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author:("mazumdar, A.")
Ancient Science of Life  2002;21(3):191-197.
The mycotoxin Citrinin was obtained from the fungus Penicillium citrinum. It was tested for it's Minimum Inhibitory Concentration (MIC) against some gram positive strains viz. Staphylococcus aureus, Bacillus pumilus, Bacillus subtillis, Bacillus cereus, Klebsiella pneumoniae, Streptococcus pneumoniae, Lactobacillus arabinosus and gram negative strains E.Coli, Shigella dysenteriae, shigella sonnei, shigella boydii, Salmonella typhimurium, Proteus mirabilis and Vibrio cholerae. Further the zones of inhibition produced by the fungal extract against the bacterial strains were assayed and compared with those produced by the standard antibiotic ciprofloxacin.
PMCID: PMC3331043  PMID: 22557053
2.  Pharmacognostical and Phytochemical Evaluation of the leaves of Bauhinia purpurea Linn. 
Ancient Science of Life  2010;30(2):28-32.
Various pharmacognostic parameters including macroscopy, microscopy, chemomicroscopy and behaviour of powdered drug on treatment with different chemical reagents were studied on the leaves of Bauhinia purpurea Linn. (Family Caesalpinaceae). Phytochemical screening of the plant part with various solvents revealed the presence of phenolic compounds, tannins, flavonoids, phytosterols, saponins and glycosides in it.
PMCID: PMC3336273  PMID: 22557422
3.  Arsenic Contamination of Ground Water and its Health Impact on Population of District of Nadia, West Bengal, India 
The global health impact and disease burden due to chronic arsenic toxicity has not been well studied in West Bengal.
To ascertain these, a scientific epidemiological study was carried out in a district of the state.
Materials and Methods:
Epidemiological study was carried out by house-to-house survey of arsenic affected villages in the district of Nadia. A stratified multi-stage design has been adopted for this survey for the selection of the participants. A total number of 2297 households of 37 arsenic affected villages in all the 17 blocks were surveyed in the district.
Out of 10469 participants examined, prevalence rate of arsenicosis was found to be 15.43%. Out of 0.84 million people suspected to be exposed to arsenic, 0.14 million people are estimated to be suffering from arsenicosis in the district. Highest level of arsenic in drinking water sources was found to be 1362 μg/l, and in 23% cases it was above 100 μg/l. Majority of the population living in the arsenic affected villages were of low socio-economic condition, inadequate education and were farmers or doing physical labour. Chronic lung disease was found in 207 (12.81%) subjects among cases and 69 (0.78%) in controls. Peripheral neuropathy was found in 257 (15.9%) cases and 136 (1.5%) controls.
Large number of people in the district of Nadia are showing arsenical skin lesion. However, insufficient education, poverty, lack of awareness and ineffective health care support are major factors causing immense plight to severely arsenic affected people.
PMCID: PMC2940197  PMID: 20922118
Arsenic; toxicants; arsenic and systemic manifestations; arsenic and socio-economic issues; disease burden; skin manifestations
4.  Anthelmintic activity of root bark of Carissa carandas 
Ancient Science of Life  2007;27(1):11-13.
The anthelmintic activity of the Imethanolic extract of the root bark of Carissa carandas was evaluated on adult Indian earthworm (Pheretima posthuma) using albendazole as a reference standard. The extract caused paralysis followed by the death of worm at the tested dose level. The extract at the highest tested concentration has anthelmintic activity comparable with that of standard drug albendazole.
PMCID: PMC3330840  PMID: 22557253
5.  Studies on Pharmacognostical features of Curcuma domestica Val. 
Ancient Science of Life  2007;26(4):37-41.
The microscopic and macroscopic characters of the rhizome of Curcuma domestica Val. were studied. The behavior of the powdered drug in the presence of various chemicals was also studied. Preliminary phytochemical screening on the various extracts of the rhizome was done in order to ascertain the various chemical constituents present. These studies were carried out to identify this plant for future research work.
PMCID: PMC3330885  PMID: 22557249
Ancient Science of Life  2005;25(2):74-78.
The leaves and seeds of Cassia tora (Family Caesalpinaceae) are used in the treatment of leprosy, ring worm, flatulence, colic, dyspepsia, constipation, cough, bronchitis and cardiac disorders in the Ayurvedic systems of medicine. The present study deals with the study of macroscopic characters of the leaves, ash values, extractive values, behavior on treatment with different chemical reagents and fluorescence characters under ultraviolet light. Preliminary phytochemical studies on different extractives of the leaves were also performed. These studies will help in the identification of the plant for further research.
PMCID: PMC3330902  PMID: 22557196
Ancient Science of Life  2003;22(4):160-165.
The methanolic extract of leaves of Mesua ferrea Linn. were tested for its antibacterial potentiality against 103 various strains of bacteria including Staphylococcus aureus, Bacillus spps. Klebsiella spps., Streptococus pneumoniae, Sarcina lutea, Lactobacilus arabinosus, Escherichia coli, shigellae, salmonellae, Proteus spps., Pseudomonas spps. and the vibrios. Significant antibacterial effects were produced by the extract against Staphylococcus aureus, Bacillus sppa., lactobacilli, Escherichia coli, shigellae and salmonellae and the results were compared with standard antibiotic ciprofloxacin. Further the extract was proved to be bacterial in its action.
PMCID: PMC3331016  PMID: 22557104
8.  ANTIMICROBIAL ACTION OF THE LEAF EXTRACT OF Lagerstroemia parviflora Roxb 
Ancient Science of Life  2002;21(3):198-201.
The benzene extract of the leaves of Lagerstroemia paviflora Roxb was tested for its Minimum Inhibitory Concentration (MIC) against Gram Positive Staphylococcus aureus, Bacillus subtilis, Bacillus cereus, Klebsiella pneumoniae, Streptococcus pneumoniae, Lactobacillus arabinosus and gram negative strains E.Coli, Shigella dysenteriae, shigella sonnei, shigella boydii, Salmonella typhimurium, Proteus mirabilis and Vibrio cholerae. Further the zones of inhibition Produced by the crude extract against four selected bacterial strains were measured and compared with those produced by the standard antibiotic Ciprofloxacin against the same bacterial strains.
PMCID: PMC3331035  PMID: 22557054
9.  Antimicrobial Potency of the Leaf – Stalk Extract of Curcuma longa (LINN) 
Ancient Science of Life  2000;20(1-2):92-96.
The methanolic extract of the leaf-stalk of curcuma longa LINN, was tested for its minimum Inhibitor concentration (MIC) against Gram positive-staphylococcus aureus, Bacillus pumilus, Bacillus subtilis, klebsiella pnemoniae, bacillus cereus, streptococcus pneumoniae, Lactobacillus arabinosus and gram negative E.coli, shigella dysenteriae, shigella sonnei, shigella boydii, salmonella typhimurium, proteus mirabilis, and Vibrio cholerae strains, further, the ones of inhibition produced by the crude extract against four selected bacterial strains were measured and compared with those produced by the standard antibiotic ciprofloxacin against the same bacterial strains.
PMCID: PMC3336426  PMID: 22557005
10.  Evaluation of the wound healing property of Commiphora guidottii Chiov. ex. Guid. 
The traditional use of the oleo-gum-resin of Commiphora guidottii Chiov. ex. Guid., which is commonly called scented myrrh, for topical treatment of wound is well documented. The major objective of the present study was to investigate the essential oil and resin obtained from C. guidottii for their potential wound healing properties. Due to their influence on the wound healing process, the anti-inflammatory and antimicrobial activities of scented myrrh have also been investigated.
Powdered oleo-gum-resin of C. guidottii was steam-distilled to obtain essential oil, and the resin was extracted from the marc with MeOH and filtered. The TLC fingerprint profile of the resin has been recorded by using silica gel GF254 as stationary phase. The essential oil components were identified and quantified by GC-MS. Ointments prepared from the essential oil (4 % v/w) and the resin (5 % w/w) were used for wound healing activity tests. Toxicity of the formulated ointments was investigated according to Draize skin irritation test. Acute anti-inflammatory effect in mice was evaluated using carrageenan induced mouse hind paw oedema model. Antimicrobial activity tests were carried out using disk diffusion and broth dilution techniques against 21 pathogenic bacterial and 4 fungal strains.
Ointment formulations of both the oil and resin were found to be non-irritant at the concentrations used and showed significant (p < 0.05-0.001) increase in wound contraction rate, shorter epithelization time and higher skin breaking strength as compared to the negative control. Overall, the antibacterial and antifungal activities of the oil and resin were comparable with the standard antibiotics ciprofloxacin and griseofulvin, respectively.
The results confirm that scented myrrh possesses genuine wound healing activity supporting the traditional use of the plant.
PMCID: PMC4538748  PMID: 26283230
Commiphora guidottii; Essential oil; Resin; Wound healing; Anti-inflammatory; Antimicrobial
11.  Structural elucidation of some antimicrobial constituents from the leaf latex of Aloe trigonantha L.C. Leach 
The incidents of drug resistant microorganisms and the need of treatments for newly emerging pathogens are of great concern to the global community. Our ability to treat infectious diseases is dependent on the development of new pharmaceuticals, and one potential source being medicinal plants with traditional claims. The leaves of Aloe trigonantha L.C. Leach, an endemic Ethiopian plant, are locally used for the treatment of infectious and inflammatory diseases. This study explores the potential of the latex of this plant and compounds isolated thereof for their in vitro antibacterial and antifungal properties.
Analytical RP-HPLC and silica gel preparative TLC were used for identification and isolation of active constituents, respectively. Characterization of the compounds was based on UV, IR, HR-ESIMS, 1H and 13C NMR, and 2D-NMR spectral assignments. Antimicrobial activity studies were carried out against 21 pathogenic bacterial and 4 fungal strains using the disk diffusion method. Minimum inhibitory concentrations (MICs) were determined by the broth dilution method.
A C-glycosylated chromone identified as aloesin, and three C-glycosylated anthrones characterized as 8-O-methy-7-hydroxyaloin A/B, aloin A/B and aloin-6’-O-acetate A/B were isolated. The latex and isolated compounds exhibited in vitro antibacterial activity against the tested pathogens. In some cases the activity of the isolated compounds (MIC = 10 μg/mL) was comparable with that of the standard drug ciprofloxacin, particularly against some of the Gram-negative bacterial strains tested. However, their activity towards the fungal pathogens tested was relatively weaker showing maximum activity against Candida albicans with MIC value of 400 μg/mL.
The present findings can be used for further research aimed at the development of new antibacterial agents, and may also justify the ethnomedicinal claim of the plant for the treatment of infectious diseases.
PMCID: PMC4533789  PMID: 26264241
Aloe trigonantha; Antimicrobial activity; 8-O-methy-7-hydroxyaloin A/B; Aloesin; Aloin A/B; Aloin-6’-O-acetate A/B; Disk diffusion
12.  The Influence of Episode Severity on Caregiver Recall, Care-seeking, and Treatment of Diarrhea among Children 2–59 Months of Age in Bihar, Gujarat, and Uttar Pradesh, India 
Increased diarrheal episode severity has been linked to better 2-week recall and improved care-seeking and treatment among caregivers of children under five. Using cross-sectional data from three Indian states, we sought to assess the relationship between episode severity and the recall, care-seeking, and treatment of childhood diarrhea. Recall error was higher for episodes with onset 8–14 days (31.2%) versus 1–7 days (4.8%) before the survey, and logistic regression analysis showed a trend toward increased severity of less recent compared with more recent episodes. This finding indicates that data collection with 2-week recall underestimates diarrhea prevalence while overestimating the proportion of severe episodes. There was a strong correlation between care-seeking and dehydration, fever, vomiting, and increased stool frequency and duration. Treatment with oral rehydration salts was associated with dehydration, vomiting, and higher stool frequency, and trends were established between therapeutic zinc supplementation and increased duration and stool frequency. However, state and care-seeking sector were stronger determinants of treatment than episode severity, illustrating the need to address disparities in treatment quality across regions and delivery channels. Our findings are of importance to researchers and diarrhea management program evaluators aiming to produce accurate estimates of diarrheal outcomes and program impact in low- and middle-income countries.
PMCID: PMC4530743  PMID: 26033018
13.  Fear of Falling Is Associated with Recurrent Falls in People with Multiple Sclerosis 
International Journal of MS Care  2015;17(4):164-170.
Background: People with multiple sclerosis (MS) fall frequently, and there are few clinically valid tools to measure the risk factors for falls. We assessed the unidimensionality of the 7-item Falls Efficacy Scale–International (FES-I), a measure of fear of falling, and determined whether the 7-item FES-I is associated with recurrent falls in people with MS.
Methods: Falls were counted prospectively for 6 months using fall calendars in 58 people with MS (age, 18–50 years; Expanded Disability Status Scale score, 0–6). The FES-I was administered at baseline, and its unidimensionality was assessed by confirmatory factor analysis. The relationship between FES-I score and future falls, after adjusting for recurrent falls in the past year, was assessed by logistic regression.
Results: Fifty-four participants who completed all assessments were included in the analysis. Goodness-of-fit indices confirmed a single-factor solution for the 7-item FES-I (discrepancy χ2, P = .101; Tucker-Lewis index, 0.953; comparative fit index, 0.969; root mean square error of approximation, 0.098). There was a significant association between fear of falling and falls in the following 3 months, independent of recurrent falls in the past year (odds ratio = 1.22, 95% confidence interval, 1.04–1.43, P = .016).
Conclusions: The 7-item FES-I demonstrates good construct validity, allowing the total score to be used as a measure of fear of falling in people with MS. Fear of falling, as measured by the 7-item FES-I, is associated with future recurrent falls independent of past recurrent falls in people with MS.
PMCID: PMC4542711  PMID: 26300702
14.  The Association between Provider Practice and Knowledge of ORS and Zinc Supplementation for the Treatment of Childhood Diarrhea in Bihar, Gujarat and Uttar Pradesh, India: A Multi-Site Cross-Sectional Study 
PLoS ONE  2015;10(6):e0130845.
Programs aimed at reducing the burden of diarrhea among children under-five in low-resource settings typically allocate resources to training community-level health workers, but studies have suggested that provider knowledge does not necessarily translate into adequate practice. A diarrhea management program implemented in Bihar, Gujarat and Uttar Pradesh, India trained private sector rural medical practitioners (RMPs) and public sector Accredited Social Health Activists (ASHAs) and Anganwadi workers (AWWs) in adequate treatment of childhood diarrhea with oral rehydration salts (ORS) and zinc. We used cross-sectional program evaluation data to determine the association between observed diarrhea treatment practices and reported knowledge of ORS and zinc among each provider cadre.
We conducted principal components analysis on providers’ responses to diarrhea treatment questions in order to generate a novel scale assessing ORS/zinc knowledge. We subsequently regressed a binary indicator of whether ORS/zinc was prescribed during direct observation onto the resulting knowledge scores, controlling for other relevant knowledge predictors.
There was a positive association between ORS/zinc knowledge score and prescribing ORS and zinc to young children with diarrhea among private sector RMPs (aOR: 2.32; 95% CI: 1.29-4.17) and public sector ASHAs and AWWs (aOR 2.48; 95% CI: 1.90-3.24). Controlling for knowledge score, receipt of training in the preceding 6 months was a good predictor of adequate prescribing in the public but not the private sector. In the public sector, direct access to ORS and zinc supplies was also highly associated with prescribing.
To enhance the management of childhood diarrhea in India, programmatic activities should center on increasing knowledge of ORS and zinc among public and private sector providers through biannual trainings but should also focus on ensuring sustained access to an adequate supply chain.
PMCID: PMC4476718  PMID: 26098305
15.  Molecular-docking study of malaria drug target enzyme transketolase in Plasmodium falciparum 3D7 portends the novel approach to its treatment 
Malaria has been a major life threatening mosquito borne disease from long since. Unavailability of any effective vaccine and recent emergence of multi drug resistant strains of malaria pathogen Plasmodium falciparum continues to cause persistent deaths in the tropical and sub-tropical region. As a result, demands for new targets for more effective anti-malarial drugs are escalating. Transketolase is an enzyme of the pentose phosphate pathway; a novel pathway which is involved in energy generation and nucleic acid synthesis. Moreover, significant difference in homology between Plasmodium falciparum transketolase (Pftk) and human (Homo sapiens) transketolase makes it a suitable candidate for drug therapy. Our present study is aimed to predict the 3D structure of Plasmodium falciparum transketolase and design an inhibitor against it.
The primary and secondary structural features of the protein is calculated by ProtParam and SOPMA respectively which revealed the protein is composed of 43.3 % alpha helix and 33.04 % random coils along with 15.62 % extended strands, 8.04 % beta turns. The three dimensional structure of the transketolase is constructed using homology modeling tool MODELLAR utilizing several available transketolase structures as templates. The structure is then subjected to deep optimization and validated by structure validation tools PROCHECK, VERIFY 3D, ERRAT, QMEAN. The predicted model scored 0.74 for global model reliability in PROCHECK analysis, which ensures the quality of the model. According to VERIFY 3D the predicted model scored 0.77 which determines good environmental profile along with ERRAT score of 78.313 which is below 95 % rejection limit. Protein-protein and residue–residue interaction networks are generated by STRING and RING server respectively. CASTp server was used to analyze active sites and His 109, Asn 108 and His 515 are found to be more positive site to dock the substrate, in addition molecular docking simulation with Autodock vina determined the estimated free energy of molecular binding was of −6.6 kcal/mol for most favorable binding of 6′-Methyl-Thiamin Diphosphate.
This predicted structure of Pftk will serve first hand in the future development of effective Pftk inhibitors with potential anti-malarial activity. However, this is a preliminary study of designing an inhibitor against Plasmodium falciparum 3D7; the results await justification by in vitro and in vivo experimentations.
PMCID: PMC4472393  PMID: 26089981
Transketolase; Plasmodium falciparum 3D7; Homology modeling; Drug target; Docking studies
16.  Appropriate Management of Acute Diarrhea in Children Among Public and Private Providers in Gujarat, India: A Cross-Sectional Survey 
Training public-sector providers to treat diarrhea in children with low-osmolarity oral rehydration salts and zinc appeared to be effective. Among private providers, drug-detailing visits by pharmaceutical representatives seemed less effective, particularly in improving knowledge of the correct dosage and duration of zinc treatment. Consistent supplies and sufficient attention to training all health care cadres, especially community health workers who may be new to diarrhea treatment and informal-sector providers who are typically excluded from formal training, are critical to improving knowledge and prescribing behaviors.
Training public-sector providers to treat diarrhea in children with low-osmolarity oral rehydration salts and zinc appeared to be effective. Among private providers, drug-detailing visits by pharmaceutical representatives seemed less effective, particularly in improving knowledge of the correct dosage and duration of zinc treatment. Consistent supplies and sufficient attention to training all health care cadres, especially community health workers who may be new to diarrhea treatment and informal-sector providers who are typically excluded from formal training, are critical to improving knowledge and prescribing behaviors.
Diarrhea remains a leading cause of morbidity and mortality among children under 5 years of age in low- and middle-income countries. In 2006, the Indian government formally endorsed the World Health Organization guidelines that introduced zinc supplementation and low-osmolarity oral rehydration salts (ORS) for the treatment of diarrhea. Despite this, zinc is rarely prescribed and has not been available in the public sector in India until very recently. The Diarrhea Alleviation Through Zinc and ORS Treatment (DAZT) project was implemented in Gujarat between 2011 and 2013 to accelerate the uptake of zinc and ORS among public and private providers in 6 rural districts. As part of an external evaluation of DAZT, we interviewed 619 randomly selected facility- and community-based public and private providers 2–3 months after a 1-day training event had been completed (or, in the case of private providers, after at least 1 drug-detailing visit by a pharmaceutical representative had occurred) and supplies were in place. The purpose of the interviews was to assess providers’ knowledge of appropriate treatment for diarrhea in children, reported treatment practices, and availability of drugs in stock. More than 80% of all providers interviewed reported they had received training or a drug-detailing visit on diarrheal treatment in the past 6 months. Most providers in all cadres (range, 68% to 100%) correctly described how to prepare ORS and nearly all (range, 90% to 100%) reported routinely prescribing it to treat diarrhea in children. Reported routine prescription of zinc was lower, ranging from 62% among private providers to 96% among auxiliary nurse-midwives. Among providers who reported ever not recommending zinc (n = 242), the 2 most frequently reported reasons for not doing so were not completely understanding zinc for diarrhea treatment and not having zinc in stock at the time of contact with the patient. In a multiple logistic regression analysis, recent training or drug-detailing visits and having zinc in stock were associated with reported zinc prescribing (P<.05). Recent training among public providers was significantly associated with having correct knowledge of zinc treatment duration and dosage, but the same was not true of drug-detailing visits among private providers. Treating diarrhea with zinc and low-osmolarity ORS is new for public and private providers in India and other low- and middle-income countries. Sufficient training and logistics support to ensure consistent supplies are critical if providers are to begin routinely treating all diarrhea episodes with zinc and ORS.
PMCID: PMC4476861  PMID: 26085020
17.  Probable Toxic Cause for Suspected Lychee-Linked Viral Encephalitis 
Emerging Infectious Diseases  2015;21(5):1817-24.
PMCID: PMC4412228  PMID: 25897979
encephalitis; lychee fruit; litchi fruit; ackee; toxin
19.  Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis 
Bio-ontologies provide terminologies for the scientific community to describe biomedical entities in a standardized manner. There are multiple initiatives that are developing biomedical terminologies for the purpose of providing better annotation, data integration and mining capabilities. Terminology resources devised for multiple purposes inherently diverge in content and structure. A major issue of biomedical data integration is the development of overlapping terms, ambiguous classifications and inconsistencies represented across databases and publications. The disease ontology (DO) was developed over the past decade to address data integration, standardization and annotation issues for human disease data. We have established a DO cancer project to be a focused view of cancer terms within the DO. The DO cancer project mapped 386 cancer terms from the Catalogue of Somatic Mutations in Cancer (COSMIC), The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium, Therapeutically Applicable Research to Generate Effective Treatments, Integrative Oncogenomics and the Early Detection Research Network into a cohesive set of 187 DO terms represented by 63 top-level DO cancer terms. For example, the COSMIC term ‘kidney, NS, carcinoma, clear_cell_renal_cell_carcinoma’ and TCGA term ‘Kidney renal clear cell carcinoma’ were both grouped to the term ‘Disease Ontology Identification (DOID):4467 / renal clear cell carcinoma’ which was mapped to the TopNodes_DOcancerslim term ‘DOID:263 / kidney cancer’. Mapping of diverse cancer terms to DO and the use of top level terms (DO slims) will enable pan-cancer analysis across datasets generated from any of the cancer term sources where pan-cancer means including or relating to all or multiple types of cancer. The terms can be browsed from the DO web site ( and downloaded from the DO’s Apache Subversion or GitHub repositories.
Database URL:
PMCID: PMC4385274  PMID: 25841438
20.  Identification of agents that promote endoplasmic reticulum stress using an assay that monitors luciferase secretion 
Journal of biomolecular screening  2013;19(4):575-584.
Disruption of protein processing in the secretory pathway is a measurable hallmark of endoplasmic reticulum (ER) stress. Activation of ER stress-mediated pathways has been implicated in numerous diseases including cancer. To identify agents that induce ER stress, we established a screen for compounds that reduce secretion of the reporter protein Gaussia luciferase (GLUC). Given the clinically validated importance of targeting ER stress-mediated pathways in the treatment of multiple myeloma (MM), we used this hematological malignancy as a model for validating our screening system. From a screen of 2000 marketed drugs and natural compounds in KMS11 and ARP1 MM cells, we identified 97 agents that reduced GLUC secretion in both cell lines by at least 30%. In order to confirm inducers of ER stress, we applied a secondary screen that assessed splicing of the unfolded protein response (UPR) transcription factor XBP1. One agent, theaflavin-3,3′–digallate (TF-3), was chosen based on its history of safe human consumption and further validated through studies of ER stress-related pathways including the UPR and apoptosis. Given these promising results, this screen could be a useful tool to identify agents targeting ER stress-related mechanisms in other cellular systems wherein ER stress plays a role in disease etiology.
PMCID: PMC4338999  PMID: 24371212
Gaussia luciferase; multiple myeloma; endoplasmic reticulum stress; protein secretion
21.  BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis 
BioXpress is a gene expression and cancer association database in which the expression levels are mapped to genes using RNA-seq data obtained from The Cancer Genome Atlas, International Cancer Genome Consortium, Expression Atlas and publications. The BioXpress database includes expression data from 64 cancer types, 6361 patients and 17 469 genes with 9513 of the genes displaying differential expression between tumor and normal samples. In addition to data directly retrieved from RNA-seq data repositories, manual biocuration of publications supplements the available cancer association annotations in the database. All cancer types are mapped to Disease Ontology terms to facilitate a uniform pan-cancer analysis. The BioXpress database is easily searched using HUGO Gene Nomenclature Committee gene symbol, UniProtKB/RefSeq accession or, alternatively, can be queried by cancer type with specified significance filters. This interface along with availability of pre-computed downloadable files containing differentially expressed genes in multiple cancers enables straightforward retrieval and display of a broad set of cancer-related genes.
Database URL:
PMCID: PMC4377087  PMID: 25819073
22.  Gaining Insights into the Codon Usage Patterns of TP53 Gene across Eight Mammalian Species 
PLoS ONE  2015;10(3):e0121709.
TP53 gene is known as the “guardian of the genome” as it plays a vital role in regulating cell cycle, cell proliferation, DNA damage repair, initiation of programmed cell death and suppressing tumor growth. Non uniform usage of synonymous codons for a specific amino acid during translation of protein known as codon usage bias (CUB) is a unique property of the genome and shows species specific deviation. Analysis of codon usage bias with compositional dynamics of coding sequences has contributed to the better understanding of the molecular mechanism and the evolution of a particular gene. In this study, the complete nucleotide coding sequences of TP53 gene from eight different mammalian species were used for CUB analysis. Our results showed that the codon usage patterns in TP53 gene across different mammalian species has been influenced by GC bias particularly GC3 and a moderate bias exists in the codon usage of TP53 gene. Moreover, we observed that nature has highly favored the most over represented codon CTG for leucine amino acid but selected against the ATA codon for isoleucine in TP53 gene across all mammalian species during the course of evolution.
PMCID: PMC4373688  PMID: 25807269
23.  Falls in people with MS—an individual data meta-analysis from studies from Australia, Sweden, United Kingdom and the United States 
Falls are common in people with multiple sclerosis (PwMS). Previous studies have generally included small samples and had varied methods.
The objectives of this paper are to compile fall rates across a broad range of ages and disease severity and to definitively assess the extent to which MS-associated and demographic factors influence fall rates.
Individual data from studies in four countries that prospectively measured falls for three months were analyzed. We determined fall rates, prevalence of fallers (≥1 falls) and frequent fallers (≥2 falls), location and timing of falls, and fall-related demographic factors.
A total of 537 participants reported 1721 falls: 56% were fallers and 37% frequent fallers. Most falls occurred indoors (65%) between 6 a.m. and 6 p.m. (75%). Primary progressive MS was associated with significantly increased odds of being a faller (odds ratio (OR) 2.02; CI 1.08–3.78). Fall risk peaked at EDSS levels of 4.0 and 6.0 with significant ORs between 5.30 (2.23–12.64) and 5.10 (2.08–12.47). The fall rate was lower in women than men (relative risk (RR) 0.80; CI 0.67–0.94) and decreased with increasing age (RR 0.97 for each year, CI 0.95–0.98).
PwMS are at high risk of falls and there are important associations between falls and MS-associated disability, gender and age.
PMCID: PMC4361466  PMID: 24948687
Accidental falls; multiple sclerosis; risk factors; cohort studies; meta-analysis
24.  Ribosomal Protein L13a Deficiency in Macrophages Promotes Atherosclerosis by Limiting Translation Control-Dependent Retardation of Inflammation 
Unresolved inflammatory response of macrophages plays a pivotal role in the pathogenesis of atherosclerosis. Previously we showed that ribosomal protein L13a-dependent translational silencing suppresses the synthesis of a cohort of inflammatory proteins in monocytes and macrophages. We also found that genetic abrogation of L13a expression in macrophages significantly compromised the resolution of inflammation in a mouse model of LPS-induced endotoxemia. However, its function in the pathogenesis of atherosclerosis is not known. Here, we examine whether L13a in macrophage has a protective role against high fat diet-induced atherosclerosis.
Approach and Results
We bred the macrophage-specific L13a knockout mice L13a Flox+/+ Cre+/+ onto apoE−/− background and generated the experimental double knockout (KO) mice L13a Flox+/+ Cre+/+ apoE−/−. L13a Flox+/+ Cre−/− mice on apoE−/− background were used as controls. Control and KO mice were subjected to high-fat diet for 10 weeks. Evaluation of aortic sinus sections and entire aorta by en face showed significantly higher atherosclerosis in the KO mice. Severity of atherosclerosis in KO mice was accompanied by thinning of the smooth muscle cell (SMC) layer in the media, larger macrophage area in the intimal plaque region and higher plasma levels of inflammatory cytokines. In addition, macrophages isolated from KO mice had higher polyribosomal abundance of several target mRNAs, thus showing defect in translation control.
Our data demonstrate that loss of L13a in macrophages increases susceptibility to atherosclerosis in apoE−/− mice, revealing an important role of L13a-dependent translational control as an endogenous protection mechanism against atherosclerosis.
PMCID: PMC3954853  PMID: 24436370
L13a; Chemokines; Translational control; Macrophages; Inflammation; Atherosclerosis
25.  Captopril in Congenital Chloride Diarrhoea: A Case Study 
An 11 months 22 days old girl presented with a history of watery diarrhoea since birth, failure to thrive, and developmental delay. Her diagnosis was congenital chloride diarrhoea (CCD) with raised level of chloride (>90 mmol/L) in stool in the absence of cystic fibrosis. Management of CCD included replacement of NaCl, KCl, and correction of dehydration. Diarrhoea of the patient was resolved with Captopril, which was initially provided to the patient for managing heart failure. To our knowledge, this is the first reported case of CCD that shows the beneficial effect of Captopril. Therefore, we suggest that further study is warranted as to the potential for Captopril as additional option in the treatment for CCD. We present this case report with the informed consent of the patient's guardian.
PMCID: PMC4438664  PMID: 25995737

Results 1-25 (229)