cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17026/ar/tectdc
title: BO AAC B.L. Tijdenskanaal Groningen
title: Aardkunde, archeologie en cultuurhistorie

description: In opdracht van Waterschap Hunze en Aa's heeft Arcadis in de periode juni 2024-januari 2026 een bureauonderzoek aardkunde, archeologie en cultuurhistorie uitgevoerd. Dit in verband met de geplande werkzaamheden rond de kades van het B.L. Tijdenskanaal in de gemeente Westerwolde. Het doel van het onderzoek is om te bepalen of de geplande werkzaamheden afbreuk doen aan de aanwezige archeologische, cultuurhistorische, aardkundige en/of landschappelijke waarden. Door te kijken naar de opbouw en ontwikkeling van het gebied en de reeds bekende archeologische gegevens wordt inzicht verkregen in de archeologische waarden binnen het onderzoeksgebied. Op basis hiervan wordt bepaald welke risico's en kansen er in het onderzoeksgebied gelden met betrekking tot aanwezige en te verwachten waarden.
DOI: 10.5061/dryad.4gh7b
title: Data from: The summary-likelihood method and its implementation in the Infusion package

description: In recent years, simulation methods such as approximate Bayesian
 computation have extensively been used to infer parameters of population
 genetic models where the likelihood is intractable. We describe an
 alternative approach, summary likelihood, that provides a likelihood-based
 analysis of the information retained in the summary statistics whose
 distribution is simulated. We provide an automated implementation as a
 standard R package, Infusion, and we test the method, in particular for a
 scenario of inference of population-size change from genetic data. We show
 that the method provides confidence intervals with controlled coverage
 independently of a prior distribution on parameters, in contrast to
 approximate Bayesian computation. We expect the method to be applicable
 for at least six-parameter models and discuss possible modifications for
 higher-dimensional inference problems.
description: R
 scriptsZipped archive of R
 scripts for simulation of samples and for analysis of simulated
 samplesscripts.zipSimulations for first iteration of the poulations-size change analyses:The simulations output is stored as an R data file, to be loaded in an R session by the load() command.PSC_simulations.rda
DOI: 10.5061/dryad.mf513
title: Data from: Plastid and seed morphology data support revised infrageneric classification and African origin of the pantropical genus Xylopia (Annonaceae)

description: The floristic treatment of Engler and Diels, published in 1901, provides
 the only infrageneric classification of the pantropical genus Xylopia
 (Annonaceae). Here we test and extend that classification using molecular
 and seed morphology characters. Phylogenetic relationships were
 reconstructed using data from four plastid regions obtained from 44 of the
 approximately 165 species in the genus, recovering four well-supported
 major clades. Seed characters were examined for these taxa, and six aril
 morphologies, three previously undocumented, were distinguished; we also
 document the presence of a sarcotesta on the seeds of many species.
 Molecular and seed data support recognition of five sections within the
 genus; one, Xylopia sect. Rugosperma, is proposed here as new. Our
 phylogenetic results suggest an African origin for the genus and reveal
 complex biogeographic patterns, likely facilitated by long-distance
 dispersal.
description: Maximum likelihood
 analysis of matKMaximum likelihood
 analysis of matK, showing bootstrap supportSuppl1_Xyl_matK.pdfMaximum likelihood analysis of ndhFMaximum likelihood analysis of ndhF, showing bootstrap supportSuppl2_Xyl_ndhF.pdfMaximum likelihood analysis of psbA-trnH spacerMaximum likelihood analysis of psbA-trnH spacer, showing bootstrap supportSuppl3_Xyl_psbA-trnH.pdfMaximum likelihood analysis of trnL-trnF spacerMaximum likelihood analysis of trnL-trnF spacer, showing bootstrap supportSuppl4_Xyl_trnLF.pdfGene-partitioned maximum likelihood analysisMaximum likelihood analysis of the four-marker data set (gene-partitioned), showing bootstrap support.Suppl5_ML_4gene_PART_clado.pdfUnpartitioned maximum likelihood analysisMaximum likelihood analysis of the four-marker data set (unpartitioned), showing bootstrap support.Suppl6_ML_4gene_UNPART_clado.pdfBayesian analysis of the four-marker data setBayesian analysis of the four-marker data set, including support values for node.Suppl7_BAYES_FOURGENE.pdfMaximum parsimony analysis of the four-marker data setMaximum parsimony analysis of the four-marker data set, including bootstrap support values.Suppl8_MP_4genes.pdfMaximum parsimony reconstruction of aril typesMaximum parsimony reconstruction of aril types, implemented in MesquiteSuppl9_aril_mesquite.pdfMaximum parsimony reconstruction of sarcotestaMaximum parsimony reconstruction of sarcotesta (presence vs. absence), implemented in MesquiteSuppl10_sarcotesta_mesquite.pdfmatK alignmentmatK multiple sequence alignmentXyl_matK_wMissingTaxa_Inframe.nexndhF alignmentndhF multiple sequence alignmentXyl_ndhF_wMissinTaxa_Inframe.nexpsbA-trnH spacer alignmentpsbA-trnH spacer multiple sequence alignmentXyl_psbA-trnH_wMissingTaxa.nextrnL-trnF spacer alignmenttrnL-trnF spacer multiple sequence alignmentXyl_trnLF_wMissingTaxa.nex
DOI: 10.5061/dryad.b2v7v
title: Data from: Millions of years behind: slow adaptation of ruminants to grasslands

description: The Late-Cretaceous appearance of grasses, followed by the Cenozoic
 advancement of grasslands as dominant biomes, has contributed to the
 evolution of a range of specialized herbivores adapted to new diets, as
 well as to increasingly open and arid habitats. Many mammals including
 ruminants, the most diversified ungulate suborder, evolved high–crowned
 (hypsodont) teeth as an adaptation to tooth–wearing diets and habitats.
 The impact of different causes of tooth wear is still a matter of debate,
 and the temporal pattern of hypsodonty evolution in relation to the
 evolution of grasslands remains unclear. We present an improved
 time–calibrated molecular phylogeny of Cetartiodactyla, with phylogenetic
 reconstruction of ancestral ruminant diets and habitats, based on
 characteristics of extant taxa. Using this timeline, as well as the fossil
 record of grasslands, we conduct phylogenetic comparative analyses showing
 that hypsodonty in ruminants evolved as an adaptation to both diet and
 habitat. Our results demonstrate a slow, perhaps constrained, evolution of
 hypsodonty towards estimated optimal states, excluding the possibility of
 immediate adaptation. This augments recent findings that slow adaptation
 is not uncommon on million–year time scales.
description: SLOUCH software
 2016Stochastic Linear
 Ornstein-Uhlenbeck Models for Comparative Hypotheses
 softwareSupplementary Table 1.
 Calibrations tableTable with fossil
 calibrations used to build the phylogenetic tree of
 Cetartiodactyla.Supplementary Table 2.
 Additional modelsTable with results from
 additional models not included in the main text.cetartiodactyla_gtr.trecetartiodactyla_gtr.xmlcoderuminants.txtinput file for codeSuppTable2c.txtinput file for codeTable2inputinput file for codeBEAST input file
DOI: 10.13140/rg.2.2.18418.77767
title: Nationesis: The Science of Regenerative Political Communities
DOI: 10.5061/dryad.3365t
title: Data from: Possible ballast water transfer of lionfish to the eastern Pacific Ocean

description: The Indo-Pacific Red Lionfish was first reported off the Florida coast in
 1985, following which it has spread across much of the SE USA, Gulf of
 Mexico, and Caribbean Sea. Lionfish negatively impact fish and
 invertebrate assemblages and abundances, thus further spread is cause for
 concern. To date, the fish has not been reported on the Pacific coast of
 North or Central America. Here we examine the possibility of ballast water
 transfer of lionfish from colonized areas in the Atlantic Ocean to USA
 ports on the Pacific coast. Over an eight-year period, we documented 27
 commercial vessel-trips in which ballast water was loaded in colonized
 sites and later discharged untreated into Pacific coast ports in the USA.
 California had the highest number of discharges including San Francisco
 Bay and Los Angeles-Long Beach. A species distribution model suggests that
 the probability of lionfish establishment is low for the western USA,
 Colombia and Panama, low to medium for Costa Rica, Nicaragua, El Salvador
 and Guatemala, medium to high for mainland Ecuador, and very high for
 western Mexico, Peru and the Galapagos Islands. Given the species’
 intolerance of freshwater conditions, we propose that ballast water
 exchange be conducted in Gatún Lake, Panama for western-bound vessels
 carrying ‘risky’ ballast water to prevent invasion of the eastern Pacific
 Ocean.
description: Ballast water
 recordsShipping data from
 Caribbean to Pacific US coast from the years 2006-2013 for ships without
 BWENBIC.xlsxLionfish occurrence and environmental dataLionfish occurrence data provided by the U.S. Geological Survey combined with environmental data provided by AquaMapsLionfish_Climate_join_cln.xlsx
DOI: 10.5061/dryad.sg280
title: Data from: Mitochondrial genotype and phenotypic plasticity of gene expression in response to cold acclimation in killifish

description: Adjustments of aerobic metabolic processes are critical components of
 organismal responses to environmental change that require tight
 co-ordination between the nuclear and mitochondrial genomes. Intraspecific
 differences in mitochondrial genotype can affect gene transcription in
 both genomes. Thus, variation in mitochondrial genotype may be associated
 with differences in the plasticity of gene expression when organisms are
 faced with changes in environmental conditions. Cold acclimation is known
 to result in metabolic responses involving increases in mitochondrial
 amount and capacity, suggesting that low temperatures may pose a
 particular challenge when co-ordinating the functions of the nuclear and
 mitochondrial genomes. In this study, we utilized RNA-seq to assess
 transcriptome-wide gene expression in the muscle of Atlantic killifish
 (Fundulus heteroclitus) from a population that contains segregating
 variation in mitochondrial genotype. We examined gene expression
 plasticity in response to 5°C acclimation and the effects of mitochondrial
 genotype on this plasticity. Cold acclimation resulted in changes in gene
 expression consistent with up-regulation of genes involved in many
 cellular functions, including spliceosomal and proteasomal processes, and
 with down-regulation of genes involved in extracellular matrix, muscle
 contraction and oxidative phosphorylation functions. There were few
 differences in gene expression between killifish with different
 mitochondrial genotypes: 14 genes demonstrated significant interactions
 between mitochondrial genotype and acclimation temperature and 3 genes
 demonstrated effects of mitochondrial genotype alone. These results
 indicate that variation in mitochondrial genotype has modest effects on
 gene expression; the majority of which are revealed as differences in
 plasticity as a result of environmental change.
description: Unique_Exon_Read_CountsRNA-seq read count data for killifish individuals with northern or southern mitochondrial genotypes that were acclimated to either 15 or 5 degrees Celsius.Gene_IDs_Names_LengthsReduced gene model information for the Fundulus heteroclitus genome containing gene IDs, gene names and gene lengths. Information was obtained from the F. heteroclitus genome assembly (http://marmot.bio.indiana.edu:7151/EvidentialGene/killifish/).GO_IDsOrthologous GO annotations for the gene models in the F. heteroclitus genome assembly (http://marmot.bio.indiana.edu:7151/EvidentialGene/killifish/).KEGG_IDsOrthologous KEGG annotations for the gene models in the F. heteroclitus genome assembly (http://marmot.bio.indiana.edu:7151/EvidentialGene/killifish/).RNA-seq and enrichment analyses R scriptR code used for analysis of RNA-seq read count data and GO/KEGG enrichment analyses. All data used in these analyses are found in the additional files associated with this Dryad submission.
DOI: 10.5061/dryad.86mh8
title: Data from: Inferring contemporary and historical genetic connectivity from juveniles

description: Measuring population connectivity is a critical task in conservation
 biology. While genetic markers can provide reliable long-term historical
 estimates of population connectivity, scientists are still limited in
 their ability to determine contemporary patterns of gene flow, the most
 practical time frame for management. Here, we tackled this issue by
 developing a new approach that only requires juvenile sampling at a single
 time period. To demonstrate the usefulness of our method, we used the
 Speartooth shark (Glyphis glyphis), a critically endangered species of
 river sharks found only in tropical northern Australia and southern Papua
 New Guinea. Contemporary adult and juvenile shark movements, estimated
 with the spatial distribution of kin pairs across and within three river
 systems, was contrasted with historical long-term connectivity patterns,
 estimated from mitogenomes and genome-wide SNP data. We found strong
 support for river fidelity in juveniles with the within-cohort
 relationship analysis. Male breeding movements were highlighted with the
 cross-cohort relationship analysis and female reproductive philopatry to
 the river systems was revealed by the mitogenomic analysis. We show that
 accounting for juvenile river fidelity and female philopatry is important
 in population structure analysis and that targeting sampling in nurseries
 and juveniles aggregation should be included in the genomic toolbox of
 threatened species management.
description: Supporting_Information_S3_ScriptR script associated with Supporting Information S3Supporting_Information_S8
DOI: 10.6084/m9.figshare.31157624
title: source data from 20-Hydroxyecdysone regulated exosomal transport of mulberry urease drives nitrogen recycling and silkworm development

description: Supporting information, including source digital research materials.
DOI: 10.6084/m9.figshare.31157624.v1
title: source data from 20-Hydroxyecdysone regulated exosomal transport of mulberry urease drives nitrogen recycling and silkworm development

description: Supporting information, including source digital research materials.
DOI: 10.5061/dryad.gg5td
title: Data from: Workshop on reconstruction schemes for magnetic resonance data: summary of findings and recommendations

description: The high-fidelity reconstruction of compressed and low-resolution magnetic
 resonance (MR) data is essential for simultaneously improving patient
 care, accuracy in diagnosis and quality in clinical research. Sponsored by
 the Royal Society through the Newton Mobility Grant Scheme, we held a
 half-day workshop on reconstruction schemes for MR data on 17 August 2016
 to discuss new ideas from related research fields that could be useful to
 overcome the shortcomings of the conventional reconstruction methods that
 have been evaluated to date. Participants were 21 university students,
 computer scientists, image analysts, engineers and physicists from
 institutions from six different countries. The discussion evolved around
 exploring new avenues to achieve high resolution, high quality and fast
 acquisition of MR imaging. In this article, we summarize the topics
 covered throughout the workshop and make recommendations for ongoing and
 future works.
description: Proactive Evolutionary
 Algorithms for Dynamic Optimization ProblemsPresentation slides that
 outline the three anticipation strategies used in proactive evolutionary
 algorithms designed for dynamic optimization problems.pfi_slides.pdfCompressed Sensing for Fast 31P-MRSI of Brain Tumors and 1H-MRSI of Mild Cognitive Impairment in Parkinson’s DiseasePresentation slides that explain compressed sensing accelerated phosphorus MR spectroscopic imaging of brain tumors, and preliminary findings in proton MR spectroscopic imaging of Parkinson's disease with mild cognitive impairment.NMG_Workshop_EOI.pdf
DOI: 10.5061/dryad.ct810
title: Data from: The positive side of a negative reference: the delay between linguistic processing and common ground

description: Interlocutors converge on names to refer to entities. For example, a
 speaker might refer to a novel looking object as the jellyfish and, once
 identified, the listener will too. The hypothesized mechanism behind such
 referential precedents is a subject of debate. The common ground view
 claims that listeners register the object as well as the identity of the
 speaker who coined the label. The linguistic view claims that, once
 established, precedents are treated by listeners like any other linguistic
 unit, i.e. without needing to keep track of the speaker. To test
 predictions from each account, we used visual-world eyetracking, which
 allows observations in real time, during a standard referential
 communication task. Participants had to select objects based on
 instructions from two speakers. In the critical condition, listeners
 sought an object with a negative reference such as not the jellyfish. We
 aimed to determine the extent to which listeners rely on the linguistic
 input, common ground or both. We found that initial interpretations were
 based on linguistic processing only and that common ground considerations
 do emerge but only after 1000 ms. Our findings support the idea that—at
 least temporally—linguistic processing can be isolated from common ground.
description: DataScriptsCompressed folder with subfolders with raw data, R scripts and results from cluster randomization analysis. Also a README.pdf file.
DOI: 10.5061/dryad.gp1mn
title: Data from: Glenohumeral joint kinematics following clavicular fracture and repairs

description: Background. The purpose of this biomechanical study was to determine the
 effect of shortened clavicle malunion on the center of rotation of the
 glenohumeral (GH) joint, and the capacity of repair to restore baseline
 kinematics. Methods. Six shoulders underwent automated abduction (ABD) and
 abbreviated throwing motion (ATM) using a 7-DoF automated upper extremity
 testing system in combination with an infrared motion capture system to
 measure the center of rotation of the GH joint. ATM was defined as pure
 lateral abduction and late cocking phase to the end of acceleration.
 Torsos with intact clavicle underwent testing to establish baseline
 kinematics. Then, the clavicles were subjected to midshaft fracture
 followed by kinematics testing. The fractured clavicles underwent repairs
 first by clavicle length restoration with plate fixation, and then by
 wiring of fragments with a 2-cm overlap to simulate shortened malunion.
 Kinematic testing was conducted after each repair technique. Center of
 rotation of the GH joint was plotted across all axes to outline 3D motion
 trajectory and area under the curve. Results. Throughout ABD, malunion
 resulted in increased posterior and superior translation compared to
 baseline. Plate fixation restored posterior and superior translations at
 lower abduction angles but resulted in excess anterior and inferior
 translation at overhead angles. Throughout ATM, all conditions were
 significantly anterior and superior to baseline. Translation with malunion
 was situated anterior to the fractured and ORIF conditions at lower angles
 of external rotation. Plate fixation did not restore baseline
 anteroposterior or superoinferior translation at any angle measured.
 Conclusions. This study illustrates the complex interplay of the clavicle
 and the GH joint. While abnormal clavicle alignment alters shoulder
 motion, restoration of clavicle length does not necessarily restore GH
 kinematics to baseline. Rehabilitation of the injured shoulder must
 address the osseous injury and the dynamic forces of the shoulder girdle.
description: CLV-GH-ATM-xCLV-GH-ATM-yCLV-GH-ATM-z
DOI: 10.5061/dryad.24767
title: Data from: From success to persistence: Identifying an evolutionary regime shift in the diverse Paleozoic aquatic arthropod group Eurypterida, driven by the Devonian biotic crisis

description: Mass extinctions have altered the trajectory of evolution a number of
 times over the Phanerozoic. During these periods of biotic upheaval a
 different selective regime appears to operate, although it is still
 unclear whether consistent survivorship rules apply across different
 extinction events. We compare variations in diversity and disparity across
 the evolutionary history of a major Paleozoic arthropod group, the
 Eurypterida. Using these data, we explore the group's transition from
 a successful, dynamic clade to a stagnant persistent lineage, pinpointing
 the Devonian as the period during which this evolutionary regime shift
 occurred. The late Devonian biotic crisis is potentially unique among the
 ‘Big Five’ mass extinctions in exhibiting a drop in speciation rates
 rather than an increase in extinction. Our study reveals eurypterids show
 depressed speciation rates throughout the Devonian but no abnormal peaks
 in extinction. Loss of morphospace occupation is random across all
 Paleozoic extinction events; however, differential origination during the
 Devonian results in a migration and subsequent stagnation of occupied
 morphospace. This shift appears linked to an ecological transition from
 euryhaline taxa to freshwater species with low morphological diversity
 alongside a decrease in endemism. These results demonstrate the importance
 of the Devonian biotic crisis in reshaping Paleozoic ecosystems.
description: Eurypterida nexus
 fileNexus file for
 phylogenetic analysis of EurypteridaEurypterida
 merged.nexSupporting Information -
 Data MatrixSpreadsheet file
 including character matrix for Eurypterida including inferred ancestors
 and the character list.Eurypterid
 MorphospaceFiles, results and
 workspaces from the morphospace analyses in R. All taxa, including
 inferred ancestors.Originator only
 Morphospace analysesFiles, results and
 workspaces from the morphospace analyses in R. Originating taxa, including
 inferred ancestors.Originator only
 Morphospace.zipSurvivor Only
 MorphospaceFiles, results and
 workspaces from the morphospace analyses in R. Surviving taxa, including
 inferred ancestors.Raw Morphospace
 Excluding Ancestors AnalysesFiles, results and
 workspaces from the morphospace analyses in R. All taxa, surviving taxa,
 and originating taxa, excluding inferred ancestors.Raw Morphospace and
 rates.zip