cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gt216
title: Data from: Characterization of breast tumors using diffusion kurtosis imaging (DKI)

description: Aim: The aim of this study was to investigate and evaluate the role of
 magnetic resonance (MR) diffusion kurtosis imaging (DKI) in characterizing
 breast lesions. Materials and Methods: One hundred and twenty-four lesions
 in 103 patients (mean age: 57±14 years) were evaluated by MR DKI performed
 with 7 b-values of 0, 250, 500, 750, 1,000, 1,500, 2,000 s/mm2 and dynamic
 contrast-enhanced (DCE) MR imaging. Breast lesions were histologically
 characterized and DKI related parameters—mean diffusivity (MD) and mean
 kurtosis (MK)—were measured. The MD and MK in normal fibroglandular breast
 tissue, benign and malignant lesions were compared by One-way analysis of
 variance (ANOVA) with Tukey's multiple comparison test. Receiver
 operating characteristic (ROC) analysis was performed to assess the
 sensitivity and specificity of MD and MK in the diagnosis of breast
 lesions. Results: The benign lesions (n = 42) and malignant lesions (n =
 82) had mean diameters of 11.4±3.4 mm and 35.8±20.1 mm, respectively. The
 MK for malignant lesions (0.88±0.17) was significantly higher than that
 for benign lesions (0.47±0.14) (P&lt;0.001), and, in contrast, MD for
 benign lesions (1.97±0.35 (10−3 mm2/s)) was higher than that for malignant
 lesions (1.20±0.31 (10−3 mm2/s)) (P&lt;0.001). At a cutoff MD/MK 1.58
 (10−3 mm2/s)/0.69, sensitivity and specificity of MD/MK for the diagnosis
 of malignant were 79.3%/84.2% and 92.9%/92.9%, respectively. The area
 under the curve (AUC) is 0.86/0.92 for MD/MK. Conclusions: DKI could
 provide valuable information on the diffusion properties related to tumor
 microenvironment and increase diagnostic confidence of breast tumors.
description: Characterization of
 Breast Tumors using Diffusion Kurtosis Imaging (DKI)Breast tumor using DKI
 Part 1DKI_data.rarDKI_201310999Breast tumor DKI part 2DKI_201309814Breast tumor DKI part 3
DOI: 10.5064/f6vanjl8/yfsdg0
title: Silan-Ciruelas_Opt1_Therapist11.pdf
DOI: 10.5064/f6vanjl8/ohtk8m
title: Silan-Ciruelas_PHL_Opt2_12A_Nica_5-10_High_Median-High.pdf
DOI: 10.5064/f6vanjl8/m8lqkg
title: Silan-Ciruelas_PHL_Opt1_2A_Nica_1_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/tvrkij
title: Silan-Ciruelas_PHL_Opt2_4A_Nica_1_High_Median-High.pdf
DOI: 10.15468/dl.qr4g8r
title: Occurrence Download

description: A dataset containing 96332 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helianthus annuus"
 ]
}

 The dataset includes 96332 records from 988 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000353-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.49r20
title: Data from: A Bayesian approach to social structure uncovers cryptic regulation of group dynamics in Drosophila melanogaster

description: Understanding the mechanisms that give rise to social structure is central
 to predicting the evolutionary and ecological outcomes of social
 interactions. Modeling this process is challenging, because all
 individuals simultaneously behave in ways that shape their social
 environments—a process called Social Niche Construction [SNC]. In previous
 work we demonstrated that aggression acts as an SNC trait in fruit flies
 (Drosophila melanogaster), but the mechanisms of that process remained
 cryptic. Here, we analyze how individual social group preferences generate
 overall social structure. We use a combination of agent-based simulation
 [ABS] and Approximate Bayesian Computation [ABC] to fit models to
 empirical data. We confirm that genetic variation in aggressive behavior
 influences social group structure. Furthermore, we find that female
 "decamping" due to male behavior may play an under-appreciated
 role in structuring social groups. Male-male aggression may sometimes
 destabilize groups, but may also be an SNC behavior for shaping desirable
 groups for females. Density intensifies female social preferences, thus
 the role of female behavior in shaping group structure may become more
 important at high densities. Our ability to model the ontogeny of group
 structure demonstrates the utility of the Bayesian model-based approach in
 social behavioral studies.
description: The output data of ABC
 MCMC for each treatmentA zipped folder
 containing two subfolders, with all the minimally processed output from
 the paper. See the readme for more details, or visit the git repository
 for the actual code.
 https://bitbucket.org/brfoley76/flyabc/flysim_results.tar.gz
DOI: 10.5064/f6vanjl8/tmdptr
title: Silan-Ciruelas_USA_Opt2_4A_Silky_1_High_Median-High.pdf
DOI: 10.18739/a2416t20v
title: Change in equilibrium-line altitude (ΔELA) for 215 Alaskan glaciers from the Little Ice Age (LIA) maximum to present (2016 to 2024)

description: The study associated with this dataset evaluates the climatic signature of the Little Ice Age (LIA; ~1250 to 1900) relative to the present (2016–2024) by reconstructing shifts in equilibrium-line altitude (ΔELA), a climate-sensitive parameter, for 215 glaciers in Alaska and adjacent Canada (southwest Yukon and northwest British Columbia) using remote sensing and a suite of geographic information system (GIS) tools. We quantify the magnitude and spatial pattern of ΔELA across Alaska’s major glaciated regions to infer centennial-scale changes in temperature and precipitation and to examine links with synoptic-scale circulation associated with the Aleutian Low.
 Data were generated in 2024–2025 at Arizona State University and Northern Arizona University as part of the NSF-funded PROGLACIAL project. The dataset includes reconstructed LIA maximum ELAs, modern end-of-summer snowline altitudes (2016–2024), and LIA–present ΔELA for 215 glaciers. LIA glacier extents were compiled from published sources and additional mapping of geomorphic evidence (terminal moraines, trimlines) using the ESRI World Imagery basemap; LIA glacier surfaces and ELAs were modeled using the GlaRe and PalaeoIce GIS toolboxes; and modern snowline altitudes were manually mapped in Sentinel-2 satellite imagery (2016-2024) and associated elevation extracted from the ArcticDEM (10 meter mosaic product).
DOI: 10.5064/f6vanjl8/qfjiar
title: Silan-Ciruelas_TUR_Opt2_21B_Anil_LGBTAnyLength_Low_Low-Median.pdf
DOI: 10.15468/dl.y3acjx
title: Occurrence Download

description: A dataset containing 4536 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carpinus orientalis"
 ]
}

 The dataset includes 4536 records from 168 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000372-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.90ps4
title: Data from: Drosophila Sulf1 is required for the termination of intestinal stem cell division during regeneration

description: Stem cell division is activated to trigger regeneration in response to
 tissue damage. The molecular mechanisms by which this stem cell mitotic
 activity is properly repressed at the end of regeneration are poorly
 understood. Here, we show that a specific modification of heparan sulfate
 is crucial for regulating Drosophila intestinal stem cell (ISC) division
 during normal midgut homeostasis and regeneration. Loss of the
 extracellular heparan sulfate endosulfatase Sulf1 resulted in increased
 ISC division during normal homeostasis, which was caused by upregulation
 of mitogenic signaling including the JAK-STAT, EGFR and Hedgehog pathways.
 Using a regeneration model, we found that ISCs failed to properly halt
 division at the termination stage in Sulf1 mutants, showing that Sulf1 is
 required for terminating ISC division at the end of regeneration. We
 propose that post-transcriptional regulation of mitogen signaling by
 heparan sulfate structural modifications provides a new regulatory step
 for precise temporal control of stem cell activity during regeneration.
description: Raw
 imagesArchive.zip
DOI: 10.5064/f6vanjl8/rjifx6
title: Silan-Ciruelas_USA_Opt1_23B_Silky_LGBTAnyLength_Low_Median-High.pdf
DOI: 10.15468/dl.pv5uvr
title: Occurrence Download

description: A dataset containing 6801 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Iguana iguana",
 "Year 2020-2026"
 ]
}

 The dataset includes 6801 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000374-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5064/f6vanjl8/xqwzyu
title: Silan-Ciruelas_USA_Opt2_11A_Haley_5-10_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/m6mkro
title: Silan-Ciruelas_BRA_Opt2_24B_Camilla_LGBT_High_Median-High.pdf
DOI: 10.5061/dryad.qq06v
title: Data from: Spatial separation without territoriality in shark communities

description: Spatial separation within predator communities can arise via
 territoriality but also from competitive interactions between and within
 species. However, linking competitive interactions to predator
 distribution patterns is difficult and theoretical models predict
 different habitat selection patterns dependent on habitat quality and how
 competition manifests itself. While models generally consider competitors
 to be either equal in ability, or for one phenotype to have a fixed
 advantage over the other, few studies consider that an animal may only
 have a competitive advantage in specific habitats. We used &gt; 10
 years of telemetry data, habitat surveys and behavioral experiments, to
 show spatial partitioning between and within two species of reef shark
 (grey reef, Carcharhinus amblyrhinchos, and blacktip reef sharks, C.
 melanopterus) at an unfished Pacific atoll. Within a species, sharks
 remained within small ‘sub-habitats’ with very few movements of
 individuals between sub-habitats, which previous models have suggested
 could be caused by intra-specific competition. Blacktip reef sharks were
 more broadly distributed across habitat types but a greater proportion
 used lagoon and backreef habitats, while grey reef sharks preferred
 forereef habitats. Grey reef sharks at a nearby atoll where blacktip reef
 sharks are absent, were distributed more broadly between habitat types
 than when both species were present. A series of individual-based models
 predict that habitat separation would only arise if there are competitive
 interactions between species that are habitat-specific, with grey reefs
 having a competitive advantage on the forereefs and blacktips in the
 lagoons and backreef. We provide compelling evidence that competition
 drives distribution patterns and spatial separation of a marine predator
 community, and highlight that competitive advantages may not be constant
 but rather dependent on habitats.
description: Palmyra Carcharhinus
 melanopterusHourly telemetry data,
 through 2015BT_Palmyra_telemetry_hourly_through2015.csvPalmyra Carcharhinus amblyrhynchosHourly telemetry data, through 2015GR_Palmyra_telemetry_hourly_through2015.csv
DOI: 10.15468/dl.ymph6v
title: Occurrence Download

description: A dataset containing 3480 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Tursiops truncatus"
 ]
}

 The dataset includes 3480 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000373-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5064/f6vanjl8/yjgmmp
title: Silan-Ciruelas_USA_Opt2_7B_Silky_1-5_Low_Median-High.pdf
DOI: 10.5064/f6vanjl8/3ircfy
title: Silan-Ciruelas_TUR_Opt2_24A_Anil_LGBT_High_Median-High.pdf
DOI: 10.5061/dryad.c8k7q
title: Data from: Genome-wide association analysis identifies potential regulatory genes for eumelanin pigmentation in chicken plumage

description: Plumage color in chicken is determined by the proportion of eumelanin and
 pheomelanin pigmentation. As the main ingredient in plumage melanin,
 eumelanin plays a key role in the dark black, brown and grey coloration.
 However, very few studies have been performed to identify the related
 genes and mutations on a genome-wide scale. Herein, a resource family
 consisting of one backcross population and two F2 cross populations
 between a black roster and Yukou Brown I parent stockbreed was constructed
 for identification of genes related to eumelanin pigmentation. Chickens
 with eumelanin in their plumage were classified as the case group, and the
 rest were considered the control group. A genome-wide association study of
 this phenotype and genotypes using Affymetrix 600K HD SNP arrays in this
 F2 family revealed 13 significantly associated SNPs and in 10 separate
 genes on chromosomes 1, 2, 3 and 5. Based on previous studies in model
 species, we inferred that genes, including NUAK family kinase 1 (NUAK1)
 and sonic hedgehog (SHH), may play roles in the development of neural
 crest cells or melanoblasts during the embryonic period, which may also
 affect the eumelanin pigmentation. Our results facilitate the
 understanding of the genetic basis of eumelanin pigmentation in chicken
 plumage.
description: Genome-wide association
 analysis identifies potential regulatory genes for eumelanin pigmentation
 in chicken plumageThe Roshal ARchive (RAR)
 contains the genotype and the phenotype of this study. Association
 analysis was conducted by the PLINK software using the “Basic case/control
 association” test after affinity adjustment. Pearson Chi-square test was
 used for significance testing, and then Bonferroni correction was used to
 adjust for multiple comparisons. The R programming codes were used to
 generate the Manhattan plot of genome wide P values.genotype and
 phenotype.rar
DOI: 10.5064/f6vanjl8/wcdr2m
title: Silan-Ciruelas_BRA_Opt2_16A_10_20_High_Median_High.pdf
DOI: 10.5064/f6vanjl8/x49qg0
title: Silan-Ciruelas_PHL_Opt2-17A-Christelle_20years_Low_Low-Median.pdf
DOI: 10.5064/f6vanjl8/dknggj
title: Silan-Ciruelas_FRA_Opt1_7A_1_5_Low_Median_High.pdf
DOI: 10.5064/f6vanjl8/ysi7ri
title: Silan-Ciruelas_PHL_Opt2-17B-Christelle_20years_Low_Low-Median.pdf
DOI: 10.5061/dryad.149m8
title: Data from: Consistency of VDJ rearrangement and substitution parameters enables accurate B cell receptor sequence annotation

description: VDJ rearrangement and somatic hypermutation work together to produce
 antibody-coding B cell receptor (BCR) sequences for a remarkable diversity
 of antigens. It is now possible to sequence these BCRs in high throughput;
 analysis of these sequences is bringing new insight into how antibodies
 develop, in particular for broadly-neutralizing antibodies against HIV and
 influenza. A fundamental step in such sequence analysis is to annotate
 each base as coming from a specific one of the V, D, or J genes, or from
 an N-addition (a.k.a. non-templated insertion). Previous work has used
 simple parametric distributions to model transitions from state to state
 in a hidden Markov model (HMM) of VDJ recombination, and assumed that
 mutations occur via the same process across sites. However, codon frame
 and other effects have been observed to violate these parametric
 assumptions for such coding sequences, suggesting that a non-parametric
 approach to modeling the recombination process could be useful. In our
 paper, we find that indeed large modern data sets suggest a model using
 parameter-rich per-allele categorical distributions for HMM transition
 probabilities and per-allele-per-position mutation probabilities, and that
 using such a model for inference leads to significantly improved results.
 We present an accurate and efficient BCR sequence annotation software
 package using a novel HMM “factorization” strategy. This package, called
 partis (https://github.com/psathyrella/partis/), is built on a new
 general-purpose HMM compiler that can perform efficient inference given a
 simple text description of an HMM.
description: Parameters and HMM
 filesParameter values and HMM
 model files for all subsets of all humans in the Adaptive and Vollmers
 data sets.parameters.tgzFull set of plotsPlots of all alleles for all humans in the Adaptive and Vollmers data sets.plots.tgz
DOI: 10.5064/f6vanjl8/mj7bs1
title: Silan-Ciruelas_Opt2_Therapist2.pdf
DOI: 10.5064/f6vanjl8/fhpqud
title: Silan-Ciruelas_PHL_Opt1-13B-Christelle_10_20_Low_Median-High.pdf
DOI: 10.5061/dryad.p1n88
title: Data from: Flight calls signal group and individual identity but not kinship in a cooperatively breeding bird

description: In many complex societies, intricate communication and recognition systems
 may evolve to help support both direct and indirect benefits of group
 membership. In cooperatively breeding species where groups typically
 comprise relatives, both learned and innate vocal signals may serve as
 reliable cues for kin recognition. Here, we investigated vocal
 communication in the plural cooperatively breeding superb starling,
 Lamprotornis superbus, where flight calls—short, stereotyped vocalizations
 used when approaching conspecifics—may communicate kin relationships,
 group membership, and/or individual identity. We found that flight calls
 were most similar within individual repertoires but were also more similar
 within groups than within the larger population. Although starlings
 responded differently to playback of calls from their own versus other
 neighboring and distant social groups, call similarity was uncorrelated
 with genetic relatedness. Additionally, immigrant females showed similar
 patterns to birds born in the study population. Together, these results
 suggest that flight calls are learned signals that reflect social
 association but may also carry a signal of individuality. Flight calls,
 therefore, provide a reliable recognition mechanism for groups and may
 also be used to recognize individuals. In complex societies comprising
 related and unrelated individuals, signaling individuality and group
 association, rather than kinship, may be a route to cooperation.
description: Acoustic recordings of
 superb starling flight call boutsbouts.zipAcoustic recordings of individual superb starling flight call motifsmotifs.zipTable of motifs, recording times, and numerical identifiers for singersmotifs.csvTable of bird identifiers, bird sex, and social groupbirds.csvTable of distances between each pair of territoriesdistances.csv
DOI: 10.5064/f6vanjl8/eflurx
title: Silan-Ciruelas_FRA_Opt1_12A_5-10_High_Median-High.pdf
DOI: 10.5064/f6vanjl8/ukmzvv
title: Silan-Ciruelas_FRA_Opt1_15B_10-20_Low_Median-High.pdf
DOI: 10.5061/dryad.4ch10
title: Data from: Using matrix and tensor factorizations for the single-trial analysis of population spike trains

description: Advances in neuronal recording techniques are leading to ever larger
 numbers of simultaneously monitored neurons. This poses the important
 analytical challenge of how to capture compactly all sensory information
 that neural population codes carry in their spatial dimension (differences
 in stimulus tuning across neurons at different locations), in their
 temporal dimension (temporal neural response variations), or in their
 combination (temporally coordinated neural population firing). Here we
 investigate the utility of tensor factorizations of population spike
 trains along space and time. These factorizations decompose a dataset of
 single-trial population spike trains into spatial firing patterns
 (combinations of neurons firing together), temporal firing patterns
 (temporal activation of these groups of neurons) and trial-dependent
 activation coefficients (strength of recruitment of such neural patterns
 on each trial). We validated various factorization methods on simulated
 data and on populations of ganglion cells simultaneously recorded in the
 salamander retina. We found that single-trial tensor space-by-time
 decompositions provided low-dimensional data-robust representations of
 spike trains that capture efficiently both their spatial and temporal
 information about sensory stimuli. Tensor decompositions with
 orthogonality constraints were the most efficient in extracting sensory
 information, whereas non-negative tensor decompositions worked well even
 on non-independent and overlapping spike patterns, and retrieved
 informative firing patterns expressed by the same population in response
 to novel stimuli. Our method showed that populations of retinal ganglion
 cells carried information in their spike timing on the
 ten-milliseconds-scale about spatial details of natural images. This
 information could not be recovered from the spike counts of these cells.
 First-spike latencies carried the majority of information provided by the
 whole spike train about fine-scale image features, and supplied almost as
 much information about coarse natural image features as firing rates.
 Together, these results highlight the importance of spike timing, and
 particularly of first-spike latencies, in retinal coding.
description: Retinal Data and
 StimuliThis dataset contains
 the visual stimuli that were used for the retina recordings and also the
 spike trains and the receptive fields of the recorded retinal ganglion
 cells.RetinaDataFactorizationsOfPopulationSpikeTrains.zip
DOI: 10.5064/f6vanjl8/9cbgaz
title: Silan-Ciruelas_TUR_Opt2_17A_Kerem_Over20_Low_Low-Median.pdf
DOI: 10.5064/f6vanjl8/lybvbi
title: Silan-Ciruelas_USA_Opt2_1A_AnaliliaReglaGutierrez_1_Median_Low-Median.pdf
DOI: 10.5061/dryad.ch110
title: Data from: The temporal signature of memories: identification of a general mechanism for dynamic memory replay in humans

description: Reinstatement of dynamic memories requires the replay of neural patterns
 that unfold over time in a similar manner as during perception. However,
 little is known about the mechanisms that guide such a temporally
 structured replay in humans, because previous studies used either
 unsuitable methods or paradigms to address this question. Here, we
 overcome these limitations by developing a new analysis method to detect
 the replay of temporal patterns in a paradigm that requires participants
 to mentally replay short sound or video clips. We show that memory
 reinstatement is accompanied by a decrease of low-frequency (8 Hz) power,
 which carries a temporal phase signature of the replayed stimulus. These
 replay effects were evident in the visual as well as in the auditory
 domain and were localized to sensory-specific regions. These results
 suggest low-frequency phase to be a domain-general mechanism that
 orchestrates dynamic memory replay in humans.
description: Analysis scripts and
 statistic data filesIn this repository you
 will find the analysis scripts as well as the group statistic data that
 were used to generate the figures in the manuscript. All files are Matlab
 based script (*.m) or data (*.mat) files.analysis_scripts_and_stats.7z
DOI: 10.5064/f6vanjl8/i8g7sk
title: Silan-Ciruelas_PHL_Opt2-24B-Nica_LGBTAnyLength_High_Median-High.pdf
DOI: 10.5064/f6vanjl8/cnphad
title: Silan-Ciruelas_Opt1_Therapist16.pdf
DOI: 10.5064/f6vanjl8/dbkauz
title: Silan-Ciruelas_USA_Opt2_18B_Marina_20_High_Low-Median.pdf