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Search Results: 1 - 10 of 932 matches for " Ruchi Chaudhary "
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Inferring Species Trees from Incongruent Multi-Copy Gene Trees Using the Robinson-Foulds Distance
Ruchi Chaudhary,J. Gordon Burleigh,David Fernández-Baca
Computer Science , 2012,
Abstract: We present a new method for inferring species trees from multi-copy gene trees. Our method is based on a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees (mul-trees), i.e., gene trees in which multiple leaves can have the same label. Unlike most previous phylogenetic methods using gene trees, this method does not assume that gene tree incongruence is caused by a single, specific biological process, such as gene duplication and loss, deep coalescence, or lateral gene transfer. We prove that it is NP-hard to compute the RF distance between two mul-trees, but it is easy to calculate the generalized RF distance between a mul-tree and a singly-labeled tree. Motivated by this observation, we formulate the RF supertree problem for mul-trees (MulRF), which takes a collection of mul-trees and constructs a species tree that minimizes the total RF distance from the input mul-trees. We present a fast heuristic algorithm for the MulRF supertree problem. Simulation experiments demonstrate that the MulRF method produces more accurate species trees than gene tree parsimony methods when incongruence is caused by gene tree error, duplications and losses, and/or lateral gene transfer. Furthermore, the MulRF heuristic runs quickly on data sets containing hundreds of trees with up to a hundred taxa.
Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis
Ruchi Chaudhary,David Fernandez-Baca,J. Gordon Burleigh
Computer Science , 2015,
Abstract: Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper provides a theoretical foundation for the use of TAGs in phylogenetics. We provide a formal definition of TAG that - unlike previous definition - does not depend on the order in which input trees are provided. In the consensus case, when all input trees have the same leaf labels, we describe algorithms for constructing majority-rule and strict consensus trees using the TAG. When the input trees do not have identical sets of leaf labels, we describe how to determine if the input trees are compatible and, if they are compatible, to construct a supertree that contains the input trees.
A Rare Case of Acute Cerebrovascular Accident in the Post-Partum Period after Primary Angioplasty during Pregnancy  [PDF]
Ruchi Gupta
International Journal of Clinical Medicine (IJCM) , 2015, DOI: 10.4236/ijcm.2015.612118
Abstract: Pregnancy-related acute myocardial infarction is rare, but a serious event. We report a case of acute myocardial infarction in a 33-year-old female with 5 months of pregnancy. Angiography, under abdominal shield, revealed 100% thrombotic occlusion in the left anterior descending artery, which was treated successfully with a stent implantation. The patient was found to have hyperhomocysteinemia within the first week of primary percutaneous coronary intervention (PCI). Rest of the follow-up was uneventful with delivery of a healthy baby by elective caesarean section at about 36 weeks of gestation. Within 7 days of post-partum period, the patient displayed signs of cerebrovascular infarction and was managed successfully. To the best of our knowledge, the association between primary PCI during pregnancy and cerebrovascular event in the postpartum period has not been reported previously.
iGTP: A software package for large-scale gene tree parsimony analysis
Ruchi Chaudhary, Mukul S Bansal, André Wehe, David Fernández-Baca, Oliver Eulenstein
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-574
Abstract: We introduce iGTP, a platform-independent software program that implements state-of-the-art algorithms that greatly speed up species tree inference under the duplication, duplication-loss, and deep coalescence reconciliation costs. iGTP significantly extends and improves the functionality and performance of existing gene tree parsimony software and offers advanced features such as building effective initial trees using stepwise leaf addition and the ability to have unrooted gene trees in the input. Moreover, iGTP provides a user-friendly graphical interface with integrated tree visualization software to facilitate analysis of the results.iGTP enables, for the first time, gene tree parsimony analyses of thousands of genes from hundreds of taxa using the duplication, duplication-loss, and deep coalescence reconciliation costs, all from within a convenient graphical user interface.The need to build species trees based on evidence from genes along entire genomes often arises in phylogenomic studies [1,2]. The problem is sometimes approached using supertree methods [3-5], which provide a way to combine several conflicting phylogenies on partially overlapping sets of taxa into a single comprehensive phylogeny. However, supertree methods (for example, the majority of those described in [6]) are typically designed to work with species trees, not gene trees, as their inputs. Unlike species trees, gene trees can contain more than one homolog of a gene from the same species. More crucially, genes are affected by complex evolutionary phenomena, such as deep coalescence (incomplete lineage sorting), gene duplication and subsequent loss, lateral gene transfer, and recombination, that can create tremendous heterogeneity in the topology of gene trees and obscure species relationships. One well-studied approach for dealing with these complications is gene tree parsimony (GTP) [7-18], which seeks a species tree that contains all taxa represented in the gene trees and implies the mini
Health related quality of life of women suffering from Uterine Prolapse before and after six months of surgery  [PDF]
Anchala Chaudhary
Health (Health) , 2014, DOI: 10.4236/health.2014.65051
Abstract:

One of the goals of health for everybody in 21st century is the improvement of quality of life. Thus, to find the best treatment for medical problems, it is not only enough to evaluate the results of interventions on morbidity and mortality in clinical studies, but also that the outcome of interventions in terms of socio-cultural aspect should be evaluated. Uterine Prolapse strikes at the heart of a woman’s sense of her own women nature and therefore her security along with her marital relationship should be guaranteed after the surgery process. After the removal of uterus women can’t find herself fulfilled though it is sick one as changes appear in women’s life both in understanding of her health as well as socio-cultural position that they gained after being as women. Many of the women who underwent surgery process are still suffering from both physical and psychological impairments. Some of them are experiencing psychological problem as they feel no longer a whole or real woman because of the removal of their reproductive organs, while others still had an orgasm from intercourse not just feeling dead. The changes to their sex life have created problem to them as they still struggle to cope with the loss they feel in their life as husbands always fed up as they argue with him. Such types of suffering and pain happen due to the socio-cultural circumstances in which a woman is brought up. They are seen as productive machine which had never been stopped though they are passing from pain and suffering. Thus, the overall issue of surgery process is to assure the quality of life of women to be them as a good wife and mother as well as good employer outside the home but before all this feeling of a whole womanhood in their life.

Impacts of Transnational Labor Migration on Learning Process: A Case Study of Nepalese Children and Women Staying Behind  [PDF]
Anchala Chaudhary
Open Journal of Social Sciences (JSS) , 2016, DOI: 10.4236/jss.2016.411007
Abstract:
Transnational migration has become an essential feature of family life in Nepal due to process of urbanization and globalization in every part of life. During this process, a network of social relationships takes place through which ideas, practices, and resources are exchanged and transformed between migrants and non-migrants. Migrants remit and support their sending households by remitting not only money but also new culture that he/she encounter in new place. This assist non migrants especially, the children and wife to demand high wages, access new opportunities such as education and better health care and reject the status quo. A wives staying behind has to be more responsible for not only to raise and educate their children but also manage their household’s chores and outside activities. In Nepal, the provision of education is embedded in the social structures and infused by cultural meanings which generally restrict women to participate more or less in formal education and move outside of home. Migration has provides ground for nurturing the women’s autonomy, self-esteem and role expansion as they started to participate in community based organizations (CBO’s), non-government organization (NGO) to learn some informal skill and knowledge such as stitching, embroidery, handicraft, and so on. Furthermore, these women are more responsible to provide better education to the children and managing the remittance. Thus, women’s staying behind has learned to manage not only economic and emotional limitations but also to organize and create new identities, alliances, space of self and communal empowerment.
The Population Decline of Gyps Vultures in India and Nepal Has Slowed since Veterinary Use of Diclofenac was Banned
Vibhu Prakash,Mohan Chandra Bishwakarma,Anand Chaudhary,Richard Cuthbert,Ruchi Dave,Mandar Kulkarni,Sashi Kumar,Khadananda Paudel,Sachin Ranade,Rohan Shringarpure,Rhys E. Green
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0049118
Abstract: Populations of oriental white-backed vulture (Gyps bengalensis), long-billed vulture (Gyps indicus) and slender-billed vulture (Gyps tenuirostris) crashed during the mid-1990s throughout the Indian subcontinent. Surveys in India, initially conducted in 1991–1993 and repeated in 2000, 2002, 2003 and 2007, revealed that the population of Gyps bengalensis had fallen by 2007 to 0.1% of its numbers in the early 1990s, with the population of Gyps indicus and G. tenuirostris combined having fallen to 3.2% of its earlier level. A survey of G. bengalensis in western Nepal indicated that the size of the population in 2009 was 25% of that in 2002. In this paper, repeat surveys conducted in 2011 were analysed to estimate recent population trends. Populations of all three species of vulture remained at a low level, but the decline had slowed and may even have reversed for G. bengalensis, both in India and Nepal. However, estimates of the most recent population trends are imprecise, so it is possible that declines may be continuing, though at a significantly slower rate. The degree to which the decline of G. bengalensis in India has slowed is consistent with the expected effects on population trend of a measured change in the level of contamination of ungulate carcasses with the drug diclofenac, which is toxic to vultures, following a ban on its veterinary use in 2006. The most recent available information indicates that the elimination of diclofenac from the vultures’ food supply is incomplete, so further efforts are required to fully implement the ban.
Asplenium nidus; The Bird’s Nest Fern: Developmental Studies and Its Conservation  [PDF]
Ruchi Srivastava, P. L. Uniyal
American Journal of Plant Sciences (AJPS) , 2013, DOI: 10.4236/ajps.2013.45A007
Abstract:

Asplenium nidus L. commonly called as Bird’s Nest Fern, is a threatened, ornamental fern, which is widely used as novel foliage ornamental plant and local people use it in worship. The taxon is threatened due to over exploitation, habitat destruction and genetic barriers. To understand the constraints in the regeneration, reproductive biology studies are made. It is observed that more sporophytes are produced in composite population (13.3%) in comparison to isolate population (10%). This pattern is suggestive of the fact that the parental sporophyte is heterozygous for recessive sporophytic lethal. On the basis of the results obtained A. nidus was initially adapted for outbreeding with the capacity for considerable amount of inbreeding. The low potential of sporophyte production in isolate gametophyte could be the constitution of the zygotic genotype.

Thermal Radiation Effects on MHD Boundary Layer Flow over an Exponentially Stretching Surface  [PDF]
Santosh Chaudhary, Sawai Singh, Susheela Chaudhary
Applied Mathematics (AM) , 2015, DOI: 10.4236/am.2015.62027
Abstract: The steady two-dimensional laminar boundary layer flow and heat transfer of a viscous incompressible electrically conducting fluid over an exponentially stretching surface in the presence of a uniform magnetic field with thermal radiation are investigated. The governing boundary layer equations are transformed to ordinary differential equations by taking suitable similarity transformation and solved numerically by shooting method. The effects of various parameters such as magnetic parameter, radiation parameter, Prandtl number and Eckert number on local skin-friction coefficient, local Nusselt number, velocity and temperature distributions are computed and represented graphically.
Analysis of Different Multiplier with Digital Filters Using VHDL Language
Ruchi Sharma
International Journal of Engineering and Advanced Technology , 2012,
Abstract: Performance as well as Area are the two main design tolls, power consumption also become a vital concern in VLSI system design. A system’s performance is generally determined by the performance of the multiplier because the multiplier is the slowest element in the system. area and speed are usually conflicting constraints so that for improving the speed of the system results in larger areas. As a result, a multipliers with optimized area & speed has been designed with fully parallel algorithms. The need for low-power VLSI system arises from two main forces.
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