cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1vhhmgqpc
title: Surface characterization and biodegradability of sodium hydroxide-treated Moso bamboo substrates

description: Alkali solution immersion is widely used in pretreatment during bamboo and
 wood product manufacturing. In this study, we performed a surface analysis
 on the bamboo chips pretreated by sodium hydroxide with different
 concentrations at room temperature (25 ℃) and evaluated the surface
 performance and biodurability. Bamboo surface rapidly changed to darker
 color at sodium hydroxide concentration (NaOH) of 5% and become rough at
 20% NaOH. The K-M curve showed absorption peak near 390-410 nm after
 alkali treatment, which was due to the presence of chromophore groups
 derived from lignin, especially from methylene quinone. X-ray diffraction
 (XRD) showed the area of the crystallization zone was enlarged rapidly at
 5% NaOH and then declined. Fourier transform infrared spectroscopy
 illustrated the conjugate structure of lignin-phenols changed after proton
 transfer in hydroxyl radical solution and this was the main reason for the
 surface color changes. During alkali treatment, lignin and hemicellulose
 in bamboo degraded to some extent, but cellulose was less affected. X-ray
 photoelectron spectroscopy demonstrated the oxygen-carbon ratio (O/C) and
 the oxygenated to unoxygenated carbon ratio (Cox/Cunox) all increased,
 indicating the decrease of extractives and lignin and surface carbon atoms
 were oxidized in alkali solution and carbon bonds were i more stable. XRD
 showed sodium hydroxide immersion can not only degrade and dissolve
 low-polymerization substances in the amorphous zone, increased the
 crystalline region, but also reached crystalline region, swell the cell
 wall, which increased the accessibility of fungi and made bamboo more
 susceptible to fungi infection. Bamboo weight loss of decay after alkali
 treatment was all larger than the control and maximized at 10% NaOH.
description: .opj files can be viewed in the software Origin
DOI: 10.5061/dryad.41ns1rn9m
title: Virtual stick balancing: Sensorimotor uncertainties related to angular displacement and velocity

description: Sensory uncertainties and imperfections in motor control play important
 roles in neural control and Bayesian approaches to neural encoding.
 However, it is diffcult to estimate these uncertainties experimentally.
 Here we show that magnitude of the uncertainties during the generation of
 motor control force can be measured for a virtual stick balancing task by
 varying the feedback delay, tau . It is shown that the shortest
 stick length that human subjects are able to balance is proportional to
 tau^2. The proportionality constant can be related to a combined effect of
 the sensory uncertainties and the error in the realization of the control
 force, based on a delayed proportional-derivative (PD) feedback model of
 the balancing task. The neural reaction delay of the human subjects were
 measured by standard reaction time tests and by visual blank out tests.
 Experimental observations provide an estimate for the upper boundary of
 the average sensorimotor uncertainty associated either with angular
 position or with angular velocity. Comparison of balancing trials with 27
 human subjects to the delayed PD model suggests that the average
 uncertainty in the control force associated purely with the angular
 position is at most 14% while that of associated purely with the angular
 velocity is at most 40%. In the general case when both uncertainties are
 present, the calculations suggest that the allowed uncertainty in angular
 velocity will always be greater than that in angular position.
DOI: 10.5061/dryad.hmgqnk9c6
title: Age-related brood parasitism and egg rejection in magpie hosts

description: When the strength or nature of a host -parasite interaction changes over
 the host life cycle, the consequences of parasitism can depend on host
 population age structure. Avian brood parasites reduce hosts’ breeding
 success, and host age may play a role in this interaction if younger hosts
 are more likely parasitized and/or less able to defend themselves. We
 analyzed whether the age of female magpies (Pica pica) hosts is associated
 with parasite attack or their ability to reject foreign eggs. We recorded
 parasitism and model egg rejection of known-age individuals over their
 lifetime, and established whether likelihood of parasitism or egg
 rejection changed with age or longevity. Parasitism probability did not
 change with female age and there was a trend for longer lived females to
 be more likely to be parasitized. However, model egg rejection probability
 increased with age for each individual female, and longer-lived females
 were more prone to reject. Most females in the population were young, and
 the majority of them accepted model eggs, suggesting that brood parasites
 exploiting younger host individuals are benefitting from a lower defensive
 level of their hosts. Our results stress that the intensity of selection
 by brood parasites may be mediated by the age-structure of host
 populations, a so far neglected aspect in brood parasite-host research.
DOI: 10.5061/dryad.98sf7m0f0
title: Genomic footprints of a biological invasion: introduction from Asia and dispersal in Europe of the topmouth gudgeon (Pseudorasbora parva)

description: Facilitated by the intensification of global trading, the introduction and
 dispersal of species to areas in which they are historically non-native is
 nowadays common. From an evolutionary standpoint, invasions are
 paradoxical: not only non-native environments could be different from
 native ones for which introduced individuals would be ill-adapted, but
 also small founding population size should be associated with reduced
 adaptive potential. As such, biological invasions are considered valuable
 real-time evolutionary experiments. Here, we investigated the population
 structure and adaptive potential of the highly invasive topmouth gudgeon
 (Pseudorasbora parva) across Europe and East Asia. We RAD-sequenced 301
 specimens from sixteen populations and three distinct within-catchment
 invaded regions as well as two locations in the native range. With 13785
 single nucleotide polymorphisms, we provide conclusive evidence for a
 genome-wide signature of two distinct invasion events, in Slovakia and
 Turkey, each originating from a specific area in the native range. A third
 invaded area, in France, appears to be the result of dispersal within the
 invasive range. Few loci showed signs of selection, the vast majority of
 which being identified in the Slovakian region. Functional annotation
 suggests that faster early stage development, resistance to pollution and
 immunocompetence contribute to the invasion success of the local habitats.
 By showing that populations in the invasive range have different
 evolutionary histories, our study reinforces the idea that populations,
 rather than species, are the units to consider in invasion biology.
DOI: 10.5061/dryad.q573n5tf4
title: Conflicting phylogenetic signals in genomic data of the coffee family (Rubiaceae)

description: Reconstructions of phylogenetic relationships in the flowering plant
 family Rubiaceae, or the coffee family, have up until now relied heavily
 on single or multi-gene data, primarily from the plastid compartment. With
 the availability of cost- and time-efficient techniques for generating
 complete genome sequences, the opportunity arises to resolve some of the
 relationships that up until now have proven problematic. Here we
 contribute new data from complete 58 plastid genome sequences representing
 55 of the currently 65 recognized tribes of the Rubiaceae. Also
 contributed are new data from the nuclear rDNA cistrons for the
 corresponding taxa. Phylogenetic analyses are conducted on two plastid
 data sets, one including data from the protein coding genes only with a
 total of 69,828 aligned characters, and a second where protein coding data
 are combined with an additional 25,666 aligned characters from non-coding
 regions, and on a nuclear rDNA data set including 6,045 aligned
 characters. Our results clearly show that simply adopting a “more
 characters” approach does not resolve the relationships in the Rubiaceae.
 More importantly, we identify conflicting phylogenetic signals in the
 data. Analyses of the same plastid data, treated as nucleotides or as
 codon degenerated data, resolve and support conflicting topologies in the
 subfamily Cinchonoideae. As these analyses use the same data, we interpret
 the conflict to result from erroneous assumptions in the models used to
 reconstruct our phylogenies. Conflicting signals are also identified in
 the analyses of the plastid vs. the nuclear rDNA data sets. These analyses
 use data from different genomic compartments, with different inheritance
 patterns, and we interpret the conflicts as representing “real” conflicts,
 reflecting biological processes of the past.
DOI: 10.5061/dryad.2280gb5nc
title: How long does it take to fix a favorable mutation, and why should we care?

description: The time taken for a selectively favorable allele to spread through a
 single population was investigated early in the history of population
 genetics. The resulting formulae are based on deterministic dynamics,
 leading to inaccuracies at allele frequencies close to zero or one. To
 remedy this problem, the properties of the stochastic phases at either
 endpoint of allele frequency need to be analysed. This paper uses a
 heuristic approach to determining the expected times spent in the
 stochastic and deterministic phases of allele frequency trajectories, for
 a model of weak selection at a single locus that is valid for inbreeding
 populations and for autosomal and sex-linked inheritance. The net fixation
 time is surprisingly insensitive to the level of dominance of a favorable
 mutation, even with random mating. Approximate expressions for the
 variance of the net fixation time are also obtained, which imply that the
 coefficient of variation can be substantial even in very large
 populations. The theoretical formulae give good approximations to
 simulations for most parameter sets. The results have implications for
 analyses of the effects of selective sweeps on variability at linked
 sites. They reveal some areas that need further investigation, to
 facilitate a full understanding of selective sweeps.
description: Computer code is provide for the calculations described in the
 American Naturalist article "How long does it take to fix a favorable
 mutation, and why should we care?"
DOI: 10.5281/zenodo.14278846
title: IPATH Dataset: 45,609 Curated Image-Text Pairs for Histopathology Applications

description: Recent advancements in artificial intelligence (AI) have enabled the identification of patterns in pathology images, improving 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, using a combination of 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 the pre-trained CLIP model using the IPATH dataset. IP-CLIP outperforms the original CLIP model in classifying new pathology images on two downstream tasks—zero-shot classification and linear probing—using two external histopathology datasets. These results surpass the CLIP baseline model and demonstrate the effectiveness of the IPATH dataset, highlighting the potential of social media data to advance AI models for medical image classification.
DOI: 10.5061/dryad.dfn2z34wj
title: Genetically determined blood pressure, antihypertensive drug classes and risk of stroke subtypes

description: Objective: We employed Mendelian Randomization to explore whether the
 effects of blood pressure (BP) and BP lowering through different
 antihypertensive drug classes on stroke risk vary by stroke etiology.
 Methods: We selected genetic variants associated with systolic and
 diastolic BP and BP-lowering variants in genes encoding antihypertensive
 drug targets from a GWAS on 757,601 individuals. Applying two-sample
 Mendelian randomization, we examined associations with any stroke (67,162
 cases; 454,450 controls), ischemic stroke and its subtypes (large artery,
 cardioembolic, small vessel stroke), intracerebral hemorrhage (ICH, deep
 and lobar), and the related small vessel disease phenotype of WMH.
 Results: Genetic predisposition to higher systolic and diastolic BP was
 associated with higher risk of any stroke, ischemic stroke, and ICH. We
 found associations between genetically determined BP and all ischemic
 stroke subtypes with a higher risk of large artery and small vessel stroke
 compared to cardioembolic stroke, as well as associations with deep, but
 not lobar ICH. Genetic proxies for calcium channel blockers, but not beta
 blockers, were associated with lower risk of any stroke and ischemic
 stroke. Proxies for CCBs showed particularly strong associations with
 small vessel stroke and the related radiological phenotype of WMH.
 Conclusions: This study supports a causal role of hypertension in all
 major stroke subtypes except lobar ICH. We find differences in the effects
 of BP and BP lowering through antihypertensive drug classes between stroke
 subtypes and identify calcium channel blockade as a promising strategy for
 preventing manifestations of cerebral small vessel disease.
DOI: 10.5061/dryad.cfxpnvx2d
title: Life history evolution, species differences and phenotypic plasticity in hemiparasitic eyebrights (Euphrasia)

description: Premise of the study: Species delimitation in parasitic organisms is
 challenging as traits used in the identification of species are often
 plastic and vary depending on the host. Here, we use species from a recent
 radiation of generalist hemiparasitic Euphrasia to investigate trait
 variation and trait plasticity. We test whether Euphrasia species show
 reliable trait differences, investigate whether these differences
 correspond to life history trade-offs between growth and reproduction, and
 quantify plasticity in response to host species. Methods: We perform
 common garden experiments to evaluate trait differences between eleven
 Euphrasia taxa grown on a common host, document phenotypic plasticity when
 a single Euphrasia species is grown on eight different hosts, and relate
 our observations to trait differences recorded in the wild. Key results:
 Euphrasia exhibit variation in life history strategies; some individuals
 transition rapidly to flower at the expense of early season growth, while
 others invest in vegetative growth and delay flowering. Life history
 differences are present between some species, though many related taxa
 lack clear-cut trait differences. Species differences are further blurred
 by phenotypic plasticity—many traits are plastic and change with host type
 or between environments. Conclusions: Phenotypic plasticity in response to
 host and environment confounds species delimitation in Euphrasia. When
 grown in a common garden environment it is possible to identify some
 morphologically distinct taxa, though others represent morphologically
 similar shallow segregates. Trait differences present between some species
 and populations demonstrates the rapid evolution of distinct life history
 strategies in response to local ecological conditions.
description: Data collection is detailed in the associated manuscript. Post
 collection data processing can be viewed at: https://github.com/Euphrasiologist/phenotypic_plasticity_euphrasia
description: "Manyhosts.csv" contains morphological measurements
 from one <em>Euphrasia arctica</em> population from North
 Berwick, Scotland, grown with eight hosts.
 "Manyspecies.csv" contains morphological measurements
 of five <em>Euphrasia</em> species and six
 natural <em>Euphrasia</em> hybrids grown on a single
 host, <em>Trifolium repens</em>.
 "Earlylate.csv" contains repeated growth
 measurements at different times of year, used in correlations of height at
 end of season. "Wildcommon.csv"
 contains <em>Euphrasia</em> species grown in the common garden
 experiment and wild collected plants for trait comparisons.
DOI: 10.5061/dryad.8kprr4xj9
title: Data from: The Fungal Endophyte Epichloë festucae var. lolii Plays a Limited Role in Mediating Crown Rust Severity in Perennial Ryegrass

description: Perennial ryegrass (Lolium perenne L.) is an important turf and forage
 species that often becomes infected with Puccinia coronata f. sp. lolii,
 the causal pathogen of crown rust. Disease control through
 clavicipitaceous endophytes has been proposed as a potential biocontrol.
 Two field experiments were designed to determine the influence of native
 Epichloë endophyte infection on natural rust development across a diverse
 panel of perennial ryegrass germplasm. Experiment 1 used an isogenic
 population design in which infected (E+) or endophyte-free (E−) clonal
 plants were nested within 14 perennial ryegrass entries. Experiment 2
 consisted of isofrequent E+ and E− progeny from isogenic parents. Results
 showed the endophyte had no consistent main effect on crown rust severity
 across or within entries; however, several isogenic host pairs did show
 either favorable or antagonistic effects. Despite these sporadic effects,
 no differences were found between isofrequent family pairs, indicating the
 presence of a host  endophyte interaction. Genotypic and phenotypic data
 revealed that endophyte isolates were similar within entry, indicating
 that host genotype could be responsible for the highly specific endophyte
 effect on crown rust. The preponderance of host resistance in mediating
 rust severity was supported by large broad (&gt;.75) and narrow-sense
 (.76) heritability estimates. These findings support the conclusion that
 endophyte infection does not play a substantial role in mediating crown
 rust severity on a population scale in perennial ryegrass.
description: See publication for details. 
description: The dataset inlcludes metadata for each column and basics on
 experimental desing. The R script that repoduces the results is attached
 to the paper and will run off the scritp without any
 modifications.
DOI: 10.5281/zenodo.18020876
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.