Abstract: Cluster analysis divides data into groups that are
meaningful, useful, or both. Analysis of biological data is creating a
new generation of epidemiologic, prognostic, diagnostic and
treatment modalities. Clustering of protein sequences is one of the
current research topics in the field of computer science. Linear
relation is valuable in rule discovery for a given data, such as if value
X goes up 1, value Y will go down 3", etc. The classical linear
regression models the linear relation of two sequences perfectly.
However, if we need to cluster a large repository of protein sequences
into groups where sequences have strong linear relationship with
each other, it is prohibitively expensive to compare sequences one by
one. In this paper, we propose a new technique named General
Regression Model Technique Clustering Algorithm (GRMTCA) to
benignly handle the problem of linear sequences clustering. GRMT
gives a measure, GR*, to tell the degree of linearity of multiple
sequences without having to compare each pair of them.
Abstract: Limited infrastructure development on peats and
organic soils is a serious geotechnical issues common to many
countries of the world especially Malaysia which distributed 1.5 mill
ha of those problematic soil. These soils have high water content and
organic content which exhibit different mechanical properties and
may also change chemically and biologically with time. Constructing
structures on peaty ground involves the risk of ground failure and
extreme settlement. Nowdays, much efforts need to be done in
making peatlands usable for construction due to increased landuse.
Deep mixing method employing cement as binders, is generally used
as measure again peaty/ organic ground failure problem. Where the
technique is widely adopted because it can improved ground
considerably in a short period of time. An understanding of
geotechnical properties as shear strength, stiffness and compressibility
behavior of these soils was requires before continues construction on
it. Therefore, 1- 1.5 meter peat soil sample from states of Johor and
an organic soil from Melaka, Malaysia were investigated. Cement
were added to the soil in the pre-mixing stage with water cement ratio
at range 3.5,7,14,140 for peats and 5,10,30 for organic soils,
essentially to modify the original soil textures and properties. The
mixtures which in slurry form will pour to polyvinyl chloride (pvc)
tube and cured at room temperature 250C for 7,14 and 28 days.
Laboratory experiments were conducted including unconfined
compressive strength and bender element , to monitor the improved
strength and stiffness of the 'stabilised mixed soils'. In between,
scanning electron miscroscopic (SEM) were observations to
investigate changes in microstructures of stabilised soils and to
evaluated hardening effect of a peat and organic soils stabilised
cement. This preliminary effort indicated that pre-mixing peat and
organic soils contributes in gaining soil strength while help the
engineers to establish a new method for those problematic ground
improvement in further practical and long term applications.
Abstract: Monitoring of microbial flora in aquacultured sea bream, in relation to the physicochemical parameters of the rearing seawater, ended to a model describing the influence of the last to the quality of the fisheries. Fishes were sampled during eight months from four aqua farms in Western Greece and analyzed for psychrotrophic, H2S producing bacteria, Salmonella sp., heterotrophic plate count (PCA), with simultaneous physical evaluation. Temperature, dissolved oxygen, pH, conductivity, TDS, salinity, NO3 - and NH4 + ions were recorded. Temperature, dissolved oxygen and conductivity were correlated, respectively, to PCA, Pseudomonas sp. and Shewanella sp. counts. These parameters were the inputs of the model, which was driving, as outputs, to the prediction of PCA, Vibrio sp., Pseudomonas sp. and Shewanella sp. counts, and fish microbiological quality. The present study provides, for the first time, a ready-to-use predictive model of fisheries hygiene, leading to an effective management system for the optimization of aquaculture fisheries quality.
Abstract: The agriculture lignocellulosic by-products are receiving increased attention, namely in the search for filter materials that retain contaminants from water. These by-products, specifically almond and hazelnut shells are abundant in Portugal once almond and hazelnuts production is a local important activity. Hazelnut and almond shells have as main constituents lignin, cellulose and hemicelluloses, water soluble extractives and tannins. Along the adsorption of heavy metals from contaminated waters, water soluble compounds can leach from shells and have a negative impact in the environment. Usually, the chemical characterization of treated water by itself may not show environmental impact caused by the discharges when parameters obey to legal quality standards for water. Only biological systems can detect the toxic effects of the water constituents. Therefore, the evaluation of toxicity by biological tests is very important when deciding the suitability for safe water discharge or for irrigation applications.
The main purpose of the present work was to assess the potential impacts of waters after been treated for heavy metal removal by hazelnut and almond shells adsorption systems, with short term acute toxicity tests.
To conduct the study, water at pH 6 with 25 mg.L-1 of lead, was treated with 10 g of shell per litre of wastewater, for 24 hours. This procedure was followed for each bark. Afterwards the water was collected for toxicological assays; namely bacterial resistance, seed germination, Lemna minor L. test and plant grow. The effect in isolated bacteria strains was determined by disc diffusion method and the germination index of seed was evaluated using lettuce, with temperature and humidity germination control for 7 days. For aquatic higher organism, Lemnas were used with 4 days contact time with shell solutions, in controlled light and temperature. For terrestrial higher plants, biomass production was evaluated after 14 days of tomato germination had occurred in soil, with controlled humidity, light and temperature.
Toxicity tests of water treated with shells revealed in some extent effects in the tested organisms, with the test assays showing a close behaviour as the control, leading to the conclusion that its further utilization may not be considered to create a serious risk to the environment.
Abstract: The study of proteomics reached unexpected levels of
interest, as a direct consequence of its discovered influence over some
complex biological phenomena, such as problematic diseases like
cancer. This paper presents the latest authors- achievements regarding
the analysis of the networks of proteins (interactome networks), by
computing more efficiently the betweenness centrality measure. The
paper introduces the concept of betweenness centrality, and then
describes how betweenness computation can help the interactome net-
work analysis. Current sequential implementations for the between-
ness computation do not perform satisfactory in terms of execution
times. The paper-s main contribution is centered towards introducing
a speedup technique for the betweenness computation, based on
modified shortest path algorithms for sparse graphs. Three optimized
generic algorithms for betweenness computation are described and
implemented, and their performance tested against real biological
data, which is part of the IntAct dataset.
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: Quantitative trait loci (QTL) experiments have yielded
important biological and biochemical information necessary for
understanding the relationship between genetic markers and
quantitative traits. For many years, most QTL algorithms only
allowed one observation per genotype. Recently, there has been an
increasing demand for QTL algorithms that can accommodate more
than one observation per genotypic distribution. The Bayesian
hierarchical model is very flexible and can easily incorporate this
information into the model. Herein a methodology is presented that
uses a Bayesian hierarchical model to capture the complexity of the
data. Furthermore, the Markov chain Monte Carlo model composition
(MC3) algorithm is used to search and identify important markers. An
extensive simulation study illustrates that the method captures the
true QTL, even under nonnormal noise and up to 6 QTL.
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: Starting from a biologically inspired framework, Gabor filters were built up from retinal filters via LMSE algorithms. Asubset of retinal filter kernels was chosen to form a particular Gabor filter by using a weighted sum. One-dimensional optimization approaches were shown to be inappropriate for the problem. All model parameters were fixed with biological or image processing constraints. Detailed analysis of the optimization procedure led to the introduction of a minimization constraint. Finally, quantization of weighting factors was investigated. This resulted in an optimized cascaded structure of a Gabor filter bank implementation with lower computational cost.
Abstract: The purpose of present paper was to investigate
perceptions of Korean secondary school students about social issues
related to biological sciences. Twenty issues were selected based on
topics of articles in the newspaper from 2005 to 2010. The issues were
categorized into biotechnology, health-disease and environment
domains. Subjects were 541 high school students (male 253 and
female 288). On the survey, students were asked to answer on 5-point
Lickert scales how they thought of the effect of biological phenomena
or events related to biological issues on the individual life and the
society. They perceived that the biological issues would be more
effectible on the society than on the individual life. Female students
had a little more perceptions than males.
Abstract: Alpfa-fetoprotein and its fragments may be an important vehicle for targeted delivery of radionuclides to the tumor. We investigated the effect of conditions on the labeling of biologically active synthetic peptide based on the (F-afp) with technetium-99m. The influence of the nature of the buffer solution, pH, concentration of reductant, concentration of the peptide and the reaction temperature on the yield of labeling was examined. As a result, the following optimal conditions for labeling of (F-afp) are found: pH 8.5 (phosphate and bicarbonate buffers) and pH from 1.7 to 7.0 (citrate buffer). The reaction proceeds with sufficient yield at room temperature for 30 min at the concentration of SnCl2 and (Fafp) (F-afp) is to be less than 10 mkg/ml and 25 mkg/ml, respectively. Investigations of the test drug accumulation in the tumor cells of human breast cancer were carried out. Results can be assumed that the in vivo study of the (F-afp) in experimental tumor lesions will show concentrations sufficient for imaging these lesions by SPECT.
Abstract: The study of proteomics reached unexpected levels of
interest, as a direct consequence of its discovered influence over
some complex biological phenomena, such as problematic diseases
like cancer. This paper presents a new technique that allows for an
accurate analysis of the human interactome network. It is basically
a two-step analysis process that involves, at first, the detection of
each protein-s absolute importance through the betweenness centrality
computation. Then, the second step determines the functionallyrelated
communities of proteins. For this purpose, we use a community
detection technique that is based on the edge betweenness
calculation. The new technique was thoroughly tested on real biological
data and the results prove some interesting properties of those proteins that are involved in the carcinogenesis process. Apart from its
experimental usefulness, the novel technique is also computationally
effective in terms of execution times. Based on the analysis- results, some topological features of cancer mutated proteins are presented
and a possible optimization solution for cancer drugs design is suggested.
Abstract: A computational platform is presented in this
contribution. It has been designed as a virtual laboratory to be used
for exploring optimization algorithms in biological problems. This
platform is built on a blackboard-based agent architecture. As a test
case, the version of the platform presented here is devoted to the
study of protein folding, initially with a bead-like description of the
chain and with the widely used model of hydrophobic and polar
residues (HP model). Some details of the platform design are
presented along with its capabilities and also are revised some
explorations of the protein folding problems with different types of
discrete space. It is also shown the capability of the platform to
incorporate specific tools for the structural analysis of the runs in
order to understand and improve the optimization process.
Accordingly, the results obtained demonstrate that the ensemble of
computational tools into a single platform is worthwhile by itself,
since experiments developed on it can be designed to fulfill different
levels of information in a self-consistent fashion. By now, it is being
explored how an experiment design can be useful to create a
computational agent to be included within the platform. These
inclusions of designed agents –or software pieces– are useful for the
better accomplishment of the tasks to be developed by the platform.
Clearly, while the number of agents increases the new version of the
virtual laboratory thus enhances in robustness and functionality.
Abstract: Bean common mosaic necrosis virus (BCMNV) is a
potyvirus with a worldwide distribution. This virus causes serious
economic losses in Iran in many leguminoses. During 20008,
samples were collected from soybeans fields in Tehran Province.
Four isolates (S1, S2 and S3) were inoculated on 15 species of
Cucurbitaceae, Chenopodiaceae, Solanacae and Leguminosae.
Chenopodium quinoa and C. amaranticolor.
Did not developed any symptoms.all isolates caused mosaic
symptoms on Phaseolus vulgaris cv. Red Kidney and P. vulgaris cv.
Bountiful. The molecular weights of coat protein using SDS-PAGE
and western blotting were estimated at 33 kDa. Reverse transcription
polymerase chain reaction (RT-PCR) was performed using one
primer pairs designed by L. XU et al. An approximately 920 bp
fragment was amplified with a specific primer.
Abstract: fibers of pure cellulose can be made from some bacteria such as acetobacter xylinum. Bacterial cellulose fibers are very pure, tens of nm across and about 0.5 micron long. The fibers are very stiff and, although nobody seems to have measured the strength of individual fibers. Their stiffness up to 70 GPa. Fundamental strengths should be at least greater than those of the best commercial polymers, but best bulk strength seems to about the same as that of steel. They can potentially be produced in industrial quantities at greatly lowered cost and water content, and with triple the yield, by a new process. This article presents a critical review of the available information on the bacterial cellulose as a biological nonwoven fabric with special emphasis on its fermentative production and applications. Characteristics of bacterial cellulose biofabric with respect to its structure and physicochemical properties are discussed. Current and potential applications of bacterial cellulose in textile, nonwoven cloth, paper, films synthetic fiber coating, food, pharmaceutical and other industries are also presented.
Abstract: The feasibility of employing solar radiation for
enhanced Fenton process in degradation of combined chlorpyrifos,
cypermethrin and chlorothalonil pesticides was examined. The effect
of various operating conditions of the process on biodegradability
improvement and mineralization of the pesticides were also
evaluated. The optimum operating conditions for treatment of
aqueous solution containing 100, 50 and 250 mg L-1 chlorpyrifos
cypermethrin and chlorothalonil, respectively were observed to be
H2O2/COD molar ratio 2, H2O2/Fe2+ molar ratio 25 and pH 3. Under
the optimum operating conditions, complete degradation of the
pesticides occurred in 1 min. Biodegradability (BOD5/COD)
increased from zero to 0.36 in 60 min, and COD and TOC removal
were 74.19 and 58.32%, respectively in 60 min. Due to
mineralization of organic carbon, decrease in ammonia-nitrogen from
22 to 4.3 mg L-1 and increase in nitrate from 0.7 to 18.1 mg L-1 in
60 min were recorded. The study indicated that solar photo-Fenton
process can be used for pretreatment of chlorpyrifos, cypermethrin
and chlorothalonil pesticides in aqueous solution for further
biological treatment.
Abstract: The characterization of κ-carrageenan could provide a
better understanding of its functions in biological, medical and
industrial applications. Chemical and physical analyses of
carrageenan from seaweeds, Euchema cottonii L., were done to offer
information on its properties and the effects of Co-60 γ-irradiation on
its thermochemical characteristics. The structural and morphological
characteristics of κ-carrageenan were determined using scanning
electron microscopy (SEM) while the composition, molecular weight
and thermal properties were determined using attenuated total
reflectance Fourier transform infrared spectroscopy (ATR-FTIR), gel
permeation chromatography (GPC), thermal gravimetric analysis
(TGA) and differential scanning calorimetry (DSC). Further chemical
analysis was done using hydrogen-1 nuclear magnetic resonance (1H
NMR) and functional characteristics in terms of biocompatibility
were evaluated using cytotoxicity test.
Abstract: Environment both endowed and built are essential for
tourism. However tourism and environment maintains a complex
relationship, where in most cases environment is at the receiving end.
Many tourism development activities have adverse environmental
effects, mainly emanating from construction of general infrastructure
and tourism facilities. These negative impacts of tourism can lead to
the destruction of precious natural resources on which it depends.
These effects vary between locations; and its effect on a hill
destination is highly critical. This study aims at developing a
Sustainable Tourism Planning Model for an environmentally
sensitive tourism destination in Kerala, India. Being part of the
Nilgiri mountain ranges, Munnar falls in the Western Ghats, one of
the biological hotspots in the world. Endowed with a unique high
altitude environment Munnar inherits highly significant ecological
wealth. Giving prime importance to the protection of this ecological
heritage, the study proposes a tourism planning model with resource
conservation and sustainability as the paramount focus. Conceiving a
novel approach towards sustainable tourism planning, the study
proposes to assess tourism attractions using Ecological Sensitivity
Index (ESI) and Tourism Attractiveness Index (TAI). Integration of
these two indices will form the Ecology – Tourism Matrix (ETM),
outlining the base for tourism planning in an environmentally
sensitive destination. The ETM Matrix leads to a classification of
tourism nodes according to its Conservation Significance and
Tourism Significance. The spatial integration of such nodes based on
the Hub & Spoke Principle constitutes sub – regions within the STZ.
Ensuing analyses lead to specific guidelines for the STZ as a whole,
specific tourism nodes, hubs and sub-regions. The study results in a
multi – dimensional output, viz., (1) Classification system for tourism
nodes in an environmentally sensitive region/ destination (2)
Conservation / Tourism Development Strategies and Guidelines for
the micro and macro regions and (3) A Sustainable Tourism Planning
Tool particularly for Ecologically Sensitive Destinations, which can
be adapted for other destinations as well.
Abstract: For many chemical and biological processes, the understanding of the mixing phenomenon and flow behavior in a stirred tank is of major importance. A three-dimensional numerical study was performed using the software Fluent, to study the flow field in a stirred tank with a Rushton turbine. In this work, we first studied the flow generated in the tank with a Rushton turbine. Then, we studied the effect of the variation of turbine’s submergence on the thermodynamic quantities defining the flow field. For that, four submergences were considered, while maintaining the same rotational speed (N =250rpm). This work intends to optimize the aeration performances of a Rushton turbine in a stirred tank.
Abstract: Cutting fluids, usually in the form of a liquid, are
applied to the chip formation zone in order to improve the cutting
conditions. Cutting fluid can be expensive and represents a biological
and environmental hazard that requires proper recycling and
disposal, thus adding to the cost of the machining operation. For
these reasons dry cutting or dry machining has become an
increasingly important approach; in dry machining no coolant or
lubricant is used. This paper discussed the effect of the dry cutting on
cutting force and tool life when machining aerospace materials
(Haynes 242) with using two different coated carbide cutting tools
(TiAlN and TiN/MT-TiCN/TiN). Response surface method (RSM)
was used to minimize the number of experiments. ParTiAlN Swarm
Optimisation (PSO) models were developed to optimize the
machining parameters (cutting speed, federate and axial depth) and
obtain the optimum cutting force and tool life. It observed that
carbide cutting tool coated with TiAlN performed better in dry
cutting compared with TiN/MT-TiCN/TiN. On other hand, TiAlN
performed more superior with using of 100 % water soluble coolant.
Due to the high temperature produced by aerospace materials, the
cutting tool still required lubricant to sustain the heat transfer from
the workpiece.