Find research datasets worth reusing

opencc-zeroAug 2023View details →

Data from: Evaluation of fecal metabarcoding for studying the diets of sympatric dusky salamanders (Desmognathus)

Amphibian diet studies often rely on visual identification of prey obtained through forced regurgitation or dissection. These approaches are somewhat invasive and often lack taxonomic specificity, which can discourage diet studies involving at-risk species and limit fine-scale investigations of diet composition. Here, we employ and assess a non-invasive molecular technique to characterize the diets of three co-occurring stream-dwelling salamander species (Desmognathus ocoee, Desmognathus monticola, and Desmognathus quadramaculatus) and investigate possible dietary partitioning within and among species. We used DNA metabarcoding to classify the arthropod prey communities from fecal samples of field-collected salamanders and investigated associations with predator species and snout-vent length (SVL). Of 200 salamanders captured and held for 24 hrs, 38 (19%) produced fecal samples containing arthropod DNA. We identified 53 prey taxa, of which 27 we could classify to species, 12 to genus, 10 to family, and 4 to order. We found no evidence of dietary partitioning among species or by SVL. Individual fecal samples generally contained few taxa, and few taxa were shared among samples, suggesting that our sample size likely limited the power of our inference. Our results support the utility of fecal metabarcoding as a non-invasive and taxonomically precise alternative to traditional diet analysis techniques. However, researchers should also consider the challenges associated with fecal metabarcoding (e.g., infrequent defecation by study organisms) before using it to complement more traditional methods.

data for the evaluation of curcumin as organogel

This project contains data for the evaluation of curcumin as organogel,  the following underlying data: As file name and content 1. amplutiude sweep.xlsx sublimantory result of amplitude sweep test.  2. Antibacterial activity of curcumin.xlsx                          Antibacterial activity of curcumin 3. ex.vivo permeation of 10 P400.xlsx           in vivo permeation of 10 P400 4. frequency sweep.xlsx       frequency sweep study           5. in vivo permeation .xlsx                   In vivo CUR permeation study 6. Oil binding capacity.xlsx          shows that the Oil binding capacity of organogels in T80 was considerably lower than the organogels in SO, OO, and P400. 7. Release of curcumin.xlsx                 spreadability and greater release of CUR

opencc-by-4.0Mar 2023View details →

Material suplementar para o artigo: Usability Evaluation of mobile banking applications in the context of the elderly in a city of Ceará

Material suplementar: <ol> <li>Questionário diagnóstico</li> <li>Questionário pós-teste</li> <li>Questionário diagnóstico questões abertas</li> <li>Questionário pós-teste questões abertas</li> <li>TCLE</li> </ol>

Data set for the publication " Evaluation of the Accuracy and Frequency Response of Medium-Voltage Instrument Transformers under the Combined Influence Factors of Temperature and Vibration"

This is dataset for paper published: Agazar, M.; Istrate, D.; Pradayrol, P. Evaluation of the Accuracy and Frequency Response of Medium-Voltage Instrument Transformers under the Combined Influence Factors of Temperature and Vibration. Energies 2023, 16, 5012. https://doi.org/10.3390/en16135012

Balancing Accuracy and Evaluation Overhead in Simulation Point Selection

This is the dataset collected for the paper "Balancing Accuracy and Evaluation Overhead in Simulation Point Selection" published at IISWC 2023. It contains 710850 SimPoint configurations and their statistics collected over 22 SPEC2017 benchmarks.

openMar 2023View details →

Dataset for Evaluating the Construct Validity of the Charité Alarm Fatigue Questionnaire

These are the datasets that we used for evaluating the construct validity of the Charité Alarm Fatigue Questionnaire (CAFQa) in a forthcoming publication. All items were answered on a 5-point Likert scale and were scored by us as follows: -2/“I do not agree at all”, -1/“I do not agree”, 0/“I agree in part”, 1/“I agree”, 2/"I very much agree". A previous version of this upload included only the data of Study 1. A new version provides the data of Study 2. Please refer to the methods section of the forthcoming publication for more details. Variable names and their corresponding item. Items marked with <table><tbody><tr> <th>Variable Name</th> <th>CAFQa Item</th> </tr> </tbody><tbody> <tr> <td>procedural_instruction</td> <td>In my ward, procedural instruction on how to deal with alarms is regularly updated and shared with all staff.a</td> </tr> <tr> <td>respond_quickly</td> <td>Responsible personnel respond quickly and appropriately to alarms.a</td> </tr> <tr> <td>motivation_decrease</td> <td>With too many alarms on my ward, my work performance, and motivation decrease.</td> </tr> <tr> <td>physical_symptoms</td> <td>Too many alarms trigger physical symptoms for me, e.g., nervousness, headaches, and sleep disturbances.</td> </tr> <tr> <td>ward_floor</td> <td>The acoustic and visual monitor alarms used on my ward floor and in my nurse station allow me to assign the patient, the device, and the situation clearly.a</td> </tr> <tr> <td>reduce_concentration</td> <td>Alarms reduce my concentration and attention.</td> </tr> <tr> <td>alarm_limits</td> <td>Alarm limits are regularly adjusted based on patients' clinical pictures (e.g., blood pressure limits for conditions after bypass surgery).a</td> </tr> <tr> <td>interrupt_workflow</td> <td>My or neighboring patients' alarms or crisis alarms frequently interrupt my workflow.</td> </tr> <tr> <td>alarms_confuse</td> <td>There are situations when alarms confuse me.</td> </tr> </tbody> </table>                       Other variables in the data set. <table><tbody><tr> <th>Variable Name</th> <th>Explanation</th> </tr> </tbody><tbody> <tr> <td>self_reported_AF</td> <td>self-estimated alarm fatigue in percent</td> </tr> <tr> <td>estimated_false_alarms</td> <td>perceived rate of false alarms in the participant's ICU</td> </tr> <tr> <td>monthly_time_on_ICU</td> <td>the average number of workdays per month in an intensive care or monitoring area</td> </tr> <tr> <td>ICU_experience</td> <td>number of years/months of ICU experience</td> </tr> <tr> <td>profession</td> <td>physician, nurse, or supporting nurse</td> </tr> </tbody> </table>               Members of the Study Group in alphabetical order: Dr. med. Mirza Aghamov1, Prof. Dr. med. Manfred Blobner2, Prof. Dr. med. Ulrich Frey3, Prof. Dr. Christian von Heymann4, Prof. Dr. med. Bettina Jungwirth1, Dr. med. Dragutin Popovic4, Prof. Dr. med. Michael Sander5. 1: Department of Anesthesiology and Intensive Care Medicine, University Hospital Ulm, Ulm University, Ulm, Germany 2: Technical University Munich, School of Medicine, Klinikum Rechts der Isar, Department of Anaesthesiology & Intensive Care Medicine, Munich, Germany 3: Department for Anesthesiology, Surgical Intensive Care, Pain and Palliative Medicine, Marien Hospital Herne – Universitätsklinikum der Ruhr-Universität Bochum, Herne, Germany 4: Department for Anaesthesiology, Intensive Care Medicine and Pain Therapy, Vivantes Klinikum im Friedrichshain, Berlin, Germany 5: Department for Anaesthesiology, Intensive Care Medicine and Pain Therapy, Justus Liebig University, Giessen, Germany

Sample data for the evaluation of pNARA v1.0

This dataset provides the sample data used in the evaluation of pNARA v1.0. For the AOD evaluation, the pNARA v1.0, MERRA-2, and CAMSRA are NARA-1.0_AOD_2016010100.nc4, MERRA2_400.inst3_2d_gas_Nx.20160101.nc4, and cams_aods_20160101.nc, respectively. The aerosol mass mixing ratios on pressure levels (at 100, 250, 400, 500, 600, 700, 850, 925, and 1000 hPa) for each product are fv3_aeros_2016010100_pll.nc (pNARA v1.0), MERRA2_aeros.20160101.nc4 (MERRA-2), and cams_aeros_20160101.nc (CAMSRA). The aerosol mixing ratios on model level for pNARA v1.0 (NARA-1.0_aero_2016010100.nc4) and MERRA-2 (MERRA2_400.inst3_3d_aer_Nv.20160101.nc4) are also included.

opencc-by-4.0Sep 2022View details →

Inferring microbial co-occurrence network from amplicon data: a systematic evaluation

Supporting data for the manuscript "Inferring microbial co-occurrence network from amplicon data: a systematic evaluation".

opencc-by-4.0Feb 2022View details →

Data from: Evaluating predator control using two non-invasive population metrics: a camera trap activity index and density estimation from scat genotyping

Includes datasets from the Wimmera and Mallee, Victoria, Australia: - Fox camera trap data used to model activity - Fox scat SECR capture and trap files used to model density

opencc-by-4.0Sep 2023View details →

Evaluating Risk Progression in Mental Health Chatbots with Escalating Prompts Dataset

Excel dataset for "Evaluating Risk Progression in Mental Health Chatbots with Escalating Prompts" manuscript.

Data from: Evaluation of breeding distribution and chronology of North American scoters

Aim: North America's scoter species are poorly monitored relative to other waterfowl. Black (Melanitta americana), surf (M. perspicillata), and white-winged (M. deglandi) scoter abundance and trend estimates are thus uncertain in many parts of these species' ranges. The most extensive source of waterfowl abundance and distribution data in North America is the Waterfowl Breeding Population and Habitat Survey (WBPHS). Although the WBPHS effectively monitors most species, both its timing and geographic coverage may not allow for accurate scoter monitoring. Therefore, our goal was to better define when and where scoters breed to help interpret survey results and optimize survey methods for scoters. Location: Canadian boreal shield, taiga shield, and low-Arctic tundra; Alaska. Taxon: Scoters (Genus: Melanitta) Methods: We integrated satellite telemetry tracking data from scoters marked at multiple molting, staging, breeding, and wintering areas along the Atlantic and Pacific coasts to quantify continent-wide breeding chronology and distribution. We also examined possible drivers of variation in timing of arrival, length of stay, and departure at nesting locations. Results: We documented a northwest-to-southeast distribution of breeding sites across Alaska and Canada. On average, scoters arrived at nest sites on June 1. Surf scoters arrived earliest, stayed for shorter periods, and departed earliest. Pacific-wintering scoters began breeding earlier than Atlantic-wintering birds. Additionally, birds arrived at nesting locations earlier in years with earlier snowmelt, and later snowmelt reduced lengths of stay for males. Breeding chronology also varied by age group, with adults arriving earlier than subadults. Main conclusions: Our study is the first to comprehensively describe spatial variation in timing of breeding of both Atlantic and Pacific populations of all three scoter species across North America. Our results increase our understanding of how current surveys enumerate scoters and will inform possible supplemental efforts to improve continental monitoring of scoter populations.

Evaluating the efficacy of using GPS satellite transmitters to assess movement of bigheaded carp in a riverine system

We have evaluated the feasibility of using GPS satellite transmitters on invasive bigheaded carp species, silver carp, and bighead carp, that could determine patterns of movement, identify potential feeding and spawning areas, and inform a comprehensive monitoring and commercial removal program in the Illinois River Waterway system in the United States. Despite a wealth of information on bigheaded carp movement from acoustic and radio telemetry, a finer-scale approach to understanding habitat use and daily surfacing trends in movement would strengthen management efforts. Custom Fastloc™-GPS data-logging transmitters (with radio telemetry capability) manufactured by Sirtrack™ were tethered to adult bigheaded carp in field experiments. Sixteen field-deployed transmitters were recovered and yielded 490 individual GPS waypoints when transmitters were attached to fish. We observed movement rates within the Dresden Island Reach of the Illinois River Waterway of approximately 16 river km, and movement in and out of backwater habitats, and the warm-water discharge of a nuclear generating station. We have demonstrated the use of this technology to monitor bigheaded carp and will use the information gained from this study to inform future work with remotely accessed, real-time, Argos satellite-linked prototypes. Fine-scale accuracies, fast acquisition speeds, and the ability to gather real-time data make this a promising tool and is one of the first uses of GPS technology to track fish movement in a riverine system. Continued exploration to improve tag retention efficiency will enhance its utility for continued invasive carp management.

opencc-by-4.0Sep 2023View details →

Evaluating plant lineage losses and gains in temperate forest understories - data and scripts

## Raw data and code to accompany the research entitled "Plant lineage losses and gains in temperate forest understories" by Padullés Cubino et al. (2023). In preparation. # There are two folders with (1) "data" and (2) "scripts". # The "data" folder contains two additional folders ("Input" and "Output") with CSV files with all the data used for analysis and produced from them. These data files are accompanied by a "metadata.xlsx" file with data descriptions. # The "scripts" folder contains three scripts for the analyses described in the manuscript: # H1_H4_H5_H6_forestreplot.R -> tests for hypotheses 1, 4, and 6. # H2_H3_forestreplot.R -> tests for hypotheses 2 and 3. # node.mean_function_forestreplot.R -> R function necessary to test H2 (load before running the code in "H2_H3_forestreplot.R". # If anything is unclear, please contact the corresponding author for clarification (padullesj@gmail.com).

opencc-by-4.0Sep 2023View details →

Evaluation of multi-season convection permitting atmosphere - mixed layer ocean simulations of the Maritime Continent.

Supporting data for figures in GMD draft paper: Evaluation of multi-season convection permitting atmosphere - mixed layer ocean simulations of the Maritime Continent.

Associated model data for: Size-selective predation effects on juvenile Chinook salmon cohort survival off Central California evaluated with an individual-based model

This dataset corresponds to the paper "Size-selective predation effects on juvenile Chinook salmon cohort survival off Central California evaluated with an individual-based model" which is in press at Fisheries Oceanography. The abstract for this paper is as follows: Variation in the recruitment of salmon is often found to be correlated with marine climate indices, but mechanisms behind environment-recruitment relationships remain unclear and correlations often break down over time. We used an ecosystem modeling approach to explore bottom-up and top-down mechanisms linking a variable environment to salmon recruitment variations. Our ecosystem model incorporates a regional ocean circulation sub-model for hydrodynamics, a nutrient-phytoplankton-zooplankton sub-model for producing planktonic prey fields, and an individual-based model (IBM) representing juvenile Chinook salmon (Oncorhynchus tshawytscha), combined with observations of foraging distributions and diet of a seabird predator. The salmon IBM consists of modules, including a juvenile salmon growth module based on temperature and salmon-prey availability, a behavior-based movement module, and a juvenile salmon predation mortality module based on juvenile salmon size distribution and predator-prey interaction probability. Seabird-salmon interactions depend on spatial overlap and juvenile salmon size, whereby salmon that grow past the size range of the prey distribution of the predator will escape predation. We used a 21-year historical simulation to explore interannual variability in juvenile Chinook salmon growth and predation-mediated survival under a range of ocean conditions for sized-based mortality scenarios. We based a series of increasingly complex predation scenarios on seabird observational data to explore variability in predation mortality on juvenile Chinook salmon. We initially included information about the predator spatial distribution, then added population size, and finally, the predator's diet percentage made up of juvenile salmon. Model agreement improves with added predator complexity, especially during periods when predator abundance is high. Overall, our model found that when the fraction of juvenile salmon in seabird diet increased relative to alternate prey (e.g., Northern anchovy Engraulis mordax, and juvenile rockfish Sebastes spp.), there was a concomitant decrease in salmon cohort survival during their first year at sea.

openmit-licenseApr 2024View details →

A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods

This repository contains all the datasets used for benchmarking drug repositioning methods based on heterogeneous networks, including drug-drug similarity, disease-disease similarity, and drug-disease associations. The repository consists of: <ol> <li>Name or keyword information for drugs and diseases information contained in the dataset</li> <li>Inputs needed for different drug repositioning methods: multiple drug similarity matrices,multiple disease similarity matrices, and drug-disease associations matrices.</li> </ol>     <blockquote> Please cite us : Yinghong Li, Yinqi Yang, Zhuohao Tong, Yu Wang, Qin Mi, Mingze Bai, Guizhao Liang, Bo Li, Kunxian Shu, A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods, Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae172, <a href="https://doi.org/10.1093/bib/bbae172">https://doi.org/10.1093/bib/bbae172</a> </blockquote>

Adders are Amazing project evaluation of attitudes and connectedness to nature

<ol> <li>Adder (Vipera berus) populations are experiencing declines in many countries, including the UK. Perceptions of adders and other venomous snakes are generally negative, making conservation of these species a challenge, and persecution remains within the top five perceived causes for adder declines in the UK. Improved understanding and attitudes are needed to support current conservation efforts. However, ensuring these positive attitudes continue into the future relies on addressing children's loss of connection to nature, and intervention at this early attitude-formation stage can be crucial for traditionally 'unpopular' species, such as snakes.</li> <li>An adder-focussed public-engagement project, Adders are Amazing!, was carried out in Pembrokeshire, UK, in 2018–19 to improve understanding and attitudes towards adders using a blended science-creative arts approach. The project included half-day primary school-based workshops to inform 111 pupils aged 8 to 11 about adder ecology, alongside creative art experiences. Questionnaires were used to measure the children's attitudes towards adders and their nature connectedness both before and after the workshops and these were compared with equivalent questionnaires carried out at a control school (57 pupils) where no workshops were conducted. </li> <li>The project demonstrated that engagement that blends both art and science can significantly change attitudes towards adders without any direct contact with the animals themselves; specifically, participants' scores for 'Wonder', 'Learning Interest' and 'Conservation Concern' increased. The workshops also significantly increased measures of the children's general connectedness to nature (specifically, 'Enjoyment of Nature' and 'Responsibility for Nature').</li> <li>We recommend conservation bodies focus on, and not shy away from, so-called 'unpopular' species, to promote understanding and acceptance of these species and support their conservation. Blended arts-science initiatives, which can be easily adapted to suit a wide range of species and the artistic practices of local communities, are an effective way to achieve this.</li> </ol>

Identifying Mozambique's most critical areas for plant conservation: An evaluation of protected areas and important plant areas

Successful protected area networks must represent biodiversity across taxonomic groups. However, too often plant species are overlooked in conservation planning, and the resulting protected areas may, as a result, fail to encompass the most important sites for plant diversity. The Mozambique Tropical Important Plant Areas project sought to promote the conservation of Mozambique's flora through the identification of Important Plant Areas (IPAs). Here, we use the Weighted Endemism including Global Endangerment (WEGE) index to identify the richest areas for rare and endemic plants in Mozambique and subsequently evaluate how well represented these hotspots are within the current protected area and IPA networks. We also examine the congruence between IPA and protected areas to identify opportunities for strengthening the conservation of plants in Mozambique. We found that high WEGE scores, representing areas rich in endemic/near‐endemic and threatened species, predict the presence of IPAs in Mozambique, but do not predict the presence of protected areas. We also find that there is limited overlap between IPAs and protected areas in Mozambique. We demonstrate how IPAs could be an important tool for ensuring priority sites for plant diversity are included within protected area network expansions, particularly following the adoption of the "30 by 30" target agreed within the post‐2020 Convention on Biological Diversity framework, with great potential for this method to be replicated elsewhere in the global tropics.

Data from: Evaluating the accuracy of methods for detecting correlated rates of molecular and morphological evolution

Determining the link between genomic and phenotypic change is a fundamental goal in evolutionary biology. Insights into this link can be gained by using a phylogenetic approach to test for correlations between rates of molecular and morphological evolution. However, there has been persistent uncertainty about the relationship between these rates, partly because conflicting results have been obtained using various methods that have not been examined in detail. We carried out a simulation study to evaluate the performance of five statistical methods for detecting correlated rates of evolution. Our simulations explored the evolution of molecular sequences and morphological characters under a range of conditions. Of the methods tested, Bayesian relaxed-clock estimation of branch rates was able to detect correlated rates of evolution correctly in the largest number of cases. This was followed by correlations of root-to-tip distances, Bayesian model selection, independent sister-pairs contrasts, and likelihood-based model selection. As expected, the power to detect correlated rates increased with the amount of data, both in terms of tree size and number of morphological characters. Likewise, greater among-lineage rate variation in the data led to improved performance of all five methods, particularly for Bayesian relaxed-clock analysis when the rate model was mismatched. We then applied these methods to a data set from flowering plants and did not find evidence of a correlation in evolutionary rates between genomic data and morphological characters. The results of our study have practical implications for phylogenetic analyses of combined molecular and morphological data sets, and highlight the conditions under which the links between genomic and phenotypic rates of evolution can be evaluated quantitatively.

Evaluating the use of non‐invasive hair sampling and ddRAD to characterize populations of endangered species: Application to a peripheral population of the European mink

The application of next‐generation sequencing (NGS) to non‐invasive samples is one of the most promising methods in conservation genomics, but these types of samples present significant challenges for NGS. The European mink (Mustela lutreola) is critically endangered throughout its range. However, important aspects such as census size and inbreeding remain still unknown in many populations, so it is crucial to develop new methods to monitor this species. In this work, we placed hair tubes along riverbanks in a border area of the Iberian population, which allowed the genetic identification of 76 European mink hair samples. We then applied a reduced representation genomic sequencing (ddRAD) technique to a subset of these samples to test whether we could extract sufficient genomic information from them. We show that several problems with the DNA, including contamination, fragmentation, oxidation, and possibly sample mixing, affected the samples. Using various bioinformatic techniques to reduce these problems, we were able to unambiguously genotype 19 hair samples belonging to six individuals. This small number of individuals showed that the demographic status of the species in this peripheral population is worse than expected. The data obtained also allowed us to perform preliminary analyses of relatedness and inbreeding. Although further improvements in sampling and analysis are needed, the application of the ddRAD technique to non‐invasively obtained hairs represents a significant advance in the genomic study of endangered species.