cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10699302
title: QCM-D-Based Metadata on Adhesion and Dispersal Patterns of Three Bacterial Species Recovered from Dairy Pasteurizer Surfaces Following Cleaning and Disinfection

description: In a research project "KILLFILM," conducted at the host institute (Flanders Research Institute for Agriculture Fisheries and Food: ILVO) in Belgium and funded by Flanders' Food, a significant number and diversity of bacterial species were recovered from food contact surfaces in the milk processing industries following cleaning and disinfection (C&D) procedures. This study involved identified dominant bacteria on the surface of dairy pasteurizers following C&D and included Stenotrophomonas rhizophila (B68), Bacillus licheniformis (B65), and Microbacterium lacticum (B30). Bacterial biofilm forming ability in monoculture and mixed culture biofilms was confirmed on polystyrene and stainless steel surfaces. We also used Quartz crystal microbaance with dissipiation (QCM-D) to study adherence and dispersal signals for the three above mentioned bacteria using the QCM-D E4 instrument (Q-sense Gothenburg, Sweden). 5 MHz AT-cut quartz crystals with silica (SiO2) and stainless steel coatings were purchased from Biolin Scientific (Gothenburg, Sweden). The sensors were cleaned according to the method described earlier Derick et al., 2023.

In each experiment, we initially stabilized the frequency shift and energy dissipation signals for at least 20 minutes in a cell-free medium, ensuring a stable baseline. After this, we introduced a suspension of cells to the sensor, maintaining a flow rate of 100 µl/min for 60 minutes. Following the cell addition, the cells were allowed to interact with the sensor surface in a static state for 18-48 h. During this period, we continuously monitored the frequency shift and energy dissipation at a controlled room temperature of approximately 19 ± 0.5 °C. For comparison, we conducted similar measurements using cell-free buffer solutions. Unless specified otherwise, our data analysis primarily focused on the 7th overtone. This particular overtone is more sensitive to the presence of the cell body compared to lower overtones, which might detect bacteria-free medium or appendages. Higher overtones, in contrast, are more sensitive to changes at the cell-body/chip interface, including any trapped medium and cell appendages. The protocol was adapted from Derick et al., 2023.

In the metadata each strain has been represented by its strains name: B68, B30 and B65. S1, S3 and S4 represent three different compartments in which the samples were run at the same time. BHI broth was for all experiments.

Reference:

Derick et al. https://onlinelibrary.wiley.com/doi/abs/10.1002/pssa.202300310.
DOI: 10.5281/zenodo.10699301
title: QCM-D-Based Metadata on Adhesion and Dispersal Patterns of Three Bacterial Species Recovered from Dairy Pasteurizer Surfaces Following Cleaning and Disinfection

description: In a research project "KILLFILM," conducted at the host institute (Flanders Research Institute for Agriculture Fisheries and Food: ILVO) in Belgium and funded by Flanders' Food, a significant number and diversity of bacterial species were recovered from food contact surfaces in the milk processing industries following cleaning and disinfection (C&D) procedures. This study involved identified dominant bacteria on the surface of dairy pasteurizers following C&D and included Stenotrophomonas rhizophila (B68), Bacillus licheniformis (B65), and Microbacterium lacticum (B30). Bacterial biofilm forming ability in monoculture and mixed culture biofilms was confirmed on polystyrene and stainless steel surfaces. We also used Quartz crystal microbaance with dissipiation (QCM-D) to study adherence and dispersal signals for the three above mentioned bacteria using the QCM-D E4 instrument (Q-sense Gothenburg, Sweden). 5 MHz AT-cut quartz crystals with silica (SiO2) and stainless steel coatings were purchased from Biolin Scientific (Gothenburg, Sweden). The sensors were cleaned according to the method described earlier Derick et al., 2023.

In each experiment, we initially stabilized the frequency shift and energy dissipation signals for at least 20 minutes in a cell-free medium, ensuring a stable baseline. After this, we introduced a suspension of cells to the sensor, maintaining a flow rate of 100 µl/min for 60 minutes. Following the cell addition, the cells were allowed to interact with the sensor surface in a static state for 18-48 h. During this period, we continuously monitored the frequency shift and energy dissipation at a controlled room temperature of approximately 19 ± 0.5 °C. For comparison, we conducted similar measurements using cell-free buffer solutions. Unless specified otherwise, our data analysis primarily focused on the 7th overtone. This particular overtone is more sensitive to the presence of the cell body compared to lower overtones, which might detect bacteria-free medium or appendages. Higher overtones, in contrast, are more sensitive to changes at the cell-body/chip interface, including any trapped medium and cell appendages. The protocol was adapted from Derick et al., 2023.

In the metadata each strain has been represented by its strains name: B68, B30 and B65. S1, S3 and S4 represent three different compartments in which the samples were run at the same time. BHI broth was for all experiments.

Reference:

Derick et al. https://onlinelibrary.wiley.com/doi/abs/10.1002/pssa.202300310.
DOI: 10.6084/m9.figshare.15104584
title: Identification of a novel lineage bat SARS-related coronaviruses that use bat ACE2 receptor

description: Severe respiratory disease coronavirus-2 (SARS-CoV-2) has been the most devastating disease COVID-19 in the century. One of the unsolved scientific questions of SARS-CoV-2 is the animal origin of this virus. Bats and pangolins are recognized as the most probable reservoir hosts that harbour highly similar SARS-CoV-2 related viruses (SARSr-CoV-2). This study identified a novel lineage of SARSr-CoVs, including RaTG15 and seven other viruses, from bats at the same location where we found RaTG13 in 2015. Although RaTG15 and the related viruses share 97.2% amino acid sequence identities with SARS-CoV-2 in the conserved ORF1b region, it only shows less than 77.6% nucleotide identity to all known SARSr-CoVs at the genome level, thus forming a distinct lineage in the <i>Sarbecovirus</i> phylogenetic tree. We found that the RaTG15 receptor-binding domain (RBD) can bind to ACE2 from <i>Rhinolophus affinis</i>, Malayan pangolin, and use it as an entry receptor, except for ACE2 from humans. However, it contains a short deletion and has different key residues responsible for ACE2 binding. In addition, we showed that none of the known viruses in bat SARSr-CoV-2 lineage discovered uses human ACE2 as efficiently as the pangolin-derived SARSr-CoV-2 or some viruses in the SARSr-CoV-1 lineage. Therefore, further systematic and longitudinal studies in bats are needed to prevent future spillover events caused by SARSr-CoVs or to understand the origin of SARS-CoV-2 better.
DOI: 10.6084/m9.figshare.15104584.v1
title: Identification of a novel lineage bat SARS-related coronaviruses that use bat ACE2 receptor

description: Severe respiratory disease coronavirus-2 (SARS-CoV-2) has been the most devastating disease COVID-19 in the century. One of the unsolved scientific questions of SARS-CoV-2 is the animal origin of this virus. Bats and pangolins are recognized as the most probable reservoir hosts that harbour highly similar SARS-CoV-2 related viruses (SARSr-CoV-2). This study identified a novel lineage of SARSr-CoVs, including RaTG15 and seven other viruses, from bats at the same location where we found RaTG13 in 2015. Although RaTG15 and the related viruses share 97.2% amino acid sequence identities with SARS-CoV-2 in the conserved ORF1b region, it only shows less than 77.6% nucleotide identity to all known SARSr-CoVs at the genome level, thus forming a distinct lineage in the <i>Sarbecovirus</i> phylogenetic tree. We found that the RaTG15 receptor-binding domain (RBD) can bind to ACE2 from <i>Rhinolophus affinis</i>, Malayan pangolin, and use it as an entry receptor, except for ACE2 from humans. However, it contains a short deletion and has different key residues responsible for ACE2 binding. In addition, we showed that none of the known viruses in bat SARSr-CoV-2 lineage discovered uses human ACE2 as efficiently as the pangolin-derived SARSr-CoV-2 or some viruses in the SARSr-CoV-1 lineage. Therefore, further systematic and longitudinal studies in bats are needed to prevent future spillover events caused by SARSr-CoVs or to understand the origin of SARS-CoV-2 better.
DOI: 10.6084/m9.figshare.6716036
title: Inositol polyphosphate-4-phosphatase type II plays critical roles in the modulation of cadherin-mediated adhesion dynamics of pancreatic ductal adenocarcinomas

description: The inositol polyphosphate-4-phosphatase type II (INPP4B) has been mostly proposed to act as a tumor suppressor whose expression is frequently dysregulated in numerous human cancers. To date, little is unveiled about whether and how INPP4B will exert its tumor suppressive function on the turnover of cadherin-based cell-cell adhesion system in pancreatic ductal adenocarcinomas (PDACs) <i>in vitro</i>. Here we provide the evidence that INPP4B manipulates cadherin switch in certain PDAC cell lines through a phosphorylated AKT-inactivation manner. The knockdown of INPP4B in AsPC-1 results in a more invasive phenotype, and overexpression of it in PANC-1 leads to partial reversion of mesenchymal status and impediment of <i>in vitro</i> invasion but not migration. More importantly, E-cadherin (Ecad) is enriched in the early and sorting endosomes containing INPP4B by which its recycling rather than degradation is enabled. Immunohistochemical analysis of 39 operatively resected PDAC specimens reveals it is poorly differentiated, non-cohesive ones in which the INPP4B and Ecad are partially or completely compromised in expression. We therefore identify INPP4B as an tumor suppressor in PDAC which attenuates AKT activation and participates in preservation of Ecad in endocytic pool and cellular membrane.
DOI: 10.6084/m9.figshare.6716036.v2
title: Inositol polyphosphate-4-phosphatase type II plays critical roles in the modulation of cadherin-mediated adhesion dynamics of pancreatic ductal adenocarcinomas

description: The inositol polyphosphate-4-phosphatase type II (INPP4B) has been mostly proposed to act as a tumor suppressor whose expression is frequently dysregulated in numerous human cancers. To date, little is unveiled about whether and how INPP4B will exert its tumor suppressive function on the turnover of cadherin-based cell-cell adhesion system in pancreatic ductal adenocarcinomas (PDACs) <i>in vitro</i>. Here we provide the evidence that INPP4B manipulates cadherin switch in certain PDAC cell lines through a phosphorylated AKT-inactivation manner. The knockdown of INPP4B in AsPC-1 results in a more invasive phenotype, and overexpression of it in PANC-1 leads to partial reversion of mesenchymal status and impediment of <i>in vitro</i> invasion but not migration. More importantly, E-cadherin (Ecad) is enriched in the early and sorting endosomes containing INPP4B by which its recycling rather than degradation is enabled. Immunohistochemical analysis of 39 operatively resected PDAC specimens reveals it is poorly differentiated, non-cohesive ones in which the INPP4B and Ecad are partially or completely compromised in expression. We therefore identify INPP4B as an tumor suppressor in PDAC which attenuates AKT activation and participates in preservation of Ecad in endocytic pool and cellular membrane.
DOI: 10.6084/m9.figshare.6716036.v1
title: Inositol polyphosphate-4-phosphatase type II plays critical roles in the modulation of cadherin-mediated adhesion dynamics of pancreatic ductal adenocarcinomas

description: The inositol polyphosphate-4-phosphatase type II (INPP4B) has been mostly proposed to act as a tumor suppressor whose expression is frequently dysregulated in numerous human cancers. To date, little is unveiled about whether and how INPP4B will exert its tumor suppressive function on the turnover of cadherin-based cell-cell adhesion system in pancreatic ductal adenocarcinomas (PDACs) <i>in vitro</i>. Here we provide the evidence that INPP4B manipulates cadherin switch in certain PDAC cell lines through a phosphorylated AKT-inactivation manner. The knockdown of INPP4B in AsPC-1 results in a more invasive phenotype, and overexpression of it in PANC-1 leads to partial reversion of mesenchymal status and impediment of <i>in vitro</i> invasion but not migration. More importantly, E-cadherin (Ecad) is enriched in the early and sorting endosomes containing INPP4B by which its recycling rather than degradation is enabled. Immunohistochemical analysis of 39 operatively resected PDAC specimens reveals it is poorly differentiated, non-cohesive ones in which the INPP4B and Ecad are partially or completely compromised in expression. We therefore identify INPP4B as an tumor suppressor in PDAC which attenuates AKT activation and participates in preservation of Ecad in endocytic pool and cellular membrane.
DOI: 10.6084/m9.figshare.20347579
title: Additional file 1 of Public health emergency and psychological distress among healthcare workers: a scoping review

description: Additional file 1.
DOI: 10.6084/m9.figshare.20347579.v1
title: Additional file 1 of Public health emergency and psychological distress among healthcare workers: a scoping review

description: Additional file 1.
DOI: 10.6084/m9.figshare.25282411
title: Avian Publishing Data

description: Publishing effort across all bird species
DOI: 10.6084/m9.figshare.25282411.v1
title: Avian Publishing Data

description: Publishing effort across all bird species
DOI: 10.6084/m9.figshare.7274651
title: Additional file 3: of Epidemiology of taeniosis/cysticercosis in Europe, a systematic review: eastern Europe

description: Table S1. List of references included in the review retrieved through online international databases. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.7274651.v1
title: Additional file 3: of Epidemiology of taeniosis/cysticercosis in Europe, a systematic review: eastern Europe

description: Table S1. List of references included in the review retrieved through online international databases. (XLSX 24 kb)
DOI: 10.7924/r49311p2m
title: Data from: A cluster-randomized trial of water, sanitation, handwashing and nutritional interventions on stress and epigenetic programming

description: A regulated stress response is essential for healthy child growth and development trajectories. We conducted a cluster-randomized trial in rural Bangladesh (funded by the Bill & Melinda Gates Foundation, ClinicalTrials.gov NCT01590095) to assess the effects of an integrated nutritional, water, sanitation, and handwashing intervention on child health. We previously reported on the primary outcomes of the trial, linear growth and caregiver-reported diarrhea. Here, we assessed additional prespecified outcomes: physiological stress response, oxidative stress, and DNA methylation (N = 759, ages 1-2 years). Eight neighboring pregnant women were grouped into a study cluster. Eight geographically adjacent clusters were block-randomized into the control or the combined nutrition, water, sanitation, and handwashing (N+WSH) intervention group (receiving nutritional counseling and lipid-based nutrient supplements, chlorinated drinking water, upgraded sanitation, and handwashing with soap). Participants and data collectors were not masked, but analyses were masked. There were 358 children (68 clusters) in the control group and 401 children (63 clusters) in the intervention group. We measured four F2-isoprostanes isomers (iPF(2α)-III; 2,3-dinor-iPF(2α)-III; iPF(2α)-VI; 8,12-iso-iPF(2α)-VI), salivary alpha-amylase and cortisol, and methylation of the glucocorticoid receptor (NR3C1) exon 1F promoter including the NGFI-A binding site. Compared with control, the N+WSH group had lower concentrations of F2-isoprostanes isomers (differences ranging from -0.16 to -0.19 log ng/mg of creatinine, P<0.01), elevated post-stressor cortisol (0.24 log µg/dl; P<0.01), higher cortisol residualized gain scores (0.06 µg/dl; P=0.023), and decreased methylation of the NGFI-A binding site (-0.04; P=0.037). The N+WSH intervention enhanced adaptive responses of the physiological stress system in early childhood.
DOI: 10.6084/m9.figshare.13531954.v1
title: Additional file 1 of Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

description: Additional file 1: Table S1. Two hundred seventeen upland cotton cultivars in this study
DOI: 10.6084/m9.figshare.13531954
title: Additional file 1 of Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

description: Additional file 1: Table S1. Two hundred seventeen upland cotton cultivars in this study
DOI: 10.6084/m9.figshare.13531963
title: Additional file 4 of Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

description: Additional file 4: Table S3. One hundred fifty-six potential candidate genes within 100 kb of flanking significant markers
DOI: 10.6084/m9.figshare.13531957
title: Additional file 2 of Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

description: Additional file 2: Table S2. Statistics of SNPs produced by GBS
DOI: 10.6084/m9.figshare.13531963.v1
title: Additional file 4 of Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

description: Additional file 4: Table S3. One hundred fifty-six potential candidate genes within 100 kb of flanking significant markers
DOI: 10.6084/m9.figshare.13531957.v1
title: Additional file 2 of Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

description: Additional file 2: Table S2. Statistics of SNPs produced by GBS
DOI: 10.6084/m9.figshare.13531972
title: Additional file 6 of Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

description: Additional file 6: Table S4. The specific primers for qRT-PCR and Virus-induced gene silencing assay
DOI: 10.6084/m9.figshare.13531972.v1
title: Additional file 6 of Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

description: Additional file 6: Table S4. The specific primers for qRT-PCR and Virus-induced gene silencing assay
DOI: 10.6084/m9.figshare.13531961.v1
title: Additional file 10 of Genome-wide association study reveals a patatin-like lipase relating to the reduction of seed oil content in Brassica napus

description: Additional file 10: Table S6. The expression values (indicated by RPKM and the number of read counts after calibration) of BnPTLs at different seed developmental stages of rapeseed.
DOI: 10.6084/m9.figshare.7274663
title: Additional file 4: of Epidemiology of taeniosis/cysticercosis in Europe, a systematic review: eastern Europe

description: Table S2. List of references included in the review made available through local sources. (XLSX 71 kb)
DOI: 10.6084/m9.figshare.13531961
title: Additional file 10 of Genome-wide association study reveals a patatin-like lipase relating to the reduction of seed oil content in Brassica napus

description: Additional file 10: Table S6. The expression values (indicated by RPKM and the number of read counts after calibration) of BnPTLs at different seed developmental stages of rapeseed.
DOI: 10.6084/m9.figshare.13531985
title: Additional file 5 of Genome-wide association study reveals a patatin-like lipase relating to the reduction of seed oil content in Brassica napus

description: Additional file 5: Table S1. The accession codes, names, origins of the 290 genetic materials and their SOC at two experimental sites.
DOI: 10.6084/m9.figshare.13531985.v1
title: Additional file 5 of Genome-wide association study reveals a patatin-like lipase relating to the reduction of seed oil content in Brassica napus

description: Additional file 5: Table S1. The accession codes, names, origins of the 290 genetic materials and their SOC at two experimental sites.
DOI: 10.6084/m9.figshare.17799501
title: Additional file 1 of Hybrid surgery with PEEK rods for lumbar degenerative diseases: a 2-year follow-up study

description: Additional file 1.
DOI: 10.6084/m9.figshare.17799501.v1
title: Additional file 1 of Hybrid surgery with PEEK rods for lumbar degenerative diseases: a 2-year follow-up study

description: Additional file 1.
DOI: 10.6084/m9.figshare.13531988
title: Additional file 6 of Genome-wide association study reveals a patatin-like lipase relating to the reduction of seed oil content in Brassica napus

description: Additional file 6: Table S2. The SNPs associated with SOC on Chr.C07 and associated gene IDs on Chr.C07.
DOI: 10.6084/m9.figshare.13531988.v1
title: Additional file 6 of Genome-wide association study reveals a patatin-like lipase relating to the reduction of seed oil content in Brassica napus

description: Additional file 6: Table S2. The SNPs associated with SOC on Chr.C07 and associated gene IDs on Chr.C07.
DOI: 10.6084/m9.figshare.13531994
title: Additional file 7 of Genome-wide association study reveals a patatin-like lipase relating to the reduction of seed oil content in Brassica napus

description: Additional file 7: Table S3. The SNPs across BnaC07g30920D.
DOI: 10.6084/m9.figshare.13531994.v1
title: Additional file 7 of Genome-wide association study reveals a patatin-like lipase relating to the reduction of seed oil content in Brassica napus

description: Additional file 7: Table S3. The SNPs across BnaC07g30920D.
DOI: 10.6084/m9.figshare.13531997
title: Additional file 8 of Genome-wide association study reveals a patatin-like lipase relating to the reduction of seed oil content in Brassica napus

description: Additional file 8: Table S4. The genome-wide analysis of 40 BnPTLs in rapeseed.
DOI: 10.15468/dl.echuse
title: Occurrence Download

description: A dataset containing 42596 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ursus americanus Pallas, 1780"
 ]
}

 The dataset includes 42596 records from 171 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0109937-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.szc8ey
title: Occurrence Download

description: A dataset containing 298168 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Luscinia luscinia (Linnaeus, 1758)",
 "HasCoordinate is true",
 "Year is greater than or equal to 2011",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 298168 records from 114 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0109938-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zb2puq
title: Occurrence Download

description: A dataset containing 3044 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Obtención de la riqueza de aves y selección de especies susceptibles de monitoreo en la zona noroeste en el estado de Chiapas"
 ]
}

 The dataset includes 3044 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0109939-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.