cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2z34tmpmv
title: Factors influencing the habitat choice of pangolins (Manis spp.) in low land of Nepal

description: Pangolins in the genus Manis are nocturnal, burrowing, insectivorous
 mammals listed as Critically Endangered or Endangered by the International
 Union for Conservation of Nature. Of the eight extant pangolin species
 worldwide, two species are found in Nepal: the Chinese pangolin (Manis
 pentadactyla) and the Indian pangolin (Manis crassicaudata). Despite
 having a great ecological role by controlling the ants or termite
 population, little attention has been given to the conservation
 interventions of both species of pangolins found in the Terai region (low
 land) of Nepal. The present study assesses habitat use and factors
 affecting the habitat choice of pangolins in low land (Terai), Nepal. The
 research was focused on Amritdharapani community forest of Chitwan
 district. Pangolin burrows were used as the indirect signs of pangolin
 presence.  A total of thirty-nine burrows were observed at
 elevations ranging from 301 to 413 m asl. Burrows were frequently
 associated with north-west aspects, gentle slope (15º to 20º), moderate
 canopy cover (51 to 75%), red-colored soil, and acidic soils with pH 6.5
 to 7. The burrows were most common in areas with weak human disturbance
 (i.e. 1500 to 1700 m from settlements), 800 to 1200 m from roads, and
 with-in 300 m from a water source and with-in 20 m from the nearest
 termitarium.   This study revealed distance to
 settlement, distance to road, soil pH, and canopy cover as major factors
 affecting the habitat choice of pangolins in the study area.
DOI: 10.5061/dryad.nzs7h44rr
title: Captivity-induced behaviour and spatial learning abilities in an enigmatic, aquifer-dwelling blind eel, Rakthamichthys digressus

description: This dataset contains data from the exploratory behaviour and spatial
 learning experiments done. We investigated the impact of captive life on
 behaviour and learning abilities in an enigmatic, aquifer-dwelling blind
 eel, Rakthamichthys digressus. Of eight major behavioural traits related
 to exploration and activity in a novel arena, four were significantly
 altered by life in captivity. While the startle response upon introduction
 into the arena and overall swimming away from the walls increased after
 captivity, inactivity exhibited immediately after the startle and the
 reaction to an external disturbance decreased. We also observed
 behavioural syndromes between startle responses and horizontal wall
 following, and between overall activity and vertical wall following;
 however, these behavioural syndromes were not altered by maintenance in
 captivity. Interestingly, this blind-eel failed to learn a simple spatial
 task in a Y-maze apparatus. Captive-associated behavioural changes in R.
 digressus may influence their survival after reintroduction into natural
 habitats, and such changes must be taken into account while developing
 protocols for ex-situ conservation and subsequent release.
DOI: 10.5061/dryad.ttdz08kzg
title: Data from: Achieving a step change in the tuberculosis epidemic through comprehensive community-wide intervention: A model-based analysis

description: Background: Global progress towards reducing tuberculosis (TB)
 incidence and mortality has consistently lagged behind World Health
 Organization targets leading to a perception that large reductions in TB
 burden cannot be achieved. However, several recent and historical trials
 suggest that intervention efforts that are comprehensive and focused can
 have substantial epidemiological impact. We aimed to quantify the
 potential epidemiological impact of an intensive but realistic,
 community-wide campaign utilizing existing tools, and designed to achieve
 a “step change” in TB burden. Methods: We developed a
 compartmental model of tuberculosis transmission in a mid-sized city in
 India, the country with the greatest absolute burden of TB worldwide. We
 modeled the impact of a campaign comprising one-time community-wide
 screening with treatment for TB disease and preventive therapy for latent
 TB infection (LTBI). This one-time intervention was followed by
 strengthening of tuberculosis-related health system achieved by leveraging
 the one-time campaign. We estimated the tuberculosis cases and deaths that
 could be averted over 10 years using this comprehensive approach and
 assessed the contributions of individual components of the intervention.
 Results: A campaign that successfully screened 70% of the adult
 population for active and latent tuberculosis and subsequently reduced
 diagnostic and treatment delays and unsuccessful treatment outcomes by 50%
 was projected to avert 7,800 (95% range: 5,450 – 10,200) cases and 1,710
 (1,290 – 2,180) tuberculosis-related deaths per 1 million population over
 10 years. Of the total averted deaths, 33.5% (28.2 – 38.3) were
 attributable to inclusion of preventive therapy and 52.9% (48.4 - 56.9) to
 health system strengthening.  Conclusions: A one-time,
 community-wide mass campaign, comprehensively designed to detect, treat,
 and prevent tuberculosis with currently existing tools can have meaningful
 and long-lasting epidemiological impact. Successful treatment of LTBI is
 critical to achieving this result. Health system strengthening is
 essential to any effort to transform the TB response.
DOI: 10.5061/dryad.02v6wwq3c
title: Repeatability and heritability of social reaction norms in a wild agamid lizard

description: In the evolutionary transition from solitary to group living, it should be
 adaptive for animals to respond to the environment and choose when to
 socialise to reduce conflict and maximise access to resources. Due to the
 associated proximate mechanisms (e.g. neural network, endocrine system),
 it is likely that this behaviour varies between individuals according to
 genetic and non-genetic factors. We used long-term behavioural and genetic
 data from a population of eastern water dragons (Intellagama lesueurii) to
 explore variation in plasticity of social behaviour, in response to sex
 ratio and density. To do so, we modelled individual variation in social
 reaction norms, which describe individuals’ mean behaviour and behavioural
 responses to changes in their environment, and partitioned variance into
 genetic and non-genetic components. We found that reaction norms were
 repeatable over multiple years, suggesting that individuals consistently
 differed in their behavioural responses to changes in the social
 environment. Despite high repeatability of reaction norm components, trait
 heritability was below our limit of detection based on power analyses (h2
 &lt; 0.12), leading to very little power to detect heritability of
 plasticity. This was in contrast to a relatively greater amount of
 variance associated with environmental effects. This could suggest that
 mechanisms such as social learning and frequency-dependence may shape
 variance in reaction norms, which will be testable as the dataset grows.
 --
DOI: 10.5061/dryad.5x69p8d39
title: Multitrophic metacommunity dataset (butterflies, flowering plants, and butterfly predators)

description: This dataset includes measures of butterfly and floral diversity and
 richness collected across 15 sites at Burnt Lands Provincial Park in
 Ontario, Canada, during the summer of 2019. It also includes information
 on the number of predator and grasshopper attacks on experimental clay
 butterfly models at each site. It also contains data on site size,
 connectivity within the site network, and distance to the closest site
 outside of the network, for the 15 sites.
description: <strong>Sampling Day</strong>: the day number on
 which the butterfly and flowering plant data was collected. The first day
 of sampling is day 1, and other day numbers indicate the number of days
 that have passed since day 1. Some larger sites (site 7 and 15)
 occasionally had to be sampled over more than one day. In this case, the
 first of these sampling days was used for the day number.
 <strong>Site Number</strong>: indicates the number
 given to each of the 15 sites, from 1 to 15.
 <strong>Butterfly Diversity</strong>: the Hill number
 that was calculated for each site for that sampling day. Some larger sites
 (site 7 and 15) occasionally had to be sampled over more than one day per
 sampling round. In this case the Hill number is caclulated for all days
 for a single sampling round. <strong>Butterfly
 Richness</strong>: the number of species observed for each site for
 that sampling day. Some larger sites (site 7 and 15) occasionally had to
 be sampled over more than one day per sampling round. In this case the
 richness includes all days for a single sampling round.
 <strong>Floral Diversity</strong>: the Hill number
 that was calculated for each site for that sampling day. Some larger sites
 (site 7 and 15) occasionally had to be sampled over more than one day per
 sampling round. In this case the Hill number is caclulated for all days
 for a single sampling round. <strong>Floral
 Richness</strong>: the number of species observed for each site for
 that sampling day. Some larger sites (site 7 and 15) occasionally had to
 be sampled over more than one day per sampling round. In this case the
 richness includes all days for a single sampling round.
 <strong>Predator Attacks</strong>: the number of clay
 butterfly models that were attacked by predators at each site.
 <strong>Grasshopper Attacks</strong>: the number of
 clay butterfly models that were attacked by grasshoppers at each
 site. <strong>Site Area</strong>: the area
 of each site, measured in hectares. <strong>Site
 Isolation</strong>: the isolation of each site within the network of
 sites. This was calulculated as the least cost path from each site to all
 other sites, and measured in units of movement costs.
 <strong>Distance to Closest External Patch</strong>:
 the distance between each site and the closest habitat patch outside of
 the site network. This was calulculated as the least cost path from each
 site to the closest external patch, and measured in units of movement
 costs.
DOI: 10.5061/dryad.j6q573ndx
title: Raw data from: Differentiating siliceous particulate matter in the diets of mammalian herbivores

description: 1. Silica is crucial to terrestrial plant life and geochemical cycling on
 Earth. It is also implicated in the evolution of mammalian teeth, but
 there is debate over which type of siliceous particle has exerted the
 strongest selective pressure on tooth morphology. 2. Debate revolves
 around the amorphous silica bodies (phytoliths) in plants and forms of
 siliceous grit––i.e., crystalline quartz (sand, soil, dust)––on plant
 surfaces. The problem is that conventional measures of silica often
 quantify both particle types simultaneously. 3. Here we describe a
 protocol that relies on heavy-liquid flotation to separate and quantify
 siliceous particulate matter in the diets of herbivores. The method is
 reproducible and well-suited to detecting species- or population-level
 differences in silica ingestion. In addition, we detected meaningful
 variation within the digestive tracts of cows, an outcome that supports
 the premise of ruminal fluid ‘washing’ of siliceous grit. 4. We used
 bootstrap resampling to estimate the sample sizes needed to compare
 species, populations, or individuals in space and time. We found that a
 minimum sample of 12 individuals is necessary if the species is a browser
 or as many as 55 if the species is a grazer, which are more variable. But
 a sample size of 20 is adequate for detecting statistical differences. We
 conclude by suggesting that our protocol for differentiating and
 quantifying silica holds promise for testing competing hypotheses on the
 evolution of dental traits.
DOI: 10.5061/dryad.3xsj3txgq
title: Capture data for American Robins (Turdus migratorius) at a fall migration banding station in Mid-Michigan from 2012 - 2019

description: At the Burke Lake Banding Station in Bath, Michigan we captured American
 robins (Turdus migratorius) during fall migration from 2011 to 2019. The
 data shared consists of capture date and age. The data are used only for
 looking at the relative ratio of hatching year (HY) to after-hatching year
 (AHY) robins captured during fall migration.  
description: Birds were captured using mist-nets (30mm-mesh; 12mL x 2.6H) at
 the Burke Lake Banding Station located in Rose Lake State Wildlife
 Research Area in Central Michigan (N 42˚48’43.1,” W 84˚23’05.7”). The
 banding station (25 mistnets) operates daily from 15 August to 15 October,
 sunrise to 5 hours post-sunrise. The habitat is an emergent scrub-shrub
 wetland dominated by native fruit-bearing shrubs (i.e.
 <em>Cornus</em> spp. <em>Lindera benzoin</em>,
 etc.). For each bird we determine species, age, and sex (if possible),
 collect morphological and body condition measurements, examine for
 ectoparasites, and then release. All animal capture and handling is
 covered by Owen Master Banding Permit with USGS (#23629), USFWS Scientific
 Collection (#MB19470), MI Scientific Collection (#SC1386), Rose Lake
 Special Use, and Michigan State University IACUC protocol
 (#07/11-145-00). 
description: Each line in this dataset represents a unique individual (i.e not
 recaptured birds) and provides their age based on molt limit, body
 plumage, and/or skull (when possible). We provide Julian day for each
 capture and then binned the data into weeks with week 1 starting with the
 first day of the banding season (15 August). The dataset is for a
 publication and does not reflect all the data collected on the
 robins.
DOI: 10.25338/b88d2v
title: Genomic dosage values of dihaploid progeny of potato accession PI 310467 reveal translocation 8-7

description: Large scale structural variations (SV), such as chromosomal
 translocations, can have profound effects on fitness and phenotype, but
 are difficult to identify and characterize. Here, we describe a simple
 method aimed at identifying translocations using only dosage variation
 information. Using sequence-based analysis of copy-number haplotypes in
 segregating populations we identify regions of the genome that exhibit
 unexpected linkage. For each dosage-polymorphic 1Mb bin, we tested linkage
 disequilibrium in nine potato (Solanum tuberosum) dihaploid families. In
 two populations we found evidence for translocation: in cv. PI 310467, a
 non-reciprocal translocation between chr. 7 and chr. 8 resulted in a 5-3
 copy number change affecting several Mb at the respective chromosome tips.
 In cv. “Alca Tarma”, the terminal arm of chr. 4 translocated to the tip of
 chr. 1. Using oligonucleotide-based fluorescent in situ hybridization
 painting probes (oligo-FISH), we tested and confirmed the predicted
 arrangement in PI 310467. Using LD analysis in 192 natural accessions of
 Arabidopsis thaliana, we identified no translocations, but also noted that
 dosage haplotypes tended to vary continuously and resulted in higher
 noise. This method should be useful in species where translocations are
 suspected because it tests linkage without the need for genotyping.
description: Experimental
 population The input table is from a segregating
 population, i.e. dihaploids produced by a potato haploid induction
 cross.  <strong>Solanum tuberosum var.
 </strong><b id="docs-internal-guid-dc7a9258-7fff-9591-7539-a2532ec94ca0">PI 310467 (listed as Desiree in the GRIN germplasm collection)</b><strong> (4x) x S. tuberosum phureja var. IvP48 (2x)</strong> the progeny individuals were sequenced and subjected to bin-by-sam analysis. These individuals had a diploid genome content and represent maternal gametes since the paternal genome was eliminated. Reads mapping in a given bin were standardized by the mean counts obtained in the same bin.
description: https://github.com/lcomai/cnv_mapping
DOI: 10.5061/dryad.7d7wm37vj
title: Avian point count data from riparian corridors of protected areas in Marin County California

description: The data set is a simplified version of avian point count data collected
 in Marin County, CA, USA between 1997 and 2019. Point count surveys (5
 minutes) were conducted twice during the breeding season (May and June)
 along transects in riparian corridors within protected areas (Point Reyes
 National Seashore, Golden Gate National Recreation Area, Mount Tamalpais
 State Park, and Bolinas Lagoon Open Space Preserve). Data were collected
 by Point Blue Conservation Science biologists and were integrated into the
 National Park Service Inventory and Monitoring Program. All individuals
 detected at any distance were recorded during the surveys, but this
 simplified data set only includes the observations analyzed for this
 publication, specifically detections (aurally and visually) within 50
 meters of each point count station for each of the fourteen species
 selected for analysis.
description: See README file and publication.
description: See README file.
DOI: 10.25909/31145029
title: Lewis_Chapter3_S1.S2.S3

description: These tables are S1 S2 and S3 from Chapter Three of Dawn Lewis's Doctoral thesis.
DOI: 10.25909/31145029.v1
title: Lewis_Chapter3_S1.S2.S3

description: These tables are S1 S2 and S3 from Chapter Three of Dawn Lewis's Doctoral thesis.
DOI: 10.5061/dryad.9ghx3ffhm
title: Data for: Imaging the short-lived hydroxyl-hydronium pair in ionized liquid water

description: The radiolysis of water is ubiquitous in nature and plays a critical role
 in numerous biochemical and technological applications. Although the
 elementary reaction pathways for the ionized water have been studied, the
 short-lived intermediate complex and structural dynamic response after the
 proton transfer reaction remain poorly understood. Using liquid-phase
 ultrafast electron diffraction technique to measure the intermolecular
 O··O and O··H bonds, we captured the short-lived radical-cation complex
 OH(H3O+) that was formed within 140 femtoseconds through a direct
 oxygen-oxygen bond contraction and proton transfer, followed by the
 radical-cation pair dissociation and the subsequent structural relaxation
 of water within 250 femtoseconds. These measurements provide direct
 evidence of capturing this metastable radical-cation complex before
 separation, thereby improving our fundamental understanding of elementary
 reaction dynamics in ionized liquid water.
description: The data is collected from the diffraction signal (electron
 counts) on 2D detector on CCD camera. Each image is saved and repeated the
 experimental condition many times (as a function of delay time). The raw
 data are 2D images and were inidividually azimuthally integrated to 1D
 array. Experiments is a repetition of 23 times at each delay time
 point and averaged to a mean value and error bar at each delay time. All
 the data uploaded are reduced to csv file.
description: For the 2D map and pair distribution, any features below ~1
 Angstrom is an artifact and should be ignored.
DOI: 10.5061/dryad.37pvmcvkj
title: Analyses of the redlegged earth mite mitogenome (Halotydeus destructor: Tucker)

description: Data and analyses for the paper:  Thia et al. (accepted) The
 mitogenome of Halotydeus destructor (Tucker) and its relationships with
 other trombidiform mites as inferred from nucleotide sequences and gene
 arrangements. Ecology and Evolution. In this work, Thia et al. described
 the first complete mitogenomic sequence of the redlegged earth mite
 (RLEM). Phylogenetic analyses were used to contextualise the evolutionary
 relationships of the RLEM mitogenome with those of other mites from the
 order Trombidiformes. Phylogenies were inferred through Bayesian inference
 using a combination of nucleotide sequences and gene order arrangements of
 protein-coding and rRNA genes.
description: The mitogenome of the redlegged earth mite was obtained through
 assembly of PacBio reads. Annotations were curated through a combination
 of <em>geneious prime</em>, <em>mitos2</em> and
 <i>Arwen</i>. Nucleotide sequences and gene order arrangements
 were analysed using <em>MrBayes</em>.
description: Data and results can be found in the
 <em>RLEMmito_Data.zip</em> file. See
 <em>RLEMmito_Data/README.pdf</em> for descriptions of data,
 analyses, and implementation. Scripts are located in
 the <em>RLEMmito_Scripts.zip </em>file.
DOI: 10.5061/dryad.34tmpg4km
title: African swine fever virus E120R protein inhibits interferon-β production by interacting with IRF3 to block its activation

description: African swine fever is a devastating disease of swine caused by African
 swine fever virus (ASFV). The pathogenesis of the disease remains largely
 unknown, leaving the uncontrolled spreading of the disease in many
 countries and regions. Here, we identified the E120R, a structural protein
 of ASFV, as a key virulent factor and late phase expression protein of the
 virus. E120R revealed an activity to suppress host antiviral response
 through blocking IFN-β production, and the 72-73 amino acid sites in the
 C-terminal domain were essential for this function. E120R interacted with
 the interferon regulatory factor 3 (IRF3) and interfered with the
 recruitment of IRF3 to TBK1, which in turn suppressed IRF3
 phosphorylation, decreasing interferon production. The recombinant mutant
 ASFV was further constructed to confirm the claimed mechanism. The ASFV
 lacking the complete E120R region could not be rescued, whereas the virus
 could tolerate the deletion of the 72nd and 73rd residuals in the E120R
 (ASFV E120R-Δ72-73aa). ASFV E120R with the two amino acids deletion failed
 to interact with IRF3 during ASFV E120R-Δ72-73aa infection, and the viral
 infection highly activated IRF3 phosphorylation and induced more robust
 type I interferon production in comparison with its parental ASFV. An
 unbiased transcriptome-wide analysis of gene expression also confirmed
 that a considerably higher level of ISGs was detected in ASFV
 E120R-Δ72-73aa-infected porcine alveolar macrophages (PAMs) than that in
 the wildtype ASFV-infected PAMs. Together, our findings found a novel
 mechanism evolved by ASFV to inhibit host antiviral response and provide a
 new target for guiding the development of ASFV live-attenuated vaccine.
description: The sequencing of ASFV WT and ASFV E120R Δ72-73aa recombinant
 virus genomes was performed using next-generation sequencing (NGS), as
 previously described. Briefly, purified DNA was used to construct Illumina
 standard shotgun library followed the NEBNext Ultra DNA Library Prep Kit
 (NEB, Catalog no. E7370), and then was sequenced using the Illumina
 NovaSeq 6000 platform with PE150 model.
description: No other files
DOI: 10.15468/dl.h6kuce
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Etmopterus compagnoi"
 ]
}

 The dataset includes 26 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002861-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.