cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p8cz8wb3r
title: Code from: Source–sink dynamics explains the coexistence of the invasive pest <em>Dryocosmus kuriphilus</em> and its biological control agent <em>Torymus sinensis</em> across French Eastern Pyrenees

description: This dataset includes the codes we developed to model the spread of a
 gall-forming hymenopteran parasite of chestnut trees, Dryocosmus
 kuriphilus, and its control agent, Torymus sinensis, across 23 natural
 forest sites located in the French Eastern Pyrenees. The model
 of D. kuriphilus - T. sinensis interactions was derived from the
 founding host-parasitoid model proposed by Nicholson-Bailey and adapted to
 account for the effects of the bottom-up and top-down factors regulating
 the invasion of D. kuriphilus. The first code then corresponds to the
 modelling of D. kuriphilus and T. sinensis population dynamic within one
 site, while the second code is an extension of the within-site modelling
 into a two-site model, allowing for the study of the effects of the pest
 and control agent dispersal between two sites on their population
 dynamics.
description: # Code from: Source–sink dynamics explains the coexistence of the invasive
 pest *Dryocosmus kuriphilus* and its biological control agent *Torymus
 sinensis* across French Eastern Pyrenees Dataset DOI:
 [10.5061/dryad.p8cz8wb3r](10.5061/dryad.p8cz8wb3r) ## Description of the
 data and file structure We developed an extension of the founding
 host-parasitoid mathematical model proposed by Nicholson-Bailey to account
 for the effects of the bottom-up and top-down factors regulating the
 invasion of *D. kuriphilus*, and its control by *T. sinensis*. To identify
 these effects and quantify their impact on the *D. kuriphilus* -*T.
 sinensis*. population dynamics , we performed a 2 years field study and
 combined ecological, genomic, statistical and epidemiological approaches.
 We then extended our model to investigate the effect of the pest and the
 control agent dispersal between two sites on their dynamics interaction.
 ### Files and variables #### File: Two_sites.R **Description:** Code for
 the Two-sites dynamical model #### File: Within_site.R
 **Description:** Code for the within site dynamical model ## Code/software
 Codes of the within site and two-sites model can be read using R version
 4.5.1 with the "tidyverse" package. Both codes are annotated to
 make them easier to understand.
DOI: 10.5061/dryad.wdbrv162f
title: Camera-traps and the city: spatiotemporal adaptations of wildlife to urban environments

description: Urbanisation significantly reshapes ecosystems, affecting biodiversity and
 profoundly altering wildlife behaviour. Nonetheless, our understanding of
 the environmental drivers of behavioural changes, as well as the
 concurrent effects upon interspecific interactions, remain limited. Here,
 we investigated the spatiotemporal adaptations of wildlife to urban
 environments, with a focus on predator-prey dynamics in response to
 urban-specific environmental characteristics, adopting a year-round
 camera-trapping campaign within the metropolitan area of Florence, Italy.
 Temporal and spatial activity patterns of predators, prey, humans, and
 domestic animals, as well as their relative overlaps, were quantified,
 revealing a marked increase in nocturnal behaviour among most wildlife
 species compared to their conspecifics in rural areas. A wide temporal
 overlap was recorded between predators and most of their prey (70–93%),
 yet limited to night hours. Contrary to more natural settings, the effects
 of moon phases were negligible upon urban mammals, and the occurrence of
 humans was a strong driver of wildlife spatiotemporal behaviour. Species
 richness was also shaped by environmental factors, with artificial light
 negatively impacting diversity, whereas the presence of herbaceous edges
 enhanced diversity of local mammal assemblages. Suburban regions emerged
 as biodiversity hotspots, highlighting the critical role of green
 corridors and thoughtful urban planning in mitigating biodiversity loss.
 Our findings analysed the complex interface between human activity and
 wildlife in urban landscapes, showing how urbanisation reshapes
 predator-prey dynamics and ecological interspecific interactions.
 Camera-trapping proved to be a fundamental tool, addressing observational
 challenges and providing an unbiased, detailed perspective on urban
 wildlife adaptations.
description: # Camera-traps and the city: spatiotemporal adaptations of wildlife to
 urban environments. --- We have submitted our raw data
 (**UrbanDataset.xlsx**). ## Descriptions ### **UrbanDataset.xlsx** *
 *Date*: date of the event * *MoonPhase*: Moon phase related to the event
 (1-4) * *Epact*: Epact day (1-29) * *SkyCoverage*: percentage of sky
 coverage * *Hour*: Solar hour of the event * *Openness*: Openness of the
 dominant habitat * *NightDay*: Nocturnal (N) or diurnal (D) event *
 *Site*: Camera trap location * *Year*: Year of the event * *Season*:
 Astronomical season of the event * *Sps*: Common name of the species
 recorded in each event * *N_ind*: Number of individuals recorded in the
 event
DOI: 10.6084/m9.figshare.30609653.v1
title: Weighted Conformational Ensembles of IDRs in BMRB entries

description: We performed NMR-based reweighting on the overlapped regions between the BMRB entries and sequences from IDRome database. We provide representative conformers—with all heavy atoms included—ranked in descending order and collectively accounting for 99.99% of the total weight.Currently under review titled as "Accurate Conformational Ensembles of Intrinsically Disordered Proteins using Reweighting based on NMR Chemical Shift"
DOI: 10.5061/dryad.t4b8gtjf8
title: Leaf conditions affect the landing success of fallen tropical ants

description: Falling to the ground is hazardous for arboreal ants. Workers of six ant
 species dropped onto leaves had the lowest landing success on inclined and
 wet leaves; epiphyll presence and ant body size had no effect.
 Consequently, landing on leaves in wet forests apparently is challenging
 for arboreal ants.
description: # Leaf conditions affect the landing success of fallen tropical ants
 Dataset DOI: [10.5061/dryad.t4b8gtjf8](10.5061/dryad.t4b8gtjf8) ##
 Description of the data and file structure Data for 'Leaf conditions
 affect the landing success of fallen tropical ants' ### Files and
 variables #### File: antdrop_trialdata.csv **Description:**  #####
 Variables * species: species of ant used in trial * colony: colony code
 for ant used in trial * ant_id: unique ID code of ant used in trial;
 inherently contains colony ID code * temp_c: ambient temperature in
 Celsius * headwidth_mm: head width of ant in millimeters for C. atratus *
 dry_wgt_g: dry weight of ant in grams * T1_0degree_clean_dry: experimental
 scenario 1: leaf at 0 degrees, clean, and dry * T2_45degree_clean_dry:
 experimental scenario 2: leaf at 45 degrees, clean, dry *
 T3_0degree_clean_wet: experimental scenario 3: leaf at 0 degrees, clean,
 wet * T4_45degree_clean_wet: experimental scenario 4: leaf at 45 degrees,
 clean, wet * T5_0degree_lichen_dry: experimental scenario 5: leaf at 0
 degrees, epiphylls present, dry * T6_45degree_lichen_dry: experimental
 scenario 6: leaf at 45 degrees, epiphylls present, dry *
 T7_0degree_lichen_wet: experimental scenario 7: leaf at 0 degrees,
 epiphylls present, wet * T8_45degree_lichen_wet: experimental scenario 8:
 leaf at 45 degrees, epiphylls present, wet
DOI: 10.15468/dl.52q86x
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Intoshia leptoplanae",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004452-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g4f4qrg2w
title: Room-temperature persistent photoconductivity of KTaO<sub>3</sub>

description: This dataset contains IR spectra of potassium tantalate (KTO3).
 KTaO3 single crystals annealed in hydrogen exhibit room
 temperature persistent photoconductivity (PPC). The oxygen-poor annealing
 environment creates oxygen vacancies that are substituted with hydrogen. A
 photon of energy near the indirect band gap (3.65 eV) can excite this
 defect, resulting in free electrons in the conduction band. This causes an
 increase in n-type conductivity of 4 orders of magnitude with a recovery
 time of 2-4 years. Hydrogen leaves the O site and forms an O–H bond that
 is observed by IR spectroscopy. In addition to the O-H peak, the IR
 spectra contain information about free-carrier absorption.
description: # Room-temperature persistent photoconductivity of KTaO~3~ Dataset DOI:
 [10.5061/dryad.g4f4qrg2w](10.5061/dryad.g4f4qrg2w) ## Description of the
 data and file structure IR spectroscopy data. **Fig2a.csv** Transmission
 (T) versus wavenumber (cm-1) after exposure to an LED with a given
 wavelength (nm). Each header is cm-1 or T for a particular LED exposure.
 X40 refers to spectra that were multiplied by a factor of 40. *Headers:*
 375 nm (cm-1) 375 nm (T) 340 nm (cm-1) 340 nm (T) 340 nm x40 (cm-1) 340 nm
 x40 (T) 300 nm x40 (cm-1) 300 nm x40 (T) 275 nm x40 (cm-1) 275 nm x40 (T)
 **Fig2b.csv** Absorbance versus wavenumber (cm-1). The ‘--' represent
 imaginary values due to taking the log of a negative number, and were
 excluded in the plot. *Headers:* cm-1 Absorbance **Fig3.csv** Absorbance
 versus wavenumber (cm-1), before and after polishing the sample.
 *Headers:* Before Polish (cm-1)  Before Polish (Absorbance)  After Polish
 (cm-1)      After Polish (Absorbance)
DOI: 10.5061/dryad.wdbrv162j
title: Supplementary tables from: Long-term outcomes of patients diagnosed with differentiated thyroid cancer in childhood and young adulthood

description: Rates of pediatric differentiated thyroid cancer (DTC) in the United
 States have been increasing while studies on this population remain
 limited by inconsistent age cut-offs, short follow-up periods, or relative
 lack of clinical data. In this manuscript, we report long-term
 outcomes in patients diagnosed with DTC at age 20 years old and younger.
 155 patients were included with a median age at diagnosis of 17 years (9
 to 20 years). The frequency of distant metastasis and larger tumor size
 were inversely related to age at diagnosis (overall stage p = 0.045,
 T-stage (size of the primary tumor ± invasion) p = 0.001). The median
 duration of follow-up was 16 years (1 to 63 years) and at last follow-up,
 52.3% of patients had excellent response and disease specific mortality
 was 0%. There was no difference in response to therapy based on histologic
 subtype or birth sex; however, younger age at diagnosis was associated
 with worse response (p = 0.046). Patients with over 50 years of follow-up
 (n = 9) had median of 36 years of stability, with progression occurring in
 6 out of 9 (67%) patients.
description: # Supplementary tables from: Long-term outcomes of patients diagnosed with
 differentiated thyroid cancer in childhood and young adulthood Dataset
 DOI: [10.5061/dryad.wdbrv162j](10.5061/dryad.wdbrv162j) ## Description of
 the data and file structure These tables contain demographic, staging,
 treatment, and response data of patients diagnosed with differentiated
 thyroid cancer at age 20 years or younger (who were enrolled in an IRB
 approved protocol) who had family history of thyroid cancer and of those
 who were diagnosed with additional cancers. Also contain clinical and
 PV/LPV information on a subset of patients.  ### Files and variables
 **Abbreviations:** DTC: differentiated thyroid cancer; PTC: papillary
 thyroid cancer; FTC: follicular thyroid cancer; FNMTC: familial non
 medullary thyroid cancer; RAI: radioactive iodine; mCi: millicurie; PV:
 pathogenic variant; LPV: likely pathogenic variant #### File:
 Supplemental_table1.csv **Description:**  Demographic, staging, treatment,
 and response data of the patients with family history of thyroid cancer.
 #### File: Supplemental_table2.csv **Description:** Demographic, staging,
 treatment, and response data of the patients diagnosed with additional
 cancers. #### File: Supplemental_table3.csv **Description:**  Clinical
 data and germline analysis (n=11). ## Code/software Notepad or equivalent
 is needed to view the files. ## Access information N/A ## Human subjects
 data All patients provided written informed consent to one or both
 IRB-approved biorepository protocols. Both consent forms include
 information about de-identified data being shared for educational or
 research purposes. No personally identifiable information is included in
 this submission.
DOI: 10.5061/dryad.2rbnzs7p2
title: Fluctuation of cellular differentiation in limb regeneration is regulated by Pde4b in urodele amphibians

description: Urodele amphibians, Pleurodeles waltl and Ambystoma mexicanum, have
 organ-level regeneration capability, such as limb regeneration.
 Multipotent cells are induced by an endogenous mechanism in amphibian limb
 regeneration. It is well known that dermal fibroblasts receive
 regenerative signals and turn into multipotent cells, called blastema
 cells. However, the induction mechanism of the blastema cells from matured
 dermal cells was unknown. We previously found that BMP2, FGF2, and FGF8
 (B2FF) could play sufficient roles in blastema induction in urodele
 amphibians. Here, we show that B2FF treatment can induce dermis-derived
 cells that can participate in multiple cell lineage in limb regeneration.
 We first established a newt dermis-derived cell line and confirmed that
 B2FF treatment on the newt cells provided plasticity in cellular
 differentiation in limb regeneration. To clarify the factors that can
 provide the plasticity in differentiation, we performed the interspecies
 comparative analysis between newt cells and mouse cells and found the
 Pde4b gene was upregulated by B2FF treatment only in the newt cells.
 Blocking PDE4B signaling by a chemical PDE4 inhibitor suppressed
 dermis-to-cartilage transformation and the mosaic knockout animals showed
 consistent results. Our results are a valuable insight into how dermal
 fibroblasts acquire multipotency during the early phase of limb
 regeneration via an endogenous program in amphibian limb regeneration.
description: # Fluctuation of cellular differentiation in limb regeneration is
 regulated by Pde4b in urodele amphibians Dataset DOI:
 [10.5061/dryad.2rbnzs7p2](10.5061/dryad.2rbnzs7p2) ## Description of the
 data and file structure The data were collected from the cultured cells
 with or without the proteins of interest.  The detail was described in the
 paper
 ([https://doi.org/10.1186/s40851-022-00190-6](https://doi.org/10.1186/s40851-022-00190-6))  * BF_1_S1_R1_001.fastq.gz ---- Newt cultured cells with BFF  * BF_2_S2_R1_001.fastq.gz---- Newt cultured cells with BFF (biological replication) * C1_S3_R1_001.fastq.gz---- Newt cultured cells without BFF (control) * C2_S4_R1_001.fastq.gz---- Newt cultured cells without BFF (control, biological replication) * Mouse.BFF_S4_R1_001.fastq.gz---- mouse cultured cells with BFF * Mouse.BFF.fastq.gz---- mouse cultured cells with BFF (biological replication) * Mouse.CTRL_S3_R1_001.fastq.gz---- mouse cultured cells without BFF * Mouse.CTRL.fastq.gz---- mouse cultured cells without BFF (biological replication) ## Code/software N/A ## Access information Data was derived from the following sources: * *Pleurodeles waltl* * *Mus musculus*
DOI: 10.15468/dl.rvet87
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Intoshia linei",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 8 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004453-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0cfxpnwfc
title: Sequencing method matters: Differential performance of DNA methylation data acquisition in epigenetic clock calibration

description: Age is an important trait, influencing an individual’s physiology,
 behavior, and survival probability. Epigenetic clocks offer a mechanism to
 estimate ages by generating accurate age estimates based on DNA
 methylation at particular CpG sites, which changes in a predictable manner
 over lifespan. Here, we compared the efficacy of two DNA methylation
 sequencing methods, whole genome enzymatic methyl sequencing (WGEM-seq)
 and epiRADseq, in calibrating epigenetic clocks for chestnut-crowned
 babbler (Pomatostomus ruficeps) nestlings (N = 56, aged 0-19 days).
 Epigenetic clocks using WGEM-seq data outperformed clocks using epiRADseq
 data, indicating that the lower resolution of epiRADseq does not allow for
 accurate clock calibration. Using WGEM-seq  data collected
 throughout a small fraction of the lifespan of chestnut-crowned babblers,
 we successfully calibrated a highly accurate epigenetic clock. These
 results open promising avenues for investigating the impact of early life
 environments and developmental stressors on aging. The insights gained
 from such studies can improve conservation and management strategies while
 deepening our understanding of avian life history strategies, ecology, and
 behavior.
description: # Sequencing method matters: Differential performance of DNA methylation
 data acquisition in epigenetic clock calibration Dataset DOI:
 [10.5061/dryad.0cfxpnwfc](10.5061/dryad.0cfxpnwfc) ## Description of the
 data and file structure Chestnut crowned babblers of known ages were bled
 between 0 and 2000 days old. DNA was extracted from blood samples and
 epiRADseq or whole genome enzymatic methylation was used to determine
 methylation of sites throughout the genome. Methylation was then used to
 generate epigenetic clocks. For both files, individual ID is listed in the
 header of each column, age in days is in the second row, and every value
 below that is the methylation at a particular CpG site for that
 individual. ### Files and variables #### File: epiRAD.csv
 **Description:** Data used to generate epigenetic clock with epiRADseq
 data. #### File: EMseq.csv **Description:** Data used to generate whole
 genome enzymatic methylation data. ## Code/software Both files are .csv
 files and can be opened with multiple software/apps.
DOI: 10.5281/zenodo.18365967
title: Dataset and code for mite trade-off paper

description: This is the dataset and code for mite trade-off paper.

 

Author list:

Mariana Reyes1†, Tanzil Malik1†, Ke-An Hung1, Syuan-Jyun Sun1* 

 

1International Degree Program in Climate Change and Sustainable Development, National Taiwan University, Taipei 106319, Taiwan

 

†These authors contributed equally to the study.

*Corresponding author: Syuan-Jyun Sun; email: sjs243@ntu.edu.tw
DOI: 10.5281/zenodo.18365968
title: Dataset and code for mite trade-off paper

description: This is the dataset and code for mite trade-off paper.

 

Author list:

Mariana Reyes1†, Tanzil Malik1†, Ke-An Hung1, Syuan-Jyun Sun1* 

 

1International Degree Program in Climate Change and Sustainable Development, National Taiwan University, Taipei 106319, Taiwan

 

†These authors contributed equally to the study.

*Corresponding author: Syuan-Jyun Sun; email: sjs243@ntu.edu.tw
DOI: 10.5061/dryad.n02v6wx9c
title: Antemortem diagnostic results for six bearded dragons (<em>Pogona vitticeps</em>) experimentally exposed to <em>Nannizziopsis guarroi</em>

description: Several fungal diagnostic assays may detect Nannizziopsis guarroir, the
 cause of mycotic dermatitis of lizards, in clinical cases, but the
 clinical performance of these assays has yet to be explored. Six adult
 bearded dragons were topically exposed to N. guarroi along the dorsal
 midline and serially sampled over five months as clinical cutaneous
 lesions developed. Diagnostic test results for fungal culture, qPCR, and
 NGS positivity and negativity are presented.
description: # Antemortem diagnostic results for six bearded dragons (*Pogona
 vitticeps*) experimentally exposed to *Nannizziopsis guarroi* Dataset DOI:
 [10.5061/dryad.n02v6wx9c](10.5061/dryad.n02v6wx9c) ## Description of the
 data and file structure ### Files and variables #### File:
 Supplementary_file_1-2.pdf **Description:** Antemortem diagnostic results
 for six bearded dragons (*Pogona vitticeps*) experimentally exposed to
 *Nannizziopsis guarroi*. Abbreviations include: DPIE = days post initial
 exposure; FC = fungal culture, PE = preexposure; NGS = next-generation
 sequencing; qPCR = quantitative polymerase chain reaction, + = positive, -
 = negative, C = contaminant, NP = not performed.
DOI: 10.5061/dryad.2jm63xt2v
title: Data from: A 3D-printed capillary tube holder for high-throughput chemotaxis assays

description: Bacterial chemotaxis is an important behavior to study to understand the
 spatial segregation of species in mixed communities and the assembly of
 host microbiomes. This is particularly relevant in the rhizosphere, where
 chemoattraction towards root exudates is an important determinant of plant
 colonization. However, current methods to screen chemoeffectors are
 limited in their throughput, creating a barrier to generating
 comprehensive datasets describing chemotactic profiles for species of
 interest. Here, we describe a novel, 3D-printed capillary tube holder
 approach, which enables up to 384 simultaneous capillary tube chemotaxis
 assays. We optimized and benchmarked our assay using Escherichia coli k12
 and Bacillus subtilis 3610 and their known chemoattractants: serine and
 aspartate. We then tested the threshold concentration of these
 chemoattractants in our assay and found we could detect chemoattraction
 towards concentrations spanning multiple orders of magnitude. In this
 paper, we describe our novel high-throughput chemotaxis assay in detail
 and provide the necessary files for 3D printing the capillary tube holder.
description: # Data from: A 3D-printed capillary tube holder for high-throughput
 chemotaxis assays Dataset DOI:
 [10.5061/dryad.2jm63xt2v](10.5061/dryad.2jm63xt2v) ## Description of the
 data and file structure #### File: Supplementary_files_S3.stl 3D printer
 design file to print the 384-well capillary tube holders used in the
 publication titled "A 3D-Printed Capillary Tube Holder for
 High-Throughput Chemotaxis Assays." ## Code/software Preview app or
 MeshLab can be used to open and view this design file.