cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nb372tc
title: Data from: Increases and decreases in marine disease reports in an era of global change

description: Outbreaks of marine infectious diseases have caused widespread mass
 mortalities, but the lack of baseline data has precluded evaluating
 whether disease is increasing or decreasing in the ocean. We use an
 established literature proxy method from Ward and Lafferty (2004) to
 analyze a 44-year global record of normalized disease reports from 1970 to
 2013. Major marine hosts are combined into nine taxonomic groups, from
 seagrasses to marine mammals, to assess disease swings, defined as
 positive or negative multi-decadal shifts in disease reports across
 related hosts. Normalized disease reports increased significantly between
 1970 and 2013 in corals and urchins, indicating positive disease swings in
 these environmentally sensitive ectotherms. Coral disease reports in the
 Caribbean correlated with increasing temperature anomalies, supporting the
 hypothesis that warming oceans drive infectious coral diseases. Meanwhile,
 disease risk may also decrease in a changing ocean. Disease reports
 decreased significantly in fish and elasmobranchs, which have experienced
 steep human-induced population declines and diminishing population density
 that, while concerning, may reduce disease. The increases and decreases in
 disease reports across the 44-year record transcend short-term
 fluctuations and regional variation. Our results show that long-term
 changes in disease reports coincide with recent decades of widespread
 environmental change in the ocean.
description: Correlation tests for
 all taxaTests of correlations
 from 1970-2013 and 2001-2013 for all taxa1. Correlations
 1-18-19.RBonferroni
 correctionsBonferonni corrections
 for correlations in Correlation file2. Bonferonni
 1-18-19.RConfidence
 intervalsConfidence intervals for
 nine taxa from 1970-2013 and echinoderms from 2001-20133. Conf_int EBU
 1-18-19.RTemperature/ Coral
 disease analysesAnalyses of link between
 temperature anomalies and Caribbean coral disease4. Temp coral disease
 1-18-19.RTemperature/ Coral
 disease dataData for analyses of
 link between temperature anomalies and Caribbean coral
 disease4.
 Temp_cordis_8-29-18.xlsxCoral
 repeatsAnalyses of repeat
 reports of coral disease5. Coral repeats check
 1-18-19.RCommon authors
 checkAnalyses of common
 authors for three example taxa6. Common authors
 1-18-19.RTaxon
 spreadsheetsSpreadsheets of Web of
 Science taxon and disease search results for 10 taxa and raccoon
 rabiesTaxon sums
 7-19-19R code for plots of
 taxon sums (Figure S3)taxon_sum_7-19-19Data sheet for plots of taxon sums (Fig S3)Title and abstract check 7-19-19Comparison of titles and abstracts (Table S6, Fig S1)Corals titles abstract 7-19-19Coral title and title+ abstract comparison for Table S6Fish titles abstracts 7-19-19Fish titles vs. titles+abstract comparisons for Table S6
DOI: 10.5061/dryad.cc1v570
title: Data from: Fullerene-like structures of Cretaceous crinoids reveal topologically limited skeletal possibilities

description: There are few cases where numbers or types of possible phenotypes are
 known, although vast state spaces have been postulated. Rarely applied in
 this context, graph theory and topology enable enumeration of possible
 phenotypes and evolutionary transitions. Here, we generate polyhedral
 calyx graphs for the Late Cretaceous, stemless
 crinoids Marsupites
 testudinarius and Uintacrinus
 socialis (Uintacrinoidea Zittel) revealing structural
 similarities to carbon fullerene and fulleroid molecules (respectively).
 The U. socialis calyx incorporates numerous
 plates (e.g. graph vertices |V| ≥ 197), which are small,
 light, low‐density and have four to eight sides. Therefore, the
 corresponding number of possible plate arrangements (number of polyhedral
 graphs) is large (≫1 × 1014). Graph vertices
 representing plates with sides &gt;6 introduce negative Gaussian
 curvature (surface saddle points) and topological instability, increasing
 buckling risk. However, observed numbers of vertices
 for Uintacrinus do not allow more stable pentaradial
 configurations. In contrast, the Marsupites calyx dual
 graph has 17 faces that are pentagonal or hexagonal. Therefore, it is
 structurally identical to a carbon fullerene, specifically C30‐D5h.
 Corresponding graph restrictions result in constraint to only three
 structural options (fullerene structures C30‐C2v 1, C30‐C2v 2 and
 C30‐D5h). Further restriction to pentaradial symmetry allows only one
 possibility: the Marsupites phenotype. This robust,
 stable topology is consistent with adaptation to predation pressures of
 the Mesozoic marine revolution. Consequently, the most plausible
 evolutionary pathway between unitacrinoid phenotypes was a mixed
 heterochronic trade‐off to fewer, larger calyx plates. Therefore,
 topological limitations radically constrained uintacrinoid skeletal
 possibilities but thereby aided evolution of a novel adaptive phenotype.
description: Supporting
 InformationCombined supporting
 information including Tables S1-S3, Figures S1-S6Table
 S4Measurements of
 disarticulated uintacrinoid platesTableS4.xlsxTable S5Marsupites calyx graphTableS5_MarsupitesCalyxGraph.csvTable S6Marsupites calyx dual graphTableS6_MarsupitesCalyxDualGraph.csvTable S7Uintacrinus calyx graphTableS7_UintacrinusCalyxGraph.csvSupplementary Computer CodeMatlab script to generate a graph dual from a triangulated graphSupplementaryComputerCode2.txt
DOI: 10.5061/dryad.c4d7cc0
title: Data from: Cost effective microsatellite isolation and genotyping by high throughput sequencing

description: High throughput sequencing (HTS) has emerged as a valuable tool for the
 rapid isolation of genetic markers for population genetics and pedigree
 analysis. HTS-based SNP (single nucleotide polymorphism) genotyping
 protocols like RAD (Restriction-site associated DNA) sequencing or hybrid
 capture, allow for the isolation of thousands of markers from any
 non-model organism. However, these protocols are relatively laborious and
 expensive and the resulting high marker density is not always necessary.
 Since HTS technology has also greatly simplified the isolation and
 genotyping process of microsatellite markers, we develop microsatellite
 markers as a cost efficient and simple alternative to SNP genotyping. We
 present low coverage genome sequencing data from seven distantly related
 spider species (Argiope bruennichi, Larinia jeskovi, Oedothorax restusus,
 Pisaura mirabilis, Australomisidia ergandros, Cheiracanthium punctorium,
 Theridion grallator) and show the utility of HTS for microsatellite
 isolation. We also present a simple Illumina amplicon sequencing protocol
 to genotype microsatellites from multiplex PCR amplicons in the Hawaiian
 happy face spider T. grallator. We discuss advantages and drawbacks of the
 use of microsatellites for a range of research questions, and highlight an
 unexpectedly fast decay and gain of repeat loci for T. grallator.
description: 454Reads_and_ContigsTheridionMicrosatReadsPaired Illumina reads containing microsatellite data for all Theridion grallator populationsAllPrimersTables containing all identified primer sequences, targeting microsatellite loci for the studied spider speciesSuppl.Table1Supplementary Table 1, containing all tested microsatellite primer sequences for the studied spider species
DOI: 10.5281/zenodo.18392932
title: Llistes d'organimses i ocurrències projecte BMSBal
DOI: 10.5281/zenodo.18392933
title: Llistes d'organimses i ocurrències projecte BMSBal
DOI: 10.5061/dryad.cb0qk1g
title: Data from: Cognitive reserve and clinical progression in Alzheimer’s disease: a paradoxical relationship

description: Objective: To investigate the relationship between cognitive reserve (CR)
 and clinical progression across the Alzheimer’s disease (AD) spectrum.
 Methods: We selected 839 Aβ-positive subjects with normal cognition (NC,
 n=175), mild cognitive impairment (MCI, n=437) or AD dementia (n=227) from
 the Alzheimer’s Disease Neuroimaging Initiative. CR was quantified using
 standardized residuals (W-scores) from a (covariate-adjusted) linear
 regression with global cognition (ADAS-Cog 13) as an independent
 variable-of-interest, and either gray matter volumes or white matter
 hyperintensity volume as dependent variables. These W-scores, reflecting
 whether an individual’s degree of cerebral damage is lower or higher than
 clinically expected, were tested as predictors of diagnostic conversion
 (i.e. NC to MCI/AD dementia, or MCI to AD dementia) and longitudinal
 changes in memory (ADNI-MEM) and executive functions (ADNI-EF). Results:
 The median follow-up period was 24 months (interquartile range: 6-42).
 Corrected for age, sex, APOE4-status and baseline cerebral damage, higher
 gray matter volume-based W-scores (i.e. greater CR) were associated with a
 lower diagnostic conversion risk (hazard ratio [HR]= .22, p&lt;.001)
 and slower decline in memory (β=.48, p&lt;.001) and executive
 functions (β=.67, p&lt;.001). Stratified by disease stage, we found
 similar results for NC (diagnostic conversion: HR=.30, p=.038; ADNI-MEM:
 β=.52, p=.028; ADNI-EF: β=.42, p=.077) and MCI (diagnostic conversion:
 HR=.21, p&lt;.001; ADNI-MEM: β=.43, p=.003; ADNI-EF: β=.59,
 p&lt;.001), but opposite findings (i.e. more rapid decline) for AD
 dementia (ADNI-MEM: β=-.91, p=.002; ADNI-EF: β=-.77, p=.081). Conclusions:
 Among Aβ-positive individuals, greater CR related to attenuated clinical
 progression in pre-dementia stages of AD, but accelerated cognitive
 decline after the onset of dementia.
description: Tables
 5-12Supplemental
 Data.docxFigure
 3Table
 e-1-8Supplemental
 Data.docxFigure
 e-1Appendix
 e-1Co-investigator
 appendix
DOI: 10.21223/p3/fyyllo
title: Dataset for: Genotypic Dataset of In Situ Native Ulluco Varieties from the Andenes de Cuyocuyo Agrobiodiversity Zone using SilicoDArT markers

description: Molecular markers dataset of 68 cultivated ullucus accessions collected in Cuyocuyo (Puno-Peru) that were genotyped with the HighDensity platform of DArTSeq markers producing 22673 SilicoDArT markers.
DOI: 10.5061/dryad.f757b6c
title: Introgression among three western North American bilberries (Vaccinium section Myrtillus)

description: Despite being dominant elements of understory communities in the
 coniferous forests of western North America, phylogenetic relationships
 among bilberries (Vaccinium section Myrtillus) remain unresolved.
 Morphological delimitation among most western bilberry species is tenuous
 and traditionally employed molecular sources of phylogenetic information
 have yielded insufficient variability. Moreover, these species are
 hypothesized to have undergone extensive introgression. We used RADseq
 data analyzed under maximum likelihood species tree estimation to examine
 the influence of introgression on relationships among Vaccinium myrtillus,
 V. scoparium, and V. caespitosum. Additionally, we used these data to
 assess whether the populations of V. myrtillus disjunct between North
 America and Eurasia are monophyletic and should continue to be recognized
 as conspecific. Significant genome-wide introgression, as determined
 through D-statistic analyses, was detected between North American samples
 of V. myrtillus and V. caespitosum, and to a lesser extent, between V.
 myrtillus and V. scoparium. No significant D-values were detected between
 V. scoparium and V. caespitosum. Accessions of Vaccinium myrtillus from
 Eurasia and North America were recovered as non-monophyletic, prompting
 our proposed resurrection of V. oreophilum for North American material.
 The long-assumed sister species relationship between V. oreophilum and V.
 scoparium was not recovered in our analysis. Instead, V. oreophilum and V.
 caespitosum were inferred to be sister taxa. This study reveals
 considerable introgression detectable in the evolutionary history of
 western North American bilberries and demonstrates the utility of RADseq
 data to resolve species level relationships in groups that undergo
 reticulate evolution such as Vaccinium.
description: Pyrad Assembly Params
 FileContains the parameter
 file used in the study "Introgression among western North American
 Bilberries (Vaccinium section Myrtillus)" to run pyrad which
 assembles RADseq reads into a concatenated matrix. This matrix was used to
 run ABBA BABA tests of introgression in pyrad, as well as ML phylogenetic
 analysis using RAxML.Introgression_NA_Bilberries_pyrad_params.txt
DOI: 10.5061/dryad.b678k40
title: Data from: An origin of citations: Darwin's collaborators and their contributions to the Origin of Species

description: Since the first edition of the Origin of Species (1859), Charles Darwin
 apologizes for not correctly referencing all the works cited in his magnum
 opus. More than 150 years later we catalogued these citations and analysed
 the resultant data. Looking for a complete selection of collaborators, a
 flexibilization of the term “citation” was necessary, and we define it as
 any reference made to a third party, independently of its form or
 function. Following the same idea, the last edition of the Origin,
 originally published in 1872 and reprinted with minor additions and
 corrections in 1876, was chosen for the research because it represents the
 end of a long debate between Darwin and his peers, naturally being the
 edition with the most number of citations and collaborators. Through a
 diverse theoric approach we hope to present a new perspective for the
 study of the Origin of Species: a bibliographic approach gives us the
 tools needed to understand the history of the book as a physical and
 cultural object; bibliometrics provides a theory of citations as well as a
 quantitative analysis; lastly, the Science Studies highlight the profound
 social aspects of science in the making. The analysis resulted in 639
 citations to 298 collaborators, although these results are only the tip of
 the iceberg of all the gathered data’s potential.
description: Table of citations
 identified in the Origin of Species (1876) In the first seventeen
 tables, the citations are organized according to each book section going
 from the Historical sketch to the last chapter. Next, there is a table
 entitled Complete Count which lists the collaborators and how many times
 they appear on each book section. The Name Count table lists how many
 times a given name appears in the Origin. Graphs showing the distribution
 per subject per chapter of citations by percentage and absolute count come
 next. Finally, the sources used for the identification of Darwin's
 collaborators are listed in the last spreadsheet.   <strong>Spreadsheets.xlsx</strong>
description: The data presented on these tables and our methodology are better
 discussed in the article "An Origin of citations: Darwin's
 collaborators and their contribution to the Origin of
 Species"
DOI: 10.5061/dryad.n4h659q
title: Genetic and functional variation across regional and local scales is associated with climate in a foundational prairie grass

description: Global change forecasts in ecosystems require knowledge of within species
 diversity, particularly of dominant species within communities. We
 assessed site-level diversity and capacity for adaptation of the dominant
 species of the shortgrass steppe biome of the Central US, Bouteloua
 gracilis. We quantified genetic diversity from 17 sites across regional
 scales, north-south from New Mexico to South Dakota, and local scales in
 Northern Colorado. We also quantified phenotype and plasticity within and
 among sites and determined the extent to which phenotypic diversity in B.
 gracilis was related to climate. Genome sequencing indicated pronounced
 population structure at the regional scale, and local differences
 indicated gene flow and/or dispersal may also be limited. Within a common
 environment, we found evidence for genetic divergence in biomass-related
 phenotypes, plasticity, and phenotypic variance, indicating functional
 divergence and different adaptive potential. Phenotypes differentiated
 according to climate, chiefly median Palmer Hydrological Drought Index and
 other aridity metrics. Our results indicate conclusive differences in
 genetic variation, phenotype, and plasticity in this species and suggest a
 mechanism explaining variation in shortgrass steppe community responses to
 global change. This analysis of B. gracilis intraspecific diversity across
 spatial scales will improve conservation and management of the shortgrass
 steppe ecosystem moving forward.
DOI: 10.5061/dryad.6br51tn
title: Data from: Deep learning for bridge load capacity estimation in post-disaster and -conflict zones

description: Many post-disaster and -conflict regions do not have sufficient data on
 their transportation infrastructure assets, hindering both mobility and
 reconstruction. In particular, as the number of aging and deteriorating
 bridges increase, it is necessary to quantify their load characteristics
 in order to inform maintenance and prevent failure. The load carrying
 capacity and the design load are considered as the main aspects of any
 civil structures. Human examination can be costly and slow when expertise
 is lacking in challenging scenarios. In this paper, we propose to employ
 deep learning as method to estimate the load carrying capacity from crowd
 sourced images. A new convolutional neural network architecture is trained
 on data from over 6000 bridges, which will benefit future research and
 applications. We tackle significant variations in the dataset (e.g. class
 interval, image completion, image colour) and quantify their impact on the
 prediction accuracy, precision, recall and F1 score. Finally, practical
 optimisation is performed by converting multiclass classification into
 binary classification to achieve a promising field use performance.
description: Bridge Images for Capacity Prediction The file
 datasets.7z contains images of bridges from the U.S. which are obtained
 from the web. These images form datasets which are employed to train and
 test bridge capacity prediction models.
DOI: 10.5061/dryad.7290t40
title: Data from: Taphonomic experiments resolve controls on the preservation of melanosomes and keratinous tissues in feathers

description: Fossils are a key source of data on the evolution of feather structure and
 function through deep time, but their ability to resolve macroevolutionary
 questions is compromised by an incomplete understanding of their
 taphonomy. Critically, the relative preservation potential of two key
 feather components, melanosomes and keratinous tissue, is not fully
 resolved. Recent studies suggesting that melanosomes are preferentially
 preserved conflict with observations that melanosomes preserve in fossil
 feathers as external moulds in an organic matrix. To date, there is no
 model to explain the latter mode of melanosome preservation. We addressed
 these issues by degrading feathers in systematic taphonomic experiments
 incorporating decay, maturation and oxidation in isolation and
 combination. Our results reveal that the production of mouldic melanosomes
 requires interactions with an oxidant and is most likely to occur prior to
 substantial maturation. This constrains the taphonomic conditions under
 which melanosomes are likely to be fossilized. Critically, our experiments
 also confirm that keratinous feather structures have a higher preservation
 potential than melanosomes under a range of diagenetic conditions,
 supporting hitherto controversial hypotheses that fossil feathers can
 retain degraded keratinous structures.
description: Fig_S1Experimental setup. A,
 schematic showing experimental pathways used. B, detailed schematic
 showing potential natural scenarios corresponding to each experimental
 pathway (indicated by numerals). DDW, distilled-deionized
 water.Fig_S2SEM images of feather
 barbules showing the paucity of obvious decay bacteria in feathers decayed
 in pH 6 and 12.2. A–B, pathway 1. C–D, pathway 2. A, decay at pH 12.2; D,
 decay at pH 6. Scale bars in A, C = 10 µm, B, D = 5 µm.Table
 S1Maximum dimensions of
 moulds and intact melanosomes, measured from transverse
 sections.Table
 S2Abundance of melanosome
 moulds in transverse sections of oxidized feather
 barbules.Table
 S3AHPO analysis of Gallus
 gallus feathers.
DOI: 10.5061/dryad.0k86k80
title: Data from: Genuine cross-frequency coupling networks in human resting-state electrophysiological recordings

description: Phase synchronization of neuronal oscillations in specific frequency bands
 coordinates anatomically distributed neuronal processing and
 communication. Typically, oscillations and synchronization take place
 concurrently in many distinct frequencies, which serve separate
 computational roles in cognitive functions. While within-frequency phase
 synchronization has been studied extensively, less is known about the
 mechanisms that govern neuronal processing distributed across frequencies
 and brain regions. Such integration of processing between frequencies
 could be achieved via cross-frequency coupling (CFC), either by
 phase-amplitude coupling (PAC) or by n:m-cross-frequency phase synchrony
 (CFS). So far, studies have mostly focused on local CFC in individual
 brain regions, whereas the presence and functional organization of CFC
 between brain areas have remained largely unknown. We posit that
 inter-areal CFC may be essential for large-scale coordination of neuronal
 activity and investigate here whether genuine CFC networks are present in
 human resting-state brain activity. To assess the functional organization
 of CFC networks, we identified brain-wide CFC networks at meso-scale
 resolution from stereo-electroencephalography (SEEG) and at macro-scale
 resolution from source-reconstructed magnetoencephalography (MEG) data. We
 developed a novel graph-theoretical method to distinguish genuine CFC from
 spurious CFC that may arise from non-sinusoidal signals ubiquitous in
 neuronal activity. We show that genuine inter-areal CFC is present in
 human resting-state activity in both MEG and SEEG data. Both CFS and PAC
 networks coupled theta and alpha oscillations with higher frequencies in
 large-scale networks connecting anterior and posterior brain regions. CFS
 and PAC networks had distinct spectral patterns and opposing distribution
 of low- and high frequency   network hubs, implying that
 they constitute distinct CFC mechanisms. The strength of CFS networks was
 also predictive of cognitive performance in a separate neuropsychological
 assessment. In conclusion, these results provide evidence for inter-areal
 CFS and PAC being two distinct mechanisms for coupling oscillations across
 frequencies in large-scale brain networks.  
description:  
description: Recording and processing of this data is described in the
 article.<br> Siebenhühner F, et
 al.: <strong>"</strong><b>Genuine
 cross-frequency coupling networks in human resting-state
 electrophysiological recordings", </b>PLoS Biology,
 2020.