Abstract: Protein 3D structure prediction has always been an
important research area in bioinformatics. In particular, the
prediction of secondary structure has been a well-studied research
topic. Despite the recent breakthrough of combining multiple
sequence alignment information and artificial intelligence algorithms
to predict protein secondary structure, the Q3 accuracy of various
computational prediction algorithms rarely has exceeded 75%. In a
previous paper [1], this research team presented a rule-based method
called RT-RICO (Relaxed Threshold Rule Induction from Coverings)
to predict protein secondary structure. The average Q3 accuracy on
the sample datasets using RT-RICO was 80.3%, an improvement
over comparable computational methods. Although this demonstrated
that RT-RICO might be a promising approach for predicting
secondary structure, the algorithm-s computational complexity and
program running time limited its use. Herein a parallelized
implementation of a slightly modified RT-RICO approach is
presented. This new version of the algorithm facilitated the testing of
a much larger dataset of 396 protein domains [2]. Parallelized RTRICO
achieved a Q3 score of 74.6%, which is higher than the
consensus prediction accuracy of 72.9% that was achieved for the
same test dataset by a combination of four secondary structure
prediction methods [2].
Abstract: A parallel computational fluid dynamics code has been
developed for the study of aerodynamic heating problem in hypersonic
flows. The code employs the 3D Navier-Stokes equations as the basic
governing equations to simulate the laminar hypersonic flow. The cell
centered finite volume method based on structured grid is applied for
spatial discretization. The AUSMPW+ scheme is used for the inviscid
fluxes, and the MUSCL approach is used for higher order spatial
accuracy. The implicit LU-SGS scheme is applied for time integration
to accelerate the convergence of computations in steady flows. A
parallel programming method based on MPI is employed to shorten
the computing time. The validity of the code is demonstrated by
comparing the numerical calculation result with the experimental data
of a hypersonic flow field around a blunt body.
Abstract: Brain ArterioVenous Malformation (BAVM) is an abnormal tangle of brain blood vessels where arteries shunt directly into veins with no intervening capillary bed which causes high pressure and hemorrhage risk. The success of treatment by embolization in interventional neuroradiology is highly dependent on the accuracy of the vessels visualization. In this paper the performance of clustering techniques on vessel segmentation from 3- D rotational angiography (3DRA) images is investigated and a new technique of segmentation is proposed. This method consists in: preprocessing step of image enhancement, then K-Means (KM), Fuzzy C-Means (FCM) and Expectation Maximization (EM) clustering are used to separate vessel pixels from background and artery pixels from vein pixels when possible. A post processing step of removing false-alarm components is applied before constructing a three-dimensional volume of the vessels. The proposed method was tested on six datasets along with a medical assessment of an expert. Obtained results showed encouraging segmentations.
Abstract: Octree compression techniques have been used
for several years for compressing large three dimensional data
sets into homogeneous regions. This compression technique
is ideally suited to datasets which have similar values in
clusters. Oil engineers represent reservoirs as a three dimensional
grid where hydrocarbons occur naturally in clusters. This
research looks at the efficiency of storing these grids using
octree compression techniques where grid cells are broken
into active and inactive regions. Initial experiments yielded
high compression ratios as only active leaf nodes and their
ancestor, header nodes are stored as a bitstream to file on
disk. Savings in computational time and memory were possible
at decompression, as only active leaf nodes are sent to the
graphics card eliminating the need of reconstructing the original
matrix. This results in a more compact vertex table, which can
be loaded into the graphics card quicker and generating shorter
refresh delay times.
Abstract: A general purpose viscous flow solver Ansys CFX
was used to solve the unsteady three-dimensional (3D) Reynolds
Averaged Navier-Stokes Equation (RANSE) for simulating a 3D
numerical viscous wave tank. A flap-type wave generator was
incorporated in the computational domain to generate the desired
incident waves. Authors have made effort to study the physical
behaviors of Flap type wave maker with governing parameters.
Dependency of the water fill depth, Time period of oscillations and
amplitude of oscillations of flap were studied. Effort has been made
to establish relations between parameters. A validation study was
also carried out against CFD methodology with wave maker theory.
It has been observed that CFD results are in good agreement with
theoretical results. Beaches of different slopes were introduced to
damp the wave, so that it should not cause any reflection from
boundary. As a conclusion this methodology can simulate the
experimental wave-maker for regular wave generation for different
wave length and amplitudes.
Abstract: 2D/3D registration is a special case of medical image
registration which is of particular interest to surgeons. Applications
of 2D/3D registration are [1] radiotherapy planning and treatment
verification, spinal surgery, hip replacement, neurointerventions and
aortic stenting. The purpose of this paper is to provide a literature
review of the main methods for image registration for the 2D/3D
case. At the end of the paper an algorithm is proposed for 2D/3D
registration based on the Chebyssev polynomials iteration loop.
Abstract: The objective of this work is to show a procedure for
mesh generation in a fluidized bed using large eddy simulations
(LES) of a filtered two-fluid model. The experimental data were
obtained by [1] in a laboratory fluidized bed. Results show that it is
possible to use mesh with less cells as compared to RANS turbulence
model with granular kinetic theory flow (KTGF). Also, the numerical
results validate the experimental data near wall of the bed, which
cannot be predicted by RANS.model.
Abstract: The main objective of this paper is to provide an efficient tool for delineating brain tumors in three-dimensional magnetic resonance images and set up compression-transmit schemes to distribute result to the remote doctor. To achieve this goal, we use basically a level-sets approach to delineating brain tumors in threedimensional. Then introduce a new compression and transmission plan of 3D brain structures based for the meshes simplification, adapted for time to the specific needs of the telemedicine and to the capacities restricted by wireless network communication. We present here the main stages of our system, and preliminary results which are very encouraging for clinical practice.
Abstract: Localized surface plasmon resonance (LSPR) is the
coherent oscillation of conductive electrons confined in noble
metallic nanoparticles excited by electromagnetic radiation, and
nanosphere lithography (NSL) is one of the cost-effective methods to
fabricate metal nanostructures for LSPR. NSL can be categorized
into two major groups: dispersed NSL and closely pack NSL. In
recent years, gold nanocrescents and gold nanoholes with vertical
sidewalls fabricated by dispersed NSL, and silver nanotriangles and
gold nanocaps on silica nanospheres fabricated by closely pack NSL,
have been reported for LSPR biosensing. This paper introduces
several novel gold nanostructures fabricated by NSL in LSPR
applications, including 3D nanostructures obtained by evaporating
gold obliquely on dispersed nanospheres, nanoholes with slant
sidewalls, and patchy nanoparticles on closely packed nanospheres,
all of which render satisfactory sensitivity for LSPR sensing. Since
the LSPR spectrum is very sensitive to the shape of the metal
nanostructures, formulas are derived and software is developed for
calculating the profiles of the obtainable metal nanostructures by
NSL, for different nanosphere masks with different fabrication
conditions. The simulated profiles coincide well with the profiles of
the fabricated gold nanostructures observed under scanning electron
microscope (SEM) and atomic force microscope (AFM), which
proves that the software is a useful tool for the process design of
different LSPR nanostructures.
Abstract: We present a new method for the fully automatic 3D
reconstruction of the coronary artery centerlines, using two X-ray
angiogram projection images from a single rotating monoplane
acquisition system. During the first stage, the input images are
smoothed using curve evolution techniques. Next, a simple yet
efficient multiscale method, based on the information of the Hessian
matrix, for the enhancement of the vascular structure is introduced.
Hysteresis thresholding using different image quantiles, is used to
threshold the arteries. This stage is followed by a thinning procedure
to extract the centerlines. The resulting skeleton image is then pruned
using morphological and pattern recognition techniques to remove
non-vessel like structures. Finally, edge-based stereo correspondence
is solved using a parallel evolutionary optimization method based on
f symbiosis. The detected 2D centerlines combined with disparity
map information allow the reconstruction of the 3D vessel
centerlines. The proposed method has been evaluated on patient data
sets for evaluation purposes.
Abstract: An experiment was implemented in a filed in the south of Morocco to evaluate the effects of domestic treated wastewater use for irrigation of amaranth crop under semi-arid conditions. Three varieties (A0020, A0057 & A211) were tested and irrigated using domestic treated wastewater EC1 (0,92 dS/m) as control, EC3 (3dS/m) and EC6 (6dS/m) obtained by adding sea water. In term of growth, an increase of the EC level of applied irrigation water reduced significantly the plant-s height, leaf area, fresh and dry weight measured at vegetative, flowering and maturity stage for all varieties. Even with the application of the EC6, yields were relatively higher in comparison with the once obtained in normal cultivation conditions. A significant accumulation of nitrate, chloride and sodium in soil layers during the crop cycle was noted. The use of treated waste water for its irrigation is proved to be possible. The variety A211 had showed to be less sensitive to salinity stress and it could be more promising its introduction to study area.
Abstract: Solidification cracking and hydrogen cracking are some defects generated in the fusion welding of ultrahigh carbon steels. However, friction stir welding (FSW) of such steels, being a solid-state technique, has been demonstrated to alleviate such problems encountered in traditional welding. FSW include different process parameters that must be carefully defined prior processing. These parameters included but not restricted to: tool feed, tool RPM, tool geometry, tool tilt angle. These parameters form a key factor behind avoiding warm holes and voids behind the tool and in achieving a defect-free weld. More importantly, these parameters directly affect the microstructure of the weld and hence the final mechanical properties of weld. For that, 3D finite element (FE) thermo-mechanical model was developed using DEFORM 3D to simulate FSW of carbon steel. At points of interest in the joint, tracking is done for history of critical state variables such as temperature, stresses, and strain rates. Typical results found include the ability to simulate different weld zones. Simulations predictions were successfully compared to experimental FSW tests. It is believed that such a numerical model can be used to optimize FSW processing parameters to favor desirable defect free weld with better mechanical properties.
Abstract: This paper focuses on the 3D reconstruction of
the architectural design of Darul Ridzuan Museum. It has
concentrated on designing exterior part of the building according
to colored digital photo of the real museum. Besides viewing the
architecture, walkthroughs are generated for the user to control
it in an easier way. User can travel through the museum to get
the feel of the environment and to explore the design of the
museum as a whole; both exterior and interior. The result has
shown positive result in terms of realism, navigation, collision
detection, suitability, usability and user-s acceptance. In brief,
the 3D virtual museum has provided an alternative to present a
real museum.
Abstract: Rapid prototyping (RP) techniques are a group of
advanced manufacturing processes that can produce custom made
objects directly from computer data such as Computer Aided Design
(CAD), Computed Tomography (CT) and Magnetic Resonance
Imaging (MRI) data. Using RP fabrication techniques, constructs
with controllable and complex internal architecture with appropriate
mechanical properties can be achieved. One of the attractive and
promising utilization of RP techniques is related to tissue engineering
(TE) scaffold fabrication. Tissue engineering scaffold is a 3D
construction that acts as a template for tissue regeneration. Although
several conventional techniques such as solvent casting and gas
forming are utilized in scaffold fabrication; these processes show
poor interconnectivity and uncontrollable porosity of the produced
scaffolds. So, RP techniques become the best alternative fabrication
methods of TE scaffolds. This paper reviews the current state of the
art in the area of tissue engineering scaffolds fabrication using
advanced RP processes, as well as the current limitations and future
trends in scaffold fabrication RP techniques.
Abstract: Stick models are widely used in studying the
behaviour of straight as well as skew bridges and viaducts subjected
to earthquakes while carrying out preliminary studies. The
application of such models to highly curved bridges continues to
pose challenging problems. A viaduct proposed in the foothills of the
Himalayas in Northern India is chosen for the study. It is having 8
simply supported spans @ 30 m c/c. It is doubly curved in horizontal
plane with 20 m radius. It is inclined in vertical plane as well. The
superstructure consists of a box section. Three models have been
used: a conventional stick model, an improved stick model and a 3D
finite element model. The improved stick model is employed by
making use of body constraints in order to study its capabilities. The
first 8 frequencies are about 9.71% away in the latter two models.
Later the difference increases to 80% in 50th mode. The viaduct was
subjected to all three components of the El Centro earthquake of May
1940. The numerical integration was carried out using the Hilber-
Hughes-Taylor method as implemented in SAP2000. Axial forces
and moments in the bridge piers as well as lateral displacements at
the bearing levels are compared for the three models. The maximum
difference in the axial forces and bending moments and
displacements vary by 25% between the improved and finite element
model. Whereas, the maximum difference in the axial forces,
moments, and displacements in various sections vary by 35%
between the improved stick model and equivalent straight stick
model. The difference for torsional moment was as high as 75%. It is
concluded that the stick model with body constraints to model the
bearings and expansion joints is not desirable in very sharp S curved
viaducts even for preliminary analysis. This model can be used only
to determine first 10 frequency and mode shapes but not for member
forces. A 3D finite element analysis must be carried out for
meaningful results.
Abstract: Both software applications and their development environment are becoming more and more distributed. This trend impacts not only the way software computes, but also how it looks. This article proposes a Human Computer Interface (HCI) template from three representative applications we have developed. These applications include a Multi-Agent System based software, a 3D Internet computer game with distributed game world logic, and a programming language environment used in constructing distributed neural network and its visualizations. HCI concepts that are common to these applications are described in abstract terms in the template. These include off-line presentation of global entities, entities inside a hierarchical namespace, communication and languages, reconfiguration of entity references in a graph, impersonation and access right, etc. We believe the metaphor that underlies an HCI concept as well as the relationships between a bunch of HCI concepts are crucial to the design of software systems and vice versa.
Abstract: This paper present an effective method to accurately reconstruct and measure the 3D curve edges of small industrial parts based on stereo vision. To effectively fit the curve of the measured parts using a series of line segments in the images, a strategy from coarse to fine is employed based on multi-scale curve fitting. After reconstructing the 3D curve of a hole through a curved surface, its axis is adjusted so that it is parallel to the Z axis with least squares error and the dimensions of the hole can be calculated on the XY plane easily. Experimental results show that the presented method can accurately measure the dimensions of round holes through a curved surface.
Abstract: The object of this research is the design and
evaluation of an immersive Virtual Learning Environment (VLE) for
deaf children. Recently we have developed a prototype immersive
VR game to teach sign language mathematics to deaf students age K-
4 [1] [2]. In this paper we describe a significant extension of the
prototype application. The extension includes: (1) user-centered
design and implementation of two additional interactive
environments (a clock store and a bakery), and (2) user-centered
evaluation including development of user tasks, expert panel-based
evaluation, and formative evaluation. This paper is one of the few to
focus on the importance of user-centered, iterative design in VR
application development, and to describe a structured evaluation
method.
Abstract: The purpose of this study is mainly to predict collision
frequency on the horizontal tangents combined with vertical curves
using artificial neural network methods. The proposed ANN models
are compared with existing regression models. First, the variables
that affect collision frequency were investigated. It was found that
only the annual average daily traffic, section length, access density,
the rate of vertical curvature, smaller curve radius before and after
the tangent were statistically significant according to related
combinations. Second, three statistical models (negative binomial,
zero inflated Poisson and zero inflated negative binomial) were
developed using the significant variables for three alignment
combinations. Third, ANN models are developed by applying the
same variables for each combination. The results clearly show that
the ANN models have the lowest mean square error value than those
of the statistical models. Similarly, the AIC values of the ANN
models are smaller to those of the regression models for all the
combinations. Consequently, the ANN models have better statistical
performances than statistical models for estimating collision
frequency. The ANN models presented in this paper are
recommended for evaluating the safety impacts 3D alignment
elements on horizontal tangents.
Abstract: Segmentation and quantification of stenosis is an
important task in assessing coronary artery disease. One of the main
challenges is measuring the real diameter of curved vessels.
Moreover, uncertainty in segmentation of different tissues in the
narrow vessel is an important issue that affects accuracy. This paper
proposes an algorithm to extract coronary arteries and measure the
degree of stenosis. Markovian fuzzy clustering method is applied to
model uncertainty arises from partial volume effect problem. The
algorithm employs: segmentation, centreline extraction, estimation of
orthogonal plane to centreline, measurement of the degree of
stenosis. To evaluate the accuracy and reproducibility, the approach
has been applied to a vascular phantom and the results are compared
with real diameter. The results of 10 patient datasets have been
visually judged by a qualified radiologist. The results reveal the
superiority of the proposed method compared to the Conventional
thresholding Method (CTM) on both datasets.