cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3g55sv8
title: Data from: CO-RIP: a riparian vegetation and corridor extent dataset for Colorado River Basin streams and rivers

description: Here we present “CO-RIP”, a novel spatial dataset delineating riparian
 corridors and riparian vegetation along large streams and rivers in the
 United States (U.S.) portion of the Colorado River Basin. The consistent
 delineation of riparian areas across large areas using remote sensing has
 been a historically complicated process partially due to differing
 definitions in the scientific and management communities regarding what a
 “riparian corridor” or “riparian vegetation” represents. We use
 valley-bottoms to define the riparian corridor and establish a riparian
 vegetation definition interpretable from aerial imagery for efficient,
 consistent, and broad-scale mapping. Riparian vegetation presence and
 absence data were collected using a systematic, flexible image
 interpretation process applicable wherever high resolution imagery is
 available. We implemented a two-step approach using existing valley bottom
 delineation methods and random forests classification models that
 integrate Landsat spectral information to delineate riparian corridors and
 vegetation across the 12 ecoregions of the Colorado River Basin. Riparian
 vegetation model accuracy was generally strong (median kappa of 0.80),
 however it varied across ecoregions (kappa range of 0.42–0.90). We offer
 suggestions for improvement in our current image interpretation and
 modelling frameworks, particularly encouraging additional research in
 mapping riparian vegetation in moist coniferous forest and deep canyon
 environments. The CO-RIP dataset created through this research is publicly
 available and can be utilized in a wide range of ecological applications.
description: CORIP: Riparian Corridor
 and Vegetation Data FilesThe riparian vegetation
 dataset is distributed in a raster format, with a value of “0”
 corresponding to riparian vegetation absence and a value of “100”
 corresponding to riparian vegetation presence for a particular pixel
 (Figure 6). Valley bottom extents, which we have defined as a proxy for
 the spatial extent of the riparian zone, are distributed as polygons in
 shapefile format. Data files can be obtained for the entire Colorado River
 Basin or for each individual ecoregion based upon the user’s
 preference.CORIP_Riparian_Corridor_Vegetation.zip
DOI: 10.5061/dryad.50r1b
title: Data from: Tolerance to gamma radiation in the tardigrade Hypsibius dujardini from embryo to adult correlate inversely with cellular proliferation

description: Tardigrades are highly tolerant to desiccation and ionizing radiation but
 the mechanisms of this tolerance are not well understood. In this paper,
 we report studies on dose responses of adults and eggs of the tardigrade
 Hypsibius dujardini exposed to gamma radiation. In adults the LD50/48h for
 survival was estimated at ~ 4200 Gy, and doses higher than 100 Gy reduced
 both fertility and hatchability of laid eggs drastically. We also
 evaluated the effect of radiation (doses 50 Gy, 200 Gy, 500 Gy) on eggs in
 the early and late embryonic stage of development, and observed a reduced
 hatchability in the early stage, while no effect was found in the late
 stage of development. Survival of juveniles from irradiated eggs was
 highly affected by a 500 Gy dose, both in the early and the late stage.
 Juveniles hatched from eggs irradiated at 50 Gy and 200 Gy developed into
 adults and produced offspring, but their fertility was reduced compared to
 the controls. Finally we measured the effect of low temperature during
 irradiation at 4000 Gy and 4500 Gy on survival in adult tardigrades, and
 observed a slight delay in the expressed mortality when tardigrades were
 irradiated on ice. Since H. dujardini is a freshwater tardigrade with
 lower tolerance to desiccation compared to limno-terrestrial tardigrades,
 the high radiation tolerance in adults, similar to limno-terrestrial
 tardigrades, is unexpected and seems to challenge the idea that
 desiccation and radiation tolerance rely on the same molecular mechanisms.
 We suggest that the higher radiation tolerance in adults and late stage
 embryos of H. dujardini (and in other studied tardigrades) compared to
 early stage embryos may partly be due to limited mitotic activity, since
 tardigrades have a low degree of somatic cell division (eutely), and
 dividing cells are known to be more sensitive to radiation.
description: Data on radiation
 tolerance in Hypsibius dujardiniThis file contains all
 data used in the study on radiation tolerance in Hypsibius dujardini, by
 Beltran-Pardo et al.Data Beltran-Pardo et
 al.xlsx
DOI: 10.5061/dryad.ch576
title: Data from: Environmental DNA from seawater samples correlate with trawl catches of subarctic, deepwater fishes

description: Remote polar and deepwater fish faunas are under pressure from ongoing
 climate change and increasing fishing effort. However, these fish
 communities are difficult to monitor for logistic and financial reasons.
 Currently, monitoring of marine fishes largely relies on invasive
 techniques such as bottom trawling, and on official reporting of global
 catches, which can be unreliable. Thus, there is need for alternative and
 non-invasive techniques for qualitative and quantitative oceanic fish
 surveys. Here we report environmental DNA (eDNA) metabarcoding of seawater
 samples from continental slope depths in Southwest Greenland. We collected
 seawater samples at depths of 188–918 m and compared seawater eDNA to
 catch data from trawling. We used Illumina sequencing of PCR products to
 demonstrate that eDNA reads show equivalence to fishing catch data
 obtained from trawling. Twenty-six families were found with both trawling
 and eDNA, while three families were found only with eDNA and two families
 were found only with trawling. Key commercial fish species for Greenland
 were the most abundant species in both eDNA reads and biomass catch, and
 interpolation of eDNA abundances between sampling sites showed good
 correspondence with catch sizes. Environmental DNA sequence reads from the
 fish assemblages correlated with biomass and abundance data obtained from
 trawling. Interestingly, the Greenland shark (Somniosus microcephalus)
 showed high abundance of eDNA reads despite only a single specimen being
 caught, demonstrating the relevance of the eDNA approach for large species
 that can probably avoid bottom trawls in most cases. Quantitative
 detection of marine fish using eDNA remains to be tested further to
 ascertain whether this technique is able to yield credible results for
 routine application in fisheries. Nevertheless, our study demonstrates
 that eDNA reads can be used as a qualitative and quantitative proxy for
 marine fish assemblages in deepwater oceanic habitats. This relates
 directly to applied fisheries as well as to monitoring effects of ongoing
 climate change on marine biodiversity—especially in polar ecosystems.
description: Greenland eDNA raw
 sequencing dataThis contains the raw
 fastq files from eDNA sequencing from the study. Data is Illumina MiSeq
 paird-end in four libraries.Greenland eDNA Miseq raw fastq
 data.zip
DOI: 10.5061/dryad.5ff8m0q
title: Data from: Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar) parrs gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods.

description: Stocking methods are used in the Province of Quebec to restore Salmo salar
 populations. However, Atlantic salmon stocked juveniles show higher
 mortality rates than wild ones when introduced into nature. Hatchery
 environment, which greatly differs from the natural environment, is
 identified as the main driver of the phenotypic mismatch between captive
 and wild parrs. The latter is also suspected to impact the gut microbiota
 composition, which can be associated with essential metabolic functions
 for their host. We hypothesized that hatchery raised parrs potentially
 recruit gut microbial communities that are different from those recruited
 in the wild. This study evaluated the impacts of artificial rearing on gut
 microbiota composition in 0+ parrs meant for stocking in two distinct
 Canadian rivers: Rimouski and Malbaie (Quebec, Canada). Striking
 differences between hatchery and wild born parrs’ gut microbiota suggest
 that microbiota could be another factor that could impact their survival
 in the targeted river, since the microbiome is narrowly related to host
 physiology. For instance, major commensals belonging to Enterobacteriaceae
 and Clostridiacea from wild parrs’ gut microbiota were substituted in
 captive parrs by lactic acid bacteria from the Lactobacillaceae family.
 Overall, captive parrs host a generalist bacterial community whereas wild
 parrs’ microbiota is much more specialized. This is the very first study
 demonstrating extensive impact of captive rearing on intestinal microbiota
 composition in Atlantic salmon intended for wild population stocking. Our
 results strongly suggest the need to implement microbial ecology concepts
 into conservation management of endangered salmon stocks supplemented with
 hatchery reared parrs.
description: 16S_reads_salmo_salar_V3_V4_gut_microbiota.tar16S paired end reads from Salmo salar gut microbiota and water samples.
DOI: 10.5061/dryad.gv78b
title: Data from: Parasite and predator risk assessment: nuanced use of olfactory cues

description: Foraging herbivores face twin threats of predation and parasite infection,
 but the risk of predation has received much more attention. We evaluated,
 experimentally, the role of olfactory cues in predator and parasite risk
 assessment on the foraging behaviour of a population of marked,
 free-ranging, red-necked wallabies (Macropus rufogriseus). The wallabies
 adjusted their behaviour according to these olfactory cues. They foraged
 less, were more vigilant and spent less time at feeders placed in the
 vicinity of faeces from dogs that had consumed wallaby or kangaroo meat
 compared with that of dogs feeding on sheep, rabbit or possum meat.
 Wallabies also showed a species-specific faecal aversion by consuming less
 food from feeders contaminated with wallaby faeces compared with sympatric
 kangaroo faeces, whose gastrointestinal parasite fauna differs from that
 of the wallabies. Combining both parasite and predation cues in a single
 field experiment revealed that these risks had an additive effect, rather
 than the wallabies compromising their response to one risk at the expense
 of the other.
description: Sharp et al 2015
 dataResults of field
 experiments investigating response of red necked wallabies to faecal
 odours.
DOI: 10.5061/dryad.v4q0r
title: Data from: The first species of Hapalodectes (Mesonychia, Mammalia) from the middle Paleocene of China (Qianshan Basin, Anhui Province) sheds light on the initial radiation of hapalodectids

description: A lower jaw of the mesonychian Hapalodectes is reported from Nongshanian
 sediments (Upper Doumu Formation; middle Paleocene) of the Qianshan Basin
 (Anhui Province, China). The fragmentary mandible is only the third
 specimen of Hapalodectidae discovered in Paleocene deposits, and the first
 in south east China; it is moreover the oldest, the two other specimens
 having been found in Gashatan (late Paleocene) localities. The premolars
 and molars of the new fossil are morphologically similar to Hapalodectes
 dux (late Paleocene of Mongolia), which has been considered to be the most
 primitive hapalodectid, but their relative proportions recall H.
 paleocenus and the Eocene Hapalodectes species. As a result, the fossil
 described herein appears to be different from the other previously
 described species of Hapalodectes in being morphologically intermediate
 between H. dux and the other Hapalodectes species, notably the Bumbanian
 Hapalodectes hetangensis and H. huanghaiensis from China; it is thus
 identified as a new species, Hapalodectes lopatini (possibly a male
 individual). Its discovery is important because it sheds light on the
 initial radiation of hapalodectids. The presence of one primitive
 hapalodectid in Mongolia previously suggested the Mongolian Plateau as the
 centre of origination of this carnivorous family, but the discovery of H.
 lopatini in older sediments from south-east China challenges this
 hypothesis. In the earliest Eocene, Hapalodectes dispersed from Asia to
 North America; this event being part of the ‘East of Eden’ dispersals.
 This event resulted in the geographical separation of two distinct
 Hapalodectes groups, in North America and south-eastern China
 respectively.
description: Matrix
 (Nexus)The matrix in Nexus file
 formatMatrix
 NexusMatrix
 TNTThe matrix formatted for
 TNTMatrix
 WincladaThe Matrix formatted for
 Winclada
DOI: 10.5281/zenodo.17484326
title: Dataset of the paper "Understanding Students' Interactions with Large Language Models for Software Engineering Tasks"

description: This dataset contains:



 Transcriptions of interviews conducted with 20 undergraduate students from the Computer Science course at [anonymized];

The answers from each participant to the proposed survey, which included questions about their profile, use of LLMs, and impressions of LLM responses.


Each transcription is provided in both Portuguese and an English version to enable access to the original content and broaden global accessibility/readership. The English versions were translated using Gemini 2.5 Pro. All content has been anonymized to protect the participants' identities. It's important to highlight that participants provided explicit consent for the anonymized publication of their data.

The file names in this dataset follow this pattern:



interview_pX_pt.txt: The Portuguese transcription for a participant. "X" represents the participant's numerical ID (ranging from 1 to 20);

interview_pX_en.txt: The English translation for a participant. "X" represents the participant's numerical ID (ranging from 1 to 20);

form_answers.xls: The file containing the survey answers for all participants. The numerical IDs in this spreadsheet correspond to the IDs used in the transcription filenames.


The qualitative coding file, generated using MAXQDA as part of the research process, is not provided here. This exclusion is necessary to protect participants' identities, as the file contains names and references to the participants.
DOI: 10.5281/zenodo.17484327
title: Dataset of the paper "Understanding Students' Interactions with Large Language Models for Software Engineering Tasks"

description: This dataset contains:



 Transcriptions of interviews conducted with 20 undergraduate students from the Computer Science course at [anonymized];

The answers from each participant to the proposed survey, which included questions about their profile, use of LLMs, and impressions of LLM responses.


Each transcription is provided in both Portuguese and an English version to enable access to the original content and broaden global accessibility/readership. The English versions were translated using Gemini 2.5 Pro. All content has been anonymized to protect the participants' identities. It's important to highlight that participants provided explicit consent for the anonymized publication of their data.

The file names in this dataset follow this pattern:



interview_pX_pt.txt: The Portuguese transcription for a participant. "X" represents the participant's numerical ID (ranging from 1 to 20);

interview_pX_en.txt: The English translation for a participant. "X" represents the participant's numerical ID (ranging from 1 to 20);

form_answers.xls: The file containing the survey answers for all participants. The numerical IDs in this spreadsheet correspond to the IDs used in the transcription filenames.


The qualitative coding file, generated using MAXQDA as part of the research process, is not provided here. This exclusion is necessary to protect participants' identities, as the file contains names and references to the participants.
DOI: 10.5061/dryad.sv515
title: Data from: Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice

description: The presence of rogue taxa (rogues) in a set of trees can frequently have
 a negative impact on the results of a bootstrap analysis (e.g., the
 overall support in consensus trees). We introduce an efficient graph-based
 algorithm for rogue taxon identification as well as an interactive
 web-service implementing this algorithm. Compared to our previous method,
 the new algorithm is up to four orders of magnitude faster, while
 returning qualitatively identical results. Because of this significant
 improvement in scalability, the new algorithm can now identify
 substantially more complex and compute-intensive rogue taxon
 constellations. On a large and diverse collection of real-world datasets,
 we show that, our method yields better supported reduced/pruned consensus
 trees than any competing rogue taxon identification method. Using the
 parallel version of our open-source code, we successfully identified rogue
 taxa in a set of 100 trees with 116,334 taxa each. Using simulated
 datasets we show that, when removing/pruning rogue taxa with our method
 from a tree set, we consistently obtain bootstrap consensus trees as well
 as maximum likelihood trees that are topologically closer to the
 respective true trees.
description: online-dataonline-appendix-v1.1online-appendix.pdf
DOI: 10.5061/dryad.8b2q1v1d
title: Data from: Within-season synchrony of a masting conifer enhances seed escape

description: Predator satiation resulting from interannual reproductive synchrony has
 been widely documented in masting plants, but how reproductive synchrony
 within a year influences seed escape is poorly understood. We evaluated
 whether the intra-annual reproductive synchrony of individual white spruce
 trees (Picea glauca) increased seed escape from their primary predispersal
 seed predator, North American red squirrels (Tamiasciurus hudsonicus).
 Trees with cones that matured synchronously relative to those of other
 trees within red squirrel territories were significantly more likely to
 escape squirrel predation in years with both low and superabundant levels
 of cone production, generating a significantly positive linear selection
 differential for increasing intra-annual reproductive synchrony. Thus,
 this masting plant escapes seed predation in numbers through interannual
 synchrony in seed production and in time through intra-annual synchrony of
 seed availability.
description: TreeINFO
DOI: 10.5061/dryad.b2s0dt4
title: Data from: Adaptation, chance, and history in experimental evolutionary reversals to unicellularity

description: Evolution is often deemed irreversible. The evolution of complex traits
 that require many mutations makes their reversal unlikely. Even in simpler
 traits, reversals might become less likely as neutral or beneficial
 mutations, with deleterious effects in the ancestral context, become fixed
 in the novel background. This is especially true in changes that involve
 large re-organizations of the organism and its interactions with the
 environment. The evolution of multicellularity involves the reorganization
 of previously autonomous cells into a more complex organism; despite the
 complexity of this change, single cells have repeatedly evolved from
 multicellular ancestors. These repeated reversals to unicellularity
 undermine the generality of Dollo’s law. In this paper we evaluated the
 dynamics of reversals to unicellularity from recently evolved
 multicellular phenotypes of the brewers' yeast Saccharomyces
 cerevisae. Even though multicellularity in this system evolved recently,
 it involves the evolution of new levels of selection. Strong selective
 pressures against multicellularity lead to rapid reversibility to single
 cells in all of our replicate lines, whereas counterselection favoring
 multicellularity led to minimal reductions to the rates of reversal.
 History and chance played an important role in the tempo and mode of
 reversibility, highlighting the interplay of deterministic and stochastic
 events in evolutionary reversals.
description: FreqUnisAllSize measurements for individual clusters of each of the populations and treatments over time.UV survival dataKillCurve_UV.csvKillCurveR code to plot UV survival curves and fit exponential decay model.Reversal rateSummarize and plot data. Fit different linear models and check assumptions.ReversalRateGraphs2.RHistoryChanceSelectionR code to calculate the relative contributions of history, chance, and selection.README
DOI: 10.5061/dryad.kq77d
title: Data from: Experience matters: context-dependent decisions explain spatial foraging patterns in the deposit-feeding crab Scopimera intermedia

description: Behavioural decisions are often context-dependent, where information from
 immediate experience is incorporated into an individual's
 decision-making, particularly in complex environments. To test whether
 such mechanism is adopted by foragers in heterogeneous environments, we
 investigated the foraging behaviour of the deposit-feeding sand-bubbler
 crab, Scopimera intermedia. An individual-based model was constructed,
 based on an optimal-patch selection criterion, which implicitly assumed
 that individuals adjust foraging decisions based on immediate past
 experience. The model's predictions were tested on the shore by
 manipulating the location of food patches, where the crab showed a strong
 context-dependent foraging pattern. When resources were randomly
 distributed, the crab responded by spending 56% of time in enriched
 patches compared with only 28% in the same area when patches were composed
 of natural sediments. Shore manipulations varying resource distribution
 supported the underlying principles of the model mechanism, and
 highlighted the benefits of such a strategy in heterogeneous environments
 such as intertidal sediments where food resources vary at different
 spatial and temporal scales. The proposed model therefore provides a
 mechanistic process, based on optimal foraging, to predict foraging
 decisions and movement patterns of animals feeding in heterogeneous
 landscapes.
description: Experimental results of
 testing the model predictionmodel_expt.xlsxSimulation results of the individual-based modelmodel_predictions.xlsxExperimental results of the experiment to test context-dependencyparameter_expt.xlsxSediment parameters for the foraging experimentssediment_params.xlsx