cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/74vy7zx9rf
title: MS results for identifying SPINK1-interacting partners

description: Raw data of mass spectrometry (MS) experiments in "SPINK1-COL18A1 Crosstalk Shapes Epigenome and Drives Cancer Stemness in Pancreatic Ductal Adenocarcinoma" project. A method of proximity dependent biotinylation with UltraID was used in PANC-1 cell line. PANC-1 cells overexpressing SPINK1-UltraID (plasmid plentiSFFV-hSPINK1-UltraID) or Ultra Ctrl (plasmid plentiSFFV-hSPINK1SP-UltraID-ALFA) were allowed to grow to ~90% confluency in 150 mm Petri dish. On the day of the experiment, cells were incubated in 50 µM biotin for 1h at 37℃. Then the biotinylated proteins were pull-down and digested on beads before MS. 

Species: Homo sapiens
Tissue: Cell culture
Cell type: Permanent cell line cell (PANC-1 cell line)
Disease: Pancreatic ductal adenocarcinoma
Subcellular: Whole cell lysate
Method: On-beads digestion
Digestion Enzyme: Trypsin
Instrument Type: Affinity purification (AP-MS)
Instrument: Q Executive HF-X

Data was analyzed using Proteome Discoverer (version 2.5)(Thermo Scientific) software and searched in-house using the Mascot algorithm (version 2.8.3) (Matrix Science). Scaffold v5.1.2 (Proteome Software Inc.) was used to validate MS/MS based peptide and protein identifications.

Ultra Ctrl (control group) associated file names: HFX24-1103_Shang_20240313_Control_Digestion.raw; HFX24-1103_Shang_20240313_Control_Digestion.mzid_HFX24-1103_Shang_20240313_Control_Digestion.MGF; HFX24-1103_Shang_20240313_Control_Digestion.mzid

SPINK1-UltraID (experiment group) associated file names: HFX24-1108_Shang_20240313_SPINK1-UltraID_Digestion; HFX24-1108_Shang_20240313_SPINK1-UltraID_Digestion.mzid_HFX24-1108_Shang_20240313_SPINK1-UltraID_Digestion.MGF; HFX24-1108_Shang_20240313_SPINK1-UltraID_Digestion.mzid
DOI: 10.17632/74vy7zx9rf.1
title: MS results for identifying SPINK1-interacting partners

description: Raw data of mass spectrometry (MS) experiments in "SPINK1-COL18A1 Crosstalk Shapes Epigenome and Drives Cancer Stemness in Pancreatic Ductal Adenocarcinoma" project. A method of proximity dependent biotinylation with UltraID was used in PANC-1 cell line. PANC-1 cells overexpressing SPINK1-UltraID (plasmid plentiSFFV-hSPINK1-UltraID) or Ultra Ctrl (plasmid plentiSFFV-hSPINK1SP-UltraID-ALFA) were allowed to grow to ~90% confluency in 150 mm Petri dish. On the day of the experiment, cells were incubated in 50 µM biotin for 1h at 37℃. Then the biotinylated proteins were pull-down and digested on beads before MS. 

Species: Homo sapiens
Tissue: Cell culture
Cell type: Permanent cell line cell (PANC-1 cell line)
Disease: Pancreatic ductal adenocarcinoma
Subcellular: Whole cell lysate
Method: On-beads digestion
Digestion Enzyme: Trypsin
Instrument Type: Affinity purification (AP-MS)
Instrument: Q Executive HF-X

Data was analyzed using Proteome Discoverer (version 2.5)(Thermo Scientific) software and searched in-house using the Mascot algorithm (version 2.8.3) (Matrix Science). Scaffold v5.1.2 (Proteome Software Inc.) was used to validate MS/MS based peptide and protein identifications.

Ultra Ctrl (control group) associated file names: HFX24-1103_Shang_20240313_Control_Digestion.raw; HFX24-1103_Shang_20240313_Control_Digestion.mzid_HFX24-1103_Shang_20240313_Control_Digestion.MGF; HFX24-1103_Shang_20240313_Control_Digestion.mzid

SPINK1-UltraID (experiment group) associated file names: HFX24-1108_Shang_20240313_SPINK1-UltraID_Digestion; HFX24-1108_Shang_20240313_SPINK1-UltraID_Digestion.mzid_HFX24-1108_Shang_20240313_SPINK1-UltraID_Digestion.MGF; HFX24-1108_Shang_20240313_SPINK1-UltraID_Digestion.mzid
DOI: 10.15468/dl.5zndvv
title: Occurrence Download

description: A dataset containing 181 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alpheus nuttingi"
 ]
}

 The dataset includes 181 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025569-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k5svhg
title: Occurrence Download

description: A dataset containing 133 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Protopolybia exigua"
 ]
}

 The dataset includes 133 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025570-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tfx35c
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Xenodermichthys copei (Gill, 1884)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((17.9945 31.4042,17.9648 31.4107,17.9648 28.8496,26.9648 28.8496,26.9648 31.9498,25.9351 32.1234,25.521 32.0431,25.1292 32.4448,23.62 32.6843,23.2184 33.1274,22.2555 33.4227,21.6592 33.4362,20.3254 32.9854,19.735 32.5293,19.425 31.8208,19.6247 31.1033,19.1159 30.7686,17.9945 31.4042))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010511-250525065834625/datasets/export for details.
DOI: 10.5281/zenodo.14162800
title: Test

description: This is a test description of the dataset!
DOI: 10.15468/dl.7ruxj8
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Xenodermichthys copei (Gill, 1884)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((35.9919 -21.4718,35.9648 -21.4413,35.9648 -24.1383,36.0558 -23.8719,35.9919 -21.4718))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010535-250525065834625/datasets/export for details.
DOI: 10.15468/dl.uqhxz3
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Clethra arborea",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001115-260126135527185/datasets/export for details.
DOI: 10.5061/dryad.rv857
title: Data from: Human face structure correlates with professional baseball performance: insights from professional Japanese baseball players

description: In our daily lives, we use faces as a major source of information about
 other people. Recent work has begun to highlight how one's facial
 width-to-height ratio (fWHR) is linked to a number of behaviours (e.g.
 deception, aggression and financial performance in firms). fWHR has also
 been linked to several factors that may be beneficial for sport (e.g.
 achievement drive, winning mentality and aggression). Despite this, few
 studies have examined the relationship between fWHR and sports
 performance, and these have focused on Caucasian sportsmen. Here, we
 investigated the relationship between fWHR and baseball performance in
 professional Japanese baseball players. We show that fWHR is positively
 related with home run performance across two consecutive seasons. The
 findings provide the first evidence linking fWHR to baseball performance
 and linking fWHR to behavioural outcomes in Asian participants.
description: Data for a paper at
 Biology LettersData for a paper titled,
 "Human face structure correlates with professional baseball
 performance: insights from professional Japanese baseball players,"
 at Biology LettersData.xlsx
DOI: 10.5061/dryad.hg6st
title: Data from: Multivariate ratio analysis reveals Trigonoderus pedicellaris Thomson (Hymenoptera, Chalcidoidea, Pteromalidae) as a valid species

description: We demonstrate by multivariate ratio analysis (MRA) the validity of two
 female colour morphs as separate species in what was previously regarded
 as a single species, Trigonoderus cyanescens (Förster, 1841) (Hymenoptera:
 Pteromalidae). As a result, T. pedicellaris Thomson, 1878 stat.r., is
 resurrected from synonymy under T. cyanescens and T. filatus binubilatus
 Erdős, 1960 syn.n. is synonymized with T. cyanescens. More than 20
 characters were measured as part of two MRA dataset analyses. The first
 analysis excluded all measurements related to the gaster, whereas the
 second included gaster length, gaster breadth and seventh gaster tergite
 breadth. The first analysis revealed that the best separating morphometric
 ratios for the two species are head breadth:metatibia length and
 OOL:parastigma length, whereas the second analysis revealed OOL:gaster
 length as the second best separating ratio. The measurement error of all
 characters was below the admissible level of 30%. Gaster length proved to
 be a good character for separating the two groups, showed the lowest
 measurement error, and its percentage coefficient of variation was not
 greater than for other characters. This indicates that gaster length
 should not be discarded out-of-hand as a morphometric character in
 Pteromalidae. The variables that gave the best separating ratios included
 different body parts; therefore we suggest that the body of a specimen
 should be taken as a whole for use in MRA analyses, where each distance
 measurement can interact freely with any other. A key, figures and
 re-descriptions of T. cyanescens and T. pedicellaris are provided.
description: Trigonoderus repeated
 measures data.txtThree measurements for
 each morphometric character (23 characters on 86 females). Column names:
 sp.id - specimen identity; repeat - repeated measures; sp.name - group
 name; spm.code - specimen code; cntry.fact - country code, descriptions of
 all other abbreviations in the paper Table 1. Cells with "NA" -
 missing data.trigonoderus_repeated_measures_data.txt
DOI: 10.5061/dryad.cj8qn
title: Data from: Reproductive behaviour indicates specificity in resource use: phylogenetic examples from temperate and tropical insects

description: Specificity (= the degree of ecological specialisation) is one of the
 fundamental concepts of the science of ecology. Ambiguities on how to
 define and measure specificity have however complicated respective
 research efforts. Here we propose that, in insects, a behavioural trait
 –adult oviposition latency in captivity without a favourable host plant –
 correlates with a species’ specificity in larval host use. In the absence
 of a suitable host, monophagous insects are expected to wait for a long
 time before commencing oviposition, with the long waiting time
 corresponding to careful host location behaviour in nature. Polyphagous
 insects, in contrast, should be selected for an increased oviposition rate
 at the expense of the quality of oviposition substrate encountered and
 will on average have a short latency time. Using experimentally derived
 data on oviposition latency, we performed a phylogenetically informed
 analysis based on Bayesian inference to show that this variable correlates
 with host specificity (larval diet breadth) in a sample of North-European
 species of geometrid moths. A closely related index – the probability to
 lay any eggs on an unfavourable substrate – shows an analogous pattern. To
 provide an example of how these indices can be applied, we compare our
 sample of geometrid moths from Northern Europe with a sample from
 equatorial Africa. A comparative analysis based on an original
 phylogenetic reconstruction found no differences between the two study
 sites in parameters of oviposition behaviour. We conclude that behavioural
 tests can provide information about ecological interactions when the
 latter cannot be directly recorded. Our example study also hints at the
 possibility that host specificity of herbivores is not necessarily higher
 in a tropical region compared to a temperate one.
description: Oviposition latency data
 for geometrid moths (Geometridae)Oviposition latency data
 measured in the lab from field collected Geometridae females for Estonian
 and Ugandan species.Appendix 1_ Geometridae species
 list and their data.docx
DOI: 10.5061/dryad.3r3v3
title: Data from: Out-group threat promotes within-group affiliation in a cooperative fish

description: In social species, conflict with outsiders is predicted to affect
 within-group interactions, and thus influence group dynamics and the
 evolution and maintenance of sociality. While empirical evidence exists
 for a relationship between out-group conflict and intragroup behaviour in
 humans, experimental tests in other animals are rare. In a model fish
 system, we show that simulated out-group intrusions cause post-conflict
 increases in intragroup affiliation, but no changes in post-conflict
 intragroup aggression. Post-conflict affiliation was greater following
 intrusions by neighbouring compared to non-neighbouring individuals;
 neighbours represent greater threats to the dominance rank and breeding
 success of residents, and are visible in the aftermath of the intrusion.
 By providing strong evidence of a link between out-group conflict and
 post-conflict intragroup behaviour, and demonstrating that intragroup
 affiliation is affected by the nature of the out-group intrusion, our
 study shows the importance of considering post-conflict behaviour for our
 understanding of cooperation and social structure.
description: Bruintjes
 Outgroup_Raw_DataRaw
 data
DOI: 10.5061/dryad.5v75d33g
title: Data from: Classification tree methods provide a multifactorial approach to predicting insular body size evolution in rodents

description: Many hypotheses have been proposed to explain size changes in insular
 mammals, but no single variable suffices to explain the diversity of
 responses, particularly within Rodentia. Here in a dataset on insular
 rodents we observe strong consistency in the direction of size change
 within islands and within species, but (outside of Heteromyidae) little
 consistency at broader taxonomic scales. Using traits of islands and of
 species in a classification-tree analysis we find the most important
 factor predicting direction of change to be mainland body mass (large
 rodents decrease, small ones increase); other variables (island climate,
 number of rodent species, and area) were significant although their roles
 as revealed by the classification tree were context-dependent. Ecological
 interactions appear relatively uninformative, and on any given island the
 largest and smallest rodent species converged or diverged in size with
 equal frequency. Our approach provides a promising framework for
 continuing examination of insular body-size evolution.
description: DurstRoth2011Database of insular rodents. See paper for collection methods and description of variables.
DOI: 10.5061/dryad.66jp1m9
title: Data from: Range-wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod

description: Recent advances in genetic and genomic analysis have greatly improved our
 understanding of spatial population structure in marine species. However,
 studies addressing phylogeographic patterns at oceanic spatial scales
 remain rare. In Atlantic cod (Gadus morhua), existing range‐wide
 examinations suggest significant transatlantic divergence, although the
 fine‐scale contemporary distribution of populations and potential for
 secondary contact are largely unresolved. Here, we explore transatlantic
 phylogeography in Atlantic cod using a data‐synthesis approach,
 integrating multiple genome‐wide single‐nucleotide polymorphism (SNP)
 datasets representative of different regions to create a single range‐wide
 dataset containing 1,494 individuals from 54 locations and genotyped at
 796 common loci. Our analysis highlights significant transatlantic
 divergence and supports the hypothesis of westward post‐glacial
 colonization of Greenland from the East Atlantic. Accordingly, our
 analysis suggests the presence of transatlantic secondary contact off
 eastern North America and supports existing perspectives on the
 phylogeographic history of Atlantic cod with an unprecedented combination
 of genetic and geographic resolution. Moreover, we demonstrate the utility
 of integrating distinct SNP databases of high comparability.
description: Cod synthesis SNP
 listA
 list of all SNPs along with genbank accession numbers linkage groups, and
 positional information. Note that positional information refers to
 position on the linkage group and that linkage and positional information
 is not available for all SNPs.
DOI: 10.5061/dryad.72j0n
title: Data from: Do deposit-feeders compete? Isotopic niche analysis of an invasion in a species-poor system

description: Successful establishment of invasive species is often related to the
 existence of vacant niches. Competition occurs when invaders use the same
 limiting resources as members of the recipient community, which will be
 reflected in some overlap of their trophic niches. The concept of isotopic
 niche has been used to study trophic niche partitioning among species.
 Here, we present a two-year field study comparing isotopic niches of the
 deposit-feeding community in a naturally species-poor system. The isotopic
 niche analyses showed no overlap between a recent polychaete invader and
 any of the native species suggesting that it has occupied a vacant niche.
 Its narrow isotopic niche suggests specialized feeding, however, the high
 d15N values compared to natives are most likely due to isotope
 fractionation effects related to nitrogen recycling and a mismatch between
 biological stoichiometry of the polychaete and the sediment nitrogen
 content. Notably, highly overlapping isotopic niches were inferred for the
 native species, which is surprising in a food-limited system. Therefore,
 our results demonstrate that invaders may broaden the community trophic
 diversity and enhance resource utilization, but also raise questions about
 the congruence between trophic and isotopic niche concepts and call for
 careful examination of assumptions underlying isotopic niche
 interpretation.
description: stable isotope data for
 deposit-feedersRawdata for each
 species, station and year: the d15N and d13C data (d13C is corrected for
 CN ratio according to Post et al. 2007 Oecologia) as well as CN
 ratiodata
 for DOI 10.1038srep09715.xlsx
DOI: 10.5061/dryad.17hn4
title: Data from: Parasite-induced inversion of geotaxis in a freshwater amphipod: a role for anaerobic metabolism?

description: Many parasites with complex life-cycles alter the phenotype of their
 intermediate hosts in ways that seem to favor transmission to a final
 host. Although there is a large literature on host manipulation, how
 parasites alter the phenotype of their hosts remains poorly known. The
 bird acanthocephalan Polymorphus minutus is known to alter geotaxis in its
 amphipod host, Gammarus roeseli. Here we examine the potential roles of
 low oxygen availability and the excretion, by the parasite, of two
 products from its own anaerobic metabolism (lactate and succinate) in
 altered geotaxis. Under hypoxia, uninfected Gammarus roeseli showed
 negative geotaxis and lower metabolic rate, two traits also altered by
 infection with P. minutus, albeit with different intensities. The
 injection of a mixture of lactate and succinate in uninfected amphipods
 mimicked the parasite-induced reversion of geotaxis, without affecting the
 metabolic rate. In addition, both P. minutus-infected gammarids and
 uninfected ones conditioned to hypoxia for two days showed elevated levels
 of lactate in the brain, but not in the hemolymph. Overall, our results
 indicate that the pathways involved in anaerobic metabolism and
 hypoxia-signalling might be responsible for the changes in geotaxis and
 metabolic rate induced by P. minutus infection. Our study emphasizes the
 need to consider the tight and complex connections between physiological
 processes and behavioural adjustments, in particular at the brain level,
 in the understanding of parasitic manipulation, and more broadly of
 behavioural changes in infected hosts.
description: Hypoxia and parasitic
 manipulation of geotaxis: datafileone Excel spreadsheet
 for each experiment - the list of abbreviations is given in the first
 datasheetDATA
 FE_MJPMetal.xlsx
DOI: 10.5061/dryad.0hm88
title: Data from: Roaming Romeos: male crickets evolving in silence show increased locomotor behaviours

description: Loss of sexual signals should be strongly selected against when these
 signals are necessary for mate attraction or acquisition. Male
 Teleogryllus oceanicus field crickets produce a long-distance calling song
 to attract females. Separate genetic mutations recently evolved on the
 Hawaiian Islands of Kauai and Oahu, rendering approximately 90% and 50% of
 males, respectively, incapable of calling. We examined whether males from
 three populations, each with a distinct prevalence of this silent
 ‘flatwing’ phenotype, show behavioural plasticity in response to being
 reared in a call-less environment. Crickets from Kauai, Oahu and Mangaia,
 a Cook Islands population without the flatwing phenotype, either were or
 were not exposed to calling song during late juvenile and early adult
 development. Movement assays showed that when males originating from Kauai
 were reared in silence, they moved sooner, moved more and spent more time
 walking during silent behaviour trials than did their counterparts reared
 with calling song. Males from Oahu and Mangaia, however, showed no such
 effect of acoustic rearing environment on these behaviours. This suggests
 that there has been directional selection on Kauai for males to respond to
 a silent environment by increasing their mobility, thus compensating for
 their lack of song and increasing their chance of encountering receptive
 females.
description: Balenger_DataDryadFile contains movement behavior data and morphological data (size and wing morph) for each individual used in this study.