cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 1 of Effect size quantification for interrupted time series analysis: implementation in R and analysis for Covid-19 research
Creators: name: Travis-Lumer, Yael
name: Goldberg, Yair
name: Levine, Stephen Z.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 1: Appendix A. Quantifying the effect size. Appendix B. Data analysis example in R. Appendix C. Additional figures for the sensitivity analysis. Figure S1. Scatterplot and Regression Fitted Values for Males then Females. Figure S2. Scatterplot and Regression Fitted Values for Males Over 60 and Females Over 60. Figure S3. Scatterplot and Regression Fitted Values for Different Age Groups. Figure S4. Scatterplot and Regression Fitted Values for Short Pre-Intervention Period. Appendix D. Simulation Study. Figure S5. Boxplot of Mean Squared Error.
Monoclonal Antibody-Based Antigenic Mapping of Norovirus GII.4-2002
Creators: name: Vinje, J.
name: Donaldson, E. F.
name: Swanstrom, J.
name: Costantini, V.
name: Baric, R. S.
name: Debbink, K.
name: Lindesmith, L. C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Noroviruses are the primary cause of epidemic gastroenteritis in humans, and GII.4 strains cause ∼80% of the overall disease burden. Surrogate neutralization assays using sera and mouse monoclonal antibodies (MAbs) suggest that antigenic variation maintains GII.4 persistence in the face of herd immunity, as the emergence of new pandemic strains is accompanied by newly evolved neutralization epitopes. To potentially identify specific blockade epitopes that are likely neutralizing and evolving between pandemic strains, mice were hyperimmunized with GII.4-2002 virus-like particles (VLPs) and the resulting MAbs were characterized by biochemical and immunologic assays. All of the MAbs but one recognized GII.4 VLPs representing strains circulating from 1987 to 2009. One MAb weakly recognized GII.4-1987 and -1997 while strongly interacting with 2002 VLPs. This antibody was highly selective and effective at blocking only GII.4-2002-ligand binding. Using bioinformatic analyses, we predicted an evolving GII.4 surface epitope composed of amino acids 407, 412, and 413 and subsequently built mutant VLPs to test the impact of the epitope on MAb binding and blockade potential. Replacement of the 2002 epitope with the epitopes found in 1987 or 2006 strains either reduced or ablated enzyme immunoassay recognition by the GII.4-2002-specific blockade MAb. These data identify a novel, evolving blockade epitope that may be associated with protective immunity, providing further support for the hypotheses that GII.4 norovirus evolution results in antigenic variation that allows the virus to escape from protective herd immunity, resulting in new epidemic strains.
Additional file 1 of 18F-FDG PET/CT metrics-based stratification of large B-cell lymphoma receiving CAR-T cell therapy: immunosuppressive tumor microenvironment as a negative prognostic indicator in patients with high tumor burden
Creators: name: Sheng, Ling-Shuang
name: Shen, Rong
name: Yan, Zi-Xun
name: Wang, Chao
name: Zheng, Xin
name: Zhang, Yi-Lun
name: Yang, Hao-Xu
name: Wu, Wen
name: Xu, Peng-Peng
name: Cheng, Shu
name: Bachy, Emmanuel
name: Sesques, Pierre
name: Jacquet-Francillon, Nicolas
name: Jiang, Xu-Feng
name: Zhao, Wei-Li
name: Wang, Li
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: Virology

description: Supplementary Material 1.
Myd88-Dependent Toll-Like Receptor 7 Signaling Mediates Protection from Severe Ross River Virus-Induced Disease in Mice
Creators: name: Heise, M. T.
name: Neighbours, L. M.
name: Whitmore, A. C.
name: Long, K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Arthralgia-associated alphaviruses, including chikungunya virus (CHIKV) and Ross River virus (RRV), pose significant public health threats because of their ability to cause explosive outbreaks of debilitating arthralgia and myalgia in human populations. Although the host inflammatory response is known to contribute to the pathogenesis of alphavirus-induced arthritis and myositis, the role that Toll-like receptors (TLRs), which are major regulators of host antiviral and inflammatory responses, play in the pathogenesis of alphavirus-induced arthritis and myositis has not been extensively studied. Using a mouse model of RRV-induced myositis/arthritis, we found that myeloid differentiation primary response gene 88 (Myd88)-dependent TLR7 signaling is involved in protection from severe RRV-associated disease. Infections of Myd88- and TLR7-deficient mouse strains with RRV revealed that both Myd88 and TLR7 significantly contributed to protection from RRV-induced mortality, and both mouse strains exhibited more severe tissue damage than wild-type (WT) mice following RRV infection. While viral loads were unchanged in either Myd88 or TLR7 knockout mice compared to WT mice at early times postinfection, both Myd88 and TLR7 knockout mice exhibited higher viral loads than WT mice at late times postinfection. Furthermore, while high levels of RRV-specific antibody were produced in TLR7-deficient mice, this antibody had very little neutralizing activity and had lower affinity than WT antibody. Additionally, TLR7- and Myd88-deficient mice showed defects in germinal center activity, suggesting that TLR7-dependent signaling is critical for the development of protective antibody responses against RRV.
Additional file 2 of 18F-FDG PET/CT metrics-based stratification of large B-cell lymphoma receiving CAR-T cell therapy: immunosuppressive tumor microenvironment as a negative prognostic indicator in patients with high tumor burden
Creators: name: Sheng, Ling-Shuang
name: Shen, Rong
name: Yan, Zi-Xun
name: Wang, Chao
name: Zheng, Xin
name: Zhang, Yi-Lun
name: Yang, Hao-Xu
name: Wu, Wen
name: Xu, Peng-Peng
name: Cheng, Shu
name: Bachy, Emmanuel
name: Sesques, Pierre
name: Jacquet-Francillon, Nicolas
name: Jiang, Xu-Feng
name: Zhao, Wei-Li
name: Wang, Li
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: Virology

description: Supplementary Material 2: Figure S1. ROC curves of screening-phase 18F-FDG PET/CT metrics with the 3-month response, PFS, and OS. (A-C) ROC curves of screening-phase 18F-FDG PET/CT metrics (Dmax, tMTV, tTLG, SUVmax, and sDmax) with PFS (A); OS (B), and 3-month response (C). (D) ROC curves of M1 18F-FDG PET/CT metrics after CAR-T cell therapy (M1 tMTV, M1 tTLG, and M1 SUVmax), (E–F) Δvalue (ΔtMTV, ΔtTLG, and ΔSUVmax) (E) and Δvalue / valuepre (ΔtMTV/tMTVpre, ΔtTLG/tTLGpre and ΔSUVmax/SUVmaxpre) (F) with PFS. ROC, receiver operating characteristic; SUVmax, maximum standardized uptake value; sDmax, the distance separating the two farthest lesions, standardized according to the body surface area.
Transition from the Infalling Envelope to the Keplerian Disk around L1551 IRS 5
Creators: name: Chou, Ti-Lin
name: Takakuwa, Shigehisa
name: Yen, Hsi-Wei
name: Ohashi, Nagayoshi
name: Ho, Paul T. P.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We present combined SubMillimeter Array (SMA) + Atacama Submillimeter Telescope Experiment (ASTE) images of the Class I protobinary L1551 IRS 5 in the CS ($J$ = 7--6) line, the submillimeter images of L1551 IRS 5 with the most complete spatial sampling ever achieved ($0''.9$ -- $36''$). The SMA image of L1551 IRS 5 in the 343 GHz dust-continuum emission is also presented, which shows an elongated feature along the northwest to southeast direction ($\sim$160 AU $\times$ 80 AU), perpendicular to the associated radio jets. The combined SMA+ASTE images show that the high-velocity ($\gtrsim$1.5 km s$^{-1}$) CS emission traces the structure of the dust component and shows a velocity gradient along the major axis, which is reproduced by a geometrically-thin Keplerian-disk model with a central stellar mass of $\sim$0.5 $M_{\odot}$. The low-velocity ($\lesssim$1.3 km s$^{-1}$) CS emission shows an extended ($\sim$1000 AU) feature that exhibits slight south (blueshifted) to north (redshifted) emission offsets, which is modeled with a rotating and infalling envelope with a conserved angular momentum. The rotational motion of the envelope connects smoothly to the inner Keplerian rotation at a radius of $\sim$64 AU. The infalling velocity of the envelope is $\sim$three times lower than the free-fall velocity toward the central stellar mass of 0.5 $M_{\odot}$. These results demonstrate transition from the infalling envelope to the Keplerian disk, consistent with the latest theoretical studies of disk formation. We suggest that sizable ($r\sim$50--200 AU) Keplerian disks are already formed when the protostars are still deeply embedded in the envelopes.
Radius constraints from high-speed photometry of 20 low-mass white dwarf binaries
Creators: name: Hermes, J. J.
name: Brown, Warren R.
name: Kilic, Mukremin
name: Gianninas, A.
name: Chote, Paul
name: Sullivan, D. J.
name: Winget, D. E.
name: Bell, Keaton J.
name: Falcon, R. E.
name: Winget, K. I.
name: Mason, Paul A.
name: Harrold, Samuel T.
name: Montgomery, M. H.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We carry out high-speed photometry on 20 of the shortest-period, detached white dwarf binaries known and discover systems with eclipses, ellipsoidal variations (due to tidal deformations of the visible white dwarf), and Doppler beaming. All of the binaries contain low-mass white dwarfs with orbital periods less than 4 hr. Our observations identify the first eight tidally distorted white dwarfs, four of which are reported for the first time here, which we use to put empirical constraints on the mass-radius relationship for extremely low-mass (<0.30 Msun) white dwarfs. We also detect Doppler beaming in several of these binaries, which confirms the high-amplitude radial-velocity variability. All of these systems are strong sources of gravitational radiation, and long-term monitoring of those that display ellipsoidal variations can be used to detect spin-up of the tidal bulge due to orbital decay.
description: 14 pages, 5 figures, accepted for publication in The Astrophysical Journal
Additional file 1 of Oral cancer patients experience mechanical and chemical sensitivity at the site of the cancer
Creators: name: Sawicki, Caroline M.
name: Janal, Malvin N.
name: Nicholson, Samuel J.
name: Wu, Angie K.
name: Schmidt, Brian L.
name: Albertson, Donna G.
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer
subject: Science Policy
subject: Hematology

description: Additional file 1.
A Technique for Extracting Highly Precise Photometry for the Two-Wheeled Kepler Mission
Creators: name: Vanderburg, Andrew
name: Johnson, John Asher
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The original Kepler mission achieved high photometric precision thanks to ultra-stable pointing enabled by use of four reaction wheels. The loss of two of these reaction wheels reduced the telescope's ability to point precisely for extended periods of time, and as a result, the photometric precision has suffered. We present a technique for generating photometric light curves from pixel-level data obtained with the two-wheeled extended Kepler mission, K2. Our photometric technique accounts for the non-uniform pixel response function of the Kepler detectors by correlating flux measurements with the spacecraft's pointing and removing the dependence. When we apply our technique to the ensemble of stars observed during the Kepler Two-Wheel Concept Engineering Test, we find improvements over raw K2 photometry by factors of 2-5, with noise properties qualitatively similar to Kepler targets at the same magnitudes. We find evidence that the improvement in photometric precision depends on each target's position in the Kepler field of view, with worst precision near the edges of the field. Overall, this technique restores the median attainable photometric precision to within a factor of two of the original Kepler photometric precision for targets ranging from 10$^{th}$ to 15$^{th}$ magnitude in the Kepler bandpass, peaking with a median precision within 35% that of Kepler for stars between 12$^{th}$ and 13$^{th}$ magnitude in the Kepler bandpass.
description: 11 pages, 8 figures. Submitted to PASP and revised based on reviewer suggestions. All processed K2 engineering data is made available to the community at http://www.cfa.harvard.edu/~avanderb/k2.html
Large deviation result for the empirical locality measure of typed random geometric graphs
Creators: name: Doku-Amponsah, Kwabena
Publisher: name: arXiv
Year: 2014
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 60F10, 05C80

description: In this article for a finite typed random geometric graph we define the empirical locality distribution, which records the number of nodes of a given type linked to a given number of nodes of each type. We find large deviation principle (LDP) for the empirical locality measure given the empirical pair measure and the empirical type measure of the typed random geometric graphs. From this LDP, we derive large deviation principles for the degree measure and the proportion of detached nodes in the classical Erdos-Renyi graph defined on [0, 1]^d. This graphs have been suggested by (Canning and Penman, 2003) as a possible extension to the randomly typed random graphs.
description: 7 pages
Persistence of Circulating Memory B Cell Clones with Potential for Dengue Virus Disease Enhancement for Decades following Infection
Creators: name: Broadwater, A. H.
name: Zhou, Y.
name: Smith, S. A.
name: Crowe, J. E.
name: de Silva, A. M.
name: Olivarez, N. P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Symptomatic dengue virus infection ranges in disease severity from an influenza-like illness to life-threatening shock. One model of the mechanism underlying severe disease proposes that weakly neutralizing, dengue serotype cross-reactive antibodies induced during a primary infection facilitate virus entry into Fc receptor-bearing cells during a subsequent secondary infection, increasing viral replication and the release of cytokines and vasoactive mediators, culminating in shock. This process has been termed antibody-dependent enhancement of infection and has significantly hindered vaccine development. Much of our understanding of this process has come from studies using mouse monoclonal antibodies (MAbs); however, antibody responses in mice typically exhibit less complexity than those in humans. A better understanding of the humoral immune response to natural dengue virus infection in humans is sorely needed. Using a high-efficiency human hybridoma technology, we isolated 37 hybridomas secreting human MAbs to dengue viruses from 12 subjects years or even decades following primary or secondary infection. The majority of the human antibodies recovered were broadly cross-reactive, directed against either envelope or premembrane proteins, and capable of enhancement of infection in vitro; few exhibited serotype-specific binding or potent neutralizing activity. Memory B cells encoding enhancing antibodies predominated in the circulation, even two or more decades following infection. Mapping the epitopes and activity of naturally occurring dengue antibodies should prove valuable in determining whether the enhancing and neutralizing activity of antibodies can be separated. Such principles could be used in the rational design of vaccines that enhance the induction of neutralizing antibodies, while lowering the risk of dengue shock syndrome.
Quantitative Analysis of the Bidirectional Viral G-Protein-Coupled Receptor and Lytic Latency-Associated Nuclear Antigen Promoter of Kaposi's Sarcoma-Associated Herpesvirus
Creators: name: Hilton, Isaac B.
name: Dittmer, Dirk P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Kaposi's sarcoma-associated herpesvirus (KSHV) establishes sustained latent persistence in susceptible cells. This is dependent on the latency-associated nuclear antigen (LANA). Understanding how LANA transcription is regulated thus aids our fundamental understanding of KSHV biology. Two hundred ninety-four base pairs are sufficient to regulate LANA transcription in response to the viral RTA protein and RBPjκ. The same region controls K14/viral G-protein-coupled receptor (vGPCR) transcription in the opposite direction. We used a quantitative analysis in conjunction with specific nucleotide substitutions and defined gain-of-function and loss-of-function RTA mutants to dissect this region. We used a bidirectional reporter driving red and green luciferase to study the LANApi and K14p promoters simultaneously. This established that LANApi/K14p functions as a canonical bidirectional promoter. Both were TATA dependent. K14p was favored by ∼50-fold in this context. Eliminating the distal LANApi TATA box increased maximal output and lowered the induction threshold ( T ) of K14p even further. Two RBPjκ binding sites were independently required; however, at high concentrations of RTA, direct interactions with an RTA-responsive element (RRE) could complement the loss of one RBPjκ binding site. Intracellular Notch (ICN) was no longer able to activate RBPjκ in the viral context. This suggests a model whereby KSHV alters ICN-RBPjκ gene regulation. When the architecture of this pair of head-to-head RBPjκ binding sites is changed, the sites now respond exclusively to the viral transactivator RTA and no longer to the host mediator ICN.
Recombinant Dengue Type 2 Viruses with Altered E Protein Domain III Epitopes Are Efficiently Neutralized by Human Immune Sera
Creators: name: Butrapet, S.
name: Huang, C.
name: Wahala, W. M. P. B.
name: White, L. J.
name: de Silva, A. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Humans develop polyclonal, serotype-specific neutralizing antibody responses after dengue virus (DENV) infection. Many mouse antibodies that neutralize DENV bind to the lateral ridge or A strand epitopes on domain III of the viral envelope (EDIII) protein. It has been assumed that these epitopes are also the main target of human neutralizing antibodies. Using recombinant dengue serotype 2 viruses with altered EDIII epitopes, we demonstrate that EDIII epitopes are not the main target of human neutralizing antibody.
Information-Theoretic Implications of Quantum Causal Structures
Creators: name: Chaves, Rafael
name: Majenz, Christian
name: Gross, David
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The correlations that can be observed between a set of variables depend on the causal structure underpinning them. Causal structures can be modeled using directed acyclic graphs, where nodes represent variables and edges denote functional dependencies. In this work, we describe a general algorithm for computing information-theoretic constraints on the correlations that can arise from a given interaction pattern, where we allow for classical as well as quantum variables. We apply the general technique to two relevant cases: First, we show that the principle of information causality appears naturally in our framework and go on to generalize and strengthen it. Second, we derive bounds on the correlations that can occur in a networked architecture, where a set of few-body quantum systems is distributed among a larger number of parties.
description: 6 pages + appendix
Additional file 3 of 18F-FDG PET/CT metrics-based stratification of large B-cell lymphoma receiving CAR-T cell therapy: immunosuppressive tumor microenvironment as a negative prognostic indicator in patients with high tumor burden
Creators: name: Sheng, Ling-Shuang
name: Shen, Rong
name: Yan, Zi-Xun
name: Wang, Chao
name: Zheng, Xin
name: Zhang, Yi-Lun
name: Yang, Hao-Xu
name: Wu, Wen
name: Xu, Peng-Peng
name: Cheng, Shu
name: Bachy, Emmanuel
name: Sesques, Pierre
name: Jacquet-Francillon, Nicolas
name: Jiang, Xu-Feng
name: Zhao, Wei-Li
name: Wang, Li
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: Virology

description: Supplementary Material 3: Figure S2. The value of 18F-FDG PET/CT metrics in predicting early progression in PR/SD patients on M1 after CAR-T cell therapy. (A-B) PFS of patients evaluated as PR/SD on M1 after CAR-T cell therapy stratified with M1 SUVmax and ΔtTLG/tTLGpre from RJ cohort (A) and Lyon cohort (B). (C-D) OS of patients evaluated as PR/SD on M1 after CAR-T cell therapy stratified with M1 SUVmax and ΔtTLG/tTLGpre from RJ cohort (C) and Lyon cohort (D). (E) A prediction model combining M1 SUVmax and tTLG clearance rate to predict early progression for patients evaluated as PR/SD at M1 after CAR-T cell therapy. PR, partial response; SD, stable disease.
PSDI Webinar: Introduction to PSDI - Slides
Creators: name: Bicarregui, Juan
name: Knight, Nicola
name: Matthews, Brian
name: Coles, Simon
name: Frey, Jeremy
name: Montanari, Barbara
name: Bunakov, Vasily
Publisher: name: Zenodo
Year: 2023

description: The Physical Sciences Data Infrastructure (PSDI - www.psdi.ac.uk) is an initiative funded by EPSRC which aims to accelerate research in the physical sciences by providing a data infrastructure that brings together and builds upon the various data systems researchers currently use. This presentation is from the Introduction to PSDI webinar which was run on 29th June 2023. https://www.psdi.ac.uk/event/webinar-introduction-to-psdi/ This content was presented by Juan Bicarregui and Nicola Knight. It was contributed to by the PSDI Investigator Team and pathfinder leads. A recording of this webinar is available on Youtube - https://youtu.be/iOg8YSE-A7I
Single Amino Acid Modification of Adeno-Associated Virus Capsid Changes Transduction and Humoral Immune Profiles
Creators: name: Hirsch, M. L.
name: Samulski, R. J.
name: Diprimio, N.
name: Li, C.
name: Bowles, D. E.
name: Agbandje-McKenna, M.
name: Asokan, A.
name: Monahan, P. E.
name: Rabinowitz, J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Adeno-associated virus (AAV) vectors have the potential to promote long-term gene expression. Unfortunately, humoral immunity restricts patient treatment and in addition provides an obstacle to the potential option of vector readministration. In this study, we describe a comprehensive characterization of the neutralizing antibody (NAb) response to AAV type 1 (AAV1) through AAV5 both in vitro and in vivo. These results demonstrated that NAbs generated from one AAV type are unable to neutralize the transduction of other types. We extended this observation by demonstrating that a rationally engineered, muscle-tropic AAV2 mutant containing 5 amino acid substitutions from AAV1 displayed a NAb profile different from those of parental AAV2 and AAV1. Here we found that a single insertion of Thr from AAV1 into AAV2 capsid at residue 265 preserved high muscle transduction, while also changing the immune profile. To better understand the role of Thr insertion at position 265, we replaced all 20 amino acids and evaluated both muscle transduction and the NAb response. Of these variants, 8 mutants induced higher muscle transduction than AAV2. Additionally, three classes of capsid NAb immune profile were defined based on the ability to inhibit transduction from AAV2 or mutants. While no relationship was found between transduction, amino acid properties, and NAb titer or its cross-reactivity, these studies map a critical capsid motif involved in all steps of AAV infectivity. Our results suggest that AAV types can be utilized not only as templates to generate mutants with enhanced transduction efficiency but also as substrates for repeat administration.
Additional file 1 of Measuring rurality in health services research: a scoping review
Creators: name: Danek, Robin
name: Blackburn, Justin
name: Greene, Marion
name: Mazurenko, Olena
name: Menachemi, Nir
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Science Policy

description: Additional file 1. Appendix of included studies.
The Death Studies Podcast Dr Xavier Aldana Reyes and the DORS 2023 Conference
Creators: name: Podcast, The Death Studies
name: Visser, Renske
name: Michael-Fox, Bethan
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 470527
subject: Popular and genre literature

description: This is an interview featured on The Death Studies Podcast. This interview is with Xavier Aldana Reyes. You can find out more about the guests and hear the full episode atwww.thedeathstudiespodcast.com or listen to the full episode wherever you find your podcasts.
Slow Manifold of a Neuronal Bursting Model
Creators: name: Ginoux, Jean-Marc
name: Rossetto, Bruno
Publisher: name: arXiv
Year: 2014
Subjects: subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics

description: Comparing neuronal bursting models (NBM) with slow-fast autonomous dynamical systems (S-FADS), it appears that the specific features of a (NBM) do not allow a determination of the analytical slow manifold equation with the singular approximation method. So, a new approach based on Differential Geometry, generally used for (S-FADS), is proposed. Adapted to (NBM), this new method provides three equivalent manners of determination of the analytical slow manifold equation. Application is made for the three-variables model of neuronal bursting elaborated by Hindmarsh and Rose which is one of the most used mathematical representation of the widespread phenomenon of oscillatory burst discharges that occur in real neuronal cells.
description: arXiv admin note: text overlap with arXiv:1408.1711
Additional file 4 of 18F-FDG PET/CT metrics-based stratification of large B-cell lymphoma receiving CAR-T cell therapy: immunosuppressive tumor microenvironment as a negative prognostic indicator in patients with high tumor burden
Creators: name: Sheng, Ling-Shuang
name: Shen, Rong
name: Yan, Zi-Xun
name: Wang, Chao
name: Zheng, Xin
name: Zhang, Yi-Lun
name: Yang, Hao-Xu
name: Wu, Wen
name: Xu, Peng-Peng
name: Cheng, Shu
name: Bachy, Emmanuel
name: Sesques, Pierre
name: Jacquet-Francillon, Nicolas
name: Jiang, Xu-Feng
name: Zhao, Wei-Li
name: Wang, Li
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: Virology

description: Supplementary Material 4:  Figure S3. Correlation of screening-phase 18F-FDG PET/CT metrics with CAR-T toxicity. (A-B) ROC curves of screening-phase 18F-FDG PET/CT metrics (Dmax, tMTV, tTLG, SUVmax, and sDmax) withCRS grade < 2 or CRS grade ≥ 2 (A) and no NT grade or any NT grade (B) in patients received axi-cel treatment. ROC curves of screening-phase 18F-FDG PET/CT metrics (Dmax, tMTV, tTLG, SUVmax and sDmax) with CRS grade < 2 or CRS grade ≥ 2 (C) and no NT grade or any NT grade (D) in patients received relma-cel treatment. (E) Occurrence of NT in patients stratified with screening-phase sDmax. (F) Correlation of screening-phase 18F-FDG PET/CT metrics with duration of CRS and NT. (G) Correlation of screening-phase 18F-FDG PET/CT metrics with onset day of CRS and NT. CRS, cytokine release syndrome; NT, neurotoxicity; Axi-cel, axicabtagene ciloleucel; relma-cel, relmacabtagene autoleucel.
Additional file 1 of Relationship between body composition indices and changes in body temperature due to hot pack use
Creators: name: Kominami, Kazuyuki
name: Sato, Kazunari
name: Takahashi, Naoaki
Publisher: name: figshare
Year: 2022
Subjects: subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Marine Biology
subject: Cancer
subject: Cardiology

description: Additional file 1. Relationships between changes in body temperature and body composition indices with significant associations.
Equivariant epsilon constant conjectures for weakly ramified extensions
Creators: name: Bley, Werner
name: Cobbe, Alessandro
Publisher: name: arXiv
Year: 2014
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics
subject: 11Y40

description: We study the local epsilon constant conjecture as formulated by Breuning. This conjecture fits into the general framework of the equivariant Tamagawa number conjecture (ETNC) and should be interpreted as a consequence of the expected compatibility of the ETNC with the functional equation of Artin-L-functions. Let K / Q_p be unramified. Under some mild technical assumption we prove Breuning's conjecture for weakly ramified abelian extensions N / K with cyclic ramification group. As a consequence of Breuning's local-global principle we obtain the validity of the global epsilon constant conjecture as formulated by Bley and Burns and of Chinburg's Omega(2)-conjecture for certain infinite families F / E of weakly and wildly ramified extensions of number fields.
description: 28 pages
Additional file 1 of Genome-wide SNPs in the spiny lobster Panulirus homarus reveal a hybrid origin for its subspecies
Creators: name: Farhadi, Ahmad
name: Jeffs, Andrew G.
name: Lavery, Shane D.
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology

description: Additional file 1. The result of supportive analysis from of mtCR sequences and SNPs in this study.
The Development of CD4 Binding Site Antibodies during HIV-1 Infection
Creators: name: Tomaras, G.
name: Schuitemaker, H.
name: Euler, Z.
name: Montefiori, D. C.
name: Kirchherr, J.
name: Tran, L.
name: Morris, L.
name: Lynch, R. M.
name: Louder, M. K.
name: Yang, Z.-Y.
name: Schmidt, S. D.
name: Abdool Karim, S.
name: Cohen, M.
name: Mascola, J. R.
name: Haynes, B. F.
name: DerSimonian, R.
name: Nabel, G. J.
name: Sibeko, S.
name: Soderberg, K.
name: Gray, E. S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Broadly neutralizing antibodies to the CD4 binding site (CD4bs) of gp120 are generated by some HIV-1-infected individuals, but little is known about the prevalence and evolution of this antibody response during the course of HIV-1 infection. We analyzed the sera of 113 HIV-1 seroconverters from three cohorts for binding to a panel of gp120 core proteins and their corresponding CD4bs knockout mutants. Among sera collected between 99 and 258 weeks post-HIV-1 infection, 88% contained antibodies to the CD4bs and 47% contained antibodies to resurfaced stabilized core (RSC) probes that react preferentially with broadly neutralizing CD4bs antibodies (BNCD4), such as monoclonal antibodies (MAbs) VRC01 and VRC-CH31. Analysis of longitudinal serum samples from a subset of 18 subjects revealed that CD4bs antibodies to gp120 arose within the first 4 to 16 weeks of infection, while the development of RSC-reactive antibodies was more varied, occurring between 10 and 152 weeks post-HIV-1 infection. Despite the presence of these antibodies, serum neutralization mediated by RSC-reactive antibodies was detected in sera from only a few donors infected for more than 3 years. Thus, CD4bs antibodies that bind a VRC01-like epitope are often induced during HIV-1 infection, but the level and potency required to mediate serum neutralization may take years to develop. An improved understanding of the immunological factors associated with the development and maturation of neutralizing CD4bs antibodies during HIV-1 infection may provide insights into the requirements for eliciting this response by vaccination.
Impact parameter space and transverse distortion
Creators: name: Dahiya, Harleen
name: Kumar, Narinder
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We investigate the GPDs in impact parameter space using the explicit light front wave functions (LFWFs) for the two-particle Fock state of the electron in QED. The Fourier transform (FT) of the GPDs gives the distribution of quarks in the transverse plane for zero longitudinal momentum transfer ($ζ=0$). We study the relationship of the spin flip GPD with the distortion of unpolarized quark distribution in the transverse plane when the target nucleon is transversely polarized and also determine the sign of distortion from the sign of anomalous magnetic moment.
description: 6 pages
Animated phase portraits of nonlinear and chaotic dynamical systems
Creators: name: Ginoux, Jean-Marc
Publisher: name: arXiv
Year: 2014
Subjects: subject: Dynamical Systems (math.DS)
subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: The aim of this section is to present programs allowing to high- light the slow-fast evolution of the solutions of nonlinear and chaotic dynamical systems such as: Van der Pol, Chua and Lorenz models. These programs provide animated phase portraits in dimension two and three, i.e. integration step by step" which are useful tools enabling to understand the dynamic of such systems.
Unexpected Maintenance of Hepatitis C Viral Diversity following Liver Transplantation
Creators: name: Fried, Michael W.
name: Salemi, Marco
name: Veras, Nazle M.
name: Goodenow, Maureen M.
name: Pybus, Oliver G.
name: Gray, Rebecca R.
name: Strickland, Samantha L.
name: Nelson, David R.
name: Lemon, Stanley M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Chronic hepatitis C virus (HCV) infection can lead to liver cirrhosis in up to 20% of individuals, often requiring liver transplantation. Although the new liver is known to be rapidly reinfected, the dynamics and source of the reinfecting virus(es) are unclear, resulting in some confusion concerning the relationship between clinical outcome and viral characteristics. To clarify the dynamics of liver reinfection, longitudinal serum viral samples from 10 transplant patients were studied. Part of the E1/E2 region was sequenced, and advanced phylogenetic analysis methods were used in a multiparameter analysis to determine the history and ancestry of reinfecting lineages. Our results demonstrated the complexity of HCV evolutionary dynamics after liver transplantation, in which a large diverse population of viruses is transmitted and maintained for months to years. As many as 30 independent lineages in a single patient were found to reinfect the new liver. Several later posttransplant lineages were more closely related to older pretransplant viruses than to viruses detected immediately after transplantation. Although our data are consistent with a number of interpretations, the persistence of high viral genetic variation over long periods of time requires an active mechanism. We discuss possible scenarios, including frequency-dependent selection or variation in selective pressure among viral subpopulations, i.e., the population structure. The latter hypothesis, if correct, could have relevance to the success of newer direct-acting antiviral therapies.
Additional file 5 of 18F-FDG PET/CT metrics-based stratification of large B-cell lymphoma receiving CAR-T cell therapy: immunosuppressive tumor microenvironment as a negative prognostic indicator in patients with high tumor burden
Creators: name: Sheng, Ling-Shuang
name: Shen, Rong
name: Yan, Zi-Xun
name: Wang, Chao
name: Zheng, Xin
name: Zhang, Yi-Lun
name: Yang, Hao-Xu
name: Wu, Wen
name: Xu, Peng-Peng
name: Cheng, Shu
name: Bachy, Emmanuel
name: Sesques, Pierre
name: Jacquet-Francillon, Nicolas
name: Jiang, Xu-Feng
name: Zhao, Wei-Li
name: Wang, Li
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: Virology

description: Supplementary Material 5: Figure S4. Correlation of screening-phase 18F-FDG PET/CT metrics with CAR-T cell expansion. Correlation of screening-phase 18F-FDG PET/CT metrics with the duration of CAR-T Cmax (A), Tmax (B), and AUC0-28d (C). Cmax, the peak CAR-T cell expansion value; Tmax, the days to peak expansion; AUC0-28d, expansion area under curve of day 0–28 after CAR-T cell therapy.
Real-Time Misbehavior Detection in IEEE 802.11e Based WLANs
Creators: name: Cao, Xianghui
name: Liu, Lu
name: Shen, Wenlong
name: Tang, Jin
name: Cheng, Yu
Publisher: name: arXiv
Year: 2014
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Computer and information sciences

description: The Enhanced Distributed Channel Access (EDCA) specification in the IEEE 802.11e standard supports heterogeneous backoff parameters and arbitration inter-frame space (AIFS), which makes a selfish node easy to manipulate these parameters and misbehave. In this case, the network-wide fairness cannot be achieved any longer. Many existing misbehavior detectors, primarily designed for legacy IEEE 802.11 networks, become inapplicable in such a heterogeneous network configuration. In this paper, we propose a novel real-time hybrid-share (HS) misbehavior detector for IEEE 802.11e based wireless local area networks (WLANs). The detector keeps updating its state based on every successful transmission and makes detection decisions by comparing its state with a threshold. We develop mathematical analysis of the detector performance in terms of both false positive rate and average detection rate. Numerical results show that the proposed detector can effectively detect both contention window based and AIFS based misbehavior with only a short detection window.
description: Accepted to IEEE Globecom 2014
Cartilha CuidaDOR
Creators: name: De Moraes Trinca, Renata
name: Ieda Francischetti
Publisher: name: Zenodo
Year: 2022
Subjects: pain
cancer pain
pain measurement
pediatric

description: Cartilha de orientações a pais e pacientes da oncologia pediátrica em relação a avaliação e tratamento da dor.
A Cluster of Virus-Encoded MicroRNAs Accelerates Acute Systemic Epstein-Barr Virus Infection but Does Not Significantly Enhance Virus-Induced Oncogenesis In Vivo
Creators: name: Krisko, J. F.
name: Delecluse, H.-J.
name: Esoda, C.
name: Martinez-Torres, F.
name: Linnstaedt, S. D.
name: Cullen, B. R.
name: Wahl, A.
name: Garcia, J. V.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Over 90% of the adult human population is chronically infected with the Epstein-Barr virus (EBV), an oncogenic herpesvirus. EBV primarily infects naive human B cells and persists latently in memory B cells. Most individuals experience an asymptomatic infection that is effectively controlled by the adaptive immune response. However, EBV-associated lymphomas can develop in immunocompromised individuals. These tumors typically express all nine EBV latent proteins (latency III). Latency III is also associated with the expression of three precursor microRNAs (miRNAs) located within the EBV BHRF1 gene locus. The role of these BHRF1 miRNAs was unclear until recent in vitro studies demonstrated that they cooperate to enhance virus-induced B cell transformation and decrease the antigenic load of virus-infected cells, indicating that the BHRF1 miRNA cluster may serve as a novel therapeutic target for the treatment of latency III EBV-associated malignancies. However, to date, it is not known if BHRF1 miRNAs enhance virus-induced oncogenesis and/or immune evasion of EBV in vivo. To understand the in vivo contribution of the BHRF1 miRNA cluster to EBV infection and EBV-associated tumorigenesis, we monitored EBV infection and assessed tumor formation in humanized mice exposed to wild-type virus and a viral mutant (Δ123) that lacks all three BHRF1 miRNAs. Our results demonstrate that while the BHRF1 miRNAs facilitate the development of acute systemic EBV infection, they do not enhance the overall oncogenic potential of EBV in vivo.
The SAMI Galaxy Survey: Towards a unified dynamical scaling relation for galaxies of all types
Creators: name: Cortese, L.
name: Fogarty, L. M. R.
name: Ho, I. -T.
name: Bekki, K.
name: Bland-Hawthorn, J.
name: Colless, M.
name: Couch, W.
name: Croom, S. M.
name: Glazebrook, K.
name: Mould, J.
name: Scott, N.
name: Sharp, R.
name: Tonini, C.
name: Allen, J. T.
name: Bloom, J.
name: Bryant, J. J.
name: Cluver, M.
name: Davies, R. L.
name: Drinkwater, M.
name: Goodwin, M.
name: Green, A.
name: Kewley, L. J.
name: Kostantopoulos, I. S.
name: Lawrence, J. S.
name: Mahajan, S.
name: Medling, A. M.
name: Owers, M.
name: Richards, S. N.
name: Sweet, S. M.
name: Wong, O. I.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We take advantage of the first data from the Sydney-AAO Multi-object Integral field (SAMI) Galaxy Survey to investigate the relation between the kinematics of gas and stars, and stellar mass in a comprehensive sample of nearby galaxies. We find that all 235 objects in our sample, regardless of their morphology, lie on a tight relation linking stellar mass ($M_{*}$) to internal velocity quantified by the $S_{0.5}$ parameter, which combines the contribution of both dispersion ($σ$) and rotational velocity ($V_{rot}$) to the dynamical support of a galaxy ($S_{0.5}=\sqrt{0.5V_{rot}^{2}+σ^{2}}$). Our results are independent of the baryonic component from which $σ$ and $V_{rot}$ are estimated, as the $S_{0.5}$ of stars and gas agree remarkably well. This represents a significant improvement compared to the canonical $M_{*}$ vs. $V_{rot}$ and $M_{*}$ vs. $σ$ relations. Not only is no sample pruning necessary, but also stellar and gas kinematics can be used simultaneously, as the effect of asymmetric drift is taken into account once $V_{rot}$ and $σ$ are combined. Our findings illustrate how the combination of dispersion and rotational velocities for both gas and stars can provide us with a single dynamical scaling relation valid for galaxies of all morphologies across at least the stellar mass range 8.5$
description: 6 pages, 4 figures. Accepted for publication in ApJ Letters
title: Sensitivity of honey bee larvae to plant protection products and impact of EFSA bee guidance document
Creators: name: Becker, Roland
name: Lückmann, Johannes
name: Miles, Mark
name: Alix, Anne
name: Weyman, Gabe
name: Pilling, Ed
name: Ruddle, Natalie
name: Dinter, Axel
name: Sharples, Amanda
name: Fritz, Stephanie
name: Oger, Laurent
Publisher: name: Julius Kühn-Institut
Year: 2018

description: In addition to other assessments, the 2013 EFSA bee guidance document requires the risk assessment of plant protection products on honey bee larvae. At the time the EFSA document was finalized, no data on honey bee larvae were available. In 2013 ECPA (the European Crop Protection Association) perfomed an impact analysis of the (then) new EFSA risk assessment and the reliability of the outcomes, using estimated endpoints derived from acute oral honey bee tests together with the usual extrapolation factors. Today, a number of honey bee larvae toxicity studies have been conducted according to the newly developed testing methods for single exposure (OECD TG 237) and repeated exposure testing (OECD GD 239). These experimental data have been used to update the ECPA impact analysis. Data on 114 active substances or formulated products were used, covering 166 worst case uses; (58 herbicides, 53 fungicides, 47 insecticides and 8 PGRs). The “pass” rates were determined according to the EFSA Bee guidance document and compared with the original outcome of the impact analysis from 2013 and with adult chronic toxicity data. When the findings of the impact analysis based on experimental data from 22 day larval tests was compared with the impact analysis from 2013 based on extrapolated data the two gave very similar results, thus indicating that the original assessment using acute data and extrapolation factors was suitably predictive.
description: Julius-Kühn-Archiv, Nr. 462 (2018): Hazards of pesticides to bees 13th International Symposium of the ICP-PR Bee Protection Group 18. - 20. October 2017, València (Spain) - Proceedings -
An Alphavirus Vector-Based Tetravalent Dengue Vaccine Induces a Rapid and Protective Immune Response in Macaques That Differs Qualitatively from Immunity Induced by Live Virus Infection
Creators: name: Mikkelsen, R.
name: Sariol, C. A.
name: Mattocks, M. D.
name: de Silva, A.
name: Collier, M. L.
name: Whitley, J.
name: White, L. J.
name: Yingsiwaphat, V.
name: Martinez, M. I.
name: Johnston, R. E.
name: Wahala M. P. B., W.
name: Rodriguez, I. V.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Despite many years of research, a dengue vaccine is not available, and the more advanced live attenuated vaccine candidate in clinical trials requires multiple immunizations with long interdose periods and provides low protective efficacy. Here, we report important contributions to the development of a second-generation dengue vaccine. First, we demonstrate that a nonpropagating vaccine vector based on Venezuelan equine encephalitis virus replicon particles (VRP) expressing two configurations of dengue virus E antigen (subviral particles [prME] and soluble E dimers [E85]) successfully immunized and protected macaques against dengue virus, while antivector antibodies did not interfere with a booster immunization. Second, compared to prME-VRP, E85-VRP induced neutralizing antibodies faster, to higher titers, and with improved protective efficacy. Third, this study is the first to map antigenic domains and specificities targeted by vaccination versus natural infection, revealing that, unlike prME-VRP and live virus, E85-VRP induced only serotype-specific antibodies, which predominantly targeted EDIII, suggesting a protective mechanism different from that induced by live virus and possibly live attenuated vaccines. Fourth, a tetravalent E85-VRP dengue vaccine induced a simultaneous and protective response to all 4 serotypes after 2 doses given 6 weeks apart. Balanced responses and protection in macaques provided further support for exploring the immunogenicity and safety of this vaccine candidate in humans.