cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12085149.v2
title: Rsp promotes the transcription of virulence factors in an <i>agr</i>-independent manner in <i>Staphylococcus aureus</i>

description: <i>Staphylococcus aureus</i> is a major human pathogen that causes a great diversity of community- and hospital-acquired infections. Rsp, a member of AraC/XylS family of transcriptional regulators (AFTRs), has been reported to play an important role in the regulation of virulence determinants in <i>S. aureus</i> via an <i>agr</i>-dependent pathway. Here we demonstrated that Rsp could bind to the <i>rsp</i> promoter to positively regulate its own expression. We then constructed an isogenic <i>rsp</i> deletion strain and compared the haemolysis in the wild-type and <i>rsp</i> mutant strains. Our results indicated that the <i>rsp</i> mutant strain displayed decreased haemolytic activity, which was correlated with a dramatic decrease in the expression of <i>hla</i> and <i>psm</i>. Furthermore, we analysed the regulatory effects of Rsp in the <i>agr</i> mutant strain and found that they are <i>agr</i>-independent. Electrophoretic mobility shift assay indicated that Rsp can directly bind to the promoter regions of <i>hla</i> and <i>psm</i>. The mouse model of subcutaneous abscess showed that the <i>rsp</i> mutant strain displayed a significant defect in virulence compared to the wild-type strain. These findings reveal that Rsp positively regulates the virulence of <i>S. aureus</i> by promoting the expression of <i>hla</i> and <i>psm</i> through direct binding to their promoter regions.
DOI: 10.6084/m9.figshare.12146112.v4
title: Jamestown Canyon virus in Massachusetts: clinical case series and vector screening

description: Jamestown Canyon virus (JCV) is a neuroinvasive arbovirus that is found throughout North America and increasingly recognized as a public health concern. From 2004 to 2012, an average of 1.7 confirmed cases were reported annually in the United States, whereas from 2013 to 2018 this figure increased over seventeen-fold to 29.2 cases per year. The rising number of reported human infections highlights the need for better understanding of the clinical manifestations and epidemiology of JCV. Here, we describe nine patients diagnosed with neuroinvasive JCV infection in Massachusetts from 2013, the year of the first reported case in the state, to 2017. Because current diagnostic testing relies on serology, which is complicated by cross-reactivity with related orthobunyaviruses and can be negative in immunosuppressed patients, we developed and evaluated an RT-qPCR assay for detection of JCV RNA. We tested this on the available archived serum from two patients, but did not detect viral RNA. JCV is transmitted by multiple mosquito species and its primary vector in Massachusetts is unknown, so we additionally applied the RT-qPCR assay and confirmatory RNA sequencing to assess JCV prevalence in a vector candidate, <i>Ochlerotatus canadensis</i>. We identified JCV in 0.6% of mosquito pools, a similar prevalence to neighboring Connecticut. We assembled the first Massachusetts JCV genome directly from a mosquito sample, finding high identity to JCV isolates collected over a 60-year period. Further studies are needed to reconcile the low vector prevalence and low rate of viral evolutionary change with the increasing number of reported cases.
DOI: 10.6084/m9.figshare.12146112.v3
title: Jamestown Canyon virus in Massachusetts: clinical case series and vector screening

description: Jamestown Canyon virus (JCV) is a neuroinvasive arbovirus that is found throughout North America and increasingly recognized as a public health concern. From 2004 to 2012, an average of 1.7 confirmed cases were reported annually in the United States, whereas from 2013 to 2018 this figure increased over seventeen-fold to 29.2 cases per year. The rising number of reported human infections highlights the need for better understanding of the clinical manifestations and epidemiology of JCV. Here, we describe nine patients diagnosed with neuroinvasive JCV infection in Massachusetts from 2013, the year of the first reported case in the state, to 2017. Because current diagnostic testing relies on serology, which is complicated by cross-reactivity with related orthobunyaviruses and can be negative in immunosuppressed patients, we developed and evaluated an RT-qPCR assay for detection of JCV RNA. We tested this on the available archived serum from two patients, but did not detect viral RNA. JCV is transmitted by multiple mosquito species and its primary vector in Massachusetts is unknown, so we additionally applied the RT-qPCR assay and confirmatory RNA sequencing to assess JCV prevalence in a vector candidate, <i>Ochlerotatus canadensis</i>. We identified JCV in 0.6% of mosquito pools, a similar prevalence to neighboring Connecticut. We assembled the first Massachusetts JCV genome directly from a mosquito sample, finding high identity to JCV isolates collected over a 60-year period. Further studies are needed to reconcile the low vector prevalence and low rate of viral evolutionary change with the increasing number of reported cases.
DOI: 10.18126/toyw-ws97
title: A mechanics-based approach to realize high-force capacity electroadhesives for robots
DOI: 10.6084/m9.figshare.21928458
title: Telomere length, oxidative stress and their links with growth and survival in a lizard facing climate warming

description: txt file is the description of data in this papar. Seven csv file is the data. Growth data.csv described growth data of all individuals. Survival.csv described survival information of all individuals. Death data.csv described death information at each developmental stage. Physiological data.csv described oxidative stress data and telomere length data of 20 individuals. Ground surface temperature.csv described monthly average ground-surface temperature in different thermal treatments from 2018-07 to 2020-09. Environment temperature.csv described monthly average environment temperature in different thermal treatments in active seasons. Humidity.csv described monthly average relative humidity in different thermal treatments in active seasons.
DOI: 10.6084/m9.figshare.21922059
title: Kuesioner anemia inggris.docx

description: Questionaire
DOI: 10.6084/m9.figshare.21922059.v1
title: Kuesioner anemia inggris.docx

description: Questionaire
DOI: 10.5281/zenodo.7553144
title: Artifact for "MAAT: A Novel Ensemble Approach to Addressing Fairness and Performance Bugs for Machine Learning Software"

description: This artifact is for the paper entitled “MAAT: A Novel Ensemble Approach to Addressing Fairness and Performance Bugs for Machine Learning Software”, which is accepted by ESEC/FSE 2022. MAAT is a novel ensemble approach to improving the fairness-performance trade-off for ML software. It outperforms state-of-the-art bias mitigation methods. The artifact has also been placed on GitHub (https://github.com/chenzhenpeng18/FSE22-MAAT) under the Apache License, publicly accessible to other researchers. In this artifact, we provide the source code of MAAT and other existing bias mitigation methods that we use in our study, as well as the intermediate results, the installation instructions, and a replication guideline (included in the README). The replication guideline provides detailed steps to replicate all the results for all the research questions.
DOI: 10.5281/zenodo.7553143
title: Artifact for "MAAT: A Novel Ensemble Approach to Addressing Fairness and Performance Bugs for Machine Learning Software"

description: This artifact is for the paper entitled “MAAT: A Novel Ensemble Approach to Addressing Fairness and Performance Bugs for Machine Learning Software”, which is accepted by ESEC/FSE 2022. MAAT is a novel ensemble approach to improving the fairness-performance trade-off for ML software. It outperforms state-of-the-art bias mitigation methods. The artifact has also been placed on GitHub (https://github.com/chenzhenpeng18/FSE22-MAAT) under the Apache License, publicly accessible to other researchers. In this artifact, we provide the source code of MAAT and other existing bias mitigation methods that we use in our study, as well as the intermediate results, the installation instructions, and a replication guideline (included in the README). The replication guideline provides detailed steps to replicate all the results for all the research questions.
DOI: 10.6084/m9.figshare.20776198
title: Empirical Study on High Performance Computing (HPC) Performance Bug Analysis - Replication Package

description: Summary results of labeled data added.
DOI: 10.6084/m9.figshare.20776198.v2
title: Empirical Study on High Performance Computing (HPC) Performance Bug Analysis - Replication Package

description: Summary results of labeled data added.
DOI: 10.6084/m9.figshare.20776198.v1
title: Empirical Study on High Performance Computing (HPC) Performance Bug Analysis - Replication Package

description: Summary results of labeled data added.
DOI: 10.6084/m9.figshare.12853655
title: The burden, admission, and outcome of COVID-19 in Africa: protocol for a systematic review and meta-analysis

description: <i>Background</i>: According to the World Health Organization (WHO), the outbreak of coronavirus disease in 2019 (COVID-19) has been declared as pandemic and public health emergency that infected more than 5 million people worldwide at the time of writing this protocol. Strong evidence for the burden, admission, and outcome of COVID-19 has not been published in Africa. Therefore, this protocol will be served as a guideline to conduct a systematic review and meta-analysis of the burden, admission, and outcome of COVID-19 in Africa. <i>Methods</i>: Published and unpublished studies on the burden, admission, and outcome of COVID-19 in Africa and written in any language will be included. Databases (PubMed / MEDLINE, Google Scholar, Google, EMBASE, Web of Science, Microsoft Academic, WHO COVID-19 database, Cochran Library, Africa Wide Knowledge, and Africa Index Medicus) from December 2019 to May 2020 will be searched. Two independent reviewers will select, screen, extract data, and assess the risk of bias. The proportion will be measured using a random-effects model. Subgroup analysis will be conducted to manage hetrogeinity. The presence of publication bias will be assessed using Egger's test and visual inspection of the funnel plots. This systematic and meta-analysis review protocol will be reported per the PRISMA-P guidelines. <i>Conclusion</i>: This systematic review and meta-analysis protocol will be expected to quantify the burden, admission, and outcome of COVID-19 in Africa. <i>Systematic review registration</i>: This protocol was submitted for registration with the International Prospective Register of Systematic Reviews (PROSPERO) in March 2020 and accepted with the registration number: CRD42020179321(https://www.crd.york.ac.uk/PROSPERO).
DOI: 10.6084/m9.figshare.12853655.v3
title: The burden, admission, and outcome of COVID-19 in Africa: protocol for a systematic review and meta-analysis

description: <i>Background</i>: According to the World Health Organization (WHO), the outbreak of coronavirus disease in 2019 (COVID-19) has been declared as pandemic and public health emergency that infected more than 5 million people worldwide at the time of writing this protocol. Strong evidence for the burden, admission, and outcome of COVID-19 has not been published in Africa. Therefore, this protocol will be served as a guideline to conduct a systematic review and meta-analysis of the burden, admission, and outcome of COVID-19 in Africa. <i>Methods</i>: Published and unpublished studies on the burden, admission, and outcome of COVID-19 in Africa and written in any language will be included. Databases (PubMed / MEDLINE, Google Scholar, Google, EMBASE, Web of Science, Microsoft Academic, WHO COVID-19 database, Cochran Library, Africa Wide Knowledge, and Africa Index Medicus) from December 2019 to May 2020 will be searched. Two independent reviewers will select, screen, extract data, and assess the risk of bias. The proportion will be measured using a random-effects model. Subgroup analysis will be conducted to manage hetrogeinity. The presence of publication bias will be assessed using Egger's test and visual inspection of the funnel plots. This systematic and meta-analysis review protocol will be reported per the PRISMA-P guidelines. <i>Conclusion</i>: This systematic review and meta-analysis protocol will be expected to quantify the burden, admission, and outcome of COVID-19 in Africa. <i>Systematic review registration</i>: This protocol was submitted for registration with the International Prospective Register of Systematic Reviews (PROSPERO) in March 2020 and accepted with the registration number: CRD42020179321(https://www.crd.york.ac.uk/PROSPERO).
DOI: 10.6084/m9.figshare.12853655.v2
title: The burden, admission, and outcome of COVID-19 in Africa: protocol for a systematic review and meta-analysis

description: <i>Background</i>: According to the World Health Organization (WHO), the outbreak of coronavirus disease in 2019 (COVID-19) has been declared as pandemic and public health emergency that infected more than 5 million people worldwide at the time of writing this protocol. Strong evidence for the burden, admission, and outcome of COVID-19 has not been published in Africa. Therefore, this protocol will be served as a guideline to conduct a systematic review and meta-analysis of the burden, admission, and outcome of COVID-19 in Africa. <i>Methods</i>: Published and unpublished studies on the burden, admission, and outcome of COVID-19 in Africa and written in any language will be included. Databases (PubMed / MEDLINE, Google Scholar, Google, EMBASE, Web of Science, Microsoft Academic, WHO COVID-19 database, Cochran Library, Africa Wide Knowledge, and Africa Index Medicus) from December 2019 to May 2020 will be searched. Two independent reviewers will select, screen, extract data, and assess the risk of bias. The proportion will be measured using a random-effects model. Subgroup analysis will be conducted to manage hetrogeinity. The presence of publication bias will be assessed using Egger's test and visual inspection of the funnel plots. This systematic and meta-analysis review protocol will be reported per the PRISMA-P guidelines. <i>Conclusion</i>: This systematic review and meta-analysis protocol will be expected to quantify the burden, admission, and outcome of COVID-19 in Africa. <i>Systematic review registration</i>: This protocol was submitted for registration with the International Prospective Register of Systematic Reviews (PROSPERO) in March 2020 and accepted with the registration number: CRD42020179321(https://www.crd.york.ac.uk/PROSPERO).
DOI: 10.6084/m9.figshare.12853721.v2
title: <i>Escherichia coli</i> ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex

description: The <i>H</i>30Rx subclade of <i>Escherichia coli</i> ST131 is a clinically important, globally dispersed pathogenic lineage that typically displays resistance to fluoroquinolones and extended spectrum β-lactams. Isolates EC233 and EC234, variants of ST131-<i>H</i>30Rx with a novel sequence type (ST) 8196, isolated from unrelated patients presenting with bacteraemia at a Sydney Hospital in 2014 are characterised here. EC233 and EC234 are phylogroup B2, serotype O25:<i>H</i>4A, and resistant to ampicillin, amoxicillin, cefoxitin, ceftazidime, ceftriaxone, ciprofloxacin, norfloxacin and gentamicin and are likely clonal. Both harbour an IncFII_2 plasmid (pSPRC_Ec234-FII) that carries most of the resistance genes on an IS<i>26</i> associated translocatable unit, two small plasmids and a novel IncI1 plasmid (pSPRC_Ec234-I). SNP-based phylogenetic analysis of the core genome of representatives within the ST131 clonal complex places both isolates in a subclade with three clinical Australian ST131-<i>H</i>30Rx clade-C isolates. A MrBayes phylogeny analysis of EC233 and EC234 indicates ST8196 share a most recent common ancestor with ST131-<i>H</i>30Rx strain EC70 isolated from the same hospital in 2013. Our study identified genomic hallmarks that define the ST131-<i>H</i>30Rx subclade in the ST8196 isolates and highlights a need for unbiased genomic surveillance approaches to identify novel high-risk MDR <i>E. coli</i> pathogens that impact healthcare facilities.
DOI: 10.6084/m9.figshare.12853721
title: <i>Escherichia coli</i> ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex

description: The <i>H</i>30Rx subclade of <i>Escherichia coli</i> ST131 is a clinically important, globally dispersed pathogenic lineage that typically displays resistance to fluoroquinolones and extended spectrum β-lactams. Isolates EC233 and EC234, variants of ST131-<i>H</i>30Rx with a novel sequence type (ST) 8196, isolated from unrelated patients presenting with bacteraemia at a Sydney Hospital in 2014 are characterised here. EC233 and EC234 are phylogroup B2, serotype O25:<i>H</i>4A, and resistant to ampicillin, amoxicillin, cefoxitin, ceftazidime, ceftriaxone, ciprofloxacin, norfloxacin and gentamicin and are likely clonal. Both harbour an IncFII_2 plasmid (pSPRC_Ec234-FII) that carries most of the resistance genes on an IS<i>26</i> associated translocatable unit, two small plasmids and a novel IncI1 plasmid (pSPRC_Ec234-I). SNP-based phylogenetic analysis of the core genome of representatives within the ST131 clonal complex places both isolates in a subclade with three clinical Australian ST131-<i>H</i>30Rx clade-C isolates. A MrBayes phylogeny analysis of EC233 and EC234 indicates ST8196 share a most recent common ancestor with ST131-<i>H</i>30Rx strain EC70 isolated from the same hospital in 2013. Our study identified genomic hallmarks that define the ST131-<i>H</i>30Rx subclade in the ST8196 isolates and highlights a need for unbiased genomic surveillance approaches to identify novel high-risk MDR <i>E. coli</i> pathogens that impact healthcare facilities.
DOI: 10.6084/m9.figshare.13221624
title: Yin-Yang 1 and HBx protein activate HBV transcription by mediating the spatial interaction of cccDNA minichromosome with cellular chromosome 19p13.11

description: HBV cccDNA stably exists in the nuclei of infected cells as an episomal munichromosome which is responsible for viral persistence and failure of current antiviral treatments. However, the regulatory mechanism of cccDNA transcription by viral and host cellular factors is not well understood. In this study, we investigated whether cccDNA could be recruited into a specific region of the nucleus via specific interaction with a cellular chromatin to regulate its transcription activity. To investigate this hypothesis, we used chromosome conformation capture (3C) technology to search for the potential interaction of cccDNA and cellular chromatin through rcccDNA transfection in hepatoma cells and found that cccDNA is specifically associated with human chromosome 19p13.11 region, which contains a highly active enhancer element. We also confirmed that cellular transcription factor Yin-Yang 1 (YY1) and viral protein HBx mediated the spatial regulation of HBV cccDNA transcription by 19p13.11 enhancer. Thus, These findings indicate that YY1 and HBx mediate the recruitment of HBV cccDNA minichromosomes to 19p13.11 region for transcription activation, and YY1 may present as a novel therapeutic target against HBV infection.
DOI: 10.6084/m9.figshare.13221624.v1
title: Yin-Yang 1 and HBx protein activate HBV transcription by mediating the spatial interaction of cccDNA minichromosome with cellular chromosome 19p13.11

description: HBV cccDNA stably exists in the nuclei of infected cells as an episomal munichromosome which is responsible for viral persistence and failure of current antiviral treatments. However, the regulatory mechanism of cccDNA transcription by viral and host cellular factors is not well understood. In this study, we investigated whether cccDNA could be recruited into a specific region of the nucleus via specific interaction with a cellular chromatin to regulate its transcription activity. To investigate this hypothesis, we used chromosome conformation capture (3C) technology to search for the potential interaction of cccDNA and cellular chromatin through rcccDNA transfection in hepatoma cells and found that cccDNA is specifically associated with human chromosome 19p13.11 region, which contains a highly active enhancer element. We also confirmed that cellular transcription factor Yin-Yang 1 (YY1) and viral protein HBx mediated the spatial regulation of HBV cccDNA transcription by 19p13.11 enhancer. Thus, These findings indicate that YY1 and HBx mediate the recruitment of HBV cccDNA minichromosomes to 19p13.11 region for transcription activation, and YY1 may present as a novel therapeutic target against HBV infection.
DOI: 10.6084/m9.figshare.12853721.v1
title: <i>Escherichia coli</i> ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex

description: The <i>H</i>30Rx subclade of <i>Escherichia coli</i> ST131 is a clinically important, globally dispersed pathogenic lineage that typically displays resistance to fluoroquinolones and extended spectrum β-lactams. Isolates EC233 and EC234, variants of ST131-<i>H</i>30Rx with a novel sequence type (ST) 8196, isolated from unrelated patients presenting with bacteraemia at a Sydney Hospital in 2014 are characterised here. EC233 and EC234 are phylogroup B2, serotype O25:<i>H</i>4A, and resistant to ampicillin, amoxicillin, cefoxitin, ceftazidime, ceftriaxone, ciprofloxacin, norfloxacin and gentamicin and are likely clonal. Both harbour an IncFII_2 plasmid (pSPRC_Ec234-FII) that carries most of the resistance genes on an IS<i>26</i> associated translocatable unit, two small plasmids and a novel IncI1 plasmid (pSPRC_Ec234-I). SNP-based phylogenetic analysis of the core genome of representatives within the ST131 clonal complex places both isolates in a subclade with three clinical Australian ST131-<i>H</i>30Rx clade-C isolates. A MrBayes phylogeny analysis of EC233 and EC234 indicates ST8196 share a most recent common ancestor with ST131-<i>H</i>30Rx strain EC70 isolated from the same hospital in 2013. Our study identified genomic hallmarks that define the ST131-<i>H</i>30Rx subclade in the ST8196 isolates and highlights a need for unbiased genomic surveillance approaches to identify novel high-risk MDR <i>E. coli</i> pathogens that impact healthcare facilities.
DOI: 10.6084/m9.figshare.13378598.v1
title: Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto<b>-</b>Beijing genotype

description: Tuberculosis disease (TB), caused by <i>Mycobacterium tuberculosis</i>, is a major public health issue in Thailand. The high prevalence of modern Beijing (Lineage 2.2.1) strains has been associated with multi- and extensively drug-resistant infections (MDR-, XDR-TB), complicating disease control. The impact of rarer proto-Beijing (L2.1) strains is less clear. In our study of thirty-seven L2.1 clinical isolates spanning thirteen years, we found a high prevalence of XDR-TB cases (32.4%). With ≤ 12 pairwise SNP distances, 43.2% of L2.1 patients belong to MDR-TB or XDR-TB transmission clusters suggesting a high level of clonal expansion across four Thai provinces. All XDR-TB (100%) were likely due to transmission rather than inadequate treatment. We found a 47 mutation signature and a partial deletion of the <i>fadD14</i> gene in the circulating XDR-TB cluster, which can be used for surveillance of this rare and resilient <i>M. tuberculosis</i> strain-type that is causing increasing health burden. We also detected three novel deletion positions, a deletion of 1285 bp within <i>desA3</i> (Rv3230c)<i>,</i> large deletions in the <i>plcB, plcA,</i> and <i>ppe38</i> gene which may play a role in the virulence, pathogenesis or evolution of the L2.1 strain-type.