cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9062765.v1
title: Papillomavirus can be transmitted through the blood and produce infections in blood recipients: Evidence from two animal models

description: Human papillomaviruses (HPV) contribute to most cervical cancers and are considered to be sexually transmitted. However, papillomaviruses are often found in cancers of internal organs, including the stomach, raising the question as to how the viruses gain access to these sites. A possible connection between blood transfusion and HPV-associated disease has not received much attention. Here we show, in rabbit and mouse models, that blood infected with papillomavirus yields infections at permissive sites with detectable viral DNA, RNA transcripts, and protein products. The rabbit skin tumours induced via blood infection displayed decreased expression of SLN, TAC1, MYH8, PGAM2, and APOBEC2 and increased expression of SDRC7, KRT16, S100A9, IL36G, and FABP9, as seen in tumours induced by local infections. Furthermore, we demonstrate that blood from infected mice can transmit the infection to uninfected animals. Finally, we demonstrate the presence of papillomavirus infections and virus-induced hyperplasia in the stomach tissues of animals infected via the blood. These results indicate that blood transmission could be another route for papillomavirus infection, implying that the human blood supply, which is not screened for papillomaviruses, could be a potential source of HPV infection as well as subsequent cancers in tissues not normally associated with the viruses.
DOI: 10.6084/m9.figshare.9252428.v1
title: Combining sequencing approaches to fully resolve a carbapenemase-encoding megaplasmid in a <i>Pseudomonas shirazica</i> clinical strain

description: Horizontal transfer of plasmids plays a pivotal role in dissemination of antibiotic resistance genes and emergence of multidrug-resistant bacteria. Plasmid sequencing is thus paramount for accurate epidemiological tracking in hospitals and routine surveillance. Combining Nanopore and Illumina sequencing allowed full assembly of a carbapenemase-encoding megaplasmid carried by multidrug-resistant clinical isolate FFUP_PS_41. Average nucleotide identity analyses revealed that FFUP_PS_41 belongs to the recently proposed new species Pseudomonas shirazica, related to the P. putida phylogenetic group. FFUP_PS_41 harbours a 498,516-bp megaplasmid (pJBCL41) with limited similarity to publicly-available plasmids. pJBCL41 contains genes predicted to encode replication, conjugation, partitioning and maintenance functions and heavy metal resistance. The |aacA7|blaVIM-2|aacA4| cassette array (resistance to carbapenems and aminoglycosides) is located within a class 1 integron that is a defective Tn402 derivative. This transposon lies within a 50,273-bp region bound by Tn3-family 38-bp inverted repeats and flanked by 5-bp direct repeats (DR) that composes additional transposon fragments, five insertion sequences and a Tn3-Derived Inverted-Repeat Miniature Element. The hybrid Nanopore/Illumina approach allowed full resolution of a carbapenemase-encoding megaplasmid from P. shirazica. Identification of novel megaplasmids sheds new light on the evolutionary effects of gene transfer and the selective forces driving antibiotic resistance.
DOI: 10.6084/m9.figshare.8320670.v1
title: Identification of a novel alphavirus related to the encephalitis complexes circulating in southern Brazil

description: In early 2017, an outbreak caused by an unknown and supposedly viral agent in the Marilena region of southern Brazil was investigated. Since the etiological agent causing the outbreak was not identified from human samples, mosquitoes from this region were collected. Three out of 121 mosquito pools collected from the region tested positive for alphavirus in molecular tests. Next generation sequencing results revealed the presence of a novel alphavirus, tentatively named here as Caainguá virus (CAAV). DNA barcoding analyses indicated that different species of <i>Culex</i> are hosts for CAAV. This new virus was basal to the New World encephalitic alphaviruses in a comprehensive and robust phylogenetic approach using complete genomes. Viral particles were observed in the cytosol and inside of intracellular compartments of cells in mosquito-derived cell cultures. Despite being noninfectious in vertebrate derived cell cultures, primary culturing of CAAV in human mononuclear cells suggests monocytes and lymphocytes as CAAV targets. However, the epidemiological link of CAAV on the human outbreak should be further explored.
DOI: 10.6084/m9.figshare.9891728.v1
title: The cytochrome d oxidase complex regulated by fexA is an Achilles' heel in the <i>in vivo</i> survival of <i>vibrio vulnificus</i>

description: <i>Vibrio vulnificus</i> is a halophilic estuarine bacterium causing severe opportunistic infections. To successfully establish an infection, <i>V. vulnificus</i> must adapt to redox fluctuations in vivo. In the present study, we show that deletion of <i>V. vulnificus</i> fexA gene caused hypersensitivity to acid and reactive oxygen species. The <i>ΔfexA</i> mutant exhibited severe in vivo survival defects. For deeper understanding the role of <i>fexA</i> gene on the successful <i>V. vulnificus</i> infection, we analyzed differentially expressed genes in <i>ΔfexA</i> mutant in comparison with wild type under aerobic, anaerobic or in vivo culture conditions by genome-scale DNA microarray analyses. Twenty-two genes were downregulated in the <i>ΔfexA</i> mutant under all three culture conditions. Among them, <i>cydAB</i> appeared to dominantly contribute to the defective phenotypes of the <i>ΔfexA</i> mutant. The <i>fexA</i> deletion induced compensatory point mutations in the <i>cydAB</i> promoter region over subcultures, suggesting essentiality. Those point mutations (P<sub>cyd</sub>SMs) restored bacterial growth, motility, cytotoxicity ATP production and mouse lethality in the <i>ΔfexA</i> mutant. These results indicate that the <i>cydAB</i> operon, being regulated by <i>FexA</i>, plays a crucial role in <i>V. vulnificus</i> survival under redox-fluctuating in vivo conditions. The FexA-CydAB axis should serve an Achilles heel in the development of therapeutic regimens against <i>V. vulnificus</i> infection.
DOI: 10.6084/m9.figshare.8015642.v1
title: Avian influenza virus detection, temporality and co-infection in poultry in Cambodian border provinces, 2017–2018

description: Avian influenza virus detection, temporality and co-infection in poultry in Cambodian border provinces, 2017–2018
DOI: 10.6084/m9.figshare.9198914.v1
title: Mapping histoplasmosis in South East Asia – implications for diagnosis in AIDS

description: Histoplasmosis caused by the fungus <i>Histoplasma capsulatum</i> is often lethal in patients with AIDS. Urine antigen testing is highly sensitive and much quicker for diagnosis than culture. Histoplasmosis has a patchy and incompletely appreciated distribution around the world especially in South East Asia. We conducted a systematic literature review of cases of all disease forms of histoplasmosis in SE Asia, not including the Indian sub-continent. We also reviewed all histoplasmin skin test mapping studies to determine localities of exposure. We found a total of 407 cases contracted or likely to have been contracted in SE Asia. Numbers of cases by country varied: Thailand (233), Malaysia (76), Indonesia (48) and Singapore (21), with few or no cases reported in other countries. Most cases (255 (63%)) were disseminated histoplasmosis and 177 (43%) cases were HIV associated. Areas of high histoplasmin skin test sensitivity prevalence were found in Myanmar, the Philippines, Indonesia, Thailand and Vietnam - 86.4%, 26.0%, 63.6%, 36.0% and 33.7%, respectively. We have drawn maps of these data. Further study is required to ascertain the extent of histoplasmosis within SE Asia. Diagnostic capability for patients with HIV infection is urgently required in SE Asia, to reduce mortality and mis-diagnosis as tuberculosis.
DOI: 10.6084/m9.figshare.7937306.v1
title: <i>Haemagogus leucocelaenus</i> and <i>Haemagogus janthinomys</i> are the primary vectors in the major yellow fever outbreak in Brazil, 2016–2018

description: The yellow fever virus (YFV) caused a severe outbreak in Brazil in 2016–2018 that rapidly spread across the Atlantic Forest in its most populated region without viral circulation for almost 80 years. A comprehensive entomological survey combining analysis of distribution, abundance and YFV natural infection in mosquitoes captured before and during the outbreak was conducted in 44 municipalities of five Brazilian states. In total, 17,662 mosquitoes of 89 species were collected. Before evidence of virus circulation, mosquitoes were tested negative but traditional vectors were alarmingly detected in 82% of municipalities, revealing high receptivity to sylvatic transmission. During the outbreak, five species were found positive in 42% of municipalities. <i>Haemagogus janthinomys</i> and <i>Hg. leucocelaenus</i> are considered the primary vectors due to their large distribution combined with high abundance and natural infection rates, concurring together for the rapid spread and severity of this outbreak. <i>Aedes taeniorhynchus</i> was found infected for the first time, but like <i>Sabethes chloropterus</i> and <i>Aedes scapularis</i>, it appears to have a potential local or secondary role because of their low abundance, distribution and infection rates. There was no evidence of YFV transmission by <i>Aedes albopictus</i> and <i>Aedes aegypti,</i> although the former was the most widespread species across affected municipalities, presenting an important overlap between the niches of the sylvatic vectors and the anthropic ones. The definition of receptive areas, expansion of vaccination in the most affected age group and exposed populations and the adoption of universal vaccination to the entire Brazilian population need to be urgently implemented.
DOI: 10.6084/m9.figshare.7936934.v1
title: Swine influenza viruses in Northern Vietnam in 2013–2014

description: Swine are an important intermediate host for emergence of pandemic influenza. Vietnam is the largest swine producer in South East Asia. Systematic virological and serological surveillance of swine influenza viruses was carried out in Northern Vietnam from May 2013 to June 2014 with monthly sampling of pigs in local and large collective slaughterhouses and in a live pig market. Influenza A seroprevalence in the local slaughterhouses and in the large collective slaughterhouse was 48.7% and 29.1%, respectively. Seventy-seven influenza A viruses were isolated, all from the large collective slaughterhouse. Genetic analysis revealed six virus genotypes including H1N1 2009 pandemic (H1N1pdm09) viruses, H1N2 with H1 of human origin, H3N2 and H1N1pdm09 reassortants, and triple-reassortant H3N2 viruses. Phylogenetic analysis of swine and human H1N1pdm09 viruses showed evidence of repeated spill-over from humans to swine rather than the establishment of H1N1pdm09 as long-term distinct lineage in swine. Surveillance at the large collective slaughterhouse proved to be the most efficient, cost-effective, and sustainable method of surveillance for swine influenza viruses in Vietnam.
DOI: 10.5281/zenodo.4712937
title: Mercury exosphere model output for meteoroid impact events

description: The Ultraviolet and Visible Spectrometer (UVVS) on the MESSENGER spacecraft observed three large transient events on Mercury’s nightside “tail,” during which exospheric brightness increased by an order of magnitude. UVVS observed enhancements of atomic sodium vapor, and, in one event, atomic sodium, magnesium and calcium. Meteoroid impacts are the most likely source given that the events can be simulated with instantaneous injections of vapor. Models for the three events are included in an attached ASCII file along with the original observations. The data consists of atomic emission time series recorded by the UVVS as its sightline was scanned back and forth across Mercury's nightside. Individual data points consist of UTC observation time and radiance in units of kilorayleighs. Each event is labeled by its atomic species and year of occurrence (2011, 2012, or 2013). The code for that produced the impactor model is available here. The work is discussed in a submitted journal article. We also include steady-state exosphere models for the three events in another ASCII file. The code that produced the steady-state models is available here. The steady-state files include the original UVVS data. More information on the original data is available on the NASA Planetary Data System with the data product ID MESS-E/V/H-MASCS-4-UVVS-DDR-V1.0.
DOI: 10.6084/m9.figshare.12851909
title: Accurate characterization of <i>Escherichia coli</i> tRNA modifications with a simple method of deep-sequencing library preparation

description: In conventional RNA high-throughput sequencing, modified bases prevent a large fraction of tRNA transcripts to be converted into cDNA libraries. Recent proposals aiming at resolving this issue take advantage of the interference of base modifications with RT enzymes to detect and identify them by establishing signals from aborted cDNA transcripts. Because some modifications, such as methyl groups, do almost not allow RT bypassing, demethylation and highly processive RT enzymes have been used to overcome these obstacles. Working with <i>Escherichia coli</i> as a model system, we show that with a conventional (albeit still engineered) RT enzyme and key optimizations in library preparation, all RT-impairing modifications can be highlighted along the entire tRNA length without demethylation procedure. This is achieved by combining deep-sequencing samples, which allows to establish aborted transcription signal of higher accuracy and reproducibility, with the potential for differentiating tiny differences in the state of modification of all cellular tRNAs. In addition, our protocol provides estimates of the relative tRNA abundance.
DOI: 10.6084/m9.figshare.12851909.v3
title: Accurate characterization of <i>Escherichia coli</i> tRNA modifications with a simple method of deep-sequencing library preparation

description: In conventional RNA high-throughput sequencing, modified bases prevent a large fraction of tRNA transcripts to be converted into cDNA libraries. Recent proposals aiming at resolving this issue take advantage of the interference of base modifications with RT enzymes to detect and identify them by establishing signals from aborted cDNA transcripts. Because some modifications, such as methyl groups, do almost not allow RT bypassing, demethylation and highly processive RT enzymes have been used to overcome these obstacles. Working with <i>Escherichia coli</i> as a model system, we show that with a conventional (albeit still engineered) RT enzyme and key optimizations in library preparation, all RT-impairing modifications can be highlighted along the entire tRNA length without demethylation procedure. This is achieved by combining deep-sequencing samples, which allows to establish aborted transcription signal of higher accuracy and reproducibility, with the potential for differentiating tiny differences in the state of modification of all cellular tRNAs. In addition, our protocol provides estimates of the relative tRNA abundance.
DOI: 10.6084/m9.figshare.12851909.v2
title: Accurate characterization of <i>Escherichia coli</i> tRNA modifications with a simple method of deep sequencing library preparation

description: In conventional RNA high-throughput sequencing, modified bases prevent a large fraction of tRNA transcripts to be converted into cDNA libraries. Recent proposals aiming at resolving this issue take advantage of the interference of base modifications with RT enzymes to detect and identify them by establishing signals from aborted cDNA transcripts. Because some modifications, such as methyl groups, do almost not allow RT bypassing, demethylation and highly processive RT enzymes have been used to overcome these obstacles. Working with <i>Escherichia coli</i> as a model system, we show that with a conventional (albeit still engineered) RT enzyme and key optimizations in library preparation, all RT-impairing modifications can be highlighted along the entire tRNA length without demethylation procedure. This is achieved by combining deep-sequencing samples, which allows to establish aborted transcription signal of higher accuracy and reproducibility, with the potential for differentiating tiny differences in the state of modification of all cellular tRNAs. In addition, our protocol provides estimates of the relative tRNA abundance.
DOI: 10.6084/m9.figshare.12851925
title: <i>Ctcf</i> haploinsufficiency mediates intron retention in a tissue-specific manner

description: CTCF is a master regulator of gene transcription and chromatin organisation with occupancy at thousands of DNA target sites genome-wide. While CTCF is essential for cell survival, CTCF haploinsufficiency is associated with tumour development and hypermethylation. Increasing evidence demonstrates CTCF as a key player in several mechanisms regulating alternative splicing (AS), however, the genome-wide impact of <i>Ctcf</i> dosage on AS has not been investigated. We examined the effect of <i>Ctcf</i> haploinsufficiency on gene expression and AS in five tissues from <i>Ctcf</i> hemizygous (<i>Ctcf</i> <sup>+/-</sup>) mice. Reduced <i>Ctcf</i> levels caused distinct tissue-specific differences in gene expression and AS in all tissues. An increase in intron retention (IR) was observed in <i>Ctcf</i> <sup>+/-</sup> liver and kidney. In liver, this specifically impacted genes associated with cytoskeletal organisation, splicing and metabolism. Strikingly, most differentially retained introns were short, with a high GC content and enriched in Ctcf binding sites in their proximal upstream genomic region. This study provides new insights into the effects of <i>CTCF</i> haploinsufficiency on organ transcriptomes and the role of CTCF in AS regulation.
DOI: 10.6084/m9.figshare.12851925.v3
title: <i>Ctcf</i> haploinsufficiency mediates intron retention in a tissue-specific manner

description: CTCF is a master regulator of gene transcription and chromatin organisation with occupancy at thousands of DNA target sites genome-wide. While CTCF is essential for cell survival, CTCF haploinsufficiency is associated with tumour development and hypermethylation. Increasing evidence demonstrates CTCF as a key player in several mechanisms regulating alternative splicing (AS), however, the genome-wide impact of <i>Ctcf</i> dosage on AS has not been investigated. We examined the effect of <i>Ctcf</i> haploinsufficiency on gene expression and AS in five tissues from <i>Ctcf</i> hemizygous (<i>Ctcf</i> <sup>+/-</sup>) mice. Reduced <i>Ctcf</i> levels caused distinct tissue-specific differences in gene expression and AS in all tissues. An increase in intron retention (IR) was observed in <i>Ctcf</i> <sup>+/-</sup> liver and kidney. In liver, this specifically impacted genes associated with cytoskeletal organisation, splicing and metabolism. Strikingly, most differentially retained introns were short, with a high GC content and enriched in Ctcf binding sites in their proximal upstream genomic region. This study provides new insights into the effects of <i>CTCF</i> haploinsufficiency on organ transcriptomes and the role of CTCF in AS regulation.
DOI: 10.6084/m9.figshare.12851925.v2
title: <i>Ctcf</i> haploinsufficiency mediates intron retention in a tissue-specific manner

description: CTCF is a master regulator of gene transcription and chromatin organisation with occupancy at thousands of DNA target sites genome-wide. While CTCF is essential for cell survival, CTCF haploinsufficiency is associated with tumour development and hypermethylation. Increasing evidence demonstrates CTCF as a key player in several mechanisms regulating alternative splicing (AS), however, the genome-wide impact of <i>Ctcf</i> dosage on AS has not been investigated. We examined the effect of <i>Ctcf</i> haploinsufficiency on gene expression and AS in five tissues from <i>Ctcf</i> hemizygous (<i>Ctcf</i> <sup>+/-</sup>) mice. Reduced <i>Ctcf</i> levels caused distinct tissue-specific differences in gene expression and AS in all tissues. An increase in intron retention (IR) was observed in <i>Ctcf</i> <sup>+/-</sup> liver and kidney. In liver, this specifically impacted genes associated with cytoskeletal organisation, splicing and metabolism. Strikingly, most differentially retained introns were short, with a high GC content and enriched in Ctcf binding sites in their proximal upstream genomic region. This study provides new insights into the effects of <i>CTCF</i> haploinsufficiency on organ transcriptomes and the role of CTCF in AS regulation.
DOI: 10.6084/m9.figshare.14770380
title: Focus group with service users madame geneva play

description: Focus group with women who are service users of drug and alcohol service providers. They viewed the show Madame geneva
DOI: 10.6084/m9.figshare.14770380.v2
title: Focus group with service users madame geneva play

description: Focus group with women who are service users of drug and alcohol service providers. They viewed the show Madame geneva
DOI: 10.6084/m9.figshare.14770380.v1
title: Untitled Item

description: Focus group with women who are service users of drug and alcohol service providers. They viewed the show Madame geneva
DOI: 10.17632/zjn2zxcgyz.1
title: ST_URA8_Dataset_part_1

description: This is a dataset for Bluetooth 5.1 DoA applications with URA8 antenna arrays. It was conceived as a starting point for developing and validating DoA algorithms for real-life scenarios. Unlike other datasets, it contains Bluetooth signals with not only varying intensity of additive white Gaussian noise, but also coherent interfering signals with random DoA coordinates. The dataset is divided into two branches, one consisting of pure sinusoidal tones and the second comprised of baseband Bluetooth signals. The Python code which generated this dataset is included. Therefore, the dataset can be expanded and also modified to suit other types of signals and simulate other types of antenna arrays. Please note that this is only the first part of the dataset. The dataset is comprised of four parts, and you need to download all of them in order to recreate the entire directory structure. Part 1: http://dx.doi.org/10.17632/zjn2zxcgyz.1 Part 2: http://dx.doi.org/10.17632/gysjfpvxpm.1 Part 3: http://dx.doi.org/10.17632/nnv3vpy4y3.1 Part 4: http://dx.doi.org/10.17632/362szwsnc4.1