Search results for: gene regulation network

Authors: Ashraf Ali, Kriti Upadhyay, Puja Sohal, Anant Mohan, Randeep Guleria

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Background: Gene silencing by aberrant promoter hypermethylation is common in lung cancer and is an initiating event in its development. Aim: To evaluate the gene promoter hypermethylation frequency in serum and tissue of lung cancer patients. Method: 95 newly diagnosed untreated advance stage lung cancer patients and 50 cancer free matched controls were studied. Bisulfite modification of tissue and serum DNA was done; modified DNA was used as a template for methylation-specific PCR analysis. Survival was assessed for one year. Results: Of 95 patients, 82% were non-small cell lung cancer (34% squamous cell carcinoma, 34% non-small cell lung cancer and 14% adenocarcinoma) and 18% were small cell lung cancer. Biopsy revealed that tissue of 89% and 75% of lung cancer patients and 85% and 52% of controls had promoter hypermethylated for MGMT (p=0.35) and p16(p<0.001) gene, respectively. In serum, 33% and 49% of lung cancer patients and 28% and 43% controls were positive for MGMT and p16 gene. No significant correlation was found between survival and clinico-pathological parameters. Conclusion: High gene promoter methylation frequency of p16 gene in tissue biopsy may be linked with early stages of carcinogenesis. Appropriate follow-up is required for confirmation of this finding.

Keywords: lung cancer, MS- PCR, methylation, molecular biology

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Authors: Aslihan Coban

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As a result of the rapid development of information communication technology, especially the internet, consumers have become an active party in commerce and in law. Consequently, the protection of consumers in cross-border contracts has become increasingly important. This paper is confined to the international jurisdiction of courts over disputes arising from electronic consumer contracts according to the ‘5718 Turkish Act on Private International Law and Civil Procedure’ and the ‘1215/2012 Council Regulation On Jurisdiction and The Recognition and Enforcement Of Judgments In Civil and Commercial Matters’ (Hereafter ‘Brussels I Regulation’). The international jurisdiction of courts for consumer contracts is recognized under both acts above-mentioned; however, there exist some differences between the said legal regulations. Firstly, while there is a specific provision for electronic consumer contracts in Brussels I Regulation, there is no specific provision in the Turkish Act. Secondly, under the Turkish Act, habitual residence, domicile, and workplace of the other party who is not a consumer are all accepted as jurisdiction elements; while domicile is the only jurisdiction element in Brussels I Regulation. Thirdly, the ability to make jurisdiction agreements in disputes arising from electronic consumer contracts is a controversial issue under the Turkish Act while it is explicitly regulated under Brussels I Regulation that such jurisdiction agreements can be concluded by complying with certain conditions.

Keywords: Brussels I Regulation, electronic consumer contracts, jurisdiction, jurisdiction agreement

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Authors: Natalia Constantinescu

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This cross-sectional study aims to explore the differences among adults with somatic symptom disorder (SSD) versus adults without SSD in terms of attachment and emotion regulation strategies. A total sample of 80 participants (40 people with SSD and 40 healthy controls), aged 20-57 years old (M = 31.69, SD = 10.55), were recruited from institutions and online groups. They completed the Romanian version of the Experiences in Close Relationships Scale – Short Form (ECR-S), Regulation of Emotion Systems Survey (RESS), Patient Health Questionnaire-15 (PHQ-15) and Somatic Symptom Disorder – B Criteria Scale (SSD-12). The results indicate significant differences between the two groups in terms of attachment and emotion regulation strategies. Adults with SSD have a higher level of attachment anxiety and avoidance compared to the nonclinical group. Moreover, people with SSD are more prone to use rumination and suppression and less prone to use reevaluation compared to healthy people. Implications for SSD prevention and treatment are discussed.

Keywords: adult attachment, emotion regulation strategies, psychosomatic disorders, somatic symptom disorder

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Authors: Rahaba Marima, Clement Penny

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The Health-related quality of life (HRQoL) for HIV positive patients has improved since the introduction of the highly active antiretroviral treatment (HAART). However, in the present HAART era, HIV co-morbidities such as lung cancer, a non-AIDS (NAIDS) defining cancer have been documented to be on the rise. Under normal physiological conditions, cells grow, repair and proliferate through the cell-cycle as cellular homeostasis is important in the maintenance and proper regulation of tissues and organs. Contrarily, the deregulation of the cell-cycle is a hallmark of cancer, including lung cancer. The association between lung cancer and the use of HAART components such as Efavirenz (EFV) is poorly understood. This study aimed at elucidating the effects of EFV on the cell-cycle genes’ expression in lung cancer. For this purpose, the human cell-cycle gene array composed of 84 genes was evaluated on both normal lung fibroblasts (MRC-5) cells and adenocarcinoma (A549) lung cells, in response to 13µM EFV or 0.01% vehicle. The ±2 up or down fold change was used as a basis of target selection, with p < 0.05. Additionally, RT-qPCR was done to validate the gene array results. Next, In-silico bio-informatics tools, Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), Reactome, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Ingenuity Pathway Analysis (IPA) were used for gene/gene interaction studies as well as to map the molecular and biological pathways influenced by the identified targets. Interestingly, the DNA damage response (DDR) pathway genes such as p53, Ataxia telangiectasia mutated and Rad3 related (ATR), Growth arrest and DNA damage inducible alpha (GADD45A), HUS1 checkpoint homolog (HUS1) and Role of radiation (RAD) genes were shown to be upregulated following EFV treatment, as revealed by STRING analysis. Additionally, functional enrichment analysis by the KEGG pathway revealed that most of the differentially expressed gene targets function at the cell-cycle checkpoint such as p21, Aurora kinase B (AURKB) and Mitotic Arrest Deficient-Like 2 (MAD2L2). Core analysis by IPA revealed that p53 downstream targets such as survivin, Bcl2, and cyclin/cyclin dependent kinases (CDKs) complexes are down-regulated, following exposure to EFV. Furthermore, Reactome analysis showed a significant increase in cellular response to stress genes, DNA repair genes, and apoptosis genes, as observed in both normal and cancerous cells. These findings implicate the genotoxic effects of EFV on lung cells, provoking the DDR pathway. Notably, the constitutive expression of this pathway (DDR) often leads to uncontrolled cell proliferation and eventually tumourigenesis, which could be the attribute of HAART components’ (such as EFV) effect on human cancers. Targeting the cell-cycle and its regulation holds a promising therapeutic intervention to the potential HAART associated carcinogenesis, particularly lung cancer.

Keywords: cell-cycle, DNA damage response, Efavirenz, lung cancer

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Authors: M. D. Asemoloye, S. G. Jonathan, A. Rafiq, O. J. Olawuyi, D. O. Adejoye

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Calmodulin is one of the intracellular calcium proteins that regulates large spectrum of enzymes and cellular functions including metabolism of cyclic nucleotides and glycogen. The potentials of calmodulin gene in fungi necessitates their genetic response and their strong cassette of enzyme secretions for pesticide degradation. Therefore, this study was carried out to investigate the ‘Transcriptomic’ response of calmodulin encoding genes in Talaromyces fungi in response to 2, 2-dichlorovinyl dimethyl phosphate (DDVP or Dichlorvos) an organophosphate pesticide and γ-Hexachlorocyclohexane (Lindane) an organochlorine pesticide. Fungi strains isolated from rhizosphere from grasses rhizosphere in pesticide polluted sites were subjected to percentage incidence test. Two most frequent fungi were further characterized using ITS gene amplification (ITS1 and ITS4 combinations), they were thereafter subjected to In-vitro DDVP and lindane tolerance tests at different concentrations. They were also screened for presence and expression of calmodulin gene (caM) using RT-PCR technique. The two Talaromyces strains had the highest incidence of 50-72% in pesticide polluted site, they were both identified as Talaromyces astroroseus asemoG and Talaromyces purpurogenum asemoN submitted in NCBI gene-bank with accession numbers KY488464 and KY488468 respectively. T. astroroseus KY488464 tolerated DDVP (1.23±0.023 cm) and lindane (1.11±0.018 cm) at 25 % concentration while T. purpurogenum KY488468 tolerated DDVP (1.33±0.061 cm) and lindane (1.54±0.077 cm) at this concentration. Calmodulin gene was detected in both strains, but RT-PCR expression of caM gene revealed at 900-1000 bp showed an under-expression of caM in T. astrorosues KY488464 but overexpressed in T. purpurogenum KY488464. Thus, the calmodulin gene response of these fungal strains to both pesticides could be considered in monitoring the potentials of fungal strains to pesticide tolerance and bioremediation of pesticide in polluted soil.

Keywords: Calmodulin gene, pesticide, RT-PCR, talaromyces, tolerance

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Authors: Sarah Devi Silvian, Hanna Shobrina Iqomatul Haq, Fara Cholidatun Nabila, Agustin Krisna Wardani

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Bacteria ability to survive in antibiotic is controlled by the presence of gene that encodes the antibiotic resistance protein. The instability of the antibiotic resistance gene can be observed by exposing the bacteria under the lethal dose of antibiotic. Low concentration of antibiotic can induce mutation, which may take a role in bacterial adaptation through the antibiotic concentration. Lactobacillus casei FNCC 0090 is one of the probiotic bacteria that has an ability to survive in tetracycline by expressing the tetM gene. The aims of this study are to observe the possibilities of mutation happened in L.casei FNCC 0090 by exposing in sub-lethal dose of tetracycline and also observing the instability of the tetM gene by comparing the sequence between the wild type and mutant. L.casei FNCC 0090 has a lethal dose in 60 µg/ml, low concentration is applied to induce the mutation, the range from 10 µg/ml, 15 µg/ml, 30 µg/ml, 45 µg/ml, and 50 µg/ml. L.casei FNCC 0090 is exposed to the low concentration from lowest to the highest concentration to induce the adaptation. Plasmid is isolated from the highest concentration culture which is 50 µg/ml by using modified alkali lysis method with the addition of lysozyme. The tetM gene is isolated by using PCR (Polymerase Chain Reaction) method, then PCR amplicon is purified and sequenced. Sequencing is done on both samples, wild type and mutant. Both sequences are compared and the mutations can be traced in the presence of nucleotides changes. The changing of the nucleotides means that the tetM gene is instable.

Keywords: L. casei FNCC 0090, probiotic, tetM, tetracycline

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Authors: Sylvie Studente, Filia J. Garivaldis

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The emotions and cognitions that underpin creative performance have been of interest for decades if not centuries, however, research evidence has still not conclusively offered reliable predictors of creativity. It is unclear whether stressors are detrimental to creative thinking, or whether some stress imposes necessary constraints to facilitate the creative process. The present research aims to examine the role of individual differences in self-regulation in influencing the links between emotions, cognitions, and creativity. Self-regulation is the capacity to disengage from moods that inhibit goal progress, and cope with failure, focus on impending intentions, and enhance the intrinsic appeal of tasks. Therefore, it is anticipated that individuals with an intuitive ability in self-regulation are able to harness their emotions and cognitions, to perform well on a creative task. In contrast, individuals with a deficiency in self-regulation will experience difficulty in such a task. Furthermore, stress in the form of positive and negative assessment feedback in the context of education will be manipulated to explore the interactive effects of environmental and individual difference factors on creative performance. The results will provide insight into the underlying factors associated with emotions and creativity, and inform future research in individual differences in cognition and emotion, and environmental triggers of creativity.

Keywords: creativity, feedback, self-regulation, stress

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Authors: Vanessa Funk, Steven Blum, Stephanie Cole, Jorge Maciel, Matthew Lux

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Paper-based synthetic gene circuits offer a new paradigm for programmable, fieldable biodetection. We demonstrate that by freeze-drying gene circuits with in vitro expression machinery, we can use complimentary RNA sequences to trigger colorimetric changes upon rehydration. We have successfully utilized both green fluorescent protein and luciferase-based reporters for easy visualization purposes in solution. Through several efforts, we are aiming to use this new platform technology to address a variety of needs in portable detection by demonstrating several more expression and reporter systems for detection functions on paper. In addition to RNA-based biodetection, we are exploring the use of various mechanisms that cells use to respond to environmental conditions to move towards all-hazards detection. Examples include explosives, heavy metals for water quality, and toxic chemicals.

Keywords: cell-free lysates, detection, gene circuits, in vitro

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Authors: Suwattana Visetnan, Premruethai Supungul, Sureerat Tang, Ikuo Hirono, Anchalee Tassanakajon, Vichien Rimphanitchayakit

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In animals, infection by Gram-negative bacteria and certain viruses activates the Imd signaling pathway wherein the a NF-κB transcription factor, Relish, is a key regulatory protein for the synthesis of antimicrobial proteins. Infection by yellow head virus (YHV) activates the Imd pathway. To investigate the expression of genes involved in YHV infection and under the influence of PmRelish regulation, RNA interference and suppression subtractive hybridization (SSH) are employed. The genes in forward library expressed in shrimp after YHV infection and under the activity of PmRelish were obtained by subtracting the cDNAs from YHV-infected and PmRelish-knockdown shrimp with cDNAs from YHV-infected shrimp. Opposite subtraction gave a reverse library whereby an alternative set of genes under YHV infection and no PmRelish expression was obtained. Sequencing of 252 and 99 cDNA clones from the respective forward and reverse libraries were done and annotated through blast search against the GenBank sequences. Genes involved in defense and homeostasis were abundant in both libraries, 31% and 23% in the forward and reverse libraries, respectively. They were predominantly antimicrobial proteins, proteinases and proteinase inhibitors. The expression of antimicrobial protein genes, ALFPm3, crustinPm1, penaeidin3 and penaeidin5 were tested under PmRelish silencing and Gram-negative bacterium V. harveyi infection. Together with the results previously reported, the expression of penaeidin5 and also penaeidin3 but not ALFPm3 and crustinPm1 were under the regulation of PmRelish in the Imd pathway.

Keywords: relish, yellow head virus, penaeus monodon, antimicrobial proteins

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Authors: Anca Dinischiotu, Sorina Nicoleta Voicu

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Silica nanoparticles (SiO2-NPs) are widely used in consumer products such as paints, plastics, insulation materials, tires, concrete production, as well as in gene delivery systems and imaging procedures. Environmental human exposure to them occurs during utilization of these products, in a time-dependent manner, the uptake being by topic and inhalation route especially. SiO2-NPs enter cells and induce membrane damage, oxidative stress and inflammatory reactions in a concentration-dependent manner. In this study, MRC-5 cells (human fetal lung fibroblasts) were exposed to amorphous SiO2-NPs at a dose of 62.5 μg/ml for 24, 48 and 72 hours. The size distribution of NPs was a lognormal function, in the range 3-14 nm. A time-dependent decrease of total reduced glutathione concentration by 36%, 50%, and 78% and an increase of NO level by 62%, 32%, respectively 24% compared to control were noticed. An up-regulation of NF-kB expression by 20%, 50% respectively 10% and of Nrf-2 by 139%, 58%, and 16% compared to control after 24, 48 and 72 hours was noticed also. The expression of IL-1β, IL-6, IL-8, and COX-2 was up-regulated in a time-dependent manner. Also, the expression of MMP-2 and MMP-9 were down-regulated after 48 and 72 hours, whereas their activities raised in a time-dependent manner. Exposure of cells to NPs up-regulated the expression of inducible NO synthase, as previously was shown, and probably this is the reason for the increased level of NO, that can react with the thiol groups of reduced glutathione molecules, diminishing its concentration Nrf2 is a transcription factor translocated in nucleus, under oxidative stress, where downstream gene expression activates in order to modulate the adaptive intracellular response against oxidative stress. The cross-talk between Nrf2 and NF-kB activities regulates the inflammatory processes. The activation of NF-kB could activate up-regulation of IL-1β, IL-6, and IL-8. The increase of COX-2 expression could be correlated with IL-1β one. Also, probably in response to the pro-inflammatory cytokines, MMP-2 and MMP-9 were induced and activated. In conclusion, the exposure of MRC-5 cells to SiO2-NPs generated inflammation in a time-dependent manner.

Keywords: inflammation, MRC-5 cells, oxidative stress, silica nanoparticles

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Authors: Romain Lestage, Marc Bourreau

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In this paper we analyze the interplay between access to the last-mile network and net neutrality in the market for Internet access. We consider two Internet Service Providers (ISPs), which act as platforms between Internet users and Content Providers (CPs). One of the ISPs is vertically integrated and provides access to its last-mile network to the other (non-integrated) ISP. We show that a lower access price increases the integrated ISP's incentives to charge CPs positive termination fees (i.e., to deviate from net neutrality), and decreases the non-integrated ISP's incentives to charge positive termination fees.

Keywords: net neutrality, access regulation, internet access, two-sided markets

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Authors: Alieh Farshbaf

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Introduction: Current anti-retroviral drugs have some restrictions for treatment of HIV-1 infection. The efficacy of retroviral drugs is not same in different infected patients and the virus rebound from latent reservoirs after stopping them. Recently, the engineering of stem cells and gene therapy provide new approaches to eliminate some drug problems by induction of resistance to HIV-1. Literature review: Up to now, AIDS-restriction genes (ARGs) were suitable candidate for gene and cell therapies, such as cc-chemokine receptor-5 (CCR5). In this manner, CCR5 provide effective cure in Berlin and Boston patients by inducing of HIV-1 resistance with allogeneic stem cell transplantation. It is showed that Zinc Finger Nuclease (ZFN) could induce HIV-1 resistance in stem cells of infected patients by homologous recombination or non-end joining mechanism and eliminate virus loading after returning the modified cells. Then, gene modification by HIV restriction factors, as TRIM5, introduced another gene candidate for HIV by interfering in infection process. These gene modifications/editing provided by stem cell futures that improve treatment in refractory disease such as HIV-1. Conclusion: Although stem cell transplantation has some complications, but in compare to retro-viral drugs demonstrated effective cure by elimination of virus loading. On the other hand, gene therapy is cost-effective for an infected patient than retroviral drugs payment in a person life-long. The results of umbilical cord blood stem cell transplantation showed that gene and cell therapy will be applied easier than previous treatment of AIDS with high efficacy.

Keywords: stem cell, AIDS, gene modification, cell engineering

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Authors: Vun Yee Thien, Kenneth Francis Rodrigues, Clemente Michael Vui Ling Wong, Wilson Thau Lym Yong

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Transcriptomes associated with the process of photosynthesis have offered insights into the mechanism of gene regulation in terrestrial plants; however, limited information is available as far as macroalgae are concerned. This investigation aims to decipher the underlying mechanisms associated with photosynthesis in the red alga, Kappaphycus alvarezii, by performing a differential expression analysis on a de novo assembled transcriptomes. Comparative analysis of gene expression was designed to examine the alteration of light qualities and its effect on physiological mechanisms in the red alga. High-throughput paired-end RNA-sequencing was applied to profile the transcriptome of K. alvarezii irradiated with different wavelengths of light (blue 492-455 nm, green 577-492 nm and red 780-622 nm) as compared to the full light spectrum, resulted in more than 60 million reads individually and assembled using Trinity and SOAPdenovo-Trans. The transcripts were annotated in the NCBI non-redundant (nr) protein, SwissProt, KEGG and COG databases with a cutoff E-value of 1e-5 and nearly 30% of transcripts were assigned to functional annotation by Blast searches. Differential expression analysis was performed using edgeR. The DEGs were designated to six categories: BL (blue light) regulated, GL (green light) regulated, RL (red light) regulated, BL or GL regulated, BL or RL regulated, GL or RL regulated, and either BL, GL or RL regulated. These DEGs were mapped to terms in KEGG database and compared with the whole transcriptome background to search for genes that regulated by light quality. The outcomes of this study will enhance our understanding of molecular mechanisms underlying light-induced responses in red algae.

Keywords: de novo transcriptome sequencing, differential gene expression, Kappaphycus alvareziired, red alga

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Authors: Habib Onsori, Somayeh Akrami, Mohammad Rahmati

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Deafness is the most common sensory disorder with the frequency of 1/1000 in many populations. Mutations in the GJB2 (CX26) gene at the DFNB1 locus on chromosome 13q12 are associated with congenital hearing loss. Approximately 80% of congenital hearing loss cases are recessively inherited and 15% dominantly inherited. Mutations of the GJB2 gene, encoding gap junction protein Connexin 26 (Cx26), are the most common cause of hereditary congenital hearing loss in many countries. This report presents two cases of different mutations from Iranian patients with bilateral hearing loss. DNA studies were performed for the GJB2 gene by PCR and sequencing methods. In one of them, direct sequencing of the gene showed a heterozygous T→C transition at nucleotide 604 resulting in a cysteine to arginine amino acid substitution at codon 202 (C202R) in the fourth extracellular domain (TM4) of the protein. The analyses indicate that the C202R mutation appeared de novo in the proband with a possible dominant effect (GenBank: KF 638275). In the other one, DNA sequencing revealed a compound heterozygous mutation (35delG, 363delC) in the Cx26 gene that is strongly associated with congenital non-syndromic hearing loss (NSHL). So screening the mutations for hearing loss individuals referring to genetics counseling centers before marriage and or pregnancy is recommended.

Keywords: CX26, deafness, GJB2, mutation

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Authors: Thomas Adi Purnomo Sidhi

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Nowadays, network is an essential need in almost every part of human daily activities. People now can seamlessly connect to others through the Internet. With advanced technology, our personal data now can be more easily accessed. One of many components we are concerned for delivering the best network is a security issue. This paper is proposing a method that provides more options for security. This research aims to improve network security by focusing on the physical layer which is the first layer of the OSI model. The layer consists of the basic networking hardware transmission technologies of a network. With the use of observation method, the research produces a schematic design for enhancing the network security through the gray code converter.

Keywords: network, network security, grey code, physical layer

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Authors: Jitendra Aswani

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In the first section of this study, impact of Global Financial Crisis (GFC) on the synchronization of fourteen Asian Stock Markets (ASM’s) of countries like Hong Kong, India, Thailand, Singapore, Taiwan, Pakistan, Bangladesh, South Korea, Malaysia, Indonesia, Japan, China, Philippines and Sri Lanka, has been analysed using the network science and its metrics like degree of node, clustering coefficient and network density. Then in the second section of this study by introducing the US stock market in existing network and developing a Minimum Spanning Tree (MST) spread of crisis from the US stock market to Asian Stock Markets (ASM) has been explained. Data used for this study is adjusted the closing price of these indices from 6th January, 2000 to 15th September, 2013 which further divided into three sub-periods: Pre, during and post-crisis. Using network analysis, it is found that Asian stock markets become more interdependent during the crisis than pre and post crisis, and also Hong Kong, India, South Korea and Japan are systemic important stock markets in the Asian region. Therefore, failure or shock to any of these systemic important stock markets can cause contagion to another stock market of this region. This study is useful for global investors’ in portfolio management especially during the crisis period and also for policy makers in formulating the financial regulation norms by knowing the connections between the stock markets and how the system of these stock markets changes in crisis period and after that.

Keywords: global financial crisis, Asian stock markets, network science, Kruskal algorithm

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Authors: Arfan Ali, Idrees Ahmad Nasir

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Potato (Solanum tuberosum) is an important cash crop and popular vegetable in Pakistan and throughout the world. Cold storage of potatoes accelerates the conversion of starch into reduced sugars (glucose and fructose). This process causes dry mass and bitter taste in the potatoes that are not acceptable to end consumers. In the current study, the phosphofructokinase B gene was cloned into the pET-30 vector for protein expression and the pCambia-1301 vector for plant expression. Amplification of a 930bp product from an E. coli strain determined the successful isolation of the phosphofructokinase B gene. Restriction digestion using NcoI and BglII along with the amplification of the 930bp product using gene specific primers confirmed the successful cloning of the PfkB gene in both vectors. The protein was expressed as a His-PfkB fusion protein. Western blot analysis confirmed the presence of the 35 Kda PfkB protein when hybridized with anti-His antibodies. The construct Fani-01 was evaluated transiently using a histochemical gus assay. The appearance of blue color in the agroinfiltrated area of potato leaves confirmed the successful expression of construct Fani-01. Further, the area displaying gus expression was evaluated for PfkB expression using ELISA. Moreover, PfkB gene expression evaluated through transient expression determined successful gene expression and highlighted its potential utilization for stable expression in potato to reduce sweetening due to long-term storage.

Keywords: potato, Solanum tuberosum, transformation, PfkB, anti-sweetening

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Authors: Syed Sameer Aga, Saniya Nissar

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The Xeroderma pigmentosum group D gene (XPD) plays a key role in nucleotide excision repair (NER) pathway of the damaged DNA. Genetic polymorphisms in the coding region of the XPD gene may alter DNA repair capacity of the protein and hence can modulate the risk of colorectal cancer (CRC) risk. The aim of the study was to determine the genetic association of XPD Lys751Gln polymorphism with the risk of colorectal cancer (CRC) development. 120 CRC patients and 160 normal controls were assessed for genotype frequencies of XPD Lys751Gln polymorphism using PCR-RFLP technique. We observed a significant association (p < 0.05) between the XPD Lys751Gln polymorphism and the risk of developing CRC (p < 0.05). Additionally, Gln/Gln genotype of the XPD gene doubled the risk for the development of CRC [p < 0.05; OR=2.25 95% CI (1.07-4.7)]. Our results suggest that there is a significant association between the XPD Lys751Gln polymorphism and the risk of CRC.

Keywords: colorectal cancer, polymorphism, RFLP, DNA Repair, NER, XPD

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Authors: Rafael Estrada, Cristian Ruiz Rueda

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Carbapenems are last-resort antibiotics used in clinical settings to treat antibiotic-resistant bacterial infections. Thus, the emergence and spread of resistance to carbapenems is a major public health concern. Here, we have studied a carbapenem-resistant Aeromonas veronii strain previously isolated from a water sample from Sam Simeon Creek (Hearst San Simeon State Park, CA). Analysis of this isolate using disk-diffusion, CarbaNP, eCIM and mCIM assays revealed that it was resistant to amoxicillin-clavulanic acid and all carbapenems tested and that this isolate produced a potentially novel carbapenemase of the Metallo-β-lactamase family. Whole genome sequencing analysis revealed that this A. veronii isolate carries a novel variant of the blacₚₕₐ class β-carbapenemase gene that was closely related to the blacₚₕₐ₇ gene of Aeromonas jandaei. This isolate also carried a novel variant of the blaₒₓₐ class D carbapenemase gene that was most closely related to the blaₒₓₐ-₉₁₂ gene found in other Aeromonas veronii isolates. Finally, we also identified a novel class C β-lactamase gene moderately related to the blaFₒₓ-₁₇ gene of Providencia stuartii and other blaFₒₓ variants identified in Klebsiella pneumoniae, Escherichia coli and other Enterobacteriaceae. Overall, our findings reveal that environmental isolates are an important reservoir of multiple carbapenemases and other β-lactamases of clinical significance.

Keywords: β-lactamases, carbapenem, antibiotic-resistant, aeromonas veronii

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Authors: Kenichiro Hida, Shin-Ichi Kuribayashi

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NFV-based network implements a variety of network functions with software on general-purpose servers, and this allows the network operator to select any capabilities and locations of network functions without any physical constraints. In this paper, we evaluate the influence of the maximum tolerable network delay on the virtual routing function deployment guidelines which the authors proposed previously. Our evaluation results have revealed the following: (1) the more the maximum tolerable network delay condition becomes severe, the more the number of areas where the route selection function is installed increases and the total network cost increases, (2) the higher the routing function cost relative to the circuit bandwidth cost, the increase ratio of total network cost becomes larger according to the maximum tolerable network delay condition.

Keywords: NFV (Network Functions Virtualization), resource allocation, virtual routing function, minimum total network cost

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Authors: Pankhudi Khandelwal

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The revenue models of digital giants such as Facebook and Google, use targeted advertising for revenues. Such a model requires huge amounts of consumer data. While the data protection law deals with the protection of personal data, however, this data is acquired by the companies on the basis of consent, performance of a contract, or legitimate interests. This paper analyses the role that competition law can play in evading these loopholes for the protection of data and privacy of online consumers. Digital markets have certain distinctive features such as network effects and feedback loop, which gives incumbents of these markets a first-mover advantage. This creates a situation where the winner takes it all, thus creating entry barriers and concentration in the market. It has been also seen that this dominant position is then used by the undertakings for leveraging in other markets. This can be harmful to the consumers in form of less privacy, less choice, and stifling innovation, as seen in the cases of Facebook Cambridge Analytica, Google Shopping, and Google Android. Therefore, the article aims to provide a legal framework wherein the data protection law and competition law can come together to provide a balance in regulating digital markets. The issue has become more relevant in light of the Facebook decision by German competition authority, where it was held that Facebook had abused its dominant position by not complying with data protection rules, which constituted an exploitative practice. The paper looks into the jurisdictional boundaries that the data protection and competition authorities can work from and suggests ex ante regulation through data protection law and ex post regulation through competition law. It further suggests a change in the consumer welfare standard where harm to privacy should be considered as an indicator of low quality.

Keywords: data protection, dominance, ex ante regulation, ex post regulation

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Authors: Jodie Stevenson, Lisa-Marie Emerson, Abigail Millings

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Mindfulness has been conceptualized as a dispositional trait, which is different across individuals. Previous research has independently identified both adult attachment orientations and emotion regulation abilities as correlates of dispositional mindfulness. Research has also presented a two-factor model of the relationship between these three constructs. The present study aimed to further develop this model and investigated theses relationships in a sample of 186 participants. Participants completed the Five Factor Mindfulness Questionnaire Short Form (FFMQ-SF), the Experiences in Close Relationships Scale for global attachment (ECR), the Emotion Regulation Questionnaire (ERC), and the Adult Disorganized Attachment scale (ADA). Exploratory factor analysis revealed a 3-factor solution accounting for 59% of the variance across scores on these measures. The first factor accounted for 32% of the variance and loaded highly on attachment and mindfulness subscales. The second factor accounted for 15% of the variance with strong loadings on emotion regulation subscales. The third factor accounted for 12% of the variance with strong loadings on disorganized attachment, and the mindfulness observes subscale. The results further confirm the relationship between attachment, mindfulness, and emotion regulation along with the unique addition of disorganized attachment. The extracted factors will then be used to predict well-being outcomes for an undergraduate student population.

Keywords: adult attachment, emotion regulation, mindfulness, well-being

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Authors: K. Iskandar, N. H. Radzi, R. Aziz, M. S. Kamaruddin, M. N. Abdullah, S. A. Jumaat

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Nowadays many developing countries have been undergoing a restructuring process in the power electricity industry. This process has involved disaggregating former state-owned monopoly utilities both vertically and horizontally and introduced competition. The restructuring process has been implemented by the Australian National Electricity Market (NEM) started from 13 December 1998, began operating as a wholesale market for supply of electricity to retailers and end-users in Queensland, New South Wales, the Australian Capital Territory, Victoria and South Australia. In this deregulated market, one of the important issues is the transmission pricing. Transmission pricing is a service that recovers existing and new cost of the transmission system. The regulation of the transmission pricing is important in determining whether the transmission service system is economically beneficial to both side of the users and utilities. Therefore, an efficient transmission pricing methodology plays an important role in the Australian NEM. In this paper, the transmission pricing methodologies that have been implemented by the Australian NEM which are the Cost Reflective Network Pricing (CRNP) and Modified Cost Reflective Network Pricing (MCRNP) methods are investigated for allocating the transmission service charges to the transmission users. A case study using 6-bus system is used in order to identify the best method that reflects a fair and equitable transmission service charge.

Keywords: cost-reflective network pricing method, modified cost-reflective network pricing method, restructuring process, transmission pricing

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Authors: M. A. I Perera, C. R. Wijesinghe, A. R. Weerasinghe

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his study was conducted to review and identify the unsupervised techniques that can be employed to analyze gene expression data in order to identify better subtypes of tumors. Identifying subtypes of cancer help in improving the efficacy and reducing the toxicity of the treatments by identifying clues to find target therapeutics. Process of gene expression data analysis described under three steps as preprocessing, clustering, and cluster validation. Feature selection is important since the genomic data are high dimensional with a large number of features compared to samples. Hierarchical clustering and K Means are often used in the analysis of gene expression data. There are several cluster validation techniques used in validating the clusters. Heatmaps are an effective external validation method that allows comparing the identified classes with clinical variables and visual analysis of the classes.

Keywords: cancer subtypes, gene expression data analysis, clustering, cluster validation

Procedia PDF Downloads 112

Authors: K. Sathishkumar, V. Thiagarasu

Abstract:

Due to recent advances in DNA microarray technology, it is now feasible to obtain gene expression profiles of tissue samples at relatively low costs. Many scientists around the world use the advantage of this gene profiling to characterize complex biological circumstances and diseases. Microarray techniques that are used in genome-wide gene expression and genome mutation analysis help scientists and physicians in understanding of the pathophysiological mechanisms, in diagnoses and prognoses, and choosing treatment plans. DNA microarray technology has now made it possible to simultaneously monitor the expression levels of thousands of genes during important biological processes and across collections of related samples. Elucidating the patterns hidden in gene expression data offers a tremendous opportunity for an enhanced understanding of functional genomics. However, the large number of genes and the complexity of biological networks greatly increase the challenges of comprehending and interpreting the resulting mass of data, which often consists of millions of measurements. A first step toward addressing this challenge is the use of clustering techniques, which is essential in the data mining process to reveal natural structures and identify interesting patterns in the underlying data. This work presents an analysis of several clustering algorithms proposed to deals with the gene expression data effectively. The existing clustering algorithms like Support Vector Machine (SVM), K-means algorithm and evolutionary algorithm etc. are analyzed thoroughly to identify the advantages and limitations. The performance evaluation of the existing algorithms is carried out to determine the best approach. In order to improve the classification performance of the best approach in terms of Accuracy, Convergence Behavior and processing time, a hybrid clustering based optimization approach has been proposed.

Keywords: microarray technology, gene expression data, clustering, gene Selection

Procedia PDF Downloads 289

Authors: Debabrata Das

Abstract:

This paper explains how to design a regulation loop for a power supply circuit. It also discusses the need of a regulation loop and the improvement of a circuit with regulation loop. A sample design is used to demonstrate how to use PSpice to design feedback loop to control output voltage of a power supply and how to check if the power supply is stable or oscillatory. A sample design is made using a specific Integrated Circuit (IC) available in the PSpice library. A designer can experiment feedback loop design using Cadence Pspice tool. PSpice is easy to use, reliable, and convenient. To test a feedback loop, generally, engineers use trial and error method with the hardware which takes a lot of time and manpower. Moreover, it is expensive because component and Printed Circuit Board (PCB) may go bad. PSpice can be used by designers to test their loop designs without using hardware circuits. A designer can save time, cost, manpower and simulate his/her power supply circuit accurately before making a real hardware using this software package.

Keywords: power electronics, feedback loop, regulation, stability, pole, zero, oscillation

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Authors: Shikha Masand, Sudesh Kumar Yadav

Abstract:

Certain protein kinases have been shown to be crucial for plant cell signaling pathways associated with plant immune responses. Here we identified a horsegram [Macrotyloma uniflorum (Lam.) Verdc.] malectin-like leucine rich receptor-like protein kinase (RLK) gene MuRLK. The functional MuRLK protein preferentially binds to mannose and N-acetyl glucosamine residues. MuRLK exists in the cytoplasm and also localizes to the plasma membrane of plant cells via its N-terminus. Over-expression of MuRLK in Arabidopsis enhances the basal resistance to infection with Pseudomonas syringae pv. tomato, Alternaria brassicicola and Hyaloperonospora arabidopsidis, are associated with elevated ROS bursts, MAPK activation, thus ultimately leading to hypersensitive cell death. Moreover, salicylic acid-dependent and jasmonic acid-dependent defense responses are also enhanced in the MuRLK-overexpressed plants that lead to HR-induced cell death. Together, these results suggest that MuRLK plays a key role in the regulation of plant cell death, early and late defense responses after the recognition of microbial pathogens.

Keywords: horsegram, Pseudomonas syringae pv. tomato, MuRLK, ROS burst, cell death, plant defense

Procedia PDF Downloads 223

Authors: M. Adjabi, A. Amiar, P. O. Logerais

Abstract:

Flexible Alternative Current Systems Transmission (FACTS) are used since nearly four decades and present very good dynamic performances. The purpose of this work is to study the behavior of a system where Static Compensator (STATCOM) is located at the midpoint of a transmission line which is the idea of the project functioning in disturbed modes with various levels of load. The studied model and starting from the analysis of various alternatives will lead to the checking of the aptitude of the STATCOM to maintain the voltage plan and to improve the power flow in electro-energetic system which is the east region of Algerian 400 kV transmission network. The steady state performance of STATCOM’s controller is analyzed through computer simulations with Matlab/Simulink program. The simulation results have demonstrated that STATCOM can be effectively applied in power transmission systems to solve the problems of poor dynamic performance and voltage regulation.

Keywords: STATCOM, reactive power, power flow, voltage plan, Algerian network

Procedia PDF Downloads 543

Authors: M. Adjabi, A. Amiar, P. O. Logerais

Abstract:

Flexible Alternative Current Systems Transmission (FACTS) are used since nearly four decades and present very good dynamic performances. The purpose of this work is to study the behavior of a system where Static Compensator (STATCOM) is located at the midpoint of a transmission line which is the idea of the project functioning in disturbed modes with various levels of load. The studied model and starting from the analysis of various alternatives will lead to the checking of the aptitude of the STATCOM to maintain the voltage plan and to improve the power flow in electro-energetic system which is the east region of Algerian 400 kV transmission network. The steady state performance of STATCOM’s controller is analyzed through computer simulations with Matlab/Simulink program. The simulation results have demonstrated that STATCOM can be effectively applied in power transmission systems to solve the problems of poor dynamic performance and voltage regulation.

Keywords: STATCOM, reactive power, power flow, voltage plan, Algerian network

Procedia PDF Downloads 571

Authors: Jie Lin, Yiwen Pan, Li Zhang, Zhangyong Xia

Abstract:

Atherosclerosis is a chronic inflammatory disease characterized by the accumulation of lipids, immune cells, and extracellular matrix in the arterial walls. This pathological process can lead to the formation of plaques that can obstruct blood flow and trigger various cardiovascular diseases such as heart attack and stroke. The underlying molecular mechanisms still remain unclear, although many studies revealed the dysfunction of endothelial cells, recruitment and activation of monocytes and macrophages, and the production of pro-inflammatory cytokines and chemokines in atherosclerosis. This study aimed to identify hub genes involved in the progression of atherosclerosis and to analyze their biological function in silico, thereby enhancing our understanding of the disease’s molecular mechanisms. Through the analysis of microarray data, we examined the gene expression in media and neo-intima from plaques, as well as distant macroscopically intact tissue, across a cohort of 32 hypertensive patients. Initially, 112 differentially expressed genes (DEGs) were identified. Subsequent immune infiltration analysis indicated a predominant presence of 27 immune cell types in the atherosclerosis group, particularly noting an increase in monocytes and macrophages. In the Weighted gene co-expression network analysis (WGCNA), 10 modules with a minimum of 30 genes were defined as key modules, with blue, dark, Oliver green and sky-blue modules being the most significant. These modules corresponded respectively to monocyte, activated B cell, and activated CD4 T cell gene patterns, revealing a strong morphological-genetic correlation. From these three gene patterns (modules morphology), a total of 2509 key genes (Gene Significance >0.2, module membership>0.8) were extracted. Six hub genes (CD36, DPP4, HMOX1, PLA2G7, PLN2, and ACADL) were then identified by intersecting 2509 key genes, 102 DEGs with lipid-related genes from the Genecard database. The bio-functional analysis of six hub genes was estimated by a robust classifier with an area under the curve (AUC) of 0.873 in the ROC plot, indicating excellent efficacy in differentiating between the disease and control group. Moreover, PCA visualization demonstrated clear separation between the groups based on these six hub genes, suggesting their potential utility as classification features in predictive models. Protein-protein interaction (PPI) analysis highlighted DPP4 as the most interconnected gene. Within the constructed key gene-drug network, 462 drugs were predicted, with ursodeoxycholic acid (UDCA) being identified as a potential therapeutic agent for modulating DPP4 expression. In summary, our study identified critical hub genes implicated in the progression of atherosclerosis through comprehensive bioinformatic analyses. These findings not only advance our understanding of the disease but also pave the way for applying similar analytical frameworks and predictive models to other diseases, thereby broadening the potential for clinical applications and therapeutic discoveries.

Keywords: atherosclerosis, hub genes, drug prediction, bioinformatics

Procedia PDF Downloads 31