cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7566285
title: Data for: Social context prevents heat hormetic effects against mutagens during fish development

description: Data for: Social context prevents heat hormetic effect against mutagens during fish development

Abstract: Global changes impose increasingly stressful environments with multiple stressors such as heat events and mutagens co-occurring. Stress levels may be increased via stress-induced “social metabolites” from congeners. Consequently, species experiencing multiple stressors within social contexts may display more adverse outcomes than anticipated. This makes it paramount to understand how social and heat stress history may amplify the negative consequences of global change-related stressors in aquatic animals when they face subsequent stressors. For this purpose, we exposed zebrafish embryos to one of three stress history treatments consisting of direct heat stress, its social context via chemical cues, and their combination, before undergoing a UVB/UVA damage/repair assay. We measured phenotypic and transcriptomic responses to these treatments, and estimated mutational damage through RNA integrity values. Compared to UV-treated controls, embryos exposed to social metabolites preceding the UV assay showed altered keratin and cell structuring-related pathways, were growing longer with over-developed pericardia and were hypoactive. Relative to UV-treated controls, direct heat stress preceding UV exposure had a hormetic effect likely involving stimulation of the cellular stress response and a facilitated DNA repair, rescuing and/or protecting embryos from UV damage, in turn improving their fitness. However, heat stress combined with social metabolites likely overwhelmed embryos in the UV assay, which annihilated the hormetic effect, damaged RNA, and lowered apparent fitness estimates. Although these findings were obtained in the laboratory, they provide a solid framework for understanding how heat and social stress history affect fitness outcomes in natural environments. This underscores the need for more research on how species adapt to intensifying stressors amidst global change in social contexts.

This archive contains the data of RNA-sequencing and phenotypic (morphology and behaviour) of zebrafish embryos exposed to stress history (heat stress and its social context) prior to being exposed to ultraviolets (UV).
description: Pleae refer to the document "Feugere.etal.2025.UVxTSxSM.metadata.PDF" for details on the content of this archive.

Briefly, the archive contains:



the data of the different metrics (phenotype, methodological development and RNA-sequencing) in the /data folder.

the R code in a .Rmd and .html extensions built in R/RStudio

the bioinformatics code used to obtain the read count data (Feugere.etal.2025.UVxTSxSM.RNAseq.ipynb/html files)

The output generated during the statistical analysis



the gene expression matrices in the /DEG output folder

the statistical analyses, the significant gene sets of interest and their functional enrichment in the Dataset S1 file

the comparison of limma and DESeq2 methods in the Dataset S2 file
DOI: 10.15468/dl.pka8hx
title: Occurrence Download

description: A dataset containing 39537 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Epilachna varivestis Mulsant, 1850, Plathypena scabra (Fabricius, 1798), Diabrotica undecimpunctata howardi Barber, 1947, Phakopsora pachyrhizi Syd. & P.Syd., Heterodera glycines Ichinohe, 1952, Bradyrhizobium japonicum_C, Riptortus pedestris (Fabricius, 1775), Etiella zinckenella (Treitschke, 1832), Dectes texanus LeConte, 1862, Alectra vogelii Benth., Crocidosema aporema (Walsingham, 1914), Cernuella virgata (Da Costa, 1778), Peronospora manshurica (Naumov) Syd., Pratylenchus sefaensis Fortuner, 1973, Phytophthora sansomeana E.M.Hansen & Reeser, Septoria glycines Hemmi, Bacillus subtilis G, Arkoola nigra J.Walker & Stovold, Aristastoma guttulosum B.Sutton, Elsinoe glycines (Kurata & Kurib.) X.L.Fan & Crous, Fusarium virguliforme O'Donnell & T.Aoki, Diaporthe longicolla (Hobbs) J.M.Santos, Vrandečić & A.J.L.Phillips, Colletotrichum glycines Hori ex Hemmi, Pythium inflatum V.D.Matthews, Fusarium brasiliense T.Aoki & O'Donnell, Eremothecium ashbyi Guillierm., Stauronematopsis sojae (Uecker & Kulik) Abbas, B.Sutton & Ghaffar, Fusarium tucumaniae T.Aoki, O'Donnell, Yosh.Homma & Lattanzi, Colletotrichum chlorophyti S.Chandra & Tandon, Fusarium crassistipitatum Scandiani, T.Aoki & O'Donnell, Bipolaris glycines (S.Naray. & Durairaj) B.A.Khasanov, Aristastoma camarographioides B.Sutton, Pratylenchus teres Khan & Singh, 1975, Calonectria morganii Crous, Alfenas & M.J.Wingf., Pratylenchus alleni Ferris, 1961, Pratylenchus agilis Thorne & Malek, 1968, Pratylenchus zeae Graham, 1951, Albonectria rigidiuscula (Berk. & Broome) Rossman & Samuels, Eremothecium coryli (Peglion) Kurtzman, Choanephora infundibulifera (Curr.) D.D.Cunn., Stachybotrys chartarum (Ehrenb.) S.Hughes, Coniothyrium glycines (R.B.Stewart) Verkley & Gruyter, Erysiphe diffusa (Cooke & Peck) U.Braun & S.Takam., Phyllosticta glycineum Tehon & Daniels, Phakopsora meibomiae (Arthur) Arthur, Fusarium pallidoroseum (Cooke) Sacc., Aproaerema anthyllidella (Hübner, 1813), Anarsia nigricana Park, 1991, Estigmene laglaizei Rothschild, 1910, Dasychira anophoeta Collenette, 1936)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 39537 records from 673 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002670-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yp8vhk
title: Occurrence Download

description: A dataset containing 6318 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aquila heliaca Savigny, 1809",
 "HasCoordinate is true",
 "Year is greater than 1989",
 "Year is less than 2026",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is Absent"
 ]
 }
 },
 "CoordinateUncertaintyInMeters is less than or equal to 1000"
 ]
}

 The dataset includes 6318 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002672-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15446848
title: Systematic Approaches for the Encoding of Chemical Groups: A Case study.

description: Herein are the data files that support a simple python package to facilitate profiling of chemicals through the ECHA ARN groupings using the Random Forest model that was developed in Karamertzanis, P, Patlewicz G, Sannicola M, Paul-Friedman K, Shah (2024) Systematic Approaches for the Encoding of Chemical Groups: A Case study. Chem. Res. Toxicol. 37, 600-619. https://doi.org/10.1021/acs.chemrestox.3c00411

The original repository supporting this publication can be found here https://github.com/pkaramertzanis/regulatory_grouping/tree/master. In https://github.com/patlewig/arn_cats/ we provide a simpler means of applying the best random forest model developed in the original study to make grouping assignments for new chemicals. 

Although the arn_cats package and associated repository provide notebooks to recreate the random forest models and necessary input files, these are provided for convenience. The dataset of REACH chemicals that was supplied in the SI of the original publication is provided here as it is useful set to verify the RF model predictions.
DOI: 10.5281/zenodo.15446849
title: Systematic Approaches for the Encoding of Chemical Groups: A Case study.

description: Herein are the data files that support a simple python package to facilitate profiling of chemicals through the ECHA ARN groupings using the Random Forest model that was developed in Karamertzanis, P, Patlewicz G, Sannicola M, Paul-Friedman K, Shah (2024) Systematic Approaches for the Encoding of Chemical Groups: A Case study. Chem. Res. Toxicol. 37, 600-619. https://doi.org/10.1021/acs.chemrestox.3c00411

The original repository supporting this publication can be found here https://github.com/pkaramertzanis/regulatory_grouping/tree/master. In https://github.com/patlewig/arn_cats/ we provide a simpler means of applying the best random forest model developed in the original study to make grouping assignments for new chemicals. 

Although the arn_cats package and associated repository provide notebooks to recreate the random forest models and necessary input files, these are provided for convenience. The dataset of REACH chemicals that was supplied in the SI of the original publication is provided here as it is useful set to verify the RF model predictions.
DOI: 10.15468/dl.7p89mg
title: Occurrence Download

description: A dataset containing 10193 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aquila nipalensis Hodgson, 1833",
 "HasCoordinate is true",
 "Year is greater than 1989",
 "Year is less than 2026",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is Absent"
 ]
 }
 },
 "CoordinateUncertaintyInMeters is less than or equal to 1000"
 ]
}

 The dataset includes 10193 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002673-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7m6ufc
title: Occurrence Download

description: A dataset containing 795538 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Xeno-canto - Bird sounds from around the world"
 ]
}

 The dataset includes 795538 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002668-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.skza4u
title: Occurrence Download

description: A dataset containing 1971 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aratinga nenday (Vieillot, 1823)",
 "HasCoordinate is true",
 "Year is greater than 1989",
 "Year is less than 2026",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is Absent"
 ]
 }
 },
 "CoordinateUncertaintyInMeters is less than or equal to 1000"
 ]
}

 The dataset includes 1971 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002676-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2bhhzx
title: Occurrence Download

description: A dataset containing 22228 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Acontia dacia Druce, 1889, Bradina adhaesalis Walker, 1858, Etiella hobsoni (Butler, 1881), Mabra charonialis Walker, 1859, Ocrasa nostralis Guenée, 1854, Omiodes poeonalis (Walker, 1859), Phalonidia curvistrigana (Stainton, 1859), Leguminivora glycinivorella (Matsumura, 1898), Clanis bilineata Walker, 1866, Synchlora frondaria Guenée, Dichomeris acuminatus (Staudinger, 1876), Bandicota indica (Bechstein, 1800), Eurema lisa (Boisduval & Le Conte, 1833), Anastatus auriceps Ashmead, 1904, Pseudocatolaccus tamabae Ishii, 1950, Pseudocatolaccus sayatamabae Ishii, 1950, Aphelinus glycinis Hopper & Woolley, 2012, Aphelinus coreae Hopper, Woolley, Hoelmer, Wu, Qiao & Lee, 2012, Eurytoma melanagromyzae Narendran, 1994, Tetrastichus obliqua Khan & Sushil, 1993, Colotrechnus agromyzae Subba Rao, 1981, Trichogramma marthae Goodpasture, 1986, Trichogramma acacioi Brun, Gomez de Moraes & Soares, 1984, Trichogramma bruni Nagaraja, 1983, Trichogramma atopovirilia Oatman & Platner, 1983, Trichomalopsis apanteloctena (Crawford, 1911), Euplectrus puttleri Gordh, 1980, Polynema boreum Girault, 1915, Trichogramma exiguum Pinto & Platner, 1978, Grotiusomyia nigricans (Howard, 1894), Euplectrus chapadae Ashmead, 1904, Trichogramma rojasi Nagaraja & Nagarkatti, 1973, Encarsia coquilletti Howard, 1895, Coruna clavata Walker, 1833, Hexacladia smithii Ashmead, 1891, Elasmus philippinensis Ashmead, 1904, Eurema alitha (Felder & Felder, 1862), Papilio mahadeva Moore, 1878, Papilio castor Westwood, 1842, Baryscapus bruchidii (Erdos, 1951), Uromyces glycyrrhizae (Rabenh.) Magnus, Lycaeides melissa (Edwards, 1873), Plebejus melissa (W.H.Edwards, 1873), Bruchophagus grisselli McDaniel & Boe, 1991, Acrocercops mechanopla Meyrick, 1934, Acrocercops telestis Meyrick, 1911, Phyllocnistis amydropa Meyrick, 1934, Endoclita chalybeatus (Moore, 1879), Ctenolita anacompa Karsch, 1896, Halseyia fimbriata (Karsch, 1896))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 22228 records from 311 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002675-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cdxnaf
title: Occurrence Download

description: A dataset containing 153097 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Trichobius costalimai Guimarães, 1938, Trichobius joblingi Wenzel, 1966, Trichobius dugesiodes Wenzel, 1966, Strebla hertigi Wenzel, 1966, Strebla mirabilis (Waterhouse, 1879), Centrocestus formosanus (Nishigori, 1924) Price, 1932, Haplorchis pumilio (Looss, 1896) Looss, 1899, Cecropia obtusa Trécul, Paratrichobius dunni (Curran, 1935), Weissella ceti A, Ypthima nikaea Moore, 1874, Euploea mulciber mulciber, Danaus affinis Fabricius, 1775, Protaetia fusca (Herbst, 1790), Coelioxys slossoni slossoni, Haplorhynchites aeneus (Boheman, 1829), Psilopsiagon aymara (Orbigny, 1839), Chrysemys picta (Schneider, 1783), Paratrichobius salvini Wenzel, 1966, Hydrobiosis parumbripennis McFarlane, 1951, Psilochorema bidens McFarlane, 1951, Cecropia pachystachya Trécul, Cecropia glaziovii Snethl., Brucella ceti, Actinobacillus delphinicola Foster et al., 1996, Brucella melitensis (Hughes, 1893) Meyer & Shaw, 1920, Bolbosoma vasculosum (Rudolphi, 1819), Dactylogyrus kurenkowi Gusev, 1955, Dactylogyrus zaccoi Ma, Li & Wang, 1982, Dactylogyrus primarius Gusev, 1955, Paradiplozoon opsariichthydis (Jiang, Wu & Wang, 1984) Jiang, Wu & Wang, 1989, Paradiplozoon parabramisi (Ling, 1973) Khotenovsky, 1985, Eleotris fusca (Forster, 1801), Dentex angolensis Poll & Maul, 1953, Pagrus major (Temminck & Schlegel, 1843), Plesiops nigricans (Rüppell, 1828), Anthurium nymphaefolium K.Koch & C.D.Bouché, 1853, Calycolpus moritzianus (O.Berg) Burret, Saurauia excelsa Willd., Piper diffamatum Trel. & Yunck., Anthurium nymphaeifolium K.Koch & C.D.Bouché, Vismia baccifera (L.) Triana & Planch., Megistopoda aranea (Coquillett, 1899), Anastrebla caudiferae Wenzel, 1976, Trichobius hispidus Wenzel, 1976, Semnorhynchus fulvopictus Champion, 1906, Polistes bahamensis Bequard & Salt, 1931, Chrysonotomyia unimaculata Paniagua & Hansson, Tropicharis cecivora Hansson, 1998, Myotis capaccinii (Bonaparte, 1837))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 153097 records from 919 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002663-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dd.2acfav
title: GBIF data of plantea occurences in the Arctic

description: GBIF data of plantea occurences in the Arctic. Occurrence data was filtered and cleaned following standard protocols (GBIF Secretariat 2021). 
Missing values in longitude, latitude and species as well as error values were discarded and fossil records/museum specimens were excluded. 
We selected for the time after 1970 and a distance uncertainty &lt; 5000 m.
DOI: 10.15468/dl.xvuutm
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Melanitta perspicillata",
 "Country is Germany",
 "HasCoordinate is true"
 ]
}

 The dataset includes 14 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031458-250811113504898/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.29143823
title: Joest et al. - Incomplete milking on udder firmness, heart-rate variability, and behavior recordings in dairy cows

description: This study aimed to evaluate the effects of automated short-term incomplete milking, with reduced milk withdrawal up to 40% on udder filling, udder firmness, and on the welfare of dairy cows, by assessing heart rate variability and behavior recordings in the milking parlor and barn in multiparous dairy cows during peak- to mid-lactation. Short-term incomplete milking led to high udder filling and firmness, indicating elevated internal udder pressure and potential discomfort. Analysis of heart rate variability revealed no alterations in the sympatho-vagal balance caused by incomplete milking. Behavioral observations in the milking parlor and barn including the brush use weren´t affected by incomplete milking. The incomplete milking protocol, including reduced milk withdrawal up to 40%, induced elevated udder firmness whereas the used indicators evaluated in this study do not suggest compromised welfare, supporting incomplete milking as a viable strategy in dairy cows.
DOI: 10.6084/m9.figshare.29143823.v1
title: Joest et al. - Incomplete milking on udder firmness, heart-rate variability, and behavior recordings in dairy cows

description: This study aimed to evaluate the effects of automated short-term incomplete milking, with reduced milk withdrawal up to 40% on udder filling, udder firmness, and on the welfare of dairy cows, by assessing heart rate variability and behavior recordings in the milking parlor and barn in multiparous dairy cows during peak- to mid-lactation. Short-term incomplete milking led to high udder filling and firmness, indicating elevated internal udder pressure and potential discomfort. Analysis of heart rate variability revealed no alterations in the sympatho-vagal balance caused by incomplete milking. Behavioral observations in the milking parlor and barn including the brush use weren´t affected by incomplete milking. The incomplete milking protocol, including reduced milk withdrawal up to 40%, induced elevated udder firmness whereas the used indicators evaluated in this study do not suggest compromised welfare, supporting incomplete milking as a viable strategy in dairy cows.
DOI: 10.15468/dl.7eatmc
title: Occurrence Download

description: A dataset containing 19008 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Ilex verticillata"
 ]
}

 The dataset includes 19008 records from 176 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031459-250811113504898/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.29966560
title: <b>Filial Piety and Acceptance of AI-Based Elderly Care: A Cultural Perspective on Consumption Intentionss</b>

description: o examine how filial piety influences consumption intentions toward AI-based elderly care services among Chinese consumers.
DOI: 10.6084/m9.figshare.29966560.v1
title: <b>Filial Piety and Acceptance of AI-Based Elderly Care: A Cultural Perspective on Consumption Intentionss</b>

description: o examine how filial piety influences consumption intentions toward AI-based elderly care services among Chinese consumers.
DOI: 10.15468/dl.3gxw9u
title: Occurrence Download

description: A dataset containing 204 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Polysticta stelleri",
 "Country is Germany",
 "HasCoordinate is true"
 ]
}

 The dataset includes 204 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031461-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57760/sciencedb.29300
title: Pathogenic CD137+ IL-17+ atypical Treg is a unique feature of immune checkpoint inhibitor-induced inflammatory arthritis and is abrogated by IL-6R blockade
title: Pathogenic CD137+ IL-17+ atypical Treg is a unique feature of immune checkpoint inhibitor-induced inflammatory arthritis and is abrogated by IL-6R blockade

description: Immune checkpoint inhibitor-induced inflammatory arthritis (ICI-IA) significantly impairs cancer therapy and patient quality of life, yet its pathogenic mechanisms remain unclear. Through integrated single-cell multi-omics analysis of paired peripheral blood, synovial fluid, and tumor samples from longitudinal ICI-IA cohorts and matched controls, we identified a unique regulatory T-cell (Treg) population co-expressing CD137 and IL-6R (AtpTreg). These cells exhibited reduced immunosuppressive capacity while aberrantly producing high level of IL-17 and promoting proinflammatory responses of synoviocytes. AtpTreg exhibits shared clonotypes and phenotypes across tissue compartments. Notably, AtpTreg frequency correlates with increased arthritis severity yet paradoxically associates with improved overall survival. Anti-IL6R therapy reduced AtpTreg levels, corresponding with improved arthritis outcomes and quality of life, without compromising anti-tumor immunity. Our findings define a pathogenic Treg subset in ICI-IA and validate IL-6R blockade as a mechanism-based therapeutic strategy, bridging mechanistic discovery to clinical translation.
description: Immune checkpoint inhibitor-induced inflammatory arthritis (ICI-IA) significantly impairs cancer therapy and patient quality of life, yet its pathogenic mechanisms remain unclear. Through integrated single-cell multi-omics analysis of paired peripheral blood, synovial fluid, and tumor samples from longitudinal ICI-IA cohorts and matched controls, we identified a unique regulatory T-cell (Treg) population co-expressing CD137 and IL-6R (AtpTreg). These cells exhibited reduced immunosuppressive capacity while aberrantly producing high level of IL-17 and promoting proinflammatory responses of synoviocytes. AtpTreg exhibits shared clonotypes and phenotypes across tissue compartments. Notably, AtpTreg frequency correlates with increased arthritis severity yet paradoxically associates with improved overall survival. Anti-IL6R therapy reduced AtpTreg levels, corresponding with improved arthritis outcomes and quality of life, without compromising anti-tumor immunity. Our findings define a pathogenic Treg subset in ICI-IA and validate IL-6R blockade as a mechanism-based therapeutic strategy, bridging mechanistic discovery to clinical translation.