cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c6fb2
title: Data from: Evaluating adaptive divergence between migratory and non-migratory ecotypes of a salmonid fish, Oncorhynchus mykiss

description: Next generation sequencing and the application of population genomic and
 association approaches have made it possible to detect selection and
 unravel the genetic basis to variable phenotypic traits. Using the two
 approaches in parallel is an especially attractive approach in non-models
 organisms that lack a sequenced and annotated genome, but only works well
 when population structure is not confounded with the phenotype of
 interest. Herein, we use population genomics in a non-model fish species,
 rainbow trout (Oncorhynchus mykiss), to better understand adaptive
 divergence between migratory and non-migratory ecotype, and to further our
 understanding about the genetic basis of migration. RAD tag sequencing was
 used to identify Single Nucleotide Polymorphisms (SNPs) in migrant and
 resident O. mykiss from two systems, one in Alaska and the other in
 Oregon, USA. A total of 7,920 and 6,755 SNPs met filtering criteria in the
 Alaska and Oregon, data sets respectively. Population genetic tests
 determined that 1,423 SNPs were candidates for selection when loci were
 compared between resident and migrant samples. Prior linkage mapping
 studies using RAD tag SNPs were available to determine the position of
 1,990 markers. Several significant SNPs are located in genome regions that
 contain QTL for migratory related traits, reinforcing the importance of
 these regions in the genetic basis of migration/residency. Annotation of
 genome regions linked to significant SNPs revealed genes involved in
 processes known to be important in migration (such as osmoregulatory
 function). This study adds to our growing knowledge on adaptive divergence
 between migratory and nonmigratory ecotypes of this species; across
 studies, this complex trait appears to be controlled by many loci of small
 effect, with some in common, but many loci not shared between populations
 studied.
description: Sashin
 steelheadQuality filtered
 Illumina single read 100bp sequences.Sashin_steelhead.zipSashin rainbowsQuality filtered Illumina 100bp single end reads.Sashin_rainbows.zipLSC steelheadQuality filtered single 100 bp readsLSC_steelhead.zipLSC rainbowsQuality filtered 100 bp Illumina single end readsLSC_rainbows.zip
DOI: 10.5061/dryad.2qg54
title: Data from: Evaluating genomic divergence and parallelism in replicate ecomorphs from young and old cichlid adaptive radiations

description: Comparative genomic studies of closely related species typically focus on
 single species pairs at one given stage of divergence. That makes it
 difficult to infer the continuum of evolutionary process during speciation
 and beyond. Here, we use whole-genome resequencing to examine genomic
 patterns of divergence in three sympatric cichlid species pairs with very
 similar functional and ecological differentiation, but different ages. We
 find a strong signature of increasing genomic divergence with time in both
 the mitochondrial genome and the nuclear genome. In contrast to many other
 systems, we find that in these cichlids regions of elevated relative
 differentiation also exhibit increased absolute differentiation. We detect
 a signature of convergent evolution in a comparison of outlier regions
 across all three species pair comparisons but the extent of it is modest,
 and regions that are strongly divergent in any one pair tend to be only
 slightly elevated in the other pairs, consistent with a repeatable but
 polygenic basis of traits that characterize the ecomorphs. Our results
 suggest that strong functional phenotypic differentiation, as seen in all
 three species pairs, is generally associated with a clear signature of
 genomic divergence, even in the youngest species pair.
description: Df and Dxy values for
 10kb blocks from Victoria pairvictoria_df_dxy.tsvDf and Dxy values for 10kb blocks from Kivu pairkivu_df_dxy.tsvDf and Dxy values for 10kb blocks from Mweru pairmweru_df_dxy.tsvData files and scriptsArchive of all data files and scripts needed to reproduce population genetic results, as well as our mitogenome tree and aligned mitogenomes. BAM files can be found in the NCBI SRA, accession PRJNA298405. Files in this archive can also be found on github, DOI: http://dx.doi.org/10.5281/zenodo.32936ulakes-master.zip
DOI: 10.5061/dryad.h4d22
title: Data from: Association between stock market gains and losses and Google searches

description: Experimental studies in the area of Psychology and Behavioral Economics
 have suggested that people change their search pattern in response to
 positive and negative events. Using Internet search data provided by
 Google, we investigated the relationship between stock-specific events and
 related Google searches. We studied daily data from 13 stocks from the
 Dow-Jones and NASDAQ100 indices, over a period of 4 trading years.
 Focusing on periods in which stocks were extensively searched (Intensive
 Search Periods), we found a correlation between the magnitude of stock
 returns at the beginning of the period and the volume, peak, and duration
 of search generated during the period. This relation between magnitudes of
 stock returns and subsequent searches was considerably magnified in
 periods following negative stock returns. Yet, we did not find that
 intensive search periods following losses were associated with more Google
 searches than periods following gains. Thus, rather than increasing
 search, losses improved the fit between people’s search behavior and the
 extent of real-world events triggering the search. The findings
 demonstrate the robustness of the attentional effect of losses.
description: classAandClassBEventStudy3_with_graphs2For each stock ticker, this shows data from the Intensive Search period (length, peak, sum) followed by data about the financial event triggering the period (negative or positive; ISNEG = 1 is negative; absolute returns).
DOI: 10.5061/dryad.cb360
title: Data from: ASSET: analysis of sequences of synchronous events in massively parallel spike trains

description: With the ability to observe the activity from large numbers of neurons
 simultaneously using modern recording technologies, the chance to identify
 sub-networks involved in coordinated processing increases. Sequences of
 synchronous spike events (SSEs) constitute one type of such coordinated
 spiking that propagates activity in a temporally precise manner. The
 synfire chain was proposed as one potential model for such network
 processing. Previous work introduced a method for visualization of SSEs in
 massively parallel spike trains, based on an intersection matrix that
 contains in each entry the degree of overlap of active neurons in two
 corresponding time bins. Repeated SSEs are reflected in the matrix as
 diagonal structures of high overlap values. The method as such, however,
 leaves the task of identifying these diagonal structures to visual
 inspection rather than to a quantitative analysis. Here we present ASSET
 (Analysis of Sequences of Synchronous EvenTs), an improved, fully
 automated method which determines diagonal structures in the intersection
 matrix by a robust mathematical procedure. The method consists of a
 sequence of steps that i) assess which entries in the matrix potentially
 belong to a diagonal structure, ii) cluster these entries into individual
 diagonal structures and iii) determine the neurons composing the
 associated SSEs. We employ parallel point processes generated by
 stochastic simulations as test data to demonstrate the performance of the
 method under a wide range of realistic scenarios, including different
 types of non-stationarity of the spiking activity and different
 correlation structures. Finally, the ability of the method to discover
 SSEs is demonstrated on complex data from large network simulations with
 embedded synfire chains. Thus, ASSET represents an effective and efficient
 tool to analyze massively parallel spike data for temporal sequences of
 synchronous activity.
description: scripts
 (Python)Code used to generate
 the stochastic data and plot the figures of the manuscript "ASSET:
 Analysis of sequences of synchronous events in massively parallel spike
 trains". The analysis results load by some scripts are stored in the
 companion data archive "performance.zip"scripts.zipperformancePerformance results of the application of ASSET on stochastic simulations and a network simulation with embedded synfire chains. Different folders relate to different data and analysis parameter. Each individual file contains the results (in terms of number of false positives and false negatives) obtained on 100 iterations on the same data type using the same analysis parameters.
DOI: 10.5061/dryad.1d52k
title: Data from: Peculiar macrophagous adaptations in a new Cretaceous pliosaurid

description: During the Middle and Late Jurassic, pliosaurid plesiosaurs evolved
 gigantic body size and a series of craniodental adaptations that have been
 linked to the occupation of an apex predator niche. Cretaceous pliosaurids
 (i.e. Brachaucheninae) depart from this morphology, being slightly smaller
 and lacking the macrophagous adaptations seen in earlier forms. However,
 the fossil record of Early Cretaceous pliosaurids is poor, concealing the
 evolution and ecological diversity of the group. Here, we report a new
 pliosaurid from the Late Hauterivian (Early Cretaceous) of Russia.
 Phylogenetic analyses using reduced consensus methods recover it as the
 basalmost brachauchenine. This pliosaurid is smaller than other derived
 pliosaurids, has tooth alveoli clustered in pairs and possesses trihedral
 teeth with complex serrated carinae. Maximum-likelihood ancestral state
 reconstruction suggests early brachauchenines retained trihedral teeth
 from their ancestors, but modified this feature in a unique way,
 convergent with macrophagous archosaurs or sphenacodontoids. Our findings
 indicate that Early Cretaceous marine reptile teeth with serrated carinae
 cannot be unequivocally assigned to metriorhynchoid crocodylomorphs.
 Furthermore, they extend the known diversity of dental adaptations seen in
 Sauropterygia, the longest lived clade of marine tetrapods.
description: Nexus_fullNexus full dataset with treesPlios_full_BL.nexNexus reducedNexus reduced dataset with treesPlios_red_BL.nexSupplementary materialAssociated bivalve remains, recoding of Anguanax zignoi, stratigraphic age data for OTUs, additional phylogeny and ancestral state reconstruction figures.SuppInfo.docxSupplementary InformationAssociated bivalve, measurements, taxon-age data, R code, supplementary phylogeny figures.SuppInfo.docx
DOI: 10.5061/dryad.7440s
title: Data from: Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster

description: Populations arrayed along broad latitudinal gradients often show patterns
 of clinal variation in phenotype and genotype. Such population
 differentiation can be generated and maintained by both historical
 demographic events and local adaptation. These evolutionary forces are not
 mutually exclusive and can in some cases produce nearly identical patterns
 of genetic differentiation among populations. Here, we investigate the
 evolutionary forces that generated and maintain clinal variation
 genome-wide among populations of Drosophila melanogaster sampled in North
 America and Australia. We contrast patterns of clinal variation in these
 continents with patterns of differentiation among ancestral European and
 African populations. Using established and novel methods we derive here,
 we show that recently derived North America and Australia populations were
 likely founded by both European and African lineages and that this
 hybridization event likely contributed to genome-wide patterns of parallel
 clinal variation between continents. The pervasive effects of admixture
 means that differentiation at only several hundred loci can be attributed
 to the operation of spatially varying selection using an FST outlier
 approach. Our results provide novel insight into the well-studied system
 of clinal differentiation in D. melanogaster and provide a context for
 future studies seeking to identify loci contributing to local adaptation
 in a wide variety of organisms, including other invasive species as well
 as temperate endemics.
description: ms code for admixture
 simulationbash script to evaluate
 accuracy of ancestry estimation from allele frequency
 data.admixture_ms.shPopulation trees for all sampled D. mel populations in Newick formatTrees are partitioned based on chromosome and inversion status.SupplementalDoc1.resub.txtDistance matrices for population treesNei's genetic distance matrices for populations used in this study. A separate file for each chromosome & inversion type is provided.daMats.tar.gzAllele frequencies for world-wide D. melanogaster populationsAllele frequency information for ~500,000 SNPs genome-wide from D. melanogaster populations sampled throughout the world. See Readme for detailed informationpopFqs.delim.gz
DOI: 10.5061/dryad.cr020
title: Data from: Sustainability of professionals’ adherence to clinical practice guidelines in medical care: a systematic review

description: Objectives: To evaluate (1) the state of the art in sustainability
 research and (2) the outcomes of professionals’ adherence to guideline
 recommendations in medical practice. Design: Systematic review. Data
 sources: Searches were conducted until August 2015 in MEDLINE, CINAHL,
 EMBASE, Cochrane Central Register of Controlled Trials (CENTRAL) and the
 Guidelines International Network (GIN) library. A snowball strategy, in
 which reference sections of other reviews and of included papers were
 searched, was used to identify additional papers. Eligibility criteria:
 Studies needed to be focused on sustainability and on professionals’
 adherence to clinical practice guidelines in medical care. Studies had to
 include at least 2 measurements: 1 before (PRE) or immediately after
 implementation (EARLY POST) and 1 measurement longer than 1 year after
 active implementation (LATE POST). Results: The search retrieved 4219
 items, of which 14 studies met the inclusion criteria, involving 18
 sustainability evaluations. The mean timeframe between the end of active
 implementation and the sustainability evaluation was 2.6 years (minimum
 1.5–maximum 7.0). The studies were heterogeneous with respect to their
 methodology. Sustainability was considered to be successful if performance
 in terms of professionals’ adherence was fully maintained in the late
 postimplementation phase. Long-term sustainability of professionals’
 adherence was reported in 7 out of 18 evaluations, adherence was not
 sustained in 6 evaluations, 4 evaluations showed mixed sustainability
 results and in 1 evaluation it was unclear whether the professional
 adherence was sustained. Conclusions: (2) Professionals’ adherence to a
 clinical practice guideline in medical care decreased after more than
 1 year after implementation in about half of the cases. (1) Owing to the
 limited number of studies, the absence of a uniform definition, the high
 risk of bias, and the mixed results of studies, no firm conclusion about
 the sustainability of professionals’ adherence to guidelines in medical
 practice can be drawn.
description: Results Systematic
 review sustainabilityFor this review, 4219
 items were retrieved and screened based on title and abstract, 185 studies
 were assessed based on full text reading and 14 studies were selected for
 analyses. This data file contains the endnote file with all items and the
 classification.
DOI: 10.5061/dryad.46pb3
title: Data from: Simulating the distribution of individual livestock farms and their populations in the united states: an example using domestic swine (Sus scrofa domesticus) farms

description: Livestock distribution in the United States (U.S.) can only be mapped at a
 county-level or worse resolution. We developed a spatial microsimulation
 model called the Farm Location and Agricultural Production Simulator
 (FLAPS) that simulated the distribution and populations of individual
 livestock farms throughout the conterminous U.S. Using domestic pigs (Sus
 scrofa domesticus) as an example species, we customized iterative
 proportional-fitting algorithms for the hierarchical structure of the U.S.
 Census of Agriculture and imputed unpublished state- or county-level
 livestock population totals that were redacted to ensure confidentiality.
 We used a weighted sampling design to collect data on the presence and
 absence of farms and used them to develop a national-scale distribution
 model that predicted the distribution of individual farms at a 100 m
 resolution. We implemented microsimulation algorithms that simulated the
 populations and locations of individual farms using output from our
 imputed Census of Agriculture dataset and distribution model.
 Approximately 19% of county-level pig population totals were unpublished
 in the 2012 Census of Agriculture and needed to be imputed. Using aerial
 photography, we confirmed the presence or absence of livestock farms at
 10,238 locations and found livestock farms were correlated with open
 areas, cropland, and roads, and also areas with cooler temperatures and
 gentler topography. The distribution of swine farms was highly variable,
 but cross-validation of our distribution model produced an area under the
 receiver-operating characteristics curve value of 0.78, which indicated
 good predictive performance. Verification analyses showed FLAPS accurately
 imputed and simulated Census of Agriculture data based on absolute percent
 difference values of &lt; 0.01% at the state-to-national scale, 3.26%
 for the county-to-state scale, and 0.03% for the individual farm-to-county
 scale. Our output data have many applications for risk management of
 agricultural systems including epidemiological studies, food safety,
 biosecurity issues, emergency-response planning, and conflicts between
 livestock and other natural resources.
description: Landscape
 characteristics associated with livestock farms in the United
 StatesThis data describes the
 environmental or anthropogenic features occurring at locations where
 livestock farms are either present or absent in the conterminous United
 States. The spatial coordinates of locations have been removed so they do
 not contain any personally identifiable information. Please see
 accompanying ReadMe file for definitions of field
 names.InputData_GeographicModel.csv
DOI: 10.5061/dryad.c0s22
title: Data from: Resilience of self-organised and top-down planned cities—a case study on London and Beijing street networks

description: The success or failure of the street network depends on its reliability.
 In this article, using resilience analysis, the author studies how the
 shape and appearance of street networks in self-organised and top-down
 planned cities influences urban transport. Considering London and Beijing
 as proxies for self-organised and top-down planned cities, the structural
 properties of London and Beijing networks first are investigated based on
 their primal and dual representations of planar graphs. The robustness of
 street networks then is evaluated in primal space and dual space by
 deactivating road links under random and intentional attack scenarios. The
 results show that the reliability of London street network differs from
 that of Beijing, which seems to rely more on its architecture and
 connectivity. It is found that top-down planned Beijing with its higher
 average degree in the dual space and assortativity in the primal space is
 more robust than self-organised London using the measures of maximum and
 second largest cluster size and network efficiency. The article offers an
 insight, from a network perspective, into the reliability of street
 patterns in self-organised and top-down planned city systems.
description: datasetThis zip file includes the raw datasets (Beijing and London street networks) and graphs created in the primal and dual space for Beijing, London, ERPG, and GRID. The raw datasets are ArcGIS shapefile format and the graphs are ‘pajek’ format.
DOI: 10.5061/dryad.vt966
title: Data from: Static allometry of unicellular green algae: scaling of cellular surface area and volume in the genus Micrasterias (Desmidiales)

description: The surface area-to-volume ratio of cells is one of the key factors
 affecting fundamental biological processes and, thus, fitness of
 unicellular organisms. One of the general models for allometric increase
 in surface-to-volume scaling involves fractal-like elaboration of cellular
 surfaces. However, specific data illustrating this pattern in natural
 populations of the unicellular organisms have not previously been
 available. This study shows that unicellular green algae of the genus
 Micrasterias (Desmidiales) have positive allometric surface-to-volume
 scaling caused by changes in morphology of individual species, especially
 in the degree of cell lobulation. This allometric pattern was also
 detected within most of the cultured and natural populations analysed.
 Values of the allometric S:V scaling within individual populations were
 closely correlated to the phylogenetic structure of the clade. In
 addition, they were related to species-specific cellular morphology.
 Individual populations differed in their allometric patterns, and their
 position in the allometric space was strongly correlated with the degree
 of allometric S:V scaling. This result illustrates that allometric shape
 patterns are an important correlate of the capacity of individual
 populations to compensate for increases in their cell volumes by
 increasing the surface area. However, variation in allometric patterns was
 not associated with phylogenetic structure. This indicates that the
 position of the populations in the allometric space was not evolutionarily
 conserved and might be influenced by environmental factors.
description: Surfaces, volumes and
 landmark data of cellsEstimated surfaces and
 volumes of Micrasterias cells (sheet 1) and the landmark data of the
 semicells (sheet 2). The first column of both tables depicts the
 population affiliation of cells.S_V-LMs.xls