cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14278845
title: IPATH Dataset: 45,609 Curated Image-Text Pairs for Histopathology Applications

description: Recent advancements in artificial intelligence (AI) have revealed important patterns in pathology images imperceptible to human observers that can improve diagnostic accuracy and decision support systems. However, progress has been limited due to the lack of publicly available medical images. To address this scarcity, we explore Instagram as a novel source of pathology images with expert annotations. We curated the IPATH dataset from Instagram, comprising 45,609 pathology image–text pairs rigorously filtered and curated for domain quality using classifiers, large language models, and manual filtering. To demonstrate the value of this dataset, we developed a multimodal AI model called IP-CLIP by fine-tuning a pretrained CLIP model using the IPATH dataset. We evaluated IP-CLIP on seven external histopathology datasets using zero shot classification and linear probing, where it consistently outperformed the original CLIP model. Furthermore, IP-CLIP matched or exceeded several recent state-of-the-art pathology vision–language models, despite being trained on a substantially smaller dataset. We also assessed image–text alignment on a 5k held-out IPATH subset using image–text retrieval, where IP-CLIP surpassed CLIP and other specialized models. These results demonstrate the effectiveness of the IPATH dataset and highlight the potential of leveraging social media data to develop AI models for medical image classification and enhance diagnostic accuracy.



What's New in Version 2.0

This is the cleaned and preprocessed version of the IPATH dataset, ready for direct use in training vision-language models. Compared to v1.0 (raw images), v2.0 includes:

✅ 1. Circular Field-of-View (FOV) Correction

Many microscope images contain circular viewing areas with black borders. V2.0 applies automated correction using:



RANSAC-based circle fitting for robust detection (handles partial circles)

Intelligent cropping to remove black borders

Background filling with tissue-appropriate colors

Works on both complete and partial circular FOVs that touch image edges


Impact: Removes distracting artifacts and focuses model attention on tissue content.

✅ 2. Text and Annotation Removal

Clinical pathology images often contain patient identifiers, scale bars, magnification markers, and other text overlays. V2.0 removes these using:



OCR-based detection (PaddleOCR) for precise text localization

Conservative fallback detection for text OCR might miss

Inpainting to seamlessly fill removed text regions

Privacy protection by automatically removing any visible text


Impact: Protects patient privacy and prevents models from learning text artifacts instead of tissue patterns.

✅ 3. Standardized Format and Resolution

All images in v2.0 are standardized to:



Format: PNG (lossless compression, no JPEG artifacts)

Resolution: 512×512 pixels

Preprocessing: Shortest side resized to 512px, maintaining aspect ratio

Quality: High-quality images suitable for model training


Impact: Consistent input format for reproducible model training.
DOI: 10.5061/dryad.1rn8pk0pt
title: Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae)

description: We present a 517-gene phylogenetic framework for the breadfruit genus
 Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from
 recent fieldwork and herbarium specimens (some up to 106 years old) to
 achieve 96% taxon sampling. We explore issues relating to assembly,
 paralogous loci, partitions, and analysis method to reconstruct a
 phylogeny that is robust to variation in data and available tools. While
 codon partitioning did not result in any substantial topological
 differences, the inclusion of flanking non-coding sequence in analyses
 significantly increased the resolution of gene trees. We also found that
 increasing the size of datasets increased convergence between analysis
 methods but did not reduce gene tree conflict. We optimized the HybPiper
 targeted-enrichment sequence assembly pipeline for short sequences derived
 from degraded DNA extracted from museum specimens. While the subgenera of
 Artocarpus were monophyletic, revision is required at finer scales,
 particularly with respect to widespread species. We expect our results to
 provide a basis for further studies in Artocarpus and provide guidelines
 for future analyses of datasets based on target enrichment data,
 particularly those using sequences from both fresh and museum material,
 counseling careful attention to the potential of off-target sequences to
 improve resolution.
DOI: 10.5061/dryad.8931zcrm2
title: A two-tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae

description: Premise of the study: Putatively single-copy nuclear (SCN) loci,
 identified using genomic resources of closely related species, are ideal
 for phylogenomic inference. However, suitable genomic resources are not
 available for many clades, including Melastomataceae. We introduce a
 versatile approach to identify SCN loci for clades with few genomic
 resources and use it to develop probes for target enrichment in the
 distantly related Memecylon and Tibouchina (Melastomataceae). Methods: We
 present a two-tiered pipeline. First, we identified putatively SCN loci
 using MarkerMiner and transcriptomes from distantly related species in
 Melastomataceae. Published loci and genes of functional
 significance were added (384 total loci). Second, using HybPiper,
 we retrieved 689 homologous template sequences for these loci
 using genome-skimming data from within the focal clades. Results: We
 sequenced 193 loci from both Memecylon and Tibouchina, with probes
 designed from 56 template sequences successfully targeting
 sequences in both clades. Probes designed from genome-skimming data within
 a focal clade were more successful than probes designed from other
 sources. Discussion: Our pipeline successfully identified and targeted SCN
 loci in Memecylon and Tibouchina, enabling phylogenomic studies in both
 clades and potentially across Melastomataceae. This pipeline could be
 easily applied to other clades with few genomic resources. 
description: The loci developed for this paper were identifying using a two
 tiered pipeline. First, MarkerMiner was used to identify putatively SCN
 loci. Second, genome-skimming reads were assembled using HybPiper to
 retrieve homologous sequences for these loci for probe design. 
   Sequences were recovered using target
 enrichment and Illumina sequencing, and assembly was conducted using
 HybPiper. The success and utility of these loci and probes for use in
 phylogenomic analysis were assessed using HybPiper scripts and custom
 scripts.  
description: This dataset includes the template sequences recovered by the
 second tier for the loci identified by the first tier in this pipeline as
 well as the probe sequences used for target enrichment. Custom scripts for
 analyzing these data are available on github at
 https://github.com/jjantzen/Probe_design. Cleaned reads are deposited on
 NCBI SRA (PRJNA592250, PRJNA573947,  PRJNA576018).
DOI: 10.5061/dryad.73n5tb2st
title: Using incidental mark-encounter data to improve survival estimation

description: 1. Obtaining robust survival estimates is critical, but sample size
 limitations often result in imprecise estimates or the failure to obtain
 estimates for population subgroups.  Concurrently, data are often
 recorded on incidental re-encounters of marked individuals, but these
 incidental data are often unused in survival analyses. 2. We evaluated the
 utility of supplementing a traditional survival dataset with incidental
 data on marked individuals that were collected ad-hoc.  We used a
 continuous time-to-event exponential survival model to leverage the
 matching information contained in both datasets and assessed differences
 in survival among adult and juvenile and resident and translocated Mojave
 desert tortoises (Gopherus agassizii). 3. Incorporation of the incidental
 mark-encounter data improved precision of all annual survival point
 estimates, with a 3.4–37.5% reduction in the spread of the 95% Bayesian
 credible intervals.  We were able to estimate annual survival for
 three subgroup combinations that were previously inestimable. 
 Point estimates between the radio-telemetry and combined datasets were
 within |0.029| percentage points of each other, suggesting minimal to no
 bias induced by the incidental data. 4. Annual survival rates were high
 (&gt; 0.89) for resident adult and juvenile tortoises in both study
 sites and for translocated adults in the southern site.  Annual
 survival rates for translocated juveniles at both sites and translocated
 adults in the northern site were between 0.73 and 0.76.  At both
 sites translocated adults and juveniles had significantly lower survival
 than resident adults.  High mortality in the northern site was
 driven primarily by a single pulse in mortalities. 5. Using exponential
 survival models to leverage matching information across traditional
 survival studies and incidental data on marked individuals may serve as a
 useful tool to improve the precision and estimability of survival
 rates.  This can improve the efficacy of understanding basic
 population ecology and population monitoring for imperiled species.
DOI: 10.5061/dryad.wwpzgmsfv
title: Data from: Accounting for multiple comparisons in statistical analysis of the extensive bioassay data on glyphosate

description: Glyphosate is a widely used herbicide worldwide. In 2015, the
 International Agency for Research on Cancer (IARC) reviewed glyphosate
 cancer bioassays and human studies, declared that the evidence for
 carcinogenicity of glyphosate is sufficient in experimental animals.
  We analyzed ten glyphosate rodent bioassays, including those in
 which IARC found evidence of carcinogenicity, using a meta-analytic
 procedure that adjusts for the large number of tumors eligible for
 statistical testing and provides valid false-positive probabilities.
  The test statistics for these global tests are functions of
 p-values from a standard test for dose-response trends applied to each
 specific type of tumor.  We evaluated three global tests, using
 as test statistics the smallest p-value from a standard statistical test
 for dose-response trend and the number of such tests for which the p-value
 is less than or equal to 0.05 or 0.01.  The false-positive
 probabilities obtained from two implementations of these three global
 tests are: smallest p-value: 0.26, 0.17, p-values ≤ 0.05: 0.08, 0.12,
 p-values ≤ 0.01: 0.06, 0.08.  In addition, we found more evidence
 for negative dose-response trends than positive.  Thus, we found
 no strong evidence that glyphosate is an animal carcinogen.  The
 main cause for the discrepancy between IARC’s finding and ours appears to
 be that IARC did not account for the large number of statistical tests
 performed in the bioassays they reviewed and the resulting multiple
 comparison problem.  This work provides a more comprehensive
 analysis of the animal carcinogenicity data for this important herbicide
 than previously available.
description: Individual animal data from rodent carcinogenicity bioassays for
 glyphosate. We extracted individual animal data from ten glyphosate rodent
 carcinogenicity bioassays. See README and Index
 documents for overview.
DOI: 10.5061/dryad.s1rn8pk3s
title: Data from: Evidence of linked selection on the Z chromosome of hybridizing hummingbirds

description: Levels of genetic differentiation vary widely along the genomes of
 recently diverged species. What processes cause this variation? Here I
 analyze geographic population structure and genome-wide patterns of
 variation in the Rufous, Allen's, and Calliope Hummingbirds
 (Selasphorus rufus/sasin/calliope) and assess evidence that linked
 selection on the Z chromosome drives patterns of genetic differentiation
 in a pair of hybridizing species. Demographic models, introgression tests,
 and genotype clustering analyses support a reticulate evolutionary history
 consistent with divergence during the late Pleistocene followed by gene
 flow across migrant Rufous and Allen's Hummingbirds during the
 Holocene. Relative genetic differentiation is elevated and
 within-population diversity depressed on the Z chromosome in all
 interspecific comparisons. The ratio of Z to autosomal within-population
 diversity is much lower than that expected from population size effects
 alone, and Tajima's D is depressed on the Z chromosome in S.
 rufus and S. calliope. These results suggest that conserved
 structural features of the genome play a prominent role in shaping genetic
 differentiation through the early stages of speciation in northern
 Selasphorus hummingbirds, and that the Z chromosome is a likely
 site of genes underlying behavioral and morphological variation in the
 group.
DOI: 10.5061/dryad.w0vt4b8md
title: Data from: Breakdown of gametophytic self-incompatibility in subdivided populations

description: In many hermaphroditic flowering plants self-fertilization is prevented by
 self-incompatibility (SI), often controlled by a single locus, the
 S-locus. In single isolated populations, the maintenance of SI depends
 chiefly on inbreeding depression and the number of SI alleles at the
 S-locus. In subdivided populations, however, population subdivision has
 complicated effects on both the number of SI alleles and the level of
 inbreeding depression, rendering the maintenance of SI difficult to
 predict. Here, we explore the conditions for the invasion of a
 self-compatible mutant in a structured population. We find that the
 maintenance of SI is strongly compromised when a population becomes
 subdivided. We show that this effect is mainly caused by the decrease of
 the local diversity of SI alleles rather than by a change in the dynamics
 of inbreeding depression. Strikingly, we also find that the diversity of
 SI alleles at the whole population level is a poor predictor of the
 maintenance of SI. We discuss the implications of our results for the
 interpretation of empirical data on the loss of SI in natural populations.
description: The general purpose of the program is to investigate the
 maintenance of a gametophytic self-incompatibility system in front of
 self-compatible mutants. The program do evolutionary simulations for
 different value of deleterious (or lethal) mutations that lead to
 inbreeding depression. recursion.cpp is the function
 for each simulation, that receive a set of parameters to test the invasion
 (or not) by the SC mutants main.cpp use fichier.cpp to
 read the parameters.csv file and to launche "recursion". main
 can investigate different value of U sequencialy or search for a critical
 value of U: the lowest value for which SI system is maintained
 Mercennes Twister.h and ranbin.cpp are for random
 numbers fichiers.cpp is to open, close, read parameters
 file. SelRec.cpp contain mainly functions for fitness
 calculation and for recombination depression.h contain function and
 structure declaration
DOI: 10.15468/dl.qkr5fp
title: Occurrence Download

description: A dataset containing 513 records in GBIF matching the query:
SELECT
 '419' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 37.42857426825602
 AND decimalLatitude &lt;= 41.89415215079384
 AND decimalLongitude &gt;= 92.10259487048747
 AND decimalLongitude &lt;= 101.89927079016302
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 513 records were derived from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002042-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.41ns1rn9n
title: Data from: Sibling rivalry: males with more brothers develop larger testes

description: When females mate with multiple partners in a reproductive cycle, the
 relative number of competing sperm from rival males is often the most
 critical factor in determining paternity. Gamete production is directly
 related to testis size in most species, and is associated with both mating
 behavior and perceived risk of competition. Deer mice, Peromyscus
 maniculatus, are naturally promiscuous and males invest significantly more
 in sperm production than males of P. polionotus, their monogamous
 sister‐species. Here, we show that the larger testes in
 P. maniculatus are retained after decades of enforced monogamy in
 captivity. While these results suggest that differences in sperm
 production between species with divergent evolutionary histories can be
 maintained in captivity, we also show that the early rearing environment
 of males can strongly influence their testis size as adults. Using a
 second‐generation hybrid population to increase variation within the
 population, we show that males reared in litters with more brothers
 develop larger testes as adults. Importantly, this difference in testis
 size is also associated with increased fertility. Together, our findings
 suggest that sperm production may be both broadly shaped by natural
 selection over evolutionary timescales and also finely tuned during early
 development.
description: See methods within the manuscript
DOI: 10.15468/dl.cejmsu
title: Occurrence Download

description: A dataset containing 250936 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Canadian National Mycological Herbarium"
 ]
}

 The dataset includes 250936 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002043-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g1jwstqmr
title: Data from: Metabolic rate shapes phenotypic covariance among physiological, behavioural, and life history traits in honeybees

description: Metabolic rate is often cited as the fundamental rate that determines the
 rate of all biological processes by shaping energetic availability for the
 various behavioral and life history traits that contribute to performance.
 It has therefore been suggested that metabolic rate drives the widely
 observed covariance among these different levels of phenotypic traits.
 However, much of the work on this topic has relied on pairwise
 correlational analysis, thereby leaving an important gap in our
 understanding regarding the functional links that shape this phenotypic
 covariance, often referred to as pace-of-life. Using honeybees as an
 experimental model, we measured a large number of behavioural, life
 history and physiological traits in individual bees and used a structural
 equation model to characterize the phenotypic covariance structure among
 these traits. Following this with a path analysis, we demonstrate that
 variation in metabolic rate plays a fundamental proximate role in driving
 this phenotypic covariance structure in honeybees. We discuss the
 importance of these findings in the context of how interindividual
 variation in terms of slow-fast phenotypes may drive the phenotype of a
 group and the functional role metabolic rate might play in shaping
 division of labour and social evolution.
description: SMDN_POL_Data  Trait values and identities of
 all subjects (honeybees)
DOI: 10.5061/dryad.w6m905qkg
title: Individual signatures outweigh social group identity in contact calls of a communally nesting parrot

description: Despite longstanding interest in the evolutionary origins and maintenance
 of vocal learning, we know relatively little about how social dynamics
 influence vocal learning processes in natural populations. The “social
 group membership” hypothesis proposes that socially learned calls evolved
 and are maintained as signals of group membership. However, in
 fission-fusion societies, individuals can interact in social groups across
 various social scales. For learned calls to signal group membership over
 multiple social scales, they must contain information about group
 membership over each of these scales, a concept termed “hierarchical
 mapping”. Monk parakeets (Myiopsitta monachus), small parrots native to
 South America, exhibit vocal mimicry in captivity and fission-fusion
 social dynamics in the wild. We examined patterns of contact call acoustic
 similarity in Uruguay to test the hierarchical mapping assumption of the
 signaling group membership hypothesis. We also asked whether geographic
 variation patterns matched regional dialects or geographic clines that
 have been documented in other vocal learning species. We used visual
 inspection, spectrographic cross-correlation and random forests, a machine
 learning approach, to evaluate contact call similarity. We compared
 acoustic similarity across social scales and geographic distance using
 Mantel tests and spatial autocorrelation. We found high similarity within
 individuals, and low, albeit significant, similarity within groups at the
 pair, flock and site social scales. Patterns of acoustic similarity over
 geographic distance did not match mosaic or graded patterns expected in
 dialectal or clinal variation. Our findings suggest that monk parakeet
 social interactions rely more heavily upon individual recognition than
 group membership at higher social scales.
DOI: 10.5061/dryad.59zw3r23m
title: Data from: Macroevolution of desiccation-related morphology in plethodontid salamanders as inferred from a novel surface area to volume ratio estimation approach

description: Evolutionary biologists have long been interested in the macroevolutionary
 consequences of various selection pressures, yet physiological responses
 to selection across deep time are not well understood. In this paper, we
 investigate how a physiologically-relevant morphological trait, surface
 area to volume ratio (SA:V) of lungless salamanders, has evolved across
 broad regional and climatic variation. SA:V directly impacts an organisms’
 ability to retain water, leading to the expectation that smaller SA:Vs
 would be advantageous in arid, water-limited environments. To explore the
 macroevolutionary patterns of SA:V, we first develop an accurate method
 for estimating SA:V from linear measurements. Next, we investigate the
 macroevolutionary patterns of SA:V across 257 salamander species,
 revealing that higher SA:Vs phylogenetically correlate with warmer, wetter
 climates. We also observe higher SA:V disparity and rate of evolution in
 tropical species, mirrored by higher climatic disparity in available and
 occupied tropical habitats. Taken together, these results suggest that the
 tropics have provided a wider range of warmer, wetter climates for
 salamanders to exploit, thereby relaxing desiccation pressures on SA:V.
 Overall, this paper provides an accurate, efficient method for quantifying
 salamander SA:V, allowing us to demonstrate the power of physiological
 selection pressures in influencing the macroevolution of morphology.
description: Attached is the full zip of all scripts and data used in this
 analysis. Previous versions of this dryad respository only included the
 raw linear measurements and the SAV R function.
   Old version of SAV.Function.R had an error
 in labeling the columns differently than described in the main text and
 supporting information. See ReadMe files for more details, or download the
 new version of SAV.Function.R (updated 8/24/20), where the column names
 have been fixed.