cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qq300
title: Data from: Construction of Taiwanese adult reference phantoms for internal dose evaluation

description: In the internal dose evaluation, the specific absorbed fraction (SAF) and
 S-value are calculated from the reference phantom based on Caucasian data.
 The differences in height and weight between Caucasian and Asian may lead
 to inaccurate dose estimation. In this study, we developed the Taiwanese
 reference phantoms. 40 volunteers were recruited. Magnetic resonance
 images (MRI) were obtained, and the contours of 15 organs were drawn. The
 Taiwanese reference man (TRM) and Taiwanese reference woman (TRW) were
 constructed. For the SAF calculation, the differences in the
 self-absorption SAF (self-SAF) between the TRM, TRW, and Oak Ridge
 National Laboratory (ORNL) adult phantom were less than 10% when the
 difference in organ mass was less than 20%. The average SAF from liver to
 pancreas of TRM was 38% larger than that of the ORNL adult phantom, and
 the result of TRW was 2.02 times higher than that of the ORNL adult
 phantom. For the S-value calculation, the ratios of TRW and ORNL adult
 phantom ranged from 0.91 to 1.57, and the ratios of TRM and ORNL adult
 phantom ranged from 1.04 to 2.29. The SAF and S-value results were
 dominantly affected by the height, weight, organ mass, and geometric
 relationship between organs. By using the TRM and TRW, the accuracy of
 internal dose evaluation can be increased for radiation protection and
 nuclear medicine.
description: SAF and S-values from
 TRM and TRWThe raw data from
 Figures 3 to 6 used in the manuscript.Raw
 data.xlsx
DOI: 10.5061/dryad.3c827
title: Data from: Female Dark-eyed Juncos (Junco hyemalis thurberi) produce male-like song in a territorial context during the early breeding season

description: Reports of female song, once considered a rarity, have recently increased
 across a variety of avian taxa. Females of many species can be induced to
 produce male-like song with exogenous testosterone, but observations of
 female song in free-living birds remain limited by incomplete sampling of
 females. Here, we report three independent observations of female
 dark-eyed juncos (Junco hyemalis) producing male-like song early in the
 breeding season (i.e. post-territory establishment, pre-nesting) in a
 recently established non-migratory, urban population. To elicit song, we
 presented 17 free-living junco pairs with a live, caged female
 conspecific. Three unique females responded to our trials by diving at the
 intruding female, chasing their (male) mate, fanning their tail feathers,
 and singing a trilled song similar in structure to male long-range
 (broadcast) song. We compared male and female songs quantitatively and
 found that the two sexes were statistically similar in many spectral and
 temporal characteristics, but female songs had significantly lower minimum
 and peak frequencies than males. This result is particularly surprising,
 as males in this urban population are known to sing at a significantly
 higher minimum frequency than males in a nearby montane population. Both
 the seasonal and social context in which these songs were observed suggest
 a potential function for female song in mate guarding and polygyny
 prevention, but more data are needed to test this hypothesis. Whether
 female song is common in all dark-eyed juncos during the early breeding
 season or if it is restricted to this particular urban and non-migratory
 population remains an important question for future research.
description: Spectral and Temporal
 Measurements of Male and Female Dark-eyed Junco Songs from San Diego,
 CaliforniaMeasurements collected
 in Raven Pro 1.4 (Cornell Lab of Ornithology) from field recordings of 22
 male and 3 female Dark-eyed Juncos. Some male subjects were recorded
 multiple times and sang different song types, which explains the repeated
 samples for certain individuals. Peak frequency was collected from
 spectrograms, and should be interpreted as the frequency with the highest
 amplitude in the song. Trill rate was calculated as the number of
 syllables (elements) divided by the song length.Reichardetal_2017_FemaleSong_Dryad.xml
DOI: 10.5061/dryad.bt51481
title: Data from: Experimental increase in baseline corticosterone level reduces oxidative damage and enhances innate immune response

description: Glucocorticoid (GC) hormones are significant regulators of homeostasis.
 The physiological effects of GCs critically depend on the time of exposure
 (short vs. long) as well as on their circulating levels (baseline vs.
 stress-induced). Previous experiments, in which chronic and high elevation
 of GC levels was induced, indicate that GCs impair both the activity of
 the immune system and the oxidative balance. Nonetheless, our knowledge on
 how mildly elevated GC levels, a situation much more common in nature,
 might influence homeostasis is limited. Therefore, we studied whether an
 increase in GC level within the baseline range suppresses or enhances
 condition (body mass, hematocrit and coccidian infestation) and
 physiological state (humoral innate immune system activity and oxidative
 balance). We implanted captive house sparrows Passer domesticus with
 either 60 days release corticosterone (CORT) or control pellets.
 CORT-treated birds had elevated baseline CORT levels one week after the
 implantation, but following this CORT returned to its pre-treatment level
 and the experimental groups had similar CORT levels one and two months
 following the implantation. The mass of tail feathers grown during the
 initial phase of treatment was smaller in treated than in control birds.
 CORT implantation had a transient negative effect on body mass and
 hematocrit, but both of these traits resumed the pre-treatment values by
 one month post-treatment. CORT treatment lowered oxidative damage to
 lipids (malondialdehyde) and enhanced constitutive innate immunity at one
 week and one month post-implantation. Our findings suggest that a
 relatively short-term (i.e. few days) elevation of baseline CORT might
 have a positive and stimulatory effect on animal physiology.
description: Data from: Experimental
 increase in baseline corticosterone level reduces oxidative damage and
 enhances innate immune responseDryad_data.xlsx
DOI: 10.5061/dryad.sv4md
title: Data from: Linking biological soil crust attributes to the multifunctionality of vegetated patches and interspaces in a semiarid shrubland

description: 1.Understanding the importance of biotic community structure on ecosystem
 functioning, and whether communities inhabiting different microhabitats in
 highly heterogeneous areas provide different ecological functions is a
 challenge in ecological research in the face of biodiversity and habitat
 loss. Biological soil crusts (BSCs) have been largely treated as unique
 entities, and have been mostly examined in interspaces between perennial
 plants, limiting current understanding of their role as drivers of
 ecosystem functioning and their relative contribution in comparison to
 vascular plants. 2.We assessed the role of BSCs on ecosystem functioning
 in vegetated patches and interspaces, and how individual soil functions
 and ecosystem multifunctionality are related to changes in BSC species-
 and community-level attributes. We contemplated nine ecosystem functions
 associated with soil water dynamics, nutrient cycling and erosion
 potential. 3.We found that vegetated patches improve infiltration rates,
 soil stability and net potential nitrogen (N) mineralization compared to
 interspaces, and thus dominate multifunctionality. However, well-developed
 BSCs improve soil moisture and N pool in both microsites, and are
 multifunctional stabilizing soils and regulating soil moisture and
 infiltration in the interspaces. BSC surface microstructure, including
 changes in total cover, species richness, morphological functional groups
 and surface discontinuities, has significant effects on soil moisture.
 Differences in soil N and phosphorous are mostly related to the presence
 of BSC-lichens. The effect of BSCs on multifunctionality varies in
 dependence of the particular set of functions that are seek to
 simultaneously maximize. 4.Our results suggest that vascular plants and
 BSCs have idiosyncratic effects on different key ecosystem functions and
 multifunction, and BSCs substitute vascular plants in stabilizing soils
 and regulating water dynamics in the interspaces. BSCs greatly contribute
 to small scale heterogeneity in the functioning of vegetated patches and
 interspaces, hence consideration of BSCs in different microsites is
 essential for enhancing our understanding of their functional relevance at
 a regional scale. In addition, quantification of BSC microstructure is
 crucial, owing to the contrasting effects of BSC species- and
 community-level attributes on different functions and multifunction.
description: Characterization of BSC
 communitiescommunity.xlsxEcosystem functions and estimation of multifunctionalityfunctionality.xlsx
DOI: 10.5061/dryad.gg47h
title: Data from: Intrauterine insemination: a UK survey on the adherence to NICE clinical guidelines by fertility clinics

description: Objective: To evaluate the awareness and response of fertility clinics in
 the UK to the National Institute for Health and Care Excellence (NICE)
 guideline recommendation that intrauterine insemination (IUI) should not
 be offered routinely, in order to report on current practice in the UK.
 Design: Online questionnaire survey of fertility clinics in the UK
 regarding their current clinical practice of IUI, formal discussion of the
 guideline recommendations, and any alterations made since the
 recommendations. Setting: 66 UK fertility clinics licensed to provide IUI.
 Participant:s 46 fertility clinics, including 6 clinic groups which
 represent 70% of all clinics and clinic groups licensed to provide IUI in
 April 2014 when the survey email was sent. Results: Of the 46 clinics that
 responded, 96% (44/46) of clinics continue to offer IUI. 98% (43/44) of
 those offering IUI also use ovarian stimulation. The most commonly used
 medications for ovarian stimulation are gonadotrophins (95%), followed by
 clomiphene citrate (49%) and letrozole (19%). 78% (36/46) of clinics had
 formally discussed NICE guideline recommendations. 17 clinics (37%) had
 made some changes to their practices; as a result, four clinics reported a
 reduction in the number of IUI cycles, six clinics had restricted the
 indications for IUI, and five clinics had begun informing patients of the
 guideline recommendations, while two did not specify. Conclusions: The
 majority of clinics were aware of the guideline recommendations. However,
 only a small proportion of clinics had made significant changes to their
 practice by reducing the number of IUI cycles or restricting the clinical
 indications for IUI. The availability of further evidence will assist NICE
 and clinicians in making recommendations on the use of IUI. There is a
 need to further explore the reasons for the lack of adherence to the
 recommendations.
description: IUI Survey response
 spreadsheet- DryadSurvey responses from
 Fertility clinics in the United Kingdom- Excel
 spreadsheet
DOI: 10.5061/dryad.s3v63
title: Data from: Saami reindeer herders cooperate with social group members and genetic kin

description: Cooperative behaviors evolve by ultimately increasing the inclusive
 fitness of performers as well as recipients of those behaviors. Such
 increases can occur via direct or indirect fitness benefits, theoretically
 explained by reciprocal altruism and kin selection, respectively. However,
 humans are known for cooperating with individuals who are not necessarily
 genetic relatives, which seemingly precludes kin selection as an
 explanation. Here, we aim to quantify the relative importance of kinship
 and social group membership as mediators of cooperative behavior. Using an
 experimental gift game, we test whether indigenous Saami reindeer herders
 in Norway give gifts to genetic relatives or to members of their
 cooperative herding group (the “siida”) or both. Membership of the same
 siida strongly increased the odds of gift giving. Kinship had a smaller,
 albeit positive, effect. Gifts were not preferentially given to younger
 family members, contrary to predictions relating to intergenerational
 resource transfers as a form of parental investment. These patterns
 suggest that social grouping can be at least as important as genetic
 factors in mediating cooperative behavior in this population. This is
 likely to reflect the importance of herding groups in day-to-day
 subsistence.
description: Herders in the
 sampleCovariates collected in
 the field. Note these data have been anonymised and so not all analysis
 code will work on this file.herders-anon.csvGift game resultsResults from experimental gift game. ID numbers link to herders.csvgifts.csvRelatedness coefficientsMatrix containing coefficients of relatedness for each dyad in the sample.relatedness.RdmpdAnalysis CodeLink to Zenodo containing analysis code written in R from GitHub.
DOI: 10.5061/dryad.r754h
title: Data from: Maternal effects alter the severity of inbreeding depression in the offspring

description: A maternal effect is a causal influence of the maternal phenotype on the
 offspring phenotype over and above any direct effects of genes. There is
 abundant evidence that maternal effects can have a major impact on
 offspring fitness. Yet, no previous study has investigated the potential
 role of maternal effects in influencing the severity of inbreeding
 depression in the offspring. Inbreeding depression is a reduction in the
 fitness of inbred offspring relative to outbred offspring. Here, we tested
 whether maternal effects due to body size alter the magnitude of
 inbreeding depression in the burying beetle Nicrophorus vespilloides. We
 found that inbreeding depression in larval survival was more severe for
 offspring of large females than offspring of small females. This might be
 due to differences in how small and large females invest in an inbred
 brood because of their different prospects for future breeding
 opportunities. To our knowledge, this is the first evidence for a causal
 effect of the maternal phenotype on the severity of inbreeding depression
 in the offspring. In natural populations that are subject to inbreeding,
 maternal effects may drive variation in inbreeding depression and
 therefore contribute to variation in the strength and direction of
 selection for inbreeding avoidance.
description: PilakoutaSmiseth2016ProceedingsBRaw data on the fitness of outbred and inbred offspring raised by either a large female or a small female in the burying beetle Nicrophorus vespilloides.
DOI: 10.5061/dryad.53q1v
title: Data from: Taxonomic and functional ant diversity along a secondary successional gradient in a tropical forest

description: The taxonomic diversity (TD) of tropical flora and fauna tends to increase
 during secondary succession. This increase may be accompanied by changes
 in functional diversity (FD), although the relationship between TD and FD
 is not well understood. To explore this relationship, we examined the
 correlations between the TD and FD of ants and forest age in secondary
 forests at the α- and β-diversity levels using single- and
 multi-trait-based approaches. Our objectives were to understand ant
 diversity patterns and to evaluate the role of secondary forests in the
 conservation of biodiversity and in the resilience of tropical forests.
 Ant assemblages were sampled across a chronosequence in the Lacandon
 region, Mexico. All species were characterized according to 12 functional
 ecomorphological traits relevant to their feeding behavior. We found that
 TD and FD were related to forest age at the alpha level, but not at the
 beta level. α-functional richness and divergence increased linearly with
 species richness and diversity, respectively. Also, the relationship
 between taxonomic and functional turnover was linear and positive. Our
 results indicated that functional traits were complementary across the
 chronosequence. The increase in FD was mainly driven by the addition of
 rare species with relevant traits. The older secondary forests did not
 recover all of the functions of old growth forest but did show a tendency
 to recovery. Because older successional stages support more TD and FD, we
 suggest developing agriculture and forestry management practices that
 facilitate rapid post-agricultural succession and thereby better preserve
 the functionality of tropical forests.
description: repository_ant_traitsFunctional traits of ants of Lacandon region
DOI: 10.6084/m9.figshare.28955141
title: XPert: Modelling drug-induced cellular perturbation responses with a biologically informed dual-branch Transformer

description: Systematic mapping of chemical perturbation responses is revolutionizing polypharmacological drug discovery, yet remains constrained by experimental scalability. Here, we introduce XPert, a biologically informed Dual-Branch Transformer model that predicts gene-specific drug responses across dose-time conditions. It generalizes to unseen cells, transfers knowledge to clinical settings, and reveals mechanistic insights, offering a scalable solution for precision medicine and perturbation-based drug discovery.

To facilitate transparency and reproducibility, we provide all relevant resources used in this study. These data are provided as supplements to our code repositories on Zenodo (https://doi.org/10.5281/zenodo.17182939) and GitHub (https://github.com/GSanShui/XPert). A summary of the available datasets is as follows:

XPert.zip: The complete XPert code repository, containing all model architectures and training scripts. This package is identical to the versions hosted on both GitHub and Zenodo.

HG_data.zip: Located under the 'XPert/' directory, this package includes the datasets used for constructing the knowledge-informed heterogeneous graph, together with the corresponding pre-trained node embeddings.

saved_model.zip: Located under the 'XPert/' directory, this package contains the trained model weights and associated pre-trained parameters.

reproducing.zip: Located under the 'XPert/' directory, this package provides the code for reproducing the main analysis and figures reported in the paper.

processed_data.zip: Located under the XPert/ directory, this package contains all processed datasets and meta used in this study.

All other files not included in the compressed archives above are provided under the 'XPert/processed_data/' directory. Users may retrieve these resources as needed and should place them in the designated file paths to ensure full reproducibility of the analyses.
DOI: 10.6084/m9.figshare.28955141.v1
title: XPert: Modelling drug-induced cellular perturbation responses with a biologically informed dual-branch Transformer

description: Systematic mapping of chemical perturbation responses is revolutionizing polypharmacological drug discovery, yet remains constrained by experimental scalability. Here, we introduce XPert, a biologically informed Dual-Branch Transformer model that predicts gene-specific drug responses across dose-time conditions. It generalizes to unseen cells, transfers knowledge to clinical settings, and reveals mechanistic insights, offering a scalable solution for precision medicine and perturbation-based drug discovery.

To facilitate transparency and reproducibility, we provide all relevant resources used in this study. These data are provided as supplements to our code repositories on Zenodo (https://doi.org/10.5281/zenodo.17182939) and GitHub (https://github.com/GSanShui/XPert). A summary of the available datasets is as follows:

XPert.zip: The complete XPert code repository, containing all model architectures and training scripts. This package is identical to the versions hosted on both GitHub and Zenodo.

HG_data.zip: Located under the 'XPert/' directory, this package includes the datasets used for constructing the knowledge-informed heterogeneous graph, together with the corresponding pre-trained node embeddings.

saved_model.zip: Located under the 'XPert/' directory, this package contains the trained model weights and associated pre-trained parameters.

reproducing.zip: Located under the 'XPert/' directory, this package provides the code for reproducing the main analysis and figures reported in the paper.

processed_data.zip: Located under the XPert/ directory, this package contains all processed datasets and meta used in this study.

All other files not included in the compressed archives above are provided under the 'XPert/processed_data/' directory. Users may retrieve these resources as needed and should place them in the designated file paths to ensure full reproducibility of the analyses.
DOI: 10.5061/dryad.g48n010
title: Data from: A novel environmental restoration method for an abandoned limestone quarry with a deep open pit and steep palisades: a case study

description: In general, exploitation of rock materials, such as limestone or granite
 exploitation, can cause serious damage to the ecological environment near
 a mine area. With economic development and the ever-increasing demand for
 ore resources, mining activities have induced very serious environmental
 issues in China. Therefore, environmental restoration work around mines in
 China is urgently required. This study explores the Chuankou open-pit
 limestone quarry in Tongchuan City, Shaanxi Province, Northwest China, as
 the engineering case. The environmental issues caused by over 40 years of
 limestone exploitation, including land degradation, land occupation, dust
 pollution and potential geological disasters, were investigated. Combining
 the characteristics of this quarry with a summary of previous studies on
 environmental restoration work, this paper proposes a novel and systematic
 method that was comprehensively carried out through engineering and
 revegetation measures. The engineering measure, that is, the construction
 of an artificial slope by using local abandoned construction materials,
 solved the environmental problems in this quarry and provided site
 conditions favourable for revegetation. The revegetation measure restored
 the local ecosystem. This method provides both a new idea for the
 sustainable development of a mining area and a useful reference for
 analogous engineering cases.
description: Statistics of rock mass
 joint (the dataset of Fig.2)This file contains the
 tendency and dip angles of the joints in study area, which is the original
 data of Fig.2.Subsidence monitor data
 of Fig.15This file contains
 subsidence dataset of four monitoring points, which is the original data
 of Fig.15.