cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sk040
title: Data from: Redesigning the ‘choice architecture’ of hospital prescription charts: a mixed methods study incorporating in-situ simulation

description: Objectives: To incorporate behavioural insights into the user-centred
 design of an inpatient prescription chart (Imperial Drug Chart Evaluation
 and Adoption Study, IDEAS chart) and to determine whether changes in the
 content and design of prescription charts could influence prescribing
 behaviour and reduce prescribing errors. Design: A mixed-methods approach
 was taken in the development phase of the project; in situ simulation was
 used to evaluate the effectiveness of the newly developed IDEAS
 prescription chart. Setting: A London teaching hospital.
 Interventions/methods: A multimodal approach comprising (1) an exploratory
 phase consisting of chart reviews, focus groups and user insight gathering
 (2) the iterative design of the IDEAS prescription chart and finally (3)
 testing of final chart with prescribers using in situ simulation. Results:
 Substantial variation was seen between existing inpatient prescription
 charts used across 15 different UK hospitals. Review of 40 completed
 prescription charts from one hospital demonstrated a number of frequent
 prescribing errors including illegibility, and difficulty in identifying
 prescribers. Insights from focus groups and direct observations were
 translated into the design of IDEAS chart. In situ simulation testing
 revealed significant improvements in prescribing on the IDEAS chart
 compared with the prescription chart currently in use in the study
 hospital. Medication orders on the IDEAS chart were significantly more
 likely to include correct dose entries (164/164 vs 166/174; p=0.0046) as
 well as prescriber's printed name (163/164 vs 0/174; p&lt;0.0001)
 and contact number (137/164 vs 55/174; p&lt;0.0001). Antiinfective
 indication (28/28 vs 17/29; p&lt;0.0001) and duration (26/28 vs 15/29;
 p&lt;0.0001) were more likely to be completed using the IDEAS chart.
 Conclusions: In a simulated context, the IDEAS prescription chart
 significantly reduced a number of common prescribing errors including
 dosing errors and illegibility. Positive behavioural change was seen
 without prior education or support, suggesting that some common
 prescription writing errors are potentially rectifiable simply through
 changes in the content and design of prescription charts.
description: Appendix
 1Comparison of design
 features of different charts used across the UK NHS
 (n=15)Appendix
 2Analysis of completed
 prescription charts in patients who were consecutively discharged from one
 medical and one surgical ward at a London hospital
 (n=40)Appendix
 3Findings from focus
 groups (selected statements)Appendix
 4Case
 study used in phase 3 of the simulation study Imperial Drug Chart
 Evaluation and Adoption Study (IDEAS)IDEAS prescription
 chartThe final IDEAS
 prescription chart template used for in-situ simulationPrescription-chart2-150611.pdf
DOI: 10.5281/zenodo.18390868
title: favorinus_auritulus_spades_01.fasta.gz
DOI: 10.5281/zenodo.18390867
title: favorinus_auritulus_spades_01.fasta.gz
DOI: 10.5061/dryad.v8j20
title: Data from: Automated stitching of microtubule centerlines across serial electron tomograms

description: Tracing microtubule centerlines in serial section electron tomography
 requires microtubules to be stitched across sections, that is lines from
 different sections need to be aligned, endpoints need to be matched at
 section boundaries to establish a correspondence between neighboring
 sections, and corresponding lines need to be connected across multiple
 sections. We present computational methods for these tasks: 1) An initial
 alignment is computed using a distance compatibility graph. 2) A fine
 alignment is then computed with a probabilistic variant of the iterative
 closest points algorithm, which we extended to handle the orientation of
 lines by introducing a periodic random variable to the probabilistic
 formulation. 3) Endpoint correspondence is established by formulating a
 matching problem in terms of a Markov random field and computing the best
 matching with belief propagation. Belief propagation is not generally
 guaranteed to converge to a minimum. We show how convergence can be
 achieved, nonetheless, with minimal manual input. In addition to stitching
 microtubule centerlines, the correspondence is also applied to transform
 and merge the electron tomograms. We applied the proposed methods to
 samples from the mitotic spindle in C. elegans, the meiotic spindle in X.
 laevis, and sub-pellicular microtubule arrays in T. brucei. The methods
 were able to stitch microtubules across section boundaries in good
 agreement with experts' opinions for the spindle samples. Results,
 however, were not satisfactory for the microtubule arrays. For certain
 experiments, such as an analysis of the spindle, the proposed methods can
 replace manual expert tracing and thus enable the analysis of microtubules
 over long distances with reasonable manual effort.
description: Supplementary
 Datasuppl-data.zip
DOI: 10.5061/dryad.j56n4
title: Data from: Genetic analysis of circadian responses to low frequency electromagnetic fields in Drosophila melanogaster

description: The blue-light sensitive photoreceptor cryptochrome (CRY) may act as a
 magneto-receptor through formation of radical pairs involving a triad of
 tryptophans. Previous genetic analyses of behavioral responses of
 Drosophila to electromagnetic fields using conditioning, circadian and
 geotaxis assays have lent some support to the radical pair model (RPM).
 Here, we describe a new method that generates consistent and reliable
 circadian responses to electromagnetic fields that differ substantially
 from those already reported. We used the Schuderer apparatus to isolate
 Drosophila from local environmental variables, and observe extremely low
 frequency (3 to 50 Hz) field-induced changes in two locomotor phenotypes,
 circadian period and activity levels. These field-induced phenotypes are
 CRY- and blue-light dependent, and are correlated with enhanced CRY
 stability. Mutational analysis of the terminal tryptophan of the triad
 hypothesised to be indispensable to the electron transfer required by the
 RPM reveals that this residue is not necessary for field responses. We
 observe that deletion of the CRY C-terminus dramatically attenuates the
 EMF-induced period changes, whereas the N-terminus underlies the
 hyperactivity. Most strikingly, an isolated CRY C-terminus that does not
 encode the Tryptophan triad nor the FAD binding domain is nevertheless
 able to mediate a modest EMF-induced period change. Finally, we observe
 that hCRY2, but not hCRY1, transformants can detect EMFs, suggesting that
 hCRY2 is blue light-responsive. In contrast, when we examined circadian
 molecular cycles in wild-type mouse suprachiasmatic nuclei slices under
 blue light, there was no field effect. Our results are therefore not
 consistent with the classical Trp triad-mediated RPM and suggest that CRYs
 act as blue-light/EMF sensors depending on trans-acting factors that are
 present in particular cellular environments.
description: Main Figures
 DataRaw data of Period and
 events of activity for main figuresMain
 Figures.7zSupplementary Figures S4
 and S5Raw Data for Per2::Luc
 bioluminescenceFig S4 and Fig
 S5.7zSupplementary Figures
 S1, S3 and S7Period data for
 supplementary figures S1 S3 S7
DOI: 10.5061/dryad.ks515
title: Data from: Seasonal dynamics of megafauna on the deep West Antarctic Peninsula shelf in response to variable phytodetrital influx

description: The deep West Antarctic Peninsula (WAP) shelf is characterized by intense
 deposition of phytodetritus during spring/summer months, while very little
 food material reaches the seafloor during winter. The response of the
 shelf benthic megafauna to this highly variable food supply is still
 poorly understood. In order to characterize the deposition of
 phytodetritus and the megabenthic community response, we deployed a
 seafloor time-lapse camera at approximately 590 m depth on the mid WAP
 shelf west of Anvers Island for 15 months. Seafloor photographs were taken
 at intervals of 12 or 24 h nearly continuously from 9 December 1999
 (austral winter) to 20 March 2001 (summer) and analysed for phytodetritus
 deposition and megafaunal dynamics. Seafloor images indicated a marked
 seasonal arrival of greenish phytodetritus, with large interannual and
 seasonal variability in the coverage of depositing phytodetrital
 particles. The surface-deposit-feeding elasipod holothurians Protelpidia
 murrayi and Peniagone vignoni dominated the epibenthic megafauna
 throughout the year, frequently constituting more than 80% of the
 megafaunal abundance, attaining total densities of up to 2.4 individuals
 m−2. Elasipod abundances were significantly higher in summer than winter.
 During summer periods of high phytodetrital flux, Pr. murrayi produced
 faecal casts at higher rates, indicating intensified population-level
 feeding activity. In March–June 2000, faecal casts lasted longest,
 suggesting lower horizontal bioturbation activity during autumn–winter.
 Our data indicate that the Pr. murrayi population increases its feeding
 rates in response to increasing amounts and/or lability of organic matter
 on the sediment surface. Assuming that this species feeds on the top
 millimetre of the sediment, we estimate that, during periods of high
 phytodetrital flux, the Pr. murrayi population reworks one square metre of
 sediment surface in approximately 287 days. We suggest that Pr. murrayi is
 an important species for organic-carbon recycling on the deep WAP shelf,
 controlling the availability of deposited labile phytodetritus to the
 broader shelf benthic community.
description: Megafauna measurements
 and densityThis contains the data
 on megafauna (specially elasipod holothurians) size and density measured
 using image analysis.TimeLapse.xlsHolothurian fecal cast dataThis presents data on fecal cast number, size, volume and production.TL_FEZES_v2.xls
DOI: 10.5061/dryad.kp854
title: Data from: Model inadequacy and mistaken inferences of trait-dependent speciation

description: Species richness varies widely across the tree of life, and there is great
 interest in identifying ecological, geographic, and other factors that
 affect rates of species proliferation. Recent methods for explicitly
 modeling the relationships among character states, speciation rates, and
 extinction rates on phylogenetic trees- BiSSE, QuaSSE, GeoSSE, and related
 models - have been widely used to test hypotheses about character
 state-dependent diversification rates. Here, we document the disconcerting
 ease with which neutral traits are inferred to have statistically
 significant associations with speciation rate. We first demonstrate this
 unfortunate effect for a known model assumption violation: shifts in
 speciation rate associated with a character not included in the model. We
 further show that for many empirical phylogenies, characters simulated in
 the absence of state-dependent diversification exhibit an even higher Type
 I error rate, indicating that the method is susceptible to additional,
 unknown model inadequacies. For traits that evolve slowly, the root cause
 appears to be a statistical framework that does not require replicated
 shifts in character state and diversification. However, spurious
 associations between character state and speciation rate arise even for
 traits that lack phylogenetic signal, suggesting that phylogenetic
 pseudoreplication alone cannot fully explain the problem. The surprising
 severity of this phenomenon suggests that many trait-diversification
 relationships reported in the literature may not be real. More generally,
 we highlight the need for diagnosing and understanding the consequences of
 model inadequacy in phylogenetic comparative methods.
description: Analysis scripts and
 simulation results for trait-dependent speciation modelsData file includes
 simulation results, code to repeat simulations, Appendix with
 supplementary methods, and supplementary results.dryad_submit.zip
DOI: 10.5061/dryad.37104
title: Data from: Performance of forest bryophytes with different geographical distributions transplanted across a topographically heterogeneous landscape

description: Most species distribution models assume a close link between climatic
 conditions and species distributions. Yet, we know little about the link
 between species' geographical distributions and the sensitivity of
 performance to local environmental factors. We studied the performance of
 three bryophyte species transplanted at south- and north-facing slopes in
 a boreal forest landscape in Sweden. At the same sites, we measured both
 air and ground temperature. We hypothesized that the two southerly
 distributed species Eurhynchium angustirete andHerzogiella seligeri
 perform better on south-facing slopes and in warm conditions, and that the
 northerly distributed species Barbilophozia lycopodioides perform better
 on north-facing slopes and in relatively cool conditions. The northern,
 but not the two southern species, showed the predicted relationship with
 slope aspect. However, the performance of one of the two southern species
 was still enhanced by warm temperatures. An important reason for the
 inconsistent results can be that microclimatic gradients across landscapes
 are complex and influenced by many climate-forcing factors. Therefore,
 comparing only north- and south-facing slopes might not capture the
 complexity of microclimatic gradients. Population growth rates and
 potential distributions are the integrated results of all vital rates.
 Still, the study of selected vital rates constitutes an important first
 step to understand the relationship between population growth rates and
 geographical distributions and is essential to better predict how climate
 change influences species distributions.
description: Performance of Forest
 BryophytesField data was collected
 between April/May and September/October 2011. In case it was processed,
 this took place in 2011-2013. Data from ArcGIS Desktop was collected in
 2011-2013. Performance data was collected in the field and processed in
 Excel, Access and GIMP. Microclimatic data (temperature) was measured in
 the field and processed in Excel and Access. The processed temperature
 data refers to the period 29th of May until 28th of September 2011. Other
 environmental data was collected both in the field and for some variables
 through ArcGIS Desktop. Data collected in the field was for a few
 variables processed in Excel. Soil and litter samples was dried for
 pH-measurements in lab (2011). We refer to the manuscript and the metadata
 of the uploaded excelfile for further details on the
 data.Data_ms1_JDKHJE_20141021.xlsx
DOI: 10.5061/dryad.jv577
title: Data from: Quantifying human mobility perturbation and resilience in Hurricane Sandy

description: Human mobility is influenced by environmental change and natural
 disasters. Researchers have used trip distance distribution, radius of
 gyration of movements, and individuals' visited locations to
 understand and capture human mobility patterns and trajectories. However,
 our knowledge of human movements during natural disasters is limited owing
 to both a lack of empirical data and the low precision of available data.
 Here, we studied human mobility using high-resolution movement data from
 individuals in New York City during and for several days after Hurricane
 Sandy in 2012. We found the human movements followed truncated power-law
 distributions during and after Hurricane Sandy, although the β value was
 noticeably larger during the first 24 hours after the storm struck. Also,
 we examined two parameters: the center of mass and the radius of gyration
 of each individual's movements. We found that their values during
 perturbation states and steady states are highly correlated, suggesting
 human mobility data obtained in steady states can possibly predict the
 perturbation state. Our results demonstrate that human movement
 trajectories experienced significant perturbations during hurricanes, but
 also exhibited high resilience. We expect the study will stimulate future
 research on the perturbation and inherent resilience of human mobility
 under the influence of hurricanes. For example, mobility patterns in
 coastal urban areas could be examined as hurricanes approach, gain or
 dissipate in strength, and as the path of the storm changes. Understanding
 nuances of human mobility under the influence of such disasters will
 enable more effective evacuation, emergency response planning and
 development of strategies and policies to reduce fatality, injury, and
 economic loss.
description: Quantifying Human
 Mobility Perturbation and Resilience in Hurricane Sandy (original
 data)The file includes both
 the lengths of displacements during and after the attack of Hurricane
 Sandy, and the de-identified active users and their geographical
 coordinates during the perturbation state and the steady
 state.
DOI: 10.5061/dryad.g7b25
title: Data from: Transcriptome analysis indicates considerable divergence in alternative splicing between duplicated genes in Arabidopsis thaliana

description: Gene and genome duplication events have created a large number of new
 genes in plants that can diverge by evolving new expression profiles and
 functions (neofunctionalization) or dividing extant ones
 (subfunctionalization). Alternative splicing (AS) generates multiple types
 of mRNA from a single type of pre-mRNA by differential intron splicing. It
 can result in new protein isoforms or down-regulation of gene expression
 by transcript decay. Using RNA-seq we investigated the degree to which
 alternative splicing patterns are conserved between duplicated genes in
 Arabidopsis thaliana. Our results revealed that 30% of AS events in alpha
 whole genome duplicates, and 33% of AS events in tandem duplicates, are
 qualitatively conserved within leaf tissue. Loss of ancestral splice
 forms, as well as asymmetric gain of new splice forms, may account for
 this divergence. Conserved events had different frequencies, as only 31%
 of shared AS events in alpha whole genome duplicates and 41% of shared AS
 events in tandem duplicates had similar frequencies in both paralogs,
 indicating considerable quantitative divergence. Analysis of published
 RNA-seq data from nonsense mediated decay (NMD) mutants indicated that 85%
 of alpha whole genome duplicates and 89% of tandem duplicates have
 diverged in their AS-induced NMD. Our results indicate that alternative
 splicing shows a high degree of divergence between paralogs such that
 qualitatively conserved alternative splicing events tend to have
 quantitative divergence. Divergence in AS patterns between duplicates may
 be a mechanism of regulating expression level divergence.
description: Repo for Tack et al.
 2014 GeneticsData and scripts from
 "Transcriptome Analysis Indicates Considerable Divergence in
 Alternative Splicing Between Duplicated Genes in Arabidopsis
 thaliana"Github_Dryad_repo.zip
DOI: 10.60555/bpn5-6m38
title: Colloidal gels:  Aging in microgravity, Structure of highly polydisperse gels

description: Data are from two projects:  one related to aging, one related to polydispersity.  The first project has data under folders with a name containing AGING.  The second has data under folders with a name containing POLYDISPERSE.

-------

Project 1: Objectives specific to aging of colloid gels
•Quantify coarsening of colloidal gels under microgravity conditions.
•Quantify changes in thermal fluctuations of colloidal gels under microgravity conditions.
•Understand aging of colloidal gels over time scales range from seconds to tens of hours.

Project 2: Objectives related to structure of polydisperse colloidal gels
•Measure fractal dimension of polydisperse colloidal gels (on Earth)
•Understand how particle size relates to contact number
•Quantify tetrahedral structures, and how particle size influences tetrahedral structure in colloidal gels
DOI: 10.5061/dryad.55h83
title: Data from: Mixed-ancestry and admixture in Kaua’i’s feral chickens: invasion of domestic genes into ancient Red Junglefowl reservoirs?

description: A major goal of invasion genetics is to determine how establishment
 histories shape non-native organisms' genotypes and phenotypes. While
 domesticated species commonly escape cultivation to invade feral habitats,
 few studies have examined how this process shapes feral gene pools and
 traits. We collected genomic and phenotypic data from feral chickens
 (Gallus gallus) on the Hawaiian island of Kauai to (i) ascertain their
 origins and (ii) measure standing variation in feral genomes, morphology
 and behaviour. Mitochondrial phylogenies (D-loop & whole Mt
 genome) revealed two divergent clades within our samples. The rare clade
 also contains sequences from Red Junglefowl (the domestic chicken's
 progenitor) and ancient DNA sequences from Kauai that predate European
 contact. This lineage appears to have been dispersed into the east Pacific
 by ancient Polynesian colonists. The more prevalent MtDNA clade occurs
 worldwide and includes domesticated breeds developed recently in Europe
 that are farmed within Hawaii. We hypothesize this lineage originates from
 recently feralized livestock and found supporting evidence for increased
 G. gallus density on Kauai within the last few decades. SNPs obtained from
 whole-genome sequencing were consistent with historic admixture between
 Kauai's divergent (G. gallus) lineages. Additionally, analyses of
 plumage, skin colour and vocalizations revealed that Kauai birds'
 behaviours and morphologies overlap with those of domestic chickens and
 Red Junglefowl, suggesting hybrid origins. Together, our data support the
 hypotheses that (i) Kauai's feral G. gallus descend from recent
 invasion(s) of domestic chickens into an ancient Red Junglefowl reservoir
 and (ii) feral chickens exhibit greater phenotypic diversity than
 candidate source populations. These findings complicate management
 objectives for Pacific feral chickens, while highlighting the potential of
 this and other feral systems for evolutionary studies of invasions.
description: Mitochondrial DNA
 alignmentsSequences and alignments
 used for whole mitochondrial and control region phylogenies. Sequences
 files in FASTA format contain Kauai sequences from this work (consensus
 sequences from mapping short reads against the chicken reference genome)
 and previously published sequences from Genbank. Sequences were aligned
 with ClustalW and are stored in nexus format.alignment.tar.gzMitochondrial DNA phylogeniesBayesian whole mitochondrial genome and control region phylogenies in nexus format.phylogeny.tar.gzNuclear variantsNuclear variants used for population genetic analyses (PCA, STRUCTURE and ADMIXTURE). One dataset contains 3000 randomly selected variants, and the other SNPs that were typed both in this study and Wragg et al (2012).variants.tar.gzSupplementary table 2Supplementary table 2 in tab-delimited text format, containing vocalization data and links to YouTube and database entry IDs for Xeno Canto sources.supplementary_vocalization_data.txt