bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental Renovascular Disease Induces Endothelial Cell Mitochondrial Damage and Impairs Endothelium-Dependent Relaxation of Renal Artery Segments
Authors: Nargesi Arash Aghajani , Zhu Xiang-Yang , Saadiq Ishran M , Jordan Kyra L , Lerman Amir , Lerman Lilach O , Eirin Alfonso 
Published: March 2020

Abstract

BACKGROUND
Mitochondria modulate endothelial cell (EC) function, but may be damaged during renal disease. We hypothesized that the ischemic and metabolic constituents of swine renovascular disease (RVD) induce mitochondrial damage and impair the function of renal artery ECs.

METHODS
Pigs were studied after 16 weeks of metabolic syndrome (MetS), renal artery stenosis (RAS), or MetS + RAS, and Lean pigs served as control (n = 6 each). Mitochondrial morphology, homeostasis, and function were measured in isolated primary stenotic-kidney artery ECs. EC functions were assessed in vitro, whereas vasoreactivity of renal artery segments was characterized in organ baths.

RESULTS
Lean + RAS and MetS + RAS ECs showed increased mitochondrial area and decreased matrix density. Mitochondrial biogenesis was impaired in MetS and MetS + RAS compared with their respective controls. Mitochondrial membrane potential similarly decreased in MetS, Lean + RAS, and MetS + RAS groups, whereas production of reactive oxygen species increased in MetS vs. Lean, but further increased in both RAS groups. EC tube formation was impaired in MetS, RAS, and MetS + RAS vs. Lean, but EC proliferation and endothelial-dependent relaxation of renal artery segments were blunted in MetS vs. Lean, but further attenuated in Lean + RAS and MetS + RAS.

CONCLUSIONS
MetS and RAS damage mitochondria in pig renal artery ECs, which may impair EC function. Coexisting MetS and RAS did not aggravate EC mitochondrial damage in the short time of our in vivo studies, suggesting that mitochondrial injury is associated with impaired renal artery EC function.
Pottery workers, ‘the Ladies’, and ‘the Middling Class of people’: production and marketing of ‘Etruscan and Grecian vases’ at Wedgwood c.1760–1820*
Authors: Petsalis-Diomidis Alexia 
Published: March 2020

Abstract
Collections of Greek vases, and their reproductions in the form of luxury publications and vessels displayed atop bookshelves in libraries, were the domain of male elites in eighteenth- and nineteenth-century Britain. Less well explored is the consumption of creative reproductions of Greek vases by elite and ‘middling’ women, and the participation of women across the social spectrum in the production of ceramics inspired by Greek vases. This article uses the Wedgwood archive to tell such stories. The subjects range from aristocratic designers through paintresses to women doing the hard labour of wedging. It argues for the importance of recognizing these engagements with Greek vases as part of the history of the reception of Greek vases in Britain. It explores the way that gender and class constrained the kind of contact women had with these materials, and it puts forward an interpretation of these engagements as independent embodied knowledge of Greek vases.
Interpretable factor models of single-cell RNA-seq via variational autoencoders
Authors: Svensson Valentine , Gayoso Adam , Yosef Nir , Pachter Lior 
Published: March 2020

Abstract

Motivation
Single-cell RNA-seq makes possible the investigation of variability in gene expression among cells, and dependence of variation on cell type. Statistical inference methods for such analyses must be scalable, and ideally interpretable.

Results
We present an approach based on a modification of a recently published highly scalable variational autoencoder framework that provides interpretability without sacrificing much accuracy. We demonstrate that our approach enables identification of gene programs in massive datasets. Our strategy, namely the learning of factor models with the auto-encoding variational Bayes framework, is not domain specific and may be useful for other applications.

Availability and implementation
The factor model is available in the scVI package hosted at https://github.com/YosefLab/scVI/.

Contact
v@nxn.se

Supplementary information
Supplementary data are available at Bioinformatics online.
TCRBuilder: multi-state T-cell receptor structure prediction
Authors: Wong Wing Ki , Marks Claire , Leem Jinwoo , Lewis Alan P , Shi Jiye , Deane Charlotte M 
Published: March 2020

Abstract

Motivation
T-cell receptors (TCRs) are immune proteins that primarily target peptide antigens presented by the major histocompatibility complex. They tend to have lower specificity and affinity than their antibody counterparts, and their binding sites have been shown to adopt multiple conformations, which is potentially an important factor for their polyspecificity. None of the current TCR-modelling tools predict this variability which limits our ability to accurately predict TCR binding.

Results
We present TCRBuilder, a multi-state TCR structure prediction tool. Given a paired αβTCR sequence, TCRBuilder returns a model or an ensemble of models covering the potential conformations of the binding site. This enables the analysis of structurally driven polyspecificity in TCRs, which is not possible with existing tools.

Availability and implementation
http://opig.stats.ox.ac.uk/resources.

Contact
deane@stats.ox.ac.uk

Supplementary information
Supplementary data are available at Bioinformatics online.
Bootstrapping M-estimators in generalized autoregressive conditional heteroscedastic models
Authors: Mukherjee K 
Published: March 2020

SummaryWe consider the weighted bootstrap approximation to the distribution of a class of M-estimators for the parameters of the generalized autoregressive conditional heteroscedastic model. We prove that the bootstrap distribution, given the data, is a consistent estimate in probability of the distribution of the M-estimator, which is asymptotically normal. We propose an algorithm for the computation of M-estimates which at the same time is useful for computing bootstrap replicates from the given data. Our simulation study indicates superior coverage rates for various weighted bootstrap schemes compared with the rates based on the normal approximation and existing bootstrap methods for the generalized autoregressive conditional heteroscedastic model, such as percentile $t$-subsampling schemes. Since some familiar bootstrap schemes are special cases of the weighted bootstrap, this paper thus provides a unified theory and algorithm for bootstrapping in generalized autoregressive conditional heteroscedastic models.
Utilization of Direct Oral Anticoagulants in People Living with Human Immunodeficiency Virus: Observational Data from the District of Columbia Cohort
Authors: George Jomy M , Kuriakose Safia S , Monroe Anne , Hou Qingjiang , Byrne Morgan , Pau Alice K , Masur Henry , Hadigan Colleen , Castel Amanda D , Horberg Michael A ,   District of Columbia (D.C.) Cohort Executive Committee, Binkley Jeffery , Taylor Rob , Rayeed Nabil , Akridge Cheryl , Purinton Stacey , Hou Qingjiang , Naughton Jeff , Parfitt David , D’Angelo Lawrence , Rahkmanina Natella , Kharfen Michael , Serlin Michael , Kumar Princy , Parenti David , Castel Amanda , Greenberg Alan , Monroe Anne , Happ Lindsey Powers , Jaurretche Maria , Wilbourn Brittany , Peterson James , Levy Matthew , Byrne Morgan , Ma Yan , Wilcox Ronald , Rana Sohail , Horberg Michael , Fernandez Ricardo , Kuriakose Safia , Hebou Annick , Dieffenbach Carl , George Jomy , Hadigan Colleen , Masur Henry , Pau Alice , Bordon Jose , Teferi Gebeyehu , Benator Debra , Ruiz Maria Elena , Goldstein Deborah 
Published: March 2020

AbstractBackgroundDirect oral anticoagulants (DOACs) have become first-line treatment for venous thrombotic events. DOAC prescribing trends among people living with human immunodeficiency virus (PWH) are not well described. The coadministration of DOACs with the antiretroviral (ARV) pharmacokinetic boosters ritonavir (RTV) or cobicistat (COBI) may be complicated by pharmacokinetic interactions.MethodsA longitudinal cohort study was conducted using the D.C. Cohort Database in Washington, D.C., from January 2011 to March 2017, to describe oral anticoagulant prescribing among PWH ≥ 18 years old and the prevalence of DOAC use with RTV or COBI. Data collection included demographic and clinical characteristics, ARV and anticoagulant prescriptions, and International Classification of Diseases Ninth and Tenth Edition diagnosis codes.ResultsAmong 8315 PWH, there were 236 anticoagulant prescriptions (96 DOAC, 140 warfarin) for 206 persons. PWH prescribed anticoagulants were predominantly Black (82%) and male (82%), with a mean age at anticoagulant initiation of 56 years. DOAC use increased from 3% of total anticoagulant prescribing in 2011 to 43% in 2016, accounting for 64% of all newly recorded anticoagulant prescriptions by 2016. There were 19 bleeding events recorded among 16 individuals. Despite the Food and Drug Administration label recommendation to avoid rivaroxaban with boosted ARVs, 41% remained on boosted ARVs after rivaroxaban initiation.ConclusionsDOAC use increased substantially in PWH by 2016. Although rivaroxaban is not recommended with RTV or COBI, concomitant use was recorded in 41% of rivaroxaban recipients in this cohort. As DOAC usage increases, clinicians need to be aware of potential DOAC/ARV interactions in order to select the most appropriate oral anticoagulant and monitoring plan for PWH.
Effects of Chinese Privet on Bees and Their Vertical Distribution in Riparian Forests
Authors: Ulyshen Michael D , Horn Scott , Hanula James L 
Published: March 2020

AbstractChinese privet (Ligustrum sinense Lour.), is known to negatively affect biodiversity near the ground in invaded forests by forming thick layers of non-native vegetation in the midstory. Whether these effects extend above the shrub layer into the canopy remains unclear. We sought to test this question by using flight-intercept traps (clear plastic panels attached to a white bucket) to sample bees at three heights (0.5, 5, and 15 m) in plots in which L. sinense had or had not been experimentally eliminated. Privet removal (i.e., restoration) resulted in significantly higher bee abundance, richness, and diversity than in invaded sites, but this effect was only observed at 0.5 m. In restored plots, bee diversity was generally higher at 5 and 15 m than near the forest floor, but there were no differences between traps at 5 and 15 m. Our findings show that bees will benefit from the removal of invasive shrubs near the forest floor but not in the canopy. Why bee diversity is higher in the canopy than near the ground in temperate deciduous forests remains unknown.Study ImplicationsChinese privet is recognized as one of the most problematic plants invading southeastern US forests where it has strong negative effects on native plant and insect diversity near the forest floor. This study tested the impacts of privet removal on the diversity of bees at three heights to determine whether the effects of removing privet extend into the canopies of temperate deciduous forests. The findings indicate that management activities aimed at eliminating Chinese privet will greatly increase bee activity near the forest floor but will not immediately impact bee numbers in the canopy.
On the Baum–Connes Conjecture for Groups Acting on CAT(0)-Cubical Spaces
Authors: Brodzki Jacek , Guentner Erik , Higson Nigel , Nishikawa Shintaro 
Published: March 2020

Abstract
We give a new proof of the Baum–Connes conjecture with coefficients for any second countable, locally compact topological group that acts properly and cocompactly on a finite-dimensional CAT(0)-cubical space with bounded geometry. The proof uses the Julg–Valette complex of a CAT(0)-cubical space introduced by the 1st three authors and the direct splitting method in Kasparov theory developed by the last author.
Determination of Some Common Heavy Metals and Radionuclides in Some Medicinal Herbs Using ICP-MS/MS
Authors: Thabit Tamer M A M , Elgeddawy Dalia I H , Shokr Shokr Abdelsalam 
Published: March 2020

Abstract
Medicinal herbs are the ancient, traditional way of treating many diseases and are now considered the first natural source of pharmaceutical active ingredients. Therefore, it is very important to focus on the hygiene of these plants so as to make sure they are safe for consumption. This work aimed to monitor the common heavy and radioactive elements in some commonly used herbs: anise, chamomile, clover, cumin, coriander, fennel, roselle, rosemary, sage, and thyme. A total of 12 elements were measured including 2 radionuclides, Al, As, Cd, Hg, Co, Cr, Ni, Pb, Sr, Th, U, and V. Heavy metals are ecologically and biologically important, and may be involved in some health disorder symptoms within the human body. Samples were digested with a microwave digester and measurements were completed with ICP-MS/MS in Helium mode to increase sensitivity, lower the background, and avoid interferences. Method validation and verification were performed through the spiking process at 2.0 µg/kg level, and then RSD, LOD, and LOQ were calculated. Recoveries ranged from 93–103% for all elements and RSD% from 2.8–9.6%. Hg and Th were not detected in all samples, while U was detected in some sample of anise, rosemary, sage, and thyme, and ranged from 0.018–0.048 mg/kg. As was detected in anise, fennel, roselle, and rosemary, and ranged from 0.0.031–5.88 mg/kg. Al, Cd, Co, Cr, Ni, Pb, Sr, and V were detected in most samples of all herbs, and ranged from 3.88–17.80, 0.122–0.654, 0.019–0.851, 0.344–2.91, 1.872–5.82, 0.120–12.56, 0.128–0.844, and 0.083–0.912 mg/kg, respectively.
Finding a Flexible Hot-Deck Imputation Method for Multinomial Data
Authors: Andridge Rebecca , Bechtel Laura , Thompson Katherine Jenny 
Published: March 2020

Abstract
Detailed breakdowns on totals are often collected in surveys, such as a breakdown of total product sales by product type. These multinomial data are often sparsely reported with wide variability in proportions across units. In addition, there are often true zeros that differ across units even within industry; for example, one establishment sells jeans but not shoes, and another sells shoes but not socks. It is quite common to have large fractions of missing data for these detailed items, even when totals are relatively completely observed. Hot-deck imputation, which fills in missing data with observed data values, is an attractive approach. The entire set of proportions can be simultaneously imputed to preserve multinomial distributions, and zero values can be imputed. However, it is not clear what variant of the hot deck is best. We describe a large set of “flavors” of the hot deck and compare them through simulation and by application to data from the 2012 Economic Census. We consider different ways to create the donor pool: choosing one nearest neighbor (NN), choosing from five NNs, or using all units as the donor pool. We also consider different ways to impute from the donor: directly impute the donor’s vector of proportions or randomly draw from a multinomial distribution using this vector of proportions. We consider scenarios where a strong predictor of these multinomial distributions exists as well as when covariate information is weak.
Prerenal acute kidney injury—still a relevant term in modern clinical practice?
Authors: Bonavia Anthony , Vece Gregory , Karamchandani Kunal 
Published: March 2020

AbstractThe traditional taxonomy of acute kidney injury (AKI) has remained pervasive in clinical nephrology. While the terms ‘prerenal’, ‘intrarenal’ and ‘postrenal’ highlight the diverse pathophysiology underlying AKI, they also imply discrete disease pathways and de-emphasize the nature of AKI as an evolving clinical syndrome with multiple, often simultaneous and overlapping, causes. In a similar vein, prerenal AKI comprises a diverse spectrum of kidney disorders, albeit one that is often managed by using a standardized clinical algorithm. We contend that the term ‘prerenal’ is too vague to adequately convey our current understanding of hypoperfusion-related AKI and that it should thus be avoided in the clinical setting. Practice patterns among nephrologists indicate that AKI-related terminology plays a significant role in the approaches that clinicians take to patients that have this complex disease. Thus, it appears that precise terminology does impact the treatment that patients receive. We will outline differences in the diagnosis and management of clinical conditions lying on the so-called prerenal disease spectrum to advocate caution when administering intravenous fluids to these clinically decompensated patients. An understanding of the underlying pathophysiology may, thus, avert clinical missteps such as fluid and vasopressor mismanagement in tenuous or critically ill patients.
A Broken Antibiotic Market: Review of Strategies to Incentivize Drug Development
Authors: Bhavnani Sujata M , Krause Kevin M , Ambrose Paul G 
Published: March 2020

Abstract
The threat posed by infections arising from antimicrobial-resistant bacteria is a global concern. Despite this trend, the future development of new antimicrobial agents is currently very uncertain. The lack of commercial success for newly launched antimicrobial agents provides little incentive to invest in the development of new agents. To address this crisis, a number of push and pull incentives have been constructed to support antimicrobial drug development. Push incentives, which are designed to lower the cost of developing new antimicrobial agents, include grants, contracts, public-private partnerships, tax credits, and clinical trial networks. Pull incentives, which are designed to facilitate higher financial returns for a newly launched antimicrobial agent, include those that decrease the time for a regulatory review, extend patent exclusivity, or provide premium pricing. Such incentives may also include direct, advanced, or milestone payments or they may be insurance-based whereby healthcare systems pay for the right to access an antimicrobial agent rather than the number of units administered. Another strategy involves the re-evaluation of interpretive criteria for in vitro susceptibility testing (susceptibility breakpoints) of old antimicrobial agents using the same standards applied to those of new agents, which will allow for an accurate determination of antimicrobial resistance. Although each of the above-described strategies will be important to ensure that antimicrobial agents are developed in the decades to come, the update of susceptibility breakpoints for old agents is a strategy that could be implemented quickly and one that could be the most effective for incentivizing drug developers and financiers to reconsider the development of antimicrobial agents.
L’assurance médicaments au Canada : le point de vue de la pédiatrie
Authors: McLaughlin Tom , Jong Geert ‘t , Gilpin Andrea , Hepburn Charlotte Moore 
Published: March 2020

Résumé
Le système d’assurance médicaments du Canada est l’un des plus coûteux au monde, mais des millions de Canadiens peinent pourtant à accéder aux médicaments dont ils ont besoin. C’est pourquoi les gouvernements fédéral, provinciaux et territoriaux envisagent des propositions de polices d’assurance médicaments publiques pour tous les Canadiens. Les polices d’assurance médicaments permettent de prioriser les enfants et les adolescents, dont les besoins pharmacologiques particuliers ont longtemps été négligés. La prise de médicaments sur ordonnance est courante au sein de cette population, puisqu’environ la moitié des enfants et des adolescents canadiens ont besoin d’au moins une ordonnance au cours d’une année donnée. La prise de médicaments demeure toutefois concentrée au sein des populations atteintes de maladies complexes, chroniques ou graves. Les enfants et les adolescents recourent largement aux préparations magistrales et aux médicaments dans un emploi non conforme à l’étiquette, ce qui a une incidence sur l’innocuité, l’efficacité, la palatabilité et les coûts. Les organes décisionnels en matière de remboursement n’accordent pas toute l’importance qu’ils devraient aux avantages uniques des médicaments pédiatriques, ce qui inclut les formulations adaptées à la pédiatrie, une meilleure qualité de vie pour les enfants et les familles et les économies à l’extérieur du système de santé. Quel que soit le modèle d’assurance médicaments finalement adopté, il est essentiel d’offrir une couverture d’assurance médicaments sur ordonnance complète, universelle et transférable pour tous les enfants et les adolescents. C’est pourquoi les experts des médicaments pédiatriques doivent créer un formulaire national de médicaments pédiatriques fondé sur des données probantes. Santé Canada doit également améliorer les processus pour que les formulations et médicaments commerciaux adaptés à la pédiatrie deviennent plus disponibles et accessibles. À cette fin, le gouvernement fédéral doit également soutenir la recherche-développement des médicaments pédiatriques.
Morphine post-conditioning-induced up-regulation of lncRNA TINCR protects cardiomyocytes from ischemia–reperfusion injury via inhibiting degradation and ubiquitination of FGF1
Authors: Wang M , Liu S , Wang H , Tang R , Chen Z 
Published: March 2020

Abstract

Background
Our previous study has demonstrated that morphine post-conditioning (MpostC) protects cardiomyocytes from ischemia/reperfusion (I/R) injury partly through activating protein kinase-epsilon (PKCε) signaling pathway and subsequently inhibiting mitochondrial permeability transition pore (mPTP) opening.

Aim
In this study, we aim to investigate the relationship between long non-coding RNA TINCR and PKCε in cardiomyocytes under MpostC-treated I/R injury.

Design
The myocardial I/R rat model was established by the ligation of lower anterior descending coronary artery for 45 min followed by the reperfusion for 1 h, and MpostC was performed before the reperfusion.

Method
H/R and MpostC were performed in the rat cardiomyocyte cell line (H9C2), and the Cytochrome-c release in cytosol and mPTP opening were determined. Cell viability was detected by using Cell Counting Kit-8, and cell apoptosis was determined by using flow cytometry or TUNEL assay.

Results
The results indicated that MpostC restored the expression of TINCR in I/R rat myocardial tissues. In cardiomyocytes, the therapeutic effect of MpostC, including reduced mPTP opening, reduced Cytochrome-c expression, increased cell viability and reduced cell apoptosis, was dramatically negated by interfering TINCR. The expression of fibroblast growth factor 1 (FGF1), a protein that activates PKCε signaling pathway, was positively correlated with TINCR. The RNA immunoprecipitation and RNA pull-down assay further confirmed the binding between FGF1 and TINCR. Furthermore, TINCR was demonstrated to inhibit the degradation and ubiquitination of FGF1 in cardiomyocytes using the cycloheximide experiment and the ubiquitination assay. The TINCR/FGF1/PKCε axis was revealed to mediate the protective effect of MpostC against hypoxia/reoxygenation injury both in vitro and in vivo.

Conclusion
In conclusion, our findings demonstrated that MpostC-induced up-regulation of TINCR protects cardiomyocytes from I/R injury via inhibiting degradation and ubiquitination of FGF1, and subsequently activating PKCε signaling pathway, which provides a novel insight in the mechanism of TINCR and PKCε during MpostC treatment of I/R injury.