Search results for: target gene database

Authors: Mohd Ritzman Abdul Karim, Zhaohui Huang

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A current focus in seismic engineering practice is the development of seismic design approach that focuses on the performance-based design. Performance-based design aims to design the structures to achieve specified performance based on the damage limit states. This damage limit is more restrictive limit than life safety and needs to be carefully estimated to avoid damage in piers due to failure in transverse reinforcement. In this paper, a different perspective of damage limit states has been explored by integrating two damage control material limit state, concrete and reinforcement by introduced parameters such as expected yield stress of transverse reinforcement where peak tension strain prior to bar buckling is introduced in a recent study. The different perspective of damage limit states with modified yield displacement and the modified plastic-hinge length is used in order to predict damage-control target displacement for reinforced concreate (RC) bridge pier. Three-dimensional (3D) finite element (FE) model has been developed for estimating damage target displacement to validate proposed damage limit states. The result from 3D FE analysis was validated with experimental study found in the literature. The validated model then was applied to predict the damage target displacement for RC bridge pier and to validate the proposed study. The tensile strain on reinforcement and compression on concrete were used to determine the predicted damage target displacement and compared with the proposed study. The result shows that the proposed damage limit states were efficient in predicting damage-control target displacement consistent with FE simulations.

Keywords: damage-control target displacement, damage limit states, reinforced concrete bridge pier, yield displacement

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Authors: Ahmad S. Mohd Noor, Emma A. Sirajudin, Nur F. Mat Zain

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Reliability is an important property for knowledge repository system. National Marine Bioinformatics System or NABTICS is a marine knowledge repository portal aimed to provide a baseline for marine biodiversity and a tool for researchers and developers. It is intended to be a large and growing online database and also a metadata system for inputs of research analysis. The trends of present large distributed systems such as Cloud computing are the delivery of computing as a service rather than a product. The goal of this research is to make NABTICS a system of greater availability by integrating it with Cloud based Neighbor Replication and Failure Recovery (NRFR). This can be achieved by implementation of NABTICS into distributed environment. As a result, the user can experience minimum downtime while using the system should the server is having a failure. Consequently the online database application is said to be highly available.

Keywords: cloud, availability, distributed system, marine repository, database replication

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Authors: Ruchi Yadav, Shivani Pandey, Prachi Srivastava

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Microarrays provide a rich source of data on the molecular working of cells. Each microarray reports on the abundance of tens of thousands of mRNAs. Virtually every human disease is being studied using microarrays with the hope of finding the molecular mechanisms of disease. Bioinformatics analysis plays an important part of processing the information embedded in large-scale expression profiling studies and for laying the foundation for biological interpretation. A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. Careful statistical design and analysis are essential to improve the efficiency and reliability of microarray experiments throughout the data acquisition and analysis process. One of the most popular platforms for microarray analysis is Bioconductor, an open source and open development software project based on the R programming language. This paper describes specific procedures for conducting quality assessment, visualization and preprocessing of Affymetrix Gene Chip and also details the different bioconductor packages used to analyze affymetrix microarray data and describe the analysis and outcome of each plots.

Keywords: microarray analysis, R language, affymetrix visualization, bioconductor

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Authors: Ahmad Ali Shahid, Mukhtar Ahmed

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The demand for long staple fiber having better strength and length is increasing with the introduction of modern spinning and weaving industry in Pakistan. Work on gene discovery from developing cotton fibers has helped to identify dozens of genes that take part in cotton fiber development and several genes have been characterized for their role in fiber development. Sucrose synthase (SuS) is a key enzyme in the metabolism of sucrose in a plant cell, in cotton fiber it catalyzes a reversible reaction, but preferentially converts sucrose and UDP into fructose and UDP-glucose. UDP-glucose (UDPG) is a nucleotide sugar act as a donor for glucose residue in many glycosylation reactions and is essential for the cytosolic formation of sucrose and involved in the synthesis of cell wall cellulose. The study was focused on successful Agrobacterium-mediated stable transformation of SuS gene in pCAMBIA 1301 into cotton under a CaMV35S promoter. Integration and expression of the gene were confirmed by PCR, GUS assay, and real-time PCR. Young leaves of SuS overexpressing lines showed increased total soluble sugars and plant biomass as compared to non-transgenic control plants. Cellulose contents from fiber were significantly increased. SEM analysis revealed that fibers from transgenic cotton were highly spiral and fiber twist number increased per unit length when compared with control. Morphological data from field plants showed that transgenic plants performed better in field conditions. Incorporation of genes related to cotton fiber length and quality can provide new avenues for fiber improvement. The utilization of this technology would provide an efficient import substitution and sustained production of long-staple fiber in Pakistan to fulfill the industrial requirements.

Keywords: agrobacterium-mediated transformation, cotton fiber, sucrose synthase gene, staple length

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Authors: Aseel Zibin, Abdel Rahman Altakhaineh

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This study analyses 30 cartoons depicting THE DEAL OF THE CENTURY as envisaged by two Jordanian cartoonists, namely, EmadHajjaj and Osama Hajjaj. Conceptual Blending Theory (CBT) and Multimodal Metaphor Theory (MMT) are adopted as a theoretical framework to interpret the metaphors and metonymies used in the target cartoons. The results reveal that the target domain THE DEAL OF THE CENTURY was conceptualized mainly through layered metaphors that have metonymic basis and event metaphors\allegories. Specifically, 6 groups were identified: OBJECT or a situation involving OBJECTS, situations involving HUMANS\HYBRIDS of HUMANS and OBJECTS, an ANIMAL OR situation involving an ANIMAL, hybrids of WEAPONS and humans, and event metaphors used to build a story\allegory. The target domain was also depicted via event metaphors used to build a story; some of which are embedded in the Jordanian culture, while others could be perceivable cross-culturally. The results also demonstrate that the most widely used configurations to construe the metaphors was the pictorial source–verbal target in line with Lan and Zuo (2016); the motivation was probably the greater conceptual density and concreteness of visual representation since the target is better captured verbally because of its abstractness. The use of cross-modal mappings of this type was attributed to the abstractness of the target domain, THE DEAL OF THE CENTURY, which makes it more construable via verbal cues rather than visual ones. In contrast, the source domains used were mainly concrete and thus perceivable pictorially rather than verbally.

Keywords: semiotics, cognitive semantics, metaphor, culture, blending, cartoon

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Authors: Neda Menbari, Ramin Mehdiabadi

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Background: breast cancer remains a critical global health issue, constituting a leading cause of cancer-related mortality in women. MicroRNAs (miRs) are natural RNA molecules that play an important role in cellular processes and regulate post-transcriptional gene expression. MiR-216b-5p is a miR that acts as a tumor suppressor. The expression levels of FoxM1 and miR-216b-5p in malignant and control cells have been evaluated by quantitative polymerase chain reaction (qPCR) technique and flow cytometry. Results: the results of this study revealed a significant downregulation of miR-216b-5p in cancerous cells compared to the control MCF-10A cells (P=0.0004). Interestingly, the expression of miR-216b-5p exhibited an inverse relationship with key clinical indicators such as tumor size, grade, and lymph node invasion. Conclusion: The study's findings showed the prognostic value of miR-216b-5p levels in breast cancer, and its reduced expression correlates with unfavorable tumor characteristics. This research recommends performing more studies on the role of FoxM1 and miR-216b-5p in breast cancer pathology which potentially paving the way for targeted therapeutic interventions.

Keywords: breast cancer, gene expression, FOXM1, microRNA

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Authors: Hamed Zolfaghari, Mojtaba Kord

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Project planners and controllers are frequently faced with the challenge of inadequate software for the preparation of automatic project progress reports based on actual project information updates. They usually make dashboards in Microsoft Excel, which is local and not applicable online. Another shortcoming is that it is not linked to planning software such as Microsoft Project, which lacks the database required for data storage. This study aimed to propose a model for the preparation of reports on automatic online project progress based on actual project information updates by the integration of Primavera P6, SQL database, and Power BI for a construction project. The designed model could be applicable to project planners and controller agents by enabling them to prepare project reports automatically and immediately after updating the project schedule using actual information. To develop the model, the data were entered into P6, and the information was stored on the SQL database. The proposed model could prepare a wide range of reports, such as earned value management, HR reports, and financial, physical, and risk reports automatically on the Power BI application. Furthermore, the reports could be published and shared online.

Keywords: primavera P6, SQL, Power BI, EVM, integration management

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Authors: Samira B. R. Prado, Paulo R. Melfi, Beatriz T. Minguzzi, João P. Fabi

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Fruit softening is the main change that occurs during papaya (Carica papaya L.) ripening. It is characterized by the depolymerization of cell wall polysaccharides, especially the pectic fractions, which causes cell wall disassembling. However, it is uncertain how the modification of the two main pectin polysaccharides fractions (water-soluble – WSF, and oxalate-soluble fractions - OSF) accounts for fruit softening. The aim of this work was to correlate molecular weight changes of WSF and OSF with the gene expression of pectin-solubilizing enzymes (pectinases) during papaya ripening. Papaya fruits obtained from a producer were harvest and storage under specific conditions. The fruits were divided in five groups according to days after harvesting. Cell walls from all groups of papaya pulp were isolated and fractionated (WSF and OSF). Expression profiles of pectinase genes were achieved according to the MIQE guidelines (Minimum Information for publication of Quantitative real-time PCR Experiments). The results showed an increased yield and a decreased molecular weight throughout ripening for WSF and OSF. Gene expression data support that papaya softening is achieved by polygalacturonases (PGs) up-regulation, in which their actions might have been facilitated by the constant action of pectinesterases (PMEs). Moreover, BGAL1 gene was up-regulated during ripening with a simultaneous galactose release, suggesting that galactosidases (GALs) could also account for pulp softening. The data suggest that a solubilization of galacturonans and a depolymerization of cell wall components were caused mainly by the action of PGs and GALs.

Keywords: carica papaya, fruit ripening, galactosidases, plant cell wall, polygalacturonases

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Authors: Yo-Seph Byun, Gyu-Phil Lee, Young-Bin Park, Gye-Chun Cho, Seong-Won Lee

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In Korea, a study on Limit State Design (LSD) for underground structures is being conducted in order to perform more effective design. In this study, as a result of MCS (Monte-Carlo Simulation) technique, failure probabilities of the structure during normal and earthquake are estimated in reliability analysis. Target reliability indexes are determined depending on load combinations for underground structure, and then, design variables such as load and material factors in LSD are decided. As a result, through the research in order to determine more reliable design variables, a specification of LSD for underground structures is able to be developed.

Keywords: design variable, limit state design, target reliability index, underground structure

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Authors: Yoshino Murakami, Takeshi Hashimoto, Steve Cole

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The autonomic nervous system (ANS), particularly the sympathetic (SNS) and parasympathetic (PNS) branches, plays a vital role in modulating immune function and physiological homeostasis. In recent years, the Conserved Transcriptional Response to Adversity (CTRA) has emerged as a key marker of the body's response to chronic stress. This gene expression profile is characterized by SNS-mediated upregulation of pro-inflammatory genes (such as IL1B and TNF) and downregulation of antiviral response genes (e.g., IFI and MX families). CTRA has been observed in individuals exposed to prolonged stressors like loneliness, social isolation, and bereavement. Some research suggests that PNS activity, as indicated by heart rate variability (HRV), may help counteract the CTRA. However, previous PNS-CTRA studies have focused on Western populations, raising questions about the generalizability of these findings across different cultural and ethnic backgrounds. This study aimed to examine the relationship between HRV and CTRA gene expression in young, healthy adults in Japan. We hypothesized that HRV would be inversely related to CTRA gene expression, similar to patterns observed in previous Western studies. A total of 49 participants aged 20 to 39 were recruited, and after data exclusions, 26 participants' HRV and CTRA data were analyzed. HRV was measured using an electrocardiogram (ECG), and two time-domain indices were utilized: the root mean square of successive differences (RMSSD) and the standard deviation of NN intervals (SDNN). Blood samples were collected for gene expression analysis, focusing on a standard set of 47 CTRA indicator gene transcripts. it findings revealed a significant inverse relationship between HRV and CTRA gene expression, with higher HRV correlating with reduced pro-inflammatory gene activity and increased antiviral response. These results are consistent with findings from Western populations and demonstrate that the relationship between ANS function and immune response generalizes to an East Asian population. The study highlights the importance of HRV as a biomarker for psychophysiological health, reflecting the body's ability to buffer stress and maintain immune balance. These findings have implications for understanding how physiological systems interact across different cultures and ethnicities. Given the influence of chronic stress in promoting inflammation and disease risk, interventions aimed at improving HRV, such as mindfulness-based practices or physical exercise, could provide significant health benefits. Future research should focus on larger sample sizes and experimental interventions to better understand the causal pathways linking HRV to CTRA gene expression, and determine whether improving HRV may help mitigate the harmful effects of stress on health by reducing inflammation.

Keywords: autonomic nervous activity, neuroendocrine system, inflammation, Japan

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Authors: Yen-Hao Su, Wan-Chun Tang, Ya-Wen Cheng, Peik Sia, Chi-Chen Huang, Yi-Chao Lee, Hsin-Yi Jiang, Ming-Heng Wu, I-Lu Lai, Jun-Wei Lee, Kuen-Haur Lee

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There is a wide range of drugs and combinations under investigation and/or approved over the last decade to treat colorectal cancer (CRC), but the 5-year survival rate remains poor at stages II–IV. Therefore, new, more efficient drugs still need to be developed that will hopefully be included in first-line therapy or overcome resistance when it appears, as part of second- or third-line treatments in the near future. In this study, we revealed that heat shock protein 90 (Hsp90) inhibitors have high therapeutic potential in CRC according to combinative analysis of NCBI's Gene Expression Omnibus (GEO) repository and chemical genomic database of Connectivity Map (CMap). We found that second generation Hsp90 inhibitor, NVP-AUY922, significantly down regulated the activities of a broad spectrum of kinases involved in regulating cell growth arrest and death of NVPAUY922-sensitive CRC cells. To overcome NVP-AUY922-induced upregulation of survivin expression which causes drug insensitivity, we found that combining berberine (BBR), a herbal medicine with potency in inhibiting survivin expression, with NVP-AUY922 resulted in synergistic antiproliferative effects for NVP-AUY922-sensitive and -insensitive CRC cells. Furthermore, we demonstrated that treatment of NVP-AUY922-insensitive CRC cells with the combination of NVP-AUY922 and BBR caused cell growth arrest through inhibiting CDK4 expression and induction of microRNA-296-5p (miR-296-5p)-mediated suppression of Pin1–β-catenin–cyclin D1 signaling pathway. Finally, we found that the expression level of Hsp90 in tumor tissues of CRC was positively correlated with CDK4 and Pin1 expression levels. Taken together, these results indicate that combination of NVP-AUY922 and BBR therapy can inhibit multiple oncogenic signaling pathways of CRC.

Keywords: berberine, colorectal cancer, connectivity map, heat shock protein 90 inhibitor

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Authors: A. Kebbeb, M. Mostefai, F. Benmerzoug, Y. Chahir

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The multimodal biometric identification is the combination of several biometric systems. The challenge of this combination is to reduce some limitations of systems based on a single modality while significantly improving performance. In this paper, we propose a new approach to the construction and the protection of a multimodal biometric database dedicated to an identification system. We use a topological watermarking to hide the relation between face image and the registered descriptors extracted from other modalities of the same person for more secure user identification.

Keywords: biometric databases, multimodal biometrics, security authentication, digital watermarking

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Authors: Dana Gabriková, Martin Mistrík, Jarmila Bernasovská, Iveta Tóthová, Jana Kisková

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The Roma (Gypsies) is a transnational minority with a high degree of consanguineous marriages. Similar to other genetically isolated founder populations, the Roma harbor a number of unique or rare genetic disorders. This paper discusses about a rare form of Charcot-Marie-Tooth disease – type 4G (CMT4G), also called Hereditary Motor and Sensory Neuropathy type Russe, an autosomal recessive disease caused by mutation private to Roma characterized by abnormally increased density of non-myelinated axons. CMT4G was originally found in Bulgarian Roma and in 2009 two putative causative mutations in the HK1 gene were identified. Since then, several cases were reported in Roma families mainly from Bulgaria and Spain. Here we present a Slovak Roma family in which CMT4G was diagnosed on the basis of clinical examination and genetic testing. This case is a further proof of the role of the HK1 gene in pathogenesis of the disease. It confirms that mutation in the HK1 gene is a common cause of autosomal recessive CMT disease in Roma and should be considered as a common part of a diagnostic procedure.

Keywords: gypsies, HK1, HSMN-Russe, rare disease

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Authors: Boukerch Haroun, Luo Qing Sheng, Li Hua Shi, Boukraa Sebti

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In this paper we present the design and the implementation of a target tracking system where the target is set to be a moving person in a video sequence. The system can be applied easily as a vision system for mobile robot. The system is composed of two major parts the first is the detection of the person in the video frame using the SVM learning machine based on the “HOG” descriptors. The second part is the tracking of a moving person it’s done by using a combination of the Kalman filter and a modified version of the Camshift tracking algorithm by adding the target motion feature to the color feature, the experimental results had shown that the new algorithm had overcame the traditional Camshift algorithm in robustness and in case of occlusion.

Keywords: camshift algorithm, computer vision, Kalman filter, object tracking

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Authors: Kay Thi Yar, Khin Mar Lar Tun

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Nowadays, social networks are so popular and widely used in all over the world. In addition, searching personal information of each person and searching connection between them (peoples’ relation in real world) becomes interesting issue in our society. In this paper, we propose a framework with three portions for exploring peoples’ relations from their connected information. The first portion focuses on the Graph database structure to store the connected data of peoples’ information. The second one proposes the graph database searching algorithm, the Modified-SoS-ACO (Sense of Smell-Ant Colony Optimization). The last portion proposes the Deductive Reasoning Algorithm to define two persons’ relationship. This study reveals the proper storage structure for connected information, graph searching algorithm and deductive reasoning algorithm to predict and analyze the personnel relationship from peoples’ relation in their connected information.

Keywords: personnel information, graph storage structure, graph searching algorithm, deductive reasoning algorithm

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Authors: Xiaoping Su, Gabriel G. Malouf

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Introduction: Breast cancer is a heterogeneous disease that can be classified in 4 subgroups using transcriptional profiling. The role of lncRNA expression in human breast cancer biology, prognosis, and molecular classification remains unknown. Methods and results: Using an integrative comprehensive analysis of lncRNA, mRNA and DNA methylation in 900 breast cancer patients from The Cancer Genome Atlas (TCGA) project, we unraveled the molecular portraits of 1,700 expressed lncRNA. Some of those lncRNAs (i.e, HOTAIR) are previously reported and others are novel (i.e, HOTAIRM1, MAPT-AS1). The lncRNA classification correlated well with the PAM50 classification for basal-like, Her-2 enriched and luminal B subgroups, in contrast to the luminal A subgroup which behaved differently. Importantly, estrogen receptor (ESR1) expression was associated with distinct lncRNA networks in lncRNA clusters III and IV. Gene set enrichment analysis for cis- and trans-acting lncRNA showed enrichment for breast cancer signatures driven by breast cancer master regulators. Almost two third of those lncRNA were marked by enhancer chromatin modifications (i.e., H3K27ac), suggesting that lncRNA expression may result in increased activity of neighboring genes. Differential analysis of gene expression profiling data showed that lncRNA HOTAIRM1 was significantly down-regulated in basal-like subtype, and DNA methylation profiling data showed that lncRNA HOTAIRM1 was highly methylated in basal-like subtype. Thus, our integrative analysis of gene expression and DNA methylation strongly suggested that lncRNA HOTAIRM1 should be a tumor suppressor in basal-like subtype. Conclusion and significance: Our study depicts the first lncRNA molecular portrait of breast cancer and shows that lncRNA HOTAIRM1 might be a novel tumor suppressor.

Keywords: lncRNA profiling, breast cancer, HOTAIRM1, tumor suppressor

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Authors: Matevž Breška, Iztok Peruš, Vlado Stankovski

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Systematic overview of existing Ground Motion Prediction Equations (GMPEs) has been published by Douglas. The number of earthquake recordings that have been used for fitting these equations has increased in the past decades. The current PF-L database contains 3550 recordings. Since the GMPEs frequently model the peak ground acceleration (PGA) the goal of the present study was to refit a selection of 44 of the existing equation models for PGA in light of the latest data. The algorithm Levenberg-Marquardt was used for fitting the coefficients of the equations and the results are evaluated both quantitatively by presenting the root mean squared error (RMSE) and qualitatively by drawing graphs of the five best fitted equations. The RMSE was found to be as low as 0.08 for the best equation models. The newly estimated coefficients vary from the values published in the original works.

Keywords: Ground Motion Prediction Equations, Levenberg-Marquardt algorithm, refitting PF-L database, peak ground acceleration

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Authors: Yun-Chin Chung, Nileema Divate, Gen-Hung Chen, Pei-Ru Huang, Rupesh Divate

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Many environmental factors, such as glucose concentration, ethanol, temperature, osmotic pressure and pH, decrease the production rate of ethanol using yeast as a starter. Fermentation starters with high tolerance to various stresses are always demanded for brewing industry. Trehalose, a storage carbohydrate in cell wall of yeast, plays an important role in tolerance of environmental stress by preserving integrity of plasma membrane and stabilizing proteins. Furan aldehydes are toxic to yeast and the growth rate of yeast is significantly reduced if furan aldehydes were present in the fermentation medium. In yeast, aldehyde reductase is involved in the detoxification of reactive aldehydes and consequently the growth of yeast is improved. The aims of this study were to construct a genetic recombinant Saccharomyces cerevisiae or Pichia pastoris with furfural and HMF degrading and high ethanol tolerance capacities. Yeast strains were engineered by genetic recombination for overexpression of trehalose-6-phosphate synthase gene (tps1) and aldehyde reductase gene (ari1). TPS1 gene was cloned from S. cerevisiae by reverse transcription-polymerase chain reaction (RT-PCR) and then ligated with pGAPZαC vector. The constructed vector, pGAPZC-tps1, was transformed to recombinant yeasts strain with overexpression of ari1. The transformants with pGAPZC-tps1-ari1 were generated called STA (S. cerevisiae) and PTA (P. pastoris) with overexpression of tps1, ari1. PCR with tps1-specific primers and western blot with his-tag confirmed the gene insertion and protein expression of tps1 in the transformants, respectively. The neutral trehalase gene (nth1) of STA was successfully deleted and the novel strain STAΔN will be used for further study, including the measurement of trehalose concentration and ethanol, furfural tolerance assay.

Keywords: genetic recombinant, yeast, ethanol tolerance, trehalase, aldehyde reductase

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Authors: Jimmy L. Caldoza, Erlito M. Albina

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Information Systems are increasingly being used to monitor and assess government projects as well as improve transparency and combat corruption. With reference to existing information systems relevant to monitoring and evaluation systems adopted by various government agencies from other countries, this research paper aims to help the Philippine government, particularly the Department of Agriculture, in assessing the impact of their programs and projects on their target beneficiaries through the development of the web-based Monitoring and Evaluation Information System with the application of a short messaging system (sms) technology.

Keywords: monitoring and evaluation system, web-based information system, short messaging system technology, database structure and management

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Authors: Jae Woong Sull, Sun Ha Jee

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High-density lipoprotein (HDL) cholesterol levels are associated with decreased risk of coronary artery disease. Several genome-wide association studies (GWAS) for HDL cholesterol levels have implicated cholesterol ester transfer protein (CETP) as possibly causal. We tested for the association between single nucleotide polymorphisms (SNPs) in CETP gene and HDL cholesterol levels in Korean population. Subjects were selected from the Korean Metabolic Syndrome Research Initiative study in the Bundang-Gu area. A total of 2,304 individuals from Bundang-Gu were recruited in 2008. Other subjects were selected from the Severance Hospital (N=4,294). SNP rs6499861 in the CETP gene was associated with mean HDL cholesterol levels (effect per allele -2.044 mg/dL, p=7.23×10-7). Subjects with the CG/GG genotype had a 1.46 -fold (range 1.24–1.72-fold) higher risk of having abnormal HDL cholesterol levels (<40 mg/dL) than subjects with the CC genotype. When analyzed by gender, the association of CETP was stronger in women than in men. When analyzed by physical activity behavior, the association with CETP was much stronger in male subjects with low physical activity (OR=1.54, 95% CI: 1.23-1.92, P=0.0001) than in male subjects with high physical activity. This study clearly demonstrates that genetic variants in CETP influence HDL cholesterol levels in Korean adults.

Keywords: CETP, HDL cholesterol, physical activity, polymorphisms

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Authors: S. A. Che Osmi, W. M. F. W. Ishak, S. F. Che Osmi

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Nowadays the issues of water quality and water pollution have been a major problem across the country. A lot of management attempt to develop their own TMDL database in order to control the river pollution. Over the past decade, the mathematical modeling has been used as the tool for the development of TMDL. This paper presents the application of water quality modeling to develop the total maximum daily load (TMDL) information. To obtain the reliable database of TMDL, the appropriate water quality modeling should choose based on the available data provided. This paper will discuss on the use of several water quality modeling such as QUAL2E, QUAL2K, and EFDC to develop TMDL. The attempts to integrate several modeling are also being discussed in this paper. Based on this paper, the differences in the application of water quality modeling based on their properties such as one, two or three dimensional are showing their ability to develop the modeling of TMDL database.

Keywords: TMDL, water quality modeling, QUAL2E, EFDC

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Authors: Dipanshu Sur, Ratnabali Chakravorty

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Background: Polycystic ovary syndrome (PCOS) is the most common metabolic abnormality such as changes in lipid profile, diabetes, hypertension and metabolic syndrome occurring in young women of reproductive age. Low vitamin D levels were found to be associated with the development of obesity and insulin resistance in women with PCOS. Variants on vitamin D receptor (VDR) gene have also been related to metabolic comorbidities in general population. Aim: The aim of this case-control study was to investigate whether the VDR gene polymorphisms are associated with susceptibility to PCOS. Methods: Women with PCOS and a control group, all aged 16-40 years, were enrolled. Genotyping of VDR Fok-I (rs2228570), VDR Apa-I (rs7975232) as well as GC (rs2282679), DHCR7 (rs12785878) SNPs between groups were determined by using direct sequencing. Serum 25-hydroxyvitamin D [25(OH)] levels were measured by ELISA. Results: Mean serum 25(OH)D in the PCOS and control samples were 19.08±7 and 23.27±6.03 (p=0.048) which were significantly lower in PCOS patients compared with controls. CC genotype of the VDR Apa-I SNP was same frequent in PCOS (25.6%) and controls (25.6%) (OR: 0.9995; 95%CI: 0.528 to 1.8921; p= 0.9987). The CC genotype was also significantly associated with both lower E2 (p=0.031) and Androstenedione levels (p=0.062). We observed a significant association of GC polymorphism with 25(OH)D levels. PCOS women carrying the GG genotype (in GC genes) had significantly higher risk for vitamin D deficiency than women carrying the TT genotype. Conclusions: In conclusion, data from this study indicate that vitamin D levels are lower, and vitamin D deficiency more frequent, in PCOS than in controls. The present findings suggest that the Apa-I, Fok-I polymorphism of the VDR gene is associated with PCOS and seems to modulate ovarian steroid secretion. Further studies are needed to better clarify the biological mechanisms by which the polymorphism influences PCOS risk.

Keywords: vitamin D receptor, polymorphism, vitamin D, polycystic ovary syndrome

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Authors: Yanwen Li, Shuguo Xie

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In electromagnetic imaging, because of the diffraction limited system, the pixel values could change slowly near the edge of the image targets and they also change with the location in the same target. Using traditional digital image segmentation methods to segment electromagnetic gradient images could result in lots of errors because of this change in pixel values. To address this issue, this paper proposes a novel image segmentation and extraction algorithm based on Mean-Shift and dictionary learning. Firstly, the preliminary segmentation results from adaptive bandwidth Mean-Shift algorithm are expanded, merged and extracted. Then the overlap rate of the extracted image block is detected before determining a segmentation region with a single complete target. Last, the gradient edge of the extracted targets is recovered and reconstructed by using a dictionary-learning algorithm, while the final segmentation results are obtained which are very close to the gradient target in the original image. Both the experimental results and the simulated results show that the segmentation results are very accurate. The Dice coefficients are improved by 70% to 80% compared with the Mean-Shift only method.

Keywords: gradient image, segmentation and extract, mean-shift algorithm, dictionary iearning

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Authors: Amir Mukhtar, Dr. Likun Xia

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An improved, robust and efficient visual target tracking algorithm using particle filtering is proposed. Particle filtering has been proven very successful in estimating non-Gaussian and non-linear problems. In this paper, the particle filter is used with color feature to estimate the target state with time. Color distributions are applied as this feature is scale and rotational invariant, shows robustness to partial occlusion and computationally efficient. The performance is made more robust by choosing the different (YIQ) color scheme. Tracking is performed by comparison of chrominance histograms of target and candidate positions (particles). Color based particle filter tracking often leads to inaccurate results when light intensity changes during a video stream. Furthermore, background subtraction technique is used for size estimation of the target. The qualitative evaluation of proposed algorithm is performed on several real-world videos. The experimental results demonstrate that the improved algorithm can track the moving objects very well under illumination changes, occlusion and moving background.

Keywords: tracking, particle filter, histogram, corner points, occlusion, illumination

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Authors: Abdullah M. Alzahrani

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Our physiopathological assumption is that u-PA, t-PA, and PAI-1 are released by calcified aortic valves and play a role in the calcification of these valves. Sixty-five calcified aortic valves were collected from patients suffering from aortic stenosis. Each valve was incubated for 24 hours in culture medium. The supernatants were used to measure u-PA, t-PA, and PAI-1 concentrations; the valve calcification was evaluated using biphotonic absorptiometry. Aortic stenosis valves expressed normal plasminogen activators concentrations and overexpressed PAI-1 (u-PA, t-PA, and PAI-1 mean concentrations were, resp., 1.69 ng/mL ± 0.80, 2.76 ng/mL ± 1.33, and 53.27 ng/mL ± 36.39). There was no correlation between u-PA and PAI-1 (r = 0.3) but t-PA and PAI-1 were strongly correlated with each other (r = 0.6). Over expression of PAI-1 was proportional to the calcium content of theAS valves. Our results demonstrate a consistent increase of PAI-1 proportional to the calcification. The over expression of PAI-1 may be useful as a predictive indicator in patients with aortic stenosis.

Keywords: aortic valve, PAI-1, tPA gene, uPA gene

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Authors: Omneya M. Helmy, Mona T. Kashef

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Aminoglycosides are used in treating a wide range of infections caused by both Gram-negative and Gram positive bacteria. The presence of 16S rRNA methyl transferases (16S-RMTase) is among the newly discovered resistance mechanisms that confer high resistance to clinically useful aminoglycosides. Cephalosporins are the most commonly used antimicrobials in Egypt; therefore, this study was conducted to determine the isolation frequency of 16S rRNA methyl transferases among third generation cephalosporin-resistant clinical isolates in Egypt. One hundred and twenty three cephalosporin resistant Gram-negative clinical isolates were screened for aminoglycoside resistance by the Kirby Bauer disk diffusion method and tested for possible production of 16S-RMTase. PCR testing and sequencing were used to confirm the presence of 16S-RMTase and the associated antimicrobial resistance determinants, as well as the genetic region surrounding the armA gene. Out of 123 isolates, 66 (53.66%) were resistant to at least one aminoglycoside antibiotic. Only one Escherichia coli isolate (E9ECMO) which was totally resistant to all tested aminoglycosides, was confirmed to have the armA gene in association with blaTEM-1, blaCTX-M-15, blaCTX-M-14 and aac(6)-Ib genes. The armA gene was found to be carried on a large A/C plasmid. Genetic mapping of the armA surrounding region revealed, for the first time, the association of armA with aac(6)-Ib on the same transposon. In Conclusion, the isolation frequency of 16S-RMTase was low among the tested cephalosporin-resistant clinical samples. However, a novel composite transposon has been detected conferring high-level aminoglycosides resistance.

Keywords: aminoglcosides, armA gene, β lactmases, 16S rRNA methyl transferases

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Authors: Mohammad Ahmad Ahmad Odah

Abstract:

Aging is a complex biological process characterized by the progressive decline of physiological functions and increased vulnerability to age-related diseases. Epigenetic changes, particularly DNA methylation alterations, play a critical role in the aging process by influencing gene expression and genomic stability. This study explores the potential of epigenetic reprogramming as a strategy to reverse aging phenotypes in human fibroblasts. Using CRISPR-Cas9 gene editing and small molecule inhibitors targeting DNA methylation and histone acetylation, we successfully induced significant changes in DNA methylation and gene expression profiles. Our results demonstrate a global reduction in DNA methylation levels and the identification of differentially methylated regions (DMRs) associated with cellular senescence and DNA repair. Additionally, treated fibroblasts exhibited enhanced proliferative capacity, reduced cellular senescence, and improved differentiation potential. These findings suggest that epigenetic reprogramming could be a promising approach for regenerative medicine, offering potential therapeutic strategies to counteract age-related decline and extend healthy lifespan.

Keywords: epigenetic reprogramming, aging, regenerative medicine, DNA methylation, cellular rejuvenation, CRISPR-Cas9, senescence

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Authors: Muhammad Shahzad Iqbal, Zobia Sarwar, Salah-ud-Din

Abstract:

Tomato spotted wilt virus (TSWV) belongs to the genus Tospoviruses (family Bunyaviridae). It is one of the most devastating pathogens of tomato (Solanum Lycopersicum) and heavily damages the crop yield each year around the globe. In this study, we retrieved 329 mature miRNA sequences from two microRNA databases (miRBase and miRSoldb) and checked the putative target sites in the downloaded-genome sequence of TSWV. A consensus of three miRNA target prediction tools (RNA22, miRanda and psRNATarget) was used to screen the false-positive microRNAs targeting sites in the TSWV genome. These tools calculated different target sites by calculating minimum free energy (mfe), site-complementarity, minimum folding energy and other microRNA-mRNA binding factors. R language was used to plot the predicted target-site data. All the genes having possible target sites for different miRNAs were screened by building a consensus table. Out of these 329 mature miRNAs predicted by three algorithms, only eight miRNAs met all the criteria/threshold specifications. MC-Fold and MC-Sym were used to predict three-dimensional structures of miRNAs and further analyzed in USCF chimera to visualize the structural and conformational changes before and after microRNA-mRNA interactions. The results of the current study show that the predicted eight miRNAs could further be evaluated by in vitro experiments to develop TSWV-resistant transgenic tomato plants in the future.

Keywords: tomato spotted wild virus (TSWV), Solanum lycopersicum, plant virus, miRNAs, microRNA target prediction, mRNA

Procedia PDF Downloads 155

Authors: İsmail İnce, Mustafa Fener, Sair Kahraman

Abstract:

The uniaxial compressive strength (UCS) of rocks is an important input parameter for the design of rock engineering project. Compressive strength can be determined in the laboratory using the uniaxial compressive strength (UCS) test. Although the test is relatively simple, the method is time consuming and expensive. Therefore many researchers have tried to assess the uniaxial compressive strength values of rocks via relatively simple and indirect tests (e.g. point load strength test, Schmidt Hammer hardness rebound test, P-wave velocity test, etc.). Pyroclastic rocks are widely exposed in the various regions of the world. Cappadocia region located in the Central Anatolia is one of the most spectacular cite of these regions. It is important to determine the mechanical behaviour of the pyroclastic rocks due to their ease of carving, heat insulation properties and building some civil engineering constructions in them. The purpose of this study is to estimate a widely varying uniaxial strength of pyroclastic rocks from Cappadocia region by means of point load strength, porosity, dry density and saturated density tests utilizing gene expression programming.

Keywords: pyroclastic rocks, uniaxial compressive strength, gene expression programming (GEP, Cappadocia region

Procedia PDF Downloads 339

Authors: Carlo Stephen O. Moneva, Sharon Rose M. Tabugo

Abstract:

The present study aims to assess polymorphism in the prolactin (C576A) gene and determine the influence of different prolactin (PRL) genotypes to milk yield performance in crossbred Anglo-Nubian dairy goats raised from Awang, Opol, Misamis Oriental and Talay, Dumaguete City, Negros Oriental. Genomic DNA was extracted from hair follicles and Polymerase Chain Reaction – Restriction Fragment Length Polymorphism (PCR-RFLP) was performed for the genotyping of the C576A polymorphism located in exon 5 of goats’ prolactin gene using Eco241 restriction enzyme. Genotypic and allelic frequencies of 0.56 for AA, 0.44 for AB, 0.78 for A, and 0.22 for B were recorded. Observed heterozygosity values were higher than the expected heterozygosity. All populations followed the Hardy–Weinberg principle at p>0.05, except for dairy goats from Farm A located in Opol, Misamis Oriental. A two-way factorial (2 x 4) in a Randomized Complete Block Design was used to be able to evaluate the relationship between genotypes and milk yield performance. PRL genotypes and parity were used as main factors and farm as the blocking factor. AB genotype goats produced significantly higher average daily milk yield and total milk production than AA genotype (p<0.05), an indication that the polymorphism in the caprine PRL (C576A) gene influenced milk yield performance in the population of crossbred Anglo-Nubian goats from Opol, Misamis Oriental and Dumaguete City, Negros Oriental. However, these results have to be validated in other dairy goat breeds.

Keywords: polymorphism, prolactin, milk yield, Anglo-Nubian, PCR-RFLP

Procedia PDF Downloads 106