A Fine-grained Data Set and Analysis of Tangling in Bug Fixing Commits

Context: Tangled commits are changes to software that address multiple concerns at once. For researchers interested in bugs, tangled commits mean that they actually study not only bugs, but also other concerns irrelevant for the study of bugs. Objective: We want to improve our understanding of the prevalence of tangling and the types of changes that are tangled within bug fixing commits. Methods: We use a crowd sourcing approach for manual labeling to validate which changes contribute to bug fixes for each line in bug fixing commits. Each line is labeled by four participants. If at least three participants agree on the same label, we have consensus. Results: We estimate that between 17% and 32% of all changes in bug fixing commits modify the source code to fix the underlying problem. However, when we only consider changes to the production code files this ratio increases to 66% to 87%. We find that about 11% of lines are hard to label leading to active disagreements between participants. Due to confirmed tangling and the uncertainty in our data, we estimate that 3% to 47% of data is noisy without manual untangling, depending on the use case. Conclusion: Tangled commits have a high prevalence in bug fixes and can lead to a large amount of noise in the data. Prior research indicates that this noise may alter results. As researchers, we should be skeptics and assume that unvalidated data is likely very noisy, until proven otherwise.Comment: Status: Accepted at Empirical Software Engineerin

4D-QSAR Study of Some Pyrazole Pyridine Carboxylic Acid Derivatives By Electron Conformational-Genetic Algorithm Method

Introduction: In the present work, pharmacophore identification and biological activity prediction for 86 pyrazole pyridine carboxylic acid derivatives were made using the electron conformational genetic algorithm approach which was introduced as a 4D-QSAR analysis by us in recent years. In the light of the data obtained from quantum chemical calculations at HF/6-311 G** level, the Electron Conformational Matrices of Congruity (ECMC) were constructed by EMRE software. Comparing the matrices, electron conformational submatrix of activity (ECSA, Pha) was revealed that are common for these compounds within a minimum tolerance. A parameter pool was generated considering the obtained pharmacophore

Novel type ketone-substituted metallophthalocyanines: synthesis, spectral, structural, computational and anticancer studies

This work reports on the synthesis and characterization of phthalocyanines (M = Cu(II) (2), Zn(II) (3) In(III) (4) and Co(II) (5)) peripherally tetra-substituted with 1-(4-hydroxyphenyl) propan-1-one. Confirmation of the synthesized phthalocyanine structures are performed with a combination of elemental analysis, FTIR, H-1-NMR, C-13-NMR, UV-vis and MALDI-MS SEM and spectral data. Their aggregation properties were examined in THF by UV-vis. Spectral and photophysical (fluorescence quantum yield) properties of complexes (2-4) were reported in THF (tetrahydrofuran). These results suggest that the metal in the core of the phthalocyanine plays an important role in the fluorescence quantum yields Phi(F) of the synthesized complexes (2-4). Also, the anticancer activities of complexes were studied on MCF-7, MG63, and L929 cell lines. Finally, all synthesized phthalocyanines were investigated by quantum chemical studies. Chemical reactivity parameters such as E-HOMO, E-LUMO, Delta E (HOMO-LUMO energy gap) were calculated by Gaussian software

Endotracheal Surfactant Combined With Budesonide for Neonatal ARDS

Acute respiratory distress syndrome (ARDS) is a clinical condition characterized by acute diffuse inflammatory lung injury and severe hypoxemia. In 2017, the Montreux Consensus defined diagnostic criteria for ARDS in the neonatal period. The management of ARDS includes strict adherence to lung-protective ventilation strategies and therapeutic agents to improve gas exchange. We report two similar cases of premature infants with gestational ages of 23 and 24 weeks diagnosed with neonatal ARDS according to the Montreux definition. These patients developed acute worsening of oxygenation on the 30th and 28th day of life, respectively, while they were ventilated on volume-guarantee assist/control mode. Chest X-rays revealed bilateral diffuse opacity, there were no cardiogenic origins for pulmonary edema, and their oxygenation indexes were >8. Both cases fulfilled the neonatal ARDS criteria and the patients' clinical conditions were associated with late onset neonatal sepsis. After lung recruitment maneuver, the infants began HFO volume-guarantee ventilation and received surfactant treatment. Since they showed a poor short-term response, intratracheal surfactant of 100 mg/kg plus budesonide of 0.25 mg/kg were administered and their oxygenation indexes were reduced stepwise. Both patients survived and were discharged home with spontaneous breathing of room air. Neonatal ARDS is generally an underdiagnosed condition associated with sepsis, pneumonia, and meconium aspiration. Impaired surfactant activity and reduced lung compliance play important roles in its pathophysiology. To our knowledge, this is the first case report indicating the possible therapeutic role of budesonide plus surfactant in ARDS treatment. Since ARDS is an entity not recognized in newborns, we want to emphasize neonatal ARDS diagnosis and underline that the combination of budesonide and surfactant may be a novel therapeutic option in the treatment of ARDS

Synthesis, characterization, biological evaluation, and molecular docking studies of some piperonyl-based 4-thiazolidinone derivatives

Heterocyclic compounds are of particular importance among pharmacologically active compounds. In this study, some piperonyl-based 4-thiazolidinone derivatives (2a-i) were synthesized and characterized by spectroscopic assays. All molecules were tested as enzyme inhibitory factors. These compounds were effective inhibitors of the enzymes acetylcholinesterase (AChE), alpha-glycosidase (alpha-Gly), and the human carbonic anhydrase I and II isoforms (hCA I and II), with K-i values in the range of 8.90-66.51 nM for alpha-Gly, 94.8-289.5 nM for hCA I, 106.3-304.6 nM for hCA II, and 0.55-2.36 nM for AChE. The synthesized molecules were also studied theoretically. Molecular docking calculations were performed to investigate the interaction between the target protein and molecules. CA inhibitor compounds have been clinically used for almost 60 years as antiglaucoma and diuretic drugs. The inhibition of the AChE enzyme results in the blockage of ACh hydrolysis. On the contrary, the design of inhibitor compounds or/and modulators for AChE is of major interest as it is one of the most popular tools to prevent Alzheimer's disease

Ground truth deficiencies in software engineering: when codifying the past can be counterproductive

Many software engineering tools build and evaluate their models based on historical data to support development and process decisions. These models help us answer numerous interesting questions, but have their own caveats. In a real-life setting, the objective function of human decision-makers for a given task might be influenced by a whole host of factors that stem from their cognitive biases, subverting the ideal objective function required for an optimally functioning system. Relying on this data as ground truth may give rise to systems that end up automating software engineering decisions by mimicking past sub-optimal behaviour. We illustrate this phenomenon and suggest mitigation strategies to raise awareness

Volume Guarantee High-Frequency Oscillatory Ventilation in Preterm Infants With RDS: Tidal Volume and DCO2 Levels for Optimal Ventilation Using Open-Lung Strategies

High frequency oscillatory ventilation with volume-guarantee (HFOV-VG) is a promising lung protective ventilator mode for the treatment of respiratory failure in newborns. However, indicators of optimal ventilation during HFOV-VG mode are not identified yet. In this study, we aimed to evaluate optimal high-frequency tidal volume (VThf) and the dissociation coefficient of CO2 (DCO2) levels to achieve normocapnia during HFOV-VG after lung recruitment in very low birthweight infants with respiratory distress syndrome (RDS). Preterm babies under the 32nd postmenstrual week with severe RDS that received HFOV-VG using open-lung strategy between January 2014 and January 2019 were retrospectively evaluated. All included patients were treated with the Drager Babylog VN500 ventilator in the HFOV-VG mode. In total, 53 infants with a mean gestational age of 26.8 +/- 2.3 weeks were evaluated. HFOV mean optimal airway pressure (MAPhf) level after lung recruitment was found to be 10.2 +/- 1.7 mbar. Overall, the mean applied VThf per kg was 1.64 +/- 0.25 mL/kg in the study sample. To provide normocapnia, the mean VThf was 1.61 +/- 0.25 mL/kg and the mean DCO(2)corr was 29.84 +/- 7.88 [mL/kg](2)/s. No significant correlation was found between pCO(2) levels with VThf (per kg) or DCO(2)corr levels. VThf levels to maintain normocarbia were significantly lower with 12 Hz frequency compared to 10 Hz frequency (1.50 +/- 0.24 vs. 1.65 +/- 0.25 mL/ kg, p < 0.001, respectively). A weak but significant positive correlation was found between mean airway pressure (MAPhf) and VThf levels. To our knowledge, this is the largest study to evaluate the optimal HFOV-VG settings in premature infants with RDS, using the open-lung strategy. According to the results, a specific set of numbers could not be recommended to achieve normocarbia. Following the trend of each patient and small adjustments according to the closely monitored pCO(2) levels seems logical