Search results for: massively parallel sequencing

Authors: Yi-Hao Wong, Li-Li Chan, Chee-Onn Leong, Stephen Ambu, Joon-Wah Mak, Priyasashi Sahu

Abstract:

Background: Acanthamoeba is a genus of amoebae which lives as a free-living in nature or as a human pathogen that causes severe brain and eye infections. Virulence potential of Acanthamoeba is not constant and can change with growth conditions. DNA methylation, an epigenetic process which adds methyl groups to DNA, is used by eukaryotic cells, including several human parasites to control their gene expression. We used qPCR, siRNA gene silencing, and RNA sequencing (RNA-Seq) to study DNA-methyltransferase gene family (DNMT) in order to indicate the possibility of its involvement in programming Acanthamoeba virulence potential. Methods: A virulence-attenuated Acanthamoeba isolate (designation: ATCC; original isolate: ATCC 50492) was subjected to mouse passages to restore its pathogenicity; a virulence-reactivated isolate (designation: AC/5) was generated. Several established factors associated with Acanthamoeba virulence phenotype were examined to confirm the succession of reactivation process. Differential gene expression of DNMT between ATCC and AC/5 isolates was performed by qPCR. Silencing on DNMT gene expression in AC/5 isolate was achieved by siRNA duplex. Total RNAs extracted from ATCC, AC/5, and siRNA-treated (designation: si-146) were subjected to RNA-Seq for comparative transcriptomic analysis in order to identify the genome-wide effect of DNMT in regulating Acanthamoeba gene expression. qPCR was performed to validate the RNA-Seq results. Results: Physiological and cytophatic assays demonstrated an increased in virulence potential of AC/5 isolate after mouse passages. DNMT gene expression was significantly higher in AC/5 compared to ATCC isolate (p ≤ 0.01) by qPCR. si-146 duplex reduced DNMT gene expression in AC/5 isolate by 30%. Comparative transcriptome analysis identified the differentially expressed genes, with 3768 genes in AC/5 vs ATCC isolate; 2102 genes in si-146 vs AC/5 isolate and 3422 genes in si-146 vs ATCC isolate, respectively (fold-change of ≥ 2 or ≤ 0.5, p-value adjusted (padj) < 0.05). Of these, 840 and 1262 genes were upregulated and downregulated, respectively, in si-146 vs AC/5 isolate. Eukaryotic orthologous group (KOG) assignments revealed a higher percentage of downregulated gene expression in si-146 compared to AC/5 isolate, were related to posttranslational modification, signal transduction and energy production. Gene Ontology (GO) terms for those downregulated genes shown were associated with transport activity, oxidation-reduction process, and metabolic process. Among these downregulated genes were putative genes encoded for heat shock proteins, transporters, ubiquitin-related proteins, proteins for vesicular trafficking (small GTPases), and oxidoreductases. Functional analysis of similar predicted proteins had been described in other parasitic protozoa for their survival and pathogenicity. Decreased expression of these genes in si146-treated isolate may account in part for Acanthamoeba reduced pathogenicity. qPCR on 6 selected genes upregulated in AC/5 compared to ATCC isolate corroborated the RNA sequencing findings, indicating a good concordance between these two analyses. Conclusion: To the best of our knowledge, this study represents the first genome-wide analysis of DNA methylation and its effects on gene expression in Acanthamoeba spp. The present data indicate that DNA methylation has substantial effect on global gene expression, allowing further dissection of the genome-wide effects of DNA-methyltransferase gene in regulating Acanthamoeba pathogenicity.

Keywords: Acanthamoeba, DNA methylation, RNA sequencing, virulence

Procedia PDF Downloads 170

Authors: Rims Janeliukstis, Deniss Mironovs, Andrejs Kovalovs

Abstract:

Operational Modal Analysis (OMA) is widely applied as a method for Structural Health Monitoring for structural damage identification and assessment by tracking the changes of the identified modal parameters over time. Unfortunately, modal parameters also depend on such external factors as temperature and loads. Any structural condition assessment using modal parameters should be done taking into consideration those external factors, otherwise there is a high chance of false positives. A method of structural reliability assessment based on anomaly detection technique called Machalanobis Squared Distance (MSD) is proposed. It requires a set of reference conditions to learn healthy state of a structure, which all future parameters are compared to. In this study, structural modal parameters (natural frequency and mode shape), as well as ambient temperature and loads acting on the structure are used as features. Numerical tests were performed on a finite element model of a carbon fibre reinforced polymer composite beam with delamination damage at various locations and of various severities. The advantages of the demonstrated approach include relatively few computational steps, ability to distinguish between healthy and damaged conditions and discriminate between different damage severities. It is anticipated to be promising in reliability assessment of massively produced structural parts.

Keywords: operational modal analysis, reliability assessment, anomaly detection, damage, mahalanobis squared distance

Procedia PDF Downloads 87

Authors: Christofas Stergianos, Jason Atkin, Herve Morvan

Abstract:

As air traffic increases, more airports are interested in utilizing optimization methods. Many processes happen in parallel at an airport, and complex models are needed in order to have a reliable solution that can be implemented for ground movement operations. The ground movement for aircraft in an airport, allocating a path to each aircraft to follow in order to reach their destination (e.g. runway or gate), is one process that could be optimized. The Quickest Path Problem with Time Windows (QPPTW) algorithm has been developed to provide a conflict-free routing of vehicles and has been applied to routing aircraft around an airport. It was subsequently modified to increase the accuracy for airport applications. These modifications take into consideration specific characteristics of the problem, such as: the pushback process, which considers the extra time that is needed for pushing back an aircraft and turning its engines on; stand holding where any waiting should be allocated to the stand; and runway sequencing, where the sequence of the aircraft that take off is optimized and has to be respected. QPPTW involves searching for the quickest path by expanding the search in all directions, similarly to Dijkstra’s algorithm. Finding a way to direct the expansion can potentially assist the search and achieve a better performance. We have further modified the QPPTW algorithm to use a heuristic approach in order to guide the search. This new algorithm is based on the A-star search method but estimates the remaining time (instead of distance) in order to assess how far the target is. It is important to consider the remaining time that it is needed to reach the target, so that delays that are caused by other aircraft can be part of the optimization method. All of the other characteristics are still considered and time windows are still used in order to route multiple aircraft rather than a single aircraft. In this way the quickest path is found for each aircraft while taking into account the movements of the previously routed aircraft. After running experiments using a week of real aircraft data from Zurich Airport, the new algorithm (A-star QPPTW) was found to route aircraft much more quickly, being especially fast in routing the departing aircraft where pushback delays are significant. On average A-star QPPTW could route a full day (755 to 837 aircraft movements) 56% faster than the original algorithm. In total the routing of a full week of aircraft took only 12 seconds with the new algorithm, 15 seconds faster than the original algorithm. For real time application, the algorithm needs to be very fast, and this speed increase will allow us to add additional features and complexity, allowing further integration with other processes in airports and leading to more optimized and environmentally friendly airports.

Keywords: a-star search, airport operations, ground movement optimization, routing and scheduling

Procedia PDF Downloads 205

Authors: Yelin Zhao, Xinxiu Li, Martin Smelik, Oleg Sysoev, Firoj Mahmud, Dina Mansour Aly, Mikael Benson

Abstract:

Background: Early diagnosis of pancreatic cancer is clinically challenging due to vague, or no symptoms, and lack of biomarkers. Polygenic risk score (PRS) scores may provide a valuable tool to assess increased or decreased risk of PC. This study aimed to develop such PRS by filtering genetic variants identified by GWAS using transcriptional programs identified by single-cell RNA sequencing (scRNA-seq). Methods: ScRNA-seq data from 24 pancreatic ductal adenocarcinoma (PDAC) tumor samples and 11 normal pancreases were analyzed to identify differentially expressed genes (DEGs) in in tumor and microenvironment cell types compared to healthy tissues. Pathway analysis showed that the DEGs were enriched for hundreds of significant pathways. These were clustered into 40 “programs” based on gene similarity, using the Jaccard index. Published genetic variants associated with PDAC were mapped to each program to generate program PRSs (pPRSs). These pPRSs, along with five previously published PRSs (PGS000083, PGS000725, PGS000663, PGS000159, and PGS002264), were evaluated in a European-origin population from the UK Biobank, consisting of 1,310 PDAC participants and 407,473 non-pancreatic cancer participants. Stepwise Cox regression analysis was performed to determine associations between pPRSs with the development of PC, with adjustments of sex and principal components of genetic ancestry. Results: The PDAC genetic variants were mapped to 23 programs and were used to generate pPRSs for these programs. Four distinct pPRSs (P1, P6, P11, and P16) and two published PRSs (PGS000663 and PGS002264) were significantly associated with an increased risk of developing PC. Among these, P6 exhibited the greatest hazard ratio (adjusted HR[95% CI] = 1.67[1.14-2.45], p = 0.008). In contrast, P10 and P4 were associated with lower risk of developing PC (adjusted HR[95% CI] = 0.58[0.42-0.81], p = 0.001, and adjusted HR[95% CI] = 0.75[0.59-0.96], p = 0.019). By comparison, two of the five published PRS exhibited an association with PDAC onset with HR (PGS000663: adjusted HR[95% CI] = 1.24[1.14-1.35], p < 0.001 and PGS002264: adjusted HR[95% CI] = 1.14[1.07-1.22], p < 0.001). Conclusion: Compared to published PRSs, scRNA-seq-based pPRSs may be used not only to assess increased but also decreased risk of PDAC.

Keywords: cox regression, pancreatic cancer, polygenic risk score, scRNA-seq, UK biobank

Procedia PDF Downloads 66

Authors: Ethel E. Phiri, Lionel Hartzenberg, Percy Chimwamuromba, Emmanuel Nepolo, Jens Kossmann, James R. Lloyd

Abstract:

Orphan crops are underresearched and underutilized food plant species that have not been categorized as major food crops, but have the potential to be economically and agronomically significant. They have been documented to have the ability to tolerate extreme environmental conditions. However, limited research has been conducted to uncover their potential as food crop species. The New Partnership for Africa’s Development (NEPAD) has classified Marama bean, Tylosema esculentum, as an orphan crop. The plant is one of the 101 African orphan crops that must have their genomes sequenced, assembled, and annotated in the foreseeable future. Marama bean is a perennial leguminous plant that primarily grows in poor, arid soils in southern Africa. The plants produce large tubers that can weigh as much as 200kg. While the foliage provides fodder, the tuber is carbohydrate rich and is a staple food source for rural communities in Namibia. Also, the edible seeds are protein- and oil-rich. Marama Bean plants respond rapidly to increased temperatures and severe water scarcity without extreme consequences. Advances in molecular biology and biotechnology have made it possible to effectively transfer technologies between model- and major crops to orphan crops. In this research, the aim was to assemble the first transcriptomic analysis of Marama Bean RNA-sequence data. Many model plant species have had their genomes sequenced and their transcriptomes assembled. Therefore the availability of transcriptome data for a non-model crop plant species will allow for gene identification and comparisons between various species. The data has been sequenced using the Ilumina Hiseq 2500 sequencing platform. Data analysis is underway. In essence, this research will eventually evaluate the potential use of Marama Bean as a crop species to improve its value in agronomy. data for a non-model crop plant species will allow for gene identification and comparisons between various species. The data has been sequenced using the Ilumina Hiseq 2500 sequencing platform. Data analysis is underway. In essence, this researc will eventually evaluate the potential use of Marama bean as a crop species to improve its value in agronomy.

Keywords: 101 African orphan crops, RNA-Seq, Tylosema esculentum, underutilised crop plants

Procedia PDF Downloads 340

Authors: Mamouni Mohammed Dhiya Eddine

Abstract:

This work aims at studying the exploitation of high-speed networks of clusters for distributed storage. Parallel applications running on clusters require both high-performance communications between nodes and efficient access to the storage system. Many studies on network technologies led to the design of dedicated architectures for clusters with very fast communications between computing nodes. Efficient distributed storage in clusters has been essentially developed by adding parallelization mechanisms so that the server(s) may sustain an increased workload. In this work, we propose to improve the performance of distributed storage systems in clusters by efficiently using the underlying high-performance network to access distant storage systems. The main question we are addressing is: do high-speed networks of clusters fit the requirements of a transparent, efficient and high-performance access to remote storage? We show that storage requirements are very different from those of parallel computation. High-speed networks of clusters were designed to optimize communications between different nodes of a parallel application. We study their utilization in a very different context, storage in clusters, where client-server models are generally used to access remote storage (for instance NFS, PVFS or LUSTRE). Our experimental study based on the usage of the GM programming interface of MYRINET high-speed networks for distributed storage raised several interesting problems. Firstly, the specific memory utilization in the storage access system layers does not easily fit the traditional memory model of high-speed networks. Secondly, client-server models that are used for distributed storage have specific requirements on message control and event processing, which are not handled by existing interfaces. We propose different solutions to solve communication control problems at the filesystem level. We show that a modification of the network programming interface is required. Data transfer issues need an adaptation of the operating system. We detail several propositions for network programming interfaces which make their utilization easier in the context of distributed storage. The integration of a flexible processing of data transfer in the new programming interface MYRINET/MX is finally presented. Performance evaluations show that its usage in the context of both storage and other types of applications is easy and efficient.

Keywords: distributed storage, remote file access, cluster, high-speed network, MYRINET, zero-copy, memory registration, communication control, event notification, application programming interface

Procedia PDF Downloads 195

Authors: Tamar Lin, Nufar Buchshtab, Yifat Elharar, Julian Nicenboim, Rotem Edgar, Iddo Weiner, Lior Zelcbuch, Ariel Cohen, Sharon Kredo-Russo, Inbar Gahali-Sass, Naomi Zak, Sailaja Puttagunta, Merav Bassan

Abstract:

Background: Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin disorder that is characterized by dry skin and flares of eczematous lesions and intense pruritus. Multiple lines of evidence suggest that AD is associated with increased colonization by Staphylococcus aureus, which contributes to disease pathogenesis through the release of virulence factors that affect both keratinocytes and immune cells, leading to disruption of the skin barrier and immune cell dysfunction. The aim of the current study is to develop a bacteriophage-based product that specifically targets S. aureus. Methods: For the discovery of phage, environmental samples were screened on 118 S. aureus strains isolated from skin samples, followed by multiple enrichment steps. Natural phages were isolated, subjected to Next-generation Sequencing (NGS), and analyzed using proprietary bioinformatics tools for undesirable genes (toxins, antibiotic resistance genes, lysogeny potential), taxonomic classification, and purity. Phage host range was determined by an efficiency of plating (EOP) value above 0.1 and the ability of the cocktail to completely lyse liquid bacterial culture under different growth conditions (e.g., temperature, bacterial stage). Results: Sequencing analysis demonstrated that the 118 S. aureus clinical strains were distributed across the phylogenetic tree of all available Refseq S. aureus (~10,750 strains). Screening environmental samples on the S. aureus isolates resulted in the isolation of 50 lytic phages from different genera, including Silviavirus, Kayvirus, Podoviridae, and a novel unidentified phage. NGS sequencing confirmed the absence of toxic elements in the phages’ genomes. The host range of the individual phages, as measured by the efficiency of plating (EOP), ranged between 41% (48/118) to 79% (93/118). Host range studies in liquid culture revealed that a subset of the phages can infect a broad range of S. aureus strains in different metabolic states, including stationary state. Combining the single-phage EOP results of selected phages resulted in a broad host range cocktail which infected 92% (109/118) of the strains. When tested in vitro in a liquid infection assay, clearance was achieved in 87% (103/118) of the strains, with no evidence of phage resistance throughout the study (24 hours). A S. aureus host was identified that can be used for the production of all the phages in the cocktail at high titers suitable for large-scale manufacturing. This host was validated for the absence of contaminating prophages using advanced NGS methods combined with multiple production cycles. The phages are produced under optimized scale-up conditions and are being used for the development of a topical formulation (BX005) that may be administered to subjects with atopic dermatitis. Conclusions: A cocktail of natural phages targeting S. aureus was effective in reducing bacterial burden across multiple assays. Phage products may offer safe and effective steroid-sparing options for atopic dermatitis.

Keywords: atopic dermatitis, bacteriophage cocktail, host range, Staphylococcus aureus

Procedia PDF Downloads 128

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

Abstract:

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

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

Procedia PDF Downloads 178

Authors: Oibar Martinez, Clara Oliver, Jose Miguel Miranda

Abstract:

In this paper, we discuss the standard improvements which can be made to reduce the earth resistance in difficult terrains for optimum lightning protection, what are the practical limitations, and how the modeling can be refined for accurate diagnostics and ground resistance minimization. Ground resistance minimization can be made via three different approaches: burying vertical electrodes connected in parallel, burying horizontal conductive plates or meshes, or modifying the own terrain, either by changing the entire terrain material in a large volume or by adding earth-enhancing compounds. The use of vertical electrodes connected in parallel pose several practical limitations. In order to prevent loss of effectiveness, it is necessary to keep a minimum distance between each electrode, which is typically around five times larger than the electrode length. Otherwise, the overlapping of the local equipotential lines around each electrode reduces the efficiency of the configuration. The addition of parallel electrodes reduces the resistance and facilitates the measurement, but the basic parallel resistor formula of circuit theory will always underestimate the final resistance. Numerical simulation of equipotential lines around the electrodes overcomes this limitation. The resistance of a single electrode will always be proportional to the soil resistivity. The electrodes are usually installed with a backfilling material of high conductivity, which increases the effective diameter. However, the improvement is marginal, since the electrode diameter counts in the estimation of the ground resistance via a logarithmic function. Substances that are used for efficient chemical treatment must be environmentally friendly and must feature stability, high hygroscopicity, low corrosivity, and high electrical conductivity. A number of earth enhancement materials are commercially available. Many are comprised of carbon-based materials or clays like bentonite. These materials can also be used as backfilling materials to reduce the resistance of an electrode. Chemical treatment of soil has environmental issues. Some products contain copper sulfate or other copper-based compounds, which may not be environmentally friendly. Carbon-based compounds are relatively inexpensive and they do have very low resistivities, but they also feature corrosion issues. Typically, the carbon can corrode and destroy a copper electrode in around five years. These compounds also have potential environmental concerns. Some earthing enhancement materials contain cement, which, after installation acquire properties that are very close to concrete. This prevents the earthing enhancement material from leaching into the soil. After analyzing different configurations, we conclude that a buried conductive ring with vertical electrodes connected periodically should be the optimum baseline solution for the grounding of a large size structure installed on a large resistivity terrain. In order to show this, a practical example is explained here where we simulate the ground resistance of a conductive ring buried in a terrain with a resistivity in the range of 1 kOhm·m.

Keywords: grounding improvements, large scale scientific instrument, lightning risk assessment, lightning standards

Procedia PDF Downloads 111

Authors: Iftikhar Hussain Gul, Syeda Aatika

Abstract:

Nickel ferrite was prepared via wet chemical co-precipitation route. Carbon Nano Fibers (CNFs) were used to prepare NiFe₂O₄/CNFs nanohybrids. Polar solvent (ortho-xylene) was used for the dispersion of CNFs in ferrite matrix. X-ray diffraction patterns confirmed the formation of NiFe₂O₄/CNFs nanohybrids without any impurity peak. FTIR patterns showed two consistent characteristic absorption bands for tetrahedral and octahedral sites, confirming the formation of spinel structure of NiFe₂O₄. Scanning Electron Microscopy (SEM) images confirmed the coating of nickel ferrite nanoparticles on CNFs, which confirms the efficiency of deployed method. The dielectric properties were measured as a function of frequency at room temperature. Pure NiFe₂O₄ showed dielectric constant of 1.79 ×10³ at 100 Hz, which increased massively to 2.92 ×10⁶ at 100 Hz with the addition of 20% by weight of CNFs, proving it to be potential candidate for applications in supercapacitors. The impedance analysis showed a considerable decrease of resistance, reactance and cole-cole plot which confirms the decline of impedance on addition of CNFs. The pure NiFe₂O₄ has highest impedance values of 5.89 ×10⁷ Ohm at 100 Hz while the NiFe₂O₄/CNFs nanohybrid with CNFs (20% by weight) has the lowest impedance values of 4.25×10³ Ohm at 100 Hz, which proves this nanohybrid is useful for high-frequency applications.

Keywords: AC impedance, co-precipitation, nanohybrid, Fourier transform infrared spectroscopy, x-ray diffraction

Procedia PDF Downloads 110

Authors: Neşe Işık, Şenol Altıok, Galip Devrim Eryılmaz, Aydın durukan, Hasan Özgür Daş

Abstract:

In this study, an active landslide zone affecting the road alignment on the Tortum-Uzundere (Erzurum/Turkey) highway was investigated. Due to the landslide movement, problems have occurred in the existing road pavement, which has caused both safety problems and reduced driving comfort in the operation of the road. In order to model the landslide, drilling, geophysical and inclinometer studies were carried out in the field within the scope of ground investigation. Laboratory tests were carried out on soil and rock samples obtained from the borings. When the drilling and geophysical studies were evaluated together, it was determined that the study area has a complex geological structure. In addition, according to the inclinometer results, the direction and speed of movement of the landslide mass were observed. In order to create an idealized geological profile, all field and laboratory studies were evaluated together and then the sliding surface of the landslide was determined by back analysis method. According to the findings obtained, it was determined that the landslide was massively large, and the movement occurred had a deep sliding surface. As a result of the numerical analyses, it was concluded that the Slope angle reduction is the most economical and environmentally friendly method for the control of the landslide mass.

Keywords: landslide, geotechnical methods, geophysics, monitoring, highway

Procedia PDF Downloads 48

Authors: Iryna P. Dzieciuch, Michael D. Putman

Abstract:

Humidity is known to degrade Navy ship electronic equipment, especially in hot moist environments. If left untreated, it can cause significant and permanent damage. Even rigorous inspection and frequent clean-up would not prevent further equipment contamination and degradation because of the constant presence of favorable growth conditions for many microorganisms. Generally, relative humidity levels of less than 60% will inhibit corrosion in electronic equipment, but because NAVY electronics often operate in hot and humid environments, prevention via dehumidification is not always possible. Currently, there is no defined research that fully describes key mechanisms which cause electronics and its coating degradation. The corrosive action of most bacteria is mainly developed through (i) mycelium adherence to the metal plates, (ii) facilitation the formation of pitting areas, (iii) production of organic acids such as citric, iso-citric, cis-aconitic, alpha-ketoglutaric, which are corrosive to electronic equipment and its components. Our approach studies corrosive action in electronic equipment: circuit-board, wires and connections that are exposed in the humid environment that gets worse during condensation. In our new approach the technical task is built on work with the bacterial communities in public areas, bacterial genetics, bioinformatics, biostatistics and Scanning Electron Microscopy (SEM) of corroded circuit boards. Based on these methods, we collect and examine environmental samples from biofilms of the corroded and non-corroded sites, where bacterial contamination of electronic equipment, such as machine racks and shore boats, is an ongoing concern. Sample collection and sample analysis is focused on addressing the key questions identified above through the following tasks: laboratory sample processing and evaluation under scanning electron microscopy, initial sequencing and data evaluation; bioinformatics and data analysis. Preliminary results from scanning electron microscopy (SEM) have revealed that metal particulates and alloys in corroded samples consists mostly of Tin ( < 40%), Silicon ( < 4%), Sulfur ( < 1%), Aluminum ( < 2%), Magnesium ( < 2%), Copper ( < 1%), Bromine ( < 2%), Barium ( <1%) and Iron ( < 2%) elements. We have also performed X 12000 magnification of the same sites and that proved existence of undisrupted biofilm organelles and crystal structures. Non-corrosion sites have revealed high presence of copper ( < 47%); other metals remain at the comparable level as on the samples with corrosion. We have performed X 1000 magnification on the non-corroded at the sites and have documented formation of copper crystals. The next step of this study, is to perform metagenomics sequencing at all sites and to compare bacterial composition present in the environment. While copper is nontoxic to the living organisms, the process of bacterial adhesion creates acidic environment by releasing citric, iso-citric, cis-aconitic, alpha-ketoglutaric acidics, which in turn release copper ions Cu++, which that are highly toxic to the bacteria and higher order living organisms. This phenomenon, might explain natural “antibiotic” properties that are lacking in elements such as tin. To prove or deny this hypothesis we will use next - generation sequencing (NGS) methods to investigate types and growth cycles of bacteria that from bacterial biofilm the on corrosive and non-corrosive samples.

Keywords: bacteria, biofilm, circuit board, copper, corrosion, electronic equipment, organic acids, tin

Procedia PDF Downloads 134

Authors: Shiji Hu, Lei Li, Wanting Zhou, DaoHong Yang

Abstract:

The data encryption, is the foundation of today’s communication. On this basis, how to improve the speed of data encryption and decryption is always a problem that scholars work for. In this paper, we proposed an elliptic curve crypto processor architecture based on SM2 prime field. In terms of hardware implementation, we optimized the algorithms in different stages of the structure. In finite field modulo operation, we proposed an optimized improvement of Karatsuba-Ofman multiplication algorithm, and shorten the critical path through pipeline structure in the algorithm implementation. Based on SM2 recommended prime field, a fast modular reduction algorithm is used to reduce 512-bit wide data obtained from the multiplication unit. The radix-4 extended Euclidean algorithm was used to realize the conversion between affine coordinate system and Jacobi projective coordinate system. In the parallel scheduling of point operations on elliptic curves, we proposed a three-level parallel structure of point addition and point double based on the Jacobian projective coordinate system. Combined with the scalar multiplication algorithm, we added mutual pre-operation to the point addition and double point operation to improve the efficiency of the scalar point multiplication. The proposed ECC hardware architecture was verified and implemented on Xilinx Virtex-7 and ZYNQ-7 platforms, and each 256-bit scalar multiplication operation took 0.275ms. The performance for handling scalar multiplication is 32 times that of CPU(dual-core ARM Cortex-A9).

Keywords: Elliptic curve cryptosystems, SM2, modular multiplication, point multiplication.

Procedia PDF Downloads 68

Authors: K. X. Cheng, A. L. Goh, K. T. Ooi

Abstract:

The effectiveness of microchannels in enhancing heat transfer has been demonstrated in the semiconductor industry. In order to tap the microscale heat transfer effects into macro geometries, overcoming the cost and technological constraints, microscale passages were created in macro geometries machined using conventional fabrication methods. A cylindrical insert was placed within a pipe, and geometrical profiles were created on the outer surface of the insert to enhance heat transfer under steady-state single-phase liquid flow conditions. However, while heat transfer coefficient values of above 10 kW/m2·K were achieved, the heat transfer enhancement was accompanied by undesirable pressure drop increment. Therefore, this study aims to address the high pressure drop issue using Constructal theory, a universal design law for both animate and inanimate systems. Two designs based on Constructal theory were developed to study the effectiveness of Constructal features in reducing the pressure drop increment as compared to parallel channels, which are commonly found in microchannel fabrication. The hydrodynamic and heat transfer performance for the Tree insert and Constructal fin (Cfin) insert were studied using experimental methods, and the underlying mechanisms were substantiated by numerical results. In technical terms, the objective is to achieve at least comparable increment in both heat transfer coefficient and pressure drop, if not higher increment in the former parameter. Results show that the Tree insert improved the heat transfer performance by more than 16 percent at low flow rates, as compared to the Tree-parallel insert. However, the heat transfer enhancement reduced to less than 5 percent at high Reynolds numbers. On the other hand, the pressure drop increment stayed almost constant at 20 percent. This suggests that the Tree insert has better heat transfer performance in the low Reynolds number region. More importantly, the Cfin insert displayed improved heat transfer performance along with favourable hydrodynamic performance, as compared to Cfinparallel insert, at all flow rates in this study. At 2 L/min, the enhancement of heat transfer was more than 30 percent, with 20 percent pressure drop increment, as compared to Cfin-parallel insert. Furthermore, comparable increment in both heat transfer coefficient and pressure drop was observed at 8 L/min. In other words, the Cfin insert successfully achieved the objective of this study. Analysis of the results suggests that bifurcation of flows is effective in reducing the increment in pressure drop relative to heat transfer enhancement. Optimising the geometries of the Constructal fins is therefore the potential future study in achieving a bigger stride in energy efficiency at much lower costs.

Keywords: constructal theory, enhanced heat transfer, microchannel, pressure drop

Procedia PDF Downloads 310

Authors: Javed Mallick

Abstract:

In metropolitan areas, rapid changes in land use and land cover (LULC) have ecological and environmental consequences. Saudi Arabia's cities have experienced tremendous urban growth since the 1990s, resulting in urban heat islands, groundwater depletion, air pollution, loss of ecosystem services, and so on. From 1990 to 2020, this study examines the variance and heterogeneity in land surface temperature (LST) caused by LULC changes in Abha-Khamis Mushyet, Saudi Arabia. LULC was mapped using the support vector machine (SVM). The mono-window algorithm was used to calculate the land surface temperature (LST). To identify LST clusters, the local indicator of spatial associations (LISA) model was applied to spatiotemporal LST maps. In addition, the parallel coordinate (PCP) method was used to investigate the relationship between LST clusters and urban biophysical variables as a proxy for LULC. According to LULC maps, urban areas increased by more than 330% between 1990 and 2018. Between 1990 and 2018, built-up areas had an 83.6% transitional probability. Furthermore, between 1990 and 2020, vegetation and agricultural land were converted into built-up areas at a rate of 17.9% and 21.8%, respectively. Uneven LULC changes in built-up areas result in more LST hotspots. LST hotspots were associated with high NDBI but not NDWI or NDVI. This study could assist policymakers in developing mitigation strategies for urban heat islands

Keywords: land use land cover mapping, land surface temperature, support vector machine, LISA model, parallel coordinate plot

Procedia PDF Downloads 50

Authors: Hanbyul Kim, Hye-Jin Kin, Taehun Park, Woo Jun Sul, Susun An

Abstract:

Skin is the largest organ of the human body and can provide the diverse habitat for various microorganisms. The ecology of the skin surface selects distinctive sets of microorganisms and is influenced by both endogenous intrinsic factors and exogenous environmental factors. The diversity of the bacterial community in the skin also depends on multiple host factors: gender, age, health status, location. Among them, age-related changes in skin structure and function are attributable to combinations of endogenous intrinsic factors and exogenous environmental factors. Skin aging is characterized by a decrease in sweat, sebum and the immune functions thus resulting in significant alterations in skin surface physiology including pH, lipid composition, and sebum secretion. The present study gives a comprehensive clue on the variation of skin microbiota and the correlations between ages by analyzing and comparing the metagenome of skin microbiome using Next Generation Sequencing method. Skin bacterial diversity and composition were characterized and compared between two different age groups: younger (20 – 30y) and older (60 - 70y) Xian, Chinese women. A total of 73 healthy women meet two conditions: (I) living in Xian, China; (II) maintaining healthy skin status during the period of this study. Based on Ribosomal Database Project (RDP) database, skin samples of 73 participants were enclosed with ten most abundant genera: Chryseobacterium, Propionibacterium, Enhydrobacter, Staphylococcus and so on. Although these genera are the most predominant genus overall, each genus showed different proportion in each group. The most dominant genus, Chryseobacterium was more present relatively in Young group than in an old group. Similarly, Propionibacterium and Enhydrobacter occupied a higher proportion of skin bacterial composition of the young group. Staphylococcus, in contrast, inhabited more in the old group. The beta diversity that represents the ratio between regional and local species diversity showed significantly different between two age groups. Likewise, The Principal Coordinate Analysis (PCoA) values representing each phylogenetic distance in the two-dimensional framework using the OTU (Operational taxonomic unit) values of the samples also showed differences between the two groups. Thus, our data suggested that the composition and diversification of skin microbiomes in adult women were largely affected by chronological and physiological skin aging.

Keywords: next generation sequencing, age, Xian, skin microbiome

Procedia PDF Downloads 121

Authors: L. Salomon, P. Sklenar

Abstract:

The Andes hold the highest plant species diversity in the world. How this occurred is one of the most intriguing questions in studies addressing the origin and patterning of plant diversity worldwide. Recently, the explosive adaptive radiations found in high Andean groups have been pointed as triggers to this spectacular diversity. The Andes is the species-richest area for the biggest genus from the Asteraceae family: Senecio. There, the genus presents an incredible diversity of species, striking growth form variation, and large niche span. Even when some studies tried to disentangle the evolutionary story for some Andean species in Senecio, they obtained partially resolved and low supported phylogenies, as expected for recently radiated groups. The high-throughput sequencing (HTS) approaches have proved to be a powerful tool answering phylogenetic questions in those groups whose evolutionary stories are recent and traditional techniques like Sanger sequencing are not informative enough. Although these tools have been used to understand the evolution of an increasing number of Andean groups, nowadays, their scope has not been applied for Senecio. This project aims to contribute to a better knowledge of the mechanisms shaping the hyper diversity of Senecio in the Andean region, using HTS focusing on Senecio ser. Culcitium (Asteraceae), recently recircumscribed. Firstly, reconstructing a highly resolved and supported phylogeny, and after assessing the role of allopatric differentiation, hybridization, and genome duplication in the diversification of the group. Using the Hyb-Seq approach, combining target enrichment using Asteraceae COS loci baits and genome skimming, more than 100 new accessions were generated. HybPhyloMaker and HybPiper pipelines were used for the phylogenetic analyses, and another pipeline in development (Paralogue Wizard) was used to deal with paralogues. RAxML was used to generate gene trees and Astral for species tree reconstruction. Phyparts were used to explore as first step of gene tree discordance along the clades. Fully resolved with moderated supported trees were obtained, showing Senecio ser. Culcitium as monophyletic. Within the group, some species formed well-supported clades with morphologically related species, while some species would not have exclusive ancestry, in concordance with previous studies using amplified fragment length polymorphism (AFLP) showing geographical differentiation. Discordance between gene trees was detected. Paralogues were detected for many loci, indicating possible genome duplications; ploidy level estimation using flow cytometry will be carried out during the next months in order to identify the role of this process in the diversification of the group. Likewise, TreeSetViz package for Mesquite, hierarchical likelihood ratio congruence test using Concaterpillar, and Procrustean Approach to Cophylogeny (PACo), will be used to evaluate the congruence among different inheritance patterns. In order to evaluate the influence of hybridization and Incomplete Lineage Sorting (ILS) in each resultant clade from the phylogeny, Joly et al.'s 2009 method in a coalescent scenario and Paterson’s D-statistic will be performed. Even when the main discordance sources between gene trees were not explored in detail yet, the data show that at least to some degree, processes such as genome duplication, hybridization, and/or ILS could be involved in the evolution of the group.

Keywords: adaptive radiations, Andes, genome duplication, hybridization, Senecio

Procedia PDF Downloads 111

Authors: Apostolos Lagarias, Anastasia Stratigea

Abstract:

Coastal urbanization is heavily affecting the Mediterranean, taking the form of linear urban sprawl along the coastal zone. This process is posing extreme pressure on ecosystems, leading to an unsustainable model of growth. The aim of this research is to analyze coastal urbanization patterns in the Mediterranean using High-resolution multi-temporal data provided by the Global Human Settlement Layer (GHSL) database. Methodology involves the estimation of a set of spatial metrics characterizing the density, aggregation/clustering and dispersion of built-up areas. As case study areas, the Spanish Coast and the Adriatic Italian Coast are examined. Coastalization profiles are examined and selected sub-areas massively affected by tourism development and suburbanization trends (Costa Blanca/Murcia, Costa del Sol, Puglia, Emilia-Romagna Coast) are analyzed and compared. Results show that there are considerable differences between the Spanish and the Italian typologies of spatial development, related to the land use structure and planning policies applied in each case. Monitoring and analyzing spatial patterns could inform integrated Mediterranean strategies for coastal areas and redirect spatial/environmental policies towards a more sustainable model of growth

Keywords: coastalization, Mediterranean, multi-temporal, urban sprawl, spatial metrics

Procedia PDF Downloads 110

Authors: Shagufta Jabeen, Faez J. Firdaus Abdullah, Zunita Zakaria, Nurulfiza M. Isa, Yung C. Tan, Wai Y. Yee, Abdul R. Omar

Abstract:

Pasteurella multocida (PM) is an important veterinary opportunistic pathogen particularly associated with septicemic pasteurellosis, pneumonic pasteurellosis and hemorrhagic septicemia in cattle and buffaloes. P. multocida serotype A has been reported to cause fatal pneumonia and septicemia. Pasteurella multocida subspecies multocida of serotype A Malaysian isolate PMTB2.1 was first isolated from buffaloes died of septicemia. In this study, the genome of P. multocida strain PMTB2.1 was sequenced using third-generation sequencing technology, PacBio RS2 system and analyzed bioinformatically via de novo analysis followed by in-depth analysis based on comparative genomics. Bioinformatics analysis based on de novo assembly of PacBio raw reads generated 3 contigs followed by gap filling of aligned contigs with PCR sequencing, generated a single contiguous circular chromosome with a genomic size of 2,315,138 bp and a GC content of approximately 40.32% (Accession number CP007205). The PMTB2.1 genome comprised of 2,176 protein-coding sequences, 6 rRNA operons and 56 tRNA and 4 ncRNAs sequences. The comparative genome sequence analysis of PMTB2.1 with nine complete genomes which include Actinobacillus pleuropneumoniae, Haemophilus parasuis, Escherichia coli and five P. multocida complete genome sequences including, PM70, PM36950, PMHN06, PM3480, PMHB01 and PMTB2.1 was carried out based on OrthoMCL analysis and Venn diagram. The analysis showed that 282 CDs (13%) are unique to PMTB2.1and 1,125 CDs with orthologs in all. This reflects overall close relationship of these bacteria and supports the classification in the Gamma subdivision of the Proteobacteria. In addition, genomic distance analysis among all nine genomes indicated that PMTB2.1 is closely related with other five Pasteurella species with genomic distance less than 0.13. Synteny analysis shows subtle differences in genetic structures among different P.multocida indicating the dynamics of frequent gene transfer events among different P. multocida strains. However, PM3480 and PM70 exhibited exceptionally large structural variation since they were swine and chicken isolates. Furthermore, genomic structure of PMTB2.1 is more resembling that of PM36950 with a genomic size difference of approximately 34,380 kb (smaller than PM36950) and strain-specific Integrative and Conjugative Elements (ICE) which was found only in PM36950 is absent in PMTB2.1. Meanwhile, two intact prophages sequences of approximately 62 kb were found to be present only in PMTB2.1. One of phage is similar to transposable phage SfMu. The phylogenomic tree was constructed and rooted with E. coli, A. pleuropneumoniae and H. parasuis based on OrthoMCL analysis. The genomes of P. multocida strain PMTB2.1 were clustered with bovine isolates of P. multocida strain PM36950 and PMHB01 and were separated from avian isolate PM70 and swine isolates PM3480 and PMHN06 and are distant from Actinobacillus and Haemophilus. Previous studies based on Single Nucleotide Polymorphism (SNPs) and Multilocus Sequence Typing (MLST) unable to show a clear phylogenetic relatedness between Pasteurella multocida and the different host. In conclusion, this study has provided insight on the genomic structure of PMTB2.1 in terms of potential genes that can function as virulence factors for future study in elucidating the mechanisms behind the ability of the bacteria in causing diseases in susceptible animals.

Keywords: comparative genomics, DNA sequencing, phage, phylogenomics

Procedia PDF Downloads 157

Authors: Pietro D'Ambrosio, Roberta D'Ambrosio

Abstract:

The upgrading of the architectural and urban heritage of the urban historic centers almost always involves the planning for the reuse and refunctionalization of the structures. Such interventions have complexities linked to the need to take into account the urban and social context in which the structure and its intrinsic characteristics such as historical and artistic value are inserted. To these, of course, we have to add the need to make a preliminary estimate of recovery costs and more generally to assess the economic and financial sustainability of the whole project of re-socialization. Particular difficulties are encountered during the pre-assessment of costs since it is often impossible to perform analytical surveys and structural tests for both structural conditions and obvious cost and time constraints. The methodology proposed in this work, based on a multidisciplinary and data-driven approach, is aimed at obtaining, at very low cost, reasonably priced economic evaluations of the interventions to be carried out. In addition, the specific features of the approach used, derived from the predictive analysis techniques typically applied in complex IT domains (big data analytics), allow to obtain as a result indirectly the evaluation process of a shared database that can be used on a generalized basis to estimate such other projects. This makes the methodology particularly indicated in those cases where it is expected to intervene massively across entire areas of historical city centers. The methodology has been partially tested during a study aimed at assessing the feasibility of a project for the reuse of the monumental complex of San Massimo, located in the historic center of Salerno, and is being further investigated.

Keywords: evaluation, methodology, restoration, reuse

Procedia PDF Downloads 152

Authors: S. Jalaja, A. M. Vijaya Prakash

Abstract:

Recursive combination of an algorithm based on Karatsuba multiplication is exploited to design a generalized transpose and parallel Finite Impulse Response (FIR) Filter. Mid-range Karatsuba multiplication and Carry Save adder based on Karatsuba multiplication reduce time complexity for higher order multiplication implemented up to n-bit. As a result, we design modified N-tap Transpose and Parallel Symmetric FIR Filter Structure using Karatsuba algorithm. The mathematical formulation of the FFA Filter is derived. The proposed architecture involves significantly less area delay product (APD) then the existing block implementation. By adopting retiming technique, hardware cost is reduced further. The filter architecture is designed by using 90 nm technology library and is implemented by using cadence EDA Tool. The synthesized result shows better performance for different word length and block size. The design achieves switching activity reduction and low power consumption by applying with and without retiming for different combination of the circuit. The proposed structure achieves more than a half of the power reduction by adopting with and without retiming techniques compared to the earlier design structure. As a proof of the concept for block size 16 and filter length 64 for CKA method, it achieves a 51% as well as 70% less power by applying retiming technique, and for CSA method it achieves a 57% as well as 77% less power by applying retiming technique compared to the previously proposed design.

Keywords: carry save adder Karatsuba multiplication, mid range Karatsuba multiplication, modified FFA and transposed filter, retiming

Procedia PDF Downloads 209

Authors: Rihab Hamdi, Amel Hadri Hamida, Fatiha Khelili, Sakina Zerouali, Ouafae Bennis

Abstract:

This paper features a comparative study performance of sliding mode controller (SMC) for closed-loop voltage control of direct current to direct current (DC-DC) three-cells buck converter connected in parallel, operating in continuous conduction mode (CCM), based on pulse-width modulation (PWM) with SMC based on hysteresis modulation (HM) where an adaptive feedforward technique is adopted. On one hand, for the PWM-based SM, the approach is to incorporate a fixed-frequency PWM scheme which is effectively a variant of SM control. On the other hand, for the HM-based SM, oncoming an adaptive feedforward control that makes the hysteresis band variable in the hysteresis modulator of the SM controller in the aim to restrict the switching frequency variation in the case of any change of the line input voltage or output load variation are introduced. The results obtained under load change, input change and reference change clearly demonstrates a similar dynamic response of both proposed techniques, their effectiveness is fast and smooth tracking of the desired output voltage. The PWM-based SM technique has greatly improved the dynamic behavior with a bit advantageous compared to the HM-based SM technique, as well as provide stability in any operating conditions. Simulation studies in MATLAB/Simulink environment have been performed to verify the concept.

Keywords: DC-DC converter, hysteresis modulation, parallel multi-cells converter, pulse-width modulation, robustness, sliding mode control

Procedia PDF Downloads 142

Authors: Siti Khadijah Che Osmi, Mohammed Ahmad Syed

Abstract:

Underground structures are crucial components which required detailed analysis and design. Tunnels, for instance, are massively constructed as transportation infrastructures and utilities network especially in urban environments. Considering their prime importance to the economy and public safety that cannot be compromised, thus any instability to these tunnels will be highly detrimental to their performance. Recent experience suggests that tunnels become vulnerable during earthquakes and blast scenarios. However, a very limited amount of studies has been carried out to study and understanding the dynamic response and performance of underground tunnels under those unpredictable extreme hazards. In view of the importance of enhancing the resilience of these structures, the overall aims of the study are to evaluate probabilistic future performance of shallow tunnels subjected to seismic and blast loads by developing detailed fragility analysis. Critical non-linear time history numerical analyses using sophisticated finite element software Midas GTS NX have been presented about the current methods of analysis, taking into consideration of structural typology, ground motion and explosive characteristics, effect of soil conditions and other associated uncertainties on the tunnel integrity which may ultimately lead to the catastrophic failure of the structures. The proposed fragility curves for both extreme loadings are discussed and compared which provide significant information the performance of the tunnel under extreme hazards which may beneficial for future risk assessment and loss estimation.

Keywords: fragility analysis, seismic loads, shallow tunnels, blast loads

Procedia PDF Downloads 316

Authors: Sergio Tovar-Pérez, Sebastian Töpfer, Markus Gräfe

Abstract:

The work proposes a technique that decreases the detection acquisition time of quantum holography schemes down to one-third; this allows the possibility to image moving objects. Since its invention, quantum holography with undetected photon schemes has gained interest in the scientific community. This is mainly due to its ability to tailor the detected wavelengths according to the needs of the scheme implementation. Yet this wavelength flexibility grants the scheme a wide range of possible applications; an important matter was yet to be addressed. Since the scheme uses digital phase-shifting techniques to retrieve the information of the object out of the interference pattern, it is necessary to acquire a set of at least four images of the interference pattern along with well-defined phase steps to recover the full object information. Hence, the imaging method requires larger acquisition times to produce well-resolved images. As a consequence, the measurement of moving objects remains out of the reach of the imaging scheme. This work presents the use and implementation of a spatial light modulator along with a digital holographic technique called quasi-parallel phase-shifting. This technique uses the spatial light modulator to build a structured phase image consisting of a chessboard pattern containing the different phase steps for digitally calculating the object information. Depending on the reduction in the number of needed frames, the acquisition time reduces by a significant factor. This technique opens the door to the implementation of the scheme for moving objects. In particular, the application of this scheme in imaging alive specimens comes one step closer.

Keywords: quasi-parallel phase shifting, quantum imaging, quantum holography, quantum metrology

Procedia PDF Downloads 88

Authors: Naghmeh Zamani, Ashkan Pourkand, David Grow

Abstract:

This paper presents the design and mechanical model of a hybrid impedance/admittance haptic device optimized for applications, like bone drilling, spinal awl probe use, and other surgical techniques were high force is required in the tool-axial direction, and low impedance is needed in all other directions. The performance levels required cannot be satisfied by existing, off-the-shelf haptic devices. This design may allow critical improvements in simulator fidelity for surgery training. The device consists primarily of two low-mass (carbon fiber) plates with a rod passing through them. Collectively, the device provides 6 DOF. The rod slides through a bushing in the top plate and it is connected to the bottom plate with a universal joint, constrained to move in only 2 DOF, allowing axial torque display the user’s hand. The two parallel plates are actuated and located by means of four cables pulled by motors. The forward kinematic equations are derived to ensure that the plates orientation remains constant. The corresponding equations are solved using the Newton-Raphson method. The static force/torque equations are also presented. Finally, we present the predicted distribution of location error, cables velocity, cable tension, force and torque for the device. These results and preliminary hardware fabrication indicate that this design may provide a revolutionary approach for haptic display of many surgical procedures by means of an architecture that allows arbitrary workspace scaling. Scaling of the height and width can be scaled arbitrarily.

Keywords: cable direct driven robot, haptics, parallel plates, bone drilling

Procedia PDF Downloads 237

Authors: H. Imad, Y. Cheah, O. Aamera

Abstract:

The aims of this research are to study the mitochondrial non-coding region by using the Sanger sequencing technique and establish the degree of variation characteristics of a fragment. FTA® Technology (FTA™ paper DNA extraction) utilized to extract DNA. A portion of a non-coding region encompassing positions 37 to 340 amplified in accordance with the Anderson reference sequence. PCR products purified by EZ-10 spin column then sequenced and detected by using the ABI 3730xL DNA Analyzer. New polymorphic positions 57, 63, and 101 are described may in future be suitable sources for identification purpose. The data obtained can be used to identify variable nucleotide positions characterized by frequent occurrence most promising for identification variants.

Keywords: encompassing nucleotide positions 37 to 340, HVII, Iraq, mitochondrial DNA, polymorphism, frequency

Procedia PDF Downloads 730

Authors: N. C. van der Merwe, J. Oosthuizen, M. F. Makhetha, J. Adams, B. K. Dajee, S-R. Schneider

Abstract:

Women representing high-risk breast cancer families, who tested negative for pathogenic mutations in BRCA1 and BRCA2, are four times more likely to develop breast cancer compared to women in the general population. Sequencing of genes involved in genomic stability and DNA repair led to the identification of novel contributors to familial breast cancer risk. These include BLM and PALB2. Bloom's syndrome is a rare homozygous autosomal recessive chromosomal instability disorder with a high incidence of various types of neoplasia and is associated with breast cancer when in a heterozygous state. PALB2, on the other hand, binds to BRCA2 and together, they partake actively in DNA damage repair. Archived DNA samples of 66 BRCA1/2 negative high-risk breast cancer patients were retrospectively selected based on the presence of an extensive family history of the disease ( > 3 affecteds per family). All coding regions and splice-site boundaries of both genes were screened using High-Resolution Melting Analysis. Samples exhibiting variation were bi-directionally automated Sanger sequenced. The clinical significance of each variant was assessed using various in silico and splice site prediction algorithms. Comprehensive screening identified a total of 11 BLM and 26 PALB2 variants. The variants detected ranged from global to rare and included three novel mutations. Three BLM and two PALB2 likely pathogenic mutations were identified that could account for the disease in these extensive breast cancer families in the absence of BRCA mutations (BLM c.11T > A, p.V4D; BLM c.2603C > T, p.P868L; BLM c.3961G > A, p.V1321I; PALB2 c.421C > T, p.Gln141Ter; PALB2 c.508A > T, p.Arg170Ter). Conclusion: The study confirmed the contribution of pathogenic mutations in BLM and PALB2 to the familial breast cancer burden in South Africa. It explained the presence of the disease in 7.5% of the BRCA1/2 negative families with an extensive family history of breast cancer. Segregation analysis will be performed to confirm the clinical impact of these mutations for each of these families. These results justify the inclusion of both these genes in a comprehensive breast and ovarian next generation sequencing cancer panel and should be screened simultaneously with BRCA1 and BRCA2 as it might explain a significant percentage of familial breast and ovarian cancer in South Africa.

Keywords: Bloom Syndrome, familial breast cancer, PALB2, South Africa

Procedia PDF Downloads 209

Authors: W. Hamaidia, T. Zebbiche

Abstract:

This paper presents the design of axisymmetric supersonic nozzles, in order to accelerate a supersonic flow to the desired Mach number and that having a small weight, in the same time gives a high thrust. The concerned nozzle gives a parallel and uniform flow at the exit section. The nozzle is divided into subsonic and supersonic regions. The supersonic portion is independent to the upstream conditions of the sonic line. The subsonic portion is used to give a sonic flow at the throat. In this case, nozzle gives a uniform and parallel flow at the exit section. It’s named by minimum length Nozzle. The study is done at high temperature, lower than the dissociation threshold of the molecules, in order to improve the aerodynamic performances. Our aim consists of improving the performances both by the increase of exit Mach number and the thrust coefficient and by reduction of the nozzle's mass. The variation of the specific heats with the temperature is considered. The design is made by the Method of Characteristics. The finite differences method with predictor-corrector algorithm is used to make the numerical resolution of the obtained nonlinear algebraic equations. The application is for air. All the obtained results depend on three parameters which are exit Mach number, the stagnation temperature, the chosen mesh in characteristics. A numerical simulation of nozzle through Computational Fluid Dynamics-FASTRAN was done to determine and to confirm the necessary design parameters.

Keywords: flux supersonic flow, axisymmetric minimum length nozzle, high temperature, method of characteristics, calorically imperfect gas, finite difference method, trust coefficient, mass of the nozzle, specific heat at constant pressure, air, error

Procedia PDF Downloads 131

Authors: Rachel Danielson, Brendan Bohannan, S.M. Tsai, Kyle Meyer, Jorge L.M. Rodrigues

Abstract:

The Amazon Rainforest is a global diversity hotspot and crucial carbon sink, but approximately 20% of its total extent has been deforested- primarily for the establishment of cattle pasture. Understanding the impact of this large-scale disturbance on soil microbial community composition and activity is crucial in understanding potentially consequential shifts in nutrient or greenhouse gas cycling, as well as adding to the body of knowledge concerning how these complex communities respond to human disturbance. In this study, surface soils (0-10cm) were collected from three forests and three 45-year-old pastures in Rondonia, Brazil (the Amazon state with the greatest rate of forest destruction) in order to determine the impact of forest conversion on microbial communities involved in nitrogen fixation. Soil chemical and physical parameters were paired with measurements of microbial activity and genetic profiles to determine how community composition and process rates relate to environmental conditions. Measuring both the natural abundance of 15N in total soil N, as well as incorporation of enriched 15N2 under incubation has revealed that conversion of primary forest to cattle pasture results in a significant increase in the rate of nitrogen fixation by free-living diazotrophs. Quantification of nifH gene copy numbers (an essential subunit encoding the nitrogenase enzyme) correspondingly reveals a significant increase of genes in pasture compared to forest soils. Additionally, genetic sequencing of both nifH genes and transcripts shows a significant increase in the diversity of the present and metabolically active diazotrophs within the soil community. Levels of both organic and inorganic nitrogen tend to be lower in pastures compared to forests, with ammonium rather than nitrate as the dominant inorganic form. However, no significant or consistent differences in total, extractable, permanganate-oxidizable, or loss-on-ignition carbon are present between the two land-use types. Forest conversion is associated with a 0.5- 1.0 unit pH increase, but concentrations of many biologically relevant nutrients such as phosphorus do not increase consistently. Increases in free-living diazotrophic community abundance and activity appear to be related to shifts in carbon to nitrogen pool ratios. Furthermore, there may be an important impact of transient, low molecular weight plant-root-derived organic carbon on free-living diazotroph communities not captured in this study. Preliminary analysis of nitrogenase gene variant composition using NovoSeq metagenomic sequencing indicates that conversion of forest to pasture may significantly enrich vanadium-based nitrogenases. This indication is complemented by a significant decrease in available soil molybdenum. Very little is known about the ecology of diazotrophs utilizing vanadium-based nitrogenases, so further analysis may reveal important environmental conditions favoring their abundance and diversity in soil systems. Taken together, the results of this study indicate a significant change in nitrogen cycling and diazotroph community composition with the conversion of the Amazon Rainforest. This may have important implications for the sustainability of cattle pastures once established since nitrogen is a crucial nutrient for forage grass productivity.

Keywords: free-living diazotrophs, land use change, metagenomic sequencing, nitrogen fixation

Procedia PDF Downloads 169

Authors: Richard Draper

Abstract:

A supercomputer can be constructed from identical building blocks which are small parallel processors connected by a network referred to as the local network. The routers have unused ports which are used to interconnect the building blocks. These connections are referred to as the global network. The address space has a global and a local component (g, l). The conventional way to connect the building blocks is to connect (g, l) to (g’,l). If there are K blocks, this requires K global ports in each router. If a block is of size M, the result is a machine with KM routers having diameter two. To increase the size of the machine to 2K blocks, each router connects to only half of the other blocks. The result is a larger machine but also one with greater diameter. This is a crude description of how the network of the CRAY XC® is designed. In this paper, a family of interconnection networks using routers with K global and M local ports is defined. Coordinates are (c,d, p) and the global connections are (c,d,p)↔(c’,p,d) which swaps p and d. The network is denoted D3(K,M) and is called a Swapped Dragonfly. D3(K,M) has KM2 routers and has diameter three, regardless of the size of K. To produce a network of size KM2 conventionally, diameter would be an increasing function of K. The family of Swapped Dragonflies has other desirable properties: 1) D3(K,M) scales linearly in K and quadratically in M. 2) If L < K, D3(K,M) contains many copies of D3(L,M). 3) If L < M, D3(K,M) contains many copies of D3(K,L). 4) D3(K,M) can perform an all-to-all exchange in KM2+KM time which is only slightly more than the time to do a one-to-all. This paper makes several contributions. It is the first time that a swap has been used to define a linearly scalable family of networks. Structural properties of this new family of networks are thoroughly examined. A synchronizing packet header is introduced. It specifies the path to be followed and it makes it possible to define highly parallel communication algorithm on the network. Among these is an all-to-all exchange in time KM2+KM. To demonstrate the effectiveness of the swap properties of the network of the CRAY XC® and D3(K,16) are compared.

Keywords: all-to-all exchange, CRAY XC®, Dragonfly, interconnection network, packet switching, swapped network, topology

Procedia PDF Downloads 99