In Silico Analysis of Differentially Expressed Genes in Colorectal Carcinoma

Background: Colorectal carcinoma (CRC) is a primary cause of morbidity and mortality worldwide. Resistance to therapy contributes to poor patient prognosis. The aim of our study is to identify the key proteins and interaction networks implicated in CRC which may serve as possible therapeutic targets and help in overcoming therapy resistance.Methods: The microarray dataset of 58 cases and 62 controls was used to identify Differentially Expressed Genes (DEGs).After constructing protein-protein interaction networks , Cytoscape analysis was done to identify the hub proteins. Based on sub graph centrality, between-ness and degree (≥10), hub proteins were selected for further literature search and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis.Results: A total of 85 up-regulated genes and 95 down-regulated genes of CRC patients were selected based on criteria of P>0.05 and fold change>2.0. The PPI analysis revealed STAT3, HNRNPA2B1, RBM8A, RBM25, ATM, HIST1H2BK, SRSF5 and HNRNPDLas hub proteins. On the basis of criteria set for cytoscape analysis, STAT3 and HNRNPA2B1 were identified as key hub proteins. KEGG pathway analysis revealed vital role of STAT3 in carcinogenesis.Conclusion: In addition of HNRNPA2B1 activation by STAT3, cross talk of STAT3 with other oncogenic signaling pathways signifies its role in colorectal carcinogenesis. Our study highlights thatSTAT3may be a possible therapeutic target which may help in overcoming the dilemma of resistance to drug treatment in advanced cases.Keywords: STAT3, drug resistance, targeted therapy, bioinformatics    

Cardiovascular disease risk factors in Pakistani population with newly diagnosed Type 2 diabetes mellitus: A cross-sectional study of selected family practitioner clinics in four provinces of Pakistan (CardiP Study)

Objective: To explore cardiovascular risk factors in people with newly-diagnosed type 2 diabetes mellitus. Methods: The cross-sectional, prospective, multicentre, study was conducted from June 2014 till July 2015 at family practice clinics in 27 cities across Pakistan, and comprised individuals aged 30-50 years diagnosed with type 2 diabetes mellitus within the preceding six months. Laboratory investigations were conducted at Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, and Aga Khan University Hospital, Karachi. The 10-year absolute risk of fatal or non-fatal coronary heart disease and stroke was calculated using the United Kingdom Prospective Diabetes Study Risk Engine version 2.0. Data were analysed using SPSS 19. Results: Out of 888 subjects, 362(40.8%) were women and 526(59.2%) were men. The overall mean presenting age was 42.4±5.8 years. After stratification by age, those ≥40 years were significantly associated with higher glycated haemoglobin (p=0.02) and those ≤39 years were associated with higher levels of very low density lipoprotein (p=0.001) and triglyceride (p=0.006). The mean risk estimate for CHD was 9.7% (95% Confidence Interval (CI) 9.0- 10.1)), for fatal CHD 4.4% (95% CI 4.0-4.6), for stroke 1.5% (95% CI 1.2-1.7), and for fatal stroke 0.25% (95% CI 0.24- 0.26). Conclusion: There is a need for screening cardiovascular risk factors even in younger age groups of newlydiagnosed diabetes

Formulation design and evaluation of Cefuroxime axetil 125 mg immediate release tablets using different concentration of sodium lauryl sulphate as solubility enhancer

Formularam-se comprimidos de liberação imediata à base de cefuroxima axetil, pelo método de compressão direta, com diferentes percentagens de lauril sulfato de sódio (LSS), tais como 0,5, 1,0, 1,5, e também sem SLS. Os lotes resultantes dos comprimidos foram avaliados por ambos os métodos da farmacopeia e não farmacopeicos para determinar as propriedades físico-mecânicas. O teste de dissolução foi realizado em meios diferentes, como HCl 0,07 M, água destilada, HCl 0,1 M com pH 1,2 e os tampões fosfato (pH 4,5 e 6,8) para observar a liberação do fármaco contra a correspondente concentração de LSS utilizado. Em seguida, as formulações de teste foram comparadas por fatores f1 (dissimilaridade) e f2 (similaridade), utilizando uma marca de referência de cefuroxima axetil. Diferenças significativas (pCefuroxime axetil immediate release tablets were formulated by direct compression method with different percentages of sodium lauryl sulphate (SLS) such as 0.5, 1.0, 1.5 and also without SLS. Resulting batches of tablets were evaluated by both pharmacopeial and non-pharmacopeial methods to ascertain the physico-mechanical properties. Dissolution test were carried out in different medium like 0.07 M HCl, distilled water, 0.1M HCl of pH 1.2 and phosphate buffers at pH 4.5 and 6.8 to observe the drug release against the respective concentration of SLS used. Later, test formulations were compared by f1 (dissimilarity) and f2 (similarity) factors using a reference brand of cefuroxime axetil. Significant differences (

HCV genotype-specific correlation with serum markers: Higher predictability for genotype 4a

Several factors have been proposed to assess the clinical outcome of HCV infection. The correlation of HCV genotypes to possible serum markers in clinical prediction is still controversial. The main objective of this study was to determine the existence of any correlation between HCV genotypes to viral load and different clinical serum markers.We performed a prospective cross-sectional and observational study. About 3160 serum HCV RNA positive patients were chosen from 4020 randomly selected anti-HCV positive patients. Statistical analysis was performed using the SPSS 16 software package. ROC (receiver operating characteristics) curves were used to compare diagnostic values of serum markers to predict genotypes.The most prevalent genotype was 3a (73.9%) followed by 1a (10.7%), 4a (6.4%) and 3b (6.1%) in Pakistani population. No correlation was found between viral load and serum markers for genotype 3a in a large no. of sample (n = 2336). While significant correlation was observed between viral load and AST in genotype 3b, ALP with viral load and ALT for genotype 1a. Patients with genotype 4a showed a significant inverse correlation with viral load and Hb level and AST with ALP. For genotype 4a, AUC (area under the curve) of ALT, ALP, AST, bilirubin, Hb level and viral load was 0.790, 0.763, 0.454, 0.664, 0.458 and 0.872 respectively.In conclusion, there was a significant variable response of HCV genotypes with serum markers. Severity of disease is independent of serum marker level in genotype 3a, while the liver damage in genotype 4a may associate with viral cytopathic effect as well as the immune-mediated process. An index using six serum markers may correctly predict genotype 4a in patients with ≥ 75% accuracy

Claudin-1 required for HCV virus entry has high potential for phosphorylation and O-glycosylation

HCV is a leading cause of hepatocellular carcinoma and cirrhosis all over the world. Claudins belong to family of tight junction's proteins that are responsible for establishing barriers for controlling the flow of molecules around cells. For therapeutic strategies, regulation of viral entry into the host cells holds a lot of promise. During HCV infection claudin-1 is highly expressed in liver and believed to be associated with HCV virus entry after HCV binding with or without co-receptor CD81. The claudin-1 assembly with tight junctions is regulated by post translational modifications. During claudins assembly and disassembly with tight junctions, phosphorylation is required at C-terminal tail. In cellular proteins, interplay between phosphorylation and O-β-GlcNAc modification is believed to be functional switch, but it is very difficult to monitor these functional and vibrant changes in vivo. Netphos 2.0 and Disphos 1.3 programs were used for potential phosphorylation; NetPhosK 1.0 and KinasePhos for kinase prediction; and YinOYang 1.2 and OGPET to predict possible O-glycosylation sites. We also identified Yin Yang sites that may have potential for O-β-GlcNAc and phosphorylation interplay at same Ser/Thr residues. We for the first time proposed that alternate phosphorylation and O-β-GlcNAc modification on Ser 192, Ser 205, Ser 206; and Thr 191 may provide an on/off switch to regulate assembly of claudin-1 at tight junctions. In addition these phosphorylation sites may be targeted by novel chemotherapeutic agents to prevent phosphorylation lead by HCV viral entry complex

Genomic Research Data Generation, Analysis and Sharing – Challenges in the African Setting

International audienceGenomics is the study of the genetic material that constitutes the genomes of organisms. This genetic material can be sequenced and it provides a powerful tool for the study of human, plant and animal evolutionary history and diseases. Genomics research is becoming increasingly commonplace due to significant advances in and reducing costs of technologies such as sequencing. This has led to new challenges including increasing cost and complexity of data. There is, therefore, an increasing need for computing infrastructure and skills to manage, store, analyze and interpret the data. In addition, there is a significant cost associated with recruitment of participants and collection and processing of biological samples, particularly for large human genetics studies on specific diseases. As a result, researchers are often reluctant to share the data due to the effort and associated cost. In Africa, where researchers are most commonly at the study recruitment, determination of phenotypes and collection of biological samples end of the genomic research spectrum, rather than the generation of genomic data, data sharing without adequate safeguards for the interests of the primary data generators is a concern. There are substantial ethical considerations in the sharing of human genomics data. The broad consent for data sharing preferred by genomics researchers and funders does not necessarily align with the expectations of researchers, research participants, legal authorities and bioethicists. In Africa, this is complicated by concerns about comprehension of genomics research studies, quality of research ethics reviews and understanding of the implications of broad consent, secondary analyses of shared data, return of results and incidental findings. Additional challenges with genomics research in Africa include the inability to transfer, store, process and analyze large-scale genomics data on the continent, because this requires highly specialized skills and expensive computing infrastructure which are often unavailable. Recently initiatives such as H3Africa and H3ABioNet which aim to build capacity for large-scale genomics projects in Africa have emerged. Here we describe such initiatives, including the challenges faced in the generation, analysis and sharing of genomic data and how these challenges are being overcome

Revised cutoff values of ALT and HBV DNA level can better differentiate HBeAg (-) chronic inactive HBV patients from active carriers

<p>Abstract</p> <p>Background and Aims</p> <p>ELISA is still used as primary test for diagnosis HBV disease. However, ELISA-positive patients were marked as HBV inactive after confirmation with PCR and vice versa. Our aim was to assess the performance of new cut-off value of ALT, HBV DNA load and significance of AST as screening tool for HBeAg (-) chronic active or inactive patients in Pakistani population.</p> <p>Materials and methods</p> <p>In a cross-sectional, cohort study, 567 HBeAg (-) patients followed for one year were selected. Patients with persistent elevated ALT than normal and HBV DNA ≥ 100,000 copies/mL were taken as active chronic. Diagnostic values for ALT, AST and HBV DNA load in HBV HBeAg (-) chronic active and inactive patients compared using receiver operation characteristic (ROC) curves.</p> <p>Results</p> <p>Of 567 HBeAg (-) patients, 228 were classified as chronic inactive and 339 as active. HBV infection was dominant in male. Serum ALT, AST and HBV DNA levels showed significant and high AUROC to differentiate chronic HBeAg (-) inactive patients from active. AUROC for Serum ALT, AST and HBV DNA were observed 0.997, 0.969 and 1.000, respectively. For revised cut off value for ALT (30 IU/L for male and 19 IU/L for female) and HBV DNA load ≥100,000 copies/mL, a PPV of 97%, NPV of 94%, a sensitivity of 98%, and a specificity of 92% was observed to discriminate active carriers from inactive carriers. We also observed 93.5% specificity, 83.1% sensitivity, 82% PPV and 89.5% NPV for AST ≤20 IU/L to differentiate inactive carriers from active ones in our study group.</p> <p>Conclusions</p> <p>Revised cut off value of ALT and NIH derived HBV DNA value can better discriminate between HBeAg (-) chronic active and inactive patients.</p

A comparison of four fibrosis indexes in chronic HCV: Development of new fibrosis-cirrhosis index (FCI)

<p>Abstract</p> <p>Background</p> <p>Hepatitis C can lead to liver fibrosis and cirrhosis. We compared readily available non-invasive fibrosis indexes for the fibrosis progression discrimination to find a better combination of existing non-invasive markers.</p> <p>Methods</p> <p>We studied 157 HCV infected patients who underwent liver biopsy. In order to differentiate HCV fibrosis progression, readily available AAR, APRI, FI and FIB-4 serum indexes were tested in the patients. We derived a new fibrosis-cirrhosis index (FCI) comprised of ALP, bilirubin, serum albumin and platelet count. FCI = [(ALP × Bilirubin) / (Albumin × Platelet count)].</p> <p>Results</p> <p>Already established serum indexes AAR, APRI, FI and FIB-4 were able to stage liver fibrosis with correlation coefficient indexes 0.130, 0.444, 0.578 and 0.494, respectively. Our new fibrosis cirrhosis index FCI significantly correlated with the histological fibrosis stages F0-F1, F2-F3 and F4 (r = 0.818, p < 0.05) with AUROCs 0.932 and 0.996, respectively. The sensitivity and PPV of FCI at a cutoff value < 0.130 for predicting fibrosis stage F0-F1 was 81% and 82%, respectively with AUROC 0.932. Corresponding value of FCI at a cutoff value ≥1.25 for the prediction of cirrhosis was 86% and 100%.</p> <p>Conclusions</p> <p>The fibrosis-cirrhosis index (FCI) accurately predicted fibrosis stages in HCV infected patients and seems more efficient than frequently used serum indexes.</p

New Hierarchical Routing Protocol Based on K-Means Clustering with Exploiting Free Time Slot for Wireless Sensor Networks

The operation time of LEACH protocol is divided into several frames. Each frame consists of a number of equal time slots where the selection of cluster heads and the re-establishment of clusters are periodic. Each member of the cluster exploits its own time slot to transmit the data, then it turns off its radio to reduce energy consumption. Here, the clusters generated are not uniformly distributed and the time slots of the dead member nodes are not allocated. We propose an improved version, which is based simultaneously on the integration of the clustering approach K-Means and the exploitation of the free time slot in favor of cluster head in the transmission phase. The results show that the proposed protocol allowed us to achieve increased throughput, improved reliability of the packet delivery ratio, low routing load and an effective reduction in energy consumption for low node density in WSNs