cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5198644.v1
title: A systematic review and combined analysis of therapeutic drug monitoring studies for long-acting risperidone

description: <b>Introduction</b>: This systematic review of therapeutic drug monitoring (TDM) identifies three long-acting injectable (LAI) risperidone formulations. <b>Areas covered</b>: Limited data is available on two formulations (RBP-7000 and <i>in Situ</i> Microparticle), but 20 TDM articles on the microsphere formulation were found. Risperidone TDM includes the serum concentrations of risperidone and its active metabolite, 9-hydroxyrisperidone, used for calculating: 1) the risperidone/9-hydroxyrisperidone (R/9-OH-R) ratio (a measure of CYP2D6; values &gt;1 are indicative of a CYP2D6 poor metabolizer) and 2) the total risperidone concentration-to-dose (C/D) ratio (a measure of risperidone clearance with a normal value around 7 in oral risperidone). The weighted mean R/9-OH-R ratio was 0.48 (approximately twice that of oral risperidone TDM) in a combined analysis from 329 patients in 6 risperidone LAI studies without major confounders. The total C/D ratios from 297 patients in 6 risperidone LAI studies ranged from 7.4 to 9.7 ng/ml/mg/day with a weighted mean of 8.8 ng/ml/mg/day. <b>Expert commentary</b>: Clinicians using TDM for risperidone LAI microsphere formulation need to: 1) consider steady state to be reached ≥ 6 weeks after the first injection, 2) pay attention to a) co-medications with inducers/inhibitors, b) severe inflammations/infections, and c) hepatic/renal impairment, and 3) use Castberg’s recommendation to calculate risperidone dosing.
DOI: 10.6084/m9.figshare.5198572
title: Prior preferences beneficially influence social and non-social learning

description: Data, stimuli, and full task and analysis code for Tarantola, Kumaran, Dayan, and De Martino. Prior preferences beneficially influence social and non-social learning. Nature Communications (2017).<br><br>The zip file contains the entire GitHub repository (minus the .git folder) for the version indicated in the file name. This version number matches the corresponding GitHub release tag.<br>
DOI: 10.6084/m9.figshare.5198566
title: 3D_Partitioning_Data.zip

description: This data includes the coarsened network data of Amsterdam that has been used for 3D partitioning study and processed speed data in three different formats - csv, mat and json. The processed speed data is aggregated from individual travel time data and gives the speed per link for consecutive time slices for 35 days. A readme is provided with the zip file for more information about the data.
DOI: 10.6084/m9.figshare.5198566.v1
title: 3D_Partitioning_Data.zip

description: This data includes the coarsened network data of Amsterdam that has been used for 3D partitioning study and processed speed data in three different formats - csv, mat and json. The processed speed data is aggregated from individual travel time data and gives the speed per link for consecutive time slices for 35 days. A readme is provided with the zip file for more information about the data.
DOI: 10.6084/m9.figshare.5198428
title: Optic flow during locomotion over rough terrain [Side-by-Side Video]

description: Optic flow during locomotion over rough terrain. <br>Left video pane shows flow in a head-centered reference frame. Right pane shows flow in a retinal reference frame.
DOI: 10.6084/m9.figshare.5198374
title: Supplementary Material for: DoriTool: A Bioinformatics Integrative Tool for Post-Association Functional Annotation

description: The emergence of high-throughput data in biology has increased the need for functional in silico analysis and prompted the development of integrative bioinformatics tools to facilitate the obtainment of biologically meaningful data. In this paper, we present DoriTool, a comprehensive, easy, and friendly pipeline integrating biological data from different functional tools. The tool was designed with the aim to maximize reproducibility and reduce the working time of the researchers, especially of those with limited bioinformatics skills, and to help them with the interpretation of the results. DoriTool is based upon an integrative strategy implemented following a modular design pattern. Using scripts written in Bash, Perl and R, it performs a functional in silico analysis annotation at mutation/variant level, gene level, pathway level and network level by combining up-to-date functional and genomic data and integrating also third-party bioinformatics tools in a pipeline. DoriTool uses GRCh37 human assembly and online mode. DoriTool provides nice visual reports including variant annotation, linkage disequilibrium proxies, gene annotation, gene ontology analysis, expression quantitative trait loci results from Genotype-Tissue Expression (GTEx) and coloured pathways. Here, we also show DoriTool functionalities by applying it to a dataset of 13 variants associated with prostate cancer. Project development, released code libraries, GitHub repository (https://github.com/doritool) and documentation are hosted at https://doritool.github.io/. DoriTool is, to our knowledge, the most complete bioinformatics tool offering functional in silico annotation of variants previously associated with a trait of interest, shedding light on the underlying biology and helping the researchers in the interpretation and discussion of the results.
DOI: 10.6084/m9.figshare.5198332
title: Supplementary Material for: Long-Term Progression of Coronary Artery Calcification Is Independent of Classical Risk Factors, C-Reactive Protein, and Parathyroid Hormone in Renal Transplant Patients

description: <b><i>Aims:</i></b> Compared to the general population, mortality is significantly increased in renal transplant recipients. In the general population, coronary artery calcification (CAC) and its evolution over time are associated with cardiovascular and all-cause mortality, and the study of this biomarker could provide useful information for describing the long-term progression of coronary heart disease in renal transplant recipients. <b><i>Methods:</i></b> We followed up a cohort of 113 renal transplant patients by performing three multi-detector computed tomography studies over 83.6 ± 6.8 months. Data analysis was performed by logistic regression analysis and by mixed linear modelling. <b><i>Results:</i></b> Progression was observed in 34.5% of patients. Baseline CAC and time-to-transplantation were the sole variables that predicted CAC evolution over time. Neither classical nor nontraditional risk factors, biomarkers of renal function (GFR) and kidney damage (albuminuria) or biomarkers of bone mineral disorder (BMD), such as serum phosphorus, calcium, and PTH, were associated with the long-term progression of coronary calcification. Serum triglycerides predicted CAC progression only in logistic regression analysis, while in addition to baseline CAC, time to transplantation was the sole variable predicting CAC progression when the data were analyzed by mixed linear modelling. These data suggested that, in addition to the background calcification burden, other unmeasured factors play major roles in promoting the evolution of coronary calcification in the transplant population. <b><i>Conclusion:</i></b> CAC progression continued over the long-term follow-up of renal transplant patients. This phenomenon was unaccounted for by classical and nontraditional risk factors, as well as by biomarkers of renal dysfunction and renal damage.
DOI: 10.6084/m9.figshare.5198374.v1
title: Supplementary Material for: DoriTool: A Bioinformatics Integrative Tool for Post-Association Functional Annotation

description: The emergence of high-throughput data in biology has increased the need for functional in silico analysis and prompted the development of integrative bioinformatics tools to facilitate the obtainment of biologically meaningful data. In this paper, we present DoriTool, a comprehensive, easy, and friendly pipeline integrating biological data from different functional tools. The tool was designed with the aim to maximize reproducibility and reduce the working time of the researchers, especially of those with limited bioinformatics skills, and to help them with the interpretation of the results. DoriTool is based upon an integrative strategy implemented following a modular design pattern. Using scripts written in Bash, Perl and R, it performs a functional in silico analysis annotation at mutation/variant level, gene level, pathway level and network level by combining up-to-date functional and genomic data and integrating also third-party bioinformatics tools in a pipeline. DoriTool uses GRCh37 human assembly and online mode. DoriTool provides nice visual reports including variant annotation, linkage disequilibrium proxies, gene annotation, gene ontology analysis, expression quantitative trait loci results from Genotype-Tissue Expression (GTEx) and coloured pathways. Here, we also show DoriTool functionalities by applying it to a dataset of 13 variants associated with prostate cancer. Project development, released code libraries, GitHub repository (https://github.com/doritool) and documentation are hosted at https://doritool.github.io/. DoriTool is, to our knowledge, the most complete bioinformatics tool offering functional in silico annotation of variants previously associated with a trait of interest, shedding light on the underlying biology and helping the researchers in the interpretation and discussion of the results.
DOI: 10.6084/m9.figshare.5198005
title: THPdb: Database of FDA Approved Peptide and Protein Therapeutics

description: THPdb is a manually curated database of Food and Drug Administration (FDA) approved therapeutic peptide and proteins. The text file contain all the data curated in THPdb.
DOI: 10.6084/m9.figshare.5198002
title: Biological responses of the marine diatom Chaetoceros socialis to changing environmental conditions: a laboratory experiment

description: The laboratory batch culture experiments on the marine diatom <i>Chaetoceros socialis</i> were performed at two temperatures (13°C and 18°C) and two pCO<sub>2</sub> corresponding to present-day (400 µatm) and near-future (800 µatm) conditions. During the growth stage of the experiments, various parameters were recorded: fluorescence, chlorophyll-a (Chl-a), cell number, nutrients (NO3, PO4 and DSi), dissolved Fe, biogenic silica (BSi), particulate organic carbon and nitrogen (POC/PN), pH, alkalinity, pCO<sub>2</sub>.
DOI: 10.6084/m9.figshare.5198002.v1
title: Biological responses of the marine diatom Chaetoceros socialis to changing environmental conditions: a laboratory experiment

description: The laboratory batch culture experiments on the marine diatom <i>Chaetoceros socialis</i> were performed at two temperatures (13°C and 18°C) and two pCO<sub>2</sub> corresponding to present-day (400 µatm) and near-future (800 µatm) conditions. During the growth stage of the experiments, various parameters were recorded: fluorescence, chlorophyll-a (Chl-a), cell number, nutrients (NO3, PO4 and DSi), dissolved Fe, biogenic silica (BSi), particulate organic carbon and nitrogen (POC/PN), pH, alkalinity, pCO<sub>2</sub>.
DOI: 10.6084/m9.figshare.5197879
title: PLOS ONE-CAD-VR Data

description: For CAD-VR Data Translation available for PLOS ONE Journal.
DOI: 10.6084/m9.figshare.5197867
title: Wing measures of 97 species of Drosophilidae (Diptera) photographed by Duda in 1924

description: The taxonomy of the Drosophilidae of New Guinea requires detailed knowledge of the fauna of neighbouring regions to the south (Australia), the east (islands of the South Pacific), the west (Indonesia) and the northwest (Philippines). The majority of species known from Indonesia were collected on Java and Sumatra by Jacobson in the period 1906–1929; he deposited all his specimens in Dutch museums and they are now at Naturalis in Leiden. De Meijere and Duda worked independently on this material in the first decades of the twentieth century and between them described most of it. Since then very little taxonomic research has focused on the drosophilid fauna of this part of the world. Duda (1924) published photographs of the wings of 103 fly species including 48 drosophilids from Southeast Asia (mainly Java and Sumatra). The venation, visible in each photo, has now been measured and tabulated here (Table 1). It is known that wing venation is variable between, but not significantly within, species and therefore provides a useful diagnostic tool. Diagnostic success is greatly enhanced when comparative analysis involves many metrics screened simultaneously. About seven standard wing indexes that describe ratios of vein lengths and sections (e.g., C, 4v, 4c, M, 5x, hb, prox.x, etc., see Table 2) are available for almost all drosophilids described since the 1950s. Standard measure-points or landmarks of the drosophilid wing are given by McEvey (2017). Datasets of wing indexes can be assembled from the literature. It is possible to interrogate such datasets with the measurements of an unknown taxon to produce a shortlist of one or several taxa that are possibly conspecific. The tables presented here list the wing indexes of all 103 species pictured by Duda (1924), many of them are given here for the first time. These metrics can be appended to available datasets greatly facilitating research on the largely undescribed drosophilid fauna of New Guinea.Table 1. Wing measures based on 104 fly wing photos published by Duda (1924, <i>Arch. Naturgesch</i>. 90(A3): 172–234). Heavy setation in the third costal section is not visible and could not be measured; in several instances dark wings obscured venation; Duda’s original 1924 figure captions are given as well as the currently valid name (Taxon); all photos are at the same scale <i>(Vergrößerung einheitlich)</i>, wing length (WL) in the <i>D. melanogaster</i> photo (Fig. 82) is, from other data, 1.63 mm and so magnification factor is 18 not 11 as stated by Duda. SEA = present in southeast Asia; * see Brake & Bächli (2008, Drosophilidae (Diptera). World Catalogue of Insects).Table 2. Key to abbreviations for wing measures and indexes used in Table 1; a vein or vein-section length is the distance between two measure-points or landmarks (see labelled diagrams of measure-points in McEvey, 2017). <br>
DOI: 10.6084/m9.figshare.5197924.v1
title: Master Chart_Updated Sept 1_ - Copy.xlsx

description: RCT of low dose MMF and CYC in LN in Nepal
DOI: 10.6084/m9.figshare.5197867.v1
title: Wing measures of 97 species of Drosophilidae (Diptera) photographed by Duda in 1924

description: The taxonomy of the Drosophilidae of New Guinea requires detailed knowledge of the fauna of neighbouring regions to the south (Australia), the east (islands of the South Pacific), the west (Indonesia) and the northwest (Philippines). The majority of species known from Indonesia were collected on Java and Sumatra by Jacobson in the period 1906–1929; he deposited all his specimens in Dutch museums and they are now at Naturalis in Leiden. De Meijere and Duda worked independently on this material in the first decades of the twentieth century and between them described most of it. Since then very little taxonomic research has focused on the drosophilid fauna of this part of the world. Duda (1924) published photographs of the wings of 103 fly species including 48 drosophilids from Southeast Asia (mainly Java and Sumatra). The venation, visible in each photo, has now been measured and tabulated here (Table 1). It is known that wing venation is variable between, but not significantly within, species and therefore provides a useful diagnostic tool. Diagnostic success is greatly enhanced when comparative analysis involves many metrics screened simultaneously. About seven standard wing indexes that describe ratios of vein lengths and sections (e.g., C, 4v, 4c, M, 5x, hb, prox.x, etc., see Table 2) are available for almost all drosophilids described since the 1950s. Standard measure-points or landmarks of the drosophilid wing are given by McEvey (2017). Datasets of wing indexes can be assembled from the literature. It is possible to interrogate such datasets with the measurements of an unknown taxon to produce a shortlist of one or several taxa that are possibly conspecific. The tables presented here list the wing indexes of all 103 species pictured by Duda (1924), many of them are given here for the first time. These metrics can be appended to available datasets greatly facilitating research on the largely undescribed drosophilid fauna of New Guinea.Table 1. Wing measures based on 104 fly wing photos published by Duda (1924, <i>Arch. Naturgesch</i>. 90(A3): 172–234). Heavy setation in the third costal section is not visible and could not be measured; in several instances dark wings obscured venation; Duda’s original 1924 figure captions are given as well as the currently valid name (Taxon); all photos are at the same scale <i>(Vergrößerung einheitlich)</i>, wing length (WL) in the <i>D. melanogaster</i> photo (Fig. 82) is, from other data, 1.63 mm and so magnification factor is 18 not 11 as stated by Duda. SEA = present in southeast Asia; * see Brake & Bächli (2008, Drosophilidae (Diptera). World Catalogue of Insects).Table 2. Key to abbreviations for wing measures and indexes used in Table 1; a vein or vein-section length is the distance between two measure-points or landmarks (see labelled diagrams of measure-points in McEvey, 2017). <br>
DOI: 10.6084/m9.figshare.5197879.v1
title: PLOS ONE-CAD-VR Data

description: For CAD-VR Data Translation available for PLOS ONE Journal.
DOI: 10.6084/m9.figshare.5197378
title: FigShare data.xlsx

description: Data associated with the Ecological Applications Paper "A pesticide paradox: Fungicides indirectly increase fungal infections" by Rohr et al. that was accepted on 7/11/2017
DOI: 10.6084/m9.figshare.5197387
title: Democratic funding

description: This is the de-identified data from our paper "Using democracy to award research funding: an observational study" published in "Research Integrity and Peer Review". DOI:10.1186/s41073-017-0040-0<br>
DOI: 10.6084/m9.figshare.5197378.v2
title: FigShare data.xlsx

description: Data associated with the Ecological Applications Paper "A pesticide paradox: Fungicides indirectly increase fungal infections" by Rohr et al. that was accepted on 7/11/2017
DOI: 10.6084/m9.figshare.5197378.v1
title: FigShare data.xlsx

description: Data associated with the Ecological Applications Paper "A pesticide paradox: Fungicides indirectly increase fungal infections" by Rohr et al. that was accepted on 7/11/2017
DOI: 10.6084/m9.figshare.5197327
title: Proteome analysis of irradiated endothelial cells reveals persistent alteration in protein degradation and the RhoGDI and NO signalling pathways

description: <b>Purpose:</b> Epidemiological studies indicate that radiation doses as low as 0.5 Gy increase the risk of cardiovascular disease decades after the exposure. The aim of the present study was to investigate whether this radiation dose causes late molecular alterations in endothelial cells that could support the population-based data. <b>Materials and methods:</b> Human coronary artery endothelial cells were irradiated at 0.5 Gy (X-ray) and radiation-induced changes in the proteome were investigated after different time intervals (1, 7 and 14 d) using ICPL technology. Key changes identified by proteomics and bioinformatics were validated by immunoblotting and ELISA. <b>Results:</b> The radiation-induced alteration of the endothelial proteome was characterized by sustained perturbation of Rho GDP-dissociation inhibitor (RhoGDI) and nitric oxide (NO) signalling pathways. At later time-points, this was accompanied by reduced proteasome activity, enhanced protein carbonylation indicating augmented oxidative stress, and senescence. <b>Conclusions:</b> These molecular changes are indicative of long-term premature endothelial dysfunction and provide a mechanistic framework to the epidemiological data showing increased risk of cardiovascular disease at 0.5 Gy. Watch the video on YouTube
DOI: 10.6084/m9.figshare.5197387.v1
title: Democratic funding

description: This is the de-identified data from our paper "Using democracy to award research funding: an observational study" published in "Research Integrity and Peer Review". DOI:10.1186/s41073-017-0040-0<br>
DOI: 10.6084/m9.figshare.5197327.v1
title: Proteome analysis of irradiated endothelial cells reveals persistent alteration in protein degradation and the RhoGDI and NO signalling pathways

description: <b>Purpose:</b> Epidemiological studies indicate that radiation doses as low as 0.5 Gy increase the risk of cardiovascular disease decades after the exposure. The aim of the present study was to investigate whether this radiation dose causes late molecular alterations in endothelial cells that could support the population-based data. <b>Materials and methods:</b> Human coronary artery endothelial cells were irradiated at 0.5 Gy (X-ray) and radiation-induced changes in the proteome were investigated after different time intervals (1, 7 and 14 d) using ICPL technology. Key changes identified by proteomics and bioinformatics were validated by immunoblotting and ELISA. <b>Results:</b> The radiation-induced alteration of the endothelial proteome was characterized by sustained perturbation of Rho GDP-dissociation inhibitor (RhoGDI) and nitric oxide (NO) signalling pathways. At later time-points, this was accompanied by reduced proteasome activity, enhanced protein carbonylation indicating augmented oxidative stress, and senescence. <b>Conclusions:</b> These molecular changes are indicative of long-term premature endothelial dysfunction and provide a mechanistic framework to the epidemiological data showing increased risk of cardiovascular disease at 0.5 Gy. Watch the video on YouTube
DOI: 10.6084/m9.figshare.5197306
title: DC resistance of silver prints

description: DC resistance of silver prints
DOI: 10.6084/m9.figshare.5197300
title: AC Impedance measurement at 1 MHz of Paste E at different particle loading

description: AC Impedance measurement at 1 MHz of Paste E at different particle loading
DOI: 10.6084/m9.figshare.5197303
title: Mechanical Testing DC resistance of carbon prints

description: Mechanical Testing DC resistance of carbon prints<br>
DOI: 10.6084/m9.figshare.5197306.v1
title: DC resistance of silver prints

description: DC resistance of silver prints
DOI: 10.6084/m9.figshare.5197297
title: The AC Impedance measurement at 1 MHz for Paste E structures cured at different temperature for 40 minutes

description: The AC Impedance measurement at 1 MHz for Paste E structures cured at different temperature for 40 minutes
DOI: 10.6084/m9.figshare.5197294
title: Phase measurement of GEM 2 paste at 95 °C

description: Phase measurement of GEM 2 paste at 95 °C
DOI: 10.6084/m9.figshare.5197300.v1
title: AC Impedance measurement at 1 MHz of Paste E at different particle loading

description: AC Impedance measurement at 1 MHz of Paste E at different particle loading
DOI: 10.6084/m9.figshare.5197303.v1
title: Mechanical Testing DC resistance of carbon prints

description: Mechanical Testing DC resistance of carbon prints<br>
DOI: 10.6084/m9.figshare.5197285
title: Phase measurement of Paste E during cure at 95 °C

description: Phase measurement of Paste E during cure at 95 °C
DOI: 10.6084/m9.figshare.5197291
title: Phase measurement of GEM 1 paste at 95 °C

description: Phase measurement of GEM 1 paste at 95 °C
DOI: 10.6084/m9.figshare.5197297.v1
title: The AC Impedance measurement at 1 MHz for Paste E structures cured at different temperature for 40 minutes

description: The AC Impedance measurement at 1 MHz for Paste E structures cured at different temperature for 40 minutes
DOI: 10.6084/m9.figshare.5197282
title: DC resistance and AC Impedance measurement of GEM 2 at 95 °C

description: DC resistance and AC Impedance measurement of GEM 2 at 95 °C
DOI: 10.6084/m9.figshare.5197285.v1
title: Phase measurement of Paste E during cure at 95 °C

description: Phase measurement of Paste E during cure at 95 °C
DOI: 10.6084/m9.figshare.5197294.v1
title: Phase measurement of GEM 2 paste at 95 °C

description: Phase measurement of GEM 2 paste at 95 °C