Search results for: high through-put

Authors: Habib Gorine, Rabia Saleh

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Mobile Ad-Hoc Networks are the special type of wireless networks which share common security requirements with other networks such as confidentiality, integrity, authentication, and availability, which need to be addressed in order to secure data transfer through the network. Their routing protocols are vulnerable to various malicious attacks which could have a devastating consequence on data security. In this paper, three types of attacks such as selfish, gray hole, and black hole attacks have been applied to the two most important routing protocols in MANET named dynamic source routing and ad-hoc on demand distance vector in order to analyse and compare the impact of these attacks on the Network performance in terms of throughput, average delay, packet loss, and consumption of energy using NS2 simulator.

Keywords: MANET, wireless networks, routing protocols, malicious attacks, wireless networks simulation

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Authors: Vijay Kumar Singh, Pooja Kushwaha, Prabhat Ranjan, Krishna Kumar Ojha, Jitendra Kumar

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Present day high-throughput genomic technologies, NGS/microarrays, are producing large volume of data that require improved analysis methods to make sense of the data. The correlation between genes and samples has been regularly used to gain insight into many biological phenomena including, but not limited to, co-expression/co-regulation, gene regulatory networks, clustering and pattern identification. However, presence of outliers and violation of assumptions underlying Pearson correlation is frequent and may distort the actual correlation between the genes and lead to spurious conclusions. Here, we report a method to measure the strength of association between genes. The method assumes that the expression values of a gene are Bernoulli random variables whose outcome depends on the sample being probed. The method considers the two genes as uncorrelated if the number of sample with same outcome for both the genes (Ns) is equal to certainly expected number (Es). The extent of correlation depends on how far Ns can deviate from the Es. The method does not assume normality for the parent population, fairly unaffected by the presence of outliers, can be applied to qualitative data and it uses the binomial distribution to assess the significance of association. At this stage, we would not claim about the superiority of the method over other existing correlation methods, but our method could be another way of calculating correlation in addition to existing methods. The method uses binomial distribution, which has not been used until yet, to assess the significance of association between two variables. We are evaluating the performance of our method on NGS/microarray data, which is noisy and pierce by the outliers, to see if our method can differentiate between spurious and actual correlation. While working with the method, it has not escaped our notice that the method could also be generalized to measure the association of more than two variables which has been proven difficult with the existing methods.

Keywords: binomial distribution, correlation, microarray, outliers, transcriptome

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Authors: Juliana Lukša, Bazilė Ravoitytė, Elena Servienė, Saulius Serva

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Totiviridae L-A virus is a persistent Saccharomyces cerevisiae dsRNA virus. It encodes the major structural capsid protein Gag and Gag-Pol fusion protein, responsible for virus replication and encapsulation. These features also enable the copying of satellite dsRNAs (called M dsRNAs) encoding a secreted toxin and immunity to it (known as killer toxin). Viral capsid pore presumably functions in nucleotide uptake and viral mRNA release. During cell division, sporogenesis, and cell fusion, the virions remain intracellular and are transferred to daughter cells. By employing high throughput RNA sequencing data analysis, we describe the influence of solely L-A virus on the expression of genes in three different S. cerevisiae hosts. We provide a new perception into Totiviridae L-A virus-related transcriptional regulation, encompassing multiple bioinformatics analyses. Transcriptional responses to L-A infection were similar to those induced upon stress or availability of nutrients. It also delves into the connection between the cell metabolism and L-A virus-conferred demands to the host transcriptome by uncovering host proteins that may be associated with intact virions. To better understand the virus-host interaction, we applied differential proteomic analysis of virus particle-enriched fractions of yeast strains that harboreither complete killer system (L-A-lus and M-2 virus), M-2 depleted orvirus-free. Our analysis resulted in the identification of host proteins, associated with structural proteins of the virus (Gag and Gag-Pol). This research was funded by the European Social Fund under the No.09.3.3-LMT-K-712-19-0157“Development of Competences of Scientists, other Researchers, and Students through Practical Research Activities” measure.

Keywords: totiviridae, killer virus, proteomics, transcriptomics

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Authors: Janos Juhasz, Sandor Pongor, Balazs Ligeti

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Next-generation sequencing, especially whole genome shotgun sequencing, is becoming a common approach to gain insight into the microbiomes in a culture-independent way, even in clinical practice. It does not only give us information about the species composition of an environmental sample but opens the possibility to detect antimicrobial resistance and novel, or currently unknown, pathogens. Accurately and reliably detecting the microbial strains is a challenging task. Here we present a sensitive approach for detecting pathogens in metagenomics samples with special regard to detecting novel variants of known pathogens. We have developed a pipeline that uses fast, short read aligner programs (i.e., Bowtie2/BWA) and comprehensive nucleotide databases. Taxonomic binning is based on the lowest common ancestor (LCA) principle; each read is assigned to a taxon, covering the most significantly hit taxa. This approach helps in balancing between sensitivity and running time. The program was tested both on experimental and synthetic data. The results implicate that our method performs as good as the state-of-the-art BLAST-based ones, furthermore, in some cases, it even proves to be better, while running two orders magnitude faster. It is sensitive and capable of identifying taxa being present only in small abundance. Moreover, it needs two orders of magnitude less reads to complete the identification than MetaPhLan2 does. We analyzed an experimental anthrax dataset (B. anthracis strain BA104). The majority of the reads (96.50%) was classified as Bacillus anthracis, a small portion, 1.2%, was classified as other species from the Bacillus genus. We demonstrate that the evaluation of high-throughput sequencing data is feasible in a reasonable time with good classification accuracy.

Keywords: metagenomics, taxonomy binning, pathogens, microbiome, B. anthracis

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Authors: Peng Hou

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Natural products produced from marine bacteria serve as an immense reservoir for anti-infective drugs and therapeutic agents. Nowadays, heterologous expression of gene clusters of interests has been widely adopted as an effective strategy for natural product discovery. Briefly, the heterologous expression flowchart would be: biosynthetic gene cluster identification, pathway construction and expression, and product detection. However, gene cluster capture using traditional Transformation-associated recombination (TAR) protocol is low-efficient (0.5% positive colony rate). To make things worse, most of these putative new natural products are only predicted by bioinformatics analysis such as antiSMASH, and their corresponding natural products biosynthetic pathways are either not expressed or expressed at very low levels under laboratory conditions. Those setbacks have inspired us to focus on seeking new technologies to efficiently edit and refractor of biosynthetic gene clusters. Recently, two cutting-edge techniques have attracted our attention - the CRISPR-Cas9 and Gibson Assembly. By now, we have tried to pretreat Brevibacillus laterosporus strain genomic DNA with CRISPR-Cas9 nucleases that specifically generated breaks near the gene cluster of interest. This trial resulted in an increase in the efficiency of gene cluster capture (9%). Moreover, using Gibson Assembly by adding/deleting certain operon and tailoring enzymes regardless of end compatibility, the silent construct (~80kb) has been successfully refactored into an active one, yielded a series of analogs expected. With the appearances of the novel molecular tools, we are confident to believe that development of a high throughput mature pipeline for DNA assembly, transformation, product isolation and identification would no longer be a daydream for marine natural product discovery.

Keywords: biosynthesis, CRISPR-Cas9, DNA assembly, refactor, TAR cloning

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Authors: Yu Li, Dongyao Wang, Xiaobao Sun, Wei Ni

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In long-term evolution (LTE), the carriers around 5GHz are planned to be utilized without licenses to further enlarge system capacity. This feature is termed licensed assisted access (LAA). The channel sensing (clean channel assessment, CCA) is required before any transmission on these unlicensed carriers, in order to make sure the harmonious co-existence of LAA with other radio access technology in the unlicensed band. Obviously, the CCA threshold is very critical, which decides whether the transmission right following CCA is delivered in time and without collisions. An improper CCA threshold may cause buffer overflow of some eNodeBs if the eNodeBs are heavily loaded with the traffic. Thus, to solve these problems, we propose an adaptive threshold adjustment method for CCA in the LAA downlink. Both the load and transmission opportunities are concerned. The trend of the LAA throughput as the threshold varies is obtained, which guides the threshold adjustment. The co-existing between LAA and Wi-Fi is particularly tested. The results from system-level simulation confirm the merits of our design, especially in heavy traffic cases.

Keywords: LTE, LAA, CCA, threshold adjustment

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Authors: B. Akturk, N. Yuzer, N. Kabay

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High temperature is one of the most detrimental effects that cause important changes in concrete’s mechanical, physical, and thermo-physical properties. As a result of these changes, especially high strength concrete (HSC), may exhibit damages such as cracks and spallings. To overcome this problem, incorporating polymer fibers such as polypropylene (PP) in concrete is a very well-known method. In this study, using RRH as a sustainable material instead of PP fiber in HSC to prevent spallings and improve physical and thermo-physical properties were investigated. Therefore, seven HSC mixtures with 0.25 water to binder ratio were prepared, incorporating silica fume and blast furnace slag. PP and RRH were used at 0.2-0.5% and 0.5-3% by weight of cement, respectively. All specimens were subjected to high temperatures (20 (control), 300, 600 and 900˚C) with a heating rate of 2.5˚C/min and after cooling, residual physical and thermo-physical properties were determined.

Keywords: high temperature, high strength concrete, polypropylene fiber, raw rice husk, thermo-physical properties

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Authors: Mwafak Shakoor

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The purpose of this study was to reduce patient waiting times, improve system throughput and improve resources utilization in radiology department. A discrete event simulation model was developed using Arena simulation software to investigate different alternatives to improve the overall system delivery based on adding resource scenarios due to the linkage between patient waiting times and resource availability. The study revealed that there is no addition investment need to procure additional scanner but hospital management deploy managerial tactics to enhance machine utilization and reduce the long waiting time in the department.

Keywords: discrete event simulation, radiology department, arena, waiting time, healthcare modeling, computed tomography

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Authors: Tei Kim, Brooklynn McNeil, Kathryn Dunn, Douglas I. Walker

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To better characterize the relationship between complex chemical exposures and disease, our laboratory uses an approach that combines low-cost, polydimethylsiloxane (silicone) wristband samplers that absorb many of the chemicals we are exposed to with untargeted high-resolution mass spectrometry (HRMS) to characterize 1000’s of chemicals at a time. In studies with human populations, these wristbands can provide an important measure of our environment: however, there is a need to use this approach in large cohorts to study exposures associated with the disease. To facilitate the use of silicone samplers in large scale population studies, the goal of this research project was to establish automated sample preparation methods that improve throughput, robustness, and scalability of analytical methods for silicone wristbands. Using the Opentron OT2 automated liquid platform, which provides a low-cost and opensource framework for automated pipetting, we created two separate workflows that translate the manual wristband preparation method to a fully automated protocol that requires minor intervention by the operator. These protocols include a sequence generation step, which defines the location of all plates and labware according to user-specified settings, and a transfer protocol that includes all necessary instrument parameters and instructions for automated solvent extraction of wristband samplers. These protocols were written in Python and uploaded to GitHub for use by others in the research community. Results from this project show it is possible to establish automated and open source methods for the preparation of silicone wristband samplers to support profiling of many environmental exposures. Ongoing studies include deployment in longitudinal cohort studies to investigate the relationship between personal chemical exposure and disease.

Keywords: bioinformatics, automation, opentrons, research

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Authors: Vyacheslav Furtak, Merja Roivainen, Olga Mirochnichenko, Majid Laassri, Bella Bidzhieva, Tatiana Zagorodnyaya, Vladimir Chizhikov, Konstantin Chumakov

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Molecular epidemiology and environmental surveillance are parts of a rational strategy to control infectious diseases. They have been widely used in the worldwide campaign to eradicate poliomyelitis, which otherwise would be complicated by the inability to rapidly respond to outbreaks and determine sources of the infection. The conventional scheme involves isolation of viruses from patients and the environment, followed by their identification by nucleotide sequences analysis to determine phylogenetic relationships. This is a tedious and time-consuming process that yields definitive results when it may be too late to implement countermeasures. Because of the difficulty of high-throughput full-genome sequencing, most such studies are conducted by sequencing only capsid genes or their parts. Therefore the important information about the contribution of other parts of the genome and inter- and intra-species recombination to viral evolution is not captured. Here we propose a new approach based on the rapid concentration of sewage samples with tangential flow filtration followed by deep sequencing and reconstruction of nucleotide sequences of viruses present in the samples. The entire nucleic acids content of each sample is sequenced, thus preserving in digital format the complete spectrum of viruses. A set of rapid algorithms was developed to separate deep sequence reads into discrete populations corresponding to each virus and assemble them into full-length consensus contigs, as well as to generate a complete profile of sequence heterogeneities in each of them. This provides an effective approach to study molecular epidemiology and evolution of natural viral populations.

Keywords: poliovirus, eradication, environmental surveillance, laboratory diagnosis

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Authors: Tanmay Raj, Vedika Gupta

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For its groundbreaking and substantial power, cloud computing is today’s most popular breakthrough. It is a sort of Internet-based computing that allows users to request and receive numerous services in a cost-effective manner. Virtualization, grid computing, and utility computing are the most widely employed emerging technologies in cloud computing, making it the most powerful. However, cloud computing still has a number of key challenges, such as security, load balancing, and non-critical failure adaption, to name a few. The massive growth of cloud computing will put an undue strain on servers. As a result, network performance will deteriorate. A good load balancing adjustment can make cloud computing more productive and in- crease client fulfillment execution. Load balancing is an important part of cloud computing because it prevents certain nodes from being overwhelmed while others are idle or have little work to perform. Response time, cost, throughput, performance, and resource usage are all parameters that may be improved using load balancing.

Keywords: cloud computing, load balancing, computing, SIP server clusters

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Authors: Zainul A. Khan, Malik Z. Abdin, Jawaid A. Khan

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Begomoviruses belonging to the family Geminiviridae, have single-stranded circular DNA genomes that are monopartite or bipartite. The large intergenic region (LIR) of the monopartite and common region (CR) of bipartite begomoviruses possess promoter activity in their genomes. In this study, we have characterized novel bidirectional promoters from Cotton leaf curl Burewala virus (CLCuBuV) genome using high-throughput software and analyzed with PlantCARE, PLACE, Cister and PlantPAN databases. The promoters (Rep and CP promoters) were assayed both in stable and transient expression systems in tobacco as well as cotton plants. Rep and CP-based promoters from the LIR sequence of CLCuBuV and 35S promoter of Cauliflower mosaic virus (CaMV) were tagged with β-glucuronidase (GUS) and green fluorescent protein (GFP) reporter genes to check the efficacy of the promoters. Histochemical staining of GUS in transformed tobacco (Nicotiana tabacum cv. Xanthi) leaves showed higher GUS expression driven by CLCuBuV Rep (complimentary sense) promoter as compared to conventional CaMV 35S promoter and CLCuBuV CP (virion sense) promoter, respectively. GUS activity in individual plant cells driven by CLCuBuV Rep, CLCuBuV CP, and CaMV 35S promoter were quantified through fluorometric GUS assay and reverse transcription quantitative real-time PCR (RT-qPCR). The expression level of GUS tagged with CLCuBuV Rep promoter in the transformed tobacco plants was obtained 2 to 4 fold higher than CaMV 35S promoter. When CLCuBuV CP promoter was used, lower expression level was monitored than that by CaMV 35S promoter. The expression of GFP-tagged with CLCuBuV promoters was also investigated through agroinfiltration. The CLCuBuV Rep promoters showed stronger consistent transient expression in the leaves of N. benthamiana, N. tabacum and Gossypium hirsutum plants when compared with CaMV 35S and CLCuBuV CP promoter.

Keywords: Begmovirus, bidirectional promoter, CaMV 35S promoter, GFP, GUS, qPCR

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Authors: Salome Schulze

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The delay of students in completing their dissertations is a worldwide problem. At the University of South Africa where this research was done, only about a third of the students complete their studies within the required period of time. This study explored the reasons why the students interrupted their studies, and why they resumed their research at a later stage. If this knowledge could be utilised to improve the throughput of doctoral students, it could have significant economic benefits for institutions of higher education while at the same time enhancing their academic prestige. To inform the investigation, attention was given to key theories concerning the learning of doctoral students, namely the situated learning theory, the social capital theory and the self-regulated learning theory, based on the social cognitive theory of learning. Ten students in the faculty of Education were purposefully selected on the grounds of their poor progress, or of having been in the system for too long. The collection of the data was in accordance with a Finnish study, since the two studies had the same aims, namely to investigate student engagement and disengagement. Graphic elicitation interviews, based on visualisations were considered appropriate to collect the data. This method could stimulate the reflection and recall of the participants’ ‘stories’ with very little input from the interviewer. The interviewees were requested to visualise, on paper, their journeys as doctoral students from the time when they first registered. They were to indicate the significant events that occurred and which facilitated their engagement or disengagement. In the interviews that followed, they were requested to elaborate on these motivating or challenging events by explaining when and why they occurred, and what prompted them to resume their studies. The interviews were tape-recorded and transcribed verbatim. Information-rich data were obtained containing visual metaphors. The data indicated that when the students suffered a period of disengagement, it was sometimes related to a lack of self-regulated learning, in particular, a lack of autonomy, and the inability to manage their time effectively. When the students felt isolated from the academic community of practice disengagement also occurred. This included poor guidance by their supervisors, which accordingly deprived them of significant social capital. The study also revealed that situational factors at home or at work were often the main reasons for the students’ procrastinating behaviour. The students, however, remained in the system. They were motivated towards a renewed engagement with their studies if they were self-regulated learners, and if they felt a connectedness with the academic community of practice because of positive relationships with their supervisors and of participation in the activities of the community (e.g., in workshops or conferences). In support of their learning, networking with significant others who were sources of information provided the students with the necessary social capital. Generally, institutions of higher education cannot address the students’ personal issues directly, but they can deal with key institutional factors in order to improve the throughput of doctoral students. It is also suggested that graphic elicitation interviews be used more often in social research that investigates the learning and development of the students.

Keywords: doctoral students, engaging and disengaging experiences, graphic elicitation interviews, student procrastination

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Authors: Zineb Jibraili, Said Ouhadi, Jorge Arana

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Introduction: Organizational performance is recognized by some theorists as one-dimensional concept, and by others as multidimensional. This concept, which is already difficult to apply in traditional companies, is even harder to identify, to measure and to manage when voluntary organizations are concerned, essentially because of the complexity of that form of organizations such as sport clubs who are characterized by the multiple goals and multiple constituencies. Indeed, the new culture of professionalization and modernization around organizational performance emerges new pressures from the state, sponsors, members and other stakeholders which have required these sport organizations to become more performance oriented, or to build their capacity in order to better manage their organizational performance. The evaluation of performance can be made by evaluating the input (e.g. available resources), throughput (e.g. processing of the input) and output (e.g. goals achieved) of the organization. In non-profit organizations (NPOs), questions of performance have become increasingly important in the world of practice. To our knowledge, most of studies used the same methods to evaluate the performance in NPSOs, but no recent study has proposed a club-specific model. Based on a review of the studies that specifically addressed the organizational performance (and effectiveness) of NPSOs at operational level, the present paper aims to provide a multidimensional framework in order to understand, analyse and measure organizational performance of sport clubs. This paper combines all dimensions founded in literature and chooses the most suited of them to our model that we will develop in Moroccan sport clubs case. Method: We propose to implicate our unified model of evaluating organizational performance that takes into account all the limitations found in the literature. On a sample of Moroccan sport clubs ‘Football, Basketball, Handball and Volleyball’, for this purpose we use a qualitative study. The sample of our study comprises data from sport clubs (football, basketball, handball, volleyball) participating on the first division of the professional football league over the period from 2011 to 2016. Each football club had to meet some specific criteria in order to be included in the sample: 1. Each club must have full financial data published in their annual financial statements, audited by an independent chartered accountant. 2. Each club must have sufficient data. Regarding their sport and financial performance. 3. Each club must have participated at least once in the 1st division of the professional football league. Result: The study showed that the dimensions that constitute the model exist in the field with some small modifications. The correlations between the different dimensions are positive. Discussion: The aim of this study is to test the unified model emerged from earlier and narrower approaches for Moroccan case. Using the input-throughput-output model for the sketch of efficiency, it was possible to identify and define five dimensions of organizational effectiveness applied to this field of study.

Keywords: organisational performance, model multidimensional, evaluation organizational performance, sport clubs

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Authors: Pedro M. Rodrigues, Claudia Raposo, Denise Schrama, Marco Cerqueira

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Farmed fish welfare is a very recent concept, widely discussed among the scientific community. Consumers’ interest regarding farmed animal welfare standards has significantly increased in the last years posing a huge challenge to producers in order to maintain an equilibrium between good welfare principles and productivity, while simultaneously achieve public acceptance. The major bottleneck of standard aquaculture is to impair considerably fish welfare throughout the production cycle and with this, the quality of fish protein. Welfare assessment in farmed fish is undertaken through the evaluation of fish stress responses. Primary and secondary stress responses include release of cortisol and glucose and lactate to the blood stream, respectively, which are currently the most commonly used indicators of stress exposure. However, the reliability of these indicators is highly dubious, due to a high variability of fish responses to an acute stress and the adaptation of the animal to a repetitive chronic stress. Our objective is to use comparative proteomics to identify and validate a fingerprint of proteins that can present an more reliable alternative to the already established welfare indicators. In this way, the culture conditions will improve and there will be a higher perception of mechanisms and metabolic pathway involved in the produced organism’s welfare. Due to its high economical importance in Portuguese aquaculture Gilthead seabream will be the elected species for this study. Protein extracts from Gilthead Seabream fish muscle, liver and plasma, reared for a 3 month period under optimized culture conditions (control) and induced stress conditions (Handling, high densities, and Hipoxia) are collected and used to identify a putative fish welfare protein markers fingerprint using a proteomics approach. Three tanks per condition and 3 biological replicates per tank are used for each analisys. Briefly, proteins from target tissue/fluid are extracted using standard established protocols. Protein extracts are then separated using 2D-DIGE (Difference gel electrophoresis). Proteins differentially expressed between control and induced stress conditions will be identified by mass spectrometry (LC-Ms/Ms) using NCBInr (taxonomic level - Actinopterygii) databank and Mascot search engine. The statistical analysis is performed using the R software environment, having used a one-tailed Mann-Whitney U-test (p < 0.05) to assess which proteins were differentially expressed in a statistically significant way. Validation of these proteins will be done by comparison of the RT-qPCR (Quantitative reverse transcription polymerase chain reaction) expressed genes pattern with the proteomic profile. Cortisol, glucose, and lactate are also measured in order to confirm or refute the reliability of these indicators. The identified liver proteins under handling and high densities induced stress conditions are responsible and involved in several metabolic pathways like primary metabolism (i.e. glycolysis, gluconeogenesis), ammonia metabolism, cytoskeleton proteins, signalizing proteins, lipid transport. Validition of these proteins as well as identical analysis in muscle and plasma are underway. Proteomics is a promising high-throughput technique that can be successfully applied to identify putative welfare protein biomarkers in farmed fish.

Keywords: aquaculture, fish welfare, proteomics, welfare biomarkers

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Authors: Aarnav Singh, Jayesh Ghatate, Tarush Pandey

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Non-Governmental Organizations (NGOs) play a crucial role in addressing societal challenges, relying heavily on financial transactions to fund their impactful initiatives. However, traditional financial systems can be cumbersome and lack transparency, hindering the efficiency and trustworthiness of NGO operations. The Ethereum main-net, while pioneering the decentralized finance landscape, grapples with inherent scalability challenges, restricting its transaction throughput to a range of 15-45 transactions per second (TPS). This limitation poses substantial obstacles for NGOs engaging in swift and dynamic financial transactions critical to their operational efficiency. This research is a comprehensive exploration of the intricacies of these scalability challenges and delves into the design and implementation of a purpose-built blockchain system explicitly crafted to surmount these constraints.

Keywords: non-governmental organizations, decentralized system, zero knowledge Ethereum virtual machine, decentralized application

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Authors: Patricia M. B. Saint-Vincent, Anna Furches, Stephanie Galanie, Erica Teixeira Prates, Piet Jones, Nancy Engle, David Kainer, Wellington Muchero, Daniel Jacobson, Timothy J. Tschaplinski

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Uridine diphosphate-glycosyltransferases (UGTs) are enzymes that catalyze sugar transfer to a variety of plant metabolites. UGT substrates, which include plant secondary metabolites involved in lignification, demonstrate new activities and incorporation when glycosylated. Knowledge of UGT function, substrate specificity, and enzyme products is important for plant engineering efforts, especially related to increasing plant biomass through lignification. UGTs in Populus trichocarpa, a biofuel feedstock, and model woody plant, were selected from a pool of gene candidates using rapid prioritization strategies. A functional genomics workflow, consisting of a metabolite genome-wide association study (mGWAS), expression of synthetic codon-optimized genes, and high-throughput biochemical assays with mass spectrometry-based analysis, was developed for determining the substrates and products of previously-uncharacterized enzymes. A total of 40 UGTs from P. trichocarpa were profiled, and the biochemical assay results were compared to predicted mGWAS connections. Assay results confirmed seven of 11 leaf mGWAS associations and demonstrated varying levels of substrate specificity among candidate UGTs. P. trichocarpa UGT substrate processing confirms the role of these newly-characterized enzymes in lignan, flavonoid, and phytohormone metabolism, with potential implications for cell wall biosynthesis, nitrogen uptake, and biotic and abiotic stress responses.

Keywords: Populus, metabolite-gene associations, GWAS, bio feedstocks, glycosyltransferase

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Authors: Mark Watson, J.-F. Bousquet, Adam Forget

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A magnetic induction based underwater communication link is evaluated using an analytical model and a custom Finite-Difference Time-Domain (FDTD) simulation tool. The analytical model is based on the Sommerfeld integral, and a full-wave simulation tool evaluates Maxwell’s equations using the FDTD method in cylindrical coordinates. The analytical model and FDTD simulation tool are then compared and used to predict the system performance for various transmitter depths and optimum frequencies of operation. To this end, the system bandwidth, signal to noise ratio, and the magnitude of the induced voltage are used to estimate the expected channel capacity. The models show that in seawater, a relatively low-power and small coils may be capable of obtaining a throughput of 40 to 300 kbps, for the case where a transmitter is at depths of 1 to 3 m and a receiver is at a height of 1 m.

Keywords: magnetic induction, FDTD, underwater communication, Sommerfeld

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Authors: N. Meddeb, A. M. Makhlouf, M. A. Ben Ayed

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Due to the real-time requirement of message in Vehicular Ad hoc NETworks (VANET), it is necessary to authenticate vehicles to achieve security, efficiency, and conditional privacy-preserving. Privacy is of utmost relevance in VANETs. For this reason, we have proposed a new protocol called ‘Multilevel Authentication Protocol’ (MAP) that considers different vehicle categories. The proposed protocol is based on our Multilevel Authentication protocol for Vehicular networks (MAVnet). But the MAP leads to human safety, where the priority is given to the ambulance vehicles. For evaluation, we used the Java language to develop a demo application and deployed it on the Network Security Simulation (Nessi2). Compared with existing authentication protocols, MAP markedly enhance the communication overhead and decreases the delay of exchanging messages while preserving conditional privacy.

Keywords: Vehicular Ad hoc NETworks (VANET), vehicle categories, safety, databases, privacy, authentication, throughput, delay

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Authors: Omojokun G. Aju, Adedayo O. Sule

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ZigBee wireless sensor and control network is one of the most popularly deployed wireless technologies in recent years. This is because ZigBee is an open standard lightweight, low-cost, low-speed, low-power protocol that allows true operability between systems. It is built on existing IEEE 802.15.4 protocol and therefore combines the IEEE 802.15.4 features and newly added features to meet required functionalities thereby finding applications in wide variety of wireless networked systems. ZigBee‘s current focus is on embedded applications of general-purpose, inexpensive, self-organising networks which requires low to medium data rates, high number of nodes and very low power consumption such as home/industrial automation, embedded sensing, medical data collection, smart lighting, safety and security sensor networks, and monitoring systems. Although the ZigBee design specification includes security features to protect data communication confidentiality and integrity, however, when simplicity and low-cost are the goals, security is normally traded-off. A lot of researches have been carried out on ZigBee technology in which emphasis has mainly been placed on ZigBee network performance characteristics such as energy efficiency, throughput, robustness, packet delay and delivery ratio in different scenarios and applications. This paper investigate and analyse the data accuracy, network implementation difficulties and security challenges of ZigBee network applications in star-based and mesh-based topologies with emphases on its home monitoring application using the ZigBee ProBee ZE-10 development boards for the network setup. The paper also expose some factors that need to be considered when designing ZigBee network applications and suggest ways in which ZigBee network can be designed to provide more resilient to network attacks.

Keywords: home monitoring, IEEE 802.14.5, topology, wireless security, wireless sensor network (WSN), ZigBee

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Authors: Vaishnavi Patil, K. M. Kurundkar

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Electrical Drives play a vital role in industry development and applications. Drives have an inevitable part in the needs of various fields such as industry, commercial, and domestic applications. The development of material technology, Power Electronics devices, and accompanying applications led to the focus of industry and researchers on high-speed electrical drives. Numerous articles charted the applications of electrical machines and various converters for high-speed applications. The choice depends on the application under study. This paper goals to highlight high-speed applications, main challenges, and some applications of electrical drives in the field.

Keywords: high-speed, electrical machines, drives, applications

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Authors: Noha Al Majid, Said Mazer, Moulhime El Bekkali, Catherine Algani, Mahmoud Mehdi

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A low noise figure (NF) and high linearity V-band Low Noise Amplifier (LNA) is reported in this article. The LNA compromises a three-stage cascode configuration. This LNA will be used as a part of a WPAN (Wireless Personal Area Network) receiver in the millimeter-wave band at 60 GHz. It is designed according to the MMIC technology (Monolithic Microwave Integrated Circuit) in PH 15 process from UMS foundry and uses a 0.15 μm GaAs PHEMT (Pseudomorphic High Electron Mobility Transistor). The particularity of this LNA compared to other LNAs in literature is its very low noise figure which is equal to 1 dB and its high linearity (IIP3 is about 22 dB). The LNA consumes 0.24 Watts, achieving a high gain which is about 23 dB, an input return loss better than -10 dB and an output return loss better than -8 dB.

Keywords: low noise amplifier, V-band, MMIC technology, LNA, amplifier, cascode, pseudomorphic high electron mobility transistor (PHEMT), high linearity

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Authors: Gilbert Makanda, Roelf Sypkens

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In this study we investigated the relevance of high school mathematics in university education. The paper particularly focused on whether the concepts taught in high school are enough for engineering courses at diploma level. The study identified particular concepts that are required in engineering courses whether they were adequately covered in high school. A questionnaire was used to investigate whether relevant topics were covered in high school. The respondents were 228 first year students at the Central University of Technology in the Faculty of Engineering and Information Technology. The study indicates that there are some topics such as integration, complex numbers and matrices that are not done at high schools and are required in engineering courses at university. It is further observed that some students did not cover the topics that are in the current syllabus. Female students enter the university less prepared than their male counterparts. More than 30% of the respondents in this study felt that high school mathematics was not useful for them to be able to do engineering courses.

Keywords: high school mathematics, university education, SPSS package, students' perceptions

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Authors: Yasir Arafat, Asma Shah, Hua Shao

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Background and Aims: Legume/cereal intercropping is used worldwide for enhancement in biomass and yield of cereal crops. However, because of intercropping, the belowground biological and chemical interactions and their effect on physiological parameters and yield of crops are limited. Methods: Wheat faba bean (WF) intercropping was designed to understand the underlying changes in the soil's chemical environment, soil microbial communities, and effect on growth and yield parameters. Experimental plots were established as having no root partition (NRP), semi-root partition (SRP), complete root partition (CRP), and their sole cropping (CK). Low molecular weight organic acids (LMWOAs) were determined by GC-MS, and high throughput sequencing of the 16S rRNA gene was carried out to screen microbial structure and composition in different root partitions of the WF intercropping system. Results: We show that intercropping induced a shift in the relative abundance of some genera of plant growth promoting rhizobacteria (PGPR) such as Allorhizobium, Neorhizobium, Pararhizobium, and Rhizobium species and resulted in better growth and yield performance of wheat. Moreover, as the plant's distance of wheat from faba beans decreased, the diversity of microbes increased, and a positive effect was observed on physiological traits and crop yield. Furthermore, an abundance and positive correlations of palmitic acid, arachidic acid, stearic acid, and 9-Octadecenoic with PGPR were recorded in the root zone of WF intercropping, which can play an important role in this facilitative mechanism of enhancing growth and yield of cereals. Conclusion: The two treatments clearly affected soil microbial and chemical composition, which can be reflected in growth and yield enhancement.

Keywords: intercropping, microbial community, LMWOAs, PGPR, soil chemical environment

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Authors: Meimei Shi

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Objectives: The identification of endangered species, especially simultaneous detection of multiple species in complex samples, plays a critical role in alleged wildlife crime incidents and prevents illegal trade. This study was to develop a multi-locus DNA metabarcoding method for endangered animal species identification. Methods: Several pairs of universal primers were designed according to the mitochondria conserved gene regions. Experimental mixtures were artificially prepared by mixing well-defined species, including endangered species, e.g., forest musk, bear, tiger, pangolin, and sika deer. The artificial samples were prepared with 1-16 well-characterized species at 1% to 100% DNA concentrations. After multiplex-PCR amplification and parameter modification, the amplified products were analyzed by capillary electrophoresis and used for NGS library preparation. The DNA metabarcoding was carried out based on Illumina MiSeq amplicon sequencing. The data was processed with quality trimming, reads filtering, and OTU clustering; representative sequences were blasted using BLASTn. Results: According to the parameter modification and multiplex-PCR amplification results, five primer sets targeting COI, Cytb, 12S, and 16S, respectively, were selected as the NGS library amplification primer panel. High-throughput sequencing data analysis showed that the established multi-locus DNA metabarcoding method was sensitive and could accurately identify all species in artificial mixtures, including endangered animal species Moschus berezovskii, Ursus thibetanus, Panthera tigris, Manis pentadactyla, Cervus nippon at 1% (DNA concentration). In conclusion, the established species identification method provides technical support for customs and forensic scientists to prevent the illegal trade of endangered animals and their products.

Keywords: DNA metabarcoding, endangered animal species, mitochondria nucleic acid, multi-locus

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Authors: Surya Prasad Sharma, Suyash Katdare, Syed Ainul Hussain

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Human-induced factors contributed to the population decline of crocodylians in India which became evident by the mid-20th century when authorities forewarned the extinction risk for the crocodile and proposed regulation in the crocodile trade. The proposed action led to the enactment of national and international wildlife regulations to prohibit the trade-in of crocodile skins and parts. Subsequently, conservation translocation programs were initiated to restore the species in the wild through a 'head-start' approach. In India, the crocodile conservation program, which began in the early 1970s, has been one of India's longest-running conservation initiatives. The gharial (Gavialis gangeticus) population has benefitted, and the gharial number increased rapidly owing to these efforts. The immediate risk of extinction was averted as the gharial has recovered due to decades-long cumulative conservation efforts, the consideration of the genetic for monitoring the recovery of the recovered populations is still lacking. Hence, we assessed the genetic diversity of the Girwa gharial population in India using six polymorphic nuclear microsatellites loci and mitochondrial control region. The number of alleles per loci ranged between 2 to 5, and the allelic richness (Ar) was 2.67 ± 0.49, and the observed (Ho) and expected (He) heterozygosities were 0.42 ± 0.08 and 0.42 ± 0.09, respectively. The M-ratio yielded a value of (0.41 ± 0.16) lower than critical M, suggesting a genetic bottleneck in the Girwa population. We observed more mitochondrial control region haplotypes in the Girwa population than previously reported in the largest gharial population in the Chambal River. Overall, our study indicates that genetic diversity remains low despite the recovery in the Girwa population. Hence, we recommend a range-wide genetic assessment of gharial populations using high-throughput techniques to identify the source population and plan future translocation programs.

Keywords: conservation translocation, recovery, crocodile, bottleneck

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Authors: Mona Almansoori, Ahmed Mustafa, Ahmad Elshamy

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Wireless sensor network was formed by a combination of nodes, systematically it transmitting the data to their base stations, this transmission data can be easily compromised if the limited processing power and the data consistency from these nodes are kept in mind; there is always a discussion to address the secure data transfer or transmission in actual time. This will present a mechanism to securely transmit the data over a chain of sensor nodes without compromising the throughput of the network by utilizing available battery resources available in the sensor node. Our methodology takes many different advantages of Z-MAC protocol for its efficiency, and it provides a unique key by sharing the mechanism using neighbor node MAC address. We present a light weighted data integrity layer which is embedded in the Z-MAC protocol to prove that our protocol performs well than Z-MAC when we introduce the different attack scenarios.

Keywords: hybrid MAC protocol, data integrity, lightweight encryption, neighbor based key sharing, sensor node dataprocessing, Z-MAC

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Authors: Wael M. Rabeh, Cesar Carrasco-Lopez, Juliana C. Ferreira, Pance Naumov

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Bioluminescence, the emission of light from a biological process, is found in various living organisms including bacteria, fireflies, beetles, fungus and different marine organisms. Luciferase is an enzyme that catalyzes a two steps oxidation of luciferin in the presence of Mg2+ and ATP to produce oxyluciferin and releases energy in the form of light. The luciferase assay is used in biological research and clinical applications for in vivo imaging, cell proliferation, and protein folding and secretion analysis. The luciferase enzyme consists of two domains, a large N-terminal domain (1-436 residues) that is connected to a small C-terminal domain (440-544) by a flexible loop that functions as a hinge for opening and closing the active site. The two domains are separated by a large cleft housing the active site that closes after binding the substrates, luciferin and ATP. Even though all insect luciferases catalyze the same chemical reaction and share 50% to 90% sequence homology and high structural similarity, they emit light of different colors from green at 560nm to red at 640 nm. Currently, the majority of the structural and biochemical studies have been conducted on green-emitting firefly luciferases. To address the color emission mechanism, we expressed and purified two luciferase enzymes with blue-shifted green and red emission from indigenous Brazilian species Amydetes fanestratus and Phrixothrix, respectively. The two enzymes naturally emit light of different colors and they are an excellent system to study the color-emission mechanism of luciferases, as the current proposed mechanisms are based on mutagenesis studies. Using a vapor-diffusion method and a high-throughput approach, we crystallized and solved the crystal structure of both enzymes, at 1.7 Å and 3.1 Å resolution respectively, using X-ray crystallography. The free enzyme adopted two open conformations in the crystallographic unit cell that are different from the previously characterized firefly luciferase. The blue-shifted green luciferase crystalized as a monomer similar to other luciferases reported in literature, while the red luciferases crystalized as an octamer and was also purified as an octomer in solution. The octomer conformation is the first of its kind for any insect’s luciferase, which might be relate to the red color emission. Structurally designed mutations confirmed the importance of the transition between the open and close conformations in the fine-tuning of the color and the characterization of other interesting mutants is underway.

Keywords: bioluminescence, enzymology, structural biology, x-ray crystallography

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Authors: S. Slimani, B. Djellouli

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Novel materials and innovative device structures has become necessary for the future of CMOS. High mobility materials like Ge is a very promising material due to its high mobility and is being considered to replace Si in the channel to achieve higher drive currents and switching speeds .Various approaches to circumvent the scaling limits to benchmark the performance of nanoscale MOSFETS with different channel materials, the optimized structure is simulated within nextnano in order to highlight the quantum effects on DG MOSFETs when Si is replaced by Ge and SiO2 is replaced by ZrO2 and HfO2as the gate dielectric. The results have shown that Ge MOSFET have the highest mobility and high permittivity oxides serve to maintain high drive current. The simulations show significant improvements compared with DGMOSFET using SiO2 gate dielectric and Si channel.

Keywords: high mobility, high-k, quantum effects, SOI-DGMOSFET

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Authors: Kerekoppa Puttaiah Bhatta Ramesha, Uday Kannegundla, Praseeda Mol, Lathika Gopalakrishnan, Jagish Kour Reen, Gourav Dey, Manish Kumar, Sakthivel Jeyakumar, Arumugam Kumaresan, Kiran Kumar M., Thottethodi Subrahmanya Keshava Prasad

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Spermatozoa are the highly specialized transcriptionally and translationally inactive haploid male gamete. The understanding of proteome of sperm is indispensable to explore the mechanism of sperm motility and fertility. Though there is a large number of human sperm proteomic studies, in-depth proteomic information on Bos indicus spermatozoa is not well established yet. Therefore, we illustrated the profile of sperm proteome in indigenous cattle, Malnad gidda (Bos Indicus), using high-resolution mass spectrometry. In the current study, two semen ejaculates from 3 breeding bulls were collected employing the artificial vaginal method. Using 45% percoll purification, spermatozoa cells were isolated. Protein was extracted using lysis buffer containing 2% Sodium Dodecyl Sulphate (SDS) and protein concentration was estimated. Fifty micrograms of protein from each individual were pooled for further downstream processing. Pooled sample was fractionated using SDS-Poly Acrylamide Gel Electrophoresis, which is followed by in-gel digestion. The peptides were subjected to C18 Stage Tip clean-up and analyzed in Orbitrap Fusion Tribrid mass spectrometer interfaced with Proxeon Easy-nano LC II system (Thermo Scientific, Bremen, Germany). We identified a total of 6773 peptides with 28426 peptide spectral matches, which belonged to 1081 proteins. Gene ontology analysis has been carried out to determine the biological processes, molecular functions and cellular components associated with sperm protein. The biological process chiefly represented our data is an oxidation-reduction process (5%), spermatogenesis (2.5%) and spermatid development (1.4%). The highlighted molecular functions are ATP, and GTP binding (14%) and the prominent cellular components most observed in our data were nuclear membrane (1.5%), acrosomal vesicle (1.4%), and motile cilium (1.3%). Seventeen percent of sperm proteins identified in this study were involved in metabolic pathways. To the best of our knowledge, this data represents the first total sperm proteome from indigenous cattle, Malnad Gidda. We believe that our preliminary findings could provide a strong base for the future understanding of bovine sperm proteomics.

Keywords: Bos indicus, Malnad Gidda, mass spectrometry, spermatozoa

Procedia PDF Downloads 196