cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7284/104346
title: INS (Inertial Navigation System) data collected during research cruise WS1101 using a Applanix POS/MV-320 V2 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/104340
title: Radiometer data collected during research cruise WS1101 using a Eppley PSP instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7155281
title: Additional file 1: of Foxf2 plays a dual role during transforming growth factor beta-induced epithelial to mesenchymal transition by promoting apoptosis yet enabling cell junction dissolution and migration

description: Figure S1. Foxf2 expression is upregulated during EMT via the canonical Smad pathway. The increased expression of Foxf2 during an EMT was assessed in normal murine mammary gland epithelial cells (NMuMG) and in murine and human breast cancer cells. Figure S2. Foxf2 is required for TGFβ-induced disruption of adherens junctions. RNAi-mediated ablation prevents an EMT as visualized by immunofluorescence staining for epithelial and mesenchymal markers. Figure S3. Foxf2 regulates the expression of Zeb1, Zeb2, Id2, and members of the miR-200 family as determined by quantitative RT-PCR of their expression during an EMT in the absence of presence of Foxf2. Figure S4. Foxf2 regulates Noxa expression and thus affects cell proliferation and apoptosis. Foxf2 regulated the expression of Noxa, and siRNA-mediated depletion of Noxa prevented an increase in cell death induced by the loss of Foxf2 expression as assessed by quantitative RT-PCR. Figure S5. EGF ligand-mediated EGF receptor signaling overcomes Foxf2-controlled cell survival. Foxf represses the expression of EGF receptor ligands as assessed by quantitative RT-PCR. Supplementary material and methods. Detailed information is given on the antibodies and reagents, on biochemical and cell biological methods, and on RNA sequencing and bioinformatics analysis used in the study. Table S1. Excel file summarizing the differential expression analysis (siFoxf2 to siCtrl after 4 days TGFβ treatment or siCtrl with vs without TGFβ for 4 days) of all transcripts detected with RNA-sequencing. Table S2. Excel file showing the list of genes belonging to the different gene signatures (modules) and the strength of their modular membership (kME values). (ZIP 14675 kb)
DOI: 10.6084/m9.figshare.7155281.v1
title: Additional file 1: of Foxf2 plays a dual role during transforming growth factor beta-induced epithelial to mesenchymal transition by promoting apoptosis yet enabling cell junction dissolution and migration

description: Figure S1. Foxf2 expression is upregulated during EMT via the canonical Smad pathway. The increased expression of Foxf2 during an EMT was assessed in normal murine mammary gland epithelial cells (NMuMG) and in murine and human breast cancer cells. Figure S2. Foxf2 is required for TGFβ-induced disruption of adherens junctions. RNAi-mediated ablation prevents an EMT as visualized by immunofluorescence staining for epithelial and mesenchymal markers. Figure S3. Foxf2 regulates the expression of Zeb1, Zeb2, Id2, and members of the miR-200 family as determined by quantitative RT-PCR of their expression during an EMT in the absence of presence of Foxf2. Figure S4. Foxf2 regulates Noxa expression and thus affects cell proliferation and apoptosis. Foxf2 regulated the expression of Noxa, and siRNA-mediated depletion of Noxa prevented an increase in cell death induced by the loss of Foxf2 expression as assessed by quantitative RT-PCR. Figure S5. EGF ligand-mediated EGF receptor signaling overcomes Foxf2-controlled cell survival. Foxf represses the expression of EGF receptor ligands as assessed by quantitative RT-PCR. Supplementary material and methods. Detailed information is given on the antibodies and reagents, on biochemical and cell biological methods, and on RNA sequencing and bioinformatics analysis used in the study. Table S1. Excel file summarizing the differential expression analysis (siFoxf2 to siCtrl after 4 days TGFβ treatment or siCtrl with vs without TGFβ for 4 days) of all transcripts detected with RNA-sequencing. Table S2. Excel file showing the list of genes belonging to the different gene signatures (modules) and the strength of their modular membership (kME values). (ZIP 14675 kb)
DOI: 10.6084/m9.figshare.7155278
title: Additional file 3: of Transcriptomic response to parasite infection in Nile tilapia (Oreochromis niloticus) depends on rearing density

description: Gene Ontology enrichment of uninfected skin tissues: Full GO enrichment results of skin genes differentially expressed between uninfected fish at high and low density. (XLSX 3920 kb)
DOI: 10.7284/104341
title: Radiometer data collected during research cruise WS1101 using a Eppley TUV instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7155275
title: Additional file 2: of Transcriptomic response to parasite infection in Nile tilapia (Oreochromis niloticus) depends on rearing density

description: Gene Ontology enrichment of uninfected gill tissues: Full GO enrichment results of gill genes differentially expressed between uninfected fish at high and low density. (XLSX 6567 kb)
DOI: 10.6084/m9.figshare.7155269
title: Additional file 13: of Transcriptomic response to parasite infection in Nile tilapia (Oreochromis niloticus) depends on rearing density

description: Dot plots of GO term enrichment: Summary of GO term enrichment in differentially expressed genes comparing uninfected and Saprolegnia-challenged fish. Dot colour intensity indicates FDR-corrected P value, dot size indicates number of genes. (XLSX 7015 kb)
DOI: 10.6084/m9.figshare.7155275.v1
title: Additional file 2: of Transcriptomic response to parasite infection in Nile tilapia (Oreochromis niloticus) depends on rearing density

description: Gene Ontology enrichment of uninfected gill tissues: Full GO enrichment results of gill genes differentially expressed between uninfected fish at high and low density. (XLSX 6567 kb)
DOI: 10.6084/m9.figshare.7155278.v1
title: Additional file 3: of Transcriptomic response to parasite infection in Nile tilapia (Oreochromis niloticus) depends on rearing density

description: Gene Ontology enrichment of uninfected skin tissues: Full GO enrichment results of skin genes differentially expressed between uninfected fish at high and low density. (XLSX 3920 kb)
DOI: 10.7284/104345
title: Radiometer data collected during research cruise WS1101 using a Eppley PIR instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7155269.v1
title: Additional file 13: of Transcriptomic response to parasite infection in Nile tilapia (Oreochromis niloticus) depends on rearing density

description: Dot plots of GO term enrichment: Summary of GO term enrichment in differentially expressed genes comparing uninfected and Saprolegnia-challenged fish. Dot colour intensity indicates FDR-corrected P value, dot size indicates number of genes. (XLSX 7015 kb)
DOI: 10.7284/104344
title: Rain Gauge data collected during research cruise WS1101 using a OSI ORG-815 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/104342
title: Water Temperature data collected during research cruise WS1101 using a Sea-Bird SBE-38 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7155251
title: Additional File 1:

description: Table S1. Results from BLASTp of Oncorhynchus mykiss protein sequences against Salmo salar and MaxQuant output after filtering contaminants, reverse sequences, proteins identified by site, and proteins with only 1 peptide for identification (3076 proteins). Table S2. Imputed protein abundance data after implementing all filtering criteria (2433 proteins). Table S3. Full statistical results from the linear model for each of the 2433 proteins included in the analysis. Table S4. Full results for GO Biological Process (GOBP) enrichment analysis. Table S5. Significantly different proteins that contribute to each significant GOBP term. Table S6. Significantly different proteins that contribute to each significant GO slim term. Table S7. Abbreviations and proteins annotations from STRING. (XLSX 3388 kb)
DOI: 10.6084/m9.figshare.7155254
title: Additional File 2:

description: Supplementary Dataset 1. Sequence alignment used for phylogenetic analysis of C3 complement sequences. (FASTA 47 kb)
DOI: 10.6084/m9.figshare.7155251.v1
title: Additional File 1:

description: Table S1. Results from BLASTp of Oncorhynchus mykiss protein sequences against Salmo salar and MaxQuant output after filtering contaminants, reverse sequences, proteins identified by site, and proteins with only 1 peptide for identification (3076 proteins). Table S2. Imputed protein abundance data after implementing all filtering criteria (2433 proteins). Table S3. Full statistical results from the linear model for each of the 2433 proteins included in the analysis. Table S4. Full results for GO Biological Process (GOBP) enrichment analysis. Table S5. Significantly different proteins that contribute to each significant GOBP term. Table S6. Significantly different proteins that contribute to each significant GO slim term. Table S7. Abbreviations and proteins annotations from STRING. (XLSX 3388 kb)
DOI: 10.6084/m9.figshare.7155254.v1
title: Additional File 2:

description: Supplementary Dataset 1. Sequence alignment used for phylogenetic analysis of C3 complement sequences. (FASTA 47 kb)
DOI: 10.7284/104343
title: TSG (Thermosalinograph) data collected during research cruise WS1101 using a Sea-Bird SBE-45 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/104347
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise WS1102 using a Sea-Bird SBE-911plus instrument system onboard the platform RV F.G. Walton Smith
DOI: 10.6084/m9.figshare.7155074
title: Adult low pH exposure influences larval abundance in Pacific oysters (Crassostrea gigas)

description: Supplement for the paper "Adult low pH exposure influences larval abundance in Pacific oysters (<i>Crassostrea gigas</i>)." This repository includes histology images, raw data for seawater chemistry, gonad maturation, and larval abundance, and code for final analyses and images.<br><b>ABSTRACT</b>: As negative effects of ocean acidification are experienced by coastal ecosystems, there is a growing trend to investigate the effect ocean acidification has on multiple generations. Parental exposure to ocean acidification has been shown to induce larval carryover effects, but whether or not an acute exposure to a stressor as an adult can influence the larval generation long after the stress has been removed has yet to be tested. To assess how a temporary exposure to experimental ocean acidification affects the ecologically and commercially relevant Pacific oyster (<i>Crassostrea gigas</i>), adult oysters were exposed to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for seven weeks. Oysters were then held for eight weeks in ambient conditions, and subsequently conditioned for four weeks at ambient pH. After reproductive conditioning, oysters were strip-spawned to create four families based on maternal and paternal ocean acidification exposure. The number of D-hinge larvae were counted eighteen hours post fertilization. A sex-specific broodstock response was observed, where female exposure to low pH conditions resulted in fewer D-hinge larvae. This study demonstrates that the effects of ocean acidification can last beyond the time from when the environmental perturbation is experienced. Broadening the understanding of environmental memory will be valuable when considering an organism’s ability to persist in the face of environmental change change.
DOI: 10.7284/104348
title: GNSS (Global Navigation Satellite System) data collected during research cruise WS1102 using a Raytheon 300 WAAS instrument system onboard the platform RV F.G. Walton Smith
DOI: 10.6084/m9.figshare.7155074.v2
title: Adult low pH exposure influences larval abundance in Pacific oysters (Crassostrea gigas)

description: Supplement for the paper "Adult low pH exposure influences larval abundance in Pacific oysters (<i>Crassostrea gigas</i>)." This repository includes histology images, raw data for seawater chemistry, gonad maturation, and larval abundance, and code for final analyses and images.<br><b>ABSTRACT</b>: As negative effects of ocean acidification are experienced by coastal ecosystems, there is a growing trend to investigate the effect ocean acidification has on multiple generations. Parental exposure to ocean acidification has been shown to induce larval carryover effects, but whether or not an acute exposure to a stressor as an adult can influence the larval generation long after the stress has been removed has yet to be tested. To assess how a temporary exposure to experimental ocean acidification affects the ecologically and commercially relevant Pacific oyster (<i>Crassostrea gigas</i>), adult oysters were exposed to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for seven weeks. Oysters were then held for eight weeks in ambient conditions, and subsequently conditioned for four weeks at ambient pH. After reproductive conditioning, oysters were strip-spawned to create four families based on maternal and paternal ocean acidification exposure. The number of D-hinge larvae were counted eighteen hours post fertilization. A sex-specific broodstock response was observed, where female exposure to low pH conditions resulted in fewer D-hinge larvae. This study demonstrates that the effects of ocean acidification can last beyond the time from when the environmental perturbation is experienced. Broadening the understanding of environmental memory will be valuable when considering an organism’s ability to persist in the face of environmental change change.
DOI: 10.6084/m9.figshare.7155062
title: Inventory of chytrid diversity in two temporary forest ponds using a multiphasic approach

description: Food webs in temporary forest ponds are driven by decomposition of terrestrial inputs. Chytrid fungi are important components of the fungal community, degrading leaf litter in streams reliant on terrestrial inputs and in lake ecosystems where they may stabilize the food web. However, little is known about chytrid fungi in temporary forest ponds. We inventoried the chytrid diversity present in two temporary forest ponds via light microscopy of baited samples and ion semiconductor (Ion Torrent) sequencing of environmental DNA. We quantified trends of chytrid alpha and beta diversity as a function of spatial and temporal factors. A total of 59 chytrid taxa were detected throughout the study. Beta diversity exhibited variation across the sampled months for both the entire fungal community as well as for chytrids alone. Shifts in community composition were also apparent, although diversity metrics and composition patterns did not meet adjusted <i>P</i> values. The results of this study highlight the diversity of chytrid fungi in temporary forest ponds and the need for further studies on the spatial and temporal dynamics of chytrid species.
DOI: 10.6084/m9.figshare.7155062.v1
title: Inventory of chytrid diversity in two temporary forest ponds using a multiphasic approach

description: Food webs in temporary forest ponds are driven by decomposition of terrestrial inputs. Chytrid fungi are important components of the fungal community, degrading leaf litter in streams reliant on terrestrial inputs and in lake ecosystems where they may stabilize the food web. However, little is known about chytrid fungi in temporary forest ponds. We inventoried the chytrid diversity present in two temporary forest ponds via light microscopy of baited samples and ion semiconductor (Ion Torrent) sequencing of environmental DNA. We quantified trends of chytrid alpha and beta diversity as a function of spatial and temporal factors. A total of 59 chytrid taxa were detected throughout the study. Beta diversity exhibited variation across the sampled months for both the entire fungal community as well as for chytrids alone. Shifts in community composition were also apparent, although diversity metrics and composition patterns did not meet adjusted <i>P</i> values. The results of this study highlight the diversity of chytrid fungi in temporary forest ponds and the need for further studies on the spatial and temporal dynamics of chytrid species.
DOI: 10.7284/104357
title: INS (Inertial Navigation System) data collected during research cruise WS1102 using a Applanix POS/MV-320 V2 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7155050
title: Dupilumab safety and efficacy in uncontrolled asthma: a systematic review and meta-analysis of randomized clinical trials

description: <i>Objective</i>: We aimed to perform a meta-analysis evaluating the efficacy and safety of dupilumab in patients with uncontrolled asthma. <i>Data source</i>: A search of electronic databases was performed using PubMed, Cochrane library and Embase. <i>Study selection</i>: The literature search was conducted independently by two reviewers. Only randomized controlled trials (RCTs) that compared between placebo and dupilumab in patients with uncontrolled asthma were included in this analysis. Pooled risk ratios (RRs) and mean differences (MDs) with their corresponding 95% confidence intervals (CIs) were calculated for dichotomous and continuous data, respectively. <i>Results</i>: A total of four RCTs representing 2,992 patients were included. Pooled analysis showed significant reductions of the annualized rate of severe asthma exacerbation in the dupilumab group compared with placebo (RR 0.44; 95% CI 0.35–0.055; P Conclusion: Among patients with uncontrolled asthma, the addition of dupilumab was associated with a reduced risk of severe asthma exacerbations and improvement in FEV1 without an increased risk of adverse events apart from injection site reactions with dupilumab.
DOI: 10.7284/104358
title: GNSS (Global Navigation Satellite System) data collected during research cruise WS1103 using a Raytheon 300 WAAS instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7155050.v1
title: Dupilumab safety and efficacy in uncontrolled asthma: a systematic review and meta-analysis of randomized clinical trials

description: <i>Objective</i>: We aimed to perform a meta-analysis evaluating the efficacy and safety of dupilumab in patients with uncontrolled asthma. <i>Data source</i>: A search of electronic databases was performed using PubMed, Cochrane library and Embase. <i>Study selection</i>: The literature search was conducted independently by two reviewers. Only randomized controlled trials (RCTs) that compared between placebo and dupilumab in patients with uncontrolled asthma were included in this analysis. Pooled risk ratios (RRs) and mean differences (MDs) with their corresponding 95% confidence intervals (CIs) were calculated for dichotomous and continuous data, respectively. <i>Results</i>: A total of four RCTs representing 2,992 patients were included. Pooled analysis showed significant reductions of the annualized rate of severe asthma exacerbation in the dupilumab group compared with placebo (RR 0.44; 95% CI 0.35–0.055; P Conclusion: Among patients with uncontrolled asthma, the addition of dupilumab was associated with a reduced risk of severe asthma exacerbations and improvement in FEV1 without an increased risk of adverse events apart from injection site reactions with dupilumab.
DOI: 10.6084/m9.figshare.7155047
title: Altered driving performance of symptomatic Huntington’s disease gene carriers in simulated road conditions

description: <b>Objective:</b> In clinical practice, patients with Huntington’s disease (HD) often decide to solely drive in their own familiar neighborhoods and not on a motorway or in an unknown area. The aim of the study was to identify differences in driving performance between HD gene carriers and healthy individuals in simulated urban and motorway environments. <b>Methods:</b> This cross-sectional study included 87 participants (28 premanifest HD, 30 manifest HD, 29 controls). All participants were active drivers and were assessed using a driving simulator, a driving history questionnaire, and the Unified Huntington’s Disease Rating Scale. The driving simulator session included urban and motorway scenarios. Analysis of variance and Kruskal-Wallis tests were used to compare urban and motorway driving across all 3 groups. <b>Results:</b> Manifest HD drove slower compared to controls and premanifest HD when speed limits increased (80 and 100 km/h) and they had a less steady speed compared to premanifest HD on the motorway and in a 30 km/h zone. Manifest HD also had a larger standard deviation of the lateral position (i.e., more weaving of the car/less vehicle control) compared to controls and premanifest HD on the motorway. <b>Conclusions:</b> Manifest HD drive more cautious in a driving simulator when speed limits increase compared to premanifest HD and controls and they have less vehicle control on the motorway. The driving simulator parameters are able to discriminate between manifest HD and healthy individuals, so a driving simulator seems a feasible tool to use when investigating changes in driving in manifest HD.
DOI: 10.7284/104359
title: GNSS (Global Navigation Satellite System) data collected during research cruise WS1103 using a Raytheon 320 WAAS instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7155047.v1
title: Altered driving performance of symptomatic Huntington’s disease gene carriers in simulated road conditions

description: <b>Objective:</b> In clinical practice, patients with Huntington’s disease (HD) often decide to solely drive in their own familiar neighborhoods and not on a motorway or in an unknown area. The aim of the study was to identify differences in driving performance between HD gene carriers and healthy individuals in simulated urban and motorway environments. <b>Methods:</b> This cross-sectional study included 87 participants (28 premanifest HD, 30 manifest HD, 29 controls). All participants were active drivers and were assessed using a driving simulator, a driving history questionnaire, and the Unified Huntington’s Disease Rating Scale. The driving simulator session included urban and motorway scenarios. Analysis of variance and Kruskal-Wallis tests were used to compare urban and motorway driving across all 3 groups. <b>Results:</b> Manifest HD drove slower compared to controls and premanifest HD when speed limits increased (80 and 100 km/h) and they had a less steady speed compared to premanifest HD on the motorway and in a 30 km/h zone. Manifest HD also had a larger standard deviation of the lateral position (i.e., more weaving of the car/less vehicle control) compared to controls and premanifest HD on the motorway. <b>Conclusions:</b> Manifest HD drive more cautious in a driving simulator when speed limits increase compared to premanifest HD and controls and they have less vehicle control on the motorway. The driving simulator parameters are able to discriminate between manifest HD and healthy individuals, so a driving simulator seems a feasible tool to use when investigating changes in driving in manifest HD.