cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7082858
title: PTPN14 regulates Roquin2 stability by tyrosine dephosphorylation

description: Protein phosphorylation regulates a variety of cellular signaling pathways and fundamental mechanisms in cells. In this paper, we demonstrate that the mRNA decay factor Roquin2 is phosphorylated at tyrosine residue in position 691 <i>in vivo</i>. This phosphorylation disrupts the interaction with KLHL6, the E3 ligase for Roquin2. Furthermore, we establish that the tyrosine phosphatase PTPN14 specifically interacts with Roquin2 through its phosphatase domain and dephosphorylates Roquin2 tyrosine 691. Overexpression of PTPN14 promotes Roquin2 degradation in a KLHL6-dependant manner by promoting interaction with KLHL6. Collectively, our findings reveal that PTPN14 negatively regulates the protein stability of Roquin2, thereby adding a new layer of regulation to the KLHL6-Roquin2 axis.
DOI: 10.6084/m9.figshare.7082858.v1
title: PTPN14 regulates Roquin2 stability by tyrosine dephosphorylation

description: Protein phosphorylation regulates a variety of cellular signaling pathways and fundamental mechanisms in cells. In this paper, we demonstrate that the mRNA decay factor Roquin2 is phosphorylated at tyrosine residue in position 691 <i>in vivo</i>. This phosphorylation disrupts the interaction with KLHL6, the E3 ligase for Roquin2. Furthermore, we establish that the tyrosine phosphatase PTPN14 specifically interacts with Roquin2 through its phosphatase domain and dephosphorylates Roquin2 tyrosine 691. Overexpression of PTPN14 promotes Roquin2 degradation in a KLHL6-dependant manner by promoting interaction with KLHL6. Collectively, our findings reveal that PTPN14 negatively regulates the protein stability of Roquin2, thereby adding a new layer of regulation to the KLHL6-Roquin2 axis.
DOI: 10.6084/m9.figshare.7082780
title: Information Improves Provider Behaviour: A Replication Study of a Community-Based Monitoring Programme in Uganda

description: In ‘Power to the People: Evidence from a Randomised Field Experiment on Community-Based Monitoring in Uganda’ (2009), Björkman and Svensson show that a relatively simple intervention – providing community-level health service delivery information and guidance on community-based monitoring – improved provider behaviour, health care utilisation, and health outcomes. In this paper we conduct a pure replication of the original study and extend the original analysis. Overall, we find that the intervention modified healthcare provider behaviours and utilisation, but that the results surrounding the programme’s impact on health outcomes appear less robust.
DOI: 10.6084/m9.figshare.7082780.v1
title: Information Improves Provider Behaviour: A Replication Study of a Community-Based Monitoring Programme in Uganda

description: In ‘Power to the People: Evidence from a Randomised Field Experiment on Community-Based Monitoring in Uganda’ (2009), Björkman and Svensson show that a relatively simple intervention – providing community-level health service delivery information and guidance on community-based monitoring – improved provider behaviour, health care utilisation, and health outcomes. In this paper we conduct a pure replication of the original study and extend the original analysis. Overall, we find that the intervention modified healthcare provider behaviours and utilisation, but that the results surrounding the programme’s impact on health outcomes appear less robust.
DOI: 10.6084/m9.figshare.7082690
title: Supplementary material for article doi:10.1371/journal.pone.0205568

description: <b>FigS1: </b>Boxplots of CPU times and idle times for the first experiment. <br><b>data_fig3: </b>Raw data for figure 3: completion times for different experimental conditions. 2XP: effect of simulation length; 4XP: effect of task deadline; 3XP: effect of batch size.<br><b>gemmel_raw: </b>Raw data for test case: population of models using a full-factorial design (fig.4 in manuscript). Data columns correspond to (1) work unit id, (2) work unit creation time, and (3) work unit completion time (see Methods in the paper for details).<br><b>config_files.rar: </b>Python scripts to generate the XML configuration files and a sample XML output.<br><b>denis-myocite-validator.cpp</b>: code to validate results.<br>
DOI: 10.6084/m9.figshare.7082684
title: Biofilm genomes

description: 479 microbial genomes recovered from marine biofilm metagenomes.
DOI: 10.6084/m9.figshare.7082678
title: Supplementary Material for: Environmental Influences on Neuromorphology in the Non-Native Starling <b><i>Sturnus vulgaris</i></b>

description: Cognitive traits are predicted to be under intense selection in animals moving into new environments and may determine the success, or otherwise, of dispersal and invasions. In particular, spatial information related to resource distribution is an important determinant of neural development. Spatial information is predicted to vary for invasive species encountering novel environments. However, few studies have tested how cognition or neural development varies intraspecifically within an invasive species. In Australia, the non-native common starling <i>Sturnus vulgaris</i> inhabits a range of habitats that vary in seasonal resource availability and distribution. We aimed to identify variations in the brain mass and hippocampus volume of starlings in Australia related to environmental variation across two substantially different habitat types. Specifically, we predicted variation in brain mass and hippocampal volume in relation to environmental conditions, latitude, and climatic variables. To test this, brain mass and volumes of the hippocampus and two control brain regions (telencephalon and tractus septomesencephalicus) were quantified from starling brains gathered from across the species’ range in south eastern Australia. When comparing across an environmental gradient, there was a significant interaction between sex and environment for overall brain mass, with greater sexual dimorphism in brain mass in inland populations compared to those at the coast. There was no significant difference in hippocampal volume in relation to environmental measures (hippocampus volume,<i> n</i> = 17) for either sex. While these data provide no evidence for intraspecific environmental drivers for changes in hippocampus volume in European starlings in Australia, they do suggest that environmental factors contribute to sex differences in brain mass. This study identifies associations between the brain volume of a non-native species and the environment; further work in this area is required to elucidate the mechanisms driving this relationship.
DOI: 10.6084/m9.figshare.7082678.v1
title: Supplementary Material for: Environmental Influences on Neuromorphology in the Non-Native Starling <b><i>Sturnus vulgaris</i></b>

description: Cognitive traits are predicted to be under intense selection in animals moving into new environments and may determine the success, or otherwise, of dispersal and invasions. In particular, spatial information related to resource distribution is an important determinant of neural development. Spatial information is predicted to vary for invasive species encountering novel environments. However, few studies have tested how cognition or neural development varies intraspecifically within an invasive species. In Australia, the non-native common starling <i>Sturnus vulgaris</i> inhabits a range of habitats that vary in seasonal resource availability and distribution. We aimed to identify variations in the brain mass and hippocampus volume of starlings in Australia related to environmental variation across two substantially different habitat types. Specifically, we predicted variation in brain mass and hippocampal volume in relation to environmental conditions, latitude, and climatic variables. To test this, brain mass and volumes of the hippocampus and two control brain regions (telencephalon and tractus septomesencephalicus) were quantified from starling brains gathered from across the species’ range in south eastern Australia. When comparing across an environmental gradient, there was a significant interaction between sex and environment for overall brain mass, with greater sexual dimorphism in brain mass in inland populations compared to those at the coast. There was no significant difference in hippocampal volume in relation to environmental measures (hippocampus volume,<i> n</i> = 17) for either sex. While these data provide no evidence for intraspecific environmental drivers for changes in hippocampus volume in European starlings in Australia, they do suggest that environmental factors contribute to sex differences in brain mass. This study identifies associations between the brain volume of a non-native species and the environment; further work in this area is required to elucidate the mechanisms driving this relationship.
DOI: 10.6084/m9.figshare.7082660
title: Supplementary Material for: Application of 3D Printing for Patient-Specific Silicone Stents: 1-Year Follow-Up on 2 Patients

description: Managing complex benign airway disease is a major challenge in interventional pulmonology. Airway stent placement can result in complications due to a variety of factors, including poor fit of the stent in the airway. We report the 1-year outcome of 2 patients with airway disease caused by granulomatosis with polyangiitis (Wegener’s) affecting the left main bronchus and secondary carina. These patients had not responded to systemic therapy or standard bronchoscopic techniques and had complications with commercially available airway stents. We describe a first-in-human, clinical experience to address these issues. Using computed tomography (CT) imaging and 3D printing technology, we generated and implanted patient-specific silicone airway stents to address airway disease. 3D patient-specific stent prescription was created using a CT scan of the patient’s chest and a proprietary software package originally developed for orthopedic surgical planning. Silicone stents were manufactured and implanted. Observation for &gt; 1 year after implantation compared to the 6 months prior to patient-specific stent implant were compared for the number, clinically required stent changes, procedure time, and general clinical improvement per usual standard of care after airway stenting. Patients showed improved durability, a shorter procedure time, and improvement of patient-reported symptoms leading to a reduced need for stent changes and modifications. The use of 3D printing technology to make patient-specific silicone stents is feasible with early clinical proof of concept noting a durable improvement over 1 year of follow-up.
DOI: 10.6084/m9.figshare.7082633
title: Supplementary Material for: Intussusceptive Pillar Formation in Developing Porcine Glomeruli

description: <b><i>Background/Aims:</i></b> Intussusceptive angiogenesis (IA) is a dynamic process which contributes to vascular expansion and remodeling. Intraluminal pillars have long been the distinctive structural indicator of IA. However, the mechanism of their formation has not been fully elucidated. <b><i>Methods:</i></b> Using light and electron microscopy, we studied intussusceptive vascular growth in the developing porcine metanephric kidney. <b><i>Results:</i></b> We observed intraluminal pillars formed by endothelial cells in the vasculature of developing glomeruli. Their diameter was &lt; 2.5 µm, consistent with the diameter of nascent pillars. TEM revealed that the majority of these pillars consisted only of endothelium. However, a central core of extracellular matrix (ECM) covered by endothelium, reminiscent of a more mature intussusceptive pillar, was also found in the lumen of a glomerular capillary. Perivascular cells or pericytes were not involved in the pillar structure during these stages of formation. <b><i>Conclusion:</i></b> This study shows ECM presence in a mature intussusceptive pillar without any perivascular cell involvement in the structure. This leads to the hypothesis that ECM deposition precedes the participation of these cells in the formation of intraluminal pillars during IA in porcine metanephric glomerular capillaries.
DOI: 10.6084/m9.figshare.7082630
title: Journaling - How I keep track of Life, MS & my Life with MS

description: A overview of how I use bullet journals to manage my symptoms and life with MS<br>
DOI: 10.6084/m9.figshare.7082627
title: Supplementary Material for: Microarray-Based Gene Expression Analysis Identifies Potential Diagnostic and Prognostic Biomarkers for Waldenström Macroglobulinemia

description: Waldenström macroglobulinemia (WM), also known as lymphoplasmacytic lymphoma, is rare but a clinicopathologically distinct B-cell malignancy. This study assessed differentially expressed genes (DEGs) to identify potential WM biomarkers and uncover the underlying the molecular mechanisms of WM progression using gene expression profiles from the Gene Expression Omnibus database. DEGs were identified using the LIMMA package and their potential functions were then analyzed by using the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses and the protein-protein interaction (PPI) network analysis by using the Search Tool for the Retrieval of Interacting Genes/Proteins database. Data showed that among 1,756 DEGs, 926 were upregulated and 830 were downregulated by comparing WM BM CD19+ with normal PB CD19+ B cell samples, whereas 241 DEGs (95 upregulated and 146 downregulated) were identified by comparing WM BM CD138+ with normal BM CD138+ plasma cell samples. The DEGs were enriched in different GO terms and pathways, including the apoptotic process, cell cycle arrest, immune response, cell adhesion, mitogen-activated protein kinase signaling pathway, toll-like receptor signaling pathway, and the gonadotropin-releasing hormone signaling pathway. Hub nodes in the PPI network included CDK1, JUN, CREBBP, EP300, CAD, CDK2, and MAPK14. Bioinformatics analysis of the GSE9656 dataset identified 7 hub genes that might play an important role in WM development and progression. Some of the candidate genes and pathways may serve as promising therapeutic targets for WM.
DOI: 10.6084/m9.figshare.7082627.v1
title: Supplementary Material for: Microarray-Based Gene Expression Analysis Identifies Potential Diagnostic and Prognostic Biomarkers for Waldenström Macroglobulinemia

description: Waldenström macroglobulinemia (WM), also known as lymphoplasmacytic lymphoma, is rare but a clinicopathologically distinct B-cell malignancy. This study assessed differentially expressed genes (DEGs) to identify potential WM biomarkers and uncover the underlying the molecular mechanisms of WM progression using gene expression profiles from the Gene Expression Omnibus database. DEGs were identified using the LIMMA package and their potential functions were then analyzed by using the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses and the protein-protein interaction (PPI) network analysis by using the Search Tool for the Retrieval of Interacting Genes/Proteins database. Data showed that among 1,756 DEGs, 926 were upregulated and 830 were downregulated by comparing WM BM CD19+ with normal PB CD19+ B cell samples, whereas 241 DEGs (95 upregulated and 146 downregulated) were identified by comparing WM BM CD138+ with normal BM CD138+ plasma cell samples. The DEGs were enriched in different GO terms and pathways, including the apoptotic process, cell cycle arrest, immune response, cell adhesion, mitogen-activated protein kinase signaling pathway, toll-like receptor signaling pathway, and the gonadotropin-releasing hormone signaling pathway. Hub nodes in the PPI network included CDK1, JUN, CREBBP, EP300, CAD, CDK2, and MAPK14. Bioinformatics analysis of the GSE9656 dataset identified 7 hub genes that might play an important role in WM development and progression. Some of the candidate genes and pathways may serve as promising therapeutic targets for WM.
DOI: 10.6084/m9.figshare.7082501
title: dataset for Maza at al.

description: Data used to write the paper entitled "On the Drivers of UK Direct Investment in the Spanish Regions: A Spatial Durbin Approach"<br>
DOI: 10.6084/m9.figshare.7082279
title: MOESM6 of Cycles of gene expression and genome response during mammalian tissue regeneration

description: Additional file 6: Table S3. Complete list of GO terms associated with genes in Sets 1â 3.7 with the associated corrected p value.
DOI: 10.6084/m9.figshare.7082279.v1
title: MOESM6 of Cycles of gene expression and genome response during mammalian tissue regeneration

description: Additional file 6: Table S3. Complete list of GO terms associated with genes in Sets 1â 3.7 with the associated corrected p value.
DOI: 10.6084/m9.figshare.7082267
title: MOESM4 of Cycles of gene expression and genome response during mammalian tissue regeneration

description: Additional file 4: Table S2. List of genes in Set 3 with their associated classification in Sets 3.1 to 3.7 plus the averaged RPKMs per time point in log2 scale.
DOI: 10.6084/m9.figshare.7082267.v1
title: MOESM4 of Cycles of gene expression and genome response during mammalian tissue regeneration

description: Additional file 4: Table S2. List of genes in Set 3 with their associated classification in Sets 3.1 to 3.7 plus the averaged RPKMs per time point in log2 scale.
DOI: 10.6084/m9.figshare.7082264
title: MOESM3 of Cycles of gene expression and genome response during mammalian tissue regeneration

description: Additional file 3: Table S1. List of genes in Set 2.
DOI: 10.6084/m9.figshare.7082264.v1
title: MOESM3 of Cycles of gene expression and genome response during mammalian tissue regeneration

description: Additional file 3: Table S1. List of genes in Set 2.
DOI: 10.6084/m9.figshare.7082237
title: Additional file 2: of Molecular surveillance and phylogenetic traits of Babesia bigemina and Babesia bovis in cattle (Bos taurus) and water buffaloes (Bubalus bubalis) from Colombia

description: Nucleotide sequences derived from a hypothetical protein of Babesia bigemina. (FAS 1 kb)
DOI: 10.6084/m9.figshare.7082237.v1
title: Additional file 2: of Molecular surveillance and phylogenetic traits of Babesia bigemina and Babesia bovis in cattle (Bos taurus) and water buffaloes (Bubalus bubalis) from Colombia

description: Nucleotide sequences derived from a hypothetical protein of Babesia bigemina. (FAS 1 kb)
DOI: 10.6084/m9.figshare.7082204
title: Additional file 2: of Genomic insights into host adaptation between the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei)

description: Table SE1. Summary of transposable elements in Puccinia striiformis f. sp. tritici and P. striiformis f. sp. hordei genomes. Table SE2. Comparison of the annotated CAZyme genes among Puccinia striiformis f. sp. tritici (Pst), P. striiformis f. sp. hordei (Psh), Blumeria graminis f. sp. tritici (Bgt) and B. graminis f. sp. hordei (Bgh). Table SE3. Mating-related genes in Puccinia striiformis f. sp. tritici (Pst), P. striiformis f. sp. hordei (Psh), Blumeria graminis f. sp. tritici (Bgt) and B. graminis f. sp. hordei (Bgh). Table SE4. Comparison of the annotated peptidases genes among Puccinia striiformis f. sp. tritici (Pst), P. striiformis f. sp. hordei (Psh), Blumeria graminis f. sp. tritici (Bgt) and B. graminis f. sp. hordei (Bgh). Table SE5. Comparison of the annotated genes in isolate Pst (93–210) (Table SE5a) and Psh (93TX-2) (Table SE5b) using the Pathogen-Host-Interaction database. Table SE6. Summary of secondary-metabolite gene classes in 17 fungal plant pathogens. Table SE7. Comparison of the annotated transcription factor genes among nine fungal species or formae speciales. Table SE8. Comparison of the annotated transporter genes among Puccinia striiformis f. sp. hordei (Psh); P. striiformis f. sp. tritici (Psh); Blumeria graminis f. sp. hordei (Bgh) and B. graminis f. sp. tritici (Bgt). Table SE9. The list of fungal genomes and their resources used in this study. Table SE10. Summary of orthologues detected in 16 fungal plant pathogens using the OrthoFinder program. Table SE11. KEGG pathways annotated using GhostKOALA for Puccinia striiformis f. sp. tritici (Pst) and P. striiformis f. sp. hordei (Psh) isolates. Table SE11a. The numbers of conserved, specific and lost genes in Pst (93–210) and Psh (93TX-2); Table SE11b. Annotation of genes of KEGG pathways in Pst (93–210); and Table SE11c. Annotation of genes of KEGG pathways in Psh (93TX-2). Table SE12. List of exclusively expressed isolate-specific genes in isolates Pst (93–210) and Psh (93Tx-2) of Puccinia striiformis absent in the genome of the opposite isolate. Table SE13. List of exclusively expressed genes in isolates Pst (93–210) and Psh (93Tx-2) of Puccinia striiformis that are present in the genomes of both isolates. (ZIP 1140 kb)
DOI: 10.6084/m9.figshare.7082204.v1
title: Additional file 2: of Genomic insights into host adaptation between the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei)

description: Table SE1. Summary of transposable elements in Puccinia striiformis f. sp. tritici and P. striiformis f. sp. hordei genomes. Table SE2. Comparison of the annotated CAZyme genes among Puccinia striiformis f. sp. tritici (Pst), P. striiformis f. sp. hordei (Psh), Blumeria graminis f. sp. tritici (Bgt) and B. graminis f. sp. hordei (Bgh). Table SE3. Mating-related genes in Puccinia striiformis f. sp. tritici (Pst), P. striiformis f. sp. hordei (Psh), Blumeria graminis f. sp. tritici (Bgt) and B. graminis f. sp. hordei (Bgh). Table SE4. Comparison of the annotated peptidases genes among Puccinia striiformis f. sp. tritici (Pst), P. striiformis f. sp. hordei (Psh), Blumeria graminis f. sp. tritici (Bgt) and B. graminis f. sp. hordei (Bgh). Table SE5. Comparison of the annotated genes in isolate Pst (93–210) (Table SE5a) and Psh (93TX-2) (Table SE5b) using the Pathogen-Host-Interaction database. Table SE6. Summary of secondary-metabolite gene classes in 17 fungal plant pathogens. Table SE7. Comparison of the annotated transcription factor genes among nine fungal species or formae speciales. Table SE8. Comparison of the annotated transporter genes among Puccinia striiformis f. sp. hordei (Psh); P. striiformis f. sp. tritici (Psh); Blumeria graminis f. sp. hordei (Bgh) and B. graminis f. sp. tritici (Bgt). Table SE9. The list of fungal genomes and their resources used in this study. Table SE10. Summary of orthologues detected in 16 fungal plant pathogens using the OrthoFinder program. Table SE11. KEGG pathways annotated using GhostKOALA for Puccinia striiformis f. sp. tritici (Pst) and P. striiformis f. sp. hordei (Psh) isolates. Table SE11a. The numbers of conserved, specific and lost genes in Pst (93–210) and Psh (93TX-2); Table SE11b. Annotation of genes of KEGG pathways in Pst (93–210); and Table SE11c. Annotation of genes of KEGG pathways in Psh (93TX-2). Table SE12. List of exclusively expressed isolate-specific genes in isolates Pst (93–210) and Psh (93Tx-2) of Puccinia striiformis absent in the genome of the opposite isolate. Table SE13. List of exclusively expressed genes in isolates Pst (93–210) and Psh (93Tx-2) of Puccinia striiformis that are present in the genomes of both isolates. (ZIP 1140 kb)
DOI: 10.6084/m9.figshare.7082153
title: Additional file 4 of GeFaST: An improved method for OTU assignment by generalising Swarmâ s fastidious clustering approach

description: Tabular data showing results on the statistical significance of differences in clustering quality on the eldermet data set. (CSV 86 KB)
DOI: 10.6084/m9.figshare.7082153.v1
title: Additional file 4 of GeFaST: An improved method for OTU assignment by generalising Swarmâ s fastidious clustering approach

description: Tabular data showing results on the statistical significance of differences in clustering quality on the eldermet data set. (CSV 86 KB)