bluuebunny/crossref_metadata_2025_split huggingface dataset:
Blood analytes of immature Kemp’s ridley sea turtles (Lepidochelys kempii) from Georgia, USA: reference intervals and body size correlations
Authors: Perrault Justin R , Arendt Michael D , Schwenter Jeffrey A , Byrd Julia L , Harms Craig A , Cray Carolyn , Tuxbury Kathryn A , Wood Lawrence D , Stacy Nicole I 
Published: October 2020

Abstract
Health assessments of wildlife species are becoming increasingly important in an ever-changing environment. Kemp’s ridley sea turtles (Lepidochelys kempii; hereafter, Kemp’s ridleys) are critically endangered and incur several on-going threats to their population recovery; therefore, it is imperative to advance the understanding of baseline blood analyte data as a diagnostic and monitoring tool. For in-water, trawl-captured, immature Kemp’s ridleys (minimum N = 31) from Georgia, USA, the objectives of this study were to (1) establish reference intervals (RIs) for packed cell volume (PCV) and 27 plasma biochemistry analytes and (2) determine length-specific relationships in blood analytes. We observed significant positive correlations between minimum straight carapace length and PCV, amylase, calcium:phosphorus ratio, cholesterol, magnesium, triglycerides, total solids, total protein and all protein fractions (e.g. alpha-, beta- and gamma-globulins); aspartate aminotransferase and chloride showed significant negative relationships. These results suggest that certain blood analytes in Kemp’s ridleys change as these animals grow, presumptively due to somatic growth and dietary shifts. The information presented herein, in due consideration of capture technique that may have impacted glucose and potassium concentrations, represents the first report of blood analyte RIs for Kemp’s ridley sea turtles established by guidelines of the American Society for Veterinary Clinical Pathology and will have direct applications for stranded individuals in rehabilitative care and for future investigations into the health status of wild individuals from this population.
Applying a gene-suite approach to examine the physiological status of wild-caught walleye (Sander vitreus)
Authors: Jeffrey Jennifer D , Carlson Hunter , Wrubleski Dale , Enders Eva C , Treberg Jason R , Jeffries Ken M 
Published: October 2020

Abstract
Molecular techniques have been increasingly used in a conservation physiology framework to provide valuable information regarding the mechanisms underlying responses of wild organisms to environmental and anthropogenic stressors. In the present study, we developed a reference gill transcriptome for walleye (Sander vitreus), allowing us to pair a gene-suite approach (i.e. multiple genes across multiple cellular processes) with multivariate statistics to examine the physiological status of wild-caught walleye. For molecular analyses of wild fish, the gill is a useful target for conservation studies, not only because of its importance as an indicator of the physiological status of fish but also because it can be biopsied non-lethally. Walleye were non-lethally sampled following short- (~1.5 months) and long-term (~3.5 months) confinement in the Delta Marsh, which is located south of Lake Manitoba in Manitoba, Canada. Large-bodied walleye are confined in the Delta Marsh from late April to early August by exclusion screens used to protect the marsh from invasive common carp (Cyprinus carpio), exposing fish to potentially stressful water quality conditions. Principal components analysis revealed patterns of transcript abundance consistent with exposure of fish to increasingly high temperature and low oxygen conditions with longer holding in the marsh. For example, longer-term confinement in the marsh was associated with increases in the mRNA levels of heat shock proteins and a shift in the mRNA abundance of aerobic to anaerobic metabolic genes. Overall, the results of the present study suggest that walleye confined in the Delta Marsh may be exhibiting sub-lethal responses to high temperature and low oxygen conditions. These results provide valuable information for managers invested in mediating impacts to a local species of conservation concern. More broadly, we highlight the usefulness of pairing transcriptomic techniques with multivariate statistics to address potential confounding factors that can affect measured physiological responses of wild-caught fish.
Cardiac fibrosis
Authors: Frangogiannis Nikolaos G 
Published: October 2020

AbstractMyocardial fibrosis, the expansion of the cardiac interstitium through deposition of extracellular matrix proteins, is a common pathophysiologic companion of many different myocardial conditions. Fibrosis may reflect activation of reparative or maladaptive processes. Activated fibroblasts and myofibroblasts are the central cellular effectors in cardiac fibrosis, serving as the main source of matrix proteins. Immune cells, vascular cells and cardiomyocytes may also acquire a fibrogenic phenotype under conditions of stress, activating fibroblast populations. Fibrogenic growth factors (such as transforming growth factor-β and platelet-derived growth factors), cytokines [including tumour necrosis factor-α, interleukin (IL)-1, IL-6, IL-10, and IL-4], and neurohumoral pathways trigger fibrogenic signalling cascades through binding to surface receptors, and activation of downstream signalling cascades. In addition, matricellular macromolecules are deposited in the remodelling myocardium and regulate matrix assembly, while modulating signal transduction cascades and protease or growth factor activity. Cardiac fibroblasts can also sense mechanical stress through mechanosensitive receptors, ion channels and integrins, activating intracellular fibrogenic cascades that contribute to fibrosis in response to pressure overload. Although subpopulations of fibroblast-like cells may exert important protective actions in both reparative and interstitial/perivascular fibrosis, ultimately fibrotic changes perturb systolic and diastolic function, and may play an important role in the pathogenesis of arrhythmias. This review article discusses the molecular mechanisms involved in the pathogenesis of cardiac fibrosis in various myocardial diseases, including myocardial infarction, heart failure with reduced or preserved ejection fraction, genetic cardiomyopathies, and diabetic heart disease. Development of fibrosis-targeting therapies for patients with myocardial diseases will require not only understanding of the functional pluralism of cardiac fibroblasts and dissection of the molecular basis for fibrotic remodelling, but also appreciation of the pathophysiologic heterogeneity of fibrosis-associated myocardial disease.
‘The Birds Were in the Net’: Reactions in the Netherlands to News of the St Bartholomew’s Day Massacre, 1572
Authors: Baars Rosanne M 
Published: October 2020

Abstract
This article analyses reactions in the Netherlands to news of the St Bartholomew’s Day massacre in 1572. Although historians have previously studied international reactions to the massacre, they have largely neglected the Netherlands due to the paucity of printed responses to the event in the Low Countries. Through the study of a great number of diaries and chronicles, this article demonstrates how news about the massacre spread rapidly throughout the Netherlands. Chroniclers in the Low Countries reflected on the content and credibility of the horrible news reports from France while writing them down. The ongoing religious wars had made them aware of manipulative strategies that influenced news and its media, including false reports that were spread deliberately by the enemy. This article argues that the study of transnational news reports illuminates contemporary questions on authority and trustworthiness in a rapidly polarizing religious climate.
Clinical Characteristics and Risk Factors for Mortality in Very Old Patients Hospitalized With COVID-19 in Spain
Authors: Ramos-Rincon Jose-Manuel , Buonaiuto Verónica , Ricci Michele , Martín-Carmona Jesica , Paredes-Ruíz Diana , Calderón-Moreno María , Rubio-Rivas Manel , Beato-Pérez José-Luis , Arnalich-Fernández Francisco , Monge-Monge Daniel , Vargas-Núñez Juan-Antonio , Acebes-Repiso Gonzalo , Mendez-Bailon Manuel , Perales-Fraile Isabel , García-García Gema-María , Guisado-Vasco Pablo , Abdelhady-Kishta Alaaeldeen , Pascual-Pérez Maria-de-los-Reyes , Rodríguez-Fernández-Viagas Cristina , Montaño-Martínez Adrián , López-Ruiz Antonio , Gonzalez-Juarez Maria-Jesus , Pérez-García Cristina , Casas-Rojo José-Manuel , Gómez-Huelgas Ricardo ,   SEMI-COVID-19 Network
Published: October 2020

Abstract

Background
Advanced age is a well-known risk factor for poor prognosis in COVID-19. However, few studies have specifically focused on very old inpatients with COVID-19. This study aims to describe the clinical characteristics of very old inpatients with COVID-19 and identify risk factors for in-hospital mortality at admission.

Methods
We conducted a nationwide, multicenter, retrospective, observational study in patients ≥ 80 years hospitalized with COVID-19 in 150 Spanish hospitals (SEMI-COVID-19) Registry (March 1–May 29, 2020). The primary outcome was in-hospital mortality. A uni- and multivariate logistic regression was performed to assess predictors of mortality at admission.

Results
A total of 2772 consecutive patients (49.4% men, median age 86.3 years) were analyzed. Rates of atherosclerotic cardiovascular disease, diabetes mellitus, dementia, and Barthel Index &lt; 60 were 30.8%, 25.6%, 30.5%, and 21.0%, respectively. The overall case-fatality rate was 46.9% (n: 1301) and increased with age (80–84 years: 41.6%; 85–90 years: 47.3%; 90–94 years: 52.7%; ≥95 years: 54.2%). After analysis, male sex and moderate-to-severe dependence were independently associated with in-hospital mortality; comorbidities were not predictive. At admission, independent risk factors for death were: oxygen saturation &lt; 90%; temperature ≥ 37.8°C; quick sequential organ failure assessment (qSOFA) score ≥ 2; and unilateral–bilateral infiltrates on chest x-rays. Some analytical findings were independent risk factors for death, including estimated glomerular filtration rate &lt; 45 mL/min/1.73 m2; lactate dehydrogenase ≥ 500 U/L; C-reactive protein ≥ 80 mg/L; neutrophils ≥ 7.5 × 103/μL; lymphocytes &lt; 0.8 × 103/μL; and monocytes &lt; 0.5 × 103/μL.

Conclusions
This first large, multicenter cohort of very old inpatients with COVID-19 shows that age, male sex, and poor preadmission functional status—not comorbidities—are independently associated with in-hospital mortality. Severe COVID-19 at admission is related to poor prognosis.
In It Together: A Qualitative Meta-Synthesis of Common and Unique Psychosocial Stressors and Adaptive Coping Strategies of Persons With Young-Onset Dementia and Their Caregivers
Authors: Bannon Sarah , Reichman Mira , Popok Paula , Wagner Juliana , Gates Melissa , Uppal Simrit , LeFeber Lisa , Wong Bonnie , Dickerson Bradford C , Vranceanu Ana-Maria 
Published: October 2020

Abstract

Background and Objectives
The common and unique psychosocial stressors and adaptive coping strategies of people with young-onset dementia (PWDs) and their caregivers (CGs) are poorly understood. This meta-synthesis used the stress and coping framework to integrate and organize qualitative data on the common and unique psychosocial stressors and adaptive coping strategies employed by PWDs and CGs after a diagnosis of young-onset dementia (YOD).

Research Design and Methods
Five electronic databases were searched for qualitative articles from inception to January 2020. Qualitative data were extracted from included articles and synthesized across articles using taxonomic analysis.

Results
A total of 486 articles were obtained through the database and hand searches, and 322 articles were screened after the removal of duplicates. Sixty studies met eligibility criteria and are included in this meta-synthesis. Four themes emerged through meta-synthesis: (a) common psychosocial stressors experienced by both PWDs and CGs, (b) unique psychosocial stressors experienced by either PWDs or CGs, (c) common adaptive coping strategies employed by both PWDs and CGs, and (d) unique adaptive coping strategies employed by either PWDs or CGs. Within each meta-synthesis theme, subthemes pertaining to PWDs, CGs, and dyads (i.e., PWD and CG as a unit) emerged.

Discussion and Implications
The majority of stressors and adaptive coping strategies of PWDs and CGs were common, supporting the use of dyadic frameworks to understand the YOD experience. Findings directly inform the development of resiliency skills interventions to promote adaptive coping in the face of a YOD diagnosis for both PWDs and CGs.
Renewable hybrid energy systems using geothermal energy: hybrid solar thermal–geothermal power plant
Authors: El Haj Assad Mamdouh , Ahmadi Mohammad Hossein , Sadeghzadeh Milad , Yassin Ameera , Issakhov Alibek 
Published: October 2020

Abstract
New and innovative solutions are being developed to overcome the challenges of detrimental effects that the traditional energy systems cause. This means that sustainable methods are implemented to do so, noting that when such developments are taken into consideration and are studied, this leads to a significant drop in the cost of renewable energy systems. In this work, a hybrid system consisting of a single flash steam geothermal power plant and a solar thermal system using a parabolic trough collector (PTC) is studied. Based on the available works in literature, the required design materials and modeling equations are chosen and discussed. The heat transfer fluid (HTF) as water is chosen as the working fluid for the PTC due to its low cost and high specific heat capacity. The calculations are carried out for the PTC on a specific day, time and location, and the simulations for the geothermal power plant (GPP) are carried out using System Advisor Model (SAM) software, assuming a specific increase in the temperature of the geofluid due to the additional heat transfer from the HTF of the PTC. The power plant output is 20 MW powered by four production wells. The results show that the energy production is ~15 GWh in January, which is the highest during the year due to the required energy demand for electricity consumption and district heating. Moreover, a mini review of the mathematical modeling of PTC and single flash geothermal power plant is presented.
A Horse of a Different Color?: Tensile Strength and Elasticity of Sloth Flexor Tendons
Authors: Mossor A M , Austin B L , Avey-Arroyo J A , Butcher M T 
Published: October 2020

AbstractTendons must be able to withstand the tensile forces generated by muscles to provide support while avoiding failure. The properties of tendons in mammal limbs must therefore be appropriate to accommodate a range of locomotor habits and posture. Tendon collagen composition provides resistance to loading that contributes to tissue strength which could, however, be modified to not exclusively confer large strength and stiffness for elastic energy storage/recovery. For example, sloths are nearly obligate suspenders and cannot run, and due to their combined low metabolic rate, body temperature, and rate of digestion, they have an extreme need to conserve energy. It is possible that sloths have a tendon “suspensory apparatus” functionally analogous to that in upright ungulates, thus allowing for largely passive support of their body weight below-branch, while concurrently minimizing muscle contractile energy expenditure. The digital flexor tendons from the fore- and hindlimbs of two-toed (Choloepus hoffmanni) and three-toed (Bradypus variegatus) sloths were loaded in tension until failure to test this hypothesis. Overall, tensile strength and elastic (Young’s) modulus of sloth tendons were low, and these material properties were remarkably similar to those of equine suspensory “ligaments.” The results also help explain previous findings in sloths showing relatively low levels of muscle activation in the digital flexors during postural suspension and suspensory walking.
Group II Introns Generate Functional Chimeric Relaxase Enzymes with Modified Specificities through Exon Shuffling at Both the RNA and DNA Level
Authors: LaRoche-Johnston Félix , Bosan Rafia , Cousineau Benoit 
Published: October 2020

AbstractGroup II introns are large self-splicing RNA enzymes with a broad but somewhat irregular phylogenetic distribution. These ancient retromobile elements are the proposed ancestors of approximately half the human genome, including the abundant spliceosomal introns and non-long terminal repeat retrotransposons. In contrast to their eukaryotic derivatives, bacterial group II introns have largely been considered as harmful selfish mobile retroelements that parasitize the genome of their host. As a challenge to this view, we recently uncovered a new intergenic trans-splicing pathway that generates an assortment of mRNA chimeras. The ability of group II introns to combine disparate mRNA fragments was proposed to increase the genetic diversity of the bacterial host by shuffling coding sequences. Here, we show that the Ll.LtrB and Ef.PcfG group II introns from Lactococcus lactis and Enterococcus faecalis respectively can both use the intergenic trans-splicing pathway to catalyze the formation of chimeric relaxase mRNAs and functional proteins. We demonstrated that some of these compound relaxase enzymes yield gain-of-function phenotypes, being significantly more efficient than their precursor wild-type enzymes at supporting bacterial conjugation. We also found that relaxase enzymes with shuffled functional domains are produced in biologically relevant settings under natural expression levels. Finally, we uncovered examples of lactococcal chimeric relaxase genes with junctions exactly at the intron insertion site. Overall, our work demonstrates that the genetic diversity generated by group II introns, at the RNA level by intergenic trans-splicing and at the DNA level by recombination, can yield new functional enzymes with shuffled exons, which can lead to gain-of-function phenotypes.
ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years
Authors: Nikam Rahul , Kulandaisamy A , Harini K , Sharma Divya , Gromiha M Michael 
Published: October 2020

Abstract
ProThermDB is an updated version of the thermodynamic database for proteins and mutants (ProTherm), which has ∼31 500 data on protein stability, an increase of 84% from the previous version. It contains several thermodynamic parameters such as melting temperature, free energy obtained with thermal and denaturant denaturation, enthalpy change and heat capacity change along with experimental methods and conditions, sequence, structure and literature information. Besides, the current version of the database includes about 120 000 thermodynamic data obtained for different organisms and cell lines, which are determined by recent high throughput proteomics techniques using whole-cell approaches. In addition, we provided a graphical interface for visualization of mutations at sequence and structure levels. ProThermDB is cross-linked with other relevant databases, PDB, UniProt, PubMed etc. It is freely available at https://web.iitm.ac.in/bioinfo2/prothermdb/index.html without any login requirements. It is implemented in Python, HTML and JavaScript, and supports the latest versions of major browsers, such as Firefox, Chrome and Safari.
3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome
Authors: Kim Kyukwang , Jang Insu , Kim Mooyoung , Choi Jinhyuk , Kim Min-Seo , Lee Byungwook , Jung Inkyung 
Published: October 2020

Abstract
Three-dimensional (3D) genome organization is tightly coupled with gene regulation in various biological processes and diseases. In cancer, various types of large-scale genomic rearrangements can disrupt the 3D genome, leading to oncogenic gene expression. However, unraveling the pathogenicity of the 3D cancer genome remains a challenge since closer examinations have been greatly limited due to the lack of appropriate tools specialized for disorganized higher-order chromatin structure. Here, we updated a 3D-genome Interaction Viewer and database named 3DIV by uniformly processing ∼230 billion raw Hi-C reads to expand our contents to the 3D cancer genome. The updates of 3DIV are listed as follows: (i) the collection of 401 samples including 220 cancer cell line/tumor Hi-C data, 153 normal cell line/tissue Hi-C data, and 28 promoter capture Hi-C data, (ii) the live interactive manipulation of the 3D cancer genome to simulate the impact of structural variations and (iii) the reconstruction of Hi-C contact maps by user-defined chromosome order to investigate the 3D genome of the complex genomic rearrangement. In summary, the updated 3DIV will be the most comprehensive resource to explore the gene regulatory effects of both the normal and cancer 3D genome. ‘3DIV’ is freely available at http://3div.kr.
Functional analysis of low-grade glioma genetic variants predicts key target genes and transcription factors
Authors: Manjunath Mohith , Yan Jialu , Youn Yeoan , Drucker Kristen L , Kollmeyer Thomas M , McKinney Andrew M , Zazubovich Valter , Zhang Yi , Costello Joseph F , Eckel-Passow Jeanette , Selvin Paul R , Jenkins Robert B , Song Jun S 
Published: October 2020

AbstractBackgroundLarge-scale genome-wide association studies (GWAS) have implicated thousands of germline genetic variants in modulating individuals’ risk to various diseases, including cancer. At least 25 risk loci have been identified for low-grade gliomas (LGGs), but their molecular functions remain largely unknown.MethodsWe hypothesized that GWAS loci contain causal single nucleotide polymorphisms (SNPs) that reside in accessible open chromatin regions and modulate the expression of target genes by perturbing the binding affinity of transcription factors (TFs). We performed an integrative analysis of genomic and epigenomic data from The Cancer Genome Atlas and other public repositories to identify candidate causal SNPs within linkage disequilibrium blocks of LGG GWAS loci. We assessed their potential regulatory role via in silico TF binding sequence perturbations, convolutional neural network trained on TF binding data, and simulated annealing–based interpretation methods.ResultsWe built an interactive website (http://education.knoweng.org/alg3/) summarizing the functional footprinting of 280 variants in 25 LGG GWAS regions, providing rich information for further computational and experimental scrutiny. We identified as case studies PHLDB1 and SLC25A26 as candidate target genes of rs12803321 and rs11706832, respectively, and predicted the GWAS variant rs648044 to be the causal SNP modulating ZBTB16, a known tumor suppressor in multiple cancers. We showed that rs648044 likely perturbed the binding affinity of the TF MAFF, as supported by RNA interference and in vitro MAFF binding experiments.ConclusionsThe identified candidate (causal SNP, target gene, TF) triplets and the accompanying resource will help accelerate our understanding of the molecular mechanisms underlying genetic risk factors for gliomas.