A Discriminative Feature Space for Detecting and Recognizing Pathologies of the Vertebral Column

Each year it has become more and more difficult for healthcare providers to determine if a patient has a pathology related to the vertebral column. There is great potential to become more efficient and effective in terms of quality of care provided to patients through the use of automated systems.

However, in many cases automated systems can allow for mis classification and force providers to have to review more causes than necessary. In this study, we analyzed methods to increase the True Positives and lower the False Positives while comparing them against state of- the-art techniques in the biomedical community. We found that by applying the studied techniques of a data-driven model, the benefits to healthcare providers are significant and align with the methodologies and techniques utilized in the current research community.

In silico Study of Bacillus brevis Xylanase - Structure Prediction and Comparative Analysis with Other Bacterial and Fungal Xylanase

The most important building block of hemicelluloses is xylan. It is broken down into xylose oligomer residues by Xylanase - an enzyme, produced by most organisms, to utilize xylose as primary source of carbon. The Xylanase produced are classified into families, viz 5, 8, 10, 11 and 43 - of Glycoside Hydrolases (GH).

Xylanase from family GH 11 are monospecific, they consist solely of Xylanase activity, exclusively active on D-xylose containing substrates.They are inactive on aryl cellobiosidase. The fungal Xylanase are produced in higher concentrations, as compared to bacterial Xylanase, but have limited use in pulp bleaching, as they affect the viscosity and strength of the product. In the present study, we have worked upon the Xylanase of Bacillus brevis, which is fulfilling all the required quality needed to be a commercial Xylanase, and thus is used by many industries. The enzyme, when studied after modelling, provided similar structural configuration with high stability. When compared with other bacterial and fungal Xylanase structures, it provided better potential to ‘activity enhancement’ and ‘in silico handling’.

Bio-Analytical Method Development and Validation for Estimation of Lume fantrine in Human Plasma by Using Lc-Ms/Ms

Lumefantrine and Glimepiride (IS) were extracted from human plasma by Precipitation followed by Solid phase extraction using Orochem (30 mg/1 CC) solid phase extraction cartridge. The chromatographic separation was performed on Hypurity C18 (50 cm×4.6 mm), 5 μ column. The mobile phase consisted of Acetonitrile: 2 mM Ammonium Acetate (pH: 3.5) (90:10, % v/v) was delivered at rate of 0.600 mL/min with Splitter. Detection and quantitation were performed by a triple quadrupole equipped with electro spray ionization and multiple reaction monitoring inpositive ionization mode (API 3000). The most intense [M-H]- transition for Lume fantrine at m/z 528.0→510.0 and for IS at m/z 491.2→352.0 were used for quantification. 

Download PDF

Role of In-silico methods in the identification of Novel Drugs

Drug designing and the molecular dynamic studies are lengthy, intensified and inter-disciplinary activity. Approaches like computational chemistry and molecular modeling are widely applied in the development of in-silico drug design because it is cost effective.  Currently, a vast number of software is used in drug design. Using in-silico drug designing techniques it is possible to produce active lead molecule right from the preclinical discovery stage to late stage clinical development. The lead molecules will be helpful in the selection of potent leads to cure particular diseases. In-silico methods thus are important in target identification and prediction of novel drugs.

Download PDF

Editorial for International Journal of biomedical Data Mining

This issue of the International Journal of Biomedical Data Mining presents two contributed articles. The first article, entitled Data Inventory for Cancer Patients Receiving Radiotherapy for Outcome Analysis and Modeling, authored by Jason Vickress, Rob Barnett and Slav Yartsev, describes a database created for storing and analyzing patient specific data related to pre-treatment condition, treatment planning, and treatment outcomes, for patients receiving radiotherapy based cancer treatment. 

The proposed database can perform automated analysis regarding quality assurance, dose accumulation for multiple treatments on different machines and can assist physicians in choosing the optimal radiation therapy for new patients. The second article, entitled Likelihood Ratio Test of Hardy-Weinberg Equilibrium Using Uncertain Genotypes for Sibship Data, authored by Qiong Li, Helene Massam and Xin Gao, is concerned with the problem of testing for Hardy-Weinberg equilibrium of genotype frequencies in the area of population genetics.

DNA/RNA Fragmentation and Cytolysis in Human Cancer Cells Treated with Diphthamide Nano Particles Derivatives

Molecular structure activity studies for some Diphthamide Nano particles derivatives indicate that the conformational characteristics along with the nature and position of the substituents on the Diphthamide Nano particles derivatives ring play an important role in their biological and biochemical activities (Figure 1). Therefore, we have calculated the optimized molecular geometries of some Diphthamide Nano particles derivatives. 

Calculations are carried out on the structures of these medical, medicinal and pharmaceutical Nano drugs using Hartree–Fock calculations and also Density Functional Theory (DFT) by performing HF, PM3, MM2, MM3, AM1, MP2, MP3, MP4, CCSD, CCSD(T), LDA, BVWN, BLYP and B3LYP levels of theory using the standard 31G, 6–31G*, 6–31+G*, 6–31G(3df, 3pd), 6–311G, 6–311G* and 6–311+G* basis sets of the Gaussian 09. The comparative heats of formation and Natural Bond Orbital (NBO) charges are calculated for these Diphthamide Nano particles derivatives. We have finally obtained some conformational rules in terms of the natures and positions of the substituents on the Diphthamide Nano particles derivatives ring.

Selenoergothionein as a Potential Inhibitor against Amyloid β-Protein (Aβ): Docking and Molecular Dynamics Studies

Alzheimer‘s disease (AD) is a progressive neurodegenerative disorder, encircling the deterioration of cognitive functions and behavioral changes, characterized by the aggregation of amyloid β-protein (Aβ) into fibrillar amyloid plaques in elected areas of the brain with the lipid-carrier protein apolipoprotein E (apoE), the microtubule associated protein tau, and the presynaptic protein α-synuclein. 

High levels of fibrillary Aβ, the main constituent of senile plaques, are deposited in the AD brain that outcome in the thrashing of synapses, neurons and destruction of neuronal role. Aβ is derived from the amyloid precursor protein through sequential protein cleavage by aspartyl protease, β-secretase and presenilin-dependent β-secretase triggering a spill of events such as oxidative damage, neurotoxicity, and inflammation that contributes to the progression of AD. Therefore the Aβ protein may be a target for anti-Alzheimer drugs.

DNA/RNA Fragmentation and Cytolysis in Human Cancer Cells Treated with Diphthamide Nano Particles Derivatives

Molecular structure activity studies for some Diphthamide Nano particles derivatives indicate that the conformational characteristics along with the nature and position of the substituents on the Diphthamide Nano particles derivatives ring play an important role in their biological and biochemical activities. 

Therefore, we have calculated the optimized molecular geometries of some Diphthamide Nano particles derivatives. Calculations are carried out on the structures of these medical, medicinal and pharmaceutical Nano drugs using Hartree–Fock calculations and also Density Functional Theory (DFT) by performing HF, PM3, MM2, MM3, AM1, MP2, MP3, MP4, CCSD, CCSD(T), LDA, BVWN, BLYP and B3LYP levels of theory using the standard 31G, 6–31G*, 6–31+G*, 6–31G(3df, 3pd), 6–311G, 6–311G* and 6–311+G* basis sets of the Gaussian 09.

Get PDF Link Here

Bioinformatics enables biotechnology and cancer research

Genomics and molecular biology has been a source of inspiration for biology and biotechnology research worldwide. Scientists and the researchers are unable to analyze this huge data manually so that innovative theraputical solutions have emerged for the data analysis. Bioinformatics come to the rescue of the scientists and researchers in digging the information efficiently. Bioinformatics is particularly capable of developing the next generation cancer research from the data and can come with innovative solutions to cure cancer.

Get PDF Link Here

Likelihood Ratio Test of Hardy-Weinberg Equilibrium Using Uncertain Genotypes for Sibship Data

Testing for Hardy-Weinberg equilibrium of genotype frequencies is a crucial first step in the study of population genetics. In this paper, we develop an Expectation-Maximization algorithm to estimate the genotype frequencies for sibship data with genotype uncertainty. 

We also develop a likelihood ratio test of Hardy-Weinberg equilibrium for sibships with no parental genotypes available and with possible genotyping errors. Simulations show that our likelihood ratio test maintains valid control of the type I error rate and good statistical power. Finally, the likelihood ratio test is extended across strata when a sample is stratified by multiple ethnic populations with different genotype frequencies.