cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4635874
title: Temporal and spatial comparisons of the reproductive biology of northern Gulf of Mexico (USA) red snapper (Lutjanus campechanus) collected a decade apart

description: <b>S1 File. Sampling dataset.</b><b>S2 File. Histology dataset.</b><b>S3 File. Gonadosomatic index (GSI) dataset.</b><b>S4 File. Maturity and spawning frequency (SF) dataset.</b><b>S5 File. Batch fecundity (BF) dataset.</b><b>S6 File. Annual fecundity (AF) dataset.</b><b>S7 File. Age composition estimates for Gulf red snapper. </b>Estimates provided by NOAA [16].<b>S8 File. Index of reproductive importance (IRI) dataset.</b>
DOI: 10.6084/m9.figshare.4635898.v1
title: tablasarticulosignoypensamiento (1).pdf

description: En estas tablas se recogen los datos sociodemográficos de la muestra participante.
DOI: 10.6084/m9.figshare.4639789.v1
title: MAPPIN: Method for Annotating, Predicting Pathogenicity, and mode of Inheritance for Nonsynonymous variants

description: This directory includes software, readme files for installation and usage, associated data files for running MAPPIN, and prediction scores for all nsSNVs. The annotate.mappin.tar.gz tarball includes all the scripts and associated data files needed to annotate missense variants. The predict.mappin.tar.gz includes all the scripts and data files need to run predictions on the annotated missense variants file. The mappin_training_data_cross-validation tarball has the training datasets and other files, which can be run for training and cross-validation using the associated R script. The hg19.mappin.prediction.scores.tar.gz file has MAPPIN prediction scores (dominant, recessive, benign) for all possible nsSNVs in the genome. The hg38.mappin.prediction.scores.tar.gz file has MAPPIN prediction scores lifted over to hg38.<br>Note: Although the license states CC BY, MAPPIN software can be used and modified freely for <b>non-commercial</b> purposes only. This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
DOI: 10.6084/m9.figshare.4635874.v2
title: Temporal and spatial comparisons of the reproductive biology of northern Gulf of Mexico (USA) red snapper (Lutjanus campechanus) collected a decade apart

description: <b>S1 File. Sampling dataset.</b><b>S2 File. Histology dataset.</b><b>S3 File. Gonadosomatic index (GSI) dataset.</b><b>S4 File. Maturity and spawning frequency (SF) dataset.</b><b>S5 File. Batch fecundity (BF) dataset.</b><b>S6 File. Annual fecundity (AF) dataset.</b><b>S7 File. Age composition estimates for Gulf red snapper. </b>Estimates provided by NOAA [16].<b>S8 File. Index of reproductive importance (IRI) dataset.</b>
DOI: 10.6084/m9.figshare.4635874.v1
title: Dataset Files

description: <b>S1 File. Sampling dataset.</b><b>S2 File. Histology dataset.</b><b>S3 File. Gonadosomatic index (GSI) dataset.</b><b>S4 File. Maturity and spawning frequency (SF) dataset.</b><b>S5 File. Batch fecundity (BF) dataset.</b><b>S6 File. Annual fecundity (AF) dataset.</b><b>S7 File. Age composition estimates for Gulf red snapper. </b>Estimates provided by NOAA [16].<b>S8 File. Index of reproductive importance (IRI) dataset.</b>
DOI: 10.6084/m9.figshare.4635670
title: MCAO ECA damage

description: Contain all raw data of the Manuscript "Extracerebral tissue damage in the intraluminal filament mouse model of middle cerebral artery occlusion" published in the Journal of Frontiers in Neurology. DOI: 10.3389/fneur.2017.00085<br><br><br>
DOI: 10.6084/m9.figshare.4635619
title: PowerPoint Slides for: Prognostic Value of the Delivery Dialysis Dose on Twice-Weekly Hemodialysis Patients

description: <b><i>Background:</i></b> Few studies have evaluated the prognostic value of dialysis dose in twice-weekly hemodialysis (HD). A single-pool Kt/V (spKt/V) over 1.70 may benefit patients receiving twice-weekly maintenance HD. <b><i>Methods:</i></b> This is a multicenter randomized controlled trial performed on 163 patients from 17 dialysis centers in Shanghai who were allocated to high- (<i>n</i> = 98) and standard-dose groups (<i>n</i> = 65) and followed through 96 weeks of study period. Therapeutic approaches were given to increase spKt/V to over 1.70 in the high-dose group. Data were collected every 12-24 weeks. The primary outcomes were all-cause mortality and major adverse cardio-cerebrovascular events (MACEs) occurrence, and secondary outcomes included residual kidney function (RKF) and health-related quality of life (HR-QOL). <b><i>Results:</i></b> The spKt/V in high-dose and standard-dose groups were 1.80 ± 0.23 and 1.55 ± 0.19, respectively, after an 8-week intervention (<i>p</i> &lt; 0.001). At the end of the study, SF-36 physical function and total score in high-dose group were 82 (69-90) and 74 (47-84), respectively, both of which were higher than those in the standard-dose group. Decline in urine volume was observed in both groups with no significant difference (<i>p</i> = 0.431). No difference was found in overall survival between the 2 groups (<i>p</i> = 0.580). The 1-year MACE-free survival for high-dose group was 84.49%, better than 76.72% for standard-dose group (<i>p</i> = 0.029). <b><i>Conclusions:</i></b> Higher spKt/V is also associated with MACE-free survival and better HR-QOL, especially in physical function aspect for twice-weekly dialysis patients. Increasing spKt/V over 1.70 in twice-weekly HD population does not cause loss of RKF.
DOI: 10.6084/m9.figshare.4635619.v1
title: PowerPoint Slides for: Prognostic Value of the Delivery Dialysis Dose on Twice-Weekly Hemodialysis Patients

description: <b><i>Background:</i></b> Few studies have evaluated the prognostic value of dialysis dose in twice-weekly hemodialysis (HD). A single-pool Kt/V (spKt/V) over 1.70 may benefit patients receiving twice-weekly maintenance HD. <b><i>Methods:</i></b> This is a multicenter randomized controlled trial performed on 163 patients from 17 dialysis centers in Shanghai who were allocated to high- (<i>n</i> = 98) and standard-dose groups (<i>n</i> = 65) and followed through 96 weeks of study period. Therapeutic approaches were given to increase spKt/V to over 1.70 in the high-dose group. Data were collected every 12-24 weeks. The primary outcomes were all-cause mortality and major adverse cardio-cerebrovascular events (MACEs) occurrence, and secondary outcomes included residual kidney function (RKF) and health-related quality of life (HR-QOL). <b><i>Results:</i></b> The spKt/V in high-dose and standard-dose groups were 1.80 ± 0.23 and 1.55 ± 0.19, respectively, after an 8-week intervention (<i>p</i> &lt; 0.001). At the end of the study, SF-36 physical function and total score in high-dose group were 82 (69-90) and 74 (47-84), respectively, both of which were higher than those in the standard-dose group. Decline in urine volume was observed in both groups with no significant difference (<i>p</i> = 0.431). No difference was found in overall survival between the 2 groups (<i>p</i> = 0.580). The 1-year MACE-free survival for high-dose group was 84.49%, better than 76.72% for standard-dose group (<i>p</i> = 0.029). <b><i>Conclusions:</i></b> Higher spKt/V is also associated with MACE-free survival and better HR-QOL, especially in physical function aspect for twice-weekly dialysis patients. Increasing spKt/V over 1.70 in twice-weekly HD population does not cause loss of RKF.
DOI: 10.6084/m9.figshare.4635670.v2
title: MCAO ECA damage

description: Contain all raw data of the Manuscript "Extracerebral tissue damage in the intraluminal filament mouse model of middle cerebral artery occlusion" published in the Journal of Frontiers in Neurology. DOI: 10.3389/fneur.2017.00085<br><br><br>
DOI: 10.6084/m9.figshare.4635670.v1
title: MCAO ECA damage

description: Contain all raw data of the Manuscript "Extracerebral tissue damage in the intraluminal filament mouse model of middle cerebral artery occlusion" published in the Journal of Frontiers in Neurology<br><br>data available after final approvel!<br>
DOI: 10.6084/m9.figshare.4635415
title: Materials from a Workshop on Research Software Management, Sharing and Sustainability held on 20th January 2017

description: A Workshop on Research Software Management, Sharing and Sustainability was held on 20th January 2017 at Engine Shed, Bristol; hosted by Prof. James Davenport (University of Bath, Software Sustainability Institute Fellow) as part of a national series of workshops funded by Jisc. This record holds material from the workshop, including: Workshop Agenda; Slides for a keynote talk from Catherine Jones: "Why is persistently identifying your research software a Good Idea?"*; Slides for a talk from Christopher Woods: "Lessons from Publishing Sire"; Slides for a talk from James Davenport: "Software Management Plans"; Transcripts of feedback from discussion groups facilitated by Zosia Beckles, James Davenport, Catherine Jones and Christopher Woods, transcribed by Richard Evans; Notes on the workshop from James Davenport; Notes on the workshop from Miquel Perello-Nieto.<br>*these slides are not included in this record but are available at: http://purl.org/net/epubs/work/31225221
DOI: 10.6084/m9.figshare.4635310
title: Data: Age- and environment-dependent changes in chemical defences of larval and post-metamorphic toads

description: We used high-performance liquid chromatography with diode-array detection and mass spectrometry (HPLC-DAD-MS) to identify and quantify bufadienolide compounds. We homogenized specimens of the common toad <i>(Bufo bufo)</i> using a VWR VDI 12 homogenizer with an IKA S12N-7S dispersing tool. After drying samples <i>in vacuo</i> at 45 °C using a Büchi Rotavapor R-134 rotary evaporator, we measured dry weight of samples using an Ohaus Pioneer PA-114 analytical balance to the nearest 0.1 mg and subsequently re-dissolved samples in 1 ml HPLC-grade absolute methanol, which was further aided by exposing the samples briefly to ultrasound in a Tesla UC005AJ1 bath sonicator. We filtered the samples using FilterBio nylon syringe filters (pore size = 0.22 μm). We identified compounds as bufadienolides by inspecting the UV spectrum of peaks (Hagman et al. 2009, Hayes et al. 2009, Bókony et al. 2016) and by using commercially acquired bufalin, bufotalin, resibufogenin, gamabufotalin, areno- and telocinobufagin (Biopurify Phytochemicals, Chengdu, China), cinobufagin (Chembest, Shanghai, China), cinobufotalin (Quality Phytochemicals, New Jersey, USA) and digitoxigenin (Santa Cruz Biotechnology, Dallas, TX, USA) as standards. Identification of compounds present in low quantities was further aided by the analysis of a sample obtained from an adult male common toad by gently massaging the parotoid glands. <br>A single-quadrupole HPLC-MS system (Model: LC-MS-2020, Shimadzu, Kyoto, Japan) equipped with a binary gradient solvent pump, a vacuum degasser, a thermostated autosampler, a column oven, a diode array detector and a mass analyser with electrospray ionization (ESI-MS) was used. Chromatographic separations were carried out at 35 °C on a Kinetex C18 2.6 µm column (100 mm x 3 mm i.d.) in series with a C18 guard column (4 mm × 3 mm i.d.) using 10 µL injections. The mobile phase consisted of water containing 0.05% formic acid (solvent A) and acetonitrile containing 0.05% formic acid (solvent B). The flow rate was 0.8 mL/min and the gradient was as follows: 0-2 min, 15-25% B; 2-15 min, 25-35% B; 15-24 min, 30-50% B; 24-25 min, 50-90% B; 25-30 min 90% B; 30-35 min 15% B. ESI worked under the following conditions: desolvation line (DL) temperature, 250 °C; heat block temperature, 400 °C; drying N2 gas flow, 15 L/min; nebulizer N2 gas flow, 1.5 L/min; positive ionization mode. Data was acquired and processed using the programme LabSolutions 5.42v (Shimadzu, Kyoto, Japan).
DOI: 10.6084/m9.figshare.4635316
title: Gps performance in yukon's arctic coast

description: This study analyses GPS performance in Yukon's Arctic coast to inform future research that uses this technology in the region. To test this, Telonics GPS collars were placed on stakes during the summers of 2009 and 2010 throughout the region for varying lengths of time. The fix records produced by these collars were then collected and cleaned, leaving 30 samples. Using these records combined with a digital elevation model, eight variables were extracted and analysed in an attempt to find relationships, such that a fix rate could be predicted throughout the landscape. The results indicated that very few strong relationships existed. Densiometer values proved to be the only relationship between an environmental variable and fix rate. Available sky and aspect data produced results that were contrary to those expected. Overall, Telonics Generation 3 collars had extremely high fix rates, high accuracy, and low positional dilution of precision. Moreover, there was little variation in these results. This means that future GPS studies in the region would likely require minimal correction for fix rate bias. However, if corrections were to be made, more data would have to be gathered to ensure the results were statistically sound. The analysis suffered from the limitations of small sample size and low sample variance, among several others. Therefore, future studies should increase the number and diversity of sites tested.
DOI: 10.6084/m9.figshare.4635316.v1
title: Gps performance in yukon's arctic coast

description: This study analyses GPS performance in Yukon's Arctic coast to inform future research that uses this technology in the region. To test this, Telonics GPS collars were placed on stakes during the summers of 2009 and 2010 throughout the region for varying lengths of time. The fix records produced by these collars were then collected and cleaned, leaving 30 samples. Using these records combined with a digital elevation model, eight variables were extracted and analysed in an attempt to find relationships, such that a fix rate could be predicted throughout the landscape. The results indicated that very few strong relationships existed. Densiometer values proved to be the only relationship between an environmental variable and fix rate. Available sky and aspect data produced results that were contrary to those expected. Overall, Telonics Generation 3 collars had extremely high fix rates, high accuracy, and low positional dilution of precision. Moreover, there was little variation in these results. This means that future GPS studies in the region would likely require minimal correction for fix rate bias. However, if corrections were to be made, more data would have to be gathered to ensure the results were statistically sound. The analysis suffered from the limitations of small sample size and low sample variance, among several others. Therefore, future studies should increase the number and diversity of sites tested.
DOI: 10.6084/m9.figshare.4635289
title: Dorsal left neuropil is activated first

description: High speed two photon imaging of the habenula at 13 hz shows light causing evoked activity in the dorsal left neuropil first which then spreads to habenula neurons. Activity to offset of light can also be seen here.
DOI: 10.6084/m9.figshare.4635307
title: Optogenetic stimulation of thalamic neurons using chr-2

description: Optogenetic stimulation of thalamic neurons labelled with channelrhodopsin-2 causes evoked activity in habenula neurons (Figure 9).<br>Access all data here : Data includes raw tiff files, Images of cells segmented and figures https://github.com/seethakris/Optogeneticstimulationofthalamus.git<br>
DOI: 10.6084/m9.figshare.4635298
title: Thalamus has light evoked activity

description: Thalamus contains evoked activity to light ON and OFF in an eye dependant manner. <br>Fish 1441 was plotted in the paper. Analysis of other examples are also provided in the folder (Figure 4)
DOI: 10.6084/m9.figshare.4635298.v1
title: Thalamus has light evoked activity

description: Thalamus contains evoked activity to light ON and OFF in an eye dependant manner. <br>Fish 1441 was plotted in the paper. Analysis of other examples are also provided in the folder (Figure 4)
DOI: 10.6084/m9.figshare.4635253
title: MDA-MB213 control

description: Raw data for MDA-MB213 control experiment.Clonogenic survival assay.<br>A total of 1.4 x 10<sup>4</sup> MDA-MB-231 cells were plated in 35 mm<sup>2</sup> dishes supplemented with complete culture medium (DMEM + 10% FBS) for 24 h. Cells were then irradiated (0-6 Gy - 160 kVp X-rays), trypsinised, counted and re-plated at pre-determined low seeding densities in 6 well plates. Individual colonies formed over 11-13 days in a humidified incubator at 37°C, 95% air/5% CO<sub>2</sub>. Colonies were then fixed and stained using 0.4% crystal violet then counted. <br>
DOI: 10.6084/m9.figshare.4635289.v1
title: Dorsal left neuropil is activated first

description: High speed two photon imaging of the habenula at 13 hz shows light causing evoked activity in the dorsal left neuropil first which then spreads to habenula neurons. Activity to offset of light can also be seen here.
DOI: 10.6084/m9.figshare.4635184
title: Relevance assessment

description: This task is designed to test the differences between novices' and experts' in formulating of relevance assessments. We employ the formulated queries obtained from the <em>query formulation</em> task to build a single system ranking of candidate relevant documents. Crowd workers were then provided with medical cases (among 113 topics) and a list of top 10 candidate relevant documents. For each query-list of top 10 results, we obtained from 2 experts and 2 novices the relevance judgement in 3-point scale. More details of this task can be found in our paper in references. Fields of the csv file: <strong>dataset</strong>: <em>CLEF_eHealth</em> or <em>OHSUMED</em> <strong>topic_id</strong>: ID of the topic (from 1 to 50 for CLEF_eHealth, from 50 to 113 for OHSUMED) <strong>answerer_type</strong>: <em>expert</em> or <em>novice</em> <strong>answerer_id</strong>: ID of crowd worker <strong>doc_id</strong>: ID of the candidate document in the dataset <strong>relevance_score</strong>: the relevance rate given by the crowd worker
DOI: 10.6084/m9.figshare.4635253.v1
title: MDA-MB213 control

description: Raw data for MDA-MB213 control experiment.Clonogenic survival assay.<br>A total of 1.4 x 10<sup>4</sup> MDA-MB-231 cells were plated in 35 mm<sup>2</sup> dishes supplemented with complete culture medium (DMEM + 10% FBS) for 24 h. Cells were then irradiated (0-6 Gy - 160 kVp X-rays), trypsinised, counted and re-plated at pre-determined low seeding densities in 6 well plates. Individual colonies formed over 11-13 days in a humidified incubator at 37°C, 95% air/5% CO<sub>2</sub>. Colonies were then fixed and stained using 0.4% crystal violet then counted. <br>
DOI: 10.6084/m9.figshare.12909431
title: SLA_10June2018

description: Gridded SLA data from cds.climate.copernicus.eu for 10 June 2018.
DOI: 10.6084/m9.figshare.12909431.v1
title: SLA_10June2018

description: Gridded SLA data from cds.climate.copernicus.eu for 10 June 2018.
DOI: 10.6084/m9.figshare.4635181
title: Query reformulation

description: This task is designed to study the impact of domain expertise on query formulation. The crowd workers, divided in two types (expert or novice in the medical domain) were asked to build the appropriate query that allows achieving the search task using a pair of facets: (1) search context and (2) information need. A total of 113 topics (of 2 datasets CLEFeHealth and OHSUMED) were submitted to 3 experts and 3 novices for self-query generation; therefore 6 queries were formulated for each topic. More details of this task can be found in our paper in references. Fields of the csv file: <strong>dataset</strong>: <em>CLEF_eHealth</em> or <em>OHSUMED</em> <strong>topic_id</strong>: ID of the topic (from 1 to 50 for CLEF_eHealth, from 50 to 113 for OHSUMED) <strong>answerer_type</strong>: <em>expert</em> or <em>novice</em> <strong>answerer_id</strong>: ID of crowd worker <strong>formulated</strong><strong>_query</strong>: query formulated by the crowd worker
DOI: 10.6084/m9.figshare.4635184.v1
title: Relevance assessment

description: This task is designed to test the differences between novices' and experts' in formulating of relevance assessments. We employ the formulated queries obtained from the <em>query formulation</em> task to build a single system ranking of candidate relevant documents. Crowd workers were then provided with medical cases (among 113 topics) and a list of top 10 candidate relevant documents. For each query-list of top 10 results, we obtained from 2 experts and 2 novices the relevance judgement in 3-point scale. More details of this task can be found in our paper in references. Fields of the csv file: <strong>dataset</strong>: <em>CLEF_eHealth</em> or <em>OHSUMED</em> <strong>topic_id</strong>: ID of the topic (from 1 to 50 for CLEF_eHealth, from 50 to 113 for OHSUMED) <strong>answerer_type</strong>: <em>expert</em> or <em>novice</em> <strong>answerer_id</strong>: ID of crowd worker <strong>doc_id</strong>: ID of the candidate document in the dataset <strong>relevance_score</strong>: the relevance rate given by the crowd worker
DOI: 10.6084/m9.figshare.4635175
title: BioCreative V.5 TIPS small dictionary

description: Reduced dictionary used by PiTagger for participation in the BioCreative V.5 BeCalm TIPS task.
DOI: 10.6084/m9.figshare.4635151
title: Metadata of Rotavirus A VP4 protein (Human)

description: Complete list of accession numbers of Rotavirus A VP4 proteins (Human) used in the statistical analysis of Pessia and Corander (2017). Statistical analysis done with Kpax3 (https://github.com/albertopessia/Kpax3.jl).<br><br>Data can be downloaded from NCBI's Virus Variation Resource database (https://www.ncbi.nlm.nih.gov/genome/viruses/variation/) and aligned with MUSCLE (http://www.drive5.com/muscle/).<br><br>Reference:<br>Pessia, A. and Corander, J. (2017). "<i>Bayesian cluster analysis of categorical data with supervised feature selection</i>". <i>Submitted</i>.<br><br>Brister, J. R., Bao, Y., Zhdanov, S. A., Ostapchuck, Y., Chetvernin, V., Kiryutin, B., Zaslavsky, L., Kimelman, M., and Tatusova, T. A. (2013). "<i>Virus Variation Resource - Recent Updates and Future Directions</i>". Nucleic Acids Research, 42(D1): D660-D665.<br><br>Edgar, R. C. (2004). "<i>MUSCLE: multiple sequence alignment with high accuracy and high throughput</i>". Nucleic Acids Research, 32(5): 1792-1797.<br>
DOI: 10.6084/m9.figshare.4635151.v1
title: Metadata of Rotavirus A VP4 protein (Human)

description: Complete list of accession numbers of Rotavirus A VP4 proteins (Human) used in the statistical analysis of Pessia and Corander (2017). Statistical analysis done with Kpax3 (https://github.com/albertopessia/Kpax3.jl).<br><br>Data can be downloaded from NCBI's Virus Variation Resource database (https://www.ncbi.nlm.nih.gov/genome/viruses/variation/) and aligned with MUSCLE (http://www.drive5.com/muscle/).<br><br>Reference:<br>Pessia, A. and Corander, J. (2017). "<i>Bayesian cluster analysis of categorical data with supervised feature selection</i>". <i>Submitted</i>.<br><br>Brister, J. R., Bao, Y., Zhdanov, S. A., Ostapchuck, Y., Chetvernin, V., Kiryutin, B., Zaslavsky, L., Kimelman, M., and Tatusova, T. A. (2013). "<i>Virus Variation Resource - Recent Updates and Future Directions</i>". Nucleic Acids Research, 42(D1): D660-D665.<br><br>Edgar, R. C. (2004). "<i>MUSCLE: multiple sequence alignment with high accuracy and high throughput</i>". Nucleic Acids Research, 32(5): 1792-1797.<br>
DOI: 10.6084/m9.figshare.4635118
title: Supplemental Data for "Modeling annual grassland phenology along the central coast of California"

description: This file contains data and parameter sets used for running the RHESSys ecohydrologic model.
DOI: 10.6084/m9.figshare.12909434
title: SLA_20June2018

description: Gridded SLA data from cds.climate.copernicus.eu for 20 June 2018.
DOI: 10.6084/m9.figshare.12909434.v1
title: SLA_20June2018

description: Gridded SLA data from cds.climate.copernicus.eu for 20 June 2018.