cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Epistemic injustice and bias towards LGBTQIA+ youth within schools
Creators: name: Forcha, Maddy
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Lesbian, gay, bisexual, transgender, queer, intersex and asexual (LGBTQIA+) youth face harm and discrimination within schools. These harms are persistent. The argument of this thesis is that the philosophical field of social epistemology and especially the concept of epistemic injustice may provide an explanation for why these harms persist, as well as helping to reveal new ways forward for addressing them. The thesis takes the failed Safe Schools Coalition Australia program (SSCA), and the public debate about the program, as a case study for understanding and addressing the problem. This thesis is comprised of three chapters. Chapter 1 sets out the persistent nature of the harms that LGBTQIA+ youth face within schools. It also introduces the two key theorists whose work will inform my argument: Miranda Fricker (2007) and José Medina (2013). In this chapter I will apply their theoretical work in social epistemology to questions about the role of ignorance in perpetuating these harms, as well as to questions about responsibility for the failure of Safe Schools, and ongoing harms towards LGBTQIA+ youth. Chapter 2 draws on Medina’s concept of a resistant imagination to provide suggestions for change at the individual level. Finally, Chapter 3 argues that the Safe Schools program was an embodiment of what Medina calls a resistant imagination, and that the program offered a promising way forward, despite its initial failure. Drawing on arguments by Louise Richardson-Self, I make a case for reviving this program (or something equivalent) despite its having failed once.
Assessing the Role of Long-Acting Cabotegravir Preexposure Prophylaxis of Human Immunodeficiency Virus: Opportunities and Aspirations
Creators: name: Landovitz, R.J.
name: Cohen, M.S.
Publisher: name: Oxford University Press
Year: 2021

description: Human immunodeficiency virus (HIV) has provided critical lessons for all novel infectious diseases. With 40 years of hindsight, it is clear that a combination of prevention efforts is required to prevent onward HIV transmission, in the absence of a vaccine. Such prevention tools include a variety of behavior changes required for risk reduction, the development of treatment as prevention both for the health of the individual and to eliminate onward transmission, and, most recently, the application of antiretroviral agents as preexposure prophylaxis (PrEP) for people at the highest risk for HIV acquisition.
Canalisation and plasticity on the developmental manifold of Caenorhabditis elegans
Creators: name: Jordan, David J.
name: Miska, Eric A.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantitative Methods (q-bio.QM)
subject: FOS: Biological sciences

description: How do the same mechanisms that faithfully regenerate complex developmental programs in spite of environmental and genetic perturbations also permit responsiveness to environmental signals, adaptation, and genetic evolution? Using the nematode Caenorhabditis elegans as a model, we explore the phenotypic space of growth and development in various genetic and environmental contexts. Our data are growth curves and developmental parameters obtained by automated microscopy. Using these, we show that among the traits that make up the developmental space, correlations within a particular context are predictive of correlations among different contexts. Further we find that the developmental variability of this animal can be captured on a relatively low dimensional phenoptypic manifold and that on this manifold, genetic and environmental contributions to plasticity can be deconvolved independently. Our perspective offers a new way of understanding the relationship between robustness and flexibility in complex systems, suggesting that projection and concentration of dimension can naturally align these forces as complementary rather than competing.
Using persistent homology and dynamical distances to analyze protein binding
Creators: name: Kovacev-Nikolic, Violeta
name: Bubenik, Peter
name: Nikolić, Dragan
name: Heo, Giseon
Publisher: name: arXiv
Year: 2014
Subjects: subject: Methodology (stat.ME)
subject: Algebraic Topology (math.AT)
subject: Biomolecules (q-bio.BM)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics
subject: FOS: Biological sciences

description: Persistent homology captures the evolution of topological features of a model as a parameter changes. The most commonly used summary statistics of persistent homology are the barcode and the persistence diagram. Another summary statistic, the persistence landscape, was recently introduced by Bubenik. It is a functional summary, so it is easy to calculate sample means and variances, and it is straightforward to construct various test statistics. Implementing a permutation test we detect conformational changes between closed and open forms of the maltose-binding protein, a large biomolecule consisting of 370 amino acid residues. Furthermore, persistence landscapes can be applied to machine learning methods. A hyperplane from a support vector machine shows the clear separation between the closed and open proteins conformations. Moreover, because our approach captures dynamical properties of the protein our results may help in identifying residues susceptible to ligand binding; we show that the majority of active site residues and allosteric pathway residues are located in the vicinity of the most persistent loop in the corresponding filtered Vietoris-Rips complex. This finding was not observed in the classical anisotropic network model.
description: 27 pages, various improvements based on referees' comments
Clinical Endpoints for Evaluating Efficacy in COVID-19 Vaccine Trials
Creators: name: Brown, E.R.
name: Janes, H.E.
name: Fleming, T.R.
name: Fay, M.P.
name: Fong, Y.
name: Annunziato, P.W.
name: Neuzil, K.M.
name: Gilbert, P.B.
name: Carpp, L.N.
name: Hartzel, J.
name: Follmann, D.
name: Carone, M.
name: Cho, I.
name: Donnell, D.
name: Nason, M.
name: Vandebosch, A.
name: Zhou, H.
name: Cohen, M.S.
name: Corey, L.
name: Hyrien, O.
name: Juraska, M.
name: Luedtke, A.
name: Han, S.
name: Hirsch, I.
name: Huang, Y.
name: Huang, Y.
name: Benkeser, D.
name: Mehrotra, D.V.
Publisher: name: American College of Physicians
Year: 2021

description: Several vaccine candidates to protect against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or coronavirus disease 2019 (COVID-19) have entered or will soon enter large-scale, phase 3, placebo-controlled randomized clinical trials. To facilitate harmonized evaluation and comparison of the efficacy of these vaccines, a general set of clinical endpoints is proposed, along with considerations to guide the selection of the primary endpoints on the basis of clinical and statistical reasoning. The plausibility that vaccine protection against symptomatic COVID-19 could be accompanied by a shift toward more SARS-CoV-2 infections that are asymptomatic is highlighted, as well as the potential implications of such a shift.
Εισαγωγή στη Θεωρία Αναπαραστάσεων Ομάδων
Creators: name: Νικομάνη, Ευτέρπη Μαρία Χριστόφορου
Publisher: name: Aristotle University of Thessaloniki
Year: 2024
Subjects: Αναπαραστάσεις ομάδων
Χαρακτήρας αναπαράστασης
Ανάγωγη αναπαράσταση
Σουρ λήμμα
Θεώρημα του Μασκε
Group representations
Character of a representation
Irreducible representation
Maschke’s Theorem
Schur’s Lemma

description: Στην παρούσα διπλωματική εργασία γίνεται μια εισαγωγή στη Θεωρία Αναπαραστάσεων Ομάδων. Ορίζουμε τις αναπαραστάσεις ομάδων και μελετάμε βασικά παραδείγματα αυτών, καθώς και αποδεικνύουμε γνωστά θεμελιώδη θεωρήματα. Στην πορεία μελετάμε τους χαρακτήρες αναπαραστάσεων ομάδων και το ερμιτιανό γινόμενο αυτών, τα οποία αποτελούν εργαλεία που απλοποιούν τις πράξεις μας και μπορούν να περιγράψουν πλήρως μια αναπαράσταση.
description: This paper aims to introduce the Group Representation Theory. More specifically, it defines group representations, studies basic examples and proves well-known fundamental theorems. Furthermore, it studies the characters of group representations and their Hermitian product, which constitute tools that simplify our operations and thoroughly describe a representation.
A Deferred-Vaccination Design to Assess Durability of COVID-19 Vaccine Effect After the Placebo Group Is Vaccinated
Creators: name: Corey, L.
name: Fay, M.P.
name: Follmann, D.
name: Donnell, D.
name: Kublin, J.G.
name: Cohen, M.S.
name: Benkeser, D.
name: Vandebosch, A.
name: Nason, M.
name: Han, S.
name: Carpp, L.N.
name: Fleming, T.R.
name: Hirsch, I.
name: Carone, M.
name: Huang, Y.
name: Hyrien, O.
name: Baden, L.R.
name: Zhou, H.
name: Gilbert, P.B.
name: Neuzil, K.M.
name: Fong, Y.
name: Gabriel, E.
name: Mehrotra, D.V.
name: Huang, Y.
name: Cho, I.
name: El Sahly, H.M.
name: Juraska, M.
name: Janes, H.E.
name: Luedtke, A.
name: Fintzi, J.
Publisher: name: American College of Physicians
Year: 2021

description: Multiple candidate vaccines to prevent COVID-19 have entered large-scale phase 3 placebo-controlled randomized clinical trials, and several have demonstrated substantial short-term efficacy. At some point after demonstration of substantial efficacy, placebo recipients should be offered the efficacious vaccine from their trial, which will occur before longer-term efficacy and safety are known. The absence of a placebo group could compromise assessment of longer-term vaccine effects. However, by continuing follow-up after vaccination of the placebo group, this study shows that placebo-controlled vaccine efficacy can be mathematically derived by assuming that the benefit of vaccination over time has the same profile for the original vaccine recipients and the original placebo recipients after their vaccination. Although this derivation provides less precise estimates than would be obtained by a standard trial where the placebo group remains unvaccinated, this proposed approach allows estimation of longer-term effect, including durability of vaccine efficacy and whether the vaccine eventually becomes harmful for some. Deferred vaccination, if done open-label, may lead to riskier behavior in the unblinded original vaccine group, confounding estimates of long-term vaccine efficacy. Hence, deferred vaccination via blinded crossover, where the vaccine group receives placebo and vice versa, would be the preferred way to assess vaccine durability and potential delayed harm. Deferred vaccination allows placebo recipients timely access to the vaccine when it would no longer be proper to maintain them on placebo, yet still allows important insights about immunologic and clinical effectiveness over time.
Mathematical modeling to reveal breakthrough mechanisms in the HIV Antibody Mediated Prevention (AMP) trials
Creators: name: Huang, Y.
name: Mayer, B.T.
name: Rolland, M.
name: Gilbert, P.B.
name: Cohen, M.S.
name: Fabian Cardozo-Ojeda, E.
name: Robb, M.L.
name: Schiffer, J.T.
name: Corey, L.
name: Mascola, J.R.
name: Boshier, F.A.
name: Swan, D.A.
name: Reeves, D.B.
name: Duke, E.R.
Publisher: name: Public Library of Science
Year: 2020

description: The ongoing Antibody Mediated Prevention (AMP) trials will uncover whether passive infusion of the broadly neutralizing antibody (bNAb) VRC01 can protect against HIV acquisition. Previous statistical simulations indicate these trials may be partially protective. In that case, it will be crucial to identify the mechanism of breakthrough infections. To that end, we developed a mathematical modeling framework to simulate the AMP trials and infer the breakthrough mechanisms using measurable trial outcomes. This framework combines viral dynamics with antibody pharmacokinetics and pharmacodynamics, and will be generally applicable to forthcoming bNAb prevention trials. We fit our model to human viral load data (RV217). Then, we incorporated VRC01 neutralization using serum pharmacokinetics (HVTN 104) and in vitro pharmacodynamics (LANL CATNAP database). We systematically explored trial outcomes by reducing in vivo potency and varying the distribution of sensitivity to VRC01 in circulating strains. We found trial outcomes could be used in a clinical trial regression model (CTRM) to reveal whether partially protective trials were caused by large fractions of VRC01-resistant (IC50>50 μg/mL) circulating strains or rather a global reduction in VRC01 potency against all strains. The former mechanism suggests the need to enhance neutralizing antibody breadth; the latter suggests the need to enhance VRC01 delivery and/or in vivo binding. We will apply the clinical trial regression model to data from the completed trials to help optimize future approaches for passive delivery of anti-HIV neutralizing antibodies.
$R$-analytic functions
Creators: name: Kaiser, Tobias
Publisher: name: arXiv
Year: 2015
Subjects: subject: Logic (math.LO)
subject: FOS: Mathematics
subject: 03C64, 14P20, 26E05, 32B05, 32B20

description: We introduce the notion of $R$-analytic functions. These are definable in an o-minimal expansion of a real closed field $R$ and are locally the restriction of a $K$-differentiable function (defined by Peterzil and Starchenko) where $K=R[\sqrt{-1}]$ is the algebraic closure of $R$. The class of these functions in this general setting exhibits the nice properties of real analytic functions. We also define strongly $R$-analytic functions. These are globally the restriction of a $K$-differentiable function. We show that in arbitrary models of important o-minimal theories strongly $R$-analytic functions abound and that the concept of analytic cell decomposition can be transferred to non-standard models.
description: Final version; to appear at Archive for Mathematical Logic
Tunable Memory and Activity of Quincke Particles in Micellar Fluid
Creators: name: Yang, Yang
name: Zhang, Meng Fei
name: Zhu, Lailai
name: Zhang, Tian Hui
Publisher: name: arXiv
Year: 2023
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Memory can remarkably modify the collective behaviors of active particles. We show that in a micellar fluid, Quincke particles driven by a square-wave electric field exhibit a frequency-dependent memory. Upon increasing the frequency, a memory of directions emerges whereas the activity of particles decreases. As the activity is dominated by interaction, Quincke particles aggregate and form dense clusters in which the memory of the direction is further enhanced due to the stronger electric interactions. The density-dependent memory and activity result in dynamic heterogeneity in flocking and offer new opportunity for study of collective motions.
description: 7 pages,5 figures, 1 movies. Chinese Phys. Lett 2023
ADSA Spring Meeting 2022 - Partnerships with Industry Feedback Summary
Creators: name: ADSA Community
Publisher: name: Zenodo
Year: 2022
Subjects: data science
industry partnership
NSF TIP

description: The Academic Data Science Alliance is a community building organization that seeks to build and support a community of researchers and educators who take responsibility for a just, equitable future where data science approaches are thoughtfully applied in all domains for the benefit of all. At the March 2022 ADSA Spring Meeting, ADSA hosted Dr. Erwin Gianchandani as a speaker for the Partnerships with Industry session. Dr. Gianchandani introduced the ADSA community to the proposed Translation, Innovation and Partnerships Directorate and asked the community to provide feedback on the program. Below is a distillation of the feedback gathered during these breakout discussions and informal conversations from the meeting, condensed into a number of major categories.
Deep Sequencing Reveals Compartmentalized HIV-1 in the Semen of Men with and without Sexually Transmitted Infection-Associated Urethritis
Creators: name: Kamwendo, D.
name: Kosakovsky Pond, S.L.
name: Swanstroma, R.
name: Zhou, S.
name: Matoga, M.
name: Council, O.D.
name: Hoffman, I.
name: Cohen, M.S.
name: Tegha, G.
name: McCann, C.D.
Publisher: name: American Society for Microbiology
Year: 2020

description: Concurrent sexually transmitted infections (STI) can increase the probability of HIV-1 transmission primarily by increasing the viral load present in semen. In this study, we explored the relationship of HIV-1 in blood and seminal plasma in the presence and absence of urethritis and after treatment of the concurrent STI. Primer ID deep sequencing of the V1/V3 region of the HIV-1 env gene was done for paired blood and semen samples from antiretroviral therapy (ART)-naive men living in Malawi with (n = 19) and without (n - 5) STI-associated urethritis; for a subset of samples, full-length env genes were generated for sequence analysis and to test entry phenotype. Cytokine concentrations in the blood and semen were also measured, and a reduction in the levels of proinflammatory cytokines was observed following STI treatment. We observed no difference in the prevalence of diverse compartmentalized semen-derived lineages in men with or without STI-associated urethritis, and these viral populations were largely stable during STI treatment. Clonal amplification of one or a few viral sequences accounted for nearly 50% of the viral population, indicating a recent bottleneck followed by limited viral replication. We conclude that the male genital tract is a site where virus can be brought in from the blood, where localized sustained replication can occur, and where specific genotypes can be amplified, perhaps initially by cellular proliferation but further by limited viral replication. IMPORTANCE HIV-1 infection is a sexually transmitted infection that coexists with other STI. Here, we examined the impact of a concurrent STI resulting in urethritis on the HIV-1 population within the male genital tract. We found that viral populations remain largely stable even with treatment of the STI. These results show that viral populations within the male genital tract are defined by factors beyond transient inflammation associated with a concurrent STI.
Mode-coupling theory for mixtures of athermal self-propelled particles
Creators: name: Debets, Vincent E.
name: Janssen, Liesbeth M. C.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Dense or glassy active matter, as a result of its remarkable resemblance to passive glass-forming materials, is enjoying increasing scientific interest. To better grasp the subtle effect of active motion on the process of vitrification, a number of active mode-coupling theories (MCTs) have recently been developed. These have proven capable of qualitatively predicting important parts of the active glassy phenomenology. However, most efforts so far have only considered single-component materials, and their derivations are arguably more complex than the standard MCT case, which might hinder broader usage. Here we present a detailed derivation of a distinct active MCT for mixtures of athermal self-propelled particles that is more transparent than previously introduced versions. The key insight is that we can follow a similar strategy for our overdamped active system as is typically used for passive underdamped MCT. Interestingly, when only considering one particle species, our theory gives the exact same result as the one obtained in previous work which employed a highly different mode-coupling strategy. Moreover, we assess the quality of the theory and its novel extension to multi-component materials by using it to predict the dynamics of a Kob-Andersen mixture of athermal active Brownian quasi-hard spheres. We demonstrate that our theory is able to capture all qualitative features, most notably the location of the optimum of the dynamics when the persistence length and cage length coincide, for each combination of particle types.
Fractal Nodal Band Structures
Creators: name: Stålhammar, Marcus
name: Smith, Cristiane Morais
Publisher: name: arXiv
Year: 2023
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Mathematical Physics (math-ph)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Non-Hermitian systems exhibit interesting band structures, where novel topological phenomena arise from the existence of exceptional points at which eigenvalues and eigenvectors coalesce. One important open question is how this would manifest at non-integer dimension. Here, we report on the appearance of fractal eigenvalue degeneracies and Fermi surfaces in Hermitian and non-Hermitian topological band structures. This might have profound implications on the physics of black holes and Fermi surface instability driven phenomena, such as superconductivity and charge density waves.
description: Article published in Physical Review Research. 5+3 pages, 5+3 figures
Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing
Creators: name: Sanchez, A.M.
name: Karagiannis, K.
name: Cohen, M.S.
name: Mazumder, R.
name: Gulzar, N.
name: Hora, B.
name: Chen, Y.
name: Gao, F.
name: Stone, M.
name: Cai, F.
name: Denny, T.N.
name: Smith, K.
name: Su, C.
name: Shah, S.A.
name: Ahmed, M., Bridge Consultants Foundation, Karachi, Pakistan
name: Simonyan, V.
Publisher: name: NLM (Medline)
Year: 2020

description: High-throughput sequencing (HTS) has been widely used to characterize HIV-1 genome sequences. There are no algorithms currently that can directly determine genotype and quasispecies population using short HTS reads generated from long genome sequences without additional software. To establish a robust subpopulation, subtype, and recombination analysis workflow, we amplified the HIV-1 3'-half genome from plasma samples of 65 HIV-1-infected individuals and sequenced the entire amplicon (∼4,500 bp) by HTS. With direct analysis of raw reads using HIVE-hexahedron, we showed that 48% of samples harbored 2 to 13 subpopulations. We identified various subtypes (17 A1s, 4 Bs, 27 Cs, 6 CRF02_AGs, and 11 unique recombinant forms) and defined recombinant breakpoints of 10 recombinants. These results were validated with viral genome sequences generated by single genome sequencing (SGS) or the analysis of consensus sequence of the HTS reads. The HIVE-hexahedron workflow is more sensitive and accurate than just evaluating the consensus sequence and also more cost-effective than SGS.IMPORTANCE The highly recombinogenic nature of human immunodeficiency virus type 1 (HIV-1) leads to recombination and emergence of quasispecies. It is important to reliably identify subpopulations to understand the complexity of a viral population for drug resistance surveillance and vaccine development. High-throughput sequencing (HTS) provides improved resolution over Sanger sequencing for the analysis of heterogeneous viral subpopulations. However, current methods of analysis of HTS reads are unable to fully address accurate population reconstruction. Hence, there is a dire need for a more sensitive, accurate, user-friendly, and cost-effective method to analyze viral quasispecies. For this purpose, we have improved the HIVE-hexahedron algorithm that we previously developed with in silico short sequences to analyze raw HTS short reads. The significance of this study is that our standalone algorithm enables a streamlined analysis of quasispecies, subtype, and recombination patterns from long HIV-1 genome regions without the need of additional sequence analysis tools. Distinct viral populations and recombination patterns identified by HIVE-hexahedron are further validated by comparison with sequences obtained by single genome sequencing (SGS).
Nilotonia (Tadjikodartia) emarginata Sokolow 1948
Creators: name: Pešić, Vladimir
name: Chatterjee, Tapas
name: Bordoloi, Sabitry
Publisher: name: Zenodo
Year: 2010
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Trombidiformes
Anisitsiellidae
Nilotonia
Nilotonia emarginata

description: Nilotonia (Tadjikodartia) emarginata (Sokolow, 1948)
Records from the study area: Himachal Pradesh, West Bengal—Panesar (2004).
Habitat: Mountain streams.
Distribution: Iran, Tadjikistan, Indian Himalaya (Panesar 2004).
description: Published as part of Pešić, Vladimir, Chatterjee, Tapas & Bordoloi, Sabitry, 2010, A checklist of the water mites (Acari: Hydrachnidia) of India, with new records and description of one new species, pp. 1-54 in Zootaxa 2617 (1) on page 10, DOI: 10.11646/zootaxa.2617.1.1, http://zenodo.org/record/197964
Initiation, discontinuation, and restarting HIV pre-exposure prophylaxis: ongoing implementation strategies
Creators: name: Dalal, S.
name: Cohen, M.S.
name: Smith, D.K.
name: Rutstein, S.E.
name: Baggaley, R.C.
Publisher: name: Elsevier Ltd
Year: 2020

description: When used appropriately, pre-exposure prophylaxis (PrEP) substantially reduces the risk of HIV acquisition. Early implementation outcomes often suggest poor PrEP adherence and persistence; however, this intervention is time-limited and the need for PrEP fluctuates as risk behaviours change. In this Viewpoint we examine the current guidelines and early programmatic outcomes after starting, stopping, and restarting PrEP, and we review the implications of PrEP in relation to HIV testing algorithms. Guidelines suggest to discontinue PrEP when a person is no longer at risk for HIV, but effectively implementing this strategy requires support tools to make the decision of stopping and restarting PrEP that considers the complex relationship between risk perceptions and risk behaviours. Safely discontinuing PrEP also requires greater understanding of the daily dosing duration that is needed to protect the person after their last HIV exposure. Additionally, clear strategies are needed to re-engage a person as their HIV exposure risk changes over time.
Conditional Generative Models for Learning Stochastic Processes
Creators: name: Certo, Salvatore
name: Pham, Anh
name: Robles, Nicolas
name: Vlasic, Andrew
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Machine Learning (cs.LG)
subject: Computational Finance (q-fin.CP)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences
subject: FOS: Economics and business

description: A framework to learn a multi-modal distribution is proposed, denoted as the Conditional Quantum Generative Adversarial Network (C-qGAN). The neural network structure is strictly within a quantum circuit and, as a consequence, is shown to represent a more efficient state preparation procedure than current methods. This methodology has the potential to speed-up algorithms, such as Monte Carlo analysis. In particular, after demonstrating the effectiveness of the network in the learning task, the technique is applied to price Asian option derivatives, providing the foundation for further research on other path-dependent options.
Landau level splitting in Cd3As2 under high magnetic fields
Creators: name: Cao, Junzhi
name: Liang, Sihang
name: Zhang, Cheng
name: Liu, Yanwen
name: Huang, Junwei
name: Jin, Zhao
name: Chen, Zhi-Gang
name: Wang, Zhijun
name: Wang, Qisi
name: Zhao, Jun
name: Li, Shiyan
name: Dai, Xi
name: Zou, Jin
name: Xia, Zhengcai
name: Li, Liang
name: Xiu, Faxian
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Three-dimensional topological Dirac semimetals (TDSs) are a new kind of Dirac materials that exhibit linear energy dispersion in the bulk and can be viewed as three-dimensional graphene. It has been proposed that TDSs can be driven to other exotic phases like Weyl semimetals, topological insulators and topological superconductors by breaking certain symmetries. Here we report the first transport experiment on Landau level splitting in TDS Cd3As2 single crystals under high magnetic fields, suggesting the removal of spin degeneracy by breaking time reversal symmetry. The detected Berry phase develops an evident angular dependence and possesses a crossover from nontrivial to trivial state under high magnetic fields, a strong hint for a fierce competition between the orbit-coupled field strength and the field-generated mass term. Our results unveil the important role of symmetry breaking in TDSs and further demonstrate a feasible path to generate a Weyl semimetal phase by breaking time reversal symmetry.
description: 31 pages
Novel Approaches for Development of Human Immunodeficiency Virus Preexposure Prophylaxis Agents
Creators: name: Cohen, M.S.
name: Donnell, D.
Publisher: name: NLM (Medline)
Year: 2020

description: The US Centers for Disease Control and Prevention estimate that there are >1 100 000 people living with human immunodeficiency virus (HIV) in the United States. In 2017, 38 739 people with a new diagnosis of HIV infection were reported [2], a number that has not changed substantially in recent years despite considerable attention to HIV prevention.
Assessing the use of surveillance data to estimate the impact of prevention interventions on HIV incidence in cluster-randomized controlled trials
Creators: name: Boily, M.-C.
name: Vittinghoff, E.
name: Moore, M.
name: Beyrer, C.
name: Cohen, M.S.
name: Hughes, J.P.
name: Donnell, D.
name: Dimitrov, D.
name: Mitchell, K.M.
name: Liu, A.
Publisher: name: Elsevier B.V.
Year: 2020

description: Background: In cluster-randomized controlled trials (C-RCTs) of HIV prevention strategies, HIV incidence is expensive to measure directly. Surveillance data on HIV diagnoses or viral suppression could provide cheaper incidence estimates. We used mathematical modelling to evaluate whether these measures can replace HIV incidence measurement in C-RCTs. Methods: We used a US HIV transmission model to simulate C-RCTs of expanded antiretroviral therapy(ART), pre-exposure prophylaxis(PrEP) and HIV testing, together or alone. We tested whether modelled reductions in total new HIV diagnoses, diagnoses with acute infection, diagnoses with early infection(CD4 > 500 cells/μl), diagnoses adjusted for testing volume, or the proportion virally non-suppressed, reflected HIV incidence reductions. Results: Over a two-year trial expanding PrEP alone, modelled reductions in total diagnoses underestimated incidence reductions by a median six percentage points(pp), with acceptable variability(95 % credible interval -14,-2pp). For trials expanding HIV testing alone or alongside ART + PrEP, greater, highly variable bias was seen[-20pp(-128,-1) and -30pp(-134,-16), respectively]. Acceptable levels of bias were only seen over longer trial durations when levels of awareness of HIV-positive status were already high. Expanding ART alone, only acute and early diagnoses reductions reflected incidence reduction well, with some bias[-3pp(-6,-1) and -8pp(-16,-3), respectively]. Early and adjusted diagnoses also reliably reflected incidence when scaling up PrEP alone[bias -5pp(-11,1) and 10pp(3,18), respectively]. For trials expanding testing (alone or with ART + PrEP), bias for all measures explored was too variable for them to replace direct incidence measures, unless using diagnoses when HIV status awareness was already high. Conclusions: Surveillance measures based on HIV diagnoses may sometimes be adequate surrogates for HIV incidence reduction in C-RCTs expanding ART or PrEP only, if adjusted for bias. However, all surveillance measures explored failed to approximate HIV incidence reductions for C-RCTs expanding HIV testing, unless levels of awareness of HIV-positive status were already high.
Planar Linkages Following a Prescribed Motion
Creators: name: Gallet, Matteo
name: Koutschan, Christoph
name: Li, Zijia
name: Regensburger, Georg
name: Schicho, Josef
name: Villamizar, Nelly
Publisher: name: arXiv
Year: 2015
Subjects: subject: Symbolic Computation (cs.SC)
subject: Computational Geometry (cs.CG)
subject: Robotics (cs.RO)
subject: Algebraic Geometry (math.AG)
subject: Rings and Algebras (math.RA)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics
subject: 70B15, 68W30, 70G55, 20G20, 16Z05, 14P05, 12Y05

description: Designing mechanical devices, called linkages, that draw a given plane curve has been a topic that interested engineers and mathematicians for hundreds of years, and recently also computer scientists. Already in 1876, Kempe proposed a procedure for solving the problem in full generality, but his constructions tend to be extremely complicated. We provide a novel algorithm that produces much simpler linkages, but works only for parametric curves. Our approach is to transform the problem into a factorization task over some noncommutative algebra. We show how to compute such a factorization, and how to use it to construct a linkage tracing a given curve.
description: 33 pages, 12 figures
Subordinate Effect of -21M HLA-B Dimorphism on NK Cell Repertoire Diversity and Function in HIV-1 Infected Individuals of African Origin
Creators: name: Peppa, D.
name: Cubero, E.M.
name: Haynes, B.F.
name: Cohen, M.S.
name: Ogbe, A.
name: Pedroza-Pacheco, I.
name: Borrow, P.
Publisher: name: Frontiers Media S.A.
Year: 2020

description: Natural Killer (NK) cells play an important role in antiviral defense and their potent effector function identifies them as key candidates for immunotherapeutic interventions in chronic viral infections. Their remarkable functional agility is achieved by virtue of a wide array of germline-encoded inhibitory and activating receptors ensuring a self-tolerant and tunable repertoire. NK cell diversity is generated by a combination of factors including genetic determinants and infections/environmental factors, which together shape the NK cell pool and functional potential. Recently a genetic polymorphism at position -21 of HLA-B, which influences the supply of HLA-E binding peptides and availability of HLA-E for recognition by the inhibitory NK cell receptor NKG2A, was shown to have a marked influence on NK cell functionality in healthy human cytomegalovirus (HCMV) seronegative Caucasian individuals. In this study, -21 methionine (M)-expressing alleles supplying HLA-E binding peptides were largely poor ligands for inhibitory killer immunoglobulin-like receptors (KIRs), and a bias to NKG2A-mediated education of functionally-potent NK cells was observed. Here, we investigated the effect of this polymorphism on the phenotype and functional capacity of peripheral blood NK cells in a cohort of 36 African individuals with human immunodeficiency virus type 1 (HIV-1)/HCMV co-infection. A similarly profound influence of dimorphism at position -21 of HLA-B on NK cells was not evident in these subjects. They predominantly expressed African specific HLA-B and -C alleles that contribute a distinct supply of NKG2A and KIR ligands, and these genetic differences were compounded by the marked effect of HIV-1/HCMV co-infection on NK cell differentiation. Together, these factors resulted in a lack of correlation of the HLA-B -21 polymorphism with surface abundance of HLA-E and loss of the NK cell functional advantage in subjects with -21M HLA-B alleles. Instead, our data suggest that during HIV/HCMV co-infection exposure of NK cells to an environment that displays altered HLA-E ligands drives adaptive NKG2C+ NK cell expansions influencing effector responses. Increased efforts to understand how NK cells are functionally calibrated to self-HLA during chronic viral infections will pave the way to developing targeted therapeutic interventions to overcome the current barriers to enhancing immune-based antiviral control.
Hydroxychloroquine for the Prevention of Covid-19 - Searching for Evidence
Creators: name: Cohen, M.S.
Publisher: name: NLM (Medline)
Year: 2020

description: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (Covid-19), has generated a worldwide pandemic. The interruption of its spread depends on a combination of pharmacologic and nonpharmacologic interventions. Initial SARSCoV-2 prevention includes social distancing, the use of face masks, environmental hygiene, and hand washing.1 Although the most important pharmacologic interventions to prevent SARSCoV-2 infection are likely to be vaccines, the repurposing of established drugs for short-term prophylaxis is another, more immediate option.
Model-Based Predictions of HIV Incidence Among African Women Using HIV Risk Behaviors and Community-Level Data on Male HIV Prevalence and Viral Suppression
Creators: name: Bekker, L.-G.
name: Donnell, D.J.
name: Delany-Moretlwe, S.
name: Celum, C.L.
name: Mitchell, K.M.
name: Mgodi, N.M.
name: Boily, M.-C.
name: Cohen, M.S.
name: Dimitrov, D.
name: El-Sadr, W.
name: Moore, J.R.
Publisher: name: Lippincott Williams and Wilkins
Year: 2020

description: Background:Pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate and emtricitabine has proven highly effective in preventing HIV acquisition and is therefore offered to all participants in the control group as part of the standard of care package in many new HIV prevention studies. We propose a methodology for predicting HIV incidence in a hypothetical "placebo arm" for open-label studies or clinical trials with active control among African women. We apply the method to an open-label PrEP study, HIV Prevention Trials Network 082, which tested strategies to improve PrEP adherence in young African women all of whom were offered PrEP.Methods:Our model predicted HIV infection risk for female study cohorts in sub-Saharan Africa using baseline behavioral risk factors and contemporary HIV prevalence and viral suppression in the local male population. The model was calibrated to HIV incidence in the Vaginal and Oral Interventions to Control the Epidemic study.Results:Our model reproduced the annual HIV incidence of 3.2%-4.8% observed over 1 year of follow-up in the placebo groups of 4 completed clinical studies. We predicted an annual HIV incidence of 3.7% (95% confidence interval: 3.2 to 4.2) among HIV Prevention Trials Network 082 participants in the absence of PrEP and other risk reduction interventions.Conclusions:We demonstrated the potential of the proposed methodology to provide HIV incidence predictions based on assessment of individual risk behaviors and community and time-specific HIV exposure risk using HIV treatment and viral suppression data. These estimates may serve as comparators in HIV prevention trials without a placebo group.
Gráfico de Controle de Regressão Estrutural
Creators: name: Carvalho Júnior, Jose Gracildo
name: Leal Soares Ramos, Edson Marcos
name: Almeida, Silvia
Publisher: name: Zenodo
Year: 2025
Subjects: Erros de Medida
Esperança Condicional
Variável Dependente

description: Resumo. Devido a necessidade de se alcançar níveis de precisão cada vez maiores, isto é, reduzir ao máximo os erros de medida, este trabalho considera o modelo de regressão com erro nas variáveis proposto disponível na literatura científica, mais especificamente o modelo aditivo estrutural e o combina a metodologia de construção de gráficos de controle de regressão já conhecido, desenvolvendo desta forma uma ferramenta inédita e inovadora, denominada gráfico de controle de regressão estrutural. Independente do erro padrão utilizado (erro padrão sobre a reta de regressão ajustada, erro padrão sobre a esperançaa condicional de Y dado X e o erro padrão sobre um valor predito da variável dependente) pode-se verificar que o gráfico de controle de regressão estrutural monitora de forma satisfatória processos com variáveis relacionadas.
Incorporation of Mn in Al$_{x}$Ga$_{1-x}$N probed by x-ray absorption and emission spectroscopy, high-resolution microscopy, x-ray diffraction and first-principles calculations
Creators: name: Rovezzi, Mauro
name: Schlögelhofer, Wolfgang
name: Devillers, Thibaut
name: Szwacki, Nevill Gonzalez
name: Li, Tian
name: Adhikari, Rajdeep
name: Glatzel, Pieter
name: Bonanni, Alberta
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Synchrotron radiation x-ray absorption and emission spectroscopy techniques, complemented by high-resolution transmission electron microscopy methods and density functional theory calculations are employed to investigate the effect of Mn in Al$_{x}$Ga$_{1-x}$N:Mn samples with an Al content up to 100%. The atomic and electronic structure of Mn is established together with its local environment and valence state. A dilute alloy without precipitation is obtained for Al$_{x}$Ga$_{1-x}$N:Mn with Al concentrations up to 82%, and the surfactant role of Mn in the epitaxial process is confirmed.
Identifying Regions of Greatest Need for Ending the HIV Epidemic: A Plan for America
Creators: name: Mitchell, K.M.
name: Donnell, D.D.
name: Moore, M.
name: Cohen, M.S.
name: Boily, M.-C.
name: Dimitrov, D.T.
Publisher: name: Lippincott Williams and Wilkins
Year: 2020

description: Background:In the 2019 State of the Union Address, President Trump announced a plan for "Ending the HIV Epidemic" in the United States, with a goal to reduce new HIV infections by 90% by 2030. Phase I of the plan set an intermediate goal of a 75% reduction within 5 years, focusing on select states and counties.Methods:We assessed the feasibility of the first phase of the plan by estimating the fraction of HIV diagnoses that occur within the targeted region, using a statistical model to predict new HIV cases in each county. We suggested new areas that should be added to the current plan, prioritizing by both a "Density Metric" of new HIV cases and a "Gap Metric" quantifying shortcomings in antiretroviral therapy and pre-exposure prophylaxis uptake.Results:We found the current plan targets less than 60% of new diagnoses. The plan should be expanded to Puerto Rico, Florida, Georgia, Louisiana, and Maryland as well as parts of New York, North Carolina, Texas, and Virginia, areas which were prioritized by both metrics.Conclusion:Many of the highest priority areas, both by density of HIV cases and by lack of viral suppression and pre-exposure prophylaxis use, were not covered by the original plan, particularly in the South. The current plan to end the HIV epidemic must be expanded to these areas to feasibly allow for a 75% reduction in new HIV cases within 5 years.
The chopthin algorithm for resampling
Creators: name: Gandy, Axel
name: Lau, F. Din-Houn
Publisher: name: arXiv
Year: 2015
Subjects: subject: Computation (stat.CO)
subject: FOS: Computer and information sciences

description: Resampling is a standard step in particle filters and more generally sequential Monte Carlo methods. We present an algorithm, called chopthin, for resampling weighted particles. In contrast to standard resampling methods the algorithm does not produce a set of equally weighted particles; instead it merely enforces an upper bound on the ratio between the weights. Simulation studies show that the chopthin algorithm consistently outperforms standard resampling methods. The algorithms chops up particles with large weight and thins out particles with low weight, hence its name. It implicitly guarantees a lower bound on the effective sample size. The algorithm can be implemented efficiently, making it practically useful. We show that the expected computational effort is linear in the number of particles. Implementations for C++, R (on CRAN), Python and Matlab are available.
description: 14 pages, 4 figures
Wie Gemeinde erneuern?
Creators: name: Hofer, Hermann
name: Mette, Norbert
name: Landman, Henk
name: Weller, Johann Gottfried
name: Baumgartner, Konrad
name: Piwowarski, Władysław
name: Rak, Romual
Publisher: name: Diakonia
Year: 1970

description: Diakonia, Bd. 19 Nr. 1 (1988): Diakonia, Band 19, Heft 1
Phase classification in the long-range Harper model using machine learning
Creators: name: Ahmed, Aamna
name: Nelson, Abee
name: Raina, Ankur
name: Sharma, Auditya
Publisher: name: arXiv
Year: 2023
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: In this work, we map the phase diagrams of one-dimensional quasiperiodic models using artificial neural networks. We observe that the multi-class classifier precisely distinguishes the various phases, namely the delocalized, multifractal, and localized phases, when trained on the eigenstates of the long-range Aubry-André Harper (LRH) model. Additionally, when this trained multi-layer perceptron is fed with the eigenstates of the Aubry-André Harper (AAH) model, it identifies various phases with reasonable accuracy. We examine the resulting phase diagrams produced using a single disorder realization and demonstrate that they are consistent with those obtained from the conventional method of fractal dimension analysis. Interestingly, when the neural network is trained using the eigenstates of the AAH model, the resulting phase diagrams for the LRH model are less exemplary than those previously obtained. Further, we study binary classification by training the neural network on the probability density corresponding to the delocalized and localized eigenstates of the AAH model. We are able to pinpoint the critical transition point by examining the metric ``accuracy" for the central eigenstate. The effectiveness of the binary classifier in identifying a previously unknown multifractal phase is then evaluated by applying it to the LRH model.
description: 11 pages, 10 figures
Magnetic Reconnection Onset via Disruption of a Forming Current Sheet by the Tearing Instability
Creators: name: Uzdensky, Dmitri A.
name: Loureiro, Nuno F.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Plasma Physics (physics.plasm-ph)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: The recent realization that Sweet-Parker current sheets are violently unstable to the secondary tearing (plasmoid) instability implies that such current sheets cannot occur in real systems. This suggests that, in order to understand the onset of magnetic reconnection, one needs to consider the growth of the tearing instability in a current layer as it is being formed. Such an analysis is performed here in the context of nonlinear resistive MHD for a generic time-dependent equilibrium representing a gradually forming current sheet. It is shown that two onset regimes, single-island and multi-island, are possible, depending on the rate of current sheet formation. A simple model is used to compute the criterion for transition between these two regimes, as well as the reconnection onset time and the current sheet parameters at that moment. For typical solar corona parameters this model yields results consistent with observations.
description: 5 pages, no figures; accepted for publication in Physical Review Letters
Guideline für Ärzte: Oshtoran-Syndrom (H63D-Syndrom Typ-3)
Creators: name: Consortium, H63D Research
name: H63D Conference 2023
name: H63D Research Team Adams
name: University (JUC), Faculty 3, Jewish
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 420304
subject: General practice
classificationCode: 420314
subject: Multimorbidity
classificationCode: 420317
subject: Patient safety
classificationCode: 420318
subject: People with disability
classificationCode: 420399
subject: Health services and systems not elsewhere classified
classificationCode: 420303
subject: Family care

description: Dies ist die offizielle Kurz-Guideline für Ärzte zum Oshtoran-Syndrom, wissenschaftlich auch als H63D-Syndrom Typ-3 bezeichnet. Stand 07/2024. Angenommen von den entscheidenden Fachgesellschaften.Peer-Review abgeschlossen am 15. Juli 2024 durch Swabian Research ✓