cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5752545
title: Additional file 2: Table S1. of Cribriform and intraductal prostate cancer are associated with increased genomic instability and distinct genomic alterations

description: Overview of genomic instability of individual chromosome arms in both TCGA and CPC-GENE datasets. Genomic instability was calculated based on a modified PGA formula (see methods). P-values are based on a Wilcon–Mann–Whitney test while log2FC represents the log2 ratio of the average PGA scores for CR/IDC positive samples and CR/IDC negative samples. PGA scores for deletions and amplifications were calculated and tested separately. (XLS 139 kb)
DOI: 10.6084/m9.figshare.5752545.v1
title: Additional file 2: Table S1. of Cribriform and intraductal prostate cancer are associated with increased genomic instability and distinct genomic alterations

description: Overview of genomic instability of individual chromosome arms in both TCGA and CPC-GENE datasets. Genomic instability was calculated based on a modified PGA formula (see methods). P-values are based on a Wilcon–Mann–Whitney test while log2FC represents the log2 ratio of the average PGA scores for CR/IDC positive samples and CR/IDC negative samples. PGA scores for deletions and amplifications were calculated and tested separately. (XLS 139 kb)
DOI: 10.6084/m9.figshare.5752452
title: Onshore-offshore trend in the evolution of calliotropid gastropods expressed in shell morphology

description: Two new species of calliotropid gastropods, <i>Calliotropis</i> (<i>Riselloidea</i>) <i>faustiankensis</i> sp. nov. and <i>Calliotropis</i> (<i>Riselloidea</i>) <i>lukovensis</i> sp. nov., are described from the Middle Jurassic (Middle Bathonian−Upper Callovian) of Poland. Additionally, new excellently preserved shells of <i>Calliotropis</i> (<i>Riselloidea</i>) <i>biarmata</i> (Münster) allow redefinition of this species. The new morphological information obtained from these three fossil species of <i>Calliotropis</i> in combination with the dataset assembled from 20 extinct and 24 living calliotropids is here summarized in quantitative multivariate and principal component analyses suggesting an onshore-offshore trend in calliotropid gastropod evolution from the Triassic to Recent times. This trend, which is expressed in the morphology of shells, shows that the Mesozoic species are mostly shallow water, while Cenozoic and Recent taxa are mostly deep water. The distinction supports earlier suggestions that the genus <i>Calliotropis</i> can be subdivided into two temporal subgenera belonging to the family Eucyclidae Koken. http://zoobank.org/urn:lsid:zoobank.org:pub:C8362FB8-966A-4322-95D5-7151CED20476
DOI: 10.6084/m9.figshare.5752452.v1
title: Onshore-offshore trend in the evolution of calliotropid gastropods expressed in shell morphology

description: Two new species of calliotropid gastropods, <i>Calliotropis</i> (<i>Riselloidea</i>) <i>faustiankensis</i> sp. nov. and <i>Calliotropis</i> (<i>Riselloidea</i>) <i>lukovensis</i> sp. nov., are described from the Middle Jurassic (Middle Bathonian−Upper Callovian) of Poland. Additionally, new excellently preserved shells of <i>Calliotropis</i> (<i>Riselloidea</i>) <i>biarmata</i> (Münster) allow redefinition of this species. The new morphological information obtained from these three fossil species of <i>Calliotropis</i> in combination with the dataset assembled from 20 extinct and 24 living calliotropids is here summarized in quantitative multivariate and principal component analyses suggesting an onshore-offshore trend in calliotropid gastropod evolution from the Triassic to Recent times. This trend, which is expressed in the morphology of shells, shows that the Mesozoic species are mostly shallow water, while Cenozoic and Recent taxa are mostly deep water. The distinction supports earlier suggestions that the genus <i>Calliotropis</i> can be subdivided into two temporal subgenera belonging to the family Eucyclidae Koken. http://zoobank.org/urn:lsid:zoobank.org:pub:C8362FB8-966A-4322-95D5-7151CED20476
DOI: 10.6084/m9.figshare.5752434
title: Data from: Do protected areas contribute to preserving traditional knowledge and gathering practices in cities?

description: Original dataset from: Cordero et al. Do protected areas contribute to preserving traditional knowledge and gathering practices in cities?
DOI: 10.6084/m9.figshare.5752434.v1
title: Data from: Do protected areas contribute to preserving traditional knowledge and gathering practices in cities?

description: Original dataset from: Cordero et al. Do protected areas contribute to preserving traditional knowledge and gathering practices in cities?
DOI: 10.6084/m9.figshare.5752413
title: Data from: Do protected areas contribute to preserving traditional knowledge and gathering practices in cities?

description: Original dataset from Cordero et al. Do protected areas contribute to preserving traditional knowledge and gathering practices in cities?
DOI: 10.6084/m9.figshare.5752410
title: A computational study of the impact of inhomogeneous internodal lengths on conduction velocity in myelinated neurons

description: Data for Figures 1 and 2. <br><br>The file fig1_data is generated using the McIntyre et al. model [McIntyre CC, Richardson AG, Grill WM. Modeling the excitability of mammalian nerve fibers: Influence of afterpotentials on the recovery cycle. J Neurophysiol. 2002;87(2):995–1006]. <br><br>The file fig2a_data is generated using the Gow and Devaux model [Gow A, Devaux J. A model of tight junction function in central nervous system myelinated axons. Neuron Glia Biol. 2008;4(4):307–317] with a g-ratio of 0.69. The file fig2b_data is generated using the Gow and Devaux model with a g-ratio of 0.86.<br>
DOI: 10.6084/m9.figshare.5752314
title: Transcatheter Aortic Valve Replacement after Transcatheter Mitral Valve Replacement

description: <b>Background:</b> Transcatheter mitral valve replacement (TMVR) in deteriorated prostheses, rings or mitral annular calcification are being performed more frequently. Inadvertently, we are starting to see patients who develop severe aortic stenosis following TMVR. Simultaneous transcatheter aortic valve replacement (TAVR)/TMVR has been previously reported, but almost all are performed in the order of TAVR first then followed by TMVR. <b>Methods:</b> We included three patients who underwent TAVR following TMVR. The patients subsequently presented with symptomatic aortic stenosis or insufficiency. All procedures were performed from September 2015 to July 2017. <b>Results:</b> All cases underwent successful TAVR after TMVR. There were several technical points. First, a balloon expandable valve was used for the initial case, but because of the interaction between the balloon and TMVR valve, we elected to use self-expandable valves for the subsequent cases. Secondly, it is critical to confirm that the wire is not traversing a cell of TMVR valve frame. This can be confirmed by fluoroscopy steered to steep left anterior oblique (LAO)/Cranial view to show that the wire is outside of any cells. Thirdly, when the space between the left ventricular outflow tract (LVOT) and the TMVR frame is narrow, there can be an interaction between the self-expanding valve nose-cone and TMVR valve which can bias the transcatheter valve towards the aorta. <b>Conclusion:</b> TAVR following TMVR poses several technical challenges. We highlight some of the obstacles encountered during the procedure, and offer potential solutions based on our experience. TAVR following previous TMVR can be safely performed with careful attention to wire position and proper valve selection.
DOI: 10.6084/m9.figshare.5752314.v2
title: Transcatheter Aortic Valve Replacement after Transcatheter Mitral Valve Replacement

description: <b>Background:</b> Transcatheter mitral valve replacement (TMVR) in deteriorated prostheses, rings or mitral annular calcification are being performed more frequently. Inadvertently, we are starting to see patients who develop severe aortic stenosis following TMVR. Simultaneous transcatheter aortic valve replacement (TAVR)/TMVR has been previously reported, but almost all are performed in the order of TAVR first then followed by TMVR. <b>Methods:</b> We included three patients who underwent TAVR following TMVR. The patients subsequently presented with symptomatic aortic stenosis or insufficiency. All procedures were performed from September 2015 to July 2017. <b>Results:</b> All cases underwent successful TAVR after TMVR. There were several technical points. First, a balloon expandable valve was used for the initial case, but because of the interaction between the balloon and TMVR valve, we elected to use self-expandable valves for the subsequent cases. Secondly, it is critical to confirm that the wire is not traversing a cell of TMVR valve frame. This can be confirmed by fluoroscopy steered to steep left anterior oblique (LAO)/Cranial view to show that the wire is outside of any cells. Thirdly, when the space between the left ventricular outflow tract (LVOT) and the TMVR frame is narrow, there can be an interaction between the self-expanding valve nose-cone and TMVR valve which can bias the transcatheter valve towards the aorta. <b>Conclusion:</b> TAVR following TMVR poses several technical challenges. We highlight some of the obstacles encountered during the procedure, and offer potential solutions based on our experience. TAVR following previous TMVR can be safely performed with careful attention to wire position and proper valve selection.
DOI: 10.6084/m9.figshare.5752314.v1
title: Cracking the Mitral Bioprosthesis in Valve-in-Valve Transcatheter Mitral Valve Replacement

description: <b>Background</b>: Transcatheter mitral valve replacement (TMVR) in deteriorated prostheses, rings or mitral annular calcification are being performed more frequently. Inadvertently, we are starting to see patients who develop severe aortic stenosis following TMVR. Simultaneous transcatheter aortic valve replacement (TAVR)/TMVR has been previously reported, but almost all are performed in the order of TAVR first then followed by TMVR. <b>Methods</b>: We included 3 patients who underwent TAVR following TMVR. Patients subsequently presented with symptomatic aortic stenosis or insufficiency. All procedures were performed from September 2015 to July 2017. <b>Results</b>: All cases underwent successful TAVR after TMVR. There were several technical points. First, balloon expandable valve was used for the initial case, but because of the interaction between the balloon and TMVR valve, we elected to use self-expandable valve for the subsequent cases. Secondly, it is critical to confirm that the wire is not traversing a cell of TMVR valve frame. This can be confirmed by fluoroscopy steered to steep LAO/Cranial view to show that the wire is outside of any cells. Thirdly, when the space between the LVOT and the TMVR frame is narrow, there can be an interaction between the self-expanding valve nose-cone and TMVR valve which can bias the transcatheter valve towards the aorta. <b>Conclusion</b>: TAVR following TMVR poses several technical challenges. We highlight some of the obstacles encountered during the procedure, and offer potential solutions based on our experience. TAVR following previous TMVR can be safely performed with careful attention to wire position and proper valve selection.
DOI: 10.6084/m9.figshare.5752218
title: Metadata

description: Data for Ward et al (2018) Limnology & Oceanography: Letters
DOI: 10.6084/m9.figshare.5752218.v1
title: Metadata

description: Data for Ward et al (2018) Limnology & Oceanography: Letters
DOI: 10.6084/m9.figshare.5752212
title: Combined pharmacophore, virtual screening and molecular dynamics studies to identify Bruton’s tyrosine kinase inhibitors

description: Bruton’s tyrosine Kinase (BTK) is a cytoplasmic, non-receptor tyrosine kinase expressed in hematopoietic cells. BTK plays a critical role in many cellular signalling pathways making it a potential target to treat autoimmune diseases and cancer. BTK signalling is important for the production of arthritis-associated antibodies, and inhibiting BTK will help the system to block the production of disease-associated antibodies. In this study, we have implemented ligand-based pharmacophore modelling and virtual screening against natural compounds followed by molecular docking, density functional theory and molecular dynamics studies for 50 ns. Four compounds with high affinity towards BTK were identified, and it could be used as a potent lead molecule for designing BTK inhibitor.
DOI: 10.6084/m9.figshare.5752212.v2
title: Combined pharmacophore, virtual screening and molecular dynamics studies to identify Bruton’s tyrosine kinase inhibitors

description: Bruton’s tyrosine Kinase (BTK) is a cytoplasmic, non-receptor tyrosine kinase expressed in hematopoietic cells. BTK plays a critical role in many cellular signalling pathways making it a potential target to treat autoimmune diseases and cancer. BTK signalling is important for the production of arthritis-associated antibodies, and inhibiting BTK will help the system to block the production of disease-associated antibodies. In this study, we have implemented ligand-based pharmacophore modelling and virtual screening against natural compounds followed by molecular docking, density functional theory and molecular dynamics studies for 50 ns. Four compounds with high affinity towards BTK were identified, and it could be used as a potent lead molecule for designing BTK inhibitor.
DOI: 10.6084/m9.figshare.5752080
title: SEEG initiative estimates of Brazilian greenhouse gas emissions: dataset from 1970 to 2015

description: This is a comprehensively dataset of Brazilian GHG emissions at national and sub-national levels for the period of 1970 to 2015 (SEEG database) for five sectors - Agriculture, Energy, Industrial Processes, Water, and Land Use. Based on the IPCC guidelines and the Brazilian National Inventory, SEEG was made by collecting raw data from multiple national official and nonofficial sources, and also organized with relevant social and economic indicators. Therefore, under simple queries, SEEG dataset allows users to search data by GHG emission sources and country activities.
DOI: 10.6084/m9.figshare.5752080.v1
title: SEEG initiative estimates of Brazilian greenhouse gas emissions: dataset from 1970 to 2015

description: This is a comprehensively dataset of Brazilian GHG emissions at national and sub-national levels for the period of 1970 to 2015 (SEEG database) for five sectors - Agriculture, Energy, Industrial Processes, Water, and Land Use. Based on the IPCC guidelines and the Brazilian National Inventory, SEEG was made by collecting raw data from multiple national official and nonofficial sources, and also organized with relevant social and economic indicators. Therefore, under simple queries, SEEG dataset allows users to search data by GHG emission sources and country activities.
DOI: 10.6084/m9.figshare.5748096
title: Coronary Artery Disease (CAD) MetaGRS

description: A genomic risk score for coronary artery disease, consisting of 1.7 million SNPs in hg19 coordinates.<br><br>Update Feb 5, 2018: one variant which was not a biallelic SNP (rs58575809) has been removed from the score.<br><br><b>References</b><b><br></b>- bioRxiv preprint: Inouye, Abraham, et al, "<b>Genomic risk prediction of coronary artery disease in nearly 500,000 adults: implications for early screening and primary prevention</b>", <i>bioRxiv</i> 2018, https://doi.org/10.1101/250712<br>- Accepted version: Inouye, Abraham, et al, "<b>Genomic Risk Prediction of CAD in Nearly 500,000 Adults: Early Screening and Primary Prevention</b>", <i>Journal of the American College of Cardiology</i>, 2018;72:1883-1893, https://doi.org/10.1016/j.jacc.2018.07.079<br> <br>
DOI: 10.6084/m9.figshare.5748096.v1
title: Coronary Artery Disease (CAD) MetaGRS

description: A genomic risk score for coronary artery disease, consisting of 1.7 million SNPs in hg19 coordinates.<br>
DOI: 10.6084/m9.figshare.5747319
title: stl file. New Bathonian (Middle Jurassic) sauropod remains from the Valtos Formation, Isle of Skye, Scotland

description: Surface models of the sauropod footprint from the Valtos Formation produced using Agisoft Photoscan software
DOI: 10.6084/m9.figshare.5747316
title: ply file. New Bathonian (Middle Jurassic) sauropod remains from the Valtos Formation, Isle of Skye, Scotland

description: Surface models of the sauropod footprint from the Valtos Formation produced using Agisoft Photoscan software
DOI: 10.6084/m9.figshare.5747313
title: obj file. New Bathonian (Middle Jurassic) sauropod remains from the Valtos Formation, Isle of Skye, Scotland

description: Surface models of the sauropod footprint from the Valtos Formation produced using Agisoft Photoscan software
DOI: 10.6084/m9.figshare.5747313.v1
title: obj file. New Bathonian (Middle Jurassic) sauropod remains from the Valtos Formation, Isle of Skye, Scotland

description: Surface models of the sauropod footprint from the Valtos Formation produced using Agisoft Photoscan software
DOI: 10.6084/m9.figshare.5747223
title: Budding yeast CENP-A<sup>Cse4</sup> interacts with the N-terminus of Sgo1 and regulates its association with centromeric chromatin

description: Shugoshin is an evolutionarily conserved protein, which is involved in tension sensing on mitotic chromosomes, kinetochore biorientation, and protection of centromeric (<i>CEN</i>) cohesin for faithful chromosome segregation. Interaction of the C-terminus of Sgo1 with phosphorylated histone H2A regulates its association with <i>CEN</i> and pericentromeric (peri-<i>CEN</i>) chromatin, whereas mutations in histone H3 selectively compromise the association of Sgo1 with peri-<i>CEN</i> but not <i>CEN</i> chromatin. Given that histone H3 is absent from <i>CEN</i> and is replaced by a histone H3 variant CENP-A<sup>Cse4</sup>, we investigated if CENP-A<sup>Cse4</sup> interacts with Sgo1 and promotes its association with the <i>CEN</i> chromatin. In this study, we found that Sgo1 interacts with CENP-A<sup>Cse4</sup> <i>in vivo</i> and <i>in vitro</i>. The N-terminus coiled-coil domain of Sgo1 without the C-terminus (<i>sgo1-NT</i>) is sufficient for its interaction with CENP-A<sup>Cse4</sup>, association with <i>CEN</i> but not the peri-<i>CEN</i>, and this <i>CEN</i> association is cell cycle dependent with maximum enrichment in mitosis. In agreement with the role of CENP-A<sup>Cse4</sup> in <i>CEN</i> maintenance of Sgo1, depletion of CENP-A<sup>Cse4</sup> results in the loss of Sgo1 and <i>sgo1-NT</i> from the <i>CEN</i> chromatin. The N-terminus of Sgo1 is required for genome stability as a mutant lacking the N-terminus (<i>sgo1-CT</i>) exhibits increased chromosome missegregation when compared to a <i>sgo1-NT</i> mutant. In summary, our results define a novel role for the N-terminus of Sgo1 in CENP-A<sup>Cse4</sup> mediated recruitment of Sgo1 to <i>CEN</i> chromatin for faithful chromosome segregation.
DOI: 10.6084/m9.figshare.5747223.v1
title: Budding yeast CENP-A<sup>Cse4</sup> interacts with the N-terminus of Sgo1 and regulates its association with centromeric chromatin

description: Shugoshin is an evolutionarily conserved protein, which is involved in tension sensing on mitotic chromosomes, kinetochore biorientation, and protection of centromeric (<i>CEN</i>) cohesin for faithful chromosome segregation. Interaction of the C-terminus of Sgo1 with phosphorylated histone H2A regulates its association with <i>CEN</i> and pericentromeric (peri-<i>CEN</i>) chromatin, whereas mutations in histone H3 selectively compromise the association of Sgo1 with peri-<i>CEN</i> but not <i>CEN</i> chromatin. Given that histone H3 is absent from <i>CEN</i> and is replaced by a histone H3 variant CENP-A<sup>Cse4</sup>, we investigated if CENP-A<sup>Cse4</sup> interacts with Sgo1 and promotes its association with the <i>CEN</i> chromatin. In this study, we found that Sgo1 interacts with CENP-A<sup>Cse4</sup> <i>in vivo</i> and <i>in vitro</i>. The N-terminus coiled-coil domain of Sgo1 without the C-terminus (<i>sgo1-NT</i>) is sufficient for its interaction with CENP-A<sup>Cse4</sup>, association with <i>CEN</i> but not the peri-<i>CEN</i>, and this <i>CEN</i> association is cell cycle dependent with maximum enrichment in mitosis. In agreement with the role of CENP-A<sup>Cse4</sup> in <i>CEN</i> maintenance of Sgo1, depletion of CENP-A<sup>Cse4</sup> results in the loss of Sgo1 and <i>sgo1-NT</i> from the <i>CEN</i> chromatin. The N-terminus of Sgo1 is required for genome stability as a mutant lacking the N-terminus (<i>sgo1-CT</i>) exhibits increased chromosome missegregation when compared to a <i>sgo1-NT</i> mutant. In summary, our results define a novel role for the N-terminus of Sgo1 in CENP-A<sup>Cse4</sup> mediated recruitment of Sgo1 to <i>CEN</i> chromatin for faithful chromosome segregation.
DOI: 10.6084/m9.figshare.5747118
title: Economic evaluation of paliperidone palmitate once monthly for treating chronic schizophrenia patients in the United Arab Emirates

description: <b>Objective:</b> Schizophrenia is one of the most debilitating diseases in the United Arab Emirates. Oral antipsychotics (OA) are commonly used in terms of pharmacotherapy; however, these treatments can be rendered ineffective by poor patient adherence. Paliperidone palmitate once monthly (PP1M) is a long acting antipsychotic which can offer an adherence advantage when compared to oral treatments. The study objective is to estimate the cost effectiveness of PP1M in the UAE setting. <b>Research design and methods:</b> A 1-year validated decision-tree model was adapted to the UAE setting using published literature and expert opinion. Patients on PP1M were compared with or without oral supplementation to patients on any oral antipsychotic. Patient outcomes studied were incremental cost per quality adjusted life years gained, incremental cost per hospitalizations, relapses, and emergency room visits averted. <b>Results:</b> After 1 year, patients on PP1M monotherapy when compared to oral antipsychotics had better outcomes (0.840 vs 0.811 QALYs; 31 relapse days averted as well as 9 and 24 percentage points of ER and hospitalizations averted, respectively), and better healthcare savings (AED 1405). PP1M economically dominated oral antipsychotics. The results were stable across a broad range of deterministic and probabilistic sensitivity analyses. PP1M plus oral antipsychotics could not be evaluated due to the absence of clinical data that would provide insight into the clinical value of combination therapy. <b>Conclusion:</b> PP1M is estimated to save the UAE healthcare system money, while at the same time improving patient outcomes.