cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8852351.v1
title: Cadmium-induced hypertension is associated with renal myosin light chain phosphatase inhibition at Thr697 and p44 mitogen-activated protein kinase elevation

description: The data provide blood pressures of Sprague-Dawley rats, taken from the tail vein using a non-invasive CODA machine. Rats received cadmium and/or potassium and were compared to a control group.
DOI: 10.6084/m9.figshare.8852354.v2
title: Supp materials final.docx

description: Supplemental information for Sorrentino et al final version<br>
DOI: 10.6084/m9.figshare.8852240
title: blast results angus 2019

description: blast results angus 2019
DOI: 10.6084/m9.figshare.8852354.v1
title: Supp materials final.docx

description: Supplemental information for Sorrentino et al final version<br>
DOI: 10.6084/m9.figshare.8852240.v1
title: blast results angus 2019

description: blast results angus 2019
DOI: 10.6084/m9.figshare.8852165
title: ncbi tax db for angus 2019

description: ncbi tax db for angus 2019
DOI: 10.6084/m9.figshare.8852168
title: RAW data.sav

description: Raw data exported from Qualtrics after gaining ethical approval for the study via the university.
DOI: 10.6084/m9.figshare.8852165.v1
title: ncbi tax db for angus 2019

description: ncbi tax db for angus 2019
DOI: 10.6084/m9.figshare.8852126
title: Data for ala porosity analysis from Macro-to-nanoscale investigation of wall-plate joints in the acorn barnacle <i>Semibalanus balanoides</i>: correlative imaging, biological form and function, and bioinspiration

description: Data generated through Avizo for porosity analysis of the ala pores
DOI: 10.6084/m9.figshare.8852126.v1
title: Data for ala porosity analysis from Macro-to-nanoscale investigation of wall-plate joints in the acorn barnacle <i>Semibalanus balanoides</i>: correlative imaging, biological form and function, and bioinspiration

description: Data generated through Avizo for porosity analysis of the ala pores
DOI: 10.6084/m9.figshare.8852114
title: Phylogenetic Analysis Matrix from <i>Borealodon osedax</i>, a new stem mysticete (Mammalia, Cetacea) from the Oligocene of Washington State and implications for fossil whale-fall communities

description: Baleen whales (mysticetes) lack teeth as adults and instead filter feed using keratinous baleen plates. They do not echolocate with ultrasonic frequencies like toothed whales but are instead known for infrasonic acoustics. Both baleen and infrasonic hearing are separately considered key innovations linked to their gigantism, evolutionary success and ecological diversity. The earliest mysticetes had teeth, and the phylogenetic position of many so-called toothed mysticetes remains debated, including those belonging to the nominal taxonomic groups Llanocetidae, Mammalodontidae and Aetiocetidae. Here, we report a new stem mysticete, <i>Borealodon osedax</i> gen. et sp. nov, from the Oligocene of Washington State, USA. <i>Borealodon</i> preserves multi-cusped teeth with apical wear; microCT scans of the inner ear indicate that the minimum frequency hearing limit of <i>Borealodon</i> was similar to mammalodontids. <i>Borealodon</i> is not recovered within a monophyletic Mammalodontidae nor a monophyletic Aetiocetidae; instead, it represents an unnamed lineage of stem Mysticeti, adding to the diversity of stem mysticetes, especially in across the Rupelian–Chattian boundary. Furthermore, the presence of a putative chemosynthetic bivalve along with <i>Osedax</i>, a bone-boring annelid, found in association with the type specimen of <i>Borealodon</i>, offer more insights into the evolution of these deep-sea whale-fall communities.
DOI: 10.6084/m9.figshare.8852114.v1
title: Phylogenetic Analysis Matrix from <i>Borealodon osedax</i>, a new stem mysticete (Mammalia, Cetacea) from the Oligocene of Washington State and implications for fossil whale-fall communities

description: Baleen whales (mysticetes) lack teeth as adults and instead filter feed using keratinous baleen plates. They do not echolocate with ultrasonic frequencies like toothed whales but are instead known for infrasonic acoustics. Both baleen and infrasonic hearing are separately considered key innovations linked to their gigantism, evolutionary success and ecological diversity. The earliest mysticetes had teeth, and the phylogenetic position of many so-called toothed mysticetes remains debated, including those belonging to the nominal taxonomic groups Llanocetidae, Mammalodontidae and Aetiocetidae. Here, we report a new stem mysticete, <i>Borealodon osedax</i> gen. et sp. nov, from the Oligocene of Washington State, USA. <i>Borealodon</i> preserves multi-cusped teeth with apical wear; microCT scans of the inner ear indicate that the minimum frequency hearing limit of <i>Borealodon</i> was similar to mammalodontids. <i>Borealodon</i> is not recovered within a monophyletic Mammalodontidae nor a monophyletic Aetiocetidae; instead, it represents an unnamed lineage of stem Mysticeti, adding to the diversity of stem mysticetes, especially in across the Rupelian–Chattian boundary. Furthermore, the presence of a putative chemosynthetic bivalve along with <i>Osedax</i>, a bone-boring annelid, found in association with the type specimen of <i>Borealodon</i>, offer more insights into the evolution of these deep-sea whale-fall communities.
DOI: 10.17633/rd.brunel.8852027
title: Data supporting "The Domain-Specificity of Face Matching Impairments in 40 Cases of Developmental Prosopagnosia"

description: This dataset contains data from a sequential same/different matching task. For full details of the procedure, see the accompanying publication "The domain-specificity of face matching impairments in 40 cases of developmental prosopangosia" or Bobak, A. K., Bennetts, R. J., Parris, B. A., Jansari, A., & Bate, S. (2016). An in-depth cognitive examination of individuals with superior face recognition skills. <i>Cortex</i>, <i>82</i>, 48-62.<b>Participants:</b> 40 individuals with developmental prosopagnosia and 60 individuals with typical face recognition ability (control). See accompanying paper for inclusion and exclusion criteria for each group. Participants are split into two age groups: younger (18-49 years old) and older (50-70 years old). The age (in years) of each participant is also included. <b>Task design: </b>There are three categories of objects included in the task: faces, hands, and houses. For each object category, there were both upright and inverted (upside-down) trials in the task. There are two version of data for the house conditions: one included all of the trials in the experiment (houses ORIG); the second (houses ADJ) included only half of the original trials, in order to equate difficulty between the face and house conditions. <b>Measures: </b>For each object/orientation combination, the following measures are included for each participant: <b>hits:</b> correct responses to trials which displayed the SAME identity in both images (as a proportion of total possible hits)<b>correct rejections (CRs):</b> correct responses to trials which displayed DIFFERENT identities in each image (as a proportion of total possible CRs)<b>dprime:</b> the signal detection theory measure d', which measures sensitivity (higher scores indicate better performance, chance performance = 0)<b>c bias:</b> the signal detection measure c, which measures response bias (scores above 0 indicate a tendency to say stimuli were not the same; scores below 0 indicate a tendency to say the stimuli were the same)<b>same RT:</b> average correct reaction time for trials in which the correct response was "same"<b>different RT:</b> average correct reaction time for trials in which the correct response was "different"<br><b>RT:</b> average correct reaction time for "same" and "different" trials<br>See accompanying paper for additional details on data processing. <br>
DOI: 10.6084/m9.figshare.8852042
title: Efficient biocatalytic synthesis of D-tagatose 1,6-diphosphate by LacC-catalysed phosphorylation of D-tagatose 6-phosphate

description: D-tagatose 1,6-diphosphate is an important metabolite which can be formed via the classical tagatose 6-phosphate pathway or via the tagatose 1-phosphate pathway discovered more recently. The chiral metabolite naturally occurs as an intermediate in the galactose metabolism of various organisms, where it is formed by a reversible condensation of dihydroxyacetone phosphate and D-glyceraldehyde 3-phosphate, whereas D-tagatose 6-phosphate has been synthesized chemically, no chemical synthetic method for further phosphorylation to the D-tagatose 1,6-diphosphate has been described so far. Therefore, a site-specific biocatalytic phosphorylation of the 1-position in D-tagatose 6-phosphate has been chosen. The <i>lacC</i> gene from <i>Lactococcus lactis</i> subsp. <i>lactis</i> was synthesized, cloned into an appropriate expression vector to allow for the production of LacC, the D-tagatose 6-phosphate kinase in <i>Escherichia coli</i>. Subsequently, an efficient biocatalytic synthesis has been developed for the phosphorylation of D-tagatose 6-phosphate at its C1-position by using the recombinant D-tagatose 6-phosphate kinase and the phosphoenolpyruvate/pyruvate kinase-system for ATP regeneration. This straightforward and scalable one-step biocatalytic synthesis of D-tagatose 1,6-diphosphate was successfully scaled up to the gram scale.
DOI: 10.6084/m9.figshare.8852024
title: Additional datasets for "Programmed DNA elimination of germline development genes in songbirds"

description: Zebra finch liver (P7359_105) and testis (P7359_106) genome assemblies as well as mitochondrial DNA alignments for the manuscript entitled "Programmed DNA elimination of germline development genes in songbirds" by Cormac M. Kinsella, Francisco J. Ruiz-Ruano, Anne-Marie Dion-Côté, Alexander J. Charles, Toni I. Gossmann, Josefa Cabrero, Dennis Kappei, Nicola Hemmings, Mirre J. P. Simons, Juan Pedro M. Camacho, Wolfgang Forstmeier and Alexander Suh<br>
DOI: 10.6084/m9.figshare.8852042.v1
title: Efficient biocatalytic synthesis of D-tagatose 1,6-diphosphate by LacC-catalysed phosphorylation of D-tagatose 6-phosphate

description: D-tagatose 1,6-diphosphate is an important metabolite which can be formed via the classical tagatose 6-phosphate pathway or via the tagatose 1-phosphate pathway discovered more recently. The chiral metabolite naturally occurs as an intermediate in the galactose metabolism of various organisms, where it is formed by a reversible condensation of dihydroxyacetone phosphate and D-glyceraldehyde 3-phosphate, whereas D-tagatose 6-phosphate has been synthesized chemically, no chemical synthetic method for further phosphorylation to the D-tagatose 1,6-diphosphate has been described so far. Therefore, a site-specific biocatalytic phosphorylation of the 1-position in D-tagatose 6-phosphate has been chosen. The <i>lacC</i> gene from <i>Lactococcus lactis</i> subsp. <i>lactis</i> was synthesized, cloned into an appropriate expression vector to allow for the production of LacC, the D-tagatose 6-phosphate kinase in <i>Escherichia coli</i>. Subsequently, an efficient biocatalytic synthesis has been developed for the phosphorylation of D-tagatose 6-phosphate at its C1-position by using the recombinant D-tagatose 6-phosphate kinase and the phosphoenolpyruvate/pyruvate kinase-system for ATP regeneration. This straightforward and scalable one-step biocatalytic synthesis of D-tagatose 1,6-diphosphate was successfully scaled up to the gram scale.
DOI: 10.17633/rd.brunel.8852027.v1
title: Data supporting "The Domain-Specificity of Face Matching Impairments in 40 Cases of Developmental Prosopagnosia"

description: This dataset contains data from a sequential same/different matching task. For full details of the procedure, see the accompanying publication "The domain-specificity of face matching impairments in 40 cases of developmental prosopangosia" or Bobak, A. K., Bennetts, R. J., Parris, B. A., Jansari, A., & Bate, S. (2016). An in-depth cognitive examination of individuals with superior face recognition skills. <i>Cortex</i>, <i>82</i>, 48-62.<b>Participants:</b> 40 individuals with developmental prosopagnosia and 60 individuals with typical face recognition ability (control). See accompanying paper for inclusion and exclusion criteria for each group. Participants are split into two age groups: younger (18-49 years old) and older (50-70 years old). The age (in years) of each participant is also included. <b>Task design: </b>There are three categories of objects included in the task: faces, hands, and houses. For each object category, there were both upright and inverted (upside-down) trials in the task. There are two version of data for the house conditions: one included all of the trials in the experiment (houses ORIG); the second (houses ADJ) included only half of the original trials, in order to equate difficulty between the face and house conditions. <b>Measures: </b>For each object/orientation combination, the following measures are included for each participant: <b>hits:</b> correct responses to trials which displayed the SAME identity in both images (as a proportion of total possible hits)<b>correct rejections (CRs):</b> correct responses to trials which displayed DIFFERENT identities in each image (as a proportion of total possible CRs)<b>dprime:</b> the signal detection theory measure d', which measures sensitivity (higher scores indicate better performance, chance performance = 0)<b>c bias:</b> the signal detection measure c, which measures response bias (scores above 0 indicate a tendency to say stimuli were not the same; scores below 0 indicate a tendency to say the stimuli were the same)<b>same RT:</b> average correct reaction time for trials in which the correct response was "same"<b>different RT:</b> average correct reaction time for trials in which the correct response was "different"<br><b>RT:</b> average correct reaction time for "same" and "different" trials<br>See accompanying paper for additional details on data processing. <br>
DOI: 10.6084/m9.figshare.8852024.v2
title: Additional datasets for "Programmed DNA elimination of germline development genes in songbirds"

description: Zebra finch liver (P7359_105) and testis (P7359_106) genome assemblies as well as mitochondrial DNA alignments for the manuscript entitled "Programmed DNA elimination of germline development genes in songbirds" by Cormac M. Kinsella, Francisco J. Ruiz-Ruano, Anne-Marie Dion-Côté, Alexander J. Charles, Toni I. Gossmann, Josefa Cabrero, Dennis Kappei, Nicola Hemmings, Mirre J. P. Simons, Juan Pedro M. Camacho, Wolfgang Forstmeier and Alexander Suh<br>
DOI: 10.6084/m9.figshare.8852084.v1
title: Replication Package - PROMISE'19

description: Replication Package of the paper "From Reports to Bug-Fix Commits: A 10 Years Dataset of Bug-Fixing Activity from 55 Apache's Open Source Projects"<br><br>ABSTRACT:<br>Bugs appear in almost any software development. Solving all or at least a large part of them requires a great deal of time, effort, and budget. Software projects typically use issue tracking systems as a way to report and monitor bug-fixing tasks. In recent years, several researchers have been conducting bug tracking analysis to better understand the problem and thus provide means to reduce costs and improve the efficiency of the bug-fixing task. In this paper, we introduce a new dataset composed of more than 70,000 bug-fix reports from 10 years of bug-fixing activity of 55 projects from the Apache Software Foundation, distributed in 9 categories. We have mined this information from Jira issue track system concerning two different perspectives of reports with closed/resolved status: static (the latest version of reports) and dynamic (the changes that have occurred in reports over time). We also extract information from the commits (if they exist) that fix such bugs from their respective version-control system (Git).We also provide a change analysis that occurs in the reports as a way of illustrating and characterizing the proposed dataset. Once the data extraction process is an error-prone nontrivial task, we believe such initiatives like this could be useful to support researchers in further more detailed investigations.<br><br>You can find the full paper at: https://doi.org/10.1145/3345629.3345639<br>If you use this dataset for your research, please reference the following paper:<pre>@inproceedings{Vieira:2019:RBC:3345629.3345639, author = {Vieira, Renan and da Silva, Ant\^{o}nio and Rocha, Lincoln and Gomes, Jo\~{a}o Paulo}, title = {From Reports to Bug-Fix Commits: A 10 Years Dataset of Bug-Fixing Activity from 55 Apache's Open Source Projects}, booktitle = {Proceedings of the Fifteenth International Conference on Predictive Models and Data Analytics in Software Engineering}, series = {PROMISE'19}, year = {2019}, isbn = {978-1-4503-7233-6}, location = {Recife, Brazil}, pages = {80--89}, numpages = {10}, url = {http://doi.acm.org/10.1145/3345629.3345639}, doi = {10.1145/3345629.3345639}, acmid = {3345639}, publisher = {ACM}, address = {New York, NY, USA}, keywords = {Bug-Fix Dataset, Mining Software Repositories, Software Traceability}, } </pre>
DOI: 10.6084/m9.figshare.8852024.v1
title: Zebra finch liver and testis genome assemblies

description: Zebra finch liver (P7359_105) and testis (P7359_106) genome assemblies for the manuscript entitled "Programmed DNA elimination of germline development genes in songbirds" by Cormac M. Kinsella, Francisco J. Ruiz-Ruano, Anne-Marie Dion-Côté, Alexander J. Charles, Toni I. Gossmann, Josefa Cabrero, Dennis Kappei, Nicola Hemmings, Mirre J. P. Simons, Juan Pedro M. Camacho, Wolfgang Forstmeier and Alexander Suh<br>
DOI: 10.6084/m9.figshare.8851853
title: Supplementary Material for: Amino Acid Loss during Continuous Venovenous Hemofiltration in Critically Ill Patients

description: <b><i>Background/Objectives:</i></b> During continuous venovenous hemofiltration (CVVH), there is unwanted loss of amino acids (AA) in the ultrafiltrate (UF). Solutes may also be removed by adsorption to the filter membrane. The aim was to quantify the total loss of AA via the CVVH circuit using a high-flux polysulfone membrane and to differentiate between the loss by ultrafiltration and adsorption. <b><i>Methods:</i></b> Prospective observational study in ten critically ill patients, receiving predilution CVVH with a new filter, blood flow 180 mL/min, and predilution flow 2,400 mL/h. Arterial blood, postfilter blood, and UF samples were taken at baseline, and 1, 8, and 24-h after CVVH initiation, to determine AA concentrations and hematocrit. Mass transfer calculations were used to determine AA loss in the filter and by UF, and the difference between these 2. <b><i>Results:</i></b> The median AA loss in the filter was 10.4 g/day, the median AA loss by UF was 13.4 g/day, and the median difference was –2.9 g/day (IQR –5.9 to –1.4 g/day). For the individual AA, the difference ranged from –1 g/day to +0.4 g/day, suggesting that some AA were consumed or adsorbed and others were generated. AA losses did not significantly change over the 24-h study period. <b><i>Conclusion:</i></b> During CVVH with a modern polysulfone membrane, the estimated AA loss was 13.4 g/day, which corresponds to a loss of about 11.2 g of protein per day. Adsorption did not play a major role. However, individual AA behaved differently, suggesting complex interactions and processes at the filter membrane or peripheral AA production.
DOI: 10.6084/m9.figshare.8851955.v1
title: Multicenter dataset of multishell diffusion magnetic resonance imaging in healthy traveling adults with identical setting

description: A multishell diffusion MRI dataset collected from three traveling subjects with identical acquisition setting in ten imaging centers. Both of the scanner type and imaging protocol for anatomical and diffusion imaging were well controlled. <br>Primary acquisition parameters:<b>T1-weighted images</b>Sequence: MP2RAGEResolution = 1x1x1.2 mm<sup>3</sup><br><b>Diffusion-weighted images</b>Sequence: SMS SE EPIResolution = 1.5x1.5x1.5 mm<sup>3</sup>b-value = 1000,2000,3000 mm<sup>2</sup>/sdirections = 30,30,30non-diffusion images = 6<br>This dataset is expected to replenish the individual reproducible study via multicenter collaborations by providing an open resource for advanced and novel microstructure and tractography quantifications.<br>
DOI: 10.6084/m9.figshare.8851841
title: S. cerevisiae reference transcripts

description: ref transcripts for angus 2019 more unix page
DOI: 10.6084/m9.figshare.8851955.v2
title: Multicenter dataset of multishell diffusion MRI in healthy traveling adults with identical setting

description: <strong>Introduction</strong>A multishell diffusion MRI dataset collected from three traveling subjects with identical acquisition setting in ten imaging centers. Both of the scanner type and imaging protocol for anatomical and diffusion imaging were well controlled.This dataset is expected to replenish the individual reproducible study via multicenter collaborations by providing an open resource for advanced and novel microstructure and tractography quantifications.<br><br><strong>Primary acquisition parameters</strong>• T1-weighted imagesSequence: MP2RAGEResolution = 1x1x1.2 mm<sup>3</sup><br>• Diffusion-weighted imagesSequence: SMS SE EPIResolution = 1.5x1.5x1.5 mm<sup>3</sup>b-value = 1000,2000,3000 mm<sup>2</sup>/sdirections = 30,30,30non-diffusion images = 6<strong><br></strong><strong>Data use agreement </strong><br>To use this dataset, we would like to follow the license CC BY-NC-SA (Attribution-NonCommercial-ShareAlike) https://creativecommons.org/licenses/by-nc-sa/4.0<br><strong>Contact</strong><br>For more information on the data collection and pre-processing procedure, you can contact Qiqi Tong (tongqq@zju.edu.cn)For other information or further cooperation with us, you can contact Dr. Hongjian He (hhezju@zju.edu.cn)<br>