bluuebunny/crossref_metadata_2025_split huggingface dataset:
NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data
Authors: Yang Qingxia , Wang Yunxia , Zhang Ying , Li Fengcheng , Xia Weiqi , Zhou Ying , Qiu Yunqing , Li Honglin , Zhu Feng 
Published: April 2020

AbstractBiological processes (like microbial growth & physiological response) are usually dynamic and require the monitoring of metabolic variation at different time-points. Moreover, there is clear shift from case-control (N=2) study to multi-class (N&gt;2) problem in current metabolomics, which is crucial for revealing the mechanisms underlying certain physiological process, disease metastasis, etc. These time-course and multi-class metabolomics have attracted great attention, and data normalization is essential for removing unwanted biological/experimental variations in these studies. However, no tool (including NOREVA 1.0 focusing only on case-control studies) is available for effectively assessing the performance of normalization method on time-course/multi-class metabolomic data. Thus, NOREVA was updated to version 2.0 by (i) realizing normalization and evaluation of both time-course and multi-class metabolomic data, (ii) integrating 144 normalization methods of a recently proposed combination strategy and (iii) identifying the well-performing methods by comprehensively assessing the largest set of normalizations (168 in total, significantly larger than those 24 in NOREVA 1.0). The significance of this update was extensively validated by case studies on benchmark datasets. All in all, NOREVA 2.0 is distinguished for its capability in identifying well-performing normalization method(s) for time-course and multi-class metabolomics, which makes it an indispensable complement to other available tools. NOREVA can be accessed at https://idrblab.org/noreva/.
To Petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics
Authors: Elworth R A Leo , Wang Qi , Kota Pavan K , Barberan C J , Coleman Benjamin , Balaji Advait , Gupta Gaurav , Baraniuk Richard G , Shrivastava Anshumali , Treangen Todd J 
Published: April 2020

AbstractAs computational biologists continue to be inundated by ever increasing amounts of metagenomic data, the need for data analysis approaches that keep up with the pace of sequence archives has remained a challenge. In recent years, the accelerated pace of genomic data availability has been accompanied by the application of a wide array of highly efficient approaches from other fields to the field of metagenomics. For instance, sketching algorithms such as MinHash have seen a rapid and widespread adoption. These techniques handle increasingly large datasets with minimal sacrifices in quality for tasks such as sequence similarity calculations. Here, we briefly review the fundamentals of the most impactful probabilistic and signal processing algorithms. We also highlight more recent advances to augment previous reviews in these areas that have taken a broader approach. We then explore the application of these techniques to metagenomics, discuss their pros and cons, and speculate on their future directions.
Single-cell RNA Analysis on ACE2 Expression Provides Insight into SARS-CoV-2 Blood Entry and Heart Injury
Authors: Guo Jieyu , Wei Xiangxiang , Li Qinhan , Li Liliang , Yang Zhaohua , Shi Yu , Qin Yue , Zhang Xinyue , Wang Xinhong , Zhi Xiuling , Meng Dan 
Published: April 2020

AbstractCOVID-19 is a global pandemic with high infectivity and pathogenicity, accounting for tens of thousands of deaths worldwide. Recent studies have found that the pathogen of COVID-19, SARS-CoV-2, shares the same cell receptor Angiotensin converting enzyme II (ACE2) with SARS-CoV. The pathological investigation of COVID-19 death showed that the lung had the characteristics of pulmonary fibrosis. However, how SARS-CoV-2 spreads from the lungs to other organs has not yet been determined. Here, we performed an unbiased evaluation of cell-type specific expression of ACE2 in healthy and fibrotic lungs, as well as in normal and failed adult human hearts, using published single-cell RNA-seq data. We found that ACE2 expression in fibrotic lungs mainly locates in arterial vascular cells, which might provide the route for bloodstream spreading of SARS-CoV-2. The failed human hearts have a higher percentage of ACE2-expressing cardiomyocytes, and SARS-CoV-2 might attack cardiomyocytes through the bloodstream in patients with heart failure.Moreover, ACE2 was highly expressed in cells infected by RSV or MERS-CoV and in mice treated by LPS. Our findings indicate that patients with pulmonary fibrosis, heart failure, and virus infection have a higher risk and are more susceptible to SARS-CoV-2 infection. SARS-CoV-2 might attack other organs by getting into the bloodstream. This work provides new insights into SARS-CoV-2 blood entry and heart injury and might propose a therapeutic strategy to prevent patients from developing severe complications.
Countrywide quarantine only mildly increased anxiety level during COVID-19 outbreak in China
Authors: Hu Wei , Su Li , Qiao Juan , Zhu Jing , Zhou Yi 
Published: April 2020

AbstractIn the recent outbreak of COVID-19, many countries have taken various kinds of quarantine measures to slow down the explosive spreading of COVID-19. Although these measures were proven to be successful in stopping the outbreak in China, the potential adverse effects of countrywide quarantine have not been thoroughly investigated. In this study, we performed an online survey to evaluate the psychological effects of quarantine in China using Zung Self-rating Anxiety Scale in February 2020 when the outbreak was nearly peaked in China. Along with the anxiety scores, limited personal information such as age, gender, region, education, occupation and specifically, the type and duration of quarantine were collected for analysis. For a total number of 992 valid questionnaires, clinical significance of anxiety symptoms was observed in 9.58% respondents according to clinical diagnostic standards in China. Statistical results showed population with different age, education level, health status and personnel category responded differently. Other characteristics such as gender, marital status, region, and acquaintance with suspected or confirmed cases of COVID-19 did not affect anxiety levels significantly. Respondents experienced different forms of quarantine showed different anxiety levels. Unexpectedly, longer durations of quarantine did not lead to significant increase of anxiety level. Our results suggest a rather mild psychological influence caused by the countrywide quarantine during COVID-19 outbreak in China and provided reference for other countries and regions to battle COVID-19.
Biological function polarity prediction of missense variants using machine learning
Authors: Ghosh Adhideb , Navarini Alexander A. 
Published: April 2020

AbstractFunctional interpretation is crucial when facing on average 20,000 missense variants per human exome, as the great majority are not associated with any underlying disease.In silicobioinformatics tools can predict the deleteriousness of variants or assess their functional impact by assigning scores, but they cannot predict whether the variant in question results in gain or loss of function at the protein level. Here, we show that machine learning can effectively predict this biological function polarity of missense variants. The new method adapts weighted gradient boosting machine approach on a set of damaging variants (1,288 loss of function and 218 gain of function variants) as annotated by the tools SIFT, PolyPhen2 and CADD. Area under the ROC curve of 0.85 illustrates high discriminative power of the classifier. Predictive performance of the classifier remains consistent against an independent set of damaging variants as highlighted by the area under the ROC curve of 0.83. This new approach may help to guide biological experiments on the clinical relevance of damaging genetic variants.Author summaryMissense variant occurs when a single genetic alteration in DNA takes place and as a result a new amino acid is translated into the protein. This amino acid change can inactivate the existing protein function causing loss-of-function or produce a new function causing gain-of-function. Therefore, it is very important to interpret these functional consequences of missense variants as they often turn out to be disease causing. Each individual’s genome sequence has thousands of missense variants, out of which very few are actually associated with any underlying disease. Various computational tools have been developed to predict whether missense variants are damaging or not, but none of them can actually predict whether the damaging missense variants cause gain-of-function or loss-of-function. We have developed a new ensemble classifier to predict this biological function polarity at the protein level. The classifier combines the prediction scores of three existing bioinformatics tools and applies machine learning to make effective predictions. We have validated our classifier against an independent data set to show its high predictive power and robustness. The predictions made by our machine learning tool can be used as indicators of biological function polarity, but with further evidence on pathogenicity.
Incorrect Molecular Weights due to inaccurate Prestained Protein Molecular Weight Markers that are used for Gel Electrophoresis and Western Blotting
Authors: Neris Rômulo Leão Silva , Kaur Ajuni , Gomes Aldrin V. 
Published: April 2020

ABSTRACTThe most widely used Western blotting protein standards are prestained proteins of known molecular mass (kDa). They are also utilized for sodium dodecyl sulphate (SDS) Polyacrylamide Gel Electrophoresis (PAGE) to determine the molecular mass of proteins separated by electrophoresis. The objective of this study was to assess the reliability of different commercially available protein standards in predicting accurate protein molecular weights. We performed this experiment by running Criterion TGX gels with five prestained protein standards (Thermo Fisher SeeBlue Plus 2, Bio-Rad Precision Plus Protein Dual-color, Thermo Fisher Spectra Multi-color, Novex-Sharp Pre-stained, and Invitrogen iBright Pre-Stained). To evaluate their accuracy, we utilized highly purified Bovine Serum Albumin (BSA, 66.44 kDa) and Cytochrome C (Cyto C, 11.62 kDa). We also made use of the dimers of BSA (132.88 kDa) and Cyt C (23.24 kDa) that are present on SDS-PAGE gels. Our results suggest that three of the standards were less accurate at higher molecular masses with the iBright marker having the highest error in determining the expected 132.88 kDa molecular weight. The SeeBlue Plus 2 was accurate at identifying the 132.88 kDa molecular weight protein band but was less reliable for the three other lower molecular weight proteins. These findings have significant implications for the determination of protein masses because researchers rely on these standards to evaluate the molecular masses of their protein(s). We suggest that at least two different protein standards should be initially used in electrophoresis gels and for Western blotting in order to get accurate protein molecular weight results.
Whole genome sequences of multi-drug resistantEscherichia coliisolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes
Authors: Iramiot Jacob Stanley , Kajumbula Henry , Bazira Joel , de Villiers Etienne P. , Asiimwe Benon B. 
Published: April 2020

AbstractBackgroundThe crisis of antimicrobial resistance is already here with us, affecting both humans and animals alike and very soon, small cuts and surgeries will become life threatening. This study aimed at determine the whole genome sequences of multi-drug resistantEscherichia coliisolated in a Pastoralist Community of Western Uganda: phylogenomic changes, virulence and resistant genes.MethodsThis was a laboratory based cross sectional study. Bacterial isolates analyzed in this study were 42 multidrug resistantE. coliisolated from stool samples from both humans and cattle in pastoralist communities collected between January 2018-March 2019. Most of the isolates (41/42) were resistant to three or more antibiotics (multi-drug resistant) and 21/42 isolates were ESBL producers; 13/42 from human and 8/42 from cattle. Whole Genome Sequencing (WGS) was carried out at the facilities of Kenya Medical Research Institute-Wellcome trust, Kilifi, to determine the phylogenomic changes, virulence and resistant genes.ResultsThe genomes of the humanE. coligenerally clustered together and away from those of cattle origin. TheE. coliisolates were assigned to eight different phylogroups: A, B1, B2, Cladel, D, E, F and G, with a majority being assigned to phylogroup A; while most of the animal isolates were assigned to phylogroup B1. The carriage of multiple AMR genes was higher from theE. colipopulation from humans than those from cattle. Among these were Beta-lactamase; blaOXA-1: Class D beta-lactamases; blaTEM-1, blaTEM-235: Beta-lactamase; catA1: chloramphenicol acetyl transferase; cmlA1: chloramphenicol efflux transporter; dfrA1, dfrA12, dfrA14, dfrA15, dfrA17, dfrA5, dfrA7, dfrA8: macrolide phosphotransferase; oqxB11: RND efflux pump conferring resistance to fluoroquinolone; qacL, qacEdelta1: quinolone efflux pump; qnrS1: quinolone resistance gene; sul1, sul2, sul3: sulfonamide resistant; tet(A), tet(B): tetracycline efflux pump.A high variation of virulence genes was registered among theE. coligenomes from humans than those of cattle origin.ConclusionTheE. coliof human and cattle origin are largely independent with different ancestral origins. Limited sharing of strains and resistance genes presents a challenge to the hypothesis that AMR in humans is as a result of antibiotic misuse on the farm.
3D cell culture models demonstrate a role for FGF and WNT signaling in regulation of lung epithelial cell fate and morphogenesis
Authors: Rabata Anas , Fedr Radek , Soucek Karel , Hampl Ales , Koledova Zuzana 
Published: April 2020

AbstractFGF signaling plays an essential role in lung development, homeostasis, and regeneration. Several FGF ligands were detected in the developing lungs, however, their roles have not been fully elucidated. We employed mouse 3D cell culture models and imaging toex vivostudy ofa)the role of FGF ligands in lung epithelial morphogenesis andb)the interplay of FGF signaling with epithelial growth factor (EGF) and WNT signaling pathways. In non-adherent conditions, FGF signaling promoted formation of lungospheres from lung epithelial stem/progenitor cells (LSPCs). Based on their architecture, we defined three distinct phenotypes of lungospheres. Ultrastructural and immunohistochemical analyses showed that LSPCs produced more differentiated lung cell progeny. In 3D extracellular matrix, FGF2, FGF7, FGF9, and FGF10 promoted lung organoid formation with similar efficiency. However, FGF9 showed reduced capacity to promote lung organoid formation, suggesting that FGF9 has a reduced ability to sustain LSPCs survival and/or initial divisions. Analysis of lung organoid phenotypes revealed that FGF7 and FGF10 produce bigger organoids and induce organoid branching with higher frequency than FGF2 and FGF9. Higher FGF concentration and/or the use of FGF2 with increased stability and affinity to FGF receptors both increased lung organoid and lungosphere formation efficiency, respectively, suggesting that the level of FGF signaling is a crucial driver of LSPC survival and differentiation, and also lung epithelial morphogenesis. EGF signaling played a supportive but nonessential role in FGF-induced lung organoid formation. Moreover, analysis of tissue architecture and cell type composition confirmed that the lung organoids contained alveolar-like regions with cells expressing alveolar type I and type II cell markers, as well as airway-like structures with club cells and ciliated cells. WNT signaling enhanced the efficiency of lung organoid formation, but in the absence of FGF10 signaling, the organoids displayed limited branching and less differentiated phenotype. In summary, we present lung 3D cell culture models as useful tools to study the role and interplay of signaling pathways in lung development and we reveal roles for FGF ligands in regulation of mouse lung morphogenesisex vivo.
A New Dynamic Echodefecography (EDF) Established by Using BK Ultrasound 8838 Transducer and its Testing Results Comparison with X-ray Defecography
Authors: Jin Heiying , Zhang Chunxia 
Published: April 2020

AbstractObjectiveTo describe a new dynamic echodefecography(EDF) using BK ultrasound 8838 transducer and compare its testing results with X-ray defecography.MethodThe BK 8838 ultrasound probe is used to evaluate the static 3D scan, dynamic 3D scan and dynamic 2D scan of pelvic floor and compare its testing results with X-ray defecography and defined its value to evaluate the pelvic floor disease.ResultsFifty-seven patients were studied (24 male and 33 female). Forty seven patients were diagnosed as anismus by EDF and 46 patients were diagnosed as anismus by X-ray defecography. Sixteen patients were diagnosed as rectocele by X-ray defecography, among which eight were classified as mild(6-15mm), 4 as moderate(16-30mm) and 4 as severe(over 30mm).Fourteen patients with constipation and 2 patients with anal pain were diagnosed as intussusception by EDF, but only 3 patients were diagnosed as intussusception by X-ray defecography. Two patients with constipation were diagnosed as perineal descent by EDF and none by X-ray defecography. Two patients were diagnosed as enterocele by EDF as well as X-ray defecography.ConclusionThe EDF established by BK 8838 ultrasound probe can show clear anatomy and real time movement of pelvic floor muscle. The EDF is more sensitive to the diagnosis of intussusception, perineal descent(PD) and anal spincter defect than X-ray defecograpgy. For anismus,rectocele and enterocele,the diagnosis results are comparable between EDF and X ray defecography. Further study is needed to determine its clinical values to evaluate the pelvic disease.
Impact of wild boar rooting on small forest‐dwelling rodents
Authors: Mori Emiliano , Ferretti Francesco , Lagrotteria Alessandro , La Greca Leonardo , Solano Emanuela , Fattorini Niccolò 
Published: April 2020

AbstractAssessing impacts of wild boar on ecosystems is a research priority worldwide, with applied implications for environmental management. We evaluated whether rooting intensity by wild boar affected a rodent community in Central Italy. Rooting intensity was measured within trap transects and all around them, following standard procedures. We live‐trapped rodents in coppiced forests with a gradient of rooting intensity (including a fenced, boar‐proof, area) and evaluated relationships between abundance and rooting for two arboreal and five ground‐dwelling species. Among those, the most abundant ones were the bank vole Myodes glareolus and the yellow‐necked wood mouse Apodemus flavicollis. Rooting within and outside transects correlated to each other, as well as with the local passage rate of the wild boar, assessed through camera‐trapping. We found a negative relationship between rooting intensity and abundance of bank voles, that is, the main food resources of some predators of conservation concern. Rooting activity may trigger effects on ground‐dwelling rodents at the population level.
Significant loss of genetic diversity and accumulation of deleterious genetic variation in a critically endangered azalea species, Rhododendron boninense, growing on the Bonin Islands
Authors: Isagi Yuji , Makino Takashi , Hamabata Tomoko , Cao Ping‐Lin , Narita Satoshi , Komaki Yoshiteru , Kurita Kazuki , Naiki Akiyo , Kameyama Yoshiaki , Kondo Toshiaki , Shibabayashi Mayu 
Published: April 2020

AbstractLoss of genetic diversity increases the risk of extinction of a population through inbreeding depression. In addition, the number of deleterious genetic variations, which might accumulate in a small population through genetic drift, can also make the population vulnerable. Rhododendron boninense is a critically endangered azalea species, which grows on the Bonin Islands, a UNESCO World Heritage Site; its population size in the wild dropped to only a single individual. Although a governmental program for species conservation has been conducted, no successful natural regeneration or population growth was achieved. We hypothesized that the reduced genetic diversity and accumulated deleterious genetic variation might cause the vulnerability of the species, and conducted comparative genetic and genomic analyses between R. boninense and its congeners. Genetic analysis using microsatellite markers indicated that the genetic diversity of R. boninense was ultimately low; microsatellite loci of this species were all fixed, whereas the congeners maintain high allelic diversity. Based on comprehensive transcriptome analysis, the amount of deleterious variation of R. boninense was significantly greater than that of R. amanoi. Repeated generation transitions of the small population of R. boninense on the oceanic islands is likely to have resulted in low genetic diversity as well as more deleterious variations in the genome, and we speculated that the accumulated deleterious variation might result in vulnerability of R. boninense. This study indicates the possibility of evaluating the feasibility of effective conservation programs based on the genetic diversity and the amount of accumulated deleterious variation in the genome of critically endangered species.
Rural non‐farm diversification, agricultural feminisation and women's autonomy in the farm: evidence from India
Authors: Neog Bhaskar Jyoti , Sahoo Bimal Kishore 
Published: April 2020

This study contributes to the literature on the interlinkage between household non‐farm diversification (HND), agricultural feminisation and female autonomy in farming. The study uses unit‐level data from the Indian Human Development Survey for the years 2004 ‐ 2005 and 2011 ‐ 2012. The paper employs instrumental variable regression methods to study such interlinkages. The results show HND to be a significant factor contributing to the feminisation of agriculture. The study finds some evidence that the phenomenon is distress driven. Further, greater participation of women in agriculture, as well as women's access to land rights, significantly contributes to female autonomy in farm decision‐making. The results are robust to the use of alternative indicators of agricultural feminisation.
Film or Film Brand? UK Consumers’ Engagement with Films as Brands
Authors: Kohli Gurdeep Singh , Yen Dorothy , Alwi Sharifah , Gupta Suraksha 
Published: April 2020

AbstractMany films are produced annually, but only a small number of films reach the state of being considered and identified by consumers as film brands. Film‐brand identification is difficult to achieve, but it leads to engagement behaviours (e.g. repetitive viewing, positive word‐of‐mouth and purchase intention of relevant merchandise/franchise). To help film‐makers better develop films as brands and benefit from their brand status, this paper takes a consumer‐centric approach to investigate how and why films are identified and engaged by consumers as brands. Using an abductive mode of reasoning, a consumer film‐brand engagement framework was developed through qualitative data collected from 35 semi‐structured interviews and then validated using survey data with 1030 participants. This consumer film‐brand engagement framework shows that film identity coherency drives film‐brand identification through the mediation effects of popularity, sequels and emotional bonding, whilst marketing effort, iconic status, franchising/merchandising activities and timelessness are highlighted as key moderators, resulting in positive brand engagement behaviour. The paper sheds new light on film‐branding literature by theoretically explaining and empirically showing a sequential and consolidated process, which consumers go through to identify and engage with films as brands, leading to several managerial and marketing implications for film‐makers.