Search results for: DNA sequence analysis

Authors: Victor Emeli, Akansel Cosgun

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This paper explores the navigation among movable obstacles (NAMO) problem and proposes joint path and push planning: which path to take and in what direction the obstacles should be pushed at, given a start and goal position. We present a planning algorithm for selecting a path and the obstacles to be pushed, where a rapidly-exploring random tree (RRT)-based heuristic is employed to calculate a minimal collision path. When it is necessary to apply a pushing force to slide an obstacle out of the way, the planners leverage means-end analysis through a dynamic physics simulation to determine the sequence of linear pushes to clear the necessary space. Simulation experiments show that our approach finds solutions in higher clutter percentages (up to 49%) compared to the straight-line push planner (37%) and RRT without pushing (18%).

Keywords: motion planning, path planning, push planning, robot navigation

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Authors: Nora Geczy

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In today’s architectural practice, during the process of designing public, educational, healthcare and cultural space, human-centered architectural designs helping spatial orientation, safe space usage and the appropriate spatial sequence of actions are gaining increasing importance. Related to the methodology of designing public buildings, several scientific experiments in spatial recognition, spatial analysis and spatial psychology with regard to the components of space producing mental and physiological effects have been going on at the Department of Architectural Design and the Interdisciplinary Student Workshop (IDM) at the Széchenyi István University, Győr since 2013. Defining the creation of preventive, anticipated spatial design and the architectural tools of spatial comfort of public buildings and their practical usability are in the limelight of our research. In the experiments applying eye-tracking cameras, we studied the way public spaces are used, especially concentrating on the characteristics of spatial behaviour, orientation, recognition, the sequence of actions, and space usage. Along with the role of mental maps, human perception, and interaction problems in public spaces (at railway stations, galleries, and educational institutions), we analyzed the spatial situations influencing psychological and ergonomic factors. We also analyzed the eye movements of the experimental subjects in dynamic situations, in spatial procession, using stairs and corridors. We monitored both the consequences and the distorting effects of the ocular dominance of the right eye on spatial orientation; we analyzed the gender-based differences of women and men’s orientation, stress-inducing spaces, spaces affecting concentration and the spatial situation influencing territorial behaviour. Based on these observations, we collected the components of creating public interior spaces, which -according to our theory- contribute to the optimal usability of public spaces. We summed up our research in criteria for design, including 10 points. Our further goals are testing design principles needed for optimizing orientation and space usage, their discussion, refinement, and practical usage.

Keywords: architecture, eye-tracking, human-centered spatial design, public interior spaces, visual perception

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Authors: Keiko Naito, Y. Nakashima, S. Yamauchi, Y. Kunitani, Y. Ishigami, K. Numata, M. Mizobe, Y. Homma, J. Takahashi, T. Inoue, T. Shiga, H. Funakoshi

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Background: A presence of severe acidemia, defined as pH < 7.2, is common during endotracheal intubation for critically ill patients in the emergency department (ED). Severe acidemia is widely recognized as a predisposing factor for intubation failure. However, it is unclear that acidemic condition itself actually makes endotracheal intubation more difficult. We aimed to evaluate if a presence of severe acidemia before intubation is associated with the lower first attempt intubation success rate in the ED. Methods: This is a retrospective observational cohort study in the ED of an urban hospital in Japan. The collected data included patient demographics, such as age, sex, and body mass index, presence of one or more factors of modified LEMON criteria for predicting difficult intubation, reasons for intubation, blood gas levels, airway equipment, intubation by emergency physician or not, and the use of the rapid sequence intubation technique. Those with any of the following were excluded from the analysis: (1) no blood gas drawn before intubation, (2) cardiopulmonary arrest, and (3) under 18 years of age. The primary outcome was the first attempt intubation success rates between a severe acidemic patients (SA) group and a non-severe acidemic patients (NA) group. Logistic regression analysis was used to test the first attempt success rates for intubations between those two groups. Results: Over 5 years, a total of 486 intubations were performed; 105 in the SA group and 381 in the NA group. The univariate analysis showed that the first attempt intubation success rate was lower in the SA group than in the NA group (71.4% vs 83.5%, p < 0.01). The multivariate logistic regression analysis identified that severe acidemia was significantly associated with the first attempt intubation failure (OR 1.9, 95% CI 1.03-3.68, p = 0.04). Conclusions: A presence of severe acidemia before endotracheal intubation lowers the first attempt intubation success rate in the ED.

Keywords: acidemia, airway management, endotracheal intubation, first-attempt intubation success rate

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Authors: Siwapech Silapaprayoon, Januluk Khanobdee, Sompid Samipak

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Chili peppers are the fruits of Capsicum pepper plants well known for their fiery burning sensation on the tongue after consumption. They are members of the Solanaceae or common nightshade family along with potato, tomato and eggplant. Thai cuisine has gained popularity for its distinct flavors due to usages of various spices and its heat from the addition of chili pepper. Though being used in little quantity for each dish, chili pepper holds a special place in Thai cuisine. There are many varieties of chili peppers in Thailand, and thirty accessions were collected at Rajamangala University of Technology Lanna, Lampang, Thailand. To effectively manage any germplasm it is essential to know the diversity and relationships among members. Thirty-six Inter Simple Sequence Repeat (ISSRs) DNA markers were used to analyze the germplasm. Total of 335 polymorphic bands was obtained giving the average of 9.3 alleles per marker. Unweighted pair-group mean arithmetic method (UPGMA) clustering of data using NTSYS-pc software indicated that the accessions showed varied levels of genetic similarity ranging from 0.57-1.00 similarity coefficient index indicating significant levels of variation. At SM coefficient of 0.81, the germplasm was separated into four groups. Phenotypic variation was discussed in context of phylogenetic tree clustering.

Keywords: diversity, germplasm, Chili pepper, ISSR

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Authors: Sulaiman Yunus

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The need for modeling response to urban fire disaster cannot be over emphasized, as recurrent fire outbreaks have gutted most cities of the world. This necessitated the need for a prompt and efficient response system in order to mitigate the impact of the disaster. Promptness, as a function of time, is seen to be the fundamental determinant for efficiency of a response system and magnitude of a fire disaster. Delay, as a result of several factors, is one of the major determinants of promptgness of a response system and also the magnitude of a fire disaster. Response Delay Model (RDM) intends to bridge the gap in urban fire disaster response system through incorporating and synchronizing the delay moments in measuring the overall efficiency of a response system and determining the magnitude of a fire disaster. The model identified two delay moments (pre-notification and Intra-reflex sequence delay) that can be elastic and collectively plays a significant role in influencing the efficiency of a response system. Due to variation in the elasticity of the delay moments, the model provides for measuring the length of delays in order to arrive at a standard average delay moment for different parts of the world, putting into consideration geographic location, level of preparedness and awareness, technological advancement, socio-economic and environmental factors. It is recommended that participatory researches should be embarked on locally and globally to determine standard average delay moments within each phase of the system so as to enable determining the efficiency of response systems and predicting fire disaster magnitudes.

Keywords: delay moment, fire disaster, reflex sequence, response, response delay moment

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Authors: Javeria Ahmad, Ayesha Maryam, Zahid Rizwan, Nadeem Nasir, Yasir Nawab, Hafiz Shehbaz Ahmad

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Mitigation of electromagnetic interference (EMI) through thin, lightweight, and cost-effective materials is critical for electronic appliances as well as human health. The present research work discusses the design of composites that are suitable to minimize EMI through various stacking sequences. The carbon fibers reinforced composite structures impregnated with dielectric (MWCNTs) and magnetic nanofillers (Fe₂O₃) were developed to investigate their microwave absorption properties. The composite structure comprising a single type of nanofillers, each of MWCNTs & Fe₂O₃, was developed, and then their layers were stacked over each other with various stacking sequences to investigate the best stacking sequence, which presents good microwave absorption characteristics. A vector network analyzer (VNA) was used to analyze the microwave absorption properties of these developed composite structures. The composite structures impregnated with the layers of a dielectric nanofiller and sandwiched between the layers of a magnetic nanofiller show the highest EMI shielding value of 59 dB and a dielectric conductivity of 35 S/cm in the frequency range of 0.1 to 13.6 GHz. The results also demonstrate that the microwave absorption properties of the developed composite structures were dominant over reflection properties. The absence of an external peak in X-ray diffraction (XRD), marked the purity of the added nanofillers.

Keywords: nanocomposites, microwave absorption, EMI shielding, skin depth, reflection loss

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Authors: Noury Bakrim

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Formalization is indeed a foundational Mathematical Linguistics as demonstrated by the pioneering works. While dialoguing with this frame, we nonetheless propone, in our approach of language as a real object, a mathematical linguistics/biosemiotics defined as a dialectical synthesis between induction and computational deduction. Therefore, relying on the parametric interaction of cycles, rules, and features giving way to a sub-hypothetic biological point of view, we first hypothesize a factorial equation as an explanatory principle within Category Mathematics of the Ergobrain: our computation proposal of Universal Grammar rules per cycle or a scalar determination (multiplying right/left columns of the determinant matrix and right/left columns of the logarithmic matrix) of the transformable matrix for rule addition/deletion and cycles within representational mapping/cycle heredity basing on the factorial example, being the logarithmic exponent or power of rule deletion/addition. It enables us to propone an extension of minimalist merge/label notions to a Language Merge (as a computing principle) within cycle recursion relying on combinatorial mapping of rules hierarchies on external Entax of the Event Sequence. Therefore, to define combinatorial maps as language merge of features and combinatorial hierarchical restrictions (governing, commanding, and other rules), we secondly hypothesize from our results feature/hierarchy exponentiation on graph representation deriving from Gromov's Symbolic Dynamics where combinatorial vertices from Fe are set to combinatorial vertices of Hie and edges from Fe to Hie such as for all combinatorial group, there are restriction maps representing different derivational levels that are subgraphs: the intersection on I defines pullbacks and deletion rules (under restriction maps) then under disjunction edges H such that for the combinatorial map P belonging to Hie exponentiation by intersection there are pullbacks and projections that are equal to restriction maps RM₁ and RM₂. The model will draw on experimental biomathematics as well as structural frames with focus on Amazigh and English (cases from phonology/micro-semantics, Syntax) shift from Structure to event (especially Amazigh formant principle resolving its morphological heterogeneity).

Keywords: rule/cycle addition/deletion, bio-mathematical methodology, general merge calculation, feature exponentiation, combinatorial maps, event sequence

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Authors: Morteza Haghi, Cigdem Yilmazbas, Ayse Zeynep Uysal, Melisa Tepedelen, Gozde Turkoz Bakirci

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Today, the increase in plastic waste accumulation is an inescapable consequence of environmental pollution; the disposal of these wastes has caused a significant problem. Variable methods have been utilized; however, biodegradation is the most environmentally friendly and low-cost method. Accordingly, the present study aimed to isolate the bacteria capable of biodegradation of plastics. In doing so, we applied the liquid carbon-free basal medium (LCFBM) prepared with deionized water for the isolation of bacterial species obtained from soil samples taken from the Izmir Menemen region. Isolates forming biofilms on plastic were selected and named (PLB3, PLF1, PLB1B) and subjected to a degradation test. FTIR analysis, 16s rDNA amplification, sequencing, identification of isolates were performed. Finally, at the end of the process, a mass loss of 16.6% in PLB3 isolate and 25% in PLF1 isolate was observed, while no mass loss was detected in PLB1B isolate. Only PLF1 and PLB1B created transparent zones on plastic texture. Considering the FTIR result, PLB3 changed plastic structure by 13.6% and PLF1 by 17%, while PLB1B did not change the plastic texture. According to the 16s rDNA sequence analysis, FLP1, PLB1B, and PLB3 isolates were identified as Streptomyces albogriseolus, Enterobacter cloacae, and Klebsiella pneumoniae, respectively.

Keywords: polyethylene, biodegradation, bacteria, 16s rDNA, FTIR

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Authors: Masih Moore, Saeed Ziaei-Rad

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In this study, the stability characteristics of a bi-stable composite plate with different asymmetric composition are considered. The interest in bi-stable structures comes from their ability that these structures can have two different stable equilibrium configurations to define a discrete set of stable shapes. The structures can easily change the first stable shape to the second one by a simple snap action. The main purpose of the current research is to consider the effect of including resin layers on the stability characteristics of bi-stable laminates. To this end and In order to determine the magnitude of the loads that are responsible for snap through and snap back phenomena between two stable shapes of the laminate, a non-linear finite element method (FEM) is utilized. An experimental investigation was also carried out to study the critical loads that caused snapping between two different stable shapes. Several specimens were manufactured from T300/5208 graphite-epoxy with [0/90]T, [-30/60]T, [-20/70]T asymmetric stacking sequence. In order to create an accurate finite element model, different thickness of resin layers created during the manufacturing process of the laminate was measured and taken into account. The geometry of each lamina and the resin layers was characterized by optical microscopy from different locations of the laminates thickness. The exact thickness of each lamina and the resin layer in all specimens with [0/90]T,[-30/60]T, [-20/70]T stacking sequence were determined by using image processing technique.

Keywords: bi-stable laminates, finite element method, graphite-epoxy plate, snap behavior

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Authors: Khabat Barkhordari, Ali Mohammad Arabzadeh

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Hepatitis delta virus (HDV) is a RNA virus that needs the function of hepatitis B virus (HBV) for its propagation and assembly. Infection by HDV can occur spontaneously with HBV infection and cause acute hepatitis or develop as secondary infection in HBV suffering patients. Based on genome sequence analysis, HDV has several genotypes which show broad geographic and diverse clinical features. The aim of current study is determine the prevalence of hepatitis delta virus genotype in patients with positive HBsAg in Kerman province of Iran. This cross-sectional study a total of 400 patients with HBV infection attending the clinic center of Besat from 2012 to 2014 were included. We carried out ELISA to detect anti-HDV antibodies. Those testing positive were analyzed further for HDV-RNA and for genotyping using restriction fragment length polymorphism (RFLP) and RT-nested PCR- sequencing. Among 400 patients in this study, 67 cases (16.75 %) were containing anti-HDV antibody which we found HDV RNA in just 7 (1.75%) serum samples. Analysis of these 7 positive HDV showed that all of them have genotype I. According to current study the HDV prevalence in Kerman is higher than the reported prevalence of 6.6% for Iran as a whole and clade 1 (genotype 1) is the predominant clade of HDV in Kerman.

Keywords: genotyping, hepatitis delta virus, molecular epidemiology, Kerman, Iran

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Authors: Cecilia Jatu, Adventino

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Gedangsari is located in Gunungkidul, Yogyakarta Province, which has several criteria to be used as a new geosite object. The research area is located in the southern mountain zone of Java, composed of 5 rock formations with Oligocene up to Middle Miocene age. The purpose of this study is to reveal the potential of geotourism and the geoheritage to be proposed as a new geosite and to make a geosite map of Gedangsari. The research method used is descriptive data collection and which includes quantitative geological data collection, geotourism, and heritage sites, then supported by petrographic analysis, geological structure, geological mapping, and SWOT analysis. The geological data proved that Gedangsari consists of igneous rock (intrusion), pyroclastic rock, and sediment rock. This condition caused many varieties and particular geomorphological platform. Geotourism that include in Gedangsari are Luweng Sampang Canyon, Gedangsari Bouma Sequence, Watugajah Columnar Joint, Gedangsari Marine Fan Sediment, and Tegalrejo Waterfall. There is also Tegalrejo Village, which can be considered as geoheritage site because of its culture and batik traditional cloth. The results of the SWOT analysis, Gedangsari geosite must be developed and appropriately promoted in order to improve the existence. The development of geosite area will have a significant impact that improve the economic growth of the surrounding community and can be used by the government as base information for sustainable development. In addition, the making of an educational map about the geological conditions and geotourism location of the Gedangsari geosite can increase the people's knowledge about Gedangsari.

Keywords: Gedangsari, geoheritage, geotourism, geosite

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Authors: Rajkumar Ghosh

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Earthquakes pose significant risks to human life and infrastructure, highlighting the importance of effective earthquake mitigation strategies. Traditional earthquake modelling and mitigation efforts have largely focused on the primary fault segments and their slip behaviour. However, earthquakes can exhibit complex rupture dynamics, including out-of-sequence thrust (OOST) events, which occur on secondary or subsidiary faults. This abstract examines the impact of OOST dynamics on earthquake mitigation strategies and their implications for hazard assessment and disaster planning. OOST events challenge conventional seismic hazard assessments by introducing additional fault segments and potential rupture scenarios that were previously unrecognized or underestimated. Consequently, these events may increase the overall seismic hazard in affected regions. The study reviews recent case studies and research findings that illustrate the occurrence and characteristics of OOST events. It explores the factors contributing to OOST dynamics, such as stress interactions between fault segments, fault geometry, and mechanical properties of fault materials. Moreover, it investigates the potential triggers and precursory signals associated with OOST events to enhance early warning systems and emergency response preparedness. The abstract also highlights the significance of incorporating OOST dynamics into seismic hazard assessment methodologies. It discusses the challenges associated with accurately modelling OOST events, including the need for improved understanding of fault interactions, stress transfer mechanisms, and rupture propagation patterns. Additionally, the abstract explores the potential for advanced geophysical techniques, such as high-resolution imaging and seismic monitoring networks, to detect and characterize OOST events. Furthermore, the abstract emphasizes the practical implications of OOST dynamics for earthquake mitigation strategies and urban planning. It addresses the need for revising building codes, land-use regulations, and infrastructure designs to account for the increased seismic hazard associated with OOST events. It also underscores the importance of public awareness campaigns to educate communities about the potential risks and safety measures specific to OOST-induced earthquakes. This sheds light on the impact of out-of-sequence thrust dynamics in earthquake mitigation. By recognizing and understanding OOST events, researchers, engineers, and policymakers can improve hazard assessment methodologies, enhance early warning systems, and implement effective mitigation measures. By integrating knowledge of OOST dynamics into urban planning and infrastructure development, societies can strive for greater resilience in the face of earthquakes, ultimately minimizing the potential for loss of life and infrastructure damage.

Keywords: earthquake mitigation, out-of-sequence thrust, seismic, satellite imagery

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Authors: P. Vit, J. Uddin, V. Zuccato, F. Maza, E. Schievano

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In Ecuador honeys are produced by Apis mellifera and stingless bees (Meliponini). We studied honey produced in beeswax combs by Apis mellifera, and honey produced in pots by Geotrigona and Scaptotrigona bees. Chloroform extracts of honey were obtained for fast NMR spectra. The 1D spectra were acquired at 298 K, with a 600 MHz NMR Bruker instrument, using a modified double pulsed field gradient spin echoes (DPFGSE) sequence. Signals of 1H NMR spectra were integrated and used as inputs for PCA, PLS-DA analysis, and labelled sets of classes were successfully identified, enhancing the separation between the three groups of honey according to the entomological origin: A. mellifera, Geotrigona and Scaptotrigona. This procedure is therefore recommended for authenticity test of honey in Ecuador.

Keywords: Apis mellifera, honey, 1H NMR, entomological origin, meliponini

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Authors: Arsyam Mawardi, Sony Suhandono, Azzania Fibriani, Fifi Fitriyah Masduki

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Malaria is an infectious disease caused by Plasmodium sp. This disease has a high prevalence in Indonesia, especially in Jayapura. The vaccine that is currently being developed has not been effective in overcoming malaria. This is due to the high polymorphism in the Plasmodium genome especially in areas that encode Plasmodium surface proteins. Merozoite Surface Protein 1 (MSP1) Plasmodium falciparum is a surface protein that plays a role in the invasion process in human erythrocytes through the interaction of Glycophorin A protein receptors and sialic acid in erythrocytes with Reticulocyte Binding Proteins (RBP) and Duffy Adhesion Protein (DAP) ligands in merozoites. MSP1 can be targeted to be a specific antigen and predicted epitope area which will be used for the development of diagnostic and malaria vaccine therapy. MSP1 consists of 17 blocks, each block is dimorphic, and has been marked as the K1 and MAD20 alleles. Exceptions only in block 2, because it has 3 alleles, among others K1, MAD20 and RO33. These polymorphisms cause allelic variations and implicate the severity of patients infected P. falciparum. In addition, polymorphism of MSP1 in Jayapura isolates has not been reported so it is interesting to be further identified and projected as a specific antigen. Therefore, in this study, we analyzed the allele polymorphism as well as detected the MSP1 epitope antigen candidate on block 2 P. falciparum. Clinical samples of selected malaria patients followed the consecutive sampling method, examining malaria parasites with blood preparations on glass objects observed through a microscope. Plasmodium DNA was isolated from the blood of malarial positive patients. The block 2 MSP1 gene was amplified using PCR method and cloned using the pGEM-T easy vector then transformed to TOP'10 E.coli. Positive colonies selection was performed with blue-white screening. The existence of target DNA was confirmed by PCR colonies and DNA sequencing methods. Furthermore, DNA sequence analysis was done through alignment and formation of a phylogenetic tree using MEGA 6 software and insilico analysis using IEDB software to predict epitope candidate for P. falciparum. A total of 15 patient samples have been isolated from Plasmodium DNA. PCR amplification results show the target gene size about ± 1049 bp. The results of MSP1 nucleotide alignment analysis reveal that block 2 MSP1 genes derived from the sample of malarial patients were distributed in four different allele family groups, K1 (7), MAD20 (1), RO33 (0) and MSP1_Jayapura (10) alleles. The most commonly appears of the detected allele is MSP1_Jayapura single allele. There was no significant association between sex variables, age, the density of parasitemia and alel variation (Mann Whitney, U > 0.05), while symptomatic signs have a significant difference as a trigger of detectable allele variation (U < 0.05). In this research, insilico study shows that there is a new epitope antigen candidate from the MSP1_Jayapura allele and it is predicted to be recognized by B cells with 17 amino acid lengths in the amino acid sequence 187 to 203.

Keywords: epitope candidate, insilico analysis, MSP1 P. falciparum, polymorphism

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Authors: Tudor Barbu

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An automatic moment-based texture segmentation approach is proposed in this paper. First, we describe the related work in this computer vision domain. Our texture feature extraction, the first part of the texture recognition process, produces a set of moment-based feature vectors. For each image pixel, a texture feature vector is computed as a sequence of area moments. Second, an automatic pixel classification approach is proposed. The feature vectors are clustered using some unsupervised classification algorithm, the optimal number of clusters being determined using a measure based on validation indexes. From the resulted pixel classes one determines easily the desired texture regions of the image.

Keywords: image segmentation, moment-based, texture analysis, automatic classification, validation indexes

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Authors: Kalaumari Mayoral-Peña, Ana I. Montejano-Montelongo, Josué Reyes-Muñoz, Gonzalo A. Ortiz-Mancilla, Mayrin Rodríguez-Cruz, Víctor Hernández-Villalobos, Jesús A. Guzmán-López, Santiago García-Jacobo, Iván Licona-Vázquez, Grisel Fierros-Romero, Rosario Flores-Vallejo

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The group B-lactamic antibiotics include some of the most frequently used small drug molecules against bacterial infections. Nevertheless, an alarming decrease in their efficacy has been reported due to the emergence of antibiotic-resistant bacteria. Infections caused by bacteria expressing extended Spectrum B-lactamases (ESBLs) are difficult to treat and account for higher morbidity and mortality rates, delayed recovery, and high economic burden. According to the Global Report on Antimicrobial Resistance Surveillance, it is estimated that mortality due to resistant bacteria will ascend to 10 million cases per year worldwide. These facts highlight the importance of developing low-cost and readily accessible detection methods of drug-resistant ESBLs bacteria to prevent their spread and promote accurate and fast diagnosis. Bacterial detection is commonly done using molecular diagnostic techniques, where PCR stands out for its high performance. However, this technique requires specialized equipment not available everywhere, is time-consuming, and has a high cost. Loop-Mediated Isothermal Amplification (LAMP) is an alternative technique that works at a constant temperature, significantly decreasing the equipment cost. It yields double-stranded DNA of several lengths with repetitions of the target DNA sequence as a product. Although positive and negative results from LAMP can be discriminated by colorimetry, fluorescence, and turbidity, there is still a large room for improvement in the point-of-care implementation. DNA origami is a technique that allows the formation of 3D nanometric structures by folding a large single-stranded DNA (scaffold) into a determined shape with the help of short DNA sequences (staples), which hybridize with the scaffold. This research aimed to generate DNA origami structures using LAMP products as scaffolds to improve the sensitivity to detect ESBLs in point-of-care diagnosis. For this study, the coding sequence of the CTM-X-15 ESBL of E. coli was used to generate the LAMP products. The set of LAMP primers were designed using PrimerExplorerV5. As a result, a target sequence of 200 nucleotides from CTM-X-15 ESBL was obtained. Afterward, eight different DNA origami structures were designed using the target sequence in the SDCadnano and analyzed with CanDo to evaluate the stability of the 3D structures. The designs were constructed minimizing the total number of staples to reduce costs and complexity for point-of-care applications. After analyzing the DNA origami designs, two structures were selected. The first one was a zig-zag flat structure, while the second one was a wall-like shape. Given the sequence repetitions in the scaffold sequence, both were able to be assembled with only 6 different staples each one, ranging between 18 to 80 nucleotides. Simulations of both structures were performed using scaffolds of different sizes yielding stable structures in all the cases. The generation of the LAMP products were tested by colorimetry and electrophoresis. The formation of the DNA structures was analyzed using electrophoresis and colorimetry. The modeling of novel detection methods through bioinformatics tools allows reliable control and prediction of results. To our knowledge, this is the first study that uses LAMP products and DNA-origami in combination to delect ESBL-producing bacterial strains, which represent a promising methodology for diagnosis in the point-of-care.

Keywords: beta-lactamases, antibiotic resistance, DNA origami, isothermal amplification, LAMP technique, molecular diagnosis

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Authors: A. R. Manu, V. K. Agrawal, K. N. Balasubramanya Murthy

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Authentication is required in stored database systems so that only authorized users can access the data and related cloud infrastructures. This paper proposes an authentication technique using multi-factor and multi-dimensional authentication system with multi-level security. The proposed technique is likely to be more robust as the probability of breaking the password is extremely low. This framework uses a multi-modal biometric approach and SMS to enforce additional security measures with the conventional Login/password system. The robustness of the technique is demonstrated mathematically using a statistical analysis. This work presents the authentication system along with the user authentication architecture diagram, activity diagrams, data flow diagrams, sequence diagrams, and algorithms.

Keywords: design, implementation algorithms, performance, biometric approach

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Authors: R. M. Srivastava, Subbanna A.R.N.S, Md Abbas Ahmad, S. P.More, Shivashankar, B. Kalyanbabu

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The similar morphology associated with high genetic variability poses problems in phylogenetic studies of Helicoverpa armigera (Hubner). To identify genetic variation of North Western Himalayan population’s, partial (Mid to terminal region) cytochrome c oxidase subunit I (COX-1) gene was amplified and sequenced for three populations collected from Pantnagar, Almora, and Chinyalisaur. The alignment of sequences with other two populations, Nagpur representing central India population and Anhui, China representing complete COX-1 sequence revealed unanimity in middle region with eleven single nucleotide polymorphisms (SNPs) in Nagpur populations. However, the consensus is missing when approaching towards terminal region, which is associated with 15 each SNPs and pair base substitutions in Chinyalisaur populations. In minimum evolution tree, all the five populations were majorly separated into two clades, one comprising of only Nagpur population and the other with rest. Amongst, North Western populations, Chinyalisaur one is promising by farming a separate clade. The pairwise genetic distance ranges from 0.025 to 0.192 with the maximum between H. armigera populations of Nagpur and Chinyalisaur. This genetic isolation of populations can be attributed to a key role of topological barriers of weather and mountain ranges and temporal barriers due to cropping patterns.

Keywords: cytochrome c oxidase subunit I, northwestern Himalayan population, Helicoverpa armigera (Noctuidae: Lepidoptera), phylogenetic relationship, genetic variation

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Authors: N. Manjunatha, K. T. Rangswamy, N. Nagaraju, H. A. Prameela, P. Rudraswamy, M. Krishnareddy

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The identification of virus in cowpea especially potyviruses is confusing. Even though there are several studies on viruses causing diseases in cowpea, difficult to distinguish based on symptoms and serological detection. The differentiation of potyviruses considering as a constraint, the present study is initiated for molecular characterization, host plant resistance and epidemiology of the BCMV infecting cowpea. The etiological agent causing cowpea mosaic was identified as Bean Common Mosaic Virus (BCMV) on the basis of RT-PCR and electron microscopy. An approximately 750bp PCR product corresponding to coat protein (CP) region of the virus and the presence of long flexuous filamentous particles measuring about 952 nm in size typical to genus potyvirus were observed under electron microscope. The characterized virus isolate genome had 10054 nucleotides, excluding the 3’ terminal poly (A) tail. Comparison of polyprotein of the virus with other potyviruses showed similar genome organization with 9 cleavage sites resulted in 10 functional proteins. The pairwise sequence comparison of individual genes, P1 showed most divergent, but CP gene was less divergent at nucleotide and amino acid level. A phylogenetic tree constructed based on multiple sequence alignments of the polyprotein nucleotide and amino acid sequences of cowpea BCMV and potyviruses showed virus is closely related to BCMV-HB. Whereas, Soybean variant of china (KJ807806) and NL1 isolate (AY112735) showed 93.8 % (5’UTR) and 94.9 % (3’UTR) homology respectively with other BCMV isolates. This virus transmitted to different leguminous plant species and produced systemic symptoms under greenhouse conditions. Out of 100 cowpea genotypes screened, three genotypes viz., IC 8966, V 5 and IC 202806 showed immune reaction in both field and greenhouse conditions. Single marker analysis (SMA) was revealed out of 4 SSR markers linked to BCMV resistance, M135 marker explains 28.2 % of phenotypic variation (R2) and Polymorphic information content (PIC) value of these markers was ranged from 0.23 to 0.37. The correlation and regression analysis showed rainfall, and minimum temperature had significant negative impact and strong relationship with aphid population, whereas weak correlation was observed with disease incidence. Path coefficient analysis revealed most of the weather parameters exerted their indirect contributions to the aphid population and disease incidence except minimum temperature. This study helps to identify specific gaps in knowledge for researchers who may wish to further analyse the science behind complex interactions between vector-virus and host in relation to the environment. The resistant genotypes identified are could be effectively used in resistance breeding programme.

Keywords: cowpea, epidemiology, genotypes, virus

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Authors: R. Rama Kishore, Sunesh

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This paper presents an optimized, robust, and secured watermarking technique. The methodology used in this work is the combination of entropy and chaotic grid map. The proposed methodology incorporates Discrete Cosine Transform (DCT) on the host image. To improve the imperceptibility of the method, the host image DCT blocks, where the watermark is to be embedded, are further optimized by considering the entropy of the blocks. Chaotic grid is used as a key to reorder the DCT blocks so that it will further increase security while selecting the watermark embedding locations and its sequence. Without a key, one cannot reveal the exact watermark from the watermarked image. The proposed method is implemented on four different images. It is concluded that the proposed method is giving better results in terms of imperceptibility measured through PSNR and found to be above 50. In order to prove the effectiveness of the method, the performance analysis is done after implementing different attacks on the watermarked images. It is found that the methodology is very strong against JPEG compression attack even with the quality parameter up to 15. The experimental results are confirming that the combination of entropy and chaotic grid map method is strong and secured to different image processing attacks.

Keywords: digital watermarking, discreate cosine transform, chaotic grid map, entropy

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Authors: Radoslaw Lukasz Staniszewski

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The aim of the research was to verify lateral extent and thickness variability of individual limestone layers within early-Jurassic medium- and thick-bedded limestone interbedded with marlstones. Location: The main research area is located in the south-central part of Poland in the south-western part of Permo-Mesozoic margin of the Holy Cross Mountains. It includes outcroppings located on the line between Mieczyn and Wola Morawicka. The analyses were carried out on six profiles (Mieczyn, Gniezdziska, Tokarnia, Wola Morawicka, Morawica and Wolica) representing three early-Jurassic links: Jasna Gora layers, grey limestone, Morawica limestone. Additionally, an attempt was made to correlate the thickness sequence from the Holy Cross Mountains to the profile from the quarry in Zawodzie located 3 km east of Czestochowa. The distance between the outermost profiles is 122 km in a straight line. Methodology of research: The Callovian-Oxfordian border was taken as the reference point during the correlation. At the same time, ammonite-based stratigraphic studies were carried out, which allowed to identify individual packages in the remote outcroppings. The analysis of data collected during fieldwork was mainly devoted to the correlation of thickness sequences of limestone layers in subsequent profiles. In order to check the objectivity of the subsequent outcroppings, the profiles have been presented in the form of the thickness functions of the subsequent layers. The generated functions were auto-correlated, and the Pearson correlation coefficient was calculated. The next step in the research was to statistically determine the percentage increment of the individual layers thickness in the subsequent profiles, and on this basis to plot the function of relative carbonate productivity. Results: The result of the above-mentioned procedures consists in illustrating the extent of 34 rock layers across the examined area in demonstrating the repeatability of their success in subsequent outcroppings. It can also be observed that the thickness of individual layers in the Holy Cross Mountains is increasing from north-west towards south-east. Despite changes in the thickness of the layers in the profiles, their relations within the sequence remain constant. The lowest matching ratio of thickness sequence calculated using the Pearson correlation coefficient formula is 0.67, while the highest is 0.84. The thickness of individual layers changes between 4% and 230% over the examined area. Interpretation: Layers in the outcroppings covered by the research show continuity throughout the examined area and it is possible to precisely correlate them, which means that the process determining the formation of the layers was regional and probably included both the fringe of the Holy Cross Mountains and the north-eastern part of the Krakow-Czestochowa Jura Upland. Local changes in the sedimentation environment affecting the productivity of the subtidal carbonate factory only cause the thickness of the layers to change without altering the thickness proportions of the profiles. Based on the percentage of changes in the thickness of individual layers in the subsequent profiles, it can be concluded that the local productivity of the subtidal carbonate factory is increasing logarithmically.

Keywords: Oxfordian, Holy Cross Mountains, carbonate factory, Limestone

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Authors: Ravinder Singh, C Rajesh, Saroj Badhan, Shailendra Mishra, Ranjit Singh Kataria

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Heat shock protein 60 and 70 are crucial chaperones that guide appropriate folding of denatured proteins under heat stress conditions. HSP60 and HSP70 provide assistance in correct folding of a multitude of denatured proteins. The heat shock factors are the family of some transcription factors which controls the regulation of gene expression of proteins involved in folding of damaged or improper folded proteins during stress conditions. Under normal condition heat shock proteins bind with HSF-1 and act as its repressor as well as aids in maintaining the HSF-1’s nonactive and monomeric confirmation. The experimental protein structure for all these proteins in Bubalus bubalis is not known till date. Therefore computational approach was explored to identify three-dimensional structure analysis of all these proteins. In this study, an extensive in silico analysis has been performed including sequence comparison among species to comparative modeling of Bubalus bubalis HSP60, HSP70 and HSF-1 protein. The stereochemical properties of proteins were assessed by utilizing several scrutiny bioinformatics tools to ensure model accuracy. Further docking approach was used to study interactions between Heat shock proteins and HSF-1.

Keywords: Bubalus bubalis, comparative modelling, docking, heat shock protein

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Authors: Niloofar Fariborzi, Hamzeh Alipour, Kourosh Azizi, Neda Eskandarzade, Abozar Ghorbani

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The family Parvoviridae consists of a large diversity of single-stranded DNA viruses, which cause mild to severe diseases in both vertebrates and invertebrates. The Parvoviridae are classified into three subfamilies: Parvovirinae infect vertebrates, Densovirinae infects invertebrates, while Hamaparovirinae infects both vertebrates and invertebrates. Except for the NS1 region, which is the prime criterion for phylogeny analysis, other parts of the parvoviruses genome, such as UTRs, are diverse even among closely related viruses or within the same genus. It is believed that host switching in parvoviruses may be related to genetic changes in regions other than NS1; therefore, whole-genome screening is valuable for studying parvoviruses' host-virus interactions. The aim of this study was to analyze genome organization and phylogeny of the complete genome sequence of the 132 Paroviridae family members, focusing on viruses that infect invertebrates. The maximum and minimum divergence within each subfamily belonged to Densovirinae and Parvovirinae, respectively. The greatest evolutionary divergence was between Hamaparovirinae and Parvovirinae. Unclassified viruses were mostly from Parovirinae and had the highest divergence to densoviruses and the lowest divergence to Parovirinae viruses. In a phylogenetic tree, all hamparoviruses were found in the center of densoviruses, with the exception of Syngnathid Ichthamaparvovirus 1 (NC_055527), which was positioned between two Parvovirinae members (NC _022089 and NC_038544). The proximity of hamparoviruses members to some densoviruses strengthens the possibility that densoviruses may be the ancestors of hamaparoviruses or vice versa. Therefore, examination and phylogeny analysis of the whole genome is necessary to understand Parvoviridae family host selection.

Keywords: densoviruses, parvoviridae, bioinformatics, phylogeny

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Authors: Asma'u Mahe, Abdullahi A. Imam, Adamu J. Alhassan, Nasiru Abdullahi, Sadiya A. Bichi, Nura Lawal, Kamaluddeen Babagana

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Malaria is a disease with global health significance. It is caused by parasites and transmitted by Anopheles mosquitoes. Increase in insecticide resistance threatens the disease vector control. The strength of selection pressure acting on a mosquito population in relation to insecticide resistance can be assess by determining the genetic diversity of a fragment spanning exon- 20 of IIS6 of the voltage gated sodium channel (VGSC). Larval samples reared to adulthood were identified and kdr (knock down resistance) profile was determined. The DNA sequences were used to assess the patterns of genetic differentiation by determining the levels of genetic variability between the Anopheles mosquitoes. Genetic differentiation of the Anopheles mosquitoes based on a portion of the voltage gated sodium channel gene was obtained. Polymorphisms were detected; sequence variation and analysis were presented as a phylogenetic tree. Phylogenetic tree of VGSC haplotypes was constructed for samples of the Anopheles mosquitoes using the maximum likelihood method in MEGA 6.0 software. DNA sequences were edited using BioEdit sequence editor. The edited sequences were aligned with reference sequence (Kisumu strain). Analyses were performed as contained in dnaSP 5.10. Results of genetic parameters of polymorphism and haplotype reconstruction were presented in count. Twenty sequences were used for the analysis. Regions selected were 1- 576, invariable (monomorphic) sites were 460 while variable (polymorphic) sites were 5 giving the number of total mutations observed in this study. Mutations obtained from the study were at codon 105: TTC- Phenylalanine replaces TCC- Serine, codon 513: TAG- Termination replaces TTG- Leucine, codon 153, 300 and 553 mutations were non-synonymous. From the constructed phylogenetic tree, some groups were shown to be closer with Exon20Gambiae Kisumu (Reference strain) having some genetic distance, while 5-Exon20Gambiae-F I13.ab1, 18-Exon20Gambiae-F C17.ab1, and 2-Exon20Gambiae-F C13.ab1 clustered together genetically differentiated away from others. Mutations observed in this study can be attributed to the high insecticide resistance profile recorded in the study areas. Haplotype networks of pattern of genetic variability and polymorphism for the fragment of the VGSC sequences of sampled Anopheles mosquitoes revealed low haplotypes for the present study. Haplotypes are set of closely linked DNA variation on X-chromosome. Haplotypes were scaled accordingly to reflect their respective frequencies. Low haplotype number, four VGSC-1014F haplotypes were observed in this study. A positive association was previously established between low haplotype number of VGSC diversity and pyrethroid resistance through kdr mechanism. Significant values at (P < 0.05) of Tajima D and Fu and Li D’ were observed for some of the results indicating possible signature of positive selection on the fragment of VGSC in the study. This is the first report of VGSC-1014F in the study site. Based on the results, the mutation was present in low frequencies. However, the roles played by the observed mutations need further investigation. Mutations, environmental factors among others can affect genetic diversity. The study area has recorded increase in insecticide resistance that can affect vector control in the area. This finding might affect the efforts made against malaria. Sequences were deposited in GenBank for Accession Number.

Keywords: anopheles mosquitoes, insecticide resistance, kdr, malaria, voltage gated sodium channel

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Authors: Bahlouli Ahmed, Bentalab Nourdin, Nigrou Mourad

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This study was aimed at investigating the effect of orientation fiber reinforced on dynamic properties of laminate composite FRP. An experimental investigation is implemented using an impulse technique. The various specimens are excited in free vibration by the use of bi-channel Analyzer. The experimental results are compared by model of finite element analysis using ANSYS. The results studies (natural frequencies measurements, vibration mode, dynamic modulus and damping ratio) show that the effects of significant parameters such as lay-up and stacking sequence, boundary conditions and excitation place of accelerometer. These results are critically examined and discussed. The accuracy of these results is demonstrated by comparing results with those available in the literature.

Keywords: natural frequency, damping ratio, laminate composite, dynamic modulus

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Authors: J. Manuel Bello-López, Julieta Rojo-Medina

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Introduction: The transplant of Umbilical Cord Blood Units (UCBU) are a therapeutic possibility for patients with oncohaematological disorders, especially in children. In Mexico, 48.5% of oncological diseases in children 1-4 years old are leukemias; whereas in patients 5-14 and 15-24 years old, lymphomas and leukemias represent the second and third cause of death in these groups respectively. Therefore it is necessary to have more registries of UCBU in order to ensure genetic diversity in the country; the above because the search for appropriate a UCBU is increasingly difficult for patients of mixed ethnicity. Objective: To estimate the genetic diversity (polymorphisms) of Human Leucocyte Antigen (HLA) Class I (A, B) and Class II (DRB1) in UCBU cryopreserved for transplant at Cord Blood Bank of the NCBT. Material and Methods: HLA typing of 533 UCBU for transplant was performed from 2003-2012 at the Histocompatibility Laboratory from the Research Department (evaluated by Los Angeles Ca. Immunogenetics Center) of the NCBT. Class I HLA-A, HLA-B and Class II HLA-DRB1 typing was performed using medium resolution Sequence-Specific Primer (SSP). In cases of an ambiguity detected by SSP; Sequence-Specific Oligonucleotide (SSO) method was carried out. A strict analysis of populations genetic parameters were done in 5 representative UCBU populations. Results: 46.5% of UCBU were collected from Mexico City, State of Mexico (30.95%), Puebla (8.06%), Morelos (6.37%) and Veracruz (3.37%). The remaining UCBU (4.75%) are represented by other states. The identified genotypes correspond to Amerindian origins (HLA-A*02, 31; HLA-B*39, 15, 48), Caucasian (HLA-A*02, 68, 01, 30, 31; HLA-B*35, 15, 40, 44, 07 y HLA-DRB1*04, 08, 07, 15, 03, 14), Oriental (HLA-A*02, 30, 01, 31; HLA-B* 35, 39, 15, 40, 44, 07,48 y HLA-DRB1*04, 07,15, 03) and African (HLA-A*30 y HLA-DRB1*03). The genetic distances obtained by Cavalli-Sforza analysis of the five states showed significant genetic differences by comparing genetic frequencies. The shortest genetic distance exists between Mexico City and the state of Puebla (0.0039) and the largest between Veracruz and Morelos (0.0084). In order to identify significant differences between this states, the ANOVA test was performed. This demonstrates that UCBU is significantly different according to their origin (P <0.05). This is shown by the divergence between arms at the Dendogram of Neighbor-Joining. Conclusions: The NCBT provides UCBU in patients with oncohaematological disorders in all the country. There is a group of patients for which not compatible UCBU can be find due to the mixed ethnic origin. For example, the population of northern Mexico is mostly Caucasian. Most of the NCBT donors are of various ethnic origins, predominantly Amerindians and Caucasians; although some ethnic minorities like Oriental, African and pure Indian ethnics are not represented. The NCBT is, therefore, establishing agreements with different states of Mexico to promote the altruistic donation of Umbilical Cord Blood in order to enrich the genetic diversity in its files.

Keywords: cord blood, genetic diversity, human leucocyte antigen, transplant

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Authors: Mondal Indranil, Bhakat Debjyoti, Mukhopadayay Asish K., Chatterjee Nabendu S.

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CS6 is the prevalent CF in our region and deciphering its molecular regulators would play a pivotal role in reducing the burden of ETEC pathogenesis. In prokaryotes, most of the genes are under the control of one operon and the promoter present upstream of the gene regulates the transcription of that gene. Here the promoter of CS6 was characterized by computational method and further analyzed by β-galactosidase assay and sequencing. Promoter constructs and deletions were prepared as required to analyze promoter activity. The effect of different additives on the CS6 promoter was analysed by the β-galactosidase assay. Bioinformatics analysis done by Softberry/BPROM predicted fur, lrp, and crp boxes, -10 and -35 region upstream of the CS6 gene. The promoter construction in no promoter plasmid pTL61T showed that region -573 to +1 is actually the promoter region as predicted. Sequential deletion of the region upstream of CS6 revealed that promoter activity remains the same when -573bp to -350bp is deleted. But after the deletion of the upstream region -350 bp to -255bp, promoter expression decreases drastically to 26%. Further deletion also decreases promoter activity up to a little range. So the region -355bp to -255bp holds the promoter sequence for the CS6 gene. Additives like iron, NaCl, etc., modulate promoter activity in a dose-dependent manner. From the promoter analysis, it can be said that the minimum region lies between -254 and +1. Important region(s) lies between -350 bp to -255 bp upstream in the promoter, which might have important elements needed to control CS6 gene expression.

Keywords: microbiology, promoter, colonization factor, ETEC

Procedia PDF Downloads 144

Authors: Lara Dutil-Fafard, Caroline Rhéaume, Patrick Archambault, Daniel Lafond, Neal W. Pollock

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Improving resources for medical autonomy of astronauts in prolonged space missions, such as a Mars mission, requires not only technology development, but also decision-making support systems. The Advanced Crew Medical System - Medical Condition Requirements study, funded by the Canadian Space Agency, aimed to create knowledge content and a scenario-based query capability to support medical autonomy of astronauts. The key objective of this study was to create a prototype tool for identifying medical infrastructure requirements in terms of medical knowledge, skills and materials. A multicriteria decision-making method was used to prioritize the highest risk medical events anticipated in a long-term space mission. Starting with those medical conditions, event sequence diagrams (ESDs) were created in the form of decision trees where the entry point is the diagnosis and the end points are the predicted outcomes (full recovery, partial recovery, or death/severe incapacitation). The ESD formalism was adapted to characterize and compare possible outcomes of medical conditions as a function of available medical knowledge, skills, and supplies in a given mission scenario. An extensive literature review was performed and summarized in a medical condition database. A PostgreSQL relational database was created to allow query-based evaluation of health outcome metrics with different medical infrastructure scenarios. Critical decision points, skill and medical supply requirements, and probable health outcomes were compared across chosen scenarios. The three medical conditions with the highest risk rank were acute coronary syndrome, sepsis, and stroke. Our efforts demonstrate the utility of this approach and provide insight into the effort required to develop appropriate content for the range of medical conditions that may arise.

Keywords: decision support system, event-sequence diagram, exploration mission, medical autonomy, scenario-based queries, space medicine

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Authors: Emma K. Sales, Nilda G. Butardo

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The project was undertaken to determine the effects of modified tissue culture protocols e.g. age of culture and hormone levels (2,4-D) in generating somaclonal variation. Moreover, the utility of molecular markers (SSR and MSAP) in sorting off types/somaclones were investigated. Results show that somaclonal variation is in effect due to prolonged subculture and high 2,4-D concentration. The resultant variation was observed to be due to high level of methylation events specifically cytosine methylation either at the internal or external cytosine and was identified by methylation sensitive amplification polymorphism (MSAP). Simple sequence repeats (SSR) on the other hand, was able to associate a marker to a trait of interest. These therefore, show that molecular markers can be an important tool in sorting out variation/mutants at an early stage.

Keywords: methylation, MSAP, somaclones, SSR, subculture, 2, 4-D

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Authors: Kah Yan How, Peh Fern Ong, Keang Peng Song

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Porphyromonas gingivalis is a black-pigmented, anaerobic Gram-negative bacterium that is important in the progression of chronic and severe periodontitis. This organism has an essential requirement for iron, which is usually obtained from hemin, using specific membrane receptors, proteases, and lipoproteins. In this study, we report the characterization of a novel 24 kDa hemin-binding protein, HmuX, in P. gingivalis W50. The hmuX gene is 651 bp long which encodes for a 217 amino acid protein. HmuX was found to be identical at the C-terminus to the previously reported HmuY protein, differing by an additional 74 amino acids at the N-terminus. Recombinant HmuX demonstrated hemin-binding ability by LDS- PAGE and TMBZ staining. Sequence analysis of HmuX revealed a putative lipoprotein attachment site, suggesting its possible role as a lipoprotein. HmuX was also localized to the outer cell surface by transmission electron microscopy. Northern analysis showed hmuX to be transcribed as a single gene and that hmuX mRNA was tightly regulated by the availability of extra-cellular hemin. P. gingivalis isogenic mutant deficient in hmuX gene exhibited significant growth retardation under hemin-limited conditions. Taken together, these results suggest that HmuX is a hemin-binding lipoprotein, important in hemin utilization for the growth of P. gingivalis.

Keywords: Porphyromonas gingivalis, periodontal diseases, HmuX, protein characterization

Procedia PDF Downloads 195