cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fqz612k41
title: Data from: Global decline in the size of sea turtles

description: Changes in mean adult body size may be a universal response to global
 warming and sometimes lead to conservation concerns. We show that size
 reductions in sea turtles are now the norm and have another explanation.
 From 18,707 measurements of nester size (curve carapace length) spanning
 30 years from Redang Island (Malaysia), where nearly all nesting
 individuals have been tagged, we show that the mean size was initially
 fairly stable and then decreased by 4.0 cm from 100.8 cm in 2005 to 96.8
 cm in 2022, which likely translates to a change in mean mass from 120 kg
 to 105 kg. At the same time, nesting increased from around 300 to 2,000
 nests per year. Consistent with this finding of a size reduction in an
 expanding population, at 27 of 31 sites across the globe where changes in
 the mean size of nesting sea turtles have been assessed, mean size is
 decreasing, and the most marked decreases are at sites where population
 size is increasing most dramatically. Taken together, these focal and
 global findings suggest that an important driver of size reductions in sea
 turtles is an influx of small first-time nesters (neophytes) in expanding
 populations, and hence, size reductions are partially a consequence of
 successful sea turtle conservation measures and population recoveries. At
 the same time, the focal observations in Malaysia show that the mean size
 of neophytes has also been getting smaller over time: from 99.6 cm to 96.8
 cm between 2005-2022, likely because of a change in foraging environments.
 While smaller turtles have lower reproductive output, this negative
 consequence of decreases in nest size will often be more than offset by
 increases in nesting numbers that are occurring widely.
description: # Global decline in the size of sea turtles Dataset DOI:
 [10.5061/dryad.fqz612k41](10.5061/dryad.fqz612k41) ## Description of the
 data and file structure Throughout 1993–2022, the body size of nesting
 green turtles (*Chelonia mydas*) was assessed at the Chagar Hutang Turtle
 Sanctuary on Redang Island, Malaysia. Every time a turtle was encountered
 nesting, the curved carapace length (CCL) was measured and included in the
 database. ### Files and variables #### File: Hays\_Table\_S2.xlsx
 **Description:** The studies assembled from the literature that included
 information on changes in mean size and abundance. Species are the green
 sea turtle *Chelonia mydas* (Cm), hawksbill *Eretmochelys imbricata* (Ei),
 leatherback *Dermochelys coriacea* (Dc), loggerhead *Caretta caretta*
 (Cc), and olive ridley *Lepidochelys olivacea* (Lo). NA means that the
 parameter was not available for that study site and the study doesn't
 pose any risks to these species. #### File: Hays\_etal\_Table\_S1.xlsx
 **Description:** Raw measurements of CCL and whether the turtle was tagged
 that year (a neophyte or first-time nester) or has been tagged in a
 previous year (a remigrant). ##### Variables * Curve carapace length (cm)
 of nesting turtles  ## Code/software Microsoft Excel for Table S1 and
 Table S2
DOI: 10.5061/dryad.qfttdz0t9
title: Large yearly fluctuations in congregation sizes of migratory Danainae butterflies in the Western Ghats, India

description: We documented the overwintering congregations of migratory Danainae
 butterflies (Nymphalidae) over six migratory seasons in the threatened
 tropical forests of the Western Ghats, India. Congregation sizes
 fluctuated drastically (&gt;90%), indicating vulnerability to chance
 events. Continued monitoring is needed to explain these fluctuations and
 identify declining trends for timely conservation action.
description: # Data from: Large yearly fluctuations in congregation sizes of migratory
 Danainae butterflies in the Western Ghats, India Authors: P. A. Vinayan,
 M. A. Yathumon, Shivani Jadeja Publication Source and Year: Biotropica,
 2025 #### Description: This dataset contains two data files that can be
 used to replicate the analysis for Vinayan et al. 2025, Large yearly
 fluctuations in congregation sizes of migratory Danainae butterflies in
 the Western Ghats, India. See Methods section of paper Vinayan et al.
 (2025) for details of sampling. ### 1. Data file name:
 20250422\_butterfly\_congregation\_size\_raw\_data.csv #### Description:
 Metadata of raw data file with data on congregation sizes (number of
 butterflies) collected during the study period. Variable names are
 described below. *site - Unique name for each congregation site
 (Categorical variable) *lat - Latitude of congregation site, low
 resolution (Degrees) (Quantitative variable) *long - Longitude of
 congregation size, low resolution (Degrees) (Quantitative variable) *alt -
 Altitude of congregation size (meters above sea level) (Quantitative
 variable) *date - Date when congregation site was visited in dd-mm-yyyy
 format (Quantitative variable) *count - Number of butterflies estimated at
 congregation site. In some cases, the number of butterflies was not
 estimated when there were too few individuals compared to earlier visits.
 In such cases count was recorded as NA. (Quantitative variable) ### 2.
 Data file name:
 20250422\_butterfly\_congregation\_size\_processed\_data.csv ####
 Description: Metadata of processed data file with data used for analysis,
 which includes maximum congregation sizes (number of butterflies) in a
 season collected across six migratory seasons. Variable names are
 described below. *site - Unique name for each congregation site
 (Categorical variable) *date - Date when maximum number of butterflies of
 the migratory season were counted at a congregation site dd-mm-yyyy format
 (Quantitative variable) *count - Number of butterflies estimated at
 congregation site (Quantitative variable) *season - Season of migration
 based on calendar year of arrival. A season was from September to May and
 was denoted by the year of arrival of the butterflies. (Quantitative
 variable)
DOI: 10.15468/dl.t7f4a8
title: Occurrence Download

description: A dataset containing 12811 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Icaricia acmon"
 ]
}

 The dataset includes 12811 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004346-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.p8cz8wb2g
title: A conceptual disease cycle model to link the size of past and future epidemics

description: Populations of humans, animals, and plants face ongoing threats from
 infectious disease epidemics. While host–parasite coevolution plays a
 central role in shaping these dynamics, epidemics are often studied in
 isolation. I propose a simple ‘Disease Cycle’ model that connects past and
 future epidemic sizes within the context of environmental change and
 evolutionary feedbacks. Drawing on recent evo-epidemiological research, I
 highlight three key themes: (i) how epidemics influence the strength and
 direction of natural selection, (ii) how host and parasite diversity shift
 through evolving resistance and infectivity, and (iii) how genetic
 diversity in either population may affect future epidemic severity.
 Although gaps remain, current evidence supports this integrative model.
 Future research should explore how the Disease Cycle applies to non-model
 organisms with low coevolutionary potential. This framework encourages a
 more holistic view of epidemics as dynamic outcomes of host–parasite
 coevolution.
description: # A conceptual disease cycle model to link the size of past and future
 epidemics ## List of filenames * Figures.Rmd *
 word-styles-reference-01.docx ## Description of files * Figures.Rmd - code
 for producing figures 2 and 4C-D, which correspond to different ways of
 measuring epidemic size and how the maintenance of genetic diversity
 depends on the mode of coevolution, respectively (within fig 4, C and D
 correspond to gene-for-gene and matching-alleles type models,
 respectively). * word-styles-reference-01.docx - used to set the
 formatting style (inherited by .Rmd) ## Software versions and packages
 required to run the files * R version 4.3.2 (2023-10-31 ucrt) * tidyverse
 version 2.0.0 * dplyr version 1.1.4 * ggplot2 version 3.5.2 * gridExtra
 version 2.3 * ggfortify version 0.4.16 * extrafont version 0.19 *
 ggpattern version 1.1.4
DOI: 10.15468/dl.taf834
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sprattus antipodum",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 38 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004347-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pcbm7m
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plagiorhynchus ponticus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004348-260126135527185/datasets/export for details.
DOI: 10.15468/dl.28hwym
title: Occurrence Download

description: A dataset containing 1308 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "TaxonKey is Alouatta palliata",
 "Year 2015-2026"
 ]
}

 The dataset includes 1308 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004349-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b7dk3q
title: Occurrence Download

description: A dataset containing 7248 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Icaricia saepiolus"
 ]
}

 The dataset includes 7248 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004351-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2ngf1vj1b
title: 3D fluorescence dataset of tissue cleared pig cochlea

description: Tissue clearing and light-sheet fluorescence microscopy were applied for
 3D profiling of intact cochleae. However, the spiral ganglion neurons
 (SGNs) remain relatively understudied compared to hair cells and
 supporting cells, especially in large animal models. Here we: 1)
 introduced collagenase treatment to the current protocol of tissue
 clearing to enhance uniform antibody staining of SGNs within the pig
 cochlea, and 2) adopted a deep learning object detection model to locate
 and count SGNs in large 3D datasets via Spiner (Spiral ganglion neuron
 profiler). This is an example pig cochlea dataset for running the designed
 Spiner workflow. The dataset is structured by TeraStitcher
 compatible two-level hierarchy of folders, and the TIFF images can be
 opened with image tools (e.g., ImageJ) that support the TIFF
 format. 
description: A cochlea from a wild-type 6-8-week-old Yorkshire pig
 was cleared and stained using a modified BoneClear protocol. The cleared
 pig cochlea was imaged using a custom-built light sheet fluorescence
 microscope by illumination of 640 nm (anti-TuJ1, AF647), with a voxel size
 of 0.65 × 0.65 × 10 μm<sup>3</sup>. 
description: # 3D fluorescence dataset of tissue cleared pig cochlea ##
 6-8w-pig-cochlea-TuJ1 3D fluorescence image dataset of a tissue cleared
 pig cochlea of a 6-8-week-old wildtype Yorkshire pig, with TuJ1 labeling
 of spiral ganglion neurons. ## Description of the data and file structure
 This is an example dataset for running the
 [Spiner](https://doi.org/10.5281/zenodo.15273059) workflow. The dataset
 contains tiff images which can be opened with image tools (e.g., ImageJ)
 that support tiff format. Each tiff file, if not empty, is a fluorescence
 image (2048 × 2048) of the pig cochlea at certain location. The 3D dataset
 was acquired using a custom-built light sheet fluorescence microscope by
 illumination of 640 nm, with a voxel size of 0.65 × 0.65 × 10 μm^3. The
 corresponding staining information is shown below. | Primary | Secondary |
 | :-------: | :-------: | | anti-TuJ1 | AF647 | The files were structured
 by [TeraStitcher compatible two-level hierarchy of
 folders](https://github.com/abria/TeraStitcher/wiki/Supported-volume-formats#two-level-hierarchy-of-folders). The first level of 5 folders, named as YYYYYY (6 digits), contains a row of tiles. The second level of 5 folders, named as YYYYYY_XXXXXX (6 + 6 digits), contains a stack of images which share the same x and y coordinates. Each stack contains 291 images at different z locations, named as YYYYYY_XXXXXX_ZZZZZZ (6 + 6 + 6 digits). In total, there are 5 × 5 × 291 tiff files.
DOI: 10.5061/dryad.9ghx3ffvq
title: Hidden in plain sight: a new Cuscuta species from southwest Utah and northwest Arizona (section Californicae, subgenus Grammica, Convolvulaceae)

description: Cuscuta nuwuviana, a new species from southwest Utah and northwest Arizona
 is described and illustrated. The phylogenetic analyses revealed that the
 new species belongs to a subclade of sect. Californicae (subg. Grammica)
 that also includes C. draconella and C. decipiens. Although not
 statistically significant, a topological incongruence between the plastid
 and nuclear data suggests that C. draconella most likely resulted from the
 homoploid hybridization of C. nuwuviana and C. decipiens, accompanied by
 plastid introgression.  Optical and scanning electron microscopy
 were employed to morphologically distinguish C. nuwuviana from C.
 draconella and C. decipiens, and an identification key was provided. Field
 investigations allowed the description of the habitat and plant community
 of the new species, which is currently known from only two populations in
 which it parasitizes solely Gutierrezia microcephala (Asteraceae).
 Evolutionary relationships, infrastaminal scales, and the presence of
 floral stomatiferous protuberances in sect. Californicae are discussed.
description: # Hidden in plain sight: a new Cuscuta species from southwest Utah and
 northwest Arizona (section Californicae, subgenus Grammica,
 Convolvulaceae) Dataset DOI:
 [10.5061/dryad.9ghx3ffvq](10.5061/dryad.9ghx3ffvq) ## Description of the
 data and file structure Files are submitted in NEXUS format. Can be
 analyzed with PAUP* or similar software. Models of DNA evolution employed
 are provided. The best tree under ML criterion is provided for each file.
 ### Files and variables #### File: nucDNA-nuwuviana-13Nov202.nex
 **Description:** ITS and 26S rDNA sequences #### File:
 ptDNA-nuwuviana-13Nov2024.nex **Description:** trnLF and rbcL sequences ##
 Code/software SeAl used for alignment PAUP used for phylogenetic analyses
DOI: 10.5061/dryad.djh9w0wbg
title: Low osmotic pressure induces calcium response states

description: Osmotic pressure is critical for maintaining cellular homeostasis, but the
 mechanisms underlying osmotic responses remain incompletely understood. We
 show that acute osmotic changes regulate intracellular calcium
 concentration in three distinct modes.  In addition, low osmotic
 pressure induces calcium flux from the endoplasmic reticulum through
 ryanodine receptors and propagates calcium signals to neighboring cells
 through gap junctions. Here, we represented raw data of calcium response
 modes under different conditions.
description: # Low osmotic pressure induces calcium response states Dataset DOI:
 [10.5061/dryad.djh9w0wbg](10.5061/dryad.djh9w0wbg) ## Description of the
 data and file structure This dataset originates from a study investigating
 how acute osmotic pressure changes influence intracellular calcium
 signaling in mammalian cells. The research identifies three distinct
 calcium response patterns triggered by osmotic shifts and characterizes a
 unique, wave-like signaling mode that enables coordinated responses across
 neighboring cells. This signaling mode is proposed to contribute to the
 early stages of osmotic stress-related organ injury. ### Files and
 variables #### File: Fig_2_wave.avi,File:
 Fig_2_silence.avi,Fig_2_spontaneity.avi,Fig_2_wave2.avi
 **Description:** Live cell calcium videos. Silence mode - response to
 hypertonic solution: No calcium activation is observed after the
 stimulation with a hypertonic solution. Spontaneous activation mode: Cells
 exhibit an auto-activation response upon adding an isotonic solution,
 displaying a sparking-like activation pattern. Wave activation mode: Cell
 activation begins in one cell, spreads to neighboring cells, and shows
 activation spreading as a wave. The scale bar is 200 μm. ### Files and
 variables #### Files: Fig_3_HUVEC.avi, Fig_3_MDCK.avi, Fig_3_RPTEC.avi
 **Description:** Live cell calcium video. RPTEC, MDCK cells, and HUVEC：
 calcium spontaneous activation mode in these cells. The scale bar is 200
 μm. #### Files:
 Fig_4-C_right_RyR2_siRNA.avi,Fig_4-A_Ca_free.avi,Fig_4-A_Gap27.avi,Fig_4-A_JTV_519.avi,Fig_4-A_18A_GA.avi **Description:** Live cell calcium video. Blocking of RyR2 and gap junction with SiRNA, JTV-519, 18α-glycyrrhetinic acid (18A-GA), and Gap 27 inhibited wave activation mode. The scale bar is 200μm.
DOI: 10.5061/dryad.1c59zw47m
title: Annotated spiral ganglion neuron training data for object detection

description: Tissue clearing and light-sheet fluorescence microscopy were applied for
 3D profiling of intact cochleae. However, the spiral ganglion neurons
 (SGNs) remain relatively understudied compared to hair cells and
 supporting cells, especially in large animal models. Here we: 1)
 introduced collagenase treatment to the current protocol of tissue
 clearing to enhance uniform antibody staining of SGNs within the pig
 cochlea, and 2) adopted a deep learning object detection model to locate
 and count SGNs in large 3D datasets via Spiner (Spiral ganglion neuron
 profiler). This dataset contains the training, validation, and test data
 for the deep learning object detection model (RetinaNet) used in the
 Spiner workflow. Bounding boxes of SGNs are annotated in the
 dataset. 
description: # Annotated spiral ganglion neuron training data for object detection
 Training, validation, and test data for RetinaNet model training, with
 annotated bounding boxes for spiral ganglion neurons in fluorescence
 images. ## Description of the data and file structure This is the
 annotated data used for training the RetinaNet model in the
 [Spiner](https://doi.org/10.5281/zenodo.15273059) workflow. The trained
 RetinaNet model was used for the automated detection of spiral ganglion
 neurons in fluorescence images. The images in this dataset were acquired
 using light sheet fluorescence microscopes, in which the spiral ganglion
 neurons (SGNs) were immunostained with PGP9.5 or TuJ1 antibody or in the
 autofluorescence channel obtained with illumination at 488nm. The dataset
 contains three folders of images (for training, validation, and test
 respectively), bounding box annotations stored in three corresponding CSV
 files, and a "classes_0.csv" specifying the class label for
 model training. Details are shown below. | | Image Folder | Annotation CSV
 | | :--------: | :----------------: | :------------: | | Train |
 sgn-train-20231006 | sgn-train.csv | | Validation | sgn-val-20230927 |
 sgn-val.csv | | Test | sgn-test-20240109 | sgn-test.csv | In the
 annotation CSV, each line contains one annotation (a boung box) in the
 image, formatted as: `path/to/image,x1,y1,x2,y2,class_name`. *
 `path/to/image`: relative path to the image * `x1,y1`: top-left
 coordinates of the rectangular bounding box * `x2,y2`: bottom-right
 coordinates of the bounding box * `class_name`: the object label,
 'SGN' as in this dataset When an image does not contain any
 labeled objects, `x1`,`y1`,`x2`,`y2`,`class_name` are left empty and the
 annotation is: `path/to/image,,,,,`. In the "classes_0.csv", the
 class indexing information is provided: `SGN,0`. ## Code/Software The
 dataset can be directly used to train a RetinaNet object detection model
 using [fizyr/keras-retinanet](https://github.com/fizyr/keras-retinanet)
 (Python).
DOI: 10.5061/dryad.jwstqjqn3
title: Adult predation shapes the evolution of swimming performance in guppies (Poecilia reticulata)

description: Predation pressure plays an important role in shaping animal behaviour and
 physiology, driving prey species to evolve stronger escape strategies.
 Swimming performance is a key trait for many aquatic organisms to evade
 predation. It is therefore intuitive that increased predation pressure
 should select for faster swimming abilities when outswimming predators is
 a viable option for prey. However, experimental evidence allowing for a
 causal link between predation and the evolution of swimming performance is
 currently lacking. Here, we used artificial selection lines of guppies
 (Poecilia reticulata) based on predation survival to test the evolutionary
 relationship between predation pressure and swimming speed. We used a swim
 tunnel with an incremental increase in water flow to test critical
 swimming speed. Our results show that predation-line females, but not
 males, outperformed those of the control lines in critical swimming speed.
 We also found that in predation-line females, the variance in critical
 swimming speed was reduced in comparison to control-line females, which is
 congruent with directional selection against slow-swimming genotypes. This
 study provides experimental evidence for the evolutionary role of
 predation pressure in enhancing swimming performance and shaping
 behavioural adaptations in prey species.
description: ## Adult predation shapes the evolution of swimming performance in guppies
 (Poecilia reticulata) Dataset
 DOI: [https://doi.org/10.5061/dryad.jwstqjqn3](https://doi.org/10.5061/dryad.jwstqjqn3) Authors: Mingfang Yang, Hannah De Waele, Arjan P. Palstra, Alexander Kotrschal Contact: Mingfang Yang: [mingfang.yang@wur.nl](mailto:mingfang.yang@wur.nl) ## Overview This repository provides access to the data and source code used for the associated manuscript [Adult predation shapes the evolution of swimming performance in guppies (*Poecilia reticulata*)]. ## File List * ucrit_emale.csv: data for critical swimming speed in females * ucrit_male.csv: data for critical swimming speed in males * ucrit_alldata.csv: data for critical swimming speed (used for output the plot) #### Variable Descriptions: selection line = artificial selection line replicate = replicate within each selection line (C, P) group = group ind = individual in each group ucrit = critical swimming speed (cm/s) standard length = standard length for each fish (cm) rep = combine selection line and replicate sex = sex (F = female, M = male) ## Code/Software * data_analysis_swimming speed.R: R script used for data analysis * output.R: R script used to output the plot R version 4.4.2 (2024-10-31 ucrt) platform: x86_64-w64-mingw32