cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vt4b8gtz1
title: Data from: The effect of initial vortex asymmetric structure on tropical cyclone intensity change in response to an imposed environmental vertical wind shear

description: Previous studies have investigated how the environmental vertical wind
 shear (VWS) may trigger the asymmetric structure in an initially
 axisymmetric tropical cyclone (TC) vortex and how TC intensity changes in
 response. In this study, the possible effect of the initial vortex
 asymmetric structure on the TC intensity change in response to an imposed
 environmental VWS is investigated based on idealized full-physics model
 simulations. Results show that the effect of the asymmetric structure in
 the initial TC vortex can either enhance or suppress the initial weakening
 of the TC in response to the imposed environmental VWS. When the initial
 asymmetric structure is in phase of the VWS-induced asymmetric structure,
 the TC weakening will be enhanced and vice versa. Our finding calls for
 realistic representation of initial TC asymmetric structure in numerical
 weather prediction models and observations to better resolve the
 asymmetric structure in TCs.
description: The original data generated by our idealized experiments using
 the WRF model is very large, so we used Fortran (you can also use Python,
 MATLAB and other tools) to preprocess the data and obtain the main
 variables needed for our research analysis. The preprocessed data is in
 binary format. The WRF model is a numerical weather
 prediction and atmospheric research model developed by organizations
 including the National Center for Atmospheric Research (NCAR) and the
 National Centers for Environmental Prediction (NCEP) in the USA. WRF is
 open-source software and can be downloaded from
 https://github.com/wrf-model/WRF/releases. The specific
 parameters and settings used to configure the WRF model runs are described
 in detail in the paper. Interested researchers can follow the settings in
 the paper to regenerate the original raw data. However, the raw data files
 are very large (tens of GB per file), making direct analysis difficult.
 Therefore, we used tools like Fortran to preprocess the raw data into
 smaller binary files containing the key variables needed for analysis,
 such as radar reflectivity, winds, etc. The binary files are around a few
 hundred MB in size. We strongly recommend that subsequent researchers
 directly use these preprocessed binary data files, which will greatly
 simplify the data processing workflow. 
description: The data can be read using Python, NCL, Grads, Fortran, Matlab
 and other tools. Here we take NCL as an
 example: To read the first, second and third variables
 in the data initial_dbz_w.d as an example:  do
 k=1,59 var1 = fbindirread(“initial_dbz_w.d”, k,
 (/300,300/),“float”) var2 =
 fbindirread(“initial_dbz_w.d”, 59+k, (/300,300/),“float”)
 var3 = fbindirread(“initial_dbz_w.d”, 2*59+k,
 (/300,300/),“float”) end do …and so
 on<br>NCL can be obtained by
 https://www.ncl.ucar.edu/Download/
DOI: 10.5061/dryad.djh9w0w5b
title: Changes in vertical and horizontal diversities mediated by the size structure of introduced fish collectively shape food-web stability

description: Species introductions can alter local food-web structure by changing the
 vertical or horizontal diversity within communities, largely driven by
 their body size distributions. Increasing vertical and horizontal
 diversities is predicted to have opposing effects on stability. However,
 their interactive effects remain largely overlooked. We investigated the
 independent and collective effects of vertical and horizontal diversities
 on food-web stability in alpine lakes stocked with variable body size
 distributions of introduced fish species. Introduced predators destabilize
 food-webs by increasing vertical diversity through food chain lengthening.
 Alternatively, increasing horizontal diversity results in more stable
 food-web topologies. A non-linear interaction between vertical and
 horizontal diversities suggests that increasing vertical diversity is most
 destabilizing when horizontal diversity is low. Our findings suggest that
 the size structure of introduced predators drives their impacts on
 stability by modifying the structure of food-webs, and highlights the
 interactive effects of vertical and horizontal diversities on stability.
DOI: 10.5061/dryad.np5hqc003
title: Model aversiveness and the evolution of imperfect Batesian mimics

description: There are numerous examples in the natural world of Batesian mimics that
 only imperfectly resemble their models. Given that inaccurate mimics are
 known to be predated more frequently than accurate ones, imperfect mimicry
 therefore poses something of a conundrum. One putative explanation, the
 relaxed selection hypothesis, predicts that when the cost of attacking a
 model is high relative to the benefit of consuming a mimic, selection
 against imperfect mimics will be relaxed, allowing mimics to be more
 imperfect for a given level of fitness. However, empirical support for
 this hypothesis is equivocal. Here we report an experimental test of the
 relaxed selection hypothesis, in which human participants were tasked with
 discriminating between artificial stimuli representing models and mimics.
 In response to ‘attacking’ a model (i.e., misclassifying it as palatable,
 or non-aversive) they received either a mild electric shock (high cost) or
 vibratory feedback (low cost). Consistent with the predictions of this
 hypothesis, we found that when the cost of attacking a model was high,
 mimetic phenotype could deviate more from the model (i.e., be more
 imperfect) for a given level of fitness than when the cost of attacking a
 model was low. Moreover, when the cost of attacking a model was high,
 participants showed an increased latency to attack. This finding shows
 that given sufficient costs, the relaxed selection hypothesis is a
 plausible explanation for the evolution of imperfect mimicry within
 certain ecological contexts.
DOI: 10.5061/dryad.r4xgxd2k5
title: Tissue-specific features of the T cell repertoire following allogeneic hematopoietic cell transplantation in human and mouse

description: T cells are the central drivers of many inflammatory diseases, but the
 repertoire of tissue-resident T cells at sites of pathology in human
 organs remains poorly understood. We examined the site-specificity of T
 cell receptor (TCR) repertoires across tissues (5-18 tissues per patient)
 in prospectively collected autopsies of patients with and without
 graft-versus-host disease (GVHD), a potentially lethal tissue-targeting
 complication of allogeneic hematopoietic cell transplantation, as well as
 in mouse models of GVHD. Anatomic similarity between tissues was a key
 determinant of TCR repertoire composition within patients, independent of
 disease or transplant status. The T cells recovered from peripheral blood
 and spleen in patients and mice captured a limited portion of the TCR
 repertoire detected in tissues. Whereas few T cell clones were shared
 across patients, motif-based clustering revealed shared repertoire
 signatures across patients in a tissue-specific fashion. T cells at
 disease sites had a tissue-resident phenotype and were of donor origin
 based on single-cell chimerism analysis. These data demonstrate the
 complex composition of T cell populations that persist in human tissues at
 the end-stage of an inflammatory disorder following lymphocyte-directed
 therapy. These findings also underscore the importance of studying T cells
 in tissues rather than blood for tissue-based pathologies and suggest the
 tissue-specific nature of both the endogenous and post-transplant T cell
 landscape.
description: Data here are aggregated from the Adaptive Biotech data found
 here: https://doi.org/10.21417/SD2022GVHD
DOI: 10.5281/zenodo.18400107
title: Validation of a handheld smartphone markerless method for quantifying thoracolumbar flexion–extension range of motion in horses at trot

description: This repository contains data associated with the study “Validation of a handheld smartphone markerless method for quantifying thoracolumbar flexion–extension range of motion in horses at trot.”

The study evaluates the performance of a vision based, markerless computer vision algorithm for quantifying thoracolumbar flexion–extension range of motion (FEROM) in horses during trot under field conditions.

The algorithm (RealHorse®) performance is assessed through comparison with a 3D optical motion capture reference system (Qualisys®), analysing FEROM at both stride and trial levels in horses trotting on a straight line and on a circle.

The dataset supports clinical and research applications in the objective assessment of equine back motion using accessible smartphone based tools.
DOI: 10.5281/zenodo.18400108
title: Validation of a handheld smartphone markerless method for quantifying thoracolumbar flexion–extension range of motion in horses at trot

description: This repository contains data associated with the study “Validation of a handheld smartphone markerless method for quantifying thoracolumbar flexion–extension range of motion in horses at trot.”

The study evaluates the performance of a vision based, markerless computer vision algorithm for quantifying thoracolumbar flexion–extension range of motion (FEROM) in horses during trot under field conditions.

The algorithm (RealHorse®) performance is assessed through comparison with a 3D optical motion capture reference system (Qualisys®), analysing FEROM at both stride and trial levels in horses trotting on a straight line and on a circle.

The dataset supports clinical and research applications in the objective assessment of equine back motion using accessible smartphone based tools.
DOI: 10.5061/dryad.jdfn2z3gg
title: Monitoring moose in Montana using hunter observations to count moose by district

description: During 2012–2016, we queried hunters of deer and elk for observations of
 groups of a non-target species, moose, across their statewide distribution
 in Montana.  We used buffer analyses to filter data according to
 independent observations in space and time and then tallied observations
 of groups by hunting district.  We then analyzed data in an
 abundance-detection framework with n-mixture models and evaluated the
 effects of covariates such as hunter effort, survey response totals,
 weekly session, and forest cover on detection probability before using
 models to predict moose abundance.  Lastly, we converted model
 predictions of group abundnace to total abundance by multiplying number of
 groups by average group size per administrative region.
description: Analyzed in Program R with the package unmarked
DOI: 10.5061/dryad.dbrv15f6k
title: Adaptations to the deep-sea alongside presence of a mega-array of homeobox genes in the genome of the cnidarian Actinernus

description: Members of the phylum Cnidaria include sea anemones, corals, and
 jellyfishes, and have successfully colonised both marine and freshwater
 habitats throughout the world. Understanding of how cnidarians adapt to
 extreme environments such as the dark, high-pressure deep-sea habitat has
 been hindered by the lack of genomic information. Here we report the first
 chromosome-level deep-sea cnidarian genome, of the anemone Actinernus.
 Analyses of homeobox genes revealed the longest chromosome hosts a
 mega-array of Hox cluster, HoxL, ParaHox, NK cluster, and NKL homeobox
 genes; until now, such an array has only been hypothesized to have existed
 in ancient ancestral genomes. Analysis of microRNAs revealed
 cnidarian-specific complements that are distinctive for nested clades of
 these animals, presumably reflecting the progressive evolution of the gene
 regulatory networks in which they are embedded. Compared to other sea
 anemones, circadian rhythm genes were lost in Actinernus, which likely
 reflects adaptation to living in the dark. This high-quality genome of a
 deep-sea cnidarian deepens our understanding of the evolution of genome
 content and organization of animals in general and cnidarians in
 particular and reveals some of the molecular adaptations of this
 ecologically important group of metazoans to the extreme deep-sea
 environment.
description: Gene models were trained and
 predicted using funannotate (v1.8.9).
DOI: 10.5061/dryad.0vt4b8h4f
title: Data from: Inhibition of the dorsomedial striatal direct pathway is essential for the execution of action sequences

description: Contrary to the previous notion that the dorsomedial striatum (DMS) is
 crucial for acquiring new learning, accumulated evidence has suggested
 that the DMS also plays a role in the execution of already learned action
 sequences. Here, we examined how the direct and indirect pathways in the
 DMS regulate action sequences using a task that requires animals to press
 a lever consecutively. Cell-type-specific bulk Ca2+ recording revealed
 that the direct pathway was inhibited at the time of sequence execution.
 The sequence-related response was blunted in trials where the sequential
 behaviors were disrupted. Optogenetic activation at the sequence start
 caused distraction of action sequences without affecting motor function or
 memory of the task structure. By contrast with the direct pathway, the
 indirect pathway was slightly activated at the start of the sequence, but
 the optogenetic suppression of such sequence-related signaling did not
 impact the behaviors. These results suggest that the inhibition of the DMS
 direct pathway promotes sequence execution potentially by suppressing the
 formation of a new association.
description: # Data from: Inhibition of the dorsomedial striatal direct pathway is
 essential for the execution of action sequences ## Description of the Data
 and file structure The .bin files named as A0234, A0241, A0246, A0249,
 A0252, A0284 and A0297 indicate photometry data of D1-YC mice. The .bin
 files named as A0182, A0201, A0202, A0253, and A0288 indicate photometry
 data of D2-YC mice. The .bin files named as A0238, A0240, A0278, A0279,
 A0280, A0281 indicate optogenetic data of D1-ChR2 mice. The .bin files
 named as A0264, A0275, A0276, A0292 and A0293 indicate optogenetic data of
 D2-ArchT mice.
DOI: 10.5061/dryad.zs7h44jfm
title: DNA metabarcoding illuminates the contribution of small and very small prey taxa to the diet of lions

description: Knowledge of food web interactions is essential for understanding the role
 of carnivores in an ecosystem and designing appropriate conservation and
 management strategies to preserve them. These interactions can only be
 understood by studying carnivores’ diets and obtaining comprehensive and
 unbiased diet data. For large carnivores – which typically rely on large
 herbivores as prey – the role of smaller prey species has not received
 attention. This study aims to quantify the contribution of small (5–50 kg)
 and very small (&lt;5 kg) prey taxa in the diet of lions (Panthera leo
 melanochaita) in four Kenyan National Parks (NPs). We use DNA
 metabarcoding to achieve higher-resolution insights into prey composition,
 which is less biased toward large prey species compared to traditional
 methods, such as carcass counts. Our study identified 24 prey taxa in a
 total of 171 lion fecal samples. Small and very small prey taxa together
 contributed 18.7% out of 278 prey occurrences in all fecal samples. With
 comparable small prey presence (ranging from 8% to 15%) in the diet for
 each NP studied. This approach proved to be useful in detecting small and
 very small prey species in the diet of lions and can therefore be used in
 future research to uncover the diverse diet composition of these large
 carnivores. The consistent presence of smaller prey species in the diet
 indicates that lions generally supplement their large prey diet with
 smaller prey.
description: Raw output of the NGS run,
 following the sequencing methods used as mentioned in the
 manuscript.
description: fastq.gz files
DOI: 10.5061/dryad.gtht76hs1
title: Data for: Weak sex-specific evolution of locomotor activity of Sepsis punctum (Diptera: Sepsidae) thermal experimental evolution lines

description: Elevated temperatures are expected to rise beyond what the physiology of
 many organisms can tolerate. Behavioural responses facilitating
 microhabitat shifts may mitigate some of this increased thermal selection
 on physiology, but behaviours are themselves mediated by physiology, and
 any behavioural response may trade-off against other fitness-related
 activities. We investigated whether experimental evolution in different
 thermal regimes (Cold: 15°C; Hot: 31°C; Intergenerational fluctuation
 15/31°C; Control: 23°C) resulted in genetic differentiation of standard
 locomotor activity in the dung fly Sepsis punctum. We assessed individual
 locomotor performance, an integral part of most behavioral repertoires,
 across eight warm temperatures from 24°C to 45°C using an automated
 device. We found no evidence for generalist-specialist trade-offs (i.e.
 changes in the breadth of the performance curve) for this trait. Instead,
 at the warmest assay temperatures, hot-selected flies showed somewhat
 higher maximal performance than all others, especially cold-selected
 flies, overall more so in males than females. Yet, the flies’ temperature
 optimum was not higher than that of the cold-selected flies, as expected
 under the ‘hotter-is-better’ hypothesis. Maximal locomotor performance
 merely weakly increased with body size. These results suggest that thermal
 performance curves are unlikely to evolve as an entity according to theory
 and that locomotor activity is a trait of limited use in revealing thermal
 adaptation.
description: We assessed individual locomotor activity or performance, an integral part of most
 behavioral repertoires, across eight warm temperatures from 24°C to 45°C
 using an automated device
 (LAMs; Trikinetics). Locomotor
 activity was automatically measured by placing individual Male or Female flies into one of
 32 rack slots of two
 different Locomotor
 Activity racks (LAMs;
 Trikinetics). Experimental flies of the dung fly species
 <em>Sepsis</em> <em>punctum</em> (Diptera:
 Sepsidae) stemmed from four experimental evolution treatments (Cold=constant 15C, Hot=constant 31°C;
 Kontrol=wildtype 23°C; Inter=switch from 15°C to 31°C from one generation
 to next; see Berger et al. 2014 JEvolBiol 10.1111/jeb.12452). Multiple
 runs (replicates) per
 treatment combination were assessed to obtain locomotor
 activity/performance Thermal Performance Curves. The hind tibia length
 (mm) of each fly was measured after the
 experiment.<br>
DOI: 10.5061/dryad.rbnzs7hhh
title: Data for: Lack of intergenerational reproductive conflict, rather than lack of inclusive fitness benefits, likely explains absence of post-reproductive lifespan in long-finned pilot whales

description: Life history theory suggests that individuals should reproduce until
 death, yet females of a small number of mammals live for a significant
 period after ceasing reproduction, a phenomenon known as post-reproductive
 lifespan. It is thought that the evolution of this trait is facilitated by
 increasing local relatedness throughout a female’s lifetime. This allows
 older females to gain inclusive fitness through helping their offspring
 (known as a mother effect) and/or grandoffspring (known as a grandmother
 effect), rather than gaining direct fitness through reproducing. However,
 older females may only benefit from stopping reproducing when their direct
 offspring compete with those of their daughters. Here, we investigate
 whether a lack of post-reproductive lifespan in long-finned pilot whales
 (Globicephala melas) results from minimal benefits incurred from the
 presence of older females, or from a lack of costs resulting from
 mother-daughter co-reproduction. Using microsatellite data, we conducted
 parentage analysis on individuals from 25 pods and find that younger
 females were more likely to have offspring if their mother was present in
 their pod, indicating that mothers may assist inexperienced daughters to
 reproduce. However, we found no evidence of reproductive conflict between
 co-reproducing mothers and daughters, indicating that females may be able
 to reproduce into old age whilst simultaneously aiding their daughters in
 reproduction. This highlights the importance of reproductive conflict in
 the evolution of a post-reproductive lifespan and demonstrates that mother
 and grandmother effects alone do not result in the evolution of a
 post-reproductive lifespan.
DOI: 10.5061/dryad.q83bk3jpd
title: Data from: Speakers of different languages remember visual scenes differently

description: Language can have a powerful effect on how people experience events. Here,
 we examine how the languages people speak guide attention and influence
 what they remember from a visual scene. When hearing a word, listeners
 activate other similar-sounding words before settling on the correct
 target. We tested whether this linguistic co-activation during a visual
 search task changes memory for objects. Bilinguals and monolinguals
 remembered English competitor words that overlapped phonologically with a
 spoken English target better than control objects without name overlap.
 High Spanish proficiency also enhanced memory for Spanish competitors that
 overlapped across languages. We conclude that linguistic diversity partly
 accounts for differences in higher cognitive functions like memory, with
 multilinguals providing a fertile ground for studying the interaction
 between language and cognition.
description: Data was analyzed using <em>R</em> and requires the
 following R packages: tidyverse
 broom lme4
 afex emmeans
 sjPlot Hmisc
 rstatix plotrix
 ggeffects ggpattern
 data.table