Search results for: spatial gene

Authors: Ivana Cabarkapa, Zorica Tomicic, Olivera Duragic

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Antimicrobial resistance represents one of the major challenges facing humanity in the last decades. Increasing antibiotic-resistant pathogens indicates the need for the development of alternative antibacterial drugs and new treatment strategies. One of the innovative emerging treatments in overcoming multidrug-resistant pathogens certainly represents the inhibition anti-quorum sensing system. For most of the food-borne pathogens, the expression of the virulence depends on their capability communication with other members of the population by means of quorum sensing (QS). QS represents a specific way of bacterial intercellular communication, which enabled owing to their ability to detect and to respond to cell population density by gene regulation. QS mechanisms are responsible for controls the pathogenesis, virulence luminescence, motility, sporulation and biofilm formation of many organisms by regulating gene expression. Therefore, research in this field is being an attractive target for the development of new natural antibacterial agents. Anti-QS compounds are known to have the ability to prohibit bacterial pathogenicity. Considering the importance of quorum sensing during bacterial pathogenesis, this research has been focused on evaluation anti - QS properties of four essential oils (EOs) Origanum heracleoticum, Origanum vulgare, Thymus vulgare, and Thymus serpyllum, using biomonitor strain of Chromobacterium violaceum CV026. Tests conducted on Luria Bertani agar supplemented with N hexanol DL homoserine lacton (HHL) 10µl/50ml of agar. The anti-QS potential of the EOs was assayed in a range of concentrations of 200 – 0.39 µl/ml using the disc diffusion method. EOs of Th. vulgaris and T. serpyllum were exhibited anti-QS activity indicated by a non- pigmented ring with a dilution-dependent manner. The lowest dilution of EOs T. vulgaris and T. serpyllum in which they exhibited visually detectable inhibition of violacein synthesis was 6.25 µl/ml for both tested EOs. EOs of O. heracleoticum and O. vulgare were displayed different active principles, i.e., antimicrobial activity indicated by the inner clear ring and anti-QS activity indicated by the outer non-pigmented ring, in a concentration-dependent manner. The lowest dilution of EOs of O. heracleoticum and O. vulgare in which exhibited visually detectable inhibition of violacein synthesis was 1.56 and 3.25 µl/ml, respectively. Considering that, the main constituents of the tested EOs represented by monoterpenes (carvacrol, thymol, γ-terpinene, and p-cymene), anti - QS properties of tested EOs can be mainly attributed to their activity. In particular, from the scientific literature, carvacrol and thymol show a sub-inhibitory effect against foodborne pathogens. Previous studies indicated that sub-lethal concentrations of carvacrol reduced the mobility of bacteria due to the ability of interference using QS mechanism between the bacterial cells, and thereby reducing the ability of biofilm formation The precise mechanism by which carvacrol inhibits biofilm formation is still not fully understood. Our results indicated that EOs displayed different active principles, i.e., antimicrobial activity indicated by the inner clear ring and anti-QS activity indicated by an outer non- pigmented ring with visually detectable inhibition of violacein. Preliminary results suggest that EOs represent a promising alternative for effective control of the emergence and spread of resistant pathogens.

Keywords: anti-quorum sensing activity, Chromobacterium violaceum, essential oils, violacein

Procedia PDF Downloads 138

Authors: Gaurav Shinde, Sai Charan Gongiguntla, Prajwal Shirur, Ahmed Hambaba

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Health issues are significantly increasing, putting a substantial strain on healthcare services. This has accelerated the integration of machine learning in healthcare, particularly following the COVID-19 pandemic. The utilization of machine learning in healthcare has grown significantly. We introduce DeClEx, a pipeline that ensures that data mirrors real-world settings by incorporating Gaussian noise and blur and employing autoencoders to learn intermediate feature representations. Subsequently, our convolutional neural network, paired with spatial attention, provides comparable accuracy to state-of-the-art pre-trained models while achieving a threefold improvement in training speed. Furthermore, we provide interpretable results using explainable AI techniques. We integrate denoising and deblurring, classification, and explainability in a single pipeline called DeClEx.

Keywords: machine learning, healthcare, classification, explainability

Procedia PDF Downloads 55

Authors: Nour Charara, Hussein Charara, Omar Abou Khaled, Hani Abdallah, Elena Mugellini

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In this paper, we present a human behavior modeling approach in videos scenes. This approach is used to model the normal behaviors in the conference halls. We exploited the Probabilistic Latent Semantic Analysis technique (PLSA), using the 'Bag-of-Terms' paradigm, as a tool for exploring video data to learn the model by grouping similar activities. Our term vocabulary consists of 3D spatio-temporal patch groups assigned by the direction of motion. Our video representation ensures the spatial information, the object trajectory, and the motion. The main importance of this approach is that it can be adapted to detect abnormal behaviors in order to ensure and enhance human security.

Keywords: activity modeling, clustering, PLSA, video representation

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Authors: Mohammad Asadpour, Gholamreza Razmi, Gholamreza Mohammadi, Abolghasem Naghibi

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Cryptosporidium Spp., protozoan parasites of the phylum Apicomplexa, have a wide spectrum of hosts including humans, domestic animals and wild mammals, birds, reptiles, amphibians and fish. Dairy cattle have been identified in numerous reports as a major source of environmental contamination with this pathogen. In this study, a Polymerase Chain Reaction (PCR), Restriction Fragment Length Polymorphism (RFLP) analysis of the Small-Subunit (SSU) rRNA gene was used to detect and identify Cryptosporidium Spp. in 300 fecal specimens from 1 to 30 days pre-wean calves in 10 farms in Mashhad, Iran. Eighty five (28.3%) and forty five (15%) of the specimens were positive for Cryptosporidium by microscopic and PCR examination respectively. Restriction digestion of the PCR products by VSPI and Ssp1 restriction enzymes and analysis of sequence data revealed the presence of C. parvum, bovine genotype in all isolates. Our findings suggest that cattle can be a source of Cryptosporidial infections for humans and animals in Mashhad area. This is the first published description of Cryptosporidium sub genotyping in Mashhad.

Keywords: cryptosporidium, genotype, dairy calves, 18S rRNA, Mashhad

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Authors: Asiye Ciftci, Zeki Kaya

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Populus nigra is one of the most economically and ecologically important forest trees in Turkey, well known for its rapid growth, good ability to vegetative propagation and the extreme uses of its wood. Due to overexploitation, loss of natural distribution area and extreme hybridization and introgression, Populus nigra is one of the most threatened tree species in Turkey and Europe. Using 20 nuclear microsatellite loci, the genetic structure of European black poplar populations along the two largest rivers of Turkey was analyzed. All tested loci were highly polymorphic, displaying 5 to 15 alleles per locus. Observed heterozygosity (overall Ho = 0.79) has been higher than the expected (overall He = 0.58) in each population. Low level of genetic differentiation among populations (FST= 0,03) and excess of heterozygotes for each river were found. Human-mediated dispersal, phenotypic selection, high level of gene flow and extensive circulations of clonal materials may cause those situations. The genetic data obtained from this study could provide the basis for efficient in situ and ex-situ conservation and restoration of species natural populations in its natural habitat as well as having sustainable breeding and poplar plantations in the future.

Keywords: populus, clonal, loci, ex situ

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Authors: Jeong-Min Son, Jeong-Hee Eum, Jin-Kyu Min, Uk-Je Sung, Ju-Eun Kim

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While various environmental problems are severe due to climate change, especially in cities where population and development are concentrated, urban thermal environment problems such as heat waves and tropical nights are particularly worsening. Accordingly, the Korean government provides basic data related to the urban thermal environment to support each local government in effectively establishing policies to cope with heat waves. However, the basic data related to the thermal environment provided by the government has limitations in establishing a regional thermal adaptation plan with a minimum unit of cities, counties, and districts. In addition, the urban heat environment perceived by people differs in each region and space. Therefore, it is necessary to prepare practical measures that can be used to establish regional-based policies for heat wave adaptation by identifying people’s heat perception in the entire city. This study aims to develop a mobile phone application (APP) to gather people’s thermal sensation information and create Korea’s first thermal map based on this information. In addition, through this APP, citizens directly propose thermal adaptation policies, and urban planners and policymakers accept citizens' opinions, so this study provides a tool to solve local thermal environment problems. To achieve this purpose, first, the composition and contents of the app were discussed by examining various existing apps and cases for citizen participation and collection of heat information. In addition, factors affecting human thermal comfort, such as spatial, meteorological, and demographic factors, were investigated to construct the APP system. Based on these results, the basic version of the APP was developed. Second, the living lab methodology was adopted to gather people’s heat perception using the developed app to conduct overall evaluation and feedback of people on the APP. The people participating in the living lab were selected as those living in Daegu Metropolitan City, which is located in South Korea and annually records high temperatures. The user interface was improved through the living lab to make the app easier to use and the thermal map was modified. This study expects to establish high-resolution thermal maps for effective policies and measures and to solve local thermal environmental problems using the APP. The collected information can be used to evaluate spatial, meteorological, and demographic characteristics that affect the perceived heat of citizens. In addition, it is expected that the research can be expanded by gathering thermal information perceived by citizens of foreign cities as well as other cities in South Korea through the APP developed in this study.

Keywords: mobile application, living lab, thermal map, climate change adaptation

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Authors: Austin Belfiori, Kevin Rinek, Zach Barcroft, Jennifer Berglind

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Diet influences the composition of the gut microbiota and host's health. Disruption of the balance among the microbiota, epithelial cells, and resident immune cells in the intestine is involved in the pathogenesis of inflammatory bowel disease (IBD). To study the role of gut microbiota in intestinal inflammation, the microbiome of control mice (C57BL6) given a gluten-containing standard diet versus C57BL6 mice given the gluten-free (GF) feed (n=10 in each group) was examined. All mice received the 3% DSS for 5 days. Throughout the study, feces were collected and processed for DNA extraction and MiSeq Illumina sequencing of V4 region of bacterial 16S rRNA gene. Alpha and beta diversities and compositional differences at phylum and genus levels were determined in intestinal microbiota. The mice receiving the GF diet showed a significantly increased abundance of Firmicutes and a decrease of Bacteroides and Lactobacillus at phylum level. Therefore, the gluten free diet led to reductions in beneficial gut bacteria populations. These findings indicate a role of wheat gluten in dysbiosis of the intestinal microbiota.

Keywords: gluten, colitis, microbiota, DSS, dextran sulphate sodium

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Authors: Varun Agarwal

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Introduction: With the advent of personalized medicine, histopathological review of whole slide images (WSIs) for cancer diagnosis presents an exceedingly time-consuming, complex task. Specifically, detecting metastatic regions in WSIs of sentinel lymph node biopsies necessitates a full-scanned, holistic evaluation of the image. Thus, digital pathology, low-level image manipulation algorithms, and machine learning provide significant advancements in improving the efficiency and accuracy of WSI analysis. Using Camelyon16 data, this paper proposes a deep learning pipeline to automate and ameliorate breast cancer metastasis localization and WSI classification. Methodology: The model broadly follows five stages -region of interest detection, WSI partitioning into image tiles, convolutional neural network (CNN) image-segment classifications, probabilistic mapping of tumor localizations, and further processing for whole WSI classification. Transfer learning is applied to the task, with the implementation of Inception-ResNetV2 - an effective CNN classifier that uses residual connections to enhance feature representation, adding convolved outputs in the inception unit to the proceeding input data. Moreover, in order to augment the performance of the transfer learning CNN, a stack of convolutional denoising autoencoders (CDAE) is applied to produce embeddings that enrich image representation. Through a saliency-detection algorithm, visual training segments are generated, which are then processed through a denoising autoencoder -primarily consisting of convolutional, leaky rectified linear unit, and batch normalization layers- and subsequently a contrast-normalization function. A spatial pyramid pooling algorithm extracts the key features from the processed image, creating a viable feature map for the CNN that minimizes spatial resolution and noise. Results and Conclusion: The simplified and effective architecture of the fine-tuned transfer learning Inception-ResNetV2 network enhanced with the CDAE stack yields state of the art performance in WSI classification and tumor localization, achieving AUC scores of 0.947 and 0.753, respectively. The convolutional feature retention and compilation with the residual connections to inception units synergized with the input denoising algorithm enable the pipeline to serve as an effective, efficient tool in the histopathological review of WSIs.

Keywords: breast cancer, convolutional neural networks, metastasis mapping, whole slide images

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Authors: Christakis Damianou, Christos Christofi, Nicos Mylonas

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The aim of this paper was to conduct a feasibility study using a flat rectangular (3x10 mm2) MRI compatible transducer operating at 5 MHz for destroying atherosclerotic plaque using the thermal effects of ultrasound in in vitro models. A parametric study was performed where the time needed to ablate the plaque was studied as a function of Spatial Average Temporal Average (SATA) intensity, and pulse duration. The time needed to ablate plaque is directly related to intensity, and pulse duration. The temperature measured close to the artery is above safe limits and therefore thermal ultrasound does not have a place in removing plaques in arteries.

Keywords: ultrasound, atherosclerotic, plaque, pulse

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Authors: Delly C. Lestari, Linosefa, Ardiana Kusumaningrum, Andi Yasmon, Anis Karuniawati

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The objective of this study is to determine the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) harboring mecA genes from screening isolates among intensive care unit (ICU) patients. All MRSA screening isolates from ICU’s patients of Cipto Mangunkusumo Hospital during 2011 and 2014 were included in this study. Identification and susceptibility test was performed using Vitek2 system (Biomereux®). PCR was conducted to characterize the SCCmec of S. aureus harboring the mecA gene on each isolate. Patient’s history of illness was traced through medical record. 24 isolates from 327 screening isolates were MRSA positive (7.3%). From PCR, we found 17 (70.8%) isolates carrying SCCmec type I, 3 (12.5%) isolates carrying SCCmec type III, and 2 (8.3%) isolates carrying SCCmec type IV. In conclusion, SCCmec type I is the most prevalent MRSA colonization among ICU patients in Cipto Mangunkusumo Hospital.

Keywords: MRSA, mecA genes, ICU, colonization

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Authors: Vitalijs Lusis, Andrejs Krasnikovs

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Fiber reinforced concrete is important material for load bearing structural elements. Usually fibers are homogeneously distributed in a concrete body having arbitrary spatial orientations. At the same time, in many situations, fiber concrete with oriented fibers is more optimal. Is obvious, that is possible to create constructions with oriented short fibers in them, in different ways. Present research is devoted to one of such approaches- fiber reinforced concrete prisms having dimensions 100 mm×100 mm×400 mm with layers of non-homogeneously distributed fibers inside them were fabricated. Simultaneously prisms with homogeneously dispersed fibers were produced for reference as well. Prisms were tested under four point bending conditions. During the tests vertical deflection at the center of every prism and crack opening were measured (using linear displacements transducers in real timescale). Prediction results were discussed.

Keywords: fiber reinforced concrete, 4-point bending, steel fiber, construction engineering

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Authors: Matthew Stephenson

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We study the electrical conductivity of strongly disordered, strongly coupled quantum field theories, holographically dual to non-perturbatively disordered uncharged black holes. The computation reduces to solving a diffusive hydrostatic equation for an emergent horizon fluid. We demonstrate that a large class of theories in two spatial dimensions have a universal conductivity independent of disorder strength, and rigorously rule out disorder-driven conductor-insulator transitions in many theories. We present a (fine-tuned) axion-dilaton bulk theory which realizes the conductor-insulator transition, interpreted as a classical percolation transition in the horizon fluid. We address aspects of strongly disordered holography that can and cannot be addressed via mean-field modeling, such as massive gravity.

Keywords: theoretical physics, black holes, holography, high energy

Procedia PDF Downloads 178

Authors: Artem Kim, Clara Savary, Christele Dubourg, Wilfrid Carre, Houda Hamdi-Roze, Valerie Dupé, Sylvie Odent, Marie De Tayrac, Veronique David

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Holoprosencephaly (HPE) is a rare congenital brain malformation resulting from the incomplete separation of the two cerebral hemispheres. It is characterized by a wide phenotypic spectrum and a high degree of locus heterogeneity. Genetic defects in 16 genes have already been implicated in HPE, but account for only 30% of cases, suggesting that a large part of genetic factors remains to be discovered. HPE has been recently redefined as a complex multigenic disorder, requiring the joint effect of multiple mutational events in genes belonging to one or several developmental pathways. The onset of HPE may result from accumulation of the effects of multiple rare variants in functionally-related genes, each conferring a moderate increase in the risk of HPE onset. In order to decipher the genetic basis of HPE, unconventional patterns of inheritance involving multiple genetic factors need to be considered. The primary objective of this study was to uncover possible disease causing combinations of multiple rare variants underlying HPE by performing trio-based Whole Exome Sequencing (WES) of familial cases where no molecular diagnosis could be established. 39 families were selected with no fully-penetrant causal mutation in known HPE gene, no chromosomic aberrations/copy number variants and without any implication of environmental factors. As the main challenge was to identify disease-related variants among a large number of nonpathogenic polymorphisms detected by WES classical scheme, a novel variant prioritization approach was established. It combined WES filtering with complementary gene-level approaches: transcriptome-driven (RNA-Seq data) and clinically-driven (public clinical data) strategies. Briefly, a filtering approach was performed to select variants compatible with disease segregation, population frequency and pathogenicity prediction to identify an exhaustive list of rare deleterious variants. The exome search space was then reduced by restricting the analysis to candidate genes identified by either transcriptome-driven strategy (genes sharing highly similar expression patterns with known HPE genes during cerebral development) or clinically-driven strategy (genes associated to phenotypes of interest overlapping with HPE). Deeper analyses of candidate variants were then performed on a family-by-family basis. These included the exploration of clinical information, expression studies, variant characteristics, recurrence of mutated genes and available biological knowledge. A novel bioinformatics pipeline was designed. Applied to the 39 families, this final integrated workflow identified an average of 11 candidate variants per family. Most of candidate variants were inherited from asymptomatic parents suggesting a multigenic inheritance pattern requiring the association of multiple mutational events. The manual analysis highlighted 5 new strong HPE candidate genes showing recurrences in distinct families. Functional validations of these genes are foreseen.

Keywords: complex genetic disorder, holoprosencephaly, multiple rare variants, whole exome sequencing

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Authors: Carolina Mayen Huerta, Clara Ivanescu, Paloma Marcos

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Due to their unique geographic challenges and the imperative to combat climate change, Small Island Developing States (SIDS) are experiencing rapid growth in the renewable energy (RE) sector. However, women's representation in formal employment within this burgeoning field remains significantly lower than their male counterparts. Conventional methodologies often overlook critical geographic data that influence women's job prospects. To address this gap, this paper introduces a Multicriteria Evaluation (MCE) framework designed to identify spatially enabling environments and restrictions affecting women's access to formal employment and business opportunities in the SIDS' RE sector. The proposed MCE framework comprises 24 key factors categorized into four dimensions: Individual, Contextual, Accessibility, and Place Characterization. "Individual factors" encompass personal attributes influencing women's career development, including caregiving responsibilities, exposure to domestic violence, and disparities in education. "Contextual factors" pertain to the legal and policy environment, influencing workplace gender discrimination, financial autonomy, and overall gender empowerment. "Accessibility factors" evaluate women's day-to-day mobility, considering travel patterns, access to public transport, educational facilities, RE job opportunities, healthcare facilities, and financial services. Finally, "Place Characterization factors" enclose attributes of geographical locations or environments. This dimension includes walkability, public transport availability, safety, electricity access, digital inclusion, fragility, conflict, violence, water and sanitation, and climatic factors in specific regions. The analytical framework proposed in this paper incorporates a spatial methodology to visualize regions within countries where conducive environments for women to access RE jobs exist. In areas where these environments are absent, the methodology serves as a decision-making tool to reinforce critical factors, such as transportation, education, and internet access, which currently hinder access to employment opportunities. This approach is designed to equip policymakers and institutions with data-driven insights, enabling them to make evidence-based decisions that consider the geographic dimensions of disparity. These insights, in turn, can help ensure the efficient allocation of resources to achieve gender equity objectives.

Keywords: gender, women, spatial analysis, renewable energy, access

Procedia PDF Downloads 69

Authors: Carolina Mayen Huerta, Clara Ivanescu, Paloma Marcos

Abstract:

Due to their unique geographic challenges and the imperative to combat climate change, Small Island Developing States (SIDS) are experiencing rapid growth in the renewable energy (RE) sector. However, women's representation in formal employment within this burgeoning field remains significantly lower than their male counterparts. Conventional methodologies often overlook critical geographic data that influence women's job prospects. To address this gap, this paper introduces a Multicriteria Evaluation (MCE) framework designed to identify spatially enabling environments and restrictions affecting women's access to formal employment and business opportunities in the SIDS' RE sector. The proposed MCE framework comprises 24 key factors categorized into four dimensions: Individual, Contextual, Accessibility, and Place Characterization. "Individual factors" encompass personal attributes influencing women's career development, including caregiving responsibilities, exposure to domestic violence, and disparities in education. "Contextual factors" pertain to the legal and policy environment, influencing workplace gender discrimination, financial autonomy, and overall gender empowerment. "Accessibility factors" evaluate women's day-to-day mobility, considering travel patterns, access to public transport, educational facilities, RE job opportunities, healthcare facilities, and financial services. Finally, "Place Characterization factors" enclose attributes of geographical locations or environments. This dimension includes walkability, public transport availability, safety, electricity access, digital inclusion, fragility, conflict, violence, water and sanitation, and climatic factors in specific regions. The analytical framework proposed in this paper incorporates a spatial methodology to visualize regions within countries where conducive environments for women to access RE jobs exist. In areas where these environments are absent, the methodology serves as a decision-making tool to reinforce critical factors, such as transportation, education, and internet access, which currently hinder access to employment opportunities. This approach is designed to equip policymakers and institutions with data-driven insights, enabling them to make evidence-based decisions that consider the geographic dimensions of disparity. These insights, in turn, can help ensure the efficient allocation of resources to achieve gender equity objectives.

Keywords: gender, women, spatial analysis, renewable energy, access

Procedia PDF Downloads 83

Authors: Apotiola Z. O., Anyakorah C. I., Kuforiji O. O.

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Sensory and microbial properties of fresh and canned Calocybe indica (milky mushroom) were evaluated. The mushroom was grown under a controlled environment with hardwood (Cola nitida) and rice bran substrate (4:1) canned in a brine solution of salt and citric acid. Analysis was carried out using standard methods. The overall acceptability ranged between 5.62 and 6.50, with sample S30 adjudged the best. In all, significant differences p<0.01 exist in the panelist judgment. Thus, the incorporation of salt and citric acid at 3.5g and 1.5g, respectively, improved sensory attributes such as texture, aroma, color, and overall acceptability. There was no coliform and fungi growth on the samples throughout the storage period. The bacterial count, on the other hand, was observed only in the fifth and sixth week of the storage period which varied between 0.2 to 0.9 x 103 cfu/g. The highest value was observed in sample S20 of the sixth week of storage, while the lowest value was recorded in sample S30 of the sixth week of storage. Based on 16S rRNA gene sequencing, bacterial species were taxonomically confirmed as Bacillus thuringiensis. The percentile compositions and Sequence ID of the bacterial species in the mushroom was 90%.

Keywords: bacterial count, microbial property, sensory, sawdust, texture

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Authors: Fatma Abdedayem

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The most effective and efficient methods in image categorization are almost based on bag-of-words (BOW) which presents image by a histogram of occurrence of visual words. In this paper, we propose a novel extension to this method. Firstly, we extract features in multi-scales by applying a color local descriptor named opponent-SIFT. Secondly, in order to represent image we use Spatial Pyramid Representation (SPR) and an extension to the BOW method which based on weighting visual words. Typically, the visual words are weighted during histogram assignment by computing the ratio of their occurrences in the image to the occurrences in the background. Finally, according to classical BOW retrieval framework, only a few words of the vocabulary is useful for image representation. Therefore, we select the useful weighted visual words that respect the threshold value. Experimentally, the algorithm is tested by using different image classes of PASCAL VOC 2007 and is compared against the classical bag-of-visual-words algorithm.

Keywords: BOW, useful visual words, weighted visual words, bag of visual words

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Authors: Aiman Alshare, Sahar Qaadan

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A curvature dependent force correction algorithm for planning force controlled grinding process with off-line programming flexibility is designed for ABB industrial robot, in order to avoid the manual interface during the process. The machining path utilizes a spline curve fit that is constructed from the CAD data of the workpiece. The fitted spline has a continuity of the second order to assure path smoothness. The implemented algorithm computes uniform forces normal to the grinding surface of the workpiece, by constructing a curvature path in the spatial coordinates using the spline method.

Keywords: ABB industrial robot, grinding process, offline programming, CAD data extraction, force correction algorithm

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Authors: Yin Ruoxi

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Buddhism, originating in ancient India, saw its most profound development in China. Similarly, Buddhist architecture, though derived from Indian prototypes, evolved distinctively as the religion reached new regions. The interaction with local traditions led to architectural forms that mirrored the unique cultural and ethnic identities of each area. Before the Sui and Tang dynasties, three prominent styles could be observed: Indian, Central Asian, and those of the northern Central Plains. This paper aims to analyze the spatial distribution of temples and the evolution of temple layouts， which means the general layout and floor plans in architecture study, with the innovation of the Pagoda in China. Through examining these transformations and their underlying causes, this paper seeks to unravel the early stages of Buddhism's adaptation to Chinese cultural contexts before the Sui dynasty.

Keywords: Buddhist architecture, early Buddhism in China, change in Buddhism with developing in architecture, temple, pagoda

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Authors: Manal Farea, Adam Husein, Ahmad S. Halim, Zurairah Berahim, Nurul A. Abdullah, Khairani I. Mokhtar, Kasmawati Mokhtar

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Endodontic furcal perforation remains both an endodontic and a periodontal problem. Regeneration of cementum is very essential for the perforation repair. The aim of this study was to investigate the role of Hertwig's epithelial root sheath (HERS) cells on the cementogenic differentiation of stem cells derived from human exfoliated deciduous teeth (SHED) in the presence of chitosan scaffold-TGFβ1. HERS cells were isolated and characterized then co-cultured with SHED with/without chitosan scaffold-TGFβ1. SHED proliferation was assessed by PrestoBlue. Alkaline phosphatase activity, mineralization behaviour and gene/protein expression of cemento/osteoblast phenotype of SHED were evaluated. Results of the present study showed that HERS cells in association with chitosan-TGFβ1 enhanced proliferation and cemento/osteogenic differentiation of SHED. Our novel co-culture system confirmed the potential effect of HERS cells to stimulate the differentiation of SHED along the cementoblastic lineage which was triggered in the presence of chitosan-TGFβ1. This approach possesses a novel therapeutic strategy for future endodontic perforation and periodontitis.

Keywords: cementogenesis, co-culture system, HERS, SHED

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Authors: Claudia Popescu, Adriana Mihaela Soaita

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Within the EU accession process, Romania, as well as other CEE countries, have embarked on the post-1990 urbanization wave aiming to reduce the gaps between ‘older’ and ‘new’ EU member states. While post-socialist urban transitions have been extensively scrutinized, little is known about the developing trajectories of these new towns across the CEE region. To start addressing this knowledge gap, we wish to bring to the fore one of the most humble expressions of urbanism, that of the small, new towns of Romania. Despite rural-to-urban reclassification, urbanization levels have remained persistently low over the last three decades. In this context, it is timely and legitimate to ask about the prospects of new towns for a ‘successful’ socioeconomic performance within the urban network and avoidance of precarity and marginalization and adequate measure of place performance within the urban/settlement network and understanding the drivers that trigger towns’ socioeconomic performances. To answer these, we create a socioeconomic index of the place in order to compare the profile of the 60 new towns with large cities, old small towns and rural. We conceive ‘successful’ and ‘precarious’ performance in terms of a locality’s index value being above or below all small towns’ index average. Second, we performed logistic regression to interrogate the relevance of some key structural factors to the new towns’ socioeconomic performance (i.e. population size, urban history, regional location, connectivity and political determination of their local governments). Related to the first research question, our findings highlight the precarity of place as a long-standing condition of living and working in the new towns of Romania, particularly evident through our cross-comparative analysis across key category along the rural-urban continuum. We have substantiated the socioeconomic condition of precarity in rural places, with the new towns still maintaining features of ‘rurality’ rather than ‘urbanity’ - except a few successful satellites of economically striving large cities, particularly the country capital of Bucharest, which benefited from spillover effects. Related to our second research question, we found that the new towns of Romania have significantly higher odds of being characterized by precarity as a socioeconomic condition than all other small towns and urban places, but less so compared to the even more marginalized rural areas. Many new towns contain resource-dependent rural communities with a poor response to the context of change. Therefore, issues pertaining to local capacity building to adapt to the new urban environment should be addressed by the spatial planning policy. Our approach allowed us to bring to the fore the idea of precarity as a condition of whole localities. Thinking of precarity of place is important as it brings the whole institutional and political apparatus of spatial planning, urban and regional, into conversation with other causative or substantive axes of precarity developed in the literature. We recommend future research on the new towns in Romania and elsewhere.

Keywords: politics of fantasy, precarity of place, urbanization, Romania

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Authors: Salam Khalifa, Naveed Ahmed

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We present a new method to reconstruct a temporally coherent 3D animation from single or multi-view RGB-D video data using unbiased feature point sampling. Given RGB-D video data, in form of a 3D point cloud sequence, our method first extracts feature points using both color and depth information. In the subsequent steps, these feature points are used to match two 3D point clouds in consecutive frames independent of their resolution. Our new motion vectors based dynamic alignment method then fully reconstruct a spatio-temporally coherent 3D animation. We perform extensive quantitative validation using novel error functions to analyze the results. We show that despite the limiting factors of temporal and spatial noise associated to RGB-D data, it is possible to extract temporal coherence to faithfully reconstruct a temporally coherent 3D animation from RGB-D video data.

Keywords: 3D video, 3D animation, RGB-D video, temporally coherent 3D animation

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Authors: Sun Ailu, Zhao Wanmin

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In the process of rapid urbanization, old urban renewal is an important task in China's urban construction. This study, using status survey and Analytic Hierarchy Process (AHP) method, taking Chongqing of China as an example, puts forward the problems faced by the old urban area from the aspects of function, facilities and environment. Further, this study summarizes the types of the old urban area and proposes space renewal strategies for three typical old urban areas, such as old residential area, old factory and old market. These old urban areas are confronted with the problems of functional layout confounding, lack of infrastructure and poor living environment. At last, this paper proposes spatial strategies for urban renewal, which are hoped to be useful for urban renewal management in China.

Keywords: old urban renewal, renewal mode, renewal strategy, Chongqing, China

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Authors: E. Baltas, E. Feloni, G. Bariamis

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The operation of a network of hydrometeorological-hydrometric stations is basic infrastructure for the management of water resources, as well as, for flood protection. The assessment of water resources potential led to the necessity of adoption management practices including a multi-criteria analysis for the optimum design of the region’s station network. This research work aims at the optimisation of a new/existing network, using GIS methods. The planning of optimum network stations is based on the guidelines of international organizations such as World Meteorological Organization (WMO). The uniform spatial distribution of the stations, the drainage basin for the hydrometric stations and criteria concerning the low terrain slope, the accessibility to the stations and proximity to hydrological interest sites, were taken into consideration for its development. The abovementioned methodology has been implemented for two different areas the Florina municipality and the Argolis area in Greece, and comparison of the results has been conducted.

Keywords: GIS, hydrometeorological, hydrometric, network, optimisation

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Authors: Doaa Hashad, Amany Elbanna, Abeer Ibrahim, Gihan Khedr

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Background: H19 is one of the long non coding RNAs (LncRNA) that is related to the progression of many diseases including cancers. This work was carried out to study the level of the long non-coding RNA; H119, in plasma of patients with gastric cancer (GC) and to assess its significance in their clinical management. Methods: A total of sixty-two participants were enrolled in the present study. The first group included thirty-two GC patients, while the second group was formed of thirty age and sex matched healthy volunteers serving as a control group. Plasma samples were used to assess H19 gene expression using real time quantitative PCR technique. Results: H19 expression was up-regulated in GC patients with positive correlation to TNM cancer stages. Conclusions: Up-regulation of H19 is closely associated with gastric cancer and correlates well with tumor staging. Convenient, efficient quantification of H19 in plasma using real time PCR technique implements its role as a potential noninvasive prognostic biomarker in gastric cancer, that predicts patient’s outcome and most importantly as a novel target in gastric cancer treatment with better performance achieved on using both CEA and H19 simultaneously.

Keywords: biomarker, gastric, cancer, LncRNA

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Authors: M. N. Hanina, M. Hairul Shahril, I. Ismatul Nurul Asyikin, A. K. Abdul Jalil, M. R. Salina, M. R. Maryam, M. Rosfarizan

Abstract:

The extracellular proteins secreted by bacteria may be increased in stressful surroundings, such as in the presence of antibiotics. It appears that many antibiotics, when used at low concentrations, have in common the ability to activate or repress gene transcription, which is distinct from their inhibitory effect. There have been comparatively few studies on the potential of antibiotics as a specific chemical signal that can trigger a variety of biological functions. Therefore, this study was carried out to determine the effect of Streptomycin Sulfate in regulating extracellular proteins secreted by Bacillus subtilis ATCC21332. Results of Microdilution assay showed that the Minimum Inhibition Concentration (MIC) of Streptomycin Sulfate on B. subtilis ATCC21332 was 2.5 mg/ml. The bacteria cells were then exposed to Streptomycin Sulfate at concentration of 0.01 MIC before being further incubated for 48h to 72 h. The extracellular proteins secreted were then isolated and analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Proteins profile revealed that three additional bands with approximate sizes of 30 kDa, 22 kDa and 23 kDa were appeared for the treated bacteria with Streptomycin Sulfate. Thus, B. subtilis ATCC21332 in stressful condition with the presence of Streptomycin Sulfate at low concentration could induce the extracellular proteins secretion.

Keywords: Bacillus subtilis ATCC21332, streptomycin sulfate, extracellular proteins, antibiotics

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Authors: Gulsen Yilmaz

Abstract:

Istanbul’s population has jumped by over 1 million in the past four years, to a level surpassing the overall population of 64 provinces in the country, according to data from the Turkish Statistical Institute (TÜİK). In this paper, Istanbul's population change and migration effects can be examined in detail Tarlabasi neighborhood cultural center of the city of Istanbul, Istiklal Street, which is located a few hundred meters away. Tarlabasi the end of the nineteenth century in the historic district with built in the early twentieth century, there are four or five storey historic buildings. Tarlabasi, here come from southeastern Turkey and the illegal African immigrants living in Roma origin by the Kurds as a residential area is used. In this area to improve the quality of life for urban renewal projects have been initiated. The aim of this paper is to explore the spatial effects of demographic change and migration with Tarlabasi example.

Keywords: migration, immigration, Tarlabaşı, urban transformation

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Authors: Najibullah M, Soumendra Nath Kuiry

Abstract:

Dams and reservoirs are perceived for their estimable alms to irrigation, water supply, flood control, electricity generation, etc. which civilize the prosperity and wealth of society across the world. Meantime the dam breach could cause devastating flood that can threat to the human lives and properties. Failures of large dams remain fortunately very seldom events. Nevertheless, a number of occurrences have been recorded in the world, corresponding in an average to one to two failures worldwide every year. Some of those accidents have caused catastrophic consequences. So it is decisive to predict the dam break flow for emergency planning and preparedness, as it poses high risk to life and property. To mitigate the adverse impact of dam break, modeling is necessary to gain a good understanding of the temporal and spatial evolution of the dam-break floods. This study will mainly deal with one-dimensional (1D) dam break modeling. Less commonly used in the hydraulic research community, another possible option for modeling the rapidly varied dam-break flows is the extended Boussinesq equations (BEs), which can describe the dynamics of short waves with a reasonable accuracy. Unlike the Shallow Water Equations (SWEs), the BEs taken into account the wave dispersion and non-hydrostatic pressure distribution. To capture the dam-break oscillations accurately it is very much needed of at least fourth-order accurate numerical scheme to discretize the third-order dispersion terms present in the extended BEs. The scope of this work is therefore to develop an 1D fourth-order accurate in both space and time Boussinesq model for dam-break flow analysis by using finite-volume / finite difference scheme. The spatial discretization of the flux and dispersion terms achieved through a combination of finite-volume and finite difference approximations. The flux term, was solved using a finite-volume discretization whereas the bed source and dispersion term, were discretized using centered finite-difference scheme. Time integration achieved in two stages, namely the third-order Adams Basforth predictor stage and the fourth-order Adams Moulton corrector stage. Implementation of the 1D Boussinesq model done using PYTHON 2.7.5. Evaluation of the performance of the developed model predicted as compared with the volume of fluid (VOF) based commercial model ANSYS-CFX. The developed model is used to analyze the risk of cascading dam failures similar to the Panshet dam failure in 1961 that took place in Pune, India. Nevertheless, this model can be used to predict wave overtopping accurately compared to shallow water models for designing coastal protection structures.

Keywords: Boussinesq equation, Coastal protection, Dam-break flow, One-dimensional model

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Authors: Khiem M. Nguyen, Ming C. Yang

Abstract:

Chloroplast pigments are extremely important during photosynthesis since they play essential roles in light absorption and energy transfer. Therefore, understanding the efficiency of chlorophyll (Chl) biosynthesis could facilitate enhancement in photo-assimilates accumulation, and ultimately, in crop yield. The Chl-deficient mutants have been used extensively to study the Chl biosynthetic pathways and the biogenesis of the photosynthetic apparatus. Rice (Oryza sativa L.) is one of the most leading food crops, serving as staple food for many parts of the world. To author’s best knowledge, Chl b–lacking rice has been found; however the molecular mechanism of Chl biosynthesis still remains unclear compared to wild-type rice. In this study, the ultrastructure analysis, photosynthetic properties, and transcriptome profile of wild-type rice (Norin No.8, N8) and its Chl b-lacking mutant (Chlorina 1, C1) were examined. The finding concluded that total Chl content and Chl b content in the C1 leaves were strongly reduced compared to N8 leaves, suggesting that reduction in the total Chl content contributes to leaf color variation at the physiological level. Plastid ultrastructure of C1 possessed abnormal thylakoid membranes with loss of starch granule, large number of vesicles, and numerous plastoglobuli. The C1 rice also exhibited thinner stacked grana, which was caused by a reduction in the number of thylakoid membranes per granum. Thus, the different Chl a/b ratio of C1 may reflect the abnormal plastid development and function. Transcriptional analysis identified 23 differentially expressed genes (DEGs) and 671 transcription factors (TFs) that were involved in Chl metabolism, chloroplast development, cell division, and photosynthesis. The transcriptome profile and DEGs revealed that the gene encoding PsbR (PSII core protein) was down-regulated, therefore suggesting that the lower in light-harvesting complex proteins are responsible for the lower photosynthetic capacity in C1. In addition, expression level of cell division protein (FtsZ) genes were significantly reduced in C1, causing chloroplast division defect. A total of 19 DEGs were identified based on KEGG pathway assignment involving Chl biosynthesis pathway. Among these DEGs, the GluTR gene was down-regulated, whereas the UROD, CPOX, and MgCH genes were up-regulated. Observation through qPCR suggested that later stages of Chl biosynthesis were enhanced in C1, whereas the early stages were inhibited. Plastid structure analysis together with transcriptomic analysis suggested that the Chl a/b ratio was amplified both by the reduction in Chl contents accumulation, owning to abnormal chloroplast development, and by the enhanced conversion of Chl b to Chl a. Moreover, the results indicated the same Chl-cycle pattern in the wild-type and C1 rice, indicating another Chl b degradation pathway. Furthermore, the results demonstrated that normal grana stacking, along with the absence of Chl b and greatly reduced levels of Chl a in C1, provide evidence to support the conclusion that other factors along with LHCII proteins are involved in grana stacking. The findings of this study provide insight into the molecular mechanisms that underlie different Chl a/b ratios in rice.

Keywords: Chl-deficient mutant, grana stacked, photosynthesis, RNA-Seq, transcriptomic analysis

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Authors: N. A. Kazemi Sefat, M. M. Mohammadi, J. Hadjati, S. Talebi, M. Ajami, H. Daneshvar

Abstract:

Colorectal cancer metastases result in a significant number of cancer related deaths. Histone deacetylase (HDAC) inhibitors induce growth arrest and apoptosis in a variety of human cancer cells. Sodium butyrate (SB) is a short chain fatty acid, belongs to HDAC inhibitors which is released in the colonic lumen as a consequence of fiber fermentation. In this study, we are about to assess the effect of sodium butyrate on HCT116 human colorectal carcinoma cell line. The viability of cells was measured by microscopic morphologic study and MTT assay. After 48 hours, treatments more than 10 mM lead to cell injury in HCT116 by increasing cell granulation and decreasing cell adhesion (p>0.05). After 72 hours, treatments at 10 mM and more lead to significant cell injury (p<0.05). Our results may suggest that the gene expression which is contributed in cell proliferation and apoptosis has been changed under pressure of HDAC inhibition.

Keywords: colorectal cancer, sodium butyrate, cytotoxicity, MTT

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