cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13145654
title: Chemical perturbations impacting histone acetylation regulate colorectal cancer differentiation

description: M60.count.Rdata: Rdata that includes the raw count, scaled CPM value and meta data of each sample. (Fig. 1 & 4)

DAP.merged.Log2FC.csv: integrated DiffBind results that shows the log2FC and P-value/FDR of peaks. (Fig. 1 & 4)

rawdata_scRNA-seq.zip: raw count data of scRNA-seq data from cellranger (labels: A: DMSO, B: MRK60, D: MRK60 + JQAD1).  (Fig. 5)
description: Histone acetylation governs broad gene expression programs in normal tissue and disease states. By applying a small chemical compound library targeting epigenetic regulators to a dual endogenous reporter system, we found that inhibiting histone deacetylase (HDAC) 1/2 initiates colorectal cancer (CRC) differentiation. Inhibiting the enzymatic pocket of HDAC1/2 induced differentiation and reduced proliferation across in vitro and in vivo models. On-target HDAC1/2 inhibition was validated using biochemical, chemical, and genetic approaches. A survey of histone posttranslational modifications from HDAC1/2 selective inhibition nominated acetylation of specific H3 and H4 lysine (K) residues as potential regulators of differentiation. Genome-wide profiles of these histone acetylation marks indicated that gains in histone 3 lysine 27 acetylation (H3K27ac) most strongly correlated to opening of chromatin and upregulation of genes associated with differentiation upon HDAC1/2 inhibition. Blocking acetylation of H3K27 by degrading its writer EP300 rescued the differentiation phenotype induced by HDAC1/2 inhibition in a patient-derived CRC model by single cell RNA-sequencing among other readouts. These results highlight the importance of specific chemically targetable histone modifications in governing cancer cell states and implicate precision targeting of H3K27ac as a potential therapeutic approach for CRC.
DOI: 10.5281/zenodo.13145655
title: Chemical perturbations impacting histone acetylation regulate colorectal cancer differentiation

description: M60.count.Rdata: Rdata that includes the raw count, scaled CPM value and meta data of each sample. (Fig. 1 & 4)

DAP.merged.Log2FC.csv: integrated DiffBind results that shows the log2FC and P-value/FDR of peaks. (Fig. 1 & 4)

rawdata_scRNA-seq.zip: raw count data of scRNA-seq data from cellranger (labels: A: DMSO, B: MRK60, D: MRK60 + JQAD1).  (Fig. 5)
description: Histone acetylation governs broad gene expression programs in normal tissue and disease states. By applying a small chemical compound library targeting epigenetic regulators to a dual endogenous reporter system, we found that inhibiting histone deacetylase (HDAC) 1/2 initiates colorectal cancer (CRC) differentiation. Inhibiting the enzymatic pocket of HDAC1/2 induced differentiation and reduced proliferation across in vitro and in vivo models. On-target HDAC1/2 inhibition was validated using biochemical, chemical, and genetic approaches. A survey of histone posttranslational modifications from HDAC1/2 selective inhibition nominated acetylation of specific H3 and H4 lysine (K) residues as potential regulators of differentiation. Genome-wide profiles of these histone acetylation marks indicated that gains in histone 3 lysine 27 acetylation (H3K27ac) most strongly correlated to opening of chromatin and upregulation of genes associated with differentiation upon HDAC1/2 inhibition. Blocking acetylation of H3K27 by degrading its writer EP300 rescued the differentiation phenotype induced by HDAC1/2 inhibition in a patient-derived CRC model by single cell RNA-sequencing among other readouts. These results highlight the importance of specific chemically targetable histone modifications in governing cancer cell states and implicate precision targeting of H3K27ac as a potential therapeutic approach for CRC.
DOI: 10.5281/zenodo.13145704
title: South American monsoon intensification during the last millennium driven by joint Pacific and Atlantic forcing

description: This archive contains the climate reconstruction of South American summer monsoon over 850–1850 CE at 5-year resolution by combining the isotope-enabled Community Earth System Model with isotopic proxy records through data assimilation. For a complete description of the experimental design, see the associated publication. Each NetCDF file corresponds to one variable. For each variable, along with the reconstruction, an estimation of the uncertainty is provided. All fields are anomalies relative to the 850–1850 CE period.
DOI: 10.5281/zenodo.13145705
title: South American monsoon intensification during the last millennium driven by joint Pacific and Atlantic forcing

description: This archive contains the climate reconstruction of South American summer monsoon over 850–1850 CE at 5-year resolution by combining the isotope-enabled Community Earth System Model with isotopic proxy records through data assimilation. For a complete description of the experimental design, see the associated publication. Each NetCDF file corresponds to one variable. For each variable, along with the reconstruction, an estimation of the uncertainty is provided. All fields are anomalies relative to the 850–1850 CE period.
DOI: 10.15468/dl.xyy2pm
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is BRA.12_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Eunectes murinus (Linnaeus, 1758)"
 ]
}

 The dataset includes 24 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043642-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bscbxq
title: Occurrence Download

description: A dataset containing 16007 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((3.84977 43.31718,47.52869 43.31718,47.52869 60.78126,3.84977 60.78126,3.84977 43.31718))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Glyceria declinata Bréb."
 ]
}

 The dataset includes 16007 records from 168 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043643-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rvzrap
title: Occurrence Download

description: A dataset containing 64517 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-769.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ulmus minor Mill."
 ]
}

 The dataset includes 64517 records from 364 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043644-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jxfp2d
title: Occurrence Download

description: A dataset containing 1035 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Occurrence evidence)",
 "Continent is North America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Lactuca sativa L.",
 "Year 1454-2024"
 ]
}

 The dataset includes 1035 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043645-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mjt5bh
title: Occurrence Download

description: A dataset containing 5897 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-131.94719 65.22706,-135.27675 64.99526,-135.67012 64.95311,-135.56475 62.23467,-128.5544 62.38218,-130.00845 63.76599,-131.94719 65.22706))",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 5897 records from 91 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043646-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13145486
title: Mechanism of Enhancing Chemotherapy Efficacy in Pancreatic Ductal Adenocarcinoma with Paricalcitol and Hydroxychloroquine: A Single Cell RNA Sequencing - PART2

description: Pancreatic ductal adenocarcinoma (PDAC) boasts a dismal five-year survival rate of less than 15%, mainly due to therapy resistance. Recent studies have highlighted hydroxychloroquine (H) and paricalcitol (P), reducing stromal density and enhancing PDAC sensitivity to chemotherapy. This investigation aimed to elucidate the molecular impacts of combining H and P, focusing on their ability to sensitize PDAC to chemotherapy. In vitro and in vivo experiments demonstrated that the HP combination significantly (p<0.001) enhanced gemcitabine (G) effects, validated in orthotopic mouse models and patient-derived xenografts (PDX). Mechanistically, GPH induced cell death via the vitamin D receptor pathway upregulated autophagy and ER stress-related transcripts and suppressed mTOR signaling. Single-cell (sc) RNAseq analyses showed GPH increased quiescent cancer associated fibroblasts and reduced autophagy related transcripts. GPH treatment modulated T-cell populations favoring antitumor immunity. Findings from clinical trial patient biopsies underscored these effects, highlighting GPH's potential as a therapeutic adjunct in PDAC management (NCT04524702).
DOI: 10.5281/zenodo.13145487
title: Mechanism of Enhancing Chemotherapy Efficacy in Pancreatic Ductal Adenocarcinoma with Paricalcitol and Hydroxychloroquine: A Single Cell RNA Sequencing - PART2

description: Pancreatic ductal adenocarcinoma (PDAC) boasts a dismal five-year survival rate of less than 15%, mainly due to therapy resistance. Recent studies have highlighted hydroxychloroquine (H) and paricalcitol (P), reducing stromal density and enhancing PDAC sensitivity to chemotherapy. This investigation aimed to elucidate the molecular impacts of combining H and P, focusing on their ability to sensitize PDAC to chemotherapy. In vitro and in vivo experiments demonstrated that the HP combination significantly (p<0.001) enhanced gemcitabine (G) effects, validated in orthotopic mouse models and patient-derived xenografts (PDX). Mechanistically, GPH induced cell death via the vitamin D receptor pathway upregulated autophagy and ER stress-related transcripts and suppressed mTOR signaling. Single-cell (sc) RNAseq analyses showed GPH increased quiescent cancer associated fibroblasts and reduced autophagy related transcripts. GPH treatment modulated T-cell populations favoring antitumor immunity. Findings from clinical trial patient biopsies underscored these effects, highlighting GPH's potential as a therapeutic adjunct in PDAC management (NCT04524702).
DOI: 10.15468/dl.sdffav
title: Occurrence Download

description: A dataset containing 375 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pristimantis danae (Duellman, 1978)"
 ]
}

 The dataset includes 375 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043649-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25345/c5vq2sn7p
title: MassIVE MSV000095498 - Investigating effects of queen exposure to QueenBoost on queen oocytes and hemolymph as well as worker antennae, hemolymph, and hypopharangeal glands
title: Queens were exposed to low doses pyriproxyfen (QueenBoost, which has been previously found to increase egg hatching rates and attentiveness of worker progeny to the queen) orally within queen monitoring cages. After treatment, queens were sampled to obtain proteomics data for hemolymph and mature oocytes (dissected from the ovaries), and workers were sampled to obtain pooled samples of antennae, hypopharangeal glands, and hemolymph. Data from worker antennae and hypopharangeal gland samples were acquired from a single plate, data from worker and queen hemolymph samples were acquired from a second plate, and oocyte data were acquired at a later date from a third plate. All samples were randomized within plates. The hemolymph, antennae, and hypopharangeal gland data were searched together (report_JF-all-tissues file) and the oocyte data were searched separately (report_JF-oocytes file). Data were all searched library-free using DIA-NN with default parameters except "unrelated runs" and "MBR" were selected, the neural network classifier was set to "double-pass mode", and protein inference was set to "protein names from FASTA".
DOI: 10.15468/dl.ud4p66
title: Occurrence Download

description: A dataset containing 62635 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Canadian Museum of Nature Fish Collection"
 ]
}

 The dataset includes 62635 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043650-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25345/c5qz22v4d
title: MassIVE MSV000095499 - First Evidence of an Involvement of the Calcitonin Gene Related Peptide in Restless Legs Syndrome
title: Restless legs syndrome (RLS) is a sensory-motor disorder characterized by an irresistible urge to move the legs, often accompanied by unpleasant sensations, particularly during rest or inactivity. This study investigates the involvement of calcitonin gene-related peptide (CGRP) and related proteins in the pathophysiology of RLS. CGRP is implicated in various neural and inflammatory processes and has been studied in other conditions like migraines. Our research employed principal component analysis to distinguish RLS patients from controls, revealing significant differences in the expression of CGRP-related proteins. A total of 13 CGRP-related proteins were identified, with eight upregulated and two downregulated in RLS patients compared to controls. Integrative proteomics and transcriptomics analyses highlighted a network of proteins and genes linked to RLS, including S100A12, pro-adrenomedullin (ADM), SRSF6, and ADM2. Among these, SRSF6 emerged as a potential central player in RLS pathogenesis. The findings suggest that CGRP may influence the sensory and motor components of RLS through interactions with dopaminergic and opioid systems and potentially modulate inflammatory pathways. Moreover, the study indicates possible cardiovascular implications of CGRP upregulation, which may serve as a compensatory mechanism in response to increased cardiovascular risk in RLS. This research proposes that targeting CGRP and its related pathways could offer new therapeutic avenues for RLS treatment. However, further studies are needed to validate these findings and explore the potential efficacy and safety of such treatments. These results underscore the importance of CGRP in the complex pathophysiology of RLS and suggest new directions for future research.
DOI: 10.15468/dl.qk6u6d
title: Occurrence Download

description: A dataset containing 177 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "GadmGid is one of (ECU.15.1.1_1, COL.1_2, PER.1_1, GUF, GUY, SUR, VEN.1_1, BRA.3_1, BRA.23_1, BRA.4_1, BRA.14_1)",
 "OccurrenceStatus is Present",
 "TaxonKey is Mollia lepidota Spruce ex Benth."
 ]
}

 The dataset includes 177 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043652-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4vm6ab
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dyckia simulans L.B.Sm."
 ]
}

 The dataset includes 14 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043653-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2fk0df
title: CCDC 2250674: Experimental Crystal Structure Determination

description: Related Article: Shiqi Xu, Zi Ye, Shuang Shang, Fengge Wang, Huan Zhang, Lianguo Chen, Hao Lin, Chen Chen, Fang Hua, Chong-Jing Zhang|2024|Chin.Chem.Lett.|35|109034|doi:10.1016/j.cclet.2023.109034
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.34740/kaggle/dsv/9077059
title: Balochi Language to English Translation Dataset
DOI: 10.15468/dl.rssf5q
title: Occurrence Download

description: A dataset containing 1068204 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2024-06-05",
 "EventDate is less than or equal to 2024-07-05",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 }
 ]
}

 The dataset includes 1068204 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043647-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13145471
title: Survey dataset
DOI: 10.5281/zenodo.13145472
title: Survey dataset
DOI: 10.15468/dl.cyddvu
title: Occurrence Download

description: A dataset containing 1447 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alsodes Bell, 1843"
 ]
}

 The dataset includes 1447 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043657-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j9rns5
title: Occurrence Download

description: A dataset containing 216 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Canadian Museum of Nature Fish Collection",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ichthyomyzon unicuspis Hubbs & Trautman, 1937"
 ]
}

 The dataset includes 216 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043658-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8gsvyn
title: Occurrence Download

description: A dataset containing 2239 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Frieseomelitta nigra (Cresson, 1879)"
 ]
}

 The dataset includes 2239 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043659-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kfy2fk
title: Occurrence Download

description: A dataset containing 3008 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "DatasetKey is Taxon occurrence data for the FungalRoot database"
 ]
}

 The dataset includes 3008 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043660-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bha9dq
title: Occurrence Download

description: A dataset listing the 32002 species recorded in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "PublishingOrg is one of (2a7e3080-28a9-11dd-97cd-b8a03c50a862, eac88d99-9f6c-4031-8fc4-8088f0e0dfe7, 9d77fdeb-100f-4b29-98ad-4effdd824457, ab13adb9-ce23-444d-87c9-ce41f03ef2b3, 278c2395-6edb-41f4-8f0a-0abd13656901, 15b278a8-1356-4f7b-ba32-3c733c3d0aac, 1106e179-e49f-461f-95a6-459bf4d53c1b, 69cbe3e1-ea7a-4f22-b4b8-47dd4df6e79b, 7a079928-aee9-418a-b083-6152d01c78d6, 03fefd3c-2809-4966-810d-a6c2205ab899, 52f50975-7f82-4945-8e98-90b983a89bfc, 47380c8a-0edd-4036-b1bc-d852cba8232f, 0bad0631-0693-41fa-afd5-54df0120c509, 6e051633-cbf0-4729-be54-f7be1e078c97, 85e6ceac-5381-4378-917c-dc3b8032affa, fbe29d53-6c40-411a-8e97-2d92a285c88e, 015d5ac7-2644-49e9-815e-79468647d6af, 4b3fc3ac-227f-477d-9853-cfa76044d108, 06867940-0867-4b4a-abb2-a57a16fcf2dc, fd66e4f3-e13e-4cf5-a3cb-d0fe0fe48aa1, e2e717bf-551a-4917-bdc9-4fa0f342c530, f072f648-b8a4-47a0-9e1c-89d790645b5a)",
 "Year 2010-2024",
 "Country is one of (Colombia)"
 ]
 }
 ]
}

 The dataset's 32002 records were derived from 779 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043654-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.l3py8i
title: Occurrence Download

description: A dataset containing 1696 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leptopogon amaurocephalus Tschudi, 1846",
 "HasGeospatialIssue is false",
 "Geometry POLYGON((-60.82 -36.87,-60.82 -4.64,-5.71 -4.64,-5.71 -36.87,-60.82 -36.87))"
 ]
}

 The dataset includes 1696 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009233-160623103540712/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s67868
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Impatiens mokimi Hook.fil."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027045-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mhcvps
title: Occurrence Download

description: A dataset containing 201 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ceanothus gloriosus var. exaltatus J.T.Howell"
 ]
}

 The dataset includes 201 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009233-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ukav5p
title: Occurrence Download

description: A dataset containing 72 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Homalium vitiense Benth."
 ]
}

 The dataset includes 72 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027067-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.