Search results for: structural genes

Authors: Al-Mutary M., Alhimaidi A., Al-Ghadi M. Iwamoto D., Javed Ahmad. Abdulaziz A. Al-Khedhairy

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The aim of the present study was to evaluate the effect of ovine follicular fluid supplementation during IVM of sheep oocytes on the resumption of meiosis, glutathione (GSH) content and expression of Bax, Bcl-2, and HSPB1 genes. Sheep ovaries were collected from Riyadh slaughterhouse, KSA. Oocytes were aspirated from 3-6 mm follicles. Ovine oocytes were cultured in maturation medium with 0% (control), 10%, 20%, 40% of ovine follicular fluid for 24 h. Results indicated that the rate of oocyte maturation was significantly (P≤0.05) decreased in 40% OFF (36.87%) versus the control (61.3%), 10% OFF (63.95%) and 20% OFF (64.08%). Supplementation of 10% OFF to IVM medium induced an intra-oocyte GSH concentration significantly higher than that found in ovine oocytes cultured with 20% OFF and 40% OFF and similar to the GSH content in oocytes cultured without FF. Real time polymerase chain reaction analysis for gene expression revealed no differences in Bax, Bcl-2, HSPB1 genes between control and 10% OFF group, whereas they were strongly expressed in 20% OFF and 40% OFF (P < 0.05) when compared to the control and 10% OFF. In conclusion the addition of 10% OFF to the IVM culture of sheep oocytes is recommended to support cytoplasmic maturation and increase oocytes competence.

Keywords: IVM, oocyte maturation, gene expression, follicular fluid

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Authors: Sittampalam Manoharan, Gary Chai, Sanaul Chowdhury, Andrew Golding

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The primary objective of this paper is to present a simplified approach to develop the structural deterioration model using traffic speed deflectometer data for flexible pavements. Maintaining assets to meet functional performance is not economical or sustainable in the long terms, and it would end up needing much more investments for road agencies and extra costs for road users. Performance models have to be included for structural and functional predicting capabilities, in order to assess the needs, and the time frame of those needs. As such structural modelling plays a vital role in the prediction of pavement performance. A structural condition is important for the prediction of remaining life and overall health of a road network and also major influence on the valuation of road pavement. Therefore, the structural deterioration model is a critical input into pavement management system for predicting pavement rehabilitation needs accurately. The Traffic Speed Deflectometer (TSD) is a vehicle-mounted Doppler laser system that is capable of continuously measuring the structural bearing capacity of a pavement whilst moving at traffic speeds. The device’s high accuracy, high speed, and continuous deflection profiles are useful for network-level applications such as predicting road rehabilitations needs and remaining structural service life. The methodology adopted in this model by utilizing time series TSD maximum deflection (D0) data in conjunction with rutting, rutting progression, pavement age, subgrade strength and equivalent standard axle (ESA) data. Then, regression analyses were undertaken to establish a correlation equation of structural deterioration as a function of rutting, pavement age, seal age and equivalent standard axle (ESA). This study developed a simple structural deterioration model which will enable to incorporate available TSD structural data in pavement management system for developing network-level pavement investment strategies. Therefore, the available funding can be used effectively to minimize the whole –of- life cost of the road asset and also improve pavement performance. This study will contribute to narrowing the knowledge gap in structural data usage in network level investment analysis and provide a simple methodology to use structural data effectively in investment decision-making process for road agencies to manage aging road assets.

Keywords: adjusted structural number (SNP), maximum deflection (D0), equant standard axle (ESA), traffic speed deflectometer (TSD)

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Authors: Nam-Hee Kim, Jang-Hoon Ko, Kwon-Hee Lee

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A relief valve is a mechanical element to keep safety by controlling high pressure. Usually, the high pressure is relieved by using the spring force and letting the fluid to flow from another way out of system. When its normal pressure is reached, the relief valve can return to initial state. The relief valve in this study has been applied for pressure vessel, evaporator, piping line, etc. The relief valve should be designed for smooth operation and should satisfy the structural safety requirement under operating condition. In general, the structural analysis is performed by following fluid flow analysis. In this process, the FSI (Fluid-Structure Interaction) is required to input the force obtained from the output of the flow analysis. Firstly, this study predicts the velocity profile and the pressure distribution in the given system. In this study, the assumptions for flow analysis are as follows: • The flow is steady-state and three-dimensional. • The fluid is Newtonian and incompressible. • The walls of the pipe and valve are smooth. The flow characteristics in this relief valve does not induce any problem. The commercial software ANSYS/CFX is utilized for flow analysis. On the contrary, very high pressure may cause structural problem due to severe stress. The relief valve is made of body, bonnet, guide, piston and nozzle, and its material is stainless steel. To investigate its structural safety, the worst case loading is considered as the pressure of 700 bar. The load is applied to inside the valve, which is greater than the load obtained from FSI. The maximum stress is calculated as 378 MPa by performing the finite element analysis. However, the value is greater than its allowable value. Thus, an alternative design is suggested to improve the structural performance through case study. We found that the sensitive design variable to the strength is the shape of the nozzle. The case study is to vary the size of the nozzle. Finally, it can be seen that the suggested design satisfy the structural design requirement. The FE analysis is performed by using the commercial software ANSYS/Workbench.

Keywords: relief valve, structural analysis, structural design, strength, safety factor

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Authors: Jin Young Kim, Kwon Kyoo Kang

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The SGR1 (STAYGREEN1) protein is a critical regulator of plant leaves in chlorophyll degradation and senescence. The functions and mechanisms of tomato SGR1 action are poorly understood and worthy of further investigation. To investigate the function of the SGR1 gene, we generated a SGR1-knockout (KO) null line via clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated gene editing and conducted RNA sequencing and gas chromatography tandem mass spectrometry (GC-MS/MS) analysis to identify the differentially expressed genes. The SlSGR1 (Solanum lycopersicum SGR1) knockout null line clearly showed a turbid brown color with significantly higher chlorophyll and carotenoid content compared to wild-type (WT) fruit. Differential gene expression analysis revealed 728 differentially expressed genes (DEGs) between WT and sgr1 #1-6 line, including 263 and 465 downregulated and upregulated genes, respectively, for which fold change was >2, and the adjusted p-value was <0.05. Most of the DEGs were related to photosynthesis and chloroplast function. In addition, the pigment, carotenoid changes in sgr1 #1-6 line was accumulated of key primary metabolites such as sucrose and its derivatives (fructose, galactinol, raffinose), glycolytic intermediates (glucose, G6P, Fru6P) and tricarboxylic acid cycle (TCA) intermediates (malate and fumarate). Taken together, the transcriptome and metabolite profiles of SGR1-KO lines presented here provide evidence for the mechanisms underlying the effects of SGR1 and molecular pathways involved in chlorophyll degradation and carotenoid biosynthesis.

Keywords: tomato, CRISPR/Cas9, null line, RNA-sequencing, metabolite profiling

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Authors: Salman Naveed, Nitant Gandhi, Grant Billings, Zachary Jones, B. Todd Campbell, Michael Jones, Sachin Rustgi

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Cotton (Gossypium spp.) is the primary source of natural fiber in the U.S. and a major crop in the Southeastern U.S. Despite constant efforts to increase the cotton fiber yield, the yield gain has stagnated. Therefore, we undertook a novel approach to improve the cotton fiber yield by altering its growth habit from perennial to annual. In this effort, we identified genotypes with high-expression alleles of five floral induction and meristem identity genes (FT, SOC1, FUL, LFY, and AP1) from an upland cotton mini-core collection and crossed them in various combinations to develop cotton lines with annual growth habit, optimal flowering time and enhanced productivity. To facilitate the characterization of genotypes with the desired combinations of stacked alleles, we identified markers associated with the gene expression traits via genome-wide association analysis using a 63K SNP Array (Hulse-Kemp et al. 2015 G3 5:1187). Over 14,500 SNPs showed polymorphism and were used for association analysis. A total of 396 markers showed association with expression traits. Out of these 396 markers, 159 mapped to genes, 50 to untranslated regions, and 187 to random genomic regions. Biased genomic distribution of associated markers was observed where more trait-associated markers mapped to the cotton D sub-genome. Many quantitative trait loci coincided at specific genomic regions. This observation has implications as these traits could be bred together. The analysis also allowed the identification of candidate regulators of the expression patterns of these floral induction and meristem identity genes whose functions will be validated via virus-induced gene silencing.

Keywords: cotton, GWAS, QTL, expression traits

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Authors: Anida Causevic-Ramosevac, Sabina Semiz

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The aim of this study was to investigate the association of four single nucleotide polymorphisms (SNPs) - rs673548, rs693 in ApoB gene, rs1800775 in CETP gene and rs4846914 in GALNT2 gene with parameters of type 2 diabetes (T2D) and diabetic dyslipidemia in the population of Bosnia and Herzegovina (BH). Materials and methods: Our study involved 352 patients with T2D and 156 healthy subjects. Biochemical and anthropometric parameters were measured in all participants. DNA was extracted from the peripheral blood for the purpose of genetic testing. Polymorphisms in ApoB (rs673548, rs693), CETP (rs1800775) and GALNT2 (rs4846914) genes were analyzed by using Sequenom IPLEX platform. Results: Our results demonstrated significant associations for rs180075 polymorphism in CETP gene with levels of fasting insulin (p = 0.020; p = 0.027; p = 0.044), triglycerides (p = 0.046) and ALT (p = 0.031) activity in control group. In group of diabetic patients, results showed a significant association of rs673548 in ApoB gene with levels of fasting insulin (p = 0.008), HOMA-IR (p = 0.013), VLDL-C (p = 0.037) and CRP (p = 0.029) and rs693 in ApoB gene with BMI (p = 0.025), systolic blood pressure (p = 0.027), fasting insulin (p = 0.037) and HOMA-IR (p = 0.023) levels. Significant associations were also observed for rs1800775 in CETP gene with triglyceride (p = 0.023) levels and rs4846914 in GALNT2 gene with HbA1C (p = 0.013) and triglyceride (p = 0.043) levels. Conclusion: In conclusion, this is the first study that examined the impact of variations of candidate genes on a wide range of metabolic parameters in BH population. Our results suggest an association of variations of ApoB, CETP and GALNT2 genes with specific markers of T2D and dyslipidemia. Further studies would be needed in order to confirm these genetic effects in other ethnic groups as well.

Keywords: ApoB, CETP, dyslipidemia, GALNT2, type 2 diabetes

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Authors: Nandini Sharma

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Monitoring the characteristics of a nanostructured material comprises measurements of structural, morphological, mechanical, optical and electronic properties of the synthesized nanopowder and different layers and coatings of nanomaterials coated on transparent conducting oxides (TCOs) substrates like fluorine doped tin oxide (FTO) or Indium doped tin oxide (ITO). This article focuses on structural and optical characterization with emphasis on measurements of the photocatalytic efficiency as a photocatalyst and their interpretation to extract relevant information about various TCOs and materials, their emitter regions, and surface passivation. It also covers a brief description of techniques based on photoluminescence that can portray high resolution pictorial graphs for application as solar energy devices. With the advancement in the scientific techniques, detailed information about the structural, morphological, and optical properties can be investigated, which is further useful for engineering and designing of an efficient device. The common principles involved in the prevalent characterization techniques aid to illustrate the range of options that can be broadened in near future for acurate device characterization and diagnosis.

Keywords: characterization, structural, optical, nanomaterial

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

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

Keywords: Methicillin-resistant Staphylococcus aureus, dihydroxyacetone kinase, essential genes, drug target, phosphoryl group donor

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Authors: Tettey Afi Pamela, Sotaro Fujii, Hidetoshi Saito, Kawaii Koichiro

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Introduction: Organisms employ adaptive mechanisms when faced with any stressor or risk of being wiped out. This has made it possible for them to survive in harsh environmental conditions such as increasing temperature, low pH, and anoxia. Some of the mechanisms they utilize include the expression of heat shock proteins, synthesis of cryoprotectants, and anhydrobiosis. Heat shock proteins (HSPs) have been widely studied to determine their involvement in stress tolerance among various organism, of which chironomid species have been no exception. We examined the survival and expression of genes encoding five (5) heat shock proteins (HSP70, HSP67, HSP60, HSP27, and HSP23) from Chironomus sulfurosus larvae reared from 1st instar at 25°C, 30°C, 35°C, and 40°C. Results: The highest survival rate was recorded at 30°C, followed by 25°C, then 35°C. Only a small percentage of C. sulfurosus survived at 40°C (14.5%). With regards to HSPs expression, some HSPs responded to an increase in high temperature. The relative expression levels were lowest at 30°C for HSP70, HSP60, HSP27, and HSP23. At 25°C and 40°C, HSP70, HSP67, HSP60, HSP27, and HSP23 had the highest expression. At 35°C, all had the lowest expression. Discussion: The expression of heat shock proteins varies from one species to another. We designated the genes HSP 70, HSP 67, HSP 60, HSP 27, and HSP 23 genes based on transcriptome analysis of C. sulfurosus. Our study can be termed as a long-heat shock study as C. sulfurosus was reared from the first instar to the fourth instar, and this might have led to a continuous induction of HSPs at 25°C. 40°C had the lowest survival but highest HSPs expression as C. sulfurosus larvae had to utilize HSPs for sustenance. These results and future high-throughput studies at both the transcriptome and proteome level will improve the information needed to predict the future geographic distribution of these species within the context of global warming.

Keywords: chironomid, heat shock proteins, high temperature, heat shock protein expression

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Authors: Rahul Agarwal, Ashutosh Singh

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Colorectal cancer (CRC) also refers as bowel cancer or colon cancer. It involves the development of abnormal growth of cells in colon or rectum part of the body. This work leads to the development of a miRNA database in colorectal cancer. We named this database- miCoRe. This database comprises of all validated colon-rectal cancer miRNAs information from various published literature with an effectual knowledge based information retrieval system. miRNAs have been collected from various published literature reports. MySQL is used for main-framework of miCoRe while the front-end was developed in PHP script. The aim of developing miCoRe is to create a comprehensive central repository of colorectal carcinoma miRNAs with all germane information of miRNAs and their target genes. The current version of miCoRe consists of 238 miRNAs which are known to be implicated in malignancy of CRC. Alongside with miRNA information, miCoRe also contains the information related to the target genes of these miRNA. miCoRe furnishes the information about the mechanism of incidence and progression of the disease, which would further help the researchers to look for colorectal specific miRNAs therapies and CRC specific targeted drug designing. Moreover, it will also help in development of biomarkers for the better and early detection of CRC and will help in better clinical management of the disease.

Keywords: colorectal cancer, database, miCoRe, miRNAs

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Authors: Angga S. Fajar, Y. Takahashi, J. Kiyono, S. Sawada

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The structural system concept of RC pier accompanied with multi sliding friction damping mechanism was developed based on numerical analysis approach. However in the implementation, to make design for such kind of this structural system consumes a lot of effort in case high of complexity. During making design, the special behaviors of this structural system should be considered including flexible small deformation, sufficient elastic deformation capacity, sufficient lateral force resistance, and sufficient energy dissipation. The confinement distribution of friction devices has significant influence to its. Optimization and prediction with multi function regression of this structural system expected capable of providing easier and simpler design method. The confinement distribution of friction devices is optimized with SNOPT in Opensees, while some design variables of the structure are predicted using multi function regression of ANN. Based on the optimization and prediction this structural system is able to be designed easily and simply.

Keywords: RC Pier, multi sliding friction device, optimal design, flexible small deformation

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Authors: Mitchell Gohnert, Ryan Bradley

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This paper reviews some fundamental concepts of structural optimization, which are based on the type of materials used in construction and the shape of the structure. The first step in structural optimization is to break down all internal forces in a structure into fundamental stresses, which are tensions and compressions. Knowing the stress patterns directs our selection of structural shapes and the most appropriate type of construction material. In our selection of materials, it is essential to understand all construction materials have flaws, or micro-cracks, which reduce the capacity of the material, especially when subjected to tensions. Because of material defects, many construction materials perform significantly better when subjected to compressive forces. Structures are also more efficient if bending moments are eliminated. Bending stresses produce high peak stresses at each face of the member, and therefore, substantially more material is required to resist bending. The shape of the structure also has a profound effect on stress levels. Stress may be reduced dramatically by simply changing the shape. Catenary, triangular and linear shapes are the fundamental structural forms to achieve optimal stress flow. If the natural flow of stress matches the shape of the structures, the most optimal shape is determined.

Keywords: arches, economy of stresses, material strength, optimization, shells

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Authors: M. Yoneda

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It is known that stationary human occupants act as dynamic mass-spring-damper systems and can change the modal properties of civil engineering structures. This paper describes the full scale measurement to explain the tuned mass damper effects of stationary people on structural damping of footbridge with center span length of 33 m. A human body can be represented by a lumped system consisting of masses, springs, and dashpots. Complex eigenvalue calculation is also conducted by using ISO5982:1981 human model (two degree of freedom system). Based on experimental and analytical results for the footbridge with the stationary people in the standing position, it is demonstrated that stationary people behave as a tuned mass damper and that ISO5982:1981 human model can explain the structural damping characteristics measured in the field.

Keywords: dynamic interaction, footbridge, stationary people, structural damping

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Authors: A. Zitouni, S. Bentata, B. Bouadjemi, T. Lantri, W. Benstaali, A. Zoubir, S. Cherid, A. Sefir

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The structural, electronic, and magnetic properties of transition metal Co and Mn doped zinc-blende semiconductor CdTe were calculated using the density functional theory (DFT) with both generalized gradient approximation (GGA). We have analyzed the structural parameters, charge and spin densities, total and partial densities of states. We find that the Co and Mn doped zinc blende CdTe show half-metallic behavior with a total magnetic moment of 6.0 and 10.0 µB, respectively.The results obtained, make the Co and Mn doped CdTe a promising candidate for application in spintronics.

Keywords: first-principles, half-metallic, diluted magnetic semiconductor, magnetic moment

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Authors: Sabit Horoz, Ahmet Ekicibil, Omer Sahin, M. Akyol

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In this study, CdZnS and Ni-doped CdZnS quantum dots(QDs) were prepared by the wet-chemical method at room temperature using mercaptoethanol as a capping agent. The structural and magnetic properties of the CdZnS and CdZnS doped with different concentrations of Ni QDs were examined by XRD and magnetic susceptibility measurements, respectively. The average particles size of cubic QDs obtained by full-width half maxima (FWHM) analysis, increases with increasing doping concentrations. The investigation of the magnetic properties showed that the Ni-doped samples exhibit signs of ferromagnetism, on the other hand, un-doped CdZnS is diamagnetic.

Keywords: un-doped and Ni doped CdZnS Quantum Dots (QDs), co-precipitation method, structural and optical properties of QDs, diluted magnetic semiconductor materials (DMSMs)

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Authors: Muhammad Shakeel Rehman Hissam

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This study aims at analyzing gender in Othello by applying Judith Butler’s Post-Structural theory of gender and gender performance. The analysis of the play provides us context by which we can examine what kinds of effects the drama have on understanding of the researchers regarding gender identity. The study sets out to examine that, is there any evidence or ground in Shakespearean selected work which leads to challenge the patriarchal taken for granted prescribed roles of gender? This would be the focal point in study of Othello that actions and performances of characters determine their gender identity rather than their sexuality. It argues that gender of Shakespearean characters has no constant, fixed and structural impression. On the contrary, they undergo consistent variations in their behavior and performance which impart fluidity and volatility to them. The focal point of the present study is Butler’s prominent work; Gender Trouble: Feminism and subversion of Identity and her post structural theory of Gender performativity as the theoretical underpinning of the text. It analyzes the selected play in Post-Structural gender perspective. The gender-centric plot of the play is riddled with fluidity of gender. The most fascinating aspect of the play is the transformations of genders on the basis of performances by different characters and through these transformations; gender identity is revealed and determined. The study reconstructs the accepted gender norms by challenging the traditional concept of gender that is based on sexual differences of characters.

Keywords: post structural, gender, performativity, socio-cultural gender norms, binaries, Othello, Butler, identity

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Authors: Ryadi Adityavarman

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The study is an analysis by using the postcolonial theoretical lens on the search for a distinctive architectural identity by architect Maclaine Pont in Indonesia in the early twentieth century. Influenced by progressive architectural thinking and enlightened humanism at the time, Pont applied the fundamental principles of Structural Rationalism by using a creative combination of traditional Indonesian architectural typology and innovative structural application. The interpretive design strategy also celebrated creative use of local building materials with sensible tropical climate design response. Moreover, his holistic architectural scheme, including inclusion of local custom of building construction, represents the notion of Gesamkunstwerk. By using such hybrid strategy, Maclaine Pont intended to preserve the essential cultural identity and vernacular architecture of the indigenous. The study will chronologically investigate the evolution of Structural Rationalism architecture philosophy of Viollet-le-Duc to Hendrik Berlage’s influential design thinking in the Dutch modern architecture, and subsequently to the Maclaine Pont’s innovative design in Indonesia. Consequently, the morphology analysis on his exemplary design works of ITB campus (1923) and Pohsarang Church (1936) is to understand the evolutionary influence of Structural Rationalism theory. The postmodern analysis method is to highlight the validity of Pont’s idea in the contemporary Indonesian architecture within the culture of globalism era.

Keywords: Indonesian modern architecture, postcolonial, structural rationalism, critical regionalism

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Authors: Abbas Pourreza

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MicroRNAs (miRNAs) are small single-stranded non-coding RNAs. They are almost 18-25 nucleotides long and very conservative through evolution. They are involved in adjusting the expression of numerous genes due to the existence of a complementary region, generally in the 3' untranslated regions (UTR) of target genes, against particular mRNAs in the cell. Also, miRNAs have been proven to be involved in cell development, differentiation, proliferation, and apoptosis. More than 2000 miRNAs have been recognized in human cells, and these miRNAs adjust approximately one-third of all genes in human cells. Dysregulation of miRNA originated from abnormal DNA methylation patterns of the locus, cause to down-regulated or overexpression of miRNAs, and it may affect tumor formation or development of it. Breast cancer (BC) is the most commonly identified cancer, the most prevalent cancer (23%), and the second-leading (14%) mortality in all types of cancer in females. BC can be classified based on the status (+/−) of the hormone receptors, including estrogen receptor (ER), progesterone receptor (PR), and the Receptor tyrosine-protein kinase erbB-2 (ERBB2 or HER2). Currently, there are four main molecular subtypes of BC: luminal A, approximately 50–60 % of BCs; luminal B, 10–20 %; HER2 positive, 15–20 %, and 10–20 % considered Basal (triple-negative breast cancer (TNBC)) subtype. Aberrant expression of miR-145, miR-21, miR-10b, miR-125a, and miR-206 was detected by Stem-loop real-time RT-PCR in BC cases. Breast tumor formation and development may result from down-regulation of a tumor suppressor miRNA such as miR-145, miR-125a, and miR-206 and/or overexpression of an oncogenic miRNA such as miR-21 and miR-10b. MiR-125a, miR-206, miR-145, miR-21, and miR-10b are hugely predicted to be new tumor markers for the diagnosis and prognosis of BC. MiR-21 and miR-125a could play a part in the treatment of HER-2-positive breast cancer cells, while miR-145 and miR-206 could speed up the evolution of cure techniques for TNBC. To conclude, miRNAs will be presented as hopeful molecules to be used in the primary diagnosis, prognosis, and treatment of BC and battle as opposed to its developed drug resistance.

Keywords: breast cancer, HER2 positive, miRNA, TNBC

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Authors: Anita Kushwaha

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We propose a new evolutionary computational model called Artificial Reproduction System which is based on the complex process of meiotic reproduction occurring between male and female cells of the living organisms. Artificial Reproduction System is an attempt towards a new computational intelligence approach inspired by the theoretical reproduction mechanism, observed reproduction functions, principles and mechanisms. A reproductive organism is programmed by genes and can be viewed as an automaton, mapping and reducing so as to create copies of those genes in its off springs. In Artificial Reproduction System, the binding mechanism between male and female cells is studied, parameters are chosen and a network is constructed also a feedback system for self regularization is established. The model then applies Mendel’s law of inheritance, allele-allele associations and can be used to perform data analysis of imbalanced data, multivariate, multiclass and big data. In the experimental study Artificial Reproduction System is compared with other state of the art classifiers like SVM, Radial Basis Function, neural networks, K-Nearest Neighbor for some benchmark datasets and comparison results indicates a good performance.

Keywords: bio-inspired computation, nature- inspired computation, natural computing, data mining

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Authors: Ashley Wei-Ting Wang, Wen-Yau Hsu

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Objectives: The current study applies and expands the Tripartite Model to elaborate the link between non-suicidal self-injury (NSSI) and suicidal behavior. We propose a structural model of NSSI and suicidal risk, in which negative affect (NA) predicts both anxiety and depression, positive affect (PA) predicts depression only, anxiety is linked to NSSI, and depression is linked to suicidal risk. Method: Four hundreds and eighty seven undergraduates participated. Data were collected by administering self-report questionnaires. We performed hierarchical regression and structural equation modeling to test the proposed structural model. Results: The results largely support the proposed structural model, with one exception: anxiety was strongly associated with NSSI and to a lesser extent with suicidal risk. Conclusions: We conclude that the co-occurrence of NSSI and suicidal risk is due to NA and anxiety, and suicidal risk can be differentiated by depression. Further theoretical and practical implications are discussed.

Keywords: non-suicidal self-injury, suicidal risk, anxiety, depression, the tripartite model, hierarchical relationship

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Authors: Lethukuthula Ngobese, Abin Gupthar, Patrick Govender

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The ability of yeast cell wall-derived mannoproteins (glycoproteins) to positively contribute to oenological properties has been a key factor that stimulates research initiatives into these industrially important glycoproteins. In addition, and from a fundamental research perspective, yeast cell wall glycoproteins are involved in a wide range of biological interactions. To date, and to the best of our knowledge, our understanding of the fine molecular structure of these mannoproteins is fairly limited. Generally, the amino acid sequences of their protein moieties have been established from structural and functional analysis of the genomic sequence of these yeasts whilst far less information is available on the glycosyl moieties of these mannoproteins. A novel strategy was devised in this study that entails the genetic engineering of yeast strains that over-express and release cell wall-associated glycoproteins into the liquid growth medium. To this end, the Flo1p mannoprotein was overexpressed in Saccharomyces cerevisiae laboratory strains bearing a specific deletion in KNR4 and GPI7 genes involved in cell wall biosynthesis that have been previously shown to extracellularly hyper-secrete cell wall-associated glycoproteins. A polymerase chain reaction (PCR) -based cloning strategy was employed to generate transgenic yeast strains in which the native cell wall FLO1 glycoprotein-encoding gene is brought under transcriptional control of the constitutive PGK1 promoter. The modified Helm’s flocculation assay was employed to assess flocculation intensities of a Flo1p over-expressing wild type and deletion mutant as an indirect measure of their abilities to release the desired mannoprotein. The flocculation intensities of the transformed strains were assessed and all the strains showed similar intensities (>98% flocculation). To assess if mannoproteins were released into the growth medium, the supernatant of each strain was subjected to the BCA protein assay and the transformed Δknr4 strain showed a considerable increase in protein levels. This study has the potential to produce mannoproteins in sufficient quantities that may be employed in future investigations to understand their molecular structures and mechanisms of interaction to the benefit of both fundamental and industrial applications.

Keywords: glycoproteins, genetic engineering, flocculation, over-expression

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Authors: Ruolan Zhou

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Trisomy of human chromosome 21 is the primary cause of Down Syndrome (DS), and this genetic disease has significantly burdened families and countries, causing great controversy. To address this problem, the research takes an approach in exploring the relationship between genetic abnormality and this disease's symptoms, adopting several techniques, including data analysis and enrichment analysis. It also explores open-source websites, such as NCBI, DAVID, SOURCE, STRING, as well as UCSC, to complement its result. This research has analyzed the variety of genes on human chromosome 21 with simple coding, and by using analysis, it has specified the protein-coding genes, their function, and their location. By using enrichment analysis, this paper has found the abundance of keratin production-related coding-proteins on human chromosome 21. By adopting past researches, this research has attempted to disclose the relationship between trisomy of human chromosome 21 and keratin production abnormality, which might be the reason for common diseases in patients with Down Syndrome. At last, by addressing the advantage and insufficiency of this research, the discussion has provided specific directions for future research.

Keywords: Down Syndrome, protein production, genome, enrichment analysis

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Authors: Daniil Karzanov

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This paper studies the effect of quarterly earnings reports on the stock price. The profitability of the stock is modeled by geometric Brownian diffusion and the Constant Elasticity of Variance model. We fit several variations of stochastic differential equations to the pre-and after-report period using the Maximum Likelihood Estimation and Grid Search of parameters method. By examining the change in the model parameters after reports’ publication, the study reveals that the reports have enough evidence to be a structural breakpoint, meaning that all the forecast models exploited are not applicable for forecasting and should be refitted shortly.

Keywords: stock market, earnings reports, financial time series, structural breaks, stochastic differential equations

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Authors: Katarína Čurová, Leonard Siegfried, Radka Vargová, Marta Kmeťová, Vladimír Hrabovský

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Introduction: Cytolethal distending toxins (CDTs) represent intracellular acting proteins which interfere with cell cycle of eukaryotic cells. They are produced by Gram-negative bacteria with afinity to mucocutaneous surfaces and could play a role in the pathogenesis of various diseases. CDTs induce DNA damage probably through DNAse activity, which causes cell cycle arrest and leads to further changes (cell distension and death, apoptosis) depending on the cell type. Five subtypes of CDT (I to V) were reported in E. coli. Methods: We examined 252 E. coli strains belonging to four different groups. Of these strains, 57 were isolated from patients with diarrhea, 65 from patients with urinary tract infections (UTI), 65 from patients with sepsis and 65 from patients with other extraintestinal infections (mostly surgical wounds, decubitus ulcers and respiratory tract infections). Identification of these strains was performed by MALDI-TOF analysis and detection of genes encoding CDTs and determination of the phylogenetic group was performed by PCR. Results: In this study, we detected presence of cdt genes in 11 of 252 E. coli strains tested (4,4 %). Four cdt positive E. coli strains were confirmed in group of UTI (6,15 %), three cdt positive E. coli strains in groups of diarrhea (5,3 %) and other extraintestinal infections (4,6 %). The lowest incidence, one cdt positive E. coli strain, was observed in group of sepsis (1,5 %). All cdt positive E. coli strains belonged to phylogenetic group B2. Conclusion: CDT-producing E. coli are isolated in a low percentage from patients with intestinal and extraintestinal infections, including sepsis and our results correspond with these studies. A weak prevalence of cdt genes suggests that CDTs are not major virulence factors but in combination with other virulence factors may increase virulence potential of E. coli. We suppose that all 11 cdt positive E. coli strains represent real pathogens because they belong to the phylogenetic group B2 which is pathogenic lineage for bacteria E. coli.

Keywords: cytolethal distending toxin, E. coli, phylogenetic group, extraintestinal infection, diarrhea

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Authors: James Kinyua Gitonga, Toshio Fujimi

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Vulnerability assessment and analysis is essential to solving the degree of damage and loss as a result of natural disasters. Urban flooding causes a major economic loss and casualties, at Mathare residential area in Nairobi, Kenya. High population caused by rural-urban migration, Unemployment, and unplanned urban development are among factors that increase flood vulnerability in Mathare area. This study aims to analyse flood risk physical vulnerabilities in Mathare based on scientific data, research data that includes the Rainfall data, River Mathare discharge rate data, Water runoff data, field survey data and questionnaire survey through sampling of the study area have been used to develop the risk curves. Three structural types of building were identified in the study area, vulnerability and risk curves were made for these three structural types by plotting the relationship between flood depth and damage for each structural type. The results indicate that the structural type with mud wall and mud floor is the most vulnerable building to flooding while the structural type with stone walls and concrete floor is least vulnerable. The vulnerability of building contents is mainly determined by the number of floors, where households with two floors are least vulnerable, and households with a one floor are most vulnerable. Therefore more than 80% of the residential buildings including the property in the building are highly vulnerable to floods consequently exposed to high risk. When estimating the potential casualties/injuries we discovered that the structural types of houses were major determinants where the mud/adobe structural type had casualties of 83.7% while the Masonry structural type had casualties of 10.71% of the people living in these houses. This research concludes that flood awareness, warnings and observing the building codes will enable reduce damage to the structural types of building, deaths and reduce damage to the building contents.

Keywords: flood loss, Mathare Nairobi, risk curve analysis, vulnerability

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Authors: H. Abbasi, K. Sennah

Abstract:

A Structural Insulated Panel (SIP) is a structural element contains of foam insulation core sandwiched between two oriented-strand boards (OSB), plywood boards, steel sheets or fibre cement boards. Superior insulation, exceptional strength and fast insulation are the specifications of a SIP-based structure. There are also many other benefits such as less total construction costs, speed of construction, less expensive HVAC equipment required, favourable energy-efficient mortgages comparing to wood-framed houses. This paper presents the experimental analysis on selected foam-timber SIPs to study their structural behaviour when used as walls in residential construction under lateral loading. The experimental program has also taken several stud panels in order to compare the performance of SIP with conventional wood-frame system. The results of lateral tests performed in this study established a database that can be used further to develop design tables of SIP wall subjected to lateral loading caused by wind or earthquake. A design table for walls subjected to lateral loading was developed. Experimental results proved that the tested SIPs are ‘as good as’ the conventional wood-frame system.

Keywords: structural insulated panel, experimental study, lateral load, design tables

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Authors: Mohammad Befkin, Alireza Momtaz

Abstract:

Structural design is the challenging aspect of every project due to limitations in dimensions, functionality of the structure, and more importantly, the allocated budget for construction. This research study aims to investigate the optimized design for three steel moment frame buildings with different number of stories using genetic algorithm code. The number and length of spans, and height of each floor were constant in all three buildings. The design of structures are carried out according to AISC code within the provisions of plastic design with allowable stress values. Genetic code for optimization is produced using MATLAB program, while buildings modeled in Opensees program and connected to the MATLAB code to perform iterations in optimization steps. In the end designs resulted from genetic algorithm code were compared with the analysis of buildings in ETABS program. The results demonstrated that suggested structural elements by the code utilize their full capacity, indicating the desirable efficiency of produced code.

Keywords: genetic algorithm, structural analysis, steel moment frame, structural design

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Authors: Amira Zrelli, Tahar Ezzedine

Abstract:

Routing protocol may enhance the lifetime of sensor network, it has a highly importance, especially in wireless sensor network (WSN). Therefore, routing protocol has a big effect in these networks, thus the choice of routing protocol must be studied before setting up our network. In this work, we implement the routing protocol collect tree protocol (CTP) which is one of the hierarchic protocols used in structural health monitoring (SHM). Therefore, to evaluate the performance of this protocol, we choice to work with Contiki system and Cooja simulator. By throughput and RSSI evaluation of each node, we will deduce about the utility of CTP in structural monitoring system.

Keywords: CTP, WSN, SHM, routing protocol

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Authors: Boitumelo Setlhare, Mduduzi P. Mokoena, Ademola O. Olaniran

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Agricultural and industrial activities have led to increasing production of xenobiotics such as 2,4-dichlorophenol (2,4-DCP), a derivative of 2,4-dichlorophenoxyacetic acid (2,4-D), which is a widely used herbicide. Bioremediation offers an efficient, cost-effective and environmentally friendly method for degradation of the compound through the activities of the various microbial enzymes involved in the catabolic pathway. The aim of this study was to isolate and characterize bacterial isolate indigenous to contaminated sites in Durban, South Africa for 2,4-DCP degradation. One bacterium capable of utilizing 2,4-DCP as sole carbon source was isolated using culture enrichment technique and identified as Pseudomonas chlororaphis strain UFB2 via PCR amplification and analysis of 16S rRNA gene sequence. This isolate was able to degrade up to 75.11% of 2,4-DCP in batch cultures within 10 days, with the degradation rate constant of 0.14 mg/l/d. Phylogenetic analysis revealed the relatedness of this bacterial isolate to other Pseudomonas sp. previously characterized for chlorophenol degradation. PCR amplification of the catabolic genes involved in 2,4-DCP degradation revealed the presence of the correct amplicons for phenol hydroxylase (600 bp), catechol 1,2-dioxygenase (214 bp), muconate isomerase (851 bp), cis-dienelactone hydrolase (577 bp), and trans-dienelactone hydrolase (491 bp) genes. Enzyme assays revealed activity as high as 21840 mU/mg, 15630 mU/mg, 2340 mU/mg and 1490 mU/mg obtained for phenol hydroxylase, catechol 1,2-dioxygenase, cis-dienelactone hydroxylase and trans-dienelactone hydroxylase, respectively. The absence of catechol 2,3-dioxygenase gene and the corresponding enzyme in this isolate suggests that the organism followed ortho-pathway for 2,4-DCP degradation. Furthermore, the absence of malaycetate reductase genes showed that the bacterium may not be able to completely mineralize 2,4-DCP. Further studies are required to optimize 2,4-DCP degradation by this isolate as well as to elucidate the mechanism of 2,4-DCP degradation.

Keywords: biodegradation, catechol 1, 2-dioxygenase, 2, 4-dichlorophenol, phenol hydroxylase, Pseudomonas chlororaphis

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Authors: Sridhar A. Malkaram, Tamer E. Fandy

Abstract:

Purpose: 5-Azacytidine (5AC) and decitabine (DC) are DNA hypomethylating agents. We recently demonstrated that both drugs increase the enzymatic activity of the histone deacetylase enzyme SIRT6. Accordingly, we are comparing the changes H3K9 acetylation changes in the whole genome induced by both drugs using leukemia cells. Description of Methods & Materials: Mononuclear cells from the bone marrow of six de-identified naive acute myeloid leukemia (AML) patients were cultured with either 500 nM of DC or 5AC for 72 h followed by ChIP-Seq analysis using a ChIP-validated acetylated-H3K9 (H3K9ac) antibody. Chip-Seq libraries were prepared from treated and untreated cells using SMARTer ThruPLEX DNA- seq kit (Takara Bio, USA) according to the manufacturer’s instructions. Libraries were purified and size-selected with AMPure XP beads at 1:1 (v/v) ratio. All libraries were pooled prior to sequencing on an Illumina HiSeq 1500. The dual-indexed single-read Rapid Run was performed with 1x120 cycles at 5 pM final concentration of the library pool. Sequence reads with average Phred quality < 20, with length < 35bp, PCR duplicates, and those aligning to blacklisted regions of the genome were filtered out using Trim Galore v0.4.4 and cutadapt v1.18. Reads were aligned to the reference human genome (hg38) using Bowtie v2.3.4.1 in end-to-end alignment mode. H3K9ac enriched (peak) regions were identified using diffReps v1.55.4 software using input samples for background correction. The statistical significance of differential peak counts was assessed using a negative binomial test using all individuals as replicates. Data & Results: The data from the six patients showed significant (Padj<0.05) acetylation changes at 925 loci after 5AC treatment versus 182 loci after DC treatment. Both drugs induced H3K9 acetylation changes at different chromosomal regions, including promoters, coding exons, introns, and distal intergenic regions. Ten common genes showed H3K9 acetylation changes by both drugs. Approximately 84% of the genes showed an H3K9 acetylation decrease by 5AC versus 54% only by DC. Figures 1 and 2 show the heatmaps for the top 100 genes and the 99 genes showing H3K9 acetylation decrease after 5AC treatment and DC treatment, respectively. Conclusion: Despite the similarity in hypomethylating activity and chemical structure, the effect of both drugs on H3K9 acetylation change was significantly different. More changes in H3K9 acetylation were observed after 5 AC treatments compared to DC. The impact of these changes on gene expression and the clinical efficacy of these drugs requires further investigation.

Keywords: DNA methylation, leukemia, decitabine, 5-Azacytidine, epigenetics

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