cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8136781
title: Raw data of Cedar Creek Experiment

description: <strong>1.-Experiment </strong> The experimental design consisted of 21 populations inoculated with 1 mL water samples taken near the Cedar Bog Lake dock on July 7th. Each population consisted of a final volume of 39 mL in transparent Greiner Bio-One vented-cap culture flasks. We used a three-by-two factorial design with three nitrogen concentrations (standard BG11 medium (17.6 mM NaNO3), a reduced nitrogen BG11 medium (9 mM NaNO3), and a BG11-0 medium (without nitrogen)) and (10 mM NaCl) and without NaCl addition. To account for the effect of nutrient addition, we added a control treatment with deionized water. Three replicates population of each experimental condition were stabilized. The experiment was run for 3 weeks. Table 1: Experimental design. <strong>dH20</strong> <strong>BG11</strong> <strong>BG11 reduce Nitrogen</strong> <strong>B11 without Nitrogen </strong> <strong>BG11 +NaCl</strong> <strong>BG11 reduce Nitrogen</strong> <strong>+NaCl</strong> <strong>B11 without Nitrogen+NaC</strong>l R1 R16 R10 R4 R19 R13 R7 R2 R17 R11 R5 R20 R14 R8 R3 R18 R12 R6 R21 R15 R9 <strong>1.1 FlowCam( Fluid Imaging Technologies) Data collection</strong> 0.15 mL aliquots of each population at week three were run through a Flowcam cytometer (Fluid Imaging Technologies) at a speed of 0.14 mL/min and collect images of individual particles and estimate biovolume using total area. The 10x magnification setting was used with a calibration factor of 0.5525. For each sample, the first 1,000 images taken by FlowCam were selected for species diversity analysis. Each folder is a separate population at T3 (21 days). It contains the original run (pictures and files) and within it can be found the classification by “groups” (pictures and files). <strong>1.2 Flotation Device Technical Description</strong> Flotation Device is a suspension system to safely maintain planktonic microbial populations to carry out studies at the water temperature and light conditions of a water body. <strong>1.3 Bradford Protein Assay Data </strong> Populations were checked weekly by sampling aliquots of all the populations and running Bradford Protein Assays as a proxy for population growth.
description: This material is based upon work supported by the Minnesota Agricultural Experiment Station, and the National Institute of Food and Agriculture, U.S. Department of Agriculture, project MIN-73-015 under accession no. 1009904 BBC was supported by the MNDrive environment grant entitled: Cyanotoxin Bioremediation with Microbes
DOI: 10.5281/zenodo.8136780
title: Raw data of Cedar Creek Experiment

description: <strong>1.-Experiment </strong> The experimental design consisted of 21 populations inoculated with 1 mL water samples taken near the Cedar Bog Lake dock on July 7th. Each population consisted of a final volume of 39 mL in transparent Greiner Bio-One vented-cap culture flasks. We used a three-by-two factorial design with three nitrogen concentrations (standard BG11 medium (17.6 mM NaNO3), a reduced nitrogen BG11 medium (9 mM NaNO3), and a BG11-0 medium (without nitrogen)) and (10 mM NaCl) and without NaCl addition. To account for the effect of nutrient addition, we added a control treatment with deionized water. Three replicates population of each experimental condition were stabilized. The experiment was run for 3 weeks. Table 1: Experimental design. <strong>dH20</strong> <strong>BG11</strong> <strong>BG11 reduce Nitrogen</strong> <strong>B11 without Nitrogen </strong> <strong>BG11 +NaCl</strong> <strong>BG11 reduce Nitrogen</strong> <strong>+NaCl</strong> <strong>B11 without Nitrogen+NaC</strong>l R1 R16 R10 R4 R19 R13 R7 R2 R17 R11 R5 R20 R14 R8 R3 R18 R12 R6 R21 R15 R9 <strong>1.1 FlowCam( Fluid Imaging Technologies) Data collection</strong> 0.15 mL aliquots of each population at week three were run through a Flowcam cytometer (Fluid Imaging Technologies) at a speed of 0.14 mL/min and collect images of individual particles and estimate biovolume using total area. The 10x magnification setting was used with a calibration factor of 0.5525. For each sample, the first 1,000 images taken by FlowCam were selected for species diversity analysis. Each folder is a separate population at T3 (21 days). It contains the original run (pictures and files) and within it can be found the classification by “groups” (pictures and files). <strong>1.2 Flotation Device Technical Description</strong> Flotation Device is a suspension system to safely maintain planktonic microbial populations to carry out studies at the water temperature and light conditions of a water body. <strong>1.3 Bradford Protein Assay Data </strong> Populations were checked weekly by sampling aliquots of all the populations and running Bradford Protein Assays as a proxy for population growth.
description: This material is based upon work supported by the Minnesota Agricultural Experiment Station, and the National Institute of Food and Agriculture, U.S. Department of Agriculture, project MIN-73-015 under accession no. 1009904 BBC was supported by the MNDrive environment grant entitled: Cyanotoxin Bioremediation with Microbes
DOI: 10.6084/m9.figshare.23700189
title: Phrynocephalus forsythii SSR Genotyping data

description: Genotyping allele dataset of 21 microsatellite loci for <em>Phrynocephalus forsythii. </em>Population information are also included.
DOI: 10.6084/m9.figshare.23700189.v1
title: Phrynocephalus forsythii SSR Genotyping data

description: Genotyping allele dataset of 21 microsatellite loci for <em>Phrynocephalus forsythii. </em>Population information are also included.
DOI: 10.6084/m9.figshare.23699991
title: LARRY LT-scRNA-seq dataset formatted for fate prediction

description: LARRY LT-scRNA-seq dataset formatted for fate prediction
DOI: 10.6084/m9.figshare.23699991.v1
title: LARRY LT-scRNA-seq dataset formatted for fate prediction

description: LARRY LT-scRNA-seq dataset formatted for fate prediction
DOI: 10.6084/m9.figshare.23306234
title: Data of underground pipelines detected using transient electromagnetic method

description: This data set was collected using a small circuit transient electromagnetic device and integrated with xls in the data format.
DOI: 10.6084/m9.figshare.23306234.v1
title: data.xls

description: This data set was collected using a small circuit transient electromagnetic device and integrated with xls in the data format.
DOI: 10.5281/zenodo.8157678
title: Single-Cell Mapping Reveals Several Immune Subsets Associated with Liver Metastasis of Pancreatic Ductal Adenocarcinoma

description: Identifying a metastasis-correlated immune cell composition within the tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) will help to develop promising and innovative therapeutic strategies. Twenty-six samples from 11 patients (including 11 primary tumor tissues, 10 blood, and 5 lymph nodes) with different stages were used to develop a multiscale immune profile. High-dimensional single-cell analysis with mass cytometry was performed to search for metastasis-correlated immune changes in the microenvironment. The details about the files uploaded are as follows: 1. panelA_Blood.zip includes 10 .fcs files from blood samples in Panel A; 2. panelA_LN.zip includes 5 .fcs files from lymph node samples in Panel A; 3. panelA_Tumor.zip includes 11 .fcs files from tumor tissue samples in Panel A; 4. panelB_Tumor.zip includes 11 .fcs files from tumor tissue samples in Panel B; 5. panel_metadata.xlsx describes marker used in Panel A and B; 6. sample_metadata.xlsx describes detailed sample information.
DOI: 10.5281/zenodo.8157679
title: Single-Cell Mapping Reveals Several Immune Subsets Associated with Liver Metastasis of Pancreatic Ductal Adenocarcinoma

description: Identifying a metastasis-correlated immune cell composition within the tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) will help to develop promising and innovative therapeutic strategies. Twenty-six samples from 11 patients (including 11 primary tumor tissues, 10 blood, and 5 lymph nodes) with different stages were used to develop a multiscale immune profile. High-dimensional single-cell analysis with mass cytometry was performed to search for metastasis-correlated immune changes in the microenvironment. The details about the files upload are as follows: 1. panelA_Blood.zip includes 10 .fcs files from blood samples in Panel A; 2. panelA_LN.zip includes 5 .fcs files from lymph node samples in Panel A; 3. panelA_Tumor.zip includes 11 .fcs files from tumor tissue samples in Panel A; 4. panelB_Tumor.zip includes 11 .fcs files from tumor tissue samples in Panel B; 5. panel_metadata.xlsx describes marker used in Panel A and B; 6. sample_metadata.xlsx describes detailed sample information.
DOI: 10.5281/zenodo.8157687
title: Single-Cell Mapping Reveals Several Immune Subsets Associated with Liver Metastasis of Pancreatic Ductal Adenocarcinoma

description: Identifying a metastasis-correlated immune cell composition within the tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) will help to develop promising and innovative therapeutic strategies. Twenty-six samples from 11 patients (including 11 primary tumor tissues, 10 blood, and 5 lymph nodes) with different stages were used to develop a multiscale immune profile. High-dimensional single-cell analysis with mass cytometry was performed to search for metastasis-correlated immune changes in the microenvironment. The details about the files uploaded are as follows: 1. panelA_Blood.zip includes 10 .fcs files from blood samples in Panel A; 2. panelA_LN.zip includes 5 .fcs files from lymph node samples in Panel A; 3. panelA_Tumor.zip includes 11 .fcs files from tumor tissue samples in Panel A; 4. panelB_Tumor.zip includes 11 .fcs files from tumor tissue samples in Panel B; 5. panel_metadata.xlsx describes marker used in Panel A and B; 6. sample_metadata.xlsx describes detailed sample information.
DOI: 10.5281/zenodo.8157645
title: Constructions Dataset

description: These are the data associated with the manuscript entitled: "<strong>Syntactic Constructions Drive Cortical Tracking in the Absence of Lexical Content: An Electrophysiological Investigation of Sentence Processing During Reading".</strong>
DOI: 10.5281/zenodo.8157644
title: Constructions Dataset

description: These are the data associated with the manuscript entitled: "<strong>Syntactic Constructions Drive Cortical Tracking in the Absence of Lexical Content: An Electrophysiological Investigation of Sentence Processing During Reading".</strong>
DOI: 10.6084/m9.figshare.23700369
title: <strong>Source data and statistics</strong>

description: Statisitcs associated with all figures displayed and unprocessed western blots for Fig.1 and Fig.4
DOI: 10.5281/zenodo.8157657
title: ACA CO(J=2-1) Mapping of the Nearest Spiral Galaxy M33. I. Initial Results and Identification of Molecular Clouds

description: (1) M33_ACA7m+IRAM_12CO21_cube_pbcor_kelvin.fits.tar.gz (661 MB): <sup>12</sup>CO(<em>J</em>=2-1) data cube obtained with the ACA 7m array combined with the IRAM 30m telescope, 7".31 x 6".50 beam, 0.7 km/s resolution<br> (2) M33_ACA7m-only_12CO21_cube_pbcor_kelvin.fits.tar.gz (660.6 MB): <sup>12</sup>CO(<em>J</em>=2-1) data cube obtained with the ACA stand-alone mode (7m array only), 7".31 x 6".50 beam, 0.7 km/s resolution<br> (3) M33_ACA7m-only_13CO21_cube_pbcor_kelvin.fits.tar.gz (331.5 MB): <sup>13</sup>CO(<em>J</em>=2-1) data cube obtained with the ACA stand-alone mode (7m array only), 7".72 x 6".86 beam, 1.4 km/s resolution<br> (4) M33_ACA7m-only_C18O21_cube_pbcor_kelvin.fits.tar.gz (289.9 MB): C<sup>18</sup>O(<em>J</em>=2-1) data cube obtained with the ACA stand-alone mode (7m array only), 7".82 x 6".96 beam, 1.6 km/s resolution
DOI: 10.5281/zenodo.8157656
title: ACA CO(J=2-1) Mapping of the Nearest Spiral Galaxy M33. I. Initial Results and Identification of Molecular Clouds

description: (1) M33_ACA7m+IRAM_12CO21_cube_pbcor_kelvin.fits.tar.gz (661 MB): <sup>12</sup>CO(<em>J</em>=2-1) data cube obtained with the ACA 7m array combined with the IRAM 30m telescope, 7".31 x 6".50 beam, 0.7 km/s resolution<br> (2) M33_ACA7m-only_12CO21_cube_pbcor_kelvin.fits.tar.gz (660.6 MB): <sup>12</sup>CO(<em>J</em>=2-1) data cube obtained with the ACA stand-alone mode (7m array only), 7".31 x 6".50 beam, 0.7 km/s resolution<br> (3) M33_ACA7m-only_13CO21_cube_pbcor_kelvin.fits.tar.gz (331.5 MB): <sup>13</sup>CO(<em>J</em>=2-1) data cube obtained with the ACA stand-alone mode (7m array only), 7".72 x 6".86 beam, 1.4 km/s resolution<br> (4) M33_ACA7m-only_C18O21_cube_pbcor_kelvin.fits.tar.gz (289.9 MB): C<sup>18</sup>O(<em>J</em>=2-1) data cube obtained with the ACA stand-alone mode (7m array only), 7".82 x 6".96 beam, 1.6 km/s resolution
DOI: 10.5281/zenodo.8070983
title: Dataset of Molecular Dynamics Simulations for the Upregulated Biomarker PSMB8: 3UNF and its G210V Mutant in Experimental Autoimmune Encephalomyelitis

description: This dataset contains molecular dynamics simulations data generated using GROMACS for the upregulated biomarker 3UNF and its G210V mutant in the context of Experimental Autoimmune Encephalomyelitis (EAE). EAE is a widely studied animal model for multiple sclerosis, and investigating the behavior of biomarkers in this model is crucial for understanding disease progression and potential therapeutic interventions. The dataset includes trajectory files, coordinate files, and relevant parameters used in the simulations. These simulations provide valuable insights into the structural dynamics, conformational changes, and interactions of the PSMB8 biomarker 3UNF and its G210V mutant within the EAE system. The data offers researchers an opportunity to analyze and explore the behavior of these biomarkers at the atomic level, aiding in the identification of potential binding partners, functional sites, and mechanisms associated with disease progression. By sharing this dataset, we aim to contribute to the scientific community by providing a valuable resource for further analysis, validation, and comparison of the molecular behavior of the upregulated biomarker 3UNF and its G210V mutant in Experimental Autoimmune Encephalomyelitis.
description: {"references": ["Paul, Shamrat Kumar, et al. \"Molecular modeling, molecular dynamics simulation, and essential dynamics analysis of grancalcin: An upregulated biomarker in experimental autoimmune encephalomyelitis mice.\" Heliyon 8.10 (2022): e11232."]}
DOI: 10.5281/zenodo.8157696
title: Performance and process-based evaluation of BARPA-R

description: Supporting data for figures in GMD draft paper: Performance and process-based evaluation of BARPA-R
DOI: 10.26180/23632287.v1
title: Role of naturally occurring dietary salicylates in Irritable Bowel Syndrome

description: Overall design: This was a pilot, double-blind, randomised, cross-over trial of low versus high-salicylate diets in IBS patients who had no previous exposure to a low chemical diet.<br> Materials: Participants were randomized by a computer-generated order to receive a diet either low or high in salicylate content for 14-days (6.6 and 27.9 g/day salicylate respectively). All food was provided. Participants and investigators were blinded to the diet. After the initial 14-days, the participants undertook a washout period of 7 days, where they resumed their habitual diet. No food was provided during this phase. During the washout phase, they completed a diary recording their symptoms and the amount and type of food they ate. This was followed by a cross-over to the alternate diet for further 14 days.<br> During the interventional dietary phases, all participants were provided with food and they completed information on the quantity of the provided foods consumed.<br> Interventional diets:<br> All foods including three main meals, morning and afternoon snacks, and drinks were provided. Detailed meal plans for high- and low-salicylate diets were provided to the participants. For some meals that included fresh salads, detailed recipes were provided for participants to prepare before consumption. They were strictly instructed to avoid eating out during the course of the study. If participants wanted to eat foods that were not specified on the supplied list, they contacted the study investigator for guidance on food choices.<br> Who provided intervention delivery & mode of delivery: The study investigator and two professional chefs prepared all foods in the commercial kitchen of Department of Dietetics, Monash University. Frozen complete meals were provided to the participants with instructions to thaw and heat before consumption. The foods were delivered bi-weekly free of charge to the participant homes.<br> The diets were designed based upon the salicylate content of foods. Both diets were free of gluten, preservatives, additives and lactose, were consistent in their levels of minimal FODMAPs (fermentable oligo- di- mono-saccharides and polyols), and contained moderate levels of amines and glutamates as per published food content to avoid any confounding factors that might affect the symptoms.<br> The average daily intake of salicylates in the low-salicylate diet was approximately 6 mg. The meal plans had an average energy value of 8 MJ daily and met the recommended serves of all food groups according to the Australian dietary guidelines.<br> Location: The intervention occurred within the participants home.<br> Personalisation: The intervention was not personalised to each patient.<br> Adherence: Compliance was monitored via the daily food diaries.
DOI: 10.26180/23632287
title: Role of naturally occurring dietary salicylates in Irritable Bowel Syndrome

description: Overall design: This was a pilot, double-blind, randomised, cross-over trial of low versus high-salicylate diets in IBS patients who had no previous exposure to a low chemical diet.<br> Materials: Participants were randomized by a computer-generated order to receive a diet either low or high in salicylate content for 14-days (6.6 and 27.9 g/day salicylate respectively). All food was provided. Participants and investigators were blinded to the diet. After the initial 14-days, the participants undertook a washout period of 7 days, where they resumed their habitual diet. No food was provided during this phase. During the washout phase, they completed a diary recording their symptoms and the amount and type of food they ate. This was followed by a cross-over to the alternate diet for further 14 days.<br> During the interventional dietary phases, all participants were provided with food and they completed information on the quantity of the provided foods consumed.<br> Interventional diets:<br> All foods including three main meals, morning and afternoon snacks, and drinks were provided. Detailed meal plans for high- and low-salicylate diets were provided to the participants. For some meals that included fresh salads, detailed recipes were provided for participants to prepare before consumption. They were strictly instructed to avoid eating out during the course of the study. If participants wanted to eat foods that were not specified on the supplied list, they contacted the study investigator for guidance on food choices.<br> Who provided intervention delivery & mode of delivery: The study investigator and two professional chefs prepared all foods in the commercial kitchen of Department of Dietetics, Monash University. Frozen complete meals were provided to the participants with instructions to thaw and heat before consumption. The foods were delivered bi-weekly free of charge to the participant homes.<br> The diets were designed based upon the salicylate content of foods. Both diets were free of gluten, preservatives, additives and lactose, were consistent in their levels of minimal FODMAPs (fermentable oligo- di- mono-saccharides and polyols), and contained moderate levels of amines and glutamates as per published food content to avoid any confounding factors that might affect the symptoms.<br> The average daily intake of salicylates in the low-salicylate diet was approximately 6 mg. The meal plans had an average energy value of 8 MJ daily and met the recommended serves of all food groups according to the Australian dietary guidelines.<br> Location: The intervention occurred within the participants home.<br> Personalisation: The intervention was not personalised to each patient.<br> Adherence: Compliance was monitored via the daily food diaries.
description: HeSANDA 1.0.0
DOI: 10.6084/m9.figshare.23700465.v1
title: Additional file 2 of The landscape of PBMC methylome in canine mammary tumors reveals the epigenetic regulation of immune marker genes and its potential application in predicting tumor malignancy

description: Additional file 2: Table S1. The information about dog donors providing blood samples used for MBD-seq. Table S2. Sequencing Coverage and Quality Statistics. Table S3. The statistics and genomic features of NT_DMR (2840 DMRs). Table S4. The statistics and genomic features of NB_DMR (3373 DMRs).Table S5. The statistics and genomic features of NC_DMR (1876 DMRs). Table S6. The statistics and genomic features of BC_DMR (168 DMRs). Table S7. The list of enriched immune-related terms with adj.p &lt;0.1. Table S8. The list of hypermethylated DMRs in immune cell type markers (Panglao DB). Table S9. The list of immune-regulating DMGs inversely correlated with gene expression. Table S10. The list of primers designed for targeted BS-sequencing. Table S11. The information of unknown dog PBMC donors (used for validation sets of NT classifier). Table S12. The list of 127 DMRs which have high feature importance in BC classifier.
DOI: 10.6084/m9.figshare.23700465
title: Additional file 2 of The landscape of PBMC methylome in canine mammary tumors reveals the epigenetic regulation of immune marker genes and its potential application in predicting tumor malignancy

description: Additional file 2: Table S1. The information about dog donors providing blood samples used for MBD-seq. Table S2. Sequencing Coverage and Quality Statistics. Table S3. The statistics and genomic features of NT_DMR (2840 DMRs). Table S4. The statistics and genomic features of NB_DMR (3373 DMRs).Table S5. The statistics and genomic features of NC_DMR (1876 DMRs). Table S6. The statistics and genomic features of BC_DMR (168 DMRs). Table S7. The list of enriched immune-related terms with adj.p &lt;0.1. Table S8. The list of hypermethylated DMRs in immune cell type markers (Panglao DB). Table S9. The list of immune-regulating DMGs inversely correlated with gene expression. Table S10. The list of primers designed for targeted BS-sequencing. Table S11. The information of unknown dog PBMC donors (used for validation sets of NT classifier). Table S12. The list of 127 DMRs which have high feature importance in BC classifier.
DOI: 10.6084/m9.figshare.23700471
title: Additional file 2 of Comparison of certainty of evidence between the net benefit approach and the traditional GRADE method using the data of Japanese Clinical Practice Guidelines for Management of Sepsis and Septic Shock 2020

description: Additional file 2. Utility tool for the net benefit approach.
DOI: 10.6084/m9.figshare.23700471.v1
title: Additional file 2 of Comparison of certainty of evidence between the net benefit approach and the traditional GRADE method using the data of Japanese Clinical Practice Guidelines for Management of Sepsis and Septic Shock 2020

description: Additional file 2. Utility tool for the net benefit approach.
DOI: 10.6084/m9.figshare.23700473
title: Additional file 1 of Dimensionality of genomic information and its impact on genome-wide associations and variant selection for genomic prediction: a simulation study

description: Additional file 1. QMSim parameter files for simul_Ne20_200QTL_h2_0.3.
DOI: 10.6084/m9.figshare.23700473.v1
title: Additional file 1 of Dimensionality of genomic information and its impact on genome-wide associations and variant selection for genomic prediction: a simulation study

description: Additional file 1. QMSim parameter files for simul_Ne20_200QTL_h2_0.3.