cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0cfxpnw1b
title: Supplemental Table: Video breakdown of 1,895 NeuroByte user satisfaction survey responses

description: Objective  To determine whether NeuroBytes is a helpful
 e-Learning tool in neurology through usage, viewer type, estimated time
 and cost of development, and post-course survey responses. 
   Background  A sustainable continuing professional
 development (CPD) system is vital in neurology due to the field’s
 expanding therapeutic options and vulnerable patient populations. In an
 effort to offer concise, evidence based updates to a wide range of
 neurology professionals, the AAN launched NeuroBytes in 2018. NeuroBytes
 are brief (&lt;5 min) videos that provide high-yield updates to AAN
 members.    Methods  NeuroBytes was beta tested
 from August–December 2018 and launched for pilot circulation from
 January–April 2019. Usage was assessed by quantifying course enrollment
 and completion rates; feasibility by cost and time required to design and
 release a module; appeal by user satisfaction; and impact by self-reported
 change in practice.    Results  A total of
 5,130 NeuroBytes enrollments (1,026±551/month) occurred from January
 11–May 28, 2019 with a median of 588 enrollments per module (interquartile
 range, 194-922) and 37% course completion. The majority of viewers were
 neurologists (54%), neurologists in training (26%), and students (8%).
 NeuroBytes took 59 hours to develop at an estimated $77.94/hour. Of the
 1,895 users who completed the survey, 82% were “extremely” or “very
 likely” to recommend NeuroBytes to a colleague and 60% agreed that the
 depth of educational content was “just right.”    
 Conclusions  NeuroBytes is a user-friendly, easily accessible CPD
 product that delivers concise updates to a broad range of neurology
 practitioners and trainees. Future efforts will explore models where
 NeuroBytes combines with other CPD programs to impact quality of training
 and clinical practice.
DOI: 10.5061/dryad.44j0zpccx
title: Caterpillar survival in the city: Attack rates on model lepidopteran larvae along an urban-rural gradient show no increase in predation with increasing urban intensity (Raw Data)

description: Growing native plants in urban gardens is often promoted as a possible
 means of increasing lepidopteran populations. However, the
 efficacy of such efforts has not been well studied. Lepidopterans vary
 widely in their ability to survive in cities, and the few previous studies
 of caterpillar abundance or biomass across an urban-rural gradient have
 yielded mixed results.  We placed clay caterpillar
 models in native plant gardens to assess whether the attack rate
 on these models varied with degree of urbanization (percent
 impervious surface within 1 km radius of each garden), and whether
 responses differed across predator taxa.  We also
 examined how garden characteristics (plant biovolume density,
 plant species richness) affected probability of
 attack.  Overall, attack rates on these models decreased
 with increasing impervious surface, although predator taxa varied in their
 sometimes complex responses. For parasitoid wasps, which accounted for 47%
 of all attacks, increasing biovolume density increased attack probability
 at impervious surface levels below 35%, but decreased the
 probability of attack at higher levels of impervious surface. In
 contrast, probabilities of attack by both predatory
 wasps and vertebrates decreased with increasing percent
 impervious surface, but did not vary with impervious surface
 for ants and spiders.  Predation on
 caterpillars in urban gardens may be lower than
 in rural ones; however, this potential increase
 in survival may be a result of declines in some predator taxa, such as
 predatory wasps and insectivorous birds. More studies across an urban
 gradient are needed to measure factors other than predation that
 influence caterpillar survival in gardens.
description: Model caterpillars were place in the field, then collected. Marks
 left in the clay were then assessed to determine predator type.
DOI: 10.5061/dryad.7m0cfxpst
title: Leaf δ13C and δ15N of aquatic macrophytes in the arid zone of northwestern China

description: Raw data of species list, life form, carbon isotope ratio (δ13C) and
 nitrogen isotope ratio (δ15N) for all observations
 examined across the arid zone of northwestern China. Multi-annual
 mean precipitation (MAP, mm), multi-annual mean temperature (MAT, oC),
 potential evapotranspiration (PET, mm), sediment total carbon (STC),
 sediment total nitrogen (STN), longitude (Long.), latitude (Lat.) and
 altitude (Alt.) across the arid zone of northwestern China were
 also provided. We examined the spatial pattern of the leaf δ13C and δ15N
 of macrophytes collected across the arid zone of northwestern China and
 tried to illustrate its relationship with environmental factors.
DOI: 10.5061/dryad.v6wwpzgv2
title: The predictive value of Modified Early Warning Score (MEWS) and Revised Trauma Score (RTS) for the short-term prognosis of emergency trauma patients: A retrospective study

description: Objectives: This study aimed to assess the predictive value of
 the Modified Early Warning Score (MEWS) and Revised Trauma Score (RTS) for
 emergency trauma patients who died within 24 hours. Design: A
 retrospective, single-centered study. Setting: This study was conducted at
 a tertiary hospital in Southern China. Participants: A total of 1739
 patients with acute trauma, aged 16 years or older who presented to the
 emergency department from November 1, 2016, to November 30, 2019, were
 included. Interventions: None. Outcome: 24-hour mortality was the primary
 outcome of trauma. Results: 1739 patients were divided into the survival
 group (1709 patients,98.27%), and the non-survival group (30
 patients,1.73%). Crude OR and adjusted OR of MEWS were 1.99, 95%CI
 (1.73-2.29), and 2.00, 95%CI (1.74-2.31), P&lt;0.001, respectively.
 Crude OR and adjusted OR of RTS were 0.62, 95%CI (0.55-0.69), and 0.61,
 95%CI (0.55-0.68), P&lt;0.001, respectively. The area under the curve
 (AUC) of MEWS was significantly higher than that of RTS (P=0.005): 0.927,
 95%CI (0.914-0.939) vs 0.799, 95%CI (0.779-0.817). Conclusions: Both MEWS
 and RTS were independent predictors of the short-term prognosis in
 emergency trauma patients, MEWS had better predictive efficacy.
DOI: 10.5061/dryad.ns1rn8prn
title: RNA-sequencing of endometrial explants

description: Seminal plasma (SP) has been shown to modulate the female reproductive
 environment in mammalian species in which the ejaculate comes into direct
 contact with the endometrium, such as mice, pigs and horses. In contrast,
 cattle ejaculate in the vagina, and it is questionable whether the fluid
 portion reaches the uterus. A recent study from our group reported that
 mating to intact, but not vasectomised, bulls modifies the endometrium
 transcriptome. However, it is not clear whether these changes are driven
 by SP molecules that bind to sperm at the time of ejaculation or not.
 Thus, the aim of the present study was to determine whether ejaculated
 sperm, which are suspended in the secretions of the accessory sex glands
 (AGs) at ejaculation, elicit a different endometrial transcriptomic
 response than epididymal sperm, which have never been exposed to SP
 factors of AG origin. To this end, endometrial explants collected from
 heifers in oestrus were (co-)incubated alone (control), or with epididymal
 or ejaculated sperm, following which RNA-sequencing analysis was
 performed. Endometrial exposure to epididymal sperm resulted in 48
 differentially expressed genes (DEGs) compared with control explants.
 Strikingly, explants exposed to ejaculated sperm exhibited no DEGs
 compared with control explants. However, incubation with ejaculated sperm
 resulted in 80 DEGs in comparison with epididymal sperm, involved in
 muscle contraction, extracellular matrix remodelling, and immune system
 pathways, among others. These data indicate that ejaculated and epididymal
 sperm induce a different response in the endometrium, likely due to the
 acquisition of SP components at the time of ejaculation.
DOI: 10.5061/dryad.j6q573ncr
title: Praomys delectorum capture-mark-recapture dataset from fieldwork on the Ukaguru Mountains, Tanzania.

description: Praomys delectorum occurs abundantly in both disturbed and intact forests
 in the Ukaguru Mountains within the Eastern Arc Mountains (EAM), Morogoro,
 Tanzania. While previous studies have reported that anthropogenic
 disturbance such as grazing, wood cutting and harvesting has a positive
 effect on the population density of P. delectorum, the impact of habitat
 disturbance on its demographic traits is still unknown. We performed a
 capture-mark-recapture study in both disturbed and intact forest from June
 2018 to February 2020 in order to investigate the effects of habitat
 disturbance on abundance as well as two demographic traits: survival and
 maturation of P. delectorum in the Ukaguru Mountains. We found no
 variation in abundance or maturation between intact and disturbed forests,
 but habitat type did affect survival. However, this effect was
 sex-dependent since female survival was higher in disturbed forests while
 male survival remained similar across the two forest types potentially due
 to differences in predation pressure or food availability between the two
 habitats. Continuous demographic monitoring of P. delectorum in EAM is
 necessary given that the increasing human population surrounding the
 landscape is leading to higher deforestation rates, and expansion of the
 pine plantation in the forest reserve.
DOI: 10.15468/dl.xhymac
title: Occurrence Download

description: A dataset containing 410 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "StateProvince is Huila",
 "TaxonKey is Pristimantis"
 ]
}

 The dataset includes 410 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002740-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8kprr4xmt
title: Tree and amino acid alignments of thioredoxin, glucose-6-phosphate dehydrogenase, and malate dehydrogenase

description: Redox regulation in phytoplankton is critical to monitor and stabilize
 metabolic pathways under changing environmental conditions. In plastids,
 the thioredoxin (TRX) system is linked to photosynthetic electron
 transport and fine tuning the metabolism to fluctuating light levels.
 Expansion of the number of redox signal transmitters and their protein
 targets, as seen in plants, is believed to increase cell robustness. In
 this study, we searched for genes related to redox regulation in the
 genome of the photosynthetic amoeba Paulinella micropora KR01 (hereafter,
 KR01). The genus Paulinella includes testate filose amoebae, in which a
 single clade acquired a photosynthetic organelle, the chromatophore, from
 an alpha cyanobacterial donor. This independent primary endosymbiosis
 occurred relatively recently (~ 124 Ma), when compared to Archaeplastida
 (&gt; 1 Ga), making photosynthetic Paulinella a valuable model for
 studying the earlier stages of primary endosymbiosis. Our comparative
 analysis demonstrates that this lineage has evolved a thioredoxin system
 similar to that from other algae, relying however on genes with diverse
 phylogenetic origins (i.e., the endosymbiont, host, bacteria, red algae).
 One TRX of eukaryotic provenance is targeted to the chromatophore,
 implicating host-endosymbiont coordination of redox regulation. A
 chromatophore targeted glucose-6-phosphate dehydrogenase of red algal
 origin suggests that Paulinella exploited the existing redox regulation
 system in Archaeplastida to foster integration. Our study elucidates the
 independent evolution of the thioredoxin system in photosynthetic
 Paulinella, whose parts derive from the existing genetic toolkit in
 diverse organisms.
description: Putative homologs for each target protein were identified using a
 BlastP search (e-value cutoff: 1e-5) against a local database, which
 contained taxa selected from NCBI RefSeq and the MMETSP database to
 provide a broad taxon sampling. CD-HIT was used to remove the redundant
 isoforms. Multiple amino acid alignments were done using Clustal
 Omega with the default options. These alignments were refined manually
 based on conserved domains. Maximum likelihood-based phylogenetic analysis
 and bootstrap resampling of the data was done using IQ-TREE with 1,000
 ultrafast bootstrap replications. The evolutionary model was automatically
 selected using the model test option incorporated in IQ-TREE. Highly
 diverged or contaminant sequences, which exhibited a long-branch or
 taxonomic misplacement in the tree were removed and the analysis done
 anew.
DOI: 10.5061/dryad.70rxwdbwn
title: Proton-transfer-reaction time-of-flight mass spectrometry (PTR-TOF-MS) as a tool for studying animal volatile organic compound (VOC) emissions

description: 1. Chemical sensing in vertebrates is crucial in their lives, and efforts
 are undertaken towards deciphering their chemical language. Volatile
 organic compounds (VOCs) is a group of chemicals believed to play an
 essential role in a wide variety of animal interactions. Therefore,
 understanding what animals sense themselves and untangling the ecological
 role of their volatile cues can be accomplished by analysing VOC
 emissions. A Proton-Transfer Reaction Time-of-Flight Mass Spectrometer
 (PTR-TOF-MS) is an instrument that measures VOCs in real-time in an air
 sample. Since this technique acts as a hyper-sensitive ‘nose’ it has a
 similar potential in deciphering the chemical language of vertebrates. 2.
 Here, we validate the use of PTR-TOF-MS as a tool to measure VOCs from
 vertebrates, which in turn will help resolve vertebrate interactions
 through VOCs. The instrument monitors and records the full spectrum of
 VOCs emitted by an individual with a high accuracy and low detection
 limit, including transient VOC emissions. We propose and test diverse
 measuring configurations that allow for measurement of VOC emissions from
 different vertebrates and their exudates: full body, specific parts of the
 body, urine and femoral pores. In addition, we test configurations for
 sudden and short-lasting processes as VOCs emitted during adder skin
 shedding as well as the emissions of skin secretions upon mechanical and
 physiological stimulation in amphibia. Our configurations work in tandem
 with Gas Chromatography Mass Spectrometry (GC-MS) to allow compound
 structure verification. 3. We discuss the configurations and methodologies
 used and conclude with recommendations for further studies, such as the
 choice of chamber size and flow. We also report the results of the
 measurements on vertebrates —that are novel to science— and discuss their
 ecological meaning. 4. We argue that PTR-TOF-MS has a high potential to
 resolve important unanswered questions in vertebrate chemical ecology with
 great adaptability to a wide range of experimental setups. If combined
 with a structure verification tool, such as GC-MS, the creative deployment
 of PTR-TOF-MS in various future study designs will lead to the
 identification of ecologically relevant VOCs.
description: In-vivo animals and their exudates where enclosed in chambers of
 different sizes and configurations to measure the volatile organic
 compound emissions in real-time with a proton-transfer reaction
 time-of-flight mass spectrometer (PTR-TOF-MS). All the methods are
 decribed and discussed in the article.
DOI: 10.5281/zenodo.18396255
title: Unprocessed TEF v1.4 Output Files for Arabidopsis Transposable Elements (Raw TEF Output)

description: Unprocessed TEF v1.4 output files underlying the processed dataset at DOI: 10.5281/zenodo.10398998.Generated from Arabidopsis thaliana herbarium specimens using the TAIR10 reference genome (downloaded from the Ensembl Plants FTP link below).These files include TEF head–tail detections for each accession, as well as TE transposition events detected in the SRR13608004 (Col‑0) control.No manual curation or reformatting has been applied. Files therefore also contain TE insertions detected in the control Col‑0 sample.

File format specifications are described at:https://akiomiyao.github.io/tef/arabidopsis.html

Reference genome acquisition:The TAIR10 reference genome sequence was obtained using the following command:



ftp ftp://ftp.ensemblgenomes.org/pub/plants/release-41/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz
DOI: 10.5061/dryad.7h44j0zt0
title: Data from: Chimpanzees behave prosocially in a group-specific manner

description: Chimpanzees act cooperatively in the wild, but whether they afford
 benefits to others, and whether their tendency to act prosocially varies
 across communities is unclear. Here, we show that chimpanzees from
 neighboring communities provide valuable resources to group members at
 personal cost, and that the magnitude of their prosocial behavior is
 group specific. Provided with a resource-donation
 experiment allowing for free (partner) choice, we observed an
 increase in prosocial acts across the study period in the majority of
 chimpanzees. When group members could profit (test condition), chimpanzees
 provided resources more frequently and for longer durations than when
 their acts produced inaccessible resources (control condition).
 Strikingly, chimpanzees’ prosocial behavior was group specific,
 with more socially tolerant groups acting more prosocially. We conclude
 that chimpanzees may purposely behave prosocially toward
 group members, and that the notion of group-specific sociality in
 nonhuman animals should crucially inform discussions on the
 evolution of prosocial behavior.
description: Experimental data in a sanctuary setting. Data have been scored
 from video.
DOI: 10.5061/dryad.p5hqbzknw
title: Data associated with: Going round the twist – An empirical analysis of shell coiling in helicospiral gastropods

description: The logarithmic helicospiral has been the most widely accepted model of
 regularly coiled mollusc form since it was proposed by Moseley (1838) and
 popularised by Thompson (1942) and Raup (1966). It is based on an explicit
 assumption that shells are isometric and grow exponentially, and an
 implicit assumption that the external form of the shell follows the
 internal shape, which implies that the parameters of the spiral could,
 theoretically, be reconstructed from the external whorl profile. In this
 contribution, we show that these assumptions fail on all 25 gastropod
 species we examine. Using a dataset of 176 fossil and modern gastropod
 shells, we construct an empirical morphospace of coiling using the
 familiar three parameters of whorl expansion rate, translation rate, and
 rate of increasing distance from coiling axis, plus rate of aperture shape
 change, from their best-fit models. We present a case study of change in
 shell form through geological time in the austral family Struthiolariidae
 to demonstrate the utility of our approach for evolutionary paleobiology.
 We fit various functions to the four shell-coiling parameters, to
 demonstrate that the best morphological model is not the same for each
 parameter. We present a set of R routines that will calculate helicospiral
 parameters from sagittal sections through coiled shells and allow workers
 to compare models and choose appropriate sets of parameters for their own
 datasets. Shell form parameters in the Struthiolariidae highlight a
 hitherto-neglected hypothesis of relationship between Antarctic
 Perissodonta and the enigmatic Australian genus Tylospira that fits the
 biogeographic and stratigraphic distribution of both genera.
description: The dataset comprises 2D images, the majority taken with a dSLR
 camera, plus a small number of digital 'slices' through
 synchrotron micro-CT scans. The dSLR camera images were retrodeformed to
 remove lens distortion (see Collins & Gazley 2017 for details of
 method).  The .tps file of landmarks was collected by
 one author (KSC) from the images included here.
description: Code files are provided as .Rmd files, which can be run in R
 Studio, and as html files which can be read in a browser without any
 coding knowledge. To run the .Rmd files, you will need
 to download the .Rmd files and the .csv files and place them in a folder
 together. Extract the zip file, and place all of its contents inside a
 folder named 'data' inside the folder containing the .Rmd and
 .csv files.
DOI: 10.5061/dryad.gmsbcc2mb
title: SARA module 3: NGS epitope sequencing: Illumina FASTQ files

description: We investigate the accumulated microbial and autoantigen antibody
 repertoire in adult-onset dermatomyositis patients sero-positive for TIF1γ
 (TRIM33) autoantibodies. We use an untargeted high-throughput approach
 which combines immunoglobulin disease-specific epitope-enrichment and
 identification of microbial and human antigens. We observe antibodies
 recognizing a wider repertoire of microbial antigens in dermatomyositis.
 Antibodies recognizing viruses and Poxviridae family species are
 significantly enriched. The identified autoantibodies recognise a large
 portion of the human proteome, including interferon regulated proteins;
 these proteins cluster in specific biological processes. In addition to
 TRIM33, we identify autoantibodies against eleven further TRIM proteins,
 including TRIM21. Some of these TRIM proteins share epitope homology with
 specific viral species including poxviruses. Our data suggest antibody
 accumulation in dermatomyositis against an expanded diversity of microbial
 and human proteins and evidence of non-random targeting of specific
 signalling pathways. Our findings indicate that molecular mimicry and
 epitope spreading events may play a role in dermatomyositis pathogenesis.
description: We
 implemented the “Serum Antibody Repertoire Analysis (SARA)” pipeline as
 outlined in our corresponding manuscript. Polyvalent
 plasmid variance regions were PCR amplified and gel-purified. PCR products
 were validated by Sanger sequencing and NanoDrop. Multiplexed DNA
 fragments were sequenced on the NextSeq 500 platform (Illumina, UK) to
 retrieve ≈24 million and ≈36 million paired end FASTQ reads for HC and DM
 respectively. This
 repository contains FASTQ zipped files. FASTQ IDs
 are: "S1_S1_": P20 pool Healthy controls (HC). "S2_S2_": P20 pool: Anti-TIF1 positive Dermatomyositis patients (DM). "S5_S5_": P10 pool: Healthy controls (HC). "S6_S6_": P10 pool: Anti-TIF1 positive Dermatomyositis patients (DM).
description: The FASTQ files contain plasmid sequence data following
 competitive biopanning of total Igs that were purified from healthy and
 disease plasma. Plasmid sequences contain a 36bp
 variance region which codes for expressed (and thus
 immunologically-relevant) peptide epitopes.