cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v8kc47p
title: Data from: Emergency Room Safer Transfer of Patients (ER-STOP): a quality improvement initiative at a community based hospital to improve the safety of emergency room patient handovers

description: Objectives: Ensure early identification and timely management of patient
 deterioration as essential components of safe effective healthcare.
 Prompted by analyses of incident reports and deterioration events, a
 multi-component organizational rescue from danger system was redesigned to
 decrease unexpected in-patient deterioration. Design: Quality improvement
 before-after unblinded trial Setting: 430 bed Canadian community teaching
 hospital Participants: All admitted adult medical-surgical patients in a
 before-after 12-month interventional study Intervention: Locally validated
 checklist (Modified Early Warning Score-MEWS + urinary catheter in-situ +
 nurse concern) with an intentional pause and explicit management options
 was deployed as a modification of an existing ward transfer of
 accountability fax report in the ED Results: Following deployment of
 ER-STOP, the risk of an unexpected CCRT (Critical Care Response Team)
 response within 24 hours of admission from ED to adult medical and
 surgical wards was significantly decreased (OR: 4.1, 95% CI: 2.17 – 7.77).
 Mean (+SD) ED wait-times (5.66+1.54 vs. 5.74+1.04 hours, p=0.30), ICU
 admission rate (3.84%, n=233 vs. 4.61%, n= 278, p=0.06) and cardiac care
 unit admission rate (9.51%, n =577 vs. 9.60%, n=579, p=0.198) were
 unchanged. Conclusions: ER-STOP improvement was out of proportion to the
 predictive value of the checklist component suggesting that effectiveness
 of this low cost sustainable tool was related to increased situational
 awareness, empowering a culture of patient safety and repurposing of an
 adjacent ED medical short stay unit use. Local adaptation within existing
 processes is essential to successful safety outcomes
description: Wait time
 data“Wait time data”
 includes ER to admission wait time (hours) and admission to inpatient unit
 transfer wait time (hours)
DOI: 10.5061/dryad.5pr17
title: Data from: Current and historical land use influence soil-based ecosystem services in an urban landscape

description: Urban landscapes are increasingly recognized as providing important
 ecosystem services (ES) to their occupants. Yet, urban ES assessments
 often ignore the complex spatial heterogeneity and land-use history of
 cities. Soil-based services may be particularly susceptible to land-use
 legacy effects. We studied indicators of three soil-based ES – carbon
 storage, water quality regulation, and runoff regulation – in a
 historically agricultural urban landscape and asked: (1) How do ES
 indicators vary with contemporary land cover and time since development?
 (2) Do ES indicators vary primarily among land-cover classes, within
 land-cover classes, or within sites? (3) What is the relative contribution
 of urban land-cover classes to potential citywide ES provision? We
 measured biophysical indicators (soil carbon (C), available phosphorus
 (P), and saturated hydraulic conductivity (Ks)) in 100 sites across 5
 land-cover classes, spanning an ~125 year gradient of time since
 development within each land-cover class. Potential for ES provision was
 substantial in urban green spaces, including developed land. Runoff
 regulation services (high Ks) were highest in forests; water quality
 regulation (low P) was highest in open spaces and grasslands; and open
 spaces and developed land (e.g., residential yards) had the highest C
 storage. In developed land covers, both C and P increased with time since
 development, indicating effects of historical land-use on contemporary ES
 and tradeoffs between two important ES. Among-site differences accounted
 for a high proportion of variance in soil properties in forests,
 grasslands, and open space, while residential areas had high within-site
 variability – underscoring the leverage city residents have to improve
 urban ES provision. Developed land covers contributed most ES supply at
 the citywide scale, even after accounting for potential impacts of
 impervious surfaces. Considering the full mosaic of urban green space and
 its history is needed to estimate the kinds and magnitude of ES provided
 in cities, and to augment regional ES assessments that often ignore or
 underestimate urban ES supply.
description: Ziter_Turner_2018_UrbanSoil_DataUrban soil data collected in Madison, WI, USA. The zipped folder contains core data used for analyses, including soil physical properties (bulk density, texture, Ksat), soil carbon, soil phosphorous, and SSURGO soil type for 100 field sites across 5 urban land-cover classes (forest, prairie, open space, low-density residential, medium-density residential).
DOI: 10.5061/dryad.51d7k
title: Data from: Mechanical reproductive isolation facilitates parallel speciation in western North American scincid lizards

description: Mechanical reproductive barriers have been dismissed as a major driver of
 animal speciation, yet the extent to which such barriers cause
 reproductive isolation in most animal groups is largely unknown and rarely
 tested. In this study, we used hierarchical Bayesian modeling of mate
 compatibility experiments to show that body size divergence in lizards of
 the Plestiodon skiltonianus complex contributes to reproductive isolation
 in at least three ways: males preferably court females that are more
 similar in size, females reject males that are highly divergent in size,
 and that the size difference of a male and female in copula constrains the
 ability to align the genitalia for intromission. We used a predictive
 model to estimate the contributions of behavioral and mechanical barriers
 to reproductive isolation between populations with differing degrees of
 size divergence. This model shows that the mechanical barrier is more
 important than the behavioral barriers at small and intermediate degrees
 of size divergence, suggesting that it acts earlier during speciation. As
 correlated divergence in size and ecology is common in animals, similar
 constraints imposed by the geometry of the mating posture may apply to a
 variety of major animal lineages and merit further attention in speciation
 research.
description: Richmond et al 2011
 DatafileThis tab-delimited text
 file contains all of the raw, scored data from laboratory mate
 compatibility trials conducted on wild caught skinks in the Plestiodon
 skiltonianus species group. A description of the categories scored during
 the mating trials (i.e. column headers) can be found in the ReadMe file.
 The data can be opened as a plain text file and executed in OPENBUGS
 3.0.7, the same software used to analyze the data in the paper. Source
 codes for running the models can be found in Appendix I that accompanies
 the paper.
DOI: 10.5061/dryad.1150
title: Data from: A test of the chromosomal rearrangement model of speciation in Drosophila pseudoobscura

description: Recent studies suggest that chromosomal rearrangements play a significant
 role in speciation by preventing recombination and maintaining species
 persistence despite interspecies gene flow. Factors conferring adaptation
 or reproductive isolation are maintained in rearranged regions in the face
 of hybridization, while such factors are eliminated from collinear
 regions. As a direct test of this rearrangement model, we evaluated the
 genetic basis of hybrid male sterility in a sympatric species pair,
 Drosophila pseudoobscura pseudoobscura and D. persimilis, and an
 allopatric species pair, D. pseudoobscura bogotana and D. persimilis. Our
 results are consistent with the proposed model: virtually all of the
 sterility factors in the former pair are associated with three inverted
 regions, whereas sterility factors are present in the collinear regions in
 the latter pair. These findings indicate recombination and selection may
 have eliminated sterility factors outside the inverted regions between D.
 p. pseudoobscura and D. persimilis, suggesting chromosomal rearrangements
 may facilitate species persistence despite hybridization.
description: BackcrossGenotypes.zip
DOI: 10.5061/dryad.ht047
title: Data from:A method for estimating Hill function-based dynamic models of gene regulatory networks

description: Gene regulatory networks (GRNs) are quite large and complex. To better
 understand and analyze GRNs, mathematical models are being employed.
 Different types of models, such as logical, continuous, and stochastic
 models, can be used to describe GRNs. In this paper, we present a new
 approach to identify continuous models, since they are more suitable for
 large number of genes and quantitative analysis. One of the most promising
 techniques for identifying continuous models of GRNs is based on Hill
 functions and generalized profiling method (GPM). The advantage of this
 approach is low computational cost and insensitivity to initial
 conditions. In the GPM, a constrained nonlinear optimization problem has
 to be solved that is usually under-determined. In this paper, we propose a
 new optimization approach in which we reformulate the optimization problem
 such that constraints are embedded implicitly in the cost function.
 Moreover, we propose to split the unknown parameter in two sets based on
 the structure of Hill functions. These two sets are estimated separately
 to resolve the issue of under-determined problem. As a case study, we
 apply the proposed technique on the SOS response in Escherichia coli and
 compare the results with the existing literature.
description: MATLAB Code for the SOT
 algorithmThe archive includes
 MATLAB script files for the proposed split optimisation technique
 algorithm.Matlab
 Code.zip
DOI: 10.5061/dryad.5k30c
title: Data from: An appraisal of the enzyme stability-activity trade-off

description: A longstanding idea in evolutionary physiology is that an enzyme cannot
 jointly optimize performance at both high and low temperatures due to a
 trade-off between stability and activity. Although a stability-activity
 trade-off has been observed for well-characterized examples, such a
 trade-off is not imposed by any physical chemical constraint. To better
 understand the pervasiveness of this trade-off, I investigated the
 stability-activity relationship for comparative biochemical studies of
 purified orthologous enzymes identified by a literature search. The nature
 of this relationship varied greatly among studies. Notably, studies of
 enzymes with low mean synonymous nucleotide sequence divergence were less
 likely to exhibit the predicted negative correlation between stability and
 activity. Similarly, a survey of directed evolution investigations of the
 stability-activity relationship indicated that these traits are often
 uncoupled among nearly identical yet phenotypically divergent enzymes.
 This suggests that the presumptive trade-off often reported for
 investigations of enzymes with high mean sequence divergence may in some
 cases instead be a consequence of the degeneration over time of enzyme
 function in unselected environments, rather than a direct effect of
 thermal adaptation. The results caution against the general assertion of a
 stability-activity trade-off during enzyme adaptation.
description: Data used for analyses
 of the enzyme stability-activity relationshipData were obtained from
 a literature search. Web of Science searches from 1968 through 2016 were
 performed under the topic terms (1) “enzyme stability” and “temperature”
 and (2) “temperature adaptation” and “protein”, respectively.To be
 included, data were required for three or more purified orthologous
 enzymes for some measure of both (1) enzyme stability and (2) enzyme
 kinetics assayed at a common garden temperature. For the former, this
 included enzyme denaturation temperature (Tm), enzyme optimal temperature
 (Topt), time to 50% enzyme inactivation (T50) or other estimate of
 residual activity, and the free energy of unfolding (GU). For the latter,
 this included enzyme catalytic turnover number (kcat), maximal rate of
 catalysis (Vmax), enzyme specific activity, and the Michaelis constant
 (Km), a measure of an enzyme’s substrate affinity (1/Km is related but not
 identical to enzyme binding affinity).Data.xlsx
DOI: 10.5061/dryad.269h9
title: Data from: Poor plant performance under simulated climate change is linked to mycorrhizal responses in a semiarid shrubland

description: 1.Warmer and drier conditions associated with ongoing climate change will
 increase abiotic stress for plants and mycorrhizal fungi in drylands
 worldwide, thereby potentially reducing vegetation cover and productivity
 and increasing the risk of land degradation and desertification.
 Rhizosphere microbial interactions and feedbacks are critical processes
 that could either mitigate or aggravate the vulnerability of dryland
 vegetation to forecasted climate change. 2.We conducted a four-year
 manipulative study in a semiarid shrubland in the Iberian Peninsula to
 assess the effects of warming (~2.5°C; W), rainfall reduction (~30%; RR)
 and their combination (W+RR) on the performance of native shrubs
 (Helianthemum squamatum) and their associated mycorrhizal fungi. 3.Warming
 (W and W+RR) decreased the net photosynthetic rates of H. squamatum shrubs
 by ~31% despite concurrent increases in stomatal conductance (~33%),
 leading to sharp decreases (~50%) in water use efficiency. Warming also
 advanced growth phenology, decreased leaf nitrogen and phosphorus contents
 per unit area, reduced shoot biomass production by ~36% and decreased
 survival during a dry year in both W and W+RR plants. Plants under RR
 showed more moderate decreases (~10-20%) in photosynthesis, stomatal
 conductance and shoot growth. 4.Warming, RR and W+RR altered
 ectomycorrhizal fungal (EMF) community structure and drastically reduced
 the relative abundance of EMF sequences obtained by high-throughput
 sequencing, a response associated with decreases in the leaf nitrogen,
 phosphorus and dry matter contents of their host plants. In contrast to
 EMF, the community structure and relative sequence abundances of other
 non-mycorrhizal fungal guilds were not significantly affected by the
 climate manipulation treatments. 5.Synthesis: Our findings highlight the
 vulnerability of both native plants and their symbiotic mycorrhizal fungi
 to climate warming and drying in semiarid shrublands, and point to the
 importance of a deeper understanding of plant-soil feedbacks to predict
 dryland vegetation responses to forecasted aridification. The
 interdependent responses of plants and ectomycorrhizal fungi to warming
 and rainfall reduction may lead to a detrimental feedback loop on
 vegetation productivity and nutrient pool size, which could amplify the
 adverse impacts of forecasted climate change on ecosystem functioning in
 EMF-dominated drylands.
description: Dataset for León-Sánchez
 et al. Journal of EcologyData was collected in a
 field climate change simulation experiment in Aranjuez, in central Spain
 (40°02′N–3°32′W, 495 m altitude). The dataset includes leaf gas exchange
 measurements, isotopic C composition, leaf nutrients (P, N), leaf
 morphological traits, plant biomass, plant survival and mycorrhizal fungi
 relative abundances.León-Sánchez_etal_dataset.xlsx
DOI: 10.5061/dryad.g0b20
title: Data from: Molecular evidence shows low species diversity of coral-associated hydroids in Acropora corals

description: A novel symbiosis between scleractinians and hydroids (Zanclea spp.) was
 recently discovered using taxonomic approaches for hydroid species
 identification. In this study, we address the question whether this is a
 species-specific symbiosis or a cosmopolitan association between Zanclea
 and its coral hosts. Three molecular markers, including mitochondrial 16S
 and nuclear 28S ribosomal genes, and internal transcribed spacer (ITS),
 were utilized to examine the existence of Zanclea species from 14 Acropora
 species and 4 other Acroporidae genera including 142 coral samples
 collected from reefs in Kenting and the Penghu Islands, Taiwan, Togian
 Island, Indonesia, and Osprey Reef and Orpheus Island on the Great Barrier
 Reef, Australia. Molecular phylogenetic analyses of the 16S and 28S genes
 showed that Acropora-associated Zanclea was monophyletic, but the genus
 Zanclea was not. Analysis of the ITS, and 16S and 28S genes showed either
 identical or extremely low genetic diversity (with mean pairwise distances
 of 0.009 and 0.006 base substitutions per site for the 16S and 28S genes,
 respectively) among Zanclea spp. collected from diverse Acropora hosts in
 different geographic locations, suggesting that a cosmopolitan and
 probably genus-specific association occurs between Zanclea hydroids and
 their coral hosts.
description: 16SAlignment of partial 16S
 ribosomal gene of Zanclea sp. associated with different Scleractinia
 species28SAlignment of partial 28S
 ribosomal gene of Zanclea sp. associated with different Scleractinia
 speciesITSAlignment of ITS region
 (partial 18S - ITS1 - 5.8S - ITS2- partial 28S) of Zanclea sp. associated
 with different Acropora speciesITS1Alignment of ITS of
 Zanclea sp. associated with different Scleractinia
 species
DOI: 10.5061/dryad.630hf
title: Data from: Intraneural stimulation elicits discrimination of textural features by artificial fingertip in intact and amputee humans

description: Restoration of touch after hand amputation is a desirable feature of ideal
 prostheses. Here, we show that texture discrimination can be artificially
 provided in human subjects by implementing a neuromorphic real-time
 mechano-neuro-transduction (MNT), which emulates to some extent the firing
 dynamics of SA1 cutaneous afferents. The MNT process was used to modulate
 the temporal pattern of electrical spikes delivered to the human median
 nerve via percutaneous microstimulation in four intact subjects and via
 implanted intrafascicular stimulation in one transradial amputee. Both
 approaches allowed the subjects to reliably discriminate spatial
 coarseness of surfaces as confirmed also by a hybrid neural model of the
 median nerve. Moreover, MNT-evoked EEG activity showed physiologically
 plausible responses that were superimposable in time and topography to the
 ones elicited by a natural mechanical tactile stimulation. These findings
 can open up novel opportunities for sensory restoration in the next
 generation of neuro-prosthetic hands.
description: Neuromorphic tactile
 stimulation patternsSequence of timestamps
 (in ms) of spikes that were delivered to the human median nerve
 (trial*.txt), resulting from a neuromorphic mechano-neuro-transduction
 process, and responses of human amputee in a 3AFC psychophysical protocol
 associated to such stimuli (DAS_3AFC_protocol.csv)DAS_3AFC_protocol.zip
DOI: 10.5061/dryad.p8j80
title: Data from: Stable isotope labeled n-alkanes to assess digesta passage kinetics through the digestive tract of ruminants

description: We describe the use of carbon stable isotope (13C) labeled n-alkanes as a
 potential internal tracer to assess passage kinetics of ingested nutrients
 in ruminants. Plant cuticular n-alkanes originating from intrinsically 13C
 labeled ryegrass plants were pulse dosed intraruminally in four
 rumen-cannulated lactating dairy cows receiving four contrasting ryegrass
 silage treatments that differed in nitrogen fertilization level (45 or 90
 kg nitrogen ha−1) and maturity (early or late). Passage kinetics through
 the gastrointestinal tract were derived from the δ13C (i.e. the ratio
 13C:12C) in apparently undigested fecal material. Isotopic enrichment was
 observed in a wide range of long-chain n-alkanes (C27–C36) and passage
 kinetics were determined for the most abundant C29, C31 and C33 n-alkanes,
 for which a sufficiently high response signal was detected by combustion
 isotope ratio mass spectrometry. Basal diet treatment and carbon chain
 length of n-alkanes did not affect fractional passage rates from the rumen
 (K1) among individual n-alkanes (3.71–3.95%/h). Peak concentration time
 and transit time showed a quantitatively small, significant (p≤0.002)
 increase with carbon chain length. K1 estimates were comparable to those
 of the 13C labeled digestible dry matter fraction (3.38%/h; r = 0.61 to
 0.71; p≤0.012). A literature review has shown that n-alkanes are not
 fermented by microorganisms in the rumen and affirms no preferential
 depletion of 13C versus 12C. Our results suggest that 13C labeled
 n-alkanes can be used as nutrient passage tracers and support the
 reliability of the δ13C signature of digestible feed nutrients as a tool
 to measure nutrient-specific passage kinetics.
description: fecal excretion data
 13C-n-alkanespone
 alkanes.csv
DOI: 10.5061/dryad.fp32k
title: Data from: Metabolic scaling of individuals vs. populations: evidence for variation in scaling exponents at different hierarchical levels

description: 1. The power scaling of metabolic rate with body mass is fundamental to
 animal biology, due to the profound influence that animal size has on
 ecology and physiolatically with cell size or metabolic intensity between
 the boundaries of 0.67 and 1. Despite this tremendous interest in the
 value of scaling exponents, little is known about metabolic scaling within
 individual animals and how this relates to population-level scaling. 2.
 Here, we conducted a long-term study that repeatedly characterised the
 complete metabolic profile of a group of 68 individual fish (cunner,
 Tautogolabrus adspersus) by measuring their standard metabolic rate (SMR),
 routine metabolic rate (RMR), active metabolic rate (AMR), and aerobic
 scope (AS) in five separate trials over 10 months (fish mass range,
 0.5–19.5 g). 3. At all levels of metabolic intensity, the mean exponents
 for the group of fish at any single point in time i.e., within trials; =
 0.89, RMR = 0.89, = 0.94, AS = 0.96) were higher than those characterising
 the group as it aged i.e., across trials; = 0.82, = 0.84, = 0.90, = 0.92),
 and both were higher than the mean exponents for individual fish as they
 grew i.e., across trials but within individuals; = 0.74, = 0.79, = 0.83, =
 0.85). 4. This variation in scaling relationships, which occurred at
 different hierarchical levels and across time as the fish aged, may have
 implications for bioenergetics and ecosystem modelling, and for individual
 ecological and physiological studies where body mass adjustments are made
 using specific scaling exponents to compare traits of interest between
 different-sized individuals. 5. The findings suggest that studies on fish
 population dynamics should apply metabolic scaling exponents that are
 significantly higher than those used in studies on individuals. However,
 the generality of this assertion should be confirmed by future work, as a
 few existing studies on endotherms (mainly birds) have reported shallower
 scaling relationships for basal metabolic rate between individuals as
 compared to within individuals.
description: Norin and Gamperl
 (2017)_Table S1_data