A Decade of Code Comment Quality Assessment: A Systematic Literature Review

Code comments are important artifacts in software systems and play a paramount role in many software engineering (SE) tasks related to maintenance and program comprehension. However, while it is widely accepted that high quality matters in code comments just as it matters in source code, assessing comment quality in practice is still an open problem. First and foremost, there is no unique definition of quality when it comes to evaluating code comments. The few existing studies on this topic rather focus on specific attributes of quality that can be easily quantified and measured. Existing techniques and corresponding tools may also focus on comments bound to a specific programming language, and may only deal with comments with specific scopes and clear goals (e.g., Javadoc comments at the method level, or in-body comments describing TODOs to be addressed). In this paper, we present a Systematic Literature Review (SLR) of the last decade of research in SE to answer the following research questions: (i) What types of comments do researchers focus on when assessing comment quality? (ii) What quality attributes (QAs) do they consider? (iii) Which tools and techniques do they use to assess comment quality?, and (iv) How do they evaluate their studies on comment quality assessment in general? Our evaluation, based on the analysis of 2353 papers and the actual review of 47 relevant ones, shows that (i) most studies and techniques focus on comments in Java code, thus may not be generalizable to other languages, and (ii) the analyzed studies focus on four main QAs of a total of 21 QAs identified in the literature, with a clear predominance of checking consistency between comments and the code. We observe that researchers rely on manual assessment and specific heuristics rather than the automated assessment of the comment quality attributes

Compounds released from Lactobacillus (L.) acidophilus, L. plantarum, L. rhamnosus and L. reuteri inhibit Candida parapsilosis pathogenic potential after infection of vaginal epithelial cells in vitro.

INTRODUCTION. Lactobacillus spp. are the most represented microorganisms in the vaginal microbiota of healthy women, where they provide a shelter against infections from several pathogens, such as the yeasts belonging to the genus Candida. The latter are responsible for the vulvovaginal candidiasis (VVC), a condition affecting up to 75% of women during their child-bearing age at least once in their lifetime. Moreover, 5-8% of such women develop the recurrent form of the disease (RVVC), consisting of at least 5 VVC episodes per year. Notwithstanding C. albicans is the main responsible of VVC cases, in the last decades, the incidence of VVC cases by non-albicans Candida (NAC) species has become prevalent, especially in some geographical areas. C. parapsilosis, in particular, has been reported to be second species most commonly isolated from women affected by VVC. However, little is known on this species, and on its role in the pathogenesis of VVC. MATERIALS AND METHODS. Cell-free supernatants (CFS) were obtained following an overnight culture of 4 different Lactobacilli species (L. acidophilus, L. plantarum, L. rhamnosus, L. reuteri). Lactobacilli-released compounds, contained in CFS, were assessed for their effect on several virulence factors of C. parapsilosis (strain CLIB214), such as growth rate, capacity to form pseudohyphae, capacity to adhere to a vaginal epithelium in vitro (A-431 cells monolayer) and to induce cell damage. The latter was evaluated by measuring lactate dehydrogenase (LDH) release from A431 cells. RESULTS. C. parapsilosis growth inhibition by L. acidophilus, L. plantarum and L. reuteri CFS was 47%, 55% and 52% respectively, whereas L. rhamnosus CFS effect was weaker (33% inhibition growth). All the Lactobacilli significantly inhibited C. parapsilosis adhesion to vaginal epithelial cells: upon incubation with CFS, only 5-7% of fungal cells adhered to epithelial cells, after 90 minutes incubation; differently, the adhesion of the control reached 19%. Interestingly, no effect on pseudohyphae formation by any of the CSF was ever observed. Finally, the C. parapsilosis-induced damage on A-431 cells was significantly reduced by the addition of the CSF. DISCUSSION AND CONCLUSIONS. Our results show that the investigated species of Lactobacilli release compounds capable to impair several C. parapsilosis virulence factors, such as growth rate and adhesion to vaginal epithelial cells; interestingly, while not affecting fungal capacity to form pseudohyphae, such compounds significantly reduce Candida-mediated epithelial damage.. These data suggest that, in the context of vaginal microbiota, these Lactobacilli species may play an important role in counteracting the onset of mucosal Candida infections

Herpes Simplex Virus-1 entrapped in Candida albicans biofilm displays decreased sensitivity to antivirals and UVA1 laser treatment

Abstract Background: Recently, we published data suggesting a mutualistic relationship between HSV-1 and Candida. albicans; in particular: (a) HSV-1 infected macrophages are inhibited in their anti-Candida effector function and (b) Candida biofilm protects HSV-1 from inactivation. The present in vitro study is aimed at testing the effects of Candida biofilm on HSV-1 sensitivity to pharmacological and physical stress, such as antiviral drugs (acyclovir and foscarnet) and laser UVA1 irradiation. We also investigated whether fungus growth pattern, either sessile or planktonic, influences HSV-1 sensitivity to antivirals. Methods: Mature Candida biofilms were exposed to HSV-1 and then irradiated with laser light (UVA1, 355 \u3bb). In another set of experiments, mature Candida biofilm were co-cultured with HSV-1 infected VERO cells in the presence of different concentrations of acyclovir or foscarnet. In both protocols, controls unexposed to laser or drugs were included. The viral yield of treated and untreated samples was evaluated by end-point titration. To evaluate whether this protective effect might occur in relation with a different growth pattern, HSV-1 infected cells were co-cultured with either sessile or planktonic forms of Candida and then assessed for susceptibility to antiviral drugs. Results: UVA1 irradiation caused a 2 Log reduction of virus yield in the control cultures whereas the reduction was only 1 Log with Candida biofilm, regardless to the laser dose applied to the experimental samples (50 or 100 J/cm2). The presence of biofilm increased the IC90 from 18.4\u201325.6 J/cm2. Acyclovir caused a 2.3 Log reduction of virus yield in the control cultures whereas with Candida biofilm the reduction was only 0.5 Log; foscarnet determined a reduction of 1.4 Log in the controls and 0.2 Log in biofilm cultures. Consequently, the ICs50 for acyclovir and foscarnet increased by 4- and 12-folds, respectively, compared to controls. When HSV-1 was exposed to either sessile or planktonic fungal cells, the antiviral treatments caused approximately the same weak reduction of virus yield. Conclusions: These data demonstrate that: (1) HSV-1 encompassed in Candida biofilm is protected from inactivation by physical (laser) and pharmacological (acyclovir or foscarnet) treatments; (2) the drug antiviral activity is reduced at a similar extent for both sessile or planktonic Candida

Real-time monitoring of Pseudomonas aeruginosa biofilm formation on endotracheal tubes in vitro

BACKGROUND: Pseudomonas aeruginosa is an opportunistic bacterial pathogen responsible for both acute and chronic infections in humans. In particular, its ability to form biofilm, on biotic and abiotic surfaces, makes it particularly resistant to host's immune defenses and current antibiotic therapies as well. Innovative antimicrobial materials, like hydrogel, silver salts or nanoparticles have been used to cover new generation catheters with promising results. Nevertheless, biofilm remains a major health problem. For instance, biofilm produced onto endotracheal tubes (ETT) of ventilated patients plays a relevant role in the onset of ventilation-associated pneumonia. Most of our knowledge on Pseudomonas aeruginosa biofilm derives from in vitro studies carried out on abiotic surfaces, such as polystyrene microplates or plastic materials used for ETT manufacturing. However, these approaches often provide underestimated results since other parameters, in addition to bacterial features (i.e. shape and material composition of ETT) might strongly influence biofilm formation. RESULTS: We used an already established biofilm development assay on medically-relevant foreign devices (CVC catheters) by a stably transformed bioluminescent (BLI)-Pseudomonas aeruginosa strain, in order to follow up biofilm formation on ETT by bioluminescence detection. Our results demonstrated that it is possible: i) to monitor BLI-Pseudomonas aeruginosa biofilm development on ETT pieces in real-time, ii) to evaluate the three-dimensional structure of biofilm directly on ETT, iii) to assess metabolic behavior and the production of microbial virulence traits of bacteria embedded on ETT-biofilm. CONCLUSIONS: Overall, we were able to standardize a rapid and easy-to-perform in vitro model for real-time monitoring Pseudomonas aeruginosa biofilm formation directly onto ETT pieces, taking into account not only microbial factors, but also ETT shape and material. Our study provides a rapid method for future screening and validation of novel antimicrobial drugs as well as for the evaluation of novel biomaterials employed in the production of new classes of ETT

Evaluation of benzydamine effects on Candida albicans adhesion, biofilm formation and persistence onto abiotic surfaces

Introduction. Candida albicans is the most abundant yeast colonizing the oral cavity. It behaves as an opportunistic pathogen, causing mucosal infections mainly in immunocompromised individuals; in addition, it is often associated to patients suffering from diabetes, oral cancer and terminally ill conditions. Benzydamine hydrochloride is a non-steroidal and anti-inflammatory agent. It has been included in the formulation of several mouthwashes because endowed with analgesic and anesthetic properties. Since benzydamine exerts antibacterial and antifungal activity in vitro, we assessed if this molecule could affect C. albicans virulence traits, such as adhesion, biofilm formation and persistence on abiotic surfaces. Materials and Methods. C. albicans CA1398, carrying the bioluminescence ACT1p-gLUC59 fusion product, was employed. Firstly, fungal cells were exposed for 1\u2019, 5\u2019, or 15\u2019 to 4 different benzydamine concentrations (0.075%, 0.15%, 0.3% and 0.6%) and then tested for their capacity to adhere to plastic (90\u2019 incubation) or to form a biofilm (24h assay). Secondly, 24 and 48h-old biofilms were exposed to the same concentrations of benzydamine and for the same times in order to assess biofilm persistence and regrowth. Benzydamine effects were quantified by measuring, in parallel, metabolically active fungal cells (bioluminescence assay) and viable cells (Colony Forming Units assay). Results. Benzydamine impaired ability to adhere to plastic and to form biofilm, in a dose-dependent fashion; such effects could be ascribed to a direct effect of benzydamine on Candida viability only when using the highest dosage. Moreover, benzydamine caused a dose-dependent decrement in the viability of Candida cells embedded in biofilm, no matter whether a 24h- or a 48h-old sessile community was tested. Discussion and Conclusions. Benzydamine not only impairs C. albicans biofilm formation, profoundly affecting the initial step of fungal cell adhesion to abiotic surfaces, but it is also able to counteract persistence and regrowth of a preformed biofilm. The capacity of benzydamine to affect C. albicans, a fungus responsible of oral diseases in several categories of susceptible subjects, makes this molecule a very interesting tool for both prevention and treatment of oral candidiasis. Studies employing benzydamine-containing mouthwashes will be carried out, in order to assess and compare the anti-Candida effects of different commercial products

A decade of code comment quality assessment : a systematic literature review

Code comments are important artifacts in software systems and play a paramount role in many software engineering (SE) tasks related to maintenance and program comprehension. However, while it is widely accepted that high quality matters in code comments just as it matters in source code, assessing comment quality in practice is still an open problem. First and foremost, there is no unique definition of quality when it comes to evaluating code comments. The few existing studies on this topic rather focus on specific attributes of quality that can be easily quantified and measured. Existing techniques and corresponding tools may also focus on comments bound to a specific programming language, and may only deal with comments with specific scopes and clear goals (e.g., Javadoc comments at the method level, or in-body comments describing TODOs to be addressed). In this paper, we present a Systematic Literature Review (SLR) of the last decade of research in SE to answer the following research questions: (i) What types of comments do researchers focus on when assessing comment quality? (ii) What quality attributes (QAs) do they consider? (iii) Which tools and techniques do they use to assess comment quality?, and (iv) How do they evaluate their studies on comment quality assessment in general? Our evaluation, based on the analysis of 2353 papers and the actual review of 47 relevant ones, shows that (i) most studies and techniques focus on comments in Java code, thus may not be generalizable to other languages, and (ii) the analyzed studies focus on four main QAs of a total of 21 QAs identified in the literature, with a clear predominance of checking consistency between comments and the code. We observe that researchers rely on manual assessment and specific heuristics rather than the automated assessment of the comment quality attributes, with evaluations often involving surveys of students and the authors of the original studies but rarely professional developers

Myb-binding protein 1A (MYBBP1A) is essential for early embryonic development, controls cell cycle and mitosis, and acts as a tumor suppressor

MYBBP1A is a predominantly nucleolar transcriptional regulator involved in rDNA synthesis and p53 activation via acetylation. However little further information is available as to its function. Here we report that MYBBP1A is developmentally essential in the mouse prior to blastocyst formation. In cell culture, down-regulation of MYBBP1A decreases the growth rate of wild type mouse embryonic stem cells, mouse embryo fibroblasts (MEFs) and of human HeLa cells, where it also promotes apoptosis. HeLa cells either arrest at G2/M or undergo delayed and anomalous mitosis. At mitosis, MYBBP1A is localized to a parachromosomal region and gene-expression profiling shows that its down-regulation affects genes controlling chromosomal segregation and cell cycle. However, MYBBP1A down-regulation increases the growth rate of the immortalized NIH3T3 cells. Such Mybbp1a down-regulated NIH3T3 cells are more susceptible to Ras-induced transformation and cause more potent Ras-driven tumors. We conclude that MYBBP1A is an essential gene with novel roles at the pre-mitotic level and potential tumor suppressor activity.NHMRC: This work was supported by Associazione Italiana Ricerche sul Cancro (AIRC) grant 8929 and European Community FP7 201681 ‘‘Prepobedia’’ to FB, the Australian National Health and Medical Research Council to RK and TJG (project ID000115). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Perinuclear Anti-Neutrophil Cytoplasmic Antibodies (pANCA) Impair Neutrophil Candidacidal Activity and Are Increased in the Cellular Fraction of Vaginal Samples from Women with Vulvovaginal Candidiasis

Vulvovaginal candidiasis (VVC) is primarily caused by Candida albicans and affects 75% of childbearing age women. Although C. albicans can colonize asymptomatically, disease is associated with an increased Candida burden, a loss of epithelial tolerance and a breakdown in vaginal microbiota homeostasis. VVC symptoms have been ascribed to a powerful inflammatory response associated with the infiltration of non-protective neutrophils (PMN). Here, we compared the immunological characteristics of vaginal fluids and cellular protein extracts obtained from 28 VVC women and from 23 healthy women colonized by Candida spp. We measured the levels of antibodies against fungal antigens and human autoantigens (anti-Saccharomyces cerevisiae antibodies (ASCA), C. albicans germ tube antibodies (CAGTAs) and perinuclear anti-neutrophil cytoplasmic antibodies (pANCA)), in addition to other immunological markers. Our results show that the pANCA levels detected in the cellular protein extracts from the vaginal fluids of symptomatic women were significantly higher than those obtained from healthy colonized women. Consistent with a potential physiologically relevant role for this pANCA, we found that specific anti-myeloperoxidase antibodies could completely neutralize the ex vivo killing capacity of polymorphonuclear cells. Collectively, this preliminary study suggests for the first time that pANCA are found in the pathogenic vaginal environment and can promptly impair neutrophil function against Candida, potentially preventing a protective response

The synthetic killer peptide KP impairs Candida albicans biofilm in vitro

Candida albicans is a commensal organism, commonly inhabiting mucosal surfaces of healthy individuals, as a part of the resident microbiota. However, in susceptible hosts, especially hospitalized and/or immunocompromised patients, it may cause a wide range of infections. The presence of abiotic substrates, such as central venous or urinary catheters, provides an additional niche for Candida attachment and persistence, particularly via biofilm development. Furthermore, Candida biofilm is poorly susceptible to most antifungals, including azoles. Here we investigated the effects of a synthetic killer peptide (KP), known to be active in vitro, ex vivo and/or in vivo against different pathogens, on C. albicans biofilm. Together with a scrambled peptide used as a negative control, KP was tested against Candida biofilm at different stages of development. A reference strain, two fluconazole-resistant and two fluconazole-susceptible C. albicans clinical isolates were used. KP-induced C. albicans oxidative stress response and membrane permeability were also analysed. Moreover, the effect of KP on transcriptional profiles of C. albicans genes involved in different stages of biofilm development, such as cell adhesion, hyphal development and extracellular matrix production, was evaluated. Our results clearly show that the treatment with KP strongly affected the capacity of C. albicans to form biofilm and significantly impairs preformed mature biofilm. KP treatment resulted in an increase in C. albicans oxidative stress response and membrane permeability; also, biofilm-related genes expression was significantly reduced. Comparable inhibitory effects were observed in all the strains employed, irrespective of their resistance or susceptibility to fluconazole. Finally, KP-mediated inhibitory effects were observed also against a catheter-associated C. albicans biofilm. This study provides the first evidence on the KP effectiveness against C. albicans biofilm, suggesting that KP may be considered as a potential novel tool for treatment and prevention of biofilm-related C. albicans infections