bluuebunny/crossref_metadata_2025_split huggingface dataset:
Silent dissemination of plasmid-borne tigecycline resistance genetet(X6) in livestock-associatedAcinetobacter towneri
Authors: Cheng Yingying , Chen Yong , Liu Yang , Song Jingjie , Guo Yuqi , Zhou Yanzi , Xiao Tingting , Zhang Shuntian , Xu Hao , Chen Yunbo , Shan Tongling , Xiao Yonghong , Zhou Kai 
Published: May 2020

AbstractA tigecycline-resistance gene,tet(X6), was detected on a 159-kb novel plasmid carried by a tigecycline-susceptible livestock-associatedAcinetobacter towneriisolate. The genetic context oftet(X6) (ΔISVsa3-tet(X6)-abh-guaA-ISVsa3) is highly similar with that of the other plasmid-bornetet(X) variants. The 23-Ala residue of the first FAD binding site conferred higher activity to Tet(X6) than the 23-Gly reside conserved in the other plasmid-bornetet(X)s. To our knowledge, this is the first report oftet(X6) carried by the plasmid.
Pre-Procedural Surveillance Testing for SARS-CoV-2 in an Asymptomatic Population Shows Low Rates of Positivity
Authors: Mays James A , Greninger Alexander L , Jerome Keith R , Lynch John B , Mathias Patrick C 
Published: May 2020

Background: Depression is a common cause of mortality and morbidity worldwide. To detect depression, we compared Beck Depression Inventory scoring as a valid tool with participants self-reporting depression.Methodology: This cross-sectional study aimed to explore the diagnostic values of self-reporting in patients' with depression comparing to Beck Depression Inventory scoring in Mazandaran Persian cohort study, with a total of 1300 samples. The sample size was determined to include 155 participants through the census method. In order to increase the test power, 310 healthy participants were included in the study through random selection. In order to evaluate the diagnostic value of self-reporting, BDI-II was completed by blind interviewing to the case group as well as to another group who reported that they were not depressed, as control.Results: sensitivity, specificity, accuracy, false positive, false negative, positive and negative predictive values of self-reporting was calculated 58.4%, 79.1%,73.4%, 20.8%, 41.6%, 51.8%, and 83.2% for the total population respectively, as well as, sensitivity, specificity, accuracy, positive and negative predictive values of self-report in males were 83.3%, 77.2%, 77.1%, 43.8% and 95.6% and 53.7%, 78.1%, 71.2%, 49.2%, and 81.1% for females, respectively.Conclusion: The positive predictive value and sensitivity of self-reporting are insufficient in total population and females, and therefore self-reporting cannot detect depressed patients, but regarding to its average positive predictive value, perhaps, it can be used to identify non-depressant individuals.
Correlation Between Blood and CSF Compartment Cytokines and Chemokines in Subjects with Cryptococcal Meningitis
Authors: Okafor Elizabeth C , Hullsiek Katherine H , Williams Darlisha A , Scriven James E , Rhein Joshua , Nabeta Henry W , Musubire Abdu K , Rajasingham Radha , Muzoora Conrad , Schutz Charlotte , Meintjes Graeme , Meya David B , Boulware David R 
Published: May 2020

ABSTRACTBackgroundThough peripheral blood is a crucial sample to study immunology, it is unclear whether the immune environment in the peripheral vasculature correlates with that at the endorgan site of infection. Utilizing cryptococcal meningitis as a model, we investigated the correlation between serum and cerebrospinal fluid biomarkers over time.MethodsWe analyzed the cerebrospinal fluid and serum of 160 subjects presenting with first episode cryptococcal meningitis for soluble cytokines and chemokines measured by Luminex assay. Specimens were collected at meningitis diagnosis, 1-week, and 2-weeks post cryptococcal diagnosis. We compared paired samples by Spearman correlation and the p-value was set at <0.01.ResultsOf the 21 analytes tested at baseline, there was no correlation detected between nearly all analytes. A weak negative correlation was found between serum and cerebrospinal fluid levels of interferon-gamma (Rho= −0.214, p= .007) and interleukin-4 (Rho= −0.232, p=. 003). There was no correlation at 1-week post cryptococcal diagnosis. However, at 2-weeks post diagnosis, there was a weak positive correlation between levels of granulocyte-macrophage colony-stimulating factor (Rho= 0.25, p= .007) between serum and cerebrospinal fluid. No cytokine or chemokine showed consistent correlation overtime.ConclusionBased on our analysis of 21 biomarkers, serum and cerebrospinal fluid immune responses do not correlate. There appears to be a distinct immune environment in terms of soluble biomarkers in the vasculature versus end-organ site of infection. While this is a model of HIV-related cryptococcal meningitis, we postulate that assuming the blood compartment is representative of the immune function at the end-organ site of infection may not be appropriate.
Total predicted MHC-I epitope load is inversely associated with population mortality from SARS-CoV-2
Authors: Wilson Eric A. , Hirneise Gabrielle , Singharoy Abhishek , Anderson Karen S. 
Published: May 2020

AbstractPolymorphisms in MHC-I protein sequences across human populations significantly impacts viral peptide binding capacity and thus alters T cell immunity to infection. Consequently, allelic variants of the MHC-I protein have been found to be associated with patient outcome to various viral infections, including SARS-CoV. In the present study, we assess the relationship between observed SARS-CoV-2 population mortality and the predicted viral binding capacities of 52 common MHC-I alleles. Potential SARS-CoV-2 MHC-I peptides were identified using a consensus MHC-I binding and presentation prediction algorithm, called EnsembleMHC. Starting with nearly 3.5 million candidates, we resolved a few hundred highly probable MHC-I peptides. By weighing individual MHC allele-specific SARS-CoV-2 binding capacity with population frequency in 23 countries, we discover a strong inverse correlation between the predicted population SARS-CoV-2 peptide binding capacity and observed mortality rate. Our computations reveal that peptides derived from the structural proteins of the virus produces a stronger association with observed mortality rate, highlighting the importance of S, N, M, E proteins in driving productive immune responses. The correlation between epitope binding capacity and population mortality risk remains robust across a range of socioeconomic and epidemiological factors. A combination of binding capacity, number of deaths due to COPD complications, gender demographics. and the proportions of the population that were over the age of 65 and overweight offered the strongest determinant of at-risk populations. These results bring to light how molecular changes in the MHC-I proteins may affect population-level outcomes of viral infection.
Genetic drift versus regional spreading dynamics of COVID-19
Authors: Pietro R. Di , Basile M. , Antolini L. , Alberti S. 
Published: May 2020

AbstractBackgroundCurrent propagation models of COVID-19 are poorly consistent with existing epidemiological data and with evidence that the SARS-CoV-2 genome is mutating, for potential aggressive evolution of the disease.MethodsWe challenged regional versus genetic evolution models of COVID-19 at a whole-population level, over 168,089 laboratory-confirmed SARS-CoV-2 infection cases in Italy, Spain and Scandinavia. Diffusion data in Germany, France and UK provided a validation dataset of 210,239 additional cases.ResultsThe mean doubling time of COVID-19 cases was 6.63 days in Northern versus 5.38 days in Southern Italy. Spain extended this trend of faster diffusion in Southern Europe, with a doubling time of 4.2 days. Slower doubling times were observed in Sweden (9.4 days), Finland (10.8 days), Norway (12.95 days). COVID-19 doubling time in Germany (7.0 days), France (7.5 days) and UK (7.2 days) supported the North/South gradient model. Clusters of SARS-CoV-2 mutations upon sequential diffusion across distinct geographic areas were not found to clearly correlate with regional distribution dynamics.ConclusionsAcquisition of mutations, upon SARS-CoV-2 spreading across distinct geographic areas, did not distinctly associate to enhanced virus aggressiveness, and failed to explain regional diffusion heterogeneity at early phases of the pandemic. Our findings indicate that COVID-19 transmission rates associate to a sharp North/South climate gradient, with faster spreading in Southern regions. Thus, warmer climate conditions may not limit SARS-CoV-2 infectivity. Very cold regions may be better spared by recurrent courses of SARS-CoV-2 infection.
Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)
Authors: Sánchez-Barreiro Fátima , Gopalakrishnan Shyam , Ramos-Madrigal Jazmín , Westbury Michael V. , de Manuel Marc , Margaryan Ashot , Ciucani Marta M. , Vieira Filipe G. , Patramanis Yannis , Kalthoff Daniela C. , Timmons Zena , Sicheritz-Pontén Thomas , Dalén Love , Ryder Oliver A. , Zhang Guojie , Marquès-Bonet Tomás , Moodley Yoshan , Gilbert M. Thomas P. 
Published: May 2020

AbstractLarge vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore suffered a remarkable population reduction in the last 150 years due to human activities. The two white rhinoceros subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly after the onset of the decline, while the SWR recovered after a severe bottleneck. Such demographic events are predicted to have an erosive effect at the genomic level, in connection with the extirpation of diversity, and increased genetic drift and inbreeding. However there is currently little empirical data available that allows us to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore to assess these effects, we generated a whole-genome, temporal dataset consisting of 52 re-sequenced white rhinoceros genomes, that represents both subspecies at two time windows: before and during/after the bottleneck. Our data not only reveals previously unknown population substructure within both subspecies, but allowed us to quantify the genomic erosion undergone by both, with post-bottleneck white rhinoceroses harbouring significantly fewer heterozygous sites, and showing higher inbreeding coefficients than pre-bottleneck individuals. Moreover, the effective population size suffered a decrease of two and three orders of magnitude in the NWR and SWR respectively, due to the recent bottleneck. Our data therefore provides much needed empirical support for theoretical predictions about the genomic consequences of shrinking populations, information that is relevant for understanding the process of population extinction. Furthermore, our findings have the potential to inform management approaches for the conservation of the remaining white rhinoceroses.
Predicting tissue-specific gene expression from whole blood transcriptome
Authors: Basu Mahashweta , Wang Kun , Ruppin Eytan , Hannenhalli Sridhar 
Published: May 2020

AbstractComplex diseases are systemic, largely mediated via transcriptional dysregulation in multiple tissues. Thus, knowledge of tissue-specific transcriptome in an individual can provide important information about an individual’s health. Unfortunately, with a few exceptions such as blood, skin, and muscle, an individual’s tissue-specific transcriptome is not accessible through non-invasive means. However, due to shared genetics and regulatory programs between tissues, the transcriptome in blood may be predictive of those in other tissues, at least to some extent. Here, based on GTEx data, we address this question in a rigorous, systematic manner, for the first time. We find that an individual’s whole blood gene expression and splicing profile can predict tissue-specific expression levels in a significant manner (beyond demographic variables) for many genes. On average, across 32 tissues, the expression of about 60% of the genes is predictable from blood expression in a significant manner, with a maximum of 81% of the genes for the musculoskeletal tissue. Remarkably, the tissue-specific expression inferred from the blood transcriptome is almost as good as the actual measured tissue expression in predicting disease state for six different complex disorders, including Hypertension and Type 2 diabetes, substantially surpassing predictors built directly from the blood transcriptome. The code for our pipeline for tissue-specific gene expression prediction – TEEBoT, is provided, enabling others to study its potential translational value in other indications.
SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is further increased by a naturally occurring elongation variant
Authors: Konno Yoriyuki , Kimura Izumi , Uriu Keiya , Fukushi Masaya , Irie Takashi , Koyanagi Yoshio , Nakagawa So , Sato Kei 
Published: May 2020

AbstractOne of the features distinguishing SARS-CoV-2 from its more pathogenic counterpart SARS-CoV is the presence of premature stop codons in itsORF3bgene. Here, we show that SARS-CoV-2ORF3bis a potent interferon antagonist, suppressing the induction of type I interferon more efficiently than its SARS-CoV ortholog. Phylogenetic analyses and functional assays revealed that SARS-CoV-2-related viruses from bats and pangolins also encode truncatedORF3bgene products with strong anti-interferon activity. Furthermore, analyses of more than 15,000 SARS-CoV-2 sequences identified a natural variant, in which a longerORF3breading frame was reconstituted. This variant was isolated from two patients with severe disease and further increased the ability of ORF3b to suppress interferon induction. Thus, our findings not only help to explain the poor interferon response in COVID-19 patients, but also describe a possibility of the emergence of natural SARS-CoV-2 quasispecies with extendedORF3bthat may exacerbate COVID-19 symptoms.HighlightsORF3b of SARS-CoV-2 and related bat and pangolin viruses is a potent IFN antagonistSARS-CoV-2 ORF3b suppresses IFN induction more efficiently than SARS-CoV orthologThe anti-IFN activity of ORF3b depends on the length of its C-terminusAn ORF3b with increased IFN antagonism was isolated from two severe COVID-19 cases
A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2
Authors: Gohl Daryl M. , Garbe John , Grady Patrick , Daniel Jerry , Watson Ray H. B. , Auch Benjamin , Nelson Andrew , Yohe Sophia , Beckman Kenneth B. 
Published: May 2020

AbstractThe global COVID-19 pandemic has led to an urgent need for scalable methods for clinical diagnostics and viral tracking. Next generation sequencing technologies have enabled large-scale genomic surveillance of SARS-CoV-2 as thousands of isolates are being sequenced around the world and deposited in public data repositories. A number of methods using both short- and long-read technologies are currently being applied for SARS-CoV-2 sequencing, including amplicon approaches, metagenomic methods, and sequence capture or enrichment methods. Given the small genome size, the ability to sequence SARS-CoV-2 at scale is limited by the cost and labor associated with making sequencing libraries. Here we describe a low-cost, streamlined, all amplicon-based method for sequencing SARS-CoV-2, which bypasses costly and time-consuming library preparation steps. We benchmark this tailed amplicon method against both the ARTIC amplicon protocol and sequence capture approaches and show that an optimized tailed amplicon approach achieves comparable amplicon balance, coverage metrics, and variant calls to the ARTIC v3 approach and represents a cost-effective and highly scalable method for SARS-CoV-2 sequencing.
Onion thrips Thrips tabaci [Thysanoptera: Thripidae] reduces yields and THC in indoor grown cannabis
Authors: McCune Frédéric , Murphy Chad , Eaves James , Fournier Valérie 
Published: May 2020

ABSTRACTCannabis (Cannabis sativa L. [Rosales: Cannabaceae]) is a newly legalized crop and requires deeper insights on its pest communities. In this preliminary study, we identified a thrips species affecting indoor grown cannabis in Canada and tested its impact on plant yield. We used three levels of initial infestation (zero, one, and five thrips) on individual plants grown in two growing mediums: normal substrate or substrate containing the biostimulant Bacillus pumilus, Meyer and Gottheil [Bacillales: Bacillaceae]. We found that the onion thrips, Thrips tabaci (Lindeman) [Thysanoptera: Thripidae] is proliferating in indoor grown cannabis. Furthermore, our results showed that fresh yields were higher for the plants that initially received zero thrips compared to those that initially received five thrips. Moreover, the biostimulant did not help reduce the impact of thrips. We highlight the importance for growers to carefully monitor thrips infestations in indoor grown cannabis. Finally, we emphasize the need for more research related to the impact of pests on cannabis yields and safe means of pest control for this strictly regulated crop.
Twin-arginine translocase component TatB performs folding quality control via a general chaperone activity
Authors: Taw May N. , Boock Jason T. , Kim Daniel , Rocco Mark A. , Waraho-Zhmayev Dujduan , DeLisa Matthew P. 
Published: May 2020

AbstractThe twin-arginine translocation (Tat) pathway involves an inbuilt quality control (QC) system that synchronizes proofreading of substrate protein folding with lipid bilayer transport. However, the molecular details of this QC mechanism remain poorly understood. Here, we hypothesized that the conformational state of Tat substrates is directly sensed by the TatB component of the bacterial Tat translocase. In support of this hypothesis, several TatB variants in which the cytoplasmic membrane-extrinsic domain was either truncated or mutated in the vicinity of a conserved, highly flexible α-helical domain were observed to form functional translocasesin vivothat had compromised QC activity as evidenced by the uncharacteristic export of several misfolded protein substrates.In vitrofolding experiments revealed that the membrane-extrinsic domain of TatB possessed general chaperone activity, transiently binding to highly structured, partially unfolded intermediates of a model protein, citrate synthase, thereby preventing its irreversible aggregation and stabilizing the active species. Collectively, these results suggest that the Tat translocase may use chaperone-like client recognition to monitor the conformational status of its substrates.
Macau gambling industry's quick V-shape rebound from 2014 to 2019
Authors: Liu Matthew Tingchi , Dong Shiying , Chang Sara Kit Peng , Tan Francis 
Published: May 2020

PurposeThe purpose of this study is to summarize the factors that result in V-shape rebound of Macau gambling industry's from 2014 to 2019. Both internal and external factors are examined and discussed by representatives from academia, industry and government.Design/methodology/approachPractitioners from the gambling industry offered their cutting-edged analysis and viewpoints with observation and comments from scholars and government representatives in gambling domain.FindingsInternally, actions are taken by both the Macau government and Macau casino operators to rebrand Macau with nongambling elements and to adjust the strategies to attract more tourists from a wider range. Externally, global economic upturn and support from the China government also enhance Macau's quick rebound. A total of nine key factors are finally recognized.Originality/valueThis study provides answers and sense-making explanations to why Macau gambling industry can recover in such a short time after a big drop in Gross Gambling Revenue in 2014. This work reveals that Macau, by learning the lessons from the dramatic decline, conducts various self-rescue action plans which contribute to the quick V-shape rebound. This study is also a self-examination of Macau gambling industry from the firsthand perspectives of scholars, government representatives and casino management.
The mediating role of employee commitment in the relationship between quality of work life and the intention to stay
Authors: Agus Arawati , Selvaraj Rajni 
Published: May 2020

PurposeThe aim of this study is to investigate the relationship between quality of work life (QWL), employee commitment and the intention to stay of nurses in private hospitals in Malaysia.Design/methodology/approachA cross-sectional survey design was used in this study. Primary data were collected through self-administered questionnaires with nurses as the respondents from four private hospitals in the states of Selangor and Kuala Lumpur, Malaysia. Out of 300 questionnaires distributed, 202 valid responses were received. Statistical analyses employed were descriptive statistics, Pearson's correlation, confirmatory factor analysis and structural equation modeling (SEM).FindingsThe strongest QWL construct that contributed significantly to the intention to stay among respondents is work context, followed by work world, work design and work life/home life. The findings further indicate that employee commitment partially mediates the relationship between QWL and the intention to stay. In conclusion, if employees are contented with their QWL, the stronger will the employee commitment be in the organization and ultimately their intention to stay.Originality/valueThis study provides robust evidence for private hospital administrators to enhance their employees' QWL, especially if they are opting to ensure that the turnover of the staff is contained.
Revisiting the mediating effect of normative commitment in B2B bank relationships in Nigeria
Authors: Ojeme Mark , Robson Julie 
Published: May 2020

PurposeThis study examines the mediating effect of normative commitment, that is, a customer's feeling of moral obligation to stay in a relationship based on the psychological feeling that it is the right thing to do. Previous studies have neglected normative commitment due to its complexity and poor fit with predominantly Western individualistic cultures.Design/methodology/approachAn empirical study was conducted in the collectivist culture of Nigeria, West Africa. The unit of analysis was the business-to-business (B2B) relationship between small to medium-sized enterprises (SMEs) and their bank.FindingsThis study arrived at two key findings. First, normative commitment is insignificant in acting as the mediator of a relationship in both overall satisfaction and social bonding on advocacy. Second, overall satisfaction and social bonding are positively significant in predicting normative commitment and advocacy.Research limitations/implicationsThis study focussed solely on an SME's perception of their relationship with their bank and does not consider the dyadic nature of such relationships, that is, the bank's perception of this relationship.Practical implicationsThis research demonstrates that the SME/bank relationship can be developed based on satisfaction and social bonding as background variables. Caution should be exercised for relationships developed on the basis of a moral obligatory commitment.Originality/valueRegardless of a collectivist cultural setting, normative commitment was found to be ineffective in enhancing relationships in a business-oriented setting in Nigeria, contrary to emerging propositions within the literature.