cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.j2un6g
title: Occurrence Download

description: A dataset containing 777 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mycena galericulata (Scop.) Gray",
 "Country is Germany",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1990"
 ]
}

 The dataset includes 777 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069035-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.29267123.v5
title: Network_Based_Multi_Axial_Cognitive_Framework.pdf

description: A Three-Axis Framework for Neural Network Organization: From Cognitive Quadrants to Clinical Applications A theoretical framework proposing that neural organization follows three orthogonal dimensions: η (control direction), τ (temporal processing), and α (processing mode). These axes generate eight distinct cognitive quadrants that operate as discrete network-level systems despite underlying neural activity being continuous. Each quadrant corresponds to specific brain networks and exhibits measurable resource allocation patterns, with cognitive resources operating under conservation principles where total allocation across all quadrants equals 100% of available processing capacity. The framework introduces dynamic resource allocation constraints that create competitive dynamics between cognitive systems - increased activation in one quadrant necessarily reduces resources available to others. This enables precise clinical predictions, including specific resource allocation dysfunction patterns for psychiatric disorders: Q2 (contemplative integrator) hyperactivation consuming 40-70% of total resources in major depressive disorder, Q1-Q3 (strategic-procedural) hyperactivation consuming 60-80% in OCD, and Q7 (reactive responder) hyperactivation with Q1 (strategic analyst) hypoactivation in ADHD. The discrete quadrant model operates at the network organizational level - the appropriate scale of abstraction for understanding consciousness and clinical applications, similar to how atomic theory provides discrete models despite quantum mechanical continuity. The framework honors both the modular reality of brain network architecture (default mode, salience, executive control networks) and phenomenological experience of bounded cognitive states, clear transitions between thinking modes, and distinct resource competition patterns. Clinical applications include precision psychiatry through individual resource allocation profiling, treatment selection based on specific network dysfunction patterns rather than symptoms alone, and targeted interventions that rebalance cognitive resources (e.g., reducing Q2 allocation from 60% to 15% while enhancing Q4 allocation from 5% to 12%). The framework generates ten functionally coherent cognitive streams through systematic anatomical pathways, enabling measurement and therapeutic targeting of complex cognitive functions. The framework provides testable hypotheses for consciousness research and represents a potential paradigm shift from symptom-focused to resource-focused psychiatric interventions that address underlying cognitive mechanisms at the network level.
DOI: 10.15468/dl.xdphp3
title: Occurrence Download

description: A dataset containing 121813 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tigrisoma mexicanum Swainson, 1834"
 ]
}

 The dataset includes 121813 records from 101 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069028-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6zfkvs
title: Occurrence Download

description: A dataset containing 780 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Nothofagus obliqua (Mirb.) Oerst."
 ]
}

 The dataset includes 780 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069036-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/fti8fa
title: Replication data for: Evaluating effects of nudging-based policies for food waste optimization: an Agent Based Modeling approach.

description: Source code for the ABM
DOI: 10.15468/dl.ybeuhj
title: Occurrence Download

description: A dataset containing 504 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "TaxonKey is Lomatia dentata (Ruiz & Pav.) R.Br."
 ]
}

 The dataset includes 504 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069037-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15741089
title: CCHF-Public Health Study
DOI: 10.5281/zenodo.15741088
title: CCHF-Public Health Study
DOI: 10.6073/pasta/eae5218f1b9410bfcfdfddf749d61495
title: Size fractionation for total Chl a within the surface layer and calculated size distribution of total Chl a from discrete bottle samples collected during CCE LTER process cruises in the CCE region, 2006 - 2024 (ongoing).

description: Water for size fractionation of chlorophyll a is sampled from ~10m depth (surface layer) in the CCE study area. The size distribution of total chlorophyll a is determined by filtering water though filters of differing pore sizes. These are then extracted in acetone and analyzed fluorometrically with Turner Designs 10-AU Fluorometer on CCE Process cruises (since 2006, ongoing). Chlorophyll a and taxon-specific pigments (chlorophylls and carotenoids) are qualitatively and quantitatively characterized in the lab onshore by several size fractions (&lt; 1µm to &gt; 20µm) utilizing High Performance Liquid Chromatography (HPLC) analysis. The samples analyzed within the CCE region are used to develop a metric for phytoplankton community structure that can be used to monitor its state and changes thereof over time.
DOI: 10.15468/dl.z96bf7
title: Occurrence Download

description: A dataset containing 295 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Russian Federation",
 "TaxonKey is Dolichophis caspius (Gmelin, 1789)"
 ]
}

 The dataset includes 295 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069038-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gbaq7g
title: Occurrence Download

description: A dataset containing 45003 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Museo Argentino de Ciencias Naturales \"Bernardino Rivadavia\" (MACN). Herpetology National Collection (MACNHe)"
 ]
}

 The dataset includes 45003 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069039-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/jjbheg
title: Assessing the role of law in reducing the practice of FGM/C in Kenya

description: This study aimed to understand how better to use criminal law to promote the abandonment of female genital mutilation/cutting (FGM/C) among men and women aged 18 years and above in Narok/Kisii and Isiolo counties in Kenya.
DOI: 10.5517/ccdc.csd.cc26nr3r
title: CCDC 2045724: Experimental Crystal Structure Determination

description: Related Article: Jia-Qi Niu, Wen-Ting An, Xiu-Juan Zhang, Yuan-Yuan Ma, Zhan-Gang Han|2021|Chem.Eng.Journal|418|129408|doi:10.1016/j.cej.2021.129408
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: 10.5281/zenodo.15741031
title: Simulation Results for "Modelling physical activity profiles in COPD patients: a basis expansion approach to variable domain functional regression models"

description: Simulation Results for "Modelling physical activity profiles in COPD patients: a basis expansion approach to variable domain functional regression models"
DOI: 10.5281/zenodo.15741032
title: Simulation Results for "Modelling physical activity profiles in COPD patients: a basis expansion approach to variable domain functional regression models"

description: Simulation Results for "Modelling physical activity profiles in COPD patients: a basis expansion approach to variable domain functional regression models"
DOI: 10.5281/zenodo.15740610
title: Data for VEGFR2 Interactions study
DOI: 10.5281/zenodo.15740611
title: Data for VEGFR2 Interactions study
DOI: 10.5281/zenodo.15311024
title: Analysis of fatty acid levels in Drosophila with PGRP-LE overexpression in enterocytes

description: We sought to determine whether activation of PGRP-LE signaling in the midgut could have impacts on systemic lipid homeostasis (the midgut is the equivalent of the small intestine in Drosophila). To test this possibility, we scored total fatty acid levels in control flies and flies with PGRP-LE overexpression in enterocytes (ECs). Progeny from the cross between virgin females carrying the EC-specific mex-GAL4 (RRID:BDSC_ 91368) and w1118 males were used as controls. For PGRP-LE overexpression in ECs, virgin females carrying mex-GAL4 were crossed with males carrying UAS-PGRP-LE (RRID:BDSC_33054). For simplicity, the later genetic condition is referred to as “mutant” in the dataset. We used 7-day-old males for these analyses. FA levels were determined by LC-ESI-MS/MS as previously described (1).

The dataset contains LC-ESI-MS/MS raw files for the 10 samples (5 controls and 5 “mutants”) in mzML format. The dataset also contains a data analysis table. This table contains the quantifications for each fatty acid (FA) species (“RawData”, Cx:y indicates the fatty acyl chains, where x is the number of carbon atoms and y is the number of double bonds), FA levels in each sample after normalization to protein content (“Values per Sample”), and plots showing relative FA levels between control and mutant conditions (“Mean + SD Plots”).  

(1) Vonolfen MC, Meyer Zu Altenschildesche FL, Nam HJ, Brodesser S, Gyenis A, Buellesbach J, Lam G, Thummel CS, Storelli G. Drosophila HNF4 acts in distinct tissues to direct a switch between lipid storage and export in the gut. Cell Rep. 2024 Sep 24;43(9):114693. doi: 10.1016/j.celrep.2024.114693. Epub 2024 Sep 4. PMID: 39235946.
DOI: 10.5281/zenodo.15311025
title: Analysis of fatty acid levels in Drosophila with PGRP-LE overexpression in enterocytes

description: We sought to determine whether activation of PGRP-LE signaling in the midgut could have impacts on systemic lipid homeostasis (the midgut is the equivalent of the small intestine in Drosophila). To test this possibility, we scored total fatty acid levels in control flies and flies with PGRP-LE overexpression in enterocytes (ECs). Progeny from the cross between virgin females carrying the EC-specific mex-GAL4 (RRID:BDSC_ 91368) and w1118 males were used as controls. For PGRP-LE overexpression in ECs, virgin females carrying mex-GAL4 were crossed with males carrying UAS-PGRP-LE (RRID:BDSC_33054). For simplicity, the later genetic condition is referred to as “mutant” in the dataset. We used 7-day-old males for these analyses. FA levels were determined by LC-ESI-MS/MS as previously described (1).

The dataset contains LC-ESI-MS/MS raw files for the 10 samples (5 controls and 5 “mutants”) in mzML format. The dataset also contains a data analysis table. This table contains the quantifications for each fatty acid (FA) species (“RawData”, Cx:y indicates the fatty acyl chains, where x is the number of carbon atoms and y is the number of double bonds), FA levels in each sample after normalization to protein content (“Values per Sample”), and plots showing relative FA levels between control and mutant conditions (“Mean + SD Plots”).  

(1) Vonolfen MC, Meyer Zu Altenschildesche FL, Nam HJ, Brodesser S, Gyenis A, Buellesbach J, Lam G, Thummel CS, Storelli G. Drosophila HNF4 acts in distinct tissues to direct a switch between lipid storage and export in the gut. Cell Rep. 2024 Sep 24;43(9):114693. doi: 10.1016/j.celrep.2024.114693. Epub 2024 Sep 4. PMID: 39235946.
DOI: 10.5281/zenodo.14563816
title: Transformation Rate Maps of Dissolved Organic Carbon in the Contiguous U.S.

description: We develop two new maps of the dissolved organic carbon (DOC) transformation rate (\(P_r\)) over the contiguous United States. Those maps are derived by combining the USGS riverine DOC observations, soil organic carbon (SOC) data from two sources—HWSD v1.2 and SoilGrids 2.0, and the watershed characteristics from two existing datasets medium-resolution NHDplus and ScienceBase, and state-of-the-art machine learning techniques. 
description: This research is supported by the Office of Science of the U.S. Department of Energy as part of the Earth System Model Development program area through the Energy Exascale Earth System Model (E3SM) project. The Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy under Contract DE-AC05-76RL01830. L. Li and H.-Y. Li also acknowledge the support from the U.S. National Science Foundation (EAR #1804560).
DOI: 10.5281/zenodo.7651875
title: Transformation Rate Maps of Dissolved Organic Carbon in the Contiguous U.S.

description: We develop two new maps of the dissolved organic carbon (DOC) transformation rate (\(P_r\)) over the contiguous United States. Those maps are derived by combining the USGS riverine DOC observations, soil organic carbon (SOC) data from two sources—HWSD v1.2 and SoilGrids 2.0, and the watershed characteristics from two existing datasets medium-resolution NHDplus and ScienceBase, and state-of-the-art machine learning techniques. 
description: This research is supported by the Office of Science of the U.S. Department of Energy as part of the Earth System Model Development program area through the Energy Exascale Earth System Model (E3SM) project. The Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy under Contract DE-AC05-76RL01830. L. Li and H.-Y. Li also acknowledge the support from the U.S. National Science Foundation (EAR #1804560).
DOI: 10.18738/t8/eu0kfb
title: Supplementary tables for chapter 2 & 4 dissertation

description: Here you can find supplementary tables for chapter 2 and 4 of my dissertation.
DOI: 10.6084/m9.figshare.29403677
title: Supplemental Material ATIRMA

description: Supplemental Material for ATIRMA
DOI: 10.6084/m9.figshare.29403677.v1
title: Supplemental Material ATIRMA

description: Supplemental Material for ATIRMA
DOI: 10.5281/zenodo.15303436
title: Metabolomics analysis of the midgut of Dredd mutant Drosophila, with or without PGRP-LE overexpression in enterocytes

description: We sought to determine whether the pattern recognition receptor PGRP-LE acts independently of Relish/NF-kB signaling to alter metabolism in the midgut (the midgut is the equivalent of the small intestine in Drosophila). To test this possibility, we performed metabolomics analyses in Dredd mutant midguts (“Dredd_mex_plus”) and Dredd mutant midguts with PGRP-LE overexpression in enterocytes (“Dredd_mex_LE”). We used a Dredd mutant background because this mutation blocks the induction of Relish/NF-kB downstream of PGRP-LE. We have used germ-free, 7-day-old males for these analyses. The following stocks were used to generate these genotypes: Dredd[D44] (RRID:BDSC_ 80924), mex-GAL4 (RRID:BDSC_ 91368) and UAS-PGRP-LE (RRID:BDSC_33054).

The dataset contains the liquid chromatography mass spectrometry (LC-MS) raw files (2 zipped files containing the Thermo .raw files from the IC-MS (anions) and the Bz-UHPLC-MS (amines) measurements). The dataset also contains two tables with the peak information of the steady state metabolite measurements (Compound name, expected RT (retention time, min), Filename, Sample type (sample, method blank (MB), quality control (pool) and reference compound mixture (Std Mix)), Injection Volume (uL), sample type, peak height (AU), peak area (AU), actual RT (min), RT Delta, formula, adduct, m/z (Expected), m/z (Apex), m/z (Delta in ppm) and S/N (signal-to-noise)).

Data were obtained using either anion chromatography coupled to high resolution mass spectrometry (for anionic compounds, including intermediates of the TCA cycle, glycolysis, pentose phosphate pathway and nucleotides) or ultra-high performance liquid chromatography (UHPLC) coupled to high resolution mass spectrometry (for amine-containing compounds, including amino acids and polyamines).
DOI: 10.5281/zenodo.15303437
title: Metabolomics analysis of the midgut of Dredd mutant Drosophila, with or without PGRP-LE overexpression in enterocytes

description: We sought to determine whether the pattern recognition receptor PGRP-LE acts independently of Relish/NF-kB signaling to alter metabolism in the midgut (the midgut is the equivalent of the small intestine in Drosophila). To test this possibility, we performed metabolomics analyses in Dredd mutant midguts (“Dredd_mex_plus”) and Dredd mutant midguts with PGRP-LE overexpression in enterocytes (“Dredd_mex_LE”). We used a Dredd mutant background because this mutation blocks the induction of Relish/NF-kB downstream of PGRP-LE. We have used germ-free, 7-day-old males for these analyses. The following stocks were used to generate these genotypes: Dredd[D44] (RRID:BDSC_ 80924), mex-GAL4 (RRID:BDSC_ 91368) and UAS-PGRP-LE (RRID:BDSC_33054).

The dataset contains the liquid chromatography mass spectrometry (LC-MS) raw files (2 zipped files containing the Thermo .raw files from the IC-MS (anions) and the Bz-UHPLC-MS (amines) measurements). The dataset also contains two tables with the peak information of the steady state metabolite measurements (Compound name, expected RT (retention time, min), Filename, Sample type (sample, method blank (MB), quality control (pool) and reference compound mixture (Std Mix)), Injection Volume (uL), sample type, peak height (AU), peak area (AU), actual RT (min), RT Delta, formula, adduct, m/z (Expected), m/z (Apex), m/z (Delta in ppm) and S/N (signal-to-noise)).

Data were obtained using either anion chromatography coupled to high resolution mass spectrometry (for anionic compounds, including intermediates of the TCA cycle, glycolysis, pentose phosphate pathway and nucleotides) or ultra-high performance liquid chromatography (UHPLC) coupled to high resolution mass spectrometry (for amine-containing compounds, including amino acids and polyamines).
DOI: 10.6084/m9.figshare.28557530
title: Sharma_2025

description: Using genome-wide association (GWA) and quantitative trait loci (QTL) mapping, we identified a major QTL on chromosome 8 containing candidate genes encoding cation/H⁺ exchangers (CHX), which are involved in ion transport and homeostasis. To validate these findings, we analyzed a mapping population derived from <i>V. acerifolia</i><i> </i>longii 9018 and the commercial rootstock GRN3, confirming the chromosome 8 locus as a major determinant of chloride exclusion. Structural variant analysis revealed key non-synonymous substitutions within CHX genes, suggesting potential functional roles in salinity tolerance. Additionally, we discovered a novel QTL on chromosome 19 enriched with G-type lectin S-receptor-like serine/threonine-protein kinases, known regulators of stress signaling. By integrating extensive phenotypic and genomic data across a diverse <i>Vitis</i> collection, this study provides novel insights into the genetic architecture of chloride exclusion and identifies valuable candidate genes for breeding salt-tolerant rootstocks.
DOI: 10.6084/m9.figshare.28557530.v2
title: Sharma_2025

description: Using genome-wide association (GWA) and quantitative trait loci (QTL) mapping, we identified a major QTL on chromosome 8 containing candidate genes encoding cation/H⁺ exchangers (CHX), which are involved in ion transport and homeostasis. To validate these findings, we analyzed a mapping population derived from <i>V. acerifolia</i><i> </i>longii 9018 and the commercial rootstock GRN3, confirming the chromosome 8 locus as a major determinant of chloride exclusion. Structural variant analysis revealed key non-synonymous substitutions within CHX genes, suggesting potential functional roles in salinity tolerance. Additionally, we discovered a novel QTL on chromosome 19 enriched with G-type lectin S-receptor-like serine/threonine-protein kinases, known regulators of stress signaling. By integrating extensive phenotypic and genomic data across a diverse <i>Vitis</i> collection, this study provides novel insights into the genetic architecture of chloride exclusion and identifies valuable candidate genes for breeding salt-tolerant rootstocks.
DOI: 10.6084/m9.figshare.28557530.v1
title: Sharma_2025

description: Using genome-wide association (GWA) and quantitative trait loci (QTL) mapping, we identified a major QTL on chromosome 8 containing candidate genes encoding cation/H⁺ exchangers (CHX), which are involved in ion transport and homeostasis. To validate these findings, we analyzed a mapping population derived from <i>V. acerifolia</i><i> </i>longii 9018 and the commercial rootstock GRN3, confirming the chromosome 8 locus as a major determinant of chloride exclusion. Structural variant analysis revealed key non-synonymous substitutions within CHX genes, suggesting potential functional roles in salinity tolerance. Additionally, we discovered a novel QTL on chromosome 19 enriched with G-type lectin S-receptor-like serine/threonine-protein kinases, known regulators of stress signaling. By integrating extensive phenotypic and genomic data across a diverse <i>Vitis</i> collection, this study provides novel insights into the genetic architecture of chloride exclusion and identifies valuable candidate genes for breeding salt-tolerant rootstocks.
DOI: 10.15468/dl.yn95es
title: Occurrence Download

description: A dataset containing 66612 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is one of (Asia, Oceania, North America, South America)",
 "TaxonKey is Gaultheria Kalm ex L."
 ]
}

 The dataset includes 66612 records from 590 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069041-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25345/c5qf8jx84
title: MassIVE MSV000098323 - Harnessing Intracellular Parasite-Host Metabolic Interplay to Uncover Tools for Mitochondrial Repair
title: This dataset was generated from mitochondria isolated from the ovaries of Drosophila infected with Wolbachia. We then purified the mitochondria using serial refined sucrose gradients to separate them from Wolbachia contamination. Finally, mitochondrial proteomics was performed using established methods, and the spectra were mapped to the Wolbachia proteome, resulting in the identification of several parasite-derived peptides within the mitochondrial fraction. Samples LUM2_1125736-40: Wol- 1-5 Samples LUM2_1125741-5: Wol+ 1-5 Samples LUM2_1125746-50: U1-5