Search results for: spatial gene

Authors: Chunxiao Wu, Dongyun Jiang, Tao Jiang, Luxia Xu, Qian Xu, Meng Zhao, Qin Zhu, Zhigang Guo, Jinlan Pan, Suning Chen

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The stability and evolution of human genetics depends on chromosomes (and chromosome-chromosome interactions). We wish to understand the spatial location of chromosomes in dividing cells in order to understand the relationship between chromosome-chromosome interactions and to further investigate the role of chromosomes and their impact on cell biological behavior. In this study, we explored the relative spatial positional relationships of chromosomes [t (9;22) and t (15;17)] in B-ALL cells by using the three-dimensions DNA in situ fluorescent hybridization (3D-FISH) method. The results showed that chromosomes [t (9;22) and t (15;17)] showed relatively stable spatial relationships. The relative stability of the spatial location of chromosomes in dividing cells may be relevant to disease.

Keywords: chromosome, human genetics, chromosome territory, 3D-FISH

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Authors: Huong M. T. Nguyen, Hoa A. P. Nguyen, Mai P. T. Nguyen, Ngoc D. Ngo, Van T. Ta, Hai T. Le, Chi V. Phan

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Wilson’s disease (WD) is an autosomal recessive disorder of the copper metabolism, which is caused by a mutation in the copper-transporting P-type ATPase (ATP7B). The mechanism of this disease is the failure of hepatic excretion of copper to bile, and leads to copper deposits in the liver and other organs. The ATP7B gene is located on the long arm of chromosome 13 (13q14.3). This study aimed to investigate the gene mutation in the Vietnamese patients with WD, and make a presymptomatic diagnosis for their familial members. Forty-three WD patients and their 65 siblings were identified as having ATP7B gene mutations. Genomic DNA was extracted from peripheral blood samples; 21 exons and exon-intron boundaries of the ATP7B gene were analyzed by direct sequencing. We recognized four mutations ([R723=; H724Tfs*34], V1042Cfs*79, D1027H, and IVS6+3A>G) in the sum of 20 detectable mutations, accounting for 87.2% of the total. Mutation S105* was determined to have a high rate (32.6%) in this study. The hotspot regions of ATP7B were found at exons 2, 16, and 8, and intron 14, in 39.6 %, 11.6 %, 9.3%, and 7 % of patients, respectively. Among nine homozygote/compound heterozygote siblings of the patients with WD, three individuals were determined as asymptomatic by screening mutations of the probands. They would begin treatment after diagnosis. In conclusion, 20 different mutations were detected in 43 WD patients. Of this number, four novel mutations were explored, including [R723=; H724Tfs*34], V1042Cfs*79, D1027H, and IVS6+3A>G. The mutation S105* is the most prevalent and has been considered as a biomarker that can be used in a rapid detection assay for diagnosis of WD patients. Exons 2, 8, and 16, and intron 14 should be screened initially for WD patients in Vietnam. Based on risk profile for WD, genetic testing for presymptomatic patients is also useful in diagnosis and treatment.

Keywords: ATP7B gene, mutation detection, presymptomatic diagnosis, Vietnamese Wilson’s disease

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Authors: Ziwei Huang

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The standard unit of Shenzhen land spatial planning has the characteristics of vertical conduction, horizontal evaluation, internal balance and supervision of implementation. It mainly assumes the role of geospatial unit, assists in promoting the complex development of the business in Shenzhen and undertakes the management and transmission of upper and lower levels of planning as well as the Urban management functions such as gap analysis of public facilities, planning evaluation and dynamic monitoring of planning information. Combining with the application examples of the analysis of gaps in public facilities in Longgang District, it can be found that the standard unit of land spatial planning in Shenzhen as a small-scale geographic basic unit, has a stronger urban spatial coupling effect. However, the universality of the application of the system is still lacking and it is necessary to propose more scientific and powerful standard unit delineation standards and planning function evaluation indicators to guide the implementation of the system's popularization and application.

Keywords: Shenzhen city, land spatial planning, standard unit system, urban delicacy management

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Authors: Mudawamah Mudawamah, Muhammad Z. Fadli, Gatot Ciptadi, Aulanni’am

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Canary breeders have spread throughout Indonesian regions for the low-middle society and become an income source for them. The interesting phenomenon of the canary market is the feather colours become one of determining factor for the price. The advantages of this research were contributed to the molecular database as a base of selection and mating for the Indonesia canary breeder. The research method was experiment with the genome obtained from canary blood isolation. The genome did the PCR amplification with PMEL marker followed by sequencing. Canaries were used 24 heads of light and dark colour feathers. Research data analyses used BioEdit and Network 4.6.0.0 software. The results showed that all samples were amplification with PMEL gene with 500 bp fragment length. In base sequence of 40 was found Cytosine(C) in the light colour canaries, while the dark colour canaries was obtained Thymine (T) in same base sequence. Sequence results had 286-415 bp fragment and 10 haplotypes. The conclusions were the PMEL gene (gene of white pigment) was likely to be used PMEL gene to detect molecular genetic variation of dark and light colour feather.

Keywords: canary, haplotype, PMEL, sequence

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Authors: Yahya A. Sadiq, Grace F. Balogun, Olufemi J. Anjorin

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This study analyzed the spatial distribution of socio-economic factors in Kogi state with a view to examining its implications on the development of the state. Consequently, questionnaires were administered on both the selected individual respondents (784) in the state and on the administrative offices (local council offices, 21) to solicit relevant information on the spatial distribution of socio-economic factors in their areas. The collected data were tabulated and analyzed using percentages. The study revealed commerce/trade, education, and health care, etc. as the major socio-economic factors in the state but with marked variation/imbalance in their spatial distribution across the study area. The rural-based local government areas have far less of such important facilities. Conclusively, it was recommended that there is need for socio-economic transformation of living conditions of people in the study area especially by positively redistributing local political power and the resources that are abound in the state will be felt by everybody including the commoners.

Keywords: development, local government areas (LGAs), spatial distribution, socio-economic factors

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Authors: Mengying Wang, Dongjing Liu, Holger Schwender, Ping Wang, Hongping Zhu, Tao Wu, Terri H Beaty

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Background: Maternal smoking is a recognized risk factor for nonsyndromic cleft lip with or without cleft palate (NSCL/P). It has been reported that the effect of maternal smoking on oral clefts is mediated through genes that influence nicotine dependence. The polymorphisms of cholinergic receptor nicotinic alpha (CHRNA) and beta (CHRNB) subunits genes have previously shown strong associations with nicotine dependence. Here, we attempted to investigate whether the above genes are associated with clefting risk through testing for potential gene-gene (G×G) and gene-environment (G×E) interaction. Methods: We selected 120 markers in 14 genes associated with nicotine dependence to conduct transmission disequilibrium tests among 806 Chinese NSCL/P case-parent trios ascertained in an international consortium which conducted a genome-wide association study (GWAS) of oral clefts. We applied Cordell’s method using “TRIO” package in R to explore G×G as well as G×E interaction involving environmental tobacco smoke (ETS) based on conditional logistic regression model. Results: while no SNP showed significant association with NSCL/P after Bonferroni correction, we found signals for G×G interaction between 10 pairs of SNPs in CHRNA3, CHRNA5, and CHRNB4 (p<10-8), among which the most significant interaction was found between RS3743077 (CHRNA3) and RS11636753 (CHRNB4, p<8.2×10-12). Linkage disequilibrium (LD) analysis revealed only low level of LD between these markers. However, there were no significant results for G×ETS interaction. Conclusion: This study fails to detect association between nicotine dependence genes and NSCL/P, but illustrates the importance of taking into account potential G×G interaction for genetic association analysis in NSCL/P. This study also suggests nicotine dependence genes should be considered as important candidate genes for NSCL/P in future studies.

Keywords: Gene-Gene Interaction, Maternal Smoking, Nicotine Dependence, Non-Syndromic Cleft Lip with or without Cleft Palate

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Authors: Moneesh Thakur, Hridayesh Prasad, Nikitasha Bora, Parimal Roy Choudhary, A. K. Samanta, Sanjeev Kumar

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Canine demodicosis is a common parasitic condition which involves dog skin. Demodicosis in dogs is due the prominent growth of Demodex. Out of various canine Demodex spp., Demodex canis is the most often involved species. Canine demodicosis can occur as either a localized or generalized form of demodicosis severely affect the dogs and in non-treated dogs may cause death. This study was planned with the aim to screen and characterize the 18S rRNA gene of isolated Demodex canis. A total of 1200 dogs were screened during this study period. The skin scrapings of all the suspected dogs were examined under a microscope at 100X magnification for the presence of Demodex canis. The skin scrapings positive for Demodex canis were examined using PCR for confirmation. A total of 35 dogs were confirmed a positive result for D. canis based on 18S rRNA gene amplification by PCR. Further, the 18S rRNA gene of isolated Demodex canis was cloned and sequenced for genome analysis. On the sequence analysis, it was found that isolated sequence (GenBank Accession No. MK177513) had close similarity (99.7%) to that of D. canis genotype of China (Accession No. MG372254).

Keywords: PCR, phylogenetic analysis, cloning and sequening, Demodex canis

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Authors: Jyoti Singh, Swati Dubey, Mukta Singh, R. P. Singh

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The freshwater microalgae Chlorella sp. is alluring considerable interest as a source for biofuel production due to its fast growth rate and high lipid content. Under nitrogen limited conditions, they can accumulate significant amounts of lipids. Thus, it is important to gain insight into the molecular mechanism of their lipid metabolism. In this study under nitrogen limited conditions, regular pattern of growth characteristics lipid accumulation and gene expression analysis of key regulatory genes of lipid biosynthetic pathway were carried out in microalgae Chlorella sp 3. Our results indicated that under nitrogen limited conditions there is a significant increase in the lipid content and lipid productivity, achieving 44.21±2.64 % and 39.34±0.66 mg/l/d at the end of the cultivation, respectively. Time-course transcript patterns of lipid biosynthesis genes i.e. acetyl coA carboxylase (accD) and diacylglycerol acyltransferase (dgat) showed that during late log phase of microalgae Chlorella sp.3 both the genes were significantly up regulated as compared to early log phase. Moreover, the transcript level of the dgat gene is two-fold higher than the accD gene. The results suggested that both the genes responded sensitively to the nitrogen limited conditions during the late log stage, which proposed their close relevance to lipid biosynthesis. Further, this transcriptome data will be useful for engineering microalgae species by targeting these genes for genetic modification to improve microalgal biofuel quality and production.

Keywords: biofuel, gene, lipid, microalgae

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Authors: Patricia M. Boechler, Heather M. Gautreau

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In this research study, postsecondary students completed an information learning task in an avatar-based 3D virtual learning environment. Three factors were of interest in relation to learning; 1) the influence of collaborative vs. independent conditions, 2) the influence of the spatial arrangement of the virtual environment (linear, random and clustered), and 3) the relationship of individual differences such as spatial skill, general computer experience and video game experience to learning. Students completed pretest measures of prior computer experience and prior spatial skill. Following the premeasure administration, students were given instruction to move through the virtual environment and study all the material within 10 information stations. In the collaborative condition, students proceeded in randomly assigned pairs, while in the independent condition they proceeded alone. After this learning phase, all students individually completed a multiple choice test to determine information retention. The overall results indicated that students in pairs did not perform any better or worse than independent students. As far as individual differences, only spatial ability predicted the performance of students. General computer experience and video game experience did not. Taking a closer look at the pairs and spatial ability, comparisons were made on pairs high/matched spatial ability, pairs low/matched spatial ability and pairs that were mismatched on spatial ability. The results showed that both high/matched pairs and mismatched pairs outperformed low/matched pairs. That is, if a pair had even one individual with strong spatial ability they would perform better than pairs with only low spatial ability individuals. This suggests that, in virtual environments, the specific individuals that are paired together are important for performance outcomes. The paper also includes a discussion of trends within the data that have implications for virtual environment education.

Keywords: avatar-based, virtual environment, paired learning, individual differences

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Authors: Beate Niemann, Fabian Pramel

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The formerly industrially or militarily used Urban Waterfront is a potential area for urban development. Extensive interventions in the urban space come along with the development of these previously inaccessible areas in the city. The development of the Urban Waterfront in the European City is not subject to any recognizable urban paradigm. In this study, the development of the Urban Waterfront as a new urban space typology is analyzed by case studies of Urban Waterfront developments in European Cities. For humans, perceptible spatial conditions are categorized and it is identified whether the themed Urban Waterfront Developments are congruent or incongruent urban design interventions and which deviations the Urban Waterfront itself induce. As congruent urban design, a design is understood, which fits in the urban fabric regarding its similar spatial conditions to the surrounding. Incongruent urban design, however, shows significantly different conditions in its shape. Finally, the spatial relationship of the themed Urban Waterfront developments and their associated environment are compared in order to identify contrasts between new and old urban space. In this way, conclusions about urban design paradigms of the new urban space typology are tried to be drawn.

Keywords: composition, congruence, identity, paradigm, spatial condition, urban design, urban development, urban waterfront

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Authors: Konstantinos Tolidis

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The mountains are amongst the most fragile environments in the world. The world’s mountain areas cover 24% of the Earth’s land surface and are home to 12% of the global population. A further 14% of the global population is estimated to live in the vicinity of their surrounding areas. As urbanization continues to increase in the world, the mountains are also key centers for recreation and tourism; their attraction is often heightened by their remarkably high levels of biodiversity. Due to the fact that the features in mountain areas vary spatially (development degree, human geography, socio-economic reality, relations of dependency and interaction with other areas-regions), the spatial planning on these areas consists of a crucial process for preserving the natural, cultural and human environment and consists of one of the major processes of an integrated spatial policy. This research has been focused on the spatial decision problem of land use allocation optimization which is an ordinary planning problem on the mountain areas. It is a matter of fact that such decisions must be made not only on what to do, how much to do, but also on where to do, adding a whole extra class of decision variables to the problem when combined with the consideration of spatial optimization. The utility of optimization as a normative tool for spatial problem is widely recognized. However, it is very difficult for planners to quantify the weights of the objectives especially when these are related to mountain areas. Furthermore, the land use allocation optimization problems at mountain areas must be addressed not only by taking into account the general development objectives but also the spatial objectives (e.g. compactness, compatibility and accessibility, etc). Therefore, the main research’s objective was to approach the land use allocation problem by utilizing a hybrid meta-heuristic optimization technique tailored to the mountain areas’ spatial characteristics. The results indicates that the proposed methodological approach is very promising and useful for both generating land use alternatives for further consideration in land use allocation decision-making and supporting spatial management plans at mountain areas.

Keywords: multiobjective land use allocation, mountain areas, spatial planning, spatial decision making, meta-heuristic methods

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Authors: Amir Bastani

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The result of the research in the field of human behavioural genetics demonstrates a genetic contribution of behavioural differences in aggression, violence, drug and substance abuse, antisocial personality disorder and other related traits. As the field of human behavioural genetics progresses and achieves credibility, the criminal accused continue to use its types of evidence into the criminal law. One of the most important genetic factors which controls certain neurotransmitters like dopamine and serotonin is the Monoamine Oxidase Acid A (MAOA) gene, known as the 'warrior gene'. The high-profile study by Caspi and colleagues in 2002 showed that the combination between one type of variation of the MAOA gene and childhood maltreatment noticeably predisposes a person to antisocial behaviour. Moreover, further scientific research shows that individuals with the MAOA gene have to some degree difficulties in controlling their impulses. Based on the evidence of MAOA, some criminal accused claimed difficulties in self-control. In the first case – the famous case of Mobley – the court rejected the MAOA evidence on the ground of the lack of scientific support. In contrast, in other cases after the Mobley trial, courts accepted the evidence of MAOA. In this paper, the issue of lack of impulse control produced by the MAOA gene and cases which relied on the MAOA evidence and successfully being accepted will be reviewed in detail. Finally, the anticipation of the paper for the future use of the MAOA evidence in criminal cases will be presented.

Keywords: genetic defence, criminal responsibility, MAOA, self-control

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Authors: Tanveer Hussain, Misbah Hussain, Masroor Ellahi Babar, Muhammad Traiq Pervez, Fiaz Hussain, Sana Zahoor, Rashid Saif

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Interleukin 2 (IL-2) is a cytokine which is produced by activated T cells, play important role in immune response against antigen. It act in both autocrine and paracrine manner. It can stimulate B cells and various other phagocytic cells like monocytes, lymphokine-activated killer cells and natural killer cells. Acting in autocrine fashion, IL-2 protein plays a crucial role in proliferation of T cells. IL-2 triggers the release of pro and anti- inflammatory cytokines by activating several pathways. In present study, exon 1 of IL-2 gene of four local Pakistani breeds (Dera Din Panah, Beetal, Nachi and Kamori) from two provinces was amplified by using reported Ovine IL-2 primers, yielding PCR product of 501 bp. The sequencing of all samples was done to identify the polymorphisms in amplified region of IL-2 gene. Analysis of sequencing data resulted in identification of one novel nucleotide substitution (T→A) in amplified non-coding region of IL-2 gene. Comparison of IL-2 gene sequence of all four breeds with other goat breeds showed high similarity in sequence. While phylogenetic analysis of our local breeds with other mammals showed that IL-2 is a variable gene which has undergone many substitutions. This high substitution rate can be due to the decreased or increased changed selective pressure. These rapid changes can also lead to the change in function of immune system. This pioneering study of Pakistani goat breeds urge for further studies on immune system of each targeted breed for fully understanding the functional role of IL-2 in goat immunity.

Keywords: interleukin 2, mutational analysis, phylogeny, goat breeds, Pakistan

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Authors: Trupti Chavan, Ramachandra Guda, Kameshwar Rao

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The lack of data is a pain problem in medical image analysis using a convolutional neural network (CNN). This work uses various spatial transformation techniques to address the medical image augmentation issue for knee detection and localization using an enhanced single shot detector (SSD) network. The spatial transforms like a negative, histogram equalization, power law, sharpening, averaging, gaussian blurring, etc. help to generate more samples, serve as pre-processing methods, and highlight the features of interest. The experimentation is done on the OpenKnee dataset which is a collection of knee images from the openly available online sources. The CNN called enhanced single shot detector (SSD) is utilized for the detection and localization of the knee joint from a given X-ray image. It is an enhanced version of the famous SSD network and is modified in such a way that it will reduce the number of prediction boxes at the output side. It consists of a classification network (VGGNET) and an auxiliary detection network. The performance is measured in mean average precision (mAP), and 99.96% mAP is achieved using the proposed enhanced SSD with spatial transformations. It is also seen that the localization boundary is comparatively more refined and closer to the ground truth in spatial augmentation and gives better detection and localization of knee joints.

Keywords: data augmentation, enhanced SSD, knee detection and localization, medical image analysis, openKnee, Spatial transformations

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Authors: Kapil Pandey, Vishnu Goyal

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Spatial and temporal data analysis is very well known in the field of satellite image processing. When spatial data are correlated with time, series analysis it gives the significant results in change detection studies. In this paper the GIS and Remote sensing techniques has been used to find the change detection using time series satellite imagery of Uttarakhand state during the years of 1990-2010. Natural vegetation, urban area, forest cover etc. were chosen as main landuse classes to study. Landuse/ landcover classes within several years were prepared using satellite images. Maximum likelihood supervised classification technique was adopted in this work and finally landuse change index has been generated and graphical models were used to present the changes.

Keywords: GIS, landuse/landcover, spatial and temporal data, remote sensing

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Authors: Maria Christofi, George Plastiras, Rafaella Elia, Vaggelis Tsiourtis, Theocharis Theocharides, Miltiadis Katsaros

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The rapidly expanding urban areas of the world constitute a challenge of how we need to make the transition to "the next urbanization", which will be defined by new analytical tools and new sources of data. This paper is about the production of a spatial application, the ‘FUMapp’, where space and its initiative will be available literally, in meters, but also abstractly, at a sensed level. While existing spatial applications typically focus on illustrations of the urban infrastructure, the suggested application goes beyond the existing: It investigates how our environment's perception adapts to the alterations of the built environment through a dataset construction of biophysical measurements (eye-tracking, heart beating), and physical metrics (spatial characteristics, size of stimuli, rhythm of mobility). It explores the intersections between architecture, cognition, and computing where future design can be improved and identifies the flexibility and livability of the ‘available space’ of specific examined urban paths.

Keywords: biophysical data, flexibility of urban, livability, next urbanization, spatial application

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Authors: Othman E. Othman, Hassan R. Darwish, Amira M. Nowier

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Lactoferrin (LF) is a multifunctional protein involved in economically production traits like milk protein composition and skeletal structure in small ruminants including sheep and goat. So, LF gene - with its genetic polymorphisms associated with production traits - is considered a candidate genetic marker used in marker-assisted selection in goats. This study aimed to identify the different alleles and genotypes of this gene in three Egyptian goat breeds using PCR-SSCP (polymerase chain reaction-single-strand conformation polymorphism) and DNA sequencing. Genomic DNA was extracted from 120 animals belonging to Barki, Zaraibi, and Damascus goat breeds. Using specific primers, PCR amplified 247-bp fragments from exon 2 of LF goat gene. The PCR products were subjected to Single-Strand Conformation Polymorphism (SSCP) technique. The results showed the presence of two genotypes GG and AG in the tested animals. The frequencies of both genotypes varied among the three tested breeds with the highest frequencies of GG genotype in all tested goat breeds. The sequence analysis of PCR products representing these two detected genotypes declared the presence of an SNP (single nucleotide polymorphisms) substitution (G/A) among G and A alleles of this gene. The association between different LF genotypes and milk composition as well as body measurement was estimated. The comparison showed that the animals possess AG genotypes are superior over those with GG genotypes for different parameters of milk protein compositions and skeletal structures. This finding declared that allele A of LF gene is considered the promising marker for the productive traits in goat. In conclusion, the Egyptian goat breeds will be needed to enhance their milk protein composition and growth trait parameters through the increasing of allele A frequency in their herds depending on the superior production traits of this allele in goats.

Keywords: lLactoferrin gene, PCR-SSCP, SNPs, Egyptian goat

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Authors: Kittitara Chunlakittiphan, Patompong Satapornpong

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Introduction: The variation of genetics affects how our body responds to pharmaceuticals elucidates the correlation between long-term use of medical cannabis and adverse drug reactions (ADRs). Medical cannabis is regarded as the treatment for chronic pain, cancer pain, acute pain, psychological disorders, multiple sclerosis and migraine management. However, previous studies have shown that delta-9-Tetrahydrocannabinol (THC), an ingredient found in cannabis, was the cause of ADRs in CB1 receptors found in humans. Previous research suggests that distributions of the cannabinoid type 1 (CB1) receptor gene and pharmacogenetic markers, which vary amongst different populations, might affect incidences of ADRs. Although there is an evident need to investigate the level of the CB1 receptor gene (rs806365), studies on the distribution of CB1-pharmacogenetics markers in Thai patients are limited. Objective: Therefore, the aim of this study is to investigate the distribution of the rs806365 polymorphism in Thai patients who have been treated with medical cannabis. Materials and Methods: We enrolled 31 Thai patients with THC-induced ADRs and 34 THC-tolerant controls to take part in this study. All patients with THC-induced ADRs were accessed through a review of medical records by physicians. EDTA blood of 3ml was collected to obtain the CNR1 gene (rs806365) and genotyping of this gene was conducted using the real-time PCR ViiA7 (ABI, Foster City, CA, USA) following the manufacturer’s instruction. Results: The sample consisted of 65 patients (40/61.54%) were females and (25/38.46%) were males, with an age range of 19-87 years, who have been treated with medical cannabis. In this study, the most common THC-induced ADRs were dry mouth and/or dry throat, tachycardia, nausea, and arrhythmia. Across the whole sample, we found that 52.31% of Thai patients carried a heterozygous variant (rs806365, CT allele). Moreover, the number of rs806365 (CC, homozygous variant) carriers totaled seventeen people (26.15%) amongst the subjects of Thai patients treated with medical cannabis. Furthermore, 17 out of 22 patients (77.27%) who experienced severe ADRs: Tachycardia and/or arrhythmia, carried an abnormal rs806365 gene (CT and CC alleles). Conclusions: The results propose that the rs806365 gene is widely distributed amongst the Thai population and there is a link between this gene and vulnerability to developing THC-induced ADRs after being treated with medical cannabis. Therefore, it is necessary to screen for the rs806365 gene before using medical cannabis to treat a patient.

Keywords: rs806365, THC-induced adverse drug reactions, CB1 receptor, Thai population

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Authors: Mohammad Talei, Neda Ranjbar Nosheri, Reza Kazemi Gorzadini

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Today municipalities are searching for the new tools for increasing the public participation in different levels of urban planning. This approach of urban planning involves the community in planning process using participatory approaches instead of the long traditional top-down planning methods. These tools can be used to obtain the particular problems of urban furniture form the residents’ point of view. One of the tools that is designed with this goal is public participation GIS (PPGIS) that enables citizen to record and following up their feeling and spatial knowledge regarding main problems of the city, specifically urban furniture, in the form of maps. However, despite the good intentions of PPGIS, its practical implementation in developing countries faces many problems including the lack of basic supporting infrastructure and services and unavailability of sophisticated public participatory models. In this research we develop a PPGIS using of Web 2 to collect voluntary geodataand to perform spatial analysis based on Spatial OnLine Analytical Processing (SOLAP) and Spatial Data Mining (SDM). These tools provide urban planners with proper informationregarding the type, spatial distribution and the clusters of reported problems. This system is implemented in a case study area in Tehran, Iran and the challenges to make it applicable and its potential for real urban planning have been evaluated. It helps decision makers to better understand, plan and allocate scarce resources for providing most requested urban furniture.

Keywords: PPGIS, spatial information, urbanizing futures, urban planning

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Authors: Manaphol Kulpraneet, Anirut Limtrakul, Surangrat Srisurapanon, Piyatida Tangteerawatana

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Tuberculosis (TB) remains a global health care disease world-wide. Control of the global TB epidemic has been impaired by the lack of an effective vaccine, by the emergence of drug resistant forms of Mycobacterium tuberculosis and by lack of sensitive and rapid diagnostics. Cytokines play a major role in defense against M. tuberculosis infection. Polymorphisms in the genes encoding various cytokines have been associated with tuberculosis susceptibility. Polymorphisms of the regulatory cytokine gene, the interleukin (IL)-10 is associated with the risk of tuberculosis (TB) in different populations. However, IL-10 gene polymorphism and susceptibility to TB in Thai is still unknown. The purpose of this study was to evaluate whether the common IL-10 promoter gene polymorphisms are associated with TB in Thai population. Forty eight patients with newly diagnosed pulmonary tuberculosis were studied. DNA samples were extracted from leukocytes and used to investigate -1087A/G, -819C/T, -252C/A (rs1800896, rs1800871, rs1800872) in IL-10 gene using restriction fragment length polymorphism (PCR-RFLP) methods. In this study, the genotype and allele frequencies of IL-10-1087A/G, -819C/T, -252C/A polymorphism did not significantly different between TB patients and healthy controls ((genotype: p=0.38, p=0.92, p=1; allele: p=0.57, p=0.77, p=0.89, respectively). The lack of association between common IL-10 promoter polymorphisms and TB susceptibility in this study may provide clue for better understanding of IL-10-1087A/G, -819C/T, -252C/A polymorphism and TB susceptibility in Thai population, which might facilitate the rationale design of vaccines. However, further studies in large scales population are required for confirmation.

Keywords: IL-10, cytokines, single nucleotide polymorphism (SNP), tuberculosis

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Authors: Mulaudzi Tshimbiluni Annah

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South African city centres depict dynamic urban spaces which reflect complex interactions between multiple actors: the state, formal businesses and informal street traders, with each competing for territorial claims and spatial dominance. The objective of the study is exploring how space is contested, negotiated and occupied between formal and informal sectors, while consequently trying to understand the implication that this has on spatial planning and spatial justice. Through a case-study analysis of the eThekwini city centre, this research examines spatial arrangement, coexistence and conflicts that shape the urban fabric. The study employs spatial justice as a theoretical lens to highlight the inequalities that are embedded within urban planning policies and how street traders are resilient to the harsh restrictive spatial frameworks. Limited evidence is known about how urban planning frameworks can integrate informal street traders in city centres and recognize them as legitimate stakeholders. The study investigates how spatial planning frameworks can be reimagined to promote spatial justice and further facilitate coexistence between formal and informal stakeholders in city centres. Primary data collection included interviews with key stakeholders, while NVivo software was used to analyse the interview data. Observations were conducted through transect walks, which allowed for insight into the spatial dynamics and daily interactions. Visual representations were depicted using GIS mapping to show areas of contestation as well as areas where formal and informal activities intersect. Furthermore, secondary data from literature enabled a comparative analysis of similar case studies through precedent studies. The study revealed continuous contestation by formal businesses and the state, who are for the most part often prioritized by planning frameworks while street traders are often marginalized regardless of their contribution towards economic development. This study therefore proposes strategies for spatial planning that supports an integrative urban framework which ensures equitable access and also a reduction of the marginalization of street traders within urban spaces. This study aims to contribute to understanding urban coexistence and further advocates for spatial planning approaches that integrates informal street traders as legitimate actors in the urban landscape while fostering spatial justice within city centres.

Keywords: coexistence, contestation, integration, spatial justice, spatial planning, street traders

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Authors: Riffat Iqbal, Sidra Ihsan, Andleeb Batool, Maryam Mukhtar

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Glaucoma is a gathering of optic neuropathies described by dynamic degeneration of retinal ganglionic cells. It is clinically and innately heterogenous illness containing a couple of particular forms each with various causes and severities. Primary open-angle glaucoma (POAG) is the most generally perceived kind of glaucoma. This study investigated the genetic association of single nucleotide polymorphisms (SNPs; rs10483727 and rs33912345) at the SIX1/SIX6 locus with primary open-angle glaucoma (POAG) in the Pakistani population. The SIX6 gene plays an important role in ocular development and has been associated with morphology of the optic nerve. A total of 100 patients clinically diagnosed with glaucoma and 100 control individuals of age over 40 were enrolled in the study. Genomic DNA was extracted by organic extraction method. The SNP genotyping was done by (i) PCR based restriction fragment length polymorphism (RFLP) and sequencing method. Significant genetic associations were observed for rs10483727 (risk allele T) and rs33912345 (risk allele C) with POAG. Hence, it was concluded that Six6 gene is genetically associated with pathogenesis of Glaucoma in Pakistan.

Keywords: genotyping, Pakistani population, primary open-angle glaucoma, SIX6 gene

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Authors: Gee-Cheol Kim, Joo-Won Kang

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Structural characteristics of spatial structure are different from that of rahmen structures and it has many factors that are unpredictable experientially. Both horizontal and vertical earthquake should be considered because of seismic behaviour characteristics of spatial structures. This experimental study is conducted about seismic response characteristics of roof structure according to the effect of columns or walls, through scale model of arch structure that has the basic dynamic characteristics of spatial structure. Though remarkable response is not occurred for horizontal direction in the region of higher frequency than the region of frequency that seismic energy is concentrated, relatively large response is occurred in vertical direction. It is proved that seismic response of arch structure with column is varied according to property of column.

Keywords: arch structure, seismic response, shaking table, spatial structure

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Authors: Reena Murali, David Peter S.

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The small interfering RNA (siRNA) alters the regulatory role of mRNA during gene expression by translational inhibition. Recent studies shows that up regulation of mRNA cause serious diseases like Cancer. So designing effective siRNA with good knockdown effects play an important role in gene silencing. Various siRNA design tools had been developed earlier. In this work, we are trying to analyze the existing good scoring second generation siRNA predicting tools and to optimize the efficiency of siRNA prediction by designing a computational model using Artificial Neural Network and whole stacking energy (ΔG), which may help in gene silencing and drug design in cancer therapy. Our model is trained and tested against a large data set of siRNA sequences. Validation of our results is done by finding correlation coefficient of experimental versus observed inhibition efficacy of siRNA. We achieved a correlation coefficient of 0.727 in our previous computational model and we could improve the correlation coefficient up to 0.753 when the threshold of whole tacking energy is greater than or equal to -32.5 kcal/mol.

Keywords: artificial neural network, double stranded RNA, RNA interference, short interfering RNA

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Authors: Hajar Hosseini Khorami

Abstract:

Porphyrins are organic, aromatic compounds found in heme, cytochrome, cobalamin, chlorophyll , and many other natural products with essential roles in biological processes that their cationic forms have been used as groups of favorable non-viral vectors recently. Cationic porphyrins are self-chromogenic reagents with a high capacity for modifications, great interaction with DNA and protection of DNA from nuclease during delivery of it into a cell with low toxicity. In order to have high efficient gene transfection into the cell while causing low toxicity, genetically manipulations of the non-viral vector, cationic porphyrin, would be useful. In this study newly modified cationic porphyrin derivative, 5, 10-dihexyl-15, 20bis (N-methyl-4-pyridyl) porphyrin was applied. Cytotoxicity of synthesized cationic porphyrin on Chinese Hamster Ovarian (CHO) cells was evaluated by using MTT assay. This cationic derivative is dose-dependent, with low cytotoxicity at the ranges from 100 μM to 0.01μM. It was uptake by cells at high concentration. Using direct non-viral gene transfection method and different concentration of cationic porphyrin were tested on transfection of CHO cells by applying derived transfection reagent with X-tremeGENE HP DNA as a positive control. However, no transfection observed by porphyrin derivative and the parameters tested except for positive control. Results of this study suggested that applying different protocol, and also trying other concentration of cationic porphyrins and DNA for forming a strong complex would increase the possibility of efficient gene transfection by using cationic porphyrins.

Keywords: cationic porphyrins, gene delivery, non-viral vectors, transfection reagents

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Authors: Mi Yuan

Abstract:

Employment issues have become increasingly severe in contemporary society, with job seekers' criteria for work environments becoming more complex. However, most studies lack an analysis from the perspective of employment spatial environment. This study employs qualitative research methods such as interviews and thematic analysis, focusing on spatial environment behavior research. By analyzing the behaviors and preferences of key employment groups in China (college graduates, migrant workers, and reemployed laid-off workers) from the perspectives of physical and socio-cultural environments, this study identifies the consistencies and differences in personal viewpoints during job selection and their impact on employment decisions. The findings indicate that college graduates tend to emphasize the macro spatial environment, while migrant workers and reemployed laid-off workers are more concerned with micro spatial environment factors. Additionally, college graduates have higher requirements for the diversity of space types and the distinction between public and private spaces. Furthermore, aside from salary considerations, key employment groups generally place less importance on the socio-cultural environment compared to the physical environment. This study aims to highlight the significance of spatial environment in job selection decisions from the perspective of diverse job seekers, providing insights for policy-making and corporate recruitment strategies.

Keywords: job-seeking populations, spatial environment behavior, micro, macro, qualitative research, physical environment, socio-cultural environment

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Authors: Ngoc Tu Truong, Nuong T. Bui, Ben Rao, Ya L. Shen

Abstract:

Quorum sensing is a phenomenon present in many gram-negative bacteria that allows bacterial communication and controlled expression of a large suite of genes through quorum sensing signals - N-acyl homoserine lactones (AHLs). In order to investigate the ability of the rhlR/rhlI quorum sensing system in Pseudomonas aeruginosa to express the ß-Galactosidase reporter gene, an engineered E. coli strain EpHL02, was genetically engineered. This engineered E. coli strain EpHL02 responded to the presence of the N-butanoyl homoserine lactone and N-hexanoyl homoserine lactone to express the ß-Galactosidase reporter gene at a concentration limit of 5x10⁻⁸ M. This was also found to be comparable to AHLs extraction from Serratia marcescens H31. Moreover, we examined this ability of this engineered E. coli strain for respond of AHLs from extractions of Pseudomonas aeruginosa ATCC9027. The results demonstrated that the rhlR/rhlI quorum sensing system can express the ß-Galactosidase reporter gene by using the N-butanoyl homoserine lactone, N-hexanoyl homoserine lactone and AHLs from extractions of Serratia marcescens H31 and Pseudomonas aeruginosa ATCC9027 in the engineered E. coli strain EpHL02.

Keywords: N-butanoyl homoserine lactone, C4-HSL, N-hexanoyl homoserine lactone, C6-HSL, Pseudomonas aeruginosa, quorum sensing, Serratia marcescens, ß-galactosidase reporter gene

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Authors: Moustafa Osman Mohammed

Abstract:

The modeling of a spatial-economic database is crucial in recitation economic network structure to social development. Sustainability within the spatial-economic model gives attention to green businesses to comply with Earth’s Systems. The natural exchange patterns of ecosystems have consistent and periodic cycles to preserve energy and materials flow in systems ecology. When network topology influences formal and informal communication to function in systems ecology, ecosystems are postulated to valence the basic level of spatial sustainable outcome (i.e., project compatibility success). These referred instrumentalities impact various aspects of the second level of spatial sustainable outcomes (i.e., participant social security satisfaction). The sustainability outcomes are modeling composite structure based on a network analysis model to calculate the prosperity of panel databases for efficiency value, from 2005 to 2025. The database is modeling spatial structure to represent state-of-the-art value-orientation impact and corresponding complexity of sustainability issues (e.g., build a consistent database necessary to approach spatial structure; construct the spatial-economic-ecological model; develop a set of sustainability indicators associated with the model; allow quantification of social, economic and environmental impact; use the value-orientation as a set of important sustainability policy measures), and demonstrate spatial structure reliability. The structure of spatial-ecological model is established for management schemes from the perspective pollutants of multiple sources through the input–output criteria. These criteria evaluate the spillover effect to conduct Monte Carlo simulations and sensitivity analysis in a unique spatial structure. The balance within “equilibrium patterns,” such as collective biosphere features, has a composite index of many distributed feedback flows. The following have a dynamic structure related to physical and chemical properties for gradual prolong to incremental patterns. While these spatial structures argue from ecological modeling of resource savings, static loads are not decisive from an artistic/architectural perspective. The model attempts to unify analytic and analogical spatial structure for the development of urban environments in a relational database setting, using optimization software to integrate spatial structure where the process is based on the engineering topology of systems ecology.

Keywords: ecological modeling, spatial structure, orientation impact, composite index, industrial ecology

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Authors: Siyuan Cai

Abstract:

This paper takes community segregation during major infectious diseases as the background, based on the physiological needs and safety needs of citizens during home segregation, and based on the selection of convenient facilities and medical facilities as the main research objects. Based on the POI data of public facilities in Chongqing, the spatial distribution characteristics of the convenience and medical facilities in the 15-minute living circle centered on three neighborhoods in Shapingba, namely Shengwei Community, Anju Commmunity and Fengtian Garden Community, were explored by means of GIS spatial analysis. The results show that the spatial distribution of convenience and medical facilities in this area has significant clustering characteristics, with a point-like distribution pattern of "dense in the west and sparse in the east", and a grouped and multi-polar spatial structure. The spatial structure is multi-polar and has an obvious tendency to the intersections and residential areas with dense pedestrian flow. This study provides a preliminary exploration of the distribution of medical and convenience facilities within the 15-minute living circle of a segregated community, which makes up for the lack of spatial research in this area.

Keywords: ArcGIS, community segregation, convenient facilities; distribution pattern, medical facilities, POI, 15-minute community life circle

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Authors: Saad Mahmud Khan, Sarah El Hajj Chehadeh, Mehera Abdulrahman, Wael Osman, Habiba Al Safar

Abstract:

Obesity is a non-communicable disease that is widely prevalent with approximately 600 million people classified as obese worldwide. Its etiology is multifactorial and involves a complex interplay between genes and the environment. Over the past few decades, obesity rates among the Emirati population have been increasing. The aim of this study was to investigate the association of candidate gene single nucleotide polymorphisms (SNPs), namely the fat mass and obesity associated (FTO) gene SNP rs9939609 and Vitamin D Receptor (VDR) gene SNP rs1544410, with obesity in the UAE population. Methods: This is a case-control study in which 414 individuals were enrolled during their routine visit to endocrinology clinics in Abu Dhabi, United Arab Emirates between the period of June 2012 and December 2013. Several biochemical tests and clinical assessments along with a lifestyle questionnaire for each participant were completed at the clinic. Genomic DNA was extracted from saliva samples of 201 obese, 114 overweight and 99 normal subjects. Genotyping for the variants was performed using TaqMan assay. Results: The mean Body Mass Index (BMI) ± SD for the obese, overweight, and normal subjects was 35.76 ± 4.54, 27.53 ± 1.45 and 22.69 ± 1.84 kg/m2, respectively. Increasing BMI values were associated with an increase in values for systolic blood pressure, diastolic blood pressure, HbA1c, and triglycerides. The SNP rs9939609 in the FTO gene was found to be significantly associated with the BMI (p=0.028), with the minor allele A having a clear additive effect on BMI values. No significant association was detected between BMI and rs1544410 of the VDR gene. Conclusions: Our study findings indicate that the minor allele A of the rs9939609 has a significant association with increasing BMI values. In addition, our findings support the fact that increasing BMI is associated with increasing risks of other comorbidities such as higher blood pressure, poorer glycemic control and higher triglycerides.

Keywords: body mass index, FTO gene, obesity, rs9939609, United Arab Emirates

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