cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Quantum transport in 3D Weyl semimetals: Is there a metal-insulator transition?
Creators: name: Ziegler, K.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We calculate the transport properties of three-dimensional Weyl fermions in a disordered environment. The resulting conductivity depends only on the Fermi energy and the scattering rate. First we study the conductivity at the spectral node for a fixed scattering rate and obtain a continuous transition from an insulator at weak disorder to a metal at stronger disorder. In the self-consistent Born approximation the scattering rate depends on the Fermi energy. Then it is crucial that the limits of the conductivity for a vanishing Fermi energy and a vanishing scattering rate do not commute. As a result, there is also metallic behavior in the phase with vanishing scattering rate and only a quantum critical point remains as an insulating state.
description: 9 pages, 5 figures
Modelos de aplicación del aula invertida
Creators: name: Fidalgo-Blanco, Ángel
name: Sein-Echaluce, Marisa
name: García-Peñalvo, Francisco José
Publisher: name: Zenodo
Year: 2021
Subjects: Flip Teaching, Flipped Classroom, Aula Invertida, Modelos de Aplicación

description: Uno de los problemas que presenta el Aula Invertida es que el modelo de aplicación es muy genérico, solo se basa en agrupar un conjunto de actividades en torno a la “lección en casa” y otro conjunto de actividades en torno a los “deberes en clase”. Este modelo genérico tiene ventajas y desventajas. Entre las ventajas citamos la flexibilidad y creatividad que permite, ya que al no definir las actividades concretas el profesorado tiene libertad para establecer las que considere más adecuadas. Como principal desventaja señalamos la gran variedad de modelos existentes en la actualidad, lo que puede ocasionar una cierta confusión entre el profesorado que desea comenzar a utilizar este método. Así pues, es necesario clasificar los distintos modelos de aplicación para facilitar su estudio y la elección del más adecuado en cada caso
The characteristics and diagnosis of adult onset primary lymphoedema of the lower limb using Indocyanine Green fluorescent lymphography
Creators: name: Mackie, Helen
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: In this study an analysis of identified ICG lymphography features of the superficial lymphatics of the lower extremity was undertaken [Table 2.2]. The absence or presence and extent of the superficial lymphatics in the limb with LLLE was assessed to identify if any of these features or combination of features were significantly associated with particular diagnostic groups of primary or secondary cancer related or secondary non-cancer related LLLE. ICG lymphography studies undertaken by the researcher (submitted for publication) had identified two compensatory lymph drainage regions, the contralateral inguinal and axillo-inguinal nodal regions, associated with secondary cancer related LLLE which were not seen or very rarely seen in clinically diagnosed primary LLLE and less so in secondary non-cancer related LLLE. Conversely, retrograde flow in lymph vessels demonstrated during the ICG lymphography procedure was not seen in secondary cancer related LLLE. These observations provided a background rationale to exploring the diagnostic capacity of ICG lymphography in LLLE. One purpose of this study was to explore the feasibility of using ICG lymphography features as a diagnostic tool. It was hoped that identified ICG lymphographic features would allow the individual presenting with persistent leg swelling of unknown causation to be able to be advised that their condition is most likely a secondary non cancer related LLLE rather than an adult onset primary LE and therefore be possibly less likely to progress or deteriorate. This may potentially provide better prognostic information and improve individualised therapeutic plans of management and support compliance (Pigott, 2021). The aim of Part A of this study was to identify the prevalence and characteristics of ICG lymphography features of the lymph vessels, position and extent of DBF and drainage patterns. In addition, Part B of this study was to explore whether using the ALERT standardised ICG lymphography technique and a structured analysis of ICG lymphography features could be translated into a simple score to distinguish the ICG pattern of adult onset primary LLLE from secondary non-cancer related LLLE.
Bin Size Independence in Intra-day Seasonalities for Relative Prices
Creators: name: Hidalgo, Esteban Guevara
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Finance (q-fin.ST)
subject: FOS: Economics and business

description: In this paper we perform a statistical analysis over the returns and relative prices of the CAC $40$ and the S\&P $500$ with the purpose of analyzing the intra-day seasonalities of single and cross-sectional stock dynamics. In order to do that, we characterized the dynamics of a stock (or a set of stocks) by the evolution of the moments of its returns (and relative prices) during a typical day. We show that these intra-day seasonalities are independent of the size of the bin, and the index we consider, (but characteristic for each index) for the case of the relative prices but not for the case of the returns. Finally, we suggest how this bin size independence could be used to characterize "atypical days" for indexes and "anomalous behaviours" in stocks.
On Lawson's area-minimizing hypercones
Creators: name: Zhang, Yongsheng
Publisher: name: arXiv
Year: 2015
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: Primary 53C38, Secondary 28A75

description: We show the area-minimality property of all homogeneous area-minimizing hypercones in Euclidean spaces (classified by Lawlor) following Lawson's original idea in his 72' Trans. A.M.S. paper "The equivariant Plateau problem and interior regularity". Moreover, each of them enjoys (coflat) calibrations singular only at the origin.
description: Improved final version, Acta Mathematica Sinica, English Series, Dec., 2016, Vol. 32
A Critical Role for Transcription Factor Smad4 in T Cell Function that Is Independent of Transforming Growth Factor β Receptor Signaling
Creators: name: Wang, Yunqi
name: Zhang, Song
name: Xiong, Hui
name: Wan, Yisong Y.
name: Curtis, Thomas A.
name: Gu, Ai-Di
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Transforming growth factor-beta (TGF-β) suppresses T cell function to maintain self-tolerance and to promote tumor immune evasion. Yet how Smad4, a transcription factor component of TGF-β signaling, regulates T cell function remains unclear. Here we have demonstrated an essential role for Smad4 in promoting T cell function during autoimmunity and anti-tumor immunity. Smad4 deletion rescued the lethal autoimmunity resulting from transforming growth factor-beta receptor (TGF-βR) deletion and compromised T-cell-mediated tumor rejection. While Smad4 was dispensable for T cell generation, homeostasis and effector function, it was essential for T cell proliferation following activation in vitro and in vivo. The transcription factor Myc was identified to mediate Smad4-controlled T cell proliferation. This study thus reveals a requirement of Smad4 for T-cell-mediated autoimmunity and tumor rejection, which is beyond the current paradigm. It highlights a TGF-βR-independent role for Smad4 in promoting T cell function, autoimmunity and anti-tumor immunity.
The Gonihedric Paradigm Extensions of the Ising Model
Creators: name: Savvidy, George
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: We suggest a generalization of the Feynman path integral to an integral over random surfaces. The proposed action is proportional to the linear size of the random surfaces and is called gonihedric. The convergence and the properties of the partition function are analysed. The model can also be formulated as a spin system with identical partition function. The spin system represents a generalisation of the Ising model with ferromagnetic, antiferromagnetic and quartic interactions. Higher symmetry of the model allows to construct dual spin systems in three and four dimensions. In three dimensions the transfer matrix describes the propagation of closed loops and we found its exact spectrum. It is a unique exact solution of the tree-dimensional statistical spin system. In three and four dimensions the system exhibits the second order phase transitions. The gonihedric spin systems have exponentially degenerated vacuum states separated by the potential barriers and can be used as a storage of binary information.
description: 19 pages, 7 figures, International Conference on Statistical Physics 2014 - SigmaPhi2014, 7-11 July 2014, Rhodes, Greece, references added
MOESM1 of Immunological features of patients affected by Barraquer-Simons syndrome
Creators: name: Corvillo, Fernando
name: Ceccarini, Giovanni
name: Nozal, Pilar
name: Magno, Silvia
name: Pelosini, Caterina
name: Garrido, Sofía
name: López-Lera, Alberto
name: Moraru, Manuela
name: Vilches, Carlos
name: Fornaciari, Silvia
name: Gabbriellini, Sabrina
name: Santini, Ferruccio
name: Araújo-Vilar, David
name: López-Trascasa, Margarita
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: Figure S1. The alternative pathway of the complement system and autoantibodies against its proteins. In the alternative pathway (AP), continuous, low-level activation of C3 by spontaneous hydrolysis of the internal C3 thioester, or C3 cleavage by plasma proteases, generates C3(H2O) or C3b. Activation by the AP leads to the generation of C3 convertase complexes (C3bBb) that cleave C3 into C3a and C3b. Additionally, the AP C3 convertase can bind properdin (P), a positive regulator that stabilizes the enzyme, extending its half-life more than 10-fold. The activation of the AP is controlled by two different soluble regulatory proteins, as factor H (FH) and factor I (FI). C3 nephritic factor (C3NeF) is one of the most known autoantibodies which recognized a neo-epitope in the C3 convertase. Other autoantibodies against complement components (C3, FB or P) and regulators (FH or FI), some of them with functional activities, have been shown in the figure. Figure S2. Lack of correlation between complement levels and age. In 20 healthy subjects no correlations were found among age and the levels of (A) C3, (B) C4 (C) factor B (FB) and (D) properdin (P). These data were obtained using the Spearman Rank correlation coefficient. P
9 New M Dwarf Planet Candidates Including 5 Gas Giants
Creators: name: Eschen, Yoshi Nike Emilia
name: Kunimoto, Michelle
name: Wilson, Thomas G.
Publisher: name: Zenodo
Year: 2024
Subjects: TESS synergies with space missions and Surveys

description: We present the detection of nine new planet candidates orbiting M dwarfs, identified using an independent search and vetting pipeline applied to TESS Full-Frame Image data from Sectors 1 to 63. Our candidates include planets as small as 1.4 R⊕, with orbital periods up to 20 d. Among the nine new candidates, we identified five gas giants, which represent a rare and unexpected outcome of planet formation. Our findings add to the growing sample of giant planets around M dwarfs found by TESS. We discuss their follow-up potential for mass measurements through radial velocity observations and atmospheric characterization through transmission spectroscopy. We highlight TIC 12999193.01 as a particularly unique gas giant candidate in an eccentric orbit and excellent potential for atmospheric characterization.
Embeddings of algebras in derived categories of surfaces
Creators: name: Belmans, Pieter
name: Raedschelders, Theo
Publisher: name: arXiv
Year: 2015
Subjects: subject: Algebraic Geometry (math.AG)
subject: Representation Theory (math.RT)
subject: FOS: Mathematics

description: By a result of Orlov there always exists an embedding of the derived category of a finite-dimensional algebra of finite global dimension into the derived category of a high-dimensional smooth projective variety. In this article we give some restrictions on those algebras whose derived categories can be embedded into the bounded derived category of a smooth projective surface. This is then applied to obtain explicit results for hereditary algebras.
description: 13 pages; revised version
Inflammasomes Coordinate Pyroptosis and Natural Killer Cell Cytotoxicity to Clear Infection by a Ubiquitous Environmental Bacterium
Creators: name: Tubbs, Alan L.
name: Maltez, Vivien I.
name: Miao, Edward A.
name: Aachoui, Youssef
name: Falcone, E. Liana
name: Holland, Steven M.
name: Whitmire, Jason K.
name: Cook, Kevin D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Defective neutrophils in patients with chronic granulomatous disease (CGD) cause susceptibility to extracellular and intracellular infections. Microbes must first be ejected from intracellular niches to expose them to neutrophil attack, so we hypothesized that inflammasomes detect certain CGD pathogens upstream of neutrophil killing. Here, we identified one such ubiquitous environmental bacterium, Chromobacterium violaceum, whose extreme virulence was fully counteracted by the NLRC4 inflammasome. Caspase-1 protected via two parallel pathways that eliminated intracellular replication niches. Pyroptosis was the primary bacterial clearance mechanism in the spleen, but both pyroptosis and interleukin-18 (IL-18)-driven natural killer (NK) cell responses were required for liver defense. NK cells cleared hepatocyte replication niches via perforin-dependent cytotoxicity, whereas interferon-γ was not required. These insights suggested a therapeutic approach: exogenous IL-18 restored perforin-dependent cytotoxicity during infection by the inflammasome-evasive bacterium Listeria monocytogenes. Therefore, inflammasomes can trigger complementary programmed cell death mechanisms, directing sterilizing immunity against intracellular bacterial pathogens.
Additional file 1 of Second opinion opportunity declined: patient typology and experiences regarding the decision-making process preceding elective surgeries in Germany
Creators: name: May, Susann
name: Bruch, Dunja
name: Muehlensiepen, Felix
name: Prediger, Barbara
name: Pieper, Dawid
name: Ronckers, Cecile
name: von Peter, Sebastian
name: Neugebauer, Edmund
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy
subject: Hematology

description: Additional file 1. Procedure of the SOD
Additional file 1 of The Invested in Diabetes Study Protocol: a cluster randomized pragmatic trial comparing standardized and patient-driven diabetes shared medical appointments
Creators: name: Kwan, Bethany
name: L. Dickinson
name: Glasgow, Russell
name: Sajatovic, Martha
name: Gritz, Mark
name: Holtrop, Jodi
name: Nease, Don
name: Ritchie, Natalie
name: Nederveld, Andrea
name: Gurfinkel, Dennis
name: Waxmonsky, Jeanette
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 1. SPIRIT 2013 Checklist: Recommended items to address in a clinical trial protocol and related documents.
Ejemplos de aplicación del método de Aula Invertida MFT.
Creators: name: Fidalgo-Blanco, Ángel
name: Sein-Echaluce, Marisa
name: García-Peñalvo, Francisco José
Publisher: name: Zenodo
Year: 2021
Subjects: Aula Invertida, Flip Teaching, Flipped Classroom, Metodologías activas, Lecciones teóricas, trabajo en equipo, clases prácticas, MOOC

description: En este documento se analizarán tres ejemplos de aplicación del método Micro Flip Teaching (MFT) de Aula Invertida. Cada ejemplo se aplica en un contexto de aprendizaje distinto: clases teóricas, clases prácticas y durante la adquisición de la competencia de trabajo en equipo. Las actividades a realizar son en todos los casos las mismas básicamente, ya que se corresponden con las actividades del modelo MFT, pero cada una tiene sus peculiaridades. El objetivo del módulo es que a partir de los ejemplos citados puedan tener una guía que les facilite la aplicación.
MOESM1 of The Invested in Diabetes Study Protocol: a cluster randomized pragmatic trial comparing standardized and patient-driven diabetes shared medical appointments
Creators: name: Kwan, Bethany
name: L. Dickinson
name: Glasgow, Russell
name: Sajatovic, Martha
name: Gritz, Mark
name: Holtrop, Jodi
name: Nease, Don
name: Ritchie, Natalie
name: Nederveld, Andrea
name: Gurfinkel, Dennis
name: Waxmonsky, Jeanette
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 1. SPIRIT 2013 Checklist: Recommended items to address in a clinical trial protocol and related documents.
T Follicular Helper Cell-Dependent Clearance of a Persistent Virus Infection Requires T Cell Expression of the Histone Demethylase UTX
Creators: name: Rager, Julia E.
name: Starmer, Joshua
name: Whitfield-Larry, Fatima
name: Conley, Bridget
name: Whitmire, Jason K.
name: Allard, Denise E.
name: Magnuson, Terry
name: Shpargel, Karl B.
name: Cook, Kevin D.
name: Su, Maureen A.
name: Fry, Rebecca C.
name: Davenport, Marsha L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Epigenetic changes, including histone methylation, control T cell differentiation and memory formation, though the enzymes that mediate these processes are not clear. We show that UTX, a histone H3 lysine 27 (H3K27) demethylase, supports T follicular helper (Tfh) cell responses that are essential for B cell antibody generation and the resolution of chronic viral infections. Mice with a T cell-specific UTX deletion had fewer Tfh cells, reduced germinal center responses, lacked virus-specific immunoglobulin G (IgG), and were unable to resolve chronic lymphocytic choriomeningitis virus infections. UTX-deficient T cells showed decreased expression of interleukin-6 receptor-α and other Tfh cell-related genes that were associated with increased H3K27 methylation. Additionally, Turner Syndrome subjects, who are predisposed to chronic ear infections, had reduced UTX expression in immune cells and decreased circulating CD4(+) CXCR5(+) T cell frequency. Thus, we identify a critical link between UTX in T cells and immunity to infection.
A non-abelian quasi-particle model for gluon plasma
Creators: name: Politis, E. P.
name: Tsagkarakis, C. E.
name: Diakonos, F. K.
name: Maintas, X. N.
name: Tsapalis, A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Lattice (hep-lat)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We propose a quasi-particle model for the thermodynamic description of the gluon plasma which takes into account non-abelian characteristics of the gluonic field. This is accomplished utilizing massive non-linear plane wave solutions of the classical equations of motion with a variable mass parameter, reflecting the scale invariance of the Yang-Mills Lagrangian. For the statistical description of the gluon plasma we interpret these non-linear waves as quasi-particles with a temperature dependent mass distribution. Quasi-Gaussian distributions with a common variance but different temperature dependent mean masses for the longitudinal and transverse modes are employed. We use recent Lattice results to fix the mean transverse and longitudinal masses while the variance is fitted to the equation of state of pure $SU(3)$ on the Lattice. Thus, our model succeeds to obtain both a consistent description of the gluon plasma energy density as well as a correct behaviour of the mass parameters near the critical point.
description: 7 pages, 2 figures
Foxp3 and Treg cells in HIV-1 infection and immuno-pathogenesis
Creators: name: Jiang, Qi
name: Su, Lishan
name: Zhang, Liguo
name: Holmes, Derek
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: FoxP3+CD4+CD25+ regulatory T (Treg) cells are implicated in a number of pathologic processes including elevated levels in cancers and infectious diseases, and reduced levels in autoimmune diseases. Treg cells are activated to modulate immune responses to avoid over-reactive immunity. However, conflicting findings are reported regarding relative levels of Treg cells during HIV-1 infection and disease progression. The role of Treg cells in HIV-1 diseases (aberrant immune activation) is poorly understood due to lack of a robust model. We summarize here the regulation and function of Foxp3 in Treg cells and in modulating HIV-1 replication. Based on recent findings from SIV/monkey and HIV/humanized mouse models, a model of the dual role of Treg cells in HIV-1 infection and immuno-pathogenesis is discussed.
Towards the $\beta$ function of SU(2) with adjoint matter using Pauli--Villars fields
Creators: name: Bennett, Ed
name: Athenodorou, Andreas
name: Bergner, Georg
name: Butti, Pietro
name: Lucini, Biagio
Publisher: name: Zenodo
Year: 2024

description: The family of SU(2) theories with matter transforming in the adjoint representation has attracted interest from many angles. The 2-flavour theory, known as Minimal Walking Technicolor, has a body of evidence pointing to it being in the conformal window with anomalous dimension $\gamma_{*}\approx0.3$. Perturbative calculations would suggest that the 1-flavour theory should be confining and chirally broken; however, lattice studies of the theory have been inconclusive. In this contribution we present a first look at efforts towards the computation of the beta function of these theories using the gradient flow methodology. Following an exploration of the phase diagram of the two theories with Wilson fermions and additional Pauli–Villars fields, we tune the bare fermion mass to near the chiral limit, and subsequently generate ensembles at five lattice volumes and a range of lattice spacings.
Well-posedness of non-autonomous linear evolution equations in uniformly convex spaces
Creators: name: Schmid, Jochen
name: Griesemer, Marcel
Publisher: name: arXiv
Year: 2015
Subjects: subject: Analysis of PDEs (math.AP)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: This paper addresses the problem of wellposedness of non-autonomous linear evolution equations $\dot x = A(t)x$ in uniformly convex Banach spaces. We assume that $A(t):D \subset X\to X$, for each $t$ is the generator of a quasi-contractive $C_0$-group where the domain $D$ and the growth exponent are independent of $t$. Well-posedness holds provided that $t\mapsto A(t)y$ is Lipschitz for all $y\in D$. Hölder continuity of degree $α<1$ is not sufficient and the assumption of uniform convexity cannot be dropped.
description: 9 pages, to appear in Math. Nachr
Triangular bases in quantum cluster algebras and monoidal categorification conjectures
Creators: name: Qin, Fan
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Algebra (math.QA)
subject: Representation Theory (math.RT)
subject: FOS: Mathematics
subject: 13F60

description: We consider the quantum cluster algebras which are injective-reachable and introduce a triangular basis in every seed. We prove that, under some initial conditions, there exists a unique common triangular basis with respect to all seeds. This basis is parametrized by tropical points as expected in the Fock-Goncharov conjecture. As an application, we prove the existence of the common triangular bases for the quantum cluster algebras arising from representations of quantum affine algebras and partially for those arising from quantum unipotent subgroups. This result implies monoidal categorification conjectures of Hernandez-Leclerc and Fomin-Zelevinsky in the corresponding cases: all cluster monomials correspond to simple modules.
description: 93 pages; minor corrections, Definition 6.1.1 and Lemma 6.4.2 updated
The regulation of autoreactive B cells during innate immune responses
Creators: name: Vilen, Barbara J.
name: Rutan, Jennifer A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Systemic lupus erythematosus (SLE) highlights the dangers of dysregulated B cells and the importance of initiating and maintaining tolerance. In addition to central deletion, receptor editing, peripheral deletion, receptor revision, anergy, and indifference, we have described a new mechanism of B cell tolerance wherein dendritic cells (DCs) and macrophages (MΦs) regulate autoreactive B cells during innate immune responses. In part, DCs and MΦs repress autoreactive B cells by releasing IL-6 and soluble CD40L (sCD40L). This mechanism is selective in that IL-6 and sCD40L do not affect Ig secretion by naïve cells during innate immune responses, allowing immunity in the absence of autoimmunity. In lupus-prone mice, DCs and MΦs are defective in secretion of IL-6 and sCD40L and cannot effectively repress autoantibody secretion suggesting that defects in DC/MΦ-mediated tolerance may contribute to the autoimmune phenotype. Further, these studies suggest that reconstituting DCs and MΦs in SLE patients might restore regulation of autoreactive B cells and provide an alternative to immunosuppressive therapies.
K-mer Genome-wide Association Study for Anthracnose and BCMV Resistance in a Phaseolus vulgaris Andean Diversity Panel
Creators: name: T. Wiersma, Andrew
name: Hamilton, John P.
name: Vaillancourt, Brieanne
name: Brose, Julia
name: Awale, Halima E.
name: M. Wright, Evan
name: D. Kelly, James
name: Buell, C. Robin
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 310899
subject: Plant biology not elsewhere classified
classificationCode: 310206
subject: Sequence analysis

description: Abstract
Limited genomic resources and closely linked marker-trait associations for common beans (Phaseolus vulgaris L.) have prevented breeders from fully utilizing molecular genetics technologies to maximize genetic gain. The emergence of more virulent races of Anthracnose (caused by Colletotrichum lindemuthianum) and Bean Common Mosaic Virus (BCMV) highlight the need for improved methods to identify and incorporate pan-genomic variation in breeding for durable disease resistance. We sequenced the P. vulgaris Andean Diversity Panel (ADP) and performed a genome-wide association study (GWAS) to identify associations for plant determinacy and resistance to BCMV and eight races of Anthracnose. Historical single nucleotide polymorphism (SNP)-chip and phenotypic data enabled a three-way comparison between SNP-chip, reference-based whole genome shotgun sequence (WGS)-SNP, and reference-free k-mer GWAS. Across all traits, there was excellent concordance between SNP-chip, WGS-SNP, and k-mer GWAS results—albeit at a much higher marker resolution for the WGS data sets. Significant k-mer haplotype variation revealed selection of the linked I-gene and Co-u traits in North American breeding lines and cultivars. Due to k-mer mapping criteria and the absence of target loci in the reference genome due to structural variation, only between 9.1 and 47.3% of the significantly associated k-mers could be mapped to the reference genome. To determine the genetic context of cis-associated k-mers, we generated whole genome assemblies of four ADP accessions and identified an expanded local repertoire of disease resistance genes associated with resistance to anthracnose and BCMV. With access to variant data in the context of a pan-genome, high resolution mapping of agronomic traits for common bean is now feasible.
Additional file 2 of Second opinion opportunity declined: patient typology and experiences regarding the decision-making process preceding elective surgeries in Germany
Creators: name: May, Susann
name: Bruch, Dunja
name: Muehlensiepen, Felix
name: Prediger, Barbara
name: Pieper, Dawid
name: Ronckers, Cecile
name: von Peter, Sebastian
name: Neugebauer, Edmund
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy
subject: Hematology

description: Additional file 2. Interview guide
Entanglement Hamiltonians for chiral fermions with zero modes
Creators: name: Klich, Israel
name: Vaman, Diana
name: Wong, Gabriel
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this Letter we study the effect of topological zero modes on entanglement Hamiltonians and entropy of free chiral fermion systems in (1+1)d. We show how Riemann-Hilbert solutions combined with finite rank perturbation theory allow us to obtain explicit expressions for entanglement Hamiltonians. We consider both chiral Majorana and Dirac fermions, and explore the effects of boundary conditions (periodic/anti-periodic for Majorana and generic for Dirac) and associated zero modes on entanglement. In the periodic sector, we derive explicitly the non-local contribution to the entanglement Hamiltonian due to the zero mode, and show an exact expression for the change in entanglement entropy due to the zero mode.
description: typos fixed
Additional file 3 of Second opinion opportunity declined: patient typology and experiences regarding the decision-making process preceding elective surgeries in Germany
Creators: name: May, Susann
name: Bruch, Dunja
name: Muehlensiepen, Felix
name: Prediger, Barbara
name: Pieper, Dawid
name: Ronckers, Cecile
name: von Peter, Sebastian
name: Neugebauer, Edmund
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy
subject: Hematology

description: Additional file 3. COREQ.
Caspase-1-induced pyroptotic cell death
Creators: name: Aderem, Alan
name: Rajan, Jayant V.
name: Miao, Edward A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Programmed cell death is a necessary part of development and tissue homeostasis enabling the removal of unwanted cells. In the setting of infectious disease, cells that have been commandeered by microbial pathogens become detrimental to the host. When macrophages and dendritic cells are compromised in this way, they can be lysed by pyroptosis, a cell death mechanism that is distinct from apoptosis and oncosis/necrosis. Pyroptosis is triggered by Caspase-1 after its activation by various inflammasomes and results in lysis of the affected cell. Both pyroptosis and apoptosis are programmed cell death mechanisms but are dependent on different caspases, unlike oncosis. Similar to oncosis and unlike apoptosis, pyroptosis results in cellular lysis and release of the cytosolic contents to the extracellular space. This event is predicted to be inherently inflammatory and coincides with interleukin-1β (IL-1β) and IL-18 secretion. We discuss the role of distinct inflammasomes, including NLRC4, NLRP3, and AIM2, as well as the role of the ASC focus in Caspase-1 signaling. We further review the importance of pyroptosis in vivo as a potent mechanism to clear intracellular pathogens.
Expansions of generalized Euler's constants into the series of polynomials in $π^{-2}$ and into the formal enveloping series with rational coefficients only
Creators: name: Blagouchine, Iaroslav V.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Number Theory (math.NT)
subject: Combinatorics (math.CO)
subject: Complex Variables (math.CV)
subject: FOS: Mathematics

description: In this work, two new series expansions for generalized Euler's constants (Stieltjes constants) $γ_m$ are obtained. The first expansion involves Stirling numbers of the first kind, contains polynomials in $π^{-2}$ with rational coefficients and converges slightly better than Euler's series $\sum n^{-2}$. The second expansion is a semi-convergent series with rational coefficients only. This expansion is particularly simple and involves Bernoulli numbers with a non-linear combination of generalized harmonic numbers. It also permits to derive an interesting estimation for generalized Euler's constants, which is more accurate than several well-known estimations. Finally, in Appendix A, the reader will also find two simple integral definitions for the Stirling numbers of the first kind, as well an upper bound for them.
description: Copy of the final journal version of the paper
Thermodynamic Geometry and Phase Transitions of AdS Braneworld Black Holes
Creators: name: Chaturvedi, Pankaj
name: Sengupta, Gautam
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The thermodynamics and phase transitions of charged RN-AdS and rotating Kerr-AdS black holes in a generalized Randall-Sundrum braneworld are investigated in the framework of thermodynamic geometry. A detailed analysis of the thermodynamics, stability and phase structures in the canonical and the grand canonical ensembles for these AdS braneworld black holes are described. The thermodynamic curvatures for both these AdS braneworld black holes are computed and studied as a function of the thermodynamic variables. Through this analysis we illustrate an interesting dependence of the phase structures on the braneworld parameter for these black holes.
description: 21 pages, 10 figures and Appendix added
Tres visiones de Aula Invertida: conceptual, aplicada e híbrida
Creators: name: Fidalgo-Blanco, Ángel
name: Sein-Echaluce, Marisa
name: García-Peñalvo, Francisco José
Publisher: name: Zenodo
Year: 2021
Subjects: Aula Invertida, Flip Teaching, Metodologías activas, MOOC

description: Si paramos a una persona por la calle y le preguntamos cuáles son los dos procesos más característicos de la formación, con toda seguridad dirá: “En clase se imparte la lección y en casa se hacen los deberes”. Esta idea es muy común a cualquier ámbito y nivel educativo. Los deberes, donde actualmente hay mucho debate sobre su conveniencia, se suelen denominar trabajos en el contexto universitario. Quizás por esta visión tan arraigada de los procesos educativos, llama la atención la descripción del método de Aula Invertida, “la lección en casa y los deberes en clase”
Non-linear effects on radiation propagation around a charged compact object
Creators: name: Cuzinatto, R. R.
name: de Melo, C. A. M.
name: de Vasconcelos, K. C.
name: Medeiros, L. G.
name: Pompeia, P. J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The propagation of non-linear electromagnetic waves is carefully analyzed on a curved spacetime created by static spherically symmetric mass and charge distribution. We compute how non-linear electrodynamics affects the geodesic deviation and the redshift of photons propagating near this massive charged object. In the first order approximation, the effects of electromagnetic self-interaction can be distinguished from the usual Reissner-Nordström terms. In the particular case of Euler-Heisenberg effective Lagrangian, we find that these self-interaction effects might be important near extremal compact charged objects.
description: 7 pages, no figures, new references added, minor corrections in some equations
Additional file 1 of INTERnational Project for the Evaluation of “activE Rehabilitation” (inter-PEER) – a protocol for a prospective cohort study of community peer-based training programmes for people with spinal cord injury
Creators: name: Divanoglou, Anestis
name: Tasiemski, Tomasz
name: Jörgensen, Sophie
Publisher: name: figshare
Year: 2020
Subjects: subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Additional file 1. The Template for Intervention Description and Replication (TIDieR) for Active Rehabilitation programmes.
Bugs in the system
Creators: name: Baric, Ralph S.
name: Menachery, Vineet D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Immunity to respiratory virus infection is governed by complex biological networks that influence disease progression and pathogenesis. Systems biology provides an opportunity to explore and understand these multifaceted interactions based on integration and modeling of multiple biological parameters. In this review, we describe new and refined systems-based approaches used to model, identify, and validate novel targets within complex networks following influenza and coronavirus infection. In addition, we propose avenues for extension and expansion that can revolutionize our understanding of infectious disease processes. Together, we hope to provide a window into the unique and expansive opportunity presented by systems biology to understand complex disease processes within the context of infectious diseases.
MOESM1 of INTERnational Project for the Evaluation of “activE Rehabilitation” (inter-PEER) – a protocol for a prospective cohort study of community peer-based training programmes for people with spinal cord injury
Creators: name: Divanoglou, Anestis
name: Tasiemski, Tomasz
name: Jörgensen, Sophie
Publisher: name: figshare
Year: 2020
Subjects: subject: Cell Biology
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology

description: Additional file 1. The Template for Intervention Description and Replication (TIDieR) for Active Rehabilitation programmes.
Man's best friend: what can pet dogs teach us about non-Hodgkin's lymphoma?
Creators: name: Suter, Steven E.
name: Richards, Kristy L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Animal models are essential for understanding lymphoma biology and testing new treatments prior to human studies. Spontaneously arising lymphomas in pet dogs represent an underutilized resource that could be used to complement current mouse lymphoma models, which do not adequately represent all aspects of the human disease. Canine lymphoma resembles human lymphoma in many important ways, including characteristic translocations and molecular abnormalities and similar therapeutic responses to chemotherapy, radiation, and newer targeted therapies (e.g. ibrutinib). Given the large number of pet dogs and high incidence of lymphoma, particularly in susceptible breeds, dogs represent a largely untapped resource for advancing the understanding and treatment of human lymphoma. This review highlights similarities in molecular biology, diagnosis, treatment, and outcomes between human and canine lymphoma. It also describes resources that are currently available to study canine lymphoma, advantages to be gained by exploiting the genetic breed structure in dogs, and current and future challenges and opportunities to take full advantage of this resource for lymphoma studies.
Endogenous antigen presenting cell-derived IL-10 inhibits T lymphocyte responses to commensal enteric bacteria
Creators: name: Albright, Carol A.
name: Sartor, R. Balfour
name: Tonkonogy, Susan L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Interleukin-10 deficient (IL-10-/-) mice develop chronic T cell-mediated colitis when colonized with normal commensal bacteria, but germ-free (GF) IL-10-/- mice remain disease-free. Antigen presenting cells (APC) secrete regulatory cytokines that help determine T lymphocyte activation or tolerance. CD4+ T cells from the mesenteric lymph nodes of inflamed IL-10-/- mice secrete more IFNγ and IL-17 when cultured with cecal bacterial lysate-pulsed splenic APC from IL-10-/- mice than when cultured with normal control APC. GF IL-10-/- APC induce similar IFNγ and IL-17 responses; therefore, the functional difference between normal and IL-10 deficient APC is inherent to the lack of IL-10 and not secondary to inflammation. Bacterial lysate-pulsed normal APC cultured with CD4+ cells from colitic IL-10-/- mice or with exogenous IFNγ secrete higher amounts of IL-10 compared to the same APC cultured with naïve T cells. APC enriched for CD11c+ cells are potent activators of IFNγ and IL-17 production by CD4+ cells from IL-10-/- mice. These APC also produce IL-12/IL-23 p40 and IL-10. Recombinant IL-10 suppressed and anti-IL-10 receptor antibody increased IFNγ, IL-17 and IL-12/IL-23 p40 production in bacterial lysate-pulsed APC and plus CD4+ T cell co-cultures. Taken together, our results show that endogenous IL-10 produced by APC inhibits responses to commensal bacteria and influences the ability of APC to stimulate IFNγ-producing effector lymphocytes, which reciprocally, induce IL-10 production by APC. Cytokines produced by APC are an important determinant of pathogenic versus protective mucosal immune responses to colonic bacterial stimulation.
On the optimality of shifted Laplacian in the class of expansion preconditioners for the Helmholtz equation
Creators: name: Cools, Siegfried
name: Vanroose, Wim
Publisher: name: arXiv
Year: 2015
Subjects: subject: Analysis of PDEs (math.AP)
subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics

description: This paper introduces and explores the class of expansion preconditioners EX(m) that forms a direct generalization to the classic complex shifted Laplace (CSL) preconditioner for Helmholtz problems. The construction of the EX(m) preconditioner is based upon a truncated Taylor series expansion of the original Helmholtz operator inverse. The expansion preconditioner is shown to significantly improve Krylov solver convergence rates for the Helmholtz problem for growing values of the number of series terms m. However, the addition of multiple terms in the expansion also increases the computational cost of applying the preconditioner. A thorough cost-benefit analysis of the addition of extra terms in the EX(m) preconditioner proves that the CSL or EX(1) preconditioner is the practically most efficient member of the expansion preconditioner class. Additionally, possible extensions to the expansion preconditioner class that further increase preconditioner efficiency are suggested.
description: 19 pages, 6 figures, 4 tables
Additional file 4 of Second opinion opportunity declined: patient typology and experiences regarding the decision-making process preceding elective surgeries in Germany
Creators: name: May, Susann
name: Bruch, Dunja
name: Muehlensiepen, Felix
name: Prediger, Barbara
name: Pieper, Dawid
name: Ronckers, Cecile
name: von Peter, Sebastian
name: Neugebauer, Edmund
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy
subject: Hematology

description: Additional file 4. Detailed socio-demographic information
Comparing traditional and participatory dissemination of a shared decision making intervention (ADAPT-NC): a cluster randomized trial
Creators: name: Mohanan, Sveta
name: Taylor, Yhenneko
name: McWilliams, Andrew
name: Dulin, Michael
name: Ludden, Thomas
name: Kuhn, Lindsay
name: Derkowski, Diane
name: Alkhazraji, Thamara
name: Tapp, Hazel
name: Halladay, Jacquie
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: BackgroundAsthma is a common disease that affects people of all ages and has significant morbidity and mortality. Poor outcomes and health disparities related to asthma result in part from the difficulty of disseminating new evidence and care delivery methods such as shared decision making (SDM) into clinical practice.This 3-year study explores the ideal framework for rapid dissemination of an evidence-based SDM toolkit for asthma management. The study leverages a partnership between the North Carolina (NC) statewide Medicaid network and the NC Network Consortium of practice-based research networks (PBRNs).Methods/designThis non-blinded study will randomize 30 primary care clinics in NC stratified by four PBRNs. We will test dissemination across these practices using a facilitator-led participatory approach to dissemination (FLOW), a novel method of participatory dissemination involving key principles of community-based participatory research, and a more typical “lunch and learn” dissemination method. Specifically, we will use cluster randomization to assign each of the 30 practices to one of three arms: (1) control, no dissemination; (2) traditional dissemination, one didactic session a year and distribution of educational material; and (3) FLOW dissemination. We hypothesize that at the unit of randomization, the clinic, patients in the FLOW dissemination arm will be more likely to share in their treatment decisions compared to patients in the traditional dissemination or control arms. All outcomes will be measured at the level of the clinic. Adoption of the SDM approach will be evaluated by 1) asthma exacerbations, 2) level of patient involvement in the decision making process, and 3) qualitative assessments from patients and providers.The research question is: What dissemination strategy most effectively increases practice level adoption of a shared decision making approach to asthma management? This study will provide important data to support best practices in dissemination of an evidence-based toolkit and implementation of shared decision making into primary care practices.Trial registrationThe trial was registered on January 27, 2014 through the United States National Institutes of Health’s ClinicalTrials.gov NCT02047929 and funded by the Patient-Centered Outcomes Research Institute (PCORI).
Notes on topological insulators
Creators: name: Kaufmann, Ralph M.
name: Li, Dan
name: Wehefritz-Kaufmann, Birgit
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 82-02, 19K56, 81V70

description: This paper is a survey of the $\mathbb{Z}_2$-valued invariant of topological insulators used in condensed matter physics. The $\mathbb{Z}$-valued topological invariant, which was originally called the TKNN invariant in physics, has now been fully understood as the first Chern number. The $\mathbb{Z}_2$ invariant is more mysterious, we will explain its equivalent descriptions from different points of view and provide the relations between them. These invariants provide the classification of topological insulators with different symmetries in which K-theory plays an important role. Moreover, we establish that both invariants are realizations of index theorems which can also be understood in terms of condensed matter physics.
description: 62 pages, 3 figures