cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zkh189389
title: Evening locomotor activity during stopover differs on pre-departure and departure days in free-living songbirds

description: The length of time songbirds remain at a migratory stopover site is likely
 regulated by a daily stay/go decision informed by fat stores and weather
 conditions, but the finer-scale timing of this decision and associated
 pre-departure behaviours are still poorly understood. Using automated
 radiotelemetry of free-living songbirds captured at a migratory stopover
 site in spring, we tested whether individuals change their locomotor
 activity near sunset on their migratory departure day compared to their
 non-departure days. To do so, we extracted precise transition times
 between diurnal activity and nocturnal inactivity, which always precedes
 departure, using changepoint analysis of radio transmission signal
 strength. Among four warbler species, individuals extended diurnal
 activity by 8-19 minutes towards sunset on their departure day. In three
 species, this extension was significant. In contrast, white-throated
 sparrows significantly shortened diurnal activity on their departure day
 by 13 min, also towards sunset. This is the first study to detect and
 quantify a change in locomotor activity schedule on departure versus
 non-departure days in free-living songbirds, and is consistent with the
 hypothesis that birds engage in pre-departure preparatory behaviours near
 sunset.
DOI: 10.5061/dryad.dbrv15f00
title: Size, sex, reproductive status and body temperature dataset

description: Climate change is impacting species globally, with many populations
 declining at an accelerated rate towards extinction. Ectothermic species
 are particularly vulnerable given their reproductive success is linked to
 environmental temperatures. Studies of the effect of temperature on
 reproductive success in oviparous squamates have focused mostly on nest
 temperatures, after eggs are deposited. However, in some species gravid
 females are known to thermoregulate differently than other adults to
 increase reproductive success.  It is essential to understand
 what influences the thermal biology of breeding adults in a population to
 implement targeted conservation strategies. The Florida scrub lizard
 Sceloporus woodi is an endemic species listed as near-threatened due to
 decreasing populations. This study is the first to document the thermal
 biology of these breeding adults in relation to size, sex, and
 reproductive status. A t-test was used to determine if sexual dimorphism
 was present in the sampled S.woodi. Full linear mixed-effects models were
 used to test the influence of size, sex and reproductive status on the
 thermal biology of S. woodi. Despite female-biased sexual size dimorphism,
 there were no sex-based differences in body temperature in the studied
 population.  Interestingly, reproductive status influenced
 thermal biology of females during the breeding season, with gravid females
 maintaining lower body temperatures compared to non-gravid females.
 However, gravid females did not regulate their body temperatures more
 precisely compared to non-gravid females. These results indicate the
 population viability of this endemic species is potentially linked to the
 different thermoregulatory requirements of gravid females as compared to
 other adults. Lower body temperatures of gravid females, exacerbated by
 their lack of thermal precision, has disconcerting conservation
 implications in the face of climate warming. Future studies focusing on
 gravid females are warranted to attain effective biodiversity conservation
 strategies mitigating the impacts of climate warming.
description: The file contains data on size, sex, reproductive status, and
 body temperature for 37 endemic Florida scrub lizards
 <em>(</em><i>Sceloporus woodi</i>).
DOI: 10.5061/dryad.ksn02v72k
title: Contrasting biomass allocation responses across ontogeny and stress gradients reveal plant adaptations to drought and cold

description: How plants allocate their biomass to different organs is essential to
 understand plant adaptation and distribution. Overall, biomass allocation
 may follow fixed rules across taxa. They are also likely to exhibit
 substantial departure from these rules during ontogeny and in response to
 particular limiting factors to optimize their growth and maximize their
 survival. However, how plants adjust their allocation priorities depending
 on size and age across stress gradients remain largely unkown in wild
 populations. We examined ontogenetic variation in biomass allocation in
 Himalayan forb Potentilla pamirica across its 5250-5900 m elevation range,
 between populations from dry steppe, wet alpine and cold subnival zone. We
 tested whether biomass allocation followed optimal partitioning or fixed
 allometric rules using organ mass in 1019 individuals spanning 1-73 years.
 We found shifting biomass fractions with plant size and age, supporting
 the optimal partitioning theory. Young plants (&lt;10 years) allocated
 similar proportions of biomass to leaves, stems, and roots,
 intermediate-aged plants (10-30 years) allocated more biomass to roots,
 while the oldest plants had 90% biomass in belowground stems. Major
 developmental processes including secondary thickening, branching and
 flowering begin 10-15 years earlier under more thermally favorable steppe
 conditions. Young steppe plants are larger than alpine and subnival
 plants, but these differences disappear in plants aged ~30, and the oldest
 alpine and subnival plants are larger than steppe plants. Plant age
 exerted significant control over biomass allocation after controlling for
 plant size. While in steppe plants the preference for stem biomass
 allocation increases with both size and age, for large alpine and subnival
 plants the stem prioritization decreases with age in favour of root and
 leaf mass fractions. We interpret the root and leaf prioritization in the
 oldest plants as a way to reduce carbon imbalances and the risk of frost
 damage to secure long life. Our analyses rejected ontogenetically ﬁxed
 allometry and instead found high variation in biomass allocation depending
 on age, size and environment, supporting optimal partitioning theory. The
 uneven allocation of resources to different structures and functions
 during ontogenesis reflects plant adaptations to different levels of
 low-temperature and water stress across species elevation range.
DOI: 10.6084/m9.figshare.31054762
title: Destructive Earthquake Catalog (2300 BC – 2024 AD) for China

description: A complete and reliable earthquake catalog is the most fundamental dataset for studying regional seismic activity. This study discloses the newly compiled catalog of destructive earthquakes (M≥4.7) for developing the next-generation seismic zonation map of ground motion parameters in China. The dataset was systematically compiled from multiple local, regional, and international sources to ensure comprehensive coverage. To ensure maximal retention of seismicity patterns, the catalog incorporates earthquake clusters, notably foreshock-aftershock sequences. The complete catalog contains 16,403 recorded earthquakes (M≥4.7) spanning 4,324 years from B.C. 2300 to A.D. 2024. The dataset spans China and adjacent zones, with longitudinal and latitudinal extents of 65°E–141°E and 3°N–57°N, respectively. As a foundational dataset, it supports two key modeling processes in developing China's new-generation seismic zonation map: (1) seismic activity characterization, and (2) potential seismic source zone identification.
DOI: 10.6084/m9.figshare.31054762.v1
title: Destructive Earthquake Catalog (2300 BC – 2024 AD) for China

description: A complete and reliable earthquake catalog is the most fundamental dataset for studying regional seismic activity. This study discloses the newly compiled catalog of destructive earthquakes (M≥4.7) for developing the next-generation seismic zonation map of ground motion parameters in China. The dataset was systematically compiled from multiple local, regional, and international sources to ensure comprehensive coverage. To ensure maximal retention of seismicity patterns, the catalog incorporates earthquake clusters, notably foreshock-aftershock sequences. The complete catalog contains 16,403 recorded earthquakes (M≥4.7) spanning 4,324 years from B.C. 2300 to A.D. 2024. The dataset spans China and adjacent zones, with longitudinal and latitudinal extents of 65°E–141°E and 3°N–57°N, respectively. As a foundational dataset, it supports two key modeling processes in developing China's new-generation seismic zonation map: (1) seismic activity characterization, and (2) potential seismic source zone identification.
DOI: 10.5061/dryad.j9kd51c9h
title: Testing for population differences in evolutionary responses to pesticide pollution in brown trout (Salmo trutta)

description: Pesticides are often toxic to non-target organisms, especially to those
 living in rivers that drain agricultural land. The brown trout (Salmo
 trutta) is a keystone species in many such rivers, and natural populations
 have hence been chronically exposed to pesticides over multiple
 generations. The introduction of pesticides decades ago could have induced
 evolutionary responses within these populations. Such a response would be
 predicted to reduce the toxicity over time but also deplete any additive
 genetic variance for the tolerance to the pesticides. If so, populations
 are now expected to differ in their susceptibility and in the variance for
 the tolerance depending on the pesticides they have been exposed to. We
 sampled breeders from seven natural populations that differ in their
 habitats and that show significant genetic differentiation. We stripped
 them for their gametes and produced 118 families by in vitro
 fertilization. We then raised 20 embryos per family singly in
 experimentally controlled conditions and exposed them to one of two
 ecologically relevant concentrations of either the herbicide S-metolachlor
 or the insecticide diazinon. Both pesticides affected embryo and larval
 development at all concentrations. We found no statistically significant
 additive genetic variance for tolerance to these stressors within or
 between populations. Tolerance to the pesticides could also not be linked
 to variation in carotenoid content of the eggs. However, pesticide
 tolerance was linked to egg size, with smaller eggs being more tolerant to
 the pesticides than larger eggs. We conclude that an evolutionary response
 to these pesticides is currently unlikely, and that (i) continuous
 selection in the past has either depleted genetic variance in all the
 populations we studied, or (ii) that exposure to the pesticides never
 induced an evolutionary response. The observed toxicity selects against
 large eggs that are typically spawned by larger and older females.
DOI: 10.5061/dryad.fn2z34ts1
title: Data from: Current distributions and future climate‐driven changes in diatoms, insects and fish in U.S. streams

description: Aim Biodiversity on Earth is threatened by climate change. Despite the
 vulnerability of freshwater habitats to human impacts, most climate change
 projections have focused on terrestrial systems. Here, we examined how the
 current distributions and biodiversity of stream taxa might change under
 mitigated, stabilizing and increasing greenhouse gas emissions. Location
 Conterminous USA. Time period Present day to 2070. Major taxa studied
 Stream diatoms, insects and fish. Methods We developed species
 distribution models for 336 freshwater taxa from 1,227 distinct stream
 localities using water chemistry, watershed and climatic variables. Models
 based only on climate were used to project changes in the distributions
 and biodiversity of cold‐ versus warm‐water taxa under representative
 concentration pathways (RCPs) ranging from 2.6 to 8.5 W/m2.
 Results In all three organismal groups, climate emerged as the strongest
 predictor of species distributions, providing comparable explanatory power
 to water chemistry and watershed variables combined. The RCP‐based
 projections suggested a widespread expansion of warm‐water taxa, outpacing
 the decline of cold‐water taxa. Consequently, overall species richness
 would increase, but beta diversity would decrease drastically with the
 severity of climate change. A closer look at individual taxa and
 functional guilds revealed that vulnerable cold‐water taxa included: (a)
 diatom guilds forming the base and bulk of the biofilm; (b)
 environmentally sensitive insects, characteristic of unimpacted streams;
 and (c) ecologically and recreationally important salmonids, which were
 forecast to diminish dramatically in source habitats. Warm‐water fish
 projected to increase their distributions include bait bucket release
 minnows and dominant predators. Main conclusions Our results suggest
 potentially devastating impacts of climate change on stream ecosystems,
 with the restructuring of diatom, insect and fish communities, diminished
 distributions of functionally important taxa and widespread expansion of
 warm‐water taxa, giving rise to biotic homogenization. Given that the
 magnitude of these biotic shifts depends on the severity of climate
 change, appropriate current policy decisions are necessary to preserve
 freshwater ecosystems.
description: Water chemistry, watershed information and individual counts for
 stream benthic diatoms, insects and fish were gathered from the National
 Water‐Quality Assessment Program of the U.S. Geological Survey (https://www.waterqualitydata.us/portal/). Climatic variables were retrieved from the WorldClim database.
description: Three datasets: diatoms, insects, and fish. Each spreadsheet
 contains data for taxa presence/absence, water chemistry, watershed
 properties, present day climate, and NorESM1‐M climate projections for
 each stream site in 2050 and 2070.
DOI: 10.5061/dryad.xpnvx0kd2
title: Scoring of 13 microsatellite loci for Tetrastigma loheri in Cebu (Philippines) based on the fragment length size of their respective alleles

description: Little is known about the effects of habitat fragmentation on the patterns
 of genetic diversity and genetic connectivity of species in the remaining
 tropical forests of Southeast Asia. This is particularly evident in Cebu,
 a Philippine island that has a long history of deforestation and has lost
 nearly all of its forest cover. To begin filling this gap, data from 13
 microsatellite loci developed for Tetrastigma loheri (Vitaceae), a common
 vine species in Philippine forests, were used to study patterns of genetic
 diversity and genetic connectivity for the four largest of the remaining
 forest areas in Cebu. Evidence of relatively high levels of inbreeding was
 found in all four areas, despite no evidence of low genetic diversity. The
 four areas are genetically differentiated, suggesting low genetic
 connectivity. The presence of inbreeding and low genetic connectivity in a
 commonly encountered species such as T. loheri in Cebu suggests that the
 impact of habitat fragmentation is likely greater on rare plant species
 with more restricted distributions in Cebu. Conservation recommendations
 for the remaining forest areas in Cebu include the establishment of
 steppingstone corridors between nearby areas to improve the movement of
 pollinators and seed dispersers among them.
description: Leaf samples from a total of 17 sampling sites in Cebu,
 Philippines were obtained from 25–47 individuals for each of the four
 forest areas. Whole genomic DNA was extracted from silica-dried
 leaves. Extracted DNA of one individual was sent to Macrogen (South Korea)
 for Next Generation Sequencing (GS-FLX Titanium). Using MSATCOMMANDER
 1.0.8-beta, the DNA sequence reads were screened for microsatellite loci
 of two to six nucleotides and M13-tagged primers were designed for them. A
 total of 13 microsatellite loci was amplified. Amplified products were
 analyzed using the ABI 3130xL Genetic Analyzer at the University of
 Canterbury in New Zealand. Geneious v.6.1.8 (Biomatters, Auckland, New
 Zealand) was used to determine fragment lengths (bp) of the amplified
 loci.
description: Files include: 1.
 Readme_for_T_loheri_microsat.pdf 2.
 T_loheri_microsat.xlsx which contains scoring of 13 microsatellite loci
 for <i>Tetrastigma loheri</i> in Cebu based on the fragment
 length size of their respective alleles.
DOI: 10.5281/zenodo.18343575
title: Example data for IDLI analysis of nucleosome distortion

description: E14 mESC SAMOSA data, subsambled to 10,000 reads, in biological duplicate, for reproducing key results from Yang, Richter, and Wang et al. 2026. Starting files are forHMM, from previously published SAMOSA pipeline (GitHub - SAMOSA), aligned.ccs.bam also included for convenience. Outputs from clustering script using 100,000 nucleosomes per sample, including output plots, are included for comparison with your own results. Processing scripts, to go from forHMM to output shown here, are available on Github - IDLI and full raw data are available at GSE288933. 

Steps for processing example data:1. run Python script: HMMv2_IDLI_forZenodo.py (go from forHMM to HMMres and footprints)2. run interactive Jupyter notebook: IDLI_clustering_forZenodo.ipynb (performs IDLI and clustering)3. run R code: ClusterPlotting_forZenodo.Rmd (plots clustering output to visualize/group nucleosome types)

The first two steps assume file paths are stored in a sample reference sheet, an example is included in this repo but make sure to adjust to match your own directories and file paths.
DOI: 10.5281/zenodo.18343574
title: Example data for IDLI analysis of nucleosome distortion

description: E14 mESC SAMOSA data, subsambled to 10,000 reads, in biological duplicate, for reproducing key results from Yang, Richter, and Wang et al. 2026. Starting files are forHMM, from previously published SAMOSA pipeline (GitHub - SAMOSA), aligned.ccs.bam also included for convenience. Outputs from clustering script using 100,000 nucleosomes per sample, including output plots, are included for comparison with your own results. Processing scripts, to go from forHMM to output shown here, are available on Github - IDLI and full raw data are available at GSE288933. 

Steps for processing example data:1. run Python script: HMMv2_IDLI_forZenodo.py (go from forHMM to HMMres and footprints)2. run interactive Jupyter notebook: IDLI_clustering_forZenodo.ipynb (performs IDLI and clustering)3. run R code: ClusterPlotting_forZenodo.Rmd (plots clustering output to visualize/group nucleosome types)

The first two steps assume file paths are stored in a sample reference sheet, an example is included in this repo but make sure to adjust to match your own directories and file paths.
DOI: 10.7272/q6h70d1j
title: The natural history of fetal gallstones: A case series and updated literature review

description: Introduction: The incidence of fetal gallstones is estimated at 0.45% and
 its clinical relevance after birth remains unknown. This study aimed to
 describe the natural history of fetal gallstones and their clinical
 sequelae after birth. Methods: We queried a database of fetuses referred
 for second and third trimester sonograms performed for high-risk
 pregnancies, and identified cases with fetal gallstones (1996-2019).
 Demographics, prenatal/postnatal imaging findings, and clinical sequelae
 were collected. A literature review was performed according to PRISMA
 guidelines. Results: We screened approximately 200,000 obstetric
 sonograms; 34 fetuses were found to have cholelithiasis. The median
 gestational age at the time of US was 35 weeks (range 22 - 38). Fifty-six
 percent were female and 11.8% were twin pregnancies with one affected
 fetus. Median maternal age was 28 years (range 17-42). Eight fetuses
 underwent postnatal imaging and 4 had persistent cholelithiasis. There was
 one case of in utero demise. Two patients had structural anomalies (renal
 and cardiac) by US. A subset of 17 patients was followed long-term (range
 3-20 years), and none developed clinical sequelae from cholelithiasis.
 Discussion/Conclusions: No child developed postnatal clinical sequelae
 related to cholelithiasis identified in utero. Fetal cholelithiasis can be
 managed expectantly without follow-up imaging in asymptomatic patients.
DOI: 10.5061/dryad.44j0zpccb
title: A dimensionless parameter coupling the south and north roofs on the thermal environment of Chinese solar greenhouse: Ridge position ratio

description: This paper clarified the mechanism of the south and north roofs on the
 thermal environment of the Chinese solar greenhouse (CSG), using a new
 parameter: ridge position ratio (RPR), which can describe the dynamic
 dependency relationship between the south and north roofs. A mathematical
 model was established by using the method of combining computational fluid
 dynamics (CFD) with experiments, which then was used to analyze the effect
 of RPR on the thermal environment of the CSG. Based on this model, we
 compared the temperature distributions of the greenhouse with different
 RPR. Furthermore, the effects of different RPR on the amount of solar
 energy that entered the greenhouse were studied. Finally, the effects of
 different RPR on heat released capacity of the greenhouse envelopes at
 different moments were analyzed. The results showed the decline rate of
 the maximum temperature of each part in different RPR intervals increased
 as the increase of RPR during the daytime. The occurrence time of the
 maximum air temperature will be delayed when RPR increases to 0.3. As RPR
 increases, the heat storage layer of the soil gradually becomes thinner,
 but that of the north wall remains unchanged. RPR has a relatively small
 effect on the minimum temperature in each part of the greenhouse during
 the nighttime. Mathematical models of the relationships between RPR and
 the solar energy that entered the greenhouse, the released heat energy of
 the enclosure structures were established, respectively. The results can
 provide theoretical guidance for the structural design of the CSG.
DOI: 10.5061/dryad.pnvx0k6k6
title: Kangaroos display gazing and gaze alternations during an unsolvable problem task

description: Domestication is generally assumed to have resulted in enhanced
 communication abilities between non-primate mammals and humans, although
 the number of species studied is very limited (e.g. cats, Felis catus;
 dogs, Canis familiaris; wolves, Canis lupus; goats, Capra hircus;
 horses, Equus caballus). In species without hands for pointing, gazing at
 humans when dealing with inaccessible food during an unsolvable task, and
 in particular gaze alternations between a human and the unsolvable task
 (considered forms of showing), are often interpreted as attempts at
 referential intentional communication. We report that kangaroos, marsupial
 mammals that have never been domesticated, actively gazed at an
 experimenter during an unsolvable problem task (10/11 kangaroos tested),
 thus challenging the notion that this behavior results from domestication.
 Nine of the ten kangaroos additionally showed gaze alternations between
 the unsolvable task and experimenter. We propose that the potential
 occurrence of these behaviors displayed towards humans has been
 underestimated, owing to a narrow focus on domestic animals, as well as a
 more general eutherian research bias.  
description: Video data were recorded during live observations of kangaroos (n
 = 11) during six training and one testing trial with an unsolvable task.
 Videos were analysed with BORIS v. 7.9.7 behavioural analysis software.
 The behaviours of six kangaroos were double coded by K.H.O and A.C.G.
 Behavioural observations including proportion of trial interacting with
 box and experimenter, and presence of gaze alternations between box and
 experimenter were exported to Microsoft Excel and statistically analysed
 with R Studio v.1.2.5042 using the 'tidyverse' package for data
 cleaning and visualisation, 'janitor' package for contingency
 tables, 'skimr' package for summary statistics.