cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.77hk7
title: Data from: Spontaneous nongenetic variation of group size creates cheater-free groups of social microbes

description: In social organisms, cheaters that gain a fitness advantage by defecting
 from the costs of cooperation reduce the average level of cooperation in a
 population. Such “cheating load” can be severe enough to cause local
 extinction events when cooperation is necessary for survival, but can also
 mediate group-level selection against cheaters across spatially structured
 groups that vary in cheater frequency. In cheater-laden populations, such
 variation could be generated by the formation of new homogeneous groups by
 small numbers of identical cells. Here we use the model social bacterium
 Myxococcus xanthus to test whether population bottlenecks inherent to the
 starvation-induced formation of multicellular fruiting bodies can generate
 cheater-free groups within an initially cheater-laden population. We first
 show that genetically identical fruiting bodies vary greatly in their
 numbers of stress-resistant spores. We further show mathematically and
 experimentally that this variation can include small cheater-free groups.
 Such non-genetic variation in group size was found to occur in a variety
 of M. xanthus isolates and Myxococcus species. Our results suggest that
 stress-induced reductions in group size may serve as a general process
 that repeatedly purges genetic diversity from a minority of social groups,
 thus recurrently generating high-relatedness social environments
 unburdened by cheating load.
description: Figure1Number of spores per individual fruiting body (column 2) across eight independent replicates (column 1: T1 to T8).Number of spores produced per natural isolateThis table contains the name of the isolate (column 1) and the number of spores in individual fruiting bodies across four indented replicates (columns 2 to 6: T1 to T4).Spores_naturalIsolates.csvNumber of cooperator and cheater per fruiting bodyNumber of spores belonging to cooperator genotype (column 4: GJV1) and cheater genotype(column 3:OC) per fruiting body (column 2: FB) and per independent experiment (column 1: Exp). Log values for cooperator and cheater are also presented (Log.GJV1 and Log.OC respectively)Cooperator_cheater.csvNumber of spores across different environmentsNumber of spores in each individual fruiting body (column 4: Logspores) per strain (column 2: Strain) in each environment(column 3: Env) per experiment (column 1: Exp)Figure5.csv
DOI: 10.5061/dryad.bg26p
title: Data from: Novel insights into relationships between egg corticosterone and timing of breeding revealed by LC-MS/MS

description: Inter- and intra-clutch variation in egg corticosterone (CORT), the major
 glucocorticoid in birds, may provide insights into how maternal stress
 levels vary with the timing of breeding and with laying order. Common
 analytical methods (e.g. immunoassays), however, suffer from
 cross-reaction with other steroids, leading to potential overestimation of
 CORT concentrations which can obscure true hormone–environment
 relationships and complicate among-study comparisons. We here apply a new
 LC-MS/MS technique, which has recently been shown to avoid the problem of
 cross-reactivity due to its high specificity, to quantify CORT
 concentrations in yolk and albumen in clutches of lesser black-backed
 gulls Larus fuscus. We found that CORT concentration exhibited a
 previously unreported U-shaped relationship with time of breeding, which
 we explain as a potential interplay of two forces exerting extra strain on
 the early and late breeders. Furthermore, results showed an increase in
 CORT with laying order indicating the energetic expense of egg production.
 The levels of CORT assessed in this study were significantly lower than
 those previously reported in studies using immunoassays for CORT analysis.
 This supports the fact that incorporating chromatography effectively
 reduces overestimation of CORT due to cross-reactivity with other steroid
 hormones, particularly in egg yolk.
description: eggdata
 CSVSee readme file for more
 information. The eggdata CSV and eggdata excel files contain the same data
 just in different formats.eggdata.csveggdata excelSee readme file for more information. The eggdata CSV and eggdata excel files contain the same data just in different formats.eggdata.xlsx
DOI: 10.5061/dryad.7nh05k6
title: Data from: Integration of homogeneous structural region identification and rock mass quality classification

description: In rock engineering projects, professionals assess the overall rock mass
 qualities using a sole value. However, the true qualities of partial rock
 masses are incompatible with such a value. To address this problem, the
 idea of regionally classifying rock mass qualities is proposed and the
 associated procedure presented. To achieve this goal, the probabilistic
 and deterministic joints within the study area were determined, and a
 three-dimensional joint network model was created. Then, the
 three-dimensional joint network model was discretised into interlocking
 subdomains, and the modified blockiness index (MBi) was used to finely
 identify the homogeneous structural regions, together with the k-means
 algorithm and the sum of squared errors (SSE). A synthetic model
 comprising homogeneous structural regions was developed and validated with
 respect to the extracted cross-sections. Next, an improved Rock Mass
 Rating system (RMRmbi) was introduced, and the viability of RMRmbi was
 supported through a significant amount of theoretical cases and several
 real cases. Finally, visualisation of regional RMRmbi classification
 results was performed. Results show that: (i) the homogeneous structural
 regions are finely demarcated in three dimensions; and (ii) the proposed
 idea can overcome the problem of rock mass quality classification using
 the conventional approach often leading to ‘overgeneralisation’.
description: Joint data used in
 Manuscript (ID RSOS-181353)data file of Manuscript (ID
 RSOS-181353).xlsx
DOI: 10.5281/zenodo.18264176
title: Plasma Proteomic Biomarkers for Predicting Immunochemotherapy Outcomes in Advanced Gastric Adenocarcinoma

description: Immune checkpoint inhibitors (ICIs) plus chemotherapy are standard first-line therapy for advanced gastric (GC) and gastroesophageal junction cancer (GEJC), yet predictive biomarkers remain limited. In this prospective single-center study, 31 patients with advanced GC/GEJC receiving PD-1 inhibitor plus chemotherapy were enrolled. Plasma samples were collected at baseline and every two cycles. Immune-related proteins were quantified using the Olink Target 96 Immuno-Oncology panel.
DOI: 10.5061/dryad.bf597
title: Data from: Patterns of variation during adaptation in functionally linked loci

description: An understanding of the distribution of natural patterns of genetic
 variation is relevant to such fundamental biological fields as evolution
 and development. One recent approach to understanding such patterns has
 been to focus on the constraints which may arise as a function of the
 network or pathway context in which genes are embedded. Despite
 theoretical expectations of higher evolutionary constraint for genes
 encoding upstream versus downstream enzymes in metabolic pathways,
 empirical results have varied. Here we combine two complementary models
 from population genetics and enzyme kinetics to explore genetic variation
 as a function of pathway position when selection acts on whole-pathway
 flux. We are able to qualitatively reproduce empirically observed patterns
 of polymorphism and divergence and suggest that expectations should vary
 depending on the evolutionary trajectory of a population. Upstream genes
 are initially more polymorphic and diverge faster after an environmental
 change, while we see the opposite trend as the population approaches its
 fitness optimum.
description: simulation of pathway
 evolutionmg.140313.tar.gz
DOI: 10.5281/zenodo.18385122
title: Gut Microbiota Phylum-Level Relative Abundance Table from MYRR-Treated DSS-Induced Ulcerative Colitis Mouse Model

description: Inflammatory bowel disease (IBD) is closely associated with gut microbiota imbalance and intestinal barrier dysfunction. Bayberries improve intestinal health, with myricitrin (MYRR) as their main active component. However, the mechanism by which MYRR modulates the microbiota-metabolite-host axis to alleviate ulcerative colitis remains unclear. This study employs a dextran sodium sulfate (DSS)-induced colitis mouse model, integrating metagenomics, metabolomics, and colonic organoid cultures to explore MYRR's effects. The results demonstrate that MYRR alleviates colitis symptoms and restores the expression of key intestinal barrier proteins, MUC2 and occludin. Multi-omics analysis reveals that MYRR reshapes the gut microbiota by enriching beneficial bacteria and modulating bile acid metabolism, particularly allocholic acid (ACA), in both serum and feces. In vitro intestinal organoid experiments further confirm that ACA enhances MUC2 expression. In conclusion, MYRR protects against colitis by regulating the microbiota-metabolite-intestinal barrier axis, offering a theoretical foundation for microbiota-based therapeutic strategies for IBD.
DOI: 10.5281/zenodo.18385123
title: Gut Microbiota Phylum-Level Relative Abundance Table from MYRR-Treated DSS-Induced Ulcerative Colitis Mouse Model

description: Inflammatory bowel disease (IBD) is closely associated with gut microbiota imbalance and intestinal barrier dysfunction. Bayberries improve intestinal health, with myricitrin (MYRR) as their main active component. However, the mechanism by which MYRR modulates the microbiota-metabolite-host axis to alleviate ulcerative colitis remains unclear. This study employs a dextran sodium sulfate (DSS)-induced colitis mouse model, integrating metagenomics, metabolomics, and colonic organoid cultures to explore MYRR's effects. The results demonstrate that MYRR alleviates colitis symptoms and restores the expression of key intestinal barrier proteins, MUC2 and occludin. Multi-omics analysis reveals that MYRR reshapes the gut microbiota by enriching beneficial bacteria and modulating bile acid metabolism, particularly allocholic acid (ACA), in both serum and feces. In vitro intestinal organoid experiments further confirm that ACA enhances MUC2 expression. In conclusion, MYRR protects against colitis by regulating the microbiota-metabolite-intestinal barrier axis, offering a theoretical foundation for microbiota-based therapeutic strategies for IBD.
DOI: 10.5061/dryad.fd548
title: Data from: Overlapping vocalizations produce far-reaching choruses: a test of the signal enhancement hypothesis

description: Many animals gather in large groups to mate. When these animals produce
 sexual signals, their signals may overlap. The signal enhancement
 hypothesis proposes that overlapping signals exhibit enhanced transmission
 properties, increasing the active space and potency of the signal. We
 tested this hypothesis using multispeaker playback to simulate a chorus of
 explosively breeding Neotropical Yellow Toads (Incilius luetkenii). We
 varied the number of simulated males and the frequency of their
 vocalizations and we rerecorded the choruses at different distances
 through this species’ native habitat in Costa Rica. Our results support
 the signal enhancement hypothesis: transmission distance increased with
 the number of simultaneous calls. Call frequency varies inversely with
 body size in many animals, including Yellow Toads, and our results reveal
 that the signal enhancement effect of overlapping calls is heightened when
 the calls are low in frequency (i.e., a chorus of large-bodied animals)
 compared to medium or high frequency (i.e., a chorus of smaller-bodied
 animals). Our findings represent the first experimental demonstration of
 chorus-level signal enhancement in the vocalizations of vertebrates.
description: Signal-to-noise Ratio
 measurements for Incilius luetkenii callsColumn A shows five
 transcripts described in the paper (1-5). Column B shows the number of
 speakers (1, 5, or 10 simulated toads). Column C shows distance between
 the loudspeakers and the microphone, in meters. Column D shows the
 frequency of the calls, either their natural frequency, or one of three
 transposed frequencies (Low, Mid, or High). Column E shows the measured
 Signal-to-noise Ratio, and Column F shows the square root transformed SNR
 values.Rehberg-Besler et al. BE
 Data.csv
DOI: 10.5061/dryad.m7qf972
title: Data from: Highly mobile insectivorous swifts perform multiple intra-tropical migrations to exploit an asynchronous African phenology

description: With timely allocated movement phases, mobile organisms can match their
 space-use with the seasonality of the environment and thereby optimise
 their resource utilisation over time. Long-distance avian migrants are
 known to move with the seasonal dynamics on an annual basis, but how
 individuals respond to seasonality within their tropical non-breeding
 range has been less studied. Here we analyse the movement pattern of a
 highly mobile aerial insectivorous bird, the pallid swift Apus pallidus,
 and its association with the local habitat phenology during the
 non-breeding period, using individual-based light-level geolocation. We
 extracted timing and location of 21 birds´ residence periods, as well as
 characteristics of the intervening movements, such as distance and speed.
 We used time series of precipitation and vegetation data for each
 residence area to extract the timing of the local end of the rainy season
 and the onset of the dry season. The pallid swifts repeatedly upgraded
 their habitat by undertaking 2-5 intra-tropical migrations correlated with
 the withdrawal of the rains and the onset of the local dry season. The
 birds arrived to the sites on average 12 days after rains ended and
 departed about two weeks after the onset of dry season suggesting that the
 birds closely tracked a spatiotemporal window presumably timed with
 optimal foraging conditions. Our results provide insights in the ways
 Palaearctic-African migrants respond to the asynchronous phenology within
 their sub-Saharan non-breeding range. We confirmed that pallid swifts
 actively respond to deteriorating conditions by repeated upgrades in
 habitat quality, which likely have substantial consequences for an
 individual´s access to an essential, spatiotemporally ephemeral food
 resource. However, the pallid swifts did not surf an apparent resource
 wave per se as would be expected in a highly mobile species, indicating
 that also other factors, such as spatial patchiness of resources, may
 influence the movement decision.
description: Intinerary_PSList of stationary sites and period of residency for pallid swifts tracked with geolocators
DOI: 10.5061/dryad.v0q5p
title: Data from: A method for estimating population sex ratio for sage-grouse using noninvasive genetic samples

description: Population sex ratio is an important metric for wildlife management and
 conservation, but estimates can be difficult to obtain, particularly for
 sexually monomorphic species or for species that differ in detection
 probability between the sexes. Noninvasive genetic sampling (NGS) using
 polymerase chain reaction (PCR) has become a common method for identifying
 sex from sources such as hair, feathers, or feces, and is a potential
 source for estimating sex ratio. If, however, PCR success is sex-biased,
 naively using NGS could lead to a biased sex ratio estimator. We measured
 PCR success rates and error rates for amplifying the W and Z chromosomes
 from greater sage-grouse (Centrocercus urophasianus) fecal samples,
 examined how success and error rates for sex identification changed in
 response to fecal sample exposure time, and used simulation models to
 evaluate precision and bias of 3 sex assignment criteria for estimating
 population sex ratio with variable sample sizes and levels of PCR
 replication. We found PCR success rates were higher for females than males
 and that choice of sex assignment criteria influenced the bias and
 precision of corresponding sex ratio estimates. Our simulations
 demonstrate the importance of considering the interplay between the
 sex-bias of PCR success, number of genotyping replicates, sample size,
 true population sex ratio, and accuracy of assignment rules for designing
 future studies. Our results suggest that using fecal DNA for estimating
 the sex ratio of sage-grouse populations has great potential and, with
 minor adaptations, should be applicable to numerous species.
description: SGmarkersData are the results from sex identification primers 1237L/1272H (Kahn et al. 1998) and 2550F/2718R (Fridolfsson & Ellegren 1999) for greater sage-grouse (Centrocercus urophasianus) fecal pellets collected at 9 time periods (day of deposition, 2, 4, 6, 8, 15, 23, 34, and 124 days post deposition).
DOI: 10.5061/dryad.337dr
title: Data from: Meta-analysis of variance: an illustration comparing the effects of two dietary interventions on variability in weight

description: Meta-analysis, which drives evidence-based practice, typically focuses on
 the average response of subjects to a treatment. For instance in
 nutritional research the difference in average weight of participants on
 different diets is typically used to draw conclusions about the relative
 efficacy of interventions. As a result of their focus on the mean,
 meta-analyses largely overlook the effects of treatments on inter-subject
 variability. Recent tools from the study of biological evolution, where
 inter-individual variability is one of the key ingredients for evolution
 by natural selection, now allow us to study inter-subject variability
 using established meta-analytic models. Here we use meta-analysis to study
 how low carbohydrate (LC) ad libitum diets and calorie restricted diets
 affect variance in mass. We find that LC ad libitum diets may have a more
 variable outcome than diets that prescribe a reduced calorie intake. Our
 results suggest that whilst LC diets are effective in a large proportion
 of the population, for a subset of individuals, calorie restricted diets
 may be more effective. There is evidence that LC ad libitum diets rely on
 appetite suppression to drive weight loss. Extending this hypothesis, we
 suggest that between-individual variability in protein appetite may drive
 the trends that we report. A priori identification of an individual’s
 target intake for protein may help define the most effective dietary
 intervention to prescribe for weight loss.
description: Data
 PackageThis is the data package
 to accompany Senior et al. 2016: Meta-analysis of variance: an
 illustration comparing the effects of two dietary interventions on
 variability in weight. The zip file contains three R files. 1)
 "Analysis.R" is the script to perform the analysis and is
 heavily commented. 2) "Data.Objects.Rdata" is a R datafile
 containing all of the necessary to replicate the analysis (see comments in
 "Analysis.R"). 3) "EffectSizeFunctions.R" contains
 various functions to calculate effect sizes, and is called in
 "Analysis.R".
DOI: 10.5061/dryad.62285
title: Data from: Echinorhynchus brayi n. sp. (Acanthocephala: Echinorhynchidae) from Pachycara crassiceps (Roule) (Zoarcidae), a deep-sea fish

description: Echinorhynchus brayi n. sp. (Palaeacanthocephala: Echinorhynchidae) is
 described from Pachycara crassiceps (Roule) (Zoarcidae) from the Porcupine
 Seabight, Northeast Atlantic. The new species closely resembles E.
 canyonensis Huffman & Kliever, 1977, a parasite of a Pacific
 zoarcid, but has longer lemnisci, larger eggs and larger testes. E. brayi
 n. sp. can be readily differentiated from the ten other Echinorhynchus
 spp. recorded from deep-sea fishes (E. abyssicola, E. gadi, E.
 longiproboscis, E. malacocephali, E. melanoglaeae, E. muraenolepisi, E.
 petrotschenkoi, E. sebastolobi, E. trachyrinci and E. truttae), because it
 has fewer hooks per longitudinal row.
description: Standard morphometric
 and meristic data from femalesMorphometric and
 meristic data from the 25 female specimens of the type-material of
 Echinorhynchus brayi Wayland, Sommerville & Gibson, 1999
 (Acanthocephala: Echinorhynchidae).Echinorhynchus_brayi_female_meristics_morphometrics.csvStandard morphometric and meristic data from malesMorphometric and meristic data from the 14 male specimens of the type-material of Echinorhynchus brayi Wayland, Sommerville & Gibson, 1999 (Acanthocephala: Echinorhynchidae). Specimens include holotype.Echinorhynchus_brayi_male_meristics_morphometrics.csvHook measurement data from femalesHook measurements from 6 female specimens of the type-material of Echinorhynchus brayi Wayland, Sommerville & Gibson, 1999 (Acanthocephala: Echinorhynchidae).Echinorhynchus_brayi_female_hook_measurements.csvHook measurement data from malesHook measurements from 7 male specimens of the type-material of Echinorhynchus brayi Wayland, Sommerville & Gibson, 1999 (Acanthocephala: Echinorhynchidae). Specimens include holotype.Echinorhynchus_brayi_male_hook_measurements.csv
DOI: 10.48764/2qk2-pv48
title: Systematic Literature Review Data on End‑User Trust and Explainability in AI Systems

description: This dataset was generated through a Systematic Literature Review (SLR) following the protocol proposed by Wohlin (2014). Wohlin defines the process as an iterative review based on the systematic tracing of citations both backward (looking at papers cited) and forward (looking at papers citing), starting from an initial set of relevant studies (start set). The full texts of the 35 papers included in the SLR were reviewed to identify: · Factors Influencing End-User Trust in AI Systems · Considerations for Designing or Evaluating AI Systems
DOI: 10.5061/dryad.d149b
title: Data from: Lichen biodiversity and ecology in the San Bernardino and San Jacinto Mountains in southern California (U.S.A.)

description: San Bernardino National Forest in southern California encompasses two
 major mountain ranges, the San Bernardino Mountains and the San Jacinto
 Mountains. Here 414 taxa of lichenized fungi are reported from San
 Bernardino National Forest as a whole; 327 from the San Jacinto Mountains
 (including the Santa Rosa Mountains), and 289 from the San Bernardino
 Mountains. Two species new to science are described: Lecanora remota and
 Lecidea stratura. Two undescribed taxa of Bellemerea and Scytinium are
 reported, both currently under study. Five species are reported new for
 North America and California: Gloeoheppia rugosa, Lecanora formosa,
 Peccania cernohorskyi, P. corallina and Psorotichia vermiculata. Peccania
 cernohorskyi is also reported new for Canada (British Columbia). Eight
 species are reported new for California: Caloplaca diphasia, C.
 isidiigera, Peltigera extenuata, Rhizocarpon simillimum, Rinodina
 lobulata, R. terrestris, Sarcogyne squamosa, and Xylographa difformis.
 Lecidea xanthococcoides is recognized as a synonym of Lecanora cadubriae.
 The California endemic Lecidea kingmanii is reported as producing
 4-0-demethylplanaic acid. Polysporina simplex is treated as Acarospora
 simplex and P. urceolata as A. urceolata. The new combination Acarospora
 gyrocarpa is proposed for Polysporina gyrocarpa.
description: data_packetThis is a zipped folder that contains the input alignment files for analyses carried out on selected Lecanora s.l. species to document the phylogenetic placement of the new sorediate species Lecanora remota. The new species was originally included within the broad concept of Lepraria friabilis (a species of the southeastern U.S. including low-elevations of the southern Appalachian Mountains), and shown with molecular data to be unrelated. The data file contains 1) the input files for maximum parsimony (MP), maximum likelihood (ML), Bayesian Inference (BI) and sequence distance analyses, and 2) the original alignment before formatting for those analyses.