bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metaball skinning of synthetic astroglial morphologies into realistic mesh models for in silico simulations and visual analytics
Authors: Abdellah Marwan , Foni Alessandro , Zisis Eleftherios , Guerrero Nadir Román , Lapere Samuel , Coggan Jay S , Keller Daniel , Markram Henry , Schürmann Felix 
Published: April 2021

Abstract

Motivation
Astrocytes, the most abundant glial cells in the mammalian brain, have an instrumental role in developing neuronal circuits. They contribute to the physical structuring of the brain, modulating synaptic activity and maintaining the blood–brain barrier in addition to other significant aspects that impact brain function. Biophysically, detailed astrocytic models are key to unraveling their functional mechanisms via molecular simulations at microscopic scales. Detailed, and complete, biological reconstructions of astrocytic cells are sparse. Nonetheless, data-driven digital reconstruction of astroglial morphologies that are statistically identical to biological counterparts are becoming available. We use those synthetic morphologies to generate astrocytic meshes with realistic geometries, making it possible to perform these simulations.

Results
We present an unconditionally robust method capable of reconstructing high fidelity polygonal meshes of astroglial cells from algorithmically-synthesized morphologies. Our method uses implicit surfaces, or metaballs, to skin the different structural components of astrocytes and then blend them in a seamless fashion. We also provide an end-to-end pipeline to produce optimized two- and three-dimensional meshes for visual analytics and simulations, respectively. The performance of our pipeline has been assessed with a group of 5000 astroglial morphologies and the geometric metrics of the resulting meshes are evaluated. The usability of the meshes is then demonstrated with different use cases.

Availability and implementation
Our metaball skinning algorithm is implemented in Blender 2.82 relying on its Python API (Application Programming Interface). To make it accessible to computational biologists and neuroscientists, the implementation has been integrated into NeuroMorphoVis, an open source and domain specific package that is primarily designed for neuronal morphology visualization and meshing.

Supplementary information
Supplementary data are available at Bioinformatics online.
Tauroursodeoxycholic acid/TGR5 signaling promotes survival and early development of glucose-stressed porcine embryos
Authors: Dicks Naomi , Gutierrez Karina , Currin Luke , de Macedo Mariana P , Glanzner Werner G , Mondadori Rafael G , Michalak Marek , Agellon Luis B , Bordignon Vilceu 
Published: April 2021

AbstractConditions of impaired energy and nutrient homeostasis, such as diabetes and obesity, are associated with infertility. Hyperglycemia increases endoplasmic reticulum stress as well as oxidative stress and reduces embryo development and quality. Oxidative stress also causes deoxyribonucleic acid damage, which impairs embryo quality and development. The natural bile acid tauroursodeoxycholic acid reduces endoplasmic reticulum stress and rescues developmentally incompetent late-cleaving embryos, as well as embryos subjected to nuclear stress, suggesting the endoplasmic reticulum stress response, or unfolded protein response, and the genome damage response are linked. Tauroursodeoxycholic acid acts via the Takeda-G-protein-receptor-5 to alleviate nuclear stress in embryos. To evaluate the role of tauroursodeoxycholic acid/Takeda-G-protein-receptor-5 signaling in embryo unfolded protein response, we used a model of glucose-induced endoplasmic reticulum stress. Embryo development was impaired by direct injection of tauroursodeoxycholic acid into parthenogenetically activated oocytes, whereas it was improved when tauroursodeoxycholic acid was added to the culture medium. Attenuation of the Takeda-G-protein-receptor-5 precluded the positive effect of tauroursodeoxycholic acid supplementation on development of parthenogenetically activated and fertilized embryos cultured under standard conditions and parthenogenetically activated embryos cultured with excess glucose. Moreover, attenuation of tauroursodeoxycholic acid/Takeda-G-protein-receptor-5 signaling induced endoplasmic reticulum stress, oxidative stress and cell survival genes, but decreased expression of pluripotency genes in parthenogenetically activated embryos cultured under excess glucose conditions. These data suggest that Takeda-G-protein-receptor-5 signaling pathways link the unfolded protein response and genome damage response. Furthermore, this study identifies Takeda-G-protein-receptor-5 signaling as a potential target for mitigating fertility issues caused by nutrient excess-associated blastomere stress and embryo death.
MicroRNAs in amniotic fluid and maternal blood plasma associated with sex determination and early gonad differentiation in cattle
Authors: Sánchez José María , Gómez-Redondo Isabel , Browne John A , Planells Benjamín , Gutiérrez-Adán Alfonso , Lonergan Pat 
Published: April 2021

Abstract
We hypothesized that sexually dimorphic differences exist in the expression of miRNAs in amniotic fluid (AF) and maternal blood plasma (MP) in association with the process of sex determination and gonad differentiation in cattle. Amniotic fluid and MP were collected from six pregnant heifers (three carrying a single male and three a single female embryo) following slaughter on Day 39 postinsemination, coinciding with the peak of SRY expression. Samples (six AF and six MP) were profiled using an miRNA Serum/Plasma Focus PCR Panel. Differentially expressed (DE) miRNAs were identified in AF (n = 5) and associated MP (n = 56) of male vs. female embryos (P &lt; 0.05). Functional analysis showed that inflammatory and immune response were among the 13 biological processes enriched by miRNAs DE in MP in the male group (FDR &lt; 0.05), suggesting that these sex-dependent DE miRNAs may be implicated in modulating the receptivity of the dam to a male embryo. Further, we compared the downstream targets of the sex-dependent DE miRNAs detected in MP with genes previously identified as DE in male vs. female genital ridges. The analyses revealed potential targets that might be important during this developmental stage such as SHROOM2, DDX3Y, SOX9, SRY, PPP1CB, JARID2, USP9X, KDM6A, and EIF2S3. Results from this study highlight novel aspects of sex determination and embryo–maternal communication in cattle such as the potential role of miRNAs in gonad development as well as in the modulation of the receptivity of the dam to a male embryo.
Adjunctive Corticosteroids for Lyme Neuroborreliosis Peripheral Facial Palsy—A Prospective Study With Historical Controls
Authors: Avellan Sanna , Bremell Daniel 
Published: April 2021

Abstract

Background
Lyme neuroborreliosis peripheral facial palsy (LNB PFP) and idiopathic PFP, Bell’s palsy (BP), are the most common causes of facial palsy in borrelia-endemic areas and are clinically similar. Early treatment with corticosteroids has been shown to be effective in Bell’s palsy, and antibiotics improve the outcome in LNB. However, there is a lack of knowledge on how the addition of corticosteroids to standard antibiotic treatment affects the outcome in LNB PFP.

Methods
This prospective, open trial with historical controls was conducted at 2 large hospitals in western Sweden between 2011 and 2018. Adults who presented with LNB PFP were included in the study group and were treated with oral doxycycline 200 mg twice daily for 10 days and prednisolone 60 mg once daily for 5 days, then tapered over 5 days. The historical controls were adult patients with LNB PFP included in previous studies and treated with oral doxycycline. Both groups underwent a follow-up lumbar puncture and were followed until complete recovery or for 12 months.

Results
Fifty-seven patients were included, 27 in the study group and 30 in the control group. Two patients (7%) in the study group and 6 patients (20%) in the control group suffered from sequelae at the end follow-up. There was no statistically significant difference between the groups, either in the proportion of patients with sequelae or in the decline in cerebrospinal fluid mononuclear cell count.

Conclusions
Adjunctive corticosteroids neither improve nor impair the outcome for patients with LNB PFP treated with doxycycline.
Does Teacher Self-Efficacy Predict Writing Practices of Teachers of Deaf and Hard of Hearing Students?
Authors: Graham Steve , Wolbers Kimberly , Dostal Hannah , Holcomb Leala 
Published: April 2021

Abstract
Forty-four elementary grade teachers of deaf and hard of hearing students were surveyed about how they taught writing and their beliefs about writing. Beliefs about writing included their self-efficacy to teach writing, attitude toward writing, and epistemological beliefs about writing. These teachers from fifteen different states in the United States slightly agreed that they were efficacious writing teachers and they were slightly positive about their writing. They slightly agreed that learning to write involves effort and process, moderately disagreed that writing development is innate or fixed, slightly disagreed that knowledge about writing is certain, and were equally split about whether writing knowledge comes from authorities and experts. On average, teachers applied the twenty-two instructional writing practices surveyed at least once a month. They reported their students wrote weekly, and their writing was supported through goal setting, feedback, and prewriting activities. Writing instruction mostly focuses on teaching grammar and how to plan compositions. Teacher self-efficacy uniquely and statistically predicted reported teaching practices after attitude toward writing, and epistemological beliefs were first controlled. Recommendations for future research and implications for practice are presented.
Exact computation of maximum rank correlation estimator
Authors: Shin Youngki , Todorov Zvezdomir 
Published: April 2021

SummaryIn this paper we provide a computation algorithm to get a global solution for the maximum rank correlation estimator using the mixed integer programming (MIP) approach. We construct a new constrained optimization problem by transforming all indicator functions into binary parameters to be estimated and show that it is equivalent to the original problem. We also consider an application of the best subset rank prediction and show that the original optimization problem can be reformulated as MIP. We derive the nonasymptotic bound for the tail probability of the predictive performance measure. We investigate the performance of the MIP algorithm by an empirical example and Monte Carlo simulations.
Fitness Cost of Chlorpyrifos Resistance in Spodoptera frugiperda (Lepidoptera: Noctuidae) on Different Host Plants
Authors: Garlet Cínthia G , Moreira Rafaella P , Gubiani Patricia da S , Palharini Ramon B , Farias Juliano R , Bernardi Oderlei 
Published: April 2021

Abstract
Spodoptera frugiperda (J. E. Smith, 1797) is a polyphagous pest of global relevance due to the damage it inflicts on agricultural crops. In South American countries, this species is one of the principal pests of maize and cotton. Currently, S. frugiperda is also emerging as an important pest of soybeans and winter cereals in Brazil. Chemical control is one of the main control tactics against S. frugiperda, even though resistance against numerous modes of action insecticides has been reported. To support insect resistance management programs, we evaluated the fitness costs of resistance of S. frugiperda to the acetylcholinesterase inhibitor chlorpyrifos. Fitness costs were quantified by comparing biological parameters of chlorpyrifos-resistant and -susceptible S. frugiperda and their F1 hybrids (heterozygotes) on non-Bt cotton, non-Bt maize, non-Bt soybean, and oats. The results revealed that the chlorpyrifos-resistant genotype showed lower pupa-to-adult and egg-to-adult survivorship and reduced larval weights on oats; longer neonate-to-pupa and egg-to-adult developmental periods, and lower pupal weights and fecundity on maize; lower pupal weights on soybean; and reduced fecundity on cotton compared with the chlorpyrifos-susceptible genotype. Fitness costs also affected fertility life table parameters of the resistant genotype, increasing the mean length of a generation on cotton and maize and reducing the potential for population growth on all hosts. These findings suggest fitness costs at the individual and population levels of chlorpyrifos resistance in S. frugiperda, indicating that removal of the selective agent from the environment would result in reduced resistance and opportunities for the restoration of susceptibility.
Peak oxygen consumption achieved at the end of cardiac rehabilitation predicts long-term survival in patients with coronary heart disease
Authors: Carbone Salvatore , Kim Youngdeok , Kachur Sergey , Billingsley Hayley , Kenyon Jonathan , De Schutter Alban , Milani Richard V , Lavie Carl J 
Published: April 2021

Abstract

Aims
Cardiac rehabilitation (CR) improves survival in patients with coronary heart disease (CHD), which is largely mediated by the improvements in cardiorespiratory fitness (CRF) defined as peak oxygen consumption (VO2). Therefore, measuring CRF is essential to predict long-term outcomes in this population. It is unclear, however, whether peak VO2 achieved at the end of CR (END-peak VO2) predicts survival or whether the changes of CRF achieved during CR provide a greater prognostic value. To determine whether END-peak VO2 independently predicts long-term survival in patients with CHD undergoing CR. We also aimed at identifying cut-offs for END-peak VO2 that could be used in clinical practice.

Methods and results
Retrospective analysis of 853 patients with CHD referred to CR who completed a maximal cardiopulmonary exercise test. Survival analysis was performed to examine the risk of all-cause mortality (average follow-up years: 6.65) based on peak VO2. The Contal and O’Quigley’s method was used to determine the optimal cut-off of END-peak VO2 based on the log-rank statistic. END-peak VO2 was inversely associated with mortality risk [hazard ratio (HR) = 0.84; 95% confidence interval (CI) = 0.78–0.90], independent of changes in peak VO2 adjusted for the baseline peak VO2. The estimated cut-off of END-peak VO2 at ≥17.6 mL/kg/min best predicted the survival with high predictive accuracy and patients with END-peak VO2 under the cut-off had a greater risk of mortality (HR = 2.93; 95% CI = 1.81–4.74).

Conclusions
In patient with CHD undergoing CR, END-peak VO2 is an independent predictor for long-term survival. Studies utilizing higher intensity CR programmes, with and without pharmacologic strategies, to increase peak VO2 to a greater degree in those achieving a suboptimal END-peak VO2, are urgently needed.
Pragmatic Adjudication of Election Cases in the European Court of Human Rights
Authors: Kurnosov Dmitry 
Published: April 2021

Abstract
During the past 30 years, the European Court of Human Rights (ECtHR) has been constantly expanding its footprint in the area of democratic rights. However, the Court’s approach to election cases has been arguably more cautious compared to its jurisprudence on freedom of speech, association and assembly. Despite a growing body of scholarship on the ECtHR and democratic processes, this caution is yet to be adequately contextualized. This article aims to fill the gap by developing a normative model of how external considerations affect the ECtHR election jurisprudence. American judge-scholar Richard Posner has proposed pragmatic adjudication as a blueprint for incorporating external considerations into political disputes before the courts. I rely on this blueprint to gauge the level of deference to respondent governments in election cases at the ECtHR between 1987 and 2020. I find that, while the Court gives states wide leeway over political competition, it is less deferential when cases concern access to political process. At the same time, the ECtHR increasingly relies on procedural oversight to detect unfair electoral practices without changing the general distribution of competences.
Perspectives on Epigenetics Alterations Associated with Smoking and Vaping
Authors: Xie Zidian , Rahman Irfan , Goniewicz Maciej L , Li Dongmei 
Published: April 2021

Abstract
Epigenetic alterations, including DNA methylation, microRNA, and long noncoding RNA, play important roles in the pathogenesis of numerous respiratory health conditions and diseases. Exposure to tobacco smoking has been found to be associated with epigenetic changes in the respiratory tract. Marketed as a less harmful alternative to combustible cigarettes, electronic cigarette (e-cigarette) has rapidly gained popularity in recent years, especially among youth and young adults. Accumulative evidence from both animal and human studies has shown that e-cigarette use (vaping) is also linked to similar respiratory health conditions as observed with cigarette smoking, including wheezing, asthma, and COPD. This review aims to provide an overview of current studies on associations of smoking and vaping with epigenetic alterations in respiratory cells and provide future research directions in epigenetic studies related to vaping.
A Transcriptomic Pipeline Adapted for Genomic Sequence Discovery of Germline-Restricted Sequence in Zebra Finch,Taeniopygia guttata
Authors: Asalone Kathryn C , Takkar Ajuni K , Saldanha Colin J , Bracht John R 
Published: April 2021

AbstractSongbirds have an unusual genomic element which is only found in their germline cells, known as the germline-restricted chromosome (GRC). Because germ cells contain both GRC and non-GRC (or A-chromosome) sequences, confidently identifying the GRC-derived elements from genome assemblies has proven difficult. Here, we introduce a new application of a transcriptomic method for GRC sequence identification. By adapting the Stringtie/Ballgown pipeline to use somatic and germline DNA reads, we find that the ratio of fragments per kilobase per million mapped reads can be used to confidently assign contigs to the GRC. Using this comparative coverage analysis, we successfully identify 733 contigs as high confidence GRC sequences (720 newly identified in this study) and 51 contigs which were validated using quantitative polymerase chain reaction. We also identified two new GRC genes, one hypothetical protein and one gene encoding an RNase H-like domain, and placed 16 previously identified but unplaced genes onto their host contigs. With the current focus on sequencing GRCs from different songbirds, our work adds to the genomic toolkit to identify GRC elements, and we provide a detailed protocol and GitHub repository at https://github.com/brachtlab/Comparative_Coverage_Analysis (last accessed May 12, 2021).
The Ca2+-Calmodulin-Activated Protein Phosphatase Calcineurin Negatively Regulates Egf Receptor Signaling in Drosophila Development
Authors: Sullivan Kathleen M C , Rubin Gerald M 
Published: April 2021

Abstract
Calcineurin is a Ca2+-calmodulin-activated, Ser-Thr protein phosphatase that is essential for the translation of Ca2+ signals into changes in cell function and development. We carried out a dominant modifier screen in the Drosophila eye using an activated form of the catalytic subunit to identify new targets, regulators, and functions of calcineurin. An examination of 70,000 mutagenized flies yielded nine specific complementation groups, four that enhanced and five that suppressed the activated calcineurin phenotype. The gene canB2, which encodes the essential regulatory subunit of calcineurin, was identified as a suppressor group, demonstrating that the screen was capable of identifying genes relevant to calcineurin function. We demonstrated that a second suppressor group was sprouty, a negative regulator of receptor tyrosine kinase signaling. Wing and eye phenotypes of ectopic activated calcineurin and genetic interactions with components of signaling pathways suggested a role for calcineurin in repressing Egf receptor/Ras signal transduction. On the basis of our results, we propose that calcineurin, upon activation by Ca2+-calmodulin, cooperates with other factors to negatively regulate Egf receptor signaling at the level of sprouty and the GTPase-activating protein Gap1.
Physical and Genetic Mapping in the Grasses Lolium perenne and Festuca pratensis
Authors: King J , Armstead I P , Donnison I S , Thomas H M , Jones R N , Kearsey M J , Roberts L A , Thomas A , Morgan W G , King I P 
Published: April 2021

Abstract
A single chromosome of the grass species Festuca pratensis has been introgressed into Lolium perenne to produce a diploid monosomic substitution line (2n = 2x = 14). In this line recombination occurs throughout the length of the F. pratensis/L. perenne bivalent. The F. pratensis chromosome and recombinants between it and its L. perenne homeologue can be visualized using genomic in situ hybridization (GISH). GISH junctions represent the physical locations of sites of recombination, enabling a range of recombinant chromosomes to be used for physical mapping of the introgressed F. pratensis chromosome. The physical map, in conjunction with a genetic map composed of 104 F. pratensis-specific amplified fragment length polymorphisms (AFLPs), demonstrated: (1) the first large-scale analysis of the physical distribution of AFLPs; (2) variation in the relationship between genetic and physical distance from one part of the F. pratensis chromosome to another (e.g., variation was observed between and within chromosome arms); (3) that nucleolar organizer regions (NORs) and centromeres greatly reduce recombination; (4) that coding sequences are present close to the centromere and NORs in areas of low recombination in plant species with large genomes; and (5) apparent complete synteny between the F. pratensis chromosome and rice chromosome 1.
Adaptive Divergence in Experimental Populations ofPseudomonas fluorescens. I. Genetic and Phenotypic Bases of Wrinkly Spreader Fitness
Authors: Spiers Andrew J , Kahn Sophie G , Bohannon John , Travisano Michael , Rainey Paul B 
Published: April 2021

AbstractA central feature of all adaptive radiations is morphological divergence, but the phenotypic innovations that are responsible are rarely known. When selected in a spatially structured environment, populations of the bacterium Pseudomonas fluorescens rapidly diverge. Among the divergent morphs is a mutant type termed “wrinkly spreader” (WS) that colonizes a new niche through the formation of self-supporting biofilms. Loci contributing to the primary phenotypic innovation were sought by screening a WS transposon library for niche-defective (WS-) mutants. Detailed analysis of one group of mutants revealed an operon of 10 genes encoding enzymes necessary to produce a cellulose-like polymer (CLP). WS genotypes overproduce CLP and overproduction of the polymer is necessary for the distinctive morphology of WS colonies; it is also required for biofilm formation and to maximize fitness in spatially structured microcosms, but overproduction of CLP alone is not sufficient to cause WS. A working model predicts that modification of cell cycle control of CLP production is an important determinant of the phenotypic innovation. Analysis of &gt;30 kb of DNA encoding traits required for expression of the WS phenotype, including a regulatory locus, has not revealed the mutational causes, indicating a complex genotype-phenotype map.