Abstract: To understand life as biological system, evolutionary
understanding is indispensable. Protein interactions data are rapidly
accumulating and are suitable for system-level evolutionary analysis.
We have analyzed yeast protein interaction network by both
mathematical and biological approaches. In this poster presentation,
we inferred the evolutionary birth periods of yeast proteins by
reconstructing phylogenetic profile. It has been thought that hub
proteins that have high connection degree are evolutionary old. But
our analysis showed that hub proteins are entirely evolutionary new.
We also examined evolutionary processes of protein complexes. It
showed that member proteins of complexes were tend to have
appeared in the same evolutionary period. Our results suggested that
protein interaction network evolved by modules that form the
functional unit. We also reconstructed standardized phylogenetic trees
and calculated evolutionary rates of yeast proteins. It showed that
there is no obvious correlation between evolutionary rates and
connection degrees of yeast proteins.
Abstract: In this paper, a bond graph dynamic model for a valvecontrolled
hydraulic cylinder has been developed. A simplified bond
graph model of the inter-actuator interactions in a multi-cylinder
hydraulic system has also been presented. The overall bond graph
model of a valve-controlled hydraulic cylinder was developed by
combining the bond graph sub-models of the pump, spool valve and
the actuator using junction structures. Causality was then assigned
in order to obtain a computational model which could be simulated.
The causal bond graph model of the hydraulic cylinder was verified
by comparing the open loop state responses to those of an ODE
model which had been developed in literature based on the same
assumptions. The results were found to correlate very well both
in the shape of the curves, magnitude and the response times,
thus indicating that the developed model represents the hydraulic
dynamics of a valve-controlled cylinder. A simplified model for interactuator
interaction was presented by connecting an effort source with
constant pump pressure to the zero-junction from which the cylinders
in a multi-cylinder system are supplied with a constant pressure from
the pump. On simulating the state responses of the developed model
under different situations of cylinder operations, indicated that such
a simple model can be used to predict the inter-actuator interactions.
Abstract: Our objectives were to evaluate the effects of sire
breed, type of protein supplement, level of supplementation and sex
on wool spinning fineness (SF), its correlations with other wool
characteristics and prediction accuracy in F1 Merino crossbred lambs.
Texel, Coopworth, White Suffolk, East Friesian and Dorset rams
were mated with 500 purebred Merino dams at a ratio of 1:100 in
separate paddocks within a single management system. The F1
progeny were raised on ryegrass pasture until weaning, before forty
lambs were randomly allocated to treatments in a 5 x 2 x 2 x 2
factorial experimental design representing 5 sire breeds, 2
supplementary feeds (canola or lupins), 2 levels of supplementation
(1% or 2% of liveweight) and sex (wethers or ewes). Lambs were
supplemented for six weeks after an initial three weeks of adjustment,
wool sampled at the commencement and conclusion of the feeding
trial and analyzed for SF, mean fibre diameter (FD), coefficient of
variation (CV), standard deviation, comfort factor (CF), fibre
curvature (CURV), and clean fleece yield. Data were analyzed using
mixed linear model procedures with sire fitted as a random effect,
and sire breed, sex, supplementary feed type, level of
supplementation and their second-order interactions as fixed effects.
Sire breed (P
Abstract: One of the most important secrets of succesful companies is the fact that cooperation with NGOs will create a good reputation for them so that they can be immunized to economic crisis. The performance of the most admired companies in the world based on the ratings of Forbes and Fortune show us that most of these firms also have close relationships with their NGOs. Today, if companies do something wrong this information spreads very quickly to do the society. If people do not like the activities of a company, it can find itself in public relations nightmare that can threaten its repuation. Since the cost of communication has dropped dramatically due to the vast use of internet, the increase in communication among stakeholders via internet makes companies more visible. These multiple and interdependent interactions among the network of stakeholders is called as the network relationships. NGOs play the role of catalyst among the stakeholders of a firm to enhance the awareness. Succesful firms are aware of this fact that NGOs have a central role in today-s business world. Firms are also aware of the fact that they can enhance their corporate reputation via cooperation with the NGOs. This fact will be illustrated in this paper by examining some of the actions of the most succesful companies in terms of their cooperations with the NGOs.
Abstract: Predicting protein-protein interactions represent a key step in understanding proteins functions. This is due to the fact that proteins usually work in context of other proteins and rarely function alone. Machine learning techniques have been applied to predict protein-protein interactions. However, most of these techniques address this problem as a binary classification problem. Although it is easy to get a dataset of interacting proteins as positive examples, there are no experimentally confirmed non-interacting proteins to be considered as negative examples. Therefore, in this paper we solve this problem as a one-class classification problem using one-class support vector machines (SVM). Using only positive examples (interacting protein pairs) in training phase, the one-class SVM achieves accuracy of about 80%. These results imply that protein-protein interaction can be predicted using one-class classifier with comparable accuracy to the binary classifiers that use artificially constructed negative examples.
Abstract: Stable bacterial polymorphism on a single limiting resource may appear if between the evolved strains metabolic interactions take place that allow the exchange of essential nutrients [8]. Towards an attempt to predict the possible outcome of longrunning evolution experiments, a network based on the metabolic capabilities of homogeneous populations of every single gene knockout strain (nodes) of the bacterium E. coli is reconstructed. Potential metabolic interactions (edges) are allowed only between strains of different metabolic capabilities. Bacterial communities are determined by finding cliques in this network. Growth of the emerged hypothetical bacterial communities is simulated by extending the metabolic flux balance analysis model of Varma et al [2] to embody heterogeneous cell population growth in a mutual environment. Results from aerobic growth on 10 different carbon sources are presented. The upper bounds of the diversity that can emerge from single-cloned populations of E. coli such as the number of strains that appears to metabolically differ from most strains (highly connected nodes), the maximum clique size as well as the number of all the possible communities are determined. Certain single gene deletions are identified to consistently participate in our hypothetical bacterial communities under most environmental conditions implying a pattern of growth-condition- invariant strains with similar metabolic effects. Moreover, evaluation of all the hypothetical bacterial communities under growth on pyruvate reveals heterogeneous populations that can exhibit superior growth performance when compared to the performance of the homogeneous wild-type population.
Abstract: The significant effects of the interactions between the
system boundaries and the near wall molecules in miniaturized
gaseous devices lead to the formation of the Knudsen layer in which
the Navier-Stokes-Fourier (NSF) equations fail to predict the correct
associated phenomena. In this paper, the well-known lattice
Boltzmann method (LBM) is employed to simulate the fluid flow and
heat transfer processes in rarefied gaseous micro media. Persuaded
by the problematic deficiency of the LBM in capturing the Knudsen
layer phenomena, present study tends to concentrate on the effective
molecular mean free path concept the main essence of which is to
compensate the incapability of this mesoscopic method in dealing
with the momentum and energy transport within the above mentioned
kinetic boundary layer. The results show qualitative and quantitative
accuracy comparable to the solutions of the linearized Boltzmann
equation or the DSMC data for the Knudsen numbers of O (1) .
Abstract: The worldwide prevalence of H3N2 influenza virus
and its increasing resistance to the existing drugs necessitates for the
development of an improved/better targeting anti-influenza drug.
H3N2 influenza neuraminidase is one of the two membrane-bound
proteins belonging to group-2 neuraminidases. It acts as key player
involved in viral pathogenicity and hence, is an important target of
anti-influenza drugs. Oseltamivir is one of the potent drugs targeting
this neuraminidase. In the present work, we have taken subtype N2
neuraminidase as the receptor and probable analogs of oseltamivir as
drug molecules to study the protein-drug interaction in anticipation of
finding efficient modified candidate compound. Oseltamivir analogs
were made by modifying the functional groups using Marvin Sketch
software and were docked using Schrodinger-s Glide. Oseltamivir
analog 10 was detected to have significant energy value (16% less
compared to Oseltamivir) and could be the probable lead molecule. It
infers that some of the modified compounds can interact in a novel
manner with increased hydrogen bonding at the active site of
neuraminidase and it might be better than the original drug. Further
work can be carried out such as enzymatic inhibition studies;
synthesis and crystallizing the drug-target complex to analyze the
interactions biologically.
Abstract: For professions of high risk industries, simulation training has always been thought in terms of high degree of fidelity regarding the real operational situation. Due to the recent progress, this way of training is changing, modifying the human-computer and software interactions: the interactions between trainees during simulation training session tend to become virtual, transforming the social-based embodiness (the way subjects integrate social skills for interpersonal relationship with co-workers). On the basis of the analysis of eight different profession trainings, a categorization of interactions has help to produce an analytical tool, the social interactions table. This tool may be very valuable to point out the changes of social interactions when the training sessions are skipping from a high fidelity simulator to a virtual simulator. In this case, it helps the designers of professional training to analyze and to assess the consequences of the potential lack the social-based embodiness.
Abstract: The human knee joint has a three dimensional
geometry with multiple body articulations that produce complex
mechanical responses under loads that occur in everyday life and
sports activities. To produce the necessary joint compliance and
stability for optimal daily function various menisci and ligaments are
present while muscle forces are used to this effect. Therefore,
knowledge of the complex mechanical interactions of these load
bearing structures is necessary when treatment of relevant diseases is
evaluated and assisting devices are designed.
Numerical tools such as finite element analysis are suitable for
modeling such joints in order to understand their physics. They have
been used in the current study to develop an accurate human knee
joint and model its mechanical behavior. To evaluate the efficacy of
this articulated model, static load cases were used for comparison
purposes with previous experimentally verified modeling works
drawn from literature.
Abstract: The interactions between input/output variables are a very common phenomenon encountered in the design of multi-loop controllers for interacting multivariable processes, which can be a serious obstacle for achieving a good overall performance of multiloop control system. To overcome this impediment, the decomposed dynamic interaction analysis is proposed by decomposing the multiloop control system into a set of n independent SISO systems with the corresponding effective open-loop transfer function (EOTF) within the dynamic interactions embedded explicitly. For each EOTF, the reduced model is independently formulated by using the proposed reduction design strategy, and then the paired multi-loop proportional-integral-derivative (PID) controller is derived quite simply and straightforwardly by using internal model control (IMC) theory. This design method can easily be implemented for various industrial processes because of its effectiveness. Several case studies are considered to demonstrate the superior of the proposed method.
Abstract: Flow through micro and mini channels requires relatively
high driving pressure due to the large fluid pressure drop
through these channels. Consequently the forces acting on the walls of
the channel due to the fluid pressure are also large. Due to these forces
there are displacement fields set up in the solid substrate containing
the channels. If the movement of the substrate is constrained at some
points, then stress fields are established in the substrate. On the other
hand, if the deformation of the channel shape is sufficiently large
then its effect on the fluid flow is important to be calculated. Such
coupled fluid-solid systems form a class of problems known as fluidstructure
interactions. In the present work a co-located finite volume
discretization procedure on unstructured meshes is described for
solving fluid-structure interaction type of problems. A linear elastic
solid is assumed for which the effect of the channel deformation
on the flow is neglected. Thus the governing equations for the
fluid and the solid are decoupled and are solved separately. The
procedure is validated by solving two benchmark problems, one from
fluid mechanics and another from solid mechanics. A fluid-structure
interaction problem of flow through a U-shaped channel embedded
in a plate is solved.
Abstract: This paper demonstrates a model of an e-Learning
system based on nowadays learning theory and distant education
practice. The relationships in the model are designed to be simple
and functional and do not necessarily represent any particular e-
Learning environments. It is meant to be a generic e-Learning
system model with implications for any distant education course
instructional design. It allows online instructors to move away from
the discrepancy between the courses and body of knowledge. The
interrelationships of four primary sectors that are at the e-Learning
system are presented in this paper. This integrated model includes
[1] pedagogy, [2] technology, [3] teaching, and [4] learning. There
are interactions within each of these sectors depicted by system loop
map.
Abstract: Bubble columns have a variety of applications in
absorption, bio-reactions, catalytic slurry reactions, and coal
liquefaction; because they are simple to operate, provide good heat
and mass transfer, having less operational cost. The use of
Computational Fluid Dynamics (CFD) for bubble column becomes
important, since it can describe the fluid hydrodynamics on both local
and global scale. Euler- Euler two-phase fluid model has been used to
simulate two-phase (air and water) transient up-flow in bubble
column (15cm diameter) using FLUENT6.3. These simulations and
experiments were operated over a range of superficial gas velocities
in the bubbly flow and churn turbulent regime (1 to16 cm/s) at
ambient conditions. Liquid velocity was varied from 0 to 16cm/s. The
turbulence in the liquid phase is described using the standard k-ε
model. The interactions between the two phases are described
through drag coefficient formulations (Schiller Neumann). The
objectives are to validate CFD simulations with experimental data,
and to obtain grid-independent numerical solutions. Quantitatively
good agreements are obtained between experimental data for hold-up
and simulation values. Axial liquid velocity profiles and gas holdup
profiles were also obtained for the simulation.
Abstract: Antimicrobial (AM) starch-based films were
developed by incorporating chitosan and lauric acid as antimicrobial
agent into starch-based film. Chitosan has wide range of applications
as a biomaterial, but barriers still exist to its broader use due to its
physical and chemical limitations. In this work, a series of
starch/chitosan (SC) blend films containing 8% of lauric acid was
prepared by casting method. The structure of the film was
characterized by Fourier transform infrared spectroscopy (FTIR), Xray
diffraction (XRD), and scanning electron microscopy (SEM).
The results indicated that there were strong interactions were present
between the hydroxyl groups of starch and the amino groups of
chitosan resulting in a good miscibility between starch and chitosan
in the blend films. Physical properties and optical properties of the
AM starch-based film were evaluated. The AM starch-based films
incorporated with chitosan and lauric acid showed an improvement in
water vapour transmission rate (WVTR) and addition of starch
content provided more transparent films while the yellowness of the
film attributed to the higher chitosan content. The improvement in
water barrier properties was mainly attributed to the hydrophobicity
of lauric acid and optimum chitosan or starch content. AM starch
based film also showed excellent oxygen barrier. Obtaining films
with good oxygen permeability would be an indication of the
potential use of these antimicrobial packaging as a natural packaging
and an alternative packaging to the synthetic polymer to protect food
from oxidation reactions
Abstract: The development of biomimetic micro-aerial-vehicles
(MAVs) with flapping wings is the future trend in military/domestic
field. The successful flight of MAVs is strongly related to the
understanding of unsteady aerodynamic performance of low Reynolds
number airfoils under dynamic flapping motion. This study explored
the effects of flapping frequency, stroke amplitude, and the inclined
angle of stroke plane on lift force and thrust force of a bio-inspiration
corrugated airfoil with 33 full factorial design of experiment and
ANOVA analysis. Unsteady vorticity flows over a corrugated thin
airfoil executing flapping motion are computed with time-dependent
two-dimensional laminar incompressible Reynolds-averaged
Navier-Stokes equations with the conformal hybrid mesh. The tested
freestream Reynolds number based on the chord length of airfoil as
characteristic length is fixed of 103. The dynamic mesh technique is
applied to model the flapping motion of a corrugated airfoil. Instant
vorticity contours over a complete flapping cycle clearly reveals the
flow mechanisms for lift force generation are dynamic stall, rotational
circulation, and wake capture. The thrust force is produced as the
leading edge vortex shedding from the trailing edge of airfoil to form a
reverse von Karman vortex. Results also indicated that the inclined
angle is the most significant factor on both the lift force and thrust
force. There are strong interactions between tested factors which mean
an optimization study on parameters should be conducted in further
runs.
Abstract: Tuberculosis (TB) is a bacterial infectious disease caused by the obligate human pathogen, Mycobacterium tuberculosis. Multidrug-resistant tuberculosis (MDR-TB) is a global reality that threatens tuberculosis control. Resistance to antibiotic Rifampicin, occurs in 95% of cases through nucleotide substitutions in an 81-bp core region of the rpoB i.e; beta subunit of DNA dependant RNA polymerase. In this paper, we studied the Rifampicin-rpoB receptor interactions In silico. First, homology modeling was performed to obtain the three dimensional structure of Mycobacterium rpoB. Sixty analogs of Rifampicin were prepared using Marvin sketch software. Both original Rifampicin and the analogs were docked with rpoB and energy values were obtained. Out of sixty analogs, 43 analogs had lesser energy values than conventional Rifampicin and hence are predicted to have greater binding affinity to rpoB. Thus, this study offers a route for the development of Rifampicin analogs against multi drug resistant Mycobacterium rpoB.
Abstract: The flow field within the combustor of scramjet
engine is very complex and poses a considerable challenge in the
design and development of a supersonic combustor with an optimized
geometry. In this paper comprehensive numerical studies on flow
field characteristics of different cavity based scramjet combustors
with transverse injection of hydrogen have been carried out for both
non-reacting and reacting flows. The numerical studies have been
carried out using a validated 2D unsteady, density based 1st-order
implicit k-omega turbulence model with multi-component finite rate
reacting species. The results show a wide variety of flow features
resulting from the interactions between the injector flows, shock
waves, boundary layers, and cavity flows. We conjectured that an
optimized cavity is a good choice to stabilize the flame in the
hypersonic flow, and it generates a recirculation zone in the scramjet
combustor. We comprehended that the cavity based scramjet
combustors having a bearing on the source of disturbance for the
transverse jet oscillation, fuel/air mixing enhancement, and flameholding
improvement. We concluded that cavity shape with
backward facing step and 45o forward ramp is a good choice to get
higher temperatures at the exit compared to other four models of
scramjet combustors considered in this study.
Abstract: Atherosclerosis was identified as a chronic inflammatory process resulting from interactions between plasma lipoproteins, cellular components (monocyte, macrophages, T lymphocytes, endothelial cells and smooth muscle cells) and the extracellular matrix of the arterial wall. Several types of genes were known to express during formation of atherosclerosis. This study is carried out to identify unknown differentially expressed gene (DEG) in atherogenesis. Rabbit’s aorta tissues were stained by H&E for histomorphology. GeneFishing™ PCR analysis was performed from total RNA extracted from the aorta tissues. The DNA fragment from DEG was cloned, sequenced and validated by Real-time PCR. Histomorphology showed intimal thickening in the aorta. DEG detected from ACP-41 was identified as cathepsin B gene and showed upregulation at week-8 and week-12 of atherogenesis. Therefore, ACP-based GeneFishing™ PCR facilitated identification of cathepsin B gene which was differentially expressed during development of atherosclerosis.
Abstract: The purpose of this study is to explore the impacts of
computer games on the mathematics instruction. First, the research
designed and implemented the web-based games according to the
content of existing textbook. And the researcher collected and
analyzed the information related to the mathematics instruction
integrating the computer games. In this study, the researcher focused
on the learning motivation of mathematics, mathematics achievement,
and pupil-teacher interactions in classroom. The results showed that
students under instruction integrating computer games significantly
improved in motivation and achievement. The teacher tended to use
less direct teaching and provide more time for student-s active
learning.