cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.80gb5mkrg
title: A peripheral immune signature of labor induction

description: Approximately 1 in 4 pregnant women in the United States undergo labor
 induction. The onset and establishment of labor, particularly
 induced labor, is a complex and dynamic process influenced by multiple
 endocrine, inflammatory, and mechanical factors as well as obstetric and
 pharmacological interventions. The duration from labor induction to the
 onset of active labor remains unpredictable. Moreover, prolonged labor is
 associated with severe complications for the mother and her offspring,
 most importantly chorioamnionitis, uterine atony, and postpartum
 hemorrhage. While maternal immune system adaptations that are critical for
 the maintenance of a healthy pregnancy have been previously characterized,
 the role of the immune system during the establishment of labor is poorly
 understood. Understanding maternal immune adaptations during labor
 initiation can have important ramifications for predicting successful
 labor induction and labor complications in both induced and spontaneous
 types of labor. The aim of this study was to characterize labor-associated
 maternal immune system dynamics from labor induction to the start of
 active labor. Serial blood samples from fifteen participants were
 collected immediately prior to labor induction (baseline) and during the
 latent phase until the start of active labor. Using high-dimensional mass
 cytometry, a total of 1,059 single-cell immune features were extracted
 from each sample. A multivariate machine-learning method was employed to
 characterize the dynamic changes of the maternal immune system after labor
 induction until the establishment of active labor. A cross-validated
 linear sparse regression model (least absolute shrinkage and selection
 operator, LASSO) predicted the minutes since induction of labor with high
 accuracy (R = 0.86, p = 6.7e-15, RMSE = 277 min). Immune features most
 informative for the model included STAT5 signaling in central memory CD8+
 T cells and pro-inflammatory STAT3 signaling responses across multiple
 adaptive and innate immune cell subsets. Our study reports a peripheral
 immune signature of labor induction, and provides important insights into
 biological mechanisms that may ultimately predict labor induction
 success as well as complications, thereby facilitating clinical
 decision-making to improve maternal and fetal well-being.
description: Please see Material and Methods section in the associated
 publication.
DOI: 10.5061/dryad.rbnzs7hbx
title: Accelerating wheat breeding for end-use quality through association mapping and multivariate genomic prediction

description: In hard winter wheat breeding, the evaluation of end-use quality is
 expensive and time-consuming, being relegated to the final stages of the
 breeding program after selection for many traits including disease
 resistance, agronomic performance and grain yield. In this study, our
 objectives were to identify genetic variants underlying baking quality
 traits through genome-wide association mapping (GWAS) and develop improved
 genomic selection (GS) models for the quality traits in hard winter
 wheat.  Advanced breeding lines (n=462) from 2015-2017
 were genotyped using genotyping-by-sequencing (GBS) and evaluated for
 baking quality.  Significant associations were detected
 for mixograph mixing time and bake mixing time; most of which were within
 or in tight linkage to glutenin and gliadin loci, and
 could be suitable for marker-assisted
 breeding.  Candidate genes for newly associated loci are
 phosphate-dependent decarboxylase and lipid transfer protein genes, which
 are believed to affect nitrogen metabolism and dough development,
 respectively.  The use of GS can both shorten the
 breeding cycle time and significantly increase the number of lines that
 could be selected for quality traits; thus we evaluated various GS models
 for end-use quality traits.  As a baseline, univariate
 GS models had 0.25 to 0.55 prediction accuracy in cross-validation and
 from 0 to 0.41 in forward-prediction.  By including
 secondary traits as additional predictor variables (univariate GS with
 covariates) or correlated response variables (multivariate GS), the
 prediction accuracies were increased relative to the univariate model
 using only genomic information.  The improved genomic
 prediction models have great potential to further accelerate wheat
 breeding for end-use quality.
description: '2015_2017 Master Quality_With corrected names for hays
 lines.csv' is the master file containing all the raw phenotypic
 data. 'quality.lines.GBS.numeric.csv'
 contains the numerically converted GBS data.
DOI: 10.5281/zenodo.18398090
title: 7-Tage-Inzidenz der COVID-19-Fälle in Deutschland

description: Im Datensatz "7-Tage-Inzidenz der COVID-19-Fälle in Deutschland" des Robert Koch-Instituts werden die täglich aktualisierten COVID-19-Inzidenzen auf Bundes-, Landes- und Landkreisebene basierend auf den Meldungen nach dem Infektionsschutzgesetz (IfSG) bereitgestellt. Die 7-Tage-Inzidenz wird definiert als Anzahl gemeldeter Fälle der letzten sieben Tage pro 100.000 Einwohner:innen und differenziert nach Altersgruppen und Regionen. Die Datenverarbeitung erfolgt vollständig elektronisch über das Deutsche Elektronische Melde- und Informationssystem (DEMIS).
DOI: 10.5061/dryad.g79cnp5qg
title: Crossing design shapes patterns of genetic variation in synthetic recombinant populations of Saccharomyces cerevisiae

description: “Synthetic recombinant” populations have emerged as a useful tool for
 dissecting the genetics of complex traits.  They can be used to
 derive inbred lines for fine QTL mapping, or the populations themselves
 can be sampled for experimental evolution.  In latter
 application, investigators generally value maximizing genetic variation in
 constructed populations. This is because in evolution experiments
 initiated from such populations, adaptation is primarily fueled by
 standing genetic variation. Despite this reality, little has been done to
 systematically evaluate how different methods of constructing synthetic
 populations shape initial patterns of variation. Here we seek to address
 this issue by comparing outcomes in synthetic recombinant Saccharomyces
 cerevisiae populations created using one of two strategies: pairwise
 crossing of isogenic strains or simple mixing of strains in equal
 proportion.  We also explore the impact of the varying the number
 of parental strains. We find that more genetic variation is initially
 present and maintained when population construction includes a round of
 pairwise crossing.  As perhaps expected, we also observe that
 increasing the number of parental strains typically increases genetic
 diversity. In summary, we suggest that when constructing populations for
 use in evolution experiments, simply mixing founder strains in equal
 proportion may limit the adaptive potential.
description: Data is from an experiment where we examine how different
 crossing strategies shape patterns of genetic variation when creating
 synthetic <i>Saccharomyces cerevisiae </i>populations.
 Specifically, we look at the effects of pairwise crossing of isogenic
 strains vs simple mixing of strains in equal proportion. Details of how
 populations were created can be found in the manuscript titled
 "Crossing design shapes patterns of genetic variation in synthetic
 recombinant populations of Saccharomyces cerevisiae" published
 through bioRxiv. This Dryad entry includes SNP tables, haplotype frequency
 estimates for synthetic populations, growth rate and sporulation data, and
 results of core statistical analyses (See ReadMe file for
 details).
DOI: 10.5061/dryad.crjdfn34q
title: Dietary availability determines metabolic conversion of long-chain polyunsaturated fatty acids in spiders: a dual compound-specific stable isotope approach

description: The following dataset contains fatty acid contents (in mg.g-1 and in %),
 stable isotopes (‰), and compound specific isotopic analyses of carbon and
 hydrogen (‰) data for insects (terrestrial and semi-aquatic) and spiders
 collected around Lake Lunz (47°85’N, 15°05’E), Austria from June to
 September 2020. Measurements were done after storage at -80°C for 2 hours,
 and  freeze drying (24h), followed by taxonomic identification.
 Analytical details can be found in "Dietary availability determines
 metabolic conversion of long-chain polyunsaturated fatty acids in spiders:
 a dual compound-specific stable isotope approach" by Mathieu-Resuge,
 Margaux; Pilecky, Matthias; Twining, Cornelia; Martin-Creuzburg, Dominik;
 Parmar, Tarn-Preet; Vitecek, Simon; Kainz, Martin. Oikos (2021), DOI:
 10.1111/oik.08513
DOI: 10.5061/dryad.cfxpnvx5s
title: Nonalcoholic fatty liver disease, sleep behaviors, and incident type 2 diabetes

description: Objectives: Nonalcoholic fatty liver disease (NAFLD) is associated with
 incident type 2 diabetes; however, the extent to which NAFLD may confer
 its risk remains uncertain, especially in Europeans. Emerging evidence
 suggests that sleep behaviors are linked to NAFLD and diabetes. We aimed
 to measure whether sleep behaviors modified the association between NAFLD
 and incident type 2 diabetes. Methods: This prospective cohort study
 included 362,834 participants without type 2 diabetes at baseline in UK
 Biobank data. Five sleep behaviors, including sleep duration, insomnia,
 snoring, chronotype, and daytime sleepiness, were collected from the
 questionnaire. Liver steatosis was based on the fatty liver index.
 Results: During a median follow-up of 10.9 years, we documented
 7,394 patients with incident type 2 diabetes. NAFLD was significantly
 associated with increased diabetes risk. Sleeping 7-8 h/day, no insomnia,
 no self-reported snoring and no frequent daytime sleepiness were
 independently associated with incident type 2 diabetes, with a 19%, 19%,
 13%, and 29% lower risk, respectively. 33.8% and 33.5% of type 2 diabetes
 events in this cohort could be attributed to NAFLD and poor sleep pattern,
 respectively. We further found significant interaction between NAFLD and
 sleep duration and insomnia (P for interaction = 0.027 and 0.025,
 respectively). Compared those with NAFLD and abnormal sleep duration (≤6 h
 or ≥9 h) or insomnia, participants with non-NAFLD and normal sleep
 duration or non-insomnia had 57% (RR 0.43, 95% CI 0.40, 0.47) or 55% (RR
 0.45, 95% CI 0.41, 0.50) lower risk of incident diabetes. These
 associations were independent of age, sex, ethnicity, education, family
 history, economic status, lifestyles, hemoglobin A1c, systolic blood
 pressure, total cholesterol, and associated medications. Conclusion: Both
 NAFLD and some sleep behaviors were risk factors for type 2 diabetes.
 Insomnia and sleep duration modified the association between NAFLD and
 type 2 diabetes.
DOI: 10.5061/dryad.ffbg79cvw
title: Functional miscibility and thermomechanical properties enhancement of substituted phthalic acetylated modified chitin filler in biopolymer composite

description: The miscibility between hydrophobic and hydrophilic biopolymers has been
 of significant challenge. This study used a novel simplified chitin
 modification method to produce phthalic - chitin using phthalic anhydride
 in a substitution reaction. The FT-IR functional group analysis was used
 to confirm the substitution reaction. The modified chitin was used as
 compatibiliser in PLA/starch biocomposite to enhance its properties. The
 biocomposite was prepared using melt extrusion and compression moulding
 technique. The biocomposite's morphological, thermomechanical, and
 water absorption properties were characterised using scanning electron
 microscope, tensile test, dynamic mechanical analysis, thermogravimetry
 analysis, differential scanning calorimetry, thickness swelling, and water
 absorption test. The FT-IR study shows a successful substitution reaction
 of the amine hydrogen ion present in the chitin as opposed to substituting
 the hydrogen ion in the hydroxide group. The tensile and impact properties
 of biocomposite incorporated with modified chitin showed better results
 compared with other samples. The SEM images showed uniform miscibility of
 the modified biocomposite. The dynamic mechanical analysis showed improved
 modulus value with the incorporation of modified chitin. The thermal
 properties showed improved thermal stability of the modified biocomposite.
 Furthermore, the percentage of water absorbed by biocomposite with
 modified chitin is reduced compared to the PLA/starch biocomposite. The
 produced biodegradable ternary blend can be used as a substitute for
 plastics in industrial applications.
description: The data set are machine generated from characterisation of
 materials properties. The data set are processed using excel software. The
 following data set were uploaded for neat chitin, modified chitin, neat
 polylactic acid, polylactic acid -starch biocomposite, polylactic starch-
 chitin biocomposite and polylactic-starch -modified chitin
 biocomposites. DMA - dynamic mechanical
 Analysis TGA- Thermogravimetry analysis
 DSC- differential scanning calorimetry
 FT-IR
description: Chitin was modified and use as compatibilizer to enhance the
 miscibility between PLA and starch. details about the result is presented
 in the affiliated manuscript
DOI: 10.5061/dryad.4xgxd259v
title: Combined palaeohistological and isotopic inferences of thermometabolism in extinct Neosuchia, using Goniopholis and Dyrosaurus (Pseudosuchia: Crocodylomorpha) as case studies

description: The evolution of thermometabolism in pseudosuchians (Late Triassic to the
 present) remains a partly unsolved issue: extant taxa (crocodilians) are
 ectothermic, but the clade was inferred ancestrally endothermic. Here we
 inferred the thermometabolic regime of two neosuchian groups,
 Goniopholididae (Early Jurassic to Late Cretaceous) and Dyrosauridae
 (Middle Cretaceous to Late Eocene), close relatives of extant
 crocodilians, in order to elucidate the evolutionary pattern across
 Metasuchia (Early Jurassic to the present), a clade comprising Neosuchia
 (Early Jurassic to the present) and Notosuchia (Middle Jurassic until Late
 Miocene). We propose a new integrative approach combining geochemical
 analyses to infer body temperature from the stable oxygen isotope
 composition of tooth phosphate and palaeohistology and phylogenetic
 comparative methods to infer resting metabolic rates (RMR) and red blood
 cells dimensions. †Dyrosaurus and †Goniopholis share with extant
 crocodilians similar lifestyles, body forms, bone tissue organization,
 body temperatures (Tb), metabolic rates and red blood cells dimensions.
 Consistently, we infer ectothermy for †Dyrosaurus and †Goniopholis with
 the parsimonious implication of neosuchians and metasuchians as being
 primitively ectothermic.
description: Data used in PEM inferences, which are the results of the
 quantification of microstructural bone structures (osteons, osteocytes
 lacunae) on pictures of femoral cross-section using ImageJ. Values were
 obtained using the equations given in the paper. V1 for Table Sup 2 and
 V1+V2 for Table Sup 3 were obtained from the literature given in the
 paper.
DOI: 10.5061/dryad.280gb5mqr
title: Focusing on individual plants to understand community scale biodiversity effects: the case of root distribution in grasslands

description: Spatial resource partitioning between species via differences in rooting
 depth is one of the main explanations for the positive
 biodiversity-productivity relationship. However, evidence for the
 importance of this mechanism is limited. This may be due to the community
 scale at which these interactions are often investigated. Community
 measures represent net outcomes of species interactions and may obscure
 the mechanisms underlying belowground interactions. Here, we assess the
 performance of ~1700 individual plants and their heterospecific neighbours
 over three growing seasons in experimental grassland plots containing one,
 four or 16 different plant species and tested whether their performance in
 mixtures compared to monocultures was related to their own rooting depth
 vs. the rooting depth of their heterospecific neighbours. Overall,
 individuals of deep-rooting species performed better in mixtures and this
 effect significantly increased when surrounded by more shallow-rooting
 species. This effect was not apparent for the shallow rooting species.
 Together, including both deep and shallow rooting species increased
 mixture performance. Our results show that taking the perspective of the
 individual rather than the community can elucidate the interactions
 between species that contribute to positive biodiversity effects,
 emphasizing the need for studies at different scales to disentangle the
 myriad interactions that take place in diverse communities.
description: These data were collected following the methods found in Bakker
 et al. 2021 Oikos. All data processing needed to produce the analyses and
 figures in this manuscript are included with the code necessary to produce
 these figures and analyses. 
description: We have included a ReadMe file and notes throughout the code. Any
 additional questions can be directed to the corresponding author of the
 paper (Liesje Mommer) or Kathryn Barry.
DOI: 10.5281/zenodo.18397899
title: Partial LFQ Proteomic Data from Serum Samples of Breast Cancer Female Patients and Healthy Female Control Subjects
DOI: 10.5281/zenodo.18397898
title: Partial LFQ Proteomic Data from Serum Samples of Breast Cancer Female Patients and Healthy Female Control Subjects
DOI: 10.5061/dryad.05qfttf3m
title: Real-time geographic settling of a hybrid zone between the invasive winter moth (Operophtera brumata L.) and the native Bruce spanworm (O. bruceata Hulst)

description: Hybridization plays an important and underappreciated role in shaping the
 evolutionary trajectories of species. Following the introduction of a
 non-native organism to a novel habitat, hybridization with a native
 congener may affect the probability of establishment of the introduced
 species. In most documented cases of hybridization between a native and a
 non-native species, a mosaic hybrid zone is formed, with hybridization
 occurring heterogeneously across the landscape. In contrast, most
 naturally occurring hybrid zones are clinal in structure. Here we report
 on a long-term microsatellite dataset that monitored hybridization between
 the invasive winter moth, Operophtera brumata (Lepidoptera: Geometridae),
 and the native Bruce spanworm, O. bruceata, over a 12-year period. Our
 results document one of the first examples of the real-time formation and
 geographic settling of a clinal hybrid zone. In addition, by comparing one
 transect in Massachusetts where extreme winter cold temperatures have been
 hypothesized to restrict the distribution of winter moth, and one in
 coastal Connecticut, where winter temperatures are moderated by Long
 Island Sound, we find that the location of the hybrid zone appears to be
 independent of environmental variables and maintained under a tension
 model wherein the stability of the hybrid zone is constrained by
 population density, reduced hybrid fitness, and low dispersal rates.
 Documenting the formation of a contemporary clinal hybrid zone may provide
 important insights into the factors that shaped other well-established
 hybrid zones.
description: From each sample, 11 polymorphic microsatellite loci were
 amplified following Havill et al. (2017), and run with the GeneScan 500
 LIZ size standard (Thermo Fisher Scientific; Waltham, MA), on a Thermo
 Fisher Scientific 3730xl DNA Analyzer at the DNA Analysis Facility on
 Science Hill at Yale University. Fragment lengths were scored in the
 software GENEIOUS v. R11 (https://www.geneious.com), using the
 microsatellite plugin.
DOI: 10.5061/dryad.b8gtht7db
title: Little Appleton Pasteuria epidemic dataset

description: Virulence, the degree to which a pathogen harms its host, is an important
 but poorly understood aspect of host-pathogen interactions. However it is
 not a static trait, instead depending on ecological context and
 potentially evolving over short periods of time (e.g., during the course
 of an epidemic). At the start of an epidemic, when susceptible hosts are
 plentiful, pathogens may evolve increased virulence, maximizing their
 intrinsic growth rate. However, if host density declines during an
 epidemic, theory predicts evolution of reduced virulence. Although
 well-studied theoretically, there is still little empirical evidence for
 virulence evolution in epidemics, especially in natural settings with
 native host and pathogen species. Here, we used a combination of field
 observations and lab experiments in the Daphnia-Pasteuria model system to
 look for evidence of virulence evolution in nature. Controlling for
 environmental conditions, we found that there was no change in parasite
 virulence when measured in terms of host lifespan or the number of
 clutches produced. There also was no evidence for evolution of host
 resistance or parasite infectivity. However, over the epidemic, the
 parasite evolved to produce significantly fewer spores in infected hosts,
 perhaps as a result of trade-offs quantified in earlier studies. Future
 studies that track evolution of parasite spore yield in more populations,
 and that link those changes with genetic changes and with predation rates,
 will yield better insight into the drivers of parasite evolution in the
 wild.
description: Dataset combines a field survey of infection prevalence with
 infection assays looking for evolution of parasite infectivity, parasite
 virulence, and/or host susceptibility.