cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fq3dq
title: Data from: The cranial morphology, phylogenetic position and biogeography of the upper Permian dicynodont Compsodon helmoedi van Hoepen (Therapsida, Anomodontia)

description: Compsodon helmoedi is an obscure dicynodont originally described based on
 a single specimen from the upper Permian of the Karoo Basin. The discovery
 of three new specimens of Compsodon from the Luangwa Basin of Zambia and
 two additional specimens from South African museum collections facilitates
 a reassessment of its cranial morphology and phylogenetic position.
 Compsodon is diagnosed by an autapomorphic secondary palate morphology:
 medial depression at anterior end of premaxillary secondary palate; medial
 anterior palatal ridges absent; lateral anterior palatal ridges prominent
 and extend to posterior end of secondary palate; Y-shaped anterior end of
 posterior median palatal ridge; embayment of palatal rim anterior to
 caniniform process divided into two depressions by a
 posteromedially-trending ridge. Other important characters include the
 presence of maxillary ‘postcanines’ and a postcaniniform keel; long
 interpterygoid vacuity; palatine pad smooth and pierced by a foramen;
 pineal foramen flanked by swollen eminences of parietals; parietals fused
 and narrowly exposed between broad postorbitals on dorsal surface of
 skull; and pocket-like depression on lateral surface of maxilla.
 Phylogenetic analysis demonstrates that Compsodon is a member of
 Emydopoidea, but underscores major outstanding problems in our
 understanding of Permian dicynodont phylogeny that require further
 attention. The cranial morphology of Compsodon converges on that of
 cryptodonts like Tropidostoma, and as such represents a unique emydopoid
 morphotype. The stratigraphic range of Compsodon probably spans the upper
 Cistecephalus and lower Daptocephalus assemblage zones, and its presence
 in South Africa and Zambia reinforces a pattern of small Permian
 dicynodonts with wide geographical ranges in southern Gondwana.
description: Angielczyk and Kammerer
 character listList of characters used
 in the phylogenetic analysisAngielczyk and Kammerer
 Data MatrixData matrix used in
 phylogenetic analysisAngielczyk and Kammerer
 jackknife and constraint resultsResults of the jackknife
 and constrained analyses described in the textAngielczyk and Kammerer
 continuous character databaseData used for coding
 continuous characters in the data matrix
DOI: 10.5061/dryad.df2jt
title: Data from: Deciphering the origin of mito-nuclear discordance in two sibling caddisfly species

description: An increasing number of phylogenetic studies have reported discordances
 among nuclear and mitochondrial markers. These discrepancies are highly
 relevant to widely used biodiversity assessment approaches, such as DNA
 barcoding, that rely almost exclusively on mitochondrial markers. Although
 the theoretical causes of mito-nuclear discordances are well understood,
 it is often extremely challenging to determine the principal underlying
 factor in a given study system. In this study, we uncovered significant
 mito-nuclear discordances in a pair of sibling caddisfly species.
 Application of genome sequencing, ddRAD, and DNA barcoding revealed
 ongoing hybridization, as well as historical hybridization in Pleistocene
 refugia, leading us to identify introgression as the ultimate cause of the
 observed discordance pattern. Our novel genomic data, the discovery of a
 European-wide hybrid zone, and the availability of established techniques
 for laboratory breeding make this species pair an ideal model system for
 studying species boundaries with ongoing gene flow.
description: Geneset of the
 Sericostoma genome assemblyGenes were predicted
 using ab initio and homology-based approaches. Augustus was used for ab
 initio predictions. For the homology-based approach, protein datasets from
 related species (Acyrthosiphon pisum, Camponotus floridanus, Nasonia
 vitripennis, Bombyx mori, and Tribolium castaneum) were aligned to the
 draft genome assemblies using BLASTp (cutoff: 10-5), and gene models were
 generated by GeneWise. A consensus gene set that merged ab initio and
 homology-based predictions was created using GLEAN. The three resulting
 data files contain a table with summary information per predicted gene
 (Sericostoma_personatum_gapClosed.gene.gff), the predicted mRNA sequences
 (Sericostoma_personatum_gapClosed.gene.cds) and the predicted protein
 sequences ( Sericostoma_personatum_gapClosed.gene.pep).geneset.zipFunctional annotation of the Sericostoma genome assemblyGene functions were assigned to the Geneset using BLASTp (cutoff: 10-5) against KEGG (release 58), non-redundant protein sequences (NCBI release 20150222), Swiss-Prot, and TrEMBL (Uniprot release 201203). Conserved protein domains were assessed by InterPro and InterProScan. Separate files are provided for each database.functional annotation.zipnuclear RNA of the Sericostoma genome assemblyNuclear RNA sequences were identified in the draft genome assembly. tRNA genes were identified using tRNAscan-SE with default parameters. miRNA and snRNA were identified using the INFERNAL software by searching against the Rfam database (release 9.1) with default parameters. rRNA genes were identified by BLASTn (cutoff: 10-5) searches against conserved invertebrate rRNA sequences. Separate files are provided for each type of RNA.ncRNA.zip
DOI: 10.5061/dryad.f9v80
title: Data from: Enzyme architecture: modeling the operation of a hydrophobic clamp in catalysis by triosephosphate isomerase

description: Triosephosphate isomerase (TIM) is a proficient catalyst of the reversible
 isomerization of dihydroxyacetone phosphate (DHAP) to d-glyceraldehyde
 phosphate (GAP), via general base catalysis by E165. Historically, this
 enzyme has been an extremely important model system for understanding the
 fundamentals of biological catalysis. TIM is activated through an
 energetically demanding conformational change, which helps position the
 side chains of two key hydrophobic residues (I170 and L230), over the
 carboxylate side chain of E165. This is critical both for creating a
 hydrophobic pocket for the catalytic base and for maintaining correct
 active site architecture. Truncation of these residues to alanine causes
 significant falloffs in TIM’s catalytic activity, but experiments have
 failed to provide a full description of the action of this clamp in
 promoting substrate deprotonation. We perform here detailed empirical
 valence bond calculations of the TIM-catalyzed deprotonation of DHAP and
 GAP by both wild-type TIM and its I170A, L230A, and I170A/L230A mutants,
 obtaining exceptional quantitative agreement with experiment. Our
 calculations provide a linear free energy relationship, with slope 0.8,
 between the activation barriers and Gibbs free energies for these
 TIM-catalyzed reactions. We conclude that these clamping side chains
 minimize the Gibbs free energy for substrate deprotonation, and that the
 effects on reaction driving force are largely expressed at the transition
 state for proton transfer. Our combined analysis of previous experimental
 and current computational results allows us to provide an overview of the
 breakdown of ground-state and transition state effects in enzyme catalysis
 in unprecedented detail, providing a molecular description of the
 operation of a hydrophobic clamp in triosephosphate isomerase.
description: Triosephosphate
 Isomerase SimulationsThe data package
 contains all input, topology and parameter files necessary for rerunning
 the simulations. It also contains coordinates, in PDB format, of all
 initial and equilibrated protein-substrate complexes, as well as of key
 stationary points along the simulation trajectories.TIM_data_package_dryad.zip
DOI: 10.5061/dryad.637r1
title: Data from: Secondary osteons scale allometrically in mammalian humerus and femur

description: Intra-cortical bone remodelling is a cell-driven process that replaces
 existing bone tissue with new bone tissue in the bone cortex, leaving
 behind histological features called secondary osteons. While the scaling
 of bone dimensions on a macroscopic scale is well known, less is known
 about how the spatial dimensions of secondary osteons vary in relation to
 the adult body size of the species. We measured the cross-sectional area
 of individual intact secondary osteons and their central Haversian canals
 in transverse sections from 40 stylopodal bones of 39 mammalian species
 (body mass 0.3–21 000 kg). Scaling analysis of our data shows that mean
 osteonal resorption area (negative allometry, exponent 0.23,R2
 0.54,p&lt;0.005) and Haversian canal area (negative allometry,
 exponent 0.31,R2 0.45,p&lt;0.005) are significantly related to body
 mass, independent of phylogeny. This study is the most comprehensive of
 its kind to date, and allows us to describe overall trends in the scaling
 behaviour of secondary osteon dimensions, supporting the inference that
 the osteonal resorption area may be limited by the need to avoid fracture
 in smaller mammalian species, but the need to maintain osteocyte viability
 in larger mammalian species.
description: Raw
 dataThe segmentations
 (ImageJ ROIs as zip) and measurements (csv files) of intact secondary
 osteons, Haversian canals and infill areas organised into folders
 "IntactOsteons", "HaversianCanals", and
 "InfilledAreas".osteon-scaling-data.zip
DOI: 10.6084/m9.figshare.30756917
title: Transcriptome in cultured pericytes after treatment with LDL cholesterol

description: Immortalized human primary brain vascular pericytes (HBPC; clone ci37) were cultured at 33 °C with 5% CO2/ 95% air in pericyte medium (Catalog number: 1201; Sciencell Research Laboratories, Carlsbad, CA, USA) containing 2% (v/v) fetal bovine serum, 1% (w/v) pericyte growth factors, and penicillin-streptomycin. Culture flasks and plates were coated with rat tail collagen type I (Catalog number: A1048301; Thermo Fisher Scientific, Darmstadt, Germany). To investigate the effects of LDL cholesterol, pericytes were cultured in 24-well plate at 2.0 × 10<sup>5</sup> cells/well. Before experiments, the culture medium was replaced with serum-free pericyte medium and cells were cultured at 37°C for 3 days to facilitate the cell differentiation. Thereafter, pericytes were treated with purified LDL from human plasma (Catalog number: SAE0053; Sigma-Aldrich Chemie GmbH, Munich, Germany) at 0 or 2 mg/ml for 24 hours. After removal of culture medium, the pericytes on the plate were immediately lysed in RTL Plus buffer for RNA isolation using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany). Thereafter, RNAseq libraries were prepared, sequenced and analyzed.The deposited file contains FPKM results for all annotated genes. Samples “Ct” and “LDL” correspond to treatments with LDL at 0 and 2 mg/mL, respectively.
DOI: 10.6084/m9.figshare.30756917.v1
title: Transcriptome in cultured pericytes after treatment with LDL cholesterol

description: Immortalized human primary brain vascular pericytes (HBPC; clone ci37) were cultured at 33 °C with 5% CO2/ 95% air in pericyte medium (Catalog number: 1201; Sciencell Research Laboratories, Carlsbad, CA, USA) containing 2% (v/v) fetal bovine serum, 1% (w/v) pericyte growth factors, and penicillin-streptomycin. Culture flasks and plates were coated with rat tail collagen type I (Catalog number: A1048301; Thermo Fisher Scientific, Darmstadt, Germany). To investigate the effects of LDL cholesterol, pericytes were cultured in 24-well plate at 2.0 × 10<sup>5</sup> cells/well. Before experiments, the culture medium was replaced with serum-free pericyte medium and cells were cultured at 37°C for 3 days to facilitate the cell differentiation. Thereafter, pericytes were treated with purified LDL from human plasma (Catalog number: SAE0053; Sigma-Aldrich Chemie GmbH, Munich, Germany) at 0 or 2 mg/ml for 24 hours. After removal of culture medium, the pericytes on the plate were immediately lysed in RTL Plus buffer for RNA isolation using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany). Thereafter, RNAseq libraries were prepared, sequenced and analyzed.The deposited file contains FPKM results for all annotated genes. Samples “Ct” and “LDL” correspond to treatments with LDL at 0 and 2 mg/mL, respectively.
DOI: 10.5061/dryad.h3j3c
title: Data from: Crowding leads to fitness benefits and reduced dispersal in a colonial spider

description: Density-dependent dispersal is a common dispersal strategy, mainly as a
 mechanism of escaping decreased fitness associated with high
 intra-specific competition. However, in group-living species, high density
 is expected to be beneficial for the individual, at least up to a certain
 threshold. A possible mechanism for maintaining an optimal density is
 negative density-dependent dispersal. In order to examine this hypothesis,
 we studied the effect of colony density on growth, dispersal and prey
 capture under different diets in the colonial spider Cyrtophora citricola
 (Forskål, 1775) (Araneidae). Colonies of C. citricola often reach high
 densities but the spiders are also capable of living solitarily. Previous
 studies showed that indirect benefits related to prey capture and predator
 defense may arise from colony-living, despite the lack of direct
 cooperation. We found that dispersal propensity of spiders decreased with
 increasing colony density, and that the effect was strongest when prey
 abundance was high. Additionally, site tenacity of spider hatchlings
 increased with greater density of adult females in colonies. Both results
 support a negative density-dependent dispersal strategy. As expected, body
 mass of spiders increased with density, suggesting that fitness increases
 with density (Allee effect). Variance in body mass was higher within dense
 colonies than among solitary spiders, therefore it is likely that spiders
 in the colony differ in their prey capture success, and consequently in
 body mass. This interplay between Allee effect, dispersal strategy and
 individual fitness may have an important role in the life history and
 distribution of colonial spiders and of other group-living species.
description: Ventura_Smith_Lubin_All
 data for BehavEcolAll data for Ventura et
 al. : Crowding leads to fitness benefits and reduced dispersal in a
 colonial spider
DOI: 10.5061/dryad.v2n27
title: Data from: Detecting ancient co-dispersals and host shifts by double dating of host and parasite phylogenies: application in proctophyllodid feather mites associated with passerine birds

description: Inferring co-phylogeographic events requires matching the timing of these
 events on both host and symbiont (e.g., parasites) phylogenies because
 divergences of hosts and their symbionts may not temporally coincide, and
 host switches may occur. We investigate a large radiation of birds
 (Passeriformes) and their permanent symbionts, the proctophyllodid feather
 mites (117 species from 116 bird species; 6 genes, 11,468 nt aligned)
 using two time-calibration strategies for mites: fossils only and host
 phylogeography only. Out of 10 putative co-phylogeographic events 4 agree
 in timing for both symbiont and host events being synchronous co-origins
 or co-dispersals; 3 were based on host shifts, but agree in timing being
 very close to the origin of modern hosts; 2 disagree; and 1 large basal
 mite split was seemingly independent from host phylogeography. Among these
 events was an ancient (21-25.3 Mya), synchronous co-dispersal from the Old
 World leading to the origin and diversifications of New World emberizoid
 passerids and their mites, the thraupis+quadratus species groups of
 Proctophyllodes. Our framework offers a more robust detection of host and
 symbiont co-phylogeographic events (as compared to host-symbiont
 reconciliation analysis and using host phylogeography for
 time-calibration) and provides independent data for testing alternative
 hypotheses on timing of host diversification and dispersal.
description: Multiple sequence
 alignment matrices: six genes and 173 mite species, 1 phylogenetic
 treeMultiple sequence
 alignments of six genes (18S, 28S, EF1-α, SRP54, HSP70, COX1) and 173 mite
 species. File also contains one time-calibrated phylognetic tree inferred
 in BEAST. Mesquite nexus format.1-Procto_173taxa_alignment_no_empty_chars.nexTime-calibrated Bayesian treeTime-calibrated Bayesian tree of Proctophyllodidae and 40 outgroups inferred in BEAST.2-Procto173_Figtree_TA_from_84650trees.newick.tre
DOI: 10.5061/dryad.9727v
title: Data from: The complex effects of demographic history on the estimation of substitution rate: concatenated gene analysis results in no more than twofold overestimation

description: Our recent estimation of the divergence time and isolation of Death Valley
 pupfishes, including the iconic Devil’s Hole pupfish (DHP), rewrote
 widespread assumptions about this group. These species were previously
 assumed to be relic populations isolated over millions of years; our
 genomic analyses indicated recent colonization of Devil’s Hole within the
 past 105–830 years and frequent gene flow among Death Valley populations
 [1]. These results understandably attracted substantial attention given
 the iconic battle for conservation and intense management of DHP [2];
 nonetheless, a young age for this species should not diminish its
 conservation value. Indeed, we argue that the unique natural history of
 this species makes it a prime candidate for exhibiting one of the fastest
 mutation rates observed in any vertebrate [3].
description: raw
 dataAll raw RADseq loci used
 for analyses and simulations.data.zipscriptsAll scripts/code used for analyses and simulations.analysis.zip
DOI: 10.5061/dryad.1h9g7
title: Data from: Production of omega-3 enriched tilapia through the dietary use of algae meal or fish oil: Improved nutrient value of fillet and offal

description: The goal of this project was to increase the nutrient value of fillets,
 by-product muscle, and offal of aquacultured tilapia. A diet that includes
 seafood with a high omega-3 (n-3) fatty acid content, more specifically
 eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), are known to
 have numerous health benefits for consumers. Improved nutrient value of
 the offal may also attract new market opportunities for the aquaculture
 industry. Tilapia were cultured on different experimental feeds that
 contained various levels of n-3 fatty acids from either fish oil (FO) or
 algae meal (AM) that were used to replace corn oil. The experimental diets
 included a control (corn oil 6.3%), FO1%, FO3%, FO5%, AM1.75%, AM5.26%,
 and AM8.77%. All diets were formulated to be isocaloric, isonitrogenous,
 and isolipid. Three hundred and fifty tilapia with an initial mean weight
 of 158±2 g were cultured in a recirculating aquaculture system (seven
 diets replicated at the tank level, 14 tanks, 25 fish per tank). For all
 of the production performance data, no differences (P&gt;0.05) were
 observed between the experimental groups which included survival (overall
 mean ± standard error, 99.4±0.3%), growth per week (45.4±1.0 g/wk), food
 conversion ratio (1.32±0.03), fillet yield (44.4±0.2%), hepatosomatic
 index (1.61±0.02), viscerosomatic index (2.86±0.06), and mesenteric fat
 index (0.97±0.04). Fillet and rib meat tissues were collected at weeks
 four and eight, and liver and mesenteric fat tissues were collected at
 week eight. Fatty acids were extracted, methylated and identified with gas
 chromatography–mass spectrometry. All tissues had improved fatty acid
 profiles (higher n-3, lower n-6, n-6:n-3) with increasing levels of FO and
 AM in the diet. For example, the best diet for significantly
 (P&lt;0.05) improving the lipid profile in tilapia fillets at week
 eight was diet AM8.77%. In the fillet, total n-3 was increased (control
 versus AM8.77%) from 151.2±19.0 to 438.7±14.2 mg per 4 ounce (113 g)
 serving and n-6:n-3 ratio was improved from 5.19±0.76 to 1.29±0.03.
description: Fatty Acid Profile
 DataData from GC-MS and
 calculations to determine and quantify fatty acid profiles in
 samples.Nutritional Profile Data
 excluding Fatty AcidsNutrient data for
 samples including proximates (protein, ash, etc.), minerals, and amino
 acids. This data set does not include fatty acid profiles. See other data
 set for this information.Fish and Production
 DataThis file includes data
 for fish production, including population of fish as a function of time,
 weight as a function of time, feed efficiency values, biometrics of
 harvested fish, and water quality data.
DOI: 10.5061/dryad.tm617
title: Data from: The genomic ancestry, landscape genetics, and invasion history of introduced mice in New Zealand

description: The house mouse (Mus musculus) provides a fascinating system for studying
 both the genomic basis of reproductive isolation, and the patterns of
 human- mediated dispersal. New Zealand has a complex history of mouse
 invasions, and the living descendants of these invaders have genetic
 ancestry from all three subspecies, although most are primarily descended
 from M. m. domesticus. We used the GigaMUGA genotyping array (~135,000
 loci) to describe the genomic ancestry of 161 mice, sampled from 34
 locations from across New Zealand (and one Australian city - Sydney). Of
 these, two populations, one in the south of the South Island, and one on
 Chatham Island, showed complete mitochondrial lineage capture, featuring
 two different lineages of M. m. castaneus mitochondrial DNA but with only
 M. m. domesticus nuclear ancestry detectable. Mice in the northern and
 southern parts of the North Island had small traces (~2-3%) of M. m.
 castaneus nuclear ancestry, and mice in the upper South Island had ~7-8%
 M. m. musculus nuclear ancestry including some Y-chromosomal ancestry –
 though no detectable M. m. musculus mitochondrial ancestry. This is the
 most thorough genomic study of introduced populations of house mice yet
 conducted, and will have relevance to studies of the isolation mechanisms
 separating subspecies of mice.
description: NZ Mouse Plink .fam
 fileNZ_GigaMUGA_cleaned_pruned.famNZ Mouse Plink .bim fileNZ_GigaMUGA_cleaned_pruned.bimNZ Mouse Plink .bed fileNZ_GigaMUGA_cleaned_pruned.bed
DOI: 10.17632/rjg4mbb46p
title: Constructivist redesign of a virtual learning environment and engagement among part time postgraduate Anaesthetic care students

description: Raw Qualtive and quantitative data for the above mention research project
DOI: 10.17632/rjg4mbb46p.1
title: Constructivist redesign of a virtual learning environment and engagement among part time postgraduate Anaesthetic care students

description: Raw Qualtive and quantitative data for the above mention research project
DOI: 10.17632/jrrfb49wmg
title: Replication Code for “Informal Loans in Thailand: Stylized Facts and Empirical Analysis”

description: This repository contains the computational code used to reproduce the empirical results in the paper “Informal Loans in Thailand: Stylized Facts and Empirical Analysis.”

The code generates all tables and figures reported in the paper, including summary statistics, stylized facts, and econometric analyses of informal borrowing behavior. The original individual-level survey data are confidential and cannot be shared publicly. Researchers with authorized access to the data may reproduce the results by running the scripts provided in this repository.