Search results for: throughput analysis

Authors: Samuel Kaspi, Sitalakshmi Venkatraman

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In-memory database systems are becoming popular due to the availability and affordability of sufficiently large RAM and processors in modern high-end servers with the capacity to manage large in-memory database transactions. While fast and reliable in-memory systems are still being developed to overcome cache misses, CPU/IO bottlenecks and distributed transaction costs, disk-based data stores still serve as the primary persistence. In addition, with the recent growth in multi-tenancy cloud applications and associated security concerns, many organisations consider the trade-offs and continue to require fast and reliable transaction processing of disk-based database systems as an available choice. For these organizations, the only way of increasing throughput is by improving the performance of disk-based concurrency control. This warrants a hybrid database system with the ability to selectively apply an enhanced disk-based data management within the context of in-memory systems that would help improve overall throughput. The general view is that in-memory systems substantially outperform disk-based systems. We question this assumption and examine how a modified variation of access invariance that we call enhanced memory access, (EMA) can be used to allow very high levels of concurrency in the pre-fetching of data in disk-based systems. We demonstrate how this prefetching in disk-based systems can yield close to in-memory performance, which paves the way for improved hybrid database systems. This paper proposes a novel EMA technique and presents a comparative study between disk-based EMA systems and in-memory systems running on hardware configurations of equivalent power in terms of the number of processors and their speeds. The results of the experiments conducted clearly substantiate that when used in conjunction with all concurrency control mechanisms, EMA can increase the throughput of disk-based systems to levels quite close to those achieved by in-memory system. The promising results of this work show that enhanced disk-based systems facilitate in improving hybrid data management within the broader context of in-memory systems.

Keywords: in-memory database, disk-based system, hybrid database, concurrency control

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Authors: Latif Adnane, Benaatou Wafa, Pla Vicent

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Handover is of great significance to achieve seamless connectivity in wireless networks. This paper gives an impression of the main factors which are being affected by the soft and the hard handovers techniques. To know and understand the handover process in The Universal Mobile Telecommunications System (UMTS) network, different statistics are calculated. This paper focuses on the quality of service (QoS) of soft and hard handover in UMTS network, which includes the analysis of received power, signal to noise radio, throughput, delay traffic, traffic received, delay, total transmit load, end to end delay and upload response time using OPNET simulator.

Keywords: handover, UMTS, mobility, simulation, OPNET modeler

Procedia PDF Downloads 322

Authors: Farshad Zeinali, Sajedeh Norouzi, Nader Mokari, Eduard Jorswieck

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The capacity of fifth-generation (5G) vehicle-to-everything (V2X) networks poses significant challenges. To ad- dress this challenge, this paper utilizes New Radio (NR) and New Radio Unlicensed (NR-U) networks to develop a heterogeneous vehicular network (HetNet). We propose a new framework, named joint BS assignment and resource allocation (JBSRA) for mobile V2X users and also consider coexistence schemes based on flexible duty cycle (DC) mechanism for unlicensed bands. Our objective is to maximize the average throughput of vehicles while guaranteeing the WiFi users' throughput. In simulations based on deep reinforcement learning (DRL) algorithms such as deep deterministic policy gradient (DDPG) and deep Q network (DQN), our proposed framework outperforms existing solutions that rely on fixed DC or schemes without consideration of unlicensed bands.

Keywords: vehicle-to-everything (V2X), resource allocation, BS assignment, new radio (NR), new radio unlicensed (NR-U), coexistence NR-U and WiFi, deep deterministic policy gradient (DDPG), deep Q-network (DQN), joint BS assignment and resource allocation (JBSRA), duty cycle mechanism

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Authors: K. K. Soundra Pandian, Bhupendra Gupta

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In the modern era, as the application data’s are massive and complex, it needs to be secured from the adversary attack. In this context, a non-recursive key based integrated spritz stream cipher with the circulant hash function using delayed feedback with carry shift register (d-FCSR) is proposed in this paper. The novelty of this proposed stream cipher algorithm is to engender the improved keystream using d-FCSR. The proposed algorithm is coded using Verilog HDL to produce dynamic binary key stream and implemented on commercially available FPGA device Virtex 5 xc5vlx110t-2ff1136. The implementation of stream cipher using d-FCSR on the FPGA device operates at a maximum frequency of 60.62 MHz. It achieved the data throughput of 492 Mbps and improved in terms of efficiency (throughput/area) compared to existing techniques. This paper also briefs the cryptanalysis of proposed circulant hash value based spritz stream cipher using d-FCSR is against the adversary attack on a hardware platform for the hardware based cryptography applications.

Keywords: cryptography, circulant function, field programmable gated array, hash value, spritz stream cipher

Procedia PDF Downloads 253

Authors: M. Imran Hamid, Muzammil Hussain, Yunpeng Wu, Meichun Xiang, Xingzhong Liu

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The rhizosphere microbiome elucidate multiple functioning in the soil suppressiveness against plant pathogens. Soybean rhizosphere microbial communities may involve in the natural suppression of soybean cyst nematode (SCN) populations in disease suppressive soils. To explore these ecological mechanisms of microbes, a long term monoculture suppressive soil were taken into account for further investigation to test the disease suppressive ability by using different treatments. The designed treatments are as, i) suppressive soil (S), ii) conducive soil (C), iii) conducive soil mixed with 10% (w/w) suppressive soil (CS), iv) suppressive soil treated at 80°C for 1 hr (S80), and v) suppressive soil treated with formalin (SF). By using an ultra-high-throughput sequencing approach, we identified the key bacterial and fungal taxa involved in SCN suppression. The Phylum-level investigation of bacteria revealed that Actinobacteria, Bacteroidetes, and Proteobacteria in the rhizosphere soil of soybean seedlings were more abundant in the suppressive soil than in the conducive soil. The phylum-level analysis of fungi in rhizosphere soil indicated that relative abundance of Ascomycota was higher in suppressive soil than in the conducive soil, where Basidiomycota was more abundant. Transferring suppressive soil to conducive soil increased the population of Ascomycota in the conducive soil by lowering the populations of Basidiomycota. The genera, such as, Pochonia, Purpureocillium, Fusarium, Stachybotrys that have been well documented as bio-control agents of plant nematodes were far more in the disease suppressive soils. Our results suggested that the plants engage a subset of functional microbial groups in the rhizosphere for initial defense upon nematode attack and protect the plant roots later on by nematodes to response for suppression of SCN in disease-suppressive soils.

Keywords: disease suppressive soil, high-throughput sequencing, rhizosphere microbiome, soybean cyst nematode

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Authors: Mohanad Alhabo, Li Zhang, Naveed Nawaz

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In this paper, a non-cooperative game method is formulated where all players compete to transmit at higher power. Every base station represents a player in the game. The game is solved by obtaining the Nash equilibrium (NE) where the game converges to optimality. The proposed method, named Power Efficient Handover Game Theoretic (PEHO-GT) approach, aims to control the handover in dense small cell networks. Players optimize their payoff by adjusting the transmission power to improve the performance in terms of throughput, handover, power consumption and load balancing. To select the desired transmission power for a player, the payoff function considers the gain of increasing the transmission power. Then, the cell selection takes place by deploying Technique for Order Preference by Similarity to an Ideal Solution (TOPSIS). A game theoretical method is implemented for heterogeneous networks to validate the improvement obtained. Results reveal that the proposed method gives a throughput improvement while reducing the power consumption and minimizing the frequent handover.

Keywords: energy efficiency, game theory, handover, HetNets, small cells

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Authors: J. S. Saini, P. P. K. Sandhu

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The multi-hop nature of Wireless Mesh Networks and the hasty progression of throughput demands results in multi- channels and multi-radios structures in mesh networks, but the main problem of co-channels interference reduces the total throughput, specifically in multi-hop networks. Quality of Service mentions a vast collection of networking technologies and techniques that guarantee the ability of a network to make available desired services with predictable results. Quality of Service (QoS) can be directed at a network interface, towards a specific server or router's performance, or in specific applications. Due to interference among various transmissions, the QoS routing in multi-hop wireless networks is formidable task. In case of multi-channel wireless network, since two transmissions using the same channel may interfere with each other. This paper has considered the Destination Sequenced Distance Vector (DSDV) routing protocol to locate the secure and optimised path. The proposed technique also utilizes the Lempel–Ziv–Welch (LZW) based lossless data compression and intra cluster data aggregation to enhance the communication between the source and the destination. The use of clustering has the ability to aggregate the multiple packets and locates a single route using the clusters to improve the intra cluster data aggregation. The use of the LZW based lossless data compression has ability to reduce the data packet size and hence it will consume less energy, thus increasing the network QoS. The MATLAB tool has been used to evaluate the effectiveness of the projected technique. The comparative analysis has shown that the proposed technique outperforms over the existing techniques.

Keywords: WMNS, QOS, flooding, collision avoidance, LZW, congestion control

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Authors: Pouya Karimi, Ramin Gasemi Shayan, Parsa Sheykhzade

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Ease shotgun DNA sequencing is changing the microbial sciences. Sequencing instruments are compelling to the point that example planning is currently the key constraining element. Here, we present a microfluidic test readiness stage that incorporates the key strides in cells to grouping library test groundwork for up to 96 examples and decreases DNA input prerequisites 100-overlay while keeping up or improving information quality. The universally useful microarchitecture we show bolsters work processes with subjective quantities of response and tidy up or catch steps. By decreasing the example amount necessities, we empowered low-input (∼10,000 cells) entire genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil miniaturized scale settlements with prevalent outcomes. We additionally utilized the upgraded throughput to succession ∼400 clinical Pseudomonas aeruginosa libraries and exhibit magnificent single-nucleotide polymorphism discovery execution that clarified phenotypically watched anti-toxin opposition. Completely coordinated lab-on-chip test arrangement beats specialized boundaries to empower more extensive organization of genomics across numerous fundamental research and translational applications.

Keywords: clinical microbiology, DNA, microbiology, microbial genomics

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Authors: Marinna Madrid, Nabiha Saklayen, Marinus Huber, Nicolas Vogel, Christos Boutopoulos, Michel Meunier, Eric Mazur

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Delivering material into cells is important for a diverse range of biological applications, including gene therapy, cellular engineering and imaging. We present a plasmonic substrate for delivering membrane-impermeable material into cells at high throughput and high efficiency while maintaining cell viability. The substrate fabrication is based on an affordable and fast colloidal self-assembly process. When illuminated with a femtosecond laser, the light interacts with the electrons at the surface of the metal substrate, creating localized surface plasmons that form bubbles via energy dissipation in the surrounding medium. These bubbles come into close contact with the cell membrane to form transient pores and enable entry of membrane-impermeable material via diffusion. We use fluorescence microscopy and flow cytometry to verify delivery of membrane-impermeable material into HeLa CCL-2 cells. We show delivery efficiency and cell viability data for a range of membrane-impermeable cargo, including dyes and biologically relevant material such as siRNA. We estimate the effective pore size by determining delivery efficiency for hard fluorescent spheres with diameters ranging from 20 nm to 2 um. To provide insight to the cell poration mechanism, we relate the poration data to pump-probe measurements of micro- and nano-bubble formation on the plasmonic substrate. Finally, we investigate substrate stability and reusability by using scanning electron microscopy (SEM) to inspect for damage on the substrate after laser treatment. SEM images show no visible damage. Our findings indicate that self-assembled plasmonic substrates are an affordable tool for high-throughput, high-efficiency delivery of material into mammalian cells.

Keywords: femtosecond laser, intracellular delivery, plasmonic, self-assembly

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Authors: Nihar Ranjan, Derrick Watkins, Dev P. Arya

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Current methods in the study of antibiotic activity of ribosome targeted antibiotics are dependent on cell based bacterial inhibition assays or various forms of ribosomal binding assays. These assays are typically independent of each other and little direct correlation between the ribosomal binding and bacterial inhibition is established with the complementary assay. We have developed novel high-throughput capable assays for ribosome targeted drug discovery. One such assay examines the compounds ability to bind to a model ribosomal RNA A-site. We have also coupled this assay to other functional orthogonal assays. Such analysis can provide valuable understanding of the relationships between two complementary drug screening methods and could be used as standard analysis to correlate the affinity of a compound for its target and the effect the compound has on a cell.

Keywords: bacterial resistance, aminoglycosides, screening, drugs

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Authors: Yi-Lin Chen, Sheng-Jou Hung, Tsunglin Liu

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Adaptive immune system recognizes a wide range of antigens via expressing a large number of structurally distinct T cell and B cell receptor genes. The distinct receptor genes arise from complex rearrangements called V(D)J recombination, and constitute the immune repertoire. A common method of profiling immune repertoire is via amplifying recombined receptor genes using multiple primers and high-throughput sequencing. This multiplex-PCR approach is efficient; however, the resulting repertoire can be distorted because of primer bias. To eliminate primer bias, 5’ RACE is an alternative amplification approach. However, the application of RACE approach is limited by its low efficiency (i.e., the majority of data are non-regular receptor sequences, e.g., containing intronic segments) and lack of the convenient tool for analysis. We propose a computational tool that can correctly identify non-regular receptor sequences in RACE data via aligning receptor sequences against the whole gene instead of only the exon regions as done in all other tools. Using our tool, the remaining regular data allow for an accurate profiling of immune repertoire. In addition, a RACE approach is improved to yield a higher fraction of regular T-cell receptor sequences. Finally, we quantify the degree of primer bias of a multiplex-PCR approach via comparing it to the RACE approach. The results reveal significant differences in frequency of VJ combination by the two approaches. Together, we provide a new experimental and computation pipeline for an unbiased profiling of immune repertoire. As immune repertoire profiling has many applications, e.g., tracing bacterial and viral infection, detection of T cell lymphoma and minimal residual disease, monitoring cancer immunotherapy, etc., our work should benefit scientists who are interested in the applications.

Keywords: immune repertoire, T-cell receptor, 5' RACE, high-throughput sequencing, sequence alignment

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Authors: Awatef Chniguir, Tarek Farah, Zouhair Ben Jemaa, Safya Belguith

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Optimal routing allows minimizing energy consumption in wireless sensor networks (WSN). Clustering has proven its effectiveness in organizing WSN by reducing channel contention and packet collision and enhancing network throughput under heavy load. Therefore, nowadays, with the emergence of the Internet of Things, heterogeneity is essential. Stable election protocol (SEP) that has increased the network stability period and lifetime is the first clustering protocol for heterogeneous WSN. SEP and its descendants, namely SEP, Threshold Sensitive SEP (TSEP), Enhanced TSEP (ETSSEP) and Current Energy Allotted TSEP (CEATSEP), were studied. These algorithms’ performance was evaluated based on different metrics, especially first node death (FND), to compare their stability. Simulations were conducted on the MATLAB tool considering two scenarios: The first one demonstrates the fraction variation of advanced nodes by setting the number of total nodes. The second considers the interpretation of the number of nodes while keeping the number of advanced nodes permanent. CEATSEP outperforms its antecedents by increasing stability and, at the same time, keeping a low throughput. It also operates very well in a large-scale network. Consequently, CEATSEP has a useful lifespan and energy efficiency compared to the other routing protocol for heterogeneous WSN.

Keywords: clustering, heterogeneous, stability, scalability, IoT, WSN

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Authors: Petr Šimek

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This work deals with the problem of synchronization of bus frames during transmission using USB (Universal Serial Bus). The principles for synchronization between USB and the non-deterministic CAN (Controller Area Network) bus will be described here. Furthermore, the work deals with ensuring the time sequence of communication frames when receiving from multiple communication bus channels. The structure of a general object for storing frames from different types of communication buses, such as CAN and LIN (Local Interconnect Network), will be described here. Finally, an evaluation of the communication throughput of bus frames for USB High speed will be performed. The creation of this architecture was based on the analysis of the communication of control units with a large number of communication buses. For the design of the architecture, a test HW with a USB-HS interface was used, which received previously known messages, which were compared with the received result. The result of this investigation is the block architecture of the control program for test HW ensuring correct data transmission via the USB bus.

Keywords: analysis, CAN, interface, LIN, synchronization, USB

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Authors: Sethu Lekshmi, Shahanas, Prettha P.

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All existing protocols in wireless networks are mainly based on Carrier Sense Multiple Access with Collision avoidance. By applying collision detection in wireless networks, the time spent on collision can be reduced and thus improves system throughput. However in a real WLAN scenario due to the use of nonlinear modulation techniques only receiver can decided whether a packet loss take place, even there are multiple transmissions. In this proposed method, the receiver or Access Point detects the collision when multiple data packets are transmitted from different wireless stations. Whenever the receiver detects a collision, it transmits a jamming signal to all the transmitting stations so that they can immediately stop their on-going transmissions. We also provide preferential access to all collided packet to reduce unfairness and to increase system throughput by reducing contention. However, this preferential access will not block the channel for the long time. Here, an in-band transmission is considered in which both the data frames and control frames are transmitted in the same channel. We also provide a simple mathematical model for the proposed protocol and give the simulation result of WLAN scenario under various capture thresholds.

Keywords: 802.11, WLAN, capture effect, collision detection, collision resolution, receiver initiated

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Authors: Muzaffar Iqbal, Essam Ezzeldin, Khalid A. Al-Rashood

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Pomalidomide is a second generation oral immunomodulatory agent, being used for the treatment of multiple myeloma in patients with disease refractory to lenalidomide and bortezomib. In this study, a sensitive UPLC-MS/MS assay was developed and validated for high-throughput determination of pomalidomide in rat plasma using celecoxib as an internal standard (IS). Liquid liquid extraction using dichloromethane as extracting agent was employed to extract pomalidomide and IS from 200 µL of plasma. Chromatographic separation was carried on Acquity BEHTM C18 column (50 × 2.1 mm, 1.7 µm) using an isocratic mobile phase of acetonitrile:10 mM ammonium acetate (80:20, v/v), at a flow rate of 0.250 mL/min. Both pomalidomide and IS were eluted at 0.66 ± 0.03 and 0.80 ± 0.03 min, respectively with a total run time of 1.5 min only. Detection was performed on a triple quadrupole tandem mass spectrometer using electrospray ionization in negative mode. The precursor to product ion transitions of m/z 272.01 → 160.89 for pomalidomide and m/z 380.08 → 316.01 for IS were used to quantify them respectively, using multiple reaction monitoring mode. The developed method was validated according to regulatory guideline for bioanalytical method validation. The linearity in plasma sample was achieved in the concentration range of 0.47–400 ng/mL (r2 ≥ 0.997). The intra and inter-day precision values were ≤ 11.1% (RSD, %) whereas accuracy values ranged from - 6.8 – 8.5% (RE, %). In addition, other validation results were within the acceptance criteria and the method was successfully applied in a pharmacokinetic study of pomalidomide in rats.

Keywords: pomalidomide, pharmacokinetics, LC-MS/MS, celecoxib

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Authors: D. Tedesco, G. Feletti, P. Trucco

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The present study aims to develop a Decision Support System (DSS) to support the operational decision of the Emergency Medical Service (EMS) regarding the assignment of medical emergency requests to Emergency Departments (ED). In the literature, this problem is also known as “hospital selection” and concerns the definition of policies for the selection of the ED to which patients who require further treatment are transported by ambulance. The employed research methodology consists of the first phase of revision of the technical-scientific literature concerning DSSs to support the EMS management and, in particular, the hospital selection decision. From the literature analysis, it emerged that current studies are mainly focused on the EMS phases related to the ambulance service and consider a process that ends when the ambulance is available after completing a request. Therefore, all the ED-related issues are excluded and considered as part of a separate process. Indeed, the most studied hospital selection policy turned out to be proximity, thus allowing to minimize the transport time and release the ambulance in the shortest possible time. The purpose of the present study consists in developing an optimization model for assigning medical emergency requests to the EDs, considering information relating to the subsequent phases of the process, such as the case-mix, the expected service throughput times, and the operational capacity of different EDs in hospitals. To this end, a Discrete Event Simulation (DES) model was created to evaluate different hospital selection policies. Therefore, the next steps of the research consisted of the development of a general simulation architecture, its implementation in the AnyLogic software and its validation on a realistic dataset. The hospital selection policy that produced the best results was the minimization of the Time To Provider (TTP), considered as the time from the beginning of the ambulance journey to the ED at the beginning of the clinical evaluation by the doctor. Finally, two approaches were further compared: a static approach, which is based on a retrospective estimate of the TTP, and a dynamic approach, which is based on a predictive estimate of the TTP determined with a constantly updated Winters model. Findings reveal that considering the minimization of TTP as a hospital selection policy raises several benefits. It allows to significantly reduce service throughput times in the ED with a minimum increase in travel time. Furthermore, an immediate view of the saturation state of the ED is produced and the case-mix present in the ED structures (i.e., the different triage codes) is considered, as different severity codes correspond to different service throughput times. Besides, the use of a predictive approach is certainly more reliable in terms of TTP estimation than a retrospective approach but entails a more difficult application. These considerations can support decision-makers in introducing different hospital selection policies to enhance EMSs performance.

Keywords: discrete event simulation, emergency medical services, forecast model, hospital selection

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Authors: Iman Farasat, Howard M. Salis

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The CRISPR/Cas9 system has revolutionized genome engineering by enabling site-directed and high-throughput genome editing, genome insertion, and gene knockdowns in several species, including bacteria, yeast, flies, worms, and human cell lines. This technology has the potential to enable human gene therapy to treat genetic diseases and cancer at the molecular level; however, the current CRISPR/Cas9 system suffers from seemingly sporadic off-target genome mutagenesis that prevents its use in gene therapy. A comprehensive mechanistic model that explains how the CRISPR/Cas9 functions would enable the rational design of the guide-RNAs responsible for target site selection while minimizing unexpected genome mutagenesis. Here, we present the first quantitative model of the CRISPR/Cas9 genome mutagenesis system that predicts how guide-RNA sequences (crRNAs) control target site selection and cleavage activity. We used statistical thermodynamics and law of mass action to develop a five-step biophysical model of cas9 cleavage, and examined it in vivo and in vitro. To predict a crRNA's binding specificities and cleavage rates, we then compiled a nearest neighbor (NN) energy model that accounts for all possible base pairings and mismatches between the crRNA and the possible genomic DNA sites. These calculations correctly predicted crRNA specificity across 5518 sites. Our analysis reveals that cas9 activity and specificity are anti-correlated, and, the trade-off between them is the determining factor in performing an RNA-mediated cleavage with minimal off-targets. To find an optimal solution, we first created a scheme of safe-design criteria for Cas9 target selection by systematic analysis of available high throughput measurements. We then used our biophysical model to determine the optimal Cas9 expression levels and timing that maximizes on-target cleavage and minimizes off-target activity. We successfully applied this approach in bacterial and mammalian cell lines to reduce off-target activity to near background mutagenesis level while maintaining high on-target cleavage rate.

Keywords: biophysical model, CRISPR, Cas9, genome editing

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Authors: Saji George, Eng Khuan Seng, Christof Luda

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Nanotechnology has been recognized as an important tool for modern agriculture and has the potential to overcome some of the pressing challenges faced by aquaculture industry. A strategy for optimizing nanotechnology-based therapeutic delivery platform for immunizing farmed fish was developed. Accordingly, a compositional library of nanomaterials of natural chemistry (Halloysite (clay), Chitosan, Hydroxyapatite, Mesoporous Silica and a composite material of clay-chitosan) was screened for their toxicity and efficiency in delivering models antigens in cellular and zebrafish embryo models using high throughput screening platforms. Through multi-parametric optimization, chitosan modified halloysite (clay) nanomaterial was identified as an optimal vaccine delivery platform. Further, studies conducted in juvenile seabass showed the potential of clay-chitosan in delivering outer membrane protein of Tenacibaculum maritimum- TIMA (pathogenic bacteria) to and its efficiency in eliciting immune responses in fish. In short, as exemplified by this work, the strategy of using compositional nanomaterial libraries and their biological profiling using high-throughput screening platform could fasten the discovery process of nanomaterials with potential applications in food and agriculture.

Keywords: nanotechnology, fish-vaccine, drug-delivery, halloysite-chitosan

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Authors: Manoj Kumar

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Routing protocols have a central role in any mobile ad hoc network (MANET). There are many routing protocols that exhibit different performance levels in different scenarios. In this paper, we compare AODV, DSDV, DSR, and ZRP routing protocol in mobile ad hoc networks to determine the best operational conditions for each protocol. We analyze these routing protocols by extensive simulations in OPNET simulator and show how to pause time and the number of nodes affect their performance. In this study, performance is measured in terms of control traffic received, control traffic sent, data traffic received, sent data traffic, throughput, retransmission attempts.

Keywords: AODV, DSDV, DSR, ZRP

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Authors: Silvina Caíno-Lores, Jesús Carretero

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Large scale computing infrastructures have been widely developed with the core objective of providing a suitable platform for high-performance and high-throughput computing. These systems are designed to support resource-intensive and complex applications, which can be found in many scientific and industrial areas. Currently, large scale data-intensive applications are hindered by the high latencies that result from the access to vastly distributed data. Recent works have suggested that improving data locality is key to move towards exascale infrastructures efficiently, as solutions to this problem aim to reduce the bandwidth consumed in data transfers, and the overheads that arise from them. There are several techniques that attempt to move computations closer to the data. In this survey we analyse the different mechanisms that have been proposed to provide data locality for large scale high-performance and high-throughput systems. This survey intends to assist scientific computing community in understanding the various technical aspects and strategies that have been reported in recent literature regarding data locality. As a result, we present an overview of locality-oriented techniques, which are grouped in four main categories: application development, task scheduling, in-memory computing and storage platforms. Finally, the authors include a discussion on future research lines and synergies among the former techniques.

Keywords: data locality, data-centric computing, large scale infrastructures, cloud computing

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Authors: Xinghui Wu, Chun Yang

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Inertial microfluidics is a competitive fluidic method with applications in separation of particles, cells and bacteria. In contrast to traditional microfluidic devices with low Reynolds number, inertial microfluidics works in the intermediate Re number range which brings about several intriguing inertial effects on particle separation/focusing to meet the throughput requirement in the real-world. Geometric modifications to make channels become irregular shapes can leverage fluid inertia to create complex secondary flow for adjusting the particle equilibrium positions and thus enhance the separation resolution and throughput. Although inertial microfluidics has been extensively studied by experiments, our current understanding of its mechanisms is poor, making it extremely difficult to build rational-design guidelines for the particle focusing locations, especially for irregularly shaped microfluidic channels. Inertial particle microfluidics in irregularly shaped channels were investigated in our group. There are several fundamental issues that require us to address. One of them is about the balance between the inertial lift forces and the secondary drag forces. Also, it is critical to quantitatively describe the dependence of the life forces on particle-particle interactions in irregularly shaped channels, such as a rectangular one. To provide physical insights into the inertial microfluidics in channels of irregular shapes, in this work the immersed boundary-lattice Boltzmann method (IB-LBM) was introduced and validated to explore the transport characteristics and the underlying mechanisms of an inertial focusing single particle in a rectangular microchannel. The transport dynamics of a finitesized particle were investigated over wide ranges of Reynolds number (20 < Re < 500) and particle size. The results show that the inner equilibrium positions are more difficult to occur in the rectangular channel, which can be explained by the secondary flow caused by the presence of a finite-sized particle. Furthermore, force decoupling analysis was utilized to study the effect of each type of lift force on the inertia migration, and a theoretical model for the lateral lift force of a finite-sized particle in the rectangular channel was established. Such theoretical model can be used to provide theoretical guidance for the design and operation of inertial microfluidics.

Keywords: inertial microfluidics, particle focuse, life force, IB-LBM

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Authors: A. Sri Janani, K. Immanuel Arokia James

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Cognitive radio ad hoc networks different unlicensed users may acquire different available channel sets. This non-uniform spectrum availability imposes special design challenges for broadcasting in CR ad hoc networks. Cognitive radio automatically detects available channels in wireless spectrum. This is a form of dynamic spectrum management. Cross-layer optimization is proposed, using this can allow far away secondary users can also involve into channel work. So it can increase the throughput and it will overcome the collision and time delay.

Keywords: cognitive radio, cross layer optimization, CR mesh network, heterogeneous spectrum, mesh topology, random routing optimization technique

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Authors: Malgorzata J. Rybak-Smith, Benedicte Thiebaut, Simon Johnson, Peter Bishop, Helen E. Townley

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Gadolinium doped titania (TiO2:Gd) nanoparticles (NPs) can be activated by X-ray radiation to generate Reactive Oxygen Species (ROS), which can be effective in killing cancer cells. As such, treatment with these NPs can be used to enhance the efficacy of conventional radiotherapy. Incorporation of the NPs in to tumour tissue will permit the extension of radiotherapy to currently untreatable tumours deep within the body, and also reduce damage to neighbouring healthy cells. In an attempt to find a fast and scalable method for the synthesis of the TiO2:Gd NPs, the use of Flame Spray Pyrolysis (FSP) was investigated. A series of TiO2 NPs were generated with 1, 2, 5 and 7 mol% gadolinium dopant. Post-synthesis, the TiO2:Gd NPs were silica-coated to improve their biocompatibility. Physico-chemical characterisation was used to determine the size and stability in aqueous suspensions of the NPs. All analysed TiO2:Gd NPs were shown to have relatively high photocatalytic activity. Furthermore, the FSP synthesized silica-coated TiO2:Gd NPs generated enhanced ROS in chemico. Studies on rhabdomyosarcoma (RMS) cell lines (RD & RH30) demonstrated that in the absence of irradiation all TiO2:Gd NPs were inert. However, application of TiO2:Gd NPs to RMS cells, followed by irradiation, showed a significant decrease in cell proliferation. Consequently, our studies showed that the X-ray-activatable TiO2:Gd NPs can be prepared by a high-throughput scalable technique to provide a novel and affordable anticancer therapy.

Keywords: cancer, gadolinium, ROS, titania nanoparticles, X-ray

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Authors: Angela U. Makolo, Temitayo A. Olagunju

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The knowledge of signaling pathways is central to understanding the biological mechanisms of organisms since it has been identified that in eukaryotic organisms, the number of signaling pathways determines the number of ways the organism will react to external stimuli. Signaling pathways are studied using protein interaction networks constructed from protein-protein interaction data obtained using high throughput experimental procedures. However, these high throughput methods are known to produce very high rates of false positive and negative interactions. In order to construct a useful protein interaction network from this noisy data, computational methods are applied to validate the protein-protein interactions. In this study, a computational technique to identify signaling pathways from a protein interaction network constructed using validated protein-protein interaction data was designed. A weighted interaction graph of the Saccharomyces cerevisiae (Baker’s Yeast) organism using the proteins as the nodes and interactions between them as edges was constructed. The weights were obtained using Bayesian probabilistic network to estimate the posterior probability of interaction between two proteins given the gene expression measurement as biological evidence. Only interactions above a threshold were accepted for the network model. A pathway was formalized as a simple path in the interaction network from a starting protein and an ending protein of interest. We were able to identify some pathway segments, one of which is a segment of the pathway that signals the start of the process of meiosis in S. cerevisiae.

Keywords: Bayesian networks, protein interaction networks, Saccharomyces cerevisiae, signalling pathways

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Authors: Gurkirat Kaur, Manoj Kumar, Manju Bala

Abstract:

Ethernet is the most influential and widely used technology in the world. With the growing demand of low latency and high throughput technologies like InfiniBand and RoCE, unique features viz. RDMA (Remote Direct Memory Access) have evolved. RDMA is an effective technology which is used for reducing system load and improving performance. InfiniBand is a well known technology which provides high-bandwidth and low-latency and makes optimal use of in-built features like RDMA. With the rapid evolution of InfiniBand technology and Ethernet lacking the RDMA and zero copy protocol, the Ethernet community has came out with a new enhancements that bridges the gap between InfiniBand and Ethernet. By adding the RDMA and zero copy protocol to the Ethernet a new networking technology is evolved, called RDMA over Converged Ethernet (RoCE). RoCE is a standard released by the IBTA standardization body to define RDMA protocol over Ethernet. With the emergence of lossless Ethernet, RoCE uses InfiniBand’s efficient transport to provide the platform for deploying RDMA technology in mainstream data centres over 10GigE, 40GigE and beyond. RoCE provide all of the InfiniBand benefits transport benefits and well established RDMA ecosystem combined with converged Ethernet. In this paper, we evaluate the heterogeneous Linux cluster, having multi nodes with fast interconnects i.e. gigabit Ethernet and Soft RoCE. This paper presents the heterogeneous Linux cluster configuration and evaluates its performance using Intel’s MPI Benchmarks. Our result shows that Soft RoCE is performing better than Ethernet in various performance metrics like bandwidth, latency and throughput.

Keywords: ethernet, InfiniBand, RoCE, RDMA, MPI, Soft RoCE

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Authors: Abhinay Puvvala, Veerendra Kumar Rai

Abstract:

A bottleneck situation arises when the outflow is lesser than the inflow in a pipe-like setup. A more practical interpretation of bottlenecks emphasizes on the realization of Service Level Objectives (SLOs) at given workloads. Our approach detects two key aspects of bottlenecks – when and where. To identify ‘when’ we continuously poll on certain key metrics such as resource utilization, processing time, request backlog and throughput at a system level. Further, when the slope of the expected sojourn time at a workload is greater than ‘K’ times the slope of expected sojourn time at the previous step of the workload while the workload is being gradually increased in discrete steps, a bottleneck situation arises. ‘K’ defines the threshold condition and is computed based on the system’s service level objectives. The second aspect of our approach is to identify the location of the bottleneck. In multi-tier systems with a complex network of layers, it is a challenging problem to locate bottleneck that affects the overall system performance. We stage the system by varying workload incrementally to draw a correlation between load increase and system performance to the point where Service Level Objectives are violated. During the staging process, multiple metrics are monitored at hardware and application levels. The correlations are drawn between metrics and the overall system performance. These correlations along with the Service Level Objectives are used to arrive at the threshold conditions for each of these metrics. Subsequently, the same method used to identify when a bottleneck occurs is used on metrics data with threshold conditions to locate bottlenecks.

Keywords: bottleneck, workload, service level objectives (SLOs), throughput, system performance

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Authors: Jonardan Koner, Avinash Purandare

Abstract:

In today’s globalized world international business is a very key area for the country's growth. Some of the strategic areas for holding up a country’s international business to grow are in the areas of connecting Ports, Road Network, and Rail Network. India’s International Business is booming both in Exports as well as Imports. Ports play a very central part in the growth of international trade and ensuring competitive ports is of critical importance. India has a long coastline which is a big asset for the country as it has given the opportunity for development of a large number of major and minor ports which will contribute to the maritime trades’ development. The National Economic Development of India requires a well-functioning seaport system. To know the comparative strength of Indian ports over South-east Asian similar ports, the study is considering the objectives of (I) to identify the key parameters of an international mega container port, (II) to compare the five selected container ports (JNPT, Chennai, Singapore, Dubai, and Colombo Ports) according to user of the ports and iii) to measure the growth of selected five container ports’ throughput over time and their comparison. The study is based on both primary and secondary databases. The linear time trend analysis is done to show the trend in quantum of exports, imports and total goods/services handled by individual ports over the years. The comparative trend analysis is done for the selected five ports of cargo traffic handled in terms of Tonnage (weight) and number of containers (TEU’s). The comparative trend analysis is done between containerized and non-containerized cargo traffic in the five selected five ports. The primary data analysis is done comprising of comparative analysis of factor ratings through bar diagrams, statistical inference of factor ratings for the selected five ports, consolidated comparative line charts of factor rating for the selected five ports, consolidated comparative bar charts of factor ratings of the selected five ports and the distribution of ratings (frequency terms). The linear regression model is used to forecast the container capacities required for JNPT Port and Chennai Port by the year 2030. Multiple regression analysis is carried out to measure the impact of selected 34 explanatory variables on the ‘Overall Performance of the Port’ for each of the selected five ports. The research outcome is of high significance to the stakeholders of Indian container handling ports. Indian container port of JNPT and Chennai are benchmarked against international ports such as Singapore, Dubai, and Colombo Ports which are the competing ports in the neighbouring region. The study has analysed the feedback ratings for the selected 35 factors regarding physical infrastructure and services rendered to the port users. This feedback would provide valuable data for carrying out improvements in the facilities provided to the port users. These installations would help the ports’ users to carry out their work in more efficient manner.

Keywords: throughput, twenty equivalent units, TEUs, cargo traffic, shipping lines, freight forwarders

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Authors: Yassine Meraihi, Dalila Acheli, Rabah Meraihi

Abstract:

MANET for Mobile Ad hoc NETwork is a collection of wireless mobile nodes that communicates with each other without using any existing infrastructure, access point or centralized administration, due to the higher mobility and limited radio transmission range, routing is an important issue in ad hoc network, so in order to ensure reliable and efficient route between to communicating nodes quickly, an appropriate routing protocol is needed. In this paper, we present the performance analysis of two mobile ad hoc network routing protocols namely DSR and OLSR using NS2.34, the performance is determined on the basis of packet delivery ratio, throughput, average jitter and end to end delay with varying pause time.

Keywords: DSR, OLSR, quality of service, routing protocols, MANET

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Authors: Kamalpreet Kaur, Harjit Pal Singh, Vikas Khullar

Abstract:

In Wireless Sensor Network (WSN), the main limitation is generally inimitable energy consumption during processing of the sensor nodes. Cluster head (CH) election is one of the main issues that can reduce the energy consumption. Therefore, discovering energy saving routing protocol is the focused area for research. In this paper, fuzzy-based energy aware routing protocol is presented, which enhances the stability and network lifetime of the network. Fuzzy logic ensures the well-organized selection of CH by taking four linguistic variables that are concentration, energy, centrality, and distance to base station (BS). The results show that the proposed protocol shows better results in requisites of stability and throughput of the network.

Keywords: ERA, fuzzy logic, network model, WSN

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Authors: A. Youseef

Abstract:

One of the most aims of IEEE 802.16 (WiMAX) is to present high-speed wireless access to cover wide range coverage. The base station (BS) and the subscriber station (SS) are the main parts of WiMAX. WiMAX uses either Point-to-Multipoint (PMP) or mesh topologies. In the PMP mode, the SSs connect to the BS to gain access to the network. However, in the mesh mode, the SSs connect to each other to gain access to the BS. The main components of QoS management in the 802.16 standard are the admission control, buffer management, and packet scheduling. There are several researches proposed to create an efficient packet scheduling schemes. Therefore, we use QualNet 5.0.2 to study the performance of different scheduling schemes, such as WFQ, SCFQ, RR, and SP when the numbers of SSs increase. We find that when the number of SSs increases, the average jitter and average end-to-end delay is increased and the throughput is reduced.

Keywords: WiMAX, scheduling scheme, QoS, QualNet

Procedia PDF Downloads 456