Search results for: multi-element expression pattern

Authors: Shengjun Yan, Xuan Wang

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Water level changes in a shallow lake always introduce dramatic land pattern changes. To achieve sustainable ecosystem service, it is necessary to evaluate habitat quality dynamic and its spatio-temporal variation resulted from water level changes, which can provide a scientific basis for protection of biodiversity and planning of wetland ecological system. Landsat data in the spring was chosen to obtain landscape data at different times based on the high, moderate and low water level of Baiyangdian Shallow Lake. We used the InVEST to evaluate the habitat quality, habitat degradation, and habitat scarcity. The result showed that: 1) the water level of shallow lake changes from high to low lead to an obvious landscape pattern changes and habitat degradation, 2) the most change area occurred in northwestward and southwest of Baiyangdian Shallow Lake, which there was a 21 percent of suitable habitat and 42 percent of moderately suitable habitat lost. Our findings show that the changes of water level in the shallow lake would have a strong relationship with the habitat quality.

Keywords: habitat quality, habitat degradation, water level changes, shallow lake

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Authors: Anna Yagodnitsyna, Alexander Kovalev, Artur Bilsky

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The efficiency of certain technological processes in two-phase microfluidics such as emulsion production, nanomaterial synthesis, nitration, extraction processes etc. depends on two-phase flow regimes in microchannels. For practical application in chemistry and biochemistry it is very important to predict the expected flow pattern for a large variety of fluids and channel geometries. In the case of immiscible liquids, the plug flow is a typical and optimal regime for chemical reactions and needs to be predicted by empirical data or correlations. In this work flow patterns of immiscible liquid-liquid flow in a rectangular microchannel with T-junction are investigated. Three liquid-liquid flow systems are considered, viz. kerosene – water, paraffin oil – water and castor oil – paraffin oil. Different flow patterns such as parallel flow, slug flow, plug flow, dispersed (droplet) flow, and rivulet flow are observed for different velocity ratios. New flow pattern of the parallel flow with steady wavy interface (serpentine flow) has been found. It is shown that flow pattern maps based on Weber numbers for different liquid-liquid systems do not match well. Weber number multiplied by Ohnesorge number is proposed as a parameter to generalize flow maps. Flow maps based on this parameter are superposed well for all liquid-liquid systems of this work and other experiments. Plug length and velocity are measured for the plug flow regime. When dispersed liquid wets channel walls plug length cannot be predicted by known empirical correlations. By means of particle tracking velocimetry technique instantaneous velocity fields in a plug flow regime were measured. Flow circulation inside plug was calculated using velocity data that can be useful for mass flux prediction in chemical reactions.

Keywords: flow patterns, hydrodynamics, liquid-liquid flow, microchannel

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Authors: Yalong Jiang, Zheru Chi

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In this paper, we study the factors which determine the capacity of a Convolutional Neural Network (CNN) model and propose the ways to evaluate and adjust the capacity of a CNN model for best matching to a specific pattern recognition task. Firstly, a scheme is proposed to adjust the number of independent functional units within a CNN model to make it be better fitted to a task. Secondly, the number of independent functional units in the capsule network is adjusted to fit it to the training dataset. Thirdly, a method based on Bayesian GAN is proposed to enrich the variances in the current dataset to increase its complexity. Experimental results on the PASCAL VOC 2010 Person Part dataset and the MNIST dataset show that, in both conventional CNN models and capsule networks, the number of independent functional units is an important factor that determines the capacity of a network model. By adjusting the number of functional units, the capacity of a model can better match the complexity of a dataset.

Keywords: CNN, convolutional neural network, capsule network, capacity optimization, character recognition, data augmentation, semantic segmentation

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Authors: Muhammad Usman

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Pattern extraction has been done in past to extract hidden and interesting patterns from large datasets. Recently, advancements are being made in these techniques by providing the ability of multi-level mining, effective dimension reduction, advanced evaluation and visualization support. This paper focuses on reviewing the current techniques in literature on the basis of these parameters. Literature review suggests that most of the techniques which provide multi-level mining and dimension reduction, do not handle mixed-type data during the process. Patterns are not extracted using advanced algorithms for large datasets. Moreover, the evaluation of patterns is not done using advanced measures which are suited for high-dimensional data. Techniques which provide visualization support are unable to handle a large number of rules in a small space. We present a theoretical model to handle these issues. The implementation of the model is beyond the scope of this paper.

Keywords: association rule mining, data mining, data warehouses, visualization of association rules

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Authors: Simona Perga, Chiara Beltramo, Floriana Fruscione, Isabella Martini, Federica Cavallo, Federica Riccardo, Paolo Buracco, Selina Iussich, Elisabetta Razzuoli, Katia Varello, Lorella Maniscalco, Elena Bozzetta, Angelo Ferrari, Paola Modesto

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Introduction: Human and canine melanoma have common clinical, histologic characteristics making dogs a good model for comparative oncology. The identification of specific genes and a better understanding of the genetic landscape, signaling pathways, and tumor–microenvironmental interactions involved in the cancer onset and progression is essential for the development of therapeutic strategies against this tumor in both species. In the present study, the differential expression of genes in spontaneously occurring canine melanoma and in paired normal tissue was investigated by targeted RNAseq. Material and Methods: Total RNA was extracted from 17 canine malignant melanoma (CMM) samples and from five paired normal tissues stored in RNA-later. In order to capture the greater genetic variability, gene expression analysis was carried out using two panels (Qiagen): Human Immuno-Oncology (HIO) and Mouse-Immuno-Oncology (MIO) and the miSeq platform (Illumina). These kits allow the detection of the expression profile of 990 genes involved in the immune response against tumors in humans and mice. The data were analyzed through the CLCbio Genomics Workbench (Qiagen) software using the Canis lupus familiaris genome as a reference. Data analysis were carried out both comparing the biologic group (tumoral vs. healthy tissues) and comparing neoplastic tissue vs. paired healthy tissue; a Fold Change greater than two and a p-value less than 0.05 were set as the threshold to select interesting genes. Results and Discussion: Using HIO 63, down-regulated genes were detected; 13 of those were also down-regulated comparing neoplastic sample vs. paired healthy tissue. Eighteen genes were up-regulated, 14 of those were also down-regulated comparing neoplastic sample vs. paired healthy tissue. Using the MIO, 35 down regulated-genes were detected; only four of these were down-regulated, also comparing neoplastic sample vs. paired healthy tissue. Twelve genes were up-regulated in both types of analysis. Considering the two kits, the greatest variation in Fold Change was in up-regulated genes. Dogs displayed a greater genetic homology with humans than mice; moreover, the results have shown that the two kits are able to detect different genes. Most of these genes have specific cellular functions or belong to some enzymatic categories; some have already been described to be correlated to human melanoma and confirm the validity of the dog as a model for the study of molecular aspects of human melanoma.

Keywords: animal model, canine melanoma, gene expression, spontaneous tumors, targeted RNAseq

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Authors: Kyle Phillips, Ndiko Ludidi

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Global climate change has resulted in altered rainfall patterns, which has resulted in annual losses in maize crop yields due to drought. Therefore it is important to produce maize cultivars that are more drought-tolerant, which is not an easily accomplished task as plants have a plethora of physical and biochemical adaptation methods. One such mechanism is the drought-induced expression of enzymatic and non-enzymatic proteins which assist plants to resist the effects of drought on their growth and development. One of these proteins is AtRD22 which has been identified in Arabidopsis thaliana. Using an in silico approach, a maize protein with 48% sequence homology to AtRD22 has been identified. This protein appears to be localized in the extracellular matrix, similarly to AtRD22. Promoter analysis of the encoding gene reveals cis-acting elements suggestive of induction of the gene’s expression by abscisic acid (ABA). Semi-quantitative transcriptomic analysis of the putative maize RD22 has revealed an increase in transcript levels after the exposure to drought. Current work elucidates the effect of up-regulation and silencing of the maize RD22 gene on the tolerance of maize to drought. The potential role of the maize RD22 gene in maize drought tolerance can be used as a tool to improve food security.

Keywords: abscisic acid, drought-responsive cis-acting elements, maize drought tolerance, RD22

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Authors: Rafia S. Al-lamki, Jun Wang, Simon Pacey, Jordan Pober, John R. Bradley

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Tumor necrosis factor alpha (TNF), signaling through TNFR2, may act an autocrine growth factor for renal tubular epithelial cells. Clear cell renal carcinomas (ccRCC) contain cancer stem cells (CSCs) that give rise to progeny which form the bulk of the tumor. CSCs are rarely in cell cycle and, as non-proliferating cells, resist most chemotherapeutic agents. Thus, recurrence after chemotherapy may result from the survival of CSCs. Therapeutic targeting of both CSCs and the more differentiated bulk tumor populations may provide a more effective strategy for treatment of RCC. In this study, we hypothesized that TNFR2 signaling will induce CSCs in ccRCC to enter cell cycle so that treatment with ligands that engage TNFR2 will render CSCs susceptible to chemotherapy. To test this hypothesis, we have utilized wild-type TNF (wtTNF) or specific muteins selective for TNFR1 (R1TNF) or TNFR2 (R2TNF) to treat either short-term organ cultures of ccRCC and adjacent normal kidney (NK) tissue or cultures of CD133+ cells isolated from ccRCC and adjacent NK, hereafter referred to as stem cell-like cells (SCLCs). The effect of cyclophosphamide (CP), currently an effective anticancer agent, was tested on CD133+SCLCs from ccRCC and NK before and after R2TNF treatment. Responses to TNF were assessed by flow cytometry (FACS), immunofluorescence, and quantitative real-time PCR, TUNEL, and cell viability assays. Cytotoxic effect of CP was analyzed by Annexin V and propidium iodide staining with FACS. In addition, we assessed the effect of TNF on isolated SCLCs differentiation using a three-dimensional (3D) culture system. Clinical samples of ccRCC contain a greater number SCLCs compared to NK and the number of SCSC increases with higher tumor grade. Isolated SCLCs show expression of stemness markers (oct4, Nanog, Sox2, Lin28) but not differentiation markers (cytokeratin, CD31, CD45, and EpCAM). In ccRCC organ cultures, wtTNF and R2TNF increase CD133 and TNFR2 expression and promote cell cycle entry whereas wtTNF and R1TNF increase TNFR1 expression and promote cell death of SCLCs. Similar findings are observed in SCLCs isolated from NK but the effect was greater in SCLCs isolated from ccRCC. Application of CP distinctly triggered apoptotic and necrotic cell death in SLCSs pre-treatment with R2TNF as compared to CP treatment alone, with SCLCs from ccRCC more sensitive to CP compared to SLCS from NK. Furthermore, TNF promotes differentiation of SCLCs to an epithelial phenotype in 3D cultures, confirmed by cytokeratin expression and loss of stemness markers Nanog and Sox2. The differentiated cells show positive expression of TNF and TNFR2. These findings provide evidence that selective engagement of TNFR2 drive CSCs to cell proliferation/differentiation, and targeting of cycling cells with TNFR2 agonist in combination with anti-cancer agents may be a potential therapy for RCC.

Keywords: cancer stem cells, ccRCC, cell cycle, cell death, TNF, TNFR1, TNFR2, CD133

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

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

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

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Authors: Lali Shanshiashvili, Marika Chikviladze, Nino Mamulashvili, Maia Sepashvili, Nana Narmania, David Mikeladze

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Purpose: During demyelinating inflammatory diseases and after the damage of the myelin sheet, myelin-derived proteins, including myelin basic protein (MBP), are secreted into the extracellular space. MBP shows extensive post-translational modifications, including the deimination of arginine residues. Deiminated MBP is structurally less ordered, susceptible to proteolytic attack, and more immunogenic than the unmodified one. It is hypothesized that MBP could change the inflammatory response in astrocytes. Methods: MBP was isolated and purified from bovine brain white matter. Primary astrocyte cultures were prepared from whole brains of 2-day-old Wistar rats. For evaluation of glutamate uptake/release in astrocytes following treatment of cells with MBP charge isomers, Glutamate Assay Kit was used. The expression of EAAT-2 (excitatory amino acid transporters), peroxisome proliferator-activated receptor gamma (PPAR- γ), inhibitor of nuclear factor kappa B (IkB), and high mobility group protein B1 (HMGB1) in astrocytes were assayed by Western Blot analysis. Results: This study investigated the action of deiminated isomer (C8) on the cultured primary astrocytes and compared its effects with the effects of unmodified C1 isomers. The study found that C8 and C1 MBP differently act on the uptake and release of glutamate in astrocytes: nonmodified C1 MBP increases the uptake of glutamate and does not change the release, whereas C8 decreases the release of glutamate but does not alter the uptake. Nevertheless, both isomers increased the expression of PPAR-γ and EAAT2 in the same intensity. However, immunostaining and Western Blots of cell lysates showed a decrease of IkB and increased expression of HMGB1 after the treatment of astrocytes by C8. Moreover, in the presence of C8, astrocytes release more nitric oxide than unmodified C1 isomers. Conclusion: These data suggest that the deiminated isomer of MBP evokes an inflammatory response and enhances the ability of astrocytes to release proinflammatory mediators through activation of NF-kB after the breakdown of myelin sheets. Acknowledgment: This research was supported by the SRNSF Georgia RF17_534 grant.

Keywords: myelin basic protein, glutamate, deimination, astrocytes, inflammation

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Authors: Sina Mahdavi

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Background and Objective: Multiple sclerosis (MS) is an inflammatory autoimmune disease of the CNS that affects the myelination process in the central nervous system (CNS). Complex interactions of various "environmental or infectious" factors may act as triggers in autoimmunity and disease progression. The association between viral infections, especially Human Herpesvirus 6 (HHV-6), and MS is one potential cause that is not well understood. In this study, we aim to summarize the available data on HHV-6 infection in MS disease progression. Materials and Methods: For this study, the keywords "Multiple sclerosis", " Human Herpesvirus 6 ", and "central nervous system" in the databases PubMed and Google Scholar between 2017 and 2022 were searched, and 12 articles were chosen, studied, and analyzed. Results: HHV 6 tends towards TCD 4+ lymphocytes and enters the CNS due to the weakening of the blood-brain barrier due to inflammatory damage. Following the observation that the HHV-6 U24 protein has a seven amino acid sequence with myelin basic protein, which is one of the main components of the myelin sheath, it could cause a molecular mimicry mechanism followed by cross-reactivity. Reactivation of HHV-6 in the CNS can cause the release of proinflammatory cytokines, including TNF-α, leading to immune-mediated demyelination in patients with MS. Conclusion: There is a high expression of endogenous retroviruses during the course of MS, which indicates the relationship between HHV-6 and MS, and that this virus can play a role in the development of MS by creating an inflammatory state. Therefore, measures to modulate the expression of HHV-6 may be effective in reducing inflammatory processes in demyelinated areas of MS patients.

Keywords: multiple sclerosis, human herpesvirus 6, central nervous system, autoimmunity

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Authors: Faheema Khan

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To investigate the ability of sensitive and tolerant genotype of Glycine max to adapt to a saline environment in a field, we examined the growth performance, water relation and activities of antioxidant enzymes in relation to photosynthetic rate, chlorophyll a fluorescence, photosynthetic pigment concentration, protein and proline in plants exposed to salt stress. Ten soybean genotypes (Pusa-20, Pusa-40, Pusa-37, Pusa-16, Pusa-24, Pusa-22, BRAGG, PK-416, PK-1042, and DS-9712) were selected and grown hydroponically. After 3 days of proper germination, the seedlings were transferred to Hoagland’s solution (Hoagland and Arnon 1950). The growth chamber was maintained at a photosynthetic photon flux density of 430 μmol m−2 s−1, 14 h of light, 10 h of dark and a relative humidity of 60%. The nutrient solution was bubbled with sterile air and changed on alternate days. Ten-day-old seedlings were given seven levels of salt in the form of NaCl viz., T1 = 0 mM NaCl, T2=25 mM NaCl, T3=50 mM NaCl, T4=75 mM NaCl, T5=100 mM NaCl, T6=125 mM NaCl, T7=150 mM NaCl. The investigation showed that genotype Pusa-24, PK-416 and Pusa-20 appeared to be the most salt-sensitive. genotypes as inferred from their significantly reduced length, fresh weight and dry weight in response to the NaCl exposure. Pusa-37 appeared to be the most tolerant genotype since no significant effect of NaCl treatment on growth was found. We observed a greater decline in the photosynthetic variables like photosynthetic rate, chlorophyll fluorescence and chlorophyll content, in salt-sensitive (Pusa-24) genotype than in salt-tolerant Pusa-37 under high salinity. Numerous primers were verified on ten soybean genotypes obtained from Operon technologies among which 30 RAPD primers shown high polymorphism and genetic variation. The Jaccard’s similarity coefficient values for each pairwise comparison between cultivars were calculated and similarity coefficient matrix was constructed. The closer varieties in the cluster behaved similar in their response to salinity tolerance. Intra-clustering within the two clusters precisely grouped the 10 genotypes in sub-cluster as expected from their physiological findings.Salt tolerant genotype Pusa-37, was further analysed by 2-Dimensional gel electrophoresis to analyse the differential expression of proteins at high salt stress. In the Present study, 173 protein spots were identified. Of these, 40 proteins responsive to salinity were either up- or down-regulated in Pusa-37. Proteomic analysis in salt-tolerant genotype (Pusa-37) led to the detection of proteins involved in a variety of biological processes, such as protein synthesis (12 %), redox regulation (19 %), primary and secondary metabolism (25 %), or disease- and defence-related processes (32 %). In conclusion, the soybean plants in our study responded to salt stress by changing their protein expression pattern. The photosynthetic, biochemical and molecular study showed that there is variability in salt tolerance behaviour in soybean genotypes. Pusa-24 is the salt-sensitive and Pusa-37 is the salt-tolerant genotype. Moreover this study gives new insights into the salt-stress response in soybean and demonstrates the power of genomic and proteomic approach in plant biology studies which finally could help us in identifying the possible regulatory switches (gene/s) controlling the salt tolerant genotype of the crop plants and their possible role in defence mechanism.

Keywords: glycine max, salt stress, RAPD, genomic and proteomic variability

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Authors: Yuliya Kovalenko

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Given the social nature of people, it is interesting to explore strategies of responding to psycho-traumatic situations in individuals of different ethnic and religious identity. This would allow to substantially expand the idea of human behavior in general, and coping behavior, in particular. This paper investigated the weighted impact of ethnic and religious identities on the patterns of coping behavior. This cross-cultural research empirically revealed intergroup differences in coping strategies and behavior in the samples of young students and teachers of different ethnic identities (Egyptians N=216 and Ukrainians N=109) and different religious identities (Egyptian Muslims N=147 and Christians, including Egyptian Christians N=68 and Ukrainian Christians N = 109). The empirical data were obtained using the questionnaires SACS and COPE. Statistical analysis and interpretation of the results were performed with IBM SPSS-23.0. It was found that, compared to the religious identity, the ethnic identity of the subjects appeared more predictive of coping behavior. It was shown that the constant exchange of information and the unity of biological and social contributed to a more homogeneous picture in the society where Christians and Muslims were integrated into a single cultural space. It was concluded that depending on their ethnic identity, individuals would form a specific hierarchy of coping strategies resulting in a specific pattern of coping with certain stressors. The Egyptian subjects revealed the following pattern of coping with various kinds of academic stress: 'seeking social support', 'problem solving', 'adapting', 'seeking information'. The coping pattern demonstrated by the Ukrainian subjects could be presented as 'seeking information', 'adapting', 'seeking social support', 'problem solving'. There was a tendency in the group of Egyptians to engage in more collectivist coping strategies (with the predominant coping strategy 'religious coping'), in contrast to the Ukrainians who displayed more individualistic coping strategies (with 'planning' and 'active coping' as the mostly used coping strategies). At the same time, it was obvious that Ukrainians should not be unambiguously attributed to the individualistic coping behavior due to their reliance on 'seeking social support' and 'social contact'. The final conclusion was also drawn from the peculiarities of developing religious identity, including religiosity, in Egyptians (formal religious education of both Muslims and Christians) and Ukrainians (more spontaneous process): Egyptians seem to learn to resort to the religious coping, which could be an indication that, in principle, it is possible and necessary to train individuals in desirable coping behavior.

Keywords: coping behavior, cross-cultural research, ethnic and religious identity, hierarchical pattern of coping

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Authors: Uswah Khairuddin, Rubiyah Yusof, Nenny Ruthfalydia Rosli

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This paper presents a comparative study between k-Nearest Neighbour (k-NN) and Multi-Layer Perceptron Neural Network (MLP-NN) classifier using Genetic Algorithm (GA) as feature selector for wood recognition system. The features have been extracted from the images using Grey Level Co-Occurrence Matrix (GLCM). The use of GA based feature selection is mainly to ensure that the database used for training the features for the wood species pattern classifier consists of only optimized features. The feature selection process is aimed at selecting only the most discriminating features of the wood species to reduce the confusion for the pattern classifier. This feature selection approach maintains the ‘good’ features that minimizes the inter-class distance and maximizes the intra-class distance. Wrapper GA is used with k-NN classifier as fitness evaluator (GA-kNN). The results shows that k-NN is the best choice of classifier because it uses a very simple distance calculation algorithm and classification tasks can be done in a short time with good classification accuracy.

Keywords: feature selection, genetic algorithm, optimization, wood recognition system

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Authors: Sumaira Zafar, Arjumand Zaidi

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During past few years, several floods have adversely affected the areas along lower Indus River. Besides other climate related anomalies, rapidly increasing urbanization and blockage of natural drains due to siltation or encroachments are two other critical causes that may be responsible for these disasters. Due to flat topography of river Indus plains and blockage of natural waterways, drainage of storm water takes time adversely affecting the crop health and soil properties of the area. Government of Sindh is taking a keen interest in revival of natural drainage network in the province and has initiated this work under Sindh Irrigation and Drainage Authority. In this paper, geospatial techniques are used to analyze landuse/land-cover changes of Larkana district over the past three decades (1980-present) and their impact on natural drainage system. Satellite derived Digital Elevation Model (DEM) and topographic sheets (recent and 1950) are used to delineate natural drainage pattern of the district. The urban landuse map developed in this study is further overlaid on drainage line layer to identify the critical areas where the natural floodwater flows are being inhibited by urbanization. Rainfall and flow data are utilized to identify areas of heavy flow, whereas, satellite data including Landsat 7 and Google Earth are used to map previous floods extent and landuse/cover of the study area. Alternatives to natural drainage systems are also suggested wherever possible. The output maps of natural drainage pattern can be used to develop a decision support system for urban planners, Sindh development authorities and flood mitigation and management agencies.

Keywords: geospatial techniques, satellite data, natural drainage, flood, urbanization

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Authors: Massimiliano Biagini, Marco Spinsanti, Gabriella De Angelis, Sara Tomei, Ilaria Ferlenghi, Maria Scarselli, Alessia Biolchi, Alessandro Muzzi, Brunella Brunelli, Silvana Savino, Marzia M. Giuliani, Isabel Delany, Paolo Costantino, Rino Rappuoli, Vega Masignani, Nathalie Norais

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The gram-negative bacterium Neisseria meningitidis serogroup B (MenB) is an exclusively human pathogen representing the major cause of meningitides and severe sepsis in infants and children but also in young adults. This pathogen is usually present in the 30% of healthy population that act as a reservoir, spreading it through saliva and respiratory fluids during coughing, sneezing, kissing. Among surface-exposed protein components of this diplococcus, factor H binding protein is a lipoprotein proved to be a protective antigen used as a component of the recently licensed Bexsero vaccine. fHbp is a highly variable meningococcal protein: to reflect its remarkable sequence variability, it has been classified in three variants (or two subfamilies), and with poor cross-protection among the different variants. Furthermore, the level of fHbp expression varies significantly among strains, and this has also been considered an important factor for predicting MenB strain susceptibility to anti-fHbp antisera. Different methods have been used to assess fHbp expression on meningococcal strains, however, all these methods use anti-fHbp antibodies, and for this reason, the results are affected by the different affinity that antibodies can have to different antigenic variants. To overcome the limitations of an antibody-based quantification, we developed a quantitative Mass Spectrometry (MS) approach. Selected Reaction Monitoring (SRM) recently emerged as a powerful MS tool for detecting and quantifying proteins in complex mixtures. SRM is based on the targeted detection of ProteoTypicPeptides (PTPs), which are unique signatures of a protein that can be easily detected and quantified by MS. This approach, proven to be highly sensitive, quantitatively accurate and highly reproducible, was used to quantify the absolute amount of fHbp antigen in total extracts derived from 105 clinical isolates, evenly distributed among the three main variant groups and selected to be representative of the fHbp circulating subvariants around the world. We extended the study at the genetic level investigating the correlation between the differential level of expression and polymorphisms present within the genes and their promoter sequences. The implications of fHbp expression on the susceptibility of the strain to killing by anti-fHbp antisera are also presented. To date this is the first comprehensive fHbp expression profiling in a large panel of Neisseria meningitidis clinical isolates driven by an antibody-independent MS-based methodology, opening the door to new applications in vaccine coverage prediction and reinforcing the molecular understanding of released vaccines.

Keywords: quantitative mass spectrometry, Neisseria meningitidis, vaccines, bexsero, molecular epidemiology

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Authors: Rita Darmayanti

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This study aims at investigating the discourse pattern and structure of research article abstracts. The characteristics of the language used in abstracts written by non-native English-speaking (NNES) novice researchers are mainly examined in terms of rhetorical moves and the degree of variability of the rhetorical features as indicated by the structure of clauses and the linguistic features of the text. To this end, 20 abstracts written by undergraduate students of the accounting department at the State Polytechnic of Malang in 2018-2019 were employed as the data of this study. Findings showed that the most frequently used pattern of the rhetorical move is I(Introduction)-P(Purpose)-M(Method)-Pr(Product or Result)-C(Conclusion) with the significant use of active sentence and present and past tense. The findings of the study are projected to be utilized for evaluating the quality of students’ abstracts and generating a pedagogical proposal of ESP writing course or at least providing a critical review of current practices in ESP program intended for non-native English students at tertiary level.

Keywords: rhetorical features, rhetorical moves, non-native English-speaking novice researchers, research abstract

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Authors: Qing Zhang, Janak L. Pathak, Macro N. Helder, Richard T. Jaspers, Yin Xiao

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Introduction: Nanomaterial-based bone regeneration is greatly influenced by the immune microenvironment. Tissue-engineered nanomaterials mediate the inflammatory response of macrophages to regulate bone regeneration. Silica nanoparticles have been widely used in tissue engineering-related preclinical studies. However, the effect of topological features on the surface of silica nanoparticles on the immune response of macrophages remains unknown. Purposes: The aims of this research are to compare the influences of normal and pollen-like silica nano-surface topography on macrophage immune responses and to obtain insight into their potential regulatory mechanisms. Method: Macrophages (RAW 264.7 cells) were exposed to mesoporous silica nanoparticles with normal morphology (MSNs) and pollen-like morphology (PMSNs). RNA-seq, RT-qPCR, and LSCM were used to assess the changes in expression levels of immune response-related genes and proteins. SEM and TEM were executed to evaluate the contact and adherence of silica nanoparticles by macrophages. For the assessment of the immunomodulation-mediated osteogenic potential, BMSCs were cultured with conditioned medium (CM) from LPS pre-stimulated macrophage cultures treated with MSNs or PMSNs. Osteoimmunomodulatory potential of MSNs and PMSNs in vivo was tested in a mouse cranial bone osteolysis model. Results: The results of the RNA-seq, RT-qPCR, and LSCM assays showed that PMSNs inhibited the expression of pro-inflammatory genes and proteins in macrophages. SEM images showed distinct macrophage membrane surface binding patterns of MSNs and PMSNs. MSNs were more evenly dispersed across the macrophage cell membrane, while PMSNs were aggregated. PMSNs-induced macrophage anti-inflammatory response was associated with upregulation of the cell surface receptor CD28 and inhibition of ERK phosphorylation. TEM images showed that both MSNs and PMSNs could be phagocytosed by macrophages, and inhibiting nanoparticle phagocytosis did not affect the expression of anti-inflammatory genes and proteins. Moreover, PMSNs-induced conditioned medium from macrophages enhanced BMP-2 expression and osteogenic differentiation mBMSCs. Similarly, PMSNs prevented LPS-induced bone resorption via downregulation of inflammatory reaction. Conclusions: PMSNs can promote bone regeneration by modulating osteoimmunological processes through surface topography. The study offers insights into how surface physical contact cues can modulate the regulation of osteoimmunology and provides a basis for the application of nanoparticles with pollen-like morphology to affect immunomodulation in bone tissue engineering and regeneration.

Keywords: physical contact, osteoimmunology, macrophages, silica nanoparticles, surface morphology, membrane receptor, osteogenesis, inflammation

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Authors: Georgi Bebrov, Rozalina Dimova

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In the field of quantum secure communication, there is no evaluation that characterizes quantum secure communication (QSC) protocols in a complete, general manner. The current paper addresses the problem concerning the lack of such an evaluation for QSC protocols by introducing an optimality evaluation, which is expressed as the average over the three main parameters of QSC protocols: efficiency, security, and practicality. For the efficiency evaluation, the common expression of this parameter is used, which incorporates all the classical and quantum resources (bits and qubits) utilized for transferring a certain amount of information (bits) in a secure manner. By using criteria approach whether or not certain criteria are met, an expression for the practicality evaluation is presented, which accounts for the complexity of the QSC practical realization. Based on the error rates that the common quantum attacks (Measurement and resend, Intercept and resend, probe attack, and entanglement swapping attack) induce, the security evaluation for a QSC protocol is proposed as the minimum function taken over the error rates of the mentioned quantum attacks. For the sake of clarity, an example is presented in order to show how the optimality is calculated.

Keywords: quantum cryptography, quantum secure communcation, quantum secure direct communcation security, quantum secure direct communcation efficiency, quantum secure direct communcation practicality

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Authors: Redouane Tlemsani, Redouane, Belkacem Kouninef, Abdelkader Benyettou

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In this paper, our system is a Markovien system which we can see it like a Dynamic Bayesian Networks. One of the major interests of these systems resides in the complete training of the models (topology and parameters) starting from training data. The Bayesian Networks are representing models of dubious knowledge on complex phenomena. They are a union between the theory of probability and the graph theory in order to give effective tools to represent a joined probability distribution on a set of random variables. The representation of knowledge bases on description, by graphs, relations of causality existing between the variables defining the field of study. The theory of Dynamic Bayesian Networks is a generalization of the Bayesians networks to the dynamic processes. Our objective amounts finding the better structure which represents the relationships (dependencies) between the variables of a dynamic bayesian network. In applications in pattern recognition, one will carry out the fixing of the structure which obliges us to admit some strong assumptions (for example independence between some variables).

Keywords: Arabic on line character recognition, dynamic Bayesian network, pattern recognition, networks

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Authors: Evans Iyamu

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Genes encoding hydrophobins play distinct roles at different stages of the life cycle of fungi, and they foster hyphal attachment to surfaces. The hydrophobin Sc4 is known to provide a hydrophobic membrane lining of the gas channels within Schizophyllum commune fruiting bodies. Here, we cultivated non-fruiting, monokaryotic S. commune 12-43 on glass surfaces that could be verified by micrography. Differential gene expression profiling of nine hydrophobin genes and the hydrophobin-like sc15 gene by quantitative PCR showed significant up-regulation of sc4 when S. commune was attached to glass surfaces, also confirmed with RNA-Seq data analysis. Another silicate, namely quartz sand, was investigated, and induction of sc4 was seen as well. The up-regulation of the hydrophobin gene sc4 may indicate involvement in S. commune hyphal attachment to glass as well as quartz surfaces. We propose that the covering of hyphae by Sc4 allows for direct interaction with the hydrophobic surfaces of silicates and that differential functions of specific hydrophobin genes depend on the surface interface involved. This study could help with the clarification of the biological functions of hydrophobins in natural surroundings, including hydrophobic surface attachment. Therefore, the analysis of growth on glass serves as a basis for understanding S. commune interaction with glass surfaces while providing the possibility to visualize the interaction microscopically.

Keywords: hydrophobin, structured glass surfaces, differential gene expression, quartz sand

Procedia PDF Downloads 121

Authors: Peter Jean-Paul, Shanaz Wahid

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The problem of division by zero can be stated as: “what is the value of 0 x 1/0?” This expression has been considered undefined by mathematicians because it can have two equally valid solutions either 0 or 1. Recently semi-structured complex number set was invented to solve “division by zero”. However, whilst the number set had some merits it was considered to have a poor theoretical foundation and did not provide a quality solution to “division by zero”. Moreover, the set lacked consistency in simple algebraic calculations producing contradictory results when dividing by zero. To overcome these issues this research starts by treating the expression " 0 x 1/0" as a quantum mechanical system that produces two tangled results 0 and 1. Dirac Notation (a tool from quantum mechanics) was then used to redefine the unstructured unit p in semi-structured complex numbers so that p represents the superposition of two results (0 and 1) and collapses into a single value when used in algebraic expressions. In the process, this paper describes a new number set called Quantum Semi-structured Complex Numbers that provides a valid solution to the problem of “division by zero”. This research shows that this new set (1) forms a “Field”, (2) can produce consistent results when solving division by zero problems, (3) can be used to accurately describe systems whose mathematical descriptions involve division by zero. This research served to provide a firm foundation for Quantum Semi-structured Complex Numbers and support their practical use.

Keywords: division by zero, semi-structured complex numbers, quantum mechanics, Hilbert space, Euclidean space

Procedia PDF Downloads 157

Authors: Montasser Mohamed Abdelwahab Mahmoud, Abdelwahab Saber Esawi

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The language of the Qur’an has a wide range of understanding, reflection, and meanings. Therefore, translation of the Qur’an is inevitably nothing but a translation of the interpretation of the meanings of the Qur’an. It requires special competencies and skills for translators so that they can get close to the intended meaning of the verse of the Qur’an and convey it with precision. In the Arabic language, the verbal noun “AlMasdar” is a very important derivative that properly expresses the verbal idea in the form of a noun. It sounds the same as the base form of the verb with minor changes in the vowel pattern. It is one of the important topics in morphology. The morphologists divided verbal nouns into auditory and analogical, and they stated that that the verbal nouns (Masadars) originating from three-letter verbs are auditory, although they set controls for some of them in order to preserve them. As for the lexicographers, they mentioned the verbal nouns while talking about the lexical materials, and in some cases, their explanation of them exceeded that made by the morphologists, especially in their discussion of structures that the morphologists did not refer to in their books. The verb kafara (disbelief), for example, has three patterns, namely: al-kufْr, al-kufrān, and al-kufūr, and it was mentioned in the Holy Qur’an with different connotations. The verb ṣāma (fasted) with his two patterns (al-ṣaūm and al-ṣīām) was mentioned in the Holy Qur’an while their semantic meaning is different. The problem discussed in this research paper lied in the "linguistic loss" committed by translators when dealing with Islamic religious texts, especially the Qur'an. The study tried to identify the strategy adopted by translators of the Holy Qur'an in translating words that were classified as verbal nouns through analyzing the translation rendered by five translations of the Qur’an into English: Yusuf Ali, Pickthall, Mohsin Khan, Muhammad Sarwar, and Shakir. This study was limited to the verbal nouns in the Quraan that originate from three-letter verbs and have different semantic meanings.

Keywords: pattern, three-letter verbs, translation of the Quran, verbal nouns

Procedia PDF Downloads 161

Authors: Amira Kalifa, Faïek Errouissi

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The seasonal changes and the daily activity of Stomoxys calcitrans (Diptera: Muscidae) were examined, using Vavoua traps, in a dairy cattle farm in Zaouiet Sousse, the Sahel area of Tunisia during May 2014 to October 2014. Over this period, a total of 4366 hematophagous diptera were captured and Stomoxys calcitrans was the most commonly trapped species (96.52%). Analysis of the seasonal activity, showed that S.calcitrans is bivoltine, with two peaks: a significant peak is recorded in May-June, during the dry season, and a second peak at the end of October, which is quite weak. This seasonal pattern would depend on climatic factors, particularly the temperature of the manure and that of the air. The activity pattern of Stomoxys calcitrans was diurnal with seasonal variations. The daily rhythm shows a peak between 11:00 am to 15:00 pm in May and between 11:00 am to 17:00 pm in June. These vector flies are important pests of livestock in Tunisia, where they are known as a mechanical vector of several pathogens and have a considerable economic and health impact on livestock. A better knowledge of their ecology is a prerequisite for more efficient control measures.

Keywords: cattle farm, daily rhythm, Stomoxys calcitrans, seasonal activity

Procedia PDF Downloads 272

Authors: A. Alyami, S. Christmas, K. Neeltje, G. Pollakis, B. Paxton, Z. Al-Bayati

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The Human leukocyte antigen-G (HLA-G) molecule plays an important role in immunomodulation. To date, 16 untranslated regions (UTR) HLA-G haplotypes have been previously defined by sequenced SNPs in the coding region. From these, UTR-1, UTR-2, UTR-3, UTR-4, UTR-5, UTR-6 and UTR-7 are the most frequent 3’UTR haplotypes at the global level. UTR-1 is associated with higher levels of soluble HLA-G and HLA-G expression, whereas UTR-5 and UTR-7 are linked with low levels of soluble HLA-G and HLA-G expression. Human immunodeficiency virus type 1 (HIV-1) infection results in the progressive loss of immune function in infected individuals. The virus escape mechanism typically includes T lymphocytes and NK cell recognition and lyses by classical HLA-A and B down-regulation, which has been associated with non-classical HLA-G molecule up-regulation, respectively. We evaluated the haplotypes of the HLA-G 3′ untranslated region frequencies observed in three HIV-1 groups from the Netherlands and their susceptibility to develop infection. The three groups are made up of mainly men who have sex with men (MSM), injection drug users (IDU) and a high-risk-seronegative (HRSN) group. DNA samples were amplified with published primers prior sequencing. According to our results, the low expresser frequencies show higher in HRSN compared to other groups. This is indicating that 3’UTR polymorphisms may be identified as potential prognostic biomarkers to determine susceptibility to HIV.

Keywords: Human leukocyte antigen-G (HLA-G) , men who have sex with men (MSM), injection drug users (IDU), high-risk-seronegative (HRSN) group, high-untranslated region (UTR)

Procedia PDF Downloads 153

Authors: Naif Al-Jomah, Falah H Al-Mohanna, Abdelilah Aboussekhra

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Active breast cancer-associated fibroblasts (CAFs), the most influential cells in breast tumor microenvironment, express/secrete high levels of the proinvasive/metastatic interleukin-6 (IL-6). Therefore, we have tested here the effect of the IL-6 receptor (IL-6R) inhibitor tocilizumab (TCZ; Actemra) on different active breast CAFs. We have shown that TCZ potently and persistently suppresses the expression of various CAF biomarkers, namely α-SMA, SDF-1 as well as the STAT3 pathway and its downstream target AUF1. TCZ also inhibited the proliferation, migration and invasion abilities of active breast CAF cells. Additionally, TCZ repressed the ability of CAF cells in promoting epithelial-to-mesenchymal transition, and enhancing the migratory/invasive and proliferative capacities of breast cancer cells in vitro. Importantly, these findings were confirmed in orthotopic humanized breast tumors in mice. Furthermore, TCZ suppressed the expression of the pro-angiogenic factor VEGF-A and its transactivator HIF-1α in CAF cells, and consequently inhibited the angiogenic-promoting effect of active CAFs both in vitro and in orthotopic tumor xenografts. These results indicate that inhibition of the IL-6/STAT3/AUF1 pathway by TCZ can normalize active breast CAFs and suppress their paracrine pro-carcinogenic effects, which paves the way toward development of specific CAF-targeting therapy, badly needed for more efficient breast cancer treatments.

Keywords: angiogenesis, interleukin-6, paracrine, cancer-associated fibroblasts

Procedia PDF Downloads 97

Authors: Seunghwan Seo, Woo-Seok Lee, Ji-Sun Shin, Young Kyoung Rhee, Chang-Won Cho, Hee-Do Hong, Kyung-Tae Lee

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Doenjang, known as traditional Korean food, is product of a natural mixed fermentation process carried out by lactic acid bacteria (LAB). Lactobacillus sakei K040706 (K040706) has been accepted as the most populous LAB in over ripened doenjang. Recently, we reported the immunostimulatory effects of K040706 in RAW 264.7 macrophages and in a cyclophosphamide-induced mouse model. In this study, we investigated the ameliorative effects of K040706 in a dextran sulfate sodium (DSS)-induced colitis mouse model. We induced colitis using DSS in 5-week-ICR mice over 14 days with or without 0.1, 1 g/kg/day K040706 orally. The body weight, stool consistency, and gross bleeding were recorded for determination of the disease activity index (DAI). At the end of treatment, animals were sacrificed and colonic tissues were collected and subjected to histological experiments and myeloperoxidase (MPO) accumulation, cytokine determination, qRT-PCR and Western blot analysis. Results showed that K040706 significantly attenuated DSS-induced DAI score, shortening of colon length, enlargement of spleen and immune cell infiltrations into colonic tissues. Histological examinations indicated that K040706 suppressed edema, mucosal damage, and the loss of crypts induced by DSS. These results were correlated with the restoration of tight junction protein expression, such as, ZO-1 and occludin in K040706-treated mice. Moreover, K040706 reduced the abnormal secretions and mRNA expressions of pro-inflammatory mediators, such as nitric oxide (NO), tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and interleukin-6 (IL-6). DSS-induced mRNA expression of intercellular adhesion molecule (ICAM) and vascular cell adhesion molecule (VCAM) in colonic tissues was also downregulated by K040706 treatment. Furthermore, K040706 suppressed the protein and mRNA expression of toll-like receptor 4 (TLR4) and phosphorylation of NF-κB and signal transducer and activator of transcription 3 (STAT3). These results suggest that K040706 has an anti-colitic effect by inhibition of intestinal inflammatory responses in DSS-induced colitic mice.

Keywords: Lactobacillus sakei, NF-κB, STAT3, ulcerative colitis

Procedia PDF Downloads 325

Authors: Dina Fatmawati, Sofia Mubarika, Mae Sri Wahyuningsih

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Chemotherapy for breast cancer is largely ineffective, but innovative combinations of chemotherapeutic agents and natural compounds represent a promising strategy. In our previous study, the combination of Doxorubicin (Dox) and ethanolic extract of Dioscorea esculenta tuber ((EED) was found to have a synergistic effect on T47D human breast cancer cell line. In this study, we investigated the apoptotic effect of the combination on T47D human breast cancer cells and normal fibroblasts cell line and its effects on the expression of Caspase-3 and cleaved poly (ADP-Ribose) Polymerase-1 (cPARP-1) protein. T47D cell lines and fibroblasts cells were treated with the combination of Dox and EED. Apoptotic effect of the combination was determined using flow cytrometry assay. Protein expressions were determined by immunocytochemistry staining. The percentage of apoptotic cells were significantly higher in T47D cell lines (75%) than that of in fibroblast cells (23%). The expression of Caspase 3 (84.53%) and cPARP-1 (83.36%) were significantly higher in the cancer cell lines than those of normal cells. These results indicate that the combination of doxorubicin and Dioscorea esculenta is a promising candidate for the treatment of breast cancer cells.

Keywords: Dioscorea esculenta, Doxorubicin, apoptosis, immunocytochemistry, cancer cells

Procedia PDF Downloads 458

Authors: P. Narrima, C. Y. Looi, M. A. Mohd, H. M. Ali

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Persea declinata (Bl.) Kosterm is a member of the Lauraceae family, widely distributed in Southeast Asia. It is from the same genus with avocado (Persea americana Mill), which is widely consumed as food and for medicinal purposes. In the present study, we examined the anticancer properties of Persea declinata (Bl.) Kosterm bark methanolic crude extract (PDM). PDM exhibited a potent antiproliferative effect in MCF-7 human breast cancer cells, with an IC50 value of 16.68 µg/mL after 48h of treatment. We observed that PDM caused cell cycle arrest and subsequent apoptosis in MCF-7 cells, as exhibited by increased population at G0/G1 phase, higher lactate dehydrogenase (LDH) release, and DNA fragmentation. Mechanistic studies showed that PDM caused significant elevation in ROS production, leading to perturbation of mitochondrial membrane potential, cell permeability, and activation of caspases-3/7. On the other hand, real-time PCR and Western blot analysis showed that PDM treatment increased the expression of the proapoptotic molecule, Bax, but decreased the expression of prosurvival proteins, Bcl-2 and Bcl-xL, in a dose-dependent manner. These findings imply that PDM could inhibit proliferation in MCF-7 cells via cell cycle arrest and apoptosis induction, indicating its potential as a therapeutic agent worthy of further development.

Keywords: antiproliferative, apoptosis, MCF-7 human breast cancer, Persea declinata

Procedia PDF Downloads 243

Authors: E. L. Albuquerque, U. L. Fulco, G. S. Ourique

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The focus of this work is on the numerical investigation of the charge transport properties of the de novo-designed alpha3 polypeptide, as well as in its variants, all of them probed by gene engineering. The theoretical framework makes use of a tight-binding model Hamiltonian, together with ab-initio calculations within quantum chemistry simulation. The alpha3 polypeptide is a 21-residue with three repeats of the seven-residue amino acid sequence Leu-Glu-Thr-Leu-Ala-Lys-Ala, forming an alpha–helical bundle structure. Its variants are obtained by Ala→Gln substitution at the e (5th) and g (7th) position, respectively, of the alpha3 polypeptide amino acid sequence. Using transmission electron microscopy and atomic force microscopy, it was observed that the alpha3 polypeptide and one of its variant do have the ability to form fibrous assemblies, while the other does not. Our main aim is to investigate whether or not the biased alpha3 polypeptide and its variants can be also identified by quantum charge transport measurements through current-voltage (IxV) curves as a pattern to characterize their fibrous assemblies. It was observed that each peptide has a characteristic current pattern, which may be distinguished by charge transport measurements, suggesting that it might be a useful tool for the development of biosensors.

Keywords: charge transport properties, electronic transmittance, current-voltage characteristics, biological sensor

Procedia PDF Downloads 665

Authors: Nandhana Vivek, Bhaskar Gogoi, Ayyavu Mahesh

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Breast cancer metastasis plays a key role in cancer progression and fatality. The present study examines the potential causes of metastasis in breast cancer by investigating the novel interactions between genes and their pathways. The gene expression profile of GSE99394, GSE1246464, and GSE103865 was downloaded from the GEO data repository to analyze the differentially expressed genes (DEGs). Protein-protein interactions, target factor interactions, pathways and gene relationships, and functional enrichment networks were investigated. The proliferation pathway was shown to be highly expressed in breast cancer progression and metastasis in all three datasets. Gene Ontology analysis revealed 11 DEGs as gene targets to control breast cancer metastasis: LYN, DLGAP5, CXCR4, CDC6, NANOG, IFI30, TXP2, AGTR1, MKI67, and FTH1. Upon studying the function, genomic and proteomic data, and pathway involvement of the target genes, DLGAP5 proved to be a promising candidate due to it being highly differentially expressed in all datasets. The study takes a unique perspective on the avenues through which DLGAP5 promotes metastasis. The current investigation helps pave the way in understanding the role DLGAP5 plays in metastasis, which leads to an increased incidence of death among breast cancer patients.

Keywords: genomics, metastasis, microarray, cancer

Procedia PDF Downloads 96