cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13602879
title: Temporal microRNA expression profile of pig peripheral blood during postnatal development

description: Gene expression profiles of blood can reflect the physiopathologic status of the immune system. The dynamic microRNA (miRNA) expression profiles of peripheral blood from pigs at different developmental stages, and how differential expression of miRNAs might relate to immune system development, are unknown. In this study, peripheral blood samples taken at five developmental stages were used to construct 15 miRNA libraries (three biological replicates/stage): 0 days (newborn), 30 days (weaning), 60 days (weaned), and 180 and 360 days (puberty). We identified 295 known mature miRNAs. Hierarchical clustering of the miRNA expression profile showed significant differences between individuals at the neonatal and postnatal stages. Functional enrichment analysis revealed that miRNAs differentially expressed between pairwise comparisons of the developmental stages were over-represented in immune-related pathways such as toll-like receptor signaling. The time-course of expression of the over-representated miRNAs exhibited a pattern of steady decline over time, for both the complete miRNA compendium and immune-related miRNAs. We identified six marker miRNAs that were highly negatively correlated with chronologic age and enriched for genes involved in immune-related pathways. This study of a peripheral blood miRNA transcriptome offers insight into immune system development in swine and provides a resource for pig genome annotation.
DOI: 10.6084/m9.figshare.13602800.v2
title: <i>In situ</i> TEM observation of phase transformation in bulk metallic glass composites

description: Transformation-induced plasticity is a fundamental solution for improving the ductility of bulk metallic glass composites (BMGCs). However, the underlying mechanism remains controversial. Here, by using <i>in situ</i> transmission electron microscopy, we present direct observation of the transformation dynamics from <i>β</i>/<i>ω</i> phase to α’ phase of the crystalline dendrites in a TiZrCuBe BMGC under uniaxial tensile deformation. The transformation redistributes the stress in the adjacent matrix, making interfacial regions potential preferential sites for shear band nucleation. The high density of nucleation sites is believed to promote the formation of shear band networks and enhance the ductility of BMGCs.
DOI: 10.6084/m9.figshare.13602782
title: Increasing prevalence of hypervirulent ST5 methicillin susceptible <i>Staphylococcus aureus</i> subtype poses a serious clinical threat

description: <i>Staphylococcus aureus</i> (<i>S. aureus</i>) is a clinical pathogen of great significance causing metastatic or complicated infections. ST5 clonotype isolates have dominated <i>S. aureus</i> infections for more than 10 years in Shanghai, China, and the proportion of methicillin-susceptible <i>S. aureus</i> (MSSA) has remarkably increased in the past decades. By whole-genome sequencing (WGS) 121 ST5 clonotype <i>S. aureus</i> isolates using next-generation sequencing (NGS) platforms and characterizing the evolutionary dynamics of ST5 linages, we found that MSSA evolved independently, making it a subtype differed from other MRSA clones. Drug resistance gene analysis by using the NGS data demonstrated that ST5 clonotype MRSA might be more tolerant under the threat of antimicrobials, which was confirmed in further <i>in vitro</i> susceptibility tests. However, MSSA subtype isolates exhibited relatively high virulence upon the analysis of virulence factors. Furthermore, MSSA subtype isolates displayed higher hemolysis capacity and higher ability to adhere to epithelial cells including A549 human alveolar epithelial cells and HaCaT human skin keratinocytes, caused more severe infections in murine abscess model. With its high virulence and enhanced magnitude in the past decades, the ST5 MSSA subtype poses a serious clinical threat hence more attention should be paid to the prevention and control.
DOI: 10.6084/m9.figshare.13602782.v1
title: Increasing prevalence of hypervirulent ST5 methicillin susceptible <i>Staphylococcus aureus</i> subtype poses a serious clinical threat

description: <i>Staphylococcus aureus</i> (<i>S. aureus</i>) is a clinical pathogen of great significance causing metastatic or complicated infections. ST5 clonotype isolates have dominated <i>S. aureus</i> infections for more than 10 years in Shanghai, China, and the proportion of methicillin-susceptible <i>S. aureus</i> (MSSA) has remarkably increased in the past decades. By whole-genome sequencing (WGS) 121 ST5 clonotype <i>S. aureus</i> isolates using next-generation sequencing (NGS) platforms and characterizing the evolutionary dynamics of ST5 linages, we found that MSSA evolved independently, making it a subtype differed from other MRSA clones. Drug resistance gene analysis by using the NGS data demonstrated that ST5 clonotype MRSA might be more tolerant under the threat of antimicrobials, which was confirmed in further <i>in vitro</i> susceptibility tests. However, MSSA subtype isolates exhibited relatively high virulence upon the analysis of virulence factors. Furthermore, MSSA subtype isolates displayed higher hemolysis capacity and higher ability to adhere to epithelial cells including A549 human alveolar epithelial cells and HaCaT human skin keratinocytes, caused more severe infections in murine abscess model. With its high virulence and enhanced magnitude in the past decades, the ST5 MSSA subtype poses a serious clinical threat hence more attention should be paid to the prevention and control.
DOI: 10.6084/m9.figshare.13602800
title: <i>In situ</i> TEM observation of phase transformation in bulk metallic glass composites

description: Transformation-induced plasticity is a fundamental solution for improving the ductility of bulk metallic glass composites (BMGCs). However, the underlying mechanism remains controversial. Here, by using <i>in situ</i> transmission electron microscopy, we present direct observation of the transformation dynamics from <i>β</i>/<i>ω</i> phase to α’ phase of the crystalline dendrites in a TiZrCuBe BMGC under uniaxial tensile deformation. The transformation redistributes the stress in the adjacent matrix, making interfacial regions potential preferential sites for shear band nucleation. The high density of nucleation sites is believed to promote the formation of shear band networks and enhance the ductility of BMGCs.
DOI: 10.6084/m9.figshare.20418613.v1
title: Mineralogy and PGE geochemistry of chromitites and peridotites of the sapat complex in the indus suture zone, northern Pakistan: implications for magmatic processes in the supra-subduction zone

description: The Sapat Complex in Northern Pakistan contains remnants of the northern Neo-Tethys Ocean, presently exposed along the Indus Suture Zone. The mantle peridotites of the Sapat Complex include harzburgites, dunites, and subordinate lherzolites. Harzburgites are the dominant peridotite variety over dunites. The dunites are hosted by harzburgites and occur exclusively as ‘envelopes’ surrounding chromitite pods. The podiform chromitites show disseminated, banded, and massive textures. Chromitites exhibit variable Cr# [Cr/(Cr + Al)] and Mg# [Mg/(Mg + Fe<sup>2+</sup>)], which range from 0.76 to 0.77, and from 0.64 to 0.66, respectively, while TiO<sub>2</sub> contents are &lt;0.2 wt.%. These features perhaps reflect crystallization of the chromian spinel from a boninitic magma. Similarly, chromian spinel in peridotites manifest a wide range of Cr# and Mg#, from 0.49 to 0.83 and 0.41 to 0.57, respectively, and are characterized by very low TiO<sub>2</sub> values, averaging at 0.1 wt.%. Chromian spinel of chromitites and peridotites of the Sapat Complex have also very low Fe<sup>3+</sup># (&lt;0.01), which indicate their crystallization under low oxygen fugacities. The platinum group elements (PGE) distributions show high (Os + Ir + Ru)/(Rh + Pt + Pd), very low Pd/Ir values, and are defined by a prominently fractionated chondritic normalized PGE pattern, hence, this deposit is a typical example of an ophiolitic chromitite. The studied peridotites are highly depleted in PGE compared to chondritic values. The Pd<sub>N</sub>/Ir<sub>N</sub> values, averaging to 1.5 in dunites are unfractionated, while PGE spidergrams of harzburgites and lherzolites depict minor positive slopes, a minor positive Ru anomaly, and have average Pd<sub>N</sub>/Ir<sub>N</sub> values of 2.3 and 2.4, respectively. Furthermore, the harzburgites, dunites, and lherzolites display generally flat chondritic and primitive mantle normalized PGE patterns, and therefore, are nearly identical to highly depleted mantle peridotites. The mineralogical and PGE geochemical imprints of Sapat Complex chromitites and peridotites establish a strong affinity to supra-subduction zone ophiolites. Moreover, calculated parental melts of the chromitites and various geochemical discrimination diagrams elucidate that the chromitites were derived from boninitic magma produced by melting of depleted mantle peridotites in an oceanic arc, characterized by low oxygen fugacity, similar to a supra-subduction zone tectonic setting. This research highlights the use of mineralogy and geochemical compositions of chromitites and peridotites to reveal deep magmatic processes in a supra-subduction zone environment.
DOI: 10.6084/m9.figshare.20418613
title: Mineralogy and PGE geochemistry of chromitites and peridotites of the sapat complex in the indus suture zone, northern Pakistan: implications for magmatic processes in the supra-subduction zone

description: The Sapat Complex in Northern Pakistan contains remnants of the northern Neo-Tethys Ocean, presently exposed along the Indus Suture Zone. The mantle peridotites of the Sapat Complex include harzburgites, dunites, and subordinate lherzolites. Harzburgites are the dominant peridotite variety over dunites. The dunites are hosted by harzburgites and occur exclusively as ‘envelopes’ surrounding chromitite pods. The podiform chromitites show disseminated, banded, and massive textures. Chromitites exhibit variable Cr# [Cr/(Cr + Al)] and Mg# [Mg/(Mg + Fe<sup>2+</sup>)], which range from 0.76 to 0.77, and from 0.64 to 0.66, respectively, while TiO<sub>2</sub> contents are &lt;0.2 wt.%. These features perhaps reflect crystallization of the chromian spinel from a boninitic magma. Similarly, chromian spinel in peridotites manifest a wide range of Cr# and Mg#, from 0.49 to 0.83 and 0.41 to 0.57, respectively, and are characterized by very low TiO<sub>2</sub> values, averaging at 0.1 wt.%. Chromian spinel of chromitites and peridotites of the Sapat Complex have also very low Fe<sup>3+</sup># (&lt;0.01), which indicate their crystallization under low oxygen fugacities. The platinum group elements (PGE) distributions show high (Os + Ir + Ru)/(Rh + Pt + Pd), very low Pd/Ir values, and are defined by a prominently fractionated chondritic normalized PGE pattern, hence, this deposit is a typical example of an ophiolitic chromitite. The studied peridotites are highly depleted in PGE compared to chondritic values. The Pd<sub>N</sub>/Ir<sub>N</sub> values, averaging to 1.5 in dunites are unfractionated, while PGE spidergrams of harzburgites and lherzolites depict minor positive slopes, a minor positive Ru anomaly, and have average Pd<sub>N</sub>/Ir<sub>N</sub> values of 2.3 and 2.4, respectively. Furthermore, the harzburgites, dunites, and lherzolites display generally flat chondritic and primitive mantle normalized PGE patterns, and therefore, are nearly identical to highly depleted mantle peridotites. The mineralogical and PGE geochemical imprints of Sapat Complex chromitites and peridotites establish a strong affinity to supra-subduction zone ophiolites. Moreover, calculated parental melts of the chromitites and various geochemical discrimination diagrams elucidate that the chromitites were derived from boninitic magma produced by melting of depleted mantle peridotites in an oceanic arc, characterized by low oxygen fugacity, similar to a supra-subduction zone tectonic setting. This research highlights the use of mineralogy and geochemical compositions of chromitites and peridotites to reveal deep magmatic processes in a supra-subduction zone environment.
DOI: 10.6084/m9.figshare.14650863.v1
title: Additional file 10 of Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori

description: Additional file 10. The top 20 enriched KEGG pathways of differentially expressed mRNAs in the two groups.
DOI: 10.6084/m9.figshare.14650866.v1
title: Additional file 11 of Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori

description: Additional file 11. The primers of the selected lncRNAs and mRNAs.
DOI: 10.6084/m9.figshare.14650869
title: Additional file 1 of Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori

description: Additional file 1. Summary of RNA-seq data of 12 silkworm samples.
DOI: 10.6084/m9.figshare.14650887.v1
title: Additional file 7 of Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori

description: Additional file 7. The significantly enriched GO terms detected in the two groups (trans).
DOI: 10.6084/m9.figshare.13078709.v1
title: Dominant and Active Methanogens in the Production Waters From a High-Temperature Petroleum Reservoir by DNA- and RNA-Based Analysis

description: Methane metabolism in deep subsurface petroleum reservoirs is of paramount interest in the global biogeochemical cycle of carbon. Methanogenesis in such habitats is driven mostly by methanogens in syntrophic association with bacteria. In the present study, methanogenic communities in production water samples from six wells of a high-temperature petroleum reservoir were analyzed based on both genomic 16S rDNA and metabolically active 16S rRNA. The PCR-amplified <i>mcrA</i> gene analysis showed that <i>Methanosaeta</i> (26%) and <i>Methanomassiliicoccus</i> (56%) were separately the dominant members in sample W2_71 and W9_18 at the DNA level. In comparison, the RNA-based analysis showed that <i>Methanosaeta</i> (63 ∼ 83%) followed by <i>Methanolinea</i> (16 ∼ 23%) were the most active methanogens, which were different from the communities of genomic DNA. While several lines of studies indicated that CO<sub>2</sub>-reducing methanogens of the genus <i>Methanothermobacter</i> was the most frequently detected phylotype in deep-subsurface petroleum reservoirs. Redundancy analysis (RDA) showed the possible correlation between active methanogens (<i>Methanosaeta</i>) and environmental factors (CO<sub>3</sub><sup>2-</sup>). The datasets indicated the importance of investigating methanogenic community by integrating DNA- and RNA-based approaches. These results provide new insight into active methanogens in high-temperature petroleum reservoirs, and promote a comprehensive understanding of methanogens as well as their potential methanogenic pathways in such environments.
DOI: 10.6084/m9.figshare.13602879.v2
title: Temporal microRNA expression profile of pig peripheral blood during postnatal development

description: Gene expression profiles of blood can reflect the physiopathologic status of the immune system. The dynamic microRNA (miRNA) expression profiles of peripheral blood from pigs at different developmental stages, and how differential expression of miRNAs might relate to immune system development, are unknown. In this study, peripheral blood samples taken at five developmental stages were used to construct 15 miRNA libraries (three biological replicates/stage): 0 days (newborn), 30 days (weaning), 60 days (weaned), and 180 and 360 days (puberty). We identified 295 known mature miRNAs. Hierarchical clustering of the miRNA expression profile showed significant differences between individuals at the neonatal and postnatal stages. Functional enrichment analysis revealed that miRNAs differentially expressed between pairwise comparisons of the developmental stages were over-represented in immune-related pathways such as toll-like receptor signaling. The time-course of expression of the over-representated miRNAs exhibited a pattern of steady decline over time, for both the complete miRNA compendium and immune-related miRNAs. We identified six marker miRNAs that were highly negatively correlated with chronologic age and enriched for genes involved in immune-related pathways. This study of a peripheral blood miRNA transcriptome offers insight into immune system development in swine and provides a resource for pig genome annotation.
DOI: 10.6084/m9.figshare.13078709
title: Dominant and Active Methanogens in the Production Waters From a High-Temperature Petroleum Reservoir by DNA- and RNA-Based Analysis

description: Methane metabolism in deep subsurface petroleum reservoirs is of paramount interest in the global biogeochemical cycle of carbon. Methanogenesis in such habitats is driven mostly by methanogens in syntrophic association with bacteria. In the present study, methanogenic communities in production water samples from six wells of a high-temperature petroleum reservoir were analyzed based on both genomic 16S rDNA and metabolically active 16S rRNA. The PCR-amplified <i>mcrA</i> gene analysis showed that <i>Methanosaeta</i> (26%) and <i>Methanomassiliicoccus</i> (56%) were separately the dominant members in sample W2_71 and W9_18 at the DNA level. In comparison, the RNA-based analysis showed that <i>Methanosaeta</i> (63 ∼ 83%) followed by <i>Methanolinea</i> (16 ∼ 23%) were the most active methanogens, which were different from the communities of genomic DNA. While several lines of studies indicated that CO<sub>2</sub>-reducing methanogens of the genus <i>Methanothermobacter</i> was the most frequently detected phylotype in deep-subsurface petroleum reservoirs. Redundancy analysis (RDA) showed the possible correlation between active methanogens (<i>Methanosaeta</i>) and environmental factors (CO<sub>3</sub><sup>2-</sup>). The datasets indicated the importance of investigating methanogenic community by integrating DNA- and RNA-based approaches. These results provide new insight into active methanogens in high-temperature petroleum reservoirs, and promote a comprehensive understanding of methanogens as well as their potential methanogenic pathways in such environments.
DOI: 10.6084/m9.figshare.24088823
title: Screening of atrial fibrillation in dental practices: a qualitative feasibility study

description: To increase the detection of unknown atrial fibrillation (AF), general practitioners have started screening their patients using small hand-held devices. It is thought that dental settings could be utilized for screening as they have regular access to patients. The aim of this study was to explore the perceptions of dental staff of screening for AF using a hand-held electronic device in primary dental care. The research took place in one large mixed NHS and private general dental practice. Views from staff including dentists, dental therapists, dental nurses, and managers were elicited via semi-structured interviews conducted face-to-face, audio recorded, and transcribed verbatim. Interviews continued until there were no new themes or patterns emerging from the data, and thematic saturation had been achieved. Eleven participants were interviewed. The main themes generated were methodology for screening, acceptability for screening within the practice, attitudes to screening, and implementation of screening. Overall, participants were positive about implementing AF screening in a dental practice but expressed concerns about time and remuneration. Staff also gave encouraging feedback regarding the simplicity of the portable screening device. Participants felt that AF screening in primary care dental practices was a good concept but may be challenging to implement in NHS Dentistry, especially due to the pandemic.
DOI: 10.6084/m9.figshare.24088823.v1
title: Screening of atrial fibrillation in dental practices: a qualitative feasibility study

description: To increase the detection of unknown atrial fibrillation (AF), general practitioners have started screening their patients using small hand-held devices. It is thought that dental settings could be utilized for screening as they have regular access to patients. The aim of this study was to explore the perceptions of dental staff of screening for AF using a hand-held electronic device in primary dental care. The research took place in one large mixed NHS and private general dental practice. Views from staff including dentists, dental therapists, dental nurses, and managers were elicited via semi-structured interviews conducted face-to-face, audio recorded, and transcribed verbatim. Interviews continued until there were no new themes or patterns emerging from the data, and thematic saturation had been achieved. Eleven participants were interviewed. The main themes generated were methodology for screening, acceptability for screening within the practice, attitudes to screening, and implementation of screening. Overall, participants were positive about implementing AF screening in a dental practice but expressed concerns about time and remuneration. Staff also gave encouraging feedback regarding the simplicity of the portable screening device. Participants felt that AF screening in primary care dental practices was a good concept but may be challenging to implement in NHS Dentistry, especially due to the pandemic.
DOI: 10.5281/zenodo.10731482
title: Example Nakajima data - uniaxial (10mm) and equibiaxial (177mm)

description: Example data used for Python script used to analyse Nakajima experiemnts at different temepratures from uniaxial – biaxial. The data is uniaxial and equibiaxial data label 10mm and 177mm due to the experimental sample diemensions. The material tested was AA7075 1.5mm sheet. This data is coupled with the driver_biaxial.py which uses the data to showcase the analysis possible with this data set.
DOI: 10.5281/zenodo.10731483
title: Example Nakajima data - uniaxial (10mm) and equibiaxial (177mm)

description: Example data used for Python script used to analyse Nakajima experiemnts at different temepratures from uniaxial – biaxial. The data is uniaxial and equibiaxial data label 10mm and 177mm due to the experimental sample diemensions. The material tested was AA7075 1.5mm sheet. This data is coupled with the driver_biaxial.py which uses the data to showcase the analysis possible with this data set.
DOI: 10.6084/m9.figshare.20418213.v1
title: Additional file 3 of Target residence of Cas9-sgRNA influences DNA double-strand break repair pathway choices in CRISPR/Cas9 genome editing

description: Additional file 3: Table S2. Junction sequences of sister chromatid fusion products in mESC by PCR targeted amplicon sequencing.
DOI: 10.15468/dl.d7mdnc
title: Occurrence Download

description: A dataset containing 4486 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "MediaType is Image",
 "ScientificName is Scabiosa ochroleuca L."
 ]
}

 The dataset includes 4486 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0110750-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10936291
title: Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM

description: This respository corresponds to the following paper: Wankowicz et al. Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM (2024). These are the qFit models. MTZ and deposited models cna be downloaded from the PDB.