Papers by elizabeth jacob
CUSAT, expert member of my Doctoral Committee for providing valuable comments and suggestions tha... more CUSAT, expert member of my Doctoral Committee for providing valuable comments and suggestions that helped in improving the quality of my work immensely. I express my sincere thanks to Rahul S., Akhil S. Karun and Jeen Mariam Mathews, my batch mates who have registered for Ph.D. in CUSAT. I thank Dr. E. V. Soniya, Scientist, Rajiv Gandhi Centre for Biotechnology for being a member of my SRF assessment committee and for her valuable suggestions.
This document contains the 1st management recommendation (MR) invitations submitted to the case s... more This document contains the 1st management recommendation (MR) invitations submitted to the case studies in the FarFish project. The purpose of these MR invitations is to offer selected operators (resource users) the opportunity to develop MRs in accordance with the responsive fisheries management system (RFMS) approach; following the "first draft general guidelines for making MRs" presented in FarFish deliverable 3.1. The RFMS is a management approach founded on the principles of results-based management (RBM). According to RFMS, the responsibility for fisheries management is partly transferred to the resource users, provided that they meet with necessary requirements set forth by the competent authorities and provide documentation confirming implementation and achievement of specified management objectives. The advantages of such an approach include facilitation of more bottom-up style of management where the actual resource users and other stakeholders are involved, whic...
This report contains basic description of the six case studies (CS) in the FarFish project. Four ... more This report contains basic description of the six case studies (CS) in the FarFish project. Four of the CS have Sustainable Fisheries Partnership Agreements (SFPA) with the EU and two are within international waters. The CS cover the Cape Verde tuna fishery (SFPA), the Senegal tuna and hake fishery (SFPA), the Mauritanian mixed fishery (SFPA), Seychelles tuna fishery (SFPA), the high-seas mixed fishery in the South West Atlantic (FAO Major Fishing Area 41) and the mixed fishery in the international waters of South East Atlantic (FAO Area 47). The information presented is primarily based on a review of the available literature and the data that will feed other FarFish work packages (WPs). This case study characterizations, which will be updated as the project progresses, includes descriptions of geography, oceanography, ecosystem characteristics, fisheries activity and production in the area. It also includes description of the existing management procedures and overall their objecti...
TABLE OF CONTENTS ACKNOWLEDGEMENT i PREFACE iv AIM AND OBJECTIVES vii OUTLINE OF THE THESIS ix TA... more TABLE OF CONTENTS ACKNOWLEDGEMENT i PREFACE iv AIM AND OBJECTIVES vii OUTLINE OF THE THESIS ix TABLE OF CONTENTS x LIST OF FIGURES xv LIST OF TABLES xvii LIST OF ABBREVIATIONS xix LIST OF ABBREVIATIONS, SYMBOLS AND PARAMETERS USED IN THE MODEL xxii xii 3.3.2 Results from simulations with symmetric division of stem cells 3.4 Conclusions 4 Application of the Crypt Model-Explaining Precancerous Changes in FAP Crypts. 4.1 Biological background 4.2 The question and the methodology 4.3 The computational model 4.4 Evolving a hypothesis on the effect of APC Mutation 4.5 Implementing the bias in favor of stem cell progeny in the model 4.6 Testing the hypothesis-Can the hypothesis resolve the contradiction? 4.7 Implementing APC mutation in the model 4.7.1 Sporadic mutation that increases biased symmetric division has a better chance of getting fixed in the crypt 4.7.2 Mutation that increases biased symmetric division increases somatic mutation rates 4.8 Conclusions 5 Multiple Roles of Adenomatous Polyposis Coli Gene in Wnt Signaling-a Computational Model. 5.1 Biological background 5.1.1The mechanisms by which APC can control β-catenin/TCF formation 5.1.2 Mutation of APC and consequent functional losses. 5.2 Computational models for the Wnt signaling network. 5.3 Methodology 5.3.1 Model for the role of APC in destruction cycle. 5.3.2 Model for the role of APC in controlling the distribution of β-catenin between adhesion and Wnt signaling. 5.3.3 Sequestration and export of ABC by nuclear APC. 5.3.4 Conceptual models of the effects of APC mutation. xiii 5.3.4.1 APC lacking 20aa and 15aa 5.3.4.2 APC lacking SAMP 5.3.4.3 APC lacking NLS 5.3.4.4 APC lacking NES 5.4 The computational model. 5.5 Results and discussion 5.5.1 Sensitivity of the results to the newly assumed rate constants. 5.5.2 Kinetic response of β-catenins to Wnt stimulation. 5.5.3 Effect of APC Mutations. 5.5.3.1 Effect of inactivation of 20aa sites. 5.5.3.2 Effect of inactivation of both 20aa and 15 aa sites. 5.5.3.3 When the Destruction Complex formation is affected by SAMP mutation. 5.5.3.4 Mutation of sites involved in nuclear shuttling. 5.6 Conclusions 5.7 Appendix 5.A-The computational model details 6 Extension of the Crypt Model-Multiple Ways in which APC Mutations Initiate Colon Cancer 6.1 Biological background-Cell functions affected by APC mutations 6.1.1 APC role in cell division driven by Wnt signaling 6.1.2 APC role in contact inhibition of proliferation and migration 6.1.3 APC role in serial differentiation 6.1.4 APC role in cell shedding 6.1.5 APC role in stem cell division 6.2 Modeling the perturbations in the colon crypt due to APC mutation 6.2.1 Modeling perturbations to cell division by Wnt signaling 6.2.2 Modeling perturbations to contact inhibition of proliferation 6.2.3 Modeling perturbations to migration xiv 6.2.4 Modeling perturbations to differentiation 6.2.5 Modeling perturbations to cell shedding 6.2.6 Modeling perturbations to stem cell division 6.3 Results and discussion 6.3.1 Perturbing the crypt processes in isolation 6.3.2 Different combinations of perturbations 6.3.2.1 Perturbing migration and contact inhibition together 6.3.2.2 Perturbing all processes except migration 6.3.2.3 Perturbing all processes except migration and stem cell division 6.3.2.4 Perturbing all the processes together 6.4 Conclusions 7 Conclusion 7.1 Summary 7.2 Future directions REFERENCES LIST OF PUBLICATIONS xv xix LIST OF ABBREVIATIONS TA Transit Amplifying APC Adenomatous Polyposis Coli CRC Colorectal Cancer Wnt Wnt Ligands TCF Transcription Factor MCC Mutated in colorectal cancer TP53 Tumor protein p53 kDa Kilo Daltons cDNA Complementary DNA kb Kilo-Base Pairs bp Base Pair GC Guanine-Cytosine
A soft computing model for data clustering and application to gene grouping
Parallel processing: Transputer and occam
Transputer - a microprocessor chip and Occam - a programming language have given a new dimension ... more Transputer - a microprocessor chip and Occam - a programming language have given a new dimension to parallel processing. They were designed together and were designed to work together. This document gives a brief overview of Transputer, Occam and Parallel Processing in general
Bioinformatics, 2016
Type 2 Diabetes, co-morbidities, Kanpur, North India Type2 Diabetes affects a huge population of ... more Type 2 Diabetes, co-morbidities, Kanpur, North India Type2 Diabetes affects a huge population of the world with India on the top of the world's list. Present study aims to gain information about the status of diabetes in the study population laying emphasis on the prevalence of co-morbidities. The study was done on 120 asymptomatic controls and 120 diabetics. A standardized questionnaire was used to collect socioeconomic and demographic details of the participants. The mean duration of diabetes was 7.07±0.5years. The mean BMI values among diabetics and controls were 27.25±0.25 kg/m 2 and 25.367±0.263 kg/m 2 respectively (p<0.001). About 24.16% patients had abnormal ECG values while 75.83% patients showed typical dyslipidemia. 60% of the affected individuals had abnormal HbA1c values (> 7) and 17.5% patients had frequent non-healing skin and soft tissue infections or ulcers of leg or foot. Kidney function tests displayed deranged values in about 11.66% patients. 62.5% diabetics belonged to the age group of 46-60 (p<0.0018) and 67.5% of them had positive family history (p<0.0001). Socio-demographic factors like marriage, education, occupation, smoking, exercise, cooking medium and consumption of junk food were found to be significantly associated with the disease. Effective treatment modalities and awareness is necessary for diabetes management in known cases and for early diagnosis in future cases.
Simulation of Side Branch Development in Thermal Dendritic Grains
Materials Science Forum, 1996
ABSTRACT Side-branch evolution in thermal dendrites of limited extent is studied using a computer... more ABSTRACT Side-branch evolution in thermal dendrites of limited extent is studied using a computer simulation. The changes in side branch spacing is seen to be primarily controlled by competitive growth as long as there is a driving force for length-wise growth of the side-...
Meta-search engines (MSEs) on Internet have improved continually with application of new methodol... more Meta-search engines (MSEs) on Internet have improved continually with application of new methodologies. Understanding and utilisation of MSEs are valuable for computer scientists and researchers, for effective information retrieval. This paper reviews functionality, working principles, growth, evolution and popularity of various MSEs.
In today's global manufacturing environment, casting buyers want foundries to deliver the parts w... more In today's global manufacturing environment, casting buyers want foundries to deliver the parts with the desired quality at short lead times. To achieve this, foundries are turning to computer simulation for analysing and optimising the design of the cast components as well as methoding (gating and feeding) design. Most of the casting simulation packages available in the international market are however, beyond the reach of small units, which form 80% of the Indian foundry industry. Keeping this in view, the computational modelling group of CSIR-NIIST has developed a highly efficient multi-physics-based software code for modelling mould filling and casting solidification, which is suitable for a wide range of metals and gravity casting processes. The software provides the filling sequence, temperature distribution, liquid fraction and cooling curves, and predicts major casting defects including air blow holes, cold shut, misrun, shrinkage porosity and hard zones. The code has been continuously improved during the last two decades and was named FLOW + , which was recently integrated with the casting design software AutoCAST. The combined programme enables foundry engineers to seamlessly carry out 3-D methods design, advanced coupled simulation, defects prediction, and casting optimisation within an extremely user-friendly environment. The mathematical model, functionality and results of the programme are briefly described in this paper, and illustrated with a few industrial case studies.
Quantitative Feeder Design for Metal Castings
Materials Science Forum, 2015
International Journal of Computer Applications, 2010
Numerous information retrieval tools like Search Engines, Web Directories and deep-web search por... more Numerous information retrieval tools like Search Engines, Web Directories and deep-web search portals exist. Meta-search engines (MSE) developed over the past years claim to automatically and simultaneously search many other such information retrieval tools and improvise the fused results.
Design and Development of a Programmable Meta Search Engine
International Journal of Computer Applications, 2013
Journal of Intelligent Manufacturing, 2000
The design of feeders for castings has been mostly based on empirical rules, heuristics and past ... more The design of feeders for castings has been mostly based on empirical rules, heuristics and past experience. This paper presents a novel approach to the problem by augmenting genetic algorithms with CAD to optimize the feeder dimensions. The synergy of CAD and genetic algorithms generates a class of optimal feeders that also satisfy the standard criteria laid down in literature. A CAD platform is used as the front-end to create the solid model of the casting, divide it into feeding sections and calculate the volume and surface area of each feeding section. The feeding sections are made such that each section satis®es the feedpath requirement and ensures a critical modulus gradient. The genetic algorithm works on this data to design feeders keeping the yield as the optimization parameter and simultaneously satisfying the constraints of minimum volume and modulus.
A fuzzy-driven genetic algorithm for sequence segmentation applied to genomic sequences
Applied Soft Computing, 2009
The fuzzy-driven genetic algorithm for sequence segmentation consists of a genetic algorithm whos... more The fuzzy-driven genetic algorithm for sequence segmentation consists of a genetic algorithm whose objective function is driven by a fuzzy fitness finder. The genetic algorithm starts with an initial population of alternate solutions where each solution is a different ...
ERROR-RATE FACTOR IN THE MANAGEMENT OF APPENDICITIS
Lancet, 1975
A fuzzy guided genetic algorithm for operon prediction
Bioinformatics/computer Applications in The Biosciences, 2005
The operon structure of the prokaryotic genome is a critical input for the reconstruction of regu... more The operon structure of the prokaryotic genome is a critical input for the reconstruction of regulatory networks at the whole genome level. As experimental methods for the detection of operons are difficult and time-consuming, efforts are being put into developing computational methods that can use available biological information to predict operons. A genetic algorithm is developed to evolve a starting population of putative operon maps of the genome into progressively better predictions. Fuzzy scoring functions based on multiple criteria are used for assessing the &amp;amp;#39;fitness&amp;amp;#39; of the newly evolved operon maps and guiding their evolution. The algorithm organizes the whole genome into operons. The fuzzy guided genetic algorithm-based approach makes it possible to use diverse biological information like genome sequence data, functional annotations and conservation across multiple genomes, to guide the organization process. This approach does not require any prior training with experimental operons. The predictions from this algorithm for Escherchia coli K12 and Bacillus subtilis are evaluated against experimentally discovered operons for these organisms. The accuracy of the method is evaluated using an ROC (receiver operating characteristic) analysis. The area under the ROC curve is around 0.9, which indicates excellent accuracy. [email protected].
In the process of interpreting simulation results, new post-processing techniques are developed. ... more In the process of interpreting simulation results, new post-processing techniques are developed. This work presents a post-processing method that analyzes the solidification pattern formed by simulation of the solidification process of molten metal in a mold to produce shaped castings. Simulations generally involve numerical solutions of differential equations which are discretized by dividing the three-dimensional computational domain into small finite volume elements using a 3D grid. The locations of the grid points and values of the solidification time at these locations are used to divide the spatial data into 3D sections such that starting from a hotspot location within the section that has high solidification time, there is a gradient outwards with lower values of solidification time. Each section is assumed to be fed by one or more feeders that must freeze only after the section has solidified completely. The volume of a feeder can be determined from the volume of the section it is supposed to feed. The volume and surface area of sections are determined approximately to calculate feeder size and dimensions. The post-processing algorithm is a simulation-based quantitative approach to feeder design which in conventional foundry practice has been more of an art than science. It is also general enough for use in other 3D segmentation applications.
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Papers by elizabeth jacob