cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3189262
title: Presentations from the inaugural Open Scholarship Initiative

description: Final presentations from OSI2016 work groups. <br>
DOI: 10.6084/m9.figshare.3189253
title: A new specimen of <i>Ichthyosaurus conybeari</i> (Reptilia, Ichthyosauria) from Watchet, Somerset, England, U.K., and a re-examination of the species

description: ABSTRACT—<i>Ichthyosaurus conybeari</i> is a rare species, previously known only from an incomplete holotype and one referred specimen, both from the Lyme Regis area of the west Dorset coast, U. K. A newly recognized, nearly complete specimen (NMW 93.5G.2) is the first occurrence of the species in Somerset, U. K. A revised diagnosis recognizes new morphological characters that distinguish the species: slender maxilla with a long, delicate premaxillary process; narrow postorbital; humerus with an anteriorly offset dorsal process that has a well-defined lip extending slightly into the shaft; fibula that is much larger dorsoventrally and mediodistally than tibia; and wide rectangular ischium that is much shorter than the pubis and femur. Notching of anterior fin elements in the forefin had been used as a diagnostic character, but a review of notching within <i>Ichthyosaurus</i> suggests that it has little taxonomic utility. Another specimen (NHMUK R15907), herein referred to the species, extends the range of <i>I. conybeari</i> from the upper Hettangian to lower Pliensbachian stages of the Lower Jurassic, the longest duration of any species of the genus. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Massare, J. A., and D. R. Lomax. 2016. A new specimen of <i>Ichthyosaurus conybeari</i> (Reptilia, Ichthyosauria) from Watchet, Somerset, England, U.K., and a reexamination of the species. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1163264.
DOI: 10.6084/m9.figshare.3189253.v1
title: A new specimen of <i>Ichthyosaurus conybeari</i> (Reptilia, Ichthyosauria) from Watchet, Somerset, England, U.K., and a re-examination of the species

description: ABSTRACT—<i>Ichthyosaurus conybeari</i> is a rare species, previously known only from an incomplete holotype and one referred specimen, both from the Lyme Regis area of the west Dorset coast, U. K. A newly recognized, nearly complete specimen (NMW 93.5G.2) is the first occurrence of the species in Somerset, U. K. A revised diagnosis recognizes new morphological characters that distinguish the species: slender maxilla with a long, delicate premaxillary process; narrow postorbital; humerus with an anteriorly offset dorsal process that has a well-defined lip extending slightly into the shaft; fibula that is much larger dorsoventrally and mediodistally than tibia; and wide rectangular ischium that is much shorter than the pubis and femur. Notching of anterior fin elements in the forefin had been used as a diagnostic character, but a review of notching within <i>Ichthyosaurus</i> suggests that it has little taxonomic utility. Another specimen (NHMUK R15907), herein referred to the species, extends the range of <i>I. conybeari</i> from the upper Hettangian to lower Pliensbachian stages of the Lower Jurassic, the longest duration of any species of the genus. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Massare, J. A., and D. R. Lomax. 2016. A new specimen of <i>Ichthyosaurus conybeari</i> (Reptilia, Ichthyosauria) from Watchet, Somerset, England, U.K., and a reexamination of the species. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1163264.
DOI: 10.6084/m9.figshare.3189262.v1
title: Presentations from the inaugural Open Scholarship Initiative

description: Final presentations from OSI2016 work groups. <br>
DOI: 10.6084/m9.figshare.3189238
title: Unraveling molecular effects of ADAR1 overexpression in HEK293T cells by label-free quantitative proteomics

description: ADAR1 is a double-stranded RNA (dsRNA) editing enzyme that specifically converts adenosine to inosine. ADAR1 is ubiquitously expressed in eukaryotes and participate in various cellular processes such as differentiation, proliferation and immune responses. We report here a new proteomics study of HEK293T cells with and without ADAR1 overexpression. The up- and down-regulated proteins by ADAR1 overexpression are identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) followed by label-free protein quantification. Totally 1,495 proteins (FDR &lt; 0.01) are identified, among which 211 are up- and 159 are down-regulated for at least 1.5-fold (n = 3, p &lt; 0.05). Gene ontology analysis reveals that these ADAR1-regulated proteins are involved in protein translation and cell cycle regulation. Bioinformatics analysis identifies a closely related network consistent for the protein translation machinery and a tightly connected network through proliferating cell nuclear antigen (PCNA)-interactions. Up-regulation of the proteins in the PCNA-mediated cell proliferation network is confirmed by Western blotting. In addition, ADAR1 overexpression is confirmed to increase cell proliferation in HEK293T cells and A549 cells. We conclude that ADAR1 overexpression modulates the protein translation and cell cycle networks through PCNA-mediated protein-protein interaction to promote cell proliferation in HEK293 cells.
DOI: 10.6084/m9.figshare.3189238.v2
title: Unraveling molecular effects of ADAR1 overexpression in HEK293T cells by label-free quantitative proteomics

description: ADAR1 is a double-stranded RNA (dsRNA) editing enzyme that specifically converts adenosine to inosine. ADAR1 is ubiquitously expressed in eukaryotes and participate in various cellular processes such as differentiation, proliferation and immune responses. We report here a new proteomics study of HEK293T cells with and without ADAR1 overexpression. The up- and down-regulated proteins by ADAR1 overexpression are identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) followed by label-free protein quantification. Totally 1,495 proteins (FDR &lt; 0.01) are identified, among which 211 are up- and 159 are down-regulated for at least 1.5-fold (n = 3, p &lt; 0.05). Gene ontology analysis reveals that these ADAR1-regulated proteins are involved in protein translation and cell cycle regulation. Bioinformatics analysis identifies a closely related network consistent for the protein translation machinery and a tightly connected network through proliferating cell nuclear antigen (PCNA)-interactions. Up-regulation of the proteins in the PCNA-mediated cell proliferation network is confirmed by Western blotting. In addition, ADAR1 overexpression is confirmed to increase cell proliferation in HEK293T cells and A549 cells. We conclude that ADAR1 overexpression modulates the protein translation and cell cycle networks through PCNA-mediated protein-protein interaction to promote cell proliferation in HEK293 cells.
DOI: 10.6084/m9.figshare.3189262.v2
title: Presentations from the inaugural Open Scholarship Initiative

description: Final presentations from OSI2016 work groups. <br>
DOI: 10.6084/m9.figshare.3189232
title: The metabolic microenvironment of melanomas: Prognostic value of MCT1 and MCT4

description: <i>BRAF</i> mutations are known drivers of melanoma development and, recently, were also described as players in the Warburg effect, while this reprogramming of energy metabolism has been identified as a possible strategy for treating melanoma patients. Therefore, the aim of this work was to evaluate the expression and prognostic value of a panel of glycolytic metabolism-related proteins in a series of melanomas. The immunohistochemical expression of MCT1, MCT4, GLUT1, and CAIX was evaluated in 356 patients presenting melanoma and 20 patients presenting benign nevi. Samples included 20 benign nevi, 282 primary melanomas, 117 lymph node and 54 distant metastases samples. <i>BRAF</i> mutation was observed in 29/92 (31.5%) melanoma patients and 17/20 (85%) benign nevi samples. <i>NRAS</i> mutation was observed in 4/36 (11.1%) melanoma patients and 1/19 (5.3%) benign nevi samples. MCT4 and GLUT1 expression was significantly increased in metastatic samples, and MCT1, MCT4 and GLUT1 were significantly associated with poor prognostic variables. Importantly, MCT1 and MCT4 were associated with shorter overall survival. In conclusion, the present study brings new insights on metabolic aspects of melanoma, paving the way for the development of new-targeted therapies.
DOI: 10.6084/m9.figshare.3189238.v1
title: Unraveling molecular effects of ADAR1 overexpression in HEK294T cells by label-free quantitative proteomics

description: ADAR1 is a double-stranded RNA (dsRNA) editing enzyme that specifically converts adenosine to inosine. ADAR1 is ubiquitously expressed in eukaryotes and participate in various cellular processes such as differentiation, proliferation and immune responses. We report here a new proteomics study of HEK293T cells with and without ADAR1 overexpression. The up- and down-regulated proteins by ADAR1 overexpression are identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) followed by label-free protein quantification. Totally 1,495 proteins (FDR&lt;0.01) are identified, among which 211 are up- and 159 are down-regulated for at least 1.5-fold (n=3, p&lt;0.05). Gene ontology analysis reveals that these ADAR1-regulated proteins are involved in protein translation and cell cycle regulation. Bioinformatics analysis identifies a closely related network consistent for the protein translation machinery and a tightly connected network through proliferating cell nuclear antigen (PCNA)-interactions. Up-regulation of the proteins in the PCNA-mediated cell proliferation network is confirmed by Western blotting. In addition, ADAR1 overexpression is confirmed to increase cell proliferation in HEK293T cells and A549 cells. We conclude that ADAR1 overexpression modulates the protein translation and cell cycle networks through PCNA-mediated protein-protein interaction to promote cell proliferation in HEK293 cells.
DOI: 10.6084/m9.figshare.3189199
title: NUTS2-level population scenarios for SSPs: Hungary

description: Population for six agegroups and five SSPs. Population in thousands.
DOI: 10.6084/m9.figshare.3189232.v2
title: The metabolic microenvironment of melanomas: Prognostic value of MCT1 and MCT4

description: <i>BRAF</i> mutations are known drivers of melanoma development and, recently, were also described as players in the Warburg effect, while this reprogramming of energy metabolism has been identified as a possible strategy for treating melanoma patients. Therefore, the aim of this work was to evaluate the expression and prognostic value of a panel of glycolytic metabolism-related proteins in a series of melanomas. The immunohistochemical expression of MCT1, MCT4, GLUT1, and CAIX was evaluated in 356 patients presenting melanoma and 20 patients presenting benign nevi. Samples included 20 benign nevi, 282 primary melanomas, 117 lymph node and 54 distant metastases samples. <i>BRAF</i> mutation was observed in 29/92 (31.5%) melanoma patients and 17/20 (85%) benign nevi samples. <i>NRAS</i> mutation was observed in 4/36 (11.1%) melanoma patients and 1/19 (5.3%) benign nevi samples. MCT4 and GLUT1 expression was significantly increased in metastatic samples, and MCT1, MCT4 and GLUT1 were significantly associated with poor prognostic variables. Importantly, MCT1 and MCT4 were associated with shorter overall survival. In conclusion, the present study brings new insights on metabolic aspects of melanoma, paving the way for the development of new-targeted therapies.
DOI: 10.6084/m9.figshare.3189199.v1
title: NUTS2-level population scenarios for SSPs: Hungary

description: Population for six agegroups and five SSPs. Population in thousands.
DOI: 10.6084/m9.figshare.3189232.v1
title: The metabolic microenvironment of melanomas: prognostic value of MCT1 and MCT4

description: <i>BRAF</i> mutations are know drivers of melanoma development and, recently, were also described as players in the Warburg effect, while this reprogramming of energy metabolism has been identified as a possible strategy for treating melanoma patients. Therefore, the aim of this work was to evaluate the expression and prognostic value of a panel of glycolytic metabolism-related proteins in a series of melanomas. The immunohistochemical expression of MCT1, MCT4, GLUT1, and CAIX was evaluated in 356 patients presenting melanoma and 20 patients presenting benign nevi. Samples included 20 benign nevi, 282 primary melanomas, 117 lymph node and 54 distant metastases samples. <i>BRAF</i> mutation was observed in 29/92 (31.5%) melanoma patients and 17/20 (85%) benign nevi samples. <i>NRAS</i> mutation was observed in 4/36 (11.1%) melanoma patients and 1/19 (5.3%) benign nevi samples. MCT4 and GLUT1 expression was significantly increased in metastatic samples, and MCT1, MCT4 and GLUT1 were significantly associated with poor prognostic variables. Importantly, MCT1 and MCT4 were associated with shorter overall survival. In conclusion, the present study brings new insights on metabolic aspects of melanoma, paving the way for the development of new-targeted therapies.
DOI: 10.6084/m9.figshare.3189262.v3
title: Presentations from the inaugural Open Scholarship Initiative

description: Final presentations from OSI2016 work groups. <br>
DOI: 10.6084/m9.figshare.3189130
title: The schedule of the graduation thesis

description: The schedule of the graduation thesis
DOI: 10.6084/m9.figshare.3189130.v1
title: The schedule of the graduation thesis

description: The schedule of the graduation thesis
DOI: 10.6084/m9.figshare.3189004
title: A bootstrap test for constant coefficients in geographically weighted regression models

description: Statistical tests for whether some coefficients really vary over space play an important role in using the geographically weighted regression (GWR) to explore spatial non-stationarity of the regression relationship. In view of some shortcomings of the existing inferential methods, we propose a residual-based bootstrap test to detect the constant coefficients in a GWR model. The proposed test is free of the assumption that the model error term is normally distributed and admits some useful extensions for identifying more complicated spatial patterns of the coefficients. Some simulation with comparison to the existing test methods is conducted to assess the test performance, including the accuracy of the bootstrap approximation to the null distribution of the test statistic, the power in identifying spatially varying coefficients and the robustness to collinearity among the explanatory variables. The simulation results demonstrate that the bootstrap test works quite well. Furthermore, a real-world data set is analyzed to illustrate the application of the proposed test.
DOI: 10.6084/m9.figshare.3189262.v4
title: Presentations from the inaugural Open Scholarship Initiative

description: Final presentations from OSI2016 work groups. <br>
DOI: 10.6084/m9.figshare.3188995
title: An efficient method for measuring the similarity of protein sequences

description: An accurate numerical descriptor for protein sequence is introduced. It is basically a set of each three successive amino acids in the sequence (triplet), starting from left to right, in addition to the distances between each two successive amino acids in the triplet such that the summation of these distances does not exceed 8. This numerical descriptor combines two features the amino acid composition and the position of each amino acid relative to the other nearby amino acids. This numerical descriptor is used to measure the similarity between protein sequences in three sets: NADH dehydrogenase subunit 5 (ND5) proteins of different species, 24 transferrin proteins from vertebrates and 12 proteins of baculoviruses. High correlation coefficient values between our results and the results of ClustalW program are obtained. These values are higher than the values obtained in many other related works.
DOI: 10.6084/m9.figshare.3189004.v1
title: A bootstrap test for constant coefficients in geographically weighted regression models

description: Statistical tests for whether some coefficients really vary over space play an important role in using the geographically weighted regression (GWR) to explore spatial non-stationarity of the regression relationship. In view of some shortcomings of the existing inferential methods, we propose a residual-based bootstrap test to detect the constant coefficients in a GWR model. The proposed test is free of the assumption that the model error term is normally distributed and admits some useful extensions for identifying more complicated spatial patterns of the coefficients. Some simulation with comparison to the existing test methods is conducted to assess the test performance, including the accuracy of the bootstrap approximation to the null distribution of the test statistic, the power in identifying spatially varying coefficients and the robustness to collinearity among the explanatory variables. The simulation results demonstrate that the bootstrap test works quite well. Furthermore, a real-world data set is analyzed to illustrate the application of the proposed test.
DOI: 10.6084/m9.figshare.3189262.v6
title: Presentations from the inaugural Open Scholarship Initiative

description: Final presentations from OSI2016 work groups. <br>
DOI: 10.6084/m9.figshare.3189262.v5
title: Presentations from the inaugural Open Scholarship Initiative

description: Final presentations from OSI2016 work groups. <br>
DOI: 10.6084/m9.figshare.3188995.v2
title: An efficient method for measuring the similarity of protein sequences

description: An accurate numerical descriptor for protein sequence is introduced. It is basically a set of each three successive amino acids in the sequence (triplet), starting from left to right, in addition to the distances between each two successive amino acids in the triplet such that the summation of these distances does not exceed 8. This numerical descriptor combines two features the amino acid composition and the position of each amino acid relative to the other nearby amino acids. This numerical descriptor is used to measure the similarity between protein sequences in three sets: NADH dehydrogenase subunit 5 (ND5) proteins of different species, 24 transferrin proteins from vertebrates and 12 proteins of baculoviruses. High correlation coefficient values between our results and the results of ClustalW program are obtained. These values are higher than the values obtained in many other related works.
DOI: 10.6084/m9.figshare.3188995.v1
title: An efficient method for measuring the similarity of protein sequences

description: An accurate numerical descriptor for protein sequence is introduced. It is basically a set of each three successive amino acids in the sequence (triplet), starting from left to right, in addition to the distances between each two successive amino acids in the triplet such that the summation of these distances does not exceed 8. This numerical descriptor combines two features the amino acid composition and the position of each amino acid relative to the other nearby amino acids. This numerical descriptor is used to measure the similarity between protein sequences in three sets: NADH dehydrogenase subunit 5 (ND5) proteins of different species, 24 transferrin proteins from vertebrates and 12 proteins of baculoviruses. High correlation coefficient values between our results and the results of ClustalW program are obtained. These values are higher than the values obtained in many other related works.
DOI: 10.6084/m9.figshare.3188923
title: Data Sharing on PLOS ONE publication "Graph theoretical analysis of structural neuroimaging in temporal lobe epilepsy with and without psychosis"

description: Data Sharing on PLOS ONE publication "Graph theoretical analysis of structural neuroimaging in temporal lobe epilepsy with and without psychosis"
DOI: 10.6084/m9.figshare.3188878
title: Drivers.xlsx

description: Summary of Literature Review on historical drivers of trade.
DOI: 10.6084/m9.figshare.3188869
title: Albumin and apolipoprotein H mRNAs in human plasma as potential clinical biomarkers of liver injury: analyses of plasma liver-specific mRNAs in patients with liver injury

description: <i>Context</i>: Plasma liver-specific mRNAs are useful biomarkers of hepatotoxicity in rats. <i>Objective</i>: To investigate the potential application of liver-specific mRNAs as biomarkers for liver injury in humans. <i>Methods</i>: We determined the plasma levels of liver-specific mRNAs by real-time qRT-PCR in healthy donors and patients with liver injury. <i>Results</i>: Plasma levels of albumin (ALB) and apolipoprotein H (APOH) mRNAs increased in patients with elevated serum alanine aminotransferase. These mRNAs also increased in plasma after transcatheter arterial chemoembolization, which induces specific injury to liver. <i>Conclusions</i>: We demonstrated the potential application of plasma ALB and APOH mRNAs as clinical biomarkers for liver injury.
DOI: 10.6084/m9.figshare.3188872
title: Number of Days Required to Estimate Habitual Activity using wrist-worn GENEActiv Accelerometer: A Cross-Sectional Study.

description: The data-set uploaded is a subset of data (data only on those with accelerometer information) from the Mitchelstown cohort, Ireland. The data-set is in long format, sorted by participant ID and day of the week. For some of the analysis this format had to be changed to wide through STATA's collapse command. This is data from Phase 1 of the Mitchelstown cohort. The link below is to the next Phase of the study and provides the necessary contact details for information on the study.<br>
DOI: 10.6084/m9.figshare.3188923.v2
title: Data Sharing on PLOS ONE publication "Graph theoretical analysis of structural neuroimaging in temporal lobe epilepsy with and without psychosis"

description: Data Sharing on PLOS ONE publication "Graph theoretical analysis of structural neuroimaging in temporal lobe epilepsy with and without psychosis"
DOI: 10.6084/m9.figshare.3188923.v1
title: PLOS_ONE.zip

description: Data Sharing on PLOS ONE publication "Graph theoretical analysis of structural neuroimaging in temporal lobe epilepsy with and without psychosis"
DOI: 10.6084/m9.figshare.3188869.v1
title: Albumin and apolipoprotein H mRNAs in human plasma as potential clinical biomarkers of liver injury: analyses of plasma liver-specific mRNAs in patients with liver injury

description: <i>Context</i>: Plasma liver-specific mRNAs are useful biomarkers of hepatotoxicity in rats. <i>Objective</i>: To investigate the potential application of liver-specific mRNAs as biomarkers for liver injury in humans. <i>Methods</i>: We determined the plasma levels of liver-specific mRNAs by real-time qRT-PCR in healthy donors and patients with liver injury. <i>Results</i>: Plasma levels of albumin (ALB) and apolipoprotein H (APOH) mRNAs increased in patients with elevated serum alanine aminotransferase. These mRNAs also increased in plasma after transcatheter arterial chemoembolization, which induces specific injury to liver. <i>Conclusions</i>: We demonstrated the potential application of plasma ALB and APOH mRNAs as clinical biomarkers for liver injury.
DOI: 10.6084/m9.figshare.3188878.v1
title: Drivers.xlsx

description: Summary of Literature Review on historical drivers of trade.
DOI: 10.6084/m9.figshare.3188830
title: Mole-rat FEA

description: Files for finite element analysis of two mole-rat species: Bathyergus suillis and Fukomys mechowi. Included in this dataset are: 3D reconstructions of the skull (made in Avizo); FE model files and project files for use in VOX-FE; resulting displacement files also from VOX-FE.
DOI: 10.6084/m9.figshare.3188824
title: MODEL A QUEST SPANISH

description: MODEL A QUEST SPANISH
DOI: 10.6084/m9.figshare.3188818
title: MODEL B QUEST SPANISH

description: MODEL B QUEST SPANISH
DOI: 10.6084/m9.figshare.3188824.v1
title: MODEL A QUEST SPANISH

description: MODEL A QUEST SPANISH