cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mk4fc3r
title: Automated detection of lameness in sheep using machine learning approaches: novel insights into behavioural differences among lame and non-lame sheep

description: Lameness in sheep is the biggest cause of concern regarding poor health
 and welfare among sheep producing countries. Best practice for lameness
 relies on rapid treatment, yet there are no objective measures of lameness
 detection. Use of accelerometers and gyroscopes have been widely used in
 human activity studies and their use is becoming increasingly common in
 livestock. In this study, we used 23 datasets (10 non-lame and 13 lame
 sheep) from an accelerometer and gyroscope-based ear sensor with a
 sampling frequency of 16 Hz to develop and compare algorithms that can
 differentiate lameness within three different activities (walking,
 standing and lying). We show for the first time that features extracted
 from accelerometer and gyroscope signals can differentiate between lame
 and non-lame sheep while standing, walking and lying. The random forest
 algorithm performed best for classifying lameness with accuracy of 84.91%
 within lying, 81.15% within standing and 76.83% within walking and overall
 correctly classified over 80% sheep within activities. Both accelerometer
 and gyroscope-based features ranked among the top 10 features for
 classification. Our results suggest that novel behavioural differences
 between lame and non-lame sheep across all three activities could be used
 to develop an automated system for lameness detection.
description: 08_05_2019_EL4LFeatureset_Ear_7_SecWindowsThe data contains feature characteristics using both the acceleration magnitude difference and the gyroscope magnitude difference providing a total of 32 feature characteristics. Additionally, it contains information about the sheep ID, lameness(LMS), sensor ID, recording day and behaviour(walking, standing and lying). The full description of the features is on the paper.
DOI: 10.5061/dryad.f4114kq
title: Data from: Variable preservation potential and richness in the fossil record of vertebrates

description: Variation in preservation and sampling probability clouds our estimates of
 past biodiversity. The most extreme examples are Lagerstätten faunas and
 floras, or Biotas as they are referred to in China. Although such deposits
 provide a wealth of information for palaeontologists and are closer to
 representing true richness than other deposits of a similar scale, they
 add a disproportionate number of taxa to wider richness counts because of
 their exceptional preservation, creating diversity peaks that might be
 mistaken for diversification events. Here, we investigate how formations
 that have previously been described as, or as hosting, Lagerstätten add to
 time series of vertebrate richness in the UK, Germany and China, the
 former two representing well-studied fossil records and the latter
 representing a region where collecting has a much shorter history. In
 fact, Lagerstätten do not drive all dramatic peaks in richness curves and
 the proportion of taxa that are unique to Lagerstätten varies through time
 and between countries. Lagerstätten uniquely contain a larger proportion
 of China’s sampled richness than in Germany and the UK, despite comprising
 a smaller proportion of fossiliferous deposits in China. Additionally,
 there is little overlap between the taxa occurring in Lagerstätten and
 “ordinary” formations within the same time bin, indicating that
 Lagerstätten preserve unusual faunas and, as expected, fragile taxa make
 up a greater proportion of richness in Lagerstätten than the remainder of
 the fossil record. Vastly different sampling probabilities through taxa,
 locations and time require serious consideration when quantitatively
 analysing richness.
description: SUPPLEMENTARY_MATERIALSRaw data and calculations for model fitting.
DOI: 10.5061/dryad.1t2p835
title: Data from: The sex determination pattern in crocodilians: a systematic review after three decades of research

description: 1. Sex in crocodilians is not determined by chromosomes, but by egg
 incubation temperature, where different temperatures produce different
 clutch sex ratios. Two patterns have been proposed to describe these
 changes in sex ratios: a 100% female proportion at low and high
 temperatures with male predominance at intermediate ones (FMF) or a
 simpler pattern with a single female to male transition (FM). Over the
 last three decades, researchers have provided empirical information to
 support either of these two patterns in different species; however, no
 consensus has been reached partly because data has not been analyzed as a
 whole. 2. Here, we aimed at gathering the existing data on these patterns
 to provide models of temperature-driven sex-determination in those
 crocodilians studied so far. 3. A preliminary literature search allowed us
 to integrate a glossary of terms related with the phenomenon under study.
 With this, we created search queries that were entered into Web of
 Knowledge, Scopus, Scielo and Science Direct. Studies that reported
 results on the sexual identity of cocodrilian hatlings obtained from
 constant-temperature incubation treatments were considered. Using
 statistical models varying in their underlying assumptions, we evaluated
 which sex-determination pattern was best supported for the studied
 crocodilians and constructed species-specific and latitud-specific models.
 4. Based on the 9030 sexed hatchlings studied throughout 30 studies, we
 show that the evidence supports a shared FMF pattern in all the
 crocodilian species thus far studied. We find that such pattern changes
 both at the species and population levels, but not at higher taxonomical
 ones. We provide single-species models of the FMF pattern, along with
 their variation at different latitudes. 5. These results suggest a
 lability of the FMF crocodilian sex determination pattern, a key feature
 under the present climate change scenario.
description: Crocodilian TSD
 DataData on
 temperature-dependent sex determination in crocodilians obtained through a
 systematic review of the existing literature.2 Crocodilian TSD
 Data.csv
DOI: 10.5061/dryad.kn4f23q
title: Data from: An enigmatic new ungulate-like mammal from the early Eocene of India

description: We report on a new genus and species of herbivorous mammal, Pahelia
 mysteriosa, from the early Eocene Cambay Shale Formation, Tadkeshwar
 Lignite Mine, Gujarat, India. The new taxon, approximately the size of a
 small phenacodontid (e.g., Ectocion parvus), is represented by three
 mandibular fragments, the most complete of which documents nearly the
 entire symphysis and mandibular body plus P3-M3. Pahelia has incipiently
 selenolophodont molars with strong exodaenodonty, absent paraconids, weak
 but distinct entolophids, and prominent ectostylids. Molar size increases
 distally, but M3 does not develop a prominent third lobe. Premolars are
 simple, with prominent protoconids and short talonids but little
 development of other trigonid cusps. The mandibular symphysis is strongly
 fused, and there is an enlarged alveolus for an anterior tooth. The
 combination of features present in the new taxon does not closely match
 that of any known mammal, but there are some similarities to a diversity
 of ungulates from Africa, Asia, Europe, and North America. Preserved
 morphology is insufficient to confidently assess the affinities of the new
 taxon, but a link to Quettacyonidae, also endemic to the Indian
 subcontinent, is morphologically and biogeographically plausible. If this
 scenario is correct, it suggests that P. mysteriosa could be a part of the
 endemic mammalian fauna of India prior to its initial faunal contact with
 Asia.
description: Pahelia Supplemental
 AppendicesThis file includes
 materials from the initial phylogenetic analyses described in the text, as
 well as a specimens examined and a full character list for the
 phylogenetic analysis presented in the main text.Pahelia Appendices for
 Dryad.docx
DOI: 10.5061/dryad.099bk53
title: Data from: Exome-chip association analysis of intracranial aneurysms

description: Objective: To investigate to what extent low-frequency genetic variants
 (with minor allele frequencies &lt;5%) affect the risk of intracranial
 aneurysms (IA). Methods: 1056 IA patients and 2097 population-based
 controls from the Netherlands were genotyped using the Illumina HumanExome
 BeadChip. After quality control (QC) of samples and single nucleotide
 variants (SNVs), we conducted a single variant analysis using Fisher’s
 exact test. We also performed the variable threshold (VT) and the sequence
 kernel association tests (SKAT) at different minor allele count (MAC)
 thresholds of ±5 and ±0 to test the hypothesis that multiple variants
 within the same gene are associated with IA risk. Significant results were
 tested in a replication cohort of 425 IA patients and 311 controls, and
 results of the two cohorts were combined in a meta-analysis. Results:
 After QC, 995 IA patients and 2080 controls remained for further analysis.
 The single variant analysis comprising 46,534 SNVs did not identify
 significant loci at the genome-wide level. The gene-based tests showed a
 statistically significant association for FBLN2 (best p=1x10-6 for the VT
 test, MAC±5). Associations were not statistically significant in the
 independent but smaller replication cohort (p±0.57), but became slightly
 stronger in a meta-analysis of the two cohorts (best p=4.8x10-7 for the
 SKAT, MAC&gt;1). Conclusion: Gene-based tests indicated an association
 for FBLN2, a gene encoding an extracellular matrix protein implicated in
 vascular wall remodeling, but independent validation in larger cohorts is
 warranted. We did not identify any significant associations for single
 low-frequency genetic variants.
description: Supplementary
 FiguresSupplementary Figures
 1-5Supplementary
 TablesSupplementary Tables
 1-3
DOI: 10.5061/dryad.0373j7r
title: Data from: A logical model of homology for comparative biology

description: There is a growing body of research on the evolution of anatomy in a wide
 variety of organisms. Discoveries in this field could be greatly
 accelerated by computational methods and resources that enable these
 findings to be compared across different studies and different organisms
 and linked with the genes responsible for anatomical modifications.
 Homology is a key concept in comparative anatomy; two important types are
 historical homology (the similarity of organisms due to common ancestry)
 and serial homology (the similarity of repeated structures within an
 organism). We explored how to most effectively represent historical and
 serial homology across anatomical structures to facilitate computational
 reasoning. We assembled a collection of homology assertions from the
 literature with a set of taxon phenotypes for vertebrate fins and limbs
 from the Phenoscape Knowledgebase (KB). Using seven competency questions,
 we evaluated the reasoning ramifications of two logical models: the
 Reciprocal Existential Axioms Homology Model (REA) and the Ancestral Value
 Axioms Homology Model (AVA). Both models returned the user-expected
 results for all but one historical homology query and one serial homology
 query. Additionally, for each competency question, the AVA model returns
 the search term and any subtypes. We identify some challenges of
 implementing complete homology queries due to limitations of OWL
 reasoning. This work lays the foundation for homology reasoning to be
 incorporated into other ontology-based tools, such as those that enable
 synthetic supermatrix construction and candidate gene discovery.
description: Supplementary Materials
 1: Phenoscape homology assertionsCollection of homology
 assertions. Each assertion relates an Entity 1 in Taxon 1 as historically
 or serially homologous (or not) to an Entity 2 in Taxon 2 based on
 evidence (annotated with terms from the Evidence and Conclusion Ontology)
 cited in the literature (Attribution).SupplementaryMaterials1.txtSupplementaryMaterials2:Fin and limb phenotypesSupplementary Materials 2. The subset of fin/limb phenotypes from the Phenoscape KB used in the demonstration homology file.SupplementaryMaterials2.tsvSupplementary Materials 3: OWL explanation regarding Uberon grouping classesSupplementary Materials 3. OWL explanation for 'length of forelimb' as phenotype of a 'pectoral fin' homolog. The explanation does not require evolutionary "grouping classes" found in Uberon, such as 'paired limb/fin'SupplementaryMaterials3.txtSupplementary Materials 4Supplementary Materials 4. OWL expressions in relation to the seven competency questions and their corresponding natural language expressions for each competency question.SupplementaryMaterials4.docx
DOI: 10.5061/dryad.56kv356
title: Data from: A pair of nonoptimal codons are necessary for the correct biosynthesis of the Aspergillus nidulans urea transporter, UreA

description: Both in prokaryotic and eukaryotic genomes synonymous codons are unevenly
 used. Such differential usage of optimal or nonoptimal codons has been
 suggested to play a role in the control of translation initiation and
 elongation, as well as at the level of transcription and mRNA stability.
 In the case of membrane proteins codon usage has been proposed to assist
 in the establishment of a pause necessary for the correct targeting of the
 nascent chains to the translocon. In this work, using as model UreA, the
 Aspergillus nidulans urea transporter, we show that the synonymous
 mutation of a pair of nonoptimal codons coding for amino acids situated at
 the limit between the N-terminus and the first transmembrane segment are
 necessary for its proper biogenesis at 37ºC. This effect is less relevant
 at 25ºC. These codons presumably regulate translation rate in order to
 allow for the correct interaction of UreA-translating ribosomes with
 factors required for the targeting and/or folding of the protein, in a
 very early stage of the biosynthesis process. Whether this mechanism would
 affect other proteins, remains to be determined.
description: Raw data_figure 1.xlsx - Contains raw data of RSCUs
 Raw data_figure3.xlsx Raw
 data_figure4.xlsx
 Supplementary_material_Sanguinetti_et_al..pdf
 Raw data_Supplementary Figure S4b.xlsx
DOI: 10.5061/dryad.k8ft12q
title: Data from: Comparing and co-analysing microsatellite and morphological data for species delimitation in the New Zealand native Myosotis pygmaea species group (Boraginaceae)

description: Delimiting species boundaries in recent plant radiations can be
 challenging. The New Zealand native Myosotis pygmaea (Boraginaceae)
 species group is a case in point. This species complex is of interest as
 it includes threatened species as well as possibly threatened unnamed
 putative taxa. Integrative taxonomic approaches using multiple lines of
 evidence are frequently used to overcome the difficulties of identifying
 lineages resulting from recent radiations. Here we analyse genotypic data
 from nearly 500 Myosotis individuals using microsatellite markers, and
 compare and co-analyse this dataset with previously published
 morphological data. Within the M. pygmaea group, several genetic clusters
 can be identified, none of which align exactly with the current taxonomy
 and morphological variation previously identified. When co-analysing the
 molecular and morphological data, M. brevis can be distinguished from the
 remainder of the M. pygmaea species group, but no other species or
 previously recognised morphological groups are supported. Other groupings
 within the molecular dataset appear to reflect geographic structure.
 Within the M. pygmaea species group, the resulting pattern of low within,
 and high between, population genetic variation is consistent with
 self-fertilization and low levels of seed dispersal.
description: Myosotis pygmaea group
 SSR dataThis data file contains
 scored SSR data of 12 markers for 497 individuals in the Myosotis pygmaea
 species group. It is formatted by GenAlEx. Missing data is represented by
 a 0. The population codes in this file are based on collector numbers,
 whereas in the related publication the populations are identified by two
 letter codes. The associated file titled "voucher information for
 specimens" translates between the two codes.MyoPygOnly497dataset.csvVoucher information for specimensThis file contains voucher information for the individuals included in the SSR datafile, as well as translating between the population codes used in the data file and those used in the publication
DOI: 10.5061/dryad.2t8c60f
title: Data from: The first skeletal record of the enigmatic Cretaceous sawfish genus Ptychotrygon (Chondrichthyes, Batoidea) from the Turonian of Morocco

description: A new fossil batoid (ray) Ptychotrygon rostrispatula sp. nov. is described
 from five exceptionally well-preserved, three-dimensional skeletal remains
 from the Turonian (Late Cretaceous) of Morocco. These specimens represent
 the first known skeletal remains for the genus Ptychotrygon and allow an
 almost complete description of the genus providing a new insight to its
 phylogenetic relations and validate its taxonomic status as a member of
 the Sclerorhynchoidei. Mechanical preparation of the fossil remains
 revealed a relatively large batoid species (estimated total length beyond
 1 meter). Overall morphology resembles that of sclerorhynchoids with a
 robust hypertrophied rostrum that lacks enlarged rostral denticles with
 enlarged paddle-like pectoral proximal elements (propterygium,
 mesopterygium and metapterygium). Never seen before details of the
 branchial skeleton are presented (large second hypobranchial without
 anterior process which was probably fused to the basibranchial and no
 evidence of articulation with other branchial element). To assess the
 phylogenetic relations of these specimens within the sclerorhynchoids a
 parsimonious analysis using TNT and PAUP software packages was performed.
 These analyses included Asflapristis cristadentis that along with
 Ptychotrygon rostrispatula sp. nov. were used as representatives of
 Ptychotrygonidae and also includes six other genera of sclerorhynchoids
 with relatively good skeletal remains. Both analyses recovered two
 monophyletic groups within sclerorhynchoids: the first contains
 Ischyrhiza, Onchopristis and Schizorhiza and a second that includes
 Micropristis, Sclerorhynchus, Libanopristis and Ptychotrygonidae.
description: matrixmatrix of characters
 used for the TNT and PAUP phylogenetic analyses (14 taxa X 23
 characters)matrixOutput of the PAUP
 analysis. File includes description of trees (tree indexes) under
 different optimisations and the Bootstrap tree. Bootstrap tree includes
 clades with less support than 50%
DOI: 10.5061/dryad.mn176dr
title: Data from: Cerebrospinal fluid dynamics disorders: relationship to Alzheimer biomarkers and cognition

description: Objectives: To determine the frequency high-convexity tight sulci (HCTS)
 in a population based sample and whether the presence of HCTS and related
 features influenced participants’ cognitive status and classification
 within the new Alzheimer-biomarker framework. Methods: We analyzed 684
 participants, ≥50, enrolled into the prospective population-based Mayo
 Clinic Study of Aging, who underwent structural MRI, amyloid PET imaging,
 and tau- PET imaging. A fully automated machine-learning algorithm that
 had been developed previously in-house was used to detect neuroimaging
 features of HCTS. Based on PET and MRI measures, participants were
 classified as having normal (A−) or abnormal (A+) amyloid, normal (T−) or
 abnormal (T+) tau, and normal (N−) or abnormal (N+) neurodegeneration. The
 neuropsychological battery assessed domain-specific and global cognitive
 scores. Gait speed also was assessed. Analyses were adjusted for age and
 sex. Results: 45/684 participants (6.6%) were classified with HCTS based
 on the automated algorithm. Patients with HCTS were older than patients
 without HCTS (mean [SD], 78.0 [8.3] vs 71.9 [10.8] years; P&lt;.001).
 More were cognitively impaired after age and sex adjustment (27% vs 9%;
 P=.005). Amyloid PET status was similar with and without HCTS, but tau PET
 SUVR was lower for those with HCTS after age and sex adjustment
 (P&lt;.001). Despite a lower tau SUVR, HCTS patients had lower
 Alzheimer disease (AD) signature cortical thickness. Using the AT(N)
 framework, HCTS was overrepresented in the T−(N)+ group, regardless of
 amyloid status. Conclusions: The HCTS pattern represents a definable
 subgroup of non-AD pathophysiology (i.e., T−[N]+) that is associated with
 cognitive impairment. HCTS may confound clinical and biomarker
 interpretation in AD clinical trials.
description: Supplemental
 TableHerein we report the
 AT(N)-biomarker profiles of the individual patients.supplement.docx
DOI: 10.5061/dryad.9nm0697
title: Data from: Relation between 20-year income volatility and brain health in midlife: the CARDIA study

description: Objective: Income volatility presents a growing public health threat. To
 our knowledge, no previous study examined the relationship between income
 volatility, cognitive function and brain integrity. Methods: We studied
 3,287 participants aged 23 to 35 years in 1990 from the Coronary Artery
 Risk Development in Young Adults prospective cohort study. Income
 volatility data were created using income data collected from 1990 to 2010
 and defined as standard deviation of percent change in income and number
 of income drops &gt;=25% (categorized as 0, 1, or 2+). In 2010,
 cognitive tests (n=3,287) and brain scans (n=716) were obtained. Results:
 After covariate adjustment, higher income volatility was associated with
 worse performances on processing speed (β=-1.09, 95%CI=-1.73, -0.44) and
 executive functioning (β=2.53, 95%CI:0.60, 4.50) but not on verbal memory
 (β=-0.02, 95%CI:-0.16, 0.11). Similarly, additional income drops were
 associated with worse performances on processing speed and executive
 functioning. Higher income volatility and more income drops were also
 associated with worse microstructural integrity of total brain and total
 white matter. All findings were similar when restricted to those with high
 education, suggesting reverse causation may not explain these findings.
 Conclusion: Income volatility over a 20-year period of formative earning
 years was associated with worse cognitive function and brain integrity in
 midlife.
description: Supplementary
 materialThis includes
 supplementary tables and figures