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Biomedical subjects

Sudhir Kumar

Publications and source records attributed to Sudhir Kumar.

At least 55 records · Page 3Linked to original sources
PubMed2004

Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations.

BACKGROUND: Modern developmental biology relies heavily on the analysis of embryonic gene expression patterns. Investigators manually inspect hundreds or thousands of expression patterns to identify those that are spatially similar and to ultimately infer potential gene interactions. However, the rapid accumulation of gene expression pattern data over the last two decades, facilitated by high-throughput techniques, has produced a need for the development of efficient approaches for direct comparison of images, rather than their textual descriptions, to identify spatially similar expression patterns. RESULTS: The effectiveness of the Binary Feature Vector (BFV) and Invariant Moment Vector (IMV) based digital representations of the gene expression patterns in finding biologically meaningful patterns was compared for a small (226 images) and a large (1819 images) dataset. For each dataset, an ordered list of images, with respect to a query image, was generated to identify overlapping and similar gene expression patterns, in a manner comparable to what a developmental biologist might do. The results showed that the BFV representation consistently outperforms the IMV representation in finding biologically meaningful matches when spatial overlap of the gene expression pattern and the genes involved are considered. Furthermore, we explored the value of conducting image-content based searches in a dataset where individual expression components (or domains) of multi-domain expression patterns were also included separately. We found that this technique improves performance of both IMV and BFV based searches. CONCLUSIONS: We conclude that the BFV representation consistently produces a more extensive and better list of biologically useful patterns than the IMV representation. The high quality of results obtained scales well as the search database becomes larger, which encourages efforts to build automated image query and retrieval systems for spatial gene expression patterns.

Algorithms↗
PubMed2004

Outcome of laparoscopic cholecystectomy in patients 80 years and older.

Advanced age is associated with an increase in postoperative complications. This study assesses the indications and outcome for laparoscopic cholecystectomy (LC) in patients aged 80 years or older. Consecutive, unselected patients aged 80 years or over undergoing LC between 1991 and 2000 were included. A retrospective case review enabled analysis of clinical and operative factors together with in-hospital morbidity, 30-day mortality, and duration of hospital stay. A series of 117 patients, 79 women and 38 men with a median age of 83 years (range 80-93 years), underwent LC. Indications for LC were chronic cholecystitis in 62 (53%) patients, acute cholecystitis in 28 (24%), gallstone pancreatitis in 12 (10%), and other conditions in 15 (13%). Six (5%) patients required conversion to an open procedure. Overall, 26 (22%) patients developed a postoperative complication. There were no bile leaks or bile duct injuries. One patient, with gangrenous cholecystitis, died after LC. The median postoperative hospital stay was 3 days (range 1-31 days). LC can be performed safely with low morbidity in patients over age 80 years.

Aged↗
PubMed2004

Prospects for inferring very large phylogenies by using the neighbor-joining method.

Current efforts to reconstruct the tree of life and histories of multigene families demand the inference of phylogenies consisting of thousands of gene sequences. However, for such large data sets even a moderate exploration of the tree space needed to identify the optimal tree is virtually impossible. For these cases the neighbor-joining (NJ) method is frequently used because of its demonstrated accuracy for smaller data sets and its computational speed. As data sets grow, however, the fraction of the tree space examined by the NJ algorithm becomes minuscule. Here, we report the results of our computer simulation for examining the accuracy of NJ trees for inferring very large phylogenies. First we present a likelihood method for the simultaneous estimation of all pairwise distances by using biologically realistic models of nucleotide substitution. Use of this method corrects up to 60% of NJ tree errors. Our simulation results show that the accuracy of NJ trees decline only by approximately 5% when the number of sequences used increases from 32 to 4,096 (128 times) even in the presence of extensive variation in the evolutionary rate among lineages or significant biases in the nucleotide composition and transition/transversion ratio. Our results encourage the use of complex models of nucleotide substitution for estimating evolutionary distances and hint at bright prospects for the application of the NJ and related methods in inferring large phylogenies.

Computer Simulation↗
PubMed2004

The spectrum of human rhodopsin disease mutations through the lens of interspecific variation.

Mutations in rhodopsin, the visual pigment found in rod cells, account for a large fraction of genetic changes underlying the human retinal diseases, Retinitis Pigmentosa (RP). The availability of rhodopsin sequences from a large number of vertebrates has allowed us to investigate factors important in the development of RP by contrasting interspecific differences (long-term evolutionary patterns) with RP disease mutation data. We find that disease mutations in rhodopsin are overabundant in highly conserved sites and that amino acid positions with any potential of variability among vertebrates are likely to harbour disease mutations less frequently. At any amino acid position in rhodopsin, the set of disease-associated amino acids does not show any commonality with the set of amino acids present among species. The disease mutations are biochemically four times more radical than the interspecific (neutral) variation. This pattern is also observed when disease mutations are categorized based on clinical classifications that reflect biochemical, physiological and psychophysical traits such as protein folding, cone electroretinogram (ERG) amplitude, pattern of visual field loss, and equivalent field diameter. We also found that for artificial mutations (those not observed in nature interspecifically), there was a positive relationship between the biochemical distance and the magnitude of blue shift in the absorption spectrum maximum. We introduce the concept of the expected chemical severity based on the normal human codon at a position. Results reveal that the analysis of disease mutations in the context of the original codon is very important for the practical application of evolutionary principles when comparing original and disease amino acid mutations. We conclude that the analysis of rhodopsin data clearly demonstrates the usefulness of molecular evolutionary analyses for understanding patterns of clinical as well as artificial mutations and underscores the biomedical insights that can be gained by using simple measures of biochemical difference in the context of evolutionary divergence.

Amino Acid Sequence↗
PubMed2004

The role of simultaneous gap arthroplasty and distraction osteogenesis in the management of temporo-mandibular joint ankylosis with mandibular deformity in children.

INTRODUCTION: Temporo-mandibular joint ankylosis is a common cause of acquired deformity in children. PURPOSE: Surgical correction of the ankylosis only leaves the patient with an uncorrected mandibular deformity. This study was to evaluate the use of distraction osteogenesis for simultaneous correction of the mandibular deformity. MATERIAL: This study was done on six children with temporo-mandibular joint ankylosis and mandibular deformity. Uniaxial double pin distractors with Schanz pins were used in this study. METHODS: The patients underwent simultaneous gap arthroplasty and mandibular osteotomy (retromolar) with distractor insertion. Distraction was started on the fifth post-operative day. The patients were put on dynamic temporo-mandibular joint exercises on the first post-operative day. RESULTS: All patients had a satisfactory mouth opening on follow-up. Satisfactory cosmetic correction of the mandibular deformity was also achieved in all these patients. Some degree of malocclusion resulted from treatment due to which the patients were placed on orthodontic treatment. CONCLUSIONS: Distraction osteogenesis can be used simultaneously with gap arthroplasty in patients with temporo-mandibular ankylosis, for the correction of the mandibular deformity.

Ankylosis↗
PubMed2004

Laparoscopic totally extraperitoneal mesh repair for femoral hernia.

BACKGROUND: The role of laparoscopic repair for femoral hernia has not been clearly defined, although the advantages of this technique for repair of inguinal hernia are well recognized. AIM: The aim of this study was to assess the outcome of laparoscopic total extraperitoneal (TEP) repair of femoral hernia. METHODS: Case records of patients who had laparoscopic TEP repair of femoral hernia between 1994 and 2002 were reviewed retrospectively. Patients' demographic details, presentation, operative details, and follow-up information were gathered from the clinical records. Postoperative complications, chronic pain, and recurrence of the hernia were assessed. RESULTS: Fifteen patients, 10 males and 5 females, with a mean age of 55 years (range, 33-84 years) underwent laparoscopic TEP femoral hernia repair. Fourteen patients (93.3%) had a primary femoral hernia, and one had a recurrent femoral hernia. In 9 (60%) patients the hernia was irreducible but not obstructed. There were no postoperative complications or chronic pain. One patient (7%) with a small (11 x 6 cm) mesh developed an inguinal recurrence. CONCLUSION: Laparoscopic TEP repair is a suitable technique for repair of femoral hernia, including irreducible but not obstructed femoral hernias.

Adult↗
PubMed2004

MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment.

With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.

Databases, Genetic↗