Abstract: In biological and biomedical research motif finding tools are important in locating regulatory elements in DNA sequences. There are many such motif finding tools available, which often yield position weight matrices and significance indicators. These indicators, p-values and E-values, describe the likelihood that a motif alignment is generated by the background process, and the expected number of occurrences of the motif in the data set, respectively. The various tools often estimate these indicators differently, making them not directly comparable. One approach for comparing motifs from different tools, is computing the E-value as the product of the p-value and the number of possible alignments in the data set. In this paper we explore the combinatorics of the motif alignment models OOPS, ZOOPS, and ANR, and propose a generic algorithm for computing the number of possible combinations accurately. We also show that using the wrong alignment model can give E-values that significantly diverge from their true values.
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: The aim of this paper is to study in depth some methodological aspects of social interventation, focusing on desirable passage from social maternage method to peer advocacy method. For this purpose, we intend analyze social and organizative components, that affect operator's professional action and that are part of his psychological environment, besides the physical and social one. In fact, operator's interventation should not be limited to a pure supply of techniques, nor to take shape as improvised action, but “full of good purposes".
Abstract: Buyer coalition with a combination of items is a group of buyers joining together to purchase a combination of items with a larger discount. The primary aim of existing buyer coalition with a combination of items research is to generate a large total discount. However, the aim is hard to achieve because this research is based on the assumption that each buyer completely knows other buyers- information or at least one buyer knows other buyers- information in a coalition by exchange of information. These assumption contrast with the real world environment where buyers join a coalition with incomplete information, i.e., they concerned only with their expected discounts. Therefore, this paper proposes a new buyer community coalition formation with a combination of items scheme, called the Community Compromised Combinatorial Coalition scheme, under such an environment of incomplete information. In order to generate a larger total discount, after buyers who want to join a coalition propose their minimum required saving, a coalition structure that gives a maximum total retail prices is formed. Then, the total discount division of the coalition is divided among buyers in the coalition depending on their minimum required saving and is a Pareto optimal. In mathematical analysis, we compare concepts of this scheme with concepts of the existing buyer coalition scheme. Our mathematical analysis results show that the total discount of the coalition in this scheme is larger than that in the existing buyer coalition scheme.
Abstract: Annotation of a protein sequence is pivotal for the understanding of its function. Accuracy of manual annotation provided by curators is still questionable by having lesser evidence strength and yet a hard task and time consuming. A number of computational methods including tools have been developed to tackle this challenging task. However, they require high-cost hardware, are difficult to be setup by the bioscientists, or depend on time intensive and blind sequence similarity search like Basic Local Alignment Search Tool. This paper introduces a new method of assigning highly correlated Gene Ontology terms of annotated protein sequences to partially annotated or newly discovered protein sequences. This method is fully based on Gene Ontology data and annotations. Two problems had been identified to achieve this method. The first problem relates to splitting the single monolithic Gene Ontology RDF/XML file into a set of smaller files that can be easy to assess and process. Thus, these files can be enriched with protein sequences and Inferred from Electronic Annotation evidence associations. The second problem involves searching for a set of semantically similar Gene Ontology terms to a given query. The details of macro and micro problems involved and their solutions including objective of this study are described. This paper also describes the protein sequence annotation and the Gene Ontology. The methodology of this study and Gene Ontology based protein sequence annotation tool namely extended UTMGO is presented. Furthermore, its basic version which is a Gene Ontology browser that is based on semantic similarity search is also introduced.
Abstract: Considering complexity of products, new geometrical
design and investment tolerances that are necessary, measuring and
dimensional controlling involve modern and more precise methods.
Photo digitizing method using two cameras to record pictures and
utilization of conventional method named “cloud points" and data
analysis by the use of ATOUS software, is known as modern and
efficient in mentioned context. In this paper, benefits of photo
digitizing method in evaluating sampling of machining processes
have been put forward. For example, assessment of geometrical
integrity surface in 5-axis milling process and measurement of
carbide tool wear in turning process, can be can be brought forward.
Advantages of this method comparing to conventional methods have
been expressed.
Abstract: Text data mining is a process of exploratory data
analysis. Classification maps data into predefined groups or classes.
It is often referred to as supervised learning because the classes are
determined before examining the data. This paper describes proposed
radial basis function Classifier that performs comparative crossvalidation
for existing radial basis function Classifier. The feasibility
and the benefits of the proposed approach are demonstrated by means
of data mining problem: direct Marketing. Direct marketing has
become an important application field of data mining. Comparative
Cross-validation involves estimation of accuracy by either stratified
k-fold cross-validation or equivalent repeated random subsampling.
While the proposed method may have high bias; its performance
(accuracy estimation in our case) may be poor due to high variance.
Thus the accuracy with proposed radial basis function Classifier was
less than with the existing radial basis function Classifier. However
there is smaller the improvement in runtime and larger improvement
in precision and recall. In the proposed method Classification
accuracy and prediction accuracy are determined where the
prediction accuracy is comparatively high.
Abstract: Walking as a type of non-motorized transportation has
various social, economical and environmental privileges. Also, today
different aspects of sustainable development have been emphasized
and promotion of sustainable transportation modes has been
considered according to this approach. Therefore, the objective of
this research is exploring the circumstance of relationship between
walking and sustainable urban transportation.For writing this article,
the most important resources related to the traits of walking have
been surveyed via a documentary method and after explaining the
concept of sustainable transportation and its indicators, benefiting
from the viewpoints of transportation experts of Tehran, as the capital
and greatest city of Iran, different modes of urban transportation have
been compared in proportion to each criterion and to each other and
have been analyzed according to AHP method. The results of this
study indicate that walking is the most sustainable mode of inner city
transportation.
Abstract: The abundance and availability of rice husk, an agricultural waste, make them as a good source for precursor of activated carbon. In this work, rice husk-based activated carbons were prepared via base treated chemical activation process prior the carbonization process. The effect of carbonization temperatures (400, 600 and 800oC) on their pore structure was evaluated through morphology analysis using scanning electron microscope (SEM). Sample carbonized at 800oC showed better evolution and development of pores as compared to those carbonized at 400 and 600oC. The potential of rice husk-based activated carbon as an alternative adsorbent was investigated for the removal of Ni(II), Zn(II) and Pb(II) from single metal aqueous solution. The adsorption studies using rice husk-based activated carbon as an adsorbent were carried out as a function of contact time at room temperature and the metal ions were analyzed using atomic absorption spectrophotometer (AAS). The ability to remove metal ion from single metal aqueous solution was found to be improved with the increasing of carbonization temperature. Among the three metal ions tested, Pb(II) ion gave the highest adsorption on rice husk-based activated carbon. The results obtained indicate the potential to utilize rice husk as a promising precursor for the preparation of activated carbon for removal of heavy metals.
Abstract: This paper describes a feasibility study that is
included with the research, development and testing of a micro
communications sonobuoy deployable by Maritime Fixed wing
Unmanned Aerial Vehicles (M-UAV) and rotor wing Quad Copters
which are both currently being developed by the University of
Adelaide. The micro communications sonobuoy is developed to act
as a seamless communication relay between an Autonomous
Underwater Vehicle (AUV) and an above water human operator
some distance away. Development of such a device would eliminate
the requirement of physical communication tethers attached to
submersible vehicles for control and data retrieval.
Abstract: This contribution deals with the relationship between
communication effectiveness and the extent of communication
among organizational units. To facilitate communication between
employees and to increase the level of understanding, the knowledge
of communication tools is necessary. Recent experience has shown
that personal communication is critical for smooth running of
companies and cannot be fully replaced by any form of technical
communication devices.
Below are presented the outcomes of the research on the
relationship between the extent of communication among
organisational units and its efficiency.
Abstract: This study aims to investigate mechanical behavior of
deep-drawn cups consisting of aluminum (A1050)/ duralumin
(A2017) multi-layered clad structures with micro- and macro-scale
functional gradients. Such multi-layered clad structures are possibly
used for a new type of crash-boxes in automobiles to effectively
absorb the impact forces generated when automobiles having
collisions. The effect of heat treatments on microstructure,
compositional gradient, micro hardness in 2 and 6-layered aluminum/
duralumin clad structures, which were fabricated by hot rolling, have
been investigated. Impact compressive behavior of deep-drawn cups
consisting of such aluminum/ duralumin clad structures has been also
investigated in terms of energy absorption and maximum force.
Deep-drawn cups consisting of 6-layerd clad structures with microand
macro-scale functional gradients exhibit superior properties in
impact compressive tests.
Abstract: Recent evidences on liquidity and valuation of securities in the capital markets clearly show the importance of stock market liquidity and valuation of firms. In this paper, relationship between transparency, liquidity, and valuation is studied by using data obtained from 70 companies listed in Tehran Stock Exchange during2003-2012. In this study, discriminatory earnings management, as a sign of lack of transparency and Tobin's Q, was used as the criteria of valuation. The results indicate that there is a significant and reversed relationship between earnings management and liquidity. On the other hand, there is a relationship between liquidity and transparency.The results also indicate a significant relationship between transparency and valuation. Transparency has an indirect effect on firm valuation alone or through the liquidity channel. Although the effect of transparency on the value of a firm was reduced by adding the variable of liquidity, the cumulative effect of transparency and liquidity increased.
Abstract: Small signal stability causes small perturbations in the
generator that can cause instability in the power network. It is
generally known that small signal stability are directly related to the
generator and load properties. This paper examines the effects of
generator input variations on power system oscillations for a small
signal stability study. Eigenvaules and eigenvectors are used to
examine the stability of the power system. The dynamic power
system's mathematical model is constructed and thus calculated using
load flow and small signal stability toolbox on MATLAB. The power
system model is based on a 3-machine 9-bus system that was
modified to suit this study. In this paper, Participation Factors are a
means to gauge the effects of variation in generation with other
parameters on the network are also incorporated.
Abstract: Ground-level tropospheric ozone is one of the air
pollutants of most concern. It is mainly produced by photochemical
processes involving nitrogen oxides and volatile organic compounds
in the lower parts of the atmosphere. Ozone levels become
particularly high in regions close to high ozone precursor emissions
and during summer, when stagnant meteorological conditions with
high insolation and high temperatures are common.
In this work, some results of a study about urban ozone
distribution patterns in the city of Badajoz, which is the largest and
most industrialized city in Extremadura region (southwest Spain) are
shown. Fourteen sampling campaigns, at least one per month, were
carried out to measure ambient air ozone concentrations, during
periods that were selected according to favourable conditions to
ozone production, using an automatic portable analyzer.
Later, to evaluate the ozone distribution at the city, the measured
ozone data were analyzed using geostatistical techniques. Thus, first,
during the exploratory analysis of data, it was revealed that they were
distributed normally, which is a desirable property for the subsequent
stages of the geostatistical study. Secondly, during the structural
analysis of data, theoretical spherical models provided the best fit for
all monthly experimental variograms. The parameters of these
variograms (sill, range and nugget) revealed that the maximum
distance of spatial dependence is between 302-790 m and the
variable, air ozone concentration, is not evenly distributed in reduced
distances. Finally, predictive ozone maps were derived for all points
of the experimental study area, by use of geostatistical algorithms
(kriging). High prediction accuracy was obtained in all cases as
cross-validation showed. Useful information for hazard assessment
was also provided when probability maps, based on kriging
interpolation and kriging standard deviation, were produced.
Abstract: Simulation of occlusal function during laboratory
material-s testing becomes essential in predicting long-term
performance before clinical usage. The aim of the study was to assess
the influence of chamfer preparation depth on failure risk of heat
pressed ceramic crowns with and without zirconia framework by
means of finite element analysis. 3D models of maxillary central
incisor, prepared for full ceramic crowns with different depths of the
chamfer margin (between 0.8 and 1.2 mm) and 6-degree tapered
walls together with the overlying crowns were generated using
literature data (Fig. 1, 2). The crowns were designed with and
without a zirconia framework with a thickness of 0.4 mm. For all
preparations and crowns, stresses in the pressed ceramic crown,
zirconia framework, pressed ceramic veneer, and dentin were
evaluated separately. The highest stresses were registered in the
dentin. The depth of the preparations had no significant influence on
the stress values of the teeth and pressed ceramics for the studied
cases, only for the zirconia framework. The zirconia framework
decreases the stress values in the veneer.
Abstract: In this paper, a fractional-order FIR differentiator
design method using the differential evolution (DE) algorithm is
presented. In the proposed method, the FIR digital filter is designed to
meet the frequency response of a desired fractal-order differentiator,
which is evaluated in the frequency domain. To verify the design
performance, another design method considered in the time-domain is
also provided. Simulation results reveal the efficiency of the proposed
method.
Abstract: In this paper, the use of beam search and look-ahead strategies for solving the strip packing problem (SPP) is investigated. Given a strip of fixed width W, unlimited length L, and a set of n circular pieces of known radii, the objective is to determine the minimum length of the initial strip that packs all the pieces. An augmented algorithm which combines beam search and a look-ahead strategies is proposed. The look-ahead is used in order to evaluate the nodes at each level of the tree search. The best nodes are then retained for branching. The computational investigation showed that the proposed augmented algorithm is able to improve the best known solutions of the literature on most instances used.
Abstract: Bacterial magnetic nanoparticles have great useful potential in biotechnological and biomedical applications. In this study, a liquid growth medium was modified for cultivation a fastidious magnetotactic bacterium that has been isolated from Anzali
lagoon, Iran in our previous research. These modifications include
change in vitamin, mineral, carbon sources and etcetera. In our
experience, the serum bottles and designed air-tight laboratory bottles
were used to create microaerobic conditions in order to development
of a method for scale-up experiment. This information may serve as a
guide to green chemistry based biological protocols for the synthesis
of magnetic nanoparticles with control over the chemical
composition, morphology and size.
Abstract: In this paper we intend to ascertain the state of the art on multifingered end-effectors, also known as robotic hands or dexterous robot hands, and propose an experimental setup for an innovative task based design approach, involving cutting edge technologies in motion capture. After an initial description of the capabilities and complexity of a human hand when grasping objects, in order to point out the importance of replicating it, we analyze the mechanical and kinematical structure of some important works carried out all around the world in the last three decades and also review the actuators and sensing technologies used. Finally we describe a new design philosophy proposing an experimental setup for the first stage using recent developments in human body motion capture systems that might lead to lighter and always more dexterous robotic hands.