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opencc-by-4.0May 2024View details →

An Exploratory Evaluation of Continuous Feedback to Enhance Machine Learning Code Smell Detection

Context: Code smells are symptoms of bad design choices implemented on the source code. To manage and enhance software quality, it is important to be aware of code smells and refactor them whenever possible. As a result, several code smell detection tools and techniques have been proposed over the years. These tools and techniques present different strategies to detect code smells. More recently, machine learning algorithms have also been proposed to support code smell detection. However, we lack empirical evidence on how expert feedback could improve detection of these machine learning based techniques. Objective: This paper aims to propose and evaluate a machine-learning based strategy to improve detection of code smells by means of continuous feedback provided by the system expert. Method: To evaluate the strategy, we follow an experimental design to compare results of the detection before and after the feedback, both when feedback is provided at once and continuously. We focus on four code smells - God Class, Long Method, Feature Envy, and Refused Bequest - detected in twenty Java systems by using five code smell detection tools. We also extracted class- and method-level metrics from the systems for training the machine learning algorithms. Results: We observed that continuous feedback improves the performance of code smell detection. For the detection of God Class, a code smell with a detection performance initially good, we achieved an average improvement of 0.13 in terms of F1. For Refused Bequest, another class-level code smell, we achieved an average improvement of 0.58 in terms of F1 after all interactions of the strategy. For the method-level code smells, Long Method and Feature Envy, we achieved an average improvement of 0.66 and 0.72 in terms of F1, respectively. Conclusions: Our promising results are a stepping stone towards the development of tools relying on continuous feedback for machine learning detection of code smells.

opencc-by-4.0Oct 2023View details →

Data Sets for Evaluation of the Psychometric Properties and Validity of the German Version of the Process Model of Emotion Regulation Scale (PMERQ)

Data files relate to an investigation of the psychometric properties of the German Version of the Process Model of Emotion Regulation Scale (PMERQ). Data set 1 (pmerq_1) contains information regarding the age, gender, ethnicity, and educational status of participants. In addition, responses to the 45 items of the initial translation of the 10-scale PMERQ are included. Data set 2 (pmerq_2) contains identical sociodemographic variables and responses to the 45 items of the revised translation of the 10-scale PMERQ. In addition, data set 2 contains responses to the 16-item German Interpersonal Emotion Regulation Questionnaire (IERQ), the 10-item German Emotion Regulation Questionnaire (ERQ), , the German version of the 10-item Big Five Inventory-10 (BFI-10), the 4-item German version of the Patient Health Questionnaire-4 (PHQ-4), the German version of the Satisfaction with Life Scale (SWLS), and the 17-item German Social Desirability Scale-17 (SES-17). Data set 2 (pmerq_2) contains identical sociodemographic variables and responses to the 45 items of the readability-improved translation of the 10-scale PMERQ. In addition, data set 2 contains responses to the German version of the Satisfaction with Life Scale (SWLS) and the German version of the 9-items UCLA Loneliness Scale (UCLA).

opencc-by-4.0Jul 2023View details →

Quality and Utility of European Cardiovascular and Orthopaedic Registries for the Regulatory Evaluation of Medical Device Safety and Performance Across the Implant Lifecycle: A Systematic Review - Dataset

Background: The European Union Medical Device Regulation (MDR) requires manufacturers to undertake post-market clinical follow-up (PMCF) to assess the safety and performance of their devices following approval and Conformité Européenne (CE) marking. The quality and reliability of device registries for this Regulation have not been reported. As part of the Coordinating Research and Evidence for Medical Devices (CORE-MD) project, we identified and reviewed European cardiovascular and orthopaedic registries to assess their structures, methods, and suitability as data sources for regulatory purposes. Methods: Regional, national and multi-country European cardiovascular (coronary stents and valve repair/replacement) and orthopaedic (hip/knee prostheses) registries were identified using a systematic literature search. Annual reports, peer-reviewed publications, and websites were reviewed to extract publicly available information for 33 items related to structure and methodology in six domains and also for reported outcomes. Results: Of the 20 cardiovascular and 26 orthopaedic registries fulfilling eligibility criteria, a median of 33% (IQR: 14%-71%) items for cardiovascular and 60% (IQR: 28%-100%) items for orthopaedic registries were reported, with large variation across domains. For instance, no cardiovascular and 16 (62%) orthopaedic registries reported patient/ procedure-level completeness. No cardiovascular and 5 (19%) orthopaedic registries reported outlier performances of devices, but each with a different outlier definition. There was large heterogeneity in reporting on items, outcomes, definitions of outcomes, and follow-up durations. Conclusion: European cardiovascular and orthopaedic device registries could improve their potential as data sources for regulatory purposes by reaching consensus on standardised reporting of structural and methodological characteristics to judge the quality of the evidence as well as outcomes.

Dataset: Testing for effects of growth rate on isotope trophic discrimination factors and evaluating the performance of Bayesian stable isotope mixing models experimentally: a moment of truth?

Discerning assimilated diets of wild animals using stable isotopes is well established where potential dietary items in food webs are isotopically distinct. With the advent of mixing models, and Bayesian extensions of such models (Bayesian Stable Isotope Mixing Models, BSIMMs), statistical techniques available for these efforts have been rapidly increasing. The accuracy with which BSIMMs quantify diet, however, depends on several factors including uncertainty in tissue discrimination factors (TDFs; Δ) and identification of appropriate error structures. Whereas performance of BSIMMs has mostly been evaluated with simulations, here we test the efficacy of BSIMMs by raising domestic broiler chicks (Gallus gallus domesticus) on four isotopically distinct diets under controlled environmental conditions, ideal for evaluating factors that affect TDFs and testing how BSIMMs allocate individual birds to diets that vary in isotopic similarity. For both liver and feather tissues, δ13C and δ 15N values differed among dietary groups. Δ13C of liver, but not feather, was negatively related to the rate at which individuals gained body mass. For Δ15N, we identified effects of dietary group, sex, and tissue type, as well as an interaction between sex and tissue type, with females having higher liver Δ15N relative to males. For both tissues, BSIMMs allocated most chicks to correct dietary groups, especially for models using combined TDFs rather than diet specific TDFs, and those applying a multiplicative error structure. These findings provide new information on how biological processes affect TDFs and confirm that adequately accounting for variability in consumer isotopes is necessary to optimize performance of BSIMMs. Moreover, they demonstrate experimentally that these types of models reliably characterize consumed diets when appropriately parameterized.

opencc-zeroApr 2024View details →

dryad36/100

Evaluating the predictors of habitat use and successful reproduction in a model bird species using a large scale automated acoustic array

The emergence of continental to global scale biodiversity data has led to growing understanding of patterns in species distributions, and the determinants of these distributions, at large spatial scales. However, identifying the specific mechanisms, including demographic processes, and determining species distributions remains difficult, as large-scale data are typically restricted to observations of only species presence. New remote automated approaches for collecting data, such as automated recording units (ARUs), provide a promising avenue towards direct measurement of demographic processes, such as reproduction, that cannot feasibly be measured at scale by traditional survey methods. In this study, we analyze data collected by ARUs from 452 survey points across an approximately 1500 km study region to compare patterns in adult and juvenile distributions in the Great Horned Owl (Bubo virginianus). We specifically examine whether habitat associated with successful reproduction is the same as that associated with adult presence. We postulated that congruence between these two distributions would suggest that all areas of the species' range contribute equally to maintenance of the population, whereas significant differences would suggest more specificity in the species' requirements for successful reproduction. We filtered adult and juvenile calls of the species for manual review using automated classification and constructed single season occupancy models to compare land cover and vegetation covariates which significantly predicted presence of each life stage. We found that habitat use by adults was significantly predicted by increasing amounts of forest cover, reduced forest basal area, and lower elevations whereas juvenile presence was significantly predicted only by decreasing amounts of forest cover, a pattern opposite that of adults. These results show that presence of adult Great Horned Owls is not a sufficient proxy for locations at which reproduction occurs, and also demonstrate a highly scalable workflow that could be used for similar analyses in other sound-producing species.

opencc-by-4.0May 2024View details →

Surpassing Threshold Barriers: Evaluating the Efficacy of Nature-Inspired Algorithms in Detecting Applied Refactorings

This page is provided as supplementary material for the article: Surpassing Threshold Barriers: Evaluating the Efficacy of Nature-Inspired Algorithms in Detecting Applied Refactorings. More specifically, we provide the results, the refactorings detected by each tool, as a downloadable JSON file.  Results.json: You can access the results comparing ACA with RefDetect, RefactoringMiner, NSGA-II, and the Greedy algorithm. <ul> <li>Overview of JSON Template: Each entry in this file provides details about commits, including their SHA-1 hash, GitHub URL, and an exhaustive list of refactorings identified in that specific commit. Refactorings are defined by their type (e.g., 'RenameClass') and are accompanied by detailed descriptions of the refactoring. Additionally, the entry specifies the tools that detected the refactoring, such as 'ACA' and 'RefactoringMiner.' The validation field indicates whether the refactoring was confirmed, using 'TP' for true positive and 'FP' for false positive. Optional comment information may be also included.</li> </ul> Times.xlsx: The Excel file containing the time taken by each tool to identify refactoring in each commit. Results.xlsx: The Excel file contains precision, recall, and F-score metrics for all identified refactoring types.

opencc-by-4.0Sep 2021View details →

Raw results of the simulation experiments performed in the educacional study evaluating a guaranteed service

This zip file contains the simulation results, gnuplot script and data files needed to generate the figures showing the simulation  results presented in [1]. [1] Suárez-González A., Rodríguez Rubio R., López-Ardao J.C., López-García C, Herrería-Alonso S. (2021). Educational case study: evaluation of guaranteed service on low earth orbit satellite networks. Proceedings of the 33rd European Modeling & Simulation Symposium (EMSS 2021), pp. 215-219. DOI: https://doi.org/10.46354/i3m.2021.emss.029

opencc-by-4.0Sep 2021View details →

Raw results of the simulation experiments performed to evaluate the Time-to-idle Control Variate ferformance in the single queue case

This zip file contains the simulation results, gnuplot script and data files needed to generate the figures showing the simulation  results presented in [1]. [1] Suárez-González A., López-García C., López-Ardao J.C., Rodríguez Rubio R., Rodríguez Pérez M. (2021). "Time-to-idle Control Variate Performance in the Single Queue Case". Proceedings of the 33rd European Modeling & Simulation Symposium (EMSS 2021), pp. 147-151. DOI: https://doi.org/10.46354/i3m.2021.emss.020

Evaluation of comparative Efficacy of two routes of administration of Carathmus Tinctorius (Medicated Enema and Nasal Administration) as an Adjuvant Therapy with Standard Care With Physiotherapy in the Rehabilitation of Thrombolytic Stroke (Pakshaghat): A Randomized Controlled Trial Protocol

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opencc-zeroAug 2023View details →

dryad36/100

Data from: Evaluating single-cell variability in proteasomal decay

Gene expression is a stochastic process that leads to variability in mRNA and protein abundances even within an isogenic population of cells grown in the same environment. This variation, often called gene-expression noise, has typically been attributed to transcriptional and translational processes while ignoring the contributions of protein decay variability across cells. Here we estimate the single-cell protein decay rates of two degron GFPs in \textit{Saccharomyces cerevisiae} using time-lapse microscopy. We find substantial cell-to-cell variability in the decay rates of the degron GFPs. We evaluate cellular features that explain the variability in the proteasomal decay and find that the amount of 20s catalytic beta subunit of the proteasome marginally explains the observed variability in the degron GFP half-lives. We propose alternate hypotheses that might explain the observed variability in the decay of the two degron GFPs. Overall, our study highlights the importance of studying the kinetics of the decay process at single-cell resolution and that decay rates vary at the single-cell level, and that the decay process is stochastic. A complex model of decay dynamics must be included when modeling stochastic gene expression to estimate gene expression noise.

opencc-by-nc-nd-4.0Jun 2024View details →

The track 1 evaluation dataset of ADD 2022

Audio deepfake detection is an emerging topic, which was included in the ASVspoof 2021. However, the recent shared tasks have not covered many real-life and challenging scenarios. The first Audio Deep synthesis Detection challenge (ADD) was motivated to fill in the gap. The ADD 2022 (<a href="http://addchallenge.cn/add2022">http://addchallenge.cn/add2022</a>) includes three tracks: low-quality fake audio detection (LF), partially fake audio detection (PF) and audio fake game (FG). The LF track focuses on dealing with bona fide and fully fake utterances with various real-world noises etc. The PF track aims to distinguish the partially fake audio from the real. The FG track is a rivalry game, which includes two tasks: an audio generation task and an audio fake detection task. In this paper, we describe the datasets, evaluation metrics, and protocols. We also report major findings that reflect the recent advances in audio deepfake detection tasks. The ADD 2022 dataset is publicly available. This data set is licensed with a CC BY-NC-ND 4.0 license. If you use this dataset, please cite the following paper: <blockquote> Jiangyan Yi, Ruibo Fu, Jianhua Tao, Shuai Nie, Haoxin Ma, Chenglong Wang, Tao Wang, Zhengkun Tian, Ye Bai, Cunhang Fan, Shan Liang, Shiming Wang, Shuai Zhang, Xinrui Yan, Le Xu, Zhengqi Wen, Haizhou Li: ADD 2022: the first Audio Deep Synthesis Detection Challenge. ICASSP 2022: 9216-9220 </blockquote>

Data for: Evaluation of Methods for Eliciting and Specifying Usability Requirements using User Stories: A Controlled Experiment

Este projeto contém os materiais utilizados na pesquisa intitulada Evaluation of Methods for Eliciting and Specifying Usability Requirements using User Stories: A Controlled Experiment: TCLE, Formulário de Caracterização, Cenário, Oráculo, User Stories, Protótipo, Storyboards, Avaliação de ferramentas em escala de Likert e Dados coletados do formulário.

Evaluation of the immunostimulant effect of microvesicles of Lactobacillus acidophilus isolated from wild Rattus norvegicus.

Lactic acid bacteria are components of the microbiota of the gastrointestinal tract in both humans and animals and are widely used as probiotics. The bacterial strain Lactobacillus sp. is the most related to probiotic activity and released membrane microvesicles (MVs). Some of their primary functions are to carry and transmit antigens to the host tissues and modulate the host defense responses. In the present study, Lactobacillus acidophilus was isolated from the ileum of free-living Rattus norvegicus to evaluate the immunostimulant effect of their MVs in two biological models. MVs from L. acidophilus were characterized using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, electron microscopy, and nanoparticle tracking analysis. The immunostimulant effect of MVs from L. acidophilus on ovine abomasal explants, previously stimulated with 30 µg/1h of MVs and subsequently challenged with third-stage larvae (L3) of Haemonchus contortus, was probed, demonstrating a decrease in the percentage of larvae association, and favoring the migration of inflammatory cells to the infection site. In contrast, cells line of the RAW 264.7 were stimulated by 10 µg/3h of MVs from L. acidophilus to evaluate their activation through the expression of transcripts coding for IL-1β and TNF-α. In both cases, the immunostimulatory effects of MVs from L. acidophilus isolated from free-living R. norvegicus were verified, demonstrating that these structures are capable of immunostimulated the evaluated biological models and could carried important antigen that can be considerate in a formulation to promote the intestinal health in livestock production.  The present study is the first report of MVs secreted by L. acidophilus isolated from free-living R. norvegicus caring that this rodent is resistant to many bacterial pathogens that normally affect the gastrointestinal tract of other mammals. In the atachment file we present the data obtained of the porcentage of asocciation and porcentage of mortality of L3 stage larvae from H. contortus in abomasal tissue stimulated with microvesicles from L. acidophilus. In the other hand the expression of IL-1β and TNFα.  mRNA from RAW 264.7 cells stimulated with microvesicles from L. acidophilus.

Evaluation of comparative efficacy of Trayodashang Guggul versus Asitaka Churna Vati in the management of Katigraha (Stiffness in Lumbar Region): A randomized controlled trial protocol

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opencc-by-4.0Dec 2020View details →

Figure 1 in Evaluation on reducing toxicity of fluoxastrobine with doped TiO2 nanoparticles

Figure 1. (A) XRD pattern, (B) SEM images of S–TiO2, and (C) SEM-EDX spectrum.

Technical and user evaluation of mobile application for pedestrian safety

This file contains the evaluation results of the tests carried out a Versailles during the Show project with external participants: <ul> <li>Technical indicators have been collected in one sheet</li> <li>Feedbacks from the user questionnaires have been collected in one other sheet</li> </ul>

opencc-by-4.0Nov 2023View details →

Figure 3 in Degrees of specialism in butterflies: a method for defining levels of specialism and an evaluation of South African species

Figure 3 – Number of South African butterfly species by ESI category.

Dataset for evaluation of AROME and SURFEX-SA forecasts

SQL Dataset for the verification of AROME (first reference) and SURFEX-SA (produced for the paper) predictions of Austrian cities (Vienna, Linz, Klagenfurt and Innsbruck) with TAWES weather station data. In addition, data from the ensemble prediction system C-LAEF are also included. AROME and C-LAEF are originally available on 2.5 km grid, but they were bilinear interpolated to the respective TAWES coodinates. Datasets can be easily read by the verification tool "harp" in R. TAWES observations are free available from the GeoSphere Austria Datahub (second reference).

" Description and evaluation of a new contrail cirrus 2 parameterization in the ARPEGE-Climat atmospheric 3 model " datasets

This repository contains the data files used for the analyses presented in the paper. The dataset includes variables of interest for the two main simulations (CONTFREE and CONTNUDGED) for the year 2019.  <ul> <li>"totcon" variable represents the integrated contrail cirrus coverage.</li> <li>"rst", respectively "rstcotra", represent the net downward shortwave radiation at the top of the atmosphere for the radiative call with contrails perturbation, respectively without perturbation. The difference between these two variables provides the contrail cirrus net downward shortwave radiation contribution. </li> <li>"rlut", respectively "rlutcotra", represent the net upward longwave radiation at the top of the atmosphere for the radiative call with contrails perturbation, respectively without perturbation. The difference between these two variables provides the contrail cirrus net upward longwave radiation contribution. </li> <li>"pissr" represents the probability of the gridbox being ice supersaturated. This variable is provided for pressure levels 200,225, and 250hPa.</li> <li>"clhcalipso" represents the integrated coverage of "high clouds" (>400hPa). </li> </ul>

Dataset for "Diurnal, seasonal, and interannual variations in δ(18O) of atmospheric O2 and its application to evaluate natural/anthropogenic changes in oxygen, carbon, and water cycles" by Ishidoya et al.

The dataset used in the paper "Diurnal, seasonal, and interannual variations in δ(18O) of atmospheric O2 and its application to evaluate natural/anthropogenic changes in oxygen, carbon, and water cycles" by Ishidoya et al. The doi of the preprint of the paper is https://doi.org/10.5194/egusphere-2024-654. The dataset contains the diurnal cycles of delta_atm(18O), delta(O2/N2), y(CO2), and delta(Ar/N2) at Tsukuba, Japan averaged for the period 2013-2022 ("data_for_Fig4.csv"), the rolling average values of delta_atm(18O) and delta(O2/N2) anomalies for 300 data at TKB during August and February, 2017 ("data_for_Fig6.csv"), and the monthly mean values of delta_atm(18O) and the delta(O2/N2) at TKB for the period 2013-2022("data_for_Fig7.csv"). The raw data before averaging are also presented ("raw_data_2013.csv" to "raw_data_2022.csv"). See text of Ishidoya et al. in more details.