Biomedical subjects

Balasubramanian Narasimhan

Publications and source records attributed to Balasubramanian Narasimhan.

14 recordsLinked to original sources

PubMed2006

Acute rejection and cardiac allograft vascular disease is reduced by suppression of subclinical cytomegalovirus infection.

BACKGROUND: Anticytomegalovirus (CMV) prophylaxis prevents the acute disease but its impact on subclinical infection and allograft outcome is unknown. We sought to determine whether CMV prophylaxis administered for three months after heart transplant would improve patient outcomes. METHODS: This prospective cohort study of 66 heart transplant recipients compared aggressive CMV prophylaxis (n = 21, CMV hyperimmune globulin [CMVIG] plus four weeks of intravenous ganciclovir followed by two months of valganciclovir); with standard prophylaxis (n = 45, intravenous ganciclovir for four weeks). Prophylaxis was based on pretransplant donor (D) and recipient (R) CMV serology: R-/D+ received aggressive prophylaxis; R+ received standard prophylaxis. Outcome measures were: CMV infection assessed by DNA-polymerase chain reaction on peripheral blood polymorphonuclear leukocytes, acute rejection, and cardiac allograft vascular disease (CAV) assessed by intravascular ultrasound. All patients completed one year of follow-up. RESULTS.: CMV infection was subclinical in all but four patients (two in each group). Aggressively treated patients had a lower incidence of CMV infection (73 +/- 10% vs. 94 +/- 4%; P = 0.038), and an independent reduced relative risk for acute rejection graded > or =3A (relative risk [95% CI] = 0.55 [0.26-0.96]; P = 0.03), as compared with the standard prophylaxis group. Aggressively prophylaxed patients also showed a slower progression of CAV, in terms of coronary artery lumen loss (lumen volume change=-21 +/- 13% vs. -10+/-14%; P = 0.05); and vessel shrinkage (vessel volume change = -15 +/- 11% vs. -3 +/- 18%; P = 0.03). CONCLUSIONS: Prolonged (val)ganciclovir plus CMVIG reduces viral levels, acute rejection, and allograft vascular disease, suggesting a role for chronic subclinical infection in the pathophysiology of the most common diseases affecting heart transplant recipients.

Cardiovascular Diseases↗

PubMed2006

Correlation of antibacterial activity of some N-[5-(2-furanyl)-2-methyl-4-oxo-4H-thieno[2,3-d]pyrimidin-3-yl]-carboxamide and 3-substituted-5-(2-furanyl)-2-methyl-3H-thieno[2,3-d]pyrimidin-4-ones with topological indices using Hansch analysis.

The antimicrobial activity of the N-[5-(2-furanyl)-2-methyl-4-oxo-4H-theino[2,3-d]pyrimidin-3-y1]-carboxamides and 3-substituted-5-(2-furanyl)-2-methyl-3H-thieno[2,3-d]pyrimidin-4-ones was correlated with different topological indices using Hansch analysis. Good correlations were obtained through a simple regression equation with third order molecular connectivity index (3chi). The developed QSAR models were crossvalidated by leave-one-out technique.

Animals↗

PubMed2006

Design, synthesis, antibacterial, and QSAR studies of myristic acid derivatives.

A series of esters and amides of myristic acid was synthesized and tested in vitro for antibacterial activity against gram-positive and gram-negative bacteria. All the compounds showed activity comparable to that of the standard drug, ciprofloxacin. The structural characteristics governing antibacterial activity of myristic acid derivatives was studied using QSAR methodology. The results showed that the antibacterial activity could be modeled using the topological descriptor, valence molecular connectivity index. The predictive ability of the models was cross-validated by construction of a test set. The low residual activity and high cross-validated r2 values (r(cv)2) observed indicated the predictive ability of the developed QSAR models.

Anti-Bacterial Agents↗

PubMed2006

CD10 expression in peripheral T-cell lymphomas complicated by a proliferation of large B-cells.

CD10 expression by the neoplastic T cells in angioimmunoblastic T-cell lymphoma was recently described. As cases of peripheral T-cell lymphoma, unspecified, fail to show similar CD10 expression, this feature helps discriminate between these two entities, particularly in cases exhibiting morphologic overlap. Given these findings, we studied CD10 expression in a subtype of peripheral T-cell lymphoma known as peripheral T-cell lymphoma complicated by a proliferation of large B cells and compared it with angioimmunoblastic T-cell lymphoma and angioimmunoblastic T-cell lymphoma with a large B-cell proliferation. A total of 33 cases were identified including peripheral T-cell lymphoma complicated by a proliferation of large B cells (10), angioimmunoblastic T-cell lymphoma (10) and angioimmunoblastic T-cell lymphoma with a large B-cell proliferation (13). Diagnoses were established by hematoxylin and eosin (H&E) stain, immunohistochemistry and/or molecular findings (polymerase chain reaction for T-cell receptor-gamma gene rearrangement). Two of 10 cases of peripheral T-cell lymphoma complicated by a proliferation of large B cells showed aberrant CD10 expression (20%) compared to 9/10 cases of angioimmunoblastic T-cell lymphoma (90%) and 8/13 of angioimmunoblastic T-cell lymphoma with a large B-cell proliferation (62%). One case each of angioimmunoblastic T-cell lymphoma and angioimmunoblastic T-cell lymphoma with a large B-cell proliferation showed a rare, but not unequivocal, CD10+ atypical cell. Four cases of angioimmunoblastic T-cell lymphoma with a large B-cell proliferation were CD10 negative. Of the 2 CD10+ peripheral T-cell lymphoma complicated by a proliferation of large B cells, one had no H&E or IHC features of angioimmunoblastic T-cell lymphoma and showed only a rare positive cell. The second case, a lung biopsy, exhibited diffuse CD10 tumor cell positivity. The predominant staining pattern in the CD10+ cases was characterized by scattered, mostly individual, morphologically neoplastic cells. A rare case showed clusters of positive cells. Our data indicate that only 20% of cases of peripheral T-cell lymphoma complicated by a proliferation of large B cells show CD10 expression by the neoplastic T cells in contrast to angioimmunoblastic T-cell lymphoma and angioimmunoblastic T-cell lymphoma with a large B-cell proliferation which exhibit CD10 staining in 90 and 62% of cases, respectively. This finding does not reach statistical significance with a P-value of 0.57 (Fisher's exact test). As these entities appear to be biologically distinct and may portend different overall survivals, CD10 expression may serve as an additional discriminating criterion.

Adult↗

PubMed2006

Antibacterial principles from Myristica fragrans seeds.

Nutmeg (Myristica fragrans) is used in food preparations for its aromatic flavor. The present investigation was undertaken to evaluate the antibacterial activity of constituents of M. fragrans seeds. Seeds of M. fragrans were powdered and extracted with chloroform to obtain trimyristin, which on saponification yielded myristic acid. The mother liquor remaining after separation of trimyristin was concentrated and column-chromatographed with petroleum ether to separate myristicin. Antibacterial activity of these isolated constituents was evaluated by determination of minimum inhibitory concentration against selected Gram-positive and Gram-negative organisms. All the constituents isolated from nutmeg exhibited good antibacterial activity. This study shows the potential of natural compounds in replacement of synthetic preservatives.

Allylbenzene Derivatives↗

PubMed2006

A QSAR approach for the prediction of stability of benzoglycolamide ester prodrugs.

A method consisting of quantitative structure-activity relationship (QSAR) (MLR) was developed to predict the hydrolytic rate constant of 37 benzoglycolamide ester prodrugs. The regression method was used as a calibration model for calculating the hydrolytic rate constant and investigating their linear characteristics. The QSAR study indicated the importance of the descriptors charge on amide nitrogen (AN), lipophilic parameter (log P) and nucleophilic frontal density (NUFD) in contribution to the ester hydrolysis with the correlation coefficient value of 0.908 for the developed MLR model. The models were validated by leave one out (LOO) technique as well as by the calculation of statistical parameters for the developed MLR models.

Drug Stability↗

PubMed2005

Signature patterns of gene expression in mouse atherosclerosis and their correlation to human coronary disease.

The propensity for developing atherosclerosis is dependent on underlying genetic risk and varies as a function of age and exposure to environmental risk factors. Employing three mouse models with different disease susceptibility, two diets, and a longitudinal experimental design, it was possible to manipulate each of these factors to focus analysis on genes most likely to have a specific disease-related function. To identify differences in longitudinal gene expression patterns of atherosclerosis, we have developed and employed a statistical algorithm that relies on generalized regression and permutation analysis. Comprehensive annotation of the array with ontology and pathway terms has allowed rigorous identification of molecular and biological processes that underlie disease pathophysiology. The repertoire of atherosclerosis-related immunomodulatory genes has been extended, and additional fundamental pathways have been identified. This highly disease-specific group of mouse genes was combined with an extensive human coronary artery data set to identify a shared group of genes differentially regulated among atherosclerotic tissues from different species and different vascular beds. A small core subset of these differentially regulated genes was sufficient to accurately classify various stages of the disease in mouse. The same gene subset was also found to accurately classify human coronary lesion severity. In addition, this classifier gene set was able to distinguish with high accuracy atherectomy specimens from native coronary artery disease vs. those collected from in-stent restenosis lesions, thus identifying molecular differences between these two processes. These studies significantly focus efforts aimed at identifying central gene regulatory pathways that mediate atherosclerotic disease, and the identification of classification gene sets offers unique insights into potential diagnostic and therapeutic strategies in atherosclerotic disease.

Animals↗

PubMed2005

A method for calling gains and losses in array CGH data.

Array CGH is a powerful technique for genomic studies of cancer. It enables one to carry out genome-wide screening for regions of genetic alterations, such as chromosome gains and losses, or localized amplifications and deletions. In this paper, we propose a new algorithm 'Cluster along chromosomes' (CLAC) for the analysis of array CGH data. CLAC builds hierarchical clustering-style trees along each chromosome arm (or chromosome), and then selects the 'interesting' clusters by controlling the False Discovery Rate (FDR) at a certain level. In addition, it provides a consensus summary across a set of arrays, as well as an estimate of the corresponding FDR. We illustrate the method using an application of CLAC on a lung cancer microarray CGH data set as well as a BAC array CGH data set of aneuploid cell strains.

Algorithms↗

PubMed2004

Mouse strain-specific differences in vascular wall gene expression and their relationship to vascular disease.

OBJECTIVE: Different strains of inbred mice exhibit different susceptibility to the development of atherosclerosis. The C3H/HeJ and C57Bl/6 mice have been used in several studies aimed at understanding the genetic basis of atherosclerosis. Under controlled environmental conditions, variations in susceptibility to atherosclerosis reflect differences in genetic makeup, and these differences must be reflected in gene expression patterns that are temporally related to the development of disease. In this study, we sought to identify the genetic pathways that are differentially activated in the aortas of these mice. METHODS AND RESULTS: We performed genome-wide transcriptional profiling of aortas from C3H/HeJ and C57Bl/6 mice. Differences in gene expression were identified at baseline as well as during normal aging and longitudinal exposure to high-fat diet. The significance of these genes to the development of atherosclerosis was evaluated by observing their temporal pattern of expression in the well-studied apolipoprotein E model of atherosclerosis. CONCLUSIONS: Gene expression differences between the 2 strains suggest that aortas of C57Bl/6 mice have a higher genetic propensity to develop inflammation in response to appropriate atherogenic stimuli. This study expands the repertoire of factors in known disease-related signaling pathways and identifies novel candidate genes for future study. To gain insights into the molecular pathways that are differentially activated in strains of mice with varied susceptibility to atherosclerosis, we performed comprehensive transcriptional profiling of their vascular wall. Genes identified through these studies expand the repertoire of factors in disease-related signaling pathways and identify novel candidate genes in atherosclerosis.

Aging↗

PubMed2004

Tree-structured supervised learning and the genetics of hypertension.

This paper is about an algorithm, FlexTree, for general supervised learning. It extends the binary tree-structured approach (Classification and Regression Trees, CART) although it differs greatly in its selection and combination of predictors. It is particularly applicable to assessing interactions: gene by gene and gene by environment as they bear on complex disease. One model for predisposition to complex disease involves many genes. Of them, most are pure noise; each of the values that is not the prevalent genotype for the minority of genes that contribute to the signal carries a "score." Scores add. Individuals with scores above an unknown threshold are predisposed to the disease. For the additive score problem and simulated data, FlexTree has cross-validated risk better than many cutting-edge technologies to which it was compared when small fractions of candidate genes carry the signal. For the model where only a precise list of aberrant genotypes is predisposing, there is not a systematic pattern of absolute superiority; however, overall, FlexTree seems better than the other technologies. We tried the algorithm on data from 563 Chinese women, 206 hypotensive, 357 hypertensive, with information on ethnicity, menopausal status, insulin-resistant status, and 21 loci. FlexTree and Logic Regression appear better than the others in terms of Bayes risk. However, the differences are not significant in the usual statistical sense.

Algorithms↗

PubMed2004

Sample classification from protein mass spectrometry, by 'peak probability contrasts'.

MOTIVATION: Early cancer detection has always been a major research focus in solid tumor oncology. Early tumor detection can theoretically result in lower stage tumors, more treatable diseases and ultimately higher cure rates with less treatment-related morbidities. Protein mass spectrometry is a potentially powerful tool for early cancer detection. We propose a novel method for sample classification from protein mass spectrometry data. When applied to spectra from both diseased and healthy patients, the 'peak probability contrast' technique provides a list of all common peaks among the spectra, their statistical significance and their relative importance in discriminating between the two groups. We illustrate the method on matrix-assisted laser desorption and ionization mass spectrometry data from a study of ovarian cancers. RESULTS: Compared to other statistical approaches for class prediction, the peak probability contrast method performs as well or better than several methods that require the full spectra, rather than just labelled peaks. It is also much more interpretable biologically. The peak probability contrast method is a potentially useful tool for sample classification from protein mass spectrometry data.

Algorithms↗

PubMed2004

Esters, amides and substituted derivatives of cinnamic acid: synthesis, antimicrobial activity and QSAR investigations.

A series of esters (I(a-k)), substituted derivatives (II(a-d)) and amides (III(a-q)) of cinnamic acid were synthesized and evaluated as antibacterial and antifungal agents. All the derivatives belonging to the series I, II and III showed antimicrobial activity comparable to the standard. Compounds I(f) and II(c) proved to be the most effective compounds. Quantitative structure-activity relationship (QSAR) investigation with multiple linear regression analysis was applied to find a correlation between different calculated physicochemical parameters of the compounds and biological activity. The quantitative models relating the structural features of cinnamic acid derivatives I(a-k), II(a-d) and III(a-q) and their antimicrobial activity showed that Gram negative Escherichia coli and Candida albicans (fungus) were the most sensitive microorganisms.

Amides↗

PubMed2002

Diagnosis of multiple cancer types by shrunken centroids of gene expression.

We have devised an approach to cancer class prediction from gene expression profiling, based on an enhancement of the simple nearest prototype (centroid) classifier. We shrink the prototypes and hence obtain a classifier that is often more accurate than competing methods. Our method of "nearest shrunken centroids" identifies subsets of genes that best characterize each class. The technique is general and can be used in many other classification problems. To demonstrate its effectiveness, we show that the method was highly efficient in finding genes for classifying small round blue cell tumors and leukemias.

Child↗

PubMed2002

Development of an internet-based protocol to facilitate randomized clinical trials in pediatric surgery.

BACKGROUND/PURPOSE: Randomized clinical trials (RCTs) perhaps are the best method available for the comparison of therapeutic interventions, yet these studies remain scarce in the pediatric surgery literature. The infrequency of surgical conditions, parents' refusal to participate, and difficulty with standardizing operative technique are potential obstacles to conducting multicenter randomized trials. Novel applications of information technology can potentially overcome these obstacles and facilitate randomized trials in pediatric surgery. METHODS: Through collaboration with our Biostatistics Department, an Internet-based protocol was developed to facilitate our own multicenter trial for the surgical treatment of necrotizing enterocolitis. A secure, on-line data entry system was developed to manage all aspects of patient care data. Data are validated during the entry phase and directly uploaded into a clinical database for safety monitoring and analysis. Multimedia resources available online were developed to encourage standardization of surgical and nonoperative therapy. Comprehensive informed consent, educational and other support resources are available on line for the parents and family members of patients. These include an 8-minute video detailing pathophysiology, treatment options, and important informed consent issues surrounding the trial. The website also provides administrative support to study centers and periodic updates on trial progress to the medical community at large. CONCLUSIONS: Internet-based protocols may facilitate trials in pediatric surgery by reducing administrative costs, improving standardization of surgical technique, and potentially increasing enrollment success rates. Future investigation will examine the impact of this protocol on the education, knowledge base, and attitudes of parents, as well as determine the efficiency and overall cost effectiveness of this data management strategy.

Clinical Protocols↗