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: Previous the 3D model texture generation from multi-view images and mapping algorithms has issues in the texture chart generation which are the self-intersection and the concentration of the texture in texture space. Also we may suffer from some problems due to the occluded areas, such as inside parts of thighs. In this paper we propose a texture mapping technique for 3D models using multi-view images on the GPU. We do texture mapping directly on the GPU fragment shader per pixel without generation of the texture map. And we solve for the occluded area using the 3D model depth information. Our method needs more calculation on the GPU than previous works, but it has shown real-time performance and previously mentioned problems do not occur.
Abstract: In recent years, there has been an increasing interest
toward the use of bovine genotyped embryos for commercial embryo
transfer programs. Biopsy of a few cells in morulla stage is essential
for preimplantation genetic diagnosis (PGD). Low amount of DNA
have limited performing the several molecular analyses within PGD
analyses. Whole genome amplification (WGA) promises to eliminate
this problem. We evaluated the possibility and performance of an
improved primer extension preamplification (I-PEP) method with a
range of starting bovine genomic DNA from 1-8 cells into the WGA
reaction. We optimized a short and simple I-PEP (ssI-PEP) procedure
(~3h). This optimized WGA method was assessed by 6 loci specific
polymerase chain reactions (PCRs), included restriction fragments
length polymorphism (RFLP). Optimized WGA procedure possesses
enough sensitivity for molecular genetic analyses through the few
input cells. This is a new era for generating characterized bovine
embryos in preimplantation stage.
Abstract: This paper presents the simulation of fragmentation
warhead using a hydrocode, Autodyn. The goal of this research is to
determine the lethal range of such a warhead. This study investigates
the lethal range of warheads with and without steel balls as
preformed fragments. The results from the FE simulation, i.e. initial
velocities and ejected spray angles of fragments, are further processed
using an analytical approach so as to determine a fragment hit density
and probability of kill of a modelled warhead. In order to simulate a
plenty of preformed fragments inside a warhead, the model requires
expensive computation resources. Therefore, this study attempts to
model the problem in an alternative approach by considering an
equivalent mass of preformed fragments to the mass of warhead
casing. This approach yields approximately 7% and 20% difference
of fragment velocities from the analytical results for one and two
layers of preformed fragments, respectively. The lethal ranges of the
simulated warheads are 42.6 m and 56.5 m for warheads with one and
two layers of preformed fragments, respectively, compared to 13.85
m for a warhead without preformed fragment. These lethal ranges are
based on the requirement of fragment hit density. The lethal ranges
which are based on the probability of kill are 27.5 m, 61 m and 70 m
for warheads with no preformed fragment, one and two layers of
preformed fragments, respectively.
Abstract: This research paper presents numerical studies of the
characteristics of warhead fragmentation in terms of initial velocities,
spray angles of fragments and fragment mass distribution of high
explosive (HE) warhead. The behavior of warhead fragmentation
depends on shape and size of warhead, thickness of casing, type of
explosive, number and position of detonator, and etc. This paper
focuses on the effects of material properties of warhead casing, i.e.
failure strain, initial yield and ultimate strength on the characteristics
of warhead fragmentation. It was found that initial yield and ultimate
strength of casing has minimal effects on the initial velocities and
spray angles of fragments. Moreover, a brittle warhead casing with
low failure strain tends to produce higher number of fragments with
less average fragment mass.
Abstract: Abstract–The objectives of the current study are to determine the
prevalence, etiological agents, drug susceptibility pattern and plasmid
profile of Acinetobacter baumannii isolates from Hospital-Acquired
Infections (HAI) at Community Hospital, Al Jouf Province, Saudi
Arabia. A total of 1890 patients had developed infection during
hospital admission and were included in the study. Among those who
developed nosocomial infections, 15(9.4), 10(2.7) and 118 (12.7) had
respiratory tract infection (RTI), blood stream infections (BSI) and
urinary tract (UTI) respectively. A total of 268 bacterial isolates were
isolated from nosocomial infection. S. aureus was reported in 23.5%
for of the total isolates followed by Klebsiella pneumoniae (17.5%), E.
coli (17.2%), P. aeruginosa (11.9%), coagulase negative
staphylococcus (9%), A. baumannii (7.1%), Enterobacter spp.
(3.4%), Citrobacter freundii (3%), Proteus mirabilis (2.6%), and
Proteus vulgaris and Enterococcous faecalis (0.7%). Isolated
organisms are multi-drug resistant, predominantly Gram-positive
pathogens with a high incidence of methicillin-resistant S. aureus,
extended spectrum beta lactamase and vancomycin resistant
enterococci organisms. The RFLP (Fragment Length Polymorphisms)
patterns of plasmid preparations from isolated A. baumannii isolates
had altered RFLP patterns, possibly due to the presence of plasmid(s).
Five A. baumannii isolates harbored plasmids all of which were not
less than 2.71kbp in molecular weight. Hence, it showed that the gene
coding for the isolates were located on the plasmid DNA while the
remaining isolates which have no plasmid might showed gene coding
for antibiotic resistance being located on chromosomal DNA.
Nosocomial infections represent a current problem in Community
Hospital, Al Jouf Province, Saudi Arabia. Problems associated with
SSI include infection with multidrug resistant pathogens which are
difficult to treat and are associated with increased mortality.
Abstract: In this paper we address the problem of musical style
classification, which has a number of applications like indexing in
musical databases or automatic composition systems. Starting from
MIDI files of real-world improvisations, we extract the melody track
and cut it into overlapping segments of equal length. From these
fragments, some numerical features are extracted as descriptors of
style samples. We show that a standard Bayesian classifier can be
conveniently employed to build an effective musical style classifier,
once this set of features has been extracted from musical data.
Preliminary experimental results show the effectiveness of the
developed classifier that represents the first component of a musical
audio retrieval system
Abstract: The aim of this study was to screen for
microorganism that able to utilize 3-N-trimethylamino-1-propanol
(homocholine) as a sole source of carbon and nitrogen. The aerobic
degradation of homocholine has been found by a gram-positive
Rhodococcus sp. bacterium isolated from soil. The isolate was
identified as Rhodococcus sp. strain A4 based on the phenotypic
features, physiologic and biochemical characteristics, and
phylogenetic analysis. The cells of the isolated strain grown on both
basal-TMAP and nutrient agar medium displayed elementary
branching mycelia fragmented into irregular rod and coccoid
elements. Comparative 16S rDNA sequencing studies indicated that
the strain A4 falls into the Rhodococcus erythropolis subclade and
forms a monophyletic group with the type-strains of R. opacus, and
R. wratislaviensis. Metabolites analysis by capillary electrophoresis,
fast atom bombardment-mass spectrometry, and gas
chromatography- mass spectrometry, showed trimethylamine (TMA)
as the major metabolite beside β-alanine betaine and
trimethylaminopropionaldehyde. Therefore, the possible degradation
pathway of trimethylamino propanol in the isolated strain is through
consequence oxidation of alcohol group (-OH) to aldehyde (-CHO)
and acid (-COOH), and thereafter the cleavage of β-alanine betaine
C-N bonds yielded trimethylamine and alkyl chain.
Abstract: Distributed Computing Systems are usually considered the most suitable model for practical solutions of many parallel algorithms. In this paper an enhanced distributed system is presented to improve the time complexity of Binary Indexed Trees (BIT). The proposed system uses multi-uniform processors with identical architectures and a specially designed distributed memory system. The analysis of this system has shown that it has reduced the time complexity of the read query to O(Log(Log(N))), and the update query to constant complexity, while the naive solution has a time complexity of O(Log(N)) for both queries. The system was implemented and simulated using VHDL and Verilog Hardware Description Languages, with xilinx ISE 10.1, as the development environment and ModelSim 6.1c, similarly as the simulation tool. The simulation has shown that the overhead resulting by the wiring and communication between the system fragments could be fairly neglected, which makes it applicable to practically reach the maximum speed up offered by the proposed model.
Abstract: On a such wide-area environment as a Grid, data
placement is an important aspect of distributed database systems. In
this paper, we address the problem of initial placement of database
no-replicated fragments in Grid architecture. We propose a graph
based approach that considers resource restrictions. The goal is to
optimize the use of computing, storage and communication
resources. The proposed approach is developed in two phases: in the
first phase, we perform fragment grouping using knowledge about
fragments dependency and, in the second phase, we determine an
efficient placement of the fragment groups on the Grid. We also
show, via experimental analysis that our approach gives solutions
that are close to being optimal for different databases and Grid
configurations.
Abstract: The paper reviews the relationship between spatial
and transportation planning in the Southern African Development
Community (SADC) region of Sub-Saharan Africa. It argues that
most urbanisation in the region has largely occurred subsequent to
the 1950s and, accordingly, urban development has been
profoundly and negatively affected by the (misguided) spatial and
institutional tenets of modernism. It demonstrates how a
considerable amount of the poor performance of these settlements
can be directly attributed to this. Two factors in particular about the
planning systems are emphasized: the way in which programmatic
land-use planning lies at the heart of both spatial and transportation
planning; and the way on which transportation and spatial planning
have been separated into independent processes. In the final
section, the paper identifies ways of improving the planning
system. Firstly, it identifies the performance qualities which
Southern African settlements should be seeking to achieve.
Secondly, it focuses on two necessary arenas of change: the need to
replace programmatic land-use planning practices with structuralspatial
approaches; and it makes a case for making urban corridors
a spatial focus of integrated planning, as a way of beginning the
restructuring and intensification of settlements which are currently
characterised by sprawl, fragmentation and separation
Abstract: Background: Dialign is a DNA/Protein alignment tool
for performing pairwise and multiple pairwise alignments through the
comparison of gap-free segments (fragments) between sequence
pairs. An alignment of two sequences is a chain of fragments, i.e
local gap-free pairwise alignments, with the highest total score.
METHOD: A new approach is defined in this article which relies on
the concept of using three-dimensional fragments – i.e. local threeway
alignments -- in the alignment process instead of twodimensional
ones. These three-dimensional fragments are gap-free
alignments constituting of equal-length segments belonging to three
distinct sequences. RESULTS: The obtained results showed good
improvments over the performance of DIALIGN.
Abstract: A. niger XP isolated from Vietnam produces very low amount of acidic phytase with optimal pH at 2.5 and 5.5. The phytase production of this strain was successfully improved through gene cloning and expression. A 1.4 - kb DNA fragment containing the coding region of the phyA gene was amplified by PCR and inserted into the expression vector pPICZαA with a signal peptide α- factor, under the control of AOX1 promoter. The recombined plasmid was transformed into the host strain P. pastoris KM71H and X33 by electroporation. Both host strains could efficiently express and secret phytase. The multicopy strains were screened for over expression of phytase. All the selected multicopy strains of P. pastoris X33 were examined for phytase activity, the maximum phytase yield of 1329 IU/ml was obtained after 4 days of incubation in medium BMM. The recombinant protein with MW of 97.4 KW showed to be the only one protein secreted in the culture broth. Multicopy transformant P. pastoris X33 supposed to be potential candidate for producing the commercial preparation of phytase.
Abstract: ICT and supply chain management (SCM) are two
notions, which have attracted much attention among both
academicians and practitioners during the last decade. However, the
discussion of the relationship between the two notions has been
limited and fragmented. In this paper, we will present a summary of
the discussion of ICT components and SCM on an extensive
literature review. Then, we will discuss the interrelation between ICT
and SCM from some major components and applications of ICT
perspective. After all, we can introduce e-SCM concept, that arisen
recently in management literature, in order to cover the whole topic.
The authors look at all of the major components of electronic supply
chain management and demonstrate that the future holds tremendous
opportunity for those firms that take advantage of all of its
possibilities.
Abstract: This paper concerns a formal model to help the
simulation of agent societies where institutional roles and
institutional links can be specified operationally. That is, this paper
concerns institutional roles that can be specified in terms of a minimal behavioral capability that an agent should have in order to
enact that role and, thus, to perform the set of institutional functions that role is responsible for. Correspondingly, the paper concerns
institutional links that can be specified in terms of a minimal
interactional capability that two agents should have in order to, while
enacting the two institutional roles that are linked by that institutional
link, perform for each other the institutional functions supported by
that institutional link. The paper proposes a cognitive architecture
approach to institutional roles and institutional links, that is, an approach in which a institutional role is seen as an abstract cognitive
architecture that should be implemented by any concrete agent (or set of concrete agents) that enacts the institutional role, and in which
institutional links are seen as interactions between the two abstract
cognitive agents that model the two linked institutional roles. We
introduce a cognitive architecture for such purpose, called the
Institutional BCC (IBCC) model, which lifts Yoav Shoham-s BCC
(Beliefs-Capabilities-Commitments) agent architecture to social
contexts. We show how the resulting model can be taken as a means
for a cognitive architecture account of institutional roles and
institutional links of agent societies. Finally, we present an example
of a generic scheme for certain fragments of the social organization
of agent societies, where institutional roles and institutional links are
given in terms of the model.
Abstract: Sports Sciences has been historically supported by the positivism idea of science, especially by the mechanistic/reductionist and becomes a field that views experimentation and measurement as the mayor research domains. The disposition to simplify nature and the world by parts has fragmented and reduced the idea of bodyathletes as machine. In this paper we intent to re-think this perception lined by Complexity Theory. We come with the idea of athletes as a reflexive and active being (corporeity-body). Therefore, the construction of a training that considers the cultural, biological, psychological elements regarding the experience of the human corporal movements in a circumspect and responsible way could bring better chances of accomplishment. In the end, we hope to help coaches understand the intrinsic complexity of the body they are training, how better deal with it, and, in the field of a deep globalization among the different types of knowledge, to respect and accepted the peculiarities of knowledge that comprise this area.
Abstract: In this paper, we proposed a method for detecting consistency violation between state machine diagrams and a sequence diagram defined in UML 2.0 using SMV. We extended a method expressing these diagrams defined in UML 1.0 with boolean formulas so that it can express a sequence diagram with combined fragments introduced in UML 2.0. This extension made it possible to represent three types of combined fragment: alternative, option and parallel. As a result of experiment, we confirmed that the proposed method could detect consistency violation correctly with SMV.
Abstract: A common way to elude the signature-based Network Intrusion Detection System is based upon changing a recognizable attack to an unrecognizable one via the IDS. For example, in order to evade sign accommodation with intrusion detection system markers, a hacker spilt the payload packet into many small pieces or hides them within messages. In this paper we try to model the main fragmentation attack and create a new module in the intrusion detection architecture system which recognizes the main fragmentation attacks through verification of integrity checking of TCP packet in order to prevent elusion of the system and also to announce the necessary alert to the system administrator.
Abstract: D-erythro-cyclohexylserine (D
chiral unnatural β-hydroxy amino acid expected for the synthesis of drug for AIDS treatment. To develop a continuous bioconversion
system with whole cell biocatalyst of D-threonine aldolase (D genes for the D-erythro-CHS production, D-threonine aldolase gene
was amplified from Ensifer arboris 100383 by direct PCR amplication using two degenerated oligonucleotide primers designed based on
genomic sequence of Shinorhizobium meliloti
Sequence analysis of the cloned DNA fragment revealed one
open-reading frame of 1059 bp and 386 amino acids. This putative
D-TA gene was cloned into NdeI and EcoRI (pEnsi
His-tag sequence or BamHI (pEnsi-DTA[2])
sequence of the pET21(a) vector. The expression level of the cloned gene was extremely overexpressed by E. coli BL21(DE3) transformed with pEnsi-DTA[1] compared to E. coli BL21(DE3) transformed with
pEnsi-DTA[2]. When the cells expressing the wild
used for D-TA enzyme activity, 12 mM glycine was successfully
detected in HPLC analysis. Moreover, the whole cells harbouring the
recombinant D-TA was able to synthesize D-erythro
of 0.6 mg/ml in a batch reaction.
Abstract: Type 2 diabetes mellitus (T2DM) is a complex
metabolic disorder that characterized by the presence of high glucose
in blood that cause from insulin resistance and insufficiency due to
deterioration β-cell Langerhans functions. T2DM is commonly
caused by the combination of inherited genetic variations as well as
our own lifestyle. Metallothionein (MT) is a known cysteine-rich
protein responsible in helping zinc homeostasis which is important in
insulin signaling and secretion as well as protection our body from
reactive oxygen species (ROS). MT scavenged ROS and free
radicals in our body happen to be one of the reasons of T2DM and its
complications. The objective of this study was to investigate the
association of MT1A and MT2A polymorphisms between T2DM and
control subjects among Malay populations. This study involved 150
T2DM and 120 Healthy individuals of Malay ethnic with mixed
genders. The genomic DNA was extracted from buccal cells and
amplified for MT1A and MT2A loci; the 347bp and 238bp banding
patterns were respectively produced by mean of the Polymerase
Chain Reaction (PCR). The PCR products were digested with Mlucl
and Tsp451 restriction enzymes respectively and producing
fragments lengths of (158/189/347bp) and (103/135/238bp)
respectively. The ANOVA test was conducted and it shown that there
was a significant difference between diabetic and control subjects for
age, BMI, WHR, SBP, FPG, HBA1C, LDL, TG, TC and family
history with (P0.05). The genotype
frequency for AA, AG and GG of MT1A polymorphisms was 72.7%,
22.7% and 4.7% in cases and 15%, 55% and 30% in control
respectively. As for MT2A, genotype frequency of GG, GC and CC
was 42.7%, 27.3% and 30% in case and 5%, 40% and 55% for
control respectively. Both polymorphisms show significant difference
between two investigated groups with (P=0.000). The Post hoc test
was conducted and shows a significant difference between the
genotypes within each polymorphism (P=0. 000). The MT1A and
MT2A polymorphisms were believed to be the reliable molecular
markers to distinguish the T2DM subjects from healthy individuals in
Malay populations.