cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0zpc866vx
title: Novel DMD mouse model carrying a multi-exonic Dmd deletion exhibit progressive muscular dystrophy and early-onset cardiomyopathy

description: Duchenne muscular dystrophy (DMD) is a life-threatening neuromuscular
 disease caused by the lack of dystrophin, resulting in progressive muscle
 wasting and locomotor dysfunctions. By adulthood, almost all patients also
 develop cardiomyopathy, which is the primary cause of death in DMD. While
 there has been extensive effort in creating animal models to study
 treatment strategies for DMD, most fail to recapitulate the complete
 skeletal and cardiac disease manifestations that are presented in affected
 patients. Here, we generated a mouse model mirroring a patient deletion
 mutation of exons 52-54 (Dmd &[Delta]52-54). The Dmd
 &[Delta]52-54 mutation led to the absence of dystrophin, resulting
 in progressive muscle deterioration with weakened muscle strength.
 Moreover, Dmd &[Delta]52-54 present with early-onset
 cardiomyopathy which is absent in current pre-clinical dystrophin
 deficient mouse models. Therefore, Dmd &[Delta]52-54 presents
 itself as an excellent pre-clinical model to evaluate the impact on
 skeletal and cardiac muscles for both mutation dependent and independent
 approaches.
description: DNA extracted from the tail of a male <i>Dmd del52-54
 </i>was utilized for whole genome sequencing (WGS), which was
 performed using the Illumina HiSeq X system (San Diego, CA) by The Centre
 for Applied Genomics (TCAG) at the Hospital for Sick Children.
description: Integrative Genomics Viewer (IGV) version 2.8.2 was used for
 analysis with GRCmm38/mm10 as the murine reference genome.
DOI: 10.5061/dryad.5dv41ns46
title: Parasite infection disrupts escape behaviour in fish shoals

description: Many prey species have evolved collective responses to avoid predation.
 They rapidly transfer information about potential predators to trigger and
 coordinate escape waves. Predation avoidance behaviour is often
 manipulated by trophically transmitted parasites, to facilitate their
 transmission to the next host. We hypothesised that the presence of
 infected, behaviourally altered individuals might disturb the spread of
 escape waves. We used the tapeworm Schistocephalus solidus, which
 increases risk-taking behaviour and decrease social responsiveness of its
 host, the three spined stickleback, to test this hypothesis. Three
 subgroups of sticklebacks were placed next to one another in separate
 compartments with shelter. The middle subgroup contained either uninfected
 or infected sticklebacks. We confronted an outer subgroup with an
 artificial bird strike, and studied how the escape response spread through
 the subgroups. With uninfected sticklebacks in the middle, escape waves
 spread rapidly through the entire shoal and fish remained in shelter
 thereafter. With infected sticklebacks in the middle, the escape wave was
 disrupted and uninfected fish did hardlyrarely used the shelter. Infected
 individuals can disrupt the transmission of flight responses, thereby not
 only increasing their own predation risk but also that of their uninfected
 shoal members. Our study uncovers a potentially far-reaching fitness
 consequence of grouping with infected individuals.
DOI: 10.15468/dl.enmpha
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Burkilliodendron album",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002484-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mw6m905v3
title: Context-dependent modulation of natural approach behavior in mice

description: Specific features of visual objects innately draw approach responses in
 animals, and provide natural signals of potential reward. However, visual
 sampling behaviors and the detection of salient, rewarding stimuli are
 context and behavioral state-dependent. The neural mechanisms underlying
 how the brain encodes naturally appetitive stimuli and conditionally
 transforms them into approach behavior remain unclear. To mechanistically
 understand this process, we probed natural approach behavior in mice by
 employing a virtual stimulus orienting paradigm based on prey capture to
 quantify the conditional expression of visual stimulus-evoked innate
 approach in freely moving mice. We found that specific combinations of
 stimulus features selectively evoked innate approach versus freezing
 behavioral responses when stimuli were unexpected. However, we discovered
 that prey capture experience, and therefore the expectation of prey in the
 environment, selectively modified a range of visually-evoked appetitive
 behaviors, as well as altered those visual features that evoked approach.
 Thus, we found that mice exhibit robust and selective orienting responses
 to parameterized visual stimuli that can be readily modified via natural
 experience. This work provides critical insight into how natural
 appetitive behaviors are driven by both visual motion and internal
 state. 
description: DeepLabCut was used to process videos of mice responding to
 two-dimensional visual stimuli moving across a video monitor that made up
 one side of an open field arena. Mouse nose, ears, tailbase and stimulus
 were tracked in 2D (x,y) pixel coordinates which were
 subsequently transformed into centimeters using customized Matlab
 scripts. These scripts were also used to determine when mice approached or
 froze in response to the stimulus. Frequencies of approach and freeze
 responses were quantified, as were mouse locomotive speeds, ranges and
 bearings with respect to the stimulus. Angular sizes and speeds of the
 visual stimulus were also calculated during each behavioral
 event.   
description: Data files with NS in the title were collected from the naive
 group of mice that were never exposed to live prey capture. 
 Data files with ES in the title were collected from the
 experienced group of mice that were given ~1 week of live prey capture
 experience. Data files with a 1 in the title are the
 low-speed stimulus trials. Data files with a 6 in the
 title are the intermediate-speed stimulus trials. Data
 files with a 25 in the title are the high-speed stimulus trials.
 Two-dimensional position coordinates (x,y) for each body part and
 the stimulus are listed in individual columns of the datafiles with text
 labels at the top.
DOI: 10.5061/dryad.sqv9s4n22
title: Experimental evidence for ecological cascades following threatened mammal reintroduction: Arachnids at Scotia Sanctuary, NSW, Australia

description: Please see the abstract from the Ecology paper: Gibb, Heloise, Silvey,
 C.J., Robinson, C., L’Hotellier, F.A. & Eldridge, D.J.
 (accepted August 2020) Experimental evidence for ecological
 cascades following threatened mammal reintroduction. This dataset
 includes: foraging pits, scorpion burrows and spider abundances from
 mensurative, exclusion and disturbance experiments at Scotia Sanctuary.
description: Please see the methods section from the Ecology paper: Gibb,
 Heloise, Silvey, C.J., Robinson, C., L’Hotellier, F.A. & Eldridge,
 D.J. (accepted August 2020) Experimental evidence for ecological cascades
 following threatened mammal reintroduction.
DOI: 10.5061/dryad.0k6djh9xk
title: A single-cell RNAseq atlas of Schistosoma mansoni identifies a key regulator of blood feeding

description: Schistosomiasis is a neglected tropical disease that infects 240 million
 people. With no vaccines and only one drug available, new therapeutic
 targets are needed. The causative agents, schistosomes, are intravascular
 flatworm parasites that feed on blood and lay eggs, causing pathology. The
 function of the parasite’s various tissues in successful parasitism are
 poorly understood, hindering identification of novel therapeutic targets.
 Using single cell RNAseq we characterize 43,642 cells from the adult
 schistosome, identifying 68 distinct cell populations including
 specialized stem cells that maintain the parasite’s blood-digesting gut.
 These stem cells express the gene hnf4, which is required for gut
 maintenance, blood feeding, and pathology in vivo.  Together,
 these data provide molecular insights into the organ systems of this
 important pathogen and identify potential therapeutic targets.
description:
DOI: 10.5061/dryad.6t1g1jwwv
title: Data from: Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data

description: Interspecific hybridization is an important evolutionary phenomenon that
 generates genetic variability in a population and fosters species
 diversity in nature. The availability of large genome scale datasets has
 revolutionized hybridization studies to shift from the examination of the
 presence or absence of hybrids in nature to the investigation of the
 genomic constitution of hybrids and their genome-specific evolutionary
 dynamics. Although a handful of methods have been proposed in an attempt
 to identify hybrids, accurate detection of hybridization from genomic data
 remains a challenging task. The available methods can be classified
 broadly as site pattern frequency based and population genetic clustering
 approaches, though the performance of the two classes of methods under
 different hybridization scenarios has not been extensively examined. Here,
 we use simulated data to comparatively evaluate the performance of four
 tools that are commonly used to infer hybridization events: the site
 pattern frequency based methods HyDe and the D-statistic (i.e.,
 the ABBA-BABA test), and the population clustering approaches
 structure and ADMIXTURE. We consider single hybridization
 scenarios that vary in the time of hybridization and the amount of
 incomplete lineage sorting (ILS) for different proportions of parental
 contributions (γ); introgressive hybridization; multiple hybridization
 scenarios; and a mixture of ancestral and recent hybridization scenarios.
 We focus on the statistical power to detect hybridization, the false
 discovery rate (FDR) for the D-statistic and HyDe, and the accuracy of the
 estimates of γ as measured by the mean squared error for HyDe, structure,
 and ADMIXTURE. Both HyDe and the D-statistic demonstrate a high
 level of detection power in all scenarios except those with high ILS,
 although the D-statistic often has an unacceptably high FDR. The estimates
 of γ in HyDe are impressively robust and accurate whereas
 structure and ADMIXTURE sometimes fail to identify hybrids,
 particularly when the proportional parental contributions are asymmetric
 (i.e., when γ is close to 0). Moreover, the posterior distribution
 estimated using structure exhibits multimodality in many
 scenarios, making interpretation difficult. Our results provide guidance
 in selecting appropriate methods for identifying hybrid populations from
 genomic data.
description: Jupyter notebook for analyses This
 repository has the Jupyter notebook that describes codes for simulating,
 processing, and analyzing all data sets conducted in this
 study.  analysis.jn.zip R
 scripts for visualizations This repository has all
 output files from the analyses and R scripts to reproduce the figures and
 table in this study. visualization.rm.zip
DOI: 10.5061/dryad.18931zcv1
title: Dunlin subspecies exhibit regional segregation and high site fidelity along the East Asian−Australasian Flyway

description: The degree that individuals migrate among particular breeding, migration,
 and wintering sites can have important implications for prioritizing
 conservation efforts. Four subspecies of Dunlin (Calidris alpina) migrate
 along the East Asian−Australasian Flyway (EAAF). Each subspecies has a
 distinct and well-defined breeding range, but their migration and winter
 ranges are poorly defined or unknown. We assessed the migratory
 connectivity of 3 of these subspecies by evaluating a dataset that
 encompasses 57 years (1960–2017), and comprises more than 28,000 Dunlin
 banding records, and 818 observations (71 recaptures and 747 band
 resightings). We present some of the first evidence that subspecific
 segregation likely occurs, with arcticola Dunlin
 wintering in areas of Japan, and
 other arcticola, actites and sakhalina Dunlin wintering in areas of the Yellow and China seas. Observations indicate that whether an arcticola Dunlin winters in Japan or the Yellow and China seas is independent of their breeding location, sex, or age. Furthermore, observations indicate that &gt;83% of arcticola Dunlin exhibit interannual site fidelity to specific wintering sites. This suggests that the degradation of specific wetland areas may negatively affect particular individuals of a particular subspecies (or combination of subspecies), and if widespread, could result in population declines. Given the possible biases inherent in analyzing band recovery data, we recommend additional flyway-wide collaboration and use of light-weight tracking devices and morphological and genetic assignment techniques to better quantify subspecies’ migratory movements and nonbreeding distributions. This information, when combined, will enable effective conservation efforts for this species across the EAAF.
description: <strong>Observation Data</strong> 
 DUNL_observations.xlsx: An excel workbook file containing Dunlin
 recapture and resighting data. A ReadMe tab is included to help guide the
 user. <strong>Summary of Dunlin
 Recoveries</strong> 
 DUNL_recoveries_by_region.pdf: Count of Dunlin
 (<em>Calidris alpina</em>) recoveries within each nonbreeding
 region during migration (July–November and March–June, combined) and
 winter (December–February). Recovery data are presented for Dunlin of both
 known and unknown subspecies, and for individuals of
 the <em>arcticola</em> subspecies.
 <strong>Summary of Dunlin Sites</strong>
 DUNL_site_info.pdf: Summary of sites where Dunlin
 (<em>Calidris alpina arcticola</em>) exhibited interannual
 site fidelity during migration (July–November and March–June, combined)
 and winter (December–February).
DOI: 10.5061/dryad.2rbnzs7kr
title: Mimicry genes reduce pre-adult survival rate in Papilio polytes: A possible new mechanism for maintaining female-limited polymorphism in Batesian mimicry

description: Batesian mimicry, in which harmless organisms resemble unpalatable or
 harmful species, is a well-studied adaptation for predation avoidance. The
 females of some Batesian mimic species comprise mimetic and non-mimetic
 individuals. Mimetic females of such polymorphic species clearly have a
 selective advantage due to decreased predation pressure, but the selective
 forces that maintain non-mimetic females in a population remain unclear.
 In the swallowtail butterfly, Papilio polytes, female polymorphism is
 controlled by the H (non-mimetic) and h (mimetic)
 alleles at a single autosomal locus. Here, we examined if the dominant
 H allele has a deleterious effect on the pre-adult survival rate
 (egg-to-adult emergence rate). We repeated an assortative mating-like
 treatment—i.e. breeding of males and females whose mothers had the same
 phenotype (mimetic or non-mimetic)—for three consecutive generations,
 while avoiding inbreeding. Results showed that pre-adult survival rate
 decreased over generations only in lines derived from mothers with the
 mimetic phenotype (hereafter, mimetic-assorted lines). This lowered
 survival was due to an increased mortality at the final instar larval
 stage and the pupal stages. Interestingly, the pre-adult mortality in the
 mimetic-assorted lines seemed to be associated with a male-biased sex
 ratio at adult emergence. These results suggest that the dominant
 H allele displays a mildly deleterious effect that is expressed
 more strongly in females and homozygous individuals than in heterozygous
 individuals. We propose that this cost of mimicry in larval and pupal
 stages contributes to the maintenance of female-limited polymorphism in P.
 polytes.
description: <em>Papilio polytes</em> survival data in the
 laboratory Survival data for butterfly species used in
 this study.
DOI: 10.5061/dryad.n5tb2rbt5
title: Stroke risk, phenotypes, and death in COVID-19: systematic review and newly reported cases

description: Objectives: To investigate the hypothesis that strokes occurring in
 patients with COVID-19 have distinctive features, we investigated stroke
 risk, clinical phenotypes, and outcomes in this population. Methods: We
 performed a systematic search resulting in 10 studies reporting stroke
 frequency among COVID-19 patients, which were pooled with one unpublished
 series from Canada. We applied random-effects meta-analyses to estimate
 the proportion of stroke among COVID-19. We performed an additional
 systematic search for cases series of stroke in COVID-19 patients (n=125)
 and we pooled these data with 35 unpublished cases from Canada, USA, and
 Iran. We analyzed clinical characteristics and in-hospital mortality
 stratified into age groups (&lt;50, 50-70, &gt;70 years). We
 applied cluster analyses to identify specific clinical phenotypes and
 their relationship with death. Results: The proportion of COVID-19
 patients with stroke (1.8%, 95%CI 0.9-3.7%) and in-hospital mortality
 (34.4%, 95%CI 27.2-42.4%) were exceedingly high. Mortality was 67% lower
 in patients &lt;50 years-old relative to those &gt;70 years-old
 (OR 0.33, 95%CI 0.12-0.94, P=0.039). Large vessel occlusion was twice as
 frequent (46.9%) as previously reported and was high across all age
 groups, even in the absence of risk factors or comorbidities. A clinical
 phenotype characterized by older age, a higher burden of comorbidities,
 and severe COVID-19 respiratory symptoms, was associated with the highest
 in-hospital mortality (58.6%) and a 3x higher risk of death than the rest
 of the cohort (OR 3.52, 95%CI 1.53-8.09, P=0.003). Conclusions: Stroke is
 frequent among COVID-19 patients and has devastating consequences across
 all ages. The interplay of older age, comorbidities and severity of
 COVID-19 respiratory symptoms is associated with an extremely elevated
 mortality.
DOI: 10.25349/d93w4z
title: LOOKing for Multi-word Expressions in American Sign Language

description: Usage-based linguistics postulates that multi-word expressions constitute
 a substantial part of language structure and use, and are formed through
 repeated chunking and stored as exemplar wholes. They are also re-used to
 produce new sequences by means of schematization. While there is extensive
 research on multi-word expressions in many spoken languages, little is
 known about the status of multi-word expressions in the mainstream U.S.
 variety of American Sign Language (ASL). This paper investigates recurring
 multi-word expressions, or sequences of multiple signs, that involve a
 high-frequency sign of visual perception glossed as LOOK and the family of
 ‘look’ signs. The LOOK sign exhibits two broad functions: LOOK/‘vision’
 references literal or metaphorical vision and LOOK/‘reaction’ signals a
 person’s reaction to a visual stimulus. Data analysis reveals that there
 are recurring sequences in distinct syntactic environments associated with
 the two functions of LOOK, suggesting that LOOK is in the process of
 grammaticalization from a verb of visual perception to a stance verb. The
 sequences demonstrate the emergence of linguistic structure from repeated
 use through the domain-general cognitive process of chunking in ASL.
description: This dataset was collected by an arbitrary sampling of assorted
 videos and video blogs (vlogs) in American Sign Language from the
 internet. These videos were coded for all tokens of the family of
 'look' and 'see' signs and the five signs preceding
 the target sign and the five signs following it. The target sign was also
 analyzed for their function in the phrasal context. The coding was entered
 as English glosses in a Microsoft Excel spreadsheet. Then the data was
 sorted for their functions and also sorted for recurring
 <em>n</em>-grams.
description: The majority of the videos are available on YouTube and Vimeo. A
 few are available through Facebook, which requires an account for logging
 in to view public posts on individual pages but not in public groups.
 Other videos are no longer available for public viewing or missing, and
 thus there are no links provided for these videos.
DOI: 10.5061/dryad.prr4xgxjq
title: Parkinson’s disease propagation using MRI biomarkers and partial least squares path modeling

description: Objectives: The classical Braak neuropathological staging model in
 Parkinson's disease (PD) suggests that brain lesions progress from
 the medulla oblongata to the cortex. An alternative model in which
 neurodegeneration first occurs in the cortex has also been proposed. These
 two models may correspond to different patient phenotypes. To test these
 two models and investigate if they were influenced by the presence of
 rapid eye movement sleep behavior disorder (RBD) we used multimodal MRI
 and Partial Least Squares Path-Modeling (PLS-PM) assuming that patients
 with RBD followed distinct neurodegeneration pattern. Methods: Fifty-four
 patients with PD (thirty-four with RBD) and twenty-five healthy volunteers
 were scanned using T1-weighted, diffusion tensor and
 neuromelanin-sensitive imaging. Volume, signal, mean, axial and radial
 diffusivities were calculated in brainstem, basal forebrain and cortical
 regions. PLS-PM, estimating a network of causal relationships between
 blocks of variables was used to build and test an analytical model based
 on Braak staging. The overall quality of the model was assessed using
 Goodness of fit coefficient (Gof). Results: PLS-PM was run on PD patients
 with RBD and without RBD separately. In PD with RBD, a brainstem-to-cortex
 model had significant Gof (0.71, p=0.01) whereas a cortex-to-brainstem
 model was not. In contrast, in PD patients without RBD, the
 brainstem-to-cortex model was not significant (Gof=0.64, p=0.27), and the
 cortex-to-brainstem model was highly significant (Gof=0.72, p=0.008).
 Conclusions: Using the PLS-PM imaging-based model, the neurodegeneration
 pattern of PD patients with RBD was consistent with the Braak
 brainstem-to-cortex model, whereas that of patients without RBD followed
 the cortex-to-brainstem model.
DOI: 10.5061/dryad.ncjsxkss0
title: Humpback whale acoustic presence in the Atlantic sector of the Southern Ocean

description: In the Atlantic Sector of the Southern Ocean (ASSO), the investigation of
 baleen whale distribution by sighting surveys is temporally restricted to
 the austral summer. The implementation of autonomous passive acoustic
 monitoring, in turn, allows studying vocal baleen whales year-round. This
 study describes the results of analyzing passive acoustic data spanning 12
 recording positions throughout the ASSO applying a
 combination of automatic and manual analysis methods to register humpback
 whale acoustic activity. Humpback whales were present at nine recording
 positions with higher acoustic activities towards lower latitudes and the
 eastern and western edges of the ASSO. During all months, except
 December, humpback whale acoustic activity was registered in
 the ASSO.