cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.60593/ur.d.31100752.v1
title: "Developmental exposure to a PFAS mixture impairs the anamnestic response to influenza A virus infection in mice": T follicular helper (Tfh) cell panel FCS files.

description: Flow cytometry standard (FCS) files for staining panel to identify CD8+ T cells, CD4+ T cells, and T follicular helper cells on days 0, 9, 70, 75, and 77 relative to primary influenza A virus infection. In the publication, the analyzed data from these files is presented in Figure 3 and Tables S5 and S6 (CD8+ T cells and CD4+ T cells) and Figure 4 and Tables S7 and S8 (Tfh cells).
DOI: 10.5061/dryad.4mw6m90h0
title: Bayesian inference under the multispecies coalescent with ancient DNA sequences

description: Ancient DNA (aDNA) is increasingly being used to investigate questions
 such as the phylogenetic relationships and divergence times of extant and
 extinct species. If aDNA samples are sufficiently old, expected branch
 lengths (in units of DNA substitutions) are reduced relative to
 contemporary samples. This can be accounted for by incorporating sample
 ages into phylogenetic analyses. Existing methods that use tip (sample)
 dates infer gene trees rather than species trees, which can lead to
 incorrect or biased inferences of the species tree. Methods using a
 multispecies coalescent (MSC) model overcome these issues. We developed an
 MSC model with tip dates and implemented it in the program bpp. The method
 performed well for a range of biologically realistic scenarios, estimating
 calibrated divergence times and mutation rates precisely. Simulations
 suggest that estimation precision can be best improved by prioritizing
 sampling of many loci and more ancient samples. Incorrectly treating
 ancient samples as contemporary in analyzing simulated data, mimicking a
 common practice of empirical analyses, led to large systematic biases in
 model parameters, including divergence times. Two genomic datasets of
 mammoths and elephants were analyzed, demonstrating the method's
 empirical utility.
description: # Bayesian Inference Under the Multispecies Coalescent with Ancient DNA
 Sequences
 [https://doi.org/10.5061/dryad.4mw6m90h0](https://doi.org/10.5061/dryad.4mw6m90h0) ## Description of the data and file structure This contains the supplemental information (on Zenodo) and the alignment of mammoth and elephant mitochondrial DNA. Most of the mtDNA was derived from the following source. The rest were downloaded from GenBank (accession numbers are included in the supplement): * [http://palaeogenetics.com/data-and-scripts/](http://palaeogenetics.com/data-and-scripts/)
DOI: 10.5061/dryad.v41ns1s2z
title: Infection success data from experimental pairings of cane toad hosts and lungworm parasites

description: By imposing novel selection pressures on both participants, biological
 invasions can disrupt evolutionary “arms races” between hosts and
 parasites. A spatially replicated cross-infection experiment reveals
 strong divergence in the ability of lungworms (Rhabdias
 pseudosphaerocephala) to infect invasive cane toads (Rhinella marina) in
 Australia. In areas colonised for &gt; 20 years, toads are more
 resistant to infection by local strains of parasites than by allopatric
 strains. The situation reverses at the invasion front, where
 super-infective parasites have evolved. Invasion-induced shifts in genetic
 diversity and selective pressures may explain why hosts win the arms race
 in long-colonised areas whereas parasites win the arms race at the
 invasion front.
description: # Cane Toad vs Rhabdias infection success data for Dryad
 This was an experimental
 cross-infection study where common-garden reared cane toads from across
 their invaded range in Australia were infected with *Rhabdias* lungworm
 parasites from across the range. The dataset contains information on the
 origins of host and parasite, their sizes and the infection success of the
 experimental pairings. **Description of the data and file structure** The
 data set is an excel file with columns for these variables- Variable
 name          Variable description ID                             
 Individual identification code for each toad  
 Litter                         The captive-bred family each toad
 originated from   toad site                    The location that the
 parental toads that produced each litter were originally captured from  
 Toad state                 The Australian state that each parental capture
 site was located in   worm site                  The location that the
 toads that donated infective Rhabdias larvae were originally captured
 from.   worm state               The Australian state that each
 Rhabdias-donating toad capture site was located in   Total
 Rhabdias          The number of adult Rhabdias present in each toads lungs
 upon euthanasia and dissection   Snout-vent length     Total body length
 (in mm) of each toad at the time of experimental infection   L3
 PC1                       Principal component describing body size
 (combination of length and width) of Rhabdias larvae used in each batch of
 experimental infections.
DOI: 10.5061/dryad.q2bvq83rg
title: Massive intein content in Anaeramoeba reveals aspects of intein mobility in eukaryotes

description: The spread of mobile genetic elements within and between the genomes of
 diverse organisms has greatly impacted biology across the tree of life.
 Inteins are an enigmatic type of mobile genetic element capable of
 self-splicing at the protein level. While inteins are generally rare in
 eukaryotes, we have discovered that three strains of the newly described
 eukaryotic microbe Anaeramoeba have many dozens of inteins encoded in
 their nuclear genomes. Genomic investigation shows that Anaeramoeba’s
 inteins were acquired by lateral transfer from viruses and bacteria, and
 subsequently spread to many different genomic locations via allelic and,
 possibly, non-allelic homing. The promiscuous nature of inteins in
 Anaeramoeba makes them promising substrates for genetic engineering and
 biotechnological applications.
description: # Massive intein content in Anaeramoeba reveals aspects of intein mobility
 in eukaryotes. ##
 Description of the data and file structure 1. INTEINS_PER_CLUSTER.tar =
 mutifasta files of inteins per cluster 2. alignment-and-iqtree_files.tar =
 multiple sequence alignment files and associated iqtree files for each
 phylogenetic tree 3. multiple-sequence-alignments_splicing-domains.tar =
 multiple sequence alignments for the splicing domains of Anaeramoeba
 inteins
DOI: 10.15468/dl.ynun6f
title: Occurrence Download

description: A dataset containing 314 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chelon richardsonii",
 "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 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 314 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003689-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9w0vt4bn8
title: Software maintenance meetings: Guide, codebook, and excerpts

description: A type of meeting that has been understudied in the software engineering
 literature to date is what we term the software maintenance meeting: a
 regularly scheduled team meeting in which emergent issues are addressed
 that are usually out of scope of the daily standup but not necessarily
 challenging enough to warrant an entirely separate meeting. This dataset
 includes the guidelines and codebook used to analyze a set of ten meetings
 of this kind. It also includes excerpts from the video transcripts that
 were analyzed as part of the study. These excerpts illustrate the nature
 of the meetings.
description: The guideline and codebook were produced by the researchers as a
 result of a thematic analysis performed over the video recordings and
 their respective transcripts. The excerpts selected from the transcripts
 illustrate the discussion held during software maintenance meetings. To
 keep subjects' identities private, these excerpts were completely
 anonymized. In summary, the process was the following,
 the videos of the ten meetings were transcribed by a professional
 transcription service, and then used as the sole sources for various kinds
 of analyses. For confidentiality reasons, the healthcare company that
 provided the video recordings did not allow their disclosure. However,
 they did give permission to share anonymized excerpts from the video
 transcripts. 
description: # Software Maintenance Meetings: Guide, Codebook, and Excerpts
 [https://doi.org/10.5061/dryad.9w0vt4bn8](https://doi.org/10.5061/dryad.9w0vt4bn8) The dataset comprises research materials produced during the study of ten video recordings about "Software Maintenance Meetings" at a healthcare software development company. Specifically, it contains the guidelines and codebook built by the researchers as part of the study, as well as a rich selection of transcript excerpts that illustrate the nature of software maintenance meetings. These supportive materials are critical to replicating the study at other software development companies. **Description of the data and file structure** The dataset contains 18 anonymized excerpts from the meeting transcripts, as well as all the guidelines and codebook used to analyze them. All these resources were compiled into a spreadsheet file with two tabs respectively labeled as “guide and codebook” and “excerpts”.
DOI: 10.6084/m9.figshare.31169701.v1
title: Spatial outliers as a pattern measure for explaining heterogeneity

description: Data and code for second-dimension outlier-driven heterogeneity (SOH) model.
DOI: 10.5061/dryad.wdbrv15vc
title: Data from: Ontogeny of color development in two green-brown polymorphic grasshopper species

description: Many insects, including several orthopterans, undergo dramatic changes in
 body coloration during ontogeny. This variation is particularly intriguing
 in gomphocerine grasshoppers, where the green and brown morphs appear to
 be genetically determined (Schielzeth & Dieker, 2020; Winter,
 Varma, & Schielzeth, 2021). A better understanding of how these
 color morphs develop during ontogeny can provide valuable insights into
 the evolution and ecology of such a widespread color polymorphism. Here,
 we focus on the color development of two green-brown polymorphic species,
 the club-legged grasshopper Gomphocerus sibiricus and the steppe
 grasshopper Chorthippus dorsatus. By following the color development of
 individuals from hatching to adulthood, we found that color morph
 differences begin to develop during the second nymphal stage, are clearly
 defined by the third nymphal stage, and remain stable throughout the life
 of an individual. Interestingly, we also observed that shed skins of late
 nymphal stages are identifiable by color morphs based on their yellowish
 coloration, rather than the green that marks green body parts.
 Furthermore, by assessing how these colors are perceived by different
 visual systems, we found that certain potential predators can
 chromatically discriminate between morphs, while others may not. These
 results suggest that the putative genes controlling color morph are active
 during the early stages of ontogeny, and that green color is likely
 composed of two components, one present in the cuticle and one not. In
 addition, the effectiveness of camouflage appears to vary depending on the
 specific predator involved.
description: There are two sets of data: 1) Data from
 spectrometric reflectance measurements of grasshoppers (recorded with a
 handheld spectrophotometer, AvaSpec-2048, Avantes). The data from the
 recording device have been compiled into 2 tables (1. included in the
 analysis and 2. excluded from the analysis). The data are ready for
 analysis using the pavo package in R. Each row refers to a wavelength
 (given in the first column) and all other columns refer to individual data
 sets (reflectance of a particular body part at a particular wavelength).
 The attributes of the data sets are encoded in the column headers (see the
 ReflectanceAnalysis_ReadMe file for details). 2) Data
 from color measurement analysis of standardized images of the lateral side
 of the head for grasshopper individuals. We used ImageJ software to
 measure the red, green, and blue (RGB) values of the images. Using the
 polygon selection tool in ImageJ, two random areas were selected: one on
 the lateral lobes of the pronotum and another on the lateral side of the
 head. The average RGB value of these selected areas was measured. This
 data set is ready to plot the ternary plot in R. See the
 TernaryPlot_ReadMe file for details.
description: There are readme files for all datasets.
DOI: 10.5061/dryad.0rxwdbs66
title: Data from: Four scenarios in which shadow competition should be prominent and factors affecting its strength

description: Shadow competition is the interception of moving prey by a predator closer
 to its arrival source, preventing its availability to predators
 downstream. Shadow competition is likely common in nature, and unlike some
 other competition types, has a strong spatial component (with the
 exception of competition for space, which clearly also has a spatial
 component). We used an individual-based spatially-explicit simulation
 model to examine whether shadow competition takes place and which factors
 affect it in four scenarios considering ambush predators and active prey.
 First, when prey capture is uncertain (‘the ricochet effect’). Here, the
 strength of shadow competition increases when it is harder to capture prey
 after the first unsuccessful capture attempt, whereas shadow competition
 is moderated if capture success is higher in successive attempts. Second,
 shadow competition becomes stronger when predators can capture prey
 arriving only from certain directions. Third, when prey tend to move along
 a barrier after encountering it. Here, predators located along this
 barrier may be more successful than those at random positions, but shadow
 competition in this scenario drastically decreases the capture success of
 predators in central positions along a barrier (i.e., having more than a
 single neighbour). Finally, in three-level systems of plants in clusters,
 herbivores searching for plants, and predators ambushing herbivores inside
 plant patches, predators with ambush locations in the periphery of plant
 patches are more successful than those at the patch center, especially at
 high predator densities. Our simulation indicates that shadow competition
 is plausibly relevant in various scenarios of ambush predators and prey,
 and that it varies based on the habitat structure and capture probability
 of prey by predators as well as the change in capture probability with
 successive encounters.
description: # Four scenarios in which shadow competition should be prominent and
 factors affecting its strength
 [https://doi.org/10.5061/dryad.0rxwdbs66](https://doi.org/10.5061/dryad.0rxwdbs66) ## Description of the data and file structure The dataset comprises the four scenarios detailed in the first Excel sheet and in the paper itself as well as the data for the sensitivity analysis presented in the Supplementary Material.
DOI: 10.15468/dl.up82fa
title: Occurrence Download

description: A dataset listing the 205 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "DatasetKey is Aves del Parque Nacional Cumbres de Monterrey, Nuevo León, México"
 ]
}

 The dataset's 205 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003667-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sunpg7
title: Occurrence Download

description: A dataset containing 893 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Coladenia"
 ]
}

 The dataset includes 893 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003690-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ffbg79d1b
title: Foraging is prioritized over nestmate rescue in desert ants and pupae are rescued more than adults

description: Social animals, and ants, in particular, exhibit a range of cooperative
 behaviors. One such behavior is the rescue of group members, which cannot
 return to the nest by themselves. However, if several group members need
 to be rescued, how do ants prioritize whom to save first? Furthermore,
 when food is offered in parallel, do ants prioritize feeding over
 rescuing? We studied the rescue behavior of the desert
 ant Cataglyphis niger. Workers invest more time in rescuing pupae
 than adult workers, perhaps because the value of brood is higher than that
 of older workers serving as foragers. Specific rescue behaviors, pulling
 the trapped individual or digging around it, differed when directed
 towards adults or pupae: rescuing workers more often pulled pupae whereas
 they dug more around trapped adults. Rescuing workers did not prioritize
 living individuals over dead ones or intact workers over injured ones
 indicating that trapped individuals were recognized chemically rather than
 by their morphology or behavior. Finally, workers prioritized foraging
 over rescuing, perhaps because fewer workers specialize in rescue behavior
 than in foraging. Our analysis indeed revealed that fewer workers both
 foraged and rescued trapped workers than expected by chance. In
 conclusion, ants that rescue others exhibit a complex set of behaviors,
 with varying attention and specific behaviors targeted at different
 individuals, perhaps according to the colony's needs. Our study is
 important for emphasizing a relatively neglected aspect of sociality
 (rescue of group members) and demonstrates that the attentions of rescues
 differ based on the trapped nestmate’s life stage.
description: # Foraging is prioritized over nestmate rescue in desert ants and pupae
 are rescued more than adults
 [https://doi.org/10.5061/dryad.ffbg79d1b](https://doi.org/10.5061/dryad.ffbg79d1b) ## Description of the data and file structure The Excel file contains the dataset for the manuscript. The dataset comprises four experiments: (a) Rescue behavior of adults, pupae, and larvae; (b) Rescue of living vs. dead workers and adults vs. pupae; (c) Rescue of intact vs. injured workers; and (d) Rescue vs. foraging. Please see the Methods for more details. In experiments a-c, colonies were exposed to different nestmates requiring rescue – larvae, pupae, adults, injured adults, and dead adults. In experiment d, colonies were also exposed to food in parallel. We measured the rescue time, divided into digging around the trapped individual and pulling of the trapped individual, and the number of ant workers involved in such activities.   Fig. S1, S2: The habitat-of-origin of the studied ants - Tel-Baruch sand dunes, a natural enclave in northwest Tel Aviv. Fig. S3, S4: Rescue attempt of a *C. niger* worker tied to a paper sheet, similar to the rescue observed in the lab.
DOI: 10.34740/kaggle/dsv/14654021
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5281/zenodo.18385835
title: Data for: Giant splitting and universal behavior of Fabry-Pérot bound states in the continuum in waveguides

description: This dataset contains all numerical data and python codes used to produce the figures in the manuscript “Giant splitting and universal behavior of Fabry-Pérot bound states in the continuum in waveguides” by N. M. Shubin, V. V. Kapaev, and A. A. Gorbatsevich.

Dependencies for the python codes include numpy, matplotlib, scipy, numba, random, and multiprocessing.
DOI: 10.5281/zenodo.18404356
title: Input files for Validation of a 3D crustal velocity model for northern Israel using wavefield simulations

description: Be3D.zip contains the par file, interfaces, and 3D tomographic model (Ben-Dor et al., 2025) used by the SPECFEM3D software in Ben-Dor et al., 2026.

Gitt1D.zip contains the par file, interfaces, and 1D velocity model (Gitterman et al., 2025) used by the SPECFEM3D software in Ben-Dor et al., 2026.

CMTSOLUTIONS.zip contains the CMTSOLUTION files used by the SPECFEM3D software in Ben-Dor et al., 2026.

 

Ben‐Dor, G., Kurzon, I., Aizenshtat‐Soffer, E., Wetzler, N., Weinberger, R., Tape, C., & Tsesarsky, M. (2025). Structure and Seismicity of the Dead Sea Fault and the Galilee Revealed by 3D Earthquake Tomography. Journal of Geophysical Research: Solid Earth, 130(7). https://doi.org/10.1029/2024JB030816.

Gitterman, Y., Pinsky, V., Amrat, A.-Q., Jaser, D., Mayyas, O., Nakanishi, K., & Hofstetter, R. (2005). Source features, scaling and location of calibration explosions in Israel and Jordan for CTBT monitoring. Israel Journal of Earth Sciences, 54, 199–217.
DOI: 10.60593/ur.d.31127236
title: "Developmental exposure to a PFAS mixture impairs the anamnestic response to influenza A virus infection in mice": Germinal center B cells and plasma cells flow cytometry panel FCS files.

description: Each folder contains flow cytometry standard (FCS) files from a staining panel to identify B cells, germinal center B cells, and plasma cells on a specific day relative to primary influenza A virus infection (day 0, day 14, day 70, day 75, day 77). In the publication, the germinal center B data is presented in Figure 5 and Table S9. The number and percentage of total B cells is presented in Tables S5 and S6 and plasma cell data is presented in Table S9.
DOI: 10.60593/ur.d.31127236.v1
title: "Developmental exposure to a PFAS mixture impairs the anamnestic response to influenza A virus infection in mice": Germinal center B cells and plasma cells flow cytometry panel FCS files.

description: Each folder contains flow cytometry standard (FCS) files from a staining panel to identify B cells, germinal center B cells, and plasma cells on a specific day relative to primary influenza A virus infection (day 0, day 14, day 70, day 75, day 77). In the publication, the germinal center B data is presented in Figure 5 and Table S9. The number and percentage of total B cells is presented in Tables S5 and S6 and plasma cell data is presented in Table S9.