Abstract: Developing an accurate classifier for high dimensional microarray datasets is a challenging task due to availability of small sample size. Therefore, it is important to determine a set of relevant genes that classify the data well. Traditionally, gene selection method often selects the top ranked genes according to their discriminatory power. Often these genes are correlated with each other resulting in redundancy. In this paper, we have proposed a hybrid method using feature ranking and wrapper method (Genetic Algorithm with multiclass SVM) to identify a set of relevant genes that classify the data more accurately. A new fitness function for genetic algorithm is defined that focuses on selecting the smallest set of genes that provides maximum accuracy. Experiments have been carried on four well-known datasets1. The proposed method provides better results in comparison to the results found in the literature in terms of both classification accuracy and number of genes selected.
Abstract: NFκB is a transcription factor regulating many
function of the vessel wall. In the normal condition , NFκB is
revealed diffuse cytoplasmic expressionsuggesting that the system is
inactive. The presence of activation NFκB provide a potential
pathway for the rapid transcriptional of a variety of genes encoding
cytokines, growth factors, adhesion molecules and procoagulatory
factors. It is likely to play an important role in chronic inflamatory
disease involved atherosclerosis. There are many stimuli with the
potential to active NFκB, including hyperlipidemia. We used 24 mice
which was divided in 6 groups. The HFD given by et libitum
procedure during 2, 4, and 6 months. The parameters in this study
were the amount of NFKB activation ,H2O2 as ROS and VCAM-1 as
a product of NFKB activation. H2O2 colorimetryc assay performed
directly using Anti Rat H2O2 ELISA Kit. The NFKB and VCAM-1
detection obtained from aorta mice, measured by ELISA kit and
imunohistochemistry. There was a significant difference activation of
H2O2, NFKB and VCAM-1 level at induce HFD after 2, 4 and 6
months. It suggest that HFD induce ROS formation and increase the
activation of NFKB as one of atherosclerosis marker that caused by
hyperlipidemia as classical atheroschlerosis risk factor.
Abstract: The relationship between tropical cyclogenesis and solar activity is addressed in this paper, analyzing the relationship between important parameters in the evolution of tropical cyclones as the CAPE, wind shear and relative vorticity, and the Dst geomagnetic index as a parameter of solar activity. The apparent relationship between all this phenomena has a different response depending on the phase of the solar cycles.
Abstract: The importance for manipulating an incorporated
scaffold and directing cell behaviors is well appreciated for tissue
engineering. Here, we developed newly nano-topographic oxidized
silicon nanosponges capable of being various chemical modifications
to provide much insight into the fundamental biology of how cells
interact with their surrounding environment in vitro. A wet etching
technique is exerted to allow us fabricated the silicon nanosponges in a
high-throughput manner. Furthermore, various organo-silane
chemicals enabled self-assembled on the surfaces by vapor deposition.
We have found that Chinese hamster ovary (CHO) cells displayed
certain distinguishable morphogenesis, adherent responses, and
biochemical properties while cultured on these chemical modified
nano-topographic structures in compared with the planar oxidized
silicon counterparts, indicating that cell behaviors can be influenced
by certain physical characteristic derived from nano-topography in
addition to the hydrophobicity of contact surfaces crucial for cell
adhesion and spreading. Of particular, there were predominant
nano-actin punches and slender protrusions formed while cells were
cultured on the nano-topographic structures. This study shed potential
applications of these nano-topographic biomaterials for controlling
cell development in tissue engineering or basic cell biology research.
Abstract: Tasks of the work were study the possible E.coli
contamination in red deer meat, identify pathogenic strains from
isolated E.coli, determine their incidence in red deer meat and
determine the presence of VT1, VT2 and eaeA genes for the
pathogenic E.coli. 8 (10%) samples were randomly selected from 80
analysed isolates of E.coli and PCR reaction was performed on them.
PCR was done both on initial materials – samples of red deer meat -
and for already isolated liqueurs. Two of analysed venison samples
contain verotoxin-producing strains of E. coli. It means that this meat
is not safe to consumer. It was proven by the sequestration reaction of
E. coli and by comparison of the obtained results with the database of
microorganism genome available on the internet that the isolated
culture corresponds to region 16S rDNS of E. coli thus presenting
correctness of the microbiological methods.
Abstract: Impaired fertility may be the result of indirect
consumption of anti-fertility agents through food. Monosodium
glutamate (MSG) has been widely used as food additive, flavour
enhancer and included in vaccines. This study focuses in determining
the gonadotoxic and cytotoxic effect of MSG on selected sperm
parameters such as sperm viability, sperm membrane integrity and
testes cytoarchitecture of male mice via histological examination to
determine its effect on spermatogenesis. Twenty-four Mus musculus
were randomly divided into 4 groups and given intraperitoneal
injections (IP) daily for 14 days of different MSG concentrations at
250, 500 and 1000mg/kg MSG to body weight to induce obesity.
Saline was given to control group. Mice were sacrificed and analysis
revealed abnormalities in values for sperm parameters and damages
to testes cytoarchitecture of male mice. The results recorded
decreased viability (p0.05) with degenerative structures in seminiferous tubule of
testes. The results indicated various implications of MSG on male
mice reproductive system which has consequences in fertility
potential.
Abstract: The Brazilian legislation has only established
diagnostic reference levels (DRLs) in terms of Multiple Scan
Average Dose (MSAD) as a quality control parameter for computed
tomography (CT) scanners. Compliance with DRLs can be verified
by measuring the Computed Tomography Kerma Index (Ca,100) with
a pencil ionization chamber or by obtaining the kerma distribution in
CT scans with radiochromic films or rod shape lithium fluoride
termoluminescent dosimeters (TLD-100). TL dosimeters were used
to record kerma profiles and to determine MSAD values of a Bright
Speed model GE CT scanner. Measurements were done with
radiochromic films and TL dosimeters distributed in cylinders
positioned in the center and in four peripheral bores of a standard
polymethylmethacrylate (PMMA) body CT dosimetry phantom.
Irradiations were done using a protocol for adult chest. The
maximum values were found at the midpoint of the longitudinal axis.
The MSAD values obtained with three dosimetric techniques were
compared.
Abstract: Biological data has several characteristics that strongly differentiate it from typical business data. It is much more complex, usually large in size, and continuously changes. Until recently business data has been the main target for discovering trends, patterns or future expectations. However, with the recent rise in biotechnology, the powerful technology that was used for analyzing business data is now being applied to biological data. With the advanced technology at hand, the main trend in biological research is rapidly changing from structural DNA analysis to understanding cellular functions of the DNA sequences. DNA chips are now being used to perform experiments and DNA analysis processes are being used by researchers. Clustering is one of the important processes used for grouping together similar entities. There are many clustering algorithms such as hierarchical clustering, self-organizing maps, K-means clustering and so on. In this paper, we propose a clustering algorithm that imitates the ecosystem taking into account the features of biological data. We implemented the system using an Ant-Colony clustering algorithm. The system decides the number of clusters automatically. The system processes the input biological data, runs the Ant-Colony algorithm, draws the Topic Map, assigns clusters to the genes and displays the output. We tested the algorithm with a test data of 100 to1000 genes and 24 samples and show promising results for applying this algorithm to clustering DNA chip data.
Abstract: This article is a piece of the doctoral thesis
"Syncretism of traditional Kazakh culture in the light of the
innovation direction of circus and choreographic art of Kazakhstan
and its integration into the world civilization", and reveals the
features of the creative personalities of the traditional culture of
shamans, sals, seris, paluans in the comparative characteristic of the
European histriones and Russian skomorokhs.
Abstract: To decompose organochlorides by bioremediation, co-culture biohydrogen producer and dehalogenation microorganisms is a useful method. In this study, we combined these two characteristics from a biohydrogen producer, Rhodopseudomonas palustris, and a dehalogenation microorganism, Pseudomonas putida, to enchance halorespiration in R. palustris. The genes encoding cytochrome P450cam system (camC, camA, and camB) from P. putida were expressed in R. palustris with designated expression plasmid. All tested strains were cultured to log phase then presented pentachloroethane (PCA) in media. The vector control strain could degrade PCA about 78% after 16 hours, however, the cytochrome P450cam system expressed strain, CGA-camCAB, could completely degrade PCA in 12 hours. While taking chlorinated aromatic, 3-chlorobenzoate, as sole carbon source or present benzoate as co-substrate, CGA-camCAB presented faster growth rate than vector control strain.
Abstract: Mechanical interaction between endothelial cells (ECs) and the extracellular matrix (or collagen gel) is known to influence the sprouting response of endothelial cells during angiogenesis. This influence is believed to impact on the capability of endothelial cells to sense soluble chemical cues. Quantitative analysis of endothelial-cell-mediated displacement of the collagen gel provides a means to explore this mechanical interaction. Existing analysis in this context is generally limited to 2D settings. In this paper, we investigate the mechanical interaction between endothelial cells and the extracellular matrix in terms of the endothelial-cellmediated displacement of the collagen gel in both 2D and 3D. Digital image correlation and Digital volume correlation are applied on confocal reflectance image stacks to analyze cell-mediated displacement of the gel. The skeleton of the sprout is extracted from phase contrast images and superimposed on the displacement field to further investigate the link between the development of the sprout and the displacement of the gel.
Abstract: Gene expression profiling is rapidly evolving into a
powerful technique for investigating tumor malignancies. The
researchers are overwhelmed with the microarray-based platforms
and methods that confer them the freedom to conduct large-scale
gene expression profiling measurements. Simultaneously,
investigations into cross-platform integration methods have started
gaining momentum due to their underlying potential to help
comprehend a myriad of broad biological issues in tumor diagnosis,
prognosis, and therapy. However, comparing results from different
platforms remains to be a challenging task as various inherent
technical differences exist between the microarray platforms. In this
paper, we explain a simple ratio-transformation method, which can
provide some common ground for cDNA and Affymetrix platform
towards cross-platform integration. The method is based on the
characteristic data attributes of Affymetrix- and cDNA- platform. In
the work, we considered seven childhood leukemia patients and their
gene expression levels in either platform. With a dataset of 822
differentially expressed genes from both these platforms, we carried
out a specific ratio-treatment to Affymetrix data, which subsequently
showed an improvement in the relationship with the cDNA data.
Abstract: Cenozoic basalts found in Jiangsu province of eastern
China include tholeiites and alkali basalts. The present paper analyzed
the major, trace elements, rare earth elements of these Cenozoic
basalts and combined with Sr-Nd isotopic compositions proposed by
Chen et al. (1990)[1] in the literatures to discuss the petrogenesis of
these basalts and the geochemical characteristics of the source mantle.
Based on major, trace elements and fractional crystallization model
established by Brooks and Nielsen (1982)[2] we suggest that the
basaltic magma has experienced olivine + clinopyroxene fractionation
during its evolution. The chemical compositions of basaltic rocks from
Jiangsu province indicate that these basalts may belong to the same
magmatic system. Spidergrams reveal that Cenozoic basalts from
Jiangsu province have geochemical characteristics similar to those of
ocean island basalts(OIB). The slight positive Nb and Ti anomalies
found in basaltic rocks of this study suggest the presence of Ti-bearing
minerals in the mantle source and these Ti-bearing minerals had
contributed to basaltic magma during partial melting, indicating a
metasomatic event might have occurred before the partial melting.
Based on the Sr vs. Nd isotopic ratio plots, we suggest that Jiangsu
basalts may be derived from partial melting of mantle source which
may represent two-end members mixing of DMM and EM-I. Some
Jiangsu basaltic magma may be derived from partial melting of EM-I
heated by the upwelling asthenospheric mantle or asthenospheric
diapirism.
Abstract: Gene, principal unit of inheritance, is an ordered
sequence of nucleotides. The genes of eukaryotic organisms include
alternating segments of exons and introns. The region of
Deoxyribonucleic acid (DNA) within a gene containing instructions
for coding a protein is called exon. On the other hand, non-coding
regions called introns are another part of DNA that regulates gene
expression by removing from the messenger Ribonucleic acid (RNA)
in a splicing process. This paper proposes to determine splice
junctions that are exon-intron boundaries by analyzing DNA
sequences. A splice junction can be either exon-intron (EI) or intron
exon (IE). Because of the popularity and compatibility of the
artificial neural network (ANN) in genetic fields; various ANN
models are applied in this research. Multi-layer Perceptron (MLP),
Radial Basis Function (RBF) and Generalized Regression Neural
Networks (GRNN) are used to analyze and detect the splice junctions
of gene sequences. 10-fold cross validation is used to demonstrate
the accuracy of networks. The real performances of these networks
are found by applying Receiver Operating Characteristic (ROC)
analysis.
Abstract: Stable nonzero populations without random deaths
caused by the Verhulst factor (Verhulst-free) are a rarity. Majority
either grow without bounds or die of excessive harmful mutations.
To delay the accumulation of bad genes or diseases, a new
environmental parameter Γ is introduced in the simulation. Current
results demonstrate that stability may be achieved by setting Γ = 0.1.
These steady states approach a maximum size that scales inversely
with reproduction age.
Abstract: A numerical method is developed for simulating
the motion of particles with arbitrary shapes in an effectively
infinite or bounded viscous flow. The particle translational and
angular motions are numerically investigated using a fluid-structure
interaction (FSI) method based on the Arbitrary-Lagrangian-Eulerian
(ALE) approach and the dynamic mesh method (smoothing and
remeshing) in FLUENT ( ANSYS Inc., USA). Also, the effects of
arbitrary shapes on the dynamics are studied using the FSI method
which could be applied to the motions and deformations of a single
blood cell and multiple blood cells, and the primary thrombogenesis
caused by platelet aggregation. It is expected that, combined with a
sophisticated large-scale computational technique, the simulation
method will be useful for understanding the overall properties of blood
flow from blood cellular level (microscopic) to the resulting
rheological properties of blood as a mass (macroscopic).
Abstract: Nowadays, Gene Ontology has been used widely by many researchers for biological data mining and information retrieval, integration of biological databases, finding genes, and incorporating knowledge in the Gene Ontology for gene clustering. However, the increase in size of the Gene Ontology has caused problems in maintaining and processing them. One way to obtain their accessibility is by clustering them into fragmented groups. Clustering the Gene Ontology is a difficult combinatorial problem and can be modeled as a graph partitioning problem. Additionally, deciding the number k of clusters to use is not easily perceived and is a hard algorithmic problem. Therefore, an approach for solving the automatic clustering of the Gene Ontology is proposed by incorporating cohesion-and-coupling metric into a hybrid algorithm consisting of a genetic algorithm and a split-and-merge algorithm. Experimental results and an example of modularized Gene Ontology in RDF/XML format are given to illustrate the effectiveness of the algorithm.
Abstract: In this study, a synthetic pathway was created by
assembling genes from Clostridium butyricum and Escherichia coli
in different combinations. Among the genes were dhaB1 and dhaB2
from C. butyricum VPI1718 coding for glycerol dehydratase (GDHt)
and its activator (GDHtAc), respectively, involved in the conversion
of glycerol to 3-hydroxypropionaldehyde (3-HPA). The yqhD gene
from E.coli BL21 was also included which codes for an NADPHdependent
1,3-propanediol oxidoreductase isoenzyme (PDORI)
reducing 3-HPA to 1,3-propanediol (1,3-PD). Molecular modeling
analysis indicated that the conformation of fusion protein of YQHD
and DHAB1 was favorable for direct molecular channeling of the
intermediate 3-HPA. According to the simulation results, the yqhD
and dhaB1 gene were assembled in the upstream of dhaB2 to express
a fusion protein, yielding the recombinant strain E. coliBL21
(DE3)//pET22b+::yqhD-dhaB1_dhaB2 (strain BP41Y3). Strain
BP41Y3 gave 10-fold higher 1,3-PD concentration than E. coliBL21
(DE3)//pET22b+::yqhD-dhaB1_dhaB2 (strain BP31Y2) expressing
the recombinant enzymes simultaneously but in a non-fusion mode.
This is the first report using a gene fusion approach to enhance the
biological conversion of glycerol to the value added compound 1,3-
PD.
Abstract: Microarray experiments are information rich; however, extensive data mining is required to identify the patterns that characterize the underlying mechanisms of action. For biologists, a key aim when analyzing microarray data is to group genes based on the temporal patterns of their expression levels. In this paper, we used an iterative clustering method to find temporal patterns of gene expression. We evaluated the performance of this method by applying it to real sporulation data and simulated data. The patterns obtained using the iterative clustering were found to be superior to those obtained using existing clustering algorithms.
Abstract: In this study, three subtypes of influenza A viruses (pH1N1, H5N1 and H3N2) which naturally infected human were analyzed by bioinformatic approaches to find candidate human cellular miRNAs targeting viral genomes. There were 76 miRNAs targeting influenza A viruses. Among these candidates, 70 miRNAs were subtypes specifically targeting each subtype of influenza A virus including 21 miRNAs targeted subtype H1N1, 27 miRNAs targeted subtype H5N1 and 22 miRNAs targeted subtype H3N2. The remaining 6 miRNAs target on multiple subtypes of influenza A viruses. Uniquely, hsa-miR-3145 is the only one candidate miRNA targeting PB1 gene of all three subtypes. Obviously, most of the candidate miRNAs are targeting on polymerase complex genes (PB2, PB1 and PA) of influenza A viruses. This study predicted potential human miRNAs targeting on different subtypes of influenza A viruses which might be useful for inhibition of viral replication and for better understanding of the interaction between virus and host cell.