Find research datasets worth reusing

Data from: Routine blood tests are associated with short term mortality and can improve emergency department triage: a cohort study of >12,000 patients

Background: Prioritization of acutely ill patients in the Emergency Department remains a challenge. We aimed to evaluate whether routine blood tests can predict mortality in unselected patients in an emergency department and to compare risk prediction with a formalized triage algorithm. Methods: A prospective observational cohort study of 12,661 consecutive admissions to the Emergency Department of Nordsjælland University Hospital during two separate periods in 2010 (primary cohort, n = 6279) and 2013 (validation cohort, n = 6383). Patients were triaged in five categories by a formalized triage algorithm. All patients with a full routine biochemical screening (albumin, creatinine, c-reactive protein, haemoglobin, lactate dehydrogenase, leukocyte count, potassium, and sodium) taken at triage were included. Information about vital status was collected from the Danish Central Office of Civil registration. Multiple logistic regressions were used to predict 30-day mortality. Validation was performed by applying the regression models on the 2013 validation cohort. Results: Thirty-day mortality was 5.3%. The routine blood tests had a significantly stronger discriminative value on 30-day mortality compared to the formalized triage (AUC 88.1 [85.7;90.5] vs. 63.4 [59.1;67.5], p < 0.01). Risk stratification by routine blood tests was able to identify a larger number of low risk patients (n = 2100, 30-day mortality 0.1% [95% CI 0.0;0.3%]) compared to formalized triage (n = 1591, 2.8% [95% CI 2.0;3.6%]), p < 0.01. Conclusions: Routine blood tests were strongly associated with 30-day mortality in acutely ill patients and discriminatory ability was significantly higher than with a formalized triage algorithm. Thus routine blood tests allowed an improved risk stratification of patients presenting in an emergency department.

Data from: Water immersion decreases sympathetic skin response during color–word Stroop Test

Water immersion alters the autonomic nervous system (ANS) response in humans. The effect of water immersion on executive function and ANS responses related to executive function tasks was unknown. Therefore, this study aimed to determine whether water immersion alters ANS response during executive tasks. Fourteen healthy participants performed color–word-matching Stroop tasks before and after non-immersion and water immersion intervention for 15 min in separate sessions. The Stroop task-related skin conductance response (SCR) was measured during every task. In addition, the skin conductance level (SCL) and electrocardiograph signals were measured over the course of the experimental procedure. The main findings of the present study were as follows: 1) water immersion decreased the executive task-related sympathetic nervous response, but did not affect executive function as evaluated by Stroop tasks, and 2) decreased SCL induced by water immersion was maintained for at least 15 min after water immersion. In conclusion, the present results suggest that water immersion decreases the sympathetic skin response during the color–word Stroop test without altering executive performance.

Data from: Improved demethylation in ecological epigenetic experiments: testing a simple and harmless foliar demethylation application

1. Experimental demethylation of plant DNA enables testing for epigenetic effects in a simple and straightforward way without the use of expensive and laborious DNA sequencing. Plants are commonly demethylated during their germination with the application of agents such as 5-azacytidine (5-azaC). However, this approach can cause unwanted effects such as underdeveloped root systems and high mortality of treated plants, hindering a full comparison with untreated plants, and can be applied only on plant reproducing by seeds. Here we test a simple alternative method of plant demethylation, designed to overcome the shortcomings of the germinating method. 2. We compared a novel method of demethylating plants, based on periodical spraying of 5-azaC aqueous solution on established seedlings, with the previous method in which seeds were germinated directly in 5-azaC solution. We quantified the amount of methylated DNA and measured various aspects of plant performance. Also, we demonstrated its applicability in ecological epigenetic experiments, by testing transgenerational effects of plant-plant competition. 3. We found that the spray application had similar DNA-demethylating efficiency than the germination method, particularly in the earlier phases of plant development, but without unwanted effects. The spray application method did not reduce plant growth and performance compared to untreated plants, as opposed to the traditional method which showed reduced growth. Also, the spray application method equalized the epigenetically-modified plant features of seedlings coming from plants grown under competition and plants growing without competition, demonstrating its application in ecological epigenetic experiments. 4. We conclude that regular spraying of 5-azaC solution onto established seedlings surpassed the germination-in-solution method in terms of vigor and fitness of treated plants. This novel method could thus be better suited for experimental studies seeking valuable insights into ecological epigenetics. Furthermore, the spray method can be suitable for clonal species reproducing asexually, and, most importantly, it opens the possibility of community-level experimental demethylation of plants.

Data from: Long-term test–retest reliability of striatal and extrastriatal dopamine D2/3 receptor binding: study with [11C]raclopride and high-resolution PET

We measured the long-term test–retest reliability of [11C]raclopride binding in striatal subregions, the thalamus and the cortex using the bolus-plus-infusion method and a high-resolution positron emission scanner. Seven healthy male volunteers underwent two positron emission tomography (PET) [11C]raclopride assessments, with a 5-week retest interval. D2/3 receptor availability was quantified as binding potential using the simplified reference tissue model. Absolute variability (VAR) and intraclass correlation coefficient (ICC) values indicated very good reproducibility for the striatum and were 4.5%/0.82, 3.9%/0.83, and 3.9%/0.82, for the caudate nucleus, putamen, and ventral striatum, respectively. Thalamic reliability was also very good, with VAR of 3.7% and ICC of 0.92. Test-retest data for cortical areas showed good to moderate reproducibility (6.1% to 13.1%). Our results are in line with previous test–retest studies of [11C]raclopride binding in the striatum. A novel finding is the relatively low variability of [11C]raclopride binding, providing suggestive evidence that extrastriatal D2/3 binding can be studied in vivo with [11C]raclopride PET to be verified in future studies.

opencc-zeroDec 2014View details →

Data from: Simulating regimes of chemical disturbance and testing impacts in the ecosystem using a novel programmable dosing system

Pollution is a global issue at the frontier between ecology, environmental science, management, engineering and policy. Legislation requires experiments to determine how much contamination an ecosystem can absorb before there are structural or functional changes. Yet, existing methods cannot realistically simulate regimes of chemical disturbance and determine impacts to assemblages in ecosystems. This is because they lack ecologically relevant species and biotic interactions, are logistically difficult to set-up, and lack environmentally relevant regimes of chemical and abiotic disturbance that organisms experience in polluted areas. We solved these long-standing environmental, logistical, experimental and ecological problems by developing a programmable dosing-system. This dosing-system simulates, in situ, regimes of chemical disturbance to assemblages by manipulating the concentration, duration, timing and frequency of pollutants to which they are exposed. Experiments with priority pollutants (the metal copper and the biocide Chlorpyrifos) and mussel assemblages revealed consistent plumes of contamination within patches of mussel. Mussels at the sources of experimental plumes of copper created by the dosing-system, accumulated 670% more copper in their tissues compared to mussels 0.5-50 m away. In addition, when mussels were exposed to increasing concentrations of copper there was a concomitant increase in the amount of copper in the tissues of mussels. Combining the dosing-system with an established hierarchy of ecotoxicological assays revealed mussel assemblages exposed to copper and/or Chlorpyrifos had 40-70% fewer worms, whilst Chlorpyrifos alone caused an 81% reduction in the number of amphipods and caused mussels to filter 48% fewer particles from the water. Combinations of copper and/or Chlorpyrifos had no effects on the abundance of crabs, the respiratory functions of assemblages or the viability of molluscan haemocytes. As global contamination accelerates we discuss how this technological advance will enable a diverse array of ecologists, mangers and policy-makers to understand and reduce pollution.

opencc-zeroDec 2017View details →

Data from: Testing and interpreting the shared space-environment fraction in variation partitioning analyses of ecological data

Variation partitioning analyses combined with spatial predictors (Moran's eigenvector maps, MEM) are commonly used in ecology to test the fractions of species abundance variation purely explained by environment and space. However, while these pure fractions can be tested using a classical residuals permutation procedure, no specific method has been developed to test the shared space-environment fraction (SSEF). Yet, the SSEF is expected to encompass a major driver of community assembly, that is, an induced spatial dependence effect (ISD; i.e. the reflection of a spatially structured habitat filter on a species distribution). A reliable test of this fraction is therefore crucial to properly test the presence of an ISD on ecological data. To bridge the gap, we propose to test the SSEF through spatially-constrained null models: torus-translations, and Moran spectral randomisations. We investigated the type I error rate and statistical power of our method based on two real environmental datasets and simulations of tree distributions. Ten types of tree distribution displaying contrasted aggregation properties were simulated, and their abundances were sampled in 153 regularly-distributed 20 × 20 m quadrats. The SSEF was tested for 1000 simulated tree distributions either unrelated to the environment, or filtered by environmental variables displaying contrasting spatial structures. The method proposed provided a correct type I error rate (< 0.05). The statistical power was high (> 0.9) when abundances were filtered by an environmental variable structured at broad scale. However, the spatial resolution allowed by the sampling design limited the power of the method when using a fine-scale filtering variable. This highlighted that an ISD can be properly detected providing that the spatial pattern of the filtering process is correctly captured by the sampling design of the study. An R function to apply the SSEF testing method is provided and detailed in a tutorial.

Data from: Testing the niche breadth-range size hypothesis: habitat specialization versus performance in Australian alpine daisies

Relatively common species within a clade are expected to perform well across a wider range of conditions than their rarer relatives, yet experimental tests of this "niche breadth—range size" hypothesis remain surprisingly scarce. Rarity may arise due to trade-offs between specialization and performance across a wide range of environments. Here we use common garden and reciprocal transplant experiments to test the niche breadth—range size hypothesis, focusing on four common and three rare endemic alpine daisies (Brachyscome spp.) from the Australian Alps. We used three experimental contexts: 1) alpine reciprocal seedling experiment: a test of seedling survival and growth in three alpine habitat types differing in environmental quality and species diversity, 2) warm environment common garden: a test of whether common daisy species have higher growth rates and phenotypic plasticity, assessed in a common garden in a warmer climate and run simultaneously with experiment 1, and 3) alpine reciprocal seed experiment: a test of seed germination capacity and viability in the same three alpine habitat types as in experiment 1. In the alpine reciprocal seedling experiment, survival of all species was highest in the open heathland habitat where overall plant diversity is high, suggesting a general, positive response to a relatively productive, low-stress environment. We found only partial support for higher survival of rare species in their habitats of origin. In the warm environment common garden, three common daisies exhibited greater growth and biomass than two rare species, but the other rare species performed as well as the common species. In the alpine reciprocal seed experiment, common daisies exhibited higher germination across most habitats, but rare species maintained a higher proportion of viable seed in all conditions, suggesting different life history strategies. These results indicate that some but not all rare, alpine endemics exhibit stress tolerance at the cost of reduced growth rates in low-stress environments compared to common species. Finally, these findings suggest the seed stage is important in the persistence of rare species, and they provide only weak support at the seedling stage for the niche breadth-range size hypothesis.

opencc-zeroDec 2013View details →

Data from: Investigating evolutionary lag using the species-pairs evolutionary lag test (SPELT)

For traits showing correlated evolution, one trait may evolve more slowly than the other, producing evolutionary lag. The species-pairs evolutionary lag test (SPELT) uses an independent contrasts based approach to detect evolutionary lag on a phylogeny. We investigated the statistical performance of SPELT in relation to degree of lag, sample size (species pairs), and strength of association between traits. We simulated trait evolution under two models: one in which trait X changes during speciation and the lagging trait Y catches up as a function of time since speciation; and another in which trait X evolves in a random walk and the lagging trait Y is a function of X at a previous time period. Type I error rates under "no lag" were close to the expected level of 5%, indicating that the method is not prone to false-positives. Simulation results suggest that reasonable statistical power (80%) is reached with around 140 species pairs, although the degree of lag and trait associations had additional influences on power. We applied the method to two datasets and discuss how estimation of a branch length scaling parameter (κ) can be used with SPELT to detect lag.

opencc-zeroDec 2018View details →

Data from: Incorporating the disease triangle framework for testing the effect of soil-borne pathogens on tree species diversity

1. The enemies-induced Janzen-Connell (JC) effect, a classic model invoking conspecific negative density dependence (CNDD) and distance dependence, is a primary biodiversity maintenance hypothesis. Yet, conflicting evidence for the JC effect leads to disagreement about its role in maintaining forest diversity. 2. We focus this review on soil-borne pathogens, which are the primary agent inducing the JC effect in many forest ecosystems. Although the test of the pathogen-induced JC effect in ecology critically rests on the seedling mortality caused by soil pathogens, what has not been explicitly explored in the early literature but has increasingly received attention is the long-recognized fact that the environment can alter virulence of pathogens and host susceptibility (and thus pathogen-host interactions), as predicted by the classic disease triangle framework enlightened by pathology research in agricultural systems. 3. Here, following the disease triangle framework we review evidence on how the pathogen-induced JC effect may be contingent on context (e.g., environmental conditions, pathogen inoculum load, and genetic divergence in host and pathogen populations). The reviewed evidence reveals and clarifies the conditions where pathogens may or may not cause disease to hosts, thus contributing to reconciling the inconsistent results about the pathogen-induced JC effect in the literature. The context-dependence of the disease triangle predicts that the pathogen-induced JC effect would change under global change. 4. Gaining insights from evidence that the pathogen-induced JC effect is context-dependent, we suggest that future tests on the JC hypothesis be conducted under the framework of disease triangle, and we stress the necessity by controlling the effect of context factors on plant-pathogen interactions when testing for the JC effect. We conclude the review by proposing three lines of future research for testing the importance of the JC effect in maintaining global forest tree species diversity, with a particular emphasis on testing the effect of global warming on the strength of pathogen-host interactions for better predicting changes of forest biodiversity under climate change.

restrictedcc-by-4.0Feb 2024View details →

Data for: Fossil samples archive functional diversity in marine ecosystems: An empirical test from a present-day coastal environment (Tyler and Kowalewski)

Data associated with "Fossil samples archive functional diversity in marine ecosystems: An empirical test from a present-day coastal environment" by Carrie L. Tyler and Michal Kowalewski. Data include GPS coordinates for sample localities, variables quantifying multivariate space for all three assemblages, trait data for all species, and the associated R code (Functional Fidelity.zip). Abundance data is available in Tyler and Kowalewski (2023) <a href="https://doi.org/10.7717/peerj.15574">10.7717/peerj.15574</a> at <a href="https://github.com/tylercl/Multi-Taxic-Fidelity">https://github.com/tylercl/Multi-Taxic-Fidelity</a> (DOI: 10.5281/zenodo.7871639).

opencc-by-4.0Jun 2023View details →

Test data of published work titled 'Automatic Detection of Colorectal Polyps with Mixed Convolutions and its Occlusion Testing'

Test data of published work titled 'Automatic Detection of Colorectal Polyps with Mixed Convolutions and its Occlusion Testing' includes:<ol><li>Gastrointestinal atlas-Colon Polyp dataset (test dataset)</li><li>Supplementary file containing information of Gastrointestinal atlas-Colon Polyp</li></ol>For more details: <a href="https://link.springer.com/article/10.1007/s00521-023-08762-z">Automatic Detection of Colorectal Polyps with Mixed Convolutions and its Occlusion Testing | Neural Computing and Applications (springer.com) </a>

opencc-by-4.0Aug 2021View details →

Prider testing data and code

The FASTA file sets and the R scripts used for the testing of the processing times of R packages Prider and openPrimeR.

openmit-licenseMay 2022View details →

Genome Annotation Workshop 2022 - Test data

Test datasets for the <a href="https://github.com/EI-CoreBioinformatics/annotation-workshop-2022/wiki">Genome Annotation Workshop 2022</a>

opencc-by-4.0May 2024View details →

Genome Annotation Workshop 2024 - Test data

Test datasets for the <a href="https://github.com/EI-CoreBioinformatics/annotation-workshop-2024/wiki">Genome Annotation Workshop 2024</a>

opencc-by-4.0Jun 2024View details →

Test Data for Comparing Simulation Speed between SPONGE and AMBER

Test Data for Comparing Simulation Speed between SPONGE and AMBER

openJul 2024View details →

Data on IEEE and Synthetic Test Power Systems for Oriol Cartiel's PhD

The data used in my PhD thesis comes from internet repositories (see within files). It is based on detailed information from both IEEE n-bus test power systems and synthetic power grid test cases developed by the scientific community. The dataset, stored in spreadsheet format (.xlsx), includes comprehensive technical details such as line impedances, equivalent internal impedances, locations of generators, load demands and their locations, and shunt element specifications. All values are normalized to per-unit (pu), assuming a base power of 100 MVA. Additionally, the reference to the internet repository is available in the same file for potential further consultation.

opencc-zeroAug 2024View details →

NanoAUV Test 1 data

Before diving into the data please refer to the description of the <a href="https://mbd.pages.rwth-aachen.de/dlr_rdm/data/NanoAUV/intro.html">NanoAUV</a> system and the <a href="https://mbd.pages.rwth-aachen.de/dlr_rdm/">TRIPLE</a> project. The data represented here describes the permittivity measured with respect to depth. The measurement was carried out on 10.09.2024 in the Neumayer station, located in Antarctica, under the campaign name TRIPLE-Phase-2. The surface ice temperature was 240K, atmospheric pressure 1 bar, and 60% humidity. The readings were taken on ice as the IceCraft moved vertically downwards by melting the ice. The data obtained can also be theoretically assessed as here(link). Column: Depth, Vertical Distance, Spatially Varying, Permittivity

opencc-by-4.0Sep 2024View details →

Data and code for training and testing a ResMLP model with experience replay for machine-learning physics parameterization

This directory contains the training data and code for training and testing a ResMLP with experience replay for creating a machine-learning physics parameterization for the Community Atmospheric Model.  The directory is structured as follows: 1. Download training and testing data: https://portal.nersc.gov/archive/home/z/zhangtao/www/hybird_GCM_ML 2. Unzip nncam_training.zip nncam_training     - models        model definition of ResMLP and other models for comparison purposes     - dataloader         utility scripts to load data into pytorch dataset     - training_scripts        scripts to train ResMLP model with/without experience replay     - offline_test        scripts to perform offline test (Table 2, Figure 2) 3. Unzip nncam_coupling.zip nncam_srcmods      - SourceMods           SourceMods to be used with CAM modules for coupling with neural network      - otherfiles           additional configuration files to setup and run SPCAM with neural network      - pythonfiles          python scripts to run neural network and couple with CAM       - ClimAnalysis           - paper_plots.ipynb              scripts to produce online evaluation figures (Figure 1, Figure 3-10)

opencc-by-4.0Dec 2021View details →

Data from Block-on-Ring Wear Tests of Victrex FG340 in Dry Sliding versus AISI 52000 steel

This is re-published copy of an existing publication (<a href="https://dx.doi.org/10.17632/nbz7hs4ckn.1">https://dx.doi.org/10.17632/nbz7hs4ckn.1</a>) The data has been collected during Block-on-Ring Wear Tests on "Victrex PEEK FG340". The tests were done in dry sliding against AISI 52000 steel rings, ground twist-free to 𝑅a = 0.14–0.19 μm, 𝑅z = 1.5–1.9 μm and with a hardness of 60–62 HRc in standard laboratory atmosphere (21–25 °C, 40–60% rH). The research objective was to determine the coefficient of friction of this material pair for use in the calculation of transient temperatures and dimensions during the process of designing a journal bearing. Test conditons were conducted on an ASTM G137-compliant Block-on-Ring tribometer from Tribologic GmbH, Germany. The tests were conducted at 1 MPa in uniform, unidirectional sliding at 1.0 m/s and lasted 6 hours each, resulting in a total sliding distance of 21,600 m for each test. Block cross section was 16 mm² and fiber orientation (if applicable) was nominally parallel (with respect to an ISO 527-1A speciment). Individual test results for the coefficient of friction, the linear, time-dependent wear rate and the counter body temperature were calculated from time-resolved sensor data. For this, data from the running-in phase of each experiment was ignored. For statistical reasons eight individual tests were conducted and - after elimination of outliers using Nalimov's variant of the Grubbs test - arithmetic mean and (frequentist) confidence intervals (95 %) were determined for the aforementioned quantities. This resulted in a COF of 0.28-0.32, a linear, time-dependent wear rate of 0.6 - 1.0 µm/h and a counter body temperature of 31.2 - 32.4 °C. For each of the 8 conducted tests, a plain-text columnar data file is provided ("*.proc"). Instead of including one or more header lines for denoting the meaning, name and unit of each column, a yaml-formatted, human-readable header file is provided ("*.yaml"). Column-indexing starts at 0, i.e. the first column of the data file is represented by index 0. Data and header files are matched by their test ids, which range from 555689 to 555696 in this data set.