Search results for: high through-put

Authors: Arash Kosari, Ali Araghi

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A mathematical model for an optical-fiber communication channel is developed which results in an expression that calculates the throughput and loss of the corresponding link. The data are assumed to be transmitted by using of separate photons with different polarizations. The derived model also shows the dependency of data throughput with length of the channel and depolarization factor. It is observed that absorption of photons affects the throughput in a more intensive way in comparison with that of depolarization. Apart from that, the probability of depolarization and the absorption of radiated photons are obtained.

Keywords: absorption, data throughput, depolarization, optical fiber

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Authors: Kehinde Peter Oyeduntan, Kayode Oshinubi

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The west African ports have been experiencing large inflow and outflow of containerized cargo in the last decades, and this has created a quest amongst the countries to attain the status of hub port for the sub-region. This study analyzed the relationship between the container throughput and Gross Domestic Products (GDP) of nine west African countries, using Simple Linear Regression (SLR), Polynomial Regression Model (PRM) and Support Vector Machines (SVM) with a time series of 20 years. The results showed that there exists a high correlation between the GDP and container throughput. The model also predicted the container throughput in west Africa for the next 20 years. The findings and recommendations presented in this research will guide policy makers and help improve the management of container ports and terminals in west Africa, thereby boosting the economy.

Keywords: container, ports, terminals, throughput

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Authors: Engin Eyceyurt, Josko Zec

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The current and future cellular mobile communication networks generate enormous amounts of data. Networks have become extremely complex with extensive space of parameters, features and counters. These networks are unmanageable with legacy methods and an enhanced design and optimization approach is necessary that is increasingly reliant on machine learning. This paper proposes that machine learning as a viable approach for uplink throughput prediction. LTE radio metric, such as Reference Signal Received Power (RSRP), Reference Signal Received Quality (RSRQ), and Signal to Noise Ratio (SNR) are used to train models to estimate expected uplink throughput. The prediction accuracy with high determination coefficient of 91.2% is obtained from measurements collected with a simple smartphone application.

Keywords: drive test, LTE, machine learning, uplink throughput prediction

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Authors: Zhijie Ma, Qinglin Zhao, Hongning Dai, Huan Zhang

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This paper proposes an APPLE scheme that aims at providing absolute and proportional throughput guarantees, and maximizing system throughput simultaneously for wireless LANs with homogeneous and heterogenous traffic. We formulate our objectives as an optimization problem, present its exact and approximate solutions, and prove the existence and uniqueness of the approximate solution. Simulations validate that APPLE scheme is accurate, and the approximate solution can well achieve the desired objectives already.

Keywords: IEEE 802.11e, throughput guarantee, priority, WLANs

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Authors: Gu Pang, Bartosz Gebka

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We forecast the demand of total container throughput at the Indonesia’s largest seaport, Tanjung Priok Port. We propose four univariate forecasting models, including SARIMA, the additive Seasonal Holt-Winters, the multiplicative Seasonal Holt-Winters and the Vector Error Correction Model. Our aim is to provide insights into whether forecasting the total container throughput obtained by historical aggregated port throughput time series is superior to the forecasts of the total throughput obtained by summing up the best individual terminal forecasts. We test the monthly port/individual terminal container throughput time series between 2003 and 2013. The performance of forecasting models is evaluated based on Mean Absolute Error and Root Mean Squared Error. Our results show that the multiplicative Seasonal Holt-Winters model produces the most accurate forecasts of total container throughput, whereas SARIMA generates the worst in-sample model fit. The Vector Error Correction Model provides the best model fits and forecasts for individual terminals. Our results report that the total container throughput forecasts based on modelling the total throughput time series are consistently better than those obtained by combining those forecasts generated by terminal-specific models. The forecasts of total throughput until the end of 2018 provide an essential insight into the strategic decision-making on the expansion of port's capacity and construction of new container terminals at Tanjung Priok Port.

Keywords: SARIMA, Seasonal Holt-Winters, Vector Error Correction Model, container throughput

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Authors: Isra Elfatih Salih Edrees, Mehmet Serdar Ufuk Türeli

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In this paper, an energy-aware method is presented, integrating energy-efficient relay-augmented techniques for correlated data routing with the goal of optimizing bottleneck throughput in wireless sensor networks. The system tackles the dual challenge of throughput optimization while considering sensor network energy consumption. A unique routing metric has been developed to enable throughput maximization while minimizing energy consumption by utilizing data correlation patterns. The paper introduces a game theoretic framework to address the NP-complete optimization problem inherent in throughput-maximizing correlation-aware routing with energy limitations. By creating an algorithm that blends energy-aware route selection strategies with the best reaction dynamics, this framework provides a local solution. The suggested technique considerably raises the bottleneck throughput for each source in the network while reducing energy consumption by choosing the best routes that strike a compromise between throughput enhancement and energy efficiency. Extensive numerical analyses verify the efficiency of the method. The outcomes demonstrate the significant decrease in energy consumption attained by the energy-efficient relay-augmented bottleneck throughput maximization technique, in addition to confirming the anticipated throughput benefits.

Keywords: correlated data aggregation, energy efficiency, game theory, relay-augmented routing, throughput maximization, wireless sensor networks

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Authors: Hyunjung Lim, Jeonghun Nam, Hyuk Choi

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High-throughput separation is an essential technique for cancer research and diagnosis. Here, we propose a viscoelastic microfluidic device for sheathless, high-throughput isolation of circulating tumor cells (CTCs) from white blood cells. Here, we demonstrate a viscoelastic method for separation and concentration of CTCs using closed-loop microfluidics. Our device is a rectangular straight channel with a low aspect ratio. Also, to achieve high-efficiency, high-throughput processing, we used a polymer solution with low viscosity. At the inlet, CTCs and white blood cells (WBCs) were randomly injected into the microchannel. Due to the viscoelasticity-induced lateral migration to the equilibrium positions, large CTCs could be collected from the side outlet while small WBCs were removed at the center outlet. By recirculating the collected CTCs from the side outlet back to the sample reservoir, continuous separation and concentration of CTCs could be achieved with high separation efficiency (~ 99%). We believe that our device has the potential to be applied in resource-limited clinical settings.

Keywords: circulating tumor cell, closed-loop microfluidics, concentration, separation, viscoelastic fluid

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Authors: Eui-Hak Lee, Jae-Hyun Ro, Hyoung-Kyu Song

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In internet of things (IoT) system, the communication scheme with reliability and low power is required to connect a terminal. Cooperative communication can achieve reliability and lower power than multiple-input multiple-output (MIMO) system. Cooperative communication increases the reliability with low power, but decreases a throughput. It has a weak point that the communication throughput is decreased. In this paper, a novel scheme is proposed to increase the communication throughput. The novel scheme is a transmission structure that increases transmission rate. And a decoding scheme according to the novel transmission structure is proposed. Simulation results show that the proposed scheme increases the throughput without bit error rate (BER) performance degradation.

Keywords: cooperative communication, IoT, STBC, transmission rate

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Authors: Arif Armagan Gozutok, Alper Kule, Burak Tos, Selman Demirel

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Wireless communication chain requires effective ways to keep throughput efficiency high while it suffers location-dependent, time-varying burst errors. Several techniques are developed in order to assure that the receiver recovers the transmitted information without errors. The most fundamental approaches are error checking and correction besides re-transmission of the non-acknowledged packets. In this paper, stop & wait (SAW) and chase combined (CC) hybrid automated repeat request (HARQ) protocols are compared and analyzed in terms of throughput and average delay for the usage of low earth orbit (LEO) mega-constellations case. Several assumptions and technological implementations are considered as well as usage of low-density parity check (LDPC) codes together with several constellation orbit configurations.

Keywords: HARQ, LEO, satellite constellation, throughput

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Authors: Tesfaw Belayneh Abebe

Abstract:

Integrating low-altitude earth orbit (LEO) satellites and unmanned aerial vehicles (UAVs) within a non-terrestrial network (NTN) with the assistance of reconfigurable intelligent surfaces (RIS), we investigate the problem of how to enhance throughput through integrated LEO satellites and UAVs with the assistance of RIS. We propose a method to jointly optimize the associations with the LEO satellite, the 3D trajectory of the UAV, and the phase shifts of the RIS to maximize communication throughput for RIS-assisted integrated LEO satellite and UAV-enabled wireless communications, which is challenging due to the time-varying changes in the position of the LEO satellite, the high mobility of UAVs, an enormous number of possible control actions, and also the large number of RIS elements. Utilizing a multi-agent double deep Q-network (MADDQN), our approach dynamically adjusts LEO satellite association, UAV positioning, and RIS phase shifts. Simulation results demonstrate that our method significantly outperforms baseline strategies in maximizing throughput. Lastly, thanks to the integrated network and the RIS, the proposed scheme achieves up to 65.66x higher peak throughput and 25.09x higher worst-case throughput.

Keywords: integrating low-altitude earth orbit (LEO) satellites, unmanned aerial vehicles (UAVs) within a non-terrestrial network (NTN), reconfigurable intelligent surfaces (RIS), multi-agent double deep Q-network (MADDQN)

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Authors: Edward P. Guillen, A. Karina Martinez Barliza

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Powerline Communications (PLC) as last mile solution to provide communication services, has the advantage of transmitting over channels already used for electrical distribution. However these channels have been not designed with this purpose, for that reason telecommunication companies in Colombia want to know how good would be using PLC in costs and network performance in comparison to cable modem or DSL. This paper analyzes PLC throughput for residential complex scenarios using a PLC network scenarios and some statistical results are shown.

Keywords: home network, power line communication, throughput analysis, power factor, cost, last mile solution

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Authors: K. Kalaiarasan, B. Pandeeswari, A. Arockia John Francis

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Wireless, Multi-hop networks consist of one or more intermediate nodes along the path that receive and forward packets via wireless links. The backpressure algorithm provides throughput optimal routing and scheduling decisions for multi-hop networks with dynamic traffic. Xpress, a cross-layer backpressure architecture was designed to reach the capacity of wireless multi-hop networks and it provides well coordination between layers of network by turning a mesh network into a wireless switch. Transmission over the network is scheduled using a throughput-optimal backpressure algorithm. But this architecture operates much below their capacity due to out-of-order packet delivery and variable packet size. In this paper, we present Xpress-T, a throughput optimal backpressure architecture with TCP support designed to reach maximum throughput of wireless multi-hop networks. Xpress-T operates at the IP layer, and therefore any transport protocol, including TCP, can run on top of Xpress-T. The proposed design not only avoids bottlenecks but also handles out-of-order packet delivery and variable packet size, optimally load-balances traffic across them when needed, improving fairness among competing flows. Our simulation results shows that Xpress-T gives 65% more throughput than Xpress.

Keywords: backpressure scheduling and routing, TCP, congestion control, wireless multihop network

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Authors: Karolis Leonavičius, Dalius Kučiauskas, Dangiras Lukošius, Arnoldas Jasiūnas, Kostas Zdanys, Rokas Stanislovas, Emilis Gegevičius, Žana Kapustina, Juozas Nainys

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Screening throughput is a common bottleneck in many research areas, including functional genomics, drug discovery, and directed evolution. High-throughput screening techniques can be classified into two main categories: (i) affinity-based screening and (ii) functional screening. The first one relies on binding assays that provide information about the affinity of a test molecule for a target binding site. Binding assays are relatively easy to establish; however, they reveal no functional activity. In contrast, functional assays show an effect triggered by the interaction of a ligand at a target binding site. Functional assays might be based on a broad range of readouts, such as cell proliferation, reporter gene expression, downstream signaling, and other effects that are a consequence of ligand binding. Screening of large cell or gene libraries based on direct activity rather than binding affinity is now a preferred strategy in many areas of research as functional assays more closely resemble the context where entities of interest are anticipated to act. Droplet sorting is the basis of high-throughput functional biological screening, yet its applicability is limited due to the technical complexity of integrating high-performance droplet analysis and manipulation systems. As a solution, the Droplet Genomics Styx platform enables custom droplet sorting workflows, which are necessary for the development of early-stage or complex biological therapeutics or industrially important biocatalysts. The poster will focus on the technical design considerations of Styx in the context of its application spectra.

Keywords: functional screening, droplet microfluidics, droplet sorting, dielectrophoresis

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Authors: Joselito Medina-Marin, Alexandr Karelin, Ana Tarasenko, Juan Carlos Seck-Tuoh-Mora, Norberto Hernandez-Romero, Eva Selene Hernandez-Gress

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A production line designer faces with several challenges in manufacturing system design. One of them is the assignment of buffer slots in between every machine of the production line in order to maximize the throughput of the whole line, which is known as the Buffer Allocation Problem (BAP). The BAP is a combinatorial problem that depends on the number of machines and the total number of slots to be distributed on the production line. In this paper, we are proposing a Petri Net (PN) Model to obtain the throughput in unreliable production lines, based on PN mathematical tools and the decomposition method. The results obtained by this methodology are similar to those presented in previous works, and the number of machines is not a hard restriction.

Keywords: buffer allocation problem, Petri Nets, throughput, production lines

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Authors: Yu Chen, Seong-Jin Kim, Jaehoon Chung

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High throughput cells counting and sizing are often required for biomedical applications. Here we report design, fabrication and validating of a micro-machined Coulter counter device with multiple-channel to realize such application for low cost. Multiple vertical through-holes were fabricated on a silicon chip, combined with the PDMS micro-fluidics channel that serves as the sensing channel. In order to avoid the crosstalk introduced by the electrical connection, instead of measuring the current passing through, the potential of each channel is monitored, thus the high throughput is possible. A peak of the output potential can be captured when the cell/particle is passing through the microhole. The device was validated by counting and sizing the polystyrene beads with diameter of 6 μm, 10 μm and 15 μm. With the sampling frequency to be set at 100 kHz, up to 5000 counts/sec for each channel can be realized. The counting and enumeration of MCF7 cancer cells are also demonstrated.

Keywords: Coulter counter, cell enumeration, high through-put, cell sizing

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Authors: B. Siva Kumar Reddy, B. Lakshmi

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WiMAX has adopted an Adaptive Modulation and Coding (AMC) in OFDM to endure higher data rates and error free transmission. AMC schemes employ the Channel State Information (CSI) to efficiently utilize the channel and maximize the throughput and for better spectral efficiency. This CSI has given to the transmitter by the channel estimators. In this paper, LSE (Least Square Error) and MMSE (Minimum Mean square Error) estimators are suggested and BER (Bit Error Rate) performance has been analyzed. Channel equalization is also integrated with with AMC-OFDM system and presented with Constant Modulus Algorithm (CMA) and Least Mean Square (LMS) algorithms with convergence rates analysis. Simulation results proved that increment in modulation scheme size causes to improvement in throughput along with BER value. There is a trade-off among modulation size, throughput, BER value and spectral efficiency. Results also reported the requirement of channel estimation and equalization in high data rate systems.

Keywords: AMC, CSI, CMA, OFDM, OFDMA, WiMAX

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Authors: Faisel Eltuhami Alzaalik, Omar Imhemed Alramli, Ahmed Mohamed Elaieb

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The IEEE 802.11 defines two modes of MAC, distributed coordination function (DCF) and point coordination function (PCF) mode. The first sub-layer of the MAC is the distributed coordination function (DCF). A contention algorithm is used via DCF to provide access to all traffic. The point coordination function (PCF) is the second sub-layer used to provide contention-free service. PCF is upper DCF and it uses features of DCF to establish guarantee access of its users. Some papers and researches that have been published in this technology were reviewed in this paper, as well as talking briefly about the distributed coordination function (DCF) technology. The simulation of the PCF function have been applied by using a simulation program called network simulator (NS2) and have been found out the throughput of a transmitter system by using this function.

Keywords: DCF, PCF, throughput, NS2

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Authors: S. Malisuwan, J. Sivaraks, N. Madan, N. Suriyakrai

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The ever going evolution of advanced wireless technologies makes it financially impossible for military operations to completely manufacture their own equipment. Therefore, Commercial-Off-The-Shelf (COTS) and Modified-Off-The-Shelf (MOTS) are being considered in military mission with low-cost modifications. In this paper, we focus on the LTE multicast systems for military communication systems under tactical environments with jamming condition. We examine the influence of the colored noise jamming on the performance of the LTE multicast systems in terms of the average throughput. The simulation results demonstrate the degradation of the average throughput for different dynamic ranges of the colored noise jamming versus average SNR.

Keywords: performance, LTE, multicast, jamming, throughput

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Authors: Shubham Dwivedi, Raghavender Medishetti, Rita Rani, Aarti Sevilimedu, Pushkar Kulkarni, Yogeeswari Perumal

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Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder of early onset, characterized by impaired sociability, cognitive function and stereotypies. There is a significant urge to develop and establish new animal models with ASD-like characteristics for better understanding of underlying mechanisms. The aim of the present study was to develop a cost and time effective zebrafish model with quantifiable parameters to facilitate mechanistic studies as well as high-throughput screening of new molecules for autism. Zebrafish embryos were treated with valproic acid and a battery of behavioral tests (anxiety, inattentive behavior, irritability and social impairment) was performed on larvae at 7th day post fertilization, followed by study of molecular markers of autism. This model shows a significant behavioural impairment in valproic acid treated larvae in comparison to control which was again supported by alteration in few marker genes and proteins of autism. The model also shows a rescue of behavioural despair with positive control drugs. The model shows robust parameters to study behavior, molecular mechanism and drug screening approach in a single frame. Thus we postulate that our 7 days zebrafish larval model for autism can help in high throughput screening of new molecules on autism.

Keywords: autism, zebrafish, valproic acid, neurodevelopment, behavioral assay

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Authors: Inkyu Kim, SangMan Moon

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This IEEE 802.11b protocol provides up to 11Mbps data rate, whereas aerospace industry wants to seek higher data rate COTS data link system in the UAV. The Total Maximum Throughput (TMT) and delay time are studied on many researchers in the past years This paper provides theoretical data throughput performance of UAV formation flight data link using the existing 802.11b performance theory. We operate the UAV formation flight with more than 30 quad copters with 802.11b protocol. We may be predicting that UAV formation flight numbers have to bound data link protocol performance limitations.

Keywords: UAV datalink, UAV formation flight datalink, UAV WLAN datalink application, UAV IEEE 802.11b datalink application

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Authors: Piotr J. Balwierz, Mikhail Pachkov, Phil Arnold, Andreas J. Gruber, Mihaela Zavolan, Erik van Nimwegen

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Understanding the key players and interactions in the regulatory networks that control gene expression and chromatin state across different cell types and tissues in metazoans remains one of the central challenges in systems biology. Our laboratory has pioneered a number of methods for automatically inferring core gene regulatory networks directly from high-throughput data by modeling gene expression (RNA-seq) and chromatin state (ChIP-seq) measurements in terms of genome-wide computational predictions of regulatory sites for hundreds of transcription factors and micro-RNAs. These methods have now been completely automated in an integrated webserver called ISMARA that allows researchers to analyze their own data by simply uploading RNA-seq or ChIP-seq data sets and provides results in an integrated web interface as well as in downloadable flat form. For any data set, ISMARA infers the key regulators in the system, their activities across the input samples, the genes and pathways they target, and the core interactions between the regulators. We believe that by empowering experimental researchers to apply cutting-edge computational systems biology tools to their data in a completely automated manner, ISMARA can play an important role in developing our understanding of regulatory networks across metazoans.

Keywords: gene expression analysis, high-throughput sequencing analysis, transcription factor activity, transcription regulation

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Authors: Sourita Ghosh, Falguni Pati, Suhanya Duraiswamy

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Spheroid, a simple three-dimensional cellular aggregate, allows us to simulate the in-vivo complexity of cellular signaling and interactions in greater detail than traditional 2D cell culture. It can be used as an in-vitro model for drug toxicity testing, tumor modeling and many other such applications specifically for cancer. Our work is focused on the development of an affordable, user-friendly, robust, reproducible, high throughput microfluidic device for water in oil droplet production, which can, in turn, be used for spheroids manufacturing. Here, we have investigated the droplet breakup between two non-Newtonian fluids, viz. silicone oil and decellularized liver matrix, which acts as our extra cellular matrix (ECM) for spheroids formation. We performed some biochemical assays to characterize the liver ECM, as well as rheological studies on our two fluids and observed a critical dependence of capillary number (Ca) on droplet breakup and homogeneous drop formation

Keywords: chip less, droplets, extracellular matrix, liver spheroid

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Authors: Jeonghun Nam, Seonggil Kim, Hyunjoo Choi, Chae Seung Lim

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Quantification and analysis of rare cells are challenging in clinical applications and cell biology due to its extremely small number in blood. In this work, we propose a viscoelastic microfluidic device for continuous cell concentration without sheath flows. Due to the viscoelastic effect on suspending cells, cells with the blockage ratio higher than 0.1 could be tightly focused at the center of the microchannel. The blockage ratio was defined as the particle diameter divided by the channel width. Finally, cells were concentrated through the center outlet and the additional suspending medium was removed to the side outlets. Since viscoelastic focusing is insensitive to the flow rate higher than 10 μl/min, the non-powered hand pump sprayer could be used with no accurate control of the flow rate, which is suitable for clinical settings in resource-limited developing countries. Using multiple concentration processes, high-throughput concentration of white blood cells in lysed blood sample was achieved by ~ 300-fold.

Keywords: cell concentration, high-throughput, non-powered, viscoelastic fluid

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Authors: M. Iruleswari, A. Jeyapaul Murugan

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Most fundamental part used in many Digital Signal Processing (DSP) application is a Finite Impulse Response (FIR) filter because of its linear phase, stability and regular structure. Designing a high-speed and hardware efficient FIR filter is a very challenging task as the complexity increases with the filter order. In most applications the higher order filters are required but the memory usage of the filter increases exponentially with the order of the filter. Using multipliers occupy a large chip area and need high computation time. Multiplier-less memory-based techniques have gained popularity over past two decades due to their high throughput processing capability and reduced dynamic power consumption. This paper describes the design and implementation of highly efficient Look-Up Table (LUT) based circuit for the implementation of FIR filter using Distributed arithmetic algorithm. It is a multiplier less FIR filter. The LUT can be subdivided into a number of LUT to reduce the memory usage of the LUT for higher order filter. Analysis on the performance of various filter orders with different address length is done using Xilinx 14.5 synthesis tool. The proposed design provides less latency, less memory usage and high throughput.

Keywords: finite impulse response, distributed arithmetic, field programmable gate array, look-up table

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Authors: Sudipto Shanker Dasgupta

Abstract:

One of the largest mining companies wanted to look at health analytics for their driverless trucks. These trucks were the key to their supply chain logistics. The automated trucks had multi-level sub-assemblies which would send out sensor information. The use case that was worked on was to capture the sensor signal from the truck subcomponents and analyze the health of the trucks from repair and replacement purview. Open source software was used to stream the data into a clustered Hadoop setup in Amazon Web Services cloud and Apache Spark SQL was used to analyze the data. All of this was achieved through a 10 node amazon 32 core, 64 GB RAM setup real-time analytics was achieved on ‘300 million records’. To check the scalability of the system, the cluster was increased to 100 node setup. This talk will highlight how Open Source software was used to achieve the above use case and the insights on the high data throughput on a cloud set up.

Keywords: streaming analytics, data science, big data, Hadoop, high throughput, sensor data

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Authors: S. Shaaban, T. McNamara, S. Hudson

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This paper reports on the performance of deliberately unbalanced, reliable, non-automated and assembly lines that merge, whose workstations differ in terms of their mean operation times. Simulations are carried out on 5- and 8-station lines with 1, 2 and 4 buffer capacity units, % degrees of line imbalance of 2, 5 and 12, and 24 different patterns of means imbalance. Data on two performance measures, namely throughput and average buffer level were gathered, statistically analysed and compared to a merging balanced line counterpart. It was found that the best configurations are a balanced line arrangement and a monotone decreasing order for each of the parallel merging lines, with the first generally resulting in a lower throughput and the second leading to a lower average buffer level than those of a balanced line.

Keywords: average buffer level, merging lines, simulation, throughput, unbalanced

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Authors: Ibrahim Isa Ali (Pantami), Abdu Jaafaru Bambale, Abimbola Alale, Danjuma Ibrahim Ndihgihdah, Muhammad Alkali, Adamu Idris Umar, Babadoko Dantala Mohammed, Moshood Kareem Olawole

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This paper dwells on the risk management required for High throughput Satellite (HTS) project, and major subsystems that pertains to the improved performance and reliability of the spacecraft. The paper gives a clear picture of high‐throughput satellites (HTS) and the associated technologies with performances as they align and differ with the traditional geostationary orbit or Geosynchronous Equatorial Orbit (GEO) Communication Satellites. The paper also highlights critical subsystems and processes in project conceptualization and execution. The paper discusses the configuration of the payload. The need for optimization of resources for the HTS project and successful integration of critical subsystems for spacecraft requires implementation of risk analysis and mitigation from the preliminary design stage; Assembly, Integration and Test (AIT); Launch and in-orbit- Management stage.

Keywords: AIT, HTS, in-orbit management, optimization

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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: 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: Ruolan Zhang, Ryo Imai, Naoko Senda, Tomoyuki Sakai

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Enzymes have attracted increasing attentions in industrial manufacturing for their applicability in catalyzing complex chemical reactions under mild conditions. Directed evolution has become a powerful approach to optimize enzymes and exploit their full potentials under the circumstance of insufficient structure-function knowledge. With the incorporation of cell-free synthetic biotechnology, rapid enzyme synthesis can be realized because no cloning procedure such as transfection is needed. Its open environment also enables direct enzyme measurement. These properties of cell-free biotechnology lead to excellent throughput of enzymes generation. However, the capabilities of current screening methods have limitations. Fluorescence-based assay needs applicable fluorescent label, and the reliability of acquired enzymatic activity is influenced by fluorescent label’s binding affinity and photostability. To acquire the natural activity of an enzyme, another method is to combine pre-screening step and high-performance liquid chromatography (HPLC) measurement. But its throughput is limited by necessary time investment. Hundreds of variants are selected from libraries, and their enzymatic activities are then identified one by one by HPLC. The turn-around-time is 30 minutes for one sample by HPLC, which limits the acquirable enzyme improvement within reasonable time. To achieve the real high-throughput enzyme screening, i.e., obtain reliable enzyme improvement within reasonable time, a widely applicable high-throughput measurement of enzymatic reactions is highly demanded. Here, a high-throughput screening method using broadband coherent anti-Stokes Raman spectroscopy (CARS) was proposed. CARS is one of coherent Raman spectroscopy, which can identify label-free chemical components specifically from their inherent molecular vibration. These characteristic vibrational signals are generated from different vibrational modes of chemical bonds. With the broadband CARS, chemicals in one sample can be identified from their signals in one broadband CARS spectrum. Moreover, it can magnify the signal levels to several orders of magnitude greater than spontaneous Raman systems, and therefore has the potential to evaluate chemical's concentration rapidly. As a demonstration of screening with CARS, alcohol dehydrogenase, which converts ethanol and nicotinamide adenine dinucleotide oxidized form (NAD+) to acetaldehyde and nicotinamide adenine dinucleotide reduced form (NADH), was used. The signal of NADH at 1660 cm⁻¹, which is generated from nicotinamide in NADH, was utilized to measure the concentration of it. The evaluation time for CARS signal of NADH was determined to be as short as 0.33 seconds while having a system sensitivity of 2.5 mM. The time course of alcohol dehydrogenase reaction was successfully measured from increasing signal intensity of NADH. This measurement result of CARS was consistent with the result of a conventional method, UV-Vis. CARS is expected to have application in high-throughput enzyme screening and realize more reliable enzyme improvement within reasonable time.

Keywords: Coherent Anti-Stokes Raman Spectroscopy, CARS, directed evolution, enzyme screening, Raman spectroscopy

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