cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j3tx95xjc
title: Discrete element models for understanding the biomechanics of fossorial animals

description: The morphological features of fossorial animals have continuously evolved
 in response to the demands of survival. However, existing methods for
 animal burrowing mechanics are not capable of addressing the large
 deformation of substrate. The discrete element method (DEM) is able to
 overcome this limitation. In this study, we used DEM to develop a general
 model to simulate the motion of an animal body part and its interaction
 with the substrate. The DEM also allowed us to easily change the forms of
 animal body parts to examine how those different forms affected the
 biomechanical functions. These capabilities of the DEM were presented
 through a case study of modelling the burrowing process of North American
 Badger. In the case study, the dynamics (forces, work, and soil
 displacements) of burrowing were predicted for different forms of badger
 claw and manus, using the model. Results showed that when extra digits are
 added to a manus, the work required for a badger to dig increases
 considerably, while the mass of soil dug only increases gradually.
 According to the proposed efficiency index (ratio of the amount of soil
 dug to the work required), the modern manus with 5 digits has indeed
 biomechanical advantage for their fossorial lifestyle, and the current
 claw curvature (25.3 mm in radius) is indeed optimal. The DEM is able to
 predict biomechanical relationships between functions and forms for any
 fossorial animals. Results can provide biomechanical evidences for
 explaining how the selective pressures for functions influence the
 morphological evolution in fossorial animals.
description: Fifteen North American Badger
 specimens were provided by the Beaty
 Biodiversity Museum (University of British Colombia, Vancouver,
 Canada). A manus from each
 badger specimen was scanned using a 3D Scanner. After 3D scanning, the
 image files were analysed to obtain the 3D models of the manus.
 Morphological characteristics (manus width and thickness, the
 claw length, width, and thickness) of the badger manus were
 measured from the 3D models.
DOI: 10.5061/dryad.g4f4qrftb
title: A hybrid structure determination approach to investigate the druggability of the nucleocapsid protein of SARS-CoV-2

description: The ongoing pandemic caused by SARS-CoV-2 has called for concerted efforts
 to generate new insights into the biology of betacoronaviruses to inform
 drug screening and development. Here, we establish a workflow to determine
 the RNA recognition and druggability of the nucleocapsid N-protein of
 SARS-CoV-2, a highly abundant protein crucial for the viral life cycle. We
 use a synergistic method that combines NMR spectroscopy and protein-RNA
 cross-linking coupled to mass spectrometry to quickly determine the RNA
 binding of two RNA recognition domains of the N-protein. Finally, we
 explore the druggability of these domains by performing an NMR fragment
 screening. This workflow identified small molecule chemotypes that bind to
 RNA binding interfaces and that have promising properties for further drug
 development. This deposition contains the NMR data acquired to determine
 the structural features of RBDs- RNA recognition as well as selected
 relevant data regarding the characterization of promising molecular
 fragments to disrupt protein-RNA interaction. Furthermore, we included the
 molecular docking files used to obtain the reported structural model.
description: The NMR folder contains raw data acquired in this study. In order
 to visualise this data, a processing software such as Topspin or similar
 is required. Please refer to the README file inside the folder to relate
 experiment name_number with data shown in the manuscript.
 The Docking folder contains the output data obtained from Haddock
 for protein-RNA and protein-ligand docking. Please consult the Haddock
 manual for interpreting these files (https://www.bonvinlab.org/software/haddock2.4/manual/). Folders are named based on Figures reported in the manuscript.  Representative models (lowest energy conformation of most representative clusters) are also included as pdb files in a separate folder (Representative models) to facilitate access.
DOI: 10.5061/dryad.k98sf7m8v
title: Data from: A field experiment exploring disturbance-and-recovery, and restoration methodology of Zostera capensis to support its role as a coastal protector

description: This DRYAD data set covers statistical analysis for the study,
 "Seagrass restoration experiment to support coastal
 protection."  Dataset attached covers row data regarding
 field experiments carried out to demonstrate the time needed for the
 seagrass to recover after disturbance (imitation of anthropogenic impact).
 The data is centered on showing the evolution (increase) of seagrass shoot
 density after a quantified period (time series over a year) where the
 pressure to seagrass is halted. Halting of pressure would resemble a total
 ban or reduction of anthropogenic impact of digging and revolving of
 seagrass; action carried out by communities, aiming to collect clams and
 other shellfish. This data covers also variation in sediments and
 epiphytes.  Additional data is provided on the seagrass
 restoration methodology that was added to the above-mentioned experiment.
 The IUCN Red listed Vulnerable seagrass species, Zostera capensis was
 tested using the plug method (a sediment-based methodology). Two size
 plugs, made of PVC tube, were tested: 4.5 cm and 7.5 cm diameter size,
 over a 12-month period (measurements carried out on four
 occasions).  The 7.5 PVC tube experiment revealed a higher
 survival rate and is therefore a more suitable method for future Z.
 capensis restoration in impacted areas. These data can be re-used as long
 as it cites the original data (this paper). To comply with best practices,
 we recommend mentioning the source of the data.
description: Field experiment was carried out within intertidal areas. 
 Control was also set ithin intertidal area. Data processing followed the
 use of ANOVA (two-factorial and one-way).
DOI: 10.5061/dryad.1ns1rn8xd
title: Data from: Odor motion sensing enhances navigation of complex plumes

description: Odor plumes in the wild are spatially complex and rapidly fluctuating
 structures carried by turbulent airflows. To successfully navigate plumes
 in search of food and mates, insects must extract and integrate multiple
 features of the odor signal, including odor identity, intensity, and
 timing. Effective navigation requires balancing these multiple streams of
 olfactory information and integrating them with other sensory inputs,
 including visual and mechanosensory cues. Studies dating back a century
 have indicated that, of these many sensory inputs, the wind provides the
 main directional cue in turbulent plumes, leading to the longstanding
 model of insect odor navigation as odor-elicited upwind motion. Here, we
 show that Drosophila shape their navigational decisions using an
 additional directional cue – the direction of motion of odors – which they
 detect using temporal correlations in the odor signal between their two
 antennae. Using a high-resolution virtual reality paradigm to deliver
 spatiotemporally complex fictive odors to freely-walking flies, we
 demonstrate that such odor direction sensing employs algorithms analogous
 to those in visual direction sensing. Combining simulations, theory, and
 experiments, we show that odor motion contains valuable directional
 information absent from the airflow alone and that both Drosophila and
 virtual agents are aided by that information in navigating naturalistic
 plumes. The generality of our findings suggests that odor direction
 sensing may exist throughout the animal kingdom and could improve
 olfactory robot navigation in uncertain environments.
DOI: 10.15468/dl.dpkrbt
title: Occurrence Download

description: A dataset containing 174897 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is one of (Harmonised freshwater fish occurrence and abundance data for 12 federal states in Germany)"
 ]
}

 The dataset includes 174897 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003265-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.xksn02vk0
title: Data from: Petrogenetic studies of Permian pegmatites in the Chinese Altay: implications for a two-stage post-collisional magmatism model

description: Understanding the petrogenesis of rare-metal pegmatites is important for
 understanding ore-forming processes and their tectonic settings. In this
 study, we performed zircon U-Pb geochronological and Hf-O isotopic
 analyses of the Xiaokalasu (XKLS), Dakalasu (DKLS) and Yelaman (YLM)
 pegmatites in the Chinese Altay orogen. These pegmatites have low εHf(t)
 values (-0.6 ~ +4.3), two-stage model ages of 989 ~ 1293
 Ma, and high δ18O values (+6.52 ~ +11.31), indicating that they
 may have been derived from the anatexis of mature sedimentary rocks in the
 deep crust, with a small amount of mantle-derived or juvenile material.
 Geochronological and Hf-O isotopic data for granitic intrusions
 in the Chinese Altay Mountains indicate that the εHf(t) values
 decreased from the Permian to the Triassic, which implies
 that two-stage post-collisional magmatism occurred in this
 region. During the Permian, the thin lower crust was cold; thus, magmatism
 likely originated in the deep crust close to the Moho surface and involved
 intense mantle-crust interactions. During the Triassic, asthenospheric
 upwelling provided heat to the lower crust, which increased the geothermal
 gradient and led to the anatexis of shallow crustal material.
description: WPS or Excel
DOI: 10.15468/dl.b5jaay
title: Occurrence Download

description: A dataset containing 98 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eminia antennulifera",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 98 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003273-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.n5tb2rbzr
title: Comparative analysis of chloroplast genomes of Sanguisorba species and insights into phylogenetic implications and molecular dating

description: Sanguisorba is a small genus, which consists of about 15 species widely
 distributed in North America and Eurasia. Previous studies on Sanguisorba
 are useful for understanding of phylogeny and chloroplast (cp) genome
 evolution of Sanguisorba. However, the cp genome resources of Sanguisorba
 are still limited, and the phylogeny and molecular dating for Sanguisorba
 and its relatives still need further explored. Here, we reported four cp
 genomes of Sanguisorba and conducted comparative analysis of the four
 Sanguisorba cp genomes plus five previously published ones. The nine cp
 genomes of Sanguisorba have typical tetrad quadripartite structure, with a
 total length of 154 282 to 155 730 bp, and their gene content, gene
 structure, and gene order are relatively conservative. The analysis of
 single copy (SC)/inverted repeat (IR) boundaries shows very slight
 boundary differences in Sanguisorba cp genomes. Eight variation hotspots
 were screened as excellent candidate markers of Sanguisorba. Phylogenetic
 analysis indicated Sanguisorba was monophyletic and was a member of tribe
 Agrimonieae subtribe Sanguisorbinae. Within Sanguisorba, S. filiformis is
 a sister group of six other taxa in the present sampling. Estimation of
 the divergence times indicated that subtribes Agrimoniinae and
 Sanguisorbinae diverged at the transition between the Oligocene and the
 Miocene, and divergent times of Agrimonieae genera ranged from the late
 Miocene to the Middle Pleistocene. This study enriches the available cp
 genome resources of Sanguisorba, and it is of great significance to
 further study the phylogeny and evolution of Sanguisorba and its
 relatives.
description: Table S1. The GenBank accession numbers of all the 36 chloroplast
 genome sequences used for phylogenetic analysis. Table
 S2. The nucleotide diversity (Pi) values of 264 homologous loci.
 Data_matrix. Data matrix used for phylogenetic analysis and
 molecular dating.
DOI: 10.5061/dryad.qjq2bvqkb
title: Regional dataset including species occurences and survey characteristics

description: While mammals are facing tremendous threats and environmental challenges
 across central Africa, we still lack a thorough understanding of how
 mammal assemblages are distributed across the region, though this
 knowledge is essential for planning coordinated conservation strategies
 and assessing where conservation gaps might persist. To fill this critical
 knowledge gap, we gathered species lists from wildlife and
 bushmeat-related surveys focusing on medium-sized to large mammals. The
 combined dataset includes 6,840 species occurrences across central Africa
 for 31 species of carnivores (out of 35 species in the study area
 according to Wilson & Mittermeier, 2009), 64 species of primates
 (out of 73 according to Mittermeier et al., 2013) and 49 species of
 artiodactyls (out of 57 according to Wilson & Mittermeier, 2011).
 We also compiled the characteristics and metadata of each survey,
 including the survey method, year and effort.
DOI: 10.5061/dryad.79cnp5hzn
title: MPM-334-1: Fossil basicranium and endocranial volumes and CT-stack (Enantiornithes, Avialae)

description: Among terrestrial vertebrates, only crown birds (Neornithes) rival mammals
 in terms of relative brain size and behavioural complexity. Relatedly, the
 anatomy of the avian central nervous system and associated sensory
 structures, such as the vestibular system of the inner ear, are highly
 modified with respect to those of other extant reptile lineages. However,
 a dearth of three-dimensional Mesozoic fossils has limited our knowledge
 of the origins of the distinctive endocranial structures of crown birds.
 Traits such as an expanded, flexed brain, a ventral connection between the
 brain and spinal column, and a modified vestibular system have been
 regarded as exclusive to Neornithes. Here, we demonstrate all of these
 ‘advanced’ traits in an undistorted braincase from an Upper Cretaceous
 enantiornithine bonebed in south-eastern Brazil. Our discovery suggests
 that these crown bird-like endocranial traits may have originated prior to
 the split between Enantiornithes and the more crownward portion of avian
 phylogeny over 140 million years ago, while coexisting with a remarkably
 plesiomorphic cranial base and posterior palate region. Altogether, our
 results support the interpretation that the distinctive endocranial
 morphologies of crown birds and their Mesozoic relatives are affected by
 complex trade-offs between spatial constraints during development.
description: MPM-334-1 was scanned using a GE Phoenix Nanotom M at the
 Molecular Imaging Center of the University of Southern California (USC).
 MPM-334-1 was scanned at 9.99 μm voxel size, 125 kV, 200 mA, exposure time
 750.36 ms, averaging two frames and skipping one frame, 360 degrees
 rotation 1440 frames and 0.1 mm Cu + Cu filter. The scans were initially
 reconstructed using GE Phoenix datos|×2 2.3.3.160. 
description: The three-dimensional reconstruction of the skull was generated
 in Avizo Lite (9.2). Digital mesh cleaning was conducted using Geomagic
 (2013). Final imaging of the volumes was conducted using Blender and Avizo
 Lite (9.2).
DOI: 10.5061/dryad.7wm37pvx5
title: High resolution ancient sedimentary DNA shows that alpine plant diversity is associated with human land use and climate change

description: The European Alps are highly rich in species, but their future may be
 threatened by ongoing changes in human land use and climate. Here, we
 reconstructed vegetation, temperature, human impact and livestock over the
 past ~12,000 years from Lake Sulsseewli, based on sedimentary ancient
 plant and mammal DNA, pollen, spores, chironomids, and microcharcoal. We
 assembled a highly-complete local DNA reference library (PhyloAlps, 3,923
 plant taxa), and used this to obtain an exceptionally rich sedaDNA record
 of 366 plant taxa. Vegetation mainly responded to climate during the early
 Holocene, while human activity had an additional influence on vegetation
 from 6 ka onwards. Land-use shifted from episodic grazing during the
 Neolithic and Bronze Age to agropastoralism in the Middle Ages. Associated
 human deforestation allowed the coexistence of plant species typically
 found at different elevational belts, leading to levels of plant richness
 that characterise the current high diversity of this region. Our findings
 indicate a positive association between low-intensity agropastoral
 activities and precipitation with the maintenance of the unique subalpine
 and alpine plant diversity of the European Alps.
description: DNA was extracted from 80 sediment samples and 8
 extraction/sampling negative controls using a modified DNeasy PowerSoil
 kit (Qiagen, Germany) protocol in the ancient DNA laboratory at TMU. DNA
 extracts and negative extraction/sampling controls, along with 8 PCR
 controls, were amplified using uniquely dual-tagged universal primer sets
 that amplify either the <em>trn</em>L P6 loop region of the
 chloroplast genome (gh primers) or a section of the mammalian
 mitochondrial 16S locus (MamP007 primers). Eight PCR replicates were
 carried out for each sample or control for <em>trn</em>L,
 whereas four replicates were performed for 16S.<br><br>The
 OBITools software package was used for the bioinformatics pipeline.
 Paired-end reads were aligned using SeqPrep (https://github.com/jstjohn/SeqPrep/releases, v1.2). Merged reads were demultiplexed according to the 8 bp unique primer tags and identical sequences were collapsed. Singleton sequences and those shorter than 10 bp were removed and putative artifactual sequences were identified and removed from the dataset. The <em>trn</em>L data were identified with 4 different reference libraries: PhyloAlps; ArctBorBryo; PhyloNorway; and the global reference library based on the EMBL rl143 database. The 16S data was only identified using the global reference library based on the EMBL rl143 database.
description: The data files are "Tab-Separated Values" (TSV) files
 and can be opened with any text editor, imported into spreadsheet
 software, analysed with stastical programs such as R, parsed with command
 line tools or scripting languages.
DOI: 10.5061/dryad.n2z34tn0j
title: Beyond the exponential horn: a bush-cricket with ear-canals which function as coupled resonators

description: Bush-crickets have dual-input, tympanal ears located in the tibia of their
 forelegs. The sound will, first of all, reach the external sides of the
 tympana, before arriving to the internal sides through the bush-cricket
 ear-canal, the acoustic trachea (AT), with a phase lapse and pressure
 gain. It has been shown that for many bush-crickets, the AT has an
 exponential horn-shaped morphology and function, producing a significant
 pressure gain above a certain cut-off frequency. However, the underlying
 mechanism of different AT designs remains elusive. In this study, we
 demonstrate that the AT of the duetting bush-cricket Pterodichopetala
 cieloi function as coupled resonators, producing sound pressure gains at
 the sex-specific conspecific calling song frequency, and attenuating the
 remainder – a functioning mechanism significantly different than an
 exponential horn. Furthermore, it is demonstrated that despite the sexual
 dimorphism between the P. cieloi AT, both male and female AT have a
 similar biophysical mechanism. The analysis was carried out using an
 interdisciplinary approach, where micro-computed tomography was used for
 the morphological properties of the P. cieloi AT, and a finite-element
 analysis was applied on the precise tracheal geometry to further justify
 the experimental results and to go beyond experimental limitations.
description: This data provides the computational models used for obtaining
 the results presented in the paper. The data file also contains the files
 required for the domain (precise bush-cricket trachea geometry).
description: Comsol Multiphysics, Version 5.6 or above.
DOI: 10.5061/dryad.44j0zpchj
title: Viet Nam: Private pharmacy TB referrals acceptability survey data

description: Pharmacies represent a key health system entry point for people with TB in
 Viet Nam, but high fragmentation hinders their broader
 engagement.  Professional networking apps may be able to
 facilitate pharmacy engagement for systematic TB screening and referral.
 Between September and December 2019, we piloted the use of a social
 networking app, SwipeRx, to recruit pharmacists for a TB referral scheme
 across four districts of Ho Chi Minh City, Viet Nam.  We measured
 chest X-ray (CXR) referrals and TB detection yields at participating
 pharmacies and fielded 100 acceptability surveys, divided into pharmacists
 who did and did not make a CXR referral.  We then fitted
 mixed-effect odds proportional models to explore acceptability factors
 that were associated with making a CXR referral.1,816 push notifications
 were sent to pharmacists via the SwipeRx app and 78 indicated their
 interest in participating; however, only one was within the pilot’s
 intervention area. Additional in-person outreach resulted in the
 recruitment of 146 pharmacists, with 54 (37.0%) making at least one CXR
 referral.  A total of 182 pharmacy customers were referred,
 resulting in a total of 64 (35.2%) CXR screens and seven people being
 diagnosed with TB. Compared to pharmacists who did not make any CXR
 referrals, pharmacists making at least one CXR referral understood the
 pilot’s objectives more clearly (aOR=2.6, 95% CI: 1.2-5.8) and they
 believed that TB screening increased customer trust (aOR=2.7, 95% CI:
 1.2-5.8), benefited their business (aOR=2.8, 95% CI: 1.3-6.2) and
 constituted a competitive advantage (aOR=4.4, 95% CI: 1.9-9.9). 
 They were also more confident in using mHealth apps (aOR=3.1, 95 CI%:
 1.4-6.8).  Pharmacies can play an important role in early and
 increased TB case finding.  It is critical to highlight the value
 proposition of TB referral schemes to their business during
 recruitment.  Digital networking platforms, such as SwipeRx, can
 facilitate referrals for TB screening by pharmacists, but their ability to
 identify and recruit pharmacists requires optimization, particularly when
 targeting specific segments of a nation-wide digital network.
description: Data can be opened using Excel and then processed using any
 statistical software package.  A Stata .do file is available as
 supplementary material in the publication.