cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22731110.v3
title: <b>Investigating Metabolic Dysregulation in Serum of Triple Transgenic Alzheimer's Disease Male Mice: Implications for Pathogenesis and Potential Biomarkers</b>

description: <strong>Introduction</strong> Alzheimer's disease (AD) is considered to be a multifactorial neurodegenerative disease that lacks effective drugs. <strong>Objective</strong> Pathological changes in the brain can be reflected in blood metabolites that are expected to explain the disease mechanisms or be candidate biomarkers. <strong>Methods</strong> Targeted metabolomics was used to quantify 256 metabolites in serum of triple transgenic AD (3×Tg-AD) male mice. <strong>Resutls</strong> Compared with control, 49 metabolites involved in bioamines and nucleoside analogues were identified as differential metabolites. They mainly were associated with purine, pyrimidine, tryptophan, cysteine and methionine and glycerophospholipid metabolism, of which the significant ones included decreased serum levels of adenosine, serotonin, N-acetyl-5-hydroxytryptamine, S-adenosine-L-homocysteine, and CDP-choline, and increased serum levels of S-adenosine-L-methionine, acetylcholine, and trimethylamine-N-oxide in AD mice. <strong>Conclusion</strong> The results revealed the changes of neuromodulators in serum, suggesting that dysregulated metabolites in periphery in AD mice may be related to the disturbances in neuroinhibition, the serotonergic system, sleep function, the cholinergic system, and the gut microbiota. The study proposed the possibility of developing peripheral biomarkers in early AD.
DOI: 10.6084/m9.figshare.22731110.v2
title: Widely targeted metabolomics approaches to investigate dysregulation of multiple metabolites in the serum of triple transgenic Alzheimer's disease male mice

description: <strong>Introduction</strong> Alzheimer's disease (AD) is considered to be a multifactorial neurodegenerative disease that lacks effective drugs. <strong>Objective</strong> Pathological changes in the brain can be reflected in blood metabolites that are expected to explain the disease mechanisms or be candidate biomarkers. <strong>Methods</strong> Targeted metabolomics was used to quantify 256 metabolites in serum of triple transgenic AD (3×Tg-AD) male mice. <strong>Resutls</strong> Compared with control, 49 metabolites involved in bioamines and nucleoside analogues were identified as differential metabolites. They mainly were associated with purine, pyrimidine, tryptophan, cysteine and methionine and glycerophospholipid metabolism, of which the significant ones included decreased serum levels of adenosine, serotonin, N-acetyl-5-hydroxytryptamine, S-adenosine-L-homocysteine, and CDP-choline, and increased serum levels of S-adenosine-L-methionine, acetylcholine, and trimethylamine-N-oxide in AD mice. <strong>Conclusion</strong> The results revealed the changes of neuromodulators in serum, suggesting that dysregulated metabolites in periphery in AD mice may be related to the disturbances in neuroinhibition, the serotonergic system, sleep function, the cholinergic system, and the gut microbiota. The study proposed the possibility of developing peripheral biomarkers in early AD.
DOI: 10.6084/m9.figshare.23896254
title: Landmark-free statistical shape modelling reveals differing effects of age and sex on whole-muscle morphology among the triceps surae

description: this is the supplementary data from the paper titled "Landmark-free statistical shape modelling reveals differing effects of age and sex on whole-muscle morphology among the triceps surae" which describes the PC's for each of the muscles for each individual in the study.
DOI: 10.5066/p9qgqrb7
title: Larval headwater stream amphibian captures from the Trask River Watershed Experimental Study of forest harvest impacts, 2008-2016

description: Forest harvest is one of the primary landscape-scale management actions affecting riparian forests of the Pacific Northwest, U.S, yet the effect of harvest on headwater steam amphibians is largely understudied. Existing information is often limited because of the difficulty separating movement and emigration processes from occupancy and abundance estimates. We designed a before-after control-impact experiment to account for instream movement in the responses of three unique headwater stream amphibians to clearcut logging as part of the Trask River Watershed Experimental Study in the Oregon Coast Range. We captured and marked larval tailed frogs (Ascaphus truei), Coastal giant salamanders (Dicamptodon tenebrosus), and Columbia torrent salamanders (Rhyacotriton kezeri) across 3,915 sampling occasions that spanned 13 study reaches and eight years.
DOI: 10.5281/zenodo.7948846
title: Shallow Slow Slip Events Identified Offshore the Osa Peninsula in Southern Costa Rica from GNSS Time Series

description: Using new continuous GNSS time series from the region, we identify 5 distinct shallow SSEs that occurred immediately offshore and beneath the Osa peninsula: an event detected by one site in 2013, and two events occurring in close succession in both 2018 and 2022 detected by multiple stations, indicating a preliminary recurrence interval of ~4-5 years. While SSEs have been observed to the north at Nicoya, this is their first documentation in southern Costa Rica. Modeled slip distributions of the 2018 and 2022 events indicate that they ruptured the same or overlapping patches of the plate interface, nearly at the trench, updip of historic earthquakes including the 1983 Mw 7.4 Osa event. Immediately offshore, the estimated cumulative slip from the 2018 and 2022 events is sufficient to close the slip deficit from tectonic loading over the recurrence interval, likely influencing the magnitude and spatial slip distribution of future large ruptures.
description: This is contains seismic catalog used in the article. The GNSS data are available with the following DOI: 10.5281/zenodo.7779495
DOI: 10.5281/zenodo.7948845
title: Shallow Slow Slip Events Identified Offshore the Osa Peninsula in Southern Costa Rica from GNSS Time Series

description: Using new continuous GNSS time series from the region, we identify 5 distinct shallow SSEs that occurred immediately offshore and beneath the Osa peninsula: an event detected by one site in 2013, and two events occurring in close succession in both 2018 and 2022 detected by multiple stations, indicating a preliminary recurrence interval of ~4-5 years. While SSEs have been observed to the north at Nicoya, this is their first documentation in southern Costa Rica. Modeled slip distributions of the 2018 and 2022 events indicate that they ruptured the same or overlapping patches of the plate interface, nearly at the trench, updip of historic earthquakes including the 1983 Mw 7.4 Osa event. Immediately offshore, the estimated cumulative slip from the 2018 and 2022 events is sufficient to close the slip deficit from tectonic loading over the recurrence interval, likely influencing the magnitude and spatial slip distribution of future large ruptures.
description: This is contains seismic catalog used in the article. The GNSS data are available with the following DOI: 10.5281/zenodo.7779495
DOI: 10.5281/zenodo.7779495
title: Shallow Slow Slip Events Identified Offshore the Osa Peninsula in Southern Costa Rica from GNSS Time Series

description: Using new continuous GNSS time series from the region, we identify 5 distinct shallow SSEs that occurred immediately offshore and beneath the Osa peninsula: an event detected by one site in 2013, and two events occurring in close succession in both 2018 and 2022 detected by multiple stations, indicating a preliminary recurrence interval of ~4-5 years. While SSEs have been observed to the north at Nicoya, this is their first documentation in southern Costa Rica. Modeled slip distributions of the 2018 and 2022 events indicate that they ruptured the same or overlapping patches of the plate interface, nearly at the trench, updip of historic earthquakes including the 1983 Mw 7.4 Osa event. Immediately offshore, the estimated cumulative slip from the 2018 and 2022 events is sufficient to close the slip deficit from tectonic loading over the recurrence interval, likely influencing the magnitude and spatial slip distribution of future large ruptures.
DOI: 10.5281/zenodo.7779494
title: Shallow Slow Slip Events Identified Offshore the Osa Peninsula in Southern Costa Rica from GNSS Time Series

description: Using new continuous GNSS time series from the region, we identify 5 distinct shallow SSEs that occurred immediately offshore and beneath the Osa peninsula: an event detected by one site in 2013, and two events occurring in close succession in both 2018 and 2022 detected by multiple stations, indicating a preliminary recurrence interval of ~4-5 years. While SSEs have been observed to the north at Nicoya, this is their first documentation in southern Costa Rica. Modeled slip distributions of the 2018 and 2022 events indicate that they ruptured the same or overlapping patches of the plate interface, nearly at the trench, updip of historic earthquakes including the 1983 Mw 7.4 Osa event. Immediately offshore, the estimated cumulative slip from the 2018 and 2022 events is sufficient to close the slip deficit from tectonic loading over the recurrence interval, likely influencing the magnitude and spatial slip distribution of future large ruptures.
DOI: 10.6084/m9.figshare.23896269
title: Robot motion data generated in the experiment

description: The data records the position of all motors, the angles of the end tool, and the force, in different methods and different parameter. The force recorded include the composition of forces and the force in three directions, and the angles in planes perpendicular to each other. Also, methods include the AIRS, PID, and our method, and different parameters tested for every method, and the best performance by each method is recorded and compared.
DOI: 10.6084/m9.figshare.23896323
title: Cox_hiv

description: Cox Regression
DOI: 10.6084/m9.figshare.23896323.v1
title: Cox_hiv

description: Cox Regression
DOI: 10.6084/m9.figshare.23896326
title: Diabetic_Retinopathy

description: Survival Analysis for Diabetic file
DOI: 10.5281/zenodo.8218414
title: Study 2 Main File

description: Dataset from employees working in an organization based in Greece that provides omnichannel customer experiences.
DOI: 10.5281/zenodo.8218415
title: Study 2 Main File

description: Dataset from employees working in an organization based in Greece that provides omnichannel customer experiences.
DOI: 10.5281/zenodo.8218408
title: Study 1 Open Ended

description: The general sentiments of employees (n=656) who worked remotely from April 2021 to November 2022.
DOI: 10.5281/zenodo.8218409
title: Study 1 Open Ended

description: The general sentiments of employees (n=656) who worked remotely from April 2021 to November 2022.
DOI: 10.5281/zenodo.6471842
title: Context-dependent 3D genome regulation by cohesin and related factors

description: Cohesin plays vital roles in chromatin folding and gene expression regulation, cooperating with such factors as cohesin loaders, unloaders, and the insulation factor CTCF. Although models of regulation have been proposed (e.g., loop extrusion), how cohesin and related factors collectively or individually regulate the hierarchical chromatin structure and gene expression remains unclear. We have depleted cohesin and related factors and then conducted a comprehensive evaluation of the resulting 3D genome, transcriptome and epigenome data. We observed substantial variation in depletion effects among factors at topologically associating domain (TAD) boundaries and on interTAD interactions, which were related to epigenomic status. Gene expression changes were highly correlated with direct cohesin binding and gain of TAD boundaries than with the loss of boundaries. Moreover, cohesin was broadly enriched in active compartment A chromosomes, which were retained after CTCF depletion. Our results demonstrate context-specific roles of cohesin for gene expression and chromatin folding.
DOI: 10.5281/zenodo.6471841
title: Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors

description: Cohesin plays vital roles in chromatin folding and gene expression regulation, cooperating with such factors as cohesin loaders, unloaders, and the insulation factor CTCF. Although models of regulation have been proposed (e.g., loop extrusion), how cohesin and related factors collectively or individually regulate the hierarchical chromatin structure and gene expression remains unclear. We have depleted cohesin and related factors and then conducted a comprehensive evaluation of the resulting 3D genome, transcriptome and epigenome data. We observed substantial variation in depletion effects among factors at topologically associating domain (TAD) boundaries and on interTAD interactions, which were related to epigenomic status. Gene expression changes were highly correlated with direct cohesin binding and gain of TAD boundaries than with the loss of boundaries. Moreover, cohesin was broadly enriched in active compartment A chromosomes, which were retained after CTCF depletion. Our results demonstrate context-specific roles of cohesin for gene expression and chromatin folding.
DOI: 10.5281/zenodo.6471928
title: Context-dependent 3D genome regulation by cohesin and related factors

description: Cohesin plays vital roles in chromatin folding and gene expression regulation, cooperating with such factors as cohesin loaders, unloaders, and the insulation factor CTCF. Although models of regulation have been proposed (e.g., loop extrusion), how cohesin and related factors collectively or individually regulate the hierarchical chromatin structure and gene expression remains unclear. We have depleted cohesin and related factors and then conducted a comprehensive evaluation of the resulting 3D genome, transcriptome and epigenome data. We observed substantial variation in depletion effects among factors at topologically associating domain (TAD) boundaries and on interTAD interactions, which were related to epigenomic status. Gene expression changes were highly correlated with direct cohesin binding and gain of TAD boundaries than with the loss of boundaries. Moreover, cohesin was broadly enriched in active compartment A chromosomes, which were retained after CTCF depletion. Our results demonstrate context-specific roles of cohesin for gene expression and chromatin folding.
DOI: 10.5281/zenodo.8038821
title: Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors

description: Cohesin plays vital roles in chromatin folding and gene expression regulation, cooperating with such factors as cohesin loaders, unloaders, and the insulation factor CTCF. Although models of regulation have been proposed (e.g., loop extrusion), how cohesin and related factors collectively or individually regulate the hierarchical chromatin structure and gene expression remains unclear. We have depleted cohesin and related factors and then conducted a comprehensive evaluation of the resulting 3D genome, transcriptome and epigenome data. We observed substantial variation in depletion effects among factors at topologically associating domain (TAD) boundaries and on interTAD interactions, which were related to epigenomic status. Gene expression changes were highly correlated with direct cohesin binding and gain of TAD boundaries than with the loss of boundaries. Moreover, cohesin was broadly enriched in active compartment A chromosomes, which were retained after CTCF depletion. Our results demonstrate context-specific roles of cohesin for gene expression and chromatin folding.
DOI: 10.5281/zenodo.8040880
title: Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors

description: Cohesin plays vital roles in chromatin folding and gene expression regulation, cooperating with such factors as cohesin loaders, unloaders, and the insulation factor CTCF. Although models of regulation have been proposed (e.g., loop extrusion), how cohesin and related factors collectively or individually regulate the hierarchical chromatin structure and gene expression remains unclear. We have depleted cohesin and related factors and then conducted a comprehensive evaluation of the resulting 3D genome, transcriptome and epigenome data. We observed substantial variation in depletion effects among factors at topologically associating domain (TAD) boundaries and on interTAD interactions, which were related to epigenomic status. Gene expression changes were highly correlated with direct cohesin binding and gain of TAD boundaries than with the loss of boundaries. Moreover, cohesin was broadly enriched in active compartment A chromosomes, which were retained after CTCF depletion. Our results demonstrate context-specific roles of cohesin for gene expression and chromatin folding.
DOI: 10.5281/zenodo.8041057
title: Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors

description: Cohesin plays vital roles in chromatin folding and gene expression regulation, cooperating with such factors as cohesin loaders, unloaders, and the insulation factor CTCF. Although models of regulation have been proposed (e.g., loop extrusion), how cohesin and related factors collectively or individually regulate the hierarchical chromatin structure and gene expression remains unclear. We have depleted cohesin and related factors and then conducted a comprehensive evaluation of the resulting 3D genome, transcriptome and epigenome data. We observed substantial variation in depletion effects among factors at topologically associating domain (TAD) boundaries and on interTAD interactions, which were related to epigenomic status. Gene expression changes were highly correlated with direct cohesin binding and gain of TAD boundaries than with the loss of boundaries. Moreover, cohesin was broadly enriched in active compartment A chromosomes, which were retained after CTCF depletion. Our results demonstrate context-specific roles of cohesin for gene expression and chromatin folding.
DOI: 10.5281/zenodo.8041088
title: Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors

description: Cohesin plays vital roles in chromatin folding and gene expression regulation, cooperating with such factors as cohesin loaders, unloaders, and the insulation factor CTCF. Although models of regulation have been proposed (e.g., loop extrusion), how cohesin and related factors collectively or individually regulate the hierarchical chromatin structure and gene expression remains unclear. We have depleted cohesin and related factors and then conducted a comprehensive evaluation of the resulting 3D genome, transcriptome and epigenome data. We observed substantial variation in depletion effects among factors at topologically associating domain (TAD) boundaries and on interTAD interactions, which were related to epigenomic status. Gene expression changes were highly correlated with direct cohesin binding and gain of TAD boundaries than with the loss of boundaries. Moreover, cohesin was broadly enriched in active compartment A chromosomes, which were retained after CTCF depletion. Our results demonstrate context-specific roles of cohesin for gene expression and chromatin folding.
DOI: 10.5281/zenodo.8218447
title: Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors

description: Cohesin plays vital roles in chromatin folding and gene expression regulation, cooperating with such factors as cohesin loaders, unloaders, and the insulation factor CTCF. Although models of regulation have been proposed (e.g., loop extrusion), how cohesin and related factors collectively or individually regulate the hierarchical chromatin structure and gene expression remains unclear. We have depleted cohesin and related factors and then conducted a comprehensive evaluation of the resulting 3D genome, transcriptome and epigenome data. We observed substantial variation in depletion effects among factors at topologically associating domain (TAD) boundaries and on interTAD interactions, which were related to epigenomic status. Gene expression changes were highly correlated with direct cohesin binding and gain of TAD boundaries than with the loss of boundaries. Moreover, cohesin was broadly enriched in active compartment A chromosomes, which were retained after CTCF depletion. Our results demonstrate context-specific roles of cohesin for gene expression and chromatin folding.
DOI: 10.6084/m9.figshare.23896416
title: Data and script

description: It provides three dataset sorted in different manners used for assessingi) variation of invertebrates across micorhabitatsii) snowfinch foraging behaviour in relation to spatio-temporal variation in invertebratesiii) foraging repeatability
DOI: 10.6084/m9.figshare.23896416.v1
title: Data and script

description: It provides three dataset sorted in different manners used for assessingi) variation of invertebrates across micorhabitatsii) snowfinch foraging behaviour in relation to spatio-temporal variation in invertebratesiii) foraging repeatability
DOI: 10.21233/jja9-xt79
title: Elatia DE peatland testate amoebae surface sample dataset

description: Raw data for the Elatia DE peatland testate amoebae surface sample dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.3886/icpsr09269.v2
title: Immigrants Admitted to the United States, 1988
title: Version 2

description: This data collection contains information on the characteristics of aliens who became legal permanent residents of the United States in fiscal year 1988 (October 1987 through September 1988). Data are presented for two types of immigrants. The first category, New Arrivals, arrived from outside the United States with valid immigrant visas issued by the United States Department of State. Those in the second category, Adjustments, were already in the United States with temporary status and were adjusted to legal permanent residence through petition to the United States Immigration and Naturalization Service. Variables include port of entry, month and year of admission, class of admission, and state and area to which immigrants were admitted. Demographic information such as age, sex, marital status, occupation, country of birth, country of last permanent residence, and nationality is also provided.
description: Datasets: DS1: Immigrants Admitted to the United States, 1988
DOI: 10.21233/js16-gn52
title: Horse Lake water chemistry dataset

description: Raw data for the Horse Lake water chemistry dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.21233/jt2x-k308
title: George diatom surface sample dataset

description: Raw data for the George diatom surface sample dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.21233/jwjr-yn51
title: West Garland P. diatom surface sample dataset

description: Raw data for the West Garland P. diatom surface sample dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.21233/jzmb-cs47
title: Thomas Lakes South pollen surface sample dataset

description: Raw data for the Thomas Lakes South pollen surface sample dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.21233/jzwt-n655
title: Hot Pond water chemistry dataset

description: Raw data for the Hot Pond water chemistry dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.21233/k30v-rr04
title: Borden Lake pollen dataset

description: Raw data for the Borden Lake pollen dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.21233/k32e-pm94
title: Sabin Pond water chemistry dataset

description: Raw data for the Sabin Pond water chemistry dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.21233/k3c3-fj87
title: South Kratt Lake plant macrofossil dataset

description: Raw data for the South Kratt Lake plant macrofossil dataset obtained from the Neotoma Paleoecology Database.