cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14729078
title: Leuk_18

description: Quantile normalized gene expression data (Affymetrix HG-U133 Plus 2.0 array) from the MILE (Microarray Innovations In LEukemia) program [1] (ArrayExpress, accession number E-GEOD-13159)

Data pre-processing and all analyses were conducted using the open-source statistical software R v3.4.3 (R Core Team, 2017a). Raw microarray data from stage I of the MILE study included 2,096 .CEL files that contained 16 acute and chronic leukemia subclasses, myelodysplastic syndromes (MDSs), and “none of the target classes” control group that included non-leukemia and healthy bone marrow. Data preparation included two main steps, namely cleaning and transformation. To perform a quality assessment for Affymetrix GeneChip data, we using the R package affy. The homogeneous distribution of signal and intensities and assessment of RNA degradation were checked. The samples were removed with dataset if their value of mean signal intensities was different than: $\pm3 \sigma$ and if threshold value for the 3. /5 ratios more then 3 for $\beta$-actin, and 1.25 for GAPDH (criterium recommended by Affymetrix). Next, we calculated the normalized values with robust rma background correction, quantile normalization, and median polish. To achieve a normal or near-normal distribution, the log2 transformation of gene expression data was performed .  After this transformation of the data, the dataset consisted of 2,077 samples and 54675 probes.

1. Kohlmann A, Kipps TJ, Rassenti LZ, Downing JR, Shurtleff SA, Mills KI, Gilkes AF, Hofmann WK, Basso G, Dell'orto MC, Foà R, Chiaretti S, De Vos J, Rauhut S, Papenhausen PR, Hernández JM, Lumbreras E, Yeoh AE, Koay ES, Li R, Liu WM, Williams PM, Wieczorek L, Haferlach T. An international standardization programme towards the application of gene expression profiling in routine leukaemia diagnostics: the Microarray Innovations in LEukemia study prephase. Br J Haematol. 2008 Sep;142(5):802-7. doi: 10.1111/j.1365-2141.2008.07261.x. PMID: 18573112; PMCID: PMC2654477.
DOI: 10.5281/zenodo.14729079
title: Leuk_18

description: Quantile normalized gene expression data (Affymetrix HG-U133 Plus 2.0 array) from the MILE (Microarray Innovations In LEukemia) program [1] (ArrayExpress, accession number E-GEOD-13159)

Data pre-processing and all analyses were conducted using the open-source statistical software R v3.4.3 (R Core Team, 2017a). Raw microarray data from stage I of the MILE study included 2,096 .CEL files that contained 16 acute and chronic leukemia subclasses, myelodysplastic syndromes (MDSs), and “none of the target classes” control group that included non-leukemia and healthy bone marrow. Data preparation included two main steps, namely cleaning and transformation. To perform a quality assessment for Affymetrix GeneChip data, we using the R package affy. The homogeneous distribution of signal and intensities and assessment of RNA degradation were checked. The samples were removed with dataset if their value of mean signal intensities was different than: $\pm3 \sigma$ and if threshold value for the 3. /5 ratios more then 3 for $\beta$-actin, and 1.25 for GAPDH (criterium recommended by Affymetrix). Next, we calculated the normalized values with robust rma background correction, quantile normalization, and median polish. To achieve a normal or near-normal distribution, the log2 transformation of gene expression data was performed .  After this transformation of the data, the dataset consisted of 2,077 samples and 54675 probes.

1. Kohlmann A, Kipps TJ, Rassenti LZ, Downing JR, Shurtleff SA, Mills KI, Gilkes AF, Hofmann WK, Basso G, Dell'orto MC, Foà R, Chiaretti S, De Vos J, Rauhut S, Papenhausen PR, Hernández JM, Lumbreras E, Yeoh AE, Koay ES, Li R, Liu WM, Williams PM, Wieczorek L, Haferlach T. An international standardization programme towards the application of gene expression profiling in routine leukaemia diagnostics: the Microarray Innovations in LEukemia study prephase. Br J Haematol. 2008 Sep;142(5):802-7. doi: 10.1111/j.1365-2141.2008.07261.x. PMID: 18573112; PMCID: PMC2654477.
DOI: 10.15468/dl.jq3yxd
title: Occurrence Download

description: A dataset containing 200 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Vietnamese insectivorous bat"
 ]
}

 The dataset includes 200 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000230-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5cwy72
title: Occurrence Download

description: A dataset containing 638 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 "TaxonKey is one of (Cebus albifrons (Humboldt, 1812))"
 ]
}

 The dataset includes 638 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000229-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jb6w6r
title: Occurrence Download

description: A dataset containing 49420 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euphorbia paralias L."
 ]
}

 The dataset includes 49420 records from 484 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000231-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4vbqwr
title: Occurrence Download

description: A dataset containing 463 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "TaxonKey is one of (Cichlasoma bimaculatum (Linnaeus, 1758), Cichlasoma dimerus (Heckel, 1840), Cichlasoma portalegrense (Hensel, 1870))",
 "Year 2000-2025"
 ]
}

 The dataset includes 463 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000232-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uxsvhv
title: Occurrence Download

description: A dataset containing 643 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Crenicichla britskii Kullander, 1982, Crenicichla acutirostris Günther, 1862, Crenicichla geayi Pellegrin, 1903, Crenicichla iguapina Kullander & Lucena, 2006, Crenicichla lacustris (Castelnau, 1855), Crenicichla lepidota Heckel, 1840, Crenicichla missioneira Lucena & Kullander, 1992, Crenicichla multispinosa Pellegrin, 1903, Crenicichla percna Kullander, 1991, Crenicichla regani Ploeg, 1989, Crenicichla saxatilis (Linnaeus, 1758), Crenicichla tigrina Ploeg, Jégu & Ferreira, 1991, Crenicichla vittata Heckel, 1840)",
 "Year 2015-2025"
 ]
}

 The dataset includes 643 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000234-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uys9xj
title: Occurrence Download

description: A dataset containing 1045 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is United States of America",
 "InstitutionCode is MSB",
 "OccurrenceStatus is Present",
 "StateProvince is Arizona",
 "TaxonKey is Anura"
 ]
}

 The dataset includes 1045 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000235-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.smp7f3
title: Occurrence Download

description: A dataset containing 249020 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Temporal variation in pesticide biodegradation"
 ]
}

 The dataset includes 249020 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000228-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p6e9a3
title: Occurrence Download

description: A dataset containing 113 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dicrossus maculatus Steindachner, 1875"
 ]
}

 The dataset includes 113 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000236-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x5jfra
title: Occurrence Download

description: A dataset containing 107 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mongolia",
 "PublishingOrg is one of (f5fc4e61-b7a0-414b-ab68-b41cb23e7fdc, fee3882f-5360-4f01-a1ca-767c48fa629c, 19a3a4e0-1908-11dc-a07b-b8a03c50a862, 8f6232c3-5523-44ad-825c-e066fc6b15ad, 943a5811-d56e-4c37-853d-bd64957d3833, 4fd82480-ea1c-11da-8db4-b8a03c50a862, 9ae75ccd-0ee8-4dd4-a412-3bbcc3ed4b26, ada9d123-ddb4-467d-8891-806ea8d94230, a2fa5b68-3ebf-4845-abc5-f456d251386f)",
 "TaxonKey is Allium polyrhizum Turcz. ex Regel"
 ]
}

 The dataset includes 107 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000237-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18112/openneuro.ds005874.v1.0.0
title: An fMRI Dataset for Appetite Neural Correlates in People Living with Motor Neuron Disease
DOI: 10.15468/dl.u9fmpk
title: Occurrence Download

description: A dataset containing 704 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Geophagus brasiliensis (Quoy & Gaimard, 1824), Geophagus harreri Gosse, 1976, Geophagus iporangensis Haseman, 1911, Geophagus megasema Heckel, 1840, Geophagus proximus (Castelnau, 1855), Geophagus steindachneri Eigenmann & Hildebrand, 1922, Geophagus surinamensis (Bloch, 1791), Geophagus sveni Lucinda, Lucena & Assis, 2010, Geophagus winemilleri López-Fernández & Taphorn, 2004)",
 "Year 2020-2025"
 ]
}

 The dataset includes 704 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000240-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fq4rqt
title: Occurrence Download

description: A dataset containing 76 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mongolia",
 "DatasetKey is one of (Moscow University Herbarium (MW), Virtual Herbarium ALTB (South-Siberian Botanical Garden), Herbarium GAT, A global database for the distributions of crop wild relatives, Foreign Asia herbarium collection in CSBG (NS), Mongolian Plant (MMNH-PL), INSDC Sequences, Ibaraki Nature Museum, Vascular Plants collection, United States National Plant Germplasm System Collection)",
 "TaxonKey is Allium mongolicum Regel"
 ]
}

 The dataset includes 76 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000241-250123221155621/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.26069006
title: Optimising the placement of additional drill holes to enhanced mineral resource classification: a case study on a porphyry copper deposit

description: In this study, we compared outcomes of optimising the placement of five additional drill holes using three geostatistical cost functions (AKV, WAKV, and CV) and the Particle Swarm Optimisation algorithm (PSO). WAKV identified locations with higher average copper grades compared to AKV. Conversely, CV suggested sites with high kriging variance and copper grade variation. Initial holes, alongside those determined by each cost function, were used to classify mineral resources. Findings underscored the effectiveness of optimising drill hole placement based on cost functions in reducing uncertainty and improving mineral resource classification.
DOI: 10.6084/m9.figshare.26069006.v1
title: Optimising the placement of additional drill holes to enhanced mineral resource classification: a case study on a porphyry copper deposit

description: In this study, we compared outcomes of optimising the placement of five additional drill holes using three geostatistical cost functions (AKV, WAKV, and CV) and the Particle Swarm Optimisation algorithm (PSO). WAKV identified locations with higher average copper grades compared to AKV. Conversely, CV suggested sites with high kriging variance and copper grade variation. Initial holes, alongside those determined by each cost function, were used to classify mineral resources. Findings underscored the effectiveness of optimising drill hole placement based on cost functions in reducing uncertainty and improving mineral resource classification.
DOI: 10.6084/m9.figshare.26096659
title: Characterisation of the internal friction angle of waste rock material from large triaxial tests using the contact dynamics method

description: The Chilean copper mining industry generates large amounts of waste rock materials. These structures must be designed, operated, and closed considering their physical stability. Although these structures generally do not present physical stability problems, superficial failures may occur, where waste rock material is subjected to low confining pressures. The identification of the internal friction angle, necessary for stability calculations, is based on the characterisation of these materials under high confining pressures. This assumption is not representative of the loading conditions in the superficial layers. To address this issue, numerical large-scale triaxial tests, using the contact dynamics method, are performed to identify the internal friction angle of these materials under low confining pressures. To model these material, irregular polyhedrons were generated using statistical data of crushed aggregates, considering the morphology and the particle size distribution from experimental waste rock materials. The proposed numerical approach was validated by comparing it to literature data for confining pressures over 0.5 MPa. Our results indicate that the internal friction angle stabilises at 39° for confining pressures below 0.1 MPa. This study provides important insights into the physical stability of waste rock dumps and contributes to the development of more accurate stability calculations for these structures.
DOI: 10.6084/m9.figshare.26096659.v1
title: Characterisation of the internal friction angle of waste rock material from large triaxial tests using the contact dynamics method

description: The Chilean copper mining industry generates large amounts of waste rock materials. These structures must be designed, operated, and closed considering their physical stability. Although these structures generally do not present physical stability problems, superficial failures may occur, where waste rock material is subjected to low confining pressures. The identification of the internal friction angle, necessary for stability calculations, is based on the characterisation of these materials under high confining pressures. This assumption is not representative of the loading conditions in the superficial layers. To address this issue, numerical large-scale triaxial tests, using the contact dynamics method, are performed to identify the internal friction angle of these materials under low confining pressures. To model these material, irregular polyhedrons were generated using statistical data of crushed aggregates, considering the morphology and the particle size distribution from experimental waste rock materials. The proposed numerical approach was validated by comparing it to literature data for confining pressures over 0.5 MPa. Our results indicate that the internal friction angle stabilises at 39° for confining pressures below 0.1 MPa. This study provides important insights into the physical stability of waste rock dumps and contributes to the development of more accurate stability calculations for these structures.
DOI: 10.15468/dl.mc3pmv
title: Occurrence Download

description: A dataset containing 44904 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euphorbia paralias L.",
 {
 "not" : {
 "Country" : [
 "is Australia"
 ]
 }
 }
 ]
}

 The dataset includes 44904 records from 459 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000242-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w57ahc
title: Occurrence Download

description: A dataset containing 107 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mongolia",
 "PublishingOrg is one of (f5fc4e61-b7a0-414b-ab68-b41cb23e7fdc, fee3882f-5360-4f01-a1ca-767c48fa629c, 19a3a4e0-1908-11dc-a07b-b8a03c50a862, 8f6232c3-5523-44ad-825c-e066fc6b15ad, 943a5811-d56e-4c37-853d-bd64957d3833, 4fd82480-ea1c-11da-8db4-b8a03c50a862, 9ae75ccd-0ee8-4dd4-a412-3bbcc3ed4b26, ada9d123-ddb4-467d-8891-806ea8d94230, a2fa5b68-3ebf-4845-abc5-f456d251386f)",
 "TaxonKey is Allium polyrhizum Turcz. ex Regel"
 ]
}

 The dataset includes 107 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000243-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/fl9ddz/aqpyog
title: GIZ_HH_Food consumption_survey _ KoboToolbox.pdf

description: Food consumption questionnaire
DOI: 10.7910/dvn/fl9ddz/z3gknz
title: Lusaka Fish Consumption Survey- XLS_QuestionnaireCodeBook.xls

description: Lusaka Fish Consumption Survey CodeBook
DOI: 10.15468/dl.6bawpx
title: Occurrence Download

description: A dataset listing the 262 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is India",
 "DatasetKey is EOD – eBird Observation Dataset",
 "Geometry POLYGON((77.76652 13.05744,77.76821 13.05518,77.77836 13.05744,77.77836 13.09207,77.76455 13.10043,77.76117 13.0963,77.75829 13.08435,77.75827 13.07572,77.76652 13.05744))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year 2000-2025"
 ]
}

 The dataset's 262 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000233-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y5a8ju
title: Occurrence Download

description: A dataset containing 9234 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CAN.2_1",
 "TaxonKey is Melanerpes lewis (G.R.Gray, 1849)"
 ]
}

 The dataset includes 9234 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000244-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hkfqs9
title: Occurrence Download

description: A dataset containing 470 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Guianacara owroewefi Kullander & Nijssen, 1989"
 ]
}

 The dataset includes 470 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000245-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gg2fvg
title: Occurrence Download

description: A dataset containing 109336 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 2024-12-29",
 "EventDate is less than or equal to 2025-01-28",
 {
 "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 109336 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000227-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.65hy48
title: Occurrence Download

description: A dataset containing 276 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "TaxonKey is one of (Gymnogeophagus balzanii (Perugia, 1891), Gymnogeophagus labiatus (Hensel, 1870), Gymnogeophagus meridionalis Reis & Malabarba, 1988, Gymnogeophagus setequedas Reis, Malabarba & Pavanelli, 1992)",
 "Year 2000-2025"
 ]
}

 The dataset includes 276 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000246-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14696862
title: Data and codes to reproduce the figures
DOI: 10.5281/zenodo.14729127
title: Stock selection for coral restoration on the Great Barrier Reef: Does phenotypic diversity align to population genetic structure?

description: Selection of corals with beneficial phenotypes is a potential strategy to increase reef resilience via active restoration. However, this approach carries the risk of reducing genetic diversity by focusing on a subset of the population. Thus, understanding the genetic consequences of selecting colonies based solely on phenotypes is crucial. Here, we applied a novel, high-throughput phenotyping device to examine differences in photophysiological performance of 174 Acropora millepora colonies from three reefs across the continental shelf of the Great Barrier Reef. Through a rapid assay, we assessed photophysiological parameters of colonies exposed to a thermal gradient, and further examined how emergent phenotypes related to the genetic structure of those corals. We show that photophysiological responses of dose-response curves varied both across and within sites (maximum range of 2.16 ºC in Fq’/Fm’ ED50), but did not align with genetic structure, as all colonies belonged to a single, highly connected population. Our findings indicate that selection of A. millepora colonies based on photophysiological phenotypic performance is unlikely to impact genetic diversity in this region, demonstrating the value of considering both phenotypic traits and genetic structure for reef management.

 

The data file included here ("Report_DAc23-8280_SNP_2") contains the raw SNP data from sampled A. millepora colonies used to assess genetic structure and diversity of the population. SNP data were generated via genome comlexity reduction-based sequencing by Diversity Arrays Technology Pty Ltd.