Abstract: We created the tool, which combines the powerful
GENESIS (GEneral NEural SImulation System) simulation language
with the up-to-date visualisation and internet techniques. Our
solution resides in the connection between the simulation output from
GENESIS, which is converted to the data-structure suitable for
WWW browsers and VRML (Virtual Reality Modelling Language)
viewers. The selected GENESIS simulations are once exported into
the VRML code, and stored in our neurovisualisation portal
(webserver). There, the loaded models, demonstrating mainly the
spread of electrical signal (action potentials, postsynaptic potentials)
along the neuronal membrane (axon, dendritic tree, neuron) could be
displayed in the client-s VRML viewer, without interacting with
original GENESIS environment. This enables the visualisation of
basic neurophysiological phenomena designed for GENESIS
simulator on the independent OS (operation system).
Abstract: Bone growth factors, such as Bone Morphogenic
Protein-2 (BMP-2) have been approved by the FDA to replace grafting for some surgical interventions, but the high dose requirement limits its use in patients. Noggin, an extracellular protein, blocks the effect of BMP-2 by binding to BMP. Preventing
the BMP-2/noggin interaction will help increase the free
concentration of BMP-2 and therefore should enhance its efficacy to
induce bone formation. The work presented here involves
computational design of novel small molecule inhibitory agents of BMP-2/noggin interaction, based on our current understanding of
BMP-2, and its known putative ligands (receptors and antagonists). A
successful acquisition of such an inhibitory agent of BMP-2/noggin interaction would allow clinicians to reduce the dose required of
BMP-2 protein in clinical applications to promote osteogenesis. The
available crystal structures of the BMPs, its receptors, and the binding partner noggin were analyzed to identify the critical residues
involved in their interaction. In presenting this study, LUDI de novo design method was utilized to perform virtual screening of a large
number of compounds from a commercially available library against the binding sites of noggin to identify the lead chemical compounds
that could potentially block BMP-noggin interaction with a high specificity.
Abstract: Attachment of the circulating monocytes to the
endothelium is the earliest detectable events during formation of
atherosclerosis. The adhesion molecules, chemokines and matrix
proteases genes were identified to be expressed in atherogenesis.
Expressions of these genes may influence structural integrity of the
luminal endothelium. The aim of this study is to relate changes in the
ultrastructural morphology of the aortic luminal surface and gene
expressions of the endothelial surface, chemokine and MMP-12 in
normal and hypercholesterolemic rabbits. Luminal endothelial
surface from rabbit aortic tissue was examined by scanning electron
microscopy (SEM) using low vacuum mode to ascertain
ultrastructural changes in development of atherosclerotic lesion. Gene
expression of adhesion molecules, MCP-1 and MMP-12 were studied
by Real-time PCR. Ultrastructural observations of the aortic luminal
surface exhibited changes from normal regular smooth intact
endothelium to irregular luminal surface including marked globular
appearance and ruptures of the membrane layer. Real-time PCR
demonstrated differentially expressed of studied genes in
atherosclerotic tissues. The appearance of ultrastructural changes in
aortic tissue of hypercholesterolemic rabbits is suggested to have
relation with underlying changes of endothelial surface molecules,
chemokine and MMP-12 gene expressions.
Abstract: Lung cancer accounts for the most cancer related deaths for men as well as for women. The identification of cancer associated genes and the related pathways are essential to provide an important possibility in the prevention of many types of cancer. In this work two filter approaches, namely the information gain and the biomarker identifier (BMI) are used for the identification of different types of small-cell and non-small-cell lung cancer. A new method to determine the BMI thresholds is proposed to prioritize genes (i.e., primary, secondary and tertiary) using a k-means clustering approach. Sets of key genes were identified that can be found in several pathways. It turned out that the modified BMI is well suited for microarray data and therefore BMI is proposed as a powerful tool for the search for new and so far undiscovered genes related to cancer.
Abstract: This paper at first presents approximate analytical
solutions for systems of fractional differential equations using the
differential transform method. The application of differential
transform method, developed for differential equations of integer
order, is extended to derive approximate analytical solutions of
systems of fractional differential equations. The solutions of our
model equations are calculated in the form of convergent series with
easily computable components. After that a drive-response
synchronization method with linear output error feedback is
presented for “generalized projective synchronization" for a class of
fractional-order chaotic systems via a scalar transmitted signal.
Genesio_Tesi and Duffing systems are used to illustrate the
effectiveness of the proposed synchronization method.
Abstract: A lot of recent research have spoken on the relation
between the increase of the homocysteinemia and some kinds of
cancer . For that, our study was based on the research of a possible
relation between the increase of the concentration of this amino-acid
in the plasma and the appearance of the disease of the Acute
Lymphoblastic Leukaemia in a part of Algerian children with Berber
origin in the East of Algeria . The study has done on 47 ill persons
with an average age of (09±06 ) years , with whom the disease has
diagnosed by blood and marrow examination in the hospital of blood
diseases in the CHU of Batna, and on 194 healthy witnesses of the
same age. The two groups were benefited by a dosage of the
concentration of the homocysteine vitamin B9 ,vitamin B12 , and
also of the study of special polymorphisms of indispensable enzymes
in the metabolism of this acid , and that by the use of the method (
Light cycler ) Real time PCR , on the following enzymes : MS (
C2756G ), MSR ( A66G ) ,MTHFR1 ( C677T ) and MTHFR2
(A1298C). The obtained results have revealed that the rate of the
homozygote muted genotype is the less frequent in the two groups ,
and that exist at list one genotype of each enzyme in the ill group and
in which the percentage exceed with remarkable way the same
genotype in the healthy group and we notice specially the muted
genotype GG of -the methionine synthetase-and the form TT of the
enzyme – methyline tetra hydrofolate reductase – We notice the
existence of considerable number of genotypes in the ill group lied
with characteristic increase of this Amino-acid ,and that for the
reduction of the biologic activity of these enzymes which become
inefficient in the transfer of the homocysteine into the methionine
and cause the diminution of the biologic activity of these enzymes
and with consequence the reduction of the percentage of methylic
radicals in the DNA of studied genes and that lead to the increase of
the activity and the capacity of transcription , and it-s so probably
that this last one is one of the factors of this disease especially if we
know that the specific check-up of vitamins is normal and similar in
the two groups , which ovoid the hypothesis of the reduction of
vitamins . We notice also that the heterozygote genotype is the less in
the sick category except the MTHFR2. Wild genotype is more
frequent in the witness group except MSR. Even these results are
partials; they open a new way in the genetic diagnosis of this
malicious disease which allow a precocious diagnosis and the use of
an effective and appropriated treatment in the same time.
Abstract: Information Retrieval has the objective of studying
models and the realization of systems allowing a user to find the
relevant documents adapted to his need of information. The
information search is a problem which remains difficult because the
difficulty in the representing and to treat the natural languages such
as polysemia. Intentional Structures promise to be a new paradigm to
extend the existing documents structures and to enhance the different
phases of documents process such as creation, editing, search and
retrieval. The intention recognition of the author-s of texts can reduce
the largeness of this problem. In this article, we present intentions
recognition system is based on a semi-automatic method of
extraction the intentional information starting from a corpus of text.
This system is also able to update the ontology of intentions for the
enrichment of the knowledge base containing all possible intentions
of a domain. This approach uses the construction of a semi-formal
ontology which considered as the conceptualization of the intentional
information contained in a text. An experiments on scientific
publications in the field of computer science was considered to
validate this approach.
Abstract: The ability to distinguish missense nucleotide
substitutions that contribute to harmful effect from those that do not
is a difficult problem usually accomplished through functional in
vivo analyses. In this study, instead current biochemical methods, the
effects of missense mutations upon protein structure and function
were assayed by means of computational methods and information
from the databases. For this order, the effects of new missense
mutations in exon 5 of PTEN gene upon protein structure and
function were examined. The gene coding for PTEN was identified
and localized on chromosome region 10q23.3 as the tumor
suppressor gene. The utilization of these methods were shown that
c.319G>A and c.341T>G missense mutations that were recognized in
patients with breast cancer and Cowden disease, could be pathogenic.
This method could be use for analysis of missense mutation in others
genes.
Abstract: A new genetic algorithm, termed the 'optimum individual monogenetic genetic algorithm' (OIMGA), is presented whose properties have been deliberately designed to be well suited to hardware implementation. Specific design criteria were to ensure fast access to the individuals in the population, to keep the required silicon area for hardware implementation to a minimum and to incorporate flexibility in the structure for the targeting of a range of applications. The first two criteria are met by retaining only the current optimum individual, thereby guaranteeing a small memory requirement that can easily be stored in fast on-chip memory. Also, OIMGA can be easily reconfigured to allow the investigation of problems that normally warrant either large GA populations or individuals many genes in length. Local convergence is achieved in OIMGA by retaining elite individuals, while population diversity is ensured by continually searching for the best individuals in fresh regions of the search space. The results given in this paper demonstrate that both the performance of OIMGA and its convergence time are superior to those of a range of existing hardware GA implementations.
Abstract: Bones are dynamic and responsive organs, they
regulate their strength and mass according to the loads which they are subjected. Because, the Wnt/β-catenin pathway has profound
effects on the regulation of bone mass, we hypothesized that mechanical loading of bone cells stimulates Wnt/β-catenin signaling, which results in the generation of new bone mass.
Mechanical loading triggers the secretion of the Wnt molecule, which after binding to transmembrane proteins, causes GSK-3β (Glycogen synthase kinase 3 beta) to cease the phosphorylation of β-catenin. β-catenin accumulation in the cytoplasm, followed by its
transport into the nucleus, binding to transcription factors (TCF/LEF)
that initiate transcription of genes related to bone formation. To test this hypothesis, we used TOPGAL (Tcf Optimal Promoter
β-galactosidase) mice in an experiment in which cyclic loads were
applied to the forearm. TOPGAL mice are reporters for cells effected
by the Wnt/β-catenin signaling pathway. TOPGAL mice are genetically engineered mice in which transcriptional activation of β-
catenin, results in the production of an enzyme, β-galactosidase. The
presence of this enzyme allows us to localize transcriptional
activation of β-catenin to individual cells, thereby, allowing us to quantify the effects that mechanical loading has on the Wnt/β-catenin pathway and new bone formation. The ulnae of loaded TOPGAL
mice were excised and transverse slices along different parts of the
ulnar shaft were assayed for the presence of β-galactosidase.
Our results indicate that loading increases β-catenin transcriptional
activity in regions where this pathway is already primed (i.e. where basal activity is already higher) in a load magnitude dependent
manner. Further experiments are needed to determine the temporal and spatial activation of this signaling in relation to bone formation.
Abstract: In the present work we report a gram negative
bacterial isolate, from soil of a dye industry, with promising
biorefining and bioremediation potential. This isolate (GBS.5) could
utilize carbazole (nitrogen containing polycyclic aromatic
hydrocarbon) as the sole source of nitrogen and carbon and utilize
almost 98% of 3mM carbazole in 100 hours. The specific activity of
our GBS.5 isolate for carbazole degradation at 30°C and pH 7.0 was
found to be 11.36 μmol/min/g dry cell weight as compared to 10.4
μmol/min/g dry cell weight, the highest reported specific activity till
date. The presence of car genes (the genes involved in
denitrogenation of carbazole) was confirmed through PCR
amplification.
Abstract: Cancers could normally be marked by a number of
differentially expressed genes which show enormous potential as
biomarkers for a certain disease. Recent years, cancer classification
based on the investigation of gene expression profiles derived by
high-throughput microarrays has widely been used. The selection of
discriminative genes is, therefore, an essential preprocess step in
carcinogenesis studies. In this paper, we have proposed a novel gene
selector using information-theoretic measures for biological
discovery. This multivariate filter is a four-stage framework through
the analyses of feature relevance, feature interdependence, feature
redundancy-dependence and subset rankings, and having been
examined on the colon cancer data set. Our experimental result show
that the proposed method outperformed other information theorem
based filters in all aspect of classification errors and classification
performance.
Abstract: In this paper we present a method for gene ranking
from DNA microarray data. More precisely, we calculate the correlation
networks, which are unweighted and undirected graphs, from
microarray data of cervical cancer whereas each network represents
a tissue of a certain tumor stage and each node in the network
represents a gene. From these networks we extract one tree for
each gene by a local decomposition of the correlation network. The
interpretation of a tree is that it represents the n-nearest neighbor
genes on the n-th level of a tree, measured by the Dijkstra distance,
and, hence, gives the local embedding of a gene within the correlation
network. For the obtained trees we measure the pairwise similarity
between trees rooted by the same gene from normal to cancerous
tissues. This evaluates the modification of the tree topology due to
progression of the tumor. Finally, we rank the obtained similarity
values from all tissue comparisons and select the top ranked genes.
For these genes the local neighborhood in the correlation networks
changes most between normal and cancerous tissues. As a result
we find that the top ranked genes are candidates suspected to be
involved in tumor growth and, hence, indicates that our method
captures essential information from the underlying DNA microarray
data of cervical cancer.
Abstract: The microbiological and physicochemical
characteristics of wetland soils in Eket Local Government Area were
studied between May 2001 and June 2003. Total heterotrophic
bacterial counts (THBC), total fungal counts (TFC), and total
actinomycetes counts (TAC) were determined from soil samples
taken from four locations at two depths in the wet and dry seasons.
Microbial isolates were characterized and identified. Particle size and
chemical parameters were also determined using standard methods.
THBC ranged from 5.2 (+0.17) x106 to 1.7 (+0.18) x107 cfu/g and
from 2.4 (+0.02) x106 to 1.4 (+0.04) x107cfu/g in the wet and dry
seasons, respectively. TFC ranged from 1.8 (+0.03) x106 to 6.6 (+
0.18) x106 cfu/g and from 1.0 (+0.04) x106 to 4.2 (+ 0.01) x106 cfu/g
in the wet and dry seasons, respectively .TAC ranged from 1.2
(+0.53) x106 to 6.0 (+0.05) x106 cfu/g and from 0.6 (+0.01) x106 to
3.2 (+ 0.12) x106 cfu/g in the wet and dry season, respectively.
Acinetobacter, Alcaligenes, Arthrobacter, Bacillus, Beijerinckja,
Enterobacter, Micrococcus, Flavobacterium, Serratia, Enterococcus,
and Pseudomonas species were predominant bacteria while
Aspergillus, Fusarium, Mucor, Penicillium, and Rhizopus were the
dominant fungal genera isolated. Streptomyces and Norcadia were
the actinomycetes genera isolated. The particle size analysis showed
high sand fraction but low silt and clay. The pH and % organic
matter were generally acidic and low, respectively at all locations.
Calcium dominated the exchangeable bases with low electrical
conductivity and micronutrients. These results provide the baseline
data of Eket wetland soils for its management for sustainable
agriculture.
Abstract: The most common result of analysis of highthroughput
data in molecular biology represents a global list of
genes, ranked accordingly to a certain score. The score can be a
measure of differential expression. Recent work proposed a new
method for selecting a number of genes in a ranked gene list from
microarray gene expression data such that this set forms the
Optimally Functionally Enriched Network (OFTEN), formed by
known physical interactions between genes or their products. Here
we present calculation results of relative connectivity of genes from
META-OFTEN network and tentative biological interpretation of the
most reproducible signal. The relative connectivity and
inbetweenness values of genes from META-OFTEN network were
estimated.
Abstract: Cancer classification to their corresponding cohorts has been key area of research in bioinformatics aiming better prognosis of the disease. High dimensionality of gene data has been makes it a complex task and requires significance data identification technique in order to reducing the dimensionality and identification of significant information. In this paper, we have proposed a novel approach for classification of oral cancer into metastasis positive and negative patients. We have used significance analysis of microarrays (SAM) for identifying significant genes which constitutes gene signature. 3 different gene signatures were identified using SAM from 3 different combination of training datasets and their classification accuracy was calculated on corresponding testing datasets using k-Nearest Neighbour (kNN), Fuzzy C-Means Clustering (FCM), Support Vector Machine (SVM) and Backpropagation Neural Network (BPNN). A final gene signature of only 9 genes was obtained from above 3 individual gene signatures. 9 gene signature-s classification capability was compared using same classifiers on same testing datasets. Results obtained from experimentation shows that 9 gene signature classified all samples in testing dataset accurately while individual genes could not classify all accurately.
Abstract: The assessment of surface waters in Enugu metropolis
for fecal coliform bacteria was undertaken. Enugu urban was divided
into three areas (A1, A2 and A3), and fecal coliform bacteria
analysed in the surface waters found in these areas for four years
(2005-2008). The plate count method was used for the analyses. Data
generated were subjected to statistical tests involving; Normality test,
Homogeneity of variance test, correlation test, and tolerance limit
test. The influence of seasonality and pollution trends were
investigated using time series plots. Results from the tolerance limit
test at 95% coverage with 95% confidence, and with respect to EU
maximum permissible concentration show that the three areas suffer
from fecal coliform pollution. To this end, remediation procedure
involving the use of saw-dust extracts from three woods namely;
Chlorophora-Excelsa (C-Excelsa),Khayan-Senegalensis,(CSenegalensis)
and Erythrophylum-Ivorensis (E-Ivorensis) in
controlling the coliforms was studied. Results show that mixture of
the acetone extracts of the woods show the most effective
antibacterial inhibitory activities (26.00mm zone of inhibition)
against E-coli. Methanol extract mixture of the three woods gave best
inhibitory activity (26.00mm zone of inhibition) against S-areus, and
25.00mm zones of inhibition against E-Aerogenes. The aqueous
extracts mixture gave acceptable zones of inhibitions against the
three bacteria organisms.
Abstract: Fourty one strains of ESBL producing P.aeruginosa
which were previously isolated from burn patients in Kerman
University general hospital, Iran were subjected to PCR, RFLP and
sequencing in order to determine the type of extended spectrum β-
lactamases (ESBL), the restriction digestion pattern and possibility of
mutation among detected genes. DNA extraction was carried out by
phenol chloroform method. PCR for detection of bla genes was
performed using specific primer for each gene. Restriction Fragment
Length Polymorphism (RFLP) for ESBL genes was carried out using
EcoRI, NheI, PVUII, EcoRV, DdeI, and PstI restriction enzymes. The
PCR products were subjected to direct sequencing of both the strands
for identification of the ESBL genes.The blaCTX-M, blaVEB-1, blaPER-1,
blaGES-1, blaOXA-1, blaOXA-4 and blaOXA-10 genes were detected in the
(n=1) 2.43%, (n=41)100%, (n=28) 68.3%, (n=10) 24.4%, (n=29)
70.7%, (n=7)17.1% and (n=38) 92.7% of the ESBL producing isolates
respectively. The RFLP analysis showed that each ESBL gene has
identical pattern of digestion among the isolated strains. Sequencing
of the ESBL genes confirmed the genuinety of PCR products and
revealed no mutation in the restriction sites of the above genes. From
results of the present investigation it can be concluded that blaVEB-1
and blaCTX-M were the most and the least frequently isolated ESBL
genes among the P.aeruginosa strains isolated from burn patients. The
RFLP and sequencing analysis revealed that same clone of the bla
genes were indeed existed among the antibiotic resistant strains.
Abstract: Bone remodeling occurs by the balanced action of
bone resorbing osteoclasts (OC) and bone-building osteoblasts.
Increased bone resorption by excessive OC activity contributes
to malignant and non-malignant diseases including osteoporosis.
To study OC differentiation and function, OC formed in
in vitro cultures are currently counted manually, a tedious
procedure which is prone to inter-observer differences. Aiming
for an automated OC-quantification system, classification of
OC and precursor cells was done on fluorescence microscope
images based on the distinct appearance of fluorescent nuclei.
Following ellipse fitting to nuclei, a combination of eight
features enabled clustering of OC and precursor cell nuclei.
After evaluating different machine-learning techniques, LOGREG
achieved 74% correctly classified OC and precursor cell
nuclei, outperforming human experts (best expert: 55%). In
combination with the automated detection of total cell areas,
this system allows to measure various cell parameters and most
importantly to quantify proteins involved in osteoclastogenesis.