Miracle-dz/UniFAR-FTUs huggingface dataset:
Do time of day and developer experience affect commit bugginess?

Modern software is often developed over many years with hundreds of thousands of commits. Commit metadata is a rich source of social characteristics, including the commit's time of day and the experience and commit frequency of its author. The "bugginess" of a commit is also a critical property of that commit. In this paper, we investigate the correlation between a commit's social characteristics and its "bugginess"; such results can be very useful for software developers and software engineering researchers. For instance, developers or code reviewers might be well-advised to thoroughly verify commits that are more likely to be buggy. In this paper, we study the correlation between a commit's bugginess and the time of day of the commit, the day of week of the commit, and the experience and commit frequency of the commit authors. We survey two widely-used open source projects: the Linux kernel and PostgreSQL. Our main findings include: (1) commits submitted between midnight and 4 AM (referred to as late-night commits) are significantly buggier and commits between 7 AM and noon are less buggy, implying that developers may want to double-check their own latenight commits; (2) daily-committing developers produce less-buggy commits, indicating that we may want to promote the practice of daily-committing developers reviewing other developers' commits; and (3) the bugginess of commits versus day-of-week varies for different software projects.
Sparse Subspace Denoising for Image Manifolds

With the increasing availability of high dimensional data and demand in sophisticated data analysis algorithms, manifold learning becomes a critical technique to perform dimensionality reduction, unraveling the intrinsic data structure. The real-world data however often come with noises and outliers, seldom, all the data live in a single linear subspace. Inspired by the recent advances in sparse subspace learning and diffusion-based approaches, we propose a new manifold denoising algorithm in which data neighborhoods are adaptively inferred via sparse subspace reconstruction, we then derive a new formulation to perform denoising to the original data. Experiments carried out on both toy and real applications demonstrate the effectiveness of our method, it is insensitive to parameter tuning and we show significant improvement over the competing algorithms.
An improved variable step size LMS algorithm

The traditional variable step size least mean square (LMS) algorithm has many weakness, such as poor convergence speed and susceptible to noise interference. In order to improve the performance of the algorithm, an improved variable step size LMS algorithm is presented, and it is applied to the noise cancelling system of communication. By using the hyperbolic tangent function, the relationship between step size and error signal is established. In this algorithm, the step size factor is adjusted by the absolute value of the product of the current and former errors. The algorithm also introduces the disturbance of the absolute estimation error to update the tapping vector of the self-adaptive filter. The simulation results show that the proposed algorithm has a faster convergence speed than traditional LMS algorithm and CTanh-LMS algorithm. And it obtains a good results in the noise cancelling system of communication.
Concentration of Antibacterial Agents in Interstitial Tissue Fluid

The concentration of antibacterial agents in the interstitial tissue fluid has been studied in an experimental model using implanted perforated Silastic capsules (tissue cages). Tissue fluid concentrations were always lower than the initial peak concentration in the serum, but for those drugs that were more slowly excreted the tissue fluid was similar to the serum concentration after six hours. In contrast the concentration in the tissue fluid for those drugs that are excreted rapidly was unpredictable, being either negligible or maintained at concentrations significantly better than in the serum. There was no evidence of accumulation in tissue fluid with regular dosage. These results indicate that the tissues may never be exposed to an adequate concentration of some antibacterial agents. This may be of clinical importance in tissue infections. Antibiotics which are rapidly excreted should be given in large enough doses and often enough for adequate blood levels to be maintained, so allowing equilibrium with tissue fluid to be achieved.
Renal Parenchymal Hypoxia, Hypoxia Response and the Progression of Chronic Kidney Disease

Renal parenchymal hypoxia, documented under a variety of clinical conditions, conceivably contributes to the progression chronic kidney disease. In this review, normal physiologic medullary hypoxia and abnormal profiles of renal pO(2) in chronic kidney diseases are presented, and the mechanisms leading to anomalous renal tissue oxygenation are discussed. Direct measurements of pO(2) with oxygen electrodes, immunostaining with pimonidazole (which binds to regions with very low pO(2)), or the detection of hypoxia-inducible factor (HIF)-alpha (which accumulates in hypoxic regions, initiating hypoxia-adaptive responses), all serve to detect the distribution and extent of renal parenchymal hypoxia under experimental settings. The use of BOLD MRI as a noninvasive tool, detecting deoxygenated hemoglobin in hypoxic renal tissues, has evolved from experimental settings to human studies. All these modalities indicate that abnormal renal oxygenation develops under conditions such as chronic glomerular, tubulointerstitial or renovascular disease, in diabetes, hypertension, aging, renal hypertrophy, anemia or obstructive uropathy. Abnormal renal tissue hypoxia modifies the pattern of regional gene expression, evoking a host of adaptive and renoprotective pathways (such as HIF-mediated erythropoietin or heme-oxygenase-1), in parallel with the induction of potentially harmful mediators that participate in the progression of chronic kidney injury. Slowing the progression of chronic kidney disease may be achieved by a better understanding of these parallel processes and the accomplishment of a selective control of such protective and maladaptive responses.
An Enhanced Semantic Layer for Hybrid Recommender Systems: Application to News Recommendation

Recommender systems have achieved success in a variety of domains, as a means to help users in information overload scenarios by proactively finding items or services on their behalf, taking into account or predicting their tastes, priorities, or goals. Challenging issues in their research agenda include the sparsity of user preference data and the lack of flexibility to incorporate contextual factors in the recommendation methods. To a significant extent, these issues can be related to a limited description and exploitation of the semantics underlying both user and item representations. The authors propose a three-fold knowledge representation, in which an explicit, semantic-rich domain knowledge space is incorporated between user and item spaces. The enhanced semantics support the development of contextualisation capabilities and enable performance improvements in recommendation methods. As a proof of concept and evaluation testbed, the approach is evaluated through its implementation in a news recommender system, in which it is tested with real users. In such scenario, semantic knowledge bases and item annotations are automatically produced from public sources.
A Protein Pre‐Organized to Trap the Nucleotide Moiety of Coenzyme B12: Refined Solution Structure of the B12‐Binding Subunit of Glutamate Mutase from Clostridium tetanomorphum

Uniformly 13C,15N‐labeled MutS, the coenzyme B12‐binding subunit of glutamate mutase from Clostridium tetanomorphum, was prepared by overexpression from an Escherichia coli strain. Multidimensional heteronuclear NMR spectroscopic experiments with aqueous solutions of 13C,15N‐labeled MutS provided signal assignments for roughly 90 % of the 1025 hydrogen, 651 carbon, and 173 nitrogen atoms and resulted in about 1800 experimental restraints. Based on the information from the NMR experiments, the structure of MutS was calculated, confirming the earlier, less detailed structure obtained with 15N‐labeled MutS. The refined analysis allowed a precise determination of the secondary and tertiary structure including several crucial side chain interactions. The structures of (the apoprotein) MutS in solution and of the B12‐binding subunit in the crystal of the corresponding homologous holoenzyme from Clostridium cochlearium differ only in a section that forms the well‐structured helix α1 in the crystal structure and that also comprises the cobalt‐coordinating histidine residue. In the apoprotein MutS, this part of the B12‐binding subunit is dynamic. The carboxy‐terminal end of this section is conformationally flexible and has significant propensity for an α‐helical structure (“nascent helix”). This dynamic section in MutS is a decisive element for the binding of the nucleotide moiety of coenzyme B12 and appears to be stabilized as a helix (α1) upon trapping of the nucleotide of the B12 cofactor.
Neandertal Humeri May Reflect Adaptation to Scraping Tasks, but Not Spear Thrusting

Unique compared with recent and prehistoric Homo sapiens, Neandertal humeri are characterised by a pronounced right-dominant bilateral strength asymmetry and an anteroposteriorly strengthened diaphyseal shape. Remodeling in response to asymmetric forces imposed during regular underhanded spear thrusting is the most influential explanatory hypothesis. The core tenet of the “Spear Thrusting Hypothesis”, that underhand thrusting requires greater muscle activity on the right side of the body compared to the left, remains untested. It is unclear whether alternative subsistence behaviours, such as hide processing, might better explain this morphology. To test this, electromyography was used to measure muscle activity at the primary movers of the humerus (pectoralis major (PM), anterior (AD) and posterior deltoid (PD)) during three distinct spear-thrusting tasks and four separate scraping tasks. Contrary to predictions, maximum muscle activity (MAX) and total muscle activity (TOT) were significantly higher (all values, p<.05) at the left (non-dominant) AD, PD and PM compared to the right side of the body during spear thrusting tasks. Thus, the muscle activity required during underhanded spearing tasks does not lend itself to explaining the pronounced right dominant strength asymmetry found in Neandertal humeri. In contrast, during the performance of all three unimanual scraping tasks, right side MAX and TOT were significantly greater at the AD (all values, p<.01) and PM (all values, p<.02) compared to the left. The consistency of the results provides evidence that scraping activities, such as hide preparation, may be a key behaviour in determining the unusual pattern of Neandertal arm morphology. Overall, these results yield important insight into the Neandertal behavioural repertoire that aided survival throughout Pleistocene Eurasia.
Evaluation of Attention‐Guiding Video Visualization

We investigate four different variants of attention‐guiding video visualization techniques that aim to help users distribute their attention equally among potential objects of interest: bounding box visualization, force‐directed visualization, top‐down visualization, grid visualization. Objects of interest are highlighted by rectangular shapes and then we concentrate on the manipulation of color, motion, and size. We conducted a controlled laboratory user study (n=25) to compare the four visualization techniques and the unmodified video material as baseline. We evaluated task performance and distribution of attention in a search task. These two properties become especially important when video material with numerous objects has to be observed. The distribution of attention was measured by eye tracking. Our results show that a more even distribution of attention between the objects can be achieved by attention‐guiding visualization, compared to unmodified video. Many participants feel more comfortable when they look at bounding boxes and the grid, but improvements in search task performance could not be confirmed.
Fast joint detection with cyclic reduction exploiting displacement structures

Joint detection with the minimum-mean square error (MMSE) criterion has been explored in previous works. Yang, Liu, Xu and Kim (see Asilomar Conference on Signals, Systems and Computers, Asilomar, CA, 1999) discussed joint detection with cyclic reduction, which has been proved to be faster than the popular Cholesky decomposition based algorithm under many scenarios. In this paper, a faster version of cyclic reduction which exploits displacement structures is presented. The proposed fast algorithm is useful when the channel length is long. Simulation results are given for a wireless communication setup.
Sensitivity of Streptococcus Mutans to Selected Nanoparticles : In Vitro Study

Background: Nanoparticles are clusters of atoms in a size range from (1-100) nm. Nano dentistry creates amazing useful structures from individual atoms or molecules (nanoparticles), which provides a new alternative and a possibly superior strategy in prevention and treatment of dental caries through management of dental plaque biofilms. The aim of the study was to test the sensitivity of Streptococcus mutans to different concentrations of hydroxyapatite and iron oxide nanoparticles suspension solutions, in comparison to chlorhexidine, and de-ionized water, in vitro. Materials and methods: Agar well technique was applied to test the sensitivity of Streptococcus mutans to different concentrations of hydroxyapatite and iron oxide nanoparticles compared with chlorhexidine 0.2% as a control positive and de-ionized water as control negative. Zone of inhibitions which is clear zone of no growth of the bacteria were measured across the diameter of each well, no zone indicated a complete resistance of bacteria to the agents. Results: Values of mean of inhibition zone for all concentrations of hydroxyapatite nanoparticles were zero. While for iron oxide nanoparticles, they were zero until reaching the last three concentrations, in which there was a respective increase with a highly significant difference between groups (p>0.01). When making multiple comparisons of the inhibition zones of iron oxide nanoparticles between groups, findings showed that the inhibition zones of 17%, 20% and 22.5% of iron oxide nanoparticles were more than all other concentrations that had no inhibition zones with a significant difference (p>0.05). There was a highly significant difference between each concentration of hydroxyapatite and iron oxide nanoparticles with chlorhexidine and de-ionized water (p>0.01). Conclusion: Streptococcus mutans were not sensitive to hydroxyapatite nanoparticles, as there was a complete resistance for the agent. While for iron oxide nanoparticles, Streptococcus mutans were sensitive to 17.5%, 20% and 22.5% and sensitivity increased with the increase in concentration with a statistically highly significant difference and this indicates an antibacterial activity of this material.
Excellent In vivo Bystander Activity of Fludarabine Phosphate against Human Glioma Xenografts that Express the Escherichia coli Purine Nucleoside Phosphorylase Gene

Escherichia coli purine nucleoside phosphorylase (PNP) expressed in tumors converts relatively nontoxic prodrugs into membrane-permeant cytotoxic compounds with high bystander activity. In the present study, we examined tumor regressions resulting from treatment with E. coli PNP and fludarabine phosphate (F-araAMP), a clinically approved compound used in the treatment of hematologic malignancies. We tested bystander killing with an adenoviral construct expressing E. coli PNP and then more formally examined thresholds for the bystander effect, using both MuLv and lentiviral vectoring. Because of the importance of understanding the mechanism of bystander action and the limits to this anticancer strategy, we also evaluated in vivo variables related to the expression of E. coli PNP (level of E. coli PNP activity in tumors, ectopic expression in liver, percentage of tumor cells transduced in situ, and accumulation of active metabolites in tumors). Our results indicate that F-araAMP confers excellent in vivo dose-dependent inhibition of bystander tumor cells, including strong responses in subcutaneous human glioma xenografts when 95 to 97.5% of the tumor mass is composed of bystander cells. These findings define levels of E. coli PNP expression necessary for antitumor activity with F-araAMP and demonstrate new potential for a clinically approved compound in solid tumor therapy.
Control of acyclic formations of mobile autonomous agents

This paper proposes distributed control laws for maintaining the shape of a formation of mobile autonomous agents in the plane for which the desired shape is defined in terms of prescribed distances between appropriately chosen pairs of agents. The formations considered are directed and acyclic where each given distance is maintained by only one of the associated pair of agents and there is no cycle in the sensing graph. It is shown that, except for a thin set of initial positions, the gradient-like control law can always cause a formation to converge to a finite limit in an equilibrium manifold for which all distance constraints are satisfied. The potential applicability of a control law using target positions is also discussed.
Isolates of Cryptococcus neoformans from Infected Animals Reveal Genetic Exchange in Unisexual, α Mating Type Populations

ABSTRACT Sexual reproduction and genetic exchange are important for the evolution of fungal pathogens and for producing potentially infective spores. Studies to determine whether sex occurs in the pathogenic yeast Cryptococcus neoformans var. grubii have produced enigmatic results, however: basidiospores are the most likely infective propagules, and clinical isolates are fertile and genetically diverse, consistent with a sexual species, but almost all populations examined consist of a single mating type and have little evidence for genetic recombination. The choice of population is critical when looking for recombination, particularly when significant asexual propagation is likely and when latency may complicate assessing the origin of an isolate. We therefore selected isolates from infected animals living in the region of Sydney, Australia, with the assumption that the relatively short life spans and limited travels of the animal hosts would provide a very defined population. All isolates were mating type α and were of molecular genotype VNI or VNII. A lack of linkage disequilibrium among loci suggested that genetic exchange occurred within both genotype groups. Four diploid VNII isolates that produced filaments and basidium-like structures when cultured in proximity to an a mating type strain were found. Recent studies suggest that compatible α-α unions can occur in C. neoformans var. neoformans populations and in populations of the sibling species Cryptococcus gattii. As a mating type strains of C. neoformans var. grubii have never been found in Australia, or in the VNII molecular type globally, the potential for α-α unions is evidence that α-α unisexual mating maintains sexual recombination and diversity in this pathogen and may produce infectious propagules.
Requirements Engineering for Pervasive Healthcare Monitoring System

A pervasive healthcare monitoring system (PHCMS) is an intrusive technology designed to provide supports to assist people with health problems. PHCMS could eventually lead to a fully monitored and supervised life within a home and thus reduce dependency of people towards healthcare institutions. Following implementation of such monitoring devices, elements of privacy, emotions and personal values of users, caregivers and family members appear to be at risk. Although requirements elicitation is a relatively mature area of requirements engineering, techniques to elicit emotions and personal values in the context of pervasive healthcare are not formally discussed. This research will use a case study of a pervasive healthcare system. Various elicitation techniques will be applied to harness emotions and personal values that affect users of a PHCMS. The final aim of this research is to recommend a toolkit that consists of requirements elicitation techniques for requirements engineers that are suitable to harness non-functional requirements for such a PHCMS.
Dentin Caries Zones: Mineral, Structure, and Properties

Caries Detector staining reveals 4 zones in dentin containing caries lesions, but characteristics of each zone are not well-defined. We therefore investigated the physical and microstructural properties of carious dentin in the 4 different zones to determine important differences revealed by Caries Detector staining. Six arrested dentin caries lesions and 2 normal controls were Caries-Detector-stained, each zone (pink, light pink, transparent, apparently normal) being analyzed by atomic force microscopy (AFM) imaging for microstructure, by AFM nano-indentation for mechanical properties, and by transverse digital microradiography (TMR) for mineral content. Microstructure changes, and nanomechanical properties and mineral content significantly decreased across zones. Hydrated elastic modulus and mineral content from normal dentin to pink Caries-Detector-stained dentin ranged from 19.5 [10.6–25.3] GPa to 1.6 [0.0–5.0] GPa and from 42.9 [39.8–44.6] vol% to 12.4 [9.1–14.2] vol%, respectively. Even the most demineralized pink zone contained considerable residual mineral.
Germline mutations of the E-cadherin(CDH1) and TP53 genes, rather than of RUNX3 and HPP1, contribute to genetic predisposition in German gastric cancer patients

Germline mutations of the cell adhesion molecule E-cadherin have been shown for the first time to underlie a hereditary diffuse type gastric cancer syndrome (HDGC) in Maori families,1 and subsequently have been reported in HDGC patients of various ethnic origins.2–9 Gastric cancer may also be associated with other hereditary tumour syndromes, which are mainly characterised by carcinomas of other organs. One of these syndromes is the HNPCC syndrome (hereditary nonpolyposis colorectal cancer syndrome), which is caused by germline mutations in DNA mismatch repair genes.10 Furthermore, gastric cancer has been observed in the context of the Li Fraumeni syndrome, a rare cancer syndrome due to germline mutations of the TP53 tumour suppressor gene,11–14 as well as in association with the FAP and Peutz–Jeghers syndrome.15 Despite known molecular genetic causes, contributing to a genetic predisposition to gastric cancer, a considerable number of familial cases have been reported that were not attributable to one of this hereditary syndromes, suggesting that unknown susceptibility genes for gastric cancer might exist. Putative tumour suppressor genes that are commonly inactivated in sporadic gastric cancers, such as the RUNX3 or HPP1 genes, are potential candidate susceptibility genes.16,17 In a previous study, we identified one E-cadherin germline mutation among seven diffuse type familial gastric cancer patients, indicating that in addition to E-cadherin , other genes might be involved in genetic predisposition to the disease in this patient group.4 There were three goals of the present study. First, we aimed to extend our analysis of E-cadherin germline mutations to a higher number of patients, to evaluate the contribution of germline mutations in this gene to German familial and early onset gastric cancer patients and to characterise identified missense mutations for their functional relevance. Secondly, we wished to analyse the role …