Search results for: Hema Subramaniam

Authors: Nur Razia Mohd Suradi, Hema Subramaniam, Marina Hassan, Siti Fatimah Omar

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Knowledge sharing culture contributes to a positive working environment. Currently, there is no platform for the Faculty of Industrial Information Technology (FIIT), Unisel academic staff to share knowledge among them. As it is done manually, the sharing process is through common meeting or by any offline discussions. There is no repository for future retrieval. However, with open source solution the development of knowledge based application may reduce the cost tremendously. In this paper we discuss about the domain on which this knowledge portal is being developed and also the deployment of open source tools such as JOOMLA, PHP programming language and MySQL. This knowledge portal is evidence that open source tools also reliable in developing knowledge based portal. These recommendations will be useful to the open source community to produce more open source products in future.

Keywords: Knowledge management, Portal, ContentManagement, JOOMLA.

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Authors: Bashirah Ishak, Jacyln JiaYing Thye, Bariah Mohd Ali, Norhani Mohidin

Abstract:

Background Contact lens (CL) wear can cause changes in blinking and corneal staining. Aims and Objectives To determine the effects of CL materials (HEMA and SiHy) on spontaneous blink rate, blinking patterns and corneal staining after 2 months of wear. Methods Ninety subjects in 3 groups (control, HEMA and SiHy) were assessed at baseline and 2-months. Blink rate was recorded using a video camera. Blinking patterns were assessed with digital camera and slit lamp biomicroscope. Corneal staining was graded using IER grading scale Results There were no significant differences in all parameters at baseline. At 2 months, CL wearers showed significant increment in average blink rate (F1.626, 47.141 = 7.250, p = 0.003; F2,58 = 6.240, p = 0.004) and corneal staining (χ2 2, n=30 = 31.921, p < 0.001; χ2 2, n=30 = 26.909, p < 0.001). Conclusion Blinking characteristics and corneal staining were not influence by soft CL materials.

Keywords: Spontaneous blinking, cornea staining, grading, soft contact lenses.

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Authors: Hema Nair

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This paper presents a new system developed in Java® for pattern recognition and pattern summarisation in multi-band (RGB) satellite images. The system design is described in some detail. Results of testing the system to analyse and summarise patterns in SPOT MS images and LANDSAT images are also discussed.

Keywords: Pattern recognition, image analysis, feature extraction, blackboard component, linguistic summary.

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Authors: Hayder Natiq Jasem, Zuriati Ahmad Zukarnain, Mohamed Othman, Shamala Subramaniam

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Congestion control is one of the fundamental issues in computer networks. Without proper congestion control mechanisms there is the possibility of inefficient utilization of resources, ultimately leading to network collapse. Hence congestion control is an effort to adapt the performance of a network to changes in the traffic load without adversely affecting users perceived utilities. AIMD (Additive Increase Multiplicative Decrease) is the best algorithm among the set of liner algorithms because it reflects good efficiency as well as good fairness. Our control model is based on the assumption of the original AIMD algorithm; we show that both efficiency and fairness of AIMD can be improved. We call our approach is New AIMD. We present experimental results with TCP that match the expectation of our theoretical analysis.

Keywords: Congestion control, Efficiency, Fairness, TCP, AIMD.

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Authors: T. V. S. Sekhar, B. Hema Sundar Raju

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Laminar natural-convective heat transfer from a horizontal cylinder is studied by solving the Navier-Stokes and energy equations using higher order compact scheme in cylindrical polar coordinates. Results are obtained for Rayleigh numbers of 1, 10, 100 and 1000 for a Prandtl number of 0.7. The local Nusselt number and mean Nusselt number are calculated and compared with available experimental and theoretical results. Streamlines, vorticity - lines and isotherms are plotted.

Keywords: Higher order compact scheme, Navier-Stokes equations, Energy equation, Natural convection, Boussinesq's approximation and Mean Nusselt number.

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Authors: Neetu Rani, Hema Setia, Marut Dutt. R.K. Wanchoo

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An empirical correlation for predicting the heat transfer coefficient for a cylinder under free convection, inclined at any arbitrary angle with the horizontal has been developed in terms of Nusselt number, Prandtl number and Grashof number. Available experimental data was used to determine the parameters for the proposed correlation. The proposed correlation predicts the available data well within ±10%, for Prandtl number in the range 0.68-0.72 and Grashof number in the range 1.4×10⁴–1.2×10¹⁰.

Keywords: Heat transfer, inclined cylinders, natural convection, Nusselt number, Prandtl number, Grashof number.

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Authors: Subramaniam Chandran

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This paper explores the social and political imperatives in the sphere of public policy relating to social justice. In India, the colonial legacy and post-colonial social and political pressures sustained the appropriation of 'caste' category in allocating public resources to the backward class of citizens. For several reasons, 'economic' category could not be placed in allocating resources. This paper examines the reasons behind the deliberative exercises and formulating policies and seeks an alternative framework in realizing social justice in terms of a unified category. This attempt can be viewed as a reconciliation of traditional and modern values for a viable alternative in public policy making.

Keywords: Social justice, caste, public policy, communal quota

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Authors: Subramaniam Chandran

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This paper examines the interplay of policy options and cost-effective technology in providing sustainable distance education. A case study has been conducted among the learners and teachers. The emergence of learning technologies through CD, internet, and mobile is increasingly adopted by distance institutes for quick delivery and cost-effective factors. Their sustainability is conditioned by the structure of learners and well as the teaching community. The structure of learners in terms of rural and urban background revealed similarity in adoption and utilization of mobile learning. In other words, the technology transcended the rural-urban dichotomy. The teaching community was divided into two groups on policy issues. This study revealed both cost-effective as well as sustainability impacts on different learners groups divided by rural and urban location.

Keywords: Distance Education, Mobile Learning, Policy, Technology

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Authors: Hema Sandhya Jagarlamudi, Mousumi Saha, Pavan Kumar Jagarlamudi

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The use of Quantum dots is a promising emerging Technology for implementing digital system at the nano level. It is effecient for attractive features such as faster speed , smaller size and low power consumption than transistor technology. In this paper, various Combinational and sequential logical structures - HALF ADDER, SR Latch and Flip-Flop, D Flip-Flop preceding NAND, NOR, XOR,XNOR are discussed based on QCA design, with comparatively less number of cells and area. By applying these layouts, the hardware requirements for a QCA design can be reduced. These structures are designed and simulated using QCA Designer Tool. By taking full advantage of the unique features of this technology, we are able to create complete circuits on a single layer of QCA. Such Devices are expected to function with ultra low power Consumption and very high speeds.

Keywords: QCA, QCA Designer, Clock, Majority Gate

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Authors: Sivapalan, S., Subramaniam, G., Clifford, M.J., Balbir Singh, M.S., Abdullah, A

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Higher education has an important role to play in advocating environmentalism. Given this responsibility, the goal of higher education should therefore be to develop graduates with the knowledge, skills and values related to environmentalism. However, research indicates that there is a lack of consciousness amongst graduates on the need to be more environmentally aware, especially when it comes to applying the appropriate knowledge and skills related to environmentalism. Although institutions of higher learning do include environmental parameters within their undergraduate and postgraduate academic programme structures, the environmental boundaries are usually confined to specific engineering majors within an engineering programme. This makes environmental knowledge, skills and values exclusive to certain quarters of the higher education system. The incorporation of environmental literacy within higher education institutions as a whole is of utmost pertinence if a nation-s human capital is to be nurtured to become change agents for the preservation of environment. This paper discusses approaches that can be adapted by institutions of higher learning to include environmental literacy within the graduate-s higher learning experience.

Keywords: Higher education, engineering education, environmental literacy, Malaysia.

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Authors: Jimaima Lako, Subramaniam Sotheeswaran, Ketan Christi

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The 15-a-side Fiji rugby team trains well in preparations for any rugby competition but rarely performs to expectations. In order to help the Fiji local based rugby players to identify some key basic areas in improving their performance, a series of workshops were conducted to assess their nutritional status and dietary habits in relation to energy demand during rugby matches. The nutrition workshop included the administration of questionnaires to 19 local based rugby players, requesting the following information: usual food intakes, training camp food intakes, carbohydrate loading, pre-game meals and post-game meals. The study revealed that poor eating habits of the players resulted in the low carbohydrate intake, which may have contributed to increase levels of fatigue leading to loss of stamina even before the second half of the game. It appears that the diet of most 15-a-side players does not provide enough energy to enable them to last the full eightyminutes of the game.

Keywords: Fiji rugby, Food habits, Physical fitness, Training meals

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Authors: V.R Gannapathy, S.K Subramaniam, A.B Mohamad Diah, M.K Suaidi, A.H Hamidon

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The picture of a perfect road construction site is the one that utilizes conventional vertical road signs and a flagman to optimize the traffic flow with minimum hazel to the public. Former research has been carried out by Department of Occupational Safety and Health (DOSH) and Ministry of Works to further enhance smoothness in traffic operations and particularly in safety issues within work zones. This paper highlights on hazardous zones in a certain road construction or road maintenance site. Most cases show that the flagman falls into high risk of fatal accidents within work zone. Various measures have been taken by both the authorities and contractors to overcome such miseries, yet it-s impossible to eliminate the usage of a flagman since it is considered the best practice. With the implementation of new technologies in automating the traffic flow in road construction site, it is possible to eliminate the usage of a flagman. The intelligent traffic light system is designed to solve problems which contribute hazardous at road construction site and to be inline with the road safety regulation which is taken into granted.

Keywords: Intelligent Traffic Light, Critical Zones, Safety Regulation, Flagman

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Authors: K. Hema Shankari, R. Thirumalaiselvi, N. V. Balasubramanian

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The present paper addresses to the research in the area of regression testing with emphasis on automated tools as well as prioritization of test cases. The uniqueness of regression testing and its cyclic nature is pointed out. The difference in approach between industry, with business model as basis, and academia, with focus on data mining, is highlighted. Test Metrics are discussed as a prelude to our formula for prioritization; a case study is further discussed to illustrate this methodology. An industrial case study is also described in the paper, where the number of test cases is so large that they have to be grouped as Test Suites. In such situations, a genetic algorithm proposed by us can be used to reconfigure these Test Suites in each cycle of regression testing. The comparison is made between a proprietary tool and an open source tool using the above-mentioned metrics. Our approach is clarified through several tables.

Keywords: APFD metric, genetic algorithm, regression testing, RFT tool, test case prioritization, selenium tool.

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Authors: Subramaniam Chandran

Abstract:

This paper explains how mobile learning assures sustainable e-education for multicultural group of students. This paper reports the impact of mobile learning on distance education in multicultural environment. The emergence of learning technologies through CD, internet, and mobile is increasingly adopted by distance institutes for quick delivery and cost-effective purposes. Their sustainability is conditioned by the structure of learners as well as the teaching community. The experimental study was conducted among the distant learners of Vinayaka Missions University located at Salem in India. Students were drawn from multicultural environment based on different languages, religions, class and communities. During the mobile learning sessions, the students, who are divided on language, religion, class and community, were dominated by play impulse rather than study anxiety or cultural inhibitions. This study confirmed that mobile learning improved the performance of the students despite their division based on region, language or culture. In other words, technology was able to transcend the relative deprivation in the multicultural groups. It also confirms sustainable e-education through mobile learning and cost-effective system of instruction. Mobile learning appropriates the self-motivation and play impulse of the young learners in providing sustainable e-education to multicultural social groups of students.

Keywords: E-Education, mobile learning, multiculturalism.

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Authors: Hema C. R., Paulraj M. P., S. Yaacob, A. H. Adom, R. Nagarajan

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Motor imagery classification provides an important basis for designing Brain Machine Interfaces [BMI]. A BMI captures and decodes brain EEG signals and transforms human thought into actions. The ability of an individual to control his EEG through imaginary mental tasks enables him to control devices through the BMI. This paper presents a method to design a four state BMI using EEG signals recorded from the C3 and C4 locations. Principle features extracted through principle component analysis of the segmented EEG are analyzed using two novel classification algorithms using Elman recurrent neural network and functional link neural network. Performance of both classifiers is evaluated using a particle swarm optimization training algorithm; results are also compared with the conventional back propagation training algorithm. EEG motor imagery recorded from two subjects is used in the offline analysis. From overall classification performance it is observed that the BP algorithm has higher average classification of 93.5%, while the PSO algorithm has better training time and maximum classification. The proposed methods promises to provide a useful alternative general procedure for motor imagery classification

Keywords: Motor Imagery, Brain Machine Interfaces, Neural Networks, Particle Swarm Optimization, EEG signal processing.

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Authors: Subramaniam Chandran

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The significance of psychology in studying politics is embedded in philosophical issues as well as behavioural pursuits. For the former is often associated with Sigmund Freud and his followers. The latter is inspired by the writings of Harold Lasswell. Political psychology or psychopolitics has its own impression on political thought ever since it deciphers the concept of human nature and political propaganda. More importantly, psychoanalysis views political thought as a textual content which needs to explore the latent from the manifest content. In other words, it reads the text symptomatically and interprets the hidden truth. This paper explains the paradigm of dream interpretation applied by Freud. The dream work is a process which has four successive activities: condensation, displacement, representation and secondary revision. The texts dealing with political though can also be interpreted on these principles. Freud's method of dream interpretation draws its source after the hermeneutic model of philological research. It provides theoretical perspective and technical rules for the interpretation of symbolic structures. The task of interpretation remains a discovery of equivalence of symbols and actions through perpetual analogies. Psychoanalysis can help in studying political thought in two ways: to study the text distortion, Freud's dream interpretation is used as a paradigm exploring the latent text from its manifest text; and to apply Freud's psychoanalytic concepts and theories ranging from individual mind to civilization, religion, war and politics.

Keywords: Psychoanalysis, political thought, dreaminterpretation, latent content, manifest content

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Authors: Subramaniam Chandran

Abstract:

This paper explores the features of political economy in the dynamics of representative politics in India. Politics is seen as enhancing economic benefits through acquiring and maintenance of power in the realm of democratic set up. The system of representation is riddled with competitive populism. Emerging leaders and parties are forced to accommodate their ideologies in coping with competitive politics. Electoral politics and voting behaviour reflect series of influences mooted by the politicians. Voters are accustomed to expect benefits outs of state exchequer. The electoral competitors show a changing phase of investment and return policy. Every elector has to spend and realize his costs in his tenure. In the case of defeated electors, even the cost recovery is not possible directly; there are indirect means to recover their costs. The series of case studies show the method of party funding, campaign financing, electoral expenditure, and cost recovery. Regulations could not restrict the level of spending. Several cases of disproportionate accumulation of wealth by the politicians reveal that money played a major part in electoral process. The political economy of representative politics hitherto ignores how a politician spends and recovers his cost and multiples his wealth. To be sure, the acquiring and maintenance of power is to enhance the wealth of the electors.

Keywords: Political economy, representative politics, costrecovery, electoral politics

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Authors: Subramaniam Chandran

Abstract:

This paper presents an assessment study conducted among the distance learners in India. Open and distance learning systems have traveled a long way since its inception and its journey has witnessed the evolution and adoption of different generations of technology. This study focuses on the distant learners in India. Sampling for this study has been derived from the mass enrollment from Tamil Nadu area, a southern state of India. Learners were chosen from dual mode universities, private universities, Tamil Nadu Open University and IGNOU. The main focus of the study is to examine the coverage and appropriation of students support services and learning aids. It explores two aspects: the facilities available and the awareness and use of such services. It includes, self-learning materials, face-to-face counseling, multimedia learning materials, website, e-learning, radio and television services etc. While exploring the student-s perspective on these learning aspects, it is important to understand the perspectives of the teachers. Two different interests are visible among the teachers. Majority of the teachers support faceto- face counseling. However, the young teachers are in favour of online learning and multimedia supports in teaching. Through the awareness is somewhat high, the actual participation in online is very low. This is due to the inadequate infrastructure as well as the traditional attitudes of the teachers. Still the face-to-face sessions remain popular than online.

Keywords: Face-to-face session, online session, distance learning, multimedia

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Authors: Subramaniam Chandran

Abstract:

This paper describes the evolution of language politics and the part played by political leaders with reference to the Dravidian parties in Tamil Nadu. It explores the interesting evolution from separatism to coalition in sustaining the values of parliamentary democracy and federalism. It seems that the appropriation of language politics is fully ascribed to the DMK leadership under Annadurai and Karunanidhi. For them, the Tamil language is a self-determining power, a terrain of nationhood, and a perennial source of social and political powers. The DMK remains a symbol of Tamil nationalist party playing language politics in the interest of the Tamils. Though electoral alliances largely determine the success, the language politics still has significant space in the politics of Tamil Nadu. Ironically, DMK moves from the periphery to centre for getting national recognition for the Tamils as well as for its own maximization of power. The evolution can be seen in two major phases as: language politics for party building; and language politics for state building with three successive political processes, namely, language politics in the process of separatism, representative politics and coalition. The much pronounced Dravidian Movement is radical enough to democratize the party ideology to survive the spirit of parliamentary democracy. This has secured its own rewards in terms of political power. The political power provides the means to achieve the social and political goal of the political party. Language politics and leadership pattern actualized this trend though the movement is shifted from separatism to coalition.

Keywords: Language politics, cultural nationalism, leadership, social justice

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Authors: Axay J Mehta, Hema A Mehta, T.C.Manjunath, C. Ardil

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In this paper, the modelling and design of artificial neural network architecture for load forecasting purposes is investigated. The primary pre-requisite for power system planning is to arrive at realistic estimates of future demand of power, which is known as Load Forecasting. Short Term Load Forecasting (STLF) helps in determining the economic, reliable and secure operating strategies for power system. The dependence of load on several factors makes the load forecasting a very challenging job. An over estimation of the load may cause premature investment and unnecessary blocking of the capital where as under estimation of load may result in shortage of equipment and circuits. It is always better to plan the system for the load slightly higher than expected one so that no exigency may arise. In this paper, a load-forecasting model is proposed using a multilayer neural network with an appropriately modified back propagation learning algorithm. Once the neural network model is designed and trained, it can forecast the load of the power system 24 hours ahead on daily basis and can also forecast the cumulative load on daily basis. The real load data that is used for the Artificial Neural Network training was taken from LDC, Gujarat Electricity Board, Jambuva, Gujarat, India. The results show that the load forecasting of the ANN model follows the actual load pattern more accurately throughout the forecasted period.

Keywords: Power system, Load forecasting, Neural Network, Neuron, Stabilization, Network structure, Load.

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Authors: Sumiko Anno, Keiji Imaoka, Takeo Tadono, Tamotsu Igarashi, Subramaniam Sivaganesh, Selvam Kannathasan, Vaithehi Kumaran, Sinnathamby Noble Surendran

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Dengue outbreaks are affected by biological, ecological, socio-economic and demographic factors that vary over time and space. These factors have been examined separately and still require systematic clarification. The present study aimed to investigate the spatial-temporal clustering relationships between these factors and dengue outbreaks in the northern region of Sri Lanka. Remote sensing (RS) data gathered from a plurality of satellites were used to develop an index comprising rainfall, humidity and temperature data. RS data gathered by ALOS/AVNIR-2 were used to detect urbanization, and a digital land cover map was used to extract land cover information. Other data on relevant factors and dengue outbreaks were collected through institutions and extant databases. The analyzed RS data and databases were integrated into geographic information systems, enabling temporal analysis, spatial statistical analysis and space-time clustering analysis. Our present results showed that increases in the number of the combination of ecological factor and socio-economic and demographic factors with above the average or the presence contribute to significantly high rates of space-time dengue clusters.

Keywords: ALOS/AVNIR-2, Dengue, Space-time clustering analysis, Sri Lanka.

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Authors: D. Sathan, A. Meetoo, R. K. Subramaniam

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Context awareness is a capability whereby mobile computing devices can sense their physical environment and adapt their behavior accordingly. The term context-awareness, in ubiquitous computing, was introduced by Schilit in 1994 and has become one of the most exciting concepts in early 21st-century computing, fueled by recent developments in pervasive computing (i.e. mobile and ubiquitous computing). These include computing devices worn by users, embedded devices, smart appliances, sensors surrounding users and a variety of wireless networking technologies. Context-aware applications use context information to adapt interfaces, tailor the set of application-relevant data, increase the precision of information retrieval, discover services, make the user interaction implicit, or build smart environments. For example: A context aware mobile phone will know that the user is currently in a meeting room, and reject any unimportant calls. One of the major challenges in providing users with context-aware services lies in continuously monitoring their contexts based on numerous sensors connected to the context aware system through wireless communication. A number of context aware frameworks based on sensors have been proposed, but many of them have neglected the fact that monitoring with sensors imposes heavy workloads on ubiquitous devices with limited computing power and battery. In this paper, we present CALEEF, a lightweight and energy efficient context aware framework for resource limited ubiquitous devices.

Keywords: Context-Aware, Energy-Efficient, Lightweight, Ubiquitous Devices.

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Authors: S. M. Shahinul Islam, Israt Ara, Narendra Tuteja, Sreeramanan Subramaniam

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Through anther and microspore culture methods, complete homozygous plants can be produced within a year as compared to the long inbreeding method. Isolated microspore culture is one of the most important techniques for rapid development of haploid plants. The efficiency of this method is influenced by several factors such as cultural conditions, growth regulators, plant media, pretreatments, physical and growth conditions of the donor plants, pollen isolation procedure, etc. The main purpose of this study was to improve the isolated microspore culture protocol in order to increase the efficiency of embryoids, its regeneration and reducing albinisms. Under this study we have tested mainly three different microspore isolation procedures by glass rod, homozeniger and by blending and found the efficiency on gametic embryogenesis. There are three types of media viz. washing, pre-culture and induction was used. The induction medium as AMC (modified MS) supplemented by 2, 4-D (2.5 mg/l), kinetin (0.5 mg/l) and higher amount of D-Manitol (90 g/l) instead of sucrose and two types of amino acids (L-glutamine and L-serine) were used. Out of three main microspore isolation procedure by homogenizer isolation (P₄) showed best performance on ELS induction (177%) and green plantlets (104%) compared with other techniques. For all cases albinisims occurred but microspore isolation from excised anthers by glass rod and homogenizer showed lesser numbers of albino plants that was also one of the important findings in this study.

Keywords: Androgenesis, pretreatment, microspore culture, regeneration, albino plants, Oryza sativa.

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Authors: Subramaniam Chandran

Abstract:

This paper analyses the structural changes in education sector since the introduction of liberalization policy in India. This paper explains how the so-called non-profit trusts and societies appropriated the liberalization policy and enhanced themselves as new capitalist class in higher education sector. Over the decades, the policy witnessed the role of private sector in terms of maintaining market equilibrium. The state also witnessed the incompatibility of the private sector in inculcating the values of social justice. The most important consequence of the policy is to witness the rise of new capitalist class and academic capitalism. When the state came to realize that it no longer cope up with market demands, it opens the entry of private sector in higher education. Concessions and tax exemptions were provided to the trusts and societies to establish higher education institutions. There is a basic difference between western countries and India in providing higher education by the trusts and societies. In western countries the big business houses contributed their surplus revenues to promote higher education and research as a complementary service to society and nation. In India, several entrepreneurs came up with business motive using education sector. Over the period, they accumulated wealth at the cost of students and concessions from the government. Four major results can now be identified: production of manpower in view of market demands; reduction of standards in higher education; bypassing the values of social justice; and the rise of new capitalist class from the business of education. This paper tries to substantiate these issues with the inputs from case studies.

Keywords: New capitalism, market, social justice, higher education

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Authors: R. Sullivan, T. Holden, G. Tremberger, Jr, E. Cheung, C. Branch, J. Burrero, G. Surpris, S. Quintana, A. Rameau, N. Gadura, H. Yao, R. Subramaniam, P. Schneider, S. A. Rotenberg, P. Marchese, A. Flamhlolz, D. Lieberman, T. Cheung

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Migration in breast cancer cell wound healing assay had been studied using image fractal dimension analysis. The migration of MDA-MB-231 cells (highly motile) in a wound healing assay was captured using time-lapse phase contrast video microscopy and compared to MDA-MB-468 cell migration (moderately motile). The Higuchi fractal method was used to compute the fractal dimension of the image intensity fluctuation along a single pixel width region parallel to the wound. The near-wound region fractal dimension was found to decrease three times faster in the MDA-MB- 231 cells initially as compared to the less cancerous MDA-MB-468 cells. The inner region fractal dimension was found to be fairly constant for both cell types in time and suggests a wound influence range of about 15 cell layer. The box-counting fractal dimension method was also used to study region of interest (ROI). The MDAMB- 468 ROI area fractal dimension was found to decrease continuously up to 7 hours. The MDA-MB-231 ROI area fractal dimension was found to increase and is consistent with the behavior of a HGF-treated MDA-MB-231 wound healing assay posted in the public domain. A fractal dimension based capacity index has been formulated to quantify the invasiveness of the MDA-MB-231 cells in the perpendicular-to-wound direction. Our results suggest that image intensity fluctuation fractal dimension analysis can be used as a tool to quantify cell migration in terms of cancer severity and treatment responses.

Keywords: Higuchi fractal dimension, box-counting fractal dimension, cancer cell migration, wound healing.

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Authors: T. Holden, G. Tremberger, Jr, E. Cheung, R. Subramaniam, R. Sullivan, N. Gadura, P. Schneider, P. Marchese, A. Flamholz, T. Cheung, D. Lieberman

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A nucleotide sequence can be expressed as a numerical sequence when each nucleotide is assigned its proton number. A resulting gene numerical sequence can be investigated for its fractal dimension in terms of evolution and chemical properties for comparative studies. We have investigated such nucleotide fluctuation in the 16S rRNA gene of archaea thermophiles. The studied archaea thermophiles were archaeoglobus fulgidus, methanothermobacter thermautotrophicus, methanocaldococcus jannaschii, pyrococcus horikoshii, and thermoplasma acidophilum. The studied five archaea-euryarchaeota thermophiles have fractal dimension values ranging from 1.93 to 1.97. Computer simulation shows that random sequences would have an average of about 2 with a standard deviation about 0.015. The fractal dimension was found to correlate (negative correlation) with the thermophile-s optimal growth temperature with R2 value of 0.90 (N =5). The inclusion of two aracheae-crenarchaeota thermophiles reduces the R2 value to 0.66 (N = 7). Further inclusion of two bacterial thermophiles reduces the R2 value to 0.50 (N =9). The fractal dimension is correlated (positive) to the sequence GC content with an R2 value of 0.89 for the five archaea-euryarchaeota thermophiles (and 0.74 for the entire set of N = 9), although computer simulation shows little correlation. The highest correlation (positive) was found to be between the fractal dimension and di-nucleotide Shannon entropy. However Shannon entropy and sequence GC content were observed to correlate with optimal growth temperature having an R2 of 0.8 (negative), and 0.88 (positive), respectively, for the entire set of 9 thermophiles; thus the correlation lacks species specificity. Together with another correlation study of bacterial radiation dosage with RecA repair gene sequence fractal dimension, it is postulated that fractal dimension analysis is a sensitive tool for studying the relationship between genotype and phenotype among closely related sequences.

Keywords: Fractal dimension, archaea thermophiles, Shannon entropy, GC content

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