Abstract: A new approach to predict the 3D structures of proteins by combining the knowledge-based method and Molecular Dynamics Simulation is presented on the chicken villin headpiece subdomain (HP-36). Comparative modeling is employed as the knowledge-based method to predict the core region (Ala9-Asn28) of the protein while the remaining residues are built as extended regions (Met1-Lys8; Leu29-Phe36) which then further refined using Molecular Dynamics Simulation for 120 ns. Since the core region is built based on a high sequence identity to the template (65%) resulting in RMSD of 1.39 Å from the native, it is believed that this well-developed core region can act as a 'nucleation center' for subsequent rapid downhill folding. Results also demonstrate that the formation of the non-native contact which tends to hamper folding rate can be avoided. The best 3D model that exhibits most of the native characteristics is identified using clustering method which then further ranked based on the conformational free energies. It is found that the backbone RMSD of the best model compared to the NMR-MDavg is 1.01 Å and 3.53 Å, for the core region and the complete protein, respectively. In addition to this, the conformational free energy of the best model is lower by 5.85 kcal/mol as compared to the NMR-MDavg. This structure prediction protocol is shown to be effective in predicting the 3D structure of small globular protein with a considerable accuracy in much shorter time compared to the conventional Molecular Dynamics simulation alone.
Abstract: HIV-1 genome is highly heterogeneous. Due to this
variation, features of HIV-I genome is in a wide range. For this
reason, the ability to infection of the virus changes depending on
different chemokine receptors. From this point of view, R5 HIV
viruses use CCR5 coreceptor while X4 viruses use CXCR5 and
R5X4 viruses can utilize both coreceptors. Recently, in
Bioinformatics, R5X4 viruses have been studied to classify by using
the experiments on HIV-1 genome.
In this study, R5X4 type of HIV viruses were classified using
Auto Regressive (AR) model through Artificial Neural Networks
(ANNs). The statistical data of R5X4, R5 and X4 viruses was
analyzed by using signal processing methods and ANNs. Accessible
residues of these virus sequences were obtained and modeled by AR
model since the dimension of residues is large and different from
each other. Finally the pre-processed data was used to evolve various
ANN structures for determining R5X4 viruses. Furthermore ROC
analysis was applied to ANNs to show their real performances. The
results indicate that R5X4 viruses successfully classified with high
sensitivity and specificity values training and testing ROC analysis
for RBF, which gives the best performance among ANN structures.
Abstract: The objective of this research was to investigate biodegradation of water hyacinth (Eichhornia crassipes) to produce bioethanol using dilute-acid pretreatment (1% sulfuric acid) results in high hemicellulose decomposition and using yeast (Pachysolen tannophilus) as bioethanol producing strain. A maximum ethanol yield of 1.14g/L with coefficient, 0.24g g-1; productivity, 0.015g l-1h-1 was comparable to predicted value 32.05g/L obtained by Central Composite Design (CCD). Maximum ethanol yield coefficient was comparable to those obtained through enzymatic saccharification and fermentation of acid hydrolysate using fully equipped fermentor. Although maximum ethanol concentration was low in lab scale, the improvement of lignocellulosic ethanol yield is necessary for large scale production.
Abstract: Efficient modulo 2n+1 adders are important for
several applications including residue number system, digital signal
processors and cryptography algorithms. In this paper we present a
novel modulo 2n+1 addition algorithm for a recently represented
number system. The proposed approach is introduced for the
reduction of the power dissipated. In a conventional modulo 2n+1
adder, all operands have (n+1)-bit length. To avoid using (n+1)-bit
circuits, the diminished-1 and carry save diminished-1 number
systems can be effectively used in applications. In the paper, we also
derive two new architectures for designing modulo 2n+1 adder, based
on n-bit ripple-carry adder. The first architecture is a faster design
whereas the second one uses less hardware. In the proposed method,
the special treatment required for zero operands in Diminished-1
number system is removed. In the fastest modulo 2n+1 adders in
normal binary system, there are 3-operand adders. This problem is
also resolved in this paper. The proposed architectures are compared
with some efficient adders based on ripple-carry adder and highspeed
adder. It is shown that the hardware overhead and power
consumption will be reduced. As well as power reduction, in some
cases, power-delay product will be also reduced.
Abstract: In this work, we consider the rational points on elliptic curves over finite fields Fp where p ≡ 5 (mod 6). We obtain results on the number of points on an elliptic curve y2 ≡ x3 + a3(mod p), where p ≡ 5 (mod 6) is prime. We give some results concerning the sum of the abscissae of these points. A similar case where p ≡ 1 (mod 6) is considered in [5]. The main difference between two cases is that when p ≡ 5 (mod 6), all elements of Fp are cubic residues.
Abstract: Viral influenza A subtypes H5N1 and pandemic
H1N1 (pH1N1) have worldwide emerged and transmitted. The most
common anti-influenza drug for treatment of both seasonal and
pandemic influenza viruses is oseltamivir that nowadays becomes
resistance to influenza neuraminidase. The novel long-acting drug,
laninamivir, was discovered for treatment of the patients infected
with influenza B and influenza A viruses. In the present study,
laninamivir complexed with wild-type strain of both H5N1 and
pH1N1 viruses were comparatively determined the structures and
drug-target interactions by means of molecular dynamics (MD)
simulations. The results show that the hydrogen bonding interactions
formed between laninamivir and its binding residues are likely
similar for the two systems. Additionally, the presence of
intermolecular interactions from laninamivir to the residues in the
binding pocket is established through their side chains in accordance
with hydrogen bond interactions.
Abstract: This study focuses on emission of black carbon (BC)
from field open burning of corn residues. Real-time BC
concentration was measured by Micro Aethalometer from field
burning and simulated open burning in a chamber (SOC)
experiments. The average concentration of BC was 1.18±0.47 mg/m3
in the field and 0.89±0.63 mg/m3 in the SOC. The deduced emission
factor from field experiments was 0.50±0.20 gBC/kgdm, and 0.56±0.33
gBC/kgdm from SOC experiment, which are in good agreement with
other studies. In 2007, the total burned area of corn crop was 8,000
ha, resulting in an emission load of BC 20 ton corresponding to 44.5
million kg CO2 equivalent. Therefore, the control of open burning in
corn field represents a significant global warming reduction option.
Abstract: The purpose of the present work was to study the
production and process parameters optimization for the synthesis of
cellulase from Trichoderma viride in solid state fermentation (SSF)
using an agricultural wheat straw as substrates; as fungal conversion
of lignocellulosic biomass for cellulase production is one among the
major increasing demand for various biotechnological applications.
An optimization of process parameters is a necessary step to get
higher yield of product. Several kinetic parameters like pretreatment,
extraction solvent, substrate concentration, initial moisture content,
pH, incubation temperature and inoculum size were optimized for
enhanced production of third most demanded industrially important
cellulase. The maximum cellulase enzyme activity 398.10±2.43
μM/mL/min was achieved when proximally analyzed lignocellulosic
substrate wheat straw inocubated at 2% HCl as pretreatment tool
along with distilled water as extraction solvent, 3% substrate
concentration 40% moisture content with optimum pH 5.5 at 45°C
incubation temperature and 10% inoculum size.
Abstract: The effects of irrigation with dairy factory wastewater on soil properties were investigated at two sites that had received irrigation for > 60 years. Two adjoining paired sites that had never received DFE were also sampled as well as another seven fields from a wider area around the factory. In comparison with paired sites that had not received effluent, long-term wastewater irrigation resulted in an increase in pH, EC, extractable P, exchangeable Na and K and ESP. These changes were related to the use of phosphoric acid, NaOH and KOH as cleaning agents in the factory. Soil organic C content was unaffected by DFE irrigation but the size (microbial biomass C and N) and activity (basal respiration) of the soil microbial community were increased. These increases were attributed to regular inputs of soluble C (e.g. lactose) present as milk residues in the wastewater. Principal component analysis (PCA) of the soils data from all 11sites confirmed that the main effects of DFE irrigation were an increase in exchangeable Na, extractable P and microbial biomass C, an accumulation of soluble salts and a liming effect. PCA analysis of soil bacterial community structure, using PCR-DGGE of 16S rDNA fragments, generally separated individual sites from one another but did not group them according to irrigation history. Thus, whilst the size and activity of the soil microbial community were increased, the structure and diversity of the bacterial community remained unaffected.
Abstract: To produce sugar and ethanol, sugarcane processing
generates several agricultural residues, being straw and bagasse is
considered as the main among them. And what to do with this
residues has been subject of many studies and experiences in an
industry that, in recent years, highlighted by the ability to transform
waste into valuable products such as electric power. Cellulose is the
main component of these materials. It is the most common organic
polymer and represents about 1.5 x 1012 tons of total production of
biomass per year and is considered an almost inexhaustible source of
raw material. Pretreatment with mineral acids is one of the most
widely used as stage of cellulose extraction from lignocellulosic
materials for solubilizing most of the hemicellulose content. This
study had as goal to find the best reaction time of sugarcane bagasse
pretreatment with sulfuric acid in order to minimize the losses of
cellulose concomitantly with the highest possible removal of
hemicellulose and lignin. It was found that the best time for this
reaction was 40 minutes, in which it was reached a loss of
hemicelluloses around 70% and lignin and cellulose, around 15%.
Over this time, it was verified that the cellulose loss increased and
there was no loss of lignin and hemicellulose.
Abstract: A comparative study on the feasibility of producing instant high fibre plantain flour for diabetic fufu by blending soy residence with different plantain (Musa spp) varieties (Horn, false Horn and French), all sieved at 60 mesh, mixed in ratio of 60:40 was analyzed for their passing properties using standard analytical method. Results show that VIIIS60 had the highest peak viscosity (303.75 RVU), Trough value (182.08 RVU), final viscosity (284.50 RVU), and lowest in breakdown viscosity (79.58 RVU), set back value (88.17 RVU), peak time (4.36min), pasting temperature (81.18°C) and differed significantly (p
Abstract: Trace element speciation of an integrated soil
amendment matrix was studied with a modified BCR sequential
extraction procedure. The analysis included pseudo-total
concentration determinations according to USEPA 3051A and
relevant physicochemical properties by standardized methods. Based
on the results, the soil amendment matrix possessed neutralization
capacity comparable to commercial fertilizers. Additionally, the
pseudo-total concentrations of all trace elements included in the
Finnish regulation for agricultural fertilizers were lower than the
respective statutory limit values. According to chemical speciation,
the lability of trace elements increased in the following order: Hg <
Cr < Co < Cu < As < Zn < Ni < Pb < Cd < V < Mo < Ba. The
validity of the BCR approach as a tool for chemical speciation was
confirmed by the additional acid digestion phase. Recovery of trace
elements during the procedure assured the validity of the approach
and indicated good quality of the analytical work.
Abstract: This paper introduces two decoders for binary linear
codes based on Metaheuristics. The first one uses a genetic algorithm
and the second is based on a combination genetic algorithm with
a feed forward neural network. The decoder based on the genetic
algorithms (DAG) applied to BCH and convolutional codes give good
performances compared to Chase-2 and Viterbi algorithm respectively
and reach the performances of the OSD-3 for some Residue
Quadratic (RQ) codes. This algorithm is less complex for linear
block codes of large block length; furthermore their performances
can be improved by tuning the decoder-s parameters, in particular the
number of individuals by population and the number of generations.
In the second algorithm, the search space, in contrast to DAG which
was limited to the code word space, now covers the whole binary
vector space. It tries to elude a great number of coding operations
by using a neural network. This reduces greatly the complexity of
the decoder while maintaining comparable performances.
Abstract: Investigations of the unimolecular decomposition of
vinyl ethyl ether (VEE), vinyl propyl ether (VPE) and vinyl butyl
ether (VBE) have shown that activation of the molecule of a ether
results in formation of a cyclic construction - the transition state (TS),
which may lead to the displacement of the thermodynamic
equilibrium towards the reaction products. The TS is obtained by
applying energy minimization relative to the ground state of an ether
under the program MM2 when taking into account the hydrogen bond
formation between a hydrogen atom of alkyl residue and the extreme
atom of carbon of the vinyl group. The dissociation of TS up to the
products is studied by energy minimization procedure using the
mathematical program Gaussian. The obtained calculation data for
VEE testify that the decomposition of this ether may be conditioned
by hydrogen bond formation for two possible versions: when α- or β-
hydrogen atoms of the ethyl group are bound to carbon atom of the
vinyl group. Applying the same calculation methods to other ethers
(VPE and VBE) it is shown that only in the case of hydrogen bonding
between α-hydrogen atom of the alkyl residue and the extreme atom
of carbon of the vinyl group (αH---C) results in decay of theses
ethers.
Abstract: Tea is a widely consumed beverage that contains many components. Caffeine belongs to this group of components called alkaloids contain nitrogen. In this study caffeine contents of three types of Turkish teas are determined by using extraction method. After condensation process, residue of caffeine and oil are obtained with evaporation. The oil which is in the residue is removed by hot water. Extraction process performed by using chloroform and the crude caffeine is obtained. From the results of experiments, caffeine contents are found in black tea, green tea and earl grey tea as 3.57±0.43%, 3.11±0.02%, 4.29±0.27%, respectively. Caffeine contents which are found in 1, 5 and 10 cups of tea are calculated. Furthermore, the daily intake of caffeine from black teas that affects human health is investigated.
Abstract: Attempt was made to improve certain characteristics of bio-oil derived from palm kernel pyrolysis by blending it with diesel fuel and alcohols. Two types of alcohol, ethanol or butanol, was used as cosolvent to stabilize the phase of ternary systems. Phase behaviors and basic fuel properties of palm kernel bio-oildiesel- alcohol systems were investigated in this study. Alcohol types showed a significant influence on the phase characteristics with palm kernel bio-oil-diesel-butanol system giving larger soluble area than that of palm kernel bio-oil-diesel-ethanol system. For fuel properties, blended fuels showed superior properties including lower values of density (~860 kg/m3 at 25°C), viscosity (~4.12 mm2/s at 40°C), carbon residue (1.02-2.53 wt%), ash (0.018-0.034 wt%) and pour point (
Abstract: In the present study, the incorporation of graphene
into blends of acrylonitrile-butadiene-styrene terpolymer with
polypropylene (ABS/PP) was investigated focusing on the
improvement of their thermomechanical characteristics and the effect
on their rheological behavior. The blends were prepared by melt
mixing in a twin-screw extruder and were characterized by measuring
the MFI as well as by performing DSC, TGA and mechanical tests.
The addition of graphene to ABS/PP blends tends to increase their
melt viscosity, due to the confinement of polymer chains motion.
Also, graphene causes an increment of the crystallization temperature
(Tc), especially in blends with higher PP content, because of the
reduction of surface energy of PP nucleation, which is a consequence
of the attachment of PP chains to the surface of graphene through the
intermolecular CH-π interaction. Moreover, the above nanofiller
improves the thermal stability of PP and increases the residue of
thermal degradation at all the investigated compositions of blends,
due to the thermal isolation effect and the mass transport barrier
effect. Regarding the mechanical properties, the addition of graphene
improves the elastic modulus, because of its intrinsic mechanical
characteristics and its rigidity, and this effect is particularly strong in
the case of pure PP.
Abstract: Organochlorine pesticides (OCPs) are known to be
persistent and bioaccumulative toxicants that may cause reproductive
impairments in wildlife as well as human. The current study uses the
snail-eating turtle Malayemys macrocephala, a long-lived animal
commonly distribute in rice field habitat in central part of Thailand,
as a sentinel to monitor OCP contamination in environment. The
nest soil, complete clutch of eggs, and blood of the turtle were
collected from agricultural areas in the Chao Phraya River Basin,
Thailand during the nesting season of 2007-2008. The novel
methods for tissue extraction by an accelerated solvent extractor
(ASE, for egg) and liquid-liquid extraction (for blood) have been
developed. The nineteen OCP residues were analyzed by gas
chromatography with micro-electron captured detector (GC-μECD).
The validated methods have met requirements of the AOAC
standard. The results indicated that significant amounts of OCPs are
still contaminated in nest soil and eggs of the turtle even though the
OCPs had been banned in this area for many years. This suggested
the potential risk to health of wildlife as well as human in the area.
Abstract: Offset Double-Disk Opener (DDO) is a popular
furrow opener in conservation tillage. It has some limitations such as
negative suction to penetrate in the soil, hair pinning and mixing seed
and fertilizer in the slot. Because of importance of separation of seed
and fertilizer in the slot, by adding two horizontal mini disks to DDO
a modified opener was made (MDO) which placed the fertilizer
between and under two rows of seed. To consider performance of
novel opener an indoor comparison test between DDO and MDO was
performed at soil bin. The experiment was conducted with three
working speeds (3, 6 and 8 km h-1), two bulk densities of soil (1.1
and 1.4 Mg m-3) and two levels of residues (1 and 2 ton ha-1). The
experimental design consisted in a (3×2×2) complete randomized
factorial with three replicates for each test. Moisture of seed furrow,
separation of seed and fertilizer, hair pinning and resultant forces
acting on the openers were used as assessing indexes. There was no
significant difference between soil moisture content in slots created
by DDO and MDO at 0-4 cm depth, but at 4-8 cm the in the slot
created by MDO moisture content was higher about 9%. Horizontal
force for both openers increased with increasing speed and soil bulk
density. Vertical force for DDO was negative so it needed additional
weight for penetrating in the soil, but vertical force for MDO was
positive and, which can solve the challenge of penetration in the soil
in DDO. In soft soil with heavy residues some trash was pushed by
DDO into seed furrow (hair pinning) but at MDO seed were placed at
clean groove. Lateral and vertical separation of seed and fertilizer
was performed effectively by MDO (4.5 and 5 cm, respectively)
while DDO put seed and fertilizer close to each other. Overall, the
Modified Offset Double-disks (MDO) had better performance. So by
adapting this opener with no-tillage drillers it would possible to have
higher yield in conservation tillage where the most appropriate
opener is disk type.
Abstract: As embedded and portable systems were emerged power consumption of circuits had been major challenge. On the other hand latency as determines frequency of circuits is also vital task. Therefore, trade off between both of them will be desirable. Modulo 2n+1 adders are important part of the residue number system (RNS) based arithmetic units with the interesting moduli set (2n-1,2n, 2n+1). In this manuscript we have introduced novel binary representation to the design of modulo 2n+1 adder. VLSI realization of proposed architecture under 180 nm full static CMOS technology reveals its superiority in terms of area, power consumption and power-delay product (PDP) against several peer existing structures.