bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selenium nanoparticles inhibit tumor metastasis in prostate cancer through upregulated miR-155-5p-related pathway
Authors: Liao Guolong , Ma He , Li Yamei , Sheng Yiyu , Chen Chujie 
Published: January 2021

ABSTRACT
Prostate cancer are the most common, malignant and lethal tumors in men, and the complexity of prostate cancer (CaP) is also due to the diverse metastasis profile. Selenium nanoparticles (SeNPs) have been reported to have potent antitumor activity, but whether it impacted the tumor metastasis is not fully clear. Here, we confirmed that SeNPs could inhibit the CaP cell migrations and invasions. Combined with our previous findings, we identified a series of microRNAs that could be upregulated significantly under SeNP treatment, among which miR-155-5p acts as a key component in mediating the SeNP-inhibited migration and invasion of CaP cells, through directly targeting IκB kinase ɛ and Sma- and Mad-related protein 2. The cell-based results were proved in xenograft mice modeling. These results have evidently signified the antitumor potential of SeNPs in the treatment of prostate cancer.
Mercator: a pipeline for multi-method, unsupervised visualization and distance generation
Authors: Abrams Zachary B. , Coombes Caitlin E. , Li Suli , Coombes Kevin R. 
Published: January 2021

Abstract

Summary
Unsupervised machine learning provides tools for researchers to uncover latent patterns in large-scale data, based on calculated distances between observations. Methods to visualize high-dimensional data based on these distances can elucidate subtypes and interactions within multi-dimensional and high-throughput data. However, researchers can select from a vast number of distance metrics and visualizations, each with their own strengths and weaknesses. The Mercator R package facilitates selection of a biologically meaningful distance from 10 metrics, together appropriate for binary, categorical and continuous data, and visualization with 5 standard and high-dimensional graphics tools. Mercator provides a user-friendly pipeline for informaticians or biologists to perform unsupervised analyses, from exploratory pattern recognition to production of publication-quality graphics.

Availabilityand implementation
Mercator is freely available at the Comprehensive R Archive Network (https://cran.r-project.org/web/packages/Mercator/index.html).
Confronting taxonomic vandalism in biology: conscientious community self-organization can preserve nomenclatural stability
Authors: Wüster Wolfgang , Thomson Scott A , O’shea Mark , Kaiser Hinrich 
Published: January 2021

Abstract
Self-published taxon descriptions, bereft of a basis of evidence, are a long-standing problem in taxonomy. The problem derives in part from the Principle of Priority in the International Code of Zoological Nomenclature, which forces the use of the oldest available nomen irrespective of scientific merit. This provides a route to ‘immortality’ for unscrupulous individuals through the mass-naming of taxa without scientific basis, a phenomenon referred to as taxonomic vandalism. Following a flood of unscientific taxon namings, in 2013 a group of concerned herpetologists organized a widely supported, community-based campaign to treat these nomina as lying outside the permanent scientific record, and to ignore and overwrite them as appropriate. Here, we review the impact of these proposals over the past 8 years. We identified 59 instances of unscientific names being set aside and overwritten with science-based names (here termed aspidonyms), and 1087 uses of these aspidonyms, compared to one instance of preference for the overwritten names. This shows that when there is widespread consultation and agreement across affected research communities, setting aside certain provisions of the Code can constitute an effective last resort defence against taxonomic vandalism and enhance the universality and stability of the scientific nomenclature.
Consequences of judging in transitional justice courts
Authors: Nyseth Brehm Hollie , Frizzell Laura C , Uggen Christopher , Gertz Evelyn 
Published: January 2021

AbstractResearch has found that participation in transitional justice (TJ) is associated with increased social capital and decreased well-being. This article extends this scholarship by examining how TJ mechanisms affect the social capital and well-being of the people who implement them via interviews with 135 Rwandan gacaca court judges. In terms of well-being, judges discuss pride and confidence yet also highlight stress and trauma. In terms of social capital, many judges are now mediators and local leaders, though numerous judges have also experienced grudges from the families of those they sentenced. These negative consequences were particularly prominent among judges with more authority.
COVID-19 pandemic era: is it time to promote home dialysis and peritoneal dialysis?
Authors: Cozzolino Mario , Conte Ferruccio , Zappulo Fulvia , Ciceri Paola , Galassi Andrea , Capelli Irene , Magnoni Giacomo , La Manna Gaetano 
Published: January 2021

AbstractThe novel coronavirus, called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared a pandemic in March 2020 by the World Health Organization. Older individuals and patients with comorbid conditions such as hypertension, heart disease, diabetes, lung disease, chronic kidney disease (CKD) and immunologic diseases are at higher risk of contracting this severe infection. In particular, patients with advanced CKD constitute a vulnerable population and a challenge in the prevention and control of the disease. Home-based renal replacement therapies offer an opportunity to manage patients remotely, thus reducing the likelihood of infection due to direct human interaction. Patients are seen less frequently, limiting the close interaction between patients and healthcare workers who may contract and spread the disease. However, while home dialysis is a reasonable choice at this time due to the advantage of isolation of patients, measures must be assured to implement the program. Despite its logistical benefits, outpatient haemodialysis also presents certain challenges during times of crises such as the coronavirus disease 2019 (COVID-19) pandemic and potentially future ones.
Prevention of esophageal stricture after circumferential endoscopic submucosal dissection using a modified self-assembling peptide
Authors: Oumrani Sarra , Barret Maximilien , Beuvon Frédéric , Nicco Carole , Chêne Charlotte , Batteux Frédéric , Prat Frédéric 
Published: January 2021

Summary
Circumferential endoscopic resection (ER) of the esophageal mucosa could find its place in the treatment of dysplastic Barrett’s esophagus or extensive squamous cell neoplasia. However, the occurrence of esophageal strictures remains a major complication after ER exceeding 75% of the circumference. The aim of this study was to assess the effect of a modified, pH = 2, self-assembling peptide matrix (4[Arg-Ala-Asp-Ala]) (SAP) on the development of esophageal stricture after circumferential ER in a swine model. We performed a circumferential ER in 35 swine under general anesthesia. Five animals were included in the control group, 11 animals received the SAP matrix immediately after the resection, and 11 received the SAP matrix associated to a local steroid immediately after the resection. Follow-up endoscopy and esophagogram were performed before slaughter and necropsy at day 14. Eight treated animals were kept alive until day 28. At day 14, 27% of the animals in the SAP group developed a symptomatic stricture versus 100% in the control group (P = 0.008) and 50% in the SAP-triamcinolone group (P = 0.11). Application of an SAP matrix after circumferential ER in the swine allowed a significant reduction of the incidence of symptomatic stricture at day 14. Adding triamcinolone brought no significant improvement.
The human side of austerity: health spending and outcomes during the Greek crisis
Authors: Perotti Roberto 
Published: January 2021

SUMMARY
The Greek crisis was the deepest in post-war Europe. Public spending on health, that had grown extremely fast in the first decade of the 2000s, was cut by almost 40% between 2010 and 2016, also an unparalleled figure in post-war Europe. Although some of the cuts were mitigated by a system of clawback on the private pharmaceutical industry and by increased household out of pocket expenditure, the provision of health services was also greatly impacted by the spread of long-term unemployment, which in the employment-based Greek system left possibly millions of individuals without access to health services, until universal coverage was effectively restored in 2016. In this paper I aim at establishing the basic facts about the health crisis. Although care must be exercised in not presenting a simplistic, uniformly bleak picture, I show that several indicators point to a substantial deterioration in the health outcomes of the Greek population during the critical years of loss of universal coverage until 2016, in particular for the more vulnerable sectors of the population.
Physician empathy and patient enablement: survey in the Portuguese primary health care
Authors: Simões José Augusto , Prazeres Filipe , Maricoto Tiago , Simões Pedro Augusto , Lourenço Joana , Romano João Pedro , Santiago Luiz Miguel 
Published: January 2021

Abstract

Background
Empathy is the capacity to understand and resonate with the experiences of other people. Patient enablement is the degree to which a patient feels strengthened in terms of being able to deal with, understand and manage their disease.

Methods
Secondary cross-sectional analysis of existing data from 2 independent datasets (456 primary health care patients), with the application of two validated questionnaires, Jefferson Scale of Patient Perceptions of Physician Empathy (JSPPPE) and Patient Enablement Instrument (PEI).

Objective
Evaluate medical empathy and patients’ enablement after consultation with their family doctors and to verify if there was an association between these two concepts.

Results
The median value of JSPPPE-VP score was 6.60 (interquartile range 1.00) and of PEI/ICC score was of 1.83 (interquartile range 0.67). Regarding empathy (JSPPPE-VP), patients taking chronic medication had a slight but significantly higher median score than patients not taking them (6.70 versus 6.60, P = 0.049), although regression modelling did not confirm any relevant predictor of JSPPPE-VP score. Regarding enablement (PEI/ICC), we found significantly higher scores on younger patients, as well as, on more educated and professionally active ones (P &lt; 0.001). Multivariable linear regression and Poisson regression modelling confirmed such variables as statistically significant potential predictors.

Conclusions
A significant positive association was found between empathy score (JSPPPE-VP) and enablement score (PEI/ICC), when adjusted to sociodemographic cofactors. On this linear regression model, age category and educational level were also significantly associated with empathy score, with the same pattern found on bivariate analysis.
Gene-level quantitative trait mapping in Caenorhabditis elegans
Authors: Noble Luke M , Rockman Matthew V , Teotónio Henrique 
Published: January 2021

Abstract
The Caenorhabditis elegans multiparental experimental evolution (CeMEE) panel is a collection of genome-sequenced, cryopreserved recombinant inbred lines useful for mapping the evolution and genetic basis of quantitative traits. We have expanded the resource with new lines and new populations, and here report the genotype and haplotype composition of CeMEE version 2, including a large set of putative de novo mutations, and updated additive and epistatic mapping simulations. Additive quantitative trait loci explaining 4% of trait variance are detected with &gt;80% power, and the median detection interval approaches single-gene resolution on the highly recombinant chromosome arms. Although CeMEE populations are derived from a long-term evolution experiment, genetic structure is dominated by variation present in the ancestral population.
De novowhole-genome assembly and resequencing resources for the roan (Hippotragus equinus), an iconic African antelope
Authors: Gonçalves Margarida , Siegismund Hans R , Jansen van Vuuren Bettine , Koepfli Klaus-Peter , Ferrand Nuno , Godinho Raquel 
Published: January 2021

AbstractRoan antelope (Hippotragus equinus) is the second-largest member of the Hippotraginae (Bovidae), and is widely distributed across sub-Saharan mesic woodlands. Despite being listed as "Least Concern" across its African range, population numbers are decreasing with many regional Red List statuses varying between Endangered and Locally Extinct. Although the roan antelope has become an economically-important game species in Southern Africa, the vast majority of wild populations are found only in fragmented protected areas, which is of conservation concern. Genomic information is crucial in devising optimal management plans. To this end, we report here the first de novo assembly and annotation of the whole-genome sequence of a male roan antelope from a captive-breeding program. Additionally, we uncover single-nucleotide variants (SNVs) through re-sequencing of five wild individuals representing five of the six described subspecies. We used 10X Genomics Chromium chemistry to produce a draft genome of 2.56 Gb consisting of 16,880 scaffolds with N50 = 8.42 Mb and a BUSCO completeness of 91.2%. The draft roan genome includes 1.1 Gbp (42.2%) repetitive sequences. De novo annotation identified 20,518 protein-coding genes. Genome synteny to the domestic cow showed an average identity of 92.7%. Re-sequencing of five wild individuals to an average sequencing depth of 9.8x resulted in the identification of a filtered set of 3.4x106 bi-allelic SNVs. The proportion of alternative homozygous SNVs for the individuals representing different subspecies, as well as differentiation as measured by PCA, were consistent with expected divergence from the reference genome and among samples. The roan antelope genome is a valuable resource for evolutionary and population genomic questions, as well as management and conservation actions.
Orphan nuclear receptorftz-f1 (NR5A3)promotes egg chamber survival in theDrosophilaovary
Authors: Beachum Allison N , Whitehead Kaitlin M , McDonald Samantha I , Phipps Daniel N , Berghout Hanna E , Ables Elizabeth T 
Published: January 2021

AbstractGamete production in mammals and insects is controlled by cell signaling pathways that facilitate communication between germ cells and somatic cells. Nuclear receptor signaling is a key mediator of many aspects of reproduction, including gametogenesis. For example, the NR5A subfamily of nuclear receptors is essential for gonad development and sex steroid production in mammals. Despite the original identification of the NR5A subfamily in the model insect Drosophila melanogaster, it has been unclear whether Drosophila NR5A receptors directly control oocyte production. Ftz-f1 is expressed throughout the ovary, including in germline stem cells, germline cysts, and several populations of somatic cells. We show that ftz-f1 is required in follicle cells prior to stage 10 to promote egg chamber survival at the mid-oogenesis checkpoint. Our data suggest that egg chamber death in the absence of ftz-f1 is due, at least in part, to failure of follicle cells to exit the mitotic cell cycle or failure to accumulate oocyte-specific factors in the germline. Taken together, these results show that, as in mammals, the NR5A subfamily promotes maximal reproductive output in Drosophila. Our data underscore the importance of nuclear receptors in the control of reproduction and highlight the utility of Drosophila oogenesis as a key model for unraveling the complexity of nuclear receptor signaling in gametogenesis.
The assembled and annotated genome of the pigeon louseColumbicola columbae, a model ectoparasite
Authors: Baldwin-Brown James G , Villa Scott M , Vickrey Anna I , Johnson Kevin P , Bush Sarah E , Clayton Dale H , Shapiro Michael D 
Published: January 2021

AbstractThe pigeon louse Columbicola columbae is a longstanding and important model for studies of ectoparasitism and host-parasite coevolution. However, a deeper understanding of its evolution and capacity for rapid adaptation is limited by a lack of genomic resources. Here, we present a high-quality draft assembly of the C. columbae genome, produced using a combination of Oxford Nanopore, Illumina, and Hi-C technologies. The final assembly is 208 Mb in length, with 12 chromosome-size scaffolds representing 98.1% of the assembly. For gene model prediction, we used a novel clustering method (wavy_choose) for Oxford Nanopore RNA-seq reads to feed into the MAKER annotation pipeline. High recovery of conserved single-copy orthologs (BUSCOs) suggests that our assembly and annotation are both highly complete and highly accurate. Consistent with the results of the only other assembled louse genome, Pediculus humanus, we find that C. columbae has a relatively low density of repetitive elements, the majority of which are DNA transposons. Also similar to P. humanus, we find a reduced number of genes encoding opsins, G protein-coupled receptors, odorant receptors, insulin signaling pathway components, and detoxification proteins in the C. columbae genome, relative to other insects. We propose that such losses might characterize the genomes of obligate, permanent ectoparasites with predictable habitats, limited foraging complexity, and simple dietary regimes. The sequencing and analysis for this genome were relatively low cost, and took advantage of a new clustering technique for Oxford Nanopore RNAseq reads that will be useful to future genome projects.
The complete genome and comparative analysis of the phage phiC120 infecting multidrug-resistant Escherichia coli and Salmonella strains
Authors: Amarillas Luis , Villicaña Claudia , Lightbourn-Rojas Luis , González-Robles Arturo , León-Félix Josefina 
Published: January 2021

Abstract
Phages infecting Salmonella and Escherichia coli are promising agents for therapeutics and biological control of these foodborne pathogens, in particular those strains with resistance to several antibiotics. In an effort to assess the potential of the phage phiC120, a virulent phage isolated from horse feces in Mexico, we characterized its morphology, host range and complete genome. Herein, we showed that phiC120 possesses strong lytic activity against several multidrug-resistant E. coli O157: H7 and Salmonella strains, and its morphology indicated that is a member of Myoviridae family. The phiC120 genome is double-stranded DNA and consists of 186,570 bp in length with a 37.6% G + C content. A total of 281 putative open reading frames (ORFs) and two tRNAs were found, where 150 ORFs encoded hypothetical proteins with unknown function. Comparative analysis showed that phiC120 shared high similarity at nucleotide and protein levels with coliphages RB69 and phiE142. Detailed phiC120 analysis revealed that ORF 94 encodes a putative depolymerase, meanwhile genes encoding factors associated with lysogeny, toxins, and antibiotic resistance were absent; however, ORF 95 encodes a putative protein with potential allergenic and pro-inflammatory properties, making needed further studies to guarantee the safety of phiC120 for human use. The characterization of phiC120 expands our knowledge about the biology of coliphages and provides novel insights supporting its potential for the development of phage-based applications to control unwanted bacteria.
Color morphs of the coral, Acropora tenuis, show different responses to environmental stress and different expression profiles of fluorescent-protein genes
Authors: Satoh Noriyuki , Kinjo Koji , Shintaku Kohei , Kezuka Daisuke , Ishimori Hiroo , Yokokura Atsushi , Hagiwara Kazutaka , Hisata Kanako , Kawamitsu Mayumi , Koizumi Koji , Shinzato Chuya , Zayasu Yuna 
Published: January 2021

Abstract
Corals of the family Acroporidae are key structural components of reefs that support the most diverse marine ecosystems. Due to increasing anthropogenic stresses, coral reefs are in decline. Along the coast of Okinawa, Japan, three different color morphs of Acropora tenuis have been recognized for decades. These include brown (N morph), yellow green (G), and purple (P) forms. The tips of axial polyps of each morph exhibit specific fluorescence spectra. This attribute is inherited asexually, and color morphs do not change seasonally. In Okinawa Prefecture, during the summer of 2017, N and P morphs experienced bleaching, in which many N morphs died. Dinoflagellates (Symbiodiniaceae) are essential partners of scleractinian corals, and photosynthetic activity of symbionts was reduced in N and P morphs. In contrast, G morphs successfully withstood the stress. Examination of the clade and type of Symbiodiniaceae indicated that the three color-morphs host similar sets of Clade-C symbionts, suggesting that beaching of N and P morphs is unlikely attributable to differences in the clade of Symbiodiniaceae the color morphs hosted. Fluorescent proteins play pivotal roles in physiological regulation of corals. Since the A. tenuis genome has been decoded, we identified five genes for green fluorescent proteins (GFPs), two for cyan fluorescent proteins (CFPs), three for red fluorescent proteins (RFPs), and seven genes for chromoprotein (ChrP). A summer survey of gene expression profiles under outdoor aquarium conditions demonstrated that (a) expression of CFP and REP was quite low during the summer in all three morphs, (b) P morphs expressed higher levels of ChrP than N and G morphs, (c) both N and G morphs expressed GFP more highly than P morphs, and (d) GFP expression in N morphs was reduced during summer whereas G morphs maintained high levels of GFP expression throughout the summer. Although further studies are required to understand the biological significance of these color morphs of A. tenuis, our results suggest that thermal stress resistance is modified by genetic mechanisms that coincidentally lead to diversification of color morphs of this coral.
Disrupting progression of the yeast Hsp90 folding pathway at different transition points results in client-specific maturation defects
Authors: Hohrman Kaitlyn , Gonçalves Davi , Morano Kevin A , Johnson Jill L 
Published: January 2021

Abstract
The protein molecular chaperone Hsp90 (Heat shock protein, 90 kilodalton) plays multiple roles in the biogenesis and regulation of client proteins impacting myriad aspects of cellular physiology. Amino acid alterations located throughout Saccharomyces cerevisiae Hsp90 have been shown to result in reduced client activity and temperature-sensitive growth defects. Although some Hsp90 mutants have been shown to affect activity of particular clients more than others, the mechanistic basis of client-specific effects is unknown. We found that Hsp90 mutants that disrupt the early step of Hsp70 and Sti1 interaction, or show reduced ability to adopt the ATP-bound closed conformation characterized by Sba1 and Cpr6 interaction, similarly disrupt activity of three diverse clients, Utp21, Ssl2, and v-src. In contrast, mutants that appear to alter other steps in the folding pathway had more limited effects on client activity. Protein expression profiling provided additional evidence that mutants that alter similar steps in the folding cycle cause similar in vivo consequences. Our characterization of these mutants provides new insight into how Hsp90 and cochaperones identify and interact with diverse clients, information essential for designing pharmaceutical approaches to selectively inhibit Hsp90 function.