cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5151157
title: Evolution of the receptors for growth hormone, prolactin, erythropoietin and thrombopoietin in relation to the vertebrate tetraploidizations

description: Evolution of the receptors for growth hormone, prolactin, erythropoietin and thrombopoietin in relation to the vertebrate tetraploidizations<br>Daniel Ocampo Daza<sup>1,*</sup> and Dan Larhammar<br>Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden.<br>* Corresponding author. E-mail address: Daniel.Ocampo.Daza@ebc.uu.se<br><sup>1</sup> Present address: Subdepartment of Evolution and Development, Department of Organismal Biology, Uppsala University, Norbyvägen 18A, SE-752 36 Uppsala, Sweden.<br>General and Comparative Endocrinology 257 (2018) 143-160https://doi.org/10.1016/j.ygcen.2017.06.021<br>Received 29 January 2017Revised 16 June 2017Accepted 22 June 2017Available online 23 June 2017<br>This document corresponds to the final published version of this article. You are free to download, print and distribute this document for any purposes under a Creative Commons Attribution 4.0 Unported License (http://creativecommons.org/licenses/by/4.0/), provided the original work is cited as specified. <br>Cite this article as: Ocampo Daza D, Larhammar D. Evolution of the receptors for growth hormone, prolactin, erythropoietin and thrombopoietin in relation to the vertebrate tetraploidizations, General and Comparative Endocrinology 257 (2018) 143-160. doi: http://dx.doi.org/10.1016/j.ygcen.2017.06.021
DOI: 10.6084/m9.figshare.5151151.v1
title: Appendix D Originele Moederdatabase Van Dinter 2017

description: An extended version of Appendix D- Section A of Van Dinter 2017 (PhD thesis) with remarks and height of vegetation horizons, elevation levels and composition of deposits, thickness and age of cultural layers and various remarks (all in Dutch).
DOI: 10.6084/m9.figshare.5151085
title: WRR - Capillary Trapping Quantification in Sandstones using NMR Relaxometry .xlsx

description: Data relating to the journal article submitted to WRR - Capillary Trapping Quantification in Sandstones using NMR Relaxometry
DOI: 10.6084/m9.figshare.5151085.v1
title: WRR - Capillary Trapping Quantification in Sandstones using NMR Relaxometry .xlsx

description: Data relating to the journal article submitted to WRR - Capillary Trapping Quantification in Sandstones using NMR Relaxometry
DOI: 10.5281/zenodo.4003042
title: Raw diffraction images of Spirochaeta YeeE

description: Crystal structure of thiosulfate transporter YeeE from Spirochaeta thermophila (PDB code 6LEO). The complete datasets were obtained by merging multiple small-wedge datasets using EIGER X 9M detector at a wavelength of 1.44 Å with a multi-crystal data collection scheme using 15×10 μm beam on BL32XU, SPring-8. For the native dataset, diffraction images of 10° rotation range with a pitch of 0.1° oscillation range were collected from each of the 515 crystals. For the SeMet dataset, diffraction images of 7° rotation range with a pitch of 0.1° oscillation range were collected from each of the 326 crystals. All the diffraction images were collected automatically by the Zoo system and then processed using KAMO with XDS. Crystal structure of a YeeE/YedE family protein engaged in thiosulfate uptake https://advances.sciencemag.org/content/6/35/eaba7637
DOI: 10.5281/zenodo.4003041
title: Raw diffraction images of Spirochaeta YeeE

description: Crystal structure of thiosulfate transporter YeeE from Spirochaeta thermophila (PDB code 6LEO). The complete datasets were obtained by merging multiple small-wedge datasets using EIGER X 9M detector at a wavelength of 1.44 Å with a multi-crystal data collection scheme using 15×10 μm beam on BL32XU, SPring-8. For the native dataset, diffraction images of 10° rotation range with a pitch of 0.1° oscillation range were collected from each of the 515 crystals. For the SeMet dataset, diffraction images of 7° rotation range with a pitch of 0.1° oscillation range were collected from each of the 326 crystals. All the diffraction images were collected automatically by the Zoo system and then processed using KAMO with XDS. Crystal structure of a YeeE/YedE family protein engaged in thiosulfate uptake https://advances.sciencemag.org/content/6/35/eaba7637
DOI: 10.6084/m9.figshare.5150644
title: T2 Distributions.xlsx

description: T2 distributions corresponding figures 8,9 and 10.
DOI: 10.6084/m9.figshare.5150644.v1
title: T2 Distributions.xlsx

description: T2 distributions corresponding figures 8,9 and 10.
DOI: 10.6084/m9.figshare.5150548
title: Internal gradients.xlsx

description: Regularised solutions for internal gradients,corresponds to figures 5,6.
DOI: 10.6084/m9.figshare.5150548.v1
title: Internal gradients.xlsx

description: Regularised solutions for internal gradients,corresponds to figures 5,6.
DOI: 10.6084/m9.figshare.5150512
title: NMR signal intensity.xlsx

description: NMR signal data corresponding to figures 2,3 and 4
DOI: 10.6084/m9.figshare.5150512.v1
title: NMR signal intensity.xlsx

description: NMR signal data corresponding to figures 2,3 and 4
DOI: 10.6084/m9.figshare.5150443
title: Missing in action: species competition is a neglected predictor variable in Species Distribution Modelling _Raw_Data

description: Presence data for buffalo (n = 93), warthog (n = 27), waterbuck (n =21), wildebeest (n = 24) and zebra (n =44) were collected via an aerial survey conducted in Gonarezhou National Park in October 2013. The aerial survey was a sample with transects spaced at 1.5 km and 2.5 km depending on animal density within sampling strata. A Cessna 185 fixed wing plane was used and two observers sitting at the right and left sides of the plane observed animals within strips of width 150 m. The observers searched for animals between two streamers fitted to the wing struts of the plane during pre-calibration flights in such a way that the search strip on the ground was 150 m wide. Each time animals were sighted, the location of the sighting was marked using a handheld GPS device (GPSmap 296, Garmin international). A full description of the method is provided in 'Norton-Griffiths M (1978) Counting animals. Handbooks on techniques currently used in African wildlife ecology. African Wildlife Leadership Foundation, Nairobi'.
DOI: 10.6084/m9.figshare.5150437
title: VRPCD for Perishable products -Test Problems Data.xlsx

description: Dataset for test problems - vehicle routing and scheduling problem with cross-docking for perishable products
DOI: 10.6084/m9.figshare.5150437.v1
title: VRPCD for Perishable products -Test Problems Data.xlsx

description: Dataset for test problems - vehicle routing and scheduling problem with cross-docking for perishable products
DOI: 10.6084/m9.figshare.5150437.v2
title: VRPCD for Perishable products -Test Problems Data.xlsx

description: Dataset for test problems - vehicle routing and scheduling problem with cross-docking for perishable products
DOI: 10.17608/k6.auckland.5150140
title: Numerical model input and output files for simulating impacts of sea-level rise on Funafuti Atoll

description: This dataset provides the simulation files and raw output files used in a numerical modeling based study focused of how sea-level rise will impact wave transformation processes and flooding on Fatato Island, Funafuti Atoll. This research utilised a phase-resolving fully nonlinear Boussinesq wave model to simulate wave transformation, runup and overtopping in context of present and future sea level, with different reef response morphologies. Simulations encompass the contemporary tidal range and future sea level rise scenarios up to 1.5 m above present spring high tide. Model outputs are presented in the form of profile and time-series data for water level and velocity data at numerous time-steps and location across. Model outputs and inputs are presented for three different reef response morphologies: 1) static reef that simply drowns with sea-level rise), 2) vertical adjustment of the outer reef flat, and 3) vertical adjustment of the full reef flat. This research does not consider adjustments to reef island morphology.<br>The model used in the research is freely available form http://basilisk.fr/src/green-naghdi.h
DOI: 10.6084/m9.figshare.5150131
title: Amphotis marginata data

description: Supporting data for <em>Hölldobler and Kwapich (2017)</em>
DOI: 10.17608/k6.auckland.5150140.v1
title: Numerical model input and output files for simulating impacts of sea-level rise on Funafuti Atoll

description: This dataset provides the simulation files and raw output files used in a numerical modeling based study focused of how sea-level rise will impact wave transformation processes and flooding on Fatato Island, Funafuti Atoll. This research utilised a phase-resolving fully nonlinear Boussinesq wave model to simulate wave transformation, runup and overtopping in context of present and future sea level, with different reef response morphologies. Simulations encompass the contemporary tidal range and future sea level rise scenarios up to 1.5 m above present spring high tide. Model outputs are presented in the form of profile and time-series data for water level and velocity data at numerous time-steps and location across. Model outputs and inputs are presented for three different reef response morphologies: 1) static reef that simply drowns with sea-level rise), 2) vertical adjustment of the outer reef flat, and 3) vertical adjustment of the full reef flat. This research does not consider adjustments to reef island morphology.<br>The model used in the research is freely available form http://basilisk.fr/src/green-naghdi.h
DOI: 10.6084/m9.figshare.5150131.v1
title: Amphotis marginata data

description: Supporting data for <em>Hölldobler and Kwapich (2017)</em>
DOI: 10.6084/m9.figshare.5150107
title: Table: Metabolic Syndrome and Renal osteodystrophy.

description: Demographic, hormonal and bone hystomorphometry data from observational cross-sectional study included 55 hemodialysis patients (28 women/27 men) who were evaluated for MetS and bone histomorphometry. Biochemical parameters included calcium, phosphorus, alkaline phosphatase, intact parathyroid hormone (iPTH), 25-hydroxyvitamin D, free serum leptin, fibroblast growth factor 23 (FGF23), intact osteocalcin, sclerostin (Scl), glucose, insulin, and thyroid hormones. A transiliac bone biopsy was performed using a Bordier trephine following a course of double labeling with tetracycline (20 mg/kg/day) for 3 days with a 10-day interval. The biopsy was performed 3-5 days after the last dose of tetracycline.
DOI: 10.6084/m9.figshare.5150107.v1
title: Table: Metabolic Syndrome and Renal osteodystrophy.

description: Demographic, hormonal and bone hystomorphometry data from observational cross-sectional study included 55 hemodialysis patients (28 women/27 men) who were evaluated for MetS and bone histomorphometry. Biochemical parameters included calcium, phosphorus, alkaline phosphatase, intact parathyroid hormone (iPTH), 25-hydroxyvitamin D, free serum leptin, fibroblast growth factor 23 (FGF23), intact osteocalcin, sclerostin (Scl), glucose, insulin, and thyroid hormones. A transiliac bone biopsy was performed using a Bordier trephine following a course of double labeling with tetracycline (20 mg/kg/day) for 3 days with a 10-day interval. The biopsy was performed 3-5 days after the last dose of tetracycline.
DOI: 10.6084/m9.figshare.5150077
title: Optimization datasets for the CPSO-DE algorithm compared with other optimization algorithms

description: Datasets including optimization results of the CPSO-DE algorithm compared with other evolutionary algorithms (CPSO-inner, CPSO-outer, PSO and DE). Data include classical and COCO benchmark functions for 30, 50 and 100 D
DOI: 10.6084/m9.figshare.5150077.v1
title: Optimization datasets for the CPSO-DE algorithm compared with other optimization algorithms

description: Datasets including optimization results of the CPSO-DE algorithm compared with other evolutionary algorithms (CPSO-inner, CPSO-outer, PSO and DE). Data include classical and COCO benchmark functions for 30, 50 and 100 D
DOI: 10.6084/m9.figshare.5150128.v1
title: S1 Table. The divisions of haplogroups comprised of 22 Y-STR loci in the Jiangsu Han population (n = 916).

description: Samples and DNA extraction<br>A total of 916 unrelated healthy male individuals of Han ancestry provided blood samples with informed consent, including 207 samples from Changzhou, 147 from Xuzhou, 111 from Suqian, 98 from Wuxi, 71 from Lianyungang, 62 from Yancheng, 55 from Huai’an, 47 from Soochow, 41 from Nanjing, 39 from Nantong, 17 from Zhenjiang, 14 from Yangzhou, and 7 from Taizhou. All individuals come from Chinese Jiangsu Han population and reside locally at least three generations. Chelex-100 protocol was adopted to extract genomic DNA. The study was conducted in accordance to the human and ethical research principles of Zhongshan City People’s Hospital and approved by the ethics committee in Zhongshan City People’s Hospital.<br><br>STR genotyping<br>Y-STR was typed for the PowerPlex Y23 System (Promega, USA) with GeneAmp PCR system 9700 (Thermofisher Scientific, Waltham, MA, USA). Amplified DNAs were separated on ABI3130XL DNA Genetic Analyzer (Thermofisher Scientific, Waltham, MA, USA) and analyzed using the GeneMapper ID-X software (Thermofisher Scientific, Waltham, MA, USA).<br><br>Statistical analysis<br>After direct count of the allele frequencies and haplotype by Arlequin 3.0, we calculated gene diversity (GD) following Nei. We also calculated several representative forensic parameters, such as haplotype diversity (HD), discrimination capacity (DC), and match probability (MP) according Sabine et al. DYS385a/b, a multi-copy locus, was analyzed as combined haplotypes. And we got the allele of DYS389II by the subtraction of DYS389I. The popular combination of computational RST values which referred to the excess similarity among alleles chosen randomly within the subgroup relative to the entire group and Multidimensional Scaling plot (MDS) was adopted as YHRD analyzed and many publications conducted. Linkage patterns and Analysis of Molecular Variance (AMOVA) which generated the pairwise RST values and according significant values were performed using Arlequin 3.0 based on detailed haplotype information of eligible individuals (samples with the null, intermediate alleles, and copy-number variations were removed). Neighbor-Joining (N-J) tree was depicted and visualized by Mega 6.0 as others conducted. Based on the matrix of RST values, we illustrated MDS as YHRD recommended and achieved values of initial stress by employing “MASS” package (https://cran.r-project.org/web/packages/MASS/index.html). <br><sup></sup>
DOI: 10.6084/m9.figshare.5150128.v2
title: S1 Table. The divisions of haplogroups comprised of 22 Y-STR loci in the Jiangsu Han population (n = 916).

description: Samples and DNA extraction<br>A total of 916 unrelated healthy male individuals of Han ancestry provided blood samples with informed consent, including 207 samples from Changzhou, 147 from Xuzhou, 111 from Suqian, 98 from Wuxi, 71 from Lianyungang, 62 from Yancheng, 55 from Huai’an, 47 from Soochow, 41 from Nanjing, 39 from Nantong, 17 from Zhenjiang, 14 from Yangzhou, and 7 from Taizhou. All individuals come from Chinese Jiangsu Han population and reside locally at least three generations. Chelex-100 protocol was adopted to extract genomic DNA. The study was conducted in accordance to the human and ethical research principles of Zhongshan City People’s Hospital and approved by the ethics committee in Zhongshan City People’s Hospital.<br><br>STR genotyping<br>Y-STR was typed for the PowerPlex Y23 System (Promega, USA) with GeneAmp PCR system 9700 (Thermofisher Scientific, Waltham, MA, USA). Amplified DNAs were separated on ABI3130XL DNA Genetic Analyzer (Thermofisher Scientific, Waltham, MA, USA) and analyzed using the GeneMapper ID-X software (Thermofisher Scientific, Waltham, MA, USA).<br><br>Statistical analysis<br>After direct count of the allele frequencies and haplotype by Arlequin 3.0, we calculated gene diversity (GD) following Nei. We also calculated several representative forensic parameters, such as haplotype diversity (HD), discrimination capacity (DC), and match probability (MP) according Sabine et al. DYS385a/b, a multi-copy locus, was analyzed as combined haplotypes. And we got the allele of DYS389II by the subtraction of DYS389I. The popular combination of computational RST values which referred to the excess similarity among alleles chosen randomly within the subgroup relative to the entire group and Multidimensional Scaling plot (MDS) was adopted as YHRD analyzed and many publications conducted. Linkage patterns and Analysis of Molecular Variance (AMOVA) which generated the pairwise RST values and according significant values were performed using Arlequin 3.0 based on detailed haplotype information of eligible individuals (samples with the null, intermediate alleles, and copy-number variations were removed). Neighbor-Joining (N-J) tree was depicted and visualized by Mega 6.0 as others conducted. Based on the matrix of RST values, we illustrated MDS as YHRD recommended and achieved values of initial stress by employing “MASS” package (https://cran.r-project.org/web/packages/MASS/index.html). <br><sup></sup>
DOI: 10.6084/m9.figshare.5150128
title: S1 Table. The divisions of haplogroups comprised of 22 Y-STR loci in the Jiangsu Han population (n = 916) . S2 Table. The distribution of 916 Jiangsu Han samples in prefecture-level geographic location.

description: Samples and DNA extraction<br>A total of 916 unrelated healthy male individuals of Han ancestry provided blood samples with informed consent, including 207 samples from Changzhou, 147 from Xuzhou, 111 from Suqian, 98 from Wuxi, 71 from Lianyungang, 62 from Yancheng, 55 from Huai’an, 47 from Soochow, 41 from Nanjing, 39 from Nantong, 17 from Zhenjiang, 14 from Yangzhou, and 7 from Taizhou. All individuals come from Chinese Jiangsu Han population and reside locally at least three generations. Chelex-100 protocol was adopted to extract genomic DNA. The study was conducted in accordance to the human and ethical research principles of Zhongshan City People’s Hospital and approved by the ethics committee in Zhongshan City People’s Hospital.<br><br>STR genotyping<br>Y-STR was typed for the PowerPlex Y23 System (Promega, USA) with GeneAmp PCR system 9700 (Thermofisher Scientific, Waltham, MA, USA). Amplified DNAs were separated on ABI3130XL DNA Genetic Analyzer (Thermofisher Scientific, Waltham, MA, USA) and analyzed using the GeneMapper ID-X software (Thermofisher Scientific, Waltham, MA, USA).<br><br>Statistical analysis<br>After direct count of the allele frequencies and haplotype by Arlequin 3.0, we calculated gene diversity (GD) following Nei. We also calculated several representative forensic parameters, such as haplotype diversity (HD), discrimination capacity (DC), and match probability (MP) according Sabine et al. DYS385a/b, a multi-copy locus, was analyzed as combined haplotypes. And we got the allele of DYS389II by the subtraction of DYS389I. The popular combination of computational RST values which referred to the excess similarity among alleles chosen randomly within the subgroup relative to the entire group and Multidimensional Scaling plot (MDS) was adopted as YHRD analyzed and many publications conducted. Linkage patterns and Analysis of Molecular Variance (AMOVA) which generated the pairwise RST values and according significant values were performed using Arlequin 3.0 based on detailed haplotype information of eligible individuals (samples with the null, intermediate alleles, and copy-number variations were removed). Neighbor-Joining (N-J) tree was depicted and visualized by Mega 6.0 as others conducted. Based on the matrix of RST values, we illustrated MDS as YHRD recommended and achieved values of initial stress by employing “MASS” package (https://cran.r-project.org/web/packages/MASS/index.html). <br><sup></sup>
DOI: 10.6084/m9.figshare.5149699.v3
title: Root crown phenotyping (AKA shovelomics) cartoon

description: This cartoon describes the field method for root crown phenotyping, including excavation of root crown by shovel, washing with water hose, and imaging in an imaging box or tent.
DOI: 10.6084/m9.figshare.5149699.v2
title: Root crown phenotyping (AKA shovelomics) cartoon

description: This cartoon describes the field method for root crown phenotyping, including excavation of root crown by shovel, washing with water hose, and imaging in an imaging box or tent.
DOI: 10.6084/m9.figshare.5149612
title: Test title

description: trying to make file set
DOI: 10.6084/m9.figshare.5149663.v1
title: Gordonia Genomics Supplemental Material 2017

description: Supplemental material including genome maps for bacteriophages of Gordonia spp.
DOI: 10.6084/m9.figshare.5149612.v2
title: Test title

description: trying to make file set
DOI: 10.6084/m9.figshare.5149612.v1
title: Test title

description: trying to make file set
DOI: 10.6084/m9.figshare.5147722
title: JOSS first-year publication data and figures

description: Data, script, and figures on articles published by the Journal of Open Source Software (JOSS) in its first year, between its release in May 2016 and May 2017.<br>Data was extracted manually from the JOSS list of accepted articles and review issues.
DOI: 10.6084/m9.figshare.5147722.v2
title: JOSS first-year publication data and figures

description: Data, script, and figures on articles published by the Journal of Open Source Software (JOSS) in its first year, between its release in May 2016 and May 2017.<br>Data was extracted manually from the JOSS list of accepted articles and review issues.
DOI: 10.6084/m9.figshare.5147722.v1
title: JOSS first-year publication data and figures

description: Data, script, and figures on articles published by the Journal of Open Source Software (JOSS) in its first year, between its release in May 2016 and May 2017.<br>Data was extracted manually from the JOSS list of accepted articles and review issues.
DOI: 10.17632/bpdttj46k7.1
title: Raw data : Omori et al

description: Raw data of the paper;Tissue and cell type-specific heterogeneity of p16high cells revealed by single-cell transcriptomes
DOI: 10.5281/zenodo.4011517
title: LC-IMPACT1.1

description: LC-Impact data
DOI: 10.6084/m9.figshare.5147305
title: RRJ Thompson et al. 2017 - stickleback Cognitive Bias data

description: Data for <b>Thompson et al. (2017) 'Net handling leaves fish ‘bold’ but not ‘optimistic’ in a novel spatial test of cognitive bias in fish</b>' are given in the file 'Thompson et al 2017 - Stickleback Cognitive Bias Data.xlsx' as follows:<br>The total latency to reach the feeding tube is in the top table, the latency to leave the start box is in the bottom table.<br>Column B gives the fish ID. Column C gives the order of testing (<b>B</b> = box; <b>N</b> = net)Column D gives the side of the test tank that was rewarded (<b>L</b>eft/<b>R</b>ight)Columns E to P give the latencies for each trial following box handling (in seconds)Columns Q to AB give the latencies for each trial following net handling (in seconds)[Unrew = trained unrewarded location]Latencies were recorded from video files by a research assistant not involved in practical experimentation and blind to treatment<br>Ethical approved granted by the University of Bristol (University Investigation Number: UB/10/020)<br>Contact for lead author:<br>ralphrjt@gmail.com
DOI: 10.6084/m9.figshare.5147311
title: data for uploading-1.pdf

description: Data set for PLoS one paper.<br>
DOI: 10.6084/m9.figshare.5147275
title: Supplemental data file 3 from Distinct spinning patterns gain differentiated loading tolerance of silk thread anchorages in spiders with different ecology

description: Morphometric data of attachment discs (csv).
DOI: 10.6084/m9.figshare.5147275.v1
title: Supplemental data file 3 from Distinct spinning patterns gain differentiated loading tolerance of silk thread anchorages in spiders with different ecology

description: Morphometric data of attachment discs (csv).