bluuebunny/crossref_metadata_2025_split huggingface dataset:
The CT Scan Lung Severity Score and Vaccination Status in COVID-19 patients in India: Perspective of an Independent Radiology Practice
Authors: Lakhia Revat T. , Trivedi Jaimin R. 
Published: July 2021

AbstractBackgroundThe COVID-19 patients often undergo a high-resolution CT scan to determine extent of their lung involvement. The aim of this study was to determine lung involvement in confirmed/suspected COVID-19 patients (encountered at an independent radiology practice) and its correlation to vaccination status amidst the second COVID-19 wave in India.MethodsWe retrospectively queried our data since April 2021 to identify adult patients (>17 years) who had confirmed (positive RT-PCR or antigen test) or suspected COVID-19 (classic symptoms but negative RT-PCR) and received a high-resolution CT scan to determine the extent of their lung involvement using the CT severity (CT-SS) score. Patients were classified in 3 groups based on their vaccination status to determine its correlation with the CT-SS score: fully vaccinated, partially vaccinated, and unvaccinated. Basic descriptive statistics, univariate tests and multivariate linear regression analysis were used.ResultsWe identified 229 patients (median age 45 years, 60% male) of which 205 (89%) had confirmed COVID-19 (positive RT-PCR) and 24 had suspected disease (negative RT-PCT but classic symptoms). Of the 229 patients 29 (13%) had complete vaccination, 38 (17%) had partial vaccination and 162 (70%) had no vaccination. The CT score of the completely vaccinated patients was significantly lower compared to partially or unvaccinated patients (median 0 v. 3.5 v. 10, respectively p<.01). A multivariate linear regression model showed that partial or fully vaccinated patients had lower CT severity score compared to unvaccinated patients (adjusted R squared = 0.47).ConclusionWe present here the real-world findings from an independent radiology practice (a unique and common practice model), in India amid the second COVID-19 wave showing significantly lower CT severity score in fully or partially vaccinated patients compared to unvaccinated patients. Complete vaccination in patients could be critical in preventing severe lung disease.
Prevalence of anti-platelet factor4/polyanionic antibodies after COVID-19 vaccination with ChAdOx1 nCoV-19 and CoronaVac in Thais
Authors: Noikongdee Phichchapha , Police Pornnapa , Phojanasenee Tichayapa , Chantrathammachart Pichika , Niparuck Pimjai , Puavilai Teeraya , Phuphuakrat Angsana , Angchaisuksiri Pantep , Boonyawat Kochawan 
Published: July 2021

AbstractIntroductionVaccine-induced thrombotic thrombocytopenia (VITT) has been reported after vaccination with the adenoviral vector COVID-19 vaccine ChAdOx1 nCoV-19 in European countries. To date, no case of VITT has been reported in Thais after COVID-19 vaccination. We determined the frequency of anti-PF4/polyanionic antibodies in the Thai population receiving the COVID-19 vaccines.MethodsWe conducted a cross-sectional study to evaluate the prevalence of anti-PF4/polyanionic antibodies in health care workers who received COVID-19 vaccination with ChAdOx1 nCoV-19 or CoronaVac within 7-35 days. A control population who had not been vaccinated was also included. Anti-PF4/polyanionic antibodies were detected using enzyme-link immunosorbent assay (ELISA). Functional assay with platelet aggregation was performed for all positive anti-PF4/polyanionic antibody ELISA tests.ResultsA total of 646 participants were included in the study. 221 received ChAdOx1 nCoV-19, 232 received CoronaVac, and 193 participants were in the control group. The prevalence of anti-PF4 antibodies was 2.3% (95% confidence interval [CI] 0.7 to 5.2), 1.7% (95% CI, 0.5 to 4.4) in the ChAdOx1 nCoV-19 and CoronaVac groups, respectively. There was no positive test in the control group. None of the PF4/polyanionic positive sera induced platelet aggregation.ConclusionWe found a low prevalence of anti-PF4 antibodies in Thais after vaccination with ChAdOx1 nCoV-19 and CoronaVac. Low titer positive PF4/polyanionic ELISA results should be interpreted with caution when screening asymptomatic individuals after vaccination against COVID-19.HighlightsHigh titer PF4/polyanion antibodies are associated with vaccine-induced immune thrombotic thrombocytopenia (VITT).Low titer PF4/polyanion antibodies occur after vaccination with ChAdOx1 nCoV-19 and CoronaVac in some vaccinees.These PF4/polyanion antibodies do not activate platelets and lack of association with VITT.Low-titer positive PF4/polyanionic ELISA results should be interpreted with caution when screening asymptomatic individuals after vaccination against COVID-19.
Body size mediates latitudinal population differences in response to Bd infection in two amphibian species
Authors: Meurling Sara , Cortazar-Chinarro Maria , Siljestam Mattias , Åhlen David , Ågren Erik , Höglund Jacob , Laurila Anssi 
Published: July 2021

AbstractPopulations of the same species may differ in their sensitivity to pathogens but the factors behind this variation are poorly understood. Moreover, infections may cause sub-lethal fitness effects even in species resistant or tolerant to disease. The chytrid fungus Batrachochytrium dendrobatidis (Bd), is a generalist pathogen which has caused amphibian population declines worldwide. In many species, Bd infection causes the disease chytridiomycosis, often leading to high mortality. We investigated how geographical origin affects tolerance to Bd by exposing newly metamorphosed individuals of two North European amphibians (moor frog Rana arvalis, common toad Bufo bufo) from two latitudinal regions to two different BdGPL strains. Bd exposure strongly lowered survival in B. bufo, and in both species survival was lower in the northern region, this difference being much stronger in B. bufo. Northern individuals were smaller in both species, and the survival difference between the regions was size-mediated with smaller individuals being more sensitive to Bd. In both species, Bd exposure led to sub-lethal effects in terms of reduced growth suggesting that even individuals surviving the infection may have reduced fitness mediated by smaller body size. Bd strain affected size-dependent mortality differently in the two regions. We discuss the possible mechanisms how body size and geographical origin can contribute to the present results.
Impact of acute visual experience on development of LGN receptive fields in the ferret
Authors: Stacy Andrea K. , Schneider Nathan A. , Gilman Noah K. , Van Hooser Stephen D. 
Published: July 2021

AbstractSelectivity for direction of motion is a key feature of primary visual cortical neurons. Visual experience is required for direction selectivity in carnivore and primate visual cortex, but the circuit mechanisms of its formation remain incompletely understood. Here we examined how developing lateral geniculate nucleus (LGN) neurons may contribute to cortical direction selectivity. Using in vivo electrophysiology techniques, we examined LGN receptive field properties of visually naïve female ferrets before and after exposure to 6 hours of motion stimuli in order to assess the effect of acute visual experience on LGN cell development. We found that acute experience with motion stimuli did not significantly affect the weak orientation or direction selectivity of LGN neurons. In addition, we found that neither latency nor sustainedness or transience of LGN neurons significantly changed with acute experience. These results suggest that the direction selectivity that emerges in cortex after acute experience is computed in cortex and cannot be explained by changes in LGN cells.Significance StatementThe development of typical neural circuitry requires experience-independent and experience-dependent factors. In the visual cortex of carnivores and primates, selectivity for motion arises as a result of experience, but we do not understand whether the major brain area that sits between the retina and the visual cortex – the lateral geniculate nucleus of the thalamus – also participates. Here we found that lateral geniculate neurons do not exhibit changes as a result of several hours of visual experience with moving stimuli, at a time when visual cortical neurons undergo a rapid change. We conclude that lateral geniculate neurons do not participate in this plasticity, and that changes in cortex are likely responsible for the development of direction selectivity in carnivores and primates.
Multiple stage hydra effect in a stage–structured prey–predator model
Authors: Costa Michel Iskin da S. , Anjos Lucas dos , Esteves Pedro V. 
Published: July 2021

AbstractIn this work, we show by means of numerical bifurcation that two alternative stable states exhibit a hydra effect in a continuous–time stage–structured predator–prey model. We denote this behavior as a stage multiple hydra effect. This concomitant effect can have significant implications in population dynamics as well as in population management.
NDC1 is necessary for the stable assembly of the nuclear pore scaffold to establish nuclear transport in early C. elegans embryos
Authors: Mauro Michael Sean , Celma Gunta , Zimyanin Vitaly , Gibson Kimberley H. , Redemann Stefanie , Bahmanyar Shirin 
Published: July 2021

SummaryNuclear pore complexes (NPCs) are large protein assemblies that facilitate transport of macromolecules across the nuclear envelope (NE) [1, 2]. How thousands of NPCs rapidly assemble after open mitosis to form a functional NE is not known. Recruitment of the Nup107-160 outer ring scaffold to chromatin initiates NPC assembly. The Nup53/93 complex bridges the outer ring to the central channel to form a functional pore [3–6]. Nup53 interacts with the conserved transmembrane nucleoporin Ndc1; however, how Ndc1 contributes to post-mitotic NPC assembly is unclear [7–9]. Here, we use C. elegans embryos to show that the timely formation of a functional NE after mitosis depends on Ndc1. Endogenously tagged Ndc1 is recruited early to the reforming NE and is highly mobile in the nuclear rim. 3D analysis of post-mitotic NE formation revealed a decreased NPC density in NEs of ndc1 deleted embryos – continuous nuclear membranes contained few holes where assembling NPCs are normally located. Nup160 is highly mobile in NEs depleted of Ndc1 and outer ring scaffold components are less enriched at the rim. When both ndc1 and nup53 are absent, nuclear assembly fails. Together, these data show that Ndc1 dynamically associates with the NE and promotes stable association of the outer ring scaffold in the NE to facilitate NPC assembly after open mitosis. Furthermore, Ndc1 and Nup53 function in parallel to drive nuclear assembly. We propose that Ndc1 is a dynamic membrane adaptor that helps recruit and promote the self-assembly of the nuclear pore scaffold to drive post-mitotic NPC assembly.
Modelling, characterization of data-dependent and process-dependent errors in DNA data storage
Authors: Wang Yixin , Noor-A-Rahim Md , Gunawan Erry , Guan Yong Liang , Poh Chueh Loo 
Published: July 2021

AbstractMotivationUsing DNA as the medium to store information has recently been recognized as a promising solution for long-term data storage. While several system prototypes have been demonstrated, the error characteristics in DNA data storage are discussed with limited content. Due to the data and process variations from experiment to experiment, the error variation and its effect on data recovery remain to be uncovered. To close the gap, we systematically investigate the storage channel, i.e., error characteristics in the storage process.ResultsWe first propose a new concept named sequence corruption to unify the error characteristics into the sequence level, easing the channel analysis. Then we derived the formulations of the data imperfection at the decoder including both sequence loss and sequence corruption, revealing the decoding demand and monitoring the data recovery. Furthermore, we extensively explored several data-dependent unevenness observed in the base error patterns and studied a few potential factors and their impacts on the data imperfection at the decoder both theoretically and experimentally. The results presented here introduce a more comprehensive channel model and offer a new angle towards the data recovery issue in DNA data storage by further elucidating the error characteristics of the storage process.Contactpoh.chuehloo@nus.edu.sg
Using a Quadruplet Codon to Expand the Genetic Code of an Animal
Authors: Xi Zhiyan , Davis Lloyd , Baxter Kieran , Tynan Ailish , Goutou Angeliki , Greiss Sebastian 
Published: July 2021

AbstractGenetic code expansion in multicellular organisms is currently limited to the use of repurposed amber stop codons. Here we introduce a system for the use of quadruplet codons to direct incorporation of non-canonical amino acids in vivo in an animal, the nematode worm Caenorhabditis elegans. We develop hybrid pyrrolysyl tRNA variants to incorporate non-canonical amino acids in response to the quadruplet codon UAGA. We demonstrate the efficiency of the quadruplet decoding system by incorporating photocaged amino acids into two proteins widely used as genetic tools. We use photocaged lysine to express photocaged Cre recombinase for the optical control of gene expression and photocaged cysteine to express photo-activatable caspase for light inducible cell ablation. Our approach will facilitate the routine adoption of quadruplet decoding for genetic code expansion in eukaryotic cells and multicellular organisms.
Phenotypic plasticity and genetic control in colorectal cancer evolution
Authors: Househam Jacob , Heide Timon , Cresswell George D , Lynn Claire , Spiteri Inmaculada , Mossner Max , Kimberley Chris , Gabbutt Calum , Lakatos Eszter , Fernandez-Mateos Javier , Chen Bingjie , Zapata Luis , James Chela , Berner Alison , Schmidt Melissa , Baker Ann-Marie , Nichol Daniel , Costa Helena , Mitchinson Miriam , Jansen Marnix , Caravagna Giulio , Shibata Darryl , Bridgewater John , Rodriguez-Justo Manuel , Magnani Luca , Sottoriva Andrea , Graham Trevor A 
Published: July 2021

AbstractCancer evolution is driven by natural selection acting upon phenotypic trait variation. However, the extent to which phenotypic variation within a tumour is a consequence of intra-tumour genetic heterogeneity remains undetermined. Here we show that colorectal cancer cells frequently have highly plastic phenotypic traitsin vivoin patient tumours. We measured the degree to which trait variation reflects genetic ancestry by quantifying the phylogenetic signal of gene expression across 297 samples with multi-region paired whole genome and transcriptome sequencing collected from 27 primary colorectal cancers. Within-tumour phylogenetic signal for genes and pathways was detected only infrequently, suggesting that the majority of intra-tumour variation in gene expression programmes was not strongly heritable. Expression quantitative trait loci analyses (eQTL) identified a small number of putative mechanisms of genetic control of gene expression due to thecis-acting coding, non-coding and structural genetic alteration, but most gene expression variation was not explained by our genetic analysis. Leveraging matched chromatin-accessibility sequencing data, enhancer mutations withcisregulatory effects on gene expression were associated with a change in chromatin accessibility, indicating that non-coding variation can have phenotypic consequence through modulation of the 3D architecture of the genome. This study maps the evolution of transcriptional variation during cancer evolution, highlighting that intra-tumour phenotypic plasticity is pervasive in colorectal malignancies, and may play key roles in further tumour evolution, from metastasis to therapy resistance.
Gene regulation is commonly selected for high plasticity and low noise
Authors: Vlková Markéta , Silander Olin K. 
Published: July 2021

AbstractBacteria often respond to dynamically changing environments by regulating gene expression. Despite this regulation being critically important for growth and survival, little is known about how selection shapes gene regulation in natural populations. To better understand the role natural selection plays in shaping bacterial gene regulation, here we compare differences in the regulatory behaviour of naturally segregating promoter variants from Escherichia coli (which have been subject to natural selection) to randomly mutated promoter variants (which have never been exposed to natural selection). We quantify gene expression phenotypes (expression level, plasticity, and noise) for hundreds of promoter variants across multiple environments, and show that segregating promoter variants are enriched for mutations with minimal effects on expression level. In many promoters, we infer that there is strong selection to maintain high levels of plasticity, and direct selection to decrease or increase cell-to-cell variability in expression. Finally, taking an integrated view, we show that across all phenotypes combined, segregating promoter variants are far more phenotypically similar than would be expected given their genetic divergence. This is the consequence of both stabilizing and directional selection acting on individual phenotypes to minimize differences among segregating variants. Taken together, these results expand our knowledge of how gene regulation is affected by natural selection and highlight the power of comparing naturally segregating polymorphisms to de novo random mutations to quantify the action of selection.
Identification of Novel Long non-coding RNAs and Expression Analyses in Rectal Neuroendocrine Tumors
Authors: Padwal Mahesh Kumar , Basu Bhakti 
Published: July 2021

AbstractAltered expression of long-non-coding RNAs (lncRNAs) is associated with various pathological conditions, including cancers. LncRNAs associated with rectal neuroendocrine tumors (rNETs) remain unexplored. Here, we report the identification of 418 high confidence novel lncRNAs by analyzing publicly available RNA-Seq datasets of primary rNETs and rNETs with lymph node or liver metastases. Novel lncRNAs had basic characteristics similar to the known lncRNAs and showed individual-specific expressions. Expression analysis in the normal rectal mucosa and pancreas NETs (pNETs) and small intestine NETs (siNETs) revealed high expression of two lncRNAs, namely MSTRG30689.1 and MSTRG341161.1. Functional characterization revealed that 9 lncRNAs could work as the ce-RNA and one as miRNAs precursor. Cis- and trans- analysis of the 9 PCG-associated lncRNAs revealed that these lncRNAs could regulate various important cancer-related genes. Further, an integrated regulatory mechanism for selected cancer hallmark genes such as SMAD3, ZEB1, TCF4 and ATM through lncRNAs is predicted. Taken together, our analyses reveal common and unique lncRNAs associated with rNETs and their metastatic variants, their PCG targets, and predict mechanisms of lncRNA mediated regulation of target PCGs.
Application of personalized differential expression analysis in human cancer proteome
Authors: Yachen Liu , Yalan Lin , Yujuan Wu , Zheyang Zhang , Mengsha Tong , Rongshan Yu 
Published: July 2021

AbstractOwing to the recent technological advances, liquid chromatography-mass spectrometry (LC-MS)-based quantitative proteomics can measure expression of thousands of proteins from biological specimens. Currently, several studies have used the LC-MS-based proteomics to measure protein expression levels in human cancer. Identifying differentially expressed proteins (DEPs) between tumors and normal controls is a common way to investigate carcinogenesis mechanisms. However, most statistical methods used for DEPs analysis can only identify deregulated proteins at the population-level and ignore the heterogeneous differential expression of proteins in individual patients. Thus, to identify patient-specific molecular defects for personalized medicine, it is necessary to perform personalized differential analysis at the scale of a single sample. To date, there is a scarcity of systematic and easy-to-handle tool that could be used to evaluate the performance of individualized difference expression analysis algorithms in human cancer proteome. Herein, we developed a user-friendly tool kit, IDEP, to enable implementation and evaluation of personalized difference expression analysis algorithms. IDEP evaluates five rank-based tools (RankComp v1/v2, PENDA, Peng and Quantile) through classic computational and functional criteria in lung, gastric and liver cancer proteome. The results show that the within-sample relative expression orderings (REOs) of protein pairs in normal tissues were highly stable, which provided the basis for individual level DEPs analysis. Moreover, these individualized difference analysis tools could reach much higher efficiency in detecting sample-specific deregulated proteins than the group-based methods. Pathway enrichment and survival analysis results were dataset and analysis method dependent. In summary, IDEP has integrated necessary toolkits for individualized identification of DEPs and supported flexible methods evaluation analysis and visualization modules. It could provide a robust and scalable framework to extract personalized deregulation patterns and could also be used for the discovery of prognostic biomarkers for personalized medicine.
Assessing and mitigating privacy risk of sparse, noisy genotypes by local alignment to haplotype databases
Authors: Emani Prashant S. , Gürsoy Gamze , Miranker Andrew , Gerstein Mark B. 
Published: July 2021

AbstractSingle nucleotide polymorphisms (SNPs) from omics data carry a high risk of reidentification for individuals and their relatives. While the ability of thousands of SNPs (especially rare ones) to identify individuals has been repeatedly demonstrated, the ready availability of small sets of noisy genotypes – such as from environmental DNA samples or functional genomics data – motivated us to quantify their informativeness. Here, we present a computational tool suite, PLIGHT (“Privacy Leakage by Inference across Genotypic HMM Trajectories”), that employs population-genetics-based Hidden Markov Models of recombination and mutation to find piecewise alignment of small, noisy query SNP sets to a reference haplotype database. We explore cases where query individuals are either known to be in a database, or not, and consider a variety of queries, including simulated genotype “mosaics” (composites from 2 source individuals) and genotypes from swabs of coffee cups from a known individual. Using PLIGHT on a database with ~5,000 haplotypes, we find for common, noise-free SNPs that only ten are sufficient to identify individuals, ~20 can identify both components in two-individual simulated mosaics, and 20-30 can identify first-order relatives (parents, children, and siblings). Using noisy coffee-cup-derived SNPs, PLIGHT identifies an individual (within the database) using ~30 SNPs. Moreover, even when the individual is not in the database, local genotype matches allow for some phenotypic information leakage based on coarse-grained GWAS SNP imputation and polygenic risk scores. Overall, PLIGHT maximizes the identifying information content of sparse SNP sets through exact or partial matches to databases. Finally, by quantifying such privacy attacks, PLIGHT helps determine the value of selectively sanitizing released SNPs without explicit assumptions about underlying population membership or allele frequencies. To make this practical, we provide a sanitization tool to remove the most identifying SNPs from a query set.