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Morphometric analysis of the cervical spine of Indian population by using computerized tomography
Partha Sarathi Banerjee,Amit Roychoudhury,Santanu Kumar Karmakar
Journal of Medical and Allied Sciences , 2012,
Abstract: The purpose of the present study was to measure the surgically important morphological parameters of cervical spine region of a representative sample of Indian population from the images obtained through computerized tomography (CT). Another purpose has been to compare the computed statistical mean, standard deviation and range of variation of these data with those of other Asian population and also European/American populations. With that aim, ninety five (95) CT scan data of Indian people (73 for male patients and 22 for female patients) pertaining to undeformed normal cervical spine has been collected from an Indian hospital. From these, 15 important morphological parameters have been measured. These values have been tabulated and their mean, standard deviation and range of variation have been computed. It has been found that pedicle dimensions of Indian people are smaller at almost all vertebra levels as compared to Caucasian people. Pedicle axis length for Indian people are found to be smaller at C3, C4 and C5 levels than those for other Asian people including Chinese people, but it is bigger at C6 and C7 levels. Indian people have longer measurements of pedicle length + lateral mass on an average than their other Asian counterparts at C5, C6 and C7 levels, but shorter measurements at C3 and C4 levels. The results of the present work may help in better understanding of morphological parameters of cervical spine region of Indian population. It may be further useful in designing spinal implants which would be biomechanically compatible to the anatomy of Indian people.
Consistency of the Maximum Likelihood Estimator of Evolutionary Tree
Arindam RoyChoudhury
Quantitative Biology , 2014,
Abstract: Maximum likelihood estimation (MLE) methods are widely used for evolutionary tree. As evolutionary tree is not a smooth parameter, the consistency of its MLE has been a topic of debate. It has been noted without proof that the classical proof of consistency by Wald holds for the MLE of evolutionary tree. Other proofs of consistency under various models were also proposed. Here we will discuss some shortcomings in some of these proofs and comment on the applicability of Wald's proof.
Change in Recessive Lethal Alleles Frequency in Inbred Populations
Arindam RoyChoudhury
Quantitative Biology , 2013,
Abstract: In a population practicing consanguineous marriage, rare recessive lethal alleles (RRLA) have higher chances of affecting phenotypes. As inbreeding causes more homozygosity and subsequently more deaths, the loss of individuals with RRLA decreases the frequency of these alleles. Although this phenomenon is well studied in general, here some hitherto unstudied cases are presented. An analytical formula for the RRLA frequency is presented for infinite monoecious population practicing several different types of inbreeding. In finite diecious populations, it is found that more severe inbreeding leads to quicker RRLA losses, making the upcoming generations healthier. A population of size 10,000 practicing 30% half-sib marriages loses more than 95% of its RRLA in 100 generations; a population practicing 30% cousin marriages loses about 75% of its RRLA. Our findings also suggest that given enough resources to grow, a small inbred population will be able to rebound while losing the RRLA.
Identifiability of a Coalescent-based Population Tree Model
Arindam RoyChoudhury
Quantitative Biology , 2013,
Abstract: Identifiability of evolutionary tree models has been a recent topic of discussion and some models have been shown to be non-identifiable. A coalescent-based rooted population tree model, originally proposed by Nielsen et al. 1998 [2], has been used by many authors in the last few years and is a simple tool to accurately model the changes in allele frequencies in the tree. However, the identifiability of this model has never been proven. Here we prove this model to be identifiable by showing that the model parameters can be expressed as functions of the probability distributions of subsamples. This a step toward proving the consistency of the maximum likelihood estimator of the population tree based on this model.
Overexpression of an abiotic-stress inducible plant protein in the bacteria Escherichia coli
A Roychoudhury, S Basu
African Journal of Biotechnology , 2008,
Abstract: The aim of our work was the overexpression of the abiotic stress-inducible dehydrin protein, namely RAB16A, from rice in the BL21 strain of Escherichia coli. The Rab16A transcript of 0.5 Kbp was amplified from the total RNA of the salt-tolerant indica rice cultivar Nonabokra by RT-PCR and cloned into the expression vector pGEX-3X. The 47 kDa protein, expressed as GST: RAB16A fusion protein, after 2 mM IPTG-mediated induction, was collected as S10 fraction and purified through glutathionesepharose affinity resin. Immunoblot analysis with the maize dehydrin antiserum showed crossreaction with the above band, but not with GST protein alone, showing functional expression of the heterologous RAB16A protein in the bacterial system.
Hemangiopericytoma of mandible
Bhutia Ongkila,Roychoudhury Ajoy
Journal of Oral and Maxillofacial Pathology , 2008,
Abstract: Hemangiopericytoma is a rare vascular neoplasm, which arises from specialized cells (pericytes) around the capillary walls. Only 5% of hemangiopericytomas in the series of Stout occurred in the oral cavity and pharynx. Several studies have revealed that due to chances of late recurrence or metastasis, long-term follow-up is necessary in patients with this tumor even after radical resection. We report a case of hemangiopericytoma of mandible in a 26-year-old woman, with 4 years′ follow-up.
Complex Codon Usage Pattern and Compositional Features of Retroviruses
Sourav RoyChoudhury,Debaprasad Mukherjee
Computational and Mathematical Methods in Medicine , 2013, DOI: 10.1155/2013/848123
Abstract: Retroviruses infect a wide range of organisms including humans. Among them, HIV-1, which causes AIDS, has now become a major threat for world health. Some of these viruses are also potential gene transfer vectors. In this study, the patterns of synonymous codon usage in retroviruses have been studied through multivariate statistical methods on ORFs sequences from the available 56 retroviruses. The principal determinant for evolution of the codon usage pattern in retroviruses seemed to be the compositional constraints, while selection for translation of the viral genes plays a secondary role. This was further supported by multivariate analysis on relative synonymous codon usage. Thus, it seems that mutational bias might have dominated role over translational selection in shaping the codon usage of retroviruses. Codon adaptation index was used to identify translationally optimal codons among genes from retroviruses. The comparative analysis of the preferred and optimal codons among different retroviral groups revealed that four codons GAA, AAA, AGA, and GGA were significantly more frequent in most of the retroviral genes inspite of some differences. Cluster analysis also revealed that phylogenetically related groups of retroviruses have probably evolved their codon usage in a concerted manner under the influence of their nucleotide composition. 1. Introduction The retroviruses are a diverse family of enveloped single stranded retro transcribing RNA viruses unique for their use of reverse transcription of the viral RNA into linear double stranded DNA during replication and the subsequent integration of the DNA into the host genome. Members of this family cause diseases in a wide range of organisms, including humans [1]. Human immunodeficiency virus 1 (HIV-1) is responsible for acquired immunodeficiency syndrome (AIDS) and is largely dependent on transmission of contaminated body fluids during sexual intercourse, pregnancy, and so forth [2]. More than 30 million people worldwide are living with HIV. Besides, retroviruses are increasingly becoming valuable tools in molecular biology and have been used successfully in gene therapy [3]. Based on morphology, pathogenicity, and molecular phylogenetics, retroviruses have been classified into two subfamilies: Orthoretrovirinae, Spumaretrovirinae and rest of the viruses are unclassified. The Orthoretrovirinae is further classified into six genera: Alpharetrovirus, Betaretrovirus, Deltaretrovirus, Epsilonretrovirus, Gammaretrovirus, and Lentivirus. The analysis of codon usage of whole organisms and/or organisms from
Construction of C operator for a PT symmetric model
R. Roychoudhury,P. Roy
Physics , 2007,
Abstract: We obtain closed form expression of the C(x,y) operator for the PT symmetric Scarf I potential. It is also shown that the eigenfunctions are complete.
PT-invariant one-dimensional Coulomb problem
Anjana Sinha,Rajkumar Roychoudhury
Physics , 2002,
Abstract: The one-dimensional Coulomb-like potential with a real coupling constant beta, and a centrifugal-like core of strength G = alpha^2 - {1/4}, viz. V(x) = {alpha^2 - (1/4)}/{(x-ic)^2} + beta/|x-ic|, is discussed in the framework of PT-symmetry. The PT-invariant exactly solvable model so formed, is found to admit a double set of real and discrete energies, numbered by a quasi-parity q = +/- 1.
WKB and MAF Quantization Rules for Spatially Confined Quantum Mechanical Systems
A. Sinha,R. Roychoudhury
Physics , 1999,
Abstract: A formalism is developed to obtain the energy eigenvalues of spatially confined quantum mechanical systems in the framework of The usual WKB and MAF methods. The technique is applied to three different cases,viz one dimensional Harmonic Oscillators,Quartic Oscillators and a boxed-in charged particle in electric field.
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