Abstract: Complex networks have been intensively studied across
many fields, especially in Internet technology, biological engineering,
and nonlinear science. Software is built up out of many interacting
components at various levels of granularity, such as functions, classes,
and packages, representing another important class of complex networks.
It can also be studied using complex network theory. Over the
last decade, many papers on the interdisciplinary research between
software engineering and complex networks have been published.
It provides a different dimension to our understanding of software
and also is very useful for the design and development of software
systems. This paper will explore how to use the complex network
theory to analyze software structure, and briefly review the main
advances in corresponding aspects.
Abstract: In this paper we investigate the influence of external
noise on the inference of network structures. The purpose of our
simulations is to gain insights in the experimental design of microarray
experiments to infer, e.g., transcription regulatory networks
from microarray experiments. Here external noise means, that the
dynamics of the system under investigation, e.g., temporal changes of
mRNA concentration, is affected by measurement errors. Additionally
to external noise another problem occurs in the context of microarray
experiments. Practically, it is not possible to monitor the mRNA
concentration over an arbitrary long time period as demanded by the
statistical methods used to learn the underlying network structure. For
this reason, we use only short time series to make our simulations
more biologically plausible.
Abstract: Repeated additions of the unfertilized bacteria led to
increase the activity of Nitrogen-fixing bacteria in the root zone with
drip irrigation system compared to traditional manual vaccination to
increase the proportion of Nitrogen from 29% to 64%, and the
efficiency of adding Nitrogen fertilizer did not exceed 9.5% while
dropped to 4%, due to the amount of fertilizer added was not exceed
20kg N/h, and the second was the existence of a large amount of
available Nitrogen in the soil by fixation, while the efficiency of
irrigation system between 2.08 to 2.26 kg/m3.
Abstract: This work contains information about the influence low-level optical irradiation on sperm motility of sturgeon fish. On the basis of given and earlier received data the following conclusion has been made. Among the photophysical processes of a resonant and not resonant nature (oriented action of light; action of gradient forces; dipole-dipole interaction; termooptical processes), which are capable to cause the photobiological effects depended on such laserspecific characteristics as polarization and coherency, determining influence belongs to oriented action of light and dipole-dipole interactions among the processes studied in the present work.
Abstract: The desulfurization of coal using biological methods is an emerging technology. The biodesulfurization process uses the catalytic activity of chemolithotrophic acidpohiles in removing sulfur and pyrite from the coal. The present study was undertaken to examine the potential of Acidithiobacillus ferrooxidans in removing the pyritic sulfur and iron from high iron and sulfur containing US coal. The experiment was undertaken in 10 L batch stirred tank reactor having 10% pulp density of coal. The reactor was operated under mesophilic conditions and aerobic conditions were maintained by sparging the air into the reactor. After 35 days of experiment, about 64% of pyrite and 21% of pyritic sulfur was removed from the coal. The findings of the present study indicate that the biodesulfurization process does have potential in treating the high pyrite and sulfur containing coal. A good mass balance was also obtained with net loss of about 5% showing its feasibility for large scale application.
Abstract: Nowadays scientific data is inevitably digital and
stored in a wide variety of formats in heterogeneous systems.
Scientists need to access an integrated view of remote or local
heterogeneous data sources with advanced data accessing, analyzing,
and visualization tools. This research suggests the use of Service
Oriented Architecture (SOA) to integrate biological data from
different data sources. This work shows SOA will solve the problems
that facing integration process and if the biologist scientists can
access the biological data in easier way. There are several methods to
implement SOA but web service is the most popular method. The
Microsoft .Net Framework used to implement proposed architecture.
Abstract: Lanthanide-doped upconversion nanoparticles which can convert near-infrared lights to visible lights have attracted growing interest because of their great potentials in fluorescence imaging. Upconversion fluorescence imaging technique with excitation in the near-infrared (NIR) region has been used for imaging of biological cells and tissues. However, improving the detection sensitivity and decreasing the absorption and scattering in biological tissues are as yet unresolved problems. In this present study, a novel NIR-reflected multispectral imaging system was developed for upconversion fluorescent imaging in small animals. Based on this system, we have obtained the high contrast images without the autofluorescence when biocompatible UCPs were injected near the body surface or deeply into the tissue. Furthermore, we have extracted respective spectra of the upconversion fluorescence and relatively quantify the fluorescence intensity with the multispectral analysis. To our knowledge, this is the first time to analyze and quantify the upconversion fluorescence in the small animal imaging.
Abstract: The paper presents the results of research on trends in shaping of multifamily buildings in Poland on the example of Wrocław, after Polish accession to the European Union. The study is conducted within the research project: “Trends in creating of multifamily housing development since 2004, on the Wrocław study case" supported by Polish Ministry of Science and Higher Education and will be completed in November 2011. The research involves multifamily buildings completed in the last decade, in term of fundamental urbanization factors such as: building-s coefficient area, useable area, green area (biologically active surface), intensity of building development, amount of dwellings, dwelling area, amount of parking places, numbers of floors, etc. The analysis of these indicators was conducted based on the date obtained in the study of approximately one hundred new housing units, completed in Wroclaw. The analysis attempts to formulate the main trends in creating of housing policy in Poland during the last 10 years in reference to local urban policy.
Abstract: In this paper we evaluated the efficacy of
photodynamic treatment of infected wounds on pig animal model by
diffuse reflectance spectrometry. The study was conducted on fifteen
wounds contaminated with Staphylococcus aureus bacteria that were
incubated for 30 min with methylene blue solution (c = 3.3 x 10-3 M)
and exposed to laser radiations (λ = 670 nm, P = 15 mW) for 15 min.
The efficiency of photodynamic inactivation of bacteria was
evaluated by microbiological exams and diffuse reflectance
spectrometry. The results of the microbiological exams showed that
the bacterial concentration has decreased from 6.93±0.138
logCFU/ml to 3.12±0.108 logCFU/ml. The spectral examination
showed that the diffuse reflectance of wounds contaminated with
Staphylococcus aureus has decreased from 5.06±0.036 % to
3.36±0.025 %. In conclusion, photodynamic therapy is an effective
method for the treatment of infected wounds and there is a correlation
between the CFU count and diffuse reflectance.
Abstract: The aim of the work presented here was to either use
existing forest dynamic simulation models or calibrate a new one
both within the SYMFOR framework with the purpose of examining
changes in stand level basal area and functional composition in
response to selective logging considering trees > 10 cm d.b.h for two
areas of undisturbed Amazonian non flooded tropical forest in Brazil
and one in Peru. Model biological realism was evaluated for forest in
the undisturbed and selectively logged state and it was concluded that
forest dynamics were realistically represented. Results of the logging
simulation experiments showed that in relation to undisturbed forest
simulation subject to no form of harvesting intervention there was a
significant amount of change over a 90 year simulation period that
was positively proportional to the intensity of logging. Areas which
had in the dynamic equilibrium of undisturbed forest a greater
proportion of a specific ecological guild of trees known as the light
hardwoods (LHW’s) seemed to respond more favorably in terms of
less deviation but only within a specific range of baseline forest
composition beyond which compositional diversity became more
important. These finds are in line partially with practical management
experience and partiality basic systematics theory respectively.
Abstract: Biological evolution has generated a rich variety of
successful solutions; from nature, optimized strategies can be
inspired. One interesting example is the ant colonies, which are able
to exhibit a collective intelligence, still that their dynamic is simple.
The emergence of different patterns depends on the pheromone trail,
leaved by the foragers. It serves as positive feedback mechanism for
sharing information.
In this paper, we use the dynamic of TASEP as a model of
interaction at a low level of the collective environment in the ant-s
traffic flow. This work consists of modifying the movement rules of
particles “ants" belonging to the TASEP model, so that it adopts with
the natural movement of ants. Therefore, as to respect the constraints
of having no more than one particle per a given site, and in order to
avoid collision within a bidirectional circulation, we suggested two
strategies: decease strategy and waiting strategy. As a third work
stage, this is devoted to the study of these two proposed strategies-
stability. As a final work stage, we applied the first strategy to the
whole environment, in order to get to the emergence of traffic flow,
which is a way of learning.
Abstract: Pentachlorophenol (PCP) is a polychlorinated
aromatic compound that is widespread in industrial effluents and is
considered to be a serious pollutant. Among the variety of industrial
effluents encountered, effluents from tanning industry are very
important and have a serious pollution potential. PCP is also formed
unintentionally in effluents of paper and pulp industries. It is highly
persistent in soils and is lethal to a wide variety of beneficial
microorganisms and insects, human beings and animals. The natural
processes that breakdown toxic chemicals in the environment have
become the focus of much attention to develop safe and environmentfriendly
deactivation technologies. Microbes and plants are among
the most important biological agents that remove and degrade waste
materials to enable their recycling in the environment. The present
investigation was carried out with the aim of developing a microbial
system for bioremediation of PCP polluted soils. A number of plant
species were evaluated for their ability to tolerate different
concentrations of pentachlorophenol (PCP) in the soil. The
experiment was conducted for 30 days under pot culture conditions.
The toxic effect of PCP on plants was studied by monitoring seed
germination, plant growth and biomass. As the concentration of PCP
was increased to 50 ppm, the inhibition of seed germination, plant
growth and biomass was also increased. Although PCP had a
negative effect on all plant species tested, maize and groundnut
showed the maximum tolerance to PCP. Other tolerating crops
included wheat, safflower, sunflower, and soybean. From the
rhizosphere soil of the tolerant seedlings, as many as twenty seven
PCP tolerant bacteria were isolated. From soybean, 8; sunflower, 3;
safflower 8; maize 2; groundnut and wheat, 3 each isolates were
made. They were screened for their PCP degradation potentials.
HPLC analyses of PCP degradation revealed that the isolate MAZ-2
degraded PCP completely. The isolate MAZ-1 was the next best
isolate with 90 per cent PCP degradation. These strains hold promise
to be used in the bioremediation of PCP polluted soils.
Abstract: An epidemiological cross sectional study was
undertaken in Yaoundé in 2002 and updated in 2005. Focused on
health within the city, the objectives were to measure diarrheal
prevalence and to identify the risk factors associated with them.
Results of microbiological examinations have revealed an urban
average prevalence rate of 14.5%. Access to basic services in the
living environment appears to be an important risk factor for
diarrheas. Statistical and spatial analyses conducted have revealed
that prevalence of diarrheal diseases vary among the two main types
of settlement (informal and planned). More importantly, this study
shows that, diarrhea prevalence rates (notably bacterial and parasitic
diarrheas) vary according to the sub- category of settlements. The
study draws a number of theoretical and policy implications for
researchers and policy decision makers.
Abstract: The k-nearest neighbors (knn) is a simple but effective method of classification. In this paper we present an extended version of this technique for chemical compounds used in High Throughput Screening, where the distances of the nearest neighbors can be taken into account. Our algorithm uses kernel weight functions as guidance for the process of defining activity in screening data. Proposed kernel weight function aims to combine properties of graphical structure and molecule descriptors of screening compounds. We apply the modified knn method on several experimental data from biological screens. The experimental results confirm the effectiveness of the proposed method.
Abstract: In most wheat growing moderate regions and
especially in the north of Iran climate, is affected grain filling by
several physical and abiotic stresses. In this region, grain filling often
occurs when temperatures are increasing and moisture supply is
decreasing. The experiment was designed in RCBD with split plot
arrangements with four replications. Four irrigation treatments
included (I0) no irrigation (check); (I1) one irrigation (50 mm) at
heading stage; (I2) two irrigation (100 mm) at heading and anthesis
stage; and (I3) three irrigation (150 mm) at heading, anthesis and
early grain filling growth stage, two wheat cultivars (Milan and
Shanghai) were cultured in the experiment. Totally raining was 453
mm during the growth season. The result indicated that biological
yield, grain yield and harvest index were significantly affected by
irrigation levels. I3 treatment produced more tillers number in m2,
fertile tillers number in m2, harvest index and biological yield. Milan
produced more tillers number in m2, fertile tillers in m2, while
Shanghai produced heavier tillers and grain 1000 weight. Plant height
was significant in wheat varieties while were not statistically
significant in irrigation levels. Milan produced more grain yield,
harvest index and biological yield. Grain yield shown that I1, I2, and
I3 produced increasing of 5228 (21%), 5460 (27%) and 5670 (29%)
kg ha-1, respectively. There was an interaction of irrigation and
cultivar on grain yields. In the absence of the irrigation reduced grain
1000 weight from 45 to 40 g. No irrigation reduced soil moisture
extraction during the grain filling stage. Current assimilation as a
source of carbon for grain filling depends on the light intercepting
viable green surfaces of the plant after anthesis that due to natural
senescence and the effect of various stresses. At the same time the
demand by the growing grain is increasing. It is concluded from
research work that wheat crop irrigated Milan cultivar could increase
the grain yield in comparison with Shanghai cultivar. Although, the
grain yield of Shanghai under irrigation was slightly lower than
Milan. This grain yield also was related to weather condition, sowing
date, plant density and location conditions and management of
fertilizers, because there was not significant difference in biological
and straw yield. The best result was produced by I1 treatment. I2 and
I3 treatments were not significantly difference with I1 treatment.
Grain yield of I1 indicated that wheat is under soil moisture
deficiency. Therefore, I1 irrigation was better than I0.
Abstract: The pollution of sediments sampled from the North
Port by polycyclic aromatic hydrocarbons (PAHs) was investigated.
Concentrations of PAHs estimated in the port sediments ranged from
199 to 2851.2 μg/kg dw. The highest concentration was found which
is closed to the Berth line, this locations affected by intensive
shipping activities and Land based runoff and they were dominated
by the high molecular weight PAHs (4–6- rings). Source
identification showed that PAHs originated mostly from the
pyrogenic source either from the combustion of fossil fuels, grass,
wood and coal (majority of the samples). Ecological Risk Assessment
on the port sediments presented that slightly adverse ecological
effects to biological community are expected to occur at the vicinity
of the stations 1 and 4. Thus PAHs are not considered as pollutants of
concern in the North Port.
Abstract: DNA microarrays allow the measurement of expression levels for a large number of genes, perhaps all genes of an organism, within a number of different experimental samples. It is very much important to extract biologically meaningful information from this huge amount of expression data to know the current state of the cell because most cellular processes are regulated by changes in gene expression. Association rule mining techniques are helpful to find association relationship between genes. Numerous association rule mining algorithms have been developed to analyze and associate this huge amount of gene expression data. This paper focuses on some of the popular association rule mining algorithms developed to analyze gene expression data.
Abstract: In this paper, we consider a new particle filter inspired
by biological evolution. In the standard particle filter, a resampling
scheme is used to decrease the degeneracy phenomenon and improve
estimation performance. Unfortunately, however, it could cause the
undesired the particle deprivation problem, as well. In order to
overcome this problem of the particle filter, we propose a novel
filtering method called the genetic filter. In the proposed filter, we
embed the genetic algorithm into the particle filter and overcome the
problems of the standard particle filter. The validity of the proposed
method is demonstrated by computer simulation.
Abstract: Recently, genetic algorithms (GA) and particle swarm optimization (PSO) technique have attracted considerable attention among various modern heuristic optimization techniques. The GA has been popular in academia and the industry mainly because of its intuitiveness, ease of implementation, and the ability to effectively solve highly non-linear, mixed integer optimization problems that are typical of complex engineering systems. PSO technique is a relatively recent heuristic search method whose mechanics are inspired by the swarming or collaborative behavior of biological populations. In this paper both PSO and GA optimization are employed for finding stable reduced order models of single-input- single-output large-scale linear systems. Both the techniques guarantee stability of reduced order model if the original high order model is stable. PSO method is based on the minimization of the Integral Squared Error (ISE) between the transient responses of original higher order model and the reduced order model pertaining to a unit step input. Both the methods are illustrated through numerical example from literature and the results are compared with recently published conventional model reduction technique.
Abstract: In cancer progress, the optical properties of tissues
like absorption and scattering coefficient change, so by these
changes, we can trace the progress of cancer, even it can be applied
for pre-detection of cancer. In this paper, we investigate the effects of
changes of optical properties on light penetrated into tissues. The
diffusion equation is widely used to simulate light propagation into
biological tissues. In this study, the boundary integral method (BIM)
is used to solve the diffusion equation. We illustrate that the changes
of optical properties can modified the reflectance or penetrating light.