cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3444s
title: Data from: The genomics of recovery from coral bleaching

description: Ecological damage from periodic environmental extremes is often repaired
 in resilient ecosystems, but the rate of return to a non-damaged state is
 critical. Measures of recovery of communities include biomass,
 productivity and diversity, while measures of recovery of individuals tend
 to focus on physiological conditions and the return to normal metabolic
 functioning. Transcriptomics offers a window into the entire physiology of
 the organism under stress and can represent a holistic view of organismal
 recovery. In this study, we track the recovery of seven colonies of
 Acropora hyacinthus following a natural bleaching event. We identified a
 large environmental stress response in the field that involved
 approximately 20% of the host transcriptome. The transcriptome remained
 largely perturbed for at least six months after temperatures had cooled
 and four months after symbiont populations had recovered. Moreover, a
 small set of genes did not recover to previous expression levels even 12
 months after the event, about the time that normal growth rates resumed.
 This study is among the first to incorporate transcriptomics into a
 longitudinal dataset of recovery from environmental stress. The data
 demonstrate large and lasting effects on coral physiology long after
 environmental conditions return to normal and symbiont populations
 recover.
description: Dataset_S1Dataset_S2Dataset_S3Dataset_S4Dataset_S5Dataset_S6Dataset_S7merged_countsRaw counts matrix based on mapping with Bowtie2. Data is not normalized.snps.bleaching_responsesingle nucleotide polymorphism genotype matrix for all tissue samples used in study (n=35 libraries).
DOI: 10.7284/166979
title: Multibeam Echosounder data collected during research cruise SKQ202519S using a Kongsberg EM710 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5061/dryad.nq3fp
title: Data from: Using human vision to detect variation in avian coloration: How bad is it?

description: Assessing variation in animal coloration is difficult as animals differ in
 their visual system properties. This has led some to propose that human
 vision can never be used to evaluate coloration, yet many studies have a
 long history of relying on human vision. To reconcile these views, we
 compared the reflectance spectra of preserved avian plumage elements with
 two measures that are humans biased: RGB values from digital photographs
 and the corresponding reflectance spectra from a field guide. We measured
 73 plumage elements across 14 bird species. The field guide reflectance
 spectra were drastically different from that of the actual birds,
 particularly for blue elements. However, principal components analyses on
 all three data sets indicated remarkably similar data structure. We
 conclude that human vision can detect much of the variation in coloration
 in the visible range, providing fodder for subsequent studies in ecology,
 evolution, behavior, and visual ecology.
description: Bergeron_Fuller_Actual.reflectance_Guide.reflectance_RGBvaluesThis excel file contains 3 sheets. The first sheet contains the average reflectance values from 300 to 750 nm (in 5nm steps) for the 'actual birds' from a museum. The second sheet contains the average reflectance values from 300 to 750 nm (in 5nm steps) for 'field guide' birds. The third sheet contains the average RGB values for the 'actual birds' from a museum. For each data type (actual reflectance, field guide reflectance, RGB), the sheets contain data for the same combination of species, sex, and patch type (e.g., wing, tail, etc.).Data_for_Dryad_means.xlsxReflectanceSpectra.Actual.v.GuideThis powerpoint file contains graphs showing the actual and field guide reflectance for all 73 species-sex-patch combinations.AllReflectanceSpectra.pptxSupplemental_Hue_AnalysesThis is an additional analysis of variation in animal coloration. In the original manuscript, we analyzed all of the data across all 73 combinations of species-sex-patch type. Here, we performed a more difficult analysis and analyzed only the reflectance curves from a single hue type (e.g., red).
DOI: 10.5061/dryad.83h1h
title: Data from: Temperature-dependent growth and fission rate plasticity drive seasonal and geographic changes in body size in a clonal sea anemone

description: The temperature-size rule is a commonly observed pattern where adult body
 size is negatively correlated with developmental temperature. In part,
 this may occur as a consequence of allometric scaling, where changes in
 the ratio of surface area to mass limit oxygen diffusion as body size
 increases. As oxygen demand increases with temperature, a smaller body
 should be favored as temperature increases. For clonal animals, small
 changes in growth and/or fission rate can rapidly alter the average body
 size of clonal descendants. Here I test the hypothesis that the clonal sea
 anemone Diadumene lineata is able to track an optimal body size through
 seasonal temperature changes using fission rate plasticity. Individuals
 from three regions (Florida, Georgia, and Massachusetts) across the
 species’ latitudinal range were grown in a year-long reciprocal common
 garden experiment mimicking seasonal temperature changes at three sites.
 Average body size was found to be smaller and fission rates higher in
 warmer conditions, consistent with the temperature-size rule pattern.
 However, seasonal size and fission patterns reflect a complex interaction
 between region-specific thermal reaction norms and the local temperature
 regime. These details provide insight into both the range of conditions
 required for oxygen limitation to contribute to a negative correlation
 between body size and temperature and the role that fission rate
 plasticity can play in tracking a rapidly changing optimal phenotype.
description: Data - Seasonal and
 geographic temperature effects on D. lineataThis excel file contains
 data from all laboratory and field activities reported in this
 publication. A metadata tab is included with descriptions of all column
 heads and variables used.2017sep2 - Recip transplant
 data for Dryad.xlsx
DOI: 10.5061/dryad.h4b5d
title: Data from: Competing opinion diffusion on social networks

description: Opinion competition is a common phenomenon in real life, such as opinions
 on controversial issues or political candidates, however modeling the
 competition remains largely unexplored. To bridge this gap, we propose a
 model of competing opinion diffusion on social networks taking into
 account the degree-dependent fitness or persuasiveness.We study the
 combined influence of social networks, individual fitnesses and
 attributes, as well as mass media on people’s opinions, and find that both
 social networks and mass media act as amplifier in opinion diffusion for
 which the amplifying effect can be quantitatively characterized. We
 analytically obtain the probability that each opinion will ultimately
 pervade the whole society when there are no committed people in networks,
 and the final proportion of each opinion at the steady state when there
 are committed people in networks. The results of numerical simulations
 show good agreement with those obtained through analytical approach. This
 study provides insight into the collective influence of individual
 attributes, local social networks and global media on opinion diffusion,
 and contributes to a comprehensive understanding of competing diffusion
 behaviors in real world.
description: The Matlab
 codecode.rar
DOI: 10.17632/tsm2tyfh7h
title: Effect of Pelvic Proprioception Training on Low Back Pain and Functional Mobility in Multiparous women : A Randomized Controlled Trial

description: This dataset contains anonymized clinical data collected from a randomized controlled trial conducted to evaluate the effect of pelvic proprioception training on low back pain and functional mobility in multiparous women with chronic low back pain. A total of 50 participants were initially recruited using simple random sampling, out of which 44 participants completed the study after accounting for dropouts. Participants were randomly allocated into two groups: an experimental group (pelvic proprioception training with conventional physiotherapy) and a control group (conventional physiotherapy only). Baseline and post-intervention data were collected over a two-week intervention period. The dataset includes demographic variables (age, body mass index, obstetric score), group allocation, and outcome measures assessed using the Numeric Pain Rating Scale (NPRS) for pain intensity and the Oswestry Disability Index (ODI) for functional mobility. All measurements were recorded at baseline (pre-test) and after completion of the intervention (post-test). The dataset is intended for reproducibility, secondary analysis, and comparison of conservative physiotherapy interventions in multiparous women with chronic low back pain.
Eligible participants were multiparous women aged above 18 years with chronic low back pain persisting for more than six months postpartum. Participants were recruited from physiotherapy outpatient departments after obtaining written informed consent. Baseline assessment included demographic details, obstetric history, pain intensity measured using NPRS, and functional disability assessed using ODI. Following baseline assessment, participants were randomized into either the experimental or control group using a lottery method. The control group received conventional physiotherapy exercises, while the experimental group received pelvic proprioception training along with conventional exercises. Post-intervention assessments using the same outcome measures were conducted after two weeks.
DOI: 10.5061/dryad.q5qm1
title: Data from: Take-off engine particle emission indices for in-service aircraft at Los Angeles International Airport

description: We present ground-based, advected aircraft engine emissions from flights
 taking off at Los Angeles International Airport. 275 discrete engine
 take-off plumes were observed on 18 and 25 May 2014 at a distance of 400 m
 downwind of the runway. CO2 measurements are used to convert the aerosol
 data into plume-average emissions indices that are suitable for modelling
 aircraft emissions. Total and non-volatile particle number EIs are of
 order 1016–1017 kg−1 and 1014–1016 kg−1, respectively.
 Black-carbon-equivalent particle mass EIs vary between 175–941 mg kg−1
 (except for the GE GEnx engines at 46 mg kg−1). Aircraft tail numbers
 recorded for each take-off event are used to incorporate aircraft- and
 engine-specific parameters into the data set. Data acquisition and
 processing follow standard methods for quality assurance. A unique aspect
 of the data set is the mapping of aerosol concentration time series to
 integrated plume EIs, aircraft and engine specifications, and
 manufacturer-reported engine emissions certifications. The integrated data
 enable future studies seeking to understand and model aircraft emissions
 and their impact on air quality.
description: LAX-Ground-Summary_TP_20140518_R01_thru20140525Assimilated aircraft engine test point data containing aircraft and engine specifications, measured particle emissions indices, and engine certification data. Each test point corresponds to an aircraft take-off event on either 18 or 25 May 2014.LAX-Ground-Summary_TS_20140518_R01_thru20140525Time series data collected on 18 May 2014 and 25 May 2014. Includes environmental data and particle and carbon dioxide concentrations.LAX-Ground-ProcessingCode_R01Data analysis code written in 'R' to generate the summary statistics and figures associated with the Data Descriptor for this data set.
DOI: 10.17632/tsm2tyfh7h.1
title: Effect of Pelvic Proprioception Training on Low Back Pain and Functional Mobility in Multiparous women : A Randomized Controlled Trial

description: This dataset contains anonymized clinical data collected from a randomized controlled trial conducted to evaluate the effect of pelvic proprioception training on low back pain and functional mobility in multiparous women with chronic low back pain. A total of 50 participants were initially recruited using simple random sampling, out of which 44 participants completed the study after accounting for dropouts. Participants were randomly allocated into two groups: an experimental group (pelvic proprioception training with conventional physiotherapy) and a control group (conventional physiotherapy only). Baseline and post-intervention data were collected over a two-week intervention period. The dataset includes demographic variables (age, body mass index, obstetric score), group allocation, and outcome measures assessed using the Numeric Pain Rating Scale (NPRS) for pain intensity and the Oswestry Disability Index (ODI) for functional mobility. All measurements were recorded at baseline (pre-test) and after completion of the intervention (post-test). The dataset is intended for reproducibility, secondary analysis, and comparison of conservative physiotherapy interventions in multiparous women with chronic low back pain.
Eligible participants were multiparous women aged above 18 years with chronic low back pain persisting for more than six months postpartum. Participants were recruited from physiotherapy outpatient departments after obtaining written informed consent. Baseline assessment included demographic details, obstetric history, pain intensity measured using NPRS, and functional disability assessed using ODI. Following baseline assessment, participants were randomized into either the experimental or control group using a lottery method. The control group received conventional physiotherapy exercises, while the experimental group received pelvic proprioception training along with conventional exercises. Post-intervention assessments using the same outcome measures were conducted after two weeks.
DOI: 10.5061/dryad.n7n85
title: Data from: Effective online Bayesian phylogenetics via sequential Monte Carlo with guided proposals

description: Modern infectious disease outbreak surveillance produces continuous
 streams of sequence data which require phylogenetic analysis as data
 arrives. Current software packages for Bayesian phylogenetic inference are
 unable to quickly incorporate new sequences as they become available,
 making them less useful for dynamically unfolding evolutionary stories.
 This limitation can be addressed by applying a class of Bayesian
 statistical inference algorithms called sequential Monte Carlo (SMC) to
 conduct online inference, wherein new data can be continuously
 incorporated to update the estimate of the posterior probability
 distribution. In this paper we describe and evaluate several different
 online phylogenetic sequential Monte Carlo (OPSMC) algorithms. We show
 that proposing new phylogenies with a density similar to the Bayesian
 prior suffers from poor performance, and we develop guided proposals that
 better match the proposal density to the posterior. Furthermore, we show
 that the simplest guided proposals can exhibit pathological behavior in
 some situations, leading to poor results, and that the situation can be
 resolved by heating the proposal density. The results demonstrate that
 relative to the widely-used MCMC-based algorithm implemented in MrBayes,
 the total time required to compute a series of phylogenetic posteriors as
 sequences arrive can be significantly reduced by the use of OPSMC, without
 incurring a significant loss in accuracy.
description: Supplementary
 resultsThis file contains
 supplementary figures and tables referenced in the main
 manuscript.supplement.pdf
DOI: 10.5061/dryad.d8j34
title: Data from: Cape buffalo (Syncerus caffer caffer) social dynamics in a flood-pulsed environment

description: Fission-fusion social dynamics allow animals to respond to short-term
 environmental changes by temporarily adjusting group size. The drivers of
 such complex social dynamics are thought to relate to resource
 availability, density effects and social interactions. During 2008-09, we
 collared 15 Cape buffalo (Syncerus caffer caffer) cows in different groups
 in the Okavango Delta, Botswana, to study social dynamics in a
 flood-pulsed ecosystem. Hierarchical clustering identified 2
 subpopulations, 1 migratory and 1 resident. We calculated Utilization
 Distribution Overlap Index (UDOI) and number and duration of fusion events
 between buffalo dyads and related them to environmental variables. Number
 of fusion events and duration of fusion periods did not vary seasonally,
 total fusion time varied seasonally and annually, and UDOI varied with
 year and subpopulation. Fission events were more likely in cluttered
 habitats, but only in the late flood season. There was more open habitat
 in home range overlap (HRO) areas than home ranges (HR) in most seasons.
 Pan density in rainy season HROs was lower and higher than in HRs in 2008
 and 2009, respectively, and in all flood seasons HRO areas were closer to
 permanent water than HRs, suggesting that fusion occurred when buffalo
 congregated on resources. Whereas previous studies described large herds
 that sometimes split, we identified numerous smaller groups that
 occasionally fused, indicating a very fluid social system. Our results
 highlight the need to understand social system flexibility to ensure
 appropriate management and understand the varying impacts of environmental
 and anthropogenic effects on subpopulations within the same geographic
 area.
description: Data for Cape buffalo
 social dynamics in a flood pulsed ecosystemThis data file contains
 1. Distances &lt;1000m between dyads of collared buffalo; 2. Utilization
 Distribution Overlap Indices and number of fusion events; 3. Data matrices
 for seasonal DCG social network calculations; 4. Details on each fusion
 event; 5. Habitat types at fission and fusion locations; 6. Habitat
 composition in home ranges and home range overlap areas; 7. Distance to
 water from fission and fusion locations; 8. Distance to water from home
 ranges and home range overlap areas
DOI: 10.17632/kt4vwsxps4
title: Single-Cell SERS Imaging Reveals Lipid-Associated Water Metabolism and Dormant Tumor Cell Signatures in Living Cancer Cells, Ruiyao Ma Study of Cellular Water Metabolism

description: Research Hypothesis
This study hypothesized that integrating surface-enhanced Raman scattering (SERS), deuterium oxide (D₂O) labeling, and a custom micropore chip would enable real-time, high-resolution visualization of intracellular water metabolism. It aimed to distinguish metabolic differences between cancer/normal cells and metastatic/dormant tumor cells, identify subcellular water metabolic hubs, and monitor cisplatin (CDDP)-induced metabolic changes.
Data Collection
Platform: Micropore chips (32 μm diameter, 25 μm depth) coated with 200 nm Ag and 100 nm Au, achieving an enhancement factor (EF) of 1.18×10⁴ vs. glass slides.
Cells: Normal (H8), cervical cancer (HeLa), metastatic (H1915-BrM), and dormant (H1915-DM) cells, cultured in D₂O-containing medium (D-DMEM) or treated with 1 mM CDDP.
Imaging: 2D/3D SERS imaging (532 nm laser) at 0–48 h; data processed via Lorentzian fitting, 7 similarity algorithms (e.g., SNR, pHash), and PCA.
Key Findings
1. Cancer cells (HeLa) showed faster D₂O uptake and higher C-D signal intensity than normal cells (H8), with a 48-hour metabolic cycle.
2. Lipid-rich cytoplasmic regions were primary water metabolic hotspots, with C-D signals strongly correlating with lipids (2840–2870 cm⁻¹) and weakly with DNA.
3. CDDP suppressed water metabolism, reduced DNA content (785 cm⁻¹ peak), and altered lipid/protein metabolism (1446, 2892 cm⁻¹ peaks).
4. Dormant cells (H1915-DM) exhibited low but sustained water metabolism, elevated proline/tyrosine, and resistance to CDDP, unlike metastatic cells (H1915-BrM).
Interpretation
C-D bond intensity reflects water incorporation into biomolecules, with lipid-rich regions driving metabolic water exchange. The platform resolves subcellular and single-cell heterogeneity, enabling drug response monitoring and dormant cell identification. It offers a non-invasive tool for studying tumor metabolism and developing precision therapies.
DOI: 10.5061/dryad.1d6d2
title: Data from: Distance-dependent seedling mortality and long-term spacing dynamics in a neotropical forest community

description: Negative distance dependence (NDisD), or reduced recruitment near adult
 conspecifics, is thought to explain the astounding diversity of tropical
 forests. While many studies show greater mortality at near vs. far
 distances from adults, these studies do not seek to track changes in the
 peak seedling curve over time, thus limiting our ability to link NDisD to
 coexistence. Using census data collected over 12 years from central Panama
 in conjunction with spatial mark-connection functions, we show evidence
 for NDisD for many species, and find that the peak seedling curve shifts
 away from conspecific adults over time. We find wide variation in the
 strength of NDisD, which was correlated with seed size and canopy
 position, but other life-history traits showed no relationship with
 variation in NDisD mortality. Our results document shifts in peak seedling
 densities over time, thus providing evidence for the hypothesized spacing
 mechanism necessary for diversity maintenance in tropical forests.
description: seedling survival from
 2001 to 2013seedlings.csv
DOI: 10.17632/kt4vwsxps4.1
title: Single-Cell SERS Imaging Reveals Lipid-Associated Water Metabolism and Dormant Tumor Cell Signatures in Living Cancer Cells, Ruiyao Ma Study of Cellular Water Metabolism

description: Research Hypothesis
This study hypothesized that integrating surface-enhanced Raman scattering (SERS), deuterium oxide (D₂O) labeling, and a custom micropore chip would enable real-time, high-resolution visualization of intracellular water metabolism. It aimed to distinguish metabolic differences between cancer/normal cells and metastatic/dormant tumor cells, identify subcellular water metabolic hubs, and monitor cisplatin (CDDP)-induced metabolic changes.
Data Collection
Platform: Micropore chips (32 μm diameter, 25 μm depth) coated with 200 nm Ag and 100 nm Au, achieving an enhancement factor (EF) of 1.18×10⁴ vs. glass slides.
Cells: Normal (H8), cervical cancer (HeLa), metastatic (H1915-BrM), and dormant (H1915-DM) cells, cultured in D₂O-containing medium (D-DMEM) or treated with 1 mM CDDP.
Imaging: 2D/3D SERS imaging (532 nm laser) at 0–48 h; data processed via Lorentzian fitting, 7 similarity algorithms (e.g., SNR, pHash), and PCA.
Key Findings
1. Cancer cells (HeLa) showed faster D₂O uptake and higher C-D signal intensity than normal cells (H8), with a 48-hour metabolic cycle.
2. Lipid-rich cytoplasmic regions were primary water metabolic hotspots, with C-D signals strongly correlating with lipids (2840–2870 cm⁻¹) and weakly with DNA.
3. CDDP suppressed water metabolism, reduced DNA content (785 cm⁻¹ peak), and altered lipid/protein metabolism (1446, 2892 cm⁻¹ peaks).
4. Dormant cells (H1915-DM) exhibited low but sustained water metabolism, elevated proline/tyrosine, and resistance to CDDP, unlike metastatic cells (H1915-BrM).
Interpretation
C-D bond intensity reflects water incorporation into biomolecules, with lipid-rich regions driving metabolic water exchange. The platform resolves subcellular and single-cell heterogeneity, enabling drug response monitoring and dormant cell identification. It offers a non-invasive tool for studying tumor metabolism and developing precision therapies.