cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k3j9kd5c6
title: Urban peregrine falcon (Falco peregrinus) breeding season diet in UK, 2020–2022

description: Diets of urban peregrine falcons in UK were monitored via nest cameras
 during the breeding season (March-June) from 2020–2022. All prey items
 were then identified to species level where possible, by Ed Drewitt. This
 dataset contains the prey items recorded during each year of the study and
 location of the sites.
DOI: 10.17632/8t4z4xd7fj
title: China's dryland soil quality: Past, present, and future

description: Soil quality serves as the cornerstone supporting the stability, biodiversity, and multifunctionality of dryland ecosystems. However, the evolution (past and present) and future trends of soil quality in dryland regions under global change remain largely unexplored. Here, we conducted a large-scale field survey across 248 sites spanning more than 4000 km geographical distance in China’s drylands–one of the world’s largest dryland regions, with the focus on long-term land treatments over the past four decades. Our findings revealed that China’s drylands have undergone a profound transformation since the initiation of large-scale land treatments in 1980, as evidenced by reduced desert areas, expanded vegetation cover, and improved soil quality. Compared to sites with no treatments, the land treatments substantially enhanced soil nutrient stocks, nutrient availability, and overall soil quality by 13%–289%, with the climate being another influencing factor. As an unintended but beneficial consequence of land treatments, widespread development of biological soil crusts (biocrusts) has further reinforced these improvements in soil quality. We also found that the land treatments would mitigate the future loss of soil quality expected to be caused by increasing aridification and grassland degradation. Together, our findings highlight the positive role of anthropogenic land treatments in improving soil quality in vast dryland regions.
DOI: 10.5061/dryad.98sf7m0nn
title: Data from: Increased male-induced harm in response to female-limited selection: interactive effects between intra- and interlocus sexual conflict?

description: Interlocus sexual conflict (IRSC) occurs because of shared interactions
 that have opposite effects on male and female fitness. Typically, it is
 assumed that loci involved in IRSC have sex-limited expression and are
 thus not directly affected by selective pressures acting on the other sex.
 However, if loci involved in IRSC have pleiotropic effects in the other
 sex, intersexual selection can shape the evolutionary dynamics of conflict
 escalation and resolution, as well as the evolution of reproductive traits
 linked to IRSC loci, and vice versa. Here we used an artificial selection
 approach in Japanese quail (Coturnix japonica) to test if female-limited
 selection on reproductive investment affects the amount of harm caused by
 males during mating. We found that males originating from lines selected
 for high female reproductive investment caused more oxidative damage in
 the female reproductive tract than males originating from lines selected
 for low female reproductive investment. This male-induced damage was
 specific to the oviduct and not found in other female tissues, suggesting
 that it was ejaculate-mediated. Our results suggest that intersexual
 selection shapes the evolution of IRSC and that male-induced harm may
 contribute to the maintenance of variation in female reproductive
 investment.
description: Dataset collected from captive Japanese quail
 (<em>Coturnix japonica</em>) artificially selected for high
 (H-line) and low (L-line) maternal egg investment. After four
 generations of selective breeding, H- and L-line females differed in egg
 size by &gt; 1 SD, but they did not differ in the number of eggs laid.
 Both L-line and H-line females were randomly paired with either a L-line
 or H-line male (2x2 design; female / male pairs: N = 11 L / L, N = 10 L /
 H, N = 10 H / H, N = 10 H / L) and kept in breeding cages for two weeks.
 From each female,
 a blood sample was obtained before breeding, and tissue samples from the
 oviduct, the liver and the spleen were obtained after breeding. Oxidative
 stress markers were analysed in the samples.
description: There are two datasets. The main information
 about the line, age, reproductive performance and oxidative stress markers
 is included in the first dataset. The information included in the second
 dataset was used only to build the correlation matrix (supplementary table
 S7), in other words, this dataset does not include new information
 non-included in the first dataset. The
 explanation of the variables is included as a comment on the variable
 name. The R code for running the models is also available.
DOI: 10.17632/8t4z4xd7fj.1
title: China's dryland soil quality: Past, present, and future

description: Soil quality serves as the cornerstone supporting the stability, biodiversity, and multifunctionality of dryland ecosystems. However, the evolution (past and present) and future trends of soil quality in dryland regions under global change remain largely unexplored. Here, we conducted a large-scale field survey across 248 sites spanning more than 4000 km geographical distance in China’s drylands–one of the world’s largest dryland regions, with the focus on long-term land treatments over the past four decades. Our findings revealed that China’s drylands have undergone a profound transformation since the initiation of large-scale land treatments in 1980, as evidenced by reduced desert areas, expanded vegetation cover, and improved soil quality. Compared to sites with no treatments, the land treatments substantially enhanced soil nutrient stocks, nutrient availability, and overall soil quality by 13%–289%, with the climate being another influencing factor. As an unintended but beneficial consequence of land treatments, widespread development of biological soil crusts (biocrusts) has further reinforced these improvements in soil quality. We also found that the land treatments would mitigate the future loss of soil quality expected to be caused by increasing aridification and grassland degradation. Together, our findings highlight the positive role of anthropogenic land treatments in improving soil quality in vast dryland regions.
DOI: 10.5061/dryad.8gtht76t2
title: Trait-dependent diversification in angiosperms: Patterns, models and data

description: Variation in species richness across the tree of life, accompanied by the
 incredible variety of ecological and morphological characteristics found
 in nature, has inspired many studies to link traits with species
 diversification. Angiosperms are a highly diverse group that has
 fundamentally shaped life on earth since the Cretaceous and illustrate how
 species diversification affects ecosystem functioning. Numerous traits and
 processes have been linked to differences in species richness within this
 group, but we know little about their relative importance and how they
 interact. Here, we synthesized data from 152 studies that used
 state-dependent speciation and extinction (SSE) models on angiosperm
 clades. Intrinsic traits related to reproduction and morphology were often
 linked to diversification but a set of universal drivers did not emerge as
 traits did not have consistent effects across clades. Importantly, SSE
 model results were correlated to dataset properties – trees that were
 larger, older, or less well-sampled tended to yield trait-dependent
 outcomes. We compared these properties to recommendations for SSE model
 use and provide a set of best practices to follow when designing studies
 and reporting results. Finally, we argue that SSE model inferences should
 be considered in a larger context incorporating species' ecology,
 demography and genetics.
DOI: 10.5061/dryad.gtht76hr3
title: Simulated eukaryotic genomic sequencing, long and short reads

description: As accuracy and throughput of nanopore sequencing improves, it is
 increasingly common to perform long-read-first de novo genome assemblies
 followed by polishing with accurate short reads (Kim et al. 2021). We
 briefly introduce FMLRC2, the successor to the original FM-index Long Read
 Corrector (FMLRC), and illustrate its performance as a fast and accurate
 de novo assembly polisher for both bacterial and eukaryotic genomes.
description: We simulated ONT data and the corresponding paired-end Illumina dataset using Badread v0.2.0 (Wick, 2019) and ART v2016-06-05 (Huang et al., 2011) as previously described (Wick and Holt, 2022). Briefly, short reads were simulated using ART with HiSeqX TruSeq preset, to 100X effective sequencing depth, 150 bp read length, 400±50(sd) bp mean fragment. Long reads were simulated using Badread with parameters “--length 20000,12000 --identity 90,98,4”.
DOI: 10.5061/dryad.r4xgxd2hm
title: The population genetics of speciation by cascade reinforcement

description: Species interactions drive diverse evolutionary outcomes. Speciation by
 cascade reinforcement represents one example of how species interactions
 can contribute to the proliferation of species. This process occurs when
 the divergence of mating traits in response to selection against
 interspecific hybridization incidentally leads to reproductive isolation
 among populations of the same species. Here, we investigated the
 population genetic outcomes of cascade reinforcement in North American
 chorus frogs (Hylidae: Pseudacris). Specifically, we estimated
 the frequency of hybridization among three taxa, assessed genetic
 structure within the focal species, P. feriarum, and
 ascertained the directionality of gene flow within P.
 feriarum across replicated contact zones via coalescent modeling.
 Through field observations and preliminary experimental crosses, we
 assessed whether hybridization is possible under natural and laboratory
 conditions. We found that hybridization occurs among P. feriarum
 and two conspecifics at a low rate in multiple contact zones and that gene
 flow within the former species is unidirectional from allopatry into
 sympatry with these other species in three of four contact zones studied.
 We found evidence of substantial genetic structuring within P.
 feriarum including a divergent western allopatric cluster, a
 behaviorally-distinct sympatric South Carolina cluster, and several
 genetically-overlapping clusters from the remainder of the distribution.
 Furthermore, we found sub-structuring between reinforced and
 non-reinforced populations in the two most intensely-sampled contact
 zones. Our literature review indicated that P.
 feriarum hybridizes with at least five heterospecifics at the
 periphery of its range providing a mechanism for further intraspecific
 diversification. This work strengthens the evidence for cascade
 reinforcement in this clade, revealing the geographic and genetic
 landscape upon which this process can contribute to the proliferation of
 species.
DOI: 10.17632/d7mrsx9hr9.2
title: Anurans in forests near cities in Peninsular Malaysia and Malaysian Borneo reflect the impact of habitat disturbance on species’ diversity and relative fitness

description: The datasets include species occurrence and biodiversity data of anuran records from two geographically distinct forests: Ayer Hitam Forest Reserve (AHFR) in Peninsular Malaysia and Universiti Putra Malaysia Bintulu Campus (UPMBC) in Malaysian Borneo.This datasets provides valuable insights into species distribution, habitat preferences, and the effects of human disturbance on anuran populations in both forest near cities.
1. A total of 466 individuals from 39 species (6 families) in AHFR and 95 individuals from 24 species (7 families) in UPMBC.
2. Long-term species records: Historical data (1975–1999) integrated with multi-year surveys (2015–2019) in AHFR and a four-year survey (2005–2009) in UPMBC.

3. Sampling and environmental data included zones in AHFR categorized by disturbance level: protected, minimally disturbed, controlled, moderately disturbed, and disturbed. The UPMBC sampling zones categorised by planted forest, Nirwana Reserve Forest and campus forest. 
4. methods of surveys for anurans within both forests using nocturnal line transect surveys along trails and streams and quadrat sampling for forest floor species inventory.

5. Morphometric dataset composed of measurements of snout-vent length (SVL), tibia length (TL), and body condition index (BCI) for various species.
6. Comparative analysis of body size and condition between disturbed and protected zones in AHFR.
7. Interspecific comparisons of morphometric traits, focusing on Limnonectes ibanorum populations in AHFR and UPMBC.
8. Statistical and analytical methods include:
(i) PCA (Principal Component Analysis) for morphological trait correlations.
(ii) Regression-based body condition index calculation due to missing weight data.
(iii) Diversity indices to assess species richness, evenness, and abundance across zones.
DOI: 10.5061/dryad.fxpnvx0wv
title: Glioblastoma-astrocytes coculture data

description: This dataset largely contains values pertaining to how migration from
 tumor spheroids in different coculture configurations with human
 astrocytes was measured. The data present relate to sphere size, the
 migration capacity or area %, and the adjusted migration distance or
 ad-distance of samples ranging over several days of measurements. Files
 are labeled to reflect data matching specific figure numbers. 
 Most of the numerical data is derived from images that were initially
 batch processed in R using known packages and further processed manually
 in ImageJ and quantified.  The Nanostring data represents gene
 expression results and needs to be further processed.
DOI: 10.17632/c9zwpz5ryv
title: Dataset of snow cover and environmental factors in frozen-ground regions of China

description: This dataset integrates meteorological observations and environmental factor information from frozen-ground regions of China. It includes geographic location (latitude and longitude), topographic characteristics (altitude, slope, and aspect), vegetation parameters (leaf area index (LAI) and fractional vegetation cover (FVC)), soil properties (bulk density, clay, silt, and sand contents, porosity, soil organic carbon (SOC), and surface soil moisture (SSM)), climatic factors (air temperature freezing index (FI_AT), wind speed, and sunshine duration), as well as snow-related variables (effective snow depth (ESD)) and ground thermal indicators (freezing index of ground surface temperature at 0 cm (FI_GT)). In addition, the dataset contains effective snow depth (ESD) and Freezing n factor (nf) data for the permafrost regions of Northeast China, the Qinghai–Tibet Plateau, and the seasonally frozen ground regions of China.
DOI: 10.17632/c9zwpz5ryv.1
title: Dataset of snow cover and environmental factors in frozen-ground regions of China

description: This dataset integrates meteorological observations and environmental factor information from frozen-ground regions of China. It includes geographic location (latitude and longitude), topographic characteristics (altitude, slope, and aspect), vegetation parameters (leaf area index (LAI) and fractional vegetation cover (FVC)), soil properties (bulk density, clay, silt, and sand contents, porosity, soil organic carbon (SOC), and surface soil moisture (SSM)), climatic factors (air temperature freezing index (FI_AT), wind speed, and sunshine duration), as well as snow-related variables (effective snow depth (ESD)) and ground thermal indicators (freezing index of ground surface temperature at 0 cm (FI_GT)). In addition, the dataset contains effective snow depth (ESD) and Freezing n factor (nf) data for the permafrost regions of Northeast China, the Qinghai–Tibet Plateau, and the seasonally frozen ground regions of China.
DOI: 10.5061/dryad.vx0k6djwt
title: Data for: Endogenous DAF-16 spatiotemporal activity quantitatively predicts lifespan extension induced by dietary restriction

description: In many organisms, dietary restriction (DR) leads to lifespan extension
 through the activation of cell protection and pro-longevity gene
 expression programs. In the nematode C. elegans, the DAF-16 transcription
 factor is a key aging regulator that governs the Insulin/IGF-1 signaling
 pathway and undergoes translocation from the cytoplasm to the nucleus of
 cells when animals are exposed to food limitation. However, how large is
 the influence of DR on DAF-16 activity, and its subsequent impact on
 lifespan has not been quantitatively determined. In this work, we assess
 the endogenous activity of DAF-16 under various DR regimes by coupling
 CRISPR/Cas9-enabled fluorescent tagging of DAF-16 with quantitative image
 analysis and machine learning. Our results indicate that DR regimes induce
 strong endogenous DAF-16 activity, although DAF-16 is less responsive in
 aged individuals. DAF-16 activity is in turn a robust predictor of mean
 lifespan in C. elegans, accounting for 78% of its variability under DR.
 Analysis of tissue-specific expression aided by a machine learning tissue
 classifier reveals that, under DR, the DAF-16 influence on lifespan
 extension mainly originates from the intestine and neurons. DR also drives
 DAF-16 activity in unexpected locations such as the germline and
 intestinal nucleoli.
DOI: 10.17632/6vhwdwfkv4.2
title: Gig Worker poor psychological health Thematic Analyses Coding File

description: This file contains the coding generated by the thematic analyses performed on 36 papers identified through a systematic literature review. The coding is performed to identify the various themes of gig worker that cause poor psychological health.
DOI: 10.5061/dryad.hqbzkh1m8
title: Data from: Downclimbing and the evolution of ape forelimb morphologies

description: Hominoids (non-human apes and hominins) are distinct from cercopithecoid
 monkeys in possessing more flexible forelimb joints, including high
 excursion angles at the shoulder and elbow. Both vertical climbing and
 forelimb suspension have been hypothesized to explain these skeletal
 differences, but field kinematic studies have found few differences in
 forelimb excursion during vertical climbs between chimpanzees and monkeys.
 Previous studies have focused largely on ascent (upclimbing) mechanics,
 while kinematic strategies employed during descents (downclimbs) are
 usually ignored. Here, we test the role that vertical climbing
 directionality plays in patterns of forelimb joint kinematics in wild
 populations of chimpanzees (Pan troglodytes) and sooty mangabeys
 (Cercocebus atys). We found that vertical descent produces greater degrees
 of elbow extension and shoulder flexion in chimpanzees compared to their
 vertical ascents, a pattern not shared with mangabeys. Chimpanzees used
 their forelimbs in kinematically similar ways to mangabeys during ascents;
 however, descent involved greater elbow extension and greater shoulder
 flexion in chimpanzees. Our results support functional hypotheses
 emphasizing the role vertical climbing–and specifically descent– plays in
 the evolution of increased forelimb mobility in apes.
DOI: 10.17632/2vr3p4nh7d
title: A Low-Cost Printed Circuit Board to Perform Functional and In-Circuit Testing

description: This dataset accompanies the paper "A Low-Cost Printed Circuit Board to Perform Functional and In-Circuit Testing ", the design and implementation of a compact, low-cost printed circuit board to perform in-circuit testing (ICT) and functional testing (FCT) of electronic assemblies during prototyping and small-scale production. The hardware integrates multiple testing functions, programmable voltage and current stimulus, relay-based switching matrices, voltage/current/resistance/capacitance measurements, and functional signal testing, all controlled by an embedded microcontroller on a single PCB.
DOI: 10.17632/2vr3p4nh7d.1
title: A Low-Cost Printed Circuit Board to Perform Functional and In-Circuit Testing

description: This dataset accompanies the paper "A Low-Cost Printed Circuit Board to Perform Functional and In-Circuit Testing ", the design and implementation of a compact, low-cost printed circuit board to perform in-circuit testing (ICT) and functional testing (FCT) of electronic assemblies during prototyping and small-scale production. The hardware integrates multiple testing functions, programmable voltage and current stimulus, relay-based switching matrices, voltage/current/resistance/capacitance measurements, and functional signal testing, all controlled by an embedded microcontroller on a single PCB.
DOI: 10.7280/d1dt3f
title: Characterizing the microbiome of patients with myeloproliferative neoplasms during a Mediterranean diet intervention

description: Myeloproliferative neoplasms (MPN) are a class of hematological
 malignancies that result in the overproduction of myeloid lineage cells.
 These malignancies result in increased cytokine production and
 inflammation, which correlate with worsened symptom burden and prognosis.
 Other than bone marrow transplantation, there is no cure for
 myeloproliferative neoplasms. As such, treatments focus on reducing
 thrombotic risk, inflammation, and symptom burden. Because current
 pharmacological treatments carry significant side-effects, there is a need
 to explore low-risk therapies. One alternative is the Mediterranean diet,
 which is rich in anti-inflammatory foods, reduces inflammatory biomarkers,
 and beneficially alters the gut microbiome. Here, we performed a 15-week
 clinical trial of 28 individuals with MPN who were randomized to dietary
 counseling based on either a Mediterranean diet or standard U.S.
 Guidelines for Americans. Our primary objective was to determine if MPN
 patients were able to adopt a Mediterranean eating style when supported
 with dietician counseling. As exploratory endpoints, we investigated the
 impact of diet and inflammation on the gut microbiome. Using shotgun
 metagenomic sequencing, we found that microbiome diversity and composition
 were stable throughout the study duration in both cohorts. Furthermore, we
 discovered significant differences in the microbiomes between MPN
 subtypes, such as increased beta-dispersion in subjects with
 myelofibrosis. Lastly, we found several significant correlations between
 the abundances of multiple bacterial taxa and cytokine levels. Together,
 this study provides insight into the interaction between diet,
 inflammation, and the gut microbiome.