cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h00mt
title: Data from: Introgression threatens the survival of the critically endangered freshwater crayfish Cherax tenuimanus (Decapoda : Parastacidae) in the wild

description: Hybridization and genetic introgression following the introduction of
 exotic species can pose a significant threat to the survival of
 geographically restricted species. A remnant population of the critically
 endangered freshwater crayfish Cherax tenuimanus in the upper reaches of
 the Margaret River in southwestern Australia is under threat following the
 introduction and spread of its congener Cherax cainii. Here, we examine
 the extent of hybridization and introgression between the two species
 using twelve polymorphic microsatellite loci. Our study reveals there are
 three times more C. cainii than C. tenuimanus at our study site in the
 upper reaches of the Margaret River. There is also evidence of
 hybridization and introgression between C. tenuimanus and C. cainii at
 this site, with F1, F2 and backcrossed individuals identified. While
 interbreeding was confirmed in this study, our simulations suggest that
 the levels of introgression are much lower than would be expected under
 random mating, indicating partial reproductive barriers exist.
 Nevertheless, it is apparent that hybridization and introgression with C.
 cainii pose a serious threat to C. tenuimanus and their survival in the
 wild will require active adaptive management and continued genetic
 monitoring to evaluate management effectiveness.
description: Marron microsatellite
 dataExcel file containing
 microsatellite genotypes for Cherax cainii and Cherax tenuimanus sampled
 from the south-west of Western Australia
DOI: 10.5061/dryad.hk16k
title: Data from: Oxygen and carbon isoscapes for the Baltic Sea: testing their applicability in fish migration studies

description: Conventional tags applied to individuals have been used to investigate
 animal movement, but these methods require tagged individuals be
 recaptured. Maps of regional isotopic variability known as “isoscapes”
 offer potential for various applications in migration research without
 tagging wherein isotope values of tissues are compared to environmental
 isotope values. In this study, we present the spatial variability in
 oxygen (math formula) and dissolved inorganic carbon (δ13CDIC) isotope
 values of Baltic Sea water. We also provide an example of how these
 isoscapes can reveal locations of individual animal via spatial
 probability surface maps, using the high-resolution salmon otolith isotope
 data from salmon during their sea-feeding phase in the Baltic Sea. A clear
 latitudinal and vertical gradient was found for both math formula and
 δ13CDIC values. The difference between summer and winter in the Baltic Sea
 math formula values was only slight, whereas δ13CDIC values exhibited
 substantial seasonal variability related to algal productivity. Salmon
 otolith δ18Ooto and δ13Coto values showed clear differences between
 feeding areas and seasons. Our example demonstrates that dual isotope
 approach offers great potential for estimating probable fish habitats once
 issues in model parameterization have been resolved.
description: R script for creating
 isocapes and probabilistic maps of salmon otolith valuesFinal_Isoscapes_paperI.R
DOI: 10.5061/dryad.8rb35rj
title: Data from: Disentangling the genetic effects of refugial isolation and range expansion in a trans-continentally distributed species

description: In wide-ranging taxa with historically dynamic ranges, past allopatric
 isolation and range expansion can both influence the current structure of
 genetic diversity. Considering alternate historical scenarios involving
 expansion from either a single refugium or from multiple refugia can be
 useful in differentiating the effects of isolation and expansion. Here, we
 examined patterns of genetic variability in the trans-continentally
 distributed painted turtle (Chrysemys picta). We utilized an existing
 phylogeographic dataset for the mitochondrial control region and generated
 additional data from nine populations for the mitochondrial control region
 (n = 302) and for eleven nuclear microsatellite loci (n = 247). We created
 a present-day ecological niche model (ENM) for C. picta and hindcast this
 model to three reconstructions of historical climate to define three
 potential scenarios with one, two, or three refugia. Finally, we employed
 spatially-explicit coalescent simulations and an approximate Bayesian
 computation (ABC) framework to test which scenario best fit the observed
 genetic data. Simulations indicated that phylogeographic and multilocus
 population-level sampling both could differentiate among refugial
 scenarios, although inferences made using mitochondrial data were less
 accurate when a longer coalescence time was assumed. Furthermore, all
 empirical genetic datasets were most consistent with expansion from a
 single refugium based on ABC. Our results indicate a stronger role for
 post-glacial range expansion, rather than isolation in allopatric refugia
 followed by range expansion, in structuring diversity in this species. To
 distinguish among complex historical scenarios, we recommend explicitly
 modeling the effects of range expansion and evaluating alternate refugial
 scenarios for wide-ranging taxa.
description: Chrysemys_allhaplotypesFiles associated with HDY-17-OR0378RR: Disentangling the effects of refusal isolation and range expansion in a trans-continentally distributed species" (Reid et al. 2018)Reid_Chrysemys_datascripts.zip
DOI: 10.5061/dryad.j92h4
title: Data from: Sexual and nonsexual cannibalism have different effects on offspring performance in redback spiders

description: Sexual cannibalism is often set apart from other forms of cannibalism;
 however, no studies have directly compared the fitness consequences of
 these 2 types of cannibalism. Here, we compared the consequences of
 cannibalism of a male by a female outside the context of mating (referred
 to as nonsexual cannibalism) and within the context of mating (referred to
 as sexual cannibalism) for the propensity to remate, fecundity, and
 offspring traits of female redback spiders Latrodectus hasselti. Although
 the timing of cannibalism relative to copulation is critical for male
 fitness, it is still unclear whether it can also influence female fitness,
 beyond the fertilization of eggs. Our results showed that sexual
 cannibalism and nonsexual cannibalism had different effects on offspring
 survival and growth. Sexually cannibalistic females produced offspring
 that survived better and grew faster than nonsexually cannibalistic or
 noncannibalistic females. By experimentally manipulating the quality of
 prey given to offspring, we showed that these effects were dependent on
 the spiderlings’ diet quality. In particular, the effects of sexual
 cannibalism on offspring growth and survival were clearer when offspring
 were, respectively, fed a high-nutrient diet and a low-nutrient diet.
 However, sexual cannibalism did not increase offspring tolerance to
 starvation. Additionally, we did not find any effect of nonsexual
 cannibalism nor sexual cannibalism on female fecundity or subsequent
 sexual receptivity. As copulation duration did not account for these
 effects on offspring performance, our findings suggest that copulation
 occurring simultaneously with cannibalism plays an essential role in the
 fitness consequences of this behavior.
description: Female_redback_dataThis dataset corresponds to the data we collected and used to test for the effect of the cannibalistic treatment on female fecundity.Receptivity_redback_dataThis dataset corresponds to the data we collected from our mating trials.Survival_redback_dataThis dataset corresponds to the data we collected and used to test for the effect of cannibalism and offspring diet quality on offspring survival.Growth_redback_dataThis dataset corresponds to the data we collected and used to test for the effect of cannibalism and offspring diet quality on offspring growth.
DOI: 10.5061/dryad.4dv51ps
title: Data from: Orientation-invariance of individual differences in three face processing tasks

description: Numerous studies have reported impairments in perception and recognition,
 and, particularly, in part-integration of faces following picture-plane
 inversion. Whether these findings support the notion that inversion
 changes face processing qualitatively remains a topic of debate. To
 examine whether associations and dissociations of the human face
 processing ability depend on stimulus orientation, we measured face
 recognition with the Cambridge Face Memory Test (CFMT), along with
 experimental tests of face perception and selective attention to faces and
 non-face objects in a sample of 314 participants. Results showed strong
 inversion effects for all face-related tasks, and modest ones for non-face
 objects. Individual differences analysis revealed that the CFMT shared
 common variance with face perception and face-selective attention,
 however, independent of orientation. Regardless of whether predictor and
 criterion had same or different orientation, face recognition was best
 predicted by the same test battery. Principal component decomposition
 revealed a common factor for face recognition and face perception, a
 second common factor for face recognition and face-selective attention,
 and two unique factors. The patterns of factor loadings were nearly
 identical for upright and inverted presentation. These results indicate
 orientation-invariance of common variance in three domains of face
 processing. Since inversion impaired performance, but did not affect
 domain-related associations and dissociations, the findings suggest
 process-specific but orientationgeneral mechanisms. Specific limitations
 by constraints of individual differences analysis and test selection are
 discussed.
description: AllTestDataDataFile: AllTestDataDataCFMT-CCP-SPP_RSOS This file contains all measurement variables and control variables of the dataset COLUMNS: A: VP-Identification Code B: Included or not in analysis (according Tukey Outlier criterion) C: Cambridge FaceMemory Test (upright) D: Cambridge FaceMemory Test (inverted) E: CCP - congruent (upright) F: CCP - congruent (inverted) G: CCP - incongruent (upright) H: CCP - incongruent (inverted) I: SPP_F - LO (upright) J: SPP_F - LO (inverted) K: SPP_F - HO (upright) L: SPP_F - HO (inverted) M: SPP_O - LO (upright) N: SPP_O - LO (inverted) O: SPP_O - HO (upright) P: SPP_O - HO (inverted)
DOI: 10.5061/dryad.mh084f6
title: Data from: Testing the assumptions of the pyrodiversity begets biodiversity hypothesis for termites in semi-arid Australia

description: Fire shapes the composition and functioning of ecosystems globally. In
 many regions, fire is actively managed to create diverse patch mosaics of
 fire-ages under the assumption that a diversity of post-fire age classes
 will provide a greater variety of habitats, thereby enabling species with
 differing habitat requirements to coexist, and enhancing species diversity
 (the pyrodiversity begets biodiversity hypothesis). However, studies
 provide mixed support for this hypothesis. Here, using termite communities
 in a semi-arid region of southeast Australia, we test four key assumptions
 of the pyrodiversity begets biodiversity hypothesis (1) that fire shapes
 vegetation structure over sufficient time frames to influence species’
 occurrence, 2) that animal species are linked to resources that are
 themselves shaped by fire and that differ at different times since fire,
 3) that species’ probability of occurrence of abundance peaks at varying
 times since fire, and 4) that providing a diverse set of fire-ages boost
 species diversity at the landscape scale. Termite species and habitat
 elements were sampled in 100 sites across a range of fire ages, nested
 within 20 landscapes chosen to represent a gradient of low to high
 pyrodiversity. We used regression modeling to explore relationships
 between termites, habitat and fire. Fire affected two habitat elements
 (coarse woody debris and the cover of woody vegetation) that were
 associated with the probability of occurrence of three termite species and
 overall species richness, thus supporting the first two assumptions of the
 pyrodiversity hypothesis. However, this did not result in those species or
 species richness being affected by fire history per se. Consequently,
 landscapes with a low diversity of fire histories had similar numbers of
 termite species as landscapes with high pyrodiversity. Our work suggests
 that encouraging a diversity of fire ages for enhancing termite species
 richness in this study region is not necessary.
description: site
 dataData used for site-scale
 analysis, including vegetation type, time since fire (TSF), species
 occurrences and habitat variablesLandscape
 dataData used in
 landscape-scale analysis. Includes landscape variables and species'
 reporting rates
DOI: 10.5061/dryad.1hc582s
title: Data from: CO2 enrichment and soil type additively regulate grassland productivity

description: Atmospheric CO2 enrichment usually increases aboveground productivity
 (ANPP) of grassland vegetation, but the magnitude of the ANPP-CO2 response
 differs among ecosystems. Soil properties affect ANPP via multiple
 mechanisms and vary over topographic to geographic gradients, but have
 received little attention as potential modifiers of the ANPP-CO2 response.
 We assessed effects of three soil types, sandy loam, silty clay, and clay,
 on the ANPP response of perennial C3/C4 grassland communities to a
 subambient to elevated CO2 gradient over 10 years in Texas, USA. We
 predicted an interactive, rather than additive, effect of CO2 and soil
 type on ANPP. Contrary to prediction, CO2 and soil additively influenced
 grassland ANPP. Increasing CO2 by 250 μL L-1 increased ANPP by 170 g m-2
 across soil types. Increased clay content from 10% to 50% among soils
 reduced ANPP by 50 g m-2. CO2 enrichment increased ANPP via a predominant
 direct effect accompanied by a smaller indirect effect mediated by
 successional shift to increased dominance of the C4 tallgrass Sorghastrum
 nutans. Our results indicate a large, positive influence of CO2 enrichment
 on grassland productivity that resulted from direct physiological benefits
 of CO2 augmented by species succession and was expressed similarly across
 soils of differing physical properties.
description: Dryad data for Polley et
 al_2018_New PhytologistData are from a 10 year
 (2006-2015) CO2 enrichment experiment of constructed communities of
 tallgrass prairie plants in central Texas, USA using the Lysimeter CO2
 enrichment gradient facility (LYCOG)
DOI: 10.5061/dryad.586f011
title: Data from: Attract or defend? Pollen and vegetative secondary chemistry of three pollen-rewarding lupines

description: PREMISE OF THE STUDY: Optimal Defense Theory predicts that selection
 should drive plants to differentially allocate resources for herbivore
 defense to tissues with high fitness values. As pollen’s primary role is
 the transport of gametes, plants may be expected to defend it from
 herbivory. However, for many animal-pollinated plants, pollen serves a
 secondary role as a pollinator reward. This may present a conflict between
 selection to defend pollen from herbivores and selection to reward
 pollinators. Here, we investigate whether pollen secondary chemistry in
 three pollen-rewarding Lupinus species better reflects the need to defend
 pollen or reward pollinators. METHODS: Lupinus (Fabaceae) species are
 nectarless, pollen-rewarding, and produce defensive quinolizidine and/or
 piperidine alkaloids throughout their tissues. We used gas chromatography
 to identify and quantitate the alkaloids in four above-ground tissues
 (pollen, flower, leaf, stem) of three western North American lupines: L.
 argenteus, L. bakeri, and L. sulphureus, and compared alkaloid
 concentrations and composition among tissues within individuals. KEY
 RESULTS: Pollen alkaloid concentrations were 11-35% of those
 concentrations in other tissues in L. argenteus and L. sulphureus. We
 detected no alkaloids in L. bakeri pollen, though they were present in
 other tissues. Alkaloid concentrations were not strongly correlated among
 tissues within individuals. We detected fewer alkaloids in pollen compared
 to other tissues and pollen contained no unique alkaloids. CONCLUSIONS:
 Our results are consistent with the hypothesis that, in these
 pollen-rewarding species, pollen secondary chemistry may reflect the need
 to attract and reward pollinators more than the need to defend pollen from
 herbivory.
description: Lupine alkaloid
 dataThis is an Excel file
 containing one sheet with 23 columns. Each row represents the data and
 metadata for a single tissue sample from a single individual. Column 1:
 specifies the species; Column 2: species the individual ID (ID numbers
 repeat across species); Column 3: specifies the tissue; Column 4:
 specifies the site that the sample was taken from; Columns 5 and 6: GPS
 coordinates (degrees.decimal); Column 7: caffeine standard; Columns 8-23:
 individual alkaloid concentrations (expressed as micrograms/gram),
 "N/D" indicates that the alkaloid corresponding to a given
 column was not detected in the sample.Heiling_etal_Lupine_alkaloid_data.xlsx
DOI: 10.5281/zenodo.17987300
title: EVENFLOW Personalised Medicine use case: Clear Cell Renal Cell Carcinoma (ccRCC, aka KIRC) datasets collection

description: These datasets contain the synthetic data generated with a VAE from the TCGA-KIRC dataset. The file Static_KIRC.csv contains a pre-processed version of the bulk-RNASeq dataset from TCGA-KIRC. nodes_metadata.csv contains the clinical information of the patients (with columns: sample name, gender, race, and stage). A synthetic dataset is available (compressed), where 50 timepoints were inferred: trajectories_forward_test.csv.tar.gz simulates the progression of RNASeq data between patients at stages early and late. Both the static and trajectory datasets where analyzed for their biological interpretation with a Differential Expression (DESeq) analysis followed by GSEA on all the pathways available in the Reactome database. The results of the static analysis are included in static_gsea_reports_kirc.csv and the results on the trajectories may be found in trajectories_gsea_reports_kirc.csv.tar.gz.

Trained models used for the synthetic data generation are available in Hugging Face.
DOI: 10.5061/dryad.jc6dt
title: Data from: Evaluation of the psychometric properties of the Brazilian version of the Oral Health Literacy Assessment in Spanish and development of a shortened form of the instrument

description: Objective: The objective of this study was to investigate the psychometric
 properties of the Oral Health Literacy Assessment in Spanish (OHLA-S) for
 the Brazilian-Portuguese language using robust analysis and with the
 results disclose possibilities to develop a shorter and more valid
 instrument. Methods: OHLA-S is an oral health literacy instrument
 comprising a word recognition section and a comprehension section. It
 consists of 24 dental words. It was translated into the
 Brazilian-Portuguese language (OHLA-B) and its psychometric properties
 were evaluated in a random sample of 250 adults aged 20–59 years. To
 assess the dimensionality and factor structure were tested by means of
 Exploratory Factor Analysis (EFA) and Confirmatory Factor Analysis (CFA).
 Reliability was assessed using two indicators: Cronbach's alpha and
 McDonald’s Omega. Results: EFA and CFA demonstrated that the OHLA-B with
 24 items did not present an adequate adjustment of the model, compromising
 its validity. In addition, reliability values at 0.50 for Cronbach's
 alpha and 0.67 for McDonald's omega were below the minimum acceptable
 rate of 0.70. As no support was found for the original structure, we
 decided to proceed with the withdrawal of individual items and successive
 reanalysis of the model until the indicators were adjusted in a shorter
 instrument. A new structure with 15 items produced an instrument with two
 dimensions and a better goodness of fit than the original instrument. The
 Alpha and Omega reliability index values increased to 0.83 and 0.80,
 respectively, and all scores were better in the OLHA-B with 15 items than
 in the instrument with 24 items. Conclusion: OLHA-B with the original
 structure composed by 24 items did not show acceptable construct validity.
 The shorter version with 15 items showed more promising results for
 assessing oral health literacy levels in the Brazilian population.
description: Database Brazilian
 version of the OLHA-S literacy instrument studyThis file in Excel
 contains the database used for the analyzes of the article entitled
 "Evaluation of the psychometric properties of the Brazilian version
 of the Oral Health Literacy Assessment in Spanish and development of a
 shortened form of the instrument "Database_Brazilian_version_of_the_OLHA-S_literacy_instrument.xlsx
DOI: 10.5281/zenodo.17987299
title: EVENFLOW Personalised Medicine use case: Clear Cell Renal Cell Carcinoma (ccRCC, aka KIRC) datasets collection

description: These datasets contain the synthetic data generated with a VAE from the TCGA-KIRC dataset. The file Static_KIRC.csv contains a pre-processed version of the bulk-RNASeq dataset from TCGA-KIRC. nodes_metadata.csv contains the clinical information of the patients (with columns: sample name, gender, race, and stage). A synthetic dataset is available (compressed), where 50 timepoints were inferred: trajectories_forward_test.csv.tar.gz simulates the progression of RNASeq data between patients at stages early and late. Both the static and trajectory datasets where analyzed for their biological interpretation with a Differential Expression (DESeq) analysis followed by GSEA on all the pathways available in the Reactome database. The results of the static analysis are included in static_gsea_reports_kirc.csv and the results on the trajectories may be found in trajectories_gsea_reports_kirc.csv.tar.gz.

Trained models used for the synthetic data generation are available in Hugging Face.
DOI: 10.5061/dryad.72v34
title: Data from: Advances in neglected tropical disease vaccines: developing relative potency and functional assays for the Na-GST-1/Alhydrogel hookworm vaccine

description: A new generation of vaccines for the neglected tropical diseases (NTDs)
 have now advanced into clinical development, with the Na-GST-1/Alhydrogel
 Hookworm Vaccine already being tested in Phase 1 studies in healthy
 adults. The current manuscript focuses on the often overlooked critical
 aspects of NTD vaccine product development, more specifically, vaccine
 stability testing programs. A key measure of vaccine stability testing is
 "relative potency" or the immunogenicity of the vaccine during
 storage. As with most NTD vaccines, the Na-GST-1/Alhydrogel Hookworm
 Vaccine was not developed by attenuation or inactivation of the pathogen
 (Necator americanus), so conventional methods for measuring relative
 potency are not relevant for this investigational product. Herein, we
 describe a novel relative potency testing program and report for the first
 time on the clinical lot of this NTD vaccine during its first 60 months of
 storage at 2–8°C. We also describe the development of a complementary
 functional assay that measures the ability of IgG from animals or humans
 immunized with Na-GST-1/Alhydrogel to neutralize this important hookworm
 enzyme. While 90% inhibition of the catalytic activity of Na-GST-1 was
 achieved in animals immunized with Na-GST-1/Alhydrogel, lower levels of
 inhibition were observed in immunized humans. Moreover, anti-Na-GST-1
 antibodies from volunteers in non-hookworm endemic areas were better able
 to inhibit catalytic activity than anti-Na-GST-1 antibodies from
 volunteers resident in hookworm endemic areas. The results described
 herein provide the critical tools for the product development of NTD
 vaccines.
description: Potency
 DataSee ReadMe
 filePotency.csvMouse Neutralization DataSee ReadMe fileMouseNeutralization.csv