cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12853320.v1
title: <i>In vitro</i> and <i>in silico</i> analysis of <i>L. donovani</i> enoyl acyl carrier protein reductase - A possible drug target

description: The emergence of increased resistance to the available drugs has created a situation that demands to find out more specific molecular drug targets for Leishmaniasis. The enoyl acyl carrier protein reductase (ENR), a regulatory enzyme in type II fatty acid synthesis, was confirmed as a novel drug target and triclosan as its specific inhibitor in many microorganisms. In this study, the triclosan was tested for the leishmanicidal property against <i>Leishmania donovani</i> (<i>L. donovani</i>) and the results of <i>in vitro</i> and <i>ex vivo</i> drug assays on promastigotes and amastigotes showed that triclosan possessed antileishmanial activity with a half minimal inhibitory concentration (IC<sub>50</sub>) of 30 µM. Consequently, adopting <i>in silico</i> approach, we have tested the triclosan’s ability to bind with the <i>L. donovani</i> enoyl acyl carrier protein reductase (<i>Ld</i>ENR). The 3D structure of <i>Ld</i>ENR was modelled, triclosan and cofactors were docked in <i>Ld</i>ENR model and molecular dynamic simulations were performed to observe the protein-ligands interactions, stability, compactness and binding energy calculation of the ligands-<i>Ld</i>ENR complexes. The observation showed that triclosan stably interacted with <i>Ld</i>ENR in presence of both the cofactors (NADPH and NADH), however, simulation results favor NADH as a preferred co-factor for <i>Ld</i>ENR. These results support that the reduction of <i>L. donovani</i> growth in the <i>in vitro</i> and <i>ex vivo</i> drug assays may be due to the interaction of triclosan with <i>Ld</i>ENR, which should be confirmed through enzymatic assays. The results of this study suggest that <i>Ld</i>ENR could be a potential drug target and triclosan as a lead for Leishmaniasis. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.10033616
title: Automated and semi-automated map georeferencing

description: Historical maps contain a wealth of information not generally available, but they must be referenced to well-known coordinate systems for maximum use in spatial analysis. Existing georeferencing tools are essentially manual, requiring considerable data entry, much panning and zooming, and precise on-screen digitizing. Here we present alternative approaches based on pattern-matching and spatial computing intended to overcome the inefficiencies of standard tools. We also describe and make available two computer programs implementing the methods discussed. The first, designed for large-scale quadrangles, locates map boundaries, finds ground control points, and produces georeferenced images without operator assistance. Experiments show that quadrangle georeferencing can be reliably automated (88% success rate in our tests). A second program, developed for general maps at any scale, uses self-learning and other approaches to overcome most of the manual aspects of georeferencing. Both programs find control points with single-pixel accuracy, yield transform errors on the order of map linewidth, and can produce warped or unwarped images as desired.
DOI: 10.5281/zenodo.5176562
title: Dataset of Russian multiword expressions for a DSM

description: The dataset consists of Russian multiword expressions selected according to the presence or absence of a 'categorical shift' between the meaning of a noun phrase and that of its head. The items with the categorical shift are intended for inclusion in the vocabulary of a distributional-semantic model (DSM) as single items. The dataset consists of 2 parts, 173 positive and 173 negative examples. The entries are additionally labeled for further categorization.
description: The research was funded by the Russian Foundation for Basic Research, grant number is 19-07-00779 A.
DOI: 10.6084/m9.figshare.10033616.v2
title: Automated and semi-automated map georeferencing

description: Historical maps contain a wealth of information not generally available, but they must be referenced to well-known coordinate systems for maximum use in spatial analysis. Existing georeferencing tools are essentially manual, requiring considerable data entry, much panning and zooming, and precise on-screen digitizing. Here we present alternative approaches based on pattern-matching and spatial computing intended to overcome the inefficiencies of standard tools. We also describe and make available two computer programs implementing the methods discussed. The first, designed for large-scale quadrangles, locates map boundaries, finds ground control points, and produces georeferenced images without operator assistance. Experiments show that quadrangle georeferencing can be reliably automated (88% success rate in our tests). A second program, developed for general maps at any scale, uses self-learning and other approaches to overcome most of the manual aspects of georeferencing. Both programs find control points with single-pixel accuracy, yield transform errors on the order of map linewidth, and can produce warped or unwarped images as desired.
DOI: 10.5281/zenodo.5176561
title: Dataset of Russian multiword expressions for a DSM

description: The dataset consists of Russian multiword expressions selected according to the presence or absence of a 'categorical shift' between the meaning of a noun phrase and that of its head. The items with the categorical shift are intended for inclusion in the vocabulary of a distributional-semantic model (DSM) as single items. The dataset consists of 2 parts, 173 positive and 173 negative examples. The entries are additionally labeled for further categorization.
description: The research was funded by the Russian Foundation for Basic Research, grant number is 19-07-00779 A.
DOI: 10.6084/m9.figshare.10033616.v1
title: Automated and semi-automated map georeferencing

description: Historical maps contain a wealth of information not generally available, but they must be referenced to well-known coordinate systems for maximum use in spatial analysis. Existing georeferencing tools are essentially manual, requiring considerable data entry, much panning and zooming, and precise on-screen digitizing. Here we present alternative approaches based on pattern-matching and spatial computing intended to overcome the inefficiencies of standard tools. We also describe and make available two computer programs implementing the methods discussed. The first, designed for large-scale quadrangles, locates map boundaries, finds ground control points, and produces georeferenced images without operator assistance. Experiments show that quadrangle georeferencing can be reliably automated (88% success rate in our tests). A second program, developed for general maps at any scale, uses self-learning and other approaches to overcome most of the manual aspects of georeferencing. Both programs find control points with single-pixel accuracy, yield transform errors on the order of map linewidth, and can produce warped or unwarped images as desired.
DOI: 10.5281/zenodo.5536246
title: Data set

description: <strong>Introduction</strong>: Mental health problems appear to be increasing in importance in Africa. Mental and substance use disorders were the leading cause of yearly lived with disability in Sub-Saharan Africa. Evidence from previous studies shows considerable variation in the prevalence of these disorders. The most acceptable explanation for this wide variation is likely to be the fact that socio cultural factors are major determinants of mental disorders. Therefore a mental disorder has to be understood in a specific setting to develop effective and tailored interventions <strong>Objective</strong>: The objective of this study was to determine the prevalence and associated factors of common mental disorders among adult residents in Silte Zone, southern Ethiopia <em><strong>Methods:</strong></em> Community based cross sectional the study was conducted in the study area. A total of 1178 adults were selected by using a three stage systematic sampling technique. Self-Reporting Questionnaire (SRQ-20) was used to determine the prevalence of common mental disorders. Data were analyzed by using SPSS version 20. Both bivariate and multiple logistic regression analyses were employed to identify factors associated with common mental disorders. <strong>Result:</strong> The prevalence of common mental disorders among adults found to be 39.7%. Increased age (OR = 1.114; 95% CI = 1.095, 1.134), being female (OR = 9.421; 95% CI = 5.947, 14.926), poor social support (OR = 1.987; 95% CI = 1.358, 2.907) and having life threatening experience (OR = 2.162; 95% CI = 1.825, 2.562) were significantly associated with common mental disorders. <strong>Conclusion:</strong> In the study, the magnitude of common mental disorders remains high in the study area. Increased age, being female, poor social support and having life threatening experience were significantly associated with common mental disorders. <strong>Key words: </strong>Common mental disorders, self-reporting questionnaire, social support, Ethiopia
DOI: 10.5281/zenodo.5536245
title: Data set

description: <strong>Introduction</strong>: Mental health problems appear to be increasing in importance in Africa. Mental and substance use disorders were the leading cause of yearly lived with disability in Sub-Saharan Africa. Evidence from previous studies shows considerable variation in the prevalence of these disorders. The most acceptable explanation for this wide variation is likely to be the fact that socio cultural factors are major determinants of mental disorders. Therefore a mental disorder has to be understood in a specific setting to develop effective and tailored interventions <strong>Objective</strong>: The objective of this study was to determine the prevalence and associated factors of common mental disorders among adult residents in Silte Zone, southern Ethiopia <em><strong>Methods:</strong></em> Community based cross sectional the study was conducted in the study area. A total of 1178 adults were selected by using a three stage systematic sampling technique. Self-Reporting Questionnaire (SRQ-20) was used to determine the prevalence of common mental disorders. Data were analyzed by using SPSS version 20. Both bivariate and multiple logistic regression analyses were employed to identify factors associated with common mental disorders. <strong>Result:</strong> The prevalence of common mental disorders among adults found to be 39.7%. Increased age (OR = 1.114; 95% CI = 1.095, 1.134), being female (OR = 9.421; 95% CI = 5.947, 14.926), poor social support (OR = 1.987; 95% CI = 1.358, 2.907) and having life threatening experience (OR = 2.162; 95% CI = 1.825, 2.562) were significantly associated with common mental disorders. <strong>Conclusion:</strong> In the study, the magnitude of common mental disorders remains high in the study area. Increased age, being female, poor social support and having life threatening experience were significantly associated with common mental disorders. <strong>Key words: </strong>Common mental disorders, self-reporting questionnaire, social support, Ethiopia
DOI: 10.5281/zenodo.5535713
title: Synthetic Escherichia coli mixture samples with variable coverage

description: This dataset contains the synthetic mixture samples and reference sequences - as well as the appropriate metadata - that were originally used in the 2021 revision of the mSWEEP manuscript.<br> <br> There are 87 samples in total, each containing 100bp paired-end Illumina sequencing reads from 10 different <em>Escherichia coli </em>strains from 10 different lineages. The number of reads is set so that the sequencing coverage of the individual strains varies between 50x and 0.10x and sums up to 100x.
DOI: 10.5281/zenodo.5535712
title: Synthetic Escherichia coli mixture samples with variable coverage

description: This dataset contains the synthetic mixture samples and reference sequences - as well as the appropriate metadata - that were originally used in the 2021 revision of the mSWEEP manuscript.<br> <br> There are 87 samples in total, each containing 100bp paired-end Illumina sequencing reads from 10 different <em>Escherichia coli </em>strains from 10 different lineages. The number of reads is set so that the sequencing coverage of the individual strains varies between 50x and 0.10x and sums up to 100x.
DOI: 10.6084/m9.figshare.8320670.v2
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.14792100.v2
title: MLSA phylogeny of 40 Agrobacterium spp.

description: For this MLSA of 40 Agrobacterium spp. strains, we extracted the CDS alignments of parE, gyrB, recA, and rpoB from the Pantagruel pangenome database and concatenated into a multi-locus alignment, totaling 9,968 positions. ML Phylogenies were then inferred based on these alignments with RAxML-NG 1.0.0 with the options ‘--model GTR+G4 --all’, implying the use of the model GTR+FO+G4m, and that 20 independent inferences were run, starting with 10 random trees and 10 parsimony-optimized tree, and retaining the the best ML tree from these 20 inferences. Branch supports were estimated with 200 Felsentein bootstrap trees.<br>
DOI: 10.6084/m9.figshare.11357432.v1
title: Antiviral potential of human IFN-α subtypes against influenza A H3N2 infection in human lung explants reveals subtype-specific activities

description: Influenza is an acute respiratory infection causing high morbidity and mortality in annual outbreaks worldwide. Antiviral drugs are limited and pose the risk of resistance development, calling for new treatment options. IFN-α subtypes are immune-stimulatory cytokines with strong antiviral activities against IAV <i>in vitro</i> and <i>in vivo.</i> However, the clinical use of IFN-α2, the only licensed subtype of this multi-gene family, could not prevent or limit IAV infections in humans. However, the other subtypes were not investigated. Therefore, this study evaluated the induction and antiviral potential of all human IFN-α subtypes during H3N2 IAV infection in human lung explants. We found that subtypes with weak antiviral activities were preferentially induced during IAV infection in human lungs. Intriguingly, non-induced subtypes α16, α5 and α4 suppressed viral replication up to 230-fold more efficiently than α2. Furthermore, our results demonstrate that subtypes with stronger antiviral activities induce higher expression of IAV-specific restriction factors and that MxA expression is a determinant of the subtype-specific antiviral activity towards H3N2 IAV. These results corroborate that IFN-α subtypes exhibit differential antiviral activities and emphasize that subtypes α16, α5 and α4 should be further investigated for the prevention and treatment of severe infections with seasonal H3N2 IAV.
DOI: 10.6084/m9.figshare.7937387.v2
title: Cumulative acquisition of pathogenicity islands has shaped virulence potential and contributed to the emergence of LEE-negative Shiga toxin-producing <i>Escherichia coli</i> strains

description: Shiga toxin-producing <i>Escherichia coli</i> (STEC) are foodborne pathogens causing severe gastroenteritis, which may lead to hemolytic uremic syndrome. The Locus of Enterocyte Effacement (LEE), a Pathogenicity Island (PAI), is a major determinant of intestinal epithelium attachment of a group of STEC strains; however, the virulence repertoire of STEC strains lacking LEE, has not been fully characterized. The incidence of LEE-negative STEC strains has increased in several countries, highlighting the relevance of their study. In order to gain insights into the basis for the emergence of LEE-negative STEC strains, we performed a large-scale genomic analysis of 367 strains isolated worldwide from humans, animals, food and the environment. We identified uncharacterized genomic islands, including two PAIs and one Integrative Conjugative Element. Additionally, the Locus of Adhesion and Autoaggregation (LAA) was the most prevalent PAI among LEE-negative strains and we found that it contributes to colonization of the mice intestine. Our comprehensive and rigorous comparative genomic and phylogenetic analyses suggest that the accumulative acquisition of PAIs has played an important, but currently unappreciated role, in the evolution of virulence in these strains. This study provides new knowledge on the pathogenicity of LEE-negative STEC strains and identifies molecular markers for their epidemiological surveillance.
DOI: 10.6084/m9.figshare.9062765.v2
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.8847455.v1
title: Comprehensive subspecies identification of 175 nontuberculous mycobacteria species based on 7547 genomic profiles

description: The prevalence of nontuberculous mycobacteria (NTM) pulmonary diseases has been increasing worldwide. NTM consist of approximately 200 species and distinguishing between them at the subspecies level is critical to treatment. In this study, we sequenced 63 NTM genomes, 27 of which were newly determined, by hybrid assembly using sequencers from Illumina and Oxford Nanopore Technologies (ONT). This analysis expanded the available genomic data to 175 NTM species and redefined their subgenus classification. We also developed a novel multi-locus sequence typing (MLST) database based on 184 genes from 7547 assemblies and an identification software, mlstverse, which can also be used for detecting other bacteria given a suitable MLST database. This method showed the highest sensitivity and specificity amongst conventional methods and demonstrated the capacity for rapid detection of NTM, 10 min of sequencing of the ONT MinION being sufficient. Application of this methodology could improve disease epidemiology and increase the cure rates of NTM diseases.
DOI: 10.6084/m9.figshare.9863981.v1
title: Active surveillance and genetic evolution of avian influenza viruses in Egypt, 2016–2018

description: Egypt is a hotspot for avian influenza virus (AIV) due to the endemicity of H5N1 and H9N2 viruses. AIVs were isolated from 329 samples collected in 2016–2018; 48% were H9N2, 37.1% were H5N8, 7.6% were H5N1, and 7.3% were co-infections with 2 of the 3 subtypes. The 32 hemagglutinin (HA) sequences of the H5N1 viruses formed a well-defined lineage within clade 2.2.1.2. The 10 HA sequences of the H5N8 viruses belonged to a subclade within 2.3.4.4. The 11 HA of H9N2 isolates showed high sequence homology with other Egyptian G1-like H9N2 viruses. The prevalence of H5N8 viruses in ducks (2.4%) was higher than in chickens (0.94%). Genetic reassortment was detected in H9N2 viruses. Antigenic analysis showed that H9N2 viruses are homogenous, antigenic drift was detected among H5N1 viruses. AI H5N8 showed higher replication rate followed by H9N2 and H5N1, respectively. H5N8 was more common in Southern Egypt, H9N2 in the Nile Delta, and H5N1 in both areas. Ducks and chickens played a significant role in transmission of H5N1 viruses. The endemicity and co-circulation of H5N1, H5N8, and H9N2 AIV coupled with the lack of a clear control strategy continues to provide avenues for further virus evolution in Egypt.
DOI: 10.6084/m9.figshare.9890444.v1
title: Genomic epidemiology of Iranian <i>Bordetella pertussis</i>: 50 years after the implementation of whole cell vaccine

description: Pertussis caused by <i>Bordetella pertussis,</i> remains a public health problem worldwide, despite high vaccine coverage in infants and children in many countries. Iran has been using whole cell vaccine for the last 50 years with more than 95% vaccination rate since 1988 and has experienced pertussis resurgence in recent years. Here, we sequenced 55 <i>B. pertussis</i> isolates mostly collected from three provinces with the highest number of pertussis cases in Iran, including Tehran, Mazandaran, and Eastern-Azarbayjan from the period of 2008-2016. Most isolates carried <i>ptxP3</i>/<i>prn2</i> alleles (42/55, 76%), the same genotype as isolates circulating in acellular vaccine-administrating countries. The second most frequent genotype was <i>ptxP3</i>/<i>prn9</i> (8/55, 14%). Only three isolates (5%) were <i>ptxP1</i>. Phylogenetic analysis showed that Iranian <i>ptxP3</i> isolates can be divided into eight clades (Clades 1-8) with no temporal association. Most of the isolates from Tehran grouped together as one distinctive clade (Clade 8) with six unique single nucleotide polymorphisms (SNPs). In addition, the <i>prn9</i> isolates were grouped together as Clade 5 with 12 clade-supporting SNPs. No pertactin deficient isolates were found among the 55 Iranian isolates. Our findings suggest that there is an ongoing adaptation and evolution of <i>B. pertussis</i> regardless of the types of vaccine used.