A trustworthy hybrid model for transparent software defect prediction: SPAM-XAI.

Maintaining quality in software development projects is becoming very difficult because the complexity of modules in the software is growing exponentially. Software defects are the primary concern, and software defect prediction (SDP) plays a crucial role in detecting faulty modules early and planning effective testing to reduce maintenance costs. However, SDP faces challenges like imbalanced data, high-dimensional features, model overfitting, and outliers. Moreover, traditional SDP models lack transparency and interpretability, which impacts stakeholder confidence in the Software Development Life Cycle (SDLC). We propose SPAM-XAI, a hybrid model integrating novel sampling, feature selection, and eXplainable-AI (XAI) algorithms to address these challenges. The SPAM-XAI model reduces features, optimizes the model, and reduces time and space complexity, enhancing its robustness. The SPAM-XAI model exhibited improved performance after experimenting with the NASA PROMISE repository's datasets. It achieved an accuracy of 98.13% on CM1, 96.00% on PC1, and 98.65% on PC2, surpassing previous state-of-the-art and baseline models with other evaluation matrices enhancement compared to existing methods. The SPAM-XAI model increases transparency and facilitates understanding of the interaction between features and error status, enabling coherent and comprehensible predictions. This enhancement optimizes the decision-making process and enhances the model's trustworthiness in the SDLC.

Impact of alkaline earth metal doping on the structural, electronic, and optical properties of all inorganic lead-free CsSnX3(X = I, Br) perovskites: a first-principles study.

Recently, researchers have focused on developing more stable, Pb-free perovskites with improved processing efficiency and notable light harvesting ability. In this regard, Sn-based (Sn-b) perovskites have gained considerable interest in developing eco-friendly perovskite solar cells (PSCs). However, the oxidation of Sn2+to Sn4+deteriorates the performance of Sn-b PSCs. Nevertheless, this issue could be mitigated by doping alkaline earth (AE) metal. Herein, we have studied the significance of AE doping on CsSnX3(X = Br, I) perovskites using density functional theory based calculations. The structural, electronic, and optical properties of CsAEySn1-yX3(y= 0, 0.25; AE = Be, Mg, Ca, Sr) compounds were systematically investigated to explore potential candidate materials for photovoltaic applications. Formation energy calculations suggested that the synthesis of other AE-doped compounds is energetically favorable except for the Be-doped compounds. The band gaps of the materials were calculated to be in the range of 0.12-1.02 eV using the generalized gradient approximation. Furthermore, the AE doping considerably lowers the exciton binding energy while remarkably enhancing the optical absorption of CsSnX3, which is beneficial for solar cells. However, in the case of Be and Mg doping, an indirect band gap is predicted. Our theoretical findings demonstrate the potential of executing AE-doped perovskites as absorber material in PSCs, which could deliver better performance than pristine CsSnX3PSCs.

Synergy of VN and Fe2O3 Enables High Performance Anodes for Asymmetric Supercapacitors.

Fe2O3 is one of the most common anode materials beyond carbons but suffers from unsatisfactory capacity and poor stability, which are associated with the insufficient utilization of active material and the structural instability caused by the phase transformation. In this work, we report an effective strategy to overcome the above issues through electronic structure optimization by constructing delicately designed Fe2O3@VN core-shell structure. The Fe2O3@VN/CC exhibits a much higher areal capacity of 254.8 mC cm-2 at 5 mA cm-2 (corresponding to 318.5 mF cm-2, or 265.4 F g-1) than the individual VN (48 mC cm-2, or 60 mF cm-2) or Fe2O3/CC (93.36 mC cm-2, or 116.7 mF cm-2), along with enhanced stability. Moreover, the assembled asymmetric supercapacitor devices based on Fe2O3@VN/CC anode and RuO2/CC cathode show a high stack energy density of 0.5 mWh cm-3 at a power density of 12.28 mW cm-3 along with good stability (80% capacitance retention after 14000 cycles at 10 mA cm-2). This work not only establishes the Fe2O3@VN as a high-performance anode material but also suggests a general strategy to enhance the electrochemical performance of traditional anodes that suffer from low capacity (capacitance) and poor stability.

PeMtb: A Database of MHC Antigenic Peptide of Mycobacterium tuberculosis.

BACKGROUND: For design of a subunit vaccine for tuberculosis, identification of antigenic Tcell epitope is of utmost importance. Several MHC prediction server are available that can accurately predict antigenic peptide of variable lengths. However, peptides predicted from one server not necessarily are predicted form another server, thus creating a confusing situation for scientists to choose a best epitope. METHOD: Keeping the above problem in mind, we developed a comprehensive database of peptides of Mycobacterial proteins. Each protein was taken from PubMed and was run through different MHC prediction servers, with the results being compiled into one database. RESULTS: For each protein, PeMtb generates a set of three different mers of variable lengths (12 mer or 13-mer) based on their ranking; with each mer being predicted for a plethora of MHC alleles. Researcher can choose the peptide (mers) that gives best binding affinity from most of the servers. CONCLUSION: The database relieves the investigators of the painstaking task of searching various MHC prediction servers for the right epitope (T-cell epitope) for a particular Mycobacterial antigen. We trust and anticipate that PeMtb will be a practical platform for trial and computational analyses of antigenic peptides for Mycobacterium tuberculosis. All the resources and information can be accessed by PeMtb home page www.pemtb-amu.org.

Multistep microsatellite mutation in the maternally transmitted locus D13S317: a case of maternal allele mismatch in the child.

Examination of a case of a paternity dispute with 17 autosomal short tandem repeats (STR) loci revealed a mismatch of the maternally transmitted allele at the locus D13S317 in the questioned child. The composition of the alleles of this locus in the mother, questioned child and suspected father was 8/8, 11/11 and 8/11, respectively. The sequence analysis of the regions flanking the locus D13S317 and peak height measurements of the paternal, maternal and child alleles at this locus excluded the possibility of null allele as a cause of the allelic mismatch inherited by the child. The results suggested expansion of the microsatellite repeat motif, TATC by three repeat units as a probable cause for the allelic mismatch in the child. This is a rare case of maternally transmitted multistep microsatellite mutation reported for the first time for this locus in the forensic DNA analysis. The mutation rate at D13S317 locus in maternal and paternal meiosis was 0.04 and 0.14%, respectively, and overall mutation rate was 0.15%. The probability of maternity and paternity were 0.999999 and 0.999999, respectively, for all the 17 autosomal STR loci analyzed. Furthermore, the sequence of two hypervariable regions of mitochondrial DNA, HV1 and HV2 and the maternal alleles of six X chromosome STR loci in the questioned child matched completely with the mother. These results conclusively proved that the mother and suspected father are the biological parents of the questioned child.

The cag pathogenicity island of Helicobacter pylori is disrupted in the majority of patient isolates from different human populations.

The cag pathogenicity island (cag-PAI) is one of the major virulence determinants of Helicobacter pylori. The chromosomal integrity of this island or the lack thereof is speculated to play an important role in the progress of the gastroduodenal pathology caused by H. pylori. We determined the integrity of the cag-PAI by using specific flanking and internally anchored PCR primers to know the biogeographical distribution of strains carrying fully integral cag-PAI with proinflammatory behavior in vivo. Genotypes based on eight selected loci were studied in 335 isolates obtained from eight different geographic regions. The cag-PAI appeared to be disrupted in the majority of patient isolates throughout the world. Conservation of cag-PAI was highest in Japanese isolates (57.1%). However, only 18.6% of the Peruvian and 12% of the Indian isolates carried an intact cag-PAI. The integrity of cag-PAI in European and African strains was minimal. All 10 strains from Costa Rica had rearrangements. Overall, a majority of the strains of East Asian ancestry were found to have intact cag-PAI compared to strains of other descent. We also found that the cagE and cagT genes were less often rearranged (18%) than the cagA gene (27%). We attempted to relate cag-PAI rearrangement patterns to disease outcome. Deletion frequencies of cagA, cagE, and cagT genes were higher in benign cases than in isolates from severe ulcers and gastric cancer. Conversely, the cagA promoter and the left end of the cag-PAI were frequently rearranged or deleted in isolates linked to severe pathology. Analysis of the cag-PAI genotypes with a different biogeoclimatic history will contribute to our understanding of the pathogen-host interaction in health and disease.

Molecular genotyping of a large, multicentric collection of tubercle bacilli indicates geographical partitioning of strain variation and has implications for global epidemiology of Mycobacterium tuberculosis.

Tuberculosis continues to be a major killer disease, despite an all-out effort launched against it in the postgenomic era. We describe here the population structure of Mycobacterium tuberculosis strains, as revealed by a chromosome-wide scan of fluorescent amplified fragment length polymorphisms (FAFLPs), for more than 1,100 independent isolates from 11 different countries. The bacterial strains were genotyped based on a total of 136 +/- 1 different FAFLP markers at the genome sequence interface, with details on IS6110 profiles, drug resistance status, clinicopathological observations, and host status integrated into the analysis process. The strains were found to cluster with possible geographic affinities, including the parameters of host species type, IS6110 profile, and drug susceptibility status. Of the five most commonly amplified fragment sets (or amplitypes), type A predominated in strains of mixed origin, deposited in The Netherlands; type B was exclusively observed for Indian isolates; type C was found mainly in strains from Peru and Australia; and types D and E predominated in European strains from France and Italy. The amplitypes were independent of certain large sequence polymorphisms representing two important deletions, TbD1 and Rd9. It appears that M. tuberculosis has a high genomic diversity with a possible geographic evolution. This may have occurred due to specific genomic deletions and synonymous substitutions selected rigorously against host defenses and environmental stresses on an evolutionary timescale. The genotypic data reported here are additionally significant for genotype-phenotype correlations and for determining whether pathogen diversity is a reflection f the host population diversity.

Genome sequence based, comparative analysis of the fluorescent amplified fragment length polymorphisms (FAFLP) of tubercle bacilli from seals provides molecular evidence for a new species within the Mycobacterium tuberculosis complex.

Tuberculosis in seals is caused by a member of the Mycobacterium tuberculosis complex referred to as the 'seal bacillus'. Fluorescent amplified-fragment length polymorphism (FAFLP) analysis was applied to isolates from four Australian and six Argentinean seals and compared with FAFLP pattern for standard strains belonging to the M. tuberculosis complex. The FAFLP profiles derived from EcoRI/MseI restricted fragments of blind coded DNA samples differentiated the seal bacillus from other members of the M. tuberculosis complex. According to the phylogenetic analysis performed using FAFLP data, seal bacilli appear to have diverged significantly from other members of the M. tuberculosis complex. We describe the suitability of a panel of 19 highly polymorphic markers for rapid identification and comparative genomic analyses of the seal bacillus strains. It is likely that these bacilli got separated from the M. tuberculosis lineage as a result of different insertion deletion events occurring on a genome wide scale. Our analysis reveals that the seal bacillus and M. bovis are genetically related and therefore, might have originated from a common ancestor. Our data additionally support the hypothesis that seal bacillus occupies a unique taxonomic position within the M. tuberculosis complex.

Distinctiveness of Mycobacterium tuberculosis genotypes from human immunodeficiency virus type 1-seropositive and -seronegative patients in Lima, Peru.

Genotypic analysis of Mycobacterium tuberculosis isolates obtained from human immunodeficiency virus type 1 (HIV-1)-seropositive (n = 80) and -seronegative (n = 25) patients from Lima, Peru, revealed two distinct genotypes correlating with the host immune status. While the level of intrastrain diversity of DNA fingerprints of HIV-seropositive isolates was less pronounced, these isolates showed many clonal groupings.

Molecular characterization of multidrug-resistant isolates of Mycobacterium tuberculosis from patients in North India.

The World Health Organization has identified India as a major hot-spot region for Mycobacterium tuberculosis infection. We have characterized the sequences of the loci associated with multidrug resistance in 126 clinical isolates of M. tuberculosis from India to identify the respective mutations. The loci selected were rpoB (rifampin), katG and the ribosomal binding site of inhA (isoniazid), gyrA and gyrB (ofloxacin), and rpsL and rrs (streptomycin). We found known as well as novel mutations at these loci. Few of the mutations at the rpoB locus could be correlated with the drug resistance levels exhibited by the M. tuberculosis isolates and occurred with frequencies different from those reported earlier. Missense mutations at codons 526 to 531 seemed to be crucial in conferring a high degree of resistance to rifampin. We identified a common Arg463Leu substitution in the katG locus and certain novel insertions and deletions. Mutations were also mapped in the ribosomal binding site of the inhA gene. A Ser95Thr substitution in the gyrA locus was the most common mutation observed in ofloxacin-resistant isolates. A few isolates showed other mutations in this locus. Seven streptomycin-resistant isolates had a silent mutation at the lysine residue at position 121. While certain mutations are widely present, pointing to the magnitude of the polymorphisms at these loci, others are not common, suggesting diversity in the multidrug-resistant M. tuberculosis strains prevalent in this region. Our results additionally have implications for the development of methods for multidrug resistance detection and are also relevant in the shaping of future clinical treatment regimens and drug design strategies.

Whole genome fingerprinting and genotyping of multiple drug resistant (MDR) isolates of Pseudomonas aeruginosa from endophthalmitis patients in India.

Genome sequence-based fluorescent amplified-fragment length polymorphism (FAFLP) analysis was investigated for fingerprinting and subtyping 42 multiple drug resistant (MDR) isolates of Pseudomonas aeruginosa from post-surgical endophthalmitis. The FAFLP profiles derived from EcoRI/MseI restricted fragments differentiated clinical isolates and were found to be extremely reproducible. Seventeen different amplification patterns (amplitypes) were observed for all the 42 isolates from 11 different patients. Also, we were able to genotype the isolates based on the differential amplification of a total of 31 FAFLP markers representing genomic fragments from the P. aeruginosa chromosome. This data appears to provide clues to the genetic diversity of endopthalmitis associated strains and could be converted into digitised fingerprints suitable for electronic manipulations and archiving.