Abstract: This paper proposes a data-driven, biology-inspired neural segmentation method of 3D drosophila Brainbow images. We use Bayesian Sequential Partitioning algorithm for probabilistic modeling, which can be used to detect somas and to eliminate
crosstalk effects. This work attempts to develop an automatic methodology for neuron image segmentation, which nowadays still
lacks a complete solution due to the complexity of the image. The proposed method does not need any predetermined, risk-prone thresholds, since biological information is inherently included inside the image processing procedure. Therefore, it is less sensitive to variations in neuron morphology; meanwhile, its flexibility would be beneficial for tracing the intertwining structure of neurons.
Abstract: Some of the main problems man contends with are the quantity (source and amount) and quality of water in Nigeria. Scarcity leads to water being obtained from various sources and microbiological contamination of the water may thus occur between the collection point and the point of usage. This study thus aims to assess the general and microbiological quality of domestic water sources and household stored water used within selected areas in Ile-Ife, South-Western part of Nigeria for microbial contaminants. Physicochemical and microbiological examination were carried out on 45 source and stored water samples collected from well and spring in three different local government areas i.e. Ife east, Ife-south and Ife-north. Physicochemical analysis included pH value, temperature, total dissolved solid, dissolved oxygen and biochemical oxygen demand. Microbiology involved most probable number analysis, total coliform, heterotrophic plate, faecal coliform and streptococcus count.
The result of the physicochemical analysis of samples showed anomalies compared to acceptable standards with the pH value of 7.20-8.60 for stored and 6.50-7.80 for source samples. The total dissolved solids (TDS of stored 20-70mg/L, source 352-691mg/L), dissolved oxygen (DO of stored 1.60-9.60mg/L, source 1.60-4.80mg/L), biochemical oxygen demand (BOD stored 0.80-3.60mg/L, source 0.60-5.40mg/L). General microbiological quality indicated that both stored and source samples with the exception of a sample were not within acceptable range as indicated by analysis of the MPN/100ml which ranges between (stored 290-1100mg/L, source 9-1100mg/L). Apart from high counts, most samples did not meet the World Health Organization standard for drinking water with the presence of some pathogenic bacteria and fungi such as Salmonella and Aspergillus spp. To annul these constraints, standard treatment methods should be adopted to make water free from contaminants. This will help identify common and likely water related infection origin within the communities and thus help guide in terms of interventions required to prevent the general populace from such infections.
Abstract: Red blood cells (RBCs) are among the most
commonly and intensively studied type of blood cells in cell biology.
Anemia is a lack of RBCs is characterized by its level compared to
the normal hemoglobin level. In this study, a system based image
processing methodology was developed to localize and extract RBCs
from microscopic images. Also, the machine learning approach is
adopted to classify the localized anemic RBCs images. Several
textural and geometrical features are calculated for each extracted
RBCs. The training set of features was analyzed using principal
component analysis (PCA). With the proposed method, RBCs were
isolated in 4.3secondsfrom an image containing 18 to 27 cells. The
reasons behind using PCA are its low computation complexity and
suitability to find the most discriminating features which can lead to
accurate classification decisions. Our classifier algorithm yielded
accuracy rates of 100%, 99.99%, and 96.50% for K-nearest neighbor
(K-NN) algorithm, support vector machine (SVM), and neural
network RBFNN, respectively. Classification was evaluated in highly
sensitivity, specificity, and kappa statistical parameters. In
conclusion, the classification results were obtained within short time
period, and the results became better when PCA was used.
Abstract: Themain goal of this article is to find efficient
methods for elemental and molecular analysis of living
microorganisms (algae) under defined environmental conditions and
cultivation processes. The overall knowledge of chemical
composition is obtained utilizing laser-based techniques, Laser-
Induced Breakdown Spectroscopy (LIBS) for acquiring information
about elemental composition and Raman Spectroscopy for gaining
molecular information, respectively. Algal cells were suspended in
liquid media and characterized using their spectra. Results obtained
employing LIBS and Raman Spectroscopy techniques will help to
elucidate algae biology (nutrition dynamics depending on cultivation
conditions) and to identify algal strains, which have the potential for
applications in metal-ion absorption (bioremediation) and biofuel
industry. Moreover, bioremediation can be readily combined with
production of 3rd generation biofuels. In order to use algae for
efficient fuel production, the optimal cultivation parameters have to
be determinedleading to high production of oil in selected
cellswithout significant inhibition of the photosynthetic activity and
the culture growth rate, e.g. it is necessary to distinguish conditions
for algal strain containing high amount of higher unsaturated fatty
acids. Measurements employing LIBS and Raman Spectroscopy were
utilized in order to give information about alga Trachydiscusminutus
with emphasis on the amount of the lipid content inside the algal cell
and the ability of algae to withdraw nutrients from its environment
and bioremediation (elemental composition), respectively. This
article can serve as the reference for further efforts in describing
complete chemical composition of algal samples employing laserablation
techniques.
Abstract: This interdisciplinary research aims to distinguish universal scale-free and field-like fundamental principles of selforganization observable across many disciplines like computer science, neuroscience, microbiology, social science, etc. Based on these universal principles we provide basic premises and postulates for designing holistic social simulation models. We also introduce pervasive information field (PIF) concept, which serves as a simulation media for contextual information storage, dynamic distribution and organization in social complex networks. PIF concept specifically is targeted for field-like uncoupled and indirect interactions among social agents capable of affecting and perceiving broadcasted contextual information. Proposed approach is expressive enough to represent contextual broadcasted information in a form locally accessible and immediately usable by network agents. This paper gives some prospective vision how system-s resources (tangible and intangible) could be simulated as oscillating processes immersed in the all pervasive information field.
Abstract: Certain sciences such as physics, chemistry or biology,
have a strong computational aspect and use computing infrastructures
to advance their scientific goals. Often, high performance and/or high
throughput computing infrastructures such as clusters and computational
Grids are applied to satisfy computational needs. In addition,
these sciences are sometimes characterised by scientific collaborations
requiring resource sharing which is typically provided by Grid
approaches. In this article, I discuss Grid computing approaches in
High Energy Physics as well as in bioinformatics and highlight some
of my experience in both scientific domains.
Abstract: Microbial air contamination of the outdoor air in Marine Durres-s Harbour (Durres, Albania) was estimated by sedimentation technique in August-October 2008. The sampling areas were: Ferry Terminal (FT), Fishery Harbor (FH), East Zone (EZ), Fuel Quay (FQ) and Apollonian Beach (AB). The aim of this study was to measure the number of aerobic plate count (mesophilic aerobic bacteria) and fungi (yeasts and molds) in the outdoor air in these areas. The number of colonies that were formed determines the number of cells at the moment in the outdoor air; respectively the number of mesophilic aerobic bacteria and yeasts and molds. The measure of bacteria and fungi used is CFU (Colony Forming Units) per Petri dish. It is said that marine harbours are very polluted areas. The aim of study was the definition of mesophilic aerobic bacteria and yeasts and molds number, and the comparison of microorganisms number in air sampling areas.
Abstract: Deoxyribonucleic Acid or DNA computing has
emerged as an interdisciplinary field that draws together chemistry,
molecular biology, computer science and mathematics. Thus, in this
paper, the possibility of DNA-based computing to solve an absolute
1-center problem by molecular manipulations is presented. This is
truly the first attempt to solve such a problem by DNA-based
computing approach. Since, part of the procedures involve with
shortest path computation, research works on DNA computing for
shortest path Traveling Salesman Problem, in short, TSP are reviewed.
These approaches are studied and only the appropriate one is adapted
in designing the computation procedures. This DNA-based
computation is designed in such a way that every path is encoded by
oligonucleotides and the path-s length is directly proportional to the
length of oligonucleotides. Using these properties, gel electrophoresis
is performed in order to separate the respective DNA molecules
according to their length. One expectation arise from this paper is that
it is possible to verify the instance absolute 1-center problem using
DNA computing by laboratory experiments.
Abstract: Pattern matching is one of the fundamental applications in molecular biology. Searching DNA related data is a common activity for molecular biologists. In this paper we explore the applicability of a new pattern matching technique called Index based Forward Backward Multiple Pattern Matching algorithm(IFBMPM), for DNA Sequences. Our approach avoids unnecessary comparisons in the DNA Sequence due to this; the number of comparisons of the proposed algorithm is very less compared to other existing popular methods. The number of comparisons rapidly decreases and execution time decreases accordingly and shows better performance.
Abstract: In many ways, biomedical analysis is analogous to possibilistic reasoning. In spite of that, there are hardly any applications of possibility theory in biology or medicine. The aim of this work is to demonstrate the use of possibility theory in an epidemiological study. In the paper, we build the possibility distribution for the controlled bloodstream concentrations of any physiologically active substance through few approximate considerations. This possibility distribution is tested later against the empirical histograms obtained from the panel study of the eight different physiologically active substances in 417 individuals.
Abstract: Modeling and simulation of biochemical reactions is of great interest in the context of system biology. The central dogma of this re-emerging area states that it is system dynamics and organizing principles of complex biological phenomena that give rise to functioning and function of cells. Cell functions, such as growth, division, differentiation and apoptosis are temporal processes, that can be understood if they are treated as dynamic systems. System biology focuses on an understanding of functional activity from a system-wide perspective and, consequently, it is defined by two hey questions: (i) how do the components within a cell interact, so as to bring about its structure and functioning? (ii) How do cells interact, so as to develop and maintain higher levels of organization and functions? In recent years, wet-lab biologists embraced mathematical modeling and simulation as two essential means toward answering the above questions. The credo of dynamics system theory is that the behavior of a biological system is given by the temporal evolution of its state. Our understanding of the time behavior of a biological system can be measured by the extent to which a simulation mimics the real behavior of that system. Deviations of a simulation indicate either limitations or errors in our knowledge. The aim of this paper is to summarize and review the main conceptual frameworks in which models of biochemical networks can be developed. In particular, we review the stochastic molecular modelling approaches, by reporting the principal conceptualizations suggested by A. A. Markov, P. Langevin, A. Fokker, M. Planck, D. T. Gillespie, N. G. van Kampfen, and recently by D. Wilkinson, O. Wolkenhauer, P. S. Jöberg and by the author.
Abstract: Bacterial molecular chaperone DnaK plays an essential role in protein folding, stress response and transmembrane targeting of proteins. DnaKs from many bacterial species, including Escherichia coli, Salmonella typhimurium and Haemophilus infleunzae are the molecular targets for the insect-derived antimicrobial peptide pyrrhocoricin. Pyrrhocoricin-like peptides bind in the substrate recognition tunnel. Despite the high degree of crossspecies sequence conservation in the substrate-binding tunnel, some bacteria are not sensitive to pyrrhocoricin. This work addresses the molecular mechanism of resistance of Helicobacter pylori DnaK to pyrrhocoricin. Homology modelling, structural and sequence analysis identify a single aminoacid substitution at the interface between the lid and the β-sandwich subdomains of the DnaK substrate-binding domain as the major determinant for its resistance.
Abstract: In this paper, a simple microfluidic device for monitoring algal cell behavior is proposed. An array of algal microwells is fabricated by PDMS soft-lithography using X-ray LIGA mold, placed on a glass substrate. Two layers of replicated PDMS and substrate are attached by oxygen plasma bonding, creating a microchannel for the microfluidic system. Algal cell are loaded into the microfluidic device, which provides positive charge on the bottom surface of wells. Algal cells, which are negative charged, can be attracted to the bottom of the wells via electrostatic interaction. By varying the concentration of algal cells in the loading suspension, it is possible to obtain wells with a single cell. Liquid medium for cells monitoring are flown continuously over the wells, providing nutrient and waste exchange between the well and the main flow. This device could lead to the uncovering of the quantitative biology of the algae, which is a key to effective and extensive algal utilizations in the field of biotechnology, food industry and bioenergy research and developments.
Abstract: The Far From Most Strings Problem (FFMSP) is to obtain a string which is far from as many as possible of a given set of strings. All the input and the output strings are of the same length, and two strings are said to be far if their hamming distance is greater than or equal to a given positive integer. FFMSP belongs to the class of sequences consensus problems which have applications in molecular biology. The problem is NP-hard; it does not admit a constant-ratio approximation either, unless P = NP. Therefore, in addition to exact and approximate algorithms, (meta)heuristic algorithms have been proposed for the problem in recent years. On the other hand, in the recent years, hybrid algorithms have been proposed and successfully used for many hard problems in a variety of domains. In this paper, a new metaheuristic algorithm, called Constructive Beam and Local Search (CBLS), is investigated for the problem, which is a hybridization of constructive beam search and local search algorithms. More specifically, the proposed algorithm consists of two phases, the first phase is to obtain several candidate solutions via the constructive beam search and the second phase is to apply local search to the candidate solutions obtained by the first phase. The best solution found is returned as the final solution to the problem. The proposed algorithm is also similar to memetic algorithms in the sense that both use local search to further improve individual solutions. The CBLS algorithm is compared with the most recent published algorithm for the problem, GRASP, with significantly positive results; the improvement is by order of magnitudes in most cases.
Abstract: This paper describes a novel approach for deriving
modules from protein-protein interaction networks, which combines
functional information with topological properties of the network.
This approach is based on weighted clustering coefficient, which
uses weights representing the functional similarities between the
proteins. These weights are calculated according to the semantic
similarity between the proteins, which is based on their Gene
Ontology terms. We recently proposed an algorithm for identification
of functional modules, called SWEMODE (Semantic WEights for
MODule Elucidation), that identifies dense sub-graphs containing
functionally similar proteins. The rational underlying this approach is
that each module can be reduced to a set of triangles (protein triplets
connected to each other). Here, we propose considering semantic
similarity weights of all triangle-forming edges between proteins. We
also apply varying semantic similarity thresholds between
neighbours of each node that are not neighbours to each other (and
hereby do not form a triangle), to derive new potential triangles to
include in module-defining procedure. The results show an
improvement of pure topological approach, in terms of number of
predicted modules that match known complexes.
Abstract: Vinegar is a precious food additive and complement as well as effective preservative against food spoilage. Recently traditional vinegar production has been improved using various natural substrates and fruits such as grape, palm, cherry, coconut, date, sugarcane, rice and balsam. These neoclassical fermentations resulted in several vinegar types with different tastes, fragrances and nutritional values because of applying various acetic acid bacteria as starters. Acetic acid bacteria include genera Acetobacter, Gluconacetobacter and Gluconobacter according to latest edition of Bergy-s Manual of Systematic Bacteriology that classifies genera on the basis of their 16s RNA differences. Acetobacter spp as the main vinegar starters belong to family Acetobacteraceae that are gram negative obligate aerobes, chemoorganotrophic bacilli that are oxidase negative and oxidize ethanol to acetic acid. In this research we isolated and identified a native Acetobacter strain with high acetic acid productivity and tolerance against high ethanol concentrations from Iranian peach as a summer delicious fruit that is very susceptible to food spoilage and decay. We used selective and specific laboratorial culture media such as Standard GYC, Frateur and Carr medium. Also we used a new industrial culture medium and a miniature fermentor with a new aeration system innovated by Pars Yeema Biotechnologists Co., Isfahan Science and Technology Town (ISTT), Isfahan, Iran. The isolated strain was successfully cultivated in modified Carr media with 2.5% and 5% ethanol simultaneously in high temperatures, 34 - 40º C after 96 hours of incubation period. We showed that the increase of ethanol concentration resulted in rising of strain sensitivity to high temperature. In conclusion we isolated and characterized a new Acetobacter strain from Iranian peach that could be considered as a potential strain for production of a new vinegar type, peach vinegar, with a delicious taste and advantageous nutritional value in food biotechnology and industrial microbiology.
Abstract: Phylogenies ; The evolutionary histories of groups of
species are one of the most widely used tools throughout the life
sciences, as well as objects of research with in systematic,
evolutionary biology. In every phylogenetic analysis reconstruction
produces trees. These trees represent the evolutionary histories of
many groups of organisms, bacteria due to horizontal gene transfer
and plants due to process of hybridization. The process of gene
transfer in bacteria and hybridization in plants lead to reticulate
networks, therefore, the methods of constructing trees fail in
constructing reticulate networks. In this paper a model has been
employed to reconstruct phylogenetic network in honey bee. This
network represents reticulate evolution in honey bee. The maximum
parsimony approach has been used to obtain this reticulate network.
Abstract: Measures of complexity and entropy have not converged to a single quantitative description of levels of organization of complex systems. The need for such a measure is increasingly necessary in all disciplines studying complex systems. To address this problem, starting from the most fundamental principle in Physics, here a new measure for quantity of organization and rate of self-organization in complex systems based on the principle of least (stationary) action is applied to a model system - the central processing unit (CPU) of computers. The quantity of organization for several generations of CPUs shows a double exponential rate of change of organization with time. The exact functional dependence has a fine, S-shaped structure, revealing some of the mechanisms of self-organization. The principle of least action helps to explain the mechanism of increase of organization through quantity accumulation and constraint and curvature minimization with an attractor, the least average sum of actions of all elements and for all motions. This approach can help describe, quantify, measure, manage, design and predict future behavior of complex systems to achieve the highest rates of self organization to improve their quality. It can be applied to other complex systems from Physics, Chemistry, Biology, Ecology, Economics, Cities, network theory and others where complex systems are present.
Abstract: The control of oxygen flow rate during growth of
titanium dioxide by mass flow controller in DC plasma sputtering
growth system is studied. The impedance of TiO2 films for inductance
effect is influenced by annealing time and oxygen flow rate. As
annealing time is increased, the inductance of TiO2 film is the more.
The growth condition of optimum and maximum inductance for TiO2
film to serve as sensing device are oxygen flow rate of 15 sccm and
large annealing time. The large inductance of TiO2 film will be
adopted to fabricate the biosensor to obtain the high sensitivity of
sensing in biology.
Abstract: Organic farmers across Saskatchewan face soil
phosphorus (P) shortages. Due to the restriction on inputs in organic
systems, farmers rely on crop rotation and naturally-occurring
arbuscular mycorrhizal fungi (AMF) for plant P supply. Crop rotation
is important for disease, pest, and weed management. Crops that are
not colonized by AMF (non-mycorrhizal) can decrease colonization
of a following crop. An experiment was performed to quantify soil P
cycling in four cropping sequences under organic management and
determine if mustard (non-mycorrhizal) was delaying the
colonization of subsequent wheat. Soils from the four cropping
sequences were measured for inorganic soil P (Pi), AMF spore
density (SD), phospholipid fatty acid analysis (PLFA, for AMF
biomarker counts), and alkaline phosphatase activity (ALPase,
related to AMF metabolic activity). Plants were measured for AMF
colonization and P content and uptake of above-ground biomass. A
lack of difference in AMF activity indicated that mustard was not
depressing colonization. Instead, AMF colonization was largely
determined by crop type and crop rotation.