bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of decidual vasculopathy in central and peripheral regions of placenta with implication of lateral growth and spiral artery remodeling
Authors: Zhang Peilin 
Published: June 2020

AbstractBackgroundDecidual vasculopathy at late gestation was shown to be associated with spiral artery remodeling at implantation. How placental lateral growth is related to spiral artery remodeling in spatiotemporal fashion is to be investigated.DesignThe central and peripheral portions of 105 placentas with decidual vasculopathy at term were examined with or without preeclampsia to see if temporal vascular regeneration was present. Central and peripheral vasculopathy and central and peripheral regeneration were compared.ResultPeripheral portion showed more decidual vasculopathy (88 of total 105, 83.8%) than central portion (72 of total 105, 68.6%, p=0.0018). However, central portion showed more vascular regeneration (51 of total 105, 48.6%) than peripheral portion (23 of total 105, 21.9%, p=0.0024). There is no difference in vasculopathy or regeneration with or without preeclampsia.ConclusionSpiral artery remodeling is non-synchronous during lateral growth and vascular regeneration. This spatiotemporal sequence may help interpretation of morphologic changes of decidual vasculopathy.
in-silicaAnalysis of SARS-CoV-2 viral strain using Reverse Vaccinology Approach: A Case Study for USA
Authors: Agarwal Ajay 
Published: June 2020

AbstractThe recent pandemic of COVID19 that has struck the world is yet to be battled by a potential cure. Countless lives have been claimed due to the existing pandemic and the societal normalcy has been damaged permanently. As a result, it becomes crucial for academic researchers in the field of bioinformatics to combat the existing pandemic. The study involved collecting the virulent strain sequence of SARS-nCoV19 for the country USA against human host through publically available bioinformatics databases. Usingin-silicaanalysis and reverse vaccinology, two leader proteins were identified to be potential vaccine candidates for development of a multi-epitope drug. The results of this study can provide further researchers better aspects and direction on developing vaccine and immune responses against COVID19. This work also aims at promoting the use of existing bioinformatics tools to faster streamline the pipeline of vaccine development.The Situation of COVID19A new infection respiratory disease was first observed in the month of December 2019, in Wuhan, situated in the Hubei province, China. Studies have indicated that the reason of this disease was the emergence of a genetically-novel coronavirus closely related to SARS-CoV. This coronavirus, now named as nCoV-19, is the reason behind the spread of this fatal respiratory disease, now named as COVID-19. The initial group of infections is supposedly linked with the Huanan seafood market, most likely due to animal contact. Eventually, human-to-human interaction occurred and resulted in the transmission of the virus to humans. [13].Since then, nCoV-19 has been rapidly spreading within China and other parts of World. At the time of writing this article (mid-March 2020), COVID-19 has spread across 146 countries. A count of 164,837 cases have been confirmed of being diagnosed with COVID-19, and a total of 6470 deaths have occurred. The cumulative cases have been depicting a rising trend and the numbers are just increasing. WHO has declared COVID-19 to be a “global health emergency”. [14].Current Scenario and ObjectivesCurrently, research is being conducted on a massive level to understand the immunology and genetic characteristics of the disease. However, no cure or vaccine of nCoV-19 has been developed at the time of writing this article.Though, nCoV-19 and SARS-CoV are almost genetically similar, the respiratory syndrome caused by both of them, COVID-19 and SARS respectively, are completely different. Studies have indicated that –“SARS was more deadly but much less infectious than COVID-19”.-World Health Organization
Antigenic evolution on global scale reveals potential natural selection of SARS-CoV-2 by pre-existing cross-reactive T cell immunity
Authors: Zhang Chengdong , Jin Xuanxuan , Chen Xianyang , Leng Qibin , Qiu Tianyi 
Published: June 2020

ABSTRACTThe mutation pattern of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is constantly changing with the places of transmission, but the reason remains to be revealed. Here, we presented the study that comprehensively analyzed the potential selective pressure of immune system restriction, which can drive mutations in circulating SARS-CoV-2 isolates. The results showed that the most common mutation sites of SARS-CoV-2 proteins were located on the non-structural protein ORF1ab and the structural protein Spike. Further analysis revealed mutations in cross-reactive epitopes between SARS-CoV-2 and seasonal coronavirus may help SARS-CoV-2 to escape cellular immunity under the long-term and large-scale community transmission. Meanwhile, the mutations on Spike protein may enhance the ability of SARS-CoV-2 to enter the host cells and escape the recognition of B-cell immunity. This study will increase the understanding of the evolutionary direction and warn about the potential immune escape ability of SARS-CoV-2, which may provide important guidance for the potential vaccine design.
The relationship between EEG and fMRI connectomes is reproducible across simultaneous EEG-fMRI studies from 1.5T to 7T
Authors: Wirsich Jonathan , Jorge João , Iannotti Giannarita , Shamshiri Elhum A , Grouiller Frédéric , Abreu Rodolfo , Lazeyras François , Giraud Anne-Lise , Gruetter Rolf , Sadaghiani Sepideh , Vulliémoz Serge 
Published: June 2020

AbstractBoth electroencephalography (EEG) and functional Magnetic Resonance Imaging (fMRI) are non-invasive methods that show complementary aspects of human brain activity. Despite measuring different proxies of brain activity, both the measured blood-oxygenation (fMRI) and neurophysiological recordings (EEG) are indirectly coupled. The electrophysiological and BOLD signal can map the underlying functional connectivity structure at the whole brain scale at different timescales. Previous work demonstrated a moderate but significant correlation between resting-state functional connectivity of both modalities, however there is a wide range of technical setups to measure simultaneous EEG-fMRI and the reliability of those measures between different setups remains unknown. This is true notably with respect to different magnetic field strengths (low and high field) and different spatial sampling of EEG (medium to high-density electrode coverage).Here, we investigated the reproducibility of the bimodal EEG-fMRI functional connectome in the most comprehensive resting-state simultaneous EEG-fMRI dataset compiled to date including a total of 72 subjects from four different imaging centers. Data was acquired from 1.5T, 3T and 7T scanners with simultaneously recorded EEG using 64 or 256 electrodes. We demonstrate that the whole-brain monomodal connectivity reproducibly correlates across different datasets and that a moderate crossmodal correlation between EEG and fMRI connectivity of r≈0.3 can be reproducibly extracted in low- and high-field scanners. The crossmodal correlation was strongest in the EEG-β frequency band but exists across all frequency bands. Both homotopic and within intrinsic connectivity network (ICN) connections contributed the most to the crossmodal relationship.This study confirms, using a considerably diverse range of recording setups, that simultaneous EEG-fMRI offers a consistent estimate of multimodal functional connectomes in healthy subjects that are dominantly linked through a functional core of ICNs across spanning across the different timescales measured by EEG and fMRI. This opens new avenues for estimating the dynamics of brain function and provides a better understanding of interactions between EEG and fMRI measures. This observed level of reproducibility also defines a baseline for the study of alterations of this coupling in pathological conditions and their role as potential clinical markers.
Nitrocellulose redox permanganometry: a simple method for reductive capacity assessment
Authors: Homolak J , Kodvanj I , Babic Perhoc A , Virag D , Knezovic A , Osmanovic Barilar J , Riederer P , Salkovic-Petrisic M 
Published: June 2020

AbstractWe propose a rapid, simple and robust method for measurement of reductive capacity of liquid and solid biological samples based on potassium permanganate reduction followed by trapping of manganese dioxide precipitate on a nitrocellulose membrane. Moreover, we discuss how nitrocellulose redox permanganometry (NRP) can be used for high-throughput analysis of biological samples and present HistoNRP, its modification used for detailed analysis of reductive capacity spatial distribution in tissue with preserved anatomical relations.
Targeting ACE2-RBD interaction as a platform for COVID19 therapeutics: Development and drug repurposing screen of an AlphaLISA proximity assay
Authors: Hanson Quinlin M. , Wilson Kelli M. , Shen Min , Itkin Zina , Eastman Richard T. , Shinn Paul , Hall Matthew D. 
Published: June 2020

AbstractThe COVID-19 pandemic, caused by SARS-CoV-2, is a pressing public health emergency garnering rapid response from scientists across the globe. Host cell invasion is initiated through direct binding of the viral spike protein to the host receptor angiotensin-converting enzyme 2 (ACE2). Disrupting the spike-ACE2 interaction is a potential therapeutic target for treating COVID-19. We have developed a proximity-based AlphaLISA assay to measure binding of SARS-CoV-2 spike protein Receptor Binding Domain (RBD) to ACE2. Utilizing this assay platform, a drug-repurposing screen against 3,384 small molecule drugs and pre-clinical compounds was performed, yielding 25 high-quality, small-molecule hits that can be evaluated in cell-based models. This established AlphaLISA RBD-ACE2 platform can facilitate evaluation of biologics or small molecules that can perturb this essential viral-host interaction to further the development of interventions to address the global health pandemic.
Quantum dot probes for the quantitative study of drug transport by the MacAB TolC efflux pump in lipid scaffolds
Authors: Souabni Hager , dos Santos William Batista , Cece Quentin , Puvanendran Dhenesh , Picard Martin 
Published: June 2020

AbstractABC tripartite efflux pumps are macromolecular membrane protein machineries that expel a large variety of drugs and export virulence factors from Gram negative bacteria. Using a lipid scaffold mimicking the two-membrane environment of the transporter and designing spectroscopic conditions allowing the monitoring of both ATP hydrolysis and substrate transport in real time, we show that MacAB-TolC accommodates transport and energy consumption with high coupling efficiency.
In-situnon-lethal rapid test to accurately detect the presence of the nematode parasite,Anguillicoloides crassus, in European eel,Anguilla anguilla
Authors: De Noia M. , Poole R. , Kaufmann J. , Waters C. , Adams C. , McGinnity P. , Llewellyn M. 
Published: June 2020

AbstractAnguillicoloides crassusis an invasive nematode parasite of the European eel,Anguilla anguilla, and one of the primary drivers of eel population collapse. The presence of the parasite has been shown to impact many features of eel physiology and life history. Early detection of the parasite is vital to limit the spread ofA. crassus. However, until recently, accurate diagnosis of infection could only be achieved via terminal dissection. To supportA. anguillafisheries management in the context ofA. crassuswe developed a rapid non-lethal and non-invasive environmental DNA method to detect the presence of the parasite in the swim bladder. Screening of 131 wild eels was undertaken between 2017 and 2019 Ireland and UK to validate the procedure. DNA extractions and PCR were conducted using both a Qiagen Stool kit at Glasgow University and in situ using Whatman qualitative filter paper No. 1 and a miniPCR DNA Discovery System™. Primers were specifically designed from the cytochrome oxidase mtDNA gene region. In situ extraction and amplification takes approx. 3h for up to 16 individuals with higher specificity and sensitivity compare to the laboratory Qiagen kit extraction. The local diagnostic procedure demonstrated Positive Predictive Values at 96% and Negative Predictive Values at 87%. Our method will be a powerful tool in the hands of fisheries managers to help protect this iconic but critically endangered species. It will allow a non-invasive monitoring of theA. crassusdispersion across the European waters.
ViR: a tool to account for intrasample variability in the detection of viral integrations
Authors: Pischedda Elisa , Crava Cristina , Carlassara Martina , Gasmi Leila , Bonizzoni Mariangela 
Published: June 2020

ABSTRACTLateral gene transfer (LT) from viruses to eukaryotic cells is a well-recognized phenomenon. Somatic integrations of viruses have been linked to persistent viral infection and genotoxic effects, including various types of cancer. As a consequence, several bioinformatic tools have been developed to identify viral sequences integrated into the human genome. Viral sequences that integrate into germline cells can be transmitted vertically, be maintained in host genomes and be co-opted for host functions. Endogenous viral elements (EVEs) have long been known, but the extent of their widespread occurrence has only been recently appreciated. Modern genomic sequencing analyses showed that eukaryotic genomes may harbor hundreds of EVEs, which derive not only from DNA viruses and retroviruses, but also from nonretroviral RNA viruses and are mostly enriched in repetitive regions of the genome. Despite being increasingly recognized as important players in different biological processes such as regulation of expression and immunity, the study of EVEs in non-model organisms has rarely gone beyond their characterization from annotated reference genomes because of the lack of computational methods suited to solve signals for EVEs in repetitive DNA. To fill this gap, we developed ViR, a pipeline which ameliorates the detection of integration sites by solving the dispersion of reads in genome assemblies that are rich of repetitive DNA. Using paired-end whole genome sequencing (WGS) data and a user-built database of viral genomes, ViR selects the best candidate couples of reads supporting an integration site by solving the dispersion of reads resulting from intrasample variability. We benchmarked ViR to work with sequencing data from both single and pooled DNA samples and show its applicability using WGS data of a non-model organism, the arboviral vectorAedes albopictus. Viral integrations predicted by ViR were molecularly validated supporting the accuracy of ViR results. Additionally, ViR can be readily adopted to detect any LT event providingad hocnon-host sequences to interrogate.
Impact of virus subtype and hostIFNL4genotype on large-scale RNA structure formation in the genome of hepatitis C virus
Authors: Simmonds P. , Cuypers L. , Irving W.L. , McLauchlan J. , Cooke G.S. , Barnes E. ,   STOP-HCV Consortium, Ansari M.A. 
Published: June 2020

ABSTRACTMechanisms underlying the ability of hepatitis C virus (HCV) to establish persistent infections and induce progressive liver disease remain poorly understood. HCV is one of several positive-stranded RNA viruses capable of establishing persistence in their immunocompetent vertebrate hosts, an attribute associated with formation of large scale RNA structure in their genomic RNA. We developed novel methods to analyse and visualise genome-scale ordered RNA structure (GORS) predicted from the increasingly large datasets of complete genome sequences of HCV. Structurally conserved RNA secondary structure in coding regions of HCV localised exclusively to polyprotein ends (core, NS5B). Coding regions elsewhere were also intensely structured based on elevated minimum folding energy difference (MFED) values, but the actual stem-loop elements involved in genome folding were structurally entirely distinct, even between subtypes 1a and 1b. Dynamic remodelling was further evident from comparison of HCV strains in different host genetic background. Significantly higher MFED values, greater suppression of UpA dinucleotide frequencies and restricted diversification were found in subjects with the TT genotype of the rs12979860 SNP in theIFNL4gene compared to the CC (non-expressing) allele. These structural and compositional associations with expression of interferon-λ4 were recapitulated on a larger scale by higher MFED values and greater UpA suppression of genotype 1 compared to genotype 3a, associated with previously reported HCV genotype-associated differences in hepatic interferon-stimulated gene induction. Associations between innate cellular responses with HCV structure and further evolutionary constraints represents an important new element in RNA virus evolution and the adaptive interplay between virus and host.
Sexually Dimorphic DNA Damage Responses and Mutation Avoidance in the Mouse Germline
Authors: Bloom Jordana C. , Schimenti John C. 
Published: June 2020

AbstractGerm cells specified during fetal development form the foundation of the mammalian germline. These primordial germ cells (PGCs) undergo rapid proliferation, yet the germline is highly refractory to mutation accumulation compared to somatic cells. Importantly, while the presence of endogenous or exogenous DNA damage has the potential to impact PGCs, there is little known about how these cells respond to stressors. To better understand the DNA damage response (DDR) in these cells, we exposed pregnant mice to ionizing radiation (IR) at specific gestational time points and assessed the DDR in PGCs. Our results show that PGCs prior to sex determination lack a G1 cell cycle checkpoint. Additionally, the response to IR-induced DNA damage differs between female and male PGCs post-sex determination. IR of female PGCs caused uncoupling of germ cell differentiation and meiotic initiation, while male PGCs exhibited repression of piRNA metabolism and transposon de-repression. We also used whole genome single-cell DNA sequencing to reveal that genetic rescue of DNA repair-deficient germ cells (Fancm-/-) leads to increased mutation incidence and biases. Importantly, our work uncovers novel insights into how PGCs exposed to DNA damage can become developmentally defective, leaving only those genetically fit cells to establish the adult germline.
An empirical test of the role of value certainty in decision making
Authors: Lee Douglas , Coricelli Giorgio 
Published: June 2020

AbstractMost contemporary models of value-based decisions are built on value estimates that are typically self-reported by the decision maker. Such models have been successful in accounting for choice accuracy and response time, and more recently choice confidence. The fundamental driver of such models is choice difficulty, which is almost always defined as the absolute value difference between the subjective value ratings of the options in a choice set. Yet a decision maker is not necessarily able to provide a value estimate with the same degree of certainty for each option that he encounters. We propose that choice difficulty is determined not only by absolute value distance of choice options, but also by their value certainty. In this study, we first demonstrate the reliability of the concept of an option-specific value certainty using three different experimental measures. We then demonstrate the influence that value certainty has on choice, including accuracy (consistency), choice confidence, response time, and choice-induced preference change (i.e., the degree to which value estimates change from pre- to post-choice evaluation). We conclude with a suggestion of how popular contemporary models of choice (e.g., race model, drift-diffusion model) could be improved by including option-specific value certainty as one of their inputs.
Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations
Authors: Shrestha Utsab R. , Smith Jeremy C. , Petridis Loukas 
Published: June 2020

ABSTRACTMolecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy in the force fields and inadequate sampling. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD led to unbiased ensembles of unprecedented accuracy, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of variable sequence properties using two recently optimized force fields. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues).
Homologous chromosomes in asexual rotiferAdineta vagasuggest automixis
Authors: Simion Paul , Narayan Jitendra , Houtain Antoine , Derzelle Alessandro , Baudry Lyam , Nicolas Emilien , Cariou Marie , Guiglielmoni Nadège , Kozlowski Djampa KL , Gaudray Florence Rodriguez , Terwagne Matthieu , Virgo Julie , Noel Benjamin , Wincker Patrick , Danchin Etienne GJ , Marbouty Martial , Hallet Bernard , Koszul Romain , Limasset Antoine , Flot Jean-François , Van Doninck Karine 
Published: June 2020

ABSTRACTThe several hundreds of species of bdelloid rotifers are notorious because they represent an ancient clade comprising only asexual lineages1. Moreover, most bdelloid species have the ability to withstand complete desiccation and high doses of ionizing radiation, being able to repair their DNA after massive genome breakage2. To better understand the impact of long-term asexuality and DNA breakage on genome evolution, a telomere-to-tolemere reference genome assembly of a bdelloid species is critical3, 4. Here we present the first, high quality chromosome-scale genome assembly for the bdelloidA. vagavalidated using three complementary assembly procedures combined with chromosome conformation capture (Hi-C) data. The different assemblies reveal the same genome architecture and using fluorescentin situhybridization (FISH), we demonstrate that theA. vagagenome is composed of six pairs of homologous chromosomes, compatible with meiosis. Moreover, the synteny between homoeologous (or ohnologous) chromosomes is also preserved, confirming their paleotetraploidy. The diploid genome structure ofA. vagaand the presence of very long homozygous tracts show that recombination between homologous chromosomes occurs in this ancient asexual scandal, either during DSB repair or during meiotic pairing. These homozygosity tracts are mainly observed towards the chromosome ends in the clonalA. vagasuggesting signatures of a parthenogenetic mode of reproduction equivalent to central fusion automixis, in which homologous chromosomes are not segregated during the meiotic division.