Molecular Docking of Known Carcinogen 4- (Methyl-nitrosamino)-1-(3-pyridyl)-1-butanone (NNK) with Cyclin Dependent Kinases towards Its Potential Role in Cell Cycle Perturbation

Cell cycle is maintained almost all the times and is controlled by various regulatory proteins and their complexes (Cdk+Cyclin) in different phases of interphase (G1, S and G2) and mitosis of cell cycle. A number of mechanisms have been proposed for the initiation and progression of carcinogenesis by abruption in cell cycle process. One of the important features of cancer/carcinogenesis is functional loss of these cell cycle regulatory proteins particularly in CDKs and cyclins. We hypothesize that there is a direct involvement of these cell cycle regulatory proteins not only at the genetic level but also proteins level, during the initiation of carcinogenesis. Therefore, it becomes significant to determine inconsistency in the functioning of regulatory proteins due to interaction with carcinogen 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). Hence, we investigated the interaction efficiency of NNK, against cell cycle regulatory proteins. We found a different value of ΔG (free energy of binding) among the studied proteins ranging between -3.29 to -7.25 kcal/mol was observed. To validate the results, we considered Human Oxy-Hemoglobin at 1.25 Å Resolution, [PDB_ID:1HHO] as a +ve control, (binding energy -6.06 kcal/mol). Finally, the CDK8 (PDB_ID:3RGF) and CDK2 (PDB_ID:3DDP) regulatory proteins showing significantly strong molecular interaction with NNK -7.25 kcal/mol, -6.19 kcal/mol respectively were analyzed in details. In this study we predicted that CDK8 protein fails to form functional complex with its complementary partner cyclin C in presence of NNK. Consequently, inconsistency of functioning in regulatory proteins might lead to the abruption in cell cycle progression; contribute to the loss of cell cycle control and subsequently increasing the possibility of carcinogenesis

Adaboost-multilayer perceptron to predict the student’s performance in software engineering

Software Engineering (SE) course is one of the backbones of today's computer technology sophistication. Effective theoretical and practical learning of this course is essential to computer students. However, there are many students fail in this course. There are many aspects that influence a student's performance. Currently, student performance analysis methods just focus on historical achievement and assessment methods given in the class. Need more research to predict student's performance to overcome the problem of student failing. The objective of this research is to perform a prediction for student's performance in the SE using enhanced Multilayer Perceptron (MLP) machine learning classification with Adaboost. This research also investigates the requirements of each student before registering in this course. This research achieved 87.76 percent accuracy in classifying the performance of SE students

Malware detection using static analysis in android: A review of FeCO (features, classification, and obfuscation)

Android is a free open-source operating system (OS), which allows an in-depth understanding of its architecture. Therefore, many manufacturers are utilizing this OS to produce mobile devices (smartphones, smartwatch, and smart glasses) in different brands, including Google Pixel, Motorola, Samsung, and Sony. Notably, the employment of OS leads to a rapid increase in the number of Android users. However, unethical authors tend to develop malware in the devices for wealth, fame, or private purposes. Although practitioners conduct intrusion detection analyses, such as static analysis, there is an inadequate number of review articles discussing the research efforts on this type of analysis. Therefore, this study discusses the articles published from 2009 until 2019 and analyses the steps in the static analysis (reverse engineer, features, and classification) with taxonomy. Following that, the research issue in static analysis is also highlighted. Overall, this study serves as the guidance for novice security practitioners and expert researchers in the proposal of novel research to detect malware through static analysis

Biomarker Changes Associated with Tuberculin Skin Test (TST) Conversion: A Two-Year Longitudinal Follow-Up Study in Exposed Household Contacts

Background:A high prevalence (50-80%) of Tuberculin Skin Test Positivity (TST+ \u3eor=10 mm indurations) has been reported in TB endemic countries. This pool forms a huge reservoir for new incident TB cases. However, immune biomarkers associated with TST conversion are largely unknown. The objective of this study was to identify immune biomarkers associated with TST conversion after acute Mycobacterium tuberculosis (MTB) Methodology/Principal Findings:A 24 month longitudinal study was carried out in a recently MTB exposed cohort of household contacts (HC = 93, 75% TST+). Control group consisted of unexposed community controls (EC = 59, 46%TST+). Cytokine secretion was assessed in whole blood cultures in response to either mycobacterial culture filtrate (CF) antigens or mitogens (PHA or LPS) using Elisa methodology. Compared to the EC group, the HC group at recruitment (Kruskal-Wallis Test) showed significantly suppressed IFN gamma (p = 0.0001), raised IL-10 (p = 0.0005) and raised TNF alpha (p = 0.001) in response to CF irrespective of their TST status. Seventeen TST-HC, showed TST conversion when retested at 6 months. Post TST conversion (paired t tests) significant increases were observed for CF induced IFN gamma (p = 0.038), IL-10 (p = 0.001) and IL-6 (p = 0.006). Cytokine responses were also compared in the exposed HC group with either recent infection [(TST converters (N = 17)] or previous infection [TST+ HC (N = 54)] at 0, 6, 12 and 24 months using ANOVA on repeated measures. Significant differences between the exposed HC groups were noted only at 6 months. CF induced IFN gamma was higher in previously infected HC group (p = 0.038) while IL-10 was higher in recently infected HC group (p = 0.041). Mitogen induced cytokine secretion showed similar differences for different group.Conclusions/Significance:Our results suggest that TST conversion is associated with early increases in IFN gamma and IL-10 responses and precedes latency by several months post exposure

Immune profiling of leprosy and tuberculosis patients to 15-mer peptides of Mycobacterium leprae and M. tuberculosis GroES in a BCG vaccinated area: implications for development of vaccine and diagnostic reagents.

Mycobacterium leprae (ML) GroES has been shown to induce strong T cell responses in tuberculoid as well as in exposed healthy contacts of leprosy patients, and therefore this antigen has been the focus of study as a potential vaccine candidate. Paradoxically, we have shown that ML GroES also induces extremely high titres of IgG1 antibody in leprosy patients across the disease spectrum, a response associated with disease progression. IgG1 antibodies in leprosy also show a negative association with interferon-gamma, a critical T cell cytokine responsible for macrophage activation and intracellular killing of mycobacteria. We therefore queried if antibody and T cell responses were being evoked by different epitopes in ML GroES proteins. To address the issue of epitope recognition in mycobacterial diseases, we have analysed 16 peptides (15-mer peptides) spanning the entire ML and M. tuberculosis GroES protein in leprosy (n = 19) and tuberculosis (n = 9) patients and healthy endemic controls (n = 8). Our analysis demonstrates clearly that the dominant peptides evokingT cell and IgG subclass antibodies were different. The target of both T and B cell responses were cross-reactive epitopes in all groups. Differences in disease and healthy states related to the strength (mean intensity) of the T cell and antibody response. IgG1 and IgG3 antibodies were associated with disseminated disease and IgG 2 and IgG4 with disease limitation. Such comprehensive immune profiling of antigen-specific responses is critical to understanding the disease pathogenesis and also if these reagents are to be exploited for either diagnostic or vaccine purposes

Longitudinal Tracking of Cytokines after Acute Exposure to Tuberculosis: Association of Distinct Cytokine Patterns with Protection and Disease Development▿

Household contacts (HCs) of patients with tuberculosis (TB) are at higher risk of infection as well as the development of active disease. Longitudinal tracking of antigen-specific cytokines after acute exposure may significantly advance our understanding of the dynamic changes in cytokine patterns associated with disease establishment. To achieve this objective, we carried out a prospective cohort study with healthy HCs after exposure to TB. The patterns of cytokines (gamma interferon [IFN-γ] and interleukin 10 [IL-10]) in response to mycobacterial antigens (culture filtrate [CF] proteins) and nonspecific mitogens (phytohemagglutinin [PHA] and lipopolysaccharide [LPS]) were assessed at 0, 6, 12, and 24 months after exposure. Seven of 109 (6.4%) HCs developed active disease. Six of the seven individuals were females, and active disease developed between 12 and 15 months after exposure in 5/20 families. The most significant findings were the exponential increases (∼1,000-fold) in both the CF protein- and the PHA- or LPS-induced IFN-γ/IL-10 ratio in healthy HCs (n = 26), which peaked at 12 months, compared to the levels in HCs who developed disease (n = 7), in whom relatively flat responses were observed during the 24-month period. Linear trends for 0 to 12 and 0 to 24 months for the CF protein-induced IFN-γ/IL-10 ratio showed significant differences between the two groups, as determined by the use of the Mantel extension test for χ2 analysis (odds ratio = 0.45; 95% confidence interval = 0.295 to 0.685; P = 0.0002). Our results strongly suggest that the magnitude of the IFN-γ/IL-10 ratio at 12 months after exposure may be a critical determinant in the resolution of infection. These studies provide new insights into the cytokine responses associated with disease establishment or the resolution of infection after natural exposure to TB and have implications for TB control programs as well vaccine efficacy studies

Association of plasma cytokines with radiological recovery in pulmonary tuberculosis patients

Background: The characterization of tuberculosis (TB) patients as slow or fast responders post anti-TB treatment has always been a matter of tremendous interest as slow responders are most likely to relapse and/or develop complications. Pulmonary tissue healing as assessed with radiology is the only available tool for tissue recovery but is not predictive at intake. The objective of the current study was to assess biomarkers associated with fast and slow recovery in TB patients at recruitment.Methods: Pulmonary TB patients (N=15) were assessed for radiological recovery serially in parallel with clinical signs and symptoms, hematological parameters, and plasma cytokines at 0months, 6months, 12months, and 24months. On the basis of differential radiological healing, patients were characterized into slow ( \u3e 12months), intermediate ( \u3c 12months), and fast ( \u3c 6months) responders.Results: Baseline plasma cytokines (interleukin [IL]-2, -4, -6, -10, tumor necrosis factor-alpha, and interferon-gamma) were determined using cytometric bead array. IL-2 and -4 were able to accurately differentiate slow and fast responders into two distinct clusters using hierarchal clustering analysis. Compared with fast responders, slow responders showed significantly high IL-2 and -4 at baseline (p=.001 Mann-Whitney U test).CONCLUSION: In-depth analysis of cytokines and its association with radiological recovery in TB patients may be useful in monitoring TB patients postchemotherapy for both clinicians and TB control program

Th1/Th2 Cytometric Bead Array can discriminate cytokine secretion from endogenously activated cells in pulmonary disease, recent and remote infection in tuberculosis

Differential T cell trafficking through the blood compartment towards infected foci may be occurring in different stages of tuberculosis disease and infection. The aim of the present study was to identify cytokine signatures in the blood compartment in tuberculosis Patients with pulmonary disease (PTB = 19), recently exposed household contacts (HC = 27) and nonexposed community controls (EC = 37). Diluted (1:10) whole blood was cultured for 2 days and cytokine secretion was assessed using Cytometric Bead Array (Th1/Th2 kit II, BD Biosciences) which included IL-2, TNF-alpha, IFN-gamma (Type1/T1),IL-4, IL-6 and IL-10 (Type2/T2). All T1/T2 cytokines were elevated in PTB (AUROC \u3e 0.9) while HC showed selective elevation of IL-6 (AUROC \u3e 0.7) compared to EC. Principal component analysis (PCA) extracted two groupings with Eigen values \u3e 1, IL-6 separated into the second component for PTB, HC and EC. After rotation, IFN-gamma was correlated with the first component for PTB and EC and the second component for HC indicating an absence of T1/T2 dichotomy. Therefore endogenous cytokine signatures may indicate differential T cell trafficking in different stages of tuberculosis infection and disease

Endogenously Activated Interleukin-4 Differentiates Disease Progressors and Non-Progressors in Tuberculosis Susceptible Families: A 2-Year Biomarkers Follow-Up Study

Objective:Dynamic cytokine profiles from endogenously activated T cells in transit from lymph node to the infected sites via the blood compartment after recent exposure to Mycobacterium tuberculosis may differentiate disease progressors from non-disease progressors in a BCG-vaccinated population. Methods: Household contacts (N = 107) from families with (six families) or without (14 families) secondary cases were assessed for Types 1 and 2 cytokines serially in plasma of whole blood cultures without exogenous stimulation. ARMS PCR was carried out for detection of single nucleotide polymorphism T/A in IFN-gamma +874. Results: In the absence of IFN-gamma expansion, raised IL-4 at 6 months was associated with disease progression in TB-susceptible families. Resistant families on the other hand showed overrepresentation of IFN-gamma +874 A allele and expansion of IFN-gamma secreting cells at 6 months followed by contraction at 12 months. Conclusion: Six months may be an important checkpoint for biomarker assessment in high-risk individuals post-exposure