Search results for: Biological clock

Authors: S. Sarumathi, M. Vaishnavi, S. Geetha, P. Ranjetha

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Machine learning is a new and exciting area of artificial intelligence nowadays. Machine learning is the most valuable, time, supervised, and cost-effective approach. It is not a narrow learning approach; it also includes a wide range of methods and techniques that can be applied to a wide range of complex realworld problems and time domains. Biological image classification, adaptive testing, computer vision, natural language processing, object detection, cancer detection, face recognition, handwriting recognition, speech recognition, and many other applications of machine learning are widely used in research, industry, and government. Every day, more data are generated, and conventional machine learning techniques are becoming obsolete as users move to distributed and real-time operations. By providing fundamental knowledge of machine learning tools and research opportunities in the field, the aim of this article is to serve as both a comprehensive overview and a guide. A diverse set of machine learning resources is demonstrated and contrasted with the key features in this survey.

Keywords: Artificial intelligence, machine learning, deep learning, machine learning algorithms, machine learning tools.

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Authors: Eka Sari, Siti Syamsiah, Hary Sulistyo, Muslikhin

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Lignocellulosic materials are considered the most abundant renewable resource available for the Bioethanol Production. Water Hyacinth is one of potential raw material of the world-s worst aquatic plant as a feedstock to produce Bioethanol. The purposed this research is obtain reduced of matter for biodegradation lignin in Biological pretreatment with White Rot Fungi eg. Phanerochaete Chrysosporium using Solid state Fermentation methods. Phanerochaete Chrysosporium is known to have the best ability to degraded lignin, but simultaneously it can also degraded cellulose and hemicelulose. During 8 weeks incubation, water hyacinth occurred loss of weight reached 34,67%, while loss of lignin reached 67,21%, loss of cellulose reached 11,01% and loss of hemicellulose reached 36,56%. The kinetic of losses lignin using regression linear plot, the results is obtained constant rate (k) of reduction lignin is -0.1053 and the equation of reduction of lignin is y = wo - 0, 1.53 x

Keywords: Biodegradation, lignin, PhanerochaeteChrysosporium, SSF, Water Hyacinth, Bioethanol

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Authors: Xiaochun Huang, Xuejun Zhao, Yun Zou, Feiyu Yang, Wenbin Liu, Nan Deng, Ming Zhang, Nengbin Cai

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A simple device termed infrared radiation (IR) was developed for rapid visualization of sweat fingerprints deposit on paper with blue light (450 nm, 11 W). In this approach, IR serves as the pretreatment device before the sweat fingerprints was illuminated by blue light. An annular blue light source was adopted for visualizing latent sweat fingerprints. Sample fingerprints were examined under various conditions after deposition, and experimental results indicate that the recovery rate of the latent sweat fingerprints is in the range of 50%-100% without chemical treatments. A mechanism for the observed visibility is proposed based on transportation and re-impregnation of fluorescer in paper at the region of water. And further exploratory experimental results gave the full support to the visible mechanism. Therefore, such a method as IR-pretreated in detecting latent fingerprints may be better for examination in the case where biological information of samples is needed for consequent testing.

Keywords: Forensic science, visualization, infrared radiation, blue light, latent sweat fingerprints, detection.

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Authors: Jin Sun Oh, Kyung Ho Lee, S ang Gug Chung, Kyehan Rhee

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Microbubbbles incorporating ultrasound have been used to increase the efficacy of targeted drug delivery, because microstreaming induced by cavitating bubbles affects the drug perfusion into the target cells and tissues. In order to clarify the physical effects of microstreaming on drug perfusion into tissues, a preliminary experimental study of perfusion enhancement by a stably oscillating microbubble was performed. Microstreaming was induced by an oscillating bubble at 15 kHz, and perfusion of dye into an agar phantom was optically measured by histology on agar phantom. Surface color intensity and the penetration length of dye in the agar phantom were increased more than 70% and 30%, respectively, due to the microstreaming induced by an oscillating bubble. The mass of dye perfused into a tissue phantom for 30 s was increased about 80% in the phantom with an oscillating bubble. This preliminary experiment shows the physical effects of steady streaming by an oscillating bubble can enhance the drug perfusion into the tissues while minimizing the biological effects.

Keywords: Bubble, Mass Transfer, Microstreaming, Drug Delivery, Acoustic Wave.

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Authors: Nichole Haag, Kimberly Velk, Tyler McCune, Chun Wu

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Methicillin/multiple-resistant Staphylococcus aureus (MRSA) are infectious bacteria that are resistant to common antibiotics. A previous in silico study in our group has identified a hypothetical protein SAV1226 as one of the potential drug targets. In this study, we reported the bioinformatics characterization, as well as cloning, expression, purification and kinetic assays of hypothetical protein SAV1226 from methicillin/vancomycin-resistant Staphylococcus aureus Mu50 strain. MALDI-TOF/MS analysis revealed a low degree of structural similarity with known proteins. Kinetic assays demonstrated that hypothetical protein SAV1226 is neither a domain of an ATP dependent dihydroxyacetone kinase nor of a phosphotransferase system (PTS) dihydroxyacetone kinase, suggesting that the function of hypothetical protein SAV1226 might be misannotated on public databases such as UniProt and InterProScan 5.

Keywords: Dihydroxyacetone kinase, essential genes, Methicillin-resistant Staphylococcus aureus, drug target.

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Authors: K. Santacruz-Gomez, E. Silva-Campa, S. Álvarez-García, V. Mata-Haro, D. Soto-Puebla, M. Pedroza-Montero

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Blood gamma irradiation is the only available method to prevent transfusion associated graft versus host disease (TAGVHD). However, when blood is irradiated, determine blood shelf time is crucial. Non irradiated blood have a self-time from 21 to 35 days when is preserved with anticoagulated solution and stored at 4°C. During their storage, red blood cells (RBC) undergo a series of biochemical, biomechanical and molecular changes involving what is known as storage lesion (SL). SL include loss of structural integrity of RBC, decrease of 2,3-diphosphatidylglyceric acid levels, and increase of both ion potassium concentration and hemoglobin (Hb). On the other hand, Atomic force Microscopy (AFM) represents a versatile tool for a nano-scale high resolution topographic analysis in biological systems. In order to evaluate SL in irradiated and nonirradiated blood, RBC topography and morphometric parameters were obtained from an AFM XE-BIO system. Cell viability was followed using flow cytometry. Our results showed that early markers as nanoscale roughness, allow us to evaluate blood quality since other perspective.

Keywords: AFM, Blood γ-irradiation, roughness, Storage lesion.

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Authors: M. Bakhouya, S. A. Bahra, T. El-Ghazawi

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The Partitioned Global Address Space (PGAS) programming paradigm offers ease-of-use in expressing parallelism through a global shared address space while emphasizing performance by providing locality awareness through the partitioning of this address space. Therefore, the interest in PGAS programming languages is growing and many new languages have emerged and are becoming ubiquitously available on nearly all modern parallel architectures. Recently, new parallel machines with multiple cores are designed for targeting high performance applications. Most of the efforts have gone into benchmarking but there are a few examples of real high performance applications running on multicore machines. In this paper, we present and evaluate a parallelization technique for implementing a local DNA sequence alignment algorithm using a PGAS based language, UPC (Unified Parallel C) on a chip multithreading architecture, the UltraSPARC T1.

Keywords: Partitioned Global Address Space, Unified Parallel C, Multicore machines, Multi-threading Architecture, Sequence alignment.

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Authors: Manuela Ciocoiu, Laur Badescu, Oana Badulescu, Magda Badescu

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The research focuses on the effects of polyphenols extracted from Sambucus nigra fruit, using an experimental arterial hypertension pattern, as well as their influence on the oxidative stress. The results reveal the normalization of the reduced glutathion concentration, as well as a considerable reduction in the malondialdehide serum concentration by the polyphenolic protection. The rat blood pressure values were recorded using a CODATM system, which uses a non-invasive blood pressure measuring method. All the measured blood pressure components revealed a biostatistically significant (p<0.05) blood pressure drop between the AHT and the AHT+P groups. The results prove that oxidative stress is considerably lower, statistically speaking, in rats with hypertension but also provided with natural polyphenolic protection from Sambucus nigra fruits than in the rats belonging to the control group. In addition to the demonstrated antioxidant effects, natural polyphenols also have other biological properties that might contribute to the cardioprotective effects.

Keywords: Arterial hypertension, Oxidative stress, Sambucus nigra

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Authors: A. Maria G. Melero, A. M. Senna, J. A. Domingues, M. A. Hausen, E. Aparecida R. Duek, V. R. Botaro

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A hydrogel from cellulose acetate cross linked with ethylenediaminetetraacetic dianhydride (HAC-EDTA) was synthesized by our research group, and submitted to characterization and biological tests. Cytocompatibility analysis was performed by confocal microscopy using human adipocyte derived stem cells (ASCs). The FTIR analysis showed characteristic bands of cellulose acetate and hydroxyl groups and the tensile tests evidence that HAC-EDTA present a Young’s modulus of 643.7 MPa. The confocal analysis revealed that there was cell growth at the surface of HAC-EDTA. After one day of culture the cells presented spherical morphology, which may be caused by stress of the sequestration of Ca²⁺ and Mg²⁺ ions at the cell medium by HAC-EDTA, as demonstrated by ICP-MS. However, after seven days and 14 days of culture, the cells present fibroblastoid morphology, phenotype expected by this cellular type. The results give efforts to indicate this new material as a potential biomaterial for tissue engineering, in the future in vivo approach.

Keywords: Cellulose acetate, hydrogel, biomaterial, cellular growth.

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Authors: Budhi Primasari, Shaliza Ibrahim, M Suffian M Annuar, Lim Xung Ian Remmie

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This study is aimed to investigate feasibility of the aerobic biological process to treat oily wastewater from palm oil food industry. Effect of aeration and sludge concentrations are studied. Raw sludge and raw wastewater was mixed and acclimatized for five days in a stirred tank reactor. The aeration rate (no aeration, low; 1.5L/min and high rate; 2L/min) and sludge concentration (3675, 7350, and 11025mg/L of VSS) were varied. Responses of process were pH, COD, oil and grease, VSS, and PHB content. It was found that the treatment can remove 85.1 to 97.1 % of COD and remove 12.9 to 54.8% of oil & grease. The PHB yield was found to be within 0.15% to 2.4% as PHB/VSS ratio and 0.01% to 0.12% as PHB/COD removed. The higher aeration results a high COD removal and oil & grease removal, while experiment without aeration gives better PHB yield. Higher sludge concentrations (11025mg/L VSS) give higher removal of oil & grease while moderate sludge concentration (7350mg/L VSS) give better result in COD removal. Higher PHB yield is obtained in low sludge concentration (3675mg/L).

Keywords: oily wastewater, COD, PHB, oil and grease

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Authors: Hanan Moawad, Naglaa M. Abd EL-Rahman

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Erwinia carotovora var. carotovora is the main cause of soft rot in potatoes. Hyphaene thebaica was studied for biocontrol of E. carotovora which inhibited growth of E. carotovora on solid medium, a comparative study of classical and ultrasound-assisted extractions of Hyphaene thebaica fruit. The use of ultrasound decreased significant the total time of treatment and increase the total amount of crude extract. The crude extract was subjected to determine the in vitro, by a bioassay technique revealed that the treatment of paper disks with ultrasound extraction of Hyphaene thebaica reduced the growth of pathogen and produced inhibition zones up to 38mm in diameter. The antioxidant activity of ultrasound-ethanolic extract of Doum fruits (Hyphaene thebaica) was determined. Data obtained showed that the extract contains the secondary metabolites such as Tannins, Saponin, Flavonoids, Phenols, Steroids, Terpenoids, Glycosides and Alkaloids.

Keywords: Ultrasound, classical extract, Biological control, Erwinia carotovora, Hyphaene thebaica.

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Authors: Ali Lemouari, Mohamed Benmohamed

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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.

Keywords: Ants system, emergence, exclusion process, pheromone.

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Authors: Shashank.B. Thakre, L.B. Bhuyar, Samir.J. Deshmukh

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The value of overall oxygen transfer Coefficient (KLa), which is the best measure of oxygen transfer in water through aeration, is obtained by a simple approach, which sufficiently explains the utility of the method to eliminate the discrepancies due to inaccurate assumption of saturation dissolved oxygen concentration. The rate of oxygen transfer depends on number of factors like intensity of turbulence, which in turns depends on the speed of rotation, size, and number of blades, diameter and immersion depth of the rotor, and size and shape of aeration tank, as well as on physical, chemical, and biological characteristic of water. An attempt is made in this paper to correlate the overall oxygen transfer Coefficient (KLa), as an independent parameter with other influencing parameters mentioned above. It has been estimated that the simulation equation developed predicts the values of KLa and power with an average standard error of estimation of 0.0164 and 7.66 respectively and with R2 values of 0.979 and 0.989 respectively, when compared with experimentally determined values. The comparison of this model is done with the model generated using Computational fluid dynamics (CFD) and both the models were found to be in good agreement with each other.

Keywords: CFD Model, Overall oxygen transfer coefficient, Power, Mathematical Model, Validation.

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Authors: N. K. Srivastava, M. K. Jha, I. D. Mall, Davinder Singh

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The treatment of the industrial wastewater can be particularly difficult in the presence of toxic compounds. Excessive concentration of Chromium in soluble form is toxic to a wide variety of living organisms. Biological removal of heavy metals using natural and genetically engineered microorganisms has aroused great interest because of its lower impact on the environment. Ralston metallidurans, formerly known as Alcaligenes eutrophus is a LProteobacterium colonizing industrial wastewater with a high content of heavy metals. Tris-buffered mineral salt medium was used for growing Alcaligenes eutrophus AE104 (pEBZ141). The cells were cultivated for 18 h at 30 oC in Tris-buffered mineral salt medium containing 3 mM disodium sulphate and 46 mM sodium gluconate as the carbon source. The cells were harvested by centrifugation, washed, and suspended in 10 mM Tris HCl, pH 7.0, containing 46 mM sodium gluconate, and 5 mM Chromium. Interaction among induction of chr resistance determinant, and chromate reduction have been demonstrated. Results of this study show that the above bacteria can be very useful for bioremediation of chromium from industrial wastewater.

Keywords: Chromium, Genetic Engineering, IndustrialWastewater, Plasmid

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Authors: V. Zamora, Z. Zhang, A. Meldrum

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The compatibility of optical resonators with microfluidic systems may be relevant for chemical and biological applications. Here, a fluorescent-core microcavity (FCM) is investigated as a refractometric sensor for heavy oils. A high-index film of silicon quantum dots (QDs) was formed inside the capillary, supporting cylindrical fluorescence whispering gallery modes (WGMs). A set of standard refractive index oils was injected into a capillary, causing a shift of the WGM resonances toward longer wavelengths. A maximum sensitivity of 240 nm/RIU (refractive index unit) was found for a nominal oil index of 1.74. As well, a sensitivity of 22 nm/RIU was obtained for a lower index of 1.48, more typical of fuel hydrocarbons. Furthermore, the observed spectra and sensitivities were compared to theoretical predictions and reproduced via FDTD simulations, showing in general an excellent agreement. This work demonstrates the potential use of FCMs for oil sensing applications and the more generally for detecting liquid solutions with a high refractive index or high viscosity.

Keywords: Oils, optical resonators, sensing applications, whispering gallery modes.

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Authors: Augustine Chioma Affam, Shamsul Rahman M. Kutty, Malay Chaudhuri

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The feasibility of employing solar radiation for enhanced Fenton process in degradation of combined chlorpyrifos, cypermethrin and chlorothalonil pesticides was examined. The effect of various operating conditions of the process on biodegradability improvement and mineralization of the pesticides were also evaluated. The optimum operating conditions for treatment of aqueous solution containing 100, 50 and 250 mg L-1 chlorpyrifos cypermethrin and chlorothalonil, respectively were observed to be H2O2/COD molar ratio 2, H2O2/Fe2+ molar ratio 25 and pH 3. Under the optimum operating conditions, complete degradation of the pesticides occurred in 1 min. Biodegradability (BOD5/COD) increased from zero to 0.36 in 60 min, and COD and TOC removal were 74.19 and 58.32%, respectively in 60 min. Due to mineralization of organic carbon, decrease in ammonia-nitrogen from 22 to 4.3 mg L-1 and increase in nitrate from 0.7 to 18.1 mg L-1 in 60 min were recorded. The study indicated that solar photo-Fenton process can be used for pretreatment of chlorpyrifos, cypermethrin and chlorothalonil pesticides in aqueous solution for further biological treatment.

Keywords: Chlorpyrifos, Cypermethrin, Chlorothalonil, Solar photo-Fenton

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

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The mathematical modeling of different biological processes is usually used to predict or assess behavior of systems in which these processes take place. This study deals with mathematical and computer modeling of bi-substrate enzymatic reactions with ping-pong mechanism, which play an important role in different biochemical pathways. Besides that, three models of competitive inhibition were designed using different software packages. The main objective of this study is to represent the results from in silico investigation of bi-substrate enzymatic reactions with ordered pingpong mechanism in the presence of competitive inhibitors, as well as to describe in details the inhibition effects. The simulation of the models with certain kinetic parameters allowed investigating the behavior of reactions as well as determined some interesting aspects concerning influence of different cases of competitive inhibition. Simultaneous presence of two inhibitors, competitive to the S1 and S2 substrates have been studied. Moreover, we have found the pattern of simultaneous influence of both inhibitors.

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

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Authors: Mária Stachová, Lukáš Sobíšek

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Data mining incorporates a group of statistical methods used to analyze a set of information, or a data set. It operates with models and algorithms, which are powerful tools with the great potential. They can help people to understand the patterns in certain chunk of information so it is obvious that the data mining tools have a wide area of applications. For example in the theoretical chemistry data mining tools can be used to predict moleculeproperties or improve computer-assisted drug design. Classification analysis is one of the major data mining methodologies. The aim of thecontribution is to create a classification model, which would be able to deal with a huge data set with high accuracy. For this purpose logistic regression, Bayesian logistic regression and random forest models were built using R software. TheBayesian logistic regression in Latent GOLD software was created as well. These classification methods belong to supervised learning methods. It was necessary to reduce data matrix dimension before construct models and thus the factor analysis (FA) was used. Those models were applied to predict the biological activity of molecules, potential new drug candidates.

Keywords: data mining, classification, drug design, QSAR

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Authors: Irfan Z. Qureshi, Fareeha A., Wajid A. Khan

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Human amniotic membrane (HAM) is a useful biological material for the reconstruction of damaged ocular surface. The processing and preservation of HAM is critical to prevent the patients undergoing amniotic membrane transplant (AMT) from cross infections. For HAM preparation human placenta is obtained after an elective cesarean delivery. Before collection, the donor is screened for seronegativity of HCV, Hbs Ag, HIV and Syphilis. After collection, placenta is washed in balanced salt solution (BSS) in sterile environment. Amniotic membrane is then separated from the placenta as well as chorion while keeping the preparation in BSS. Scrapping of HAM is then carried out manually until all the debris is removed and clear transparent membrane is acquired. Nitrocellulose membrane filters are then placed on the stromal side of HAM, cut around the edges with little membrane folded towards other side making it easy to separate during surgery. HAM is finally stored in solution of glycerine and Dulbecco-s Modified Eagle Medium (DMEM) in 1:1 ratio containing antibiotics. The capped borosil vials containing HAM are kept at -80°C until use. This vial is thawed to room temperature and opened under sterile operation theatre conditions at the time of surgery.

Keywords: HAM, AMT, ocular transplant

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Authors: Inas S. Khayal, Weiping Zhou, Jonathan Skinner

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Healthcare delivery systems around the world are in crisis. The need to improve health outcomes while decreasing healthcare costs have led to an imminent call to action to transform the healthcare delivery system. While Bioinformatics and Biomedical Engineering have primarily focused on biological level data and biomedical technology, there is clear evidence of the importance of the delivery of care on patient outcomes. Classic singular decomposition approaches from reductionist science are not capable of explaining complex systems. Approaches and methods from systems science and systems engineering are utilized to structure healthcare delivery system data. Specifically, systems architecture is used to develop a multi-scale and multi-dimensional characterization of the healthcare delivery system, defined here as the Healthcare Delivery System Knowledge Base. This paper is the first to contribute a new method of structuring and visualizing a multi-dimensional and multi-scale healthcare delivery system using systems architecture in order to better understand healthcare delivery.

Keywords: Health informatics, systems thinking, systems architecture, healthcare delivery system, data analytics.

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Authors: H. Yousefnia, S. Zolghadri, A. Golabi Dezfuli

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Abstract—[Tris (1,10-phenanthroline) lanthanum(III)] trithiocyanate is a new compound that has shown high ability for stopping the synthesis of DNA and also acting as a photosensitizer. Nowadays, the radiation dose assessment resource (RADAR) method is known as the most common method for absorbed dose calculation. 177Lu was produced by (n, gamma) reaction in a research reactor. 177Lu-PL3 was prepared in the optimized condition. The radiochemical yield was checked by ITLC method. The biodistribution of the complex was investigated by intravenously injection to wild-type rats via their tail veins. In this study, the absorbed dose of 177Lu-PL3 to human organs was estimated by RADAR method. 177Lu was prepared with a specific activity of 2.6-3 GBq.mg-1 and radionuclide purity of 99.98 %. Final preparation of the radiolabelled complex showed high radiochemical purity of > 99%. The results show that liver and spleen have received the highest absorbed dose of 1.051 and 0.441 mSv/MBq, respectively. The absorbed dose values for these two dose-limiting tissues suggest more biological studies special in tumor-bearing animals.

Keywords: Internal dosimetry, Lutetium-177, radar.

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Authors: Chiu-Wen Chen, Chih-Feng Chen, Cheng-Di Dong

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Surface sediment samples were collected from the Canon River mouth, Taiwan and analyzed for polycyclic aromatic hydrocarbons (PAHs). Total PAHs concentrations varied from 337 to 1,252 ng/g dry weight, with a mean concentration of 827 ng/g dry weight. The spatial distribution of PAHs reveals that the PAHs concentration is relatively high in the river mouth region, and gradually diminishes toward the harbor region. Diagnostic ratios showed that the possible source of PAHs in the Canon River mouth could be petroleum combustion. The toxic equivalent concentrations (TEQcarc) of PAHs varied from 47 to 112 ng TEQ/g dry weight. Higher total TEQcarc values were found in the river mouth region. As compared with the US Sediment Quality Guidelines (SQGs), the observed levels of PAHs at Canon River mouth were lower than the effects range low (ERL), and would probably not exert adverse biological effects.

Keywords: PAHs, sediment, river mouth, sediment quality guidelines (SQGs), toxic equivalent (TEQcarc)

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Authors: Minsoo Lee, Yearn Jeong Kim, Yun-mi Kim, Sujeung Cheong, Sookyung Song

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Bio-chips are used for experiments on genes and contain various information such as genes, samples and so on. The two-dimensional bio-chips, in which one axis represent genes and the other represent samples, are widely being used these days. Instead of experimenting with real genes which cost lots of money and much time to get the results, bio-chips are being used for biological experiments. And extracting data from the bio-chips with high accuracy and finding out the patterns or useful information from such data is very important. Bio-chip analysis systems extract data from various kinds of bio-chips and mine the data in order to get useful information. One of the commonly used methods to mine the data is classification. The algorithm that is used to classify the data can be various depending on the data types or number characteristics and so on. Considering that bio-chip data is extremely large, an algorithm that imitates the ecosystem such as the ant algorithm is suitable to use as an algorithm for classification. This paper focuses on finding the classification rules from the bio-chip data using the Ant Colony algorithm which imitates the ecosystem. The developed system takes in consideration the accuracy of the discovered rules when it applies it to the bio-chip data in order to predict the classes.

Keywords: Ant Colony System, DNA chip data, Classification.

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Authors: Vishwesh Kulkarni, Nikhil Bellarykar

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Cellular complexity stems from the interactions among thousands of different molecular species. Thanks to the emerging fields of systems and synthetic biology, scientists are beginning to unravel these regulatory, signaling, and metabolic interactions and to understand their coordinated action. Reverse engineering of biological networks has has several benefits but a poor quality of data combined with the difficulty in reproducing it limits the applicability of these methods. A few years back, many of the commonly used predictive algorithms were tested on a network constructed in the yeast Saccharomyces cerevisiae (S. cerevisiae) to resolve this issue. The network was a synthetic network of five genes regulating each other for the so-called in vivo reverse-engineering and modeling assessment (IRMA). The network was constructed in S. cereviase since it is a simple and well characterized organism. The synthetic network included a variety of regulatory interactions, thus capturing the behaviour of larger eukaryotic gene networks on a smaller scale. We derive a new set of algorithms by solving a nonlinear optimization problem and show how these algorithms outperform other algorithms on these datasets.

Keywords: Synthetic gene network, network identification, nonlinear modeling, optimization.

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Authors: D.Nuketaeva, A.Kanagatova, I.Khan, B.Kylyshbayeva, G.Bektenova

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This article describes the aspects of the formation of the national idea and national identity through the prism of gender control and its contradistinction to the obsolete, Soviet component. The role of females in ethnic and national projects is considered from the point of view of Dr. Nira Yuval-Davis: as biological reproducers of the ethnic communities- members; as reproducers of the boarders of ethnic/national groups; as central participants in the ideological reproduction of community and transducers of its culture; as symbols in ideology, reproduction and transformation of ethnic/national categories; and as participants of national, economical, political and military combats. The society of the transitional type uses the symbolic resources of the formation of gender component in the national project. The gender patterns act like cultural codes, executing the important ideological function in formation of the national female- image, i.e. the discussion on hijab - it-s not just the discussion on control over the female body, it-s the discussion on the metaphor of social order.

Keywords: nation, gender, hijab, Islam, ideology, politics, national idea, national identity, society of the transitional type

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Authors: Dean J. Callaghan, Mark M. McGrath

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Sensorized instruments that accurately measure the interaction forces (between biological tissue and instrument endeffector) during surgical procedures offer surgeons a greater sense of immersion during minimally invasive robotic surgery. Although there is ongoing research into force measurement involving surgical graspers little corresponding effort has been carried out on the measurement of forces between scissor blades and tissue. This paper presents the design and development of a force measurement test apparatus, which will serve as a sensor characterization and evaluation platform. The primary aim of the experiments is to ascertain whether the system can differentiate between tissue samples with differing mechanical properties in a reliable, repeatable manner. Force-angular displacement curves highlight trends in the cutting process as well the forces generated along the blade during a cutting procedure. Future applications of the test equipment will involve the assessment of new direct force sensing technologies for telerobotic surgery.

Keywords: Force measurement, minimally invasive surgery, scissor blades, tissue cutting.

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Authors: Ines Hamdi, Mohamed Ben Ahmed

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The understanding of the system level of biological behavior and phenomenon variously needs some elements such as gene sequence, protein structure, gene functions and metabolic pathways. Challenging problems are representing, learning and reasoning about these biochemical reactions, gene and protein structure, genotype and relation between the phenotype, and expression system on those interactions. The goal of our work is to understand the behaviors of the interactions networks and to model their evolution in time and in space. We propose in this study an ontological meta-model for the knowledge representation of the genetic regulatory networks. Ontology in artificial intelligence means the fundamental categories and relations that provide a framework for knowledge models. Domain ontology's are now commonly used to enable heterogeneous information resources, such as knowledge-based systems, to communicate with each other. The interest of our model is to represent the spatial, temporal and spatio-temporal knowledge. We validated our propositions in the genetic regulatory network of the Aarbidosis thaliana flower

Keywords: Ontological model, spatio-temporal modeling, Genetic Regulatory Networks (GRNs), knowledge representation.

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Authors: Ghazaleh Monazami Tehrani, Reza Khani Jazani, Rosli Hashim , Ahmad Savari, Belin Tavakoly Sany, Parastoo Parivar, Zhamak Monazami Tehrani

Abstract:

This study investigated the presence of polycyclic aromatic hydrocarbons (PAHs) in the sediments of the Musa Bay (around the PETZONE coastal area) from Feb 2010 to Jun 2010. Concentrations of PAHs recorded in the Musa Bay sediments ranged from 537.89 to 26,659.06 ng/g dry weight with a mean value of 3990.74 ng/g. the highest concentration of PAHs was observed at station 4, which is located near the aromatic outlet of Imam Khomeini petrochemical company (station 4: BI-PC Aromatic effluent outlet) in which its concentration level was more than the NOAA sediment quality guideline value (ERL= 4022 ng/g dry weight). Owing to the concentration of PAHs in the study area, its concentration level was still meet the NOAA sediment quality guideline value (ERL: 4022 ng/g dry weight); however, according to the PELq factor, slightly adverse biological effects are associated with the exposure to PAHs levels in the study area (0.1< PELq= 0.24 > 0.5).

Keywords: Musa Bay, PAHs, PETZONE, NOAA, PELq.

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Authors: Imanda H. Pradana, Tillana Adilaviana, Christine Pretty Ballerena

Abstract:

Ever since industrial revolution began, our ecosystem has changed. And indeed, the negatives outweigh the positives. Industrial waste usually released into all kinds of body of water, such as river or sea. Tempeh waste is one example of waste that carries many hazardous and unwanted substances that will affect the surrounding environment. Tempeh is a popular fermented food in Asia which is rich in nutrients and active substances. Tempeh liquid waste- in particular- can cause an air pollution, and if penetrates through the soil, it will contaminates ground-water, making it unavailable for the water to be consumed. Moreover, bacteria will thrive within the polluted water, which often responsible for causing many kinds of diseases. The treatment used for this chemical waste is biological treatment such as constructed wetland and activated sludge. These kinds of treatment are able to reduce both physical and chemical parameters altogether such as temperature, TSS, pH, BOD, COD, NH3-N, NO3-N, and PO4-P. These treatments are implemented before the waste is released into the water. The result is a comparation between constructed wetland and activated sludge, along with determining which method is better suited to reduce the physical and chemical subtances of the waste.

Keywords: activated sludge, constructed wetland, waste, watertreatment

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Authors: Anna H. Tadevosyan, Stepan K. Mayrapetyan, Michael P. Schellenberg, Laura M. Ghalachyan, Albert H. Hovsepyan, Khachatur S. Mayrapetyan

Abstract:

The possibility of radionuclides-related contamination of lands at agricultural holdings defines the necessity to apply special protective measures in plant growing. The aim of researches is to elucidate the influence of polymers applying on biological migration of man-made anthropogenic radionuclides 90Sr and 137Cs in the system water - soil – plant. The tests are being carried out under field conditions with and without application of polymers in root-inhabited media in more radioecological tension zone (with the radius of 7 km from the Armenian Nuclear Power Plant). The polymers on the base of K+, Caµ, KµCaµ ions were tested. Productivity of pepper depending on the presence and type of polymer material, content of artificial radionuclides in waters, soil and plant material has been determined. The character of different polymers influence on the artificial radionuclides migration and accumulation in the system water-soil-plant and accumulation in the plants has been cleared up.

Keywords: accumulation of artificial radionuclides, pepper, polymer, water-soil-plant system

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