Search results for: container throughput

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: Bruno R. Mendes, Francisco J. Caldeira, Rita S. Luís

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Population ageing is directly correlated to an increase in medicine consumption. Beyond the latter and the polymedicated profile of elderly, it is possible to see a need for pharmacotherapeutic monitoring due to cognitive and physical impairment. In this sense, the tracking, organization and administration of medicines become a daily challenge and the pill-box dispenser system a solution. The pill-box dispenser (system) consists in a small compartmentalized container to unit dose organization, which means a container able to correlate the patient’s prescribed dose regimen and the time schedule of intake. In many European countries, this system is part of pharmacist’s role in clinical pharmacy. Despite this simple solution, therapy compliance is only possible if the patient adheres to the system, so it is important to establish a qualitative and quantitative analysis on the perception of the patient on the benefits and risks of the pill-box dispenser as well as the identification of the ideal system. The analysis was conducted through an observational study, based on the application of a standardized questionnaire structured with the numerical scale of Likert (5 levels) and previously validated on the population. The study was performed during a limited period of time and under a randomized sample of 188 participants. The questionnaire consisted of 22 questions: 6 background measures and 16 specific measures. The standards for the final comparative analysis were obtained through the state-of-the-art on the subject. The study carried out using the Likert scale afforded a degree of agreement and discordance between measures (Sample vs. Standard) of 56,25% and 43,75%, respectively. It was concluded that the pill-box dispenser has greater acceptance among a younger population, that was not the initial target of the system. However, this allows us to guarantee a high adherence in the future. Additionally, it was noted that the cost associated with this service is not a limiting factor for its use. The pill-box dispenser system, as currently implemented, demonstrates an important weakness regarding the quality and effectiveness of the medicines, which is not understood by the patient, revealing a significant lack of literacy when it concerns with medicine area. The characteristics of an ideal system remain unchanged, which means that the size, appearance and availability of information in the pill-box continue to be indispensable elements for the compliance with the system. The pill-box dispenser remains unsuitable regarding container size and the type of treatment to which it applies. Despite that, it might be a future standard for clinical pharmacy, allowing a differentiation of the pharmacist role, as well as a wider range of applications to other age groups and treatments.

Keywords: clinical pharmacy, medicines, patient safety, pill-box dispenser

Procedia PDF Downloads 168

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: 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: Mayesha Tahsin, A.S. Mollah

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Recently, a 1.5x1.5 inch NaI(Tl) detector based gamma-ray spectroscopy system has been installed in the laboratory of the Nuclear Science and Engineering Department of the Military Institute of Science and Technology for radioactivity detection purposes. The newly installed NaI(Tl) detector has a circular lead shield of 22 mm width. An important consideration of any gamma-ray spectroscopy is the minimization of natural background radiation not originating from the radioactive sample that is being measured. Natural background gamma-ray radiation comes from naturally occurring or man-made radionuclides in the environment or from cosmic sources. Moreover, the main problem with this system is that it is not suitable for measurements of radioactivity with a large sample container like Petridish or Marinelli beaker geometry. When any laboratory installs a new detector or/and new shield, it “must” first carry out quality and performance tests for the detector and shield. This paper describes a new portable shielding system with lead that can reduce the background radiation. Intensity of gamma radiation after passing the shielding will be calculated using shielding equation I=Ioe-µx where Io is initial intensity of the gamma source, I is intensity after passing through the shield, µ is linear attenuation coefficient of the shielding material, and x is the thickness of the shielding material. The height and width of the shielding will be selected in order to accommodate the large sample container. The detector will be surrounded by a 4π-geometry low activity lead shield. An additional 1.5 mm thick shield of tin and 1 mm thick shield of copper covering the inner part of the lead shielding will be added in order to remove the presence of characteristic X-rays from the lead shield.

Keywords: shield, NaI (Tl) detector, gamma radiation, intensity, linear attenuation coefficient

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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

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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: Kun Li, Yuzheng Liu, Xiuqi Fan

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High-security standard and high efficiency of screening seem to be contradictory to each other in the airport security check process. Improving the efficiency as far as possible while maintaining the same security standard is significantly meaningful. This paper utilizes the knowledge of Operation Research and Stochastic Process to establish mathematical models to explore this problem. We analyze the current process of airport security check and use the M/G/1 and M/G/k models in queuing theory to describe the process. Then we find the least efficient part is the pre-check lane, the bottleneck of the queuing system. To improve passenger throughput and reduce the variance of passengers’ waiting time, we adjust our models and use Monte Carlo method, then put forward three modifications: adjust the ratio of Pre-Check lane to regular lane flexibly, determine the optimal number of security check screening lines based on cost analysis and adjust the distribution of arrival and service time based on Monte Carlo simulation results. We also analyze the impact of cultural differences as the sensitivity analysis. Finally, we give the recommendations for the current process of airport security check process.

Keywords: queue theory, security check, stochatic process, Monte Carlo simulation

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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: Pablo Chico De Guzman, Cesar Sanchez

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Microservices are a software development methodology in which applications are built by composing a set of independently deploy-able, small, modular services. Each service runs a unique process and it gets instantiated and deployed in one or more machines (we assume that different microservices are deployed into different machines). Microservices are becoming the de facto standard for developing distributed cloud applications due to their reduced release cycles. In principle, the responsibility of a microservice can be as simple as implementing a single function, which can lead to the following issues: - Resource fragmentation due to the virtual machine boundary. - Poor communication performance between microservices. Two composition techniques can be used to optimize resource fragmentation and communication performance: aggregation and embedding of microservices. Aggregation allows the deployment of a set of microservices on the same machine using a proxy server. Aggregation helps to reduce resource fragmentation, and is particularly useful when the aggregated services have a similar scalability behavior. Embedding deals with communication performance by deploying on the same virtual machine those microservices that require a communication channel (localhost bandwidth is reported to be about 40 times faster than cloud vendor local networks and it offers better reliability). Embedding can also reduce dependencies on load balancer services since the communication takes place on a single virtual machine. For example, assume that microservice A has two instances, a1 and a2, and it communicates with microservice B, which also has two instances, b1 and b2. One embedding can deploy a1 and b1 on machine m1, and a2 and b2 are deployed on a different machine m2. This deployment configuration allows each pair (a1-b1), (a2-b2) to communicate using the localhost interface without the need of a load balancer between microservices A and B. Aggregation and embedding techniques are complex since different microservices might have incompatible runtime dependencies which forbid them from being installed on the same machine. There is also a security concern since the attack surface between microservices can be larger. Luckily, container technology allows to run several processes on the same machine in an isolated manner, solving the incompatibility of running dependencies and the previous security concern, thus greatly simplifying aggregation/embedding implementations by just deploying a microservice container on the same machine as the aggregated/embedded microservice container. Therefore, a wide variety of deployment configurations can be described by combining aggregation and embedding to create an efficient and robust microservice architecture. This paper presents a formal method that receives a declarative definition of a microservice architecture and proposes different optimized deployment configurations by aggregating/embedding microservices. The first prototype is based on i2kit, a deployment tool also submitted to ICWS 2018. The proposed prototype optimizes the following parameters: network/system performance, resource usage, resource costs and failure tolerance.

Keywords: aggregation, deployment, embedding, resource allocation

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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: 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: 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: Xiaoqian Cheng, Jon Kleppe, Ole Torsæter

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The properties of rocks have effects on efficiency of surfactant. One objective of this study is to analyze the effects of rock properties (permeability, porosity, initial water saturation) on surfactant spontaneous imbibition at laboratory scale. The other objective is to evaluate existing upscaling methods and establish a modified upscaling method. A core is put in a container that is full of surfactant solution. Assume there is no space between the bottom of the core and the container. The core is modelled as a cuboid matrix with a length of 3.5 cm, a width of 3.5 cm, and a height of 5 cm. The initial matrix, brine and oil properties are set as the properties of Ekofisk Field. The simulation results of matrix permeability show that the oil recovery rate has a strong positive linear relationship with matrix permeability. Higher oil recovery is obtained from the matrix with higher permeability. One existing upscaling method is verified by this model. The study on matrix porosity shows that the relationship between oil recovery rate and matrix porosity is a negative power function. However, the relationship between ultimate oil recovery and matrix porosity is a positive power function. The initial water saturation of matrix has negative linear relationships with ultimate oil recovery and enhanced oil recovery. However, the relationship between oil recovery and initial water saturation is more complicated with the imbibition time because of the transition of dominating force from capillary force to gravity force. Modified upscaling methods are established. The work here could be used as a reference for the surfactant application in fractured reservoirs. And the description of the relationships between properties of matrix and the oil recovery rate and ultimate oil recovery helps to improve upscaling methods.

Keywords: initial water saturation, permeability, porosity, surfactant EOR

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Authors: Abdolhamid Anazadehsayed, Jamal Naser

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An integrated computational fluid dynamics model is developed for a combined simulation of Plateau borders, films, and transitional areas between the film and the Plateau borders to reduce the simplifications and shortcomings of available models for foam drainage in micro-scale. Additionally, the counter-flow related to the Marangoni effect in the transitional area is investigated. The results of this combined model show the contribution of the films, the exterior Plateau borders, and Marangoni flow in the drainage process more accurately since the inter-influence of foam's elements is included in this study. The exterior Plateau borders flow rate can be four times larger than the interior ones. The exterior bubbles can be more prominent in the drainage process in cases where the number of the exterior Plateau borders increases due to the geometry of container. The ratio of the Marangoni counter-flow to the Plateau border flow increases drastically with an increase in the mobility of air-liquid interface. However, the exterior bubbles follow the same trend with much less intensity since typically, the flow is less dependent on the interface of air-liquid in the exterior bubbles. Moreover, the Marangoni counter-flow in a near-wall transition area is less important than an internal one. The influence of air-liquid interface mobility on the average velocity of interior foams is attained with more accuracy with more realistic boundary condition. Then it has been compared with other numerical and analytical results. The contribution of films in the drainage is significant for the mobile foams as the velocity of flow in the film has the same order of magnitude as the velocity in the Plateau border. Nevertheless, for foams with rigid interfaces, film's contribution in foam drainage is insignificant, particularly for the films near the wall of the container.

Keywords: foam, plateau border, film, Marangoni, CFD, bubble

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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: Han-Qin Zheng, Yi-Fan Chiang-Hsieh, Chia-Hung Chien, Wen-Chi Chang

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As the most important non-vascular plants, algae have many research applications, including high species diversity, biofuel sources, adsorption of heavy metals and, following processing, health supplements. With the increasing availability of next-generation sequencing (NGS) data for algae genomes and transcriptomes, an integrated resource for retrieving gene expression data and metabolic pathway is essential for functional analysis and systems biology in algae. However, gene expression profiles and biological pathways are displayed separately in current resources, and making it impossible to search current databases directly to identify the cellular response mechanisms. Therefore, this work develops a novel AlgaePath database to retrieve gene expression profiles efficiently under various conditions in numerous metabolic pathways. AlgaePath, a web-based database, integrates gene information, biological pathways, and next-generation sequencing (NGS) datasets in Chlamydomonasreinhardtii and Neodesmus sp. UTEX 2219-4. Users can identify gene expression profiles and pathway information by using five query pages (i.e. Gene Search, Pathway Search, Differentially Expressed Genes (DEGs) Search, Gene Group Analysis, and Co-Expression Analysis). The gene expression data of 45 and 4 samples can be obtained directly on pathway maps in C. reinhardtii and Neodesmus sp. UTEX 2219-4, respectively. Genes that are differentially expressed between two conditions can be identified in Folds Search. Furthermore, the Gene Group Analysis of AlgaePath includes pathway enrichment analysis, and can easily compare the gene expression profiles of functionally related genes in a map. Finally, Co-Expression Analysis provides co-expressed transcripts of a target gene. The analysis results provide a valuable reference for designing further experiments and elucidating critical mechanisms from high-throughput data. More than an effective interface to clarify the transcript response mechanisms in different metabolic pathways under various conditions, AlgaePath is also a data mining system to identify critical mechanisms based on high-throughput sequencing.

Keywords: next-generation sequencing (NGS), algae, transcriptome, metabolic pathway, co-expression

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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: 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: Rowen Naicker, Dhiren Allopi

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One of the major problems the Port of Durban is experiencing is addressing shallow spots aggravated by megaships that berth. In the recent years, the vessels that call at the Port have increased in size which calls for draughts that are much deeper. For this reason, these larger vessels can only berth under high tide to avoid the risk of running aground. In addition to this, the ships cannot sail in fully laden which does not make it feasible for ship owners. Further during the berthing materials are displaced from the seabed which result in shallow spots being developed. The permitted draft (under-keel allowance) for the Durban Container Terminal (DCT) is currently 12.2 m. Transnet National Ports Authority (TNPA) are currently investing in a dredging fleet worth almost two billion rand. One of the highlights of this investment would be the building of grab hopper dredger that would be dedicated to the Port by 2017. TNPA are trying various techniques to dissolve the reduction of draughts by implementing dredging maintenance projects but is this sufficient? The ideal resolution would be the deepening and widening of the berths. Plans for this project is in place, but the implementation process is a matter of urgency. The intention of this project will be to accommodate three big vessels rather than two which in turn will improve the turnaround time in the port. The berthing will then no longer depend on high tide to avoid ships running aground. The aim of this paper is to prove the implementation of deepening and widening of the Port of Durban is a matter of urgency. If the plan to deepen and widen the berths at DCT is delayed it will mean a loss of business for the South African economy. If larger vessels cannot be accommodated in the Port of Durban, it will bypass the busiest container handling facility in the Southern hemisphere. Shipping companies are compelled to use larger ships as opposed to smaller vessels to lower port and fuel costs. A delay in the expansion of DCT could also result in an escalation of costs.

Keywords: DCT, deepening, berth, port

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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

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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

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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: Xavier A. Conlan

Abstract:

Speed of analysis is a significant limitation to current high-performance liquid chromatography/mass spectrometry (HPLC/MS) and ultra-high-pressure liquid chromatography (UHPLC)/MS systems both of which are used in many forensic investigations. The flow rate limitations of MS detection require a compromise in the chromatographic flow rate, which in turn reduces throughput, and when using modern columns, a reduction in separation efficiency. Commonly, this restriction is combated through the post-column splitting of flow prior to entry into the mass spectrometer. However, this results in a loss of sensitivity and a loss in efficiency due to the post-extra column dead volume. A new chromatographic column format known as 'parallel segmented flow' involves the splitting of eluent flow within the column outlet end fitting, and in this study we present its application in order to interrogate the provenience of methamphetamine samples with mass spectrometry detection. Using parallel segmented flow, column flow rates as high as 3 mL/min were employed in the analysis of amino acids without post-column splitting to the mass spectrometer. Furthermore, when parallel segmented flow chromatography columns were employed, the sensitivity was more than twice that of conventional systems with post-column splitting when the same volume of mobile phase was passed through the detector. These finding suggest that this type of column technology will particularly enhance the capabilities of modern LC/MS enabling both high-throughput and sensitive mass spectral detection.

Keywords: chromatography, mass spectrometry methamphetamine, parallel segmented outlet flow column, forensic sciences

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Authors: Paula Marín, Mohammad Saffari, Alvaro de Gracia, Luisa F. Cabeza, Svetlana Ushak

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Climate control represents an important issue when referring to energy consumption of buildings and associated expenses, both in installation or operation periods. The climate control of a building relies on several factors. Among them, localization, orientation, architectural elements, sources of energy used, are considered. In order to study the thermal behaviour of a building set up, the present study proposes the use of energy simulation program Energy Plus. In recent years, energy simulation programs have become important tools for evaluation of thermal/energy performance of buildings and facilities. Besides, the need to find new forms of passive conditioning in buildings for energy saving is a critical component. The use of phase change materials (PCMs) for heat storage applications has grown in importance due to its high efficiency. Therefore, the climatic conditions of Northern Chile: high solar radiation and extreme temperature fluctuations ranging from -10°C to 30°C (Calama city), low index of cloudy days during the year are appropriate to take advantage of solar energy and use passive systems in buildings. Also, the extensive mining activities in northern Chile encourage the use of large numbers of containers to harbour workers during shifts. These containers are constructed with lightweight construction systems, requiring heating during night and cooling during day, increasing the HVAC electricity consumption. The use of PCM can improve thermal comfort and reduce the energy consumption. The objective of this study was to evaluate the thermal and energy performance of containers of 2.5×2.5×2.5 m3, located in four cities of Chile: Antofagasta, Calama, Santiago, and Concepción. Lightweight envelopes, typically used in these building prototypes, were evaluated considering a container without PCM inclusion as the reference building and another container with PCM-enhanced envelopes as a test case, both of which have a door and a window in the same wall, orientated in two directions: North and South. To see the thermal response of these containers in different seasons, the simulations were performed considering a period of one year. The results show that higher energy savings for the four cities studied are obtained when the distribution of door and window in the container is in the north direction because of higher solar radiation incidence. The comparison of HVAC consumption and energy savings in % for north direction of door and window are summarised. Simulation results show that in the city of Antofagasta 47% of heating energy could be saved and in the cities of Calama and Concepción the biggest savings in terms of cooling could be achieved since PCM reduces almost all the cooling demand. Currently, based on simulation results, four containers have been constructed and sized with the same structural characteristics carried out in simulations, that are, containers with/without PCM, with door and window in one wall. Two of these containers will be placed in Antofagasta and two containers in a copper mine near to Calama, all of them will be monitored for a period of one year. The simulation results will be validated with experimental measurements and will be reported in the future.

Keywords: energy saving, lightweight construction, PCM, simulation

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Authors: Anupam Chanda

Abstract:

Presently Packaging plays a significant role for drug discoveries. The process of selecting materials and the type of packaging also offers an opportunity for the Packaging scientist to look for biological delivery choices. Most injectable protein products were supplied in some sort of glass vial, prefilled syringe, cartridge. Those product having high Ph content there is a chance of “delamination “from inner surface of glass vial. With protein-based drugs, the biggest issue is the effect of packaging derivatives on the protein’s threedimensional and surface structure. These are any effects that relate to denaturation or aggregation of the protein due to oxidation or interactions from contaminants or impurities in the preparation. The potential for these effects needs to be carefully considered in choosing the container and the container closure system to avoid putting patients in jeopardy. Cause of Delamination : -Formulations with a high pH include phosphate and citrate buffers increase the risk of glass delamination. -High alkali content in glass could accelerate erosion. -High temperature during the vial-forming process increase the risk of glass delamination. -Terminal sterilization (irradiated at 20-40 kGy for 150 min) also is a risk factor for specific products(veterinary parenteral administration),could cause delamination. -High product-storage temperatures and long exposure times can increase the rate and severity of glass delamination. How to prevent Delamination -Treating the surface of the glass vials with materials, such as ammonium sulfate or siliconization can reduce the rate of glass erosion. -Consider alternative sterilization methods only in rare cases. -The correct specification for the glass to ensure its suitability for the pH of the product. -Use Cyclic olefin copolymer(COC)/Cyclic olefin Polymer(COP) Adsorption of protein and Solutions: Option#1 Coat with linear methoxylated polyglycerol and hyperbranchedmethoxylated polyglycerol. Option#2 Thehyperbranched non-methoxylated coating performed best. Option#3 Coat with hyperbranched polyglycerol Option#4 Right selection of Sterilization of glass vial/syringe.

Keywords: delamination of glass, ptrotien adoptions inside the glass surface, extractable & leachable solutions, injectable designs for new drugs

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Authors: Kréhi Serge Agbli, Samuel Portebos, Michaël Salomon

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Here a methodology is considered aiming at evaluating the economic benefit of the provision of a primary frequency control unit using a Battery Energy Storage System (BESS). In this methodology, two control types (basic and hysteresis) are implemented and the corresponding minimum energy storage system power allowing to maintain the frequency drop inside a given threshold under a given contingency is identified and compared using DigSilent’s PowerFactory software. Following this step, the corresponding energy storage capacity (in MWh) is calculated. As PowerFactory is dedicated to dynamic simulation for transient analysis, a first order model related to the IEEE 9 bus grid used for the analysis under PowerFactory is characterized and implemented on MATLAB-Simulink. Primary frequency control is simulated using the two control types over one-month grid's frequency deviation data on this Simulink model. This simulation results in the energy throughput both basic and hysteresis BESSs. It emerges that the 15 minutes operation band of the battery capacity allocated to frequency control is sufficient under the considered disturbances. A sensitivity analysis on the width of the control deadband is then performed for the two control types. The deadband width variation leads to an identical sizing with the hysteresis control showing a better frequency control at the cost of a higher delivered throughput compared to the basic control. An economic analysis comparing the cost of the sized BESS to the potential revenues is then performed.

Keywords: battery energy storage system, electrical network frequency stability, frequency control unit, PowerFactor

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Authors: Christina Killian, Katie Wall, Séamus Fanning, Guerrino Macori

Abstract:

Deep-level metagenomics offers a useful technical approach to explore the three dynamic One Health axes: healthcare, domiciliary and veterinary. There is currently limited understanding of the composition of complex biofilms, natural abundance of AMR genes and gene transfer occurrence in these ecological niches. By using a newly established small-scale complex biofilm model, COMBAT has the potential to provide new information on microbial diversity, antimicrobial resistance (AMR)-encoding gene abundance, and their transfer in complex biofilms of importance to these three One Health axes. Shotgun metagenomics has been used to sample the genomes of all microbes comprising the complex communities found in each biofilm source. A comparative analysis between untreated and biocide-treated biofilms is described. The basic steps include the purification of genomic DNA, followed by library preparation, sequencing, and finally, data analysis. The use of long-read sequencing facilitates the completion of metagenome-assembled genomes (MAG). Samples were sequenced using a PromethION platform, and following quality checks, binning methods, and bespoke bioinformatics pipelines, we describe the recovery of individual MAGs to identify mobile gene elements (MGE) and the corresponding AMR genotypes that map to these structures. High-throughput sequencing strategies have been deployed to characterize these communities. Accurately defining the profiles of these niches is an essential step towards elucidating the impact of the microbiota on each niche biofilm environment and their evolution.

Keywords: COMBAT, biofilm, metagenomics, high-throughput sequencing

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Authors: Emanuel Teixeira, Anderson Ramos, Marisa Lourenço, Fernando J. Velez, Jon M. Peha

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This article discusses the benefit cost analysis aspects of millimetre wavebands (mmWaves) and Super High Frequency (SHF). The devaluation along the distance of the carrier-to-noise-plus-interference ratio with the coverage distance is assessed by considering two different path loss models, the two-slope urban micro Line-of-Sight (UMiLoS) for the SHF band and the modified Friis propagation model, for frequencies above 24 GHz. The equivalent supported throughput is estimated at the 5.62, 28, 38, 60 and 73 GHz frequency bands and the influence of carrier-to-noise-plus-interference ratio in the radio and network optimization process is explored. Mostly owing to the lessening caused by the behaviour of the two-slope propagation model for SHF band, the supported throughput at this band is higher than at the millimetre wavebands only for the longest cell lengths. The benefit cost analysis of these pico-cellular networks was analysed for regular cellular topologies, by considering the unlicensed spectrum. For shortest distances, we can distinguish an optimal of the revenue in percentage terms for values of the cell length, R ≈ 10 m for the millimeter wavebands and for longest distances an optimal of the revenue can be observed at R ≈ 550 m for the 5.62 GHz. It is possible to observe that, for the 5.62 GHz band, the profit is slightly inferior than for millimetre wavebands, for the shortest Rs, and starts to increase for cell lengths approximately equal to the ratio between the break-point distance and the co-channel reuse factor, achieving a maximum for values of R approximately equal to 550 m.

Keywords: millimetre wavebands, SHF band, SINR, cost benefit analysis, 5G

Procedia PDF Downloads 114