Search results for: gene clusters

Authors: Gholamhossein Hosseini

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Two earliness cotton genotypes I and II, which had been developed by hybridization and backcross methods between sindise-80 as an early maturing gene parent and two other lines i.e. Red leaf and Bulgare-557 as a second parent, are subjected to different environmental conditions. The early maturing genotypes with coded names of I and II were compared with four native cotton cultivars in randomized complete block design (RCBD) with four replications in three ecological regions of Iran from 2016-2017. Two early maturing genotypes along with four native cultivars viz. Varamin, Oltan, Sahel and Arya were planted in Agricultural Research Station of Varamin, Moghan and Kashmar for evaluation. Earliness data were collected for six treatments during two years in the three regions except missing data for the second year of Kashmar. Therefore, missed data were estimated and imputed. For testing the homogeneity of error variances, each experiment at a given location or year is analyzed separately using Hartley and Bartlett’s Chi-square tests and both tests confirmed homogeneity of variance. Combined analysis of variance showed that genotypes I and II were superior in Varamin, Moghan and Kashmar regions. Earliness means and their interaction effects were compared with Duncan’s multiple range tests. Finally combined analysis of variance showed that genotypes I and II were superior in Varamin, Moghan and Kashmar regions. Earliness means and their interaction effects are compared with Duncan’s multiple range tests.

Keywords: Cotton, combined, analysis, earliness.

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Authors: Kanthida Kusonmano, Michael Netzer, Bernhard Pfeifer, Christian Baumgartner, Klaus R. Liedl, Armin Graber

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Availability of high dimensional biological datasets such as from gene expression, proteomic, and metabolic experiments can be leveraged for the diagnosis and prognosis of diseases. Many classification methods in this area have been studied to predict disease states and separate between predefined classes such as patients with a special disease versus healthy controls. However, most of the existing research only focuses on a specific dataset. There is a lack of generic comparison between classifiers, which might provide a guideline for biologists or bioinformaticians to select the proper algorithm for new datasets. In this study, we compare the performance of popular classifiers, which are Support Vector Machine (SVM), Logistic Regression, k-Nearest Neighbor (k-NN), Naive Bayes, Decision Tree, and Random Forest based on mock datasets. We mimic common biological scenarios simulating various proportions of real discriminating biomarkers and different effect sizes thereof. The result shows that SVM performs quite stable and reaches a higher AUC compared to other methods. This may be explained due to the ability of SVM to minimize the probability of error. Moreover, Decision Tree with its good applicability for diagnosis and prognosis shows good performance in our experimental setup. Logistic Regression and Random Forest, however, strongly depend on the ratio of discriminators and perform better when having a higher number of discriminators.

Keywords: Classification, High dimensional data, Machine learning

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Authors: Aliaa M. El-Borai, Ehab A. Beltagy, Eman E. Gadallah, Samy A. ElAssar

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Bioremediation technology is now used for treatment instead of traditional metal removal methods. A strain was isolated from Marsa Alam, Red sea, Egypt showed high resistance to high lead concentration and was identified by the 16S rRNA gene sequencing technique as Halomonas sp. ES015. Medium optimization was carried out using Plackett-Burman design, and the most significant factors were yeast extract, casamino acid and inoculums size. The optimized media obtained by the statistical design raised the removal efficiency from 84% to 99% from initial concentration 250 ppm of lead. Moreover, Box-Behnken experimental design was applied to study the relationship between yeast extract concentration, casamino acid concentration and inoculums size. The optimized medium increased removal efficiency to 97% from initial concentration 500 ppm of lead. Immobilized Halomonas sp. ES015 cells on sponge cubes, using optimized medium in loop bioremediation column, showed relatively constant lead removal efficiency when reused six successive cycles over the range of time interval. Also metal removal efficiency was not affected by flow rate changes. Finally, the results of this research refer to the possibility of lead bioremediation by free or immobilized cells of Halomonas sp. ES015. Also, bioremediation can be done in batch cultures and semicontinuous cultures using column technology.

Keywords: Bioremediation, lead, Box–Behnken, Halomonas sp. ES015, loop bioremediation, Plackett-Burman.

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Authors: A. Dashti, M. Eskandari, L. Farahmand, P. Parvin, A. Jafargholi

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Breast Cancer is one of the most considerable diseases in the United States and other countries and is the second leading cause of death in women. Common breast cancer treatments would lead to adverse side effects such as loss of hair, nausea, and weakness. These complications arise because these cancer treatments damage some healthy cells while eliminating the cancer cells. In an effort to address these complications, laser radiation was utilized and tested as a targeted cancer treatment for breast cancer. In this regard, tissue engineering approaches are being employed by using an electrospun scaffold in order to facilitate the growth of breast cancer cells. Polycaprolacton (PCL) was used as a material for scaffold fabricating because of its biocompatibility, biodegradability, and supporting cell growth. The specific breast cancer cells have the ability to create a three-dimensional cell cluster due to the spontaneous accumulation of cells in the porosity of the scaffold under some specific conditions. Therefore, we are looking for a higher density of porosity and larger pore size. Fibers showed uniform diameter distribution and final scaffold had optimum characteristics with approximately 40% porosity. The images were taken by SEM and the density and the size of the porosity were determined with the Image. After scaffold preparation, it has cross-linked by glutaraldehyde. Then, it has been washed with glycine and phosphate buffer saline (PBS), in order to neutralize the residual glutaraldehyde. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromidefor (MTT) results have represented approximately 91.13% viability of the scaffolds for cancer cells. In order to create a cluster, Michigan Cancer Foundation-7 (MCF-7, breast cancer cell line) and Michigan Cancer Foundation-10A (MCF-10A, human mammary epithelial cell line) cells were cultured on the scaffold in 24 well plate for five days. Then, we have exposed the cluster to the laser diode 808 nm radiation to investigate the effect of laser on the tumor with different power and time. Under the same conditions, cancer cells lost their viability more than the healthy ones. In conclusion, laser therapy is a viable method to destroy the target cells and has a minimum effect on the healthy tissues and cells and it can improve the other method of cancer treatments limitations.

Keywords: Breast cancer, electrospun scaffold, polycaprolacton, laser diode, cancer treatment.

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Authors: First G.M. Karthik, Second Ramachandra.V.Pujeri, Dr.

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Generalized Center String (GCS) problem are generalized from Common Approximate Substring problem and Common substring problems. GCS are known to be NP-hard allowing the problems lies in the explosion of potential candidates. Finding longest center string without concerning the sequence that may not contain any motifs is not known in advance in any particular biological gene process. GCS solved by frequent pattern-mining techniques and known to be fixed parameter tractable based on the fixed input sequence length and symbol set size. Efficient method known as Bpriori algorithms can solve GCS with reasonable time/space complexities. Bpriori 2 and Bpriori 3-2 algorithm are been proposed of any length and any positions of all their instances in input sequences. In this paper, we reduced the time/space complexity of Bpriori algorithm by Constrained Based Frequent Pattern mining (CBFP) technique which integrates the idea of Constraint Based Mining and FP-tree mining. CBFP mining technique solves the GCS problem works for all center string of any length, but also for the positions of all their mutated copies of input sequence. CBFP mining technique construct TRIE like with FP tree to represent the mutated copies of center string of any length, along with constraints to restraint growth of the consensus tree. The complexity analysis for Constrained Based FP mining technique and Bpriori algorithm is done based on the worst case and average case approach. Algorithm's correctness compared with the Bpriori algorithm using artificial data is shown.

Keywords: Constraint Based Mining, FP tree, Data mining, GCS problem, CBFP mining technique.

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Authors: M. Sangeetha, D. Chamundeeswari, C. Saravanababu, C. Rose, V. Gopal

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Rheumatoid arthritis (RA) is a chronic, progressive, systemic inflammatory disorder affecting the synovial joints and typically producing symmetrical arthritis that leads to joint destruction, which is responsible for the deformity and disability. Despite improvements in the treatment of RA over the past decade, there still is a need for new therapeutic agents that are efficacious, less expensive, and free of severe adverse reactions. The present study aimed to investigate role of inflammatory markers in arthritic rats treated with ethanolic bark extract of Albizia procera. The protective effect of ethanolic bark extract of Albizia procera against complete Freund’s adjuvant (CFA) induced arthritis in rats. Arthritis was induced by an intradermal injection of 0.1 ml FCA in the foot pad of left hind limb of rats. ETBE (100 and 200 mg/kg b.wt./p.o) and the reference drug diclofenac (25 mg/kg b.wt./p.o) were administered to arthritic rats. Paw volume was measured for all the animals before inducing arthritis and thereafter once in seven days by using plethysmometer for 42 days. Gene expression of inflammatory markers such as IL-1β and IL-10 were investigated in paw tissues. Up regulation of IL-1β and Down regulation IL-10 were observed in CFA injected rats when compared to normal rats. ETBE attenuated these alterations dose dependently when compared to the vehicle treated rats. These results provide insights into the mechanism of anti-arthritic activity, and unravel potential therapeutic use of Albizia procera in arthritis.

Keywords: CFA-Complete Freund’s adjuvant, ETBE, Ethanolic Bark Extract, IL- Interleukins, RA-Rheumatoid Arthritis.

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Authors: Oluyemi O. Awolusi, Abimbola M. Enitan, Sheena Kumari, Faizal Bux

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Nitrification is essential to biological processes designed to remove ammonia and/or total nitrogen. It removes excess nitrogenous compound in wastewater which could be very toxic to the aquatic fauna or cause serious imbalance of such aquatic ecosystem. Efficient nitrification is linked to an in-depth knowledge of the structure and dynamics of the nitrifying community structure within the wastewater treatment systems. In this study, molecular technique was employed for characterizing the microbial structure of activated sludge [ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB)] in a municipal wastewater treatment with intention of linking it to the plant efficiency. PCR based phylogenetic analysis was also carried out. The average operating and environmental parameters as well as specific nitrification rate of plant was investigated during the study. During the investigation the average temperature was 23±1.5oC. Other operational parameters such as mixed liquor suspended solids and chemical oxygen demand inversely correlated with ammonia removal. The dissolved oxygen level in the plant was constantly lower than the optimum (between 0.24 and 1.267 mg/l) during this study. The plant was treating wastewater with influent ammonia concentration of 31.69 and 24.47 mg/L. The influent flow rates (ML/Day) was 96.81 during period. The dominant nitrifiers include: Nitrosomonas spp. Nitrobacter spp. and Nitrospira spp. The AOB had correlation with nitrification efficiency and temperature. This study shows that the specific ammonia oxidizing rate and the specific nitrate formation rates can serve as good indicator of the plant overall nitrification performance.

Keywords: Ammonia monooxygenase α-subunit (amoA) gene, ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), specific nitrification rate, PCR.

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Authors: Yanju Zhang, Joost M. Woltering, Fons J. Verbeek

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It has been established that microRNAs (miRNAs) play an important role in gene expression by post-transcriptional regulation of messengerRNAs (mRNAs). However, the precise relationships between microRNAs and their target genes in sense of numbers, types and biological relevance remain largely unclear. Dissecting the miRNA-target relationships will render more insights for miRNA targets identification and validation therefore promote the understanding of miRNA function. In miRBase, miRanda is the key algorithm used for target prediction for Zebrafish. This algorithm is high-throughput but brings lots of false positives (noise). Since validation of a large scale of targets through laboratory experiments is very time consuming, several computational methods for miRNA targets validation should be developed. In this paper, we present an integrative method to investigate several aspects of the relationships between miRNAs and their targets with the final purpose of extracting high confident targets from miRanda predicted targets pool. This is achieved by using the techniques ranging from statistical tests to clustering and association rules. Our research focuses on Zebrafish. It was found that validated targets do not necessarily associate with the highest sequence matching. Besides, for some miRNA families, the frequency of their predicted targets is significantly higher in the genomic region nearby their own physical location. Finally, in a case study of dre-miR-10 and dre-miR-196, it was found that the predicted target genes hoxd13a, hoxd11a, hoxd10a and hoxc4a of dre-miR- 10 while hoxa9a, hoxc8a and hoxa13a of dre-miR-196 have similar characteristics as validated target genes and therefore represent high confidence target candidates.

Keywords: MicroRNA targets validation, microRNA-target relationships, dre-miR-10, dre-miR-196.

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Authors: Feng-Sheng Wang, Wu-Hsiung Wu, Kai-Cheng Hsu

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The optimization of biological systems, which is a branch of metabolic engineering, has generated a lot of industrial and academic interest for a long time. In the last decade, metabolic engineering approaches based on mathematical optimizations have been used extensively for the analysis and manipulation of metabolic networks. In practical optimization of metabolic reaction networks, designers have to manage the nature of uncertainty resulting from qualitative characters of metabolic reactions, e.g., the possibility of enzyme effects. A deterministic approach does not give an adequate representation for metabolic reaction networks with uncertain characters. Fuzzy optimization formulations can be applied to cope with this problem. A fuzzy multi-objective optimization problem can be introduced for finding the optimal engineering interventions on metabolic network systems considering the resilience phenomenon and cell viability constraints. The accuracy of optimization results depends heavily on the development of essential kinetic models of metabolic networks. Kinetic models can quantitatively capture the experimentally observed regulation data of metabolic systems and are often used to find the optimal manipulation of external inputs. To address the issues of optimizing the regulatory structure of metabolic networks, it is necessary to consider qualitative effects, e.g., the resilience phenomena and cell viability constraints. Combining the qualitative and quantitative descriptions for metabolic networks makes it possible to design a viable strain and accurately predict the maximum possible flux rates of desired products. Considering the resilience phenomena in metabolic networks can improve the predictions of gene intervention and maximum synthesis rates in metabolic engineering. Two case studies will present in the conference to illustrate the phenomena.

Keywords: Fuzzy multi-objective optimization problem, kinetic model, metabolic engineering.

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Authors: M. Jarrar, S. Behl, N. Shaheen, A. Fatima, R. Nasab

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Skin aging is a slow multifactorial process influenced by both internal as well as external factors. Ultra-violet radiations (UV), diet, smoking and personal habits are the most common environmental factors that affect skin aging. Fat contents and fibrous proteins as collagen and elastin are core internal structural components. The direct influence of UV on elastin integrity and health is central on aging of skin especially by time. The deposition of abnormal elastic material is a major marker in a photo-aged skin. Searching for compounds that may protect against cutaneous photodamage is exceedingly valued. Retinoids and alpha hydroxy acids have been endorsed by some researchers as possible candidates for protecting and or repairing the effect of UV damaged skin. For consolidating a better system of anti- and protective effects of such anti-aging agents, we evaluated the combinatory effects of various dosages of lactic acid and retinol on the dermal fibroblast’s elastin levels exposed to UV. The UV exposed cells showed significant reduction in the elastin levels. A combination of drugs with a higher concentration of lactic acid (30 -35 mM) and a lower concentration of retinol (10-15mg/mL) showed to work better in maintaining elastin concentration in UV exposed cells. We assume this preservation could be the result of increased tropo-elastin gene expression stimulated by retinol whereas lactic acid probably repaired the UV irradiated damage by enhancing the amount and integrity of the elastin fibers.

Keywords: Alpha Hydroxy Acid, Elastin, Retinol, Ultraviolet radiations.

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Authors: Abu Salim Mustafa

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Rv3873 is a relatively large size protein (371 amino acids in length) and its gene is located in the immunodominant genomic region of difference (RD)1 that is present in the genome of Mycobacterium tuberculosis but deleted from the genomes of all the vaccine strains of Bacillus Calmette Guerin (BCG) and most other mycobacteria. However, when tested for cellular immune responses using peripheral blood mononuclear cells from tuberculosis patients and BCG-vaccinated healthy subjects, this protein was found to be a major stimulator of cell mediated immune responses in both groups of subjects. In order to further identify the sequence of immunodominant epitopes and explore their Human Leukocyte Antigen (HLA)-restriction for epitope recognition, 24 peptides (25-mers overlapping with the neighboring peptides by 10 residues) covering the sequence of Rv3873 were synthesized chemically using fluorenylmethyloxycarbonyl chemistry and tested in cell mediated immune responses. The results of these experiments helped in the identification of an immunodominant peptide P9 that was recognized by people expressing varying HLA-DR types. Furthermore, it was also predicted to be a promiscuous binder with multiple epitopes for binding to HLA-DR, HLA-DP and HLA-DQ alleles of HLA-class II molecules that present antigens to T helper cells, and to HLA-class I molecules that present antigens to T cytotoxic cells. In addition, the evaluation of peptide P9 using an immunogenicity predictor server yielded a high score (0.94), which indicated a greater probability of this peptide to elicit a protective cellular immune response. In conclusion, P9, a peptide with multiple epitopes and ability to bind several HLA class I and class II molecules for presentation to cells of the cellular immune response, may be useful as a peptide-based vaccine against tuberculosis.

Keywords: Mycobacterium tuberculosis, Rv3873, peptides, vaccine

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Authors: M. Areekijseree, M. Pumipaiboon, S. Nuamsukon, K. Kittiwattanawong, C. Thongchai, S. Sikiwat, T. Chuen-Im

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There are few studies on eggshell of leatherback turtle which is endangered species in Thailand. This study was focusing on the ultrastructure and elemental composition of leatherback turtle eggshells collected from Andaman Sea Shore, Thailand during the nesting season using scanning electron microscope (SEM). Three eggshell layers of leatherback turtle; the outer cuticle layer or calcareous layer, the middle layer or middle multistrata layer and the inner fibrous layer were recognized. The outer calcareous layer was thick and porosity which consisted of loose nodular units of various crystal shapes and sizes. The loose attachment between these units resulted in numerous spaces and openings. The middle layer was compact thick with several multistrata and contained numerous openings connecting to both outer cuticle layer and inner fibrous layer. The inner fibrous layer was compact and thin, and composed of numerous reticular fibers. Energy dispersive X-ray microanalysis detector revealed energy spectrum of X-rays character emitted from all elements on each layer. The percentages of all elements were found in the following order: carbon (C) > oxygen (O) > calcium (Ca) > sulfur (S) > potassium (K) > aluminum (Al) > iodine (I) > silicon (Si) > chlorine (Cl) > sodium (Na) > fluorine (F) > phosphorus (P) > magnesium (Mg). Each layer consisted of high percentage of CaCO3 (approximately 98%) implying that it was essential for turtle embryonic development. A significant difference was found in the percentages of Ca and Mo in the 3layers. Moreover, transition metal, metal and toxic non-metal contaminations were found in leatherback turtle eggshell samples. These were palladium (Pd), molybdenum (Mo), copper (Cu), aluminum (Al), lead (Pb), and bromine (Br). The contamination elements were seen in the outer layers except for Mo. All elements were readily observed and mapped using Smiling program. X-ray images which mapped the location of all elements were showed. Calcium containing in the eggshell appeared in high contents and was widely distributing in clusters of the outer cuticle layer to form CaCO3 structure. Moreover, the accumulation of Na and Cl was observed to form NaCl which was widely distributing in 3 eggshell layers. The results from this study would be valuable on assessing the emergent success in this endangered species.

Keywords: Leatherback turtle (Dermochelys coriacea), SEM (SEI/EDX), turtle eggshell.

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Authors: K. Vallianou, T. Alexopoulos, V. Plaka, M. K. Seleventi, V. Skanavis, C. Skanavis

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The present research addresses the role of place attachment and emotions in community resiliency and recovery within the context of a disaster. Natural disasters represent a disruption in the normal functioning of a community, leading to a general feeling of disorientation. This study draws on the trauma caused by a natural hazard such as a forest fire. The changes of the sense of togetherness are being assessed. Finally this research determines how the place attachment of the inhabitants was affected during the reorientation process of the community. The case study area is Mati, a small coastal town in eastern Attica, Greece. The fire broke out on July 23^rd, 2018. A quantitative research was conducted through questionnaires via phone interviews, one year after the disaster, to address community resiliency in the long-run. The sample was composed of 159 participants from the rural community of Mati plus 120 coming from Skyros Island that was used as a control group. Inhabitants were prompted to answer items gauging their emotions related to the event, group identification and emotional significance of their community, and place attachment before and a year after the fire took place. Importantly, the community recovery and reorientation were examined within the context of a relative absence of government backing and official support. Emotions related to the event were aggregated into 4 clusters related to: activation/vigilance, distress/disorientation, indignation, and helplessness. The findings revealed a decrease in the level of place attachment in the impacted area of Mati as compared to the control group of Skyros Island. Importantly, initial distress caused by the fire prompted the residents to identify more with their community and to report more positive feelings toward their community. Moreover, a mediation analysis indicated that the positive effect of community cohesion on place attachment one year after the disaster was mediated by the positive feelings toward the community. Finally, place attachment contributes to enhanced optimism and a more positive perspective concerning Mati’s future prospects. Despite an insufficient state support to this affected area, the findings suggest an important role of emotions and place attachment during the process of recovery. Implications concerning the role of emotions and social dynamics in meshing place attachment during the disaster recovery process as well as community resiliency are discussed.

Keywords: Community resilience, natural disasters, place attachment, wildfire.

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Authors: Muhammad Fiaz, Baseerat Rizwan, Naqvi Najam Abbas, Yang Naiding

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The aspiration of this research article is to target and focus the gains of university-Industry (U-I) collaborations and exploring those hurdles which are the obstacles for attaining these gains. University-Industry collaborations have attained great importance since 1980 in USA due to its application in all fields of life. U-I collaboration is a bilateral process where academia is a proactive member to make such alliances. Universities want to ameliorate their academic-base with the technicalities of technobabbles. U-I collaboration is becoming an essential lane for achieving innovative goals in this century. Many developed nations have set successful examples to prove this phenomenon as a catalyst to reduce costs, efforts and personnel for R&D projects. This study is exploits amplitudes of UI collaboration incentives in the light of success stories of developed countries. Many universities in USA, UK, Canada and various European Countries have been engaged with enterprises for numerous collaborative agreements. A long list of strategic and short term R&D projects has been executed in developed countries to accomplish their intended purposes. Due to the lack of intentions, genuine research and research-oriented environment, the mentioned field could not grow very well in developing countries. During last decade, a new wave of research has induced the institutes of developing countries to promote R&D culture especially in Pakistan. Higher Education Commission (HEC) has initiated many projects and funding supports for universities which have collaborative intentions with industry. Findings show that rapid innovation, overwhelm the technological complexities and articulated intellectual-base are major incentives which steer both partners to establish faculty-industry alliances. Everchanging technologies, concerned about intellectual property, different research environment and culture, research relevancy (Basic or applied), exposure differences and diversity of knowledge (bookish or practical) are main barriers to establish and retain joint ventures. Findings also concluded that, it is dire need to support and enhance cooperation among academia and industry to promote highly coordinated research behaviors. Author has proposed a roadmap for developing countries to promote R&D clusters among faculty and industry to deal the technological challenges and innovation complexities. Based on our research findings, Model for R&D Collaboration for developing countries also have been proposed to promote articulated R&D environment. If developing countries follow this phenomenon, rapid innovations can be achieved with limited R&D budget heads.

Keywords: University-Industry Collaboration, Academia, Innovation, R&D Barriers

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Authors: Achitphol Chookaew, Paramee Thongsukhsai, Patamarerk Engsontia, Narongwit Nakwan, Pritsana Raugrut

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Lung cancer is one of the most common malignancies and primary cause of death due to cancer worldwide. Non-small cell lung cancer (NSCLC) is the main subtype in which majority of patients present with advanced-stage disease. Herein, we analyzed differentially expressed genes to find potential biomarkers for lung cancer diagnosis as well as prognostic markers. We used transcriptome data from our 2 NSCLC patients and public data (GSE81089) composing of 8 NSCLC and 10 normal lung tissues. Differentially expressed genes (DEGs) between NSCLC and normal tissue and between early-stage and late-stage NSCLC were analyzed by the DESeq2. Pairwise correlation was used to find the DEGs with false discovery rate (FDR) adjusted p-value £ 0.05 and |log2 fold change| ³ 4 for NSCLC versus normal and FDR adjusted p-value £ 0.05 with |log2 fold change| ³ 2 for early versus late-stage NSCLC. Bioinformatic tools were used for functional and pathway analysis. Moreover, the top ten genes in each comparison group were verified the expression and survival analysis via GEPIA. We found 150 up-regulated and 45 down-regulated genes in NSCLC compared to normal tissues. Many immnunoglobulin-related genes e.g., IGHV4-4, IGHV5-10-1, IGHV4-31, IGHV4-61, and IGHV1-69D were significantly up-regulated. 22 genes were up-regulated, and five genes were down-regulated in late-stage compared to early-stage NSCLC. The top five DEGs genes were KRT6B, SPRR1A, KRT13, KRT6A and KRT5. Keratin 6B (KRT6B) was the most significantly increased gene in the late-stage NSCLC. From GEPIA analysis, we concluded that IGHV4-31 and IGKV1-9 might be used as diagnostic biomarkers, while KRT6B and KRT6A might be used as prognostic biomarkers. However, further clinical validation is needed.

Keywords: Bioinformatics, differentially expressed genes, non-small cell lung cancer, transcriptomics.

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Authors: Norsakinah Mohammad Osman, Ali Etemad, Patimah Ismail

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Type 2 diabetes mellitus (T2DM) is a complex metabolic disorder that characterized by the presence of high glucose in blood that cause from insulin resistance and insufficiency due to deterioration β-cell Langerhans functions. T2DM is commonly caused by the combination of inherited genetic variations as well as our own lifestyle. Metallothionein (MT) is a known cysteine-rich protein responsible in helping zinc homeostasis which is important in insulin signaling and secretion as well as protection our body from reactive oxygen species (ROS). MT scavenged ROS and free radicals in our body happen to be one of the reasons of T2DM and its complications. The objective of this study was to investigate the association of MT1A and MT2A polymorphisms between T2DM and control subjects among Malay populations. This study involved 150 T2DM and 120 Healthy individuals of Malay ethnic with mixed genders. The genomic DNA was extracted from buccal cells and amplified for MT1A and MT2A loci; the 347bp and 238bp banding patterns were respectively produced by mean of the Polymerase Chain Reaction (PCR). The PCR products were digested with Mlucl and Tsp451 restriction enzymes respectively and producing fragments lengths of (158/189/347bp) and (103/135/238bp) respectively. The ANOVA test was conducted and it shown that there was a significant difference between diabetic and control subjects for age, BMI, WHR, SBP, FPG, HBA1C, LDL, TG, TC and family history with (P<0.05). While the HDL, CVD risk ratio and DBP does not show any significant difference with (P>0.05). The genotype frequency for AA, AG and GG of MT1A polymorphisms was 72.7%, 22.7% and 4.7% in cases and 15%, 55% and 30% in control respectively. As for MT2A, genotype frequency of GG, GC and CC was 42.7%, 27.3% and 30% in case and 5%, 40% and 55% for control respectively. Both polymorphisms show significant difference between two investigated groups with (P=0.000). The Post hoc test was conducted and shows a significant difference between the genotypes within each polymorphism (P=0. 000). The MT1A and MT2A polymorphisms were believed to be the reliable molecular markers to distinguish the T2DM subjects from healthy individuals in Malay populations.

Keywords: Type 2 Diabetes Mellitus (T2DM), Metallothionein (MT), MT1A (rs11076161), MT2A (rs10636), Malay, Genetic Polymorphism.

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Authors: Eryati Darwin, Eka Fithra Elfi, Indria Hafizah

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Background: Physical exercise induces a pattern of hormonal and immunological responses that prevent endothelial dysfunction by maintaining the availability of nitric oxide (NO). Regular and moderate exercise stimulates NO release, that can be considered as protective factor of cardiovascular diseases, while strenuous exercise induces increased levels in a number of pro-inflammatory and anti-inflammatory cytokines. Pro-inflammatory cytokines tumor necrosis factor-α (TNF-α) triggers endothelial activation which results in an increased vascular permeability. Nuclear gene factor kappa B (NF-κB) activates biological effect of TNF-α. Aim of Study: To determine the effect of physical exercise on the endothelial and skeletal muscle, we measured the level of NF-κB on rats’ serum, macrophages, and myocytes after strenuous physical exercise. Methods: 30 male Rattus norvegicus in the age of eight weeks were randomly divided into five groups (each containing six), and there were treated groups (T) and control group (C). The treated groups obtain strenuous physical exercise by ran on treadmill at 32 m/minutes for 1 hour or until exhaustion. Blood samples, myocytes of gastrocnemius muscle, and intraperitoneal macrophages were collected sequentially. There were investigated immediately, 2 hours, 6 hours, and 24 hours (T1, T2, T3, and T4) after sacrifice. The levels of NF-κB were measured by ELISA methods. Results: From our study, we found that the levels of NF-κB on myocytes in treated group from which its specimen was taken immediately (T1), 2 hours after treadmill (T2), and 6 hours after treadmill (T3) were significantly higher than control group (p<0.05), while the group from which its specimen was taken 24 hours after treadmill, was no significantly different (p>0.05). Also on macrophages, NF-κB in treated groups T1, T2, and T3 was significantly higher than control group (p<0.05), but there was no difference between T4 and control group (p>0.05). The level of serum NF-κB was not significantly different between treatment group as well as compared to control group (p>0.05). Serum NF-κB was significantly higher than the level on macrophages and myocytes (p<0.05). Conclusion: This study demonstrated that strenuous physical exercise stimulates the activation of NF-κB that plays a role in vascular inflammation and muscular damage, and may be recovered after resting period.

Keywords: Endothelial function, inflammation, NF-κB, physical exercise.

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Authors: Moustafa Osman Mohammed

Abstract:

This paper introduces Luhmann’s autopoietic social systems starting with the original concept of autopoiesis by biologists and scientists, including the modification of general systems based on socialized medicine. A specific type of autopoietic system is explained in the three existing groups of the ecological phenomena: interaction, social and medical sciences. This hypothesis model, nevertheless, has a nonlinear interaction with its natural environment ‘interactional cycle’ for the exchange of photon energy with molecular without any changes in topology. The external forces in the systems environment might be concomitant with the natural fluctuations’ influence (e.g. radioactive radiation, electromagnetic waves). The cantilever sensor deploys insights to the future chip processor for prevention of social metabolic systems. Thus, the circuits with resonant electric and optical properties are prototyped on board as an intra–chip inter–chip transmission for producing electromagnetic energy approximately ranges from 1.7 mA at 3.3 V to service the detection in locomotion with the least significant power losses. Nowadays, therapeutic systems are assimilated materials from embryonic stem cells to aggregate multiple functions of the vessels nature de-cellular structure for replenishment. While, the interior actuators deploy base-pair complementarity of nucleotides for the symmetric arrangement in particular bacterial nanonetworks of the sequence cycle creating double-stranded DNA strings. The DNA strands must be sequenced, assembled, and decoded in order to reconstruct the original source reliably. The design of exterior actuators have the ability in sensing different variations in the corresponding patterns regarding beat-to-beat heart rate variability (HRV) for spatial autocorrelation of molecular communication, which consists of human electromagnetic, piezoelectric, electrostatic and electrothermal energy to monitor and transfer the dynamic changes of all the cantilevers simultaneously in real-time workspace with high precision. A prototype-enabled dynamic energy sensor has been investigated in the laboratory for inclusion of nanoscale devices in the architecture with a fuzzy logic control for detection of thermal and electrostatic changes with optoelectronic devices to interpret uncertainty associated with signal interference. Ultimately, the controversial aspect of molecular frictional properties is adjusted to each other and forms its unique spatial structure modules for providing the environment mutual contribution in the investigation of mass temperature changes due to pathogenic archival architecture of clusters.

Keywords: Autopoiesis, quantum photonics, portable energy, photonic structure, photodynamic therapeutic system.

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Authors: Songdi Li, Louise Spry, Tony Woodall

Abstract:

Nowadays, Corporate Social responsibility (CSR) is becoming a buzz word, and more and more academics are putting efforts on CSR studies. It is believed that CSR could influence Corporate Reputation (CR), and they hold a favourable view that CSR leads to a positive CR. To be specific, the CSR related activities in the reputational context have been regarded as ways that associate to excellent financial performance, value creation, etc. Also, it is argued that CSR and CR are two sides of one coin; hence, to some extent, doing CSR is equal to establishing a good reputation. Still, there is no consensus of the CSR-CR relationship in the literature; thus, a systematic literature review is highly in need. This research conducts a systematic literature review with both bibliometric and content analysis. Data are selected from English language sources, and academic journal articles only, then, keyword combinations are applied to identify relevant sources. Data from Scopus and WoS are gathered for bibliometric analysis. Scopus search results were saved in RIS and CSV formats, and Web of Science (WoS) data were saved in TXT format and CSV formats in order to process data in the Bibexcel software for further analysis which later will be visualised by the software VOSviewer. Also, content analysis was applied to analyse the data clusters and the key articles. In terms of the topic of CSR-CR, this literature review with bibliometric analysis has made four achievements. First, this paper has developed a systematic study which quantitatively depicts the knowledge structure of CSR and CR by identifying terms closely related to CSR-CR (such as ‘corporate governance’) and clustering subtopics emerged in co-citation analysis. Second, content analysis is performed to acquire insight on the findings of bibliometric analysis in the discussion section. And it highlights some insightful implications for the future research agenda, for example, a psychological link between CSR-CR is identified from the result; also, emerging economies and qualitative research methods are new elements emerged in the CSR-CR big picture. Third, a multidisciplinary perspective presents through the whole bibliometric analysis mapping and co-word and co-citation analysis; hence, this work builds a structure of interdisciplinary perspective which potentially leads to an integrated conceptual framework in the future. Finally, Scopus and WoS are compared and contrasted in this paper; as a result, Scopus which has more depth and comprehensive data is suggested as a tool for future bibliometric analysis studies. Overall, this paper has fulfilled its initial purposes and contributed to the literature. To the author’s best knowledge, this paper conducted the first literature review of CSR-CR researches that applied both bibliometric analysis and content analysis; therefore, this paper achieves its methodological originality. And this dual approach brings advantages of carrying out a comprehensive and semantic exploration in the area of CSR-CR in a scientific and realistic method. Admittedly, its work might exist subjective bias in terms of search terms selection and paper selection; hence triangulation could reduce the subjective bias to some degree.

Keywords: Corporate social responsibility, corporate reputation, bibliometric analysis, software data analysis.

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Authors: Moustafa Osman Mohammed

Abstract:

This paper introduces topological order in descried social systems starting with the original concept of autopoiesis by biologists and scientists, including the modification of general systems based on socialized medicine. Topological order is important in describing the physical systems for exploiting optical systems and improving photonic devices. The stats of topologically order have some interesting properties of topological degeneracy and fractional statistics that reveal the entanglement origin of topological order, etc. Topological ideas in photonics form exciting developments in solid-state materials, that being; insulating in the bulk, conducting electricity on their surface without dissipation or back-scattering, even in the presence of large impurities. A specific type of autopoiesis system is interrelated to the main categories amongst existing groups of the ecological phenomena interaction social and medical sciences. The hypothesis, nevertheless, has a nonlinear interaction with its natural environment ‘interactional cycle’ for exchange photon energy with molecules without changes in topology (i.e., chemical transformation into products do not propagate any changes or variation in the network topology of physical configuration). The engineering topology of a biosensor is based on the excitation boundary of surface electromagnetic waves in photonic band gap multilayer films. The device operation is similar to surface Plasmonic biosensors in which a photonic band gap film replaces metal film as the medium when surface electromagnetic waves are excited. The use of photonic band gap film offers sharper surface wave resonance leading to the potential of greatly enhanced sensitivity. So, the properties of the photonic band gap material are engineered to operate a sensor at any wavelength and conduct a surface wave resonance that ranges up to 470 nm. The wavelength is not generally accessible with surface Plasmon sensing. Lastly, the photonic band gap films have robust mechanical functions that offer new substrates for surface chemistry to understand the molecular design structure, and create sensing chips surface with different concentrations of DNA sequences in the solution to observe and track the surface mode resonance under the influences of processes that take place in the spectroscopic environment. These processes led to the development of several advanced analytical technologies, which are automated, real-time, reliable, reproducible and cost-effective. This results in faster and more accurate monitoring and detection of biomolecules on refractive index sensing, antibody–antigen reactions with a DNA or protein binding. Ultimately, the controversial aspect of molecular frictional properties is adjusted to each other in order to form unique spatial structure and dynamics of biological molecules for providing the environment mutual contribution in investigation of changes due the pathogenic archival architecture of cell clusters.

Keywords: autopoiesis, engineering topology, photonic system molecular structure, biosensor

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Authors: Elif Gencturk, Ekin Yurdakul, Ahmet Y. Celik, Senol Mutlu, Kutlu O. Ulgen

Abstract:

Yeast cells are generally used as a model system of eukaryotes due to their complex genetic structure, rapid growth ability in optimum conditions, easy replication and well-defined genetic system properties. Thus, yeast cells increased the knowledge of the principal pathways in humans. During fermentation, carbohydrates (hexoses and pentoses) degrade into some toxic by-products such as 5-hydroxymethylfurfural (5-HMF or HMF) and furfural. HMF influences the ethanol yield, and ethanol productivity; it interferes with microbial growth and is considered as a potent inhibitor of bioethanol production. In this study, yeast single cell behavior under HMF application was monitored by using a continuous flow single phase microfluidic platform. Microfluidic device in operation is fabricated by hot embossing and thermo-compression techniques from cyclo-olefin polymer (COP). COP is biocompatible, transparent and rigid material and it is suitable for observing fluorescence of cells considering its low auto-fluorescence characteristic. The response of yeast cells was recorded through Red Fluorescent Protein (RFP) tagged Nop56 gene product, which is an essential evolutionary-conserved nucleolar protein, and also a member of the box C/D snoRNP complexes. With the application of HMF, yeast cell proliferation continued but HMF slowed down the cell growth, and after HMF treatment the cell proliferation stopped. By the addition of fresh nutrient medium, the yeast cells recovered after 6 hours of HMF exposure. Thus, HMF application suppresses normal functioning of cell cycle but it does not cause cells to die. The monitoring of Nop56 expression phases of the individual cells shed light on the protein and ribosome synthesis cycles along with their link to growth. Further computational study revealed that the mechanisms underlying the inhibitory or inductive effects of HMF on growth are enriched in functional categories of protein degradation, protein processing, DNA repair and multidrug resistance. The present microfluidic device can successfully be used for studying the effects of inhibitory agents on growth by single cell tracking, thus capturing cell to cell variations. By metabolic engineering techniques, engineered strains can be developed, and the metabolic network of the microorganism can thus be manipulated such that chemical overproduction of target metabolite is achieved along with the maximum growth/biomass yield.  

Keywords: COP, HMF, ribosome biogenesis, thermoplastic microbioreactor, yeast.

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Authors: Chau-Kuang Chen, Juanita Buford, Colette Davis, Raisha Allen, John Hughes, Jr., James Tyus, Dexter Samuels

Abstract:

During the post-Civil War era, the city of Nashville, Tennessee, had the highest mortality rate in the United States. The elevated death and disease rates among former slaves were attributable to lack of quality healthcare. To address the paucity of healthcare services, Meharry Medical College, an institution with the mission of educating minority professionals and serving the underserved population, was established in 1876. Purpose: The social ecological framework and partial least squares (PLS) path modeling were used to quantify the impact of socioeconomic status and adverse health outcome on primary care professionals serving the disadvantaged community. Thus, the study results could demonstrate the accomplishment of the College’s mission of training primary care professionals to serve in underserved areas. Methods: Various statistical methods were used to analyze alumni data from 1975 – 2013. K-means cluster analysis was utilized to identify individual medical and dental graduates in the cluster groups of the practice communities (Disadvantaged or Non-disadvantaged Communities). Discriminant analysis was implemented to verify the classification accuracy of cluster analysis. The independent t-test was performed to detect the significant mean differences of respective clustering and criterion variables. Chi-square test was used to test if the proportions of primary care and non-primary care specialists are consistent with those of medical and dental graduates practicing in the designated community clusters. Finally, the PLS path model was constructed to explore the construct validity of analytic model by providing the magnitude effects of socioeconomic status and adverse health outcome on primary care professionals serving the disadvantaged community. Results: Approximately 83% (3,192/3,864) of Meharry Medical College’s medical and dental graduates from 1975 to 2013 were practicing in disadvantaged communities. Independent t-test confirmed the content validity of the cluster analysis model. Also, the PLS path modeling demonstrated that alumni served as primary care professionals in communities with significantly lower socioeconomic status and higher adverse health outcome (p < .001). The PLS path modeling exhibited the meaningful interrelation between primary care professionals practicing communities and surrounding environments (socioeconomic statues and adverse health outcome), which yielded model reliability, validity, and applicability. Conclusion: This study applied social ecological theory and analytic modeling approaches to assess the attainment of Meharry Medical College’s mission of training primary care professionals to serve in underserved areas, particularly in communities with low socioeconomic status and high rates of adverse health outcomes. In summary, the majority of medical and dental graduates from Meharry Medical College provided primary care services to disadvantaged communities with low socioeconomic status and high adverse health outcome, which demonstrated that Meharry Medical College has fulfilled its mission. The high reliability, validity, and applicability of this model imply that it could be replicated for comparable universities and colleges elsewhere.

Keywords: Disadvantaged Community, K-means Cluster Analysis, PLS Path Modeling, Primary care.

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