Abstract: Yeast cells live in a constantly changing environment that requires the continuous adaptation of their genomic program in order to sustain their homeostasis, survive and proliferate. Due to the advancement of high throughput technologies, there is currently a large amount of data such as gene expression, gene deletion and protein-protein interactions for S. Cerevisiae under various environmental conditions. Mining these datasets requires efficient computational methods capable of integrating different types of data, identifying inter-relations between different components and inferring functional groups or 'modules' that shape intracellular processes. This study uses computational methods to delineate some of the mechanisms used by yeast cells to respond to environmental changes. The GRAM algorithm is first used to integrate gene expression data and ChIP-chip data in order to find modules of coexpressed and co-regulated genes as well as the transcription factors (TFs) that regulate these modules. Since transcription factors are themselves transcriptionally regulated, a three-layer regulatory cascade consisting of the TF-regulators, the TFs and the regulated modules is subsequently considered. This three-layer cascade is then modeled quantitatively using artificial neural networks (ANNs) where the input layer corresponds to the expression of the up-stream transcription factors (TF-regulators) and the output layer corresponds to the expression of genes within each module. This work shows that (a) the expression of at least 33 genes over time and for different stress conditions is well predicted by the expression of the top layer transcription factors, including cases in which the effect of up-stream regulators is shifted in time and (b) identifies at least 6 novel regulatory interactions that were not previously associated with stress-induced changes in gene expression. These findings suggest that the combination of gene expression and protein-DNA interaction data with artificial neural networks can successfully model biological pathways and capture quantitative dependencies between distant regulators and downstream genes.
Abstract: Many natural language expressions are ambiguous, and
need to draw on other sources of information to be interpreted.
Interpretation of the e word تعاون to be considered as a noun or a verb
depends on the presence of contextual cues. To interpret words we
need to be able to discriminate between different usages. This paper
proposes a hybrid of based- rules and a machine learning method for
tagging Arabic words. The particularity of Arabic word that may be
composed of stem, plus affixes and clitics, a small number of rules
dominate the performance (affixes include inflexional markers for
tense, gender and number/ clitics include some prepositions,
conjunctions and others). Tagging is closely related to the notion of
word class used in syntax. This method is based firstly on rules (that
considered the post-position, ending of a word, and patterns), and
then the anomaly are corrected by adopting a memory-based learning
method (MBL). The memory_based learning is an efficient method to
integrate various sources of information, and handling exceptional
data in natural language processing tasks. Secondly checking the
exceptional cases of rules and more information is made available to
the learner for treating those exceptional cases. To evaluate the
proposed method a number of experiments has been run, and in
order, to improve the importance of the various information in
learning.
Abstract: Expression data analysis is based mostly on the
statistical approaches that are indispensable for the study of
biological systems. Large amounts of multidimensional data resulting
from the high-throughput technologies are not completely served by
biostatistical techniques and are usually complemented with visual,
knowledge discovery and other computational tools. In many cases,
in biological systems we only speculate on the processes that are
causing the changes, and it is the visual explorative analysis of data
during which a hypothesis is formed. We would like to show the
usability of multidimensional visualization tools and promote their
use in life sciences. We survey and show some of the
multidimensional visualization tools in the process of data
exploration, such as parallel coordinates and radviz and we extend
them by combining them with the self-organizing map algorithm. We
use a time course data set of transitional cell carcinoma of the bladder
in our examples. Analysis of data with these tools has the potential to
uncover additional relationships and non-trivial structures.
Abstract: In mechanical and environmental engineering, mixed
convection is a frequently encountered thermal fluid phenomenon
which exists in atmospheric environment, urban canopy flows, ocean
currents, gas turbines, heat exchangers, and computer chip cooling
systems etc... . This paper deals with a numerical investigation of
mixed convection in a vertical heated channel. This flow results from
the mixing of the up-going fluid along walls of the channel with the
one issued from a flat nozzle located in its entry section. The fluiddynamic
and heat-transfer characteristics of vented vertical channels
are investigated for constant heat-flux boundary conditions, a
Rayleigh number equal to 2.57 1010, for two jet Reynolds number
Re=3 103 and 2104 and the aspect ratio in the 8-20 range. The system
of governing equations is solved with a finite volumes method and an
implicit scheme. The obtained results show that the turbulence and
the jet-wall interaction activate the heat transfer, as does the drive of
ambient air by the jet. For low Reynolds number Re=3 103, the
increase of the aspect Ratio enhances the heat transfer of about 3%,
however; for Re=2 104, the heat transfer enhancement is of about
12%. The numerical velocity, pressure and temperature fields are
post-processed to compute the quantities of engineering interest such
as the induced mass flow rate, and average Nusselt number, in terms
of Rayleigh, Reynolds numbers and dimensionless geometric
parameters are presented.
Abstract: In this experimental investigation shake table tests
were conducted on two reduced models that represent normal single
room building constructed by Compressed Stabilized Earth Block
(CSEB) from locally available soil. One model was constructed with
earthquake resisting features (EQRF) having sill band, lintel band and
vertical bands to control the building vibration and another one was
without Earthquake Resisting Features. To examine the seismic
capacity of the models particularly when it is subjected to long-period
ground motion by large amplitude by many cycles of repeated
loading, the test specimen was shaken repeatedly until the failure.
The test results from Hi-end Data Acquisition system show that
model with EQRF behave better than without EQRF. This modified
masonry model with new material combined with new bands is used
to improve the behavior of masonry building.
Abstract: Reinforced Concrete (RC) structures strengthened
with fiber reinforced polymer (FRP) lack in thermal resistance under
elevated temperatures in the event of fire. This phenomenon led to
the lining of strengthened concrete with thin high performance
cementitious composites (THPCC) to protect the substrate against
elevated temperature. Elevated temperature effects on THPCC, based
on different cementitious materials have been studied in the past but
high-alumina cement (HAC)-based THPCC have not been well
characterized. This research study will focus on the THPCC based on
HAC replaced by 60%, 70%, 80% and 85% of ground granulated
blast furnace slag (GGBS). Samples were evaluated by the
measurement of their mechanical strength (28 & 56 days of curing)
after exposed to 400°C, 600°C and 28°C of room temperature for
comparison and corroborated by their microstructure study. Results
showed that among all mixtures, the mix containing only HAC
showed the highest compressive strength after exposed to 600°C as
compared to other mixtures. However, the tensile strength of THPCC
made of HAC and 60% GGBS content was comparable to the
THPCC with HAC only after exposed to 600°C. Field emission
scanning electron microscopy (FESEM) images of THPCC
accompanying Energy Dispersive X-ray (EDX) microanalysis
revealed that the microstructure deteriorated considerably after
exposure to elevated temperatures which led to the decrease in
mechanical strength.
Abstract: As the web continues to grow exponentially, the idea
of crawling the entire web on a regular basis becomes less and less
feasible, so the need to include information on specific domain,
domain-specific search engines was proposed. As more information
becomes available on the World Wide Web, it becomes more difficult
to provide effective search tools for information access. Today,
people access web information through two main kinds of search
interfaces: Browsers (clicking and following hyperlinks) and Query
Engines (queries in the form of a set of keywords showing the topic
of interest) [2]. Better support is needed for expressing one's
information need and returning high quality search results by web
search tools. There appears to be a need for systems that do reasoning
under uncertainty and are flexible enough to recover from the
contradictions, inconsistencies, and irregularities that such reasoning
involves. In a multi-view problem, the features of the domain can be
partitioned into disjoint subsets (views) that are sufficient to learn the
target concept. Semi-supervised, multi-view algorithms, which
reduce the amount of labeled data required for learning, rely on the
assumptions that the views are compatible and uncorrelated. This
paper describes the use of semi-structured machine learning approach
with Active learning for the “Domain Specific Search Engines". A
domain-specific search engine is “An information access system that
allows access to all the information on the web that is relevant to a
particular domain. The proposed work shows that with the help of
this approach relevant data can be extracted with the minimum
queries fired by the user. It requires small number of labeled data and
pool of unlabelled data on which the learning algorithm is applied to
extract the required data.
Abstract: Nozzle is the main part of various spinning systems
such as air-jet and Murata air vortex systems. Recently, many
researchers worked on the usage of the nozzle on different spinning
systems such as conventional ring and compact spinning systems. In
these applications, primary purpose is to improve the yarn quality. In
present study, it was produced the yarns with two different nozzle
types and determined the changes in yarn properties. In order to
explain the effect of the nozzle, airflow structure in the nozzle was
modelled and airflow variables were determined. In numerical
simulation, ANSYS 12.1 package program and Fluid Flow (CFX)
analysis method was used. As distinct from the literature, Shear
Stress Turbulent (SST) model is preferred. And also air pressure at
the nozzle inlet was measured by electronic mass flow meter and
these values were used for the simulation of the airflow. At last, the
yarn was modelled and the area from where the yarn is passing was
included to the numerical analysis.
Abstract: In this paper, a study on the modes of collapse of
compress- expand members are presented. Compress- expand member
is a compact, multiple-combined cylinders, to be proposed as energy
absorbers. Previous studies on the compress- expand member have
clarified its energy absorption efficiency, proposed an approximate
equation to describe its deformation characteristics and also
highlighted the improvement that it has brought. However, for the
member to be practical, the actual range of geometrical dimension that
it can maintain its applicability must be investigated. In this study,
using a virtualized materials that comply the bilinear hardening law,
Finite element Method (FEM) analysis on the collapse modes of
compress- expand member have been conducted. Deformation maps
that plotted the member's collapse modes with regards to the member's
geometric and material parameters were then presented in order to
determine the dimensional range of each collapse modes.
Abstract: The paper presents the study of synthetic transmit
aperture method applying the Golay coded transmission for medical
ultrasound imaging. Longer coded excitation allows to increase the
total energy of the transmitted signal without increasing the peak
pressure. Signal-to-noise ratio and penetration depth are improved
maintaining high ultrasound image resolution.
In the work the 128-element linear transducer array with 0.3 mm
inter-element spacing excited by one cycle and the 8 and 16-bit
Golay coded sequences at nominal frequencies 4 MHz was used.
Single element transmission aperture was used to generate a spherical
wave covering the full image region and all the elements received the
echo signals. The comparison of 2D ultrasound images of the wire
phantom as well as of the tissue mimicking phantom is presented to
demonstrate the benefits of the coded transmission. The results were
obtained using the synthetic aperture algorithm with transmit and
receive signals correction based on a single element directivity
function.
Abstract: Endovascular aneurysm repair is a new and minimally invasive repair for patients with abdominal aortic aneurysm (AAA). This method has potential advantages that are incomparable with other repair methods. However, the enlargement of aneurysm in the absence of endoleak, which is known as endotension, may occur as one of post-operative compliances of this method. Typically, endotension is mainly as a result of pressure transmitted to aneurysm sac by endovascular installed graft. After installation of graft the aneurysm sac reduces significantly but remains non-zero. There are some factors which affect this pressure transmitted. In this study, the geometry features of installed vascular graft have been considered. It is inferred that graft neck angle and iliac bifurcation angle are two factors which can affect the drag force on graft and consequently the pressure transmitted to aneurysm.
Abstract: Ten lactating multiparous Holstein cows were used in
a cross-over design with two dietary treatments and 28-d periods
(with 14 d as an adaptation) to study the effect of restaurant fat on
milk production and composition. Each cow was offered 14.7 kg
DM /d of the basal concentrate diet based on barley and corn (crude
protein = 17.7%, neutral detergent fiber = 23.5%, and acid detergent
fiber = 5.8% of dry matter) with free access to alfalfa. Dietary
treatments were arranged as supplying each cow with 0 (CONTROL)
or 150 g/day (RF) of restaurant fat. Supplemental RF did not
significantly (P > 0.25) affect milk yield, composition, and
composition yields, except for milk fat contents. Milk fat contents
were depressed (P < 0.05) with supplemental RF. Our results indicate
that RF could depress milk fat without affecting milk yield and that
the depression in milk fat in response to RF precedes the depression
in milk yield.
Abstract: Reliability assessment and risk analysis of rotating
machine rotors in various overload and malfunction situations
present challenge to engineers and operators. In this paper a new
analytical method for evaluation of rotor under large deformation is
addressed. Model is presented in general form to include also
composite rotors. Presented simulation procedure is based on
variational work method and has capability to account for geometric
nonlinearity, large displacement, nonlinear support effect and rotor
contacting other machine components. New shape functions are
presented which capable to predict accurate nonlinear profile of
rotor. The closed form solutions for various operating and
malfunction situations are expressed. Analytical simulation results
are discussed
Abstract: A novel file splitting technique for the reduction of the nth-order entropy of text files is proposed. The technique is based on mapping the original text file into a non-ASCII binary file using a new codeword assignment method and then the resulting binary file is split into several subfiles each contains one or more bits from each codeword of the mapped binary file. The statistical properties of the subfiles are studied and it is found that they reflect the statistical properties of the original text file which is not the case when the ASCII code is used as a mapper. The nth-order entropy of these subfiles are determined and it is found that the sum of their entropies is less than that of the original text file for the same values of extensions. These interesting statistical properties of the resulting subfiles can be used to achieve better compression ratios when conventional compression techniques are applied to these subfiles individually and on a bit-wise basis rather than on character-wise basis.
Abstract: Efforts to secure supervisory control and data acquisition
(SCADA) systems must be supported under the guidance of
sound security policies and mechanisms to enforce them. Critical
elements of the policy must be systematically translated into a format
that can be used by policy enforcement components. Ideally, the
goal is to ensure that the enforced policy is a close reflection of
the specified policy. However, security controls commonly used to
enforce policies in the IT environment were not designed to satisfy
the specific needs of the SCADA environment. This paper presents
a language, based on the well-known XACML framework, for the
expression of authorization policies for SCADA systems.
Abstract: The present work is motivated by the idea that the
layer deformation in anisotropic elasticity can be estimated from the
theory of interfacial dislocations. In effect, this work which is an
extension of a previous approach given by one of the authors
determines the anisotropic displacement fields and the critical
thickness due to a complex biperiodic network of MDs lying just
below the free surface in view of the arrangement of dislocations.
The elastic fields of such arrangements observed along interfaces
play a crucial part in the improvement of the physical properties of
epitaxial systems. New results are proposed in anisotropic elasticity
for hexagonal networks of MDs which contain intrinsic and extrinsic
stacking faults. We developed, using a previous approach based on
the relative interfacial displacement and a Fourier series formulation
of the displacement fields, the expressions of elastic fields when
there is a possible dissociation of MDs. The numerical investigations
in the case of the observed system Si/(111)Si with low twist angles
show clearly the effect of the anisotropy and thickness when the
misfit networks are dissociated.
Abstract: In this paper, a novel approach is presented
for designing multiplier-free state-space digital filters. The
multiplier-free design is obtained by finding power-of-2 coefficients
and also quantizing the state variables to power-of-2
numbers. Expressions for the noise variance are derived for the
quantized state vector and the output of the filter. A “structuretransformation
matrix" is incorporated in these expressions. It
is shown that quantization effects can be minimized by properly
designing the structure-transformation matrix. Simulation
results are very promising and illustrate the design algorithm.
Abstract: In most rule-induction algorithms, the only operator used against nominal attributes is the equality operator =. In this paper, we first propose the use of the inequality operator, ≠, in addition to the equality operator, to increase the expressiveness of induced rules. Then, we present a new method, Binary Coding, which can be used along with an arbitrary rule-induction algorithm to make use of the inequality operator without any need to change the algorithm. Experimental results suggest that the Binary Coding method is promising enough for further investigation, especially in cases where the minimum number of rules is desirable.
Abstract: We present an explicit expression to estimate driving voltage attenuation through RC networks representation of an ultrahigh- speed image sensor. Elmore delay metric for a fundamental RC chain is employed as the first-order approximation. By application of dimensional analysis to SPICE simulation data, we found a simple expression that significantly improves the accuracy of the approximation. Estimation error of the resultant expression for uniform RC networks is less than 2%. Similarly, another simple closed-form model to estimate 50 % delay through fundamental RC networks is also derived with sufficient accuracy. The framework of this analysis can be extended to address delay or attenuation issues of other VLSI structures.
Abstract: Background: Blunt aortic trauma (BAT) includes
various morphological changes that occur during deceleration,
acceleration and/or body compression in traffic accidents. The
various forms of BAT, from limited laceration of the intima to
complete transection of the aorta, depends on the force acting on the
vessel wall and the tolerance of the aorta to injury. The force depends
on the change in velocity, the dynamics of the accident and of the
seating position in the car. Tolerance to aortic injury depends on the
anatomy, histological structure and pathomorphological alterations
due to aging or disease of the aortic wall.
An overview of the literature and medical documentation reveals
that different terms are used to describe certain forms of BAT, which
can lead to misinterpretation of findings or diagnoses. We therefore,
propose a classification that would enable uniform systematic
screening of all forms of BAT. We have classified BAT into three
morphologycal types: TYPE I (intramural), TYPE II (transmural) and
TYPE III (multiple) aortic ruptures with appropriate subtypes.
Methods: All car accident casualties examined at the Institute of
Forensic Medicine from 2001 to 2009 were included in this
retrospective study. Autopsy reports were used to determine the
occurrence of each morphological type of BAT in deceased drivers,
front seat passengers and other passengers in cars and to define the
morphology of BAT in relation to the accident dynamics and the age
of the fatalities.
Results: A total of 391 fatalities in car accidents were included in
the study. TYPE I, TYPE II and TYPE III BAT were observed in
10,9%, 55,6% and 33,5%, respectively. The incidence of BAT in
drivers, front seat and other passengers was 36,7%, 43,1% and
28,6%, respectively. In frontal collisions, the incidence of BAT was
32,7%, in lateral collisions 54,2%, and in other traffic accidents
29,3%. The average age of fatalities with BAT was 42,8 years and of
those without BAT 39,1 years.
Conclusion: Identification and early recognition of the risk factors
of BAT following a traffic accident is crucial for successful treatment
of patients with BAT. Front seat passengers over 50 years of age who
have been injured in a lateral collision are the most at risk of BAT.