Search results for: Biological clock

Authors: R. Lotfi, M. Loukid, M.K. Hilali

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The reproductive aging of women is a biological process which is expressed by the loss of ovarian function and therefore the loss of the possibility of procreation. The present work aims to evaluate the effect of menopause on sexual health of rural women and to examine the determinants of female sexuality after menopause. A survey was conducted among 527 women in the rural area of Marrakech. The average age of women was 51.92 ± 7.24 years. It appears from this study that sexual activity in menopausal women decreases with age, 20% of women had no sexual activity after menopause. 72% of respondents reported having sex by obligation, 71% of women say they are not satisfied with their sexuality, while 29 % are very satisfied. The most common sexual complaints are represented by the decreased libido (81%), vaginal dryness (54%), and pain (22,7%). Of the 511 women with sexual dysfunction, only 34 (6, 4%) consulted for this disorder. Many factors may influence sex include menopause and all the biological changes but also the roles of culture, social constructions and perception of sexuality after menopause are complicated.

Keywords: Keywords—Reproductive aging, menopause, sexuality, rural women.

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Authors: Rou-Han Lee, Jie, Chung Lou, Huang-Ming Fang

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This study uses natural water and the surface properties of powdered activated carbon to acclimatize organics, forming biofilms on the surface of powdered activated carbon. To investigate the influence of different hydraulic retention times on the removal efficacy of trace organics in raw water, and to determine the optimal hydraulic retention time of a biological powdered activated carbon system, this study selects ozone-treated water processed by Feng-shan Advanced Water Purification Plant in southern Taiwan for the experiment. The evaluation indicators include assimilable organic carbon, dissolved organic carbon, and total organic carbon. The results of this study can improve the quality of drinking water treated using advanced water purification procedures.

Keywords: Water Purification Procedures, Biological Powdered Activated Carbon System, Assimilable Organic Carbon

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Authors: E. Binaeian, A.M. Rashidi, H. Attar

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A comparative evaluation of acute toxicity of synthesized nano silvers using two different procedures (biological and chemical reduction methods) and silver ions on bacteria Vibrio fischeri was investigated. The bacterial light inhibition test as a toxicological endpoint was used by applying of a homemade luminometer. To compare the toxicity effects as a quantitative parameter, a nominal effective concentrations (EC) of chemicals and a susceptibility constant (Z-value) of bacteria, after 5 min and 30 min exposure times, were calculated. After 5 and 30 min contact times, the EC50 values of two silver nanoparticles and the EC20 values were about similar. It demonstrates that toxicity of silvers was independent of their procedure. The EC values of nanoparticles were larger than those of the silver ions. The susceptibilities(Z- Values) of V.fischeri (L/mg) to the silver ions were greater than those of the nano silvers. According to the EC and Z values, the toxicity of silvers decreased in the following order: Silver ions >> silver nanoparticles from chemical reduction method ~ silver nanoparticles from biological method.

Keywords: Bioluminescence, Luminometer, silver nano particles, Toxicity, Vibrio fischeri

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Authors: Makkia, Ahmad, Al-Falahi, Abdullah Abdelaziz Muharram

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Healthcare workers (HCWs) in Yemen are exposed to a myriad of occupational health hazards, including biological, physical, ergonomic, chemical and psychosocial hazards. HCWs operate in an environment that is considered to be one of the most hazardous occupational settings. The current study aimed to assess sng the prevalence of ‎occupational health hazards among Health care workers and associated ‎risk factors in public hospitals in Sana'a City, Yemen. Descriptive cross-sectional design was utilized; out of 5443 totals of HCWs 396 were selected by multistage sampling technique was carried out in the public hospitals in Sana'a city, Yemen. More the half (60.6%) of HCWs were aged between 20-30 years, 50.8% were males, 56.3% were married, and 45.5% had a diploma qualification, while 65.2% of HCWs had less than 6 years of experience. The results show a high prevalence of occupational hazards (99%); ergonomic hazards (93.4%), biological hazards (87.6%), psychosocial (86.65%), physical hazards (83.3%), and chemical hazards (73.5%). There were no statistically significant differences between demographic characteristics and the prevalence of occupational hazards (p > 0.05). The study revealed that occupational hazards were highly prevalent among the participants. The most common biological hazard was exposure to sharp-related injuries, while the predominant physical hazard was slip, trip, and fall incidents. Ergonomic hazards manifested as back or neck pain during work. Chemical hazards were represented by allergic reactions to medical gloves powder. Psychosocial hazards included experiencing verbal and physical harassment. In conclusion, the study emphasized the importance of raising awareness among HCWs and conducting training courses to prevent occupational hazards.

Keywords: Health workers, occupational hazard, prevalence, risk factors.

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Authors: Seyedeh Belin Tavakoly Sany, H. Rosli, R. Majid, S. Aishah

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In this study, water monitoring was performed from Nov. 2012 to Oct. 2013 to assess water quality and evaluate the spatial and temporal distribution of physicochemical and biological variables in water. Water samples were collected from 10 coastal water stations of West Port. In the case of water-quality assessment, multi-metric indices and operational indicators have been proposed to classify the trophic status at different stations. The trophic level of West Port coastal water ranges from eutrophic to hypertrophic. Chl-a concentration was used to estimate the biological response of phytoplankton biomass and indicated eutrophic conditions in West Port and mesotrophic conditions at the control site. During the study period, no eutrophication events or secondary symptoms occurred, which may be related to hydrodynamic turbulence and water exchange, which prevent the development of eutrophic conditions in the West Port.

Keywords: Water quality, multi-metric indices, operational indicator, Malaysia, West Port.

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Authors: S. I. V. Sousa, F.G. Martins, M. C. Pereira, M. C. M. Alvim-Ferraz, H. Ribeiro, M. Oliveira, I. Abreu

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Exposure to ambient air pollution has been linked to a number of health outcomes, starting from modest transient changes in the respiratory tract and impaired pulmonary function, continuing to restrict activity/reduce performance and to the increase emergency rooms visits, hospital admissions or mortality. The increase of allergenic symptoms has been associated with air contaminants such as ozone, particulate matter, fungal spores and pollen. Considering the potential relevance of crossed effects of nonbiological pollutants and airborne pollens and fungal spores on allergy worsening, the aim of this work was to evaluate the influence of non-biological pollutants (O3 and PM10) and meteorological parameters on the concentrations of pollen and fungal spores using multiple linear regressions. The data considered in this study were collected in Oporto which is the second largest Portuguese city, located in the North. Daily mean of O3, PM10, pollen and fungal spore concentrations, temperature, relative humidity, precipitation, wind velocity, pollen and fungal spore concentrations, for 2003, 2004 and 2005 were considered. Results showed that the 90th percentile of the adjusted coefficient of determination, P90 (R2aj), of the multiple regressions varied from 0.613 to 0.916 for pollen and from 0.275 to 0.512 for fungal spores. O3 and PM10 showed to have some influence on the biological pollutants. Among the meteorological parameters analysed, temperature was the one that most influenced the pollen and fungal spores airborne concentrations. Relative humidity also showed to have some influence on the fungal spore dispersion. Nevertheless, the models for each pollen and fungal spore were different depending on the analysed period, which means that the correlations identified as statistically significant can not be, even so, consistent enough.

Keywords: Air pollutants, meteorological parameters, biologicalpollutants, multiple linear correlations.

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Authors: Soichi Ogishima, Takeshi Hase, So Nakagawa, Yasuhiro Suzuki, Hiroshi Tanaka

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To understand life as biological system, evolutionary understanding is indispensable. Protein interactions data are rapidly accumulating and are suitable for system-level evolutionary analysis. We have analyzed yeast protein interaction network by both mathematical and biological approaches. In this poster presentation, we inferred the evolutionary birth periods of yeast proteins by reconstructing phylogenetic profile. It has been thought that hub proteins that have high connection degree are evolutionary old. But our analysis showed that hub proteins are entirely evolutionary new. We also examined evolutionary processes of protein complexes. It showed that member proteins of complexes were tend to have appeared in the same evolutionary period. Our results suggested that protein interaction network evolved by modules that form the functional unit. We also reconstructed standardized phylogenetic trees and calculated evolutionary rates of yeast proteins. It showed that there is no obvious correlation between evolutionary rates and connection degrees of yeast proteins.

Keywords: Protein interaction network, evolution, modularity, evolutionary rate, connection degrees.

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Authors: Nazar Zaki, Safaai Deris

Abstract:

The amount of the information being churned out by the field of biology has jumped manifold and now requires the extensive use of computer techniques for the management of this information. The predominance of biological information such as protein sequence similarity in the biological information sea is key information for detecting protein evolutionary relationship. Protein sequence similarity typically implies homology, which in turn may imply structural and functional similarities. In this work, we propose, a learning method for detecting remote protein homology. The proposed method uses a transformation that converts protein sequence into fixed-dimensional representative feature vectors. Each feature vector records the sensitivity of a protein sequence to a set of amino acids substrings generated from the protein sequences of interest. These features are then used in conjunction with support vector machines for the detection of the protein remote homology. The proposed method is tested and evaluated on two different benchmark protein datasets and it-s able to deliver improvements over most of the existing homology detection methods.

Keywords: Protein homology detection; support vectormachine; string kernel.

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Authors: F. Allag, S. Bouharati, M. Belmahdi, R. Zegadi

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The rapid expansion of deserts in recent decades as a result of human actions combined with climatic changes has highlighted the necessity to understand biological processes in arid environments. Whereas physical processes and the biology of flora and fauna have been relatively well studied in marginally used arid areas, knowledge of desert soil micro-organisms remains fragmentary. The objective of this study is to conduct a diversity analysis of bacterial communities in unvegetated arid soils. Several biological phenomena in hot deserts related to microbial populations and the potential use of micro-organisms for restoring hot desert environments. Dry land ecosystems have a highly heterogeneous distribution of resources, with greater nutrient concentrations and microbial densities occurring in vegetated than in bare soils. In this work, we found it useful to use techniques of artificial intelligence in their treatment especially artificial neural networks (ANN). The use of the ANN model, demonstrate his capability for addressing the complex problems of uncertainty data.

Keywords: Desert soil, Climatic changes, Bacteria, Vegetation, Artificial neural networks.

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Authors: Razvan Bocu, Dr Sabin Tabirca

Abstract:

The study of proteomics reached unexpected levels of interest, as a direct consequence of its discovered influence over some complex biological phenomena, such as problematic diseases like cancer. This paper presents the latest authors- achievements regarding the analysis of the networks of proteins (interactome networks), by computing more efficiently the betweenness centrality measure. The paper introduces the concept of betweenness centrality, and then describes how betweenness computation can help the interactome net- work analysis. Current sequential implementations for the between- ness computation do not perform satisfactory in terms of execution times. The paper-s main contribution is centered towards introducing a speedup technique for the betweenness computation, based on modified shortest path algorithms for sparse graphs. Three optimized generic algorithms for betweenness computation are described and implemented, and their performance tested against real biological data, which is part of the IntAct dataset.

Keywords: Betweenness centrality, interactome networks, protein-protein interactions, sub-communities, sparse networks, speedup tech-nique, IntAct.

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Authors: Razvan Bocu, Sabin Tabirca

Abstract:

The study of proteomics reached unexpected levels of interest, as a direct consequence of its discovered influence over some complex biological phenomena, such as problematic diseases like cancer. This paper presents a new technique that allows for an accurate analysis of the human interactome network. It is basically a two-step analysis process that involves, at first, the detection of each protein-s absolute importance through the betweenness centrality computation. Then, the second step determines the functionallyrelated communities of proteins. For this purpose, we use a community detection technique that is based on the edge betweenness calculation. The new technique was thoroughly tested on real biological data and the results prove some interesting properties of those proteins that are involved in the carcinogenesis process. Apart from its experimental usefulness, the novel technique is also computationally effective in terms of execution times. Based on the analysis- results, some topological features of cancer mutated proteins are presented and a possible optimization solution for cancer drugs design is suggested.

Keywords: Betweenness centrality, interactome networks, proteinprotein interactions, protein communities, cancer.

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Authors: A.Qaderi, A. Heydarinasab, M. Ardjmand

Abstract:

Poly-β-hydroxybutyrate (PHB) is one of the most famous biopolymers that has various applications in production of biodegradable carriers. The most important strategy for enhancing efficiency in production process and reducing the price of PHB, is the accurate expression of kinetic model of products formation and parameters that are effective on it, such as Dry Cell Weight (DCW) and substrate consumption. Considering the high capabilities of artificial neural networks in modeling and simulation of non-linear systems such as biological and chemical industries that mainly are multivariable systems, kinetic modeling of microbial production of PHB that is a complex and non-linear biological process, the three layers perceptron neural network model was used in this study. Artificial neural network educates itself and finds the hidden laws behind the data with mapping based on experimental data, of dry cell weight, substrate concentration as input and PHB concentration as output. For training the network, a series of experimental data for PHB production from Hydrogenophaga Pseudoflava by glucose carbon source was used. After training the network, two other experimental data sets that have not intervened in the network education, including dry cell concentration and substrate concentration were applied as inputs to the network, and PHB concentration was predicted by the network. Comparison of predicted data by network and experimental data, indicated a high precision predicted for both fructose and whey carbon sources. Also in present study for better understanding of the ability of neural network in modeling of biological processes, microbial production kinetic of PHB by Leudeking-Piret experimental equation was modeled. The Observed result indicated an accurate prediction of PHB concentration by artificial neural network higher than Leudeking- Piret model.

Keywords: Kinetic Modeling, Poly-β-Hydroxybutyrate (PHB), Hydrogenophaga Pseudoflava, Artificial Neural Network, Leudeking-Piret

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Authors: M. S. Hosseini, M. Tazzoli-Shadpour, I. Amjadi, A. A. Katbab, E. Jaefargholi-Rangraz

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Bionanotechnology deals with nanoscopic interactions between nanostructured materials and biological systems. Polymer nanocomposites with optimized biological activity have attracted great attention. Nanoclay is considered as reinforcing nanofiller in manufacturing of high performance nanocomposites. In current study, organomodified-nanoclay with negatively charged silicate layers was incorporated into biomedical grade silicone rubber. Nanoparticle loading has been tailored to enhance cell behavior. Addition of nanoparticles led to improved mechanical properties of substrate with enhanced strength and stiffness while no toxic effects was observed. Results indicated improved viability and proliferation of cells by addition of nanofillers. The improved mechanical properties of the matrix result in proper cell response through adjustment and arrangement of cytoskeletal fibers. Results can be applied in tissue engineering when enhanced substrates are required for improvement of cell behavior for in vivo applications.

Keywords: Biocompatibility, Composite, Organomodified- Nanoclay, Proliferation

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Authors: Akın Kuyulu, Hanife Genç

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In present study, it was aimed to evaluate the gamma radiation impacts on tomato leaf miner at different biological stages. The laboratory colony of tomato leaf miner was used to set up the experiments. Different biological stages of the insects (eggs, 4^th instars and pupae) were irradiated using Cobalt-60 at doses of 0 (control), 100 Gray (Gy), 200 Gy, 300 Gy and 400 Gy in Cos-44HH-N source, at dose rate of 480 Gy/h. After irradiation, the eggs were incubated until hatching; the mature larvae were reared to complete their developments. Adult emergences from irradiated pupae were also evaluated. The results showed that there were no egg hatching at all tested irradiation doses. Although, the pupal percentages of irradiated mature larvae were 54%, 15% and 8% at doses of 100 Gy, 200 Gy and 300 Gy respectively, there were no adult emergences from irradiated mature larvae. On the other hand, the adult emergences were observed from irradiated pupae, decreased as radiation doses increased along with malformed adult appearance. Male and female individuals were out crossed with laboratory reared adults. Fecundity was correlated with radiation doses.

Keywords: Irradiation, tomato, tomato leafminer, Tuta absoluta.

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Authors: Abbas Ghanbari-Malidarreh

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.

Keywords: anthesis, grain yield, irrigation, supplementary, Wheat.

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Authors: F. Lops, G. Disciglio, A. Carlucci, G. Gatta, L. Frabboni, A. Tarantino, E. Tarantino

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Phelipanche ramosa L. Pomel is a root holoparasitic weed plant of many cultivations, particularly of tomato (Lycopersicum esculentum L.) crop. In Italy, Phelipanche problem is increasing, both in density and in acreage. The biological control of this parasitic weed involves the use of living organisms as numerous fungi and bacteria that can infect the parasitic weed, while it may improve the crop growth. This paper deals with the biocontrol with microorganism, including Arbuscular mycorrhizal (AM) fungi and fungal pathogens as Fusarium oxisporum spp. Colonization of crop roots by AM fungi can provide protection of crops against parasitic weeds because of a reduction in their seed germination and attachment, while F. oxisporum, isolated from diseased broomrape tubercles, proved to be highly virulent on P. ramosa. The experimental trial was carried out in open field at Foggia province (Apulia Region, Southern Italy), during the spring-summer season 2016, in order to evaluate the effect of four biological treatments: AM fungi and Fusarium oxisporum applied in the soil alone or combined together, and Rizosum Max^® product, compared with the untreated control, to reduce the P. ramosa infestation in processing tomato crop. The principal results to be drawn from this study under field condition, in contrast of those reported previously under laboratory and greenhouse conditions, show that both AM fungi and F. oxisporum do not provide the reduction of the number of emerged shoots of P. ramosa. This can arise probably from the low efficacy seedling of the agent pathogens for the control of this parasite in the field. On the contrary, the Rizosum Max^® product, containing AM fungi and some rizophere bacteria combined with several minerals and organic substances, appears to be most effective for the reduction of P. ramosa infestation.

Keywords: Arbuscular mycorrhizal fungi, biocontrol methods, Phelipanche ramosa, F. oxisporum spp.

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Authors: Najari Moghadam Sh., Qomi M., Raofie F., Khadiv J.

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In this study, a liquid phase microextraction by hollow fiber (HF-LPME) combined with high performance liquid chromatography-UV detector was applied to preconcentrate and determine trace levels of Cyproheptadine in human urine and plasma samples. Cyproheptadine was extracted from 10 mL alkaline aqueous solution (pH: 9.81) into an organic solvent (n-octnol) which was immobilized in the wall pores of a hollow fiber. Then was back-extracted into an acidified aqueous solution (pH: 2.59) located inside the lumen of the hollow fiber. This method is simple, efficient and cost-effective. It is based on pH gradient and differences between two aqueous phases. In order to optimize the HF-LPME some affecting parameters including the pH of donor and acceptor phases, the type of organic solvent, ionic strength, stirring rate, extraction time and temperature were studied and optimized. Under optimal conditions enrichment factor, limit of detection (LOD) and relative standard deviation (RSD(%), n=3) were up to 112, 15 μg.L⁻¹ and 2.7, respectively.

Keywords: Biological samples, Cyproheptadine, hollow fiber, liquid phase microextraction.

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Authors: R. Balamurugan, A. M. Natarajan, K. Premalatha

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Microarray gene expression data play a vital in biological processes, gene regulation and disease mechanism. Biclustering in gene expression data is a subset of the genes indicating consistent patterns under the subset of the conditions. Finding a biclustering is an optimization problem. In recent years, swarm intelligence techniques are popular due to the fact that many real-world problems are increasingly large, complex and dynamic. By reasons of the size and complexity of the problems, it is necessary to find an optimization technique whose efficiency is measured by finding the near optimal solution within a reasonable amount of time. In this paper, the algorithmic concepts of the Particle Swarm Optimization (PSO), Shuffled Frog Leaping (SFL) and Cuckoo Search (CS) algorithms have been analyzed for the four benchmark gene expression dataset. The experiment results show that CS outperforms PSO and SFL for 3 datasets and SFL give better performance in one dataset. Also this work determines the biological relevance of the biclusters with Gene Ontology in terms of function, process and component.

Keywords: Particle swarm optimization, Shuffled frog leaping, Cuckoo search, biclustering, gene expression data.

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Authors: Mehran Bakhshi, Mohammad Raouf Hosseini, Mohammadhosein Rahimi

Abstract:

The cadmium sulfide nanoparticles were synthesized from the nickel-cadmium cake of a hydrometallurgical zinc producing plant and sodium sulfide as Cd²⁺ and S^-2 sources, respectively. Also, the synthesis process was performed by using the secretions of Bacillus licheniformis as bio-surfactant. Initially, in order to obtain a cadmium rich solution, two following steps were carried out: 1) Alkaline leaching for the removal of zinc oxide from the cake, and 2) acidic leaching to dissolve cadmium from the remained solid residue. Afterward, the obtained CdSO₄ solution was used for the nanoparticle biosynthesis. Nanoparticles were characterized by the energy dispersive spectroscopy (EDS) and X-ray diffraction (XRD) to confirm the formation of CdS crystals with cubic structure. Also, transmission electron microscopy (TEM) was applied to determine the particle sizes which were in 2-10 nm range. Moreover, the presence of the protein containing bio-surfactants was approved by using infrared analysis (FTIR). In addition, the absorbance below 400 nm confirms quantum particles’ size. Finally, it was shown that valuable CdS quantum dots could be obtained from the industrial waste products via environment-friendly biological approaches.

Keywords: Biosynthesis, cadmium cake, cadmium sulfide, nanoparticle, zinc smelter.

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Authors: B. Tayebani, N. Hosseinibalam, D. Mostofinejad

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Interest in using bacteria in cement materials due to its positive influences has been increased. Cement materials such as mortar and concrete basically suffer from higher porosity and water absorption compared to other building materials such as steel materials. Because of the negative side-effects of certain chemical techniques, biological methods have been proposed as a desired and environmentally friendly strategy for reducing concrete porosity and diminishing water absorption. This paper presents the results of an experimental investigation carried out to evaluate the influence of Sporosarcina pasteurii bacteria on the behaviour of two types of concretes (light weight aggregate concrete and normal weight concrete). The resistance of specimens to water penetration by testing water absorption and evaluating the electrical resistance of those concretes was examined and compared. As a conclusion, 20% increase in electrical resistance and 10% reduction in water absorption of lightweight aggregate concrete (LWAC) and for normal concrete the results show 7% decrease in water absorption and almost 10% increase in electrical resistance.

Keywords: Bacteria, biological method, normal weight concrete, lightweight aggregate concrete, water absorption, electrical resistance.

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Authors: A. Ghaffari, A. S. Mostafavi

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Complex assemblies of interacting proteins carry out most of the interesting jobs in a cell, such as metabolism, DNA synthesis, mitosis and cell division. These physiological properties play out as a subtle molecular dance, choreographed by underlying regulatory networks that control the activities of cyclin-dependent kinases (CDK). The network can be modeled by a set of nonlinear differential equations and its behavior predicted by numerical simulation. In this paper, an innovative approach has been proposed that uses genetic algorithms to mine a set of behavior data output by a biological system in order to determine the kinetic parameters of the system. In our approach, the machine learning method is integrated with the framework of existent biological information in a wiring diagram so that its findings are expressed in a form of system dynamic behavior. By numerical simulations it has been illustrated that the model is consistent with experiments and successfully shown that such application of genetic algorithms will highly improve the performance of mathematical model of the cell division cycle to simulate such a complicated bio-system.

Keywords: Cell cycle, Cyclin-dependent kinase, Fission yeast, Genetic algorithms, Mathematical modeling, Wiring diagram

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Authors: Billel Kenidra, Mohamed Benmohammed

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Data mining technique used in the field of clustering is a subject of active research and assists in biological pattern recognition and extraction of new knowledge from raw data. Clustering means the act of partitioning an unlabeled dataset into groups of similar objects. Each group, called a cluster, consists of objects that are similar between themselves and dissimilar to objects of other groups. Several clustering methods are based on partitional clustering. This category attempts to directly decompose the dataset into a set of disjoint clusters leading to an integer number of clusters that optimizes a given criterion function. The criterion function may emphasize a local or a global structure of the data, and its optimization is an iterative relocation procedure. The K-Means algorithm is one of the most widely used partitional clustering techniques. Since K-Means is extremely sensitive to the initial choice of centers and a poor choice of centers may lead to a local optimum that is quite inferior to the global optimum, we propose a strategy to initiate K-Means centers. The improved K-Means algorithm is compared with the original K-Means, and the results prove how the efficiency has been significantly improved.

Keywords: Microarray data mining, biological pattern recognition, partitional clustering, k-means algorithm, centroid initialization.

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Authors: Sameh Abu El-Soud, Zahra Zayed, Safwan Khedr, Adel M. Belal

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The population increase in Egypt is urging for horizontal land development which became a demand to allow the benefit of different natural resources and expand from the narrow Nile valley. However, this development is facing challenges preventing land development and agriculture development. Desertification and moving sand dunes in the west sector of Egypt are considered the major obstacle that is blocking the ideal land use and development. In the proposed research, the sandy soil is treated biologically using Bacillus pasteurii bacteria as these bacteria have the ability to bond the sand partials to change its state of loose sand to cemented sand, which reduces the moving ability of the sand dunes. The procedure of implementing the Microbial Induced Carbonate Precipitation Technique (MICP) technique is examined, and the different factors affecting on this process such as the medium of bacteria sample preparation, the optical density (OD600), the reactant concentration, injection rates and intervals are highlighted. Based on the findings of the MICP treatment for sandy soil, conclusions and future recommendations are reached.

Keywords: Soil stabilization, biological treatment, MICP, sand cementation.

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Authors: Rafayel A. Azizyan, Aram E. Gevorgyan, Valeri B. Arakelyan, Emil S. Gevorgyan

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Currently, mathematical and computer modeling are widely used in different biological studies to predict or assess behavior of such a complex systems as a biological are. This study deals with mathematical and computer modeling of bi-substrate enzymatic reactions, which play an important role in different biochemical pathways. The main objective of this study is to represent the results from in silico investigation of bi-substrate enzymatic reactions in the presence of uncompetitive inhibitors, as well as to describe in details the inhibition effects. Four models of uncompetitive inhibition were designed using different software packages. Particularly, uncompetitive inhibitor to the first [ES₁] and the second ([ES₁S₂]; [FS₂]) enzyme-substrate complexes have been studied. The simulation, using the same kinetic parameters for all models allowed investigating the behavior of reactions as well as determined some interesting aspects concerning influence of different cases of uncompetitive inhibition. Besides, it has been shown that uncompetitive inhibitors exhibit specific selectivity depending on mechanism of bi-substrate enzymatic reaction. 

Keywords: Mathematical modeling, bi-substrate enzymatic reactions, sequential mechanism, ping-pong mechanism, uncompetitive inhibition.

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Authors: Kittiwann Nimkerdphol, Masahiro Nakagawa

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Biological reactions of individuals of a testing animal to toxic substance are unique and can be used as an indication of the existing of toxic substance. However, to distinguish such phenomenon need a very complicate system and even more complicate to analyze data in 3 dimensional. In this paper, a system to evaluate in vitro biological activities to acute toxicity of stochastic self-affine non-stationary signal of 3D goldfish swimming by using fractal analysis is introduced. Regular digital camcorders are utilized by proposed algorithm 3DCCPC to effectively capture and construct 3D movements of the fish. A Critical Exponent Method (CEM) has been adopted as a fractal estimator. The hypothesis was that the swimming of goldfish to acute toxic would show the fractal property which related to the toxic concentration. The experimental results supported the hypothesis by showing that the swimming of goldfish under the different toxic concentration has fractal properties. It also shows that the fractal dimension of the swimming related to the pH value of FD Ôëê 0.26pH + 0.05. With the proposed system, the fish is allowed to swim freely in all direction to react to the toxic. In addition, the trajectories are precisely evaluated by fractal analysis with critical exponent method and hence the results exhibit with much higher degree of confidence.

Keywords: 3D locomotion, bioassay, critical exponent method, CEM, fractal analysis, goldfish.

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Authors: A. F. Ali, D. M. Shawky

Abstract:

Discovering new biological knowledge from the highthroughput biological data is a major challenge to bioinformatics today. To address this challenge, we developed a new approach for protein classification. Proteins that are evolutionarily- and thereby functionally- related are said to belong to the same classification. Identifying protein classification is of fundamental importance to document the diversity of the known protein universe. It also provides a means to determine the functional roles of newly discovered protein sequences. Our goal is to predict the functional classification of novel protein sequences based on a set of features extracted from each protein sequence. The proposed technique used datasets extracted from the Structural Classification of Proteins (SCOP) database. A set of spectral domain features based on Fast Fourier Transform (FFT) is used. The proposed classifier uses multilayer back propagation (MLBP) neural network for protein classification. The maximum classification accuracy is about 91% when applying the classifier to the full four levels of the SCOP database. However, it reaches a maximum of 96% when limiting the classification to the family level. The classification results reveal that spectral domain contains information that can be used for classification with high accuracy. In addition, the results emphasize that sequence similarity measures are of great importance especially at the family level.

Keywords: Bioinformatics, Artificial Neural Networks, Protein Sequence Analysis, Feature Extraction.

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Authors: Dmitry Yu. Korulkin, Raissa A. Muzychkina, Evgenii N. Kojaev

Abstract:

In review the generalized data about biological activity of anthraquinone-containing plants and specimens on their basis is presented. Data of traditional medicine, results of bioscreening and clinical researches of specimens are analyzed.

Keywords: Anthraquinones, physiologically active substances, phytopreparation, Ramon.

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Authors: A. H. Tadevosyan, S. K. Mayrapetyan, N. B. Tavakalyan, K. I. Pyuskyulyan, A. H. Hovsepyan, S. N. Sergeeva

Abstract:

Soil contamination with radiocesium has a long-term radiological impact due to its long physical half-life (30.1 years for ¹³⁷Cs and 2 years for ¹³⁴Cs) and its high biological availability. ¹³⁷Cs causes the largest concerns because of its deleterious effect on agriculture and stock farming, and, thus, human life for decades. One of the important aspects of the problem of contaminated soils remediation is understand of protective actions aimed at the reduction of biological migration of radionuclides in soil-plant system. The most effective way to bind radionuclides is the use of selective sorbents. The proposed research mainly aims to achieve control on transfer of ¹³⁷Cs in a system growing media – plant due to counter ions variation in the polymeric sorbents. As research object Japanese basil - Perilla frutescens was chosen. Productivity of plants depending on the presence (control-without presence of polymer) and type of polymer material, as well as content of ¹³⁷Cs in plant material has been determined. The character of different polymers influences on the ¹³⁷Cs migration in growing media – plant system as well as accumulation in the plants has been cleared up.

Keywords: Radioceaseum, Japanese basil, polymer, soil-plant system.

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Authors: Terna T. Paul, Iloechuba P. Ngozika

Abstract:

A study was carried out to evaluate the growth and yield performance of Pleurotus ostreatus spawn on different organic substrates in Lafia, Nasarawa State, Nigeria. 50 g each of four different substrates namely; corncobs, rice straw, sugarcane bagasse and sawdust sourced locally from farmlands and processing sites, were amended with 2% calcium carbonate and calcium sulphide and sterilized using three sterilization methods namely; hot water, steam, and lime. Five grams of P. ostreatus spawn were inoculated unto treated substrates, incubated in the dark for 16 days and in light for 19 days at 25 ⁰C for the commencement of pinhead and fruit body formations respectively. Growth and yield parameters such as days to full colonization, days to pinhead formation and days to fruit body formation were recorded. Cap diameter and fresh weight of mature mushrooms were also measured for a total count of four flushes. P. ostreatus spawn grown on sugarcane bagasse recorded the highest mean cap diameter (4.69 cm), highest mean fresh weight (34.68 g), highest biological efficiency (69.37%) and highest production rate (2.83 g per day). Spawn grown on rice straw recorded the least number of days to full substrate colonization (11.00). Spawn grown on corn cobs recorded the least mean number of days to pin head (18.75) and fruiting body formations (20.25). There were no significant differences (P ≤ 0.05) among the evaluated substrates with respect to growth and yield performance of P. ostreatus. Substrates sterilized with hot water supported the highest mean cap diameter (5.64 cm), highest biological efficiency (87.04%) and highest production rate (3.43 g per day) of P. ostreatus. Significant differences (P ≤ 0.05) were observed in cap diameter, fresh weight, biological efficiency and production rates among the evaluated sterilization methods. Hot water sterilization of sugarcane bagasse could be adopted for enhanced yield of oyster mushrooms, especially among indigent farming communities in Nigeria and beyond.

Keywords: Agro wastes, growth, Pleurotus ostreatus, sterilization methods, yield.

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Authors: Asok Adak, Debabrata Mazumder, Pratip Bandyopadhyay

Abstract:

Anaerobic Digestion has become a promising technology for biological transformation of organic fraction of the municipal solid wastes (MSW). In order to represent the kinetic behavior of such biological process and thereby to design a reactor system, development of a mathematical model is essential. Addressing this issue, a simplistic mathematical model has been developed for anaerobic digestion of MSW in a continuous flow reactor unit under homogeneous steady state condition. Upon simulated hydrolysis, the kinetics of biomass growth and substrate utilization rate are assumed to follow first order reaction kinetics. Simulation of this model has been conducted by studying sensitivity of various process variables. The model was simulated using typical kinetic data of anaerobic digestion MSW and typical MSW characteristics of Kolkata. The hydraulic retention time (HRT) and solid retention time (SRT) time were mainly estimated by varying different model parameters like efficiency of reactor, influent substrate concentration and biomass concentration. Consequently, design table and charts have also been prepared for ready use in the actual plant operation.

Keywords: Anaerobic digestion, municipal solid waste (MSW), process design model, simulation study, hydraulic retention time(HRT), solid retention time (SRT).

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