Abstract: In this research, Response Surface Methodology (RSM) is used to investigate the effect of four controllable input variables namely: discharge current, pulse duration, pulse off time and applied voltage Surface Roughness (SR) of on Electrical Discharge Machined surface. To study the proposed second-order polynomial model for SR, a Central Composite Design (CCD) is used to estimation the model coefficients of the four input factors, which are alleged to influence the SR in Electrical Discharge Machining (EDM) process. Experiments were conducted on AISI D2 tool steel with copper electrode. The response is modeled using RSM on experimental data. The significant coefficients are obtained by performing Analysis of Variance (ANOVA) at 5% level of significance. It is found that discharge current, pulse duration, and pulse off time and few of their interactions have significant effect on the SR. The model sufficiency is very satisfactory as the Coefficient of Determination (R2) is found to be 91.7% and adjusted R2-statistic (R2 adj ) 89.6%.
Abstract: In this work, the autoregressive vectors are used to
know dynamics of the Agricultural export and import, and the real
effective exchange rate (REER). In order to analyze the interactions,
the impulse- response function is used in decomposition of variance,
causality of Granger as well as the methodology of Johansen to know
the relations co integration. The REER causes agricultural export and
import in the sense of Granger. The influence displays the
innovations of the REER on the agricultural export and import is not
very great and the duration of the effects is short. It displays that
REER has an immediate positive effect, after the tenth year it
displays smooth results on the agricultural export. Evidence of a
vector exists co integration, In short run, REER has smaller effects
on export and import, compared to the long-run effects.
Abstract: Growth and mineral nutrient elemental content were
studied in Mokara chark kuan pink terrestrial orchid and wild
Lantana camara weed agroecosystem. The treated subplots were
encircled with L. camara plants and sprayed weekly with L. camara
10% leaf aqueous extract. Allelopathic interactions were possible
through extensive invading root of L. camara plants into the treated
orchid subplots and weekly L. camara leaf aqueous extract
sprayings. Orchid growth was not significantly different in between
the control and treated plots, but chlorosis and yellowish patches of
leaves were observed in control orchid leaves. Nitrogen content in L.
camara leaf was significantly higher than in orchid leaf, the order of
importance of mineral nutrient contents in L. camara leaf was
K>Mg>Na>N. In treated orchid leaf, the order of importance was
N>K>Mg>Na. Orchid leaf N content from the treated plot was
higher than control, but Mg and Na contents were almost similar.
Abstract: A new strategy for oriented immobilization of proteins was proposed. The strategy contains two steps. The first step is to search for a docking site away from the active site on the protein surface. The second step is trying to find a ligand that is able to grasp the targeted site of the protein. To avoid ligand binding to the active site of protein, the targeted docking site is selected to own opposite charges to those near the active site. To enhance the ligand-protein binding, both hydrophobic and electrostatic interactions need to be included. The targeted docking site should therefore contain hydrophobic amino acids. The ligand is then selected through the help of molecular docking simulations. The enzyme α-amylase derived from Aspergillus oryzae (TAKA) was taken as an example for oriented immobilization. The active site of TAKA is surrounded by negatively charged amino acids. All the possible hydrophobic sites on the surface of TAKA were evaluated by the free energy estimation through benzene docking. A hydrophobic site on the opposite side of TAKA-s active site was found to be positive in net charges. A possible ligand, 3,3-,4,4- – Biphenyltetra- carboxylic acid (BPTA), was found to catch TAKA by the designated docking site. Then, the BPTA molecules were grafted onto silica gels and measured the affinity of TAKA adsorption and the specific activity of thereby immobilized enzymes. It was found that TAKA had a dissociation constant as low as 7.0×10-6 M toward the ligand BPTA on silica gel. The increase in ionic strength has little effect on the adsorption of TAKA, which indicated the existence of hydrophobic interaction between ligands and proteins. The specific activity of the immobilized TAKA was compared with the randomly adsorbed TAKA on primary amine containing silica gel. It was found that the orderly immobilized TAKA owns a specific activity twice as high as the one randomly adsorbed by ionic interaction.
Abstract: Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In the light of the clustering data, we have verified some interactions which were not identified as core interactions in DIP and also, we have characterized some functionally unknown proteins according to the interaction data and functional correlation. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins, also to predict new interactions and to characterize functions of unknown proteins.
Abstract: A gene network gives the knowledge of the regulatory
relationships among the genes. Each gene has its activators and
inhibitors that regulate its expression positively and negatively
respectively. Genes themselves are believed to act as activators and
inhibitors of other genes. They can even activate one set of genes and
inhibit another set. Identifying gene networks is one of the most
crucial and challenging problems in Bioinformatics. Most work done
so far either assumes that there is no time delay in gene regulation or
there is a constant time delay. We here propose a Dynamic Time-
Lagged Correlation Based Method (DTCBM) to learn the gene
networks, which uses time-lagged correlation to find the potential
gene interactions, and then uses a post-processing stage to remove
false gene interactions to common parents, and finally uses dynamic
correlation thresholds for each gene to construct the gene network.
DTCBM finds correlation between gene expression signals shifted in
time, and therefore takes into consideration the multi time delay
relationships among the genes. The implementation of our method is
done in MATLAB and experimental results on Saccharomyces
cerevisiae gene expression data and comparison with other methods
indicate that it has a better performance.
Abstract: Integral Abutment Bridges (IAB) are defined as
simple or multiple span bridges in which the bridge deck is cast
monolithically with the abutment walls. This kind of bridges are
becoming very popular due to different aspects such as good
response under seismic loading, low initial costs, elimination of
bearings, and less maintenance. However the main issue related to
the analysis of this type of structures is dealing with soil-structure
interaction of the abutment walls and the supporting piles. Various
soil constitutive models have been used in studies of soil-structure
interaction in this kind of structures by researchers. This paper is an
effort to review the implementation of various finite elements model
which explicitly incorporates the nonlinear soil and linear structural
response considering various soil constitutive models and finite
element mesh.
Abstract: This paper analyses the non linear properties
exhibited by a drill string system under various un balanced mass
conditions. The drill string is affected by continuous friction in the
form of drill bit and well bore hole interactions. This paper proves
the origin of limit cycling and increase of non linearity with increase
in speed of the drilling in the presence of friction. The spectrum of
the frequency response is also studied to detect the presence of
vibration abnormalities arising during the drilling process.
Abstract: Simultaneous Saccharification and Fermentation (SSF) of sugarcane bagasse by cellulase and Pachysolen tannophilus MTCC *1077 were investigated in the present study. Important process variables for ethanol production form pretreated bagasse were optimized using Response Surface Methodology (RSM) based on central composite design (CCD) experiments. A 23 five level CCD experiments with central and axial points was used to develop a statistical model for the optimization of process variables such as incubation temperature (25–45°) X1, pH (5.0–7.0) X2 and fermentation time (24–120 h) X3. Data obtained from RSM on ethanol production were subjected to the analysis of variance (ANOVA) and analyzed using a second order polynomial equation and contour plots were used to study the interactions among three relevant variables of the fermentation process. The fermentation experiments were carried out using an online monitored modular fermenter 2L capacity. The processing parameters setup for reaching a maximum response for ethanol production was obtained when applying the optimum values for temperature (32°C), pH (5.6) and fermentation time (110 h). Maximum ethanol concentration (3.36 g/l) was obtained from 50 g/l pretreated sugarcane bagasse at the optimized process conditions in aerobic batch fermentation. Kinetic models such as Monod, Modified Logistic model, Modified Logistic incorporated Leudeking – Piret model and Modified Logistic incorporated Modified Leudeking – Piret model have been evaluated and the constants were predicted.
Abstract: The minimal condition for symmetry breaking in morphogenesis of cellular population was investigated using cellular automata based on reaction-diffusion dynamics. In particular, the study looked for the possibility of the emergence of branching structures due to mechanical interactions. The model used two types of cells an external gradient. The results showed that the external gradient influenced movement of cell type-I, also revealed that clusters formed by cells type-II worked as barrier to movement of cells type-I.
Abstract: Using Dynamic Bayesian Networks (DBN) to model genetic regulatory networks from gene expression data is one of the major paradigms for inferring the interactions among genes. Averaging a collection of models for predicting network is desired, rather than relying on a single high scoring model. In this paper, two kinds of model searching approaches are compared, which are Greedy hill-climbing Search with Restarts (GSR) and Markov Chain Monte Carlo (MCMC) methods. The GSR is preferred in many papers, but there is no such comparison study about which one is better for DBN models. Different types of experiments have been carried out to try to give a benchmark test to these approaches. Our experimental results demonstrated that on average the MCMC methods outperform the GSR in accuracy of predicted network, and having the comparable performance in time efficiency. By proposing the different variations of MCMC and employing simulated annealing strategy, the MCMC methods become more efficient and stable. Apart from comparisons between these approaches, another objective of this study is to investigate the feasibility of using DBN modeling approaches for inferring gene networks from few snapshots of high dimensional gene profiles. Through synthetic data experiments as well as systematic data experiments, the experimental results revealed how the performances of these approaches can be influenced as the target gene network varies in the network size, data size, as well as system complexity.
Abstract: Detecting protein-protein interactions is a central problem in computational biology and aberrant such interactions may have implicated in a number of neurological disorders. As a result, the prediction of protein-protein interactions has recently received considerable attention from biologist around the globe. Computational tools that are capable of effectively identifying protein-protein interactions are much needed. In this paper, we propose a method to detect protein-protein interaction based on substring similarity measure. Two protein sequences may interact by the mean of the similarities of the substrings they contain. When applied on the currently available protein-protein interaction data for the yeast Saccharomyces cerevisiae, the proposed method delivered reasonable improvement over the existing ones.
Abstract: Academia-industry relationship is not like that of
technology donator-acceptor, but is of interactive and collaborative
nature, acknowledging and ensuring mutual respect for each other-s
role and contributions with an eye to attaining the true purpose of
such relationships, namely, bringing about research-outcome
synergy. Indeed, academia-industry interactions are a system that
requires active and collaborative participations of all the
stakeholders.
This paper examines various issues associated with academic
institutions and industry collaboration with special attention to the
nature of resources and potentialities of stakeholders in the context of
knowledge management. This paper also explores the barriers of
academia-industry interaction. It identifies potential areas where
industry-s participation with academia would be most effective for
synergism. Lastly, this paper proposes an integrated model of several
new collaborative approaches that are possible, mainly in the Indian
scenario to strengthen academia-industry interface.
Abstract: Testing is an activity that is required both in the
development and maintenance of the software development life cycle
in which Integration Testing is an important activity. Integration
testing is based on the specification and functionality of the software
and thus could be called black-box testing technique. The purpose of
integration testing is testing integration between software
components. In function or system testing, the concern is with overall
behavior and whether the software meets its functional specifications
or performance characteristics or how well the software and
hardware work together. This explains the importance and necessity
of IT for which the emphasis is on interactions between modules and
their interfaces. Software errors should be discovered early during
IT to reduce the costs of correction. This paper introduces a new type
of integration error, presenting an overview of Integration Testing
techniques with comparison of each technique and also identifying
which technique detects what type of error.
Abstract: In this paper we discuss the problems of the long-term management policy of Lake Peipsi and the roles of natural and anthropogenic factors in the ecological state of the lake. The reduction of the pollution during the last 15 years could not give significant changes of the chemical composition of the water, what implicates the essential role that natural factors have on the ecological state of lake. One of the most important factors having impact on the hydrochemical cycles and ecological state is the hydrological regime which is clearly expressed in L. Peipsi. The absence on clear interrelations of climate cycles and nutrients suggest that complex abiotic and biotic interactions, which take place in the lake ecosystem, plays a significant role in the matter circulation mechanism within lake.
Abstract: The UML modeling of complex distributed systems often is a great challenge due to the large amount of parallel real-time operating components. In this paper the problems of verification of such systems are discussed. ECPN, an Extended Colored Petri Net is defined to formally describe state transitions of components and interactions among components. The relationship between sequence diagrams and Free Choice Petri Nets is investigated. Free Choice Petri Net theory helps verifying the liveness of sequence diagrams. By converting sequence diagrams to ECPNs and then comparing behaviors of sequence diagram ECPNs and statecharts, the consistency among models is analyzed. Finally, a verification process for an example model is demonstrated.
Abstract: The inherent complexity in nowadays- business
environments is forcing organizations to be attentive to the dynamics
in several fronts. Therefore, the management of technological
innovation is continually faced with uncertainty about the future.
These issues lead to a need for a systemic perspective, able to analyze
the consequences of interactions between different factors. The field
of technology foresight has proposed methods and tools to deal with
this broader perspective. In an attempt to provide a method to analyze
the complex interactions between events in several areas, departing
from the identification of the most strategic competencies, this paper
presents a methodology based on the Delphi method and Quality
Function Deployment. This methodology is applied in a sheet metal
processing equipment manufacturer, as a case study.
Abstract: The importance for manipulating an incorporated
scaffold and directing cell behaviors is well appreciated for tissue
engineering. Here, we developed newly nano-topographic oxidized
silicon nanosponges capable of being various chemical modifications
to provide much insight into the fundamental biology of how cells
interact with their surrounding environment in vitro. A wet etching
technique is exerted to allow us fabricated the silicon nanosponges in a
high-throughput manner. Furthermore, various organo-silane
chemicals enabled self-assembled on the surfaces by vapor deposition.
We have found that Chinese hamster ovary (CHO) cells displayed
certain distinguishable morphogenesis, adherent responses, and
biochemical properties while cultured on these chemical modified
nano-topographic structures in compared with the planar oxidized
silicon counterparts, indicating that cell behaviors can be influenced
by certain physical characteristic derived from nano-topography in
addition to the hydrophobicity of contact surfaces crucial for cell
adhesion and spreading. Of particular, there were predominant
nano-actin punches and slender protrusions formed while cells were
cultured on the nano-topographic structures. This study shed potential
applications of these nano-topographic biomaterials for controlling
cell development in tissue engineering or basic cell biology research.
Abstract: We developed a new method based on quasimolecular
modeling to simulate the cavity flow in three cavity
shapes: rectangular, half-circular and bucket beer in cgs units. Each
quasi-molecule was a group of particles that interacted in a fashion
entirely analogous to classical Newtonian molecular interactions.
When a cavity flow was simulated, the instantaneous velocity vector
fields were obtained by using an inverse distance weighted
interpolation method. In all three cavity shapes, fluid motion was
rotated counter-clockwise. The velocity vector fields of the three
cavity shapes showed a primary vortex located near the upstream
corners at time t ~ 0.500 s, t ~ 0.450 s and t ~ 0.350 s, respectively.
The configurational kinetic energy of the cavities increased as time
increased until the kinetic energy reached a maximum at time t ~
0.02 s and, then, the kinetic energy decreased as time increased. The
rectangular cavity system showed the lowest kinetic energy, while
the half-circular cavity system showed the highest kinetic energy.
The kinetic energy of rectangular, beer bucket and half-circular
cavities fluctuated about stable average values 35.62 x 103, 38.04 x
103 and 40.80 x 103 ergs/particle, respectively. This indicated that the
half-circular shapes were the most suitable shape for a shrimp pond
because the water in shrimp pond flows best when we compared with
rectangular and beer bucket shape.
Abstract: Reverse engineering of full-genomic interaction networks based on compendia of expression data has been successfully applied for a number of model organisms. This study adapts these approaches for an important non-model organism: The major human fungal pathogen Candida albicans. During the infection process, the pathogen can adapt to a wide range of environmental niches and reversibly changes its growth form. Given the importance of these processes, it is important to know how they are regulated. This study presents a reverse engineering strategy able to infer fullgenomic interaction networks for C. albicans based on a linear regression, utilizing the sparseness criterion (LASSO). To overcome the limited amount of expression data and small number of known interactions, we utilize different prior-knowledge sources guiding the network inference to a knowledge driven solution. Since, no database of known interactions for C. albicans exists, we use a textmining system which utilizes full-text research papers to identify known regulatory interactions. By comparing with these known regulatory interactions, we find an optimal value for global modelling parameters weighting the influence of the sparseness criterion and the prior-knowledge. Furthermore, we show that soft integration of prior-knowledge additionally improves the performance. Finally, we compare the performance of our approach to state of the art network inference approaches.