bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sparse covariance estimation in logit mixture models
Authors: Aboutaleb Youssef M , Danaf Mazen , Xie Yifei , Ben-Akiva Moshe E 
Published: March 2021

SummaryThis paper introduces a new data-driven methodology for estimating sparse covariance matrices of the random coefficients in logit mixture models. Researchers typically specify covariance matrices in logit mixture models under one of two extreme assumptions: either an unrestricted full covariance matrix (allowing correlations between all random coefficients), or a restricted diagonal matrix (allowing no correlations at all). Our objective is to find optimal subsets of correlated coefficients for which we estimate covariances. We propose a new estimator, called MISC (mixed integer sparse covariance), that uses a mixed-integer optimization (MIO) program to find an optimal block diagonal structure specification for the covariance matrix, corresponding to subsets of correlated coefficients, for any desired sparsity level using Markov Chain Monte Carlo (MCMC) posterior draws from the unrestricted full covariance matrix. The optimal sparsity level of the covariance matrix is determined using out-of-sample validation. We demonstrate the ability of MISC to correctly recover the true covariance structure from synthetic data. In an empirical illustration using a stated preference survey on modes of transportation, we use MISC to obtain a sparse covariance matrix indicating how preferences for attributes are related to one another.
Class Altruism and Redistribution
Authors: Ghiglino Christian , Juárez-Luna David , Müller Andreas 
Published: March 2021

AbstractWhy do tax rates vary so much across countries? We study the role of other-regarding preferences and ethnic fragmentation in redistribution. A government is elected by altruistic voters and chooses a redistributive income tax. Altruism is directed towards social identity groups. Three main factors yield low levels of redistribution: (i) strong in-group altruism among rich voters—referred to as class altruism; (ii) weak universal altruism—in particular among the rich; and (iii) ethnic fragmentation among poor voters. We document survey evidence that the pattern of altruism in the United States and the European Union is consistent with the observed differences in taxes.
Chromosome Level Assembly of the Comma Butterfly (Polygonia c-album)
Authors: Celorio-Mancera Maria de la Paz , Rastas Pasi , Steward Rachel A , Nylin Soren , Wheat Christopher W 
Published: March 2021

Abstract
The comma butterfly (Polygonia c-album, Nymphalidae, Lepidoptera) is a model insect species, most notably in the study of phenotypic plasticity and plant-insect coevolutionary interactions. In order to facilitate the integration of genomic tools with a diverse body of ecological and evolutionary research, we assembled the genome of a Swedish comma using 10X sequencing, scaffolding with matepair data, genome polishing, and assignment to linkage groups using a high-density linkage map. The resulting genome is 373 Mb in size, with a scaffold N50 of 11.7 Mb and contig N50 of 11,2Mb. The genome contained 90.1% of single-copy Lepidopteran orthologs in a BUSCO analysis of 5,286 genes. A total of 21,004 gene-models were annotated on the genome using RNA-Seq data from larval and adult tissue in combination with proteins from the Arthropoda database, resulting in a high-quality annotation for which functional annotations were generated. We further documented the quality of the chromosomal assembly via synteny assessment with Melitaea cinxia. The resulting annotated, chromosome-level genome will provide an important resource for investigating coevolutionary dynamics and comparative analyses in Lepidoptera.
Using Technology to Measure Older Adults’ Social Networks for Health and Well-Being: A Scoping Review
Authors: Wei Sijia , Kang Bada , Bailey Donald E , Caves Kevin , Lin Yufen , McConnell Eleanor S , Thurow Maria , Woodward Amanda , Wright-Freeman Kayla , Xue Tingzhong (Michelle) , Corazzini Kirsten N 
Published: March 2021

AbstractBackground and ObjectivesSocial networks affect the health and well-being of older adults. Advancements in technology (e.g., digital devices and mHealth) enrich our ability to collect social networks and health data. The purpose of this scoping review was to identify and map the use of technology in measuring older adults’ social networks for health and social care.Research Design and MethodsThe Joanna Briggs Institute methodology was followed. PubMed (MEDLINE), Sociological Abstracts, SocINDEX, CINAHL, and Web of Science were searched for relevant articles. Conference abstracts and proceedings were searched via Conference Papers Index, the American Sociological Society, and The Gerontological Society of America. Studies published in English from January 2004 to March 2020 that aimed to improve health or social care for older adults and used technology to measure social networks were included. Data were extracted by 2 independent reviewers using an a priori extraction tool.ResultsThe majority of the 18 reviewed studies were pilot or simulation research conducted in Europe that focused on older adults living in the community. The various types of technologies used can be categorized as environment-based, person-based, and data-based.Discussion and ImplicationsTechnology facilitates objective and longitudinal data collection on the social interactions and activities of older adults. The use of technology to measure older adults’ social networks, however, is primarily in an exploratory phase. Multidisciplinary collaborations are needed to overcome operational, analytical, and implementation challenges. Future studies should leverage technologies for addressing social isolation and care for older adults, especially during the coronavirus disease 2019 pandemic.
Spinocerebellar Ataxia Type 1 protein Ataxin-1 is signaled to DNA damage by ataxia-telangiectasia mutated kinase
Authors: Suart Celeste E , Perez Alma M , Al-Ramahi Ismael , Maiuri Tamara , Botas Juan , Truant Ray 
Published: March 2021

Abstract
Spinocerebellar Ataxia Type 1 (SCA1) is an autosomal dominant neurodegenerative disorder caused by a polyglutamine expansion in the ataxin-1 protein. Recent genetic correlational studies have implicated DNA damage repair pathways in modifying the age at onset of disease symptoms in SCA1 and Huntington’s Disease, another polyglutamine expansion disease. We demonstrate that both endogenous and transfected ataxin-1 localizes to sites of DNA damage, which is impaired by polyglutamine expansion. This response is dependent on ataxia-telangiectasia mutated (ATM) kinase activity. Further, we characterize an ATM phosphorylation motif within ataxin-1 at serine 188. We show reduction of the Drosophila ATM homolog levels in a ATXN1[82Q] Drosophila model through shRNA or genetic cross ameliorates motor symptoms. These findings offer a possible explanation as to why DNA repair was implicated in SCA1 pathogenesis by past studies. The similarities between the ataxin-1 and the huntingtin responses to DNA damage provide further support for a shared pathogenic mechanism for polyglutamine expansion diseases.
Global Dynamics for the Two-dimensional Stochastic Nonlinear Wave Equations
Authors: Gubinelli Massimiliano , Koch Herbert , Oh Tadahiro , Tolomeo Leonardo 
Published: March 2021

AbstractWe study global-in-time dynamics of the stochastic nonlinear wave equations (SNLW) with an additive space-time white noise forcing, posed on the two-dimensional torus. Our goal in this paper is two-fold. (1) By introducing a hybrid argument, combining the $I$-method in the stochastic setting with a Gronwall-type argument, we first prove global well-posedness of the (renormalized) cubic SNLW in the defocusing case. Our argument yields a double exponential growth bound on the Sobolev norm of a solution. (2) We then study the stochastic damped nonlinear wave equations (SdNLW) in the defocusing case. In particular, by applying Bourgain’s invariant measure argument, we prove almost sure global well-posedness of the (renormalized) defocusing SdNLW with respect to the Gibbs measure and invariance of the Gibbs measure.
Universal Rings of Invariants
Authors: Meir Ehud 
Published: March 2021

Abstract
Let $K$ be an algebraically closed field of characteristic zero. Algebraic structures of a specific type (e.g., algebras or coalgebras) on a given vector space $W$ over $K$ can be encoded as points in an affine space $U(W)$. This space is equipped with a $\textrm{GL} (W)$ action, and two points define isomorphic structures if and only if they lie in the same orbit. This leads to study the ring of invariants $K[U(W)]^{\textrm{GL} (W)}$. We describe this ring by generators and relations. We then construct combinatorially a commutative ring $K[X]$, which specializes to all rings of invariants of the form $K[U(W)]^{\textrm{GL} (W)}$. We show that the commutative ring $K[X]$ has a richer structure of a Hopf algebra with additional coproduct, grading, and an inner product, which makes it into a rational PSH-algebra, generalizing a structure introduced by Zelevinsky. We finish with a detailed study of $K[X]$ in the case of an algebraic structure consisting of a single endomorphism and show how the rings of invariants $K[U(W)]^{\textrm{GL} (W)}$ can be calculated explicitly from $K[X]$ in this case.
Comparison of Strategies for Typhoid Conjugate Vaccine Introduction in India: A Cost-Effectiveness Modeling Study
Authors: Ryckman Theresa , Karthikeyan Arun S , Kumar Dilesh , Cao Yanjia , Kang Gagandeep , Goldhaber-Fiebert Jeremy D , John Jacob , Lo Nathan C , Andrews Jason R 
Published: March 2021

Abstract

Background
Typhoid fever causes substantial global mortality, with almost half occurring in India. New typhoid vaccines are highly effective and recommended by the World Health Organization for high-burden settings. There is a need to determine whether and which typhoid vaccine strategies should be implemented in India.

Methods
We assessed typhoid vaccination using a dynamic compartmental model, parameterized by and calibrated to disease and costing data from a recent multisite surveillance study in India. We modeled routine and 1-time campaign strategies that target different ages and settings. The primary outcome was cost-effectiveness, measured by incremental cost-effectiveness ratios (ICERs) benchmarked against India’s gross national income per capita (US$2130).

Results
Both routine and campaign vaccination strategies were cost-saving compared to the status quo, due to averted costs of illness. The preferred strategy was a nationwide community-based catchup campaign targeting children aged 1–15 years alongside routine vaccination, with an ICER of $929 per disability-adjusted life-year averted. Over the first 10 years of implementation, vaccination could avert 21–39 million cases and save $1.6–$2.2 billion. These findings were broadly consistent across willingness-to-pay thresholds, epidemiologic settings, and model input distributions.

Conclusions
Despite high initial costs, routine and campaign typhoid vaccination in India could substantially reduce mortality and was highly cost-effective.
Antibody Responses to Severe Acute Respiratory Syndrome Coronavirus 2 in the Serum and Cerebrospinal Fluid of Patients With Coronavirus Disease 2019 and Neurological Symptoms
Authors: Cunningham Janet L , Virhammar Johan , Rönnberg Bengt , Dopico Xaquin Castro , Kolstad Linda , Albinsson Bo , Kumlien Eva , Nääs Anja , Klang Andrea , Westman Gabriel , Zetterberg Henrik , Frithiof Robert , Lundkvist Åke , Karlsson Hedestam Gunilla B , Rostami Elham 
Published: March 2021

AbstractAntibody responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in serum and cerebrospinal fluid (CSF) samples from 16 patients with coronavirus disease 2019 and neurological symptoms were assessed using 2 independent methods. Immunoglobulin G (IgG) specific for the virus spike protein was found in 81% of patients in serum and in 56% in CSF. SARS-CoV-2 IgG in CSF was observed in 2 patients with negative serological findings. Levels of IgG in both serum and CSF were associated with disease severity (P &lt; .05). All patients with elevated markers of central nervous system damage in CSF also had CSF antibodies (P = .002), and CSF antibodies had the highest predictive value for neuronal damage markers of all tested clinical variables.
Correlation Between TIGIT Expression on CD8+ T Cells and Higher Cytotoxic Capacity
Authors: Blazkova Jana , Huiting Erin D , Boddapati Arun Kumar , Shi Victoria , Whitehead Emily J , Justement Jesse S , Nordstrom Jeffrey L , Moir Susan , Lack Justin , Chun Tae-Wook 
Published: March 2021

Abstract
Persistent exposure to antigen leads to T-cell exhaustion and immunologic dysfunction. We examined the immune exhaustion markers T cell immunoglobulin and ITIM domain (TIGIT) and programmed cell death protein 1 (PD-1) in human immunodeficiency virus (HIV)–infected and healthy individuals and the relationship with cytotoxic CD8+ T-lymphocyte activity. Frequencies of TIGIT but not PD-1 were positively correlated with CD8+ T-lymphocyte activity in HIV-aviremic and healthy individuals; however, there was no correlation in HIV-viremic individuals. Transcriptome analyses revealed up-regulation of genes associated with antiviral immunity in TIGIT+CD8+ versus TIGIT−CD8+ T cells. Our data suggest that TIGIT+CD8+ T cells do not necessarily represent a state of immune exhaustion and maintain an intrinsic cytotoxicity in HIV-infected individuals.
Coronavirus Occurrence in the Household Influenza Vaccine Evaluation (HIVE) Cohort of Michigan Households: Reinfection Frequency and Serologic Responses to Seasonal and Severe Acute Respiratory Syndrome Coronaviruses
Authors: Petrie Joshua G , Bazzi Latifa A , McDermott Adrian B , Follmann Dean , Esposito Dominic , Hatcher Christian , Mateja Allyson , Narpala Sandeep R , O’Connell Sarah E , Martin Emily T , Monto Arnold S 
Published: March 2021

Abstract

Background
We investigated frequency of reinfection with seasonal human coronaviruses (HCoVs) and serum antibody response following infection over 8 years in the Household Influenza Vaccine Evaluation (HIVE) cohort.

Methods
Households were followed annually for identification of acute respiratory illness with reverse-transcription polymerase chain reaction–confirmed HCoV infection. Serum collected before and at 2 time points postinfection were tested using a multiplex binding assay to quantify antibody to seasonal, severe acute respiratory syndrome coronavirus (SARS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike proteins and SARS-CoV-2 spike subdomains and N protein.

Results
Of 3418 participants, 40% were followed for ≥3 years. A total of 1004 HCoV infections were documented; 303 (30%) were reinfections of any HCoV type. The number of HCoV infections ranged from 1 to 13 per individual. The mean time to reinfection with the same type was estimated at 983 days for 229E, 578 days for HKU1, 615 days for OC43, and 711 days for NL63. Binding antibody levels to seasonal HCoVs were high, with little increase postinfection, and were maintained over time. Homologous, preinfection antibody levels did not significantly correlate with odds of infection, and there was little cross-response to SARS-CoV-2 proteins.

Conclusions
Reinfection with seasonal HCoVs is frequent. Binding anti-spike protein antibodies do not correlate with protection from seasonal HCoV infection.
Genetic features of the poxtA linezolid resistance gene in human enterococci from France
Authors: Dejoies Loren , Sassi Mohamed , Schutz Sacha , Moreaux Julie , Zouari Asma , Potrel Sophie , Collet Anaïs , Lecourt Maxime , Auger Gabriel , Cattoir Vincent 
Published: March 2021

Abstract

Objectives
To describe the prevalence of poxtA among clinical linezolid-resistant enterococci (LRE) collected in France from 2016 to 2020 and to extensively characterize its genetic supports and environments.

Methods
All LRE clinical isolates received at the National Reference Centre for Enterococci from French hospitals between 2016 and 2020 were included. LRE isolates were screened for linezolid resistance genes (cfr-like, optrA and poxtA) by real-time PCR and phenotypically characterized. A collection of 11 representative poxtA-positive isolates (10 Enterococcus faecium and 1 Enterococcus faecalis) underwent WGS by hybrid assembly combining short-read (Illumina MiSeq) and long-read (MinION) approaches. Transferability of poxtA was attempted by filter-mating experiments.

Results
Out of 466 LRE received at the National Reference Centre for Enterococci over the period, 47 (10.1%) were poxtA-positive, including 42 E. faecium. The 11 isolates characterized by WGS were confirmed to be epidemiologically unrelated by core genome analysis and eight different STs were assigned to E. faecium isolates. The poxtA gene was found to be plasmid carried and flanked by IS1216E transposase genes in all isolates and frequently linked with fexB, tet(M) and tet(L). A total of seven distinct poxtA-harbouring plasmids were obtained after hybrid assembly and plasmid transfer of poxtA was successful in three cases. For the two poxtA/optrA-positive isolates, those genes were carried by different plasmids.

Conclusions
The poxtA gene has been circulating among clinical enterococci in France since at least 2016, mostly in E. faecium and independently from optrA. The poxtA-carrying plasmids often co-carried resistance genes to phenicols and tetracyclines, and could have been co-selected through their veterinary use.
Towards automatic diagnosis of rheumatic heart disease on echocardiographic exams through video-based deep learning
Authors: Martins João Francisco B S , Nascimento Erickson R , Nascimento Bruno R , Sable Craig A , Beaton Andrea Z , Ribeiro Antônio L , Meira Wagner , Pappa Gisele L 
Published: March 2021

AbstractObjectiveRheumatic heart disease (RHD) affects an estimated 39 million people worldwide and is the most common acquired heart disease in children and young adults. Echocardiograms are the gold standard for diagnosis of RHD, but there is a shortage of skilled experts to allow widespread screenings for early detection and prevention of the disease progress. We propose an automated RHD diagnosis system that can help bridge this gap.Materials and MethodsExperiments were conducted on a dataset with 11 646 echocardiography videos from 912 exams, obtained during screenings in underdeveloped areas of Brazil and Uganda. We address the challenges of RHD identification with a 3D convolutional neural network (C3D), comparing its performance with a 2D convolutional neural network (VGG16) that is commonly used in the echocardiogram literature. We also propose a supervised aggregation technique to combine video predictions into a single exam diagnosis.ResultsThe proposed approach obtained an accuracy of 72.77% for exam diagnosis. The results for the C3D were significantly better than the ones obtained by the VGG16 network for videos, showing the importance of considering the temporal information during the diagnostic. The proposed aggregation model showed significantly better accuracy than the majority voting strategy and also appears to be capable of capturing underlying biases in the neural network output distribution, balancing them for a more correct diagnosis.ConclusionAutomatic diagnosis of echo-detected RHD is feasible and, with further research, has the potential to reduce the workload of experts, enabling the implementation of more widespread screening programs worldwide.
Sweet modification and regulation of death receptor signalling pathway
Authors: Moriwaki Kenta , Chan Francis K M , Miyoshi Eiji 
Published: March 2021

Abstract
Death receptors, members of the tumour necrosis factor receptor (TNFR) superfamily, are characterized by the presence of a death domain in the cytosolic region. TNFR1, Fas and TNF-related apoptosis-inducing ligand receptors, which are prototypical death receptors, exert pleiotropic functions in cell death, inflammation and immune surveillance. Hence, they are involved in several human diseases. The activation of death receptors and downstream intracellular signalling is regulated by various posttranslational modifications, such as phosphorylation, ubiquitination and glycosylation. Glycosylation is one of the most abundant and versatile modifications to proteins and lipids, and it plays a critical role in the development and physiology of organisms, as well as the pathology of many human diseases. Glycans control a number of cellular events, such as receptor activation, signal transduction, endocytosis, cell recognition and cell adhesion. It has been demonstrated that oligo- and monosaccharides modify death receptors and intracellular signalling proteins and regulate their functions. Here, we review the current understanding of glycan modifications of death receptor signalling and their impact on signalling activity.
‘Seeing the Wood for the Trees’: Revisiting the Consistency of Australia’s Illegal Logging Act with the Law of the World Trade Organization
Authors: Gascoigne Catherine E 
Published: March 2021

Abstract
In the absence of coordinated multilateral action, many countries seek to address environmental harm occurring in foreign jurisdictions by introducing measures that regulate the importation of certain products. In Australia, the Illegal Logging Prohibition Act 2012 (Cth) and the Illegal Logging Prohibition Regulation 2012 (Cth) prohibit the import of timber that has been harvested in a manner that is contrary to the laws of the harvesting country. One unsettled question is whether the measure is inconsistent with the law of the World Trade Organization. This article considers this question ahead of the Commonwealth Government’s 10-year review of the Measure. To this end, the article examines the consistency of the Act with the General Agreement on Tariffs and Trade and the Agreement on Technical Barriers to Trade. The findings of the article are relevant to Australia and to other countries that design and implement measures to regulate the importation of products for environmental objectives.
Morphological evolution of supermassive black hole merger hosts and multimessenger signatures
Authors: DeGraf Colin , Sijacki Debora , Di Matteo Tiziana , Holley-Bockelmann Kelly , Snyder Greg , Springel Volker 
Published: March 2021

ABSTRACT
With projects such as Laser Interferometer Space Antenna (LISA) and Pulsar Timing Arrays (PTAs) expected to detect gravitational waves from supermassive black hole mergers in the near future, it is key that we understand what we expect those detections to be, and maximize what we can learn from them. To address this, we study the mergers of supermassive black holes in the Illustris simulation, the overall rate of mergers, and the correlation between merging black holes and their host galaxies. We find these mergers occur in typical galaxies along the MBH−M* relation, and that between LISA and PTAs we expect to probe the full range of galaxy masses. As galaxy mergers can trigger star formation, we find that galaxies hosting low-mass black hole mergers tend to show a slight increase in star formation rates compared to a mass-matched sample. However, high-mass merger hosts have typical star formation rates, due to a combination of low gas fractions and powerful active galactic nucleus feedback. Although minor black hole mergers do not correlate with disturbed morphologies, major mergers (especially at high-masses) tend to show morphological evidence of recent galaxy mergers which survive for ∼500 Myr. This is on the same scale as the infall/hardening time of merging black holes, suggesting that electromagnetic follow-ups to gravitational wave signals may not be able to observe this correlation. We further find that incorporating a realistic time-scale delay for the black hole mergers could shift the merger distribution towards higher masses, decreasing the rate of LISA detections while increasing the rate of PTA detections.