cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kc826
title: Data from: Parallel molecular routes to cold adaptation in eight genera of New Zealand stick insects

description: The acquisition of physiological strategies to tolerate novel thermal
 conditions allows organisms to exploit new environments. As a result,
 thermal tolerance is a key determinant of the global distribution of
 biodiversity, yet the constraints on its evolution are not well
 understood. Here we investigate parallel evolution of cold tolerance in
 New Zealand stick insects, an endemic radiation containing three
 montane-occurring species. Using a phylogeny constructed from 274
 orthologous genes, we show that stick insects have independently colonized
 montane environments at least twice. We compare supercooling point and
 survival of internal ice formation among ten species from eight genera,
 and identify both freeze tolerance and freeze avoidance in separate
 montane lineages. Freeze tolerance is also verified in both lowland and
 montane populations of a single, geographically widespread, species.
 Transcriptome sequencing following cold shock identifies a set of
 structural cuticular genes that are both differentially regulated and
 under positive sequence selection in each species. However, while
 cuticular proteins in general are associated with cold shock across the
 phylogeny, the specific genes at play differ among species. Thus, while
 processes related to cuticular structure are consistently associated with
 adaptation for cold, this may not be the consequence of shared ancestral
 genetic constraints.
description: 11_Transcriptome_AssembliesTranscriptome assemblies, each constructed from 6 individuals: 3 control and 3 cold shocked (1 h + 1 h recovery). Acanthoxyla sp (6Acanth_Trinity_cdhit.fasta) Argosarchus horridus (6Argo_Trinity_cdhit.fasta) Asteliaphasma jucundum (6Ast_Trinity_cdhit.fasta) Clitarchus hookeri (6Cli_Trinity_cdhit.fasta) Micrarchus hystriculeus (6Paeng_cdhit.fasta) Micrarchus nov. sp. 2. Sewell Peak (6Sewell_cdhit.fasta) Spinotectarchus acornutus (6spino_Trinity_cdhit.fasta) Tectarchus ovobesus (6Tovo_Trinity_cdhit.fasta) Tectarchus salebrossus (6Tsal_Trinity_cdhit.fasta) Micrarchus nov. sp. 2. Mt. Arthur (12Arthur_cdhit.fasta)* Niveahpasma annulata (21Niv_Trinity_cdhit.fasta)** * Micrarchus nov. sp. 2. Mt. Arthur assembly constructed from 6 control and 6 cold shocked individuals ** Niveahpasma annulata assembly constructed from 6 individuals (3 treatment, 3 control) from two locales (Dunedin and Remarkables), plus 9 additional individuals from an unpublished dataset (Nevis)fasta_trinity_alignments.zip
DOI: 10.5061/dryad.1205
title: Data from: Nonsense-mediated decay enables intron gain in Drosophila

description: Intron number varies considerably among genomes, but despite their
 fundamental importance, the mutational mechanisms and evolutionary
 processes underlying the expansion of intron number remain unknown. Here
 we show that Drosophila, in contrast to most eukaryotic lineages, is still
 undergoing a dramatic rate of intron gain. These novel introns carry
 significantly weaker splice sites that may impede their identification by
 the spliceosome. Novel introns are more likely to encode a premature
 termination codon (PTC), indicating that nonsense-mediated decay (NMD)
 functions as a backup for weak splicing of new introns. Our data suggest
 that new introns originate when genomic insertions with weak splice sites
 are hidden from selection by NMD. This mechanism reduces the sequence
 requirement imposed on novel introns and implies that the capacity of the
 spliceosome to recognize weak splice sites was a prerequisite for intron
 gain during eukaryotic evolution.
description: Drosophila_annotation.zip
DOI: 10.15468/8dq4sq
title: Captive Lithobates sevosus Final Mass (2004-2020) at Memphis Zoo

description: This occurrence data includes birth and death dates, final mass if available, and whether the individual was born in the wild or captivity for Dusky Gopher Frogs (Lithobates sevosus) housed in captivity between 2004-2020 at the Memphis Zoo.
DOI: 10.5061/dryad.7hv4c
title: Data from: A new tealliocaridid crustacean from the Late Carboniferous of North China and its biogeographic implications

description: A new tealliocaridid eumalacostracan is described from the Late
 Carboniferous Tupo Formation (Ningxia, China). Laevitealliocaris
 xiaheyanensis gen. et sp. nov. is represented by a single specimen,
 characterised by the possession of a short rostrum without dorsal spine, a
 short postcervical carina and only one weak branchial carina, both
 tuberculate, and a short sixth pleonal somite. This is the first
 unequivocal record of tealliocaridids outside Euramerica, which occurrence
 along the eastern inner margin of the Palaeotethys suggests that these
 crustaceans were more widely distributed than previously recognised, very
 likely extending to the whole intertropical area. One can therefore expect
 to find tealliocaridids in Turkey, Arabia, Australia, Japan and
 Kazakhstan. The new occurrence also demonstrates that tealliocaridids had
 strong dispersal capacities, interestingly challenging their affinities
 with peracarids, which today do not have free-living larvae, unlike
 decapod crustaceans.
description: RTI files
 Laevitealliocaris xiaheyanensis CNU-NX1-540c telson
 detailsThe data set proposes a
 close-up of distal pleon and telson of Laevitealliocaris xiaheyanensis
 gen. et sp. nov. documented using reflectance transformation imaging
 (RTI), which allows a modification of light orientation at will to best
 see fine anatomical details. Particularly interesting views (reproduced in
 Fig. 2E–H of the associated paper) are bookmarked in the file, so that the
 user can access them just by a single click.Yang-etal-RTI-files-Laevitealliocaris-xiaheyanensis-CNU-NX1-540c-telson-details.zip
DOI: 10.5061/dryad.h86746g
title: Data from: Trends in anesthesiology research: a machine learning approach to theme discovery and summarization

description: Objectives: Traditionally, summarization of research themes and trends
 within a given discipline was accomplished by manual review of scientific
 works in the field. However, with the ushering in of the age of “big
 data”, new methods for discovery of such information become necessary as
 traditional techniques become increasingly difficult to apply due to the
 exponential growth of document repositories. Our objectives are to develop
 a pipeline for unsupervised theme extraction and summarization of thematic
 trends in document repositories, and to test it by applying it to a
 specific domain. Methods: To that end, we detail a pipeline, which
 utilizes machine learning and natural language processing for unsupervised
 theme extraction, and a novel method for summarization of thematic trends,
 and network mapping for visualization of thematic relations. We then apply
 this pipeline to a collection of anesthesiology abstracts. Results: We
 demonstrate how this pipeline enables discovery of major themes and
 temporal trends in anesthesiology research and facilitates document
 classification and corpus exploration. Discussion: The relation of
 prevalent topics and extracted trends to recent events in both
 anesthesiology, and healthcare in general, demonstrates the pipeline’s
 utility. Furthermore, the agreement between the unsupervised thematic
 grouping and human-assigned classification validates the pipeline’s
 accuracy and demonstrates another potential use. Conclusion: The described
 pipeline enables summarization and exploration of large document
 repositories, facilitates classification, aids in trend identification. A
 more robust and user-friendly interface will facilitate the expansion of
 this methodology to other domains. This will be the focus of future work
 for our group.
description: Rusanov et
 alData from "Trends
 in anesthesiology research: A machine learning approach to theme discovery
 and summarization" by Rusanov, Alexander, Miotto, Riccardo, Weng,
 Chunhua
DOI: 10.5061/dryad.t2s33
title: Data from: Squamate phylogenetics, molecular branch lengths, and molecular apomorphies: a response to McMahan et al. (2015)

description: Morphology-based studies of squamate phylogenetics recover very different
 topologies from studies that use molecular or combined molecular and
 morphological data. This has led to some stimulating dialogue regarding
 the respective merits of the alternative hypotheses, with the primary
 point of disagreement being the placement of Iguania. Molecular
 phylogenetic studies place Iguania in a highly nested position as a member
 of the clade Toxicofera, additionally containing Anguimorpha and
 Serpentes, whereas morphology-only studies have traditionally placed
 Iguania as sister to all remaining squamates. McMahan and colleagues
 recently posited that the molecular phylogenetic hypothesis of the
 placement of Iguania is a result of incorrect root placement. These
 authors mapped molecular data (i.e., DNA sequence data) onto phylogenetic
 hypotheses and identified more molecular apomorphies on the basal branches
 of the morphology-based phylogeny. They concluded from this result that
 the molecular data support the morphological phylogenetic hypothesis of
 Iguania being sister to all remaining squamates. Here, we map molecular
 data onto additional phylogenetic hypotheses and show that the conclusions
 of McMahan and colleagues are flawed for three key reasons: 1) they
 misinterpreted a measure of branch length as a measure of branch support;
 2) they considered only two phylogenetic hypotheses; and 3) their counts
 of molecular apomorphies are severely biased by their decision to collapse
 clades into large polytomies. We demonstrate that counting the molecular
 apomorphies along a given branch is a poor measure of support for a clade
 and that the molecular data do not provide support for the
 morphology-based squamate phylogeny as the optimal topology.
description: File S1. Unrooted RAxML
 tree from REA dataFile S1. This file
 contains the unrooted phylogeny estimated from the REA data using RAxML
 with outgroups excluded.File_S1_Unrooted_tree_from_REA_data.treFile S2. PBW trees and outputFile S2. This file contains the trees for all analyses of the PBW dataset, as well as the resulting PAUP* output. Individual files are described in the readme within the zip file.File_S2_PBW_trees_and_output.zipFile S3. REA trees and outputFile S3. This file contains the trees for all analyses of the REA dataset, as well as the resulting PAUP* output. Individual files are described in the readme within the zip file.File_S3_REA_trees_and_output.zipTable S1. Number of apomorphies inferred under DELTRAN optimiziation.Table S1. Number of apomorphies inferred under DELTRAN optimiziation on the two basal branches within Squamata under different rootings. Rootings specified as "collapsed" refer to topologies in which Squamata is treated as two unresolved clades, whereas all others represent results from fully-resolved topologies.Table S1 - DELTRAN results.xlsx
DOI: 10.5061/dryad.3t251
title: Data from: Achilles tendon moment arm in humans is not affected by inversion/eversion of the foot: a short report

description: The triceps surae primarily acts as plantarflexor of the ankle joint.
 However, the group also causes inversion and eversion at the subtalar
 joint. Despite this, the Achilles tendon moment arm is generally measured
 without considering the potential influence of inversion/eversion of the
 foot during plantarflexion. This study investigated the effect of foot
 inversion and eversion on the plantarflexion Achilles tendon moment arm.
 Achilles tendon moment arms were determined using the centre-of-rotation
 method in magnetic resonance images of the left ankle of 11 participants.
 The foot was positioned at 15° dorsiflexion, 0° or 15° plantarflexion
 using a Styrofoam wedge. In each of these positions, the foot was either
 10° inverted, neutral or 10° everted using an additional Styrofoam wedge.
 Achilles tendon moment arm in neutral foot position was 47.93 ± 4.54 mm
 and did not differ significantly when the foot was positioned in 10°
 inversion and 10° eversion. Hence, inversion/eversion position of the foot
 may not considerably affect the length of the Achilles tendon moment arm.
 This information could be useful in musculoskeletal models of the human
 lower leg and foot and when estimating Achilles tendon forces during
 plantarflexion with the foot positioned in inversion or eversion.
description: DICOM
 filesAll MR image series for
 all participants (anonymised)DICOM.zipAT moment armsResults of analysis of all data: plantarflexion Achilles tendon moment arms for all participants in all foot positions.
DOI: 10.5061/dryad.db17m
title: Data from: An evolutionary modelling approach to understanding the factors behind plant invasiveness and community susceptibility to invasion

description: Ecologists have had limited success in understanding which introduced
 species may become invasive. An evolutionary model is used to investigate
 which traits are associated with invasiveness. Translocation experiments
 were simulated in which species were moved into similar but evolutionary
 younger communities. The main findings were that species that had
 previously been the most abundant in their original communities have
 significantly higher rates of establishment than did species that had
 previously occurred at low abundance in their original community. However
 if establishment did occur, previously abundant and previously low
 abundance species were equally likely to become dominant and were equally
 likely to exclude other species from their new community. There was a
 suggestion that the species that were most likely to establish and exclude
 others were “genetically” different. When species that had evolved in
 different simulations (but with identical environmental conditions), were
 transplanted into communities that had also evolved in different
 simulations of the same conditions, the outcomes were difficult to
 predict. Observed rates of establishment and subsequent competitive
 dominance were observed to be species and community combination specific.
 This evolutionary study represents a novel in silico attempt to tackle
 invasiveness in an experimental framework, and may provide a new
 methodology for tackling these issues.
description: invasion model
 data
DOI: 10.5061/dryad.s3rs0
title: Data from: Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture

description: RNA viruses rapidly diversify into quasispecies of related genotypes. This
 genetic diversity has long been known to facilitate adaptation, but recent
 studies have suggested that cooperation between variants might also
 increase population fitness. Here, we demonstrate strong cooperation
 between two H3N2 influenza variants that differ by a single mutation at
 residue 151 in neuraminidase, which normally mediates viral exit from host
 cells. Residue 151 is often annotated as an ambiguous amino acid in
 sequenced isolates, indicating mixed viral populations. We show that mixed
 populations grow better than either variant alone in cell culture. Pure
 populations of either variant generate the other through mutation and then
 stably maintain a mix of the two genotypes. We suggest that cooperation
 arises because mixed populations combine one variant’s proficiency at cell
 entry with the other’s proficiency at cell exit. Our work demonstrates a
 specific cooperative interaction between defined variants in a viral
 quasispecies.
description: Figure_1-source_data_1Figure 1 – source data 1. This 7-zip archive contains the data and source code used for Figure 1 (the analysis of mutation frequencies at site 151 in naturally occurring sequences).Figure_3-source_data_1Figure 3 – source data 1. This 7-zip archive contains the data and source code used for Figure 3 (the analysis of mutation frequencies at site 151 after serial passage in the lab).
DOI: 10.5061/dryad.042vn
title: Data from: The neuropathic diabetic foot ulcer microbiome is associated with clinical factors.

description: Nonhealing diabetic foot ulcers (DFUs) are a common and costly
 complication of diabetes. Microbial burden, or "bioburden," is
 believed to underlie delayed healing, although little is known of those
 clinical factors that may influence microbial load, diversity, and/or
 pathogenicity. We profiled the microbiomes of neuropathic nonischemic DFUs
 without clinical evidence of infection in 52 individuals using
 high-throughput sequencing of the bacterial 16S ribosomal RNA gene.
 Comparatively, wound cultures, the standard diagnostic in the clinic,
 vastly underrepresent microbial load, microbial diversity, and the
 presence of potential pathogens. DFU microbiomes were heterogeneous, even
 in our tightly restricted study population, but partitioned into three
 clusters distinguished primarily by dominant bacteria and diversity. Ulcer
 depth was associated with ulcer cluster, positively correlated with
 abundance of anaerobic bacteria, and negatively correlated with abundance
 of Staphylococcus. Ulcer duration was positively correlated with bacterial
 diversity, species richness, and relative abundance of Proteobacteria, but
 was negatively correlated with relative abundance of Staphylococcus.
 Finally, poor glycemic control was associated with ulcer cluster, with
 poorest median glycemic control concentrating to Staphylococcus-rich and
 Streptococcus-rich ulcer clusters. Analyses of microbial community
 membership and structure may provide the most useful metrics in
 prospective studies to delineate problematic bioburden from benign
 colonization that can then be used to drive clinical treatment.
description: DFU 16S
 SequencesContains fasta formatted
 sequences.DFU_16S.fastaDFU Group FileMaps sequence identifiers to Subject IDDFU_16S.groupsDFU clinical factorsContains all clinical factors examined and their values for each Subject.DFU metadata Gardner et al.txt
DOI: 10.5061/dryad.37p17
title: Data from: Insecticide resistance mediated by an exon skipping event

description: Many genes increase coding capacity by alternate exon usage. The gene
 encoding the insect nicotinic acetylcholine receptor (nAChR) α6 subunit,
 target of the bio-insecticide spinosad, is one example of this and expands
 protein diversity via alternative splicing of mutually exclusive exons.
 Here, we show that spinosad resistance in the tomato leaf miner, Tuta
 absoluta is associated with aberrant regulation of splicing of Taα6
 resulting in a novel form of insecticide resistance mediated by exon
 skipping. Sequencing of the α6 subunit cDNA from spinosad selected and
 unselected strains of T. absoluta revealed all Taα6 transcripts of the
 selected strain were devoid of exon 3, with comparison of genomic DNA and
 mRNA revealing this is a result of exon skipping. Exon skipping
 cosegregated with spinosad resistance in survival bioassays, and
 functional characterization of this alteration using modified human nAChR
 α7, a model of insect α6, demonstrated that exon 3 is essential for
 receptor function and hence spinosad sensitivity. DNA and RNA sequencing
 analyses suggested that exon skipping did not result from genetic
 alterations in intronic or exonic cis-regulatory elements, but rather was
 associated with a single epigenetic modification downstream of exon 3a,
 and quantitative changes in the expression of trans-acting proteins that
 have known roles in the regulation of alternative splicing. Our results
 demonstrate that the intrinsic capacity of the α6 gene to generate
 transcript diversity via alternative splicing can be readily exploited
 during the evolution of resistance and identifies exon skipping as a
 molecular alteration conferring insecticide resistance.
description: T_absoluta_assemblies_and_BLAST_annotationData file contains two Tuta absoluta transcriptome assemblies (as fasta files: T_absoluta_assembly_1.fasta and T_absoluta_assembly_2.fasta) and corresponding annotation files (as csv files: T. absoluta_assembly_1_BLAST_annotation.csv and T. absoluta_assembly_2_BLAST_annotation.csv ). For information a third csv file (alignment_statistics.csv) contains information on the primary assembly statistics.
DOI: 10.5061/dryad.0hb5n
title: Data from: The effects of pastoral intensification on the feeding interactions of generalist predators in streams

description: Land use change can alter trophic interactions with wide-ranging
 functional consequences, yet the consequences for aquatic food webs have
 been little-studied. In part, this may reflect the challenges of resolving
 the diets of aquatic organisms using classical gut contents analysis,
 especially for soft-bodied prey. We used next generation sequencing to
 resolve prey use in nearly 400 individuals of two predatory invertebrates
 (the Caddisfly, Rhyacophila dorsalis, and the Stonefly Dinocras
 cephalotes) in streams draining land with increasingly intensive livestock
 farming. Rhyacophila dorsalis occurred in all streams, whereas D.
 cephalotes was restricted to low intensities, allowing us to test whether:
 i) apparent sensitivity to agriculture in the latter species reflects a
 more specialised diet and ii) diet in R. dorsalis varied between sites
 with and without D. cephalotes. DNA was extracted from dissected gut
 contents, amplified without blocking probes and sequenced using Ion
 Torrent technology. Both predators were generalists, consuming 30 prey
 taxa with preference for taxa that were abundant in all streams or that
 increased with intensification. Where both predators were present, their
 diets were nearly-identical, and R. dorsalis’s diet was virtually
 unchanged in the absence of D. cephalotes. The loss of D. cephalotes from
 more intensive sites was probably due to physicochemical stressors, such
 as sedimentation, rather than to dietary specialization, although wider
 biotic factors (e.g. competition with other predatory taxa) could not be
 excluded. This study provides a uniquely detailed description of predator
 diets along a land use intensity gradient, offering new insights into how
 anthropogenic stressors affect stream communities.
description: Forward multiplex
 identifier sequenceSixteen forward primers
 were designed, each consisting of ion torrent primer A, LCO-1490 primer
 and a unique ten base pair multiplex identifier sequence (MID). This file
 provides the MID sequences.Forward
 MIDs.txtReverse Multiplex
 Identifier SequencesFifteen reverse primers,
 each with the ion torrent primer B linked to the HCO-1777 primer and a
 unique Multiplex Identifier Sequences were designed. This file provides
 the MIDsReverse
 MID.txtMID allocation to each
 predator individualThe unique forward and
 reverse MID combination used to identify sequences from each individual
 predatorMID
 allocation.xlsxAbundance of prey taxa
 across all sites/season combinationsThe number of each
 potential prey items at each site in each season
 sampled.Allpreyabundance.csvSite physicochemical characteristicsMeasured habitat and water chemistry variables at each siteNGS SequencesNGS sequences collapsed into unique sequences with MIDs and primersPearson et al sequences.fasta