Abstract: This paper describes a novel approach for deriving
modules from protein-protein interaction networks, which combines
functional information with topological properties of the network.
This approach is based on weighted clustering coefficient, which
uses weights representing the functional similarities between the
proteins. These weights are calculated according to the semantic
similarity between the proteins, which is based on their Gene
Ontology terms. We recently proposed an algorithm for identification
of functional modules, called SWEMODE (Semantic WEights for
MODule Elucidation), that identifies dense sub-graphs containing
functionally similar proteins. The rational underlying this approach is
that each module can be reduced to a set of triangles (protein triplets
connected to each other). Here, we propose considering semantic
similarity weights of all triangle-forming edges between proteins. We
also apply varying semantic similarity thresholds between
neighbours of each node that are not neighbours to each other (and
hereby do not form a triangle), to derive new potential triangles to
include in module-defining procedure. The results show an
improvement of pure topological approach, in terms of number of
predicted modules that match known complexes.
Abstract: In this study rack systems that are structural storage
units of warehouses have been analyzed as structural with Finite
Element Method (FEA). Each cell of discussed rack system storages
pallets which have from 800 kg to 1000 kg weights and
0.80x1.15x1.50 m dimensions. Under this load, total deformations
and equivalent stresses of structural elements and principal stresses,
tensile stresses and shear stresses of connection elements have been
analyzed. The results of analyses have been evaluated according to
resistance limits of structural and connection elements. Obtained
results have been presented as visual and magnitude.
Abstract: In this paper, a robust watermarking algorithm using
the wavelet transform and edge detection is presented. The efficiency
of an image watermarking technique depends on the preservation of
visually significant information. This is attained by embedding the
watermark transparently with the maximum possible strength. The
watermark embedding process is carried over the subband
coefficients that lie on edges, where distortions are less noticeable,
with a subband level dependent strength. Also, the watermark is
embedded to selected coefficients around edges, using a different
scale factor for watermark strength, that are captured by a
morphological dilation operation. The experimental evaluation of the
proposed method shows very good results in terms of robustness and
transparency to various attacks such as median filtering, Gaussian
noise, JPEG compression and geometrical transformations.
Abstract: Quasigroups are algebraic structures closely related to
Latin squares which have many different applications. The
construction of block cipher is based on quasigroup string
transformation. This article describes a block cipher based
Quasigroup of order 256, suitable for fast software encryption of
messages written down in universal ASCII code. The novelty of this
cipher lies on the fact that every time the cipher is invoked a new set
of two randomly generated quasigroups are used which in turn is
used to create a pair of quasigroup of dual operations. The
cryptographic strength of the block cipher is examined by calculation
of the xor-distribution tables. In this approach some algebraic
operations allows quasigroups of huge order to be used without any
requisite to be stored.
Abstract: Organ motion, especially respiratory motion, is a technical challenge to radiation therapy planning and dosimetry. This motion induces displacements and deformation of the organ tissues within the irradiated region which need to be taken into account when simulating dose distribution during treatment. Finite element modeling (FEM) can provide a great insight into the mechanical behavior of the organs, since they are based on the biomechanical material properties, complex geometry of organs, and anatomical boundary conditions. In this paper we present an original approach that offers the possibility to combine image-based biomechanical models with particle transport simulations. We propose a new method to map material density information issued from CT images to deformable tetrahedral meshes. Based on the principle of mass conservation our method can correlate density variation of organ tissues with geometrical deformations during the different phases of the respiratory cycle. The first results are particularly encouraging, as local error quantification of density mapping on organ geometry and density variation with organ motion are performed to evaluate and validate our approach.
Abstract: Graph rewriting-based visual model processing is a
widely used technique for model transformation. Visual model
transformations often need to follow an algorithm that requires a
strict control over the execution sequence of the transformation steps.
Therefore, in Visual Model Processors (VMPs) the execution order
of the transformation steps is crucial. This paper presents the visual
control flow support of Visual Modeling and Transformation System
(VMTS), which facilitates composing complex model
transformations of simple transformation steps and executing them.
The VMTS Visual Control Flow Language (VCFL) uses stereotyped
activity diagrams to specify control flow structures and OCL
constraints to choose between different control flow branches. This
paper introduces VCFL, discusses its termination properties and
provides an algorithm to support the termination analysis of VCFL
transformations.
Abstract: Hypertension is characterized with stress on the heart and blood vessels thus increasing the risk of heart attack and renal diseases. The Renin angiotensin system (RAS) plays a major role in blood pressure control. Renin is the enzyme that controls the RAS at the rate-limiting step. Our aim is to develop new drug-like leads which can inhibit renin and thereby emerge as therapeutics for hypertension. To achieve this, molecular dynamics (MD) simulation and receptor-based pharmacophore modeling were implemented, and three rennin-inhibitor complex structures were selected based on IC50 value and scaffolds of inhibitors. Three pharmacophore models were generated considering conformations induced by inhibitor. The compounds mapped to these models were selected and subjected to drug-like screening. The identified hits were docked into the active site of renin. Finally, hit1 satisfying the binding mode and interaction energy was selected as possible lead candidate to be used in novel renin inhibitors.
Abstract: Metal cutting is a severe plastic deformation process
involving large strains, high strain rates, and high temperatures.
Conventional analysis of the chip formation process is based on bulk
material deformation disregarding the inhomogeneous nature of the
material microstructure. A series of orthogonal cutting tests of AISI
1045 and 1144 steel were conducted which yielded similar process
characteristics and chip formations. With similar shear angles and cut
chip thicknesses, shear strains for both chips were found to range
from 2.0 up to 2.8. The manganese-sulfide (MnS) precipitate in the
1144 steel has a very distinct and uniform shape which allows for
comparison before and after chip formation. From close observations
of MnS precipitates in the cut chips it is shown that the conventional
approach underestimates plastic strains in metal cutting.
Experimental findings revealed local shear strains around a value of
6. These findings and their implications are presented and discussed.
Abstract: The urban transformation processes in its framework
and its general significance became a fundamental and vital subject
of consideration for both the developed and the developing societies.
It has become important to regulate the architectural systems adopted
by the city, to sustain the present development on one hand, and on
the other hand, to facilitate its future growth.
Thus, the study dealt with the phenomenon of urban
transformation of the Mediterranean cities, and the city of Alexandria
in particular, because of its significant historical and cultural legacy,
its historical architecture and its contemporary urbanization.
This article investigates the entirety of cities in the Mediterranean
region through the analysis of the relationship between inflation and
growth of these cities and the extent of the complexity of the city
barriers. We hope to analyze not only the internal transformations,
but the external relationships (both imperial and post-colonial) that
have shaped Alexandria city growth from the nineteenth century until
today.
Abstract: Bursa, since the establishment of the Ottoman Empire,
being on the important trade roads and having a capital accumulation
as a result of silk production, was one of the first cities of
modernization activities applied. Bursa maintained its importance
even during the Republican Period and became one of the most
important cities of the country and today is the fourth biggest and the
industrialized city in Turkey. Social, political, economical and
cultural changes occured with the reforms starting with the 1839
Edict of Tanzimat that aimed at modernizing the society and the
government and centralizing the political power began in the
Ottoman Empire. After the Tanzimat Reforms transformation of the
city changed and planning processes began in Bursa according to the
vision of Governors. The theresholds of the city are very important
data for a sustainable planning for the city planners. Main aim of this
study is to investigate the changes and transformations of the city
according to the changes in the socio-economical and cultural
properties for the city planners.
Abstract: This paper examines the forced convection flow of
incompressible, electrically conducting viscous fluid past a sharp
wedge in the presence of heat generation or absorption with an
applied magnetic field. The system of partial differential equations
governing Falkner - Skan wedge flow and heat transfer is first
transformed into a system of ordinary differential equations using
similarity transformations which is later solved using an implicit
finite - difference scheme, along with quasilinearization technique.
Numerical computations are performed for air (Pr = 0.7) and
displayed graphically to illustrate the influence of pertinent physical
parameters on local skin friction and heat transfer coefficients and,
also on, velocity and temperature fields. It is observed that the
magnetic field increases both the coefficients of skin friction and heat
transfer. The effect of heat generation or absorption is found to be
very significant on heat transfer, but its effect on the skin friction is
negligible. Indeed, the occurrence of overshoot is noticed in the
temperature profiles during heat generation process, causing the
reversal in the direction of heat transfer.
Abstract: Safety Critical hard Real-Time Systems are ever
present in the avionics industry. The Model Driven Architecture
(MDA) offers different levels of model abstraction and generation.
This paper discusses our concerns relating to model development and
generation when using the MDA approach in the avionics industry.
These concerns are based on our experience when looking into
adopting the MDA as part of avionics systems development. We
place emphasis on transformations between model types and discuss
possible benefits of adopting an MDA approach as part of the
software development life cycle.
Abstract: This paper presents strategies for dynamically creating, managing and removing mesh cells during computations in the context of the Material Point Method (MPM). The dynamic meshing approach has been developed to help address problems involving motion of a finite size body in unbounded domains in which the extent of material travel and deformation is unknown a priori, such as in the case of landslides and debris flows. The key idea is to efficiently instantiate and search only cells that contain material points, thereby avoiding unneeded storage and computation. Mechanisms for doing this efficiently are presented, and example problems are used to demonstrate the effectiveness of dynamic mesh management relative to alternative approaches.
Abstract: The purpose of this paper is to propose a framework for constructing correct parallel processing programs based on Equivalent Transformation Framework (ETF). ETF regards computation as In the framework, a problem-s domain knowledge and a query are described in definite clauses, and computation is regarded as transformation of the definite clauses. Its meaning is defined by a model of the set of definite clauses, and the transformation rules generated must preserve meaning. We have proposed a parallel processing method based on “specialization", a part of operation in the transformations, which resembles substitution in logic programming. The method requires “Memo-tree", a history of specialization to maintain correctness. In this paper we proposes the new method for the specialization-base parallel processing without Memo-tree.
Abstract: A new method identifies coupled fluid-structure system with a reduced set of state variables is presented. Assuming that the structural model is known a priori either from an analysis or a test and using linear transformations between structural and aeroelastic states, it is possible to deduce aerodynamic information from sampled time histories of the aeroelastic system. More specifically given a finite set of structural modes the method extracts generalized aerodynamic force matrix corresponding to these mode shapes. Once the aerodynamic forces are known, an aeroelastic reduced-order model can be constructed in discrete-time, state-space format by coupling the structural model and the aerodynamic system. The resulting reduced-order model is suitable for constant Mach, varying density analysis.
Abstract: Modeling and vibration of a flexible link manipulator
with tow flexible links and rigid joints are investigated which can
include an arbitrary number of flexible links. Hamilton principle and
finite element approach is proposed to model the dynamics of
flexible manipulators. The links are assumed to be deflection due to
bending. The association between elastic displacements of links is
investigated, took into account the coupling effects of elastic motion
and rigid motion. Flexible links are treated as Euler-Bernoulli beams
and the shear deformation is thus abandoned. The dynamic behavior
due to flexibility of links is well demonstrated through numerical
simulation. The rigid-body motion and elastic deformations are
separated by linearizing the equations of motion around the rigid
body reference path. Simulation results are shown on for both
position and force trajectory tracking tasks in the presence of varying
parameters and unknown dynamics remarkably well. The proposed
method can be used in both dynamic simulation and controller
design.
Abstract: This paper investigates the relationship between state and business in the context of structural and institutional transformations in Indonesia following the collapse of the New Order regime in 1998. Since 1998, Indonesia has embarked on a shift from an authoritarian to democratic polity and from a centralised to a decentralised system of governance, transforming the country into the third largest democracy and one of the most decentralised states in the world. This paper examines whether the transformation of the Indonesian state has altered the pattern of state and business relations with focus on clientism and corruption as the key dependent variable, and probes how/to what extent this has changed as a result of the transformation and the ensuring shifts in business and state relations. Based on interviews with key government and business actors as well as prominent scholars in Indonesia, it is found that since the demise of the New Order, business associations in Indonesia have become more independent of state control and more influential in public decision-making whereas the government has become more responsive of business concerns and more committed to combat corruption and clientism. However, these changes have not necessarily rendered business people completely leave individualclientelistic relationship with the government, and simply pursue wider sectoral and business-wide collectivism as an alternative way of channelling their aspirations, which is expected to help reduce corruption and clientism in Indonesia. This paper concludes that democratisation and a more open politics may have helped reduce corruption and clientism in Indonesia through changes in government. However, it is still difficult to imply that such political transformation has fostered business collective action and a broader, more encompassing pattern of business lobbying and activism, which is expected to help reduce corruption and clientism.
Abstract: Extended Kalman Filter (EKF) is probably the most
widely used estimation algorithm for nonlinear systems. However,
not only it has difficulties arising from linearization but also many
times it becomes numerically unstable because of computer round off
errors that occur in the process of its implementation. To overcome
linearization limitations, the unscented transformation (UT) was
developed as a method to propagate mean and covariance
information through nonlinear transformations. Kalman filter that
uses UT for calculation of the first two statistical moments is called
Unscented Kalman Filter (UKF). Square-root form of UKF (SRUKF)
developed by Rudolph van der Merwe and Eric Wan to
achieve numerical stability and guarantee positive semi-definiteness
of the Kalman filter covariances. This paper develops another
implementation of SR-UKF for sequential update measurement
equation, and also derives a new UD covariance factorization filter
for the implementation of UKF. This filter is equivalent to UKF but
is computationally more efficient.
Abstract: An automatic speech recognition system for the
formal Arabic language is needed. The Quran is the most formal
spoken book in Arabic, it is spoken all over the world. In this
research, an automatic speech recognizer for Quranic based speakerindependent
was developed and tested. The system was developed
based on the tri-phone Hidden Markov Model and Maximum
Likelihood Linear Regression (MLLR). The MLLR computes a set
of transformations which reduces the mismatch between an initial
model set and the adaptation data. It uses the regression class tree, as
well as, estimates a set of linear transformations for the mean and
variance parameters of a Gaussian mixture HMM system. The 30th
Chapter of the Quran, with five of the most famous readers of the
Quran, was used for the training and testing of the data. The chapter
includes about 2000 distinct words. The advantages of using the
Quranic verses as the database in this developed recognizer are the
uniqueness of the words and the high level of orderliness between
verses. The level of accuracy from the tested data ranged 68 to 85%.
Abstract: This paper analyses the unsteady, two-dimensional
stagnation point flow of an incompressible viscous fluid over a flat
sheet when the flow is started impulsively from rest and at the same
time, the sheet is suddenly stretched in its own plane with a velocity
proportional to the distance from the stagnation point. The partial
differential equations governing the laminar boundary layer forced
convection flow are non-dimensionalised using semi-similar
transformations and then solved numerically using an implicit finitedifference
scheme known as the Keller-box method. Results
pertaining to the flow and heat transfer characteristics are computed
for all dimensionless time, uniformly valid in the whole spatial region
without any numerical difficulties. Analytical solutions are also
obtained for both small and large times, respectively representing the
initial unsteady and final steady state flow and heat transfer.
Numerical results indicate that the velocity ratio parameter is found
to have a significant effect on skin friction and heat transfer rate at
the surface. Furthermore, it is exposed that there is a smooth
transition from the initial unsteady state flow (small time solution) to
the final steady state (large time solution).