Assessing the Reproducibility of Clustering of Molecular Dynamics Conformations on Self-Organizing Maps

The goal of most clustering algorithms is to find the optimal number of clusters (i.e. fewest number of clusters). However, analysis of molecular conformations of biological macromolecules obtained from computer simulations may benefit from a larger array of clusters. The Self-Organizing Map (SOM) clustering method has the advantage of generating large numbers of clusters, but often gives ambiguous results. In this work, SOMs have been shown to be reproducible when the same conformational dataset is independently clustered multiple times (~100), with the help of the Cramérs V-index (C_v). The ability of C_v to determine which SOMs are reproduced is generalizable across different SOM source codes. The conformational ensembles produced from MD (molecular dynamics) and REMD (replica exchange molecular dynamics) simulations of the penta peptide Met-enkephalin (MET) and the 34 amino acid protein human Parathyroid Hormone (hPTH) were used to evaluate SOM reproducibility. The training length for the SOM has a huge impact on the reproducibility. Analysis of MET conformational data definitively determined that toroidal SOMs cluster data better than bordered maps due to the fact that toroidal maps do not have an edge effect. For the source code from MATLAB, it was determined that the learning rate function should be LINEAR with an initial learning rate factor of 0.05 and the SOM should be trained by a sequential algorithm. The trained SOMs can be used as a supervised classification for another dataset. The toroidal 10×10 hexagonal SOMs produced from the MATLAB program for hPTH conformational data produced three sets of reproducible clusters (27%, 15%, and 13% of 100 independent runs) which find similar partitionings to those of smaller 6×6 SOMs. The χ^2 values produced as part of the C_v calculation were used to locate clusters with identical conformational memberships on independently trained SOMs, even those with different dimensions. The χ^2 values could relate the different SOM partitionings to each other.

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Evaluating perceptual maps of asymmetries for gait symmetry quantification and pathology detection

Le mouvement de la marche est un processus essentiel de l'activité humaine et aussi le résultat de nombreuses interactions collaboratives entre les systèmes neurologiques, articulaires et musculo-squelettiques fonctionnant ensemble efficacement. Ceci explique pourquoi une analyse de la marche est aujourd'hui de plus en plus utilisée pour le diagnostic (et aussi la prévention) de différents types de maladies (neurologiques, musculaires, orthopédique, etc.). Ce rapport présente une nouvelle méthode pour visualiser rapidement les différentes parties du corps humain liées à une possible asymétrie (temporellement invariante par translation) existant dans la démarche d'un patient pour une possible utilisation clinique quotidienne. L'objectif est de fournir une méthode à la fois facile et peu dispendieuse permettant la mesure et l'affichage visuel, d'une manière intuitive et perceptive, des différentes parties asymétriques d'une démarche. La méthode proposée repose sur l'utilisation d'un capteur de profondeur peu dispendieux (la Kinect) qui est très bien adaptée pour un diagnostique rapide effectué dans de petites salles médicales car ce capteur est d'une part facile à installer et ne nécessitant aucun marqueur. L'algorithme que nous allons présenter est basé sur le fait que la marche saine possède des propriétés de symétrie (relativement à une invariance temporelle) dans le plan coronal.

Investigations on the Dynamics of Combination Maps and the Analysis of Bifurcation in a Discontinuous Logistic Map

This thesis is a study of discrete nonlinear systems represented by one dimensional mappings.As one dimensional interative maps represent Poincarre sections of higher dimensional flows,they offer a convenient means to understand the dynamical evolution of many physical systems.It highlighting the basic ideas of deterministic chaos.Qualitative and quantitative measures for the detection and characterization of chaos in nonlinear systems are discussed.Some simple mathematical models exhibiting chaos are presented.The bifurcation scenario and the possible routes to chaos are explained.It present the results of the numerical computational of the Lyapunov exponents (λ) of one dimensional maps.This thesis focuses on the results obtained by our investigations on combinations maps,scaling behaviour of the Lyapunov characteristic exponents of one dimensional maps and the nature of bifurcations in a discontinous logistic map.It gives a review of the major routes to chaos in dissipative systems,namely, Period-doubling ,Intermittency and Crises.This study gives a theoretical understanding of the route to chaos in discontinous systems.A detailed analysis of the dynamics of a discontinous logistic map is carried out, both analytically and numerically ,to understand the route it follows to chaos.The present analysis deals only with the case of the discontinuity parameter applied to the right half of the interval of mapping.A detailed analysis for the n –furcations of various periodicities can be made and a more general theory for the map with discontinuities applied at different positions can be on a similar footing

Scaling relations in the Lyapunov exponents of one dimensional maps

We establish numerically the validity of Huberman-Rudnick scaling relation for Lyapunov exponents during the period doubling route to chaos in one dimensional maps. We extend our studies to the context of a combination map. where the scaling index is found to be different.

Post Environmental Evaluation of the Rajjaprabha Dam in Thailand

This thesis Entitled Post-Environmental Evaluation of The Rajjaprabha Dam In Thailand. This post evaluation of environmental consequences of Rajjaprabha dam IS conducted ten years after its commencement. The Rajjaprabha dam project was planned and implemented as a multipurpose project, mainly for hydropower production, flood protection, fisheries, recreation and irrigation. The project includes the dam and reservoir with a 240 MW hydropower plant located about 90 km upstream from Surat Thani province, and irrigation systems covering the coastal plain in Surat Thani. The upstream storage reservoir (with about 5,639 mcm storage) and the hydropower plant had already been implemented. The first phase of irrigation system covers an area of 23,100 hectares. The second phase is envisaged to cover about 50,000 hectares. This study was conducted with the following objectives: (I) to assess all existing environmental resources and their values with the help of input-output analysis (2) to findout the beneficial impacts of the project (3) to evaluate the actual positive effects vis-a-vis the estimated effects before the project was implemented and (4) to identify all significant changes in relatives to the impacts previously assessed. The study area includes the Phum Duang river basin of about 4,668 km2 (placed on the areas that are upstream and downstream to the damsite), The duration of study is limited to 10 years after the dam has become operational i.e. from 1987-1997. The results of the study reveal that there is no significant changes in climatic and ground water resources, with respect to the study area inspte of the fact that the physical and chemical properties of the soil have slightly changed. Sedimentation in the reservoir does not have much effect on the function of the dam.

Analytical Studies on Diffusion and lntermittency in Chaotic Maps

The study of simple chaotic maps for non-equilibrium processes in statistical physics has been one of the central themes in the theory of chaotic dynamical systems. Recently, many works have been carried out on deterministic diffusion in spatially extended one-dimensional maps This can be related to real physical systems such as Josephson junctions in the presence of microwave radiation and parametrically driven oscillators. Transport due to chaos is an important problem in Hamiltonian dynamics also. A recent approach is to evaluate the exact diffusion coefficient in terms of the periodic orbits of the system in the form of cycle expansions. But the fact is that the chaotic motion in such spatially extended maps has two complementary aspects- - diffusion and interrnittency. These are related to the time evolution of the probability density function which is approximately Gaussian by central limit theorem. It is noticed that the characteristic function method introduced by Fujisaka and his co-workers is a very powerful tool for analysing both these aspects of chaotic motion. The theory based on characteristic function actually provides a thermodynamic formalism for chaotic systems It can be applied to other types of chaos-induced diffusion also, such as the one arising in statistics of trajectory separation. It was noted that there is a close connection between cycle expansion technique and characteristic function method. It was found that this connection can be exploited to enhance the applicability of the cycle expansion technique. In this way, we found that cycle expansion can be used to analyse the probability density function in chaotic maps. In our research studies we have successfully applied the characteristic function method and cycle expansion technique for analysing some chaotic maps. We introduced in this connection, two classes of chaotic maps with variable shape by generalizing two types of maps well known in literature.

Characteristics, socioeconomic benefits and household livelihoods of beef buffalo and beef cattle farming in Northeast Thailand

Since the Thai economy experiences rapid growth, agricultural systems, i.e. crop-livestock systems, are changing rapidly. On account of these changes, buffalo and cattle production has to be re-examined in terms of performance characteristics and roles of livestock for farm households in order to initiate suitable development programmes. Therefore, this study aimed to investigate the present characteristics of beef buffalo and beef cattle farms in Northeast Thailand. Using a semi-structured questionnaire, 121 randomly selected beef buffalo and beef cattle farms were interviewed in Nakhon Ratchasima province between October 2007 and May 2008. Both buffaloes and cattle were mostly integrated in mixed crop-livestock systems with medium to large farm sizes (7.9 ha), whereof less than half of the area was used for livestock. Family members were mainly responsible for the different activities of livestock farming and salaried labourers were only found on large-scale farms. The dominant roles of livestock were income generation to build up wealth or savings, the coverage of expected and unexpected expenses and earning of regular and additional income. Another important issue was the improvement of the social status, which increased with herd size. In order to improve farmers’ livelihoods and develop sustainable farming systems in Northeast Thailand the changing economic circumstances of cattle and especially buffalo production should receive more attention of researchers, governmental institutions and stakeholders.

Nitrogen requirements of cassava in selected soils of Thailand

Cassava (Manihot esculenta) is one of the most important export crops in Thailand, yet the nitrogen requirement is unknown and not considered by growers and producers. Cassava requirements for N were determined in field experiments during a period of four years and four sites on the Satuk (Suk), Don Chedi (Dc), Pak Chong (Pc),and Ban Beung (BBg) soil series in Lopburi, Supanburi, Nakhon Ratchasima, and Chonburi sites, respectively. The fertilizer treatment structure comprised 0, 62.5, 125, 187.5, 250 and 312.5 kg N ha^(-1) as urea. At each site cassava was harvested at nine months and yield parameters and the minimum datasets were taken. The fertilizer rate which resulted in maximum yield ranged from 187.5 kg N ha^(-1) in Supanburi and Chonburi (fresh weight yield of 47,500 and 30,000 kg ha^(-1) respectively) to 250 kg N ha^(-1) in Lopburi and Nakhon Ratchasima (fresh weight yield of 64,100 and 46,700 kg ha^(-1) respectively). Yield appeared to decrease at the higher, 312 kg ha^(-1), at Supanburi and Lopburi, and 250 kg ha^(-1) (Chonburi) fertilizer N rates. Net revenue was 70.4 and 72.9 % higher than where no N was appliedLopburi and Nakhon Ratchasima sites. Net revenue at the Supanburi and Chonburi sites were 53.8 and 211.0 % higher than that where no N was applied. This study suggests that at all sites improved cassava production and net revenue could be obtained with the judicious application of higher quantities of N. The results provide needed guidance to nitrogen fertilization of the important industrial crop cassava in Thailand.

Factors affecting farmers’ decisions on utilization of rice straw compost in Northeastern Thailand

Rice straw is used in Northeastern Thailand as an alternative to organic fertilizer for crop production. This enables farmers to reduce the use of chemical fertilizers which leads to a decrease in production costs. In spite of the beneficial effects in agricultural production, rice straw compost cannot be produced in large amounts because the burning of rice straws is a common farming practice. The decisions of farmers who use rice straw compost have been investigated by interviewing 120 households belonging to the members of an organic fertilizer user group using a household questionnaire. The study was conducted to evaluate the factors that affect the use of rice straw compost in Khon Kaen Province in Northeastern Thailand. Results of the logit model showed that the farmers’ education, number of rice straw compost trainings in which the farmer participated, lack of knowledge about technology, insufficient labour and difficulty in making rice straw compost had a significant impact on the farmer’s decision to use rice straw compost. Difficulty in making rice straw compost appeared to be the root cause because the procedure of making rice straw compost is complex and labour intensive. Repeated trainings thus, will have a positive and significant influence on farmers’ adoption of the technology. Training provides more knowledge and will presumably change the perception of the farmers towards new technologies and the awareness of positive effects of rice straw compost utilization.

Integrated Livelihoods and Landscape Approach for Smallholders in Northern Thailand

This paper examines the strategies and techniques researched and implemented by the International Union for Conservation of Nature (IUCN) in villages in the vicinity of Doi Mae Salong in Chiang Rai Province, Thailand. The strategies revolve around the paradigm linking poverty alleviation, conservation and landscape restoration. IUCN and its partners specifically researched and implemented schemes directed toward diversification of the household economy through alternative and sustainable intensified agriculture techniques based on balancing conservation and livelihood objectives. The projects aimed to reduce poverty and build the resilience of smallholders through decentralised governance arrangements including land use planning schemes and stakeholder negotiation. Considering the agro-ecological system on a catchment-wide scale enhances the conceptual understanding of each component, collectively forming a landscape matrix with requisite benefits for biodiversity, smallholder livelihoods and ecosystem services. In particular, the role of enhancing ecosystem services and functions in building socio-ecological resilience to vulnerabilities such as climate and economic variability is paramount in the process.

The prediction of seasonal and inter-annual climate variations and their impacts on the water resources in the eastern seaboard of Thailand

The research of this thesis dissertation covers developments and applications of short-and long-term climate predictions. The short-term prediction emphasizes monthly and seasonal climate, i.e. forecasting from up to the next month over a season to up to a year or so. The long-term predictions pertain to the analysis of inter-annual- and decadal climate variations over the whole 21st century. These two climate prediction methods are validated and applied in the study area, namely, Khlong Yai (KY) water basin located in the eastern seaboard of Thailand which is a major industrial zone of the country and which has been suffering from severe drought and water shortage in recent years. Since water resources are essential for the further industrial development in this region, a thorough analysis of the potential climate change with its subsequent impact on the water supply in the area is at the heart of this thesis research. The short-term forecast of the next-season climate, such as temperatures and rainfall, offers a potential general guideline for water management and reservoir operation. To that avail, statistical models based on autoregressive techniques, i.e., AR-, ARIMA- and ARIMAex-, which includes additional external regressors, and multiple linear regression- (MLR) models, are developed and applied in the study region. Teleconnections between ocean states and the local climate are investigated and used as extra external predictors in the ARIMAex- and the MLR-model and shown to enhance the accuracy of the short-term predictions significantly. However, as the ocean state – local climate teleconnective relationships provide only a one- to four-month ahead lead time, the ocean state indices can support only a one-season-ahead forecast. Hence, GCM- climate predictors are also suggested as an additional predictor-set for a more reliable and somewhat longer short-term forecast. For the preparation of “pre-warning” information for up-coming possible future climate change with potential adverse hydrological impacts in the study region, the long-term climate prediction methodology is applied. The latter is based on the downscaling of climate predictions from several single- and multi-domain GCMs, using the two well-known downscaling methods SDSM and LARS-WG and a newly developed MLR-downscaling technique that allows the incorporation of a multitude of monthly or daily climate predictors from one- or several (multi-domain) parent GCMs. The numerous downscaling experiments indicate that the MLR- method is more accurate than SDSM and LARS-WG in predicting the recent past 20th-century (1971-2000) long-term monthly climate in the region. The MLR-model is, consequently, then employed to downscale 21st-century GCM- climate predictions under SRES-scenarios A1B, A2 and B1. However, since the hydrological watershed model requires daily-scale climate input data, a new stochastic daily climate generator is developed to rescale monthly observed or predicted climate series to daily series, while adhering to the statistical and geospatial distributional attributes of observed (past) daily climate series in the calibration phase. Employing this daily climate generator, 30 realizations of future daily climate series from downscaled monthly GCM-climate predictor sets are produced and used as input in the SWAT- distributed watershed model, to simulate future streamflow and other hydrological water budget components in the study region in a multi-realization manner. In addition to a general examination of the future changes of the hydrological regime in the KY-basin, potential future changes of the water budgets of three main reservoirs in the basin are analysed, as these are a major source of water supply in the study region. The results of the long-term 21st-century downscaled climate predictions provide evidence that, compared with the past 20th-reference period, the future climate in the study area will be more extreme, particularly, for SRES A1B. Thus, the temperatures will be higher and exhibit larger fluctuations. Although the future intensity of the rainfall is nearly constant, its spatial distribution across the region is partially changing. There is further evidence that the sequential rainfall occurrence will be decreased, so that short periods of high intensities will be followed by longer dry spells. This change in the sequential rainfall pattern will also lead to seasonal reductions of the streamflow and seasonal changes (decreases) of the water storage in the reservoirs. In any case, these predicted future climate changes with their hydrological impacts should encourage water planner and policy makers to develop adaptation strategies to properly handle the future water supply in this area, following the guidelines suggested in this study.