cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7800920.v1
title: ReadMe_Clinical data_USPIO-enhanced MRI dataset

description: Supplemental information about the variables provided in the clinical dataset file.
DOI: 10.6084/m9.figshare.7800830
title: Fossil evidence of elytra reduction in ship-timber beetles

description: Higher resolution images for "<b>Fossil evidence of elytra reduction in ship-timber beetles</b>" in <i>Scientific Reports</i> by S. Yamamoto.<br>https://www.nature.com/articles/s41598-019-41310-1https://doi.org/10.1038/s41598-019-41310-1<br><br><b>Abstract</b>Beetles (Coleoptera) comprise about one quarter of all described animal species. One of the main contributors to their evolutionary success is the elytra, or hardened forewings, which have protective functions while maintaining their ability to fly. Unlike other beetles, some ship-timber beetles (Lymexylidae) have extremely small elytra and largely exposed functional hindwings. There is little fossil evidence illuminating the evolutionary history of short elytra in lymexylids. Here, I report five well-preserved lymexylid fossils in mid-Cretaceous and Cenozoic ambers from Myanmar (ca. 99 million years ago [Mya]), Russia (ca. 44 Mya), and the Dominican Republic (ca. 16 Mya). Three Cretaceous fossils have strongly reduced, shortened elytra, with unexpected variation in elytral size and shape, whereas very small, modified elytra are found only in much younger Dominican amber. These morphologically diverse extinct lymexylids shed new light on the early origin and evolutionary history of elytra reduction and its diverse variation in the ship-timber beetles. Based on the striking morphological similarities with extant lymexylids, these extinct taxa might have had the same, or similar, ecological, behavioural, and flight modes as the extant ship-timber beetles.<br><br><b>Note:</b><b><br></b>Fig. 1. Photos credits: (g,h) by Udo Schmidt,licensed under the Creative Commons Attribution-Share Alike 2.0 Generic license (CC BY-SA 2.0, https://creativecommons.org/licenses/by-sa/2.0/), derived from Wikimedia Commons, (h) modified.<br><br>
DOI: 10.6084/m9.figshare.7800917.v1
title: Clinical data for USPIO-enhanced MRI dataset

description: Clinical data for the 5 head and neck squamous cell carcinoma (HNSCC) patients, representing our cohort. Patients and disease identifiers are detailed in this *.csv file.
DOI: 10.6084/m9.figshare.7800830.v1
title: Fossil evidence of elytra reduction in ship-timber beetles

description: High resolution images.<br>Fig. 1. Photos credits: (g,h) by Udo Schmidt,licensed under the Creative Commons Attribution-Share Alike 2.0 Generic license (CC BY-SA 2.0, https://creativecommons.org/licenses/by-sa/2.0/), derived from Wikimedia Commons, (h) modified.
DOI: 10.25376/hra.7800752
title: The allosteric glycogen synthase kinase-3 inhibitor NP12 limits myocardial remodeling and promotes angiogenesis in an acute myocardial infarction model

description: A key feature of acute myocardial infarction (AMI) is an alteration in cardiac architecture. Signaling events that result in the inhibition of glycogen synthase kinase-3b (GSK-3) represent an adaptive response that might limit the extent of adverse remodeling in the aftermath of AMI. Here, we report that an allosteric inhibitor of GSK-3b, 4-benzyl-2-(naphthalene-1-yl)-1,2,4-thiadiazolidine-3,5-dione (NP12), lessens the magnitude of adverse myocardial remodeling and promotes angiogenesis. Male and female mice 8–10 weeks old were grouped (six animals in each group) into sham surgery (sham group), left anterior descending (LAD) ligation of the coronary artery followed by intramyocardial PBS injections (control group), and LAD ligation followed by NP12 administration (NP12 group). After 7 and 14 days, the extents of fibrosis and integrity of blood vessels were determined. Intramyocardial administration of NP12 increased phosphorylation of GSK-3b, reduced fibrosis, and restored diastolic function in the mice that had experienced an AMI. Morphometric analyses revealed increased CD31 and Ki67 vascular structures and decreased apoptosis in these mice. NP12 administration mediated proliferation of reparative cells in the AMI hearts. In a time-course analysis, Wnt3a and NP12 stabilized b-catenin and increased expression of both Nanog and VEGFR2. Moreover, NP12 increased the expression of -catenin and Nanog in myocardium from AMI mice. Finally, loss- and gain-of-function experiments indicated that the NP12-mediated benefit is, in part, Nanog-specific. These findings indicate that NP12 reduces fibrosis, reestablishes coronary blood flow, and improves ventricular function following an AMI. We conclude that NP12 might be useful for limiting ventricular remodeling after an AMI.
DOI: 10.25376/hra.7800752.v1
title: The allosteric glycogen synthase kinase-3 inhibitor NP12 limits myocardial remodeling and promotes angiogenesis in an acute myocardial infarction model

description: A key feature of acute myocardial infarction (AMI) is an alteration in cardiac architecture. Signaling events that result in the inhibition of glycogen synthase kinase-3b (GSK-3) represent an adaptive response that might limit the extent of adverse remodeling in the aftermath of AMI. Here, we report that an allosteric inhibitor of GSK-3b, 4-benzyl-2-(naphthalene-1-yl)-1,2,4-thiadiazolidine-3,5-dione (NP12), lessens the magnitude of adverse myocardial remodeling and promotes angiogenesis. Male and female mice 8–10 weeks old were grouped (six animals in each group) into sham surgery (sham group), left anterior descending (LAD) ligation of the coronary artery followed by intramyocardial PBS injections (control group), and LAD ligation followed by NP12 administration (NP12 group). After 7 and 14 days, the extents of fibrosis and integrity of blood vessels were determined. Intramyocardial administration of NP12 increased phosphorylation of GSK-3b, reduced fibrosis, and restored diastolic function in the mice that had experienced an AMI. Morphometric analyses revealed increased CD31 and Ki67 vascular structures and decreased apoptosis in these mice. NP12 administration mediated proliferation of reparative cells in the AMI hearts. In a time-course analysis, Wnt3a and NP12 stabilized b-catenin and increased expression of both Nanog and VEGFR2. Moreover, NP12 increased the expression of -catenin and Nanog in myocardium from AMI mice. Finally, loss- and gain-of-function experiments indicated that the NP12-mediated benefit is, in part, Nanog-specific. These findings indicate that NP12 reduces fibrosis, reestablishes coronary blood flow, and improves ventricular function following an AMI. We conclude that NP12 might be useful for limiting ventricular remodeling after an AMI.
DOI: 10.6084/m9.figshare.7800704
title: Supplemental Table S7

description: <b>Supplemental Table 7. </b>Top 10 significantly (p-value &lt;0.05) enriched Ingenuity Canonical Pathways in the HFD:HFD+DHA (39 total enriched pathways), the HFD:HFD+EPA (5 total enriched pathways), and the HFD+DHA:HFD+EPA (61 enriched pathways) comparisons of skeletal muscle transcriptomes. Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript and blue indicates downregulation.
DOI: 10.6084/m9.figshare.7800701
title: EPOS Software Artifact

description: This dataset is the software artifact of I-EPOS, the <i>Iterative Economic Planning and Optimized Selections</i>. EPOS is collective learning algorithm for decentralized combinatorial optimization problems.<br>http://epos-net.org<br>
DOI: 10.6084/m9.figshare.7800704.v1
title: Supplemental Table S7

description: <b>Supplemental Table 7. </b>Top 10 significantly (p-value &lt;0.05) enriched Ingenuity Canonical Pathways in the HFD:HFD+DHA (39 total enriched pathways), the HFD:HFD+EPA (5 total enriched pathways), and the HFD+DHA:HFD+EPA (61 enriched pathways) comparisons of skeletal muscle transcriptomes. Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript and blue indicates downregulation.
DOI: 10.6084/m9.figshare.7800698
title: Supplemental Table S6

description: <b>Supplemental Table 6. </b>Top 10 significantly (p-value &lt;0.05) enriched Ingenuity Canonical Pathways in the HFD:HFD+DHA (14 total enriched pathways), the HFD:HFD+EPA (9 enriched pathways), and the HFD+DHA:HFD+EPA (15 enriched pathways) comparisons of liver transcriptomes. Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript in the reference group (listed first) and blue indicates downregulation.
DOI: 10.6084/m9.figshare.7800641
title: CCDB_1035.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7800698.v1
title: Supplemental Table S6

description: <b>Supplemental Table 6. </b>Top 10 significantly (p-value &lt;0.05) enriched Ingenuity Canonical Pathways in the HFD:HFD+DHA (14 total enriched pathways), the HFD:HFD+EPA (9 enriched pathways), and the HFD+DHA:HFD+EPA (15 enriched pathways) comparisons of liver transcriptomes. Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript in the reference group (listed first) and blue indicates downregulation.
DOI: 10.6084/m9.figshare.7800632
title: Supplemental Table S5

description: <b>Supplemental Table 5. </b>Top 10<b> </b>significantly (p&lt;0.05) enriched Ingenuity Canonical Pathways for the 76 transcripts that were differentially expressed in the HFD:control comparison of skeletal muscle transcriptomes but not the HFD+EPA:control comparison (total of 21 enriched pathways), and for the 216 transcripts differentially expressed in the HFD+EPA:control comparison of skeletal muscle transcriptomes, but not the HFD:Control comparison (total of 116 enriched pathways). Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript and blue indicates downregulation.<b></b>
DOI: 10.6084/m9.figshare.7800635
title: CCDB_1034.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7800629
title: Supplemental Table S4

description: <b>Supplemental Table 4. </b>Top 10<b> </b>significantly (p&lt;0.05) enriched Ingenuity Canonical Pathways for the 152 transcripts that were differentially expressed in the HFD:control comparison of skeletal muscle transcriptomes but not the HFD+DHA:control comparison (total of 59 enriched pathways), and for the 67 transcripts differentially expressed in the HFD+DHA:control comparison of skeletal muscle transcriptomes, but not the HFD:Control comparison (total of 44 enriched pathways). Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript and blue indicates downregulation.<b></b>
DOI: 10.6084/m9.figshare.7800635.v1
title: CCDB_1034.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7800641.v1
title: CCDB_1035.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7800626
title: Supplemental Table S3

description: <b>Supplemental Table 3.</b> Top 10<b> </b>significantly (p&lt;0.05) enriched Ingenuity Canonical Pathways for the 92 transcripts that were differentially expressed in the HFD:control comparison of liver transcriptomes but not the HFD+EPA:control comparison (total of 25 enriched pathways), and for the 264 transcripts differentially expressed in the HFD+EPA:control comparison of liver transcriptomes, but not the HFD:Control comparison (total of 33 enriched pathways). Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript and blue indicates downregulation.<b></b>
DOI: 10.6084/m9.figshare.7800629.v1
title: Supplemental Table S4

description: <b>Supplemental Table 4. </b>Top 10<b> </b>significantly (p&lt;0.05) enriched Ingenuity Canonical Pathways for the 152 transcripts that were differentially expressed in the HFD:control comparison of skeletal muscle transcriptomes but not the HFD+DHA:control comparison (total of 59 enriched pathways), and for the 67 transcripts differentially expressed in the HFD+DHA:control comparison of skeletal muscle transcriptomes, but not the HFD:Control comparison (total of 44 enriched pathways). Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript and blue indicates downregulation.<b></b>
DOI: 10.6084/m9.figshare.7800632.v1
title: Supplemental Table S5

description: <b>Supplemental Table 5. </b>Top 10<b> </b>significantly (p&lt;0.05) enriched Ingenuity Canonical Pathways for the 76 transcripts that were differentially expressed in the HFD:control comparison of skeletal muscle transcriptomes but not the HFD+EPA:control comparison (total of 21 enriched pathways), and for the 216 transcripts differentially expressed in the HFD+EPA:control comparison of skeletal muscle transcriptomes, but not the HFD:Control comparison (total of 116 enriched pathways). Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript and blue indicates downregulation.<b></b>
DOI: 10.6084/m9.figshare.7800611
title: Supplemental Table S2

description: <b>Supplemental Table 2. </b>Top 10<b> </b>significantly (p&lt;0.05) enriched Ingenuity Canonical Pathways for the 193 transcripts that were differentially expressed in the HFD:control comparison of liver transcriptomes but not the HFD+DHA:control comparison (total of 24 enriched pathways), and for the 179 transcripts differentially expressed in the HFD+DHA:control comparison of liver transcriptomes, but not the HFD:Control comparison (total of 16 enriched pathways). Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript and blue indicates downregulation.
DOI: 10.6084/m9.figshare.7800626.v1
title: Supplemental Table S3

description: <b>Supplemental Table 3.</b> Top 10<b> </b>significantly (p&lt;0.05) enriched Ingenuity Canonical Pathways for the 92 transcripts that were differentially expressed in the HFD:control comparison of liver transcriptomes but not the HFD+EPA:control comparison (total of 25 enriched pathways), and for the 264 transcripts differentially expressed in the HFD+EPA:control comparison of liver transcriptomes, but not the HFD:Control comparison (total of 33 enriched pathways). Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript and blue indicates downregulation.<b></b>
DOI: 10.6084/m9.figshare.7800626.v2
title: Supplemental Table S3

description: <b>Supplemental Table 3.</b> Top 10<b> </b>significantly (p&lt;0.05) enriched Ingenuity Canonical Pathways for the 92 transcripts that were differentially expressed in the HFD:control comparison of liver transcriptomes but not the HFD+EPA:control comparison (total of 25 enriched pathways), and for the 264 transcripts differentially expressed in the HFD+EPA:control comparison of liver transcriptomes, but not the HFD:Control comparison (total of 33 enriched pathways). Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript and blue indicates downregulation.<b></b>
DOI: 10.6084/m9.figshare.7800605
title: Acosta.etal.Feb2019 Basiliscus vittatus assembled male and female genomes

description: Assembled genomes of 1 male and 1 female Basiliscus vittatus using SOAP de novo (v.2; default parameters) (Luo, et al. 2012)<br><br>
DOI: 10.6084/m9.figshare.7800608
title: CCDB_1033.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7800608.v1
title: CCDB_1033.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7800611.v1
title: Supplemental Table S2

description: <b>Supplemental Table 2. </b>Top 10<b> </b>significantly (p&lt;0.05) enriched Ingenuity Canonical Pathways for the 193 transcripts that were differentially expressed in the HFD:control comparison of liver transcriptomes but not the HFD+DHA:control comparison (total of 24 enriched pathways), and for the 179 transcripts differentially expressed in the HFD+DHA:control comparison of liver transcriptomes, but not the HFD:Control comparison (total of 16 enriched pathways). Transcriptomic analysis was performed on N=4 for each group. Ratio = number of differentially expressed genes/total genes in pathway. Red indicates predicted positive activation of the pathway and upregulation of an individual transcript and blue indicates downregulation.
DOI: 10.6084/m9.figshare.7800590
title: The Evolution of Evolvability: Changing Environments Promote Rapid Adaptation in Digital Organisms - Data Archive

description: Dataset supporting The Evolution of Evolvability: Changing Environments Promote Rapid Adaptation in Digital Organisms - Data Archive.<br>Includes raw data, Avida configuration files, intermediate data, and Jupyter Notebooks used to generate figures and analyses for the paper.<br>A live repository for this dataset (absent the large raw datafiles) can be found at https://github.com/voidptr/ce_rapid_adaptation_data
DOI: 10.6084/m9.figshare.7800605.v1
title: Acosta.etal.Feb2019 Basiliscus vittatus assembled male and female genomes

description: Assembled genomes of 1 male and 1 female Basiliscus vittatus using SOAP de novo (v.2; default parameters) (Luo, et al. 2012)<br><br>
DOI: 10.6084/m9.figshare.7800590.v1
title: The Evolution of Evolvability: Changing Environments Promote Rapid Adaptation in Digital Organisms - Data Archive

description: Dataset supporting The Evolution of Evolvability: Changing Environments Promote Rapid Adaptation in Digital Organisms - Data Archive.<br>Includes raw data, Avida configuration files, intermediate data, and Jupyter Notebooks used to generate figures and analyses for the paper.<br>A live repository for this dataset (absent the large raw datafiles) can be found at https://github.com/voidptr/ce_rapid_adaptation_data
DOI: 10.6084/m9.figshare.7800554
title: pubchemAssaysRAW.zip

description: PubChem HTS assays referenced in publication.these files were used for training, testing, and validation of the model.
DOI: 10.6084/m9.figshare.7800554.v1
title: pubchemAssaysRAW.zip

description: PubChem HTS assays referenced in publication.these files were used for training, testing, and validation of the model.
DOI: 10.6084/m9.figshare.7799774
title: Metacademy-prerequisite-pairs-transformed-to-wikipedia.csv

description: This is a new evaluation set for prerequisites based on a semi-automatic mapping of an expert-generated concept graph(Metacademy) to Wikipedia. It was initially introduced in the paper 'Finding Prerequisite Relations using the Wikipedia Clickstream'.<br><br>
DOI: 10.6084/m9.figshare.7799129
title: ColPortal_Microbiome_analyzed

description: Table with genus and species abundance by samples<br>
DOI: 10.6084/m9.figshare.7799138
title: ColPortal_ClinicalCases_RawData

description: Clinical cases<br>
DOI: 10.6084/m9.figshare.7799774.v1
title: Metacademy-prereq-pairs-transoformed-to-wiki.csv

description: This is a new evaluation set for prerequisites based on a semi-automatic mapping of an expert-generated concept graph(Metacademy) to Wikipedia. It was initially introduced in the paper 'Finding Prerequisite Relations using the Wikipedia Clickstream'.<br><br>
DOI: 10.6084/m9.figshare.7799138.v1
title: ColPortal_ClinicalCases_RawData

description: Clinical cases<br>
DOI: 10.6084/m9.figshare.7799126
title: Rscripts

description: Scripts used in the different analyses.<br>
DOI: 10.6084/m9.figshare.7799129.v1
title: ColPortal_Microbiome_analyzed

description: Table with genus and species abundance by samples<br>
DOI: 10.6084/m9.figshare.7799138.v3
title: ColPortal_ClinicalCases_RawData

description: Clinical cases<br>
DOI: 10.6084/m9.figshare.7799774.v2
title: Metacademy-prereq-pairs-transoformed-to-wiki.csv

description: This is a new evaluation set for prerequisites based on a semi-automatic mapping of an expert-generated concept graph(Metacademy) to Wikipedia. It was initially introduced in the paper 'Finding Prerequisite Relations using the Wikipedia Clickstream'.<br><br>
DOI: 10.6073/pasta/19d09dcbffdc157de384d4f6dae8f3e8
title: Surface soil nitrogen analyses under mesquite bush canopies and interspaces at the Jornada Basin LTER, 1986

description: This data package contains soil nitrogen data for soils collected under, or near, mesquite at the Jornada Basin LTER site (LTER-I and II) in 1986. The purpose of this study was to analyze nitrogen concentration in soils associated with mesquite (Prosopis glandulosa). The mesquite soils were sampled at 4 habitats - playa, coppice dune, arroyo, and grassland. An ecosystem dominated by the non-legume, Larrea tridentata, and lacking mesquite was included as a reference. Samples were taken from two depths (0-15cm, 15-30cm) for three beneath canopy positions (stem base, mid-canopy, and edge of canopy) and one non-vegetated interzone position for each shrub. Four shrubs were sampled at each site. The soils were analyzed for Total Kjeldahl Nitrogen (TKN), N03 nitrate, NH4 ammonium. The data set was collected on October 1, 1986 and this study is now complete.
DOI: 10.6084/m9.figshare.7799138.v2
title: ColPortal_ClinicalCases_RawData

description: Clinical cases<br>
DOI: 10.6084/m9.figshare.7799111
title: Supplemental Table S1

description: <strong>Supplemental Table 1. </strong>Dietary composition of the purified diets for the control, HFD, HFD+EPA, and HFD+DHA groups.
DOI: 10.6084/m9.figshare.7799123
title: ColPortal_microbiome_RawData

description: Microbiome raw data<br>
DOI: 10.6084/m9.figshare.7799774.v3
title: Metacademy-prereq-pairs-transoformed-to-wiki.csv

description: This is a new evaluation set for prerequisites based on a semi-automatic mapping of an expert-generated concept graph(Metacademy) to Wikipedia. It was initially introduced in the paper 'Finding Prerequisite Relations using the Wikipedia Clickstream'.<br><br>