Search results for: spatial gene

Authors: Agostinho Antunes

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The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of selected marine animal species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

Keywords: comparative genomics, adaptive evolution, bioinformatics, phylogenetics, genome mining

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Authors: Ankush Kalra, Mirza Masroor, Usha Manaktala, B. C. Koner, T. K. Mishra

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Introduction: Pre-eclampsia affects 3-5% of pregnancies worldwide and increases maternal-fetal morbidity and mortality. Reduced placental perfusion induces the release of biomolecules by the placenta into maternal circulation causing endothelial dysfunction. Zinc dependent matrix metalloproteinase-2 (MMP-2) may be up-regulated and interact with circulating factors of oxidative stress and inflammation to produce endothelial dysfunction in pre-eclampsia. Aim: To study the functional genetic polymorphism of MMP-2 gene (g-1306 C>T) in pre-eclampsia and its effect on serum MMP-2 levels in these patients. Method: Hundred pre-eclampsia patients and hundred age and gestation period matched healthy pregnant women with their consent were recruited in the study. Serum MMP-2 levels in all subjects were estimated using standard ELISA kits. MMP-2 gene (g.- 1306 C>T) SNPs were genotyped using whole blood by ASO-PCR. Result: The pre-eclampsia patients had higher serum levels of MMP-2 compared to the healthy pregnant (p < 0.05). Also the MMP-2 genotype was associated with significant alteration in the serum MMP-2 concentration in these patients (p < 0.05). Conclusion: This study results suggest an association of MMP-2 genetic polymorphism and serum levels of MMP-2 to the path physiology of hypertensive disorder of pregnancy.

Keywords: allele specific oligonucleotide polymerase chain reaction (ASO-PCR), enzyme linked immunosorbent assay (ELISA), matrix metalloproteinase-2 (MMP-2), pre-eclampsia

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Authors: Jialin Ma, Jia Meng

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Genomic features, the genome-based coordinates, are commonly used for the representation of biological features such as genes, RNA transcripts and transcription factor binding sites. For the analysis of RNA-related genomic features, such as RNA modification sites, a common task is to correlate these features with transcript components (5'UTR, CDS, 3'UTR) to explore their distribution characteristics in terms of transcriptomic coordinates, e.g., to examine whether a specific type of biological feature is enriched near transcription start sites. Existing approaches for performing these tasks involve the manipulation of a gene database, conversion from genome-based coordinate to transcript-based coordinate, and visualization methods that are capable of showing RNA transcript components and distribution of the features. These steps are complicated and time consuming, and this is especially true for researchers who are not familiar with relevant tools. To overcome this obstacle, we develop a dedicated web app TARF, which represents web toolkit for annotating RNA-related genomic features. TARF web tool intends to provide a web-based way to easily annotate and visualize RNA-related genomic features. Once a user has uploaded the features with BED format and specified a built-in transcript database or uploaded a customized gene database with GTF format, the tool could fulfill its three main functions. First, it adds annotation on gene and RNA transcript components. For every features provided by the user, the overlapping with RNA transcript components are identified, and the information is combined in one table which is available for copy and download. Summary statistics about ambiguous belongings are also carried out. Second, the tool provides a convenient visualization method of the features on single gene/transcript level. For the selected gene, the tool shows the features with gene model on genome-based view, and also maps the features to transcript-based coordinate and show the distribution against one single spliced RNA transcript. Third, a global transcriptomic view of the genomic features is generated utilizing the Guitar R/Bioconductor package. The distribution of features on RNA transcripts are normalized with respect to RNA transcript landmarks and the enrichment of the features on different RNA transcript components is demonstrated. We tested the newly developed TARF toolkit with 3 different types of genomics features related to chromatin H3K4me3, RNA N6-methyladenosine (m6A) and RNA 5-methylcytosine (m5C), which are obtained from ChIP-Seq, MeRIP-Seq and RNA BS-Seq data, respectively. TARF successfully revealed their respective distribution characteristics, i.e. H3K4me3, m6A and m5C are enriched near transcription starting sites, stop codons and 5’UTRs, respectively. Overall, TARF is a useful web toolkit for annotation and visualization of RNA-related genomic features, and should help simplify the analysis of various RNA-related genomic features, especially those related RNA modifications.

Keywords: RNA-related genomic features, annotation, visualization, web server

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Authors: M. Kouyate, M. Sangare, S. Samake, S. Keita, H. G. Kim, D. H. Geschwind

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Background & Objectives: Human genetic studies can be expensive, even unaffordable, in developing countries, partly due to the sequencing costs. Our aim is to pilot the use of bioinformatics tools to guide scientifically valid, locally relevant, and economically sound autism genetic research in Mali. Methods: The following databases, NCBI, HGMD, and LSDB, were used to identify hot point mutations. Phenotype, transmission pattern, theoretical protein expression in the brain, the impact of the mutation on the 3D structure of the protein) were used to prioritize selected autism genes. We used the protein database, Modeller, and clustal W. Results: We found Mef2c (Gly27Ala/Leu38Gln), Pten (Thr131IIle), Prodh (Leu289Met), Nme1 (Ser120Gly), and Dhcr7 (Pro227Thr/Glu224Lys). These mutations were associated with endonucleases BseRI, NspI, PfrJS2IV, BspGI, BsaBI, and SpoDI, respectively. Gly27Ala/Leu38Gln mutations impacted the 3D structure of the Mef2c protein. Mef2c protein sequences across species showed a high percentage of similarity with a highly conserved MADS domain. Discussion: Mef2c, Pten, Prodh, Nme1, and Dhcr 7 gene mutation frequencies in the Malian population will be very informative. PCR coupled with restriction enzyme digestion can be used to screen the targeted gene mutations. Sanger sequencing will be used for confirmation only. This will cut down considerably the sequencing cost for gene-to-gene mutation screening. The knowledge of the 3D structure and potential impact of the mutations on Mef2c protein informed the protein family and altered function (ex. Leu38Gln). Conclusion & Future Work: Bio-informatics will positively impact autism research in Mali. Our approach can be applied to another neuropsychiatric disorder.

Keywords: bioinformatics, endonucleases, autism, Sanger sequencing, point mutations

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Authors: Hamidreza Saberkari, Mousa Shamsi, Hossein Ahmadi, Saeed Vaali, , MohammadHossein Sedaaghi

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In the recent years, using signal processing tools for accurate identification of the protein coding regions has become a challenge in bioinformatics. Most of the genomic signal processing methods is based on the period-3 characteristics of the nucleoids in DNA strands and consequently, spectral analysis is applied to the numerical sequences of DNA to find the location of periodical components. In this paper, a novel ensemble algorithm for gene selection in DNA sequences has been presented which is based on the combination of Goertzel algorithm and anti-notch filter (ANF). The proposed algorithm has many advantages when compared to other conventional methods. Firstly, it leads to identify the coding protein regions more accurate due to using the Goertzel algorithm which is tuned at the desired frequency. Secondly, faster detection time is achieved. The proposed algorithm is applied on several genes, including genes available in databases BG570 and HMR195 and their results are compared to other methods based on the nucleotide level evaluation criteria. Implementation results show the excellent performance of the proposed algorithm in identifying protein coding regions, specifically in identification of small-scale gene areas.

Keywords: protein coding regions, period-3, anti-notch filter, Goertzel algorithm

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Authors: Neda Mozaffari

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This study represents an investigation into the poetics of space within Annie Ernaux's autobiographical work La honte, highlighting the intricate interplay among space, the individual, and society. The research aims to dissect the spatial dimension of the town Yvetot, the referential locale of the author's childhood, drawing upon the frameworks of geocriticism and geopoetics. Our analysis exposes a profound dialectical tension fundamentally predicated on the binaries of "interior/exterior" and "here/there," emphasizing how space and its occupants may reciprocally influence each other. This endeavor aspires to attribute meaning to space in Ernaux's writing in La honte and to forge a connection between spatial elements and the author's autobiographical perspective, heavily imprinted by social dynamics. Ernaux's approach fluctuates between certain binaries that segment space according to the collective perception of social hierarchy, thus unveiling the author's preoccupation with social distancing. Consequently, space transforms into a structured milieu that transfers fear and insecurity to the child, where spatial and architectural segregation further cements class divisions in terms of the language employed by its inhabitants. Ernaux's depiction of space serves both as a repository of collective memory and an instrument of social distinction, where her autobiographical perception echoes within a collective geography marked by class determinism and culture.

Keywords: geocriticism, literary study, social class, social space, spatial analysis

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Authors: JingWei Yu, Hong Yang Yu

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At present, the increasingly serious air pollution in various cities of China has made people pay more attention to the air quality index(hereinafter referred to as AQI) of their living areas. To face this situation, it is of great significance to predict air pollution in heavily polluted areas. In this paper, based on the time series model of LSTM, a spatiotemporal prediction model of PM2.5 concentration in Mianyang, Sichuan Province, is established. The model fully considers the temporal variability and spatial distribution characteristics of PM2.5 concentration. The spatial correlation of air quality at different locations is based on the Air quality status of other nearby monitoring stations, including AQI and meteorological data to predict the air quality of a monitoring station. The experimental results show that the method has good prediction accuracy that the fitting degree with the actual measured data reaches more than 0.7, which can be applied to the modeling and prediction of the spatial and temporal distribution of regional PM2.5 concentration.

Keywords: LSTM, PM2.5, neural networks, spatio-temporal prediction

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Authors: Nebojsa Stefanovic, Sasa Milijic, Natasa Danilovic Hristic

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Spatial plan of the special purpose area constitutes a basic tool in the planning of infrastructure corridor of a highway. The aim of the plan is to define the planning basis and provision of spatial conditions for the construction and operation of the highway, as well as for developing other infrastructure systems in the corridor. This paper presents a methodology and approach to the preparation of the Spatial Plan for the special purpose area for the infrastructure corridor of the highway E-80, Section Niš-Merdare in Serbia. The applied methodological approach is based on the combined application of the integrative and participatory method in the decision-making process on the sustainable development of the highway corridor. It was found that, for the planning and management of the infrastructure corridor, a key problem is coordination of spatial and urban planning, strategic environmental assessment and sectoral traffic planning and designing. Through the development of the plan, special attention is focused on increasing the accessibility of the local and regional surrounding, reducing the adverse impacts on the development of settlements and the economy, protection of natural resources, natural and cultural heritage, and the development of other infrastructure systems in the corridor of the highway. As a result of the applied methodology, this paper analyzes the basic features such as coverage, the concept, protected zones, service facilities and objects, the rules of development and construction, etc. Special emphasis is placed to methodology and results of the Strategic Environmental Assessment of the Spatial Plan, and to the importance of protection measures, with the special significance of air and noise protection measures. For evaluation in the Strategic Environmental Assessment, a multicriteria expert evaluation (semi-quantitative method) of planned solutions was used in relation to the set of goals and relevant indicators, based on the basic set of indicators of sustainable development. Evaluation of planned solutions encompassed the significance and size, spatial conditions and probability of the impact of planned solutions on the environment, and the defined goals of strategic assessment. The framework of the implementation of the Spatial Plan is presented, which is determined for the simultaneous elaboration of planning solutions at two levels: the strategic level of the spatial plan and detailed urban plan level. It is also analyzed the relationship of the Spatial Plan to other applicable planning documents for the planning area. The effects of this methodological approach relate to enabling integrated planning of the sustainable development of the infrastructure corridor of the highway and its surrounding area, through coordination of spatial, urban and sectoral traffic planning and design, as well as the participation of all key actors in the adoption and implementation of planned decisions. By the conclusions of the paper, it is pointed to the direction for further research, particularly in terms of harmonizing methodology of planning documentation and preparation of technical-design documentation.

Keywords: corridor, environment, highway, impact, methodology, spatial plan, urban

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Authors: Shashank. S. Bagane, H. N. Rajendra Prasad

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Building Information Modeling (BIM) has currently developed into a potent solution. The consistent development of BIM technology in the sphere of Architecture, Engineering, and Construction (AEC) industry has enhanced the effectiveness of construction and decision making. However, aggrandized global warming and energy crisis has impacted on building energy analysis. It is now becoming an important factor to be considered in the AEC industry. Amalgamating energy analysis in the planning and design phase of a structure has become a necessity. In the current construction industry, estimating energy usage and reducing its footprint is of high priority. The construction industry is giving more prominence to sustainability alongside energy efficiency. This demand is compelling the designers, planners, and engineers to inspect the sustainable performance throughout the building's life cycle. The current study primarily focuses on energy consumption, space arrangement, and spatial geometry of a residential building. Most commonly residential structures in India are constructed considering Vastu Shastra. Vastu designs are intended to integrate architecture with nature and utilizing geometric patterns, symmetry, and directional alignments. In the current study, a residential brick masonry structure is considered for BIM analysis, Architectural model of the structure will be created using Revit software, later the orientation and spatial arrangement will be finalized based on Vastu principles. Furthermore, the structure will be investigated for the impact of building orientation and spatial arrangements on energy using Green Building Studio software. Based on the BIM analysis of the structure, energy consumption of subsequent building orientations will be understood. A well-orientated building having good spatial arrangement can save a considerable amount of energy throughout its life cycle and reduces the need for heating and lighting which will prove to diminish energy usage and improve the energy efficiency of the residential building.

Keywords: building information modeling, energy impact, spatial geometry, vastu

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Authors: Aminah Salim, Idrees Ahmed Nasir, Abdul Qayyum Rao, Muhammad Ali, Muhammad Sohail Anjum, Ayesha Hameed, Bushra Tabassum, Anwar Khan, Arfan Ali, Mariyam Zameer, Tayyab Husnain

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Risk assessment of transgenic herbicide tolerant sugarcane having CEMB codon optimized cp4EPSPS gene was done in present study. Fifteen days old chicks taken from K&Ns Company were randomly assorted into four groups with eight chicks in each group namely control chicken group fed with commercial diet, non-transgenic group fed with non-experimental sugarcane and transgenic group fed with transgenic sugarcane with minimum and maximum level. Body weights, biochemical analysis for Urea, alkaline phosphatase, alanine transferase, aspartate transferase, creatinine and bilirubin determination and histological examination of chicks fed with four types of feed was taken at fifteen days interval and no significant difference was observed in body weight biochemical and histological studies of all four groups. Protein isolated from the serum sample was analyzed through dipstick and SDS-PAGE, showing the absence of transgene protein in the serum sample of control and experimental groups. Moreover the amplification of cp4EPSPS gene with gene specific primers of DNA isolated from chicks blood and also from commercial diet was done to determine the presence and mobility of any nucleotide fragment of the transgene in/from feed and no amplification was obtained in feed as well as in blood extracted DNA of any group. Also no mRNA expression of cp4EPSPS gene was obtained in any tissue of four groups of chicks. From the results it is clear that there is no deleterious or harmful effect of the CEMB codon optimized transgenic cp4EPSPS sugarcane on the chicks health.

Keywords: chicks, cp4EPSPS, glyphosate, sugarcane

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Authors: B. Sanchez, D. Zambrana-Vasquez, J. Fresner, C. Krenn, F. Morea, L. Mercatelli

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Local administrations are facing established targets on sustainable development from different disciplines at the heart of different city departments. Nevertheless, some of these targets, such as CO₂ reduction, relate to two or more disciplines, as it is the case of sustainable mobility and energy plans (SUMP & SECAP/SEAP). This opens up the possibility to efficiently cooperate among different city departments and to create and develop harmonized spatial plans by using available resources and together achieving more ambitious goals in cities. The steps of the harmonization processes developed result in the identification of areas to achieve common strategic objectives. Harmonization, in other words, helps different departments in local authorities to work together and optimize the use or resources by sharing the same vision, involving key stakeholders, and promoting common data assessment to better optimize the resources. A methodology to promote resilient city planning via the harmonization of sustainable mobility and energy plans is presented in this paper. In order to validate the proposed methodology, a representative city engaged in an innovation process in efficient spatial planning is used as a case study. The harmonization process of sustainable mobility and energy plans covers identifying matching targets between different fields, developing different spatial plans with dual benefit and common indicators guaranteeing the continuous improvement of the harmonized plans. The proposed methodology supports local administrations in consistent spatial planning, considering both energy efficiency and sustainable mobility. Thus, municipalities can use their human and economic resources efficiently. This guarantees an efficient upgrade of land use plans integrating energy and mobility aspects in order to achieve sustainability targets, as well as to improve the wellbeing of its citizens.

Keywords: integrated multi-sector planning, spatial plans harmonization, sustainable energy and climate action plan, sustainable urban mobility plan

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Authors: Abdelkader Mendas

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The integration of MultiCriteria Decision Making (MCDM) approaches in a Geographical Information System (GIS) provides a powerful spatial decision support system which offers the opportunity to efficiently produce the land suitability maps for agriculture. Indeed, GIS is a powerful tool for analyzing spatial data and establishing a process for decision support. Because of their spatial aggregation functions, MCDM methods can facilitate decision making in situations where several solutions are available, various criteria have to be taken into account and decision-makers are in conflict. The parameters and the classification system used in this work are inspired from the FAO (Food and Agriculture Organization) approach dedicated to a sustainable agriculture. A spatial decision support system has been developed for establishing the land suitability map for agriculture. It incorporates the multicriteria analysis method ELECTRE Tri (ELimitation Et Choix Traduisant la REalité) in a GIS within the GIS program package environment. The main purpose of this research is to propose a conceptual and methodological framework for the combination of GIS and multicriteria methods in a single coherent system that takes into account the whole process from the acquisition of spatially referenced data to decision-making. In this context, a spatial decision support system for developing land suitability maps for agriculture has been developed. The algorithm of ELECTRE Tri is incorporated into a GIS environment and added to the other analysis functions of GIS. This approach has been tested on an area in Algeria. A land suitability map for durum wheat has been produced. Through the obtained results, it appears that ELECTRE Tri method, integrated into a GIS, is better suited to the problem of land suitability for agriculture. The coherence of the obtained maps confirms the system effectiveness.

Keywords: multicriteria decision analysis, decision support system, geographical information system, land suitability for agriculture

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Authors: D. Tohlob, E. Abo Hashem, N. Ghareeb, M. Ghanem, R. Elfarahaty, S. A. Roberts, P. Pemberton, L. Mohiyiddeen, W. G. Newman

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Gonadotropin stimulation is used in females undergoing assisted reproductive treatment for ovulation induction, but ovarian response is variable and unpredictable in these women. More effective protocols and individualization of treatment are needed to increase the success rate of IVF/ICSI cycles. We genotyped seven variants reported in previous studies to be associated with ovarian response (number of ova retrieved and total gonadotropin dose) in women undergoing IVF treatment including FSHR variants Asn 680 Ser (c.2039 A > G), Thr 307 Ala (c. 919 > A), -29 G > A, HRG c.610 C > T gene, BMP15 -9 C > G, AMH Ile 49 Ser (c.146 G > T), and AMHR -489A˃G in 118 Egyptian females attending Mansoura Integrated Fertility Center in Egypt, these females were undergoing their first cycle of controlled ovarian hyper stimulation for IVF/ICSI treatment. They were analyzed by TaqMan allelic discrimination assay in Manchester Center of Genomic Medicine. We found no evidence of any significant difference (p value < 0.05) in the number of eggs retrieved or the gonadotropin dose used between individuals in all genotypes except for HRG c.610 C > T gene polymorphism where regression analysis gives a p value of 0.04 with a fewer eggs number in TT genotyped females. These results indicate that these variants do not provide sufficient clinically relevant data to individualize the treatment protocols.

Keywords: controlled ovarian hyperstimulation, gene variants, ovarian response, assisted reproduction

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Authors: Nikhil Padhye, Ellen Kintz, Dan Dorci

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Recent years have seen a rising interest in study and applications of materially uniform thin-structures (plates/shells) subject to finite-bending and stretching deformations. We introduce a well-posed 2D-model involving finite-bending and stretching of thin-structures to approximate the three-dimensional equilibria. Key features of this approach include: Non-Uniform Rational B-Spline (NURBS)-based spatial discretization for finite elements, method of dynamic relaxation to predict stable equilibria, and no a priori kinematic assumption on the deformation fields. The approach is validated against the benchmark problems,and the use of NURBS for spatial discretization facilitates exact spatial representation and computation of curvatures (due to C1-continuity of interpolated displacements) for this higher-order accuracy 2D-model.

Keywords: Isogeometric Analysis, Plates/Shells , Finite Element Methods, Dynamic Relaxation

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Authors: Hieu Van Dong, Giang Thi Huong Tran, Giap Van Nguyen, Tung Duy Dao, Vuong Nghia Bui, Le Thi My Huynh, Yohei Takeda, Haruko Ogawa, Kunitoshi Imai

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Chicken anemia virus (CAV) has a ubiquitous and worldwide distribution in chicken production. Our group previously reported high seroprevalence of CAV in chickens in northern Vietnam. In the present study, 330 tissue samples collected from commercial and breeder chicken farms in eleven provinces in northern Vietnam were tested for the CAV infection. We found that 157 out of 330 (47.58%) chickens were positive with CAV genes by real-time PCR method. Nine CAV strains obtained from the different location and time were forwarded to the full-length sequence of CAV VP1 gene. Phylogenetic analysis of the Vietnamese CAV vp1 gene indicated that the CAVs circulating in northern Vietnam were divided into three distinct genotypes, II, III, and V, but not clustered with the vaccine strains. Among the three genotypes, genotype III was the major one widely spread in Vietnam, and that included three sub-genotypes, IIIa, IIIb, and IIIc. The Vietnamese CAV strains were closely related to the Chinese, Taiwanese, and USA strains. All the CAV isolates had glutamine at amino acid position 394 in the VP1 gene, suggesting that they might be highly pathogenic strains. One strain was defined to be genotype V, which had not been reported for Vietnamese CAVs. Additional studies are required to further evaluate the pathogenicity of CAV strains circulating in Vietnam.

Keywords: chicken anemia virus, genotype, genetic characteristics, Vietnam

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Authors: Elsher Lawson-Boyd

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In the wake of the Human Genome Project, the life sciences have undergone some fascinating changes. In particular, conventional beliefs relating to gene expression are being challenged by advances in postgenomic sciences, especially by the field of epigenetics. Epigenetics is the modification of gene expression without changes in the DNA sequence. In other words, epigenetics dictates that gene expression, the process by which the instructions in DNA are converted into products like proteins, is not solely controlled by DNA itself. Unlike gene-centric theories of heredity that characterized much of the 20th Century (where the genes were considered as having almost god-like power to create life), gene expression in epigenetics insists on environmental ‘signals’ or ‘exposures’, a point that radically deviates from gene-centric thinking. Science and Technology Studies (STS) scholars have shown that epigenetic research is having vast implications for the ways in which chronic, non-communicable diseases are conceptualized, treated, and governed. However, to the author’s knowledge, there have not yet been any in-depth sociological engagements with neuroepigenetics that examine how the field is affecting mental health and trauma discourse. In this paper, the author discusses preliminary findings from a doctoral ethnographic study on neuroepigenetics, trauma, and embodiment. Specifically, this study investigates the kinds of causal relations neuroepigenetic researchers are making between experiences of trauma and the development of mental illnesses like complex post-traumatic stress disorder (PTSD), both throughout a human’s lifetime and across generations. Using qualitative interviews and nonparticipant observation, the author focuses on two public-facing research centers based in Melbourne: Florey Institute of Neuroscience and Mental Health (FNMH), and Murdoch Children’s Research Institute (MCRI). Preliminary findings indicate that a great deal of ambiguity characterizes this infant field, particularly when animal-model experiments are employed and the results are translated into human frameworks. Nevertheless, researchers at the FNMH and MCRI strongly suggest that adverse and traumatic life events have a significant effect on gene expression, especially when experienced during early development. Furthermore, they predict that neuroepigenetic research will have substantial implications for the ways in which mental illnesses like complex PTSD are diagnosed and treated. These preliminary findings shed light on why medical and health sociologists have good reason to be chiming in, engaging with and de-black-boxing ideations emerging from postgenomic sciences, as they may indeed have significant effects for vulnerable populations not only in Australia but other developing countries in the Global South.

Keywords: genetics, mental illness, neuroepigenetics, trauma

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Authors: Mohamad Reza Mohamed Afla, Putri Haryati Ibrahim, Azila Ahmad Sarkawi

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This study examines the standard procedure involved in terms of planning and management at selected Muslim cemeteries within the Kuala Lumpur Metropolitan Area. It focuses on sustainable design practice for the provision of burial infrastructures at public cemeteries, which emphasizes the inclusion of society, economy, and environment. The escalating issues of overcrowding, lack of space, and land shortage for full-body burial in the urbanized area of Kuala Lumpur have raised a concern to this alarming situation. There is a necessity to address these problems through the incorporation of sustainable development in the making of urban cemeteries to ensure a holistic approach. Recorded site observation of cemeteries’ area has been employed as a means of data collection and interpreted by conducting spatial analysis. The spatial analysis entails the assessment of form and function in accordance with sustainable design principles. The finding exhibits the dimensional layout of Muslim cemeteries were problematics due to the tension that exists between ritual practices and space organization set-up by the local authorities. This article concludes by providing conceptual guidelines for the purpose of Muslim cemetery development in the future.

Keywords: cemetery, metropolitan, spatial analysis, sustainable design practice

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Authors: Hannah R. Devens, Phillip L. Davidson, Dione Deaker, Kathryn E. Smith, Gregory A. Wray, Maria Byrne

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Marine invertebrate species with calcifying larvae are especially vulnerable to ocean acidification (OA) caused by rising atmospheric CO₂ levels. Acidic conditions can delay development, suppress metabolism, and decrease the availability of carbonate ions in the ocean environment for skeletogenesis. These stresses often result in increased larval mortality, which may lead to significant ecological consequences including alterations to the larval settlement, population distribution, and genetic connectivity. Importantly, many of these physiological and developmental effects are caused by genetic and molecular level changes. Although many studies have examined the effect of near-future oceanic pH levels on gene expression in marine invertebrates, little is known about the impact of OA on gene expression in a developmental context. Here, we performed mRNA-sequencing to investigate the impact of environmental acidity on gene expression across three developmental stages in the sea urchin Heliocidaris erythrogramma. We collected RNA from gastrula, early larva, and 1-day post-metamorphic juvenile sea urchins cultured at present-day and predicted future oceanic pH levels (pH 8.1 and 7.7, respectively). We assembled an annotated reference transcriptome encompassing development from egg to ten days post-metamorphosis by combining these data with datasets from two previous developmental transcriptomic studies of H. erythrogramma. Differential gene expression and time course analyses between pH conditions revealed significant alterations to developmental transcription that are potentially associated with pH stress. Consistent with previous investigations, genes involved in biomineralization and ion transport were significantly upregulated under acidic conditions. Differences in gene expression between the two pH conditions became more pronounced post-metamorphosis, suggesting a development-dependent effect of OA on gene expression. Furthermore, many differences in gene expression later in development appeared to be a result of broad downregulation at pH 7.7: of 539 genes differentially expressed at the juvenile stage, 519 of these were lower in the acidic condition. Time course comparisons between pH 8.1 and 7.7 samples also demonstrated over 500 genes were more lowly expressed in pH 7.7 samples throughout development. Of the genes exhibiting stage-dependent expression level changes, over 15% of these diverged from the expected temporal pattern of expression in the acidic condition. Through these analyses, we identify novel candidate genes involved in development, metabolism, and transcriptional regulation that are possibly affected by pH stress. Our results demonstrate that pH stress significantly alters gene expression dynamics throughout development. A large number of genes differentially expressed between pH conditions in juveniles relative to earlier stages may be attributed to the effects of acidity on transcriptional regulation, as a greater proportion of mRNA at this later stage has been nascent transcribed rather than maternally loaded. Also, the overall downregulation of many genes in the acidic condition suggests that OA-induced developmental delay manifests as suppressed mRNA expression, possibly from lower transcription rates or increased mRNA degradation in the acidic environment. Further studies will be necessary to determine in greater detail the extent of OA effects on early developing marine invertebrates.

Keywords: development, gene expression, ocean acidification, RNA-sequencing, sea urchins

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Authors: Natalia Sáez, Dina Shulfman

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There is an important research gap regarding accessible pedagogical techniques for teaching foreign languages to adults with visual impairments. English as a foreign language (EFL), in particular, is needed in many countries to expand occupational opportunities and improve living standards. Within EFL research, teaching and learning prepositions have only recently gained momentum, considering that they constitute one of the most difficult structures to learn in a foreign language and are fundamental for communicating about spatial relations in the world, both on the physical and imaginary levels. Learning to use prepositions would not only facilitate communication when referring to the surrounding tangible environment but also when conveying ideas about abstract topics (e.g., justice, love, society), for which students’ sociocultural knowledge about space could play an important role. By potentiating visually impaired students’ ability to construe mental spatial imagery, this study made efforts to explore pedagogical techniques that cater to their strengths, helping them create new worlds by welcoming and expanding their sociocultural funds of knowledge as they learn to use English prepositions. Fifteen visually impaired adults living in Chile participated in the study. Their first language was Spanish, and they were learning English at the intermediate level of proficiency in an EFL workshop at La Biblioteca Central para Ciegos (The Central Library for the Blind). Within this workshop, a series of activities and interviews were designed and implemented with the intention of uncovering students’ spatial funds of knowledge when learning literal/physical uses of three English prepositions, namely “in,” “at,” and “on”. The activities and interviews also explored whether students used their original spatial funds of knowledge when learning metaphorical uses of these prepositions and if their use of spatial imagery changed throughout the learning activities. Over the course of approximately half a year, it soon became clear that the students construed mental images of space when learning both literal/physical and metaphorical uses of these prepositions. This research could inform a new approach to inclusive language education using pedagogical methods that are relevant and accessible to students with visual impairments.

Keywords: EFL, funds of knowledge, prepositions, spatial cognition, visually impaired students

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Authors: Ljiljana Seric, Vladimir Divic, Marin Bugaric

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This paper presents methodology for spatial analysis of GIS data that is used for assessing the microlocation risk index from potential damages of high winds. The analysis is performed on freely available GIS data comprising information about wind load, terrain cover and topography of the area. The methodology utilizes the legislation of Eurocode norms for determination of wind load of buildings and constructions. The core of the methodology is adoption of the wind load parameters related to location on geographical spatial grid. Presented work is a part of the Wind Risk Project, supported by the European Commission under the Civil Protection Financial Instrument of the European Union (ECHO). The partners involved in Wind Risk project performed Wind Risk assessment and proposed action plan for three European countries – Slovenia, Croatia and Germany. The proposed method is implemented in GRASS GIS open source GIS software and demonstrated for Case study area of wider area of Split, Croatia. Obtained Wind Risk Index is visualized and correlated with critical infrastructures like buildings, roads and power lines. The results show good correlation between high Wind Risk Index with recent incidents related to wind.

Keywords: Eurocode norms, GIS, spatial analysis, wind distribution, wind risk

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Authors: Saad Algharib, Jay Lee

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Urbanization is a complex phenomenon that occurs during the city’s development from one form to another. In other words, it is the process when the activities in the land use/land cover change from rural to urban. Since the oil exploration, Kuwait City has been growing rapidly due to its urbanization and population growth by both natural growth and inward immigration. The main objective of this study is to detect changes in urban land use/land cover and to examine the changing spatial patterns of urban growth in and around Kuwait City between 1989 and 2001. In addition, this study also evaluates the spatial patterns of the changes detected and how they can be related to the spatial configuration of the city. Recently, the use of remote sensing and geographic information systems became very useful and important tools in urban studies because of the integration of them can allow and provide the analysts and planners to detect, monitor and analyze the urban growth in a region effectively. Moreover, both planners and users can predict the trends of the growth in urban areas in the future with remotely sensed and GIS data because they can be effectively updated with required precision levels. In order to identify the new urban areas between 1989 and 2001, the study uses satellite images of the study area and remote sensing technology for classifying these images. Unsupervised classification method was applied to classify images to land use and land cover data layers. After finishing the unsupervised classification method, GIS overlay function was applied to the classified images for detecting the locations and patterns of the new urban areas that developed during the study period. GIS was also utilized to evaluate the distribution of the spatial patterns. For example, Moran’s index was applied for all data inputs to examine the urban growth distribution. Furthermore, this study assesses if the spatial patterns and process of these changes take place in a random fashion or with certain identifiable trends. During the study period, the result of this study indicates that the urban growth has occurred and expanded 10% from 32.4% in 1989 to 42.4% in 2001. Also, the results revealed that the largest increase of the urban area occurred between the major highways after the forth ring road from the center of Kuwait City. Moreover, the spatial distribution of urban growth occurred in cluster manners.

Keywords: geographic information systems, remote sensing, urbanization, urban growth

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Authors: Debasish Pradhan, Shaktiprasad Pradhan, Rakesh Kumar Pradhan, Gitanjali Tripathy

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Suppressors of cytokine signalling (SOCS1), a newly indentified antiapoptotic molecule is a downstream effector of the receptor tyrosine kinase-Ras signalling pathway. The current study has uncovered that SOCS1 may have wide and imperative capacities, particularly because of its close correlation with malignant tumors. To investigate the impact of SOCS1 on MDR, we analyzed the expression of P-gp and SOCS1 by immunohistochemistry and found there was a positive correlation between them. At that point, we effectively interfered with RNA translation by the contamination of siRNA of SOCS1 into MCF7/ADM breast cancer cell lines through a lentivirus, and the expression of the target gene was significantly inhibited. After RNAi, the drug resistance was reduced altogether and the expression of MDR1 mRNA and P-gp in MCF7/ADM cell lines demonstrated a significant decrease. Likewise, the expression of P53 protein increased in a statistically significant manner (p ≤ 0.01) after RNAi exposure. Moreover, flow cytometry analysis uncovers that cell cycle and anti-apoptotic enhancing capacity of cells changed after RNAi treatment. These outcomes proposed SOCS1 may take part in breast cancer MDR by managing MDR1 and P53 expression, changing cell cycle and enhancing the anti-apoptotic ability.

Keywords: breast cancer, multidrug resistance, SOCS1 gene, MDR1 gene, RNA interference

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Authors: Agostinho Antunes

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The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of selected marine animal species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

Keywords: marine genomics, evolutionary bioinformatics, human genome sequencing, genomic analyses

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Authors: Fei Gao, Xinyang Dong, Yisu Ge, Shufang Lu, Libo Weng

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Vehicle color recognition plays an important role in traffic accident investigation. However, due to the influence of illumination, weather, and noise, vehicle color recognition still faces challenges. In this paper, a vehicle color classification network based on spatial cluster loss and channel attention mechanism (SCNet) is proposed for vehicle color recognition. A channel attention module is applied to extract the features of vehicle color representative regions and reduce the weight of nonrepresentative color regions in the channel. The proposed loss function, called spatial clustering loss (SC-loss), consists of two channel-specific components, such as a concentration component and a diversity component. The concentration component forces all feature channels belonging to the same class to be concentrated through the channel cluster. The diversity components impose additional constraints on the channels through the mean distance coefficient, making them mutually exclusive in spatial dimensions. In the comparison experiments, the proposed method can achieve state-of-the-art performance on the public datasets, VCD, and VeRi, which are 96.1% and 96.2%, respectively. In addition, the ablation experiment further proves that SC-loss can effectively improve the accuracy of vehicle color recognition.

Keywords: feature extraction, convolutional neural networks, intelligent transportation, vehicle color recognition

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Authors: K. S. Vimal, D. Bodhini, K. Ramya, N. Lakshmipriya, R. M. Anjana, V. Sudha, J. A. Lovegrove, V. Mohan, V. Radha

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Gene-lifestyle interaction studies have been carried out in various populations. However, to date there are no studies in an Asian Indian population. Hence, we examined whether lifestyle factors such as diet and physical activity modify the association between fat mass and obesity–associated (FTO) gene variants and obesity and type 2 diabetes (T2D) in an Asian Indian population. We studied 734 unrelated T2D and 884 normal glucose-tolerant (NGT) participants randomly selected from the Chennai Urban Rural Epidemiology Study (CURES) in Southern India. Obesity was defined according to the World Health Organization Asia Pacific Guidelines (non-obese, BMI < 25 kg/m2; obese, BMI ≥ 25 kg/m2). Six single nucleotide polymorphisms (SNPs) in the FTO gene (rs9940128, rs7193144, rs8050136, rs918031, rs1588413 and rs11076023) identified from recent genome-wide association studies for T2D were genotyped by polymerase chain reaction-restriction fragment length polymorphism and direct sequencing. Dietary assessment was carried out using a validated food frequency questionnaire and physical activity was based upon the self-report. Interaction analyses were performed by including the interaction terms in the model. A joint likelihood ratio test of the main SNP effects and the SNP-diet/physical activity interaction effects was used in the linear regression analyses to maximize statistical power. Statistical analyses were performed using STATA version 13. There was a significant interaction between FTO SNP rs8050136 and carbohydrate energy percentage (Pinteraction=0.04) on obesity, where the ‘A’ allele carriers of the SNP rs8050136 had 2.46 times higher risk of obesity than those with ‘CC’ genotype (P=3.0x10-5) among individuals in the highest tertile of carbohydrate energy percentage. Furthermore, among those who had lower levels of physical activity, the ‘A’ allele carriers of the SNP rs8050136 had 1.89 times higher risk of obesity than those with ‘CC’ genotype (P=4.0x10-5). We also found a borderline interaction between SNP rs11076023 and carbohydrate energy percentage (Pinteraction=0.08) on T2D, where the ‘A’ allele carriers in the highest tertile of carbohydrate energy percentage, had 1.57 times higher risk of T2D than those with ‘TT’ genotype (P=0.002). There was also a significant interaction between SNP rs11076023 and physical activity (Pinteraction=0.03) on T2D. No further significant interactions between SNPs and macronutrient intake or physical activity on obesity and T2D were observed. In conclusion, this is the first study to provide evidence for a gene-diet and gene-physical activity interaction on obesity and T2D in an Asian Indian population. These findings suggest that the association between FTO gene variants and obesity and T2D is influenced by carbohydrate intake and physical activity levels. Greater understanding of how FTO gene influences obesity and T2D through dietary and exercise interventions will advance the development of behavioral intervention and personalised lifestyle strategies predicted to reduce the development of metabolic diseases in ‘A’ allele carriers of both SNPs in this Asian Indian population.

Keywords: dietary intake, FTO, obesity, physical activity, type 2 diabetes, Asian Indian.

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Authors: Ge Cui, Mei Fang Chien, Chihiro Inoue

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In this research, enrichment culture using an inorganic liquid medium collected soil contaminated with 1,2-dichlorobenzene (1,2-DCB) in Sendai, Japan, was added 1,2-DCB as the sole carbon source to create a stable consortium. The purpose of this research is to analysis dominant microorganisms in the stable consortium and enzyme system which play a role in the degradation of DCBs. The consortium is now at 30 generation and is still being cultured. By the result of PCR-DGGE and clone library, two bacteria are dominant. The bacteria named sk1 was isolated. 40mg/l of 1,2-DCB and 40mg/l of 1,4-DCB were completely degraded after 32 hours and 50 hours, respectively, but no degradation occurred in the case of 1,3-DCB. By PCR, tecA1 (α-subunit of DCB dioxygenase) gene which plays a role degrading DCB to DCB dihydrodiol, and tecB (dehydrogenase) gene which plays a role degrading DCB dihydrodiol to dichlorocatechol were amplified from strain sk1. Bacteria named sk100 was also isolated. 40mg/l of 1,2-DCB was completely degraded after 32 hours, but no degradation occurred in case of 1,3-DCB and 1,4-DCB. By the result of the catalytic core region of dioxygenase amplified by PCR, gene played a role degrading DCB was analyzed. The results of this study concluded that the isolated strains which have not been reported are able to degrade 1,2-DCB stably, and the characterization of degradation and the genomic analysis which is now in progress is helpful to have an overall view of this microbial degradation.

Keywords: DCB, 1, 2-DCB degrading strains, DCB dioxygenase, enrichment culture

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Authors: Tobias Strübing, Fatemeh Ziaeetabar

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Humans usually manipulate objects with their hands. To represent these actions in a simple and understandable way, we need to use a semantic framework. For this purpose, the Semantic Event Chain (SEC) method has already been presented which is done by consideration of touching and non-touching relations between manipulated objects in a scene. This method was improved by a computational model, the so-called enriched Semantic Event Chain (eSEC), which incorporates the information of static (e.g. top, bottom) and dynamic spatial relations (e.g. moving apart, getting closer) between objects in an action scene. This leads to a better action prediction as well as the ability to distinguish between more actions. Each eSEC manipulation descriptor is a huge matrix with thirty rows and a massive set of the spatial relations between each pair of manipulated objects. The current eSEC framework has so far only been used in the category of manipulation actions, which eventually involve two hands. Here, we would like to extend this approach to a whole body action descriptor and make a conjoint activity representation structure. For this purpose, we need to do a statistical analysis to modify the current eSEC by summarizing while preserving its features, and introduce a new version called Enhanced eSEC or (e2SEC). This summarization can be done from two points of the view: 1) reducing the number of rows in an eSEC matrix, 2) shrinking the set of possible semantic spatial relations. To achieve these, we computed the importance of each matrix row in an statistical way, to see if it is possible to remove a particular one while all manipulations are still distinguishable from each other. On the other hand, we examined which semantic spatial relations can be merged without compromising the unity of the predefined manipulation actions. Therefore by performing the above analyses, we made the new e2SEC framework which has 20% fewer rows, 16.7% less static spatial and 11.1% less dynamic spatial relations. This simplification, while preserving the salient features of a semantic structure in representing actions, has a tremendous impact on the recognition and prediction of complex actions, as well as the interactions between humans and robots. It also creates a comprehensive platform to integrate with the body limbs descriptors and dramatically increases system performance, especially in complex real time applications such as human-robot interaction prediction.

Keywords: enriched semantic event chain, semantic action representation, spatial relations, statistical analysis

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Authors: M. Marjaneh, M. Y. Narazah, H. Shahrul

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Array-based gene expression analysis is a powerful tool to profile expression of genes and to generate information on therapeutic effects of new anti-cancer compounds. Anti-apoptotic effect of thymoquinone was studied in MCF7 breast cancer cell line using gene expression profiling with cDNA micro array. The purity and yield of RNA samples were determined using RNeasyPlus Mini kit. The Agilent RNA 6000 Nano LabChip kit evaluated the quantity of the RNA samples. AffinityScript RT oligo-dT promoter primer was used to generate cDNA strands. T7 RNA polymerase was used to convert cDNA to cRNA. The cRNA samples and human universal reference RNA were labelled with Cy-3-CTP and Cy-5-CTP, respectively. Feature Extraction and GeneSpring software analysed the data. The single experiment analysis revealed involvement of 64 pathways with up-regulated genes and 78 pathways with down-regulated genes. The MAPK and p38-MAPK pathways were inhibited due to the up-regulation of PTPRR gene. The inhibition of p38-MAPK suggested up-regulation of TGF-ß pathway. Inhibition of p38 - MAPK caused up-regulation of TP53 and down-regulation of Bcl2 genes indicating involvement of intrinsic apoptotic pathway. Down-regulation of CARD16 gene as an adaptor molecule regulated CASP1 and suggested necrosis-like programmed cell death and involvement of caspase in apoptosis. Furthermore, down-regulation of GPCR, EGF-EGFR signalling pathways suggested reduction of ER. Involvement of AhR pathway which control cytochrome P450 and glucuronidation pathways showed metabolism of Thymoquinone. The findings showed differential expression of several genes in apoptosis pathways with thymoquinone treatment in estrogen receptor-positive breast cancer cells.

Keywords: cDNA microarray, thymoquinone, CARD16, PTPRR, CASP10

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Authors: Z. I Jeeva

Abstract:

The establishment of municipalities in South Africa has been a long and difficult process; 25 years later, it still appears to be evolving. In 1994, the new democratic government undertook to restructure the country’s racially segregated administrative structure by integrating areas to form cohesive municipal entities that would allow for the more efficient administration management of the regions. It planned to achieve this within a short seven-year period from 1993 to 2000, which was to be divided into three phases, namely, the pre-interim phase from 1994 to1995, the interim phase from 1996 to 1999, and the post-interim phase from 2000 onwards. However, the extensive integrated municipal approach was easier to pen on paper than to implement in practice. This paper seeks to explore the South African spatial reform process from 1993 to 2020, by analyzing policy documents and literature in order to determine how exactly the government attempted to achieve this. The study found that the spatial restructuring process was particularly complex since the democratic government inherited an unequal society located on a fragmented spatial landscape of which there was limited knowledge with many unresolved issues. Furthermore, the study found that there is a lack of literature on the topic from an urban planning perspective and calls for further research to ensure the formation of more efficient administrative regions.

Keywords: categorization, demarcation, municipalities, racial integration, spatial reform

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Authors: Deepak K. Gupta, T. R. Ravindran

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Holographic Optical Tweezers (HOTs) in general use iterative algorithms such as weighted Gerchberg-Saxton (WGS) to generate multiple traps, which produce traps with 99% uniformity theoretically. But in experiments, it is the phase response of the spatial light modulator (SLM) which ultimately determines the efficiency, uniformity, and quality of the trap spots. In general, SLMs show a nonlinear phase response behavior, and they may even have asymmetric phase modulation depth before and after π. This affects the resolution with which the gray levels are addressed before and after π, leading to a degraded trap performance. We present a method to optimize the SLM for a linear phase response behavior along with a symmetric phase modulation depth around π. Further, we optimize the SLM for its varying phase response over different spatial regions by optimizing the brightness/contrast and gamma of the hologram in different subsections. We show the effect of the optimization on an array of trap spots resulting in improved efficiency and uniformity. We also calculate the spot sharpness metric and trap performance metric and show a tightly focused spot with reduced aberration. The trap performance is compared by calculating the trap stiffness of a trapped particle in a given trap spot before and after aberration correction. The trap stiffness is found to improve by 200% after the optimization.

Keywords: spatial light modulator, optical trapping, aberration, phase modulation

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