cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kg943
title: Data from: Not the time or the place: the missing spatio-temporal link in publicly available genetic data

description: Genetic data are being generated at unprecedented rates. Policies of many
 journals, institutions and funding bodies aim to ensure that these data
 are publicly archived so that published results are reproducible.
 Additionally, publicly archived data can be ‘repurposed’ to address new
 questions in the future. In 2011, along with other leading journals in
 ecology and evolution, Molecular Ecology implemented mandatory public data
 archiving (the Joint Data Archiving Policy). To evaluate the effect of
 this policy, we assessed the genetic, spatial and temporal data archived
 for 419 data sets from 289 articles in Molecular Ecology from 2009 to
 2013. We then determined whether archived data could be used to reproduce
 analyses as presented in the manuscript. We found that the journal's
 mandatory archiving policy has had a substantial positive impact,
 increasing genetic data archiving from 49 (pre-2011) to 98%
 (2011–present). However, 31% of publicly archived genetic data sets could
 not be recreated based on information supplied in either the manuscript or
 public archives, with incomplete data or inconsistent codes linking
 genetic data and metadata as the primary reasons. While the majority of
 articles did provide some geographic information, 40% did not provide this
 information as geographic coordinates. Furthermore, a large proportion of
 articles did not contain any information regarding date of sampling (40%).
 Although the inclusion of spatio-temporal data does require an increase in
 effort, we argue that the enduring value of publicly accessible genetic
 data to the molecular ecology field is greatly compromised when such
 metadata are not archived alongside genetic data.
description: Data_ME15-008_finalThis excel file contains information obtained from reviewing ME articles to determine rate of public data archiving, and patio-temporal data provision. The first page contains all data plus notes, details of which are outlined in the readme file. The second page can be downloaded as a .csv for use in our R script.All results ME15-008_final R scriptThis R script can be run to generate all results presented in our publication, and includes notes to clarify how these calculations were performed.All results ME15-008_final.RRDatThis data file can be used alongside our R script to generate the results produced in our article. This is identical to page two of our final data excel file. The readme file associated with the excel file should be used to understand the categories here.
DOI: 10.5061/dryad.1g5kb
title: Data from: Allometry of animal-microbe interactions and global census of animal-associated microbes

description: Animals live in close association with microorganisms, mostly prokaryotes,
 living in or on them as commensals, mutualists or parasites, and
 profoundly affecting host fitness. Most animal–microbe studies focus on
 microbial community structure; for this project, allometry (scaling of
 animal attributes with animal size) was applied to animal–microbe
 relationships across a range of species spanning 12 orders of magnitude in
 animal mass, from nematodes to whales. Microbial abundances per individual
 animal were gleaned from published literature and also microscopically
 counted in three species. Abundance of prokaryotes/individual versus
 animal mass scales as a nearly linear power function (exponent = 1.07, R2
 = 0.94). Combining this power function with allometry of animal abundance
 indicates that macrofauna have an outsized share of animal-associated
 microorganisms. The total number of animal-associated prokaryotes in
 Earth's land animals was calculated to be 1.3–1.4 × 1025 cells and
 the total of marine animal-associated microbes was calculated to be
 8.6–9.0 × 1024 cells. Animal-associated microbes thus total 2.1–2.3 × 1025
 of the approximately 1030 prokaryotes on the Earth. Microbes associated
 with humans comprise 3.3–3.5% of Earth's animal-associated microbes,
 and domestic animals harbour 14–20% of all animal-associated microbes,
 adding a new dimension to the scale of human impact on the biosphere. This
 novel allometric power function may reflect underlying mechanisms
 involving the transfer of energy and materials between microorganisms and
 their animal hosts. Microbial diversity indices of animal gut communities
 and gut microbial species richness for 60 mammals did not indicate
 significant scaling relationships with animal body mass; however, further
 research in this area is warranted.
description: Kieft and Simmons
 diversity dataDiversity data
 calculated from MG-RAST dataLey diversity
 data-1Species richness data
 from Ley et al., 2008 Supplemental information
DOI: 10.5061/dryad.ng3r749
title: Data from: Creating a multi-track classical music performance dataset for multi-modal music analysis: challenges, insights, and applications

description: We introduce a dataset for facilitating audio-visual analysis of musical
 performances. The dataset comprises 44 simple multi-instrument classical
 music pieces assembled from coordinated but separately recorded
 performances of individual tracks. For each piece, we provide the musical
 score in MIDI format, the audio recordings of the individual tracks, the
 audio and video recording of the assembled mixture, and ground- truth
 annotation files including frame-level and note-level tran- scriptions. We
 describe our methodology for the creation of the dataset, particularly
 highlighting our approaches for addressing the challenges involved in
 maintaining synchronization and ex- pressiveness. We demonstrate the high
 quality of synchronization achieved with our proposed approach by
 comparing the dataset against existing widely-used music audio datasets.
 We anticipate that the dataset will be useful for the devel- opment and
 evaluation of existing music information retrieval (MIR) tasks, as well as
 for novel multi-modal tasks. We bench- mark two existing MIR tasks
 (multi-pitch analysis and score- informed source separation) on the
 dataset and compare against other existing music audio datasets.
 Additionally, we consider two novel multi-modal MIR tasks (visually
 informed multi-pitch analysis and polyphonic vibrato analysis) enabled by
 the dataset and provide evaluation measures and baseline systems for
 future comparisons (from our recent work). Finally, we propose several
 emerging research directions that the dataset enables.
description: URMP
 DatasetWe introduce a dataset
 for facilitating audio-visual analysis of musical performances. The
 dataset comprises a number of simple multi-instrument musical pieces
 assembled from coordinated but separately recorded performances of
 individual tracks. For each piece, we provide the musical score in MIDI
 format, the high-quality individual instrument audio recordings and the
 videos of the assembled pieces. We anticipate that the dataset will be
 useful for multi-modal information retrieval techniques such as music
 source separation, transcription, performance analysis and also serve as
 ground-truth for evaluating performances.Dataset.tar.gz
DOI: 10.5061/dryad.5j8321f
title: Data from: An analysis of the impacts of Cretaceous Oceanic Anoxic Events on global molluscan diversity dynamics

description: Oceanic Anoxic Events (OAEs) are contemporaneous with 11 of the 18 largest
 Phanerozoic extinction events, but the magnitude and selectivity of their
 paleoecological impact remains disputed. OAEs are associated with abrupt,
 rapid warming and increased CO2 flux to the atmosphere, thus insights from
 this study may clarify the impact of current anthropogenic climate change
 on the biosphere. We investigated the influence of the Late Cretaceous
 Bonarelli Event (OAE2; Cenomanian – Turonian stage boundary; ~ 94 Ma) on
 generic- and species-level molluscan diversity, extinction rates, and
 ecological turnover. Cenomanian – Turonian results were compared with
 changes across all Cretaceous stage boundaries, some of which are
 coincident with less severe OAEs. We found increased generic turnover, but
 not species-level turnover, associated with several Cretaceous OAEs. The
 absence of a species-level pattern may reflect species occurrence data
 that are too temporally coarse to robustly detect patterns. Five
 hypotheses of ecological selectivity relating anoxia to survivorship were
 tested across stage boundaries with respect to faunality, mobility and
 diet using generalized linear models. Increasingly benthic taxa were
 consistently selected against throughout the Cretaceous regardless of the
 presence or absence of OAEs. These results suggest that: (1) the
 Cenomanian – Turonian boundary (OAE2) was associated with a decline in
 mollusk diversity, and increase in extinction rate, that was significantly
 more severe than Cretaceous background levels; and (2) no differential
 ecological selectivity was associated with OAE-related diversity declines
 among the variables tested here.
description: Table
 S1The
 raw occurrence data downloaded from the Paleobiology Database (PBDB) on 6
 August 2018. Please see README for search parameters and requested
 attribution for PBDB.Table
 S2The
 occurrence dataset used from the Paleobiology Database (PBDB) that has
 been filtered, validated, and has had stratigraphic singletons removed.
 Please see README for requested attribution for PBDB.Table
 S3Summary statistics of
 the 999 bootstrap replicates of μ3 and μg extinction rates. Blank cells
 indicate time bins where extinction rates could not be
 calculated.Methods
 AppendixAdditional clarification
 of the methods of taxonomic diversity and extinction rate
 calculations.
DOI: 10.5061/dryad.2hb2br7
title: Data from: Coadapted genomes and selection on hybrids: Fisher's geometric model explains a variety of empirical patterns

description: Natural selection plays a variety of roles in hybridization, speciation
 and admixture. Most research has focused on two extreme cases: crosses
 between closely-related inbred lines, where hybrids are fitter than their
 parents, or crosses between effectively isolated species, where hybrids
 suffer severe breakdown. But many natural populations must fall into
 intermediate regimes, with multiple types of gene interaction, and these
 are more difficult to study. Here, we develop a simple fitness landscape
 model, and show that it naturally interpolates between previous modeling
 approaches, which were designed for the extreme cases, and invoke either
 mildly deleterious recessives, or discrete hybrid incompatibilities. Our
 model yields several new predictions, which we test with genomic data from
 Mytilus mussels, and published data from plants (Zea, Populus and Senecio)
 and animals (Mus, Teleogryllus and Drosophila). The predictions are
 generally supported, and the model explains a number of surprising
 empirical patterns. Our approach enables novel and complementary uses of
 genome-wide datasets, which do not depend on identifying outlier loci, or
 "speciation genes" with anomalous effects. Given its simplicity
 and flexibility, and its predictive successes with a wide range of data,
 the approach should be readily extendable to other outstanding questions
 in the study of hybridization.
description: Simon2018_Evolution_LettersDatasets and code used to produce figures of the paper. The README file details the organization of the folders.
DOI: 10.5061/dryad.1tn7123
title: Data from: Rates of evolution: a quantitative synthesis

description: One-generation step intervals, differences, and rates; longer base
 intervals, differences, and rates; and overlapping net intervals,
 differences, and rates for selection experiments (file 1: 15,431 rates),
 field studies (file 2: 12,461 rates), and fossil studies (file 3: 47,854
 rates).
description: Rates of Evolution in
 Experimental LineagesTime intervals
 (generations), differences (standard deviation units), and resulting rate
 quotients (in haldanes or standard deviation units per generation) for all
 intervals and differences in 14 high- and low-line experimental selection
 studies.Gingerich2019_Rates_Archive_ExperimentalStudies.csvRates of Evolution in Field StudiesTime intervals (generations), differences (standard deviation units), and resulting rate quotients (in haldanes or standard deviation units per generation) for all intervals and differences in 57 field studies.Gingerich2019_Rates_Archive_FieldStudies.csvRates of Evolution in Fossil StudiesTime intervals (generations), differences (standard deviation units), and resulting rate quotients (in haldanes or standard deviation units per generation) for all intervals and differences in 34 fossil studies.Gingerich2019_Rates_Archive_FossilStudies.csvFiles for Rate AnalysesZipped file of source-data, scripts, and functions providing complete documentation for derivation of the Dryad-archived Rates of Evolution rate files. When downloaded and unzipped, some 214 small Excel source-data files and R scripts and functions are provided, organized in folders corresponding to the Rates of Evolution archive files. File names and data files are keyed to numbered sections within chapters 7, 8, and 9 of *Rates of Evolution: A Quantitative Synthesis*.Files_for_Rate_Analyses.zip
DOI: 10.5061/dryad.7fp676d
title: Data from: Feeding strategies of brown howler monkeys in response to variations in food availability

description: Primates display varying degrees of behavioral flexibility that allow them
 to adjust their diet to temporal changes in food availability. This trait
 might be critical for the survival of folivorous-frugivorous species
 inhabiting small forest fragments, where the availability of food
 resources tends to be lower than in large fragments and continuous
 forests. However, the scarcity of studies addressing this issue hampers
 our understanding of the adaptive behaviors that favor the survival of
 these primates in low-quality habitats. We conducted a 36-mo study testing
 the hypothesis that brown howler monkeys (Alouatta guariba clamitans) are
 able to adjust their diet in response to local and seasonal changes in
 resource availability. We compared the diet of six free-ranging groups
 inhabiting three small (&lt;10 ha) and three large (&gt;90 ha)
 Atlantic forest fragments in southern Brazil and estimated the temporal
 availability of their top food species (i.e., those species that together
 contribute ≥80% of total feeding records). We found that brown howlers
 exploited similarly rich diets in small (45, 54, and 57 plant species) and
 large (48, 51, and 56 species) fragments. However, intermonth diet
 similarity was higher for groups in small fragments, where howlers also
 fed on plant items from nine alien species. Fruits and leaves were the
 most consumed plant items in both small (42% and 49% of feeding records,
 respectively) and large (51% and 41%, respectively) fragments. The
 consumption of young leaves was higher in small than in large fragments,
 whereas the consumption of other plant items did not show a pattern
 related to fragment size. Regarding the contribution of growth forms as
 food sources, only the exploitation of palms showed a pattern related to
 fragment size. Palms contributed more to the diet of groups inhabiting
 large fragments. The availability of seasonal food items–ripe fruits and
 young leaves–influenced their consumption in both habitat types.
 Therefore, brown howlers cope with local and seasonal fluctuations in food
 availability by opportunistically exploiting resources. We believe that
 this feeding flexibility is a key component of the phenotypic plasticity
 that enables howlers to thrive in disturbed habitat patches, where periods
 of scarcity of preferred foods shall be more common.
description: database_feeding_behaviorHere we provided a single database on the feeding behavior and other activities of six wild groups of brown howler monkeys (Alouatta guariba clamitans). This research was conducted during a 36-month period in three small (&lt;10 ha: S1, S2, and S3) and three large (&gt;90 ha: L1,L2, and L3) Atlantic forest fragments in Rio Grande do Sul State, southern Brazil.Diet_and_behavior_data_brown_howlers_nov18.xlsxdataset_plant_phenologyDataset on the phenology of food plant species exploited by brown howlers during the study period.DATASET_plant_phenology_Chaves_and_Bicca-Marques_Dryad_f.xlsx
DOI: 10.5061/dryad.r837vv7
title: Data from: The N-end Rule Pathway and Ubr1 enforce protein compartmentalization via P2-encoded cellular location signals

description: The Arg/N-end Rule Pathway and Ubr1, an E3 ligase conserved from yeast to
 humans, is involved in the degradation of misfolded proteins in the
 cytosol. However, the root physiological purpose of this activity is not
 completely understood. Through a systematic examination of single residue
 P2-position mutants of misfolded proteins, and global and targeted
 bioinformatic analyses of the yeast proteome, we determined that Ubr1
 preferentially targets mistranslocated secretory and mitochondrial
 proteins in the cytosol. Degradation by Ubr1 is dependent on the
 recognition of cellular location signals that are naturally embedded into
 the 2nd amino acid residue of most proteins. This P2-encoded location
 signaling mechanism may shed light on how Ubr1 and the N-end rule pathway
 are involved in neurodegenerative diseases such as Alzheimer's and
 Parkinson's. A corollary to this discovery is that the N-end rule
 pathway enforces the compartmentalization of secretory and mitochondrial
 proteins by degrading those that fail to reach their intended sub-cellular
 locations. The N-end rule pathway is therefore likely to have been
 critical to the evolution of endosymbiotic relationships that paved the
 way for advanced eukaryotic cellular life.
description: Supplementary Tables
 S1-S32 (Tran 2019, Journal of Cell Science, doi:10.1242/jcs.231662
 )This archive contains
 the following: 1) Lists of yeast proteins and their associated P2-residues
 and localizations based on a global GFP-localization study; 2) P2-residue
 frequencies in the Saccharomyces cerevisiae proteome based on sub-cellular
 localization and/or compatibility with Ubr1; 3) Protein abundance levels
 based on a global GFP-localization study; 4) Topological analyses and
 P2-residue frequency analyses of a signal-sequence bearing protein set; 5)
 Raw statistical calculations; 6) Yeast strains, plasmids, and primers used
 in the studySupplementary_Tables_S1-S32_TranA_JCS_2019_231662.zip
DOI: 10.5061/dryad.8v04m
title: Data from: EuMIXFOR empirical forest mensuration and ring width data from pure and mixed stands of Scots pine (Pinus sylvestris L.) and European beech (Fagus sylvatica L.) through Europe

description: This data set provides unique empirical data from triplets of Scots pine
 (Pinus sylvestris L.) and European beech (Fagus sylvatica L.) across
 Europe. Dendrometric variables are provided for 32 triplets, 96 plots,
 7555 trees and 4695 core samples. These data contribute to our
 understanding of mixed stand dynamics.
description: EuMIXFOR Scots pine -
 European beech data.This data set provides
 unique empirical data from triplets of Scots pine (Pinus sylvestris L.)
 and European beech (Fagus sylvatica L.) across Europe. Dendrometric
 variables are provided for 32 triplets, 96 plots, 7555 trees and 4695 core
 samples. These data contribute to our understanding of mixed stand
 dynamics.EuMIXFOR_Scots_pine-European_beech_data_v2.zip
DOI: 10.5061/dryad.hv18jn6
title: Data from: Variations of thermophysical properties and heat transfer performance of nanoparticle-enhanced ionic liquids

description: The ionic liquid 1-ethyl-3-methylimidazolium acetate ([EMIm]Ac) was
 investigated as a promising absorbent for absorption refrigeration. To
 improve the thermal conductivity of pure [EMIm]Ac, ionic-liquid-based
 nanofluids (ionanofluids) were prepared by adding graphene nanoplatelets.
 The thermal stability of the ionic liquid and ionanofluids was analysed.
 The variations of the thermal conductivity, viscosity and specific heat
 capacity resulting from the addition of the graphene nanoplatelets were
 then measured over a wide range of temperatures and mass fractions. The
 measured data were fitted with appropriate equations and compared with the
 corresponding classical models. The results revealed that the ionic liquid
 and ionanofluids were thermally stable over the measurement range. The
 thermal conductivity greatly increased with increasing mass fraction,
 while only slightly changed with increasing temperature. A maximum
 enhancement in thermal conductivity of 43.2% was observed at a temperature
 of 373.15 K for the ionanofluid with a mass fraction of 5%. The numerical
 results revealed that the dispersion of the graphene nanoplatelets in the
 pure ionic liquid effectively improved the local heat transfer coefficient
 by up to 28.6%.
description: nanoparticle-enhanced
 ionic liquidsdatasets.zip
DOI: 10.5061/dryad.84q73s8
title: Data from: Neuromuscular adverse events associated with Anti-PD-1 monoclonal antibodies: systematic review

description: Neuromuscular adverse events following cancer treatment with
 anti–programmed cell death protein 1 (PD-1) monoclonal antibodies are
 relatively rare, yet potentially fatal. We performed a systematic review
 to characterize the clinical presentation, diagnostic workup, and
 management of neuromuscular disorders (NMDs) in patients treated with
 nivolumab or pembrolizumab monotherapy or concurrent with other
 immunologic agents, such as ipilimumab. Sixty-one publications on 85
 patients (mean age 66.9 years [range 34–86]; male/female 2.6:1; 59%
 metastatic melanoma) were identified from selected indexing databases
 until June 2018. Forty-eight patients had received nivolumab and 39
 pembrolizumab. The mean number of PD-1 inhibitor treatment cycles prior to
 onset of symptoms was 3.6 (range 1–28). Symptoms included oculomotor
 (47%), respiratory (43%), bulbar (35%), and proximal weakness (35%), as
 well as muscle pain (28%). Diagnoses were categorized as myasthenia gravis
 (27%), neuropathy (23%), myopathy (34%), or a combination of these (16%).
 After a critical review of the data, however, evidence did not support the
 stated NMD diagnosis in 13% of cases, while up to 25% of patients had
 signs of additional NMDs. Cardiac complications occurred in more than 30%
 of patients diagnosed with myasthenia gravis or myositis. Mortality was
 high in these patients, despite adequate treatment strategies including
 corticosteroid, IV immunoglobulins, and plasma exchange. The clinical
 presentation of NMDs associated with PD-1 inhibitors is often atypical,
 with considerable overlap between myasthenia gravis and myopathy, and
 cardiac/respiratory complications are common.
description: Data_DryadSearch protocolFlow-chart of the systematic literature searchReferences e61-e88PRISMA 2009 checklist