Optimization based automated curation of metabolic reconstructions

<p>Abstract</p> <p>Background</p> <p>Currently, there exists tens of different microbial and eukaryotic metabolic reconstructions (e.g., <it>Escherichia coli, Saccharomyces cerevisiae</it>, <it>Bacillus subtilis</it>) with many more under development. All of these reconstructions are inherently incomplete with some functionalities missing due to the lack of experimental and/or homology information. A key challenge in the automated generation of genome-scale reconstructions is the elucidation of these gaps and the subsequent generation of hypotheses to bridge them.</p> <p>Results</p> <p>In this work, an optimization based procedure is proposed to identify and eliminate network gaps in these reconstructions. First we identify the metabolites in the metabolic network reconstruction which cannot be produced under any uptake conditions and subsequently we identify the reactions from a customized multi-organism database that restores the connectivity of these metabolites to the parent network using four mechanisms. This connectivity restoration is hypothesized to take place through four mechanisms: a) reversing the directionality of one or more reactions in the existing model, b) adding reaction from another organism to provide functionality absent in the existing model, c) adding external transport mechanisms to allow for importation of metabolites in the existing model and d) restore flow by adding intracellular transport reactions in multi-compartment models. We demonstrate this procedure for the genome- scale reconstruction of <it>Escherichia coli </it>and also <it>Saccharomyces cerevisiae </it>wherein compartmentalization of intra-cellular reactions results in a more complex topology of the metabolic network. We determine that about 10% of metabolites in <it>E. coli </it>and 30% of metabolites in <it>S. cerevisiae </it>cannot carry any flux. Interestingly, the dominant flow restoration mechanism is directionality reversals of existing reactions in the respective models.</p> <p>Conclusion</p> <p>We have proposed systematic methods to identify and fill gaps in genome-scale metabolic reconstructions. The identified gaps can be filled both by making modifications in the existing model and by adding missing reactions by reconciling multi-organism databases of reactions with existing genome-scale models. Computational results provide a list of hypotheses to be queried further and tested experimentally.</p

Statistical Results of Multivariate Fox-H Function for Exact Performance Analysis of RIS-Assisted Wireless Communication

Existing research provides statistical results on the sum of single-variate Fox-H functions to analyze the performance of diversity receivers and reconfigurable intelligent surfaces (RIS) based wireless systems. There is a research gap in exact performance analysis when more than a single-variate Fox-H function represents the statistical characterization of wireless systems. In this paper, we propose a novel approach to obtain the distribution of the sum of independent and non-identically distributed (i.ni.d) random variables characterized by the multivariate Fox-H function. Further, we develop a general framework for an exact analysis of the ergodic capacity when the multivariate Fox-H function characterizes the statistics of signal-to-noise ratio (SNR). We apply the derived results to conduct an exact performance analysis of outage probability and ergodic capacity, taking an example of RIS-assisted communication over Rician fading channels with phase errors. We conduct computer simulations to validate the exact analysis and demonstrate performance of the RIS-assisted system under various practically relevant scenarios for a better performance assessment

Evaluation of antioxidant activity of ormeloxifene: in vitro study

Background: Ormeloxifene (Centchroman) is a Selective Estrogen Receptor Modulator (SERM) which acts as estrogen antagonist and having anti progestogenic activity also. It is being used in the management of dysfunctional uterine bleeding and as nonhormonal oral contraceptive. It is also being investigated for the indications such as osteoporosis, breast and endometrial carcinoma. In this study, we have evaluated the Antioxidant potential of drug by using DPPH and NO synthase Assay. It was found that ormeloxifene has significant antioxidant activity which could be cause for its use in various gynaecological and other conditions.Methods: In this study, we have demonstrated in vitro antioxidant activity of ormeloxifene. DPPH and NO synthase assay tests were done for different concentrations of ormeloxifene.Results: In our study, it showed that the free radical scavenging activity of ormeloxifene was less in lower concentration and increased in the higher concentration in DPPH assay. The free radical scavenging activity of drug ormeloxifene was 22% at 100µg/ml and 27% for the concentrations of 1000µg/ml in DPPH assay. No scavenging activity was 3% at 100µg/ml and 11% at 1000µg/ml.Conclusions: The invitro antioxidant analysis of ormeloxifene, was proved to be a potent antioxidant

Comparison of diagnostic accuracy of APRI and Transient Elastography for prediction of esophageal variceal bleed in liver cirrhosis

Background: Liver Cirrhosis is the end-stage for chronic liver disease. Repeated course of endoscopy is recommended, as this intervention is expensive and often poorly accepted by patients, there is a need for non-invasive methods to predicts the progression of portal hypertension as well as the presence and size of esophageal varices. This study was aimed to assess the APRI and Transient Elastography for predicting esophageal variceal bleed in cirrhotic patients. Objectives of the study were to study Diagnostic accuracy of APRI for Prediction of esophageal variceal bleed in liver cirrhosis, diagnostic accuracy of Transient Elastography for Prediction of esophageal variceal bleed in liver cirrhosis, comparison of diagnostic accuracy of APRI and Transient Elastography for Prediction of esophageal variceal bleed in liver cirrhosis. Methods: It was a Single centre, observational study in 35 patients of chronic liver disease. Patients were included in the study after fulfilling inclusion and exclusion criteria. CBC, LFT, KFT, SE, viral marker, USG whole abdomen, UGIE, Transient Elastography was done. APRI was calculated for every patient. Results: The APRI and Transient Elastography showed moderate diagnostic accuracy in predicting the presence of esophageal variceal bleed. Transient Elastography performed better for prediction of esophageal variceal bleed. Conclusions: The APRI and Transient Elastography showed moderate diagnostic accuracy in predicting the presence of esophageal variceal bleed. They help in starting prophylactic therapy earlier to prevent the bleeding and other complications of varices. These non-invasive parameters can also play an effective role in conjunction with endoscopy in predicting the presence of esophageal varices

PQ improvement by moderation of multi-level inverter controlling techniques and intensifying the performance of DVR

A novel control scheme is proposed for the enhancement of Dynamic Voltage Restorer (DVR) performance. In this paper, the moderation of inverter controlling techniques has been adopted to intensify the DVR characteristics and thereby to improve the Power Quality. The proposed model verification has been obtained by simulation of the PWM patterns which provides the better utilization of the device (DVR) for the compensation of voltage deviations during voltage sag. Also, it has been shown that Dynamic Voltage Restorer can be worked as a harmonic compensator for the compensation of the current and voltage harmonics. Obtained simulation results verify that the control approach gives very effective regulation and performs excellent voltage compensation by adopting multilevel inverter

Solvent extraction and separation of zinc and cobalt from ammoniacal solution

A process was developed to recover Zn and Co by solvent extraction from the raffinate generated during processing of sea nodules. From a model ammoniacal solution containing 0.2 g/L Zn or 0.2 g/L Co, extraction of Zn and Co by Versatic acid was studied. A maximum of 87% Zn was extracted with 1M Versatic acid in single stage, whereas extraction of Co was negligible due to its higher oxidation state. When Co(III) was reduced to Co(II) by the addition of cobalt powder, 1M Versatic acid extracted 76% Co in a single stage. From the McCabe Thiele diagram number of counter current extraction stages required for complete recovery of Zn and Co from ammoniacal solution was determined. Simulation of counter current extraction of Zn and Co was also carried out. Thus, this process can be used to recover Zn, leaving Co in the raffinate. Then Co can be recovered by solvent extraction with Versatic acid after reducing Co(III) to Co(II) state

Isolation and molecular characterization of symbiotic bacterial isolates associated with entomopathogenic nematodes in agro climatic zone 5 of Karnataka

The investigation was carried out to study the biochemical characterization of symbiotic bacteria associated with entomopathogenic nematodes isolated from agro climatic zone 5 of Karnataka. Twenty two entomopathogenic nematodes were isolated by insect bait method using fifth instar larvae of Galleria mellonella. Twenty symbiotic bacteria were isolated from these entomopathogenic nematodes and named based on the source place. These isolates were identified based on microscopic observation, biochemical and physiological characters like Gelatin liquefaction test, Catalase test, Lactose fermentation test, Urease test, Motility test and Colony morphology studies on Nutrient agar, NBTA and Mac Conkey agar media. The diversity of these isolates was characterized by using RAPD markers. Primer screening was carried out using 13 decamer random primers, out of which 7 primers were detected for RAPD analysis. A total of 44 bands were scored out of which 42 bands were found to be polymorphic. Statistical analysis of RAPD data clearly depicted that all the 20 symbiotic bacterial isolates formed four major clusters. The percent polymorphism observed in the isolates was 95.45% which is quiet high and suggests that the symbiotic bacterial population exhibit high genetic diversity

CD4+ T-lymphocytes exhibit biphasic kinetics post-myocardial infarction

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