cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7762748
title: MySQL Dump of main dataset

description: SQL Dump, with three tables:<br>+-----------------+| Tables_in_OODev |+-----------------+| FileID || ProjectID || summary |+-----------------+<br>Desc of each:mysql&gt; desc FileID;+----------+---------+------+-----+---------+-------+| Field | Type | Null | Key | Default | Extra |+----------+---------+------+-----+---------+-------+| Project | int(11) | YES | | NULL | || FullPath | text | YES | | NULL | || ID | int(11) | YES | | NULL | |+----------+---------+------+-----+---------+-------+<br>mysql&gt; desc ProjectID;+-------+---------+------+-----+---------+-------+| Field | Type | Null | Key | Default | Extra |+-------+---------+------+-----+---------+-------+| Name | text | YES | | NULL | || ID | int(11) | YES | | NULL | |+-------+---------+------+-----+---------+-------+<br>mysql&gt; desc summary;+-----------+---------+------+-----+---------+-------+| Field | Type | Null | Key | Default | Extra |+-----------+---------+------+-----+---------+-------+| Project | int(11) | YES | | NULL | || Type | text | YES | | NULL | || ClassName | text | YES | | NULL | || FileID | int(11) | YES | | NULL | || Authors | int(11) | YES | | NULL | || IFANIN | int(11) | YES | | NULL | || CBO | int(11) | YES | | NULL | || NOC | int(11) | YES | | NULL | || NIM | int(11) | YES | | NULL | || NIV | int(11) | YES | | NULL | || WMC | int(11) | YES | | NULL | || RFC | int(11) | YES | | NULL | || DIT | int(11) | YES | | NULL | || LCOM | int(11) | YES | | NULL | |+-----------+---------+------+-----+---------+-------+<br>
DOI: 10.6084/m9.figshare.7762757.v1
title: PIM-The Nrf2 pathway is required for intracellular replication of Toxoplasma gondii in activated macrophages.rar

description: The data have been used in The Nrf2 pathway is required for intracellular replication of Toxoplasma gondii in activated macrophages.<b></b>
DOI: 10.7284/108414
title: Winch data collected during research cruise AE1120 using a Markey DUSH-5 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7762733
title: Standardized sperm area in the lumen of the paired vasa deferentia of Lithodes santolla after the corresponding time periods at 9°C and 12°C from Temperature-dependent seminal recovery in the southern king crab <i>Lithodes santolla</i>

description: Male-biased fishery management can provoke depletion of seminal reserves, which is the primary cause of sperm limitation. Therefore, identifying factors which contribute to the vulnerability to depletion of seminal reserves is a priority. The present study aimed to determine the effect of temperature on the recovery rate of sperm and seminal reserves after their depletion in <i>Lithodes santolla</i>, an important fishery resource in southern Chile. Sperm and seminal reserves were not fully recovered within 30 days. Temperature significantly affected seminal recovery: after 30 days the recovery index increased to 40% and 21% at 9°C and 12°C, respectively. The twice as fast seminal recovery at 9°C may be explained by the zone of origin of the individuals in this study (northern distributional limit), and 12°C may be close to the threshold of temperature tolerance. <i>Lithodes santolla</i> populations subject to intense male-only fisheries may be vulnerable to depletion of seminal reserves and a climate change scenario could additionally aggravate the risk of seminal depletion in <i>L. santolla</i> in its northern distributional limit.
DOI: 10.6084/m9.figshare.7762733.v1
title: Standardized sperm area in the lumen of the paired vasa deferentia of Lithodes santolla after the corresponding time periods at 9°C and 12°C from Temperature-dependent seminal recovery in the southern king crab <i>Lithodes santolla</i>

description: Male-biased fishery management can provoke depletion of seminal reserves, which is the primary cause of sperm limitation. Therefore, identifying factors which contribute to the vulnerability to depletion of seminal reserves is a priority. The present study aimed to determine the effect of temperature on the recovery rate of sperm and seminal reserves after their depletion in <i>Lithodes santolla</i>, an important fishery resource in southern Chile. Sperm and seminal reserves were not fully recovered within 30 days. Temperature significantly affected seminal recovery: after 30 days the recovery index increased to 40% and 21% at 9°C and 12°C, respectively. The twice as fast seminal recovery at 9°C may be explained by the zone of origin of the individuals in this study (northern distributional limit), and 12°C may be close to the threshold of temperature tolerance. <i>Lithodes santolla</i> populations subject to intense male-only fisheries may be vulnerable to depletion of seminal reserves and a climate change scenario could additionally aggravate the risk of seminal depletion in <i>L. santolla</i> in its northern distributional limit.
DOI: 10.6084/m9.figshare.7762736
title: Dry weight of the left vasa deferentia after the corresponding time periods at 9°C and 12°C in Lithodes santolla from Temperature-dependent seminal recovery in the southern king crab <i>Lithodes santolla</i>

description: Male-biased fishery management can provoke depletion of seminal reserves, which is the primary cause of sperm limitation. Therefore, identifying factors which contribute to the vulnerability to depletion of seminal reserves is a priority. The present study aimed to determine the effect of temperature on the recovery rate of sperm and seminal reserves after their depletion in <i>Lithodes santolla</i>, an important fishery resource in southern Chile. Sperm and seminal reserves were not fully recovered within 30 days. Temperature significantly affected seminal recovery: after 30 days the recovery index increased to 40% and 21% at 9°C and 12°C, respectively. The twice as fast seminal recovery at 9°C may be explained by the zone of origin of the individuals in this study (northern distributional limit), and 12°C may be close to the threshold of temperature tolerance. <i>Lithodes santolla</i> populations subject to intense male-only fisheries may be vulnerable to depletion of seminal reserves and a climate change scenario could additionally aggravate the risk of seminal depletion in <i>L. santolla</i> in its northern distributional limit.
DOI: 10.6084/m9.figshare.7762757.v2
title: PIM-The Nrf2 pathway is required for intracellular replication of Toxoplasma gondii in activated macrophages

description: The data have been used in The Nrf2 pathway is required for intracellular replication of Toxoplasma gondii in activated macrophages.<b></b>
DOI: 10.7284/108421
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AE1121 using a Hawaii UHDAS instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7762730
title: Dry weight of the hepatopancreas of Lithodes santolla after the corresponding time periods at 9°C and 12°C from Temperature-dependent seminal recovery in the southern king crab <i>Lithodes santolla</i>

description: Male-biased fishery management can provoke depletion of seminal reserves, which is the primary cause of sperm limitation. Therefore, identifying factors which contribute to the vulnerability to depletion of seminal reserves is a priority. The present study aimed to determine the effect of temperature on the recovery rate of sperm and seminal reserves after their depletion in <i>Lithodes santolla</i>, an important fishery resource in southern Chile. Sperm and seminal reserves were not fully recovered within 30 days. Temperature significantly affected seminal recovery: after 30 days the recovery index increased to 40% and 21% at 9°C and 12°C, respectively. The twice as fast seminal recovery at 9°C may be explained by the zone of origin of the individuals in this study (northern distributional limit), and 12°C may be close to the threshold of temperature tolerance. <i>Lithodes santolla</i> populations subject to intense male-only fisheries may be vulnerable to depletion of seminal reserves and a climate change scenario could additionally aggravate the risk of seminal depletion in <i>L. santolla</i> in its northern distributional limit.
DOI: 10.6084/m9.figshare.7762730.v1
title: Dry weight of the hepatopancreas of Lithodes santolla after the corresponding time periods at 9°C and 12°C from Temperature-dependent seminal recovery in the southern king crab <i>Lithodes santolla</i>

description: Male-biased fishery management can provoke depletion of seminal reserves, which is the primary cause of sperm limitation. Therefore, identifying factors which contribute to the vulnerability to depletion of seminal reserves is a priority. The present study aimed to determine the effect of temperature on the recovery rate of sperm and seminal reserves after their depletion in <i>Lithodes santolla</i>, an important fishery resource in southern Chile. Sperm and seminal reserves were not fully recovered within 30 days. Temperature significantly affected seminal recovery: after 30 days the recovery index increased to 40% and 21% at 9°C and 12°C, respectively. The twice as fast seminal recovery at 9°C may be explained by the zone of origin of the individuals in this study (northern distributional limit), and 12°C may be close to the threshold of temperature tolerance. <i>Lithodes santolla</i> populations subject to intense male-only fisheries may be vulnerable to depletion of seminal reserves and a climate change scenario could additionally aggravate the risk of seminal depletion in <i>L. santolla</i> in its northern distributional limit.
DOI: 10.7284/108422
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AE1121 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7762736.v1
title: Dry weight of the left vasa deferentia after the corresponding time periods at 9°C and 12°C in Lithodes santolla from Temperature-dependent seminal recovery in the southern king crab <i>Lithodes santolla</i>

description: Male-biased fishery management can provoke depletion of seminal reserves, which is the primary cause of sperm limitation. Therefore, identifying factors which contribute to the vulnerability to depletion of seminal reserves is a priority. The present study aimed to determine the effect of temperature on the recovery rate of sperm and seminal reserves after their depletion in <i>Lithodes santolla</i>, an important fishery resource in southern Chile. Sperm and seminal reserves were not fully recovered within 30 days. Temperature significantly affected seminal recovery: after 30 days the recovery index increased to 40% and 21% at 9°C and 12°C, respectively. The twice as fast seminal recovery at 9°C may be explained by the zone of origin of the individuals in this study (northern distributional limit), and 12°C may be close to the threshold of temperature tolerance. <i>Lithodes santolla</i> populations subject to intense male-only fisheries may be vulnerable to depletion of seminal reserves and a climate change scenario could additionally aggravate the risk of seminal depletion in <i>L. santolla</i> in its northern distributional limit.
DOI: 10.7284/108420
title: Fluorometer data collected during research cruise AE1121 using a Turner 10-AU instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7762619
title: MOESM7 of SpotCard: an optical mark recognition tool to improve field data collection speed and accuracy

description: Additional file 7. The configuration file for the SpotCard used in Sample Data Set 2.
DOI: 10.6084/m9.figshare.7762622
title: MOESM8 of SpotCard: an optical mark recognition tool to improve field data collection speed and accuracy

description: Additional file 8. The CSV file generated from running SpotCard_Analyse.ijm on Sample Data Set 2.
DOI: 10.6084/m9.figshare.7762619.v1
title: MOESM7 of SpotCard: an optical mark recognition tool to improve field data collection speed and accuracy

description: Additional file 7. The configuration file for the SpotCard used in Sample Data Set 2.
DOI: 10.6084/m9.figshare.7762622.v1
title: MOESM8 of SpotCard: an optical mark recognition tool to improve field data collection speed and accuracy

description: Additional file 8. The CSV file generated from running SpotCard_Analyse.ijm on Sample Data Set 2.
DOI: 10.6084/m9.figshare.7762610
title: MOESM4 of SpotCard: an optical mark recognition tool to improve field data collection speed and accuracy

description: Additional file 4. The configuration file for the SpotCard used in Sample Data Set 1.
DOI: 10.6084/m9.figshare.7762613
title: MOESM5 of SpotCard: an optical mark recognition tool to improve field data collection speed and accuracy

description: Additional file 5. The CSV file generated from running SpotCard_Analyse.ijm on Sample Data Set 1. (Sample Data Set 1 Flood Fills and Sample Data Set 1 Flowers are available on GitHub).
DOI: 10.7284/106541
title: GNSS (Global Navigation Satellite System) data collected during research cruise AE1121 using a Furuno GP-90 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7762613.v1
title: MOESM5 of SpotCard: an optical mark recognition tool to improve field data collection speed and accuracy

description: Additional file 5. The CSV file generated from running SpotCard_Analyse.ijm on Sample Data Set 1. (Sample Data Set 1 Flood Fills and Sample Data Set 1 Flowers are available on GitHub).
DOI: 10.6084/m9.figshare.7762601
title: MOESM2 of SpotCard: an optical mark recognition tool to improve field data collection speed and accuracy

description: Additional file 2. The ImageJ macro code to read SpotCards.
DOI: 10.6084/m9.figshare.7762610.v1
title: MOESM4 of SpotCard: an optical mark recognition tool to improve field data collection speed and accuracy

description: Additional file 4. The configuration file for the SpotCard used in Sample Data Set 1.
DOI: 10.7284/108418
title: TSG (Thermosalinograph) data collected during research cruise AE1121 using a Sea-Bird SBE-21 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7762598
title: MOESM1 of SpotCard: an optical mark recognition tool to improve field data collection speed and accuracy

description: Additional file 1. The ImageJ macro code to createÂ SpotCards.
DOI: 10.6084/m9.figshare.7762601.v1
title: MOESM2 of SpotCard: an optical mark recognition tool to improve field data collection speed and accuracy

description: Additional file 2. The ImageJ macro code to read SpotCards.
DOI: 10.6084/m9.figshare.7762589
title: Additional file 3: of Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa

description: Table S2. Nanostring nCounter results. Table summarizing the results of Nanostring nCounter experiments used to validate the RNA-Seq dataset. The table consists of the probe name as well as the pertinent identifiers, including xloc and tcons and a binary T/F flag indicating whether the probe was determined to be working. The observed fold change in expression from anterior and posterior fragments relative to controls at 0, 3, and 6 dpb are shown (e.g., a0_c0, a3_c3, etc). Finally the sequence of each probe is indicated along with the Nanostring probe accession. (CSV 23 kb)
DOI: 10.6084/m9.figshare.7762598.v1
title: MOESM1 of SpotCard: an optical mark recognition tool to improve field data collection speed and accuracy

description: Additional file 1. The ImageJ macro code to createÂ SpotCards.
DOI: 10.7284/108419
title: Winch data collected during research cruise AE1121 using a Markey DUSH-5 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7762586
title: Additional file 2: of Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa

description: Table S1. RNA-Seq results. Table summarizing results of P. minata RNA-Seq experiments including each identified gene (“xloc”) along with a human-readable gene name and corresponding PMI accession based on Echinobase Pmin v1.0 annotations. For each gene, it is indicated whether it was found to be differentially expressed in any sample (“DE”) along with the fold change values for anterior and posterior regenerating fragments, relative to controls, for 0, 3, and 6 dpb. In addition, for each gene, if an ortholog was identified by reciprocal best blast in S. purpuratus, S. mediterranea, H. magnipapillata, or M. musculus, the accession of the identified ortholog is indicated. (CSV 4973 kb)
DOI: 10.6084/m9.figshare.7762589.v1
title: Additional file 3: of Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa

description: Table S2. Nanostring nCounter results. Table summarizing the results of Nanostring nCounter experiments used to validate the RNA-Seq dataset. The table consists of the probe name as well as the pertinent identifiers, including xloc and tcons and a binary T/F flag indicating whether the probe was determined to be working. The observed fold change in expression from anterior and posterior fragments relative to controls at 0, 3, and 6 dpb are shown (e.g., a0_c0, a3_c3, etc). Finally the sequence of each probe is indicated along with the Nanostring probe accession. (CSV 23 kb)
DOI: 10.6084/m9.figshare.7762586.v1
title: Additional file 2: of Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa

description: Table S1. RNA-Seq results. Table summarizing results of P. minata RNA-Seq experiments including each identified gene (“xloc”) along with a human-readable gene name and corresponding PMI accession based on Echinobase Pmin v1.0 annotations. For each gene, it is indicated whether it was found to be differentially expressed in any sample (“DE”) along with the fold change values for anterior and posterior regenerating fragments, relative to controls, for 0, 3, and 6 dpb. In addition, for each gene, if an ortholog was identified by reciprocal best blast in S. purpuratus, S. mediterranea, H. magnipapillata, or M. musculus, the accession of the identified ortholog is indicated. (CSV 4973 kb)
DOI: 10.6084/m9.figshare.7762571
title: Additional file 6: of Priming with Toll-like receptor 3 agonist or interferon-gamma enhances the therapeutic effects of human mesenchymal stem cells in a murine model of atopic dermatitis

description: Table S3. A full list of principal molecular and cellular functions associated with upstream regulators expressed in interferon-gamma (IFN-Îł)-primed Whartonâ s jelly-derived mesenchymal stem cells (WJ-MSCs). (XLS 34 kb)
DOI: 10.7284/108426
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AE1122 using a Hawaii UHDAS instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7762571.v1
title: Additional file 6: of Priming with Toll-like receptor 3 agonist or interferon-gamma enhances the therapeutic effects of human mesenchymal stem cells in a murine model of atopic dermatitis

description: Table S3. A full list of principal molecular and cellular functions associated with upstream regulators expressed in interferon-gamma (IFN-Îł)-primed Whartonâ s jelly-derived mesenchymal stem cells (WJ-MSCs). (XLS 34 kb)
DOI: 10.7284/108427
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AE1122 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7762556
title: Additional file 4: of Priming with Toll-like receptor 3 agonist or interferon-gamma enhances the therapeutic effects of human mesenchymal stem cells in a murine model of atopic dermatitis

description: Table S2. Upstream regulators of key cytokines that are expressed in interferon-gamma (IFN-Îł)-primed Whartonâ s jelly-derived mesenchymal stem cells (WJ-MSCs). (XLS 49 kb)
DOI: 10.6084/m9.figshare.7762556.v1
title: Additional file 4: of Priming with Toll-like receptor 3 agonist or interferon-gamma enhances the therapeutic effects of human mesenchymal stem cells in a murine model of atopic dermatitis

description: Table S2. Upstream regulators of key cytokines that are expressed in interferon-gamma (IFN-Îł)-primed Whartonâ s jelly-derived mesenchymal stem cells (WJ-MSCs). (XLS 49 kb)
DOI: 10.7284/108425
title: Fluorometer data collected during research cruise AE1122 using a Turner 10-AU instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7762550
title: Additional file 3: of Priming with Toll-like receptor 3 agonist or interferon-gamma enhances the therapeutic effects of human mesenchymal stem cells in a murine model of atopic dermatitis

description: Table S1. Upstream regulators of key cytokines that are expressed in poly I:C-primed Whartonâ s jelly-derived mesenchymal stem cells (WJ-MSCs). (XLS 31 kb)
DOI: 10.6084/m9.figshare.7762550.v1
title: Additional file 3: of Priming with Toll-like receptor 3 agonist or interferon-gamma enhances the therapeutic effects of human mesenchymal stem cells in a murine model of atopic dermatitis

description: Table S1. Upstream regulators of key cytokines that are expressed in poly I:C-primed Whartonâ s jelly-derived mesenchymal stem cells (WJ-MSCs). (XLS 31 kb)
DOI: 10.7284/106542
title: GNSS (Global Navigation Satellite System) data collected during research cruise AE1122 using a Furuno GP-90 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108423
title: TSG (Thermosalinograph) data collected during research cruise AE1122 using a Sea-Bird SBE-21 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108424
title: Winch data collected during research cruise AE1122 using a Markey DUSH-5 instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108431
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AE1123 using a Hawaii UHDAS instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7762493
title: MOESM2 of Combined analysis of dissimilar promoter accessibility and gene expression profiles identifies tissue-specific genes and actively repressed networks

description: Additional file 2. Includes the supplemental tables S1â 7. Table S1. Enriched Binding Motifs. Table S2. Enriched Motifs in HAâ ME promoters. Table S3. Nextera adapters used for ATAC-seq. Table S4. Read counts for ATAC-seq data. Table S5. Datasets used for ATAC-seq analysis. Table S6. Datasets used for RNA-seq analysis. Table S7. H3K27me3 primers.
DOI: 10.7284/108432
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AE1123 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantic Explorer

description: Original (unprocessed) data collected during a Field_expedition