cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4nb96c1
title: Data from: Lower extremity muscle pathology in myotonic dystrophy type 1 assessed by quantitative MRI

description: Objective: To determine the value of quantitative MRI to provide imaging
 biomarkers for disease in 20 different upper and lower leg muscles of
 myotonic dystrophy type 1 (DM1) patients. Methods: We acquired images
 covering these muscles in 33 genetically and clinically well-characterized
 DM1 patients and 10 unaffected controls. MR images were recorded with a
 Dixon method to determine muscle fat fraction, muscle volume and
 contractile muscle volume, and a multi-spin echo sequence to determine T2
 water relaxation time (T2water), reflecting putative oedema. Results:
 Muscles in DM1 patients had higher fat fractions than muscles of controls
 (15.6%±11.1% vs. 3.7%±1.5%). Also, patients had smaller muscle volumes
 (902±232 cm3 vs. 1097±251 cm3), contractile muscle volumes (779±247 cm3
 vs. 1054±246 cm3), and increased T2water (33.4±1.0 ms vs. 31.9±0.6 ms),
 indicating atrophy and oedema, respectively. Lower leg muscles were
 affected most frequently, especially the gastrocnemius medialis and
 soleus. Distribution of fat content per muscle indicated gradual fat
 infiltration in DM1. Between-patient variation in fat fraction was
 explained by age (~45%), and another ~14% by estimated progenitor CTG
 repeat length (r2 = 0.485) and somatic instability (r2 = 0.590). Fat
 fraction correlated with the six-minute walk test (r = -0.553) and
 muscular impairment rating scale (r = 0.537), and revealed subclinical
 muscle involvement. Conclusion: This cross-sectional quantitative MRI
 study of 20 different lower extremity muscles in DM1 patients revealed
 abnormal values for muscle fat fraction, volume and T2water, which
 therefore may serve as objective biomarkers to assess disease state of
 skeletal muscles in these patients.
description: Supplementary
 DataThe supplementary data
 file contains 1) A more detailed description of the applied T2water
 fitting approach to quantify putative oedema in the lower extremity
 muscles, 2) MRI outcome measures depicted for the 20 individual lower
 extremity muscles, 3) Detailed outcomes of the multivariate linear
 regression model used to assess the effect of age and CTG repeat length on
 lower extremity muscle fat fraction, 4) Effect of AciI-sensitive variant
 repeats in the expanded allele on lower extremity muscle fat fraction. 5)
 Detailed overview of the correlation between the 6MWT and the fat fraction
 in four functional muscle groups (quadriceps, hamstrings, anterior
 compartment of the lower leg, and triceps surae).Supplementary
 Material.pdf
DOI: 10.5061/dryad.v1265j8
title: Data from: Nature and timing of biotic recovery in Antarctic benthic marine ecosystems following the Cretaceous–Palaeogene mass extinction

description: Taxonomic and ecological recovery from the Cretaceous-Paleogene (K–Pg)
 mass extinction 66 million years ago shaped the composition and structure
 of modern ecosystems. The timing and nature of recovery has been linked to
 many factors including palaeolatitude, geographic range, the ecology of
 survivors, incumbency, and palaeoenvironmental setting. Using a temporally
 constrained fossil dataset from one of the most expanded
 Cretaceous–Paleogene successions in the world, integrated with
 palaeoenvironmental information, we provide the most detailed examination
 of the patterns and timing of recovery from the K–Pg mass extinction event
 in the high southern latitudes of Antarctica. The timing of biotic
 recovery was influenced by global stabilisation of the wider Earth system
 following severe environmental perturbations, apparently regardless of
 latitude or local environment. Extinction intensity and ecological change
 were decoupled, with community scale ecological change less distinct
 compared to other locations, even if the taxonomic severity of the
 extinction was the same as at lower latitudes. This is consistent with a
 degree of geographic heterogeneity in the recovery from the K–Pg mass
 extinction. Recovery in Antarctica was influenced by local factors (such
 as water depth changes, local volcanism, and possibly incumbency and
 pre-adaptation to seasonality of the local benthic molluscan population),
 and also showed global signals, for example the radiation of the
 Neogastropoda within the first million years of the Danian, and a shift in
 dominance between bivalves and gastropods.
description: Supplementary Data Excel
 fileSupplementary data for:
 NATURE AND TIMING OF BIOTIC RECOVERY IN ANTARCTIC BENTHIC MARINE
 ECOSYSTEMS FOLLOWING THE CRETACEOUS-PALEOGENE (K–PG) MASS
 EXTINCTIONSupplementary
 data.xlsxSupplementary figures
 and tablesSupplementary figures
 and tables for: NATURE AND TIMING OF BIOTIC RECOVERY IN ANTARCTIC BENTHIC
 MARINE ECOSYSTEMS FOLLOWING THE CRETACEOUS-PALEOGENE (K–PG) MASS
 EXTINCTIONSupplementary.docx
DOI: 10.5061/dryad.k24b5k2
title: Data from: Assortative mating frames establishment in a young island bird population

description: Successful island colonizations are key events to understand range dynamic
 processes, but studying a young population right after it reaches
 establishment is a rare opportunity in natural systems. However, the
 genetic structure of a recently established population may offer unique
 insights into its colonization history and demographic processes important
 for a successful colonization. Here, we studied the population genetics of
 a recently established island population of Eurasian blackbirds (Aves:
 Turdus merula) located on the island of Heligoland in the German North
 Sea. Using microsatellites, we genotyped the majority of the island
 population, including the nestlings, over a four-year period between 2004
 and 2007. We also genotyped high numbers of migrants on stopover and
 mainland individuals, as they are potential founders of the island
 population. We identified two genetic clusters that comply with the
 migrating and mainland birds respectively. While most of the island birds
 belong to the mainland cluster, some breeding individuals and a low
 fraction of the offspring belong to the genetic cluster found in migrating
 individuals with almost no admixture between the two, pointing to
 assortative mating acting on the island population. We did not find any
 evidence for founder events and detected deviations from Hardy-Weinberg
 equilibrium that disappeared in cohorts of older age that coincide with a
 lower number of siblings in older cohorts. The observed genetic patterns
 unravel a complex colonization history to which migratory and mainland
 birds have contributed and which is characterized by assortative mating.
 Further research will be directed towards habitat selection and phenotypic
 differences as potential drivers of assortative mating in this island
 population.
description: Blackbird
 genotypesExcel file of genotype
 by scored alleles for each individual (n tot = 822). The last seven
 columns provide data for each microsatellite used with biallelic scores
 written in a format to be read by / transformed to most population
 genetics software packages. A value of 999 indicated a missing (i.e. NA)
 value. The column "pop_name_paper" provides information on the
 population the individual belongs as named in the
 paper.genotype_cr_t4.xlsx
DOI: 10.5061/dryad.m42t6tm
title: Data from: The giants of the phylum Brachiopoda: a matter of diet?

description: The species of the brachiopod Gigantoproductus are giants within the
 Palaeozoic sedentary benthos. This presents a dilemma as living
 brachiopods have low-energy lifestyles. Although brachiopod metabolic
 rates were probably higher during the Palaeozoic than today, the massive
 size reached by species of Gigantoproductus is nevertheless unusual. By
 examining the diet of Gigantoproductus species from the Visean
 (Mississippian, Carboniferous) of Derbyshire (UK), we seek to understand
 the mechanisms that enabled those low-metabolism brachiopod species to
 become giants. Were they suspension feeders, similar to all other
 brachiopods or did endosymbiosis provide a lifestyle that allowed them to
 have higher metabolic rates and become giants? We suggest that the answer
 to this conundrum may be solved by the identiﬁcation of the biogeochemical
 signatures of symbionts, through combined analyses of the carbon- and
 nitrogen-isotopic compositions of the occluded organic matrix within their
 calcite shells. The shells are formed of remarkably long, and a few
 hundreds of micrometres wide, substructured columnar units deemed to be
 mostly pristine based on multiple analyses [petrography,
 cathodoluminescence (CL), Scanning Electron Microscopy (SEM), Electron
 Backscatter Diffraction (EBSD), Transmission Electron Microscopy (TEM)];
 they contain occluded organic fractions detected by TEM, Nuclear Magnetic
 Resonance (NMR), and Gas Chromatography Mass Spectrometry (GC-MS)
 analyses. We conclude that the gigantic size reached by the species of
 Gigantoproductus is likely the result of a mixotroph lifestyle, by which
 they could rely on the energy and nutrients derived both from
 photosymbiotic microbes and from filtered particulate food.
description: Fig. S1
 petroAdditional parallel and
 crossed polarizers photomicrographsFig. S2
 CLAdditional
 cathodoluminescence photomicrographsFig. S3
 XRDX
 Ray Powder Diffraction (XRPD) analysesFig. S4
 SEMAdditional SEM
 photomicrographsFig. S5 trace
 elementsTrace elements of
 selected specimens (Mn, Fe, Sr).
DOI: 10.5061/dryad.67k2f74
title: Data from: Hot tops, cold bottoms: synergistic climate warming and shielding effects increase carbon burial in lakes

description: In this article, we challenge the notion that global warming stimulates
 organic matter min-eralization and increases greenhouse gas emissions in
 lakes via direct temperature effects. We show that the interactive effects
 of warming and transparency loss due to eutrophica-tion or browning
 override effects of atmospheric warming alone. Thermal shielding ena-bles
 a longer and more stable stratification that results in bottom-water
 cooling, prolonged anoxia and enhanced carbon preservation in a large
 proportion of global lakes. These ef-fects are strongest in shallow lakes
 where an additional burial of 4.5 Tg C y-1 increases current global
 estimates by 9%. Despite more burial, the net global warming potential of
 lakes will increase via enhanced methane production, related to prolonged
 periods of an-oxia, rather than warming. Our understanding of how
 whole-lake carbon cycling responds to climate change needs revision, as
 the synergistic influence of warming and transparency loss has much
 broader ecosystem level functional consequences.
description: FLake Model Simulation
 5, 20 and 100m for LOLLakeDepthDataSet Data
 FOR LOLMetadata-LO-Letters-dataMetadata file
DOI: 10.5061/dryad.6s5651k
title: Data from: Fossil liberation: a model to explain high biodiversity in the Triassic Cassian Formation

description: With 1429 animal species, the Triassic Cassian Formation in the Dolomites,
 Southern Alps (Italy), yields the highest species richness reported from
 any spatially constrained pre-Quaternary formation known to science. The
 high preserved diversity is partly attributable to a high primary
 diversity governed by the tropical setting, increasing alpha diversity,
 and the breadth of habitats spurring beta diversity. More important is the
 excellent preservation of fossils and the ease with which they can be
 extracted from the poorly lithified sediments. We propose the term
 liberation lagerstätten to capture this preservational window. In contrast
 to conservation lagerstätten, liberation lagerstätten like the Cassian
 Formation originate from normal marine conditions but low-grade
 diagenesis. Molluscs contribute substantially to species richness,
 comprising 67% of all invertebrate species in the Cassian Formation. The
 gastropod dominance (39% of all species) is nearly as great as in Recent
 tropical settings, contradicting the concept of a substantial Cenozoic
 rise.
description: Appendix S1: Species
 list, Cassian FormationA list of species
 described from the Late Triassic Cassian Formation, Dolomites, Northern
 Italy, was compiled by the authors of the accompanying publication. This
 list is used for analysis in the main text. It is intended to facilitate
 comparisons with other fossil lagerstätten not only in terms of taxonomic
 richness but also in terms of clade proportions and the distribution of
 primary shell mineralogy.Appendix_S1_Species_list_Cassian_Roden_et_al.csvAppendix S2: Explanatory notes and referencesAppendix S2 provides details on the compiled list of species from the Cassian Formation (Appendix S1), including information on the localities and methods. It lists the references used for the literature compilation.Appendix_S2_Cassian_Roden_et_al_2019.pdfREADME_Roden_et_al_2019
DOI: 10.5061/dryad.j5m024n
title: Data from: Destabilitation and energy characteristics of coal pillar in roadway driving along gob based on rockburst risk assessment

description: Roadway driving along adjacent goafs is an effective method to develop the
 recovery rate of coal resources. However, rock burst triggered by dynamic
 destabilization of coal pillars poses serious threats to safe and
 efficient mining, thereby significantly restricting the sustainable
 development of coal mines. In this study, from the perspectives of energy
 accumulation and dissipation, a mathematic model of coal pillar is
 established and the energy equilibrium relationship of the mechanical
 system is analyzed. The rock burst mechanism of coal pillars in gob-side
 entry is obtained based on a fold catastrophe mathematical model. Results
 indicate that the rock burst triggered by the instability is a
 destabilization phenomenon. If the stiffness factor of the mechanical
 system is less than 1 and the external force is enough to lead coal
 pillars to the peak stress point, then rock burst disaster occurs. The
 engineering analysis and numerical simulation are conducted to study the
 rock burst in the gob-side entry that occurred in Xin’an coal mine. Stress
 release caused by mining can reduce the risk of rock burst to a certain
 extent. The amount of elastic energy released is 6.4512×107 J, which is
 close to the observation data and verifies the correctness and rationality
 of the research method. The research result provides a theoretical basis
 and technical guidance for rock burst prevention and control in roadway
 driving along adjacent goafs.
description: Numerical
 parameters
DOI: 10.82518/ttacdo
title: Tool wear in drilling of Inconel 718 plates

description: Curated dataset from an experiment of tool wear in drilling of Inconel 718. Seven (7) drill bits were tested under different cutting conditions. The dataset includes measurements of flank tool wear as well as machine signals recorded during the drilling of each hole.

For more information, see README.md
DOI: 10.5061/dryad.8pf04d3
title: Data from: In the land of giants: habitat use and selection of the Aldabra giant tortoise on Aldabra Atoll

description: With habitat loss and fragmentation among the greatest threats to
 biodiversity, a better understanding of the habitat use of keystone
 species is critical in any conservation management strategy. Aldabra
 Atoll, in the Seychelles archipelago, has the largest population worldwide
 of giant tortoises. This endemic species (Aldabrachelys gigantea) could be
 vulnerable to habitat fragmentation and loss induced by climate change
 related reduction in rainfall. Here, we assess habitat use and selection
 by A. gigantea in its natural environment on Aldabra. We quantified the
 habitat areas of A. gigantea based on the first high-resolution
 terrestrial habitat map of Aldabra, produced for this purpose using
 satellite imagery. The resulting map was combined with four years of
 movement data to assess A. gigantea habitat use and selection at landscape
 and home range scales. Grassland or ‘tortoise turf’ habitat was most
 preferred by A. gigantea on Aldabra, at the landscape scale across
 seasons, followed by open mixed scrub. These two habitats cover only 30
 km2 (19.2%) of the surface of the atoll (total area: 155.5 km2). At the
 home range scale, there was no significant preference shown and habitat
 was used randomly. Our results suggest that Aldabra’s grassland habitat,
 despite its small area, is of great importance to A. gigantea.
 Conservation management actions for A. gigantea on Aldabra and elsewhere
 should therefore focus on the protection and maintenance of this habitat.
description: 2019_Walton_AldabraAtollTerrestrialHabitatcovermapClassified habitat map generated using ENVI image analysis software from GeoEye satellite images. Ground truthing and validation points collected in the field. Final map package produced in ArcMap 10.6. For more detail please see methods section in Walton et al. (2019) In the land of giants: habitat use and selection of the Aldabra giant tortoise on Aldabra Atoll. Biodiversity and Conservation, in review.2019_Walton_AldabraAtollTerrestrialHabitatcovermap_twopagesFinal pdf version of terrestrial habitat map of Aldabra Atoll (original files in map package) with habitat classes described.
DOI: 10.5061/dryad.4nm4vv0
title: Data from: New Palaeogene caviomorphs (Rodentia, Hystricognathi) from Santa Rosa, Peru: systematics, biochronology, biogeography and early evolutionary trends

description: The origin and early evolution of South American rodents are ongoing
 subjects of debate. The caviomorphs of the Peruvian localities of Santa
 Rosa and Contamana are the oldest South American rodents so far known. The
 Santa Rosa rodents are abundant and diverse, but dating was based on
 biostratigraphy (?Eocene), whereas in various Contamana sites radiometric
 dates, vertebrate biochronology and palynostratigraphy suggest an age of
 41.6–40.94 Ma (late middle Eocene). Previous faunal comparisons between
 the localities have identified few shared taxa. Here we studied new and
 previously described rodent fossils from Santa Rosa and analysed their
 biochronological and biogeographical implications. We recognize five new
 taxa and three genera for Santa Rosa, four of them previously known only
 from the Eocene Contamana region. Thus, the Santa Rosa and the late middle
 Eocene Contamana assemblages appear to be chronologically closer than
 previously thought. An ?Eocene age for Santa Rosa is substantiated by
 other mammals reported from Santa Rosa. With 11 named genera and 15
 species, the Santa Rosa rodents represent the most species‐rich South
 American Palaeogene rodent assemblage known. The Eocene radiation in the
 Neotropics that gave rise to this diversity was not associated with an
 immediate geographical dispersion to higher latitudes, perhaps because
 different biogeographical barriers or factors of competition delayed their
 dispersal. Evidence suggests that replacement, rather than a persistence
 of conservative long‐lasting lineages, was the dominant process among
 Palaeogene tropical caviomorph rodents.
description: R1 Appendix 1- Arnal et
 al.Appendix 1. List of new
 and some previously described fossil specimens studied in this work. *
 indicate those fossils figured by Frailey & Campbell (2004). **
 indicates holotype. Measurements are in millimeters
 (mm).
DOI: 10.5061/dryad.315v28r
title: Data from: Analysis of gene expression in rheumatoid arthritis and related conditions offers insights into sex-bias, gene biotypes and co-expression patterns

description: The era of next-generation sequencing has mounted the foundation of many
 gene expression studies. In rheumatoid arthritis research, this has led to
 the discovery of important candidate genes which offered novel insights
 into mechanisms and their possible roles in the cure of the disease. In
 the last years, data generation has outstripped data analysis and while
 many studies focused on specific aspects of the disease, a global picture
 of the disease is not yet accomplished. Here, we analyzed and compared a
 collection of gene expression information from healthy individuals and
 from patients suffering under different arthritis conditions from
 published studies containing the following clinical conditions: early and
 established rheumatoid arthritis, osteoarthritis and arthralgia. We show
 comprehensive overviews of this data collection and give new insights
 specifically on gene expression in the early stage, into sex-dependent
 gene expression, and we describe general differences in expression of
 different biotypes of genes. Many genes that are related to cytoskeleton
 changes (actin filament related genes) are differently expressed in early
 rheumatoid arthritis in comparison to healthy subjects; interestingly,
 eight of these genes reverse their expression ratio significantly between
 men and women compared early rheumatoid arthritis and healthy subjects.
 There are some slighter changes between men and woman between the
 conditions early and established rheumatoid arthritis. Another aspect are
 miRNAs and other gene biotypes which are not only promising candidates for
 diagnoses but also change their expression grossly in average at
 rheumatoid arthritis and arthralgia compared to the healthy condition.
 With a selection of intersecting genes, we were able to generate simple
 classification models to distinguish between healthy and rheumatoid
 arthritis as well as between early rheumatoid arthritis to other
 arthritides based on gene expression.
description: Supplementary
 ArchiveSupplementary figures
 and tables; readme files are in the archive;supplement.zip
DOI: 10.5061/dryad.37c840g
title: Data from: Skeletal completeness of the non‐avian theropod dinosaur fossil record

description: Non‐avian theropods were a highly successful clade of bipedal,
 predominantly carnivorous, dinosaurs. Their diversity and
 macroevolutionary patterns have been the subject of many studies. Changes
 in fossil specimen completeness through time and space can bias our
 understanding of macroevolution. Here, we quantify the completeness of 455
 non‐avian theropod species using the skeletal completeness metric (SCM),
 which calculates the proportion of a complete skeleton preserved for a
 specimen. Temporal patterns of theropod skeletal completeness show peaks
 in the Carnian, Oxfordian–Kimmeridgian and Barremian–Aptian, and lows in
 the Berriasian and Hauterivian. Lagerstätten primarily drive the peaks in
 completeness and observed taxonomic diversity in the
 Oxfordian–Kimmeridgian and the Barremian–Aptian. Theropods have a
 significantly lower distribution of completeness scores than contemporary
 sauropodomorph dinosaurs but change in completeness through time for the
 two groups shows a significant correlation when conservation Lagerstätten
 are excluded, possibly indicating that both records are primarily driven
 by geology and sampling availability. Our results reveal relatively weak
 temporal sampling biases acting on the theropod record but relatively
 strong spatial and environmental biases. Asia has a significantly more
 complete record than any other continent, the mid northern latitudes have
 the highest abundance of finds, and most complete theropod skeletons come
 from lacustrine and aeolian environments. We suggest that these patterns
 result from historical research focus, modern climate dynamics, and
 depositional transportation energy plus association with conservation
 Lagerstätten, respectively. Furthermore, we find possible ecological
 biases acting on different theropod subgroups, but body size does not
 influence theropod completeness on a global scale.
description: Theropod skeletal
 completeness datasheetSpecimen information,
 completeness scores, and spatial and temporal occurrence data for
 non-avian theropod dinosaursTheropod_Completeness_Datasheet.xlsxSupplementary materialSupplementary figures and tables, R code, subgroup justification, and specimen scoring methodologySupplementary_material_13.06.19.pdf