Abstract: Protein-protein interactions (PPI) play a crucial role in many biological processes such as cell signalling, transcription, translation, replication, signal transduction, and drug targeting, etc. Structural information about protein-protein interaction is essential for understanding the molecular mechanisms of these processes. Structures of protein-protein complexes are still difficult to obtain by biophysical methods such as NMR and X-ray crystallography, and therefore protein-protein docking computation is considered an important approach for understanding protein-protein interactions. However, reliable prediction of the protein-protein complexes is still under way. In the past decades, several grid-based docking algorithms based on the Katchalski-Katzir scoring scheme were developed, e.g., FTDock, ZDOCK, HADDOCK, RosettaDock, HEX, etc. However, the success rate of protein-protein docking prediction is still far from ideal. In this work, we first propose a more practical measure for evaluating the success of protein-protein docking predictions,the rate of first success (RFS), which is similar to the concept of mean first passage time (MFPT). Accordingly, we have assessed the ZDOCK bound and unbound benchmarks 2.0 and 3.0. We also createda new benchmark set for protein-protein docking predictions, in which the complexes have experimentally determined binding affinity data. We performed free energy calculation based on the solution of non-linear Poisson-Boltzmann equation (nlPBE) to improve the binding mode prediction. We used the well-studied thebarnase-barstarsystem to validate the parameters for free energy calculations. Besides,thenlPBE-based free energy calculations were conducted for the badly predicted cases by ZDOCK and ZRANK. We found that direct molecular mechanics energetics cannot be used to discriminate the native binding pose from the decoys.Our results indicate that nlPBE-based calculations appeared to be one of the promising approaches for improving the success rate of binding pose predictions.
Abstract: In a 10-week (May – August, 2008) Phase I trial, 840, 1+ rainbow trout, Oncorhynchus mykiss, received a commercial oral immunomodulator, Fin Immune™, at four different dosages (0, 10, 20 and 30 mg g-1) to evaluate immune response and growth. The overall objective of was to determine an optimal dosage of this product for rainbow trout that provides enhanced immunity with maximal growth and health. Biweekly blood samples were taken from 10 randomly selected fish in each tank (30 samples per treatment) to evaluate the duration of enhanced immunity conferred by Fin-Immune™. The immunological assessment included serum white blood cell (lymphocyte, neutrophil) densities and blood hematocrit (packed cell volume %). Of these three variables, only lymphocyte density increased significantly among trout fed Fin- Immune™ at 20 and 30 mg g-1 which peaked at week 6. At week 7, all trout were switched to regular feed (lacking Fin-Immune™) and by week 10, lymphocyte levels decreased among all levels but were still greater than at week 0. There was growth impairment at the highest dose of Fin-Immune™ tested (30 mg g-1) which can be associated with a physiological compensatory mechanism due to a dose-specific threshold level. Thus, our main objective of this Phase I study was achieved, the 20 mg g-1 dose of Fin-Immune™ should be the most efficacious (of those we tested) to use for a Phase II disease challenge trial.
Abstract: In this paper we study the inverse eigenvalue problem for symmetric special matrices and introduce sufficient conditions for obtaining nonnegative matrices. We get the HROU algorithm from [1] and introduce some extension of this algorithm. If we have some eigenvectors and associated eigenvalues of a matrix, then by this extension we can find the symmetric matrix that its eigenvalue and eigenvectors are given. At last we study the special cases and get some remarkable results.
Abstract: The Constraints imposed by non-thermal
leptogenesis on the survival of the neutrino mass models describing
the presently available neutrino mass patterns, are studied
numerically. We consider the Majorana CP violating phases coming
from right-handed Majorana mass matrices to estimate the baryon
asymmetry of the universe, for different neutrino mass models
namely quasi-degenerate, inverted hierarchical and normal
hierarchical models, with tribimaximal mixings. Considering two
possible diagonal forms of Dirac neutrino mass matrix as either
charged lepton or up-quark mass matrix, the heavy right-handed
mass matrices are constructed from the light neutrino mass matrix.
Only the normal hierarchical model leads to the best predictions of
baryon asymmetry of the universe, consistent with observations in
non-thermal leptogenesis scenario.
Abstract: Banyan networks are really attractive for serving as
the optical switching architectures due to their unique properties of
small depth and absolute signal loss uniformity. The fact has been
established that the limitations of blocking nature and the nonavailability
of proper connections due to non-rearrangeable property
can be easily ruled out using electro-optic MZI switches as basic
switching elements. Combination of the horizontal expansion and
vertical stacking of optical banyan networks is an appropriate scheme
for constructing non-blocking banyan-based optical switching
networks. The interconnected banyan switching fabrics (IBSF) have
been considered and analyzed to best serve the purpose of optical
switching with electro-optic MZI basic elements. The cross/bar state
interchange for the switches has been facilitated by appropriate
voltage switching or the by the switching of operating wavelength.
The paper is dedicated to the modification of the basic switching
element being used as well as the architecture of the switching
network.
Abstract: This paper contributes to our knowledge about buyerseller
relations by identifying barriers and conflict situations
associated with maintaining and developing durable business
relationships by small companies. The contribution of prior studies
with regard to negative aspects of marketing relationships is
presented in the first section. The international research results are
discussed with regard to the existing conceptualizations and main
research implications identified at the end.
Abstract: In the present paper, Fatigue life assessment of an
anti-roll bar component of a passenger vehicle, is investigated by
ANSYS 11 software. A stress analysis is also carried out by the
finite element technique for the determination of highly stressed
regions on the bar. Anti-roll bar is a suspension element used at the
front, rear, or at both ends of a car that reduces body roll by resisting
any unequal vertical motion between the pair of wheels to which it is
connected. As a first stage, fatigue damage models proposed by some
well-known references and the corresponding assumptions are
discussed and some enhancements are proposed. Then, fracture
analysis of an anti-roll bar of an automobile is carried out. The
analysed type of the anti-roll bar is especially important as many
cases are reported about the fracture after a 100,000 km of travel
fatigue and fracture conditions. This paper demonstrates fatigue life
of an anti-roll bar and then evaluated by experimental analytically
results from other researcher.
Abstract: Leprosy is an infectious disease caused by
Mycobacterium Leprae, this disease, generally, compromises
the neural fibers, leading to the development of disability.
Disabilities are changes that limit daily activities or social life
of a normal individual. When comes to leprosy, the study of
disability considered the functional limitation (physical
disabilities), the limitation of activity and social participation,
which are measured respectively by the scales: EHF, SALSA
and PARTICIPATION SCALE. The objective of this work is
to propose an on-line monitoring of leprosy patients, which is
based on information scales EHF, SALSA and
PARTICIPATION SCALE. It is expected that the proposed
system is applied in monitoring the patient during treatment
and after healing therapy of the disease. The correlations that
the system is between the scales create a variety of
information, presented the state of the patient and full of
changes or reductions in disability. The system provides
reports with information from each of the scales and the
relationships that exist between them. This way, health
professionals, with access to patient information, can
intervene with techniques for the Prevention of Disability.
Through the automated scale, the system shows the level of
the patient and allows the patient, or the responsible, to take a
preventive measure. With an online system, it is possible take
the assessments and monitor patients from anywhere.
Abstract: WikID is a wiki for industrial design engineers. An
important aspect for the viability of a wiki is the loyalty of the user
community to share their information and knowledge by adding this
knowledge to the wiki. For the initiators of a wiki it is therefore
important to use every aspect to stimulate the user community to
actively participate. In this study the focus is on the styling of the
website. The central question is: How could the WikID website be
visually designed to achieve a user experience which will incite the
user to actively participate in the WikID community? After a
literature study on the influencing factors of a website, a new
interface has been designed by applying the rules found, in order to
expand this website-s active user community. An online
questionnaire regarding the old or the new website gave insights in
the opinions of users. As expected, the new website was rated more
positively than the old website. However, the differences are limited.
Abstract: Chikungunya virus (CHICKV) is an arboviruses belonging to family Tagoviridae and is transmitted to human through by mosquito (Aedes aegypti and Aedes albopictus) bite. A large outbreak of chikungunya has been reported in India between 2006 and 2007, along with several other countries from South-East Asia and for the first time in Europe. It was for the first time that the CHICKV outbreak has been reported with mortality from Reunion Island and increased mortality from Asian countries. CHICKV affects all age groups, and currently there are no specific drugs or vaccine to cure the disease. The need of antiviral agents for the treatment of CHICKV infection and the success of virtual screening against many therapeutically valuable targets led us to carry out the structure based drug design against Chikungunya nSP2 protease (PDB: 3TRK). Highthroughput virtual screening of publicly available databases, ZINC12 and BindingDB, has been carried out using the Openeye tools and Schrodinger LLC software packages. Openeye Filter program has been used to filter the database and the filtered outputs were docked using HTVS protocol implemented in GLIDE package of Schrodinger LLC. The top HITS were further used for enriching the similar molecules from the database through vROCS; a shape based screening protocol implemented in Openeye. The approach adopted has provided different scaffolds as HITS against CHICKV protease. Three scaffolds: Indole, Pyrazole and Sulphone derivatives were selected based on the docking score and synthetic feasibility. Derivatives of Pyrazole were synthesized and submitted for antiviral screening against CHICKV.
Abstract: This study investigated morphology of the Spanner Barb (Puntius lateristriga Valenciennes, 1842) and water quality at Thepchana waterfall. This study was conducted at Thepchana Waterfall, Khao Nan National Park from March to May 2007. There were 40 Spanner Barb collected with 20 males and 20 females. Males had an average of 5.57 cm in standard length, 6.62 cm in total length and 5.18 g in total body weight. Females had an average of 7.25 cm in standard length, 8.24 cm in total length and 10.96 g in total body weight. The length (L) – weight (W) relationships for combining sexes, males and females were LogW = -2.137 + 3.355logL, log W = -0.068 + 3.297logL, and log W = -2.068 + 3.297logL, respectively. The Spanner Barb were smaller size fish with a compressed form; terminal mouth; villiform teeth; ctenoid scale; concave tail; general body color yellowish olive, with slight reddish tint to fins; vertical band beginning below dorsal and horizontal stripe from base of tail almost to vertical band. They also had a vertical band midway between the eye and first vertical band. There was a black spot above anal fin. The bladder looked like J-shape. Inside of the bladder was found small insects and insect lava. The body length and the bowels length was 1:1 ratio. The water temperature ranged from 25.00 – 27.00 °C which was appropriate for their habitat characteristics. Acid - alkalinity ranged from 6.65 – 6.90 mg/l. Dissolved oxygen ranged from 4.55 – 4.70 mg/l. Water hardness ranged from 31.00 – 48.00 mg/l. The amount of ammonia was about 0.25 mg/l.
Abstract: A major challenge in biomaterials research is the
regulation of protein adsorption which is a key factor for controlling
the subsequent cell adhesion at implant surfaces. The aim of the
present study was to control the adsorption of fibronectin (FN) and
the attachment of MG-63 osteoblasts with an electronic
nanostructure. Shallow doping line lattices with a period of 260 nm
were produced for this purpose by implantation of phosphorous in
silicon wafers. Protein coverage was determined after incubating the
substrate with FN by means of an immunostaining procedure and the
measurement of the fluorescence intensity with a TECAN analyzer.
We observed an increased amount of adsorbed FN on the
nanostructure compared to control substrates. MG-63 osteoblasts
were cultivated for 24h on FN-incubated substrates and their
morphology was assessed by SEM. Preferred orientation and
elongation of the cells in direction of the doping lattice lines was
observed on FN-coated nanostructures.
Abstract: Thermally insulating ceramic coatings also known as
thermal barrier coatings (TBCs) have been essential technologies to
improve the performance and efficiency of advanced gas turbines in
service at extremely high temperatures. The damage mechanisms of
air-plasma sprayed YSZ thermal barrier coatings (TBC) with various
microstructures were studied by microscopic techniques after thermal
cycling. The typical degradation of plasma TBCs that occurs during
cyclic furnace testing of an YSZ and alumina coating on a Titanium
alloy are analyzed. During the present investigation the effects of
topcoat thickness, bond coat oxidation, thermal cycle lengths and test
temperature are investigated using thermal cycling. These results
were correlated with stresses measured by a spectroscopic technique
in order to understand specific damage mechanism. The failure
mechanism of former bond coats was found to involve fracture
initiation at the thermally grown oxide (TGO) interface and at the
TGO bond coat interface. The failure mechanism of the YZ was
found to involve combination of fracture along the interface between
TGO and bond coat.
Abstract: Tip vortex cavitation is one of well known patterns of
cavitation phenomenon which occurs in axial pumps. This pattern of
cavitation occurs due to pressure difference between the pressure and
suction sides of blades of an axial pump. Since the pressure in the
pressure side of the blade is higher than the pressure in its suction
side, thus a very small portion of liquid flow flows back from
pressure side to the suction side. This fact is cause of tip vortex
cavitation and gap cavitation that may occur in axial pumps. In this
paper the results of our experimental investigation about movement
of tip vortex cavitation along blade edge due to reduction of pump
flow rate in an axial pump is reported. Results show that reduction of
pump flow rate in conjunction with increasing of outlet pressure
causes movement of tip vortex cavitation along blade edge towards
the blade tip. Results also show that by approaching tip vortex
cavitation to the blade tip, vortex tip pattern of cavitation replaces
with a cavitation phenomenon on the blade tip. Furthermore by
further reduction of pump flow rate and increasing of outlet pressure,
an unstable cavitation phenomenon occurs between each blade
leading edge and the next blade trailing edge.
Abstract: Polyphenolics and sugar are the components of many
fruit juices. In this work, the performance of ultra-filtration (UF) for
separating phenolic compounds from apple juice was studied by
performing batch experiments in a membrane module with an area of
0.1 m2 and fitted with a regenerated cellulose membrane of 1 kDa
MWCO. The effects of various operating conditions: transmembrane
pressure (3, 4, 5 bar), temperature (30, 35, 40 ºC), pH (2, 3, 4, 5),
feed concentration (3, 5, 7, 10, 15 ºBrix for apple juice) and feed flow
rate (1, 1.5, 1.8 L/min) on the performance were determined.
The optimum operating conditions were: transmembrane pressure
4 bar, temperature 30 ºC, feed flow rate 1 – 1.8 L/min, pH 3 and 10
Brix (apple juice). After performing ultrafiltration under these
conditions, the concentration of polyphenolics in retentate was
increased by a factor of up to 2.7 with up to 70% recovered in the
permeate and with approx. 20% of the sugar in that stream..
Application of diafiltration (addition of water to the concentrate) can
regain the flux by a factor of 1.5, which has been decreased due to
fouling. The material balance performed on the process has shown
the amount of deposits on the membrane and the extent of fouling in
the system. In conclusion, ultrafiltration has been demonstrated as a
potential technology to separate the polyphenolics and sugars from
their mixtures and can be applied to remove sugars from fruit juice.
Abstract: Conventional concentrically-braced frame (CBF)
systems have limited drift capacity before brace buckling and related
damage leads to deterioration in strength and stiffness. Self-centering
concentrically-braced frame (SC-CBF) systems have been developed
to increase drift capacity prior to initiation of damage and minimize
residual drift. SC-CBFs differ from conventional CBFs in that the
SC-CBF columns are designed to uplift from the foundation at a
specified level of lateral loading, initiating a rigid-body rotation
(rocking) of the frame. Vertically-aligned post-tensioning bars resist
uplift and provide a restoring force to return the SC-CBF columns to
the foundation (self-centering the system). This paper presents a
parametric study of different prototype buildings using SC-CBFs.
The bay widths of the SC-CBFs have been varied in these buildings
to study different geometries. Nonlinear numerical analyses of the
different SC-CBFs are presented to illustrate the effect of frame
geometry on the behavior and dynamic response of the SC-CBF
system.
Abstract: Polymer-like organic thin films were deposited on both
aluminum alloy type 6061 and glass substrates at room temperature by
Plasma Enhanced Chemical Vapor Deposition (PECVD) methodusing
benzene and hexamethyldisiloxane (HMDSO) as precursor materials.
The surface and physical properties of plasma-polymerized organic
thin films were investigated at different r.f. powers. The effects of
benzene/argon ratio on the properties of plasma polymerized benzene
films were also investigated. It is found that using benzene alone
results in a non-coherent and non-adherent powdery deposited
material. The chemical structure and surface properties of the asgrown
plasma polymerized thin films were analyzed on glass
substrates with FTIR and contact angle measurements. FTIR spectra
of benzene deposited film indicated that the benzene rings are
preserved when increasing benzene ratio and/or decreasing r.f.
powers. FTIR spectra of HMDSO deposited films indicated an
increase of the hydrogen concentration and a decrease of the oxygen
concentration with the increase of r.f. power. The contact angle (θ) of
the films prepared from benzene was found to increase by about 43%
as benzene ratio increases from 10% to 20%. θ was then found to
decrease to the original value (51°) when the benzene ratio increases
to 100%. The contact angle, θ, for both benzene and HMDSO
deposited films were found to increase with r.f. power. This signifies
that the plasma polymerized organic films have substantially low
surface energy as the r.f power increases. The corrosion resistance of
aluminum alloy substrate both bare and covered with plasma
polymerized thin films was carried out by potentiodynamic
polarization measurements in standard 3.5 wt. % NaCl solution at
room temperature. The results indicate that the benzene and HMDSO
deposited films are suitable for protection of the aluminum substrate
against corrosion. The changes in the processing parameters seem to
have a strong influence on the film protective ability. Surface
roughness of films deposited on aluminum alloy substrate was
investigated using scanning electron microscopy (SEM). The SEM
images indicate that the surface roughness of benzene deposited films
increase with decreasing the benzene ratio. SEM images of benzene
and HMDSO deposited films indicate that the surface roughness
decreases with increasing r.f. power. Studying the above parameters
indicate that the films produced are suitable for specific practical
applications.
Abstract: The hidden-point bar method is useful in many
surveying applications. The method involves determining the
coordinates of a hidden point as a function of horizontal and vertical
angles measured to three fixed points on the bar. Using these
measurements, the procedure involves calculating the slant angles,
the distances from the station to the fixed points, the coordinates of
the fixed points, and then the coordinates of the hidden point. The
propagation of the measurement errors in this complex process has
not been fully investigated in the literature. This paper evaluates the
effect of the bar geometry on the position accuracy of the hidden
point which depends on the measurement errors of the horizontal and
vertical angles. The results are used to establish some guidelines
regarding the inclination angle of the bar and the location of the
observed points that provide the best accuracy.
Abstract: This paper proposes a bi-objective model for the
facility location problem under a congestion system. The idea of the
model is motivated by applications of locating servers in bank
automated teller machines (ATMS), communication networks, and so
on. This model can be specifically considered for situations in which
fixed service facilities are congested by stochastic demand within
queueing framework. We formulate this model with two perspectives
simultaneously: (i) customers and (ii) service provider. The
objectives of the model are to minimize (i) the total expected
travelling and waiting time and (ii) the average facility idle-time.
This model represents a mixed-integer nonlinear programming
problem which belongs to the class of NP-hard problems. In addition,
to solve the model, two metaheuristic algorithms including nondominated
sorting genetic algorithms (NSGA-II) and non-dominated
ranking genetic algorithms (NRGA) are proposed. Besides, to
evaluate the performance of the two algorithms some numerical
examples are produced and analyzed with some metrics to determine
which algorithm works better.
Abstract: In order to meet environmental norms, Indian fuel
policy aims at producing ultra low sulphur diesel (ULSD) in near
future. A catalyst for meeting such requirements has been developed
and kinetics of this catalytic process is being looked into. In the
present investigations, effect of mass transfer on kinetics of ultra deep
hydrodesulphurization (UDHDS) to produce ULSD has been studied
to determine intrinsic kinetics over a pre-sulphided catalyst.
Experiments have been carried out in a continuous flow micro reactor
operated in the temperature range of 330 to 3600C, whsv of 1 hr-1 at a
pressure of 35 bar, and its parameters estimated. Based on the derived
rate expression and estimated parameters optimum operation range
has been determined for this UDHDS catalyst to obtain ULSD
product.