Search results for: axillary lymph node dissection

Authors: Waqas Ahmed Khan Afridi, Subhas Chandra Mukhopadhyay, Bandita Mainali

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The research paper presents a unique approach to evapotranspiration (ET) prediction using a Support Vector Machine (SVM) learning algorithm. The study leverages real-time sensor node data to develop an accurate and adaptable prediction model, addressing the inherent challenges of traditional ET estimation methods. The integration of the SVM algorithm with real-time sensor node data offers great potential to improve spatial and temporal resolution in ET predictions. In the model development, key input features are measured and computed using mathematical equations such as Penman-Monteith (FAO56) and soil water balance (SWB), which include soil-environmental parameters such as; solar radiation (Rs), air temperature (T), atmospheric pressure (P), relative humidity (RH), wind speed (u2), rain (R), deep percolation (DP), soil temperature (ST), and change in soil moisture (∆SM). The one-year field data are split into combinations of three proportions i.e. train, test, and validation sets. While kernel functions with tuning hyperparameters have been used to train and improve the accuracy of the prediction model with multiple iterations. This paper also outlines the existing methods and the machine learning techniques to determine Evapotranspiration, data collection and preprocessing, model construction, and evaluation metrics, highlighting the significance of SVM in advancing the field of ET prediction. The results demonstrate the robustness and high predictability of the developed model on the basis of performance evaluation metrics (R2, RMSE, MAE). The effectiveness of the proposed model in capturing complex relationships within soil and environmental parameters provide insights into its potential applications for water resource management and hydrological ecosystem.

Keywords: evapotranspiration, FAO56, KNIME, machine learning, RStudio, SVM, sensors

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Authors: M. Sulieman, H. Arabiyat, H. Ali, K. Potiszil, I. Abbas, R. English, P. King, I. Brown, P. Drew

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Introduction: The incidence of breast ductal Carcinoma in Situ (DCIS) has been increasing; it currently represents up 20-25% of all breast carcinomas. Some aspects of DCIS management are still controversial, mainly due to the heterogeneity of its clinical presentation and of its biological and pathological characteristics. In DCIS, histological diagnosis obtained preoperatively, carries the risk of sampling error if the presence of invasive cancer is subsequently diagnosed. The mammographic extent over than 4–5 cm and the presence of architectural distortion, focal asymmetric density or mass on mammography are proven important risk factors of preoperative histological under staging. Intracystic papillary cancer (IPC) is a rare form of breast carcinoma. Despite being previously compared to DCIS it has been shown to present histologically with invasion of the basement membrane and even metastasis. SLNB – Carries the risk of associated comorbidity that should be considered when planning surgery for DCIS and IPC. Objectives: The aim of this Audit was to better define a ‘high risk’ group of patients with pre-op diagnosis of non-invasive cancer undergoing breast conserving surgery, who would benefit from sentinel node biopsy. Method: Retrospective data collection of all patients with ductal carcinoma in situ over 5 years. 636 patients identified, and after exclusion criteria applied: 394 patients were included. High risk defined as: Extensive micro-calcification >40mm OR any mass forming DCIS. IPC: Winpath search from for the term ‘papillary carcinoma’ in any breast specimen for 5 years duration;.29 patients were included in this group. Results: DCIS: 188 deemed high risk due to >40mm calcification or a mass forming (radiological or palpable) 61% of those had a mastectomy and 32% BCS. Overall, in that high-risk group - the number with invasive disease was 38%. Of those high-risk DCIS pts 85% had a SLN - 80% at the time of surgery and 5% at a second operation. For the BCS patients - 42% had SLN at time of surgery and 13% (8 patients) at a second operation. 15 (7.9%) pts in the high-risk group had a positive SLNB, 11 having a mastectomy and 4 having BCS. IPC: The provisional diagnosis of encysted papillary carcinoma is upgraded to an invasive carcinoma on final histology in around a third of cases. This has may have implications when deciding whether to offer sentinel node removal at the time of therapeutic surgery. Conclusions: We have defined a ‘high risk’ group of pts with pre-op diagnosis of non-invasive cancer undergoing BCS, who would benefit from SLNB at the time of the surgery. In patients with high-risk features; the risk of invasive disease is up to 40% but the risk of nodal involvement is approximately 8%. The risk of morbidity from SLN is up to about 5% especially the risk of lymphedema.

Keywords: breast ductal carcinoma in Situ (DCIS), intracystic papillary carcinoma (IPC), sentinel node biopsy (SLNB), high-risk, non-invasive, cancer disease

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Authors: Smriti Agarwal, Ashish Payal, B. V. R. Reddy

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IEEE 802.15.4 is a Low Rate Wireless Personal Area Networks (LR-WPAN) standard combined with ZigBee, which is going to enable new applications in Wireless Sensor Networks (WSNs) and Internet of Things (IoT) domain. In recent years, it has become a popular standard for WSNs. Wireless communication among sensor motes, enabled by IEEE 802.15.4 standard, is extensively replacing the existing wired technology in a wide range of monitoring and control applications. Researchers have proposed a routing framework and mechanism that interacts with the IEEE 802.15.4 standard using software platform. In this paper, we have designed and implemented MAC based routing (MBR) based on IEEE 802.15.4 standard using a hardware platform “SENSEnuts”. The experimental results include data through light and temperature sensors obtained from communication between PAN coordinator and source node through coordinator, MAC address of some modules used in the experimental setup, topology of the network created for simulation and the remaining battery power of the source node. Our experimental effort on a WSN Testbed has helped us in bridging the gap between theoretical and practical aspect of implementing IEEE 802.15.4 for WSNs applications.

Keywords: IEEE 802.15.4, routing, WSN, ZigBee

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Authors: K. Gomathi

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Mobile Ad hoc Networks (MANET) is defined as collection of routable wireless mobile nodes with no centralized administration and communicate each other using radio signals. Especially MANETs deployed in hostile environments where hackers will try to disturb the secure data transfer and drain the valuable network resources. Since MANET is battery operated network, preserving the network resource is essential one. For resource constrained computation, efficient routing and to increase the network stability, the network is divided into smaller groups called clusters. The clustering architecture consists of Cluster Head(CH), ordinary node and gateway. The CH is responsible for inter and intra cluster routing. CH election is a prominent research area and many more algorithms are developed using many different metrics. The CH with longer life sustains network lifetime, for this purpose Secondary Cluster Head(SCH) also elected and it is more economical. To nominate efficient CH, a Enhanced Distributed Weighted Clustering Algorithm (EDWCA) has been proposed. This approach considers metrics like battery power, degree difference and speed of the node for CH election. The proficiency of proposed one is evaluated and compared with existing algorithm using Network Simulator(NS-2).

Keywords: MANET, EDWCA, clustering, cluster head

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Authors: Jorge R. Santos, Pedro Sebastiao

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In recent years there has been a great growth in the use of drones, being used in several areas such as security, agriculture, or research. The existence of some systems that allow the remote control of drones is a reality; however, these systems are quite simple and directed to specific functionality. This paper proposes the development of a web platform made in Vue.js and Node.js to control, manage, and monitor drones in real time. Using a microservice architecture, the proposed project will be able to integrate algorithms that allow the optimization of processes. Communication with remote devices is suggested via HTTP through 3G, 4G, and 5G networks and can be done in real time or by scheduling routes. This paper addresses the case of forest fires as one of the services that could be included in a system similar to the one presented. The results obtained with the elaboration of this project were a success. The communication between the web platform and drones allowed its remote control and monitoring. The incorporation of the fire detection algorithm in the platform proved possible a real time analysis of the images captured by the drone without human intervention. The proposed system has proved to be an asset to the use of drones in fire detection. The architecture of the application developed allows other algorithms to be implemented, obtaining a more complex application with clear expansion.

Keywords: drone control, microservices, node.js, unmanned aerial vehicles, vue.js

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Authors: Raveendranath Veeramani, Sunil Jonathan Holla, Parkash Chand, Sunil Chumber

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Gray’s Anatomy for Students has been a well-appreciated book among undergraduate students of anatomy in Asia. However, the current curricular requirements of anatomy require a more focused and organized approach. The editors of the first South Asia edition of Gray’s Anatomy for Students hereby highlight the modifications and importance of this edition. There is an emphasis on active learning by making the clinical relevance of anatomy explicit. Learning anatomy in context has been fostered by the association between anatomists and clinicians in keeping with the emerging integrated curriculum of the 21st century. The language has been simplified to aid students who have studied in the vernacular. The original illustrations have been retained, and few illustrations have been added. There are more figure numbers mentioned in the text to encourage students to refer to the illustrations while learning. The text has been made more student-friendly by adding generalizations, classifications and summaries. There are useful review materials at the beginning of the chapters which include digital resources for self-study. There are updates on imaging techniques to encourage students to appreciate the importance of essential knowledge of the relevant anatomy to interpret images, due emphasis has been laid on dissection. Additional importance has been given to the cranial nerves, by describing their relevant details with several additional illustrations and flowcharts. This new edition includes innovative features such as set inductions, outlines for subchapters and flowcharts to facilitate learning. Set inductions are mostly clinical scenarios to create interest in the need to study anatomy for healthcare professions. The outlines are a modern multimodal facilitating approach towards various topics to empower students to explore content and direct their learning and include learning objectives and material for review. The components of the outline encourage the student to be aware of the need to create solutions to clinical problems. The outlines help students direct their learning to recall facts, demonstrate and analyze relationships, use reason to explain concepts, appreciate the significance of structures and their relationships and apply anatomical knowledge. The 'structures to be identified in a dissection' are given as Level I, II and III which represent the 'must know, desirable to know and nice to know' content respectively. The flowcharts have been added to get an overview of the course of a structure, recapitulate important details about structures, and as an aid to recall. There has been a great effort to balance the need to have content that would enable students to understand concepts as well as get the basic material for the current condensed curriculum.

Keywords: Grays anatomy, South Asia, human anatomy, students anatomy

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Authors: Shirin Jalili, Ramin Ghasemi Shayan

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Atrial fibrillation is the foremost common arrhythmia around the world, with expanding recurrence famous with age. Thromboembolic occasions and strokes are the number one cause of mortality and morbidity. For patients who don't react to restorative treatment for rate and beat control, the maze method offers an elective treatment mediation. pharmaco-medical treatment for atrial fibrillation is pointed at the control of rate or cadence, intrusive treatment for atrial fibrillation is pointed at cadence control. An obtrusive approach may comprise of percutaneous catheter treatment, surgery, or a crossover approach. Since the maze method is recognized as the foremost successful way to dispense with AF, combining the maze strategy amid major cardiac surgeries has been received in clinical hone. the maze strategy, moreover known as Cox¬maze iii or the ‘cut¬and¬sew’ method, involves making different incisions within the atria to make an arrangement of scars that dispose of each potential zone of re¬entry. The electrical drive is constrained through a maze of scars that coordinates the electrical drive from the sinus node to the av node. By settling the headstrong period between ranges of scar, re¬entry is disposed of. in this article, we evaluate the Maze surgery method that's the surgical method of choice for the treatment of restorative atrial fibrillation.

Keywords: atrial fibrillation, congenital heart disease, procedure, maze surgery, treatment

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Authors: Auxeeliya Jesudoss, Ashraph Sulaiman, Ratnakar Kotnana

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V2V communication brings up several questions of scalability issues although message sharing in vehicular ad-hoc networks comprises of both Vehicle-to-Vehicle communications (V2V) and Vehicle to Infrastructure communication (V2I). It is not an easy task for a vehicle to verify all signatures of the messages sent by its neighboring vehicles in a timely manner, without resulting in message loss. Moreover, the communication overhead of a vehicle to authenticate another vehicle would increase together with the security of the system. Another issue to be addressed is the continuous mobility of vehicles which requires at least some information on the node’s own position to be revealed to the neighboring vehicles. This may facilitate the attacker to congregate information on a node’s position or its mobility patterns. In order to tackle these issues, this paper introduces a RSU aggregated message deliverance scheme called RAMeD. With RAMeD, roadside units (RSUs) are responsible for verifying the identity of the vehicles entering in its range, collect messages from genuine vehicles and to aggregate similar messages into groups before sending them to all the vehicles in its communication range. This aggregation will tremendously improve the rate of message delivery and reduce the message lose ratio by avoiding similar messages being sent to the vehicles redundantly. The proposed protocol is analyzed extensively to evaluate its merits and efficiency for vehicular communication.

Keywords: vehicular ad-hoc networks, V2V, V2I, VANET communication, scalability, message aggregation

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Authors: Hosein Hamisheh Bahar, Mohammad Hossein Fazel Zarandi, Akbar Esfahanipour

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In this paper, a hybrid expert system is developed by using fuzzy genetic network programming with reinforcement learning (GNP-RL). In this system, the frame-based structure of the system uses the trading rules extracted by GNP. These rules are extracted by using technical indices of the stock prices in the training time period. For developing this system, we applied fuzzy node transition and decision making in both processing and judgment nodes of GNP-RL. Consequently, using these method not only did increase the accuracy of node transition and decision making in GNP's nodes, but also extended the GNP's binary signals to ternary trading signals. In the other words, in our proposed Fuzzy GNP-RL model, a No Trade signal is added to conventional Buy or Sell signals. Finally, the obtained rules are used in a frame-based system implemented in Kappa-PC software. This developed trading system has been used to generate trading signals for ten companies listed in Tehran Stock Exchange (TSE). The simulation results in the testing time period shows that the developed system has more favorable performance in comparison with the Buy and Hold strategy.

Keywords: fuzzy genetic network programming, hybrid expert system, technical trading signal, Tehran stock exchange

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Authors: Guler D. Uzel, Andrew G. Parker, Robert L. Mach, Adly Abd-Alla

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Several tsetse fly species (Diptera: Glossinidae) in natural or colonized populations can be infected with the salivary gland hypertrophy virus (SGHV), a circular dsDNA virus (Hytrosaviridae). The virus infection is mainly asymptomatic but, in some species under certain conditions, the infection can produce salivary gland hypertrophy (SGH) symptoms. In the laboratory colonized tsetse, flies with SGH have reduced fertility, which negatively affects colony performance. Therefore, a high prevalence of SGH in insect mass rearing represents a major challenge for tsetse control using the sterile insect technique. The main objective of this study is to analyze the impact of Glossina pallidipes SGHV infection in various tsetse species on mortality and productivity and its impact on the symbiotic bacteria. Hypertropied salivary glands (SG) were collected from G. pallidipes into phosphate buffered saline (PBS) to prepare suspension; 2 µl aliquots were injected into adults of several tsetse species (G. pallidipes (Gp), G. p. gambiensis (Gpg), G. brevipalpis (Gb), G. morsitans morsitans (Gmm), G. morsitans centralis (Gmc) and G. fuscipes (Gf)) and the change in virus and symbiont titers were analyzed using qPCR. The development of SGH in the F1 was detected by dissection 10 days after emergence and virus infection was confirmed by PCR. The impact of virus infection on fly mortality and productivity was recorded. 2 µl aliquots were also injected into 3rd instar larvae of the different species and the adult SGs assayed by PCR for virus. Virus positive SGs from each species were homogenized in PBS and pooled within species for injection into larvae of the same species. Flies injected with PBS were used as control. Injecting teneral flies with SGHV caused increasing virus titer over time in all species but no SGH was detected. Dissection of the F1 also showed no development of SGH except in Gp (the homologous host). Injection of SGHV did not have any impact on the prevalence of the tsetse symbionts, but an increase in Sodalis titer was observed correlated with fly age regardless of virus infection. The virus infection had a negative impact on productivity and mortality. SGHV injection into larvae of the different species produced SGHV infected glands in the adults determined by PCR with a rate of 60%, 27%, 16%, 7% and 7% for Gp, Gf, Gpg, Gmm and Gmc, respectively. Virus positive SGs observed in the heterologous species were smaller than SGH found in Gp. No virus positive SG was detected by PCR in Gb and no SGH was observed in any adults except in Gp. Injecting virus suspension from the virus positive SGs into conspecific larvae did not produce any adults with infected SGs (except in Gp). SGHV can infect all tested tsetse species. Although the virus can infect and increase in titer in other tsetse species and affect fly mortality and productivity, no vertical virus transmission was observed in other tsetse species with might indicate a transmission barrier in these species, and virus collected from flies injected as larvae was not infective by injection.

Keywords: DNA viruses, glossina, hytrosaviridae, symbiotic bacteria, tsetse

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Authors: Dragan Ribarić

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We employ the so-called problem-dependent linked interpolation concept to develop two cubic 4-node quadrilateral Mindlin plate finite elements with 12 external degrees of freedom. In the problem-independent linked interpolation, the interpolation functions are independent of any problem material parameters and the rotation fields are not expressed in terms of the nodal displacement parameters. On the contrary, in the problem-dependent linked interpolation, the interpolation functions depend on the material parameters and the rotation fields are expressed in terms of the nodal displacement parameters. Two cubic 4-node quadrilateral plate elements are presented, named Q4-U3 and Q4-U3R5. The first one is modelled with one displacement and two rotation degrees of freedom in every of the four element nodes and the second element has five additional internal degrees of freedom to get polynomial completeness of the cubic form and which can be statically condensed within the element. Both elements are able to pass the constant-bending patch test exactly as well as the non-zero constant-shear patch test on the oriented regular mesh geometry in the case of cylindrical bending. In any mesh shape, the elements have the correct rank and only the three eigenvalues, corresponding to the solid body motions are zero. There are no additional spurious zero modes responsible for instability of the finite element models. In comparison with the problem-independent cubic linked interpolation implemented in Q9-U3, the nine-node plate element, significantly less degrees of freedom are employed in the model while retaining the interpolation conformity between adjacent elements. The presented elements are also compared to the existing problem-independent quadratic linked-interpolation element Q4-U2 and to the other known elements that also use the quadratic or the cubic linked interpolation, by testing them on several benchmark examples. Simple functional upgrading from the quadratic to the cubic linked interpolation, implemented in Q4-U3 element, showed no significant improvement compared to the quadratic linked form of the Q4-U2 element. Only when the additional bubble terms are incorporated in the displacement and rotation function fields, which complete the full cubic linked interpolation form, qualitative improvement is fulfilled in the Q4-U3R5 element. Nevertheless, the locking problem exists even for the both presented elements, like in all pure displacement elements when applied to very thin plates modelled by coarse meshes. But good and even slightly better performance can be noticed for the Q4-U3R5 element when compared with elements from the literature, if the model meshes are moderately dense and the plate thickness not extremely thin. In some cases, it is comparable to or even better than Q9-U3 element which has as many as 12 more external degrees of freedom. A significant improvement can be noticed in particular when modeling very skew plates and models with singularities in the stress fields as well as circular plates with distorted meshes.

Keywords: Mindlin plate theory, problem-independent linked interpolation, problem-dependent interpolation, quadrilateral displacement-based plate finite elements

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Authors: Ji-yang Yu, Dan Huang, Guo-ping Feng, Xin Li, Lu-yuan Wang

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The navigation satellite network, especially the Beidou MEO Constellation, can relay data effectively with wide coverage and is applied in navigation, detection, and position widely. But the constellation has not been completed, and the amount of satellites on-board is not enough to cover the earth, which makes the data-relay disrupted or delayed in the transition process. The data-relay function needs to tolerant the delay or disruption in some extension, which make the Beidou MEO Constellation a delay/disruption-tolerant network (DTN). The traditional DTN designs mainly employ the relay table as the basic of data path schedule computing. But in practical application, especially in critical condition, such as the war-time or the infliction heavy losses on the constellation, parts of the nodes may become invalid, then the traditional DTN design could be useless. Furthermore, when transmitting the critical message in the navigation system, the maximum priority strategy is used, but the nodes still inquiry the relay table to design the path, which makes the delay more than minutes. Under this circumstances, it needs a function which could compute the optimum data path on-board in real-time according to the constellation states. The on-board critical message transmission design for navigation satellite delay/disruption-tolerant network (DTN) is proposed, according to the characteristics of navigation satellite network. With the real-time computation of parameters in the network link, the least-delay transition path is deduced to retransmit the critical message in urgent conditions. First, the DTN model for constellation is established based on the time-varying matrix (TVM) instead of the time-varying graph (TVG); then, the least transition delay data path is deduced with the parameters of the current node; at last, the critical message transits to the next best node. For the on-board real-time computing, the time delay and misjudges of constellation states in ground stations are eliminated, and the residual information channel for each node can be used flexibly. Compare with the minute’s delay of traditional DTN; the proposed transmits the critical message in seconds, which improves the re-transition efficiency. The hardware is implemented in FPGA based on the proposed model, and the tests prove the validity.

Keywords: critical message, DTN, navigation satellite, on-board, real-time

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Authors: Diogo Ferreira Lima Filho, José Roberto Amazonas

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Nanotechnology opens the door to new paradigms that introduces a variety of novel tools enabling a plethora of potential applications in the biomedical, industrial, environmental, and military fields. This work proposes an integrated node model by applying the same concepts of TCNet to networks of nanodevices where the nodes are cooperatively interconnected with a low-complexity Mealy Machine (MM) topology integrating in the same electronic system the modules necessary for independent operation in wireless sensor networks (WSNs), consisting of Rectennas (RF to DC power converters), Code Generators based on Finite State Machine (FSM) & Trellis Decoder and On-chip Transmit/Receive with autonomy in terms of energy sources applying the Energy Harvesting technique. This approach considers the use of a Graphene Composite Substrate (GCS) for the integrated electronic circuits meeting the following characteristics: mechanical flexibility, miniaturization, and optical transparency, besides being ecological. In addition, graphene consists of a layer of carbon atoms with the configuration of a honeycomb crystal lattice, which has attracted the attention of the scientific community due to its unique Electrical Characteristics.

Keywords: composite substrate, energy harvesting, finite state machine, graphene, nanotechnology, rectennas, wireless sensor networks

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Authors: Min Kyung An

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In Wireless Sensor Networks which consist of tiny wireless sensor nodes with limited battery power, one of the most fundamental applications is data aggregation which collects nearby environmental conditions and aggregates the data to a designated destination, called a sink node. Important issues concerning the data aggregation are time efficiency and energy consumption due to its limited energy, and therefore, the related problem, named Minimum Latency Aggregation Scheduling (MLAS), has been the focus of many researchers. Its objective is to compute the minimum latency schedule, that is, to compute a schedule with the minimum number of timeslots, such that the sink node can receive the aggregated data from all the other nodes without any collision or interference. For the problem, the two interference models, the graph model and the more realistic physical interference model known as Signal-to-Interference-Noise-Ratio (SINR), have been adopted with different power models, uniform-power and non-uniform power (with power control or without power control), and different antenna models, omni-directional antenna and directional antenna models. In this survey article, as the problem has proven to be NP-hard, we present and compare several state-of-the-art approximation algorithms in various models on the basis of latency as its performance measure.

Keywords: data aggregation, convergecast, gathering, approximation, interference, omni-directional, directional

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Authors: Christi Jackson, Chuka Onaga

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Introduction: We report a case of delayed diagnosis of extra-pulmonary INH-mono-resistant Tuberculosis (TB) in a South African patient with drug-resistant HIV. Case Presentation: A 36-year old male was initiated on 1st line (NNRTI-based) anti-retroviral therapy (ART) in September 2009 and switched to 2nd line (PI-based) ART in 2011, according to local guidelines. He was following up at the outpatient wellness unit of a public hospital, where he was diagnosed with Protease Inhibitor resistant HIV in March 2016. He had an HIV viral load (HIVVL) of 737000 copies/mL, CD4-count of 10 cells/µL and presented with complaints of productive cough, weight loss, chronic diarrhoea and a septic buttock wound. Several investigations were done on sputum, stool and pus samples but all were negative for TB. The patient was treated with antibiotics and the cough and the buttock wound improved. He was subsequently started on a 3rd-line ART regimen of Darunavir, Ritonavir, Etravirine, Raltegravir, Tenofovir and Emtricitabine in May 2016. He continued losing weight, became too weak to stand unsupported and started complaining of abdominal pain. Further investigations were done in September 2016, including a urine specimen for Line Probe Assay (LPA), which showed M. tuberculosis sensitive to Rifampicin but resistant to INH. A lymph node biopsy also showed histological confirmation of TB. Management and outcome: He was started on Rifabutin, Pyrazinamide and Ethambutol in September 2016, and Etravirine was discontinued. After 6 months on ART and 2 months on TB treatment, his HIVVL had dropped to 286 copies/mL, CD4 improved to 179 cells/µL and he showed clinical improvement. Pharmacy supply of his individualised drugs was unreliable and presented some challenges to continuity of treatment. He successfully completed his treatment in June 2017 while still maintaining virological suppression. Discussion: Several laboratory-related factors delayed the diagnosis of TB, including the unavailability of urine-lipoarabinomannan (LAM) and urine-GeneXpert (GXP) tests at this facility. Once the diagnosis was made, it presented a treatment dilemma due to the expected drug-drug interactions between his 3rd-line ART regimen and his INH-resistant TB regimen, and specialist input was required. Conclusion: TB is more difficult to diagnose in patients with severe immunosuppression, therefore additional tests like urine-LAM and urine-GXP can be helpful in expediting the diagnosis in these cases. Patients with non-standard drug regimens should always be discussed with a specialist in order to avoid potentially harmful drug-drug interactions.

Keywords: drug-resistance, HIV, line probe assay, tuberculosis

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Authors: R. O. Ocaya, J. J. Terblans

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The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

Keywords: C language, molecular dynamics, simulation, embedded atom method

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Authors: Takaaki Nemoto

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Case presentation: A 69-year-old Japanese man presented with a low-grade fever and fatigue that had persisted for one month. The patient had an aortic dissection on the aortic arch 13 years prior, an abdominal aortic aneurysm seven years prior, and an aortic dissection on the distal aortic arch one year prior, which were all treated with artificial blood-vessel replacement surgery. Laboratory tests revealed an inflammatory response (CRP 7.61 mg/dl), high serum creatinine (Cr 1.4 mg/dL), and elevated transaminase (AST 47 IU/L, ALT 45 IU/L). The patient was admitted to our hospital on suspicion of prosthetic vascular graft infection. Following further workups on the inflammatory response, an enhanced chest computed tomography (CT) and a non-enhanced chest DWI (MRI) were performed. The patient was diagnosed with a pulmonary fistula and a prosthetic vascular graft infection on the distal aortic arch. After admission, the patient was administered Ceftriaxion and Vancomycine for 10 days, but his fever and inflammatory response did not improve. On day 13 of hospitalization, a lung fistula repair surgery and an omental filling operation were performed, and Meropenem and Vancomycine were administered. The fever and inflammatory response continued, and therefore we took repeated blood cultures. M. fortuitum was detected in a blood culture on day 16 of hospitalization. As a result, we changed the treatment regimen to Amikacin (400 mg/day), Meropenem (2 g/day), and Cefmetazole (4 g/day), and the fever and inflammatory response began to decrease gradually. We performed a test of sensitivity for Mycobacterium fortuitum, and found that the MIC was low for fluoroquinolone antibacterial agent. The clinical course was good, and the patient was discharged after a total of 8 weeks of intravenous drug administration. At discharge, we changed the treatment regimen to Levofloxacin (500 mg/day) and Clarithromycin (800 mg/day), and prescribed these two drugs as a long life suppressive therapy. Discussion: There are few cases of prosthetic vascular graft infection caused by mycobacteria, and a standard therapy remains to be established. For prosthetic vascular graft infections, it is ideal to provide surgical and medical treatment in parallel, but in this case, surgical treatment was difficult and, therefore, a conservative treatment was chosen. We attempted to increase the treatment success rate of this refractory disease by conducting a susceptibility test for mycobacteria and treating with different combinations of antimicrobial agents, which was ultimately effective. With our treatment approach, a good clinical course was obtained and continues at the present stage. Conclusion: Although prosthetic vascular graft infection resulting from mycobacteria is a refractory infectious disease, it may be curative to administer appropriate antibiotics based on the susceptibility test in addition to surgical treatment.

Keywords: prosthetic vascular graft infection, lung fistula, Mycobacterium fortuitum, conservative treatment

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Authors: Varun Agarwal

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Introduction: With the advent of personalized medicine, histopathological review of whole slide images (WSIs) for cancer diagnosis presents an exceedingly time-consuming, complex task. Specifically, detecting metastatic regions in WSIs of sentinel lymph node biopsies necessitates a full-scanned, holistic evaluation of the image. Thus, digital pathology, low-level image manipulation algorithms, and machine learning provide significant advancements in improving the efficiency and accuracy of WSI analysis. Using Camelyon16 data, this paper proposes a deep learning pipeline to automate and ameliorate breast cancer metastasis localization and WSI classification. Methodology: The model broadly follows five stages -region of interest detection, WSI partitioning into image tiles, convolutional neural network (CNN) image-segment classifications, probabilistic mapping of tumor localizations, and further processing for whole WSI classification. Transfer learning is applied to the task, with the implementation of Inception-ResNetV2 - an effective CNN classifier that uses residual connections to enhance feature representation, adding convolved outputs in the inception unit to the proceeding input data. Moreover, in order to augment the performance of the transfer learning CNN, a stack of convolutional denoising autoencoders (CDAE) is applied to produce embeddings that enrich image representation. Through a saliency-detection algorithm, visual training segments are generated, which are then processed through a denoising autoencoder -primarily consisting of convolutional, leaky rectified linear unit, and batch normalization layers- and subsequently a contrast-normalization function. A spatial pyramid pooling algorithm extracts the key features from the processed image, creating a viable feature map for the CNN that minimizes spatial resolution and noise. Results and Conclusion: The simplified and effective architecture of the fine-tuned transfer learning Inception-ResNetV2 network enhanced with the CDAE stack yields state of the art performance in WSI classification and tumor localization, achieving AUC scores of 0.947 and 0.753, respectively. The convolutional feature retention and compilation with the residual connections to inception units synergized with the input denoising algorithm enable the pipeline to serve as an effective, efficient tool in the histopathological review of WSIs.

Keywords: breast cancer, convolutional neural networks, metastasis mapping, whole slide images

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Authors: Ella Tyuryumina, Alexey Neznanov

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This study is an attempt to obtain reliable data on the natural history of breast cancer growth. We analyze the opportunities for using classical mathematical models (exponential and logistic tumor growth models, Gompertz and von Bertalanffy tumor growth models) to try to describe growth of the primary tumor and the secondary distant metastases of human breast cancer. The research aim is to improve predicting accuracy of breast cancer progression using an original mathematical model referred to CoMPaS and corresponding software. We are interested in: 1) modelling the whole natural history of the primary tumor and the secondary distant metastases; 2) developing adequate and precise CoMPaS which reflects relations between the primary tumor and the secondary distant metastases; 3) analyzing the CoMPaS scope of application; 4) implementing the model as a software tool. The foundation of the CoMPaS is the exponential tumor growth model, which is described by determinate nonlinear and linear equations. The CoMPaS corresponds to TNM classification. It allows to calculate different growth periods of the primary tumor and the secondary distant metastases: 1) ‘non-visible period’ for the primary tumor; 2) ‘non-visible period’ for the secondary distant metastases; 3) ‘visible period’ for the secondary distant metastases. The CoMPaS is validated on clinical data of 10-years and 15-years survival depending on the tumor stage and diameter of the primary tumor. The new predictive tool: 1) is a solid foundation to develop future studies of breast cancer growth models; 2) does not require any expensive diagnostic tests; 3) is the first predictor which makes forecast using only current patient data, the others are based on the additional statistical data. The CoMPaS model and predictive software: a) fit to clinical trials data; b) detect different growth periods of the primary tumor and the secondary distant metastases; c) make forecast of the period of the secondary distant metastases appearance; d) have higher average prediction accuracy than the other tools; e) can improve forecasts on survival of breast cancer and facilitate optimization of diagnostic tests. The following are calculated by CoMPaS: the number of doublings for ‘non-visible’ and ‘visible’ growth period of the secondary distant metastases; tumor volume doubling time (days) for ‘non-visible’ and ‘visible’ growth period of the secondary distant metastases. The CoMPaS enables, for the first time, to predict ‘whole natural history’ of the primary tumor and the secondary distant metastases growth on each stage (pT1, pT2, pT3, pT4) relying only on the primary tumor sizes. Summarizing: a) CoMPaS describes correctly the primary tumor growth of IA, IIA, IIB, IIIB (T1-4N0M0) stages without metastases in lymph nodes (N0); b) facilitates the understanding of the appearance period and inception of the secondary distant metastases.

Keywords: breast cancer, exponential growth model, mathematical model, metastases in lymph nodes, primary tumor, survival

Procedia PDF Downloads 336

Authors: Jessica Arthur, Duke Amegah, Kingsley Akenten Wiafe

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Background: Vanilla planifolia is the only edible fruit of the orchid family (Orchidaceae) among the over 35,000 Orchidaceae species found worldwide. In Ghana, Vanilla was discovered in the wild, but it is underutilized for commercial production, most likely due to a lack of knowledge on the best NAA and BAP combinations for in vitro propagation to promote successfully regenerated plant acclimatization. The growing interest and global demand for elite Vanilla planifolia plants and natural vanilla flavour emphasize the need for an effective industrial-scale micropropagation protocol. Tissue culture systems are increasingly used to grow disease-free plants and reliable in vitro methods can also produce plantlets with typically modest proliferation rates. This study sought to develop an efficient protocol for in vitro propagation of vanilla using nodal explants by testing different concentrations of NAA and BAP, for the proliferation of the entire plant. Methods: Nodal explants with dormant axillary buds were obtained from year-old laboratory-grown Vanilla planifolia plants. MS media was prepared with a nutrient stock solution (containing macronutrients, micronutrients, iron solution and vitamins) and semi-solidified using phytagel. It was supplemented with different concentrations of NAA and BAP to induce multiple shoots and roots (0.5mg/L BAP with NAA at 0, 0.5, 1, 1.5, 2.0mg/L and vice-versa). The explants were sterilized, cultured in labelled test tubes and incubated at 26°C ± 2°C with 16/8 hours light/dark cycle. Data on shoot and root growth, leaf number, node number, and survival percentage were collected over three consecutive two-week periods. The data were square root transformed and subjected to ANOVA and LSD at a 5% significance level using the R statistical package. Results: Shoots emerged at 8 days and roots at 12 days after inoculation with 94% survival rate. It was discovered that for the NAA treatments, MS media supplemented with 2.00 mg/l NAA resulted in the highest shoot length (10.45cm), maximum root number (1.51), maximum shoot number (1.47) and the highest number of leaves (1.29). MS medium containing 1.00 mg/l NAA produced the highest number of nodes (1.62) and root length (14.27cm). Also, a similar growth pattern for the BAP treatments was observed. MS medium supplemented with 1.50 mg/l BAP resulted in the highest shoot length (14.98 cm), the highest number of nodes (4.60), the highest number of leaves (1.75) and the maximum shoot number (1.57). MS medium containing 0.50 mg/l BAP and 1.0 mg/l BAP generated a maximum root number (1.44) and the highest root length (13.25cm), respectively. However, the best concentration combination for maximizing shoot and root was media containing 1.5mg/l BAP combined with 0.5mg/l NAA, and 1.0mg/l NAA combined with 0.5mg/l of BAP respectively. These concentrations were optimum for in vitro growth and production of Vanilla planifolia. Significance: This study presents a standardized protocol for labs to produce clean vanilla plantlets, enhancing cultivation in Ghana and beyond. It provides insights into Vanilla planifolia's growth patterns and hormone responses, aiding future research and cultivation.

Keywords: Vanilla planifolia, In vitro propagation, plant hormones, MS media

Procedia PDF Downloads 58

Authors: Ahmad R. Zamani, Luigi Sanguigno, Angelo R. Maligno

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A 3D woven composite, designed for automotive applications, is studied using Abaqus Finite Element (FE) software suite. Python scripts were developed to build FE models of the woven composite in Complete Abaqus Environment (CAE). They can read TexGen or WiseTex files and automatically generate consistent meshes of the fabric and the matrix. A user menu is provided to help define parameters for the FE models, such as type and size of the elements in fabric and matrix as well as the type of matrix-fabric interaction. Node-to-node constraints were imposed to guarantee periodicity of the deformed shapes at the boundaries of the representative volume element of the composite. Tensile loads in three axes and biaxial loads in x-y directions have been applied at different Fibre Volume Fractions (FVFs). A simple damage model was implemented via an Abaqus user material (UMAT) subroutine. Existing tools for homogenization were also used, including voxel mesh generation from TexGen as well as Abaqus Micromechanics plugin. Linear relations between homogenised elastic properties and the FVFs are given. The FE models of composite exhibited balanced behaviour with respect to warp and weft directions in terms of both stiffness and strength.

Keywords: 3D woven composite (3DWC), meso-scale finite element model, homogenisation of elastic material properties, Abaqus Python scripting

Procedia PDF Downloads 136

Authors: Vladimir Kulyukin, Tanwir Zaman, Sarat Kiran Andhavarapu

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Research on nutrition label use identifies four factors that impede comprehension and retention of nutrition information by consumers: label’s location on the package, presentation of information within the label, label’s surface size, and surrounding visual clutter. In this paper, a system is presented that makes nutrition label use more effective for nutrition information comprehension and retention. The system’s front end is a smartphone application. The system’s back end is a four node Linux cluster for image recognition and data storage. Image frames captured on the smartphone are sent to the back end for skewed or aligned barcode recognition. When barcodes are recognized, corresponding nutrition labels are retrieved from a cloud database and presented to the user on the smartphone’s touchscreen. Each displayed nutrition label is positioned centrally on the touchscreen with no surrounding visual clutter. Wikipedia links to important nutrition terms are embedded to improve comprehension and retention of nutrition information. Standard touch gestures (e.g., zoom in/out) available on mainstream smartphones are used to manipulate the label’s surface size. The nutrition label database currently includes 200,000 nutrition labels compiled from public web sites by a custom crawler. Stress test experiments with the node cluster are presented. Implications for proactive nutrition management and food policy are discussed.

Keywords: mobile computing, cloud computing, nutrition label use, nutrition management, barcode scanning

Procedia PDF Downloads 366

Authors: Dhivyalakshmi Gnanasekaran, Sonali Adole Prasante, Raveendranath Veeramamani, H. Y. Suma

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A rare case of intestinal malrotation with midline descending colon and right sided sigmoid colon was observed in an adult male cadaver aged around 55 years during routine dissection. The descending colon began from the splenic flexure and gradually descended downwards to occupy the midline position and turned to the right side to be continued as sigmoid colon at the level of the fifth lumbar vertebra. In the right iliac fossa some part of loop of sigmoid colon displaced into the right lumbar region before entering into the true pelvis to continue as rectum. This anomalous descending and sigmoid colon was supplied by varying branching pattern of inferior mesenteric artery. It is extremely important to consider this embryological anomaly before any interventional diagnostic procedures like colonoscopy and to enhance the safety of colonic surgery.

Keywords: sigmoid colon, descending colon, hindgut, malrotation

Procedia PDF Downloads 248

Authors: Colin Smith, Linsey S Passarella

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Due to the proliferation and decentralized nature of academic publication, no widely accepted scheme exists for organizing papers by their scientific field of study (FoS) to the author’s best knowledge. While many academic journals require author provided keywords for papers, these keywords range wildly in scope and are not consistent across papers, journals, or field domains, necessitating alternative approaches to paper classification. Past attempts to perform field-of-study (FoS) classification on scientific texts have largely used a-hierarchical FoS schemas or ignored the schema’s inherently hierarchical structure, e.g. by compressing the structure into a single layer for multi-label classification. In this paper, we introduce an application of a Layered Neural Network (LNN) to the problem of performing supervised hierarchical classification of scientific fields of study (FoS) on research papers. In this approach, paper embeddings from a pretrained language model are fed into a top-down LNN. Beginning with a single neural network (NN) for the highest layer of the class hierarchy, each node uses a separate local NN to classify the subsequent subfield child node(s) for an input embedding of concatenated paper titles and abstracts. We compare our LNN-FOS method to other recent machine learning methods using the Microsoft Academic Graph (MAG) FoS hierarchy and find that the LNN-FOS offers increased classification accuracy at each FoS hierarchical level.

Keywords: hierarchical classification, layer neural network, scientific field of study, scientific taxonomy

Procedia PDF Downloads 126

Authors: Pallavi Bhogaram, Xiaolong Wu, Min He, Onyedikachi Okenwa

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A transportation network is a realization of a spatial network, describing a structure which permits either vehicular movement or flow of some commodity. Examples include road networks, railways, air routes, pipelines, and many more. The transportation network plays a vital role in maintaining the vigor of the nation’s economy. Hence, ensuring the network stays resilient all the time, especially in the face of challenges such as heavy traffic loads and large scale natural disasters, is of utmost importance. In this paper, we used the Neo4j application to develop the graph. Neo4j is the world's leading open-source, NoSQL, a native graph database that implements an ACID-compliant transactional backend to applications. The Southern California network model is developed using the Neo4j application and obtained the most critical and optimal nodes and paths in the network using centrality algorithms. The edge betweenness centrality algorithm calculates the critical or optimal paths using Yen's k-shortest paths algorithm, and the node betweenness centrality algorithm calculates the amount of influence a node has over the network. The preliminary study results confirm that the Neo4j application can be a suitable tool to study the important nodes and the critical paths for the major congested metropolitan area.

Keywords: critical path, transportation network, connectivity reliability, network model, Neo4j application, edge betweenness centrality index

Procedia PDF Downloads 131

Authors: Neerja Gupta

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Objective-Reconstruction of large cavities of the breast without contralateral symmetrisation Background- Reconstruction of breast includes a wide spectrum of procedures from displacement to regional and distant flaps. The pedicled Perforator flaps cover a wide spectrum of reconstruction surgery for all quadrants of the breast, especially in patients with comorbidities. These axial flaps singly or adjunct are based on a near constant perforator vessel, a ratio of 2:1 at its entry in a flap is good to maintain vascularity. The perforators of lateral chest wall viz LICAP, LTAP have overlapping perfurosomes without clear demarcation. LTAP is localized in the narrow zone between the lateral breast fold and anterior axillary line,2.5-3.8cm from the fold. MICAP are localized at 1-2 cm from sternum. Being 1-2mm in diameter, a Single perforator is good to maintain the flap. LICAP has a dominant perforator in 6th-11th spaces, while LTAP has higher placed dominant perforators in 4th and 5th spaces. Methodology-Six consecutive patients who underwent reconstruction of the breast with pedicled perforator flaps were retrospectively analysed. Selections of the flap was done based on the size and locations of the tumour, anticipated volume loss, willingness to undergo contralateral symmetrisation, cosmetic expectations, and finances available.3 patients underwent vertical LTAP, the distal limit of the flap being the inframammary crease. 3 patients underwent MICAP, oriented along the axis of rib, the distal limit being the anterior axillary line. Preoperative identification was done using a unidirectional hand held doppler. The flap was raised caudal to cranial, the pivot point of rotation being the vessel entry into the skin. The donor area is determined by the skin pinch. Flap harvest time was 20-25 minutes. Intra operative vascularity was assessed with dermal bleed. The patient immediate pre, post-operative and follow up pics were compared independently by two breast surgeons. Patients were given a breast Q questionnaire (licensed) for scoring. Results-The median age of six patients was 46. Each patient had a hospital stay of 24 hours. None of the patients was willing for contralateral symmetrisation. The specimen dimensions were from 8x6.8x4 cm to 19x16x9 cm. The breast volume reconstructed range was 30 percent to 45 percent. All wide excision had free margins on frozen. The mean flap dimensions were 12x5x4.5 cm. One LTAP underwent marginal necrosis and delayed wound healing due to seroma. Three patients were phyllodes, of which one was borderline, and 2 were benign on final histopathology. All other 3 patients were invasive ductal cancer and have completed their radiation. The median follow up is 7 months the satisfaction scores at median follow of 7 months are 90 for physical wellbeing and 85 for surgical results. Surgeons scored fair to good in Harvard score. Conclusion- Pedicled perforator flaps are a valuable option for 3/8th volume of breast defects. LTAP is preferred for tumours at the Central, upper, and outer quadrants of the breast and MICAP for the inner and lower quadrant. The vascularity of the flap is dependent on the angiosomalterritories; adequate venous and cavity drainage.

Keywords: breast, oncoplasty, pedicled, perforator

Procedia PDF Downloads 183

Authors: El Miloudi Djelloul

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The computer network play an important position for practical implementations of the differently system. To implement a system into network above all is needed to know all the configurations, which is responsible to be a part of the system, and to give adequate information and solution in realtime. So if want to implement this system for example in the school or relevant institutions, the first step is to analyze the types of model which is needed to be configured and another important step is to organize the works in the context of devices, as a part of the general system. Often before configuration, as important point is descriptions and documentations from all the works into the respective process, and then to organize in the aspect of problem-solving. The computer network as critic infrastructure is very specific so the paper present the effectiveness solutions in the structured aspect viewed from one side, and another side is, than the paper reflect the positive aspect in the context of modeling and block schema presentations as an better alternative to solve the specific problem because of continually distortions of the system from the line of devices, programs and signals or packed collisions, which are in movement from one computer node to another nodes.

Keywords: local area networks, LANs, block schema presentations, computer network system, computer node, critical infrastructure packed collisions, structural control system representations, computer network, implementations, modeling structural representations, companies, computers, context, control systems, internet, software

Procedia PDF Downloads 355

Authors: Armanul Hoque Shaon, Md Baizid Mahmud, Askander Nobi, Md. Raju Ahmed, Md. Jiabul Hoque

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In the Internet of Things (IoT), devices are linked to the internet through a wireless network, allowing them to collect and transmit data without the need for a human operator. Agriculture relies heavily on wireless sensors, which are a vital component of the Internet of Things (IoT). This kind of wireless sensor network monitors physical or environmental variables like temperatures, sound, vibration, pressure, or motion without relying on a central location or sink and collaboratively passes its data across the network to be analyzed. As the primary source of plant nutrients, the soil is critical to the agricultural industry's continued growth. We're excited about the prospect of developing an Internet of Things (IoT) solution. To arrange the network, the sink node collects groundwater levels and sends them to the Gateway, which centralizes the data and forwards it to the sensor nodes. The sink node gathers soil moisture data, transmits the mean to the Gateways, and then forwards it to the website for dissemination. The web server is in charge of storing and presenting the moisture in the soil data to the web application's users. Soil characteristics may be collected using a networked method that we developed to improve rice production. Paddy land is running out as the population of our nation grows. The success of this project will be dependent on the appropriate use of the existing land base.

Keywords: IoT based agriculture monitoring, intelligent irrigation, communicating network, rice production

Procedia PDF Downloads 151

Authors: Mayank Mundhra, Chester Rebeiro

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Cryptocurrencies are rapidly finding wide application in areas such as Real Time Gross Settlements and Payments Systems. Ripple is a cryptocurrency that has gained prominence with banks and payment providers. It solves the Byzantine General’s Problem with its Ripple Protocol Consensus Algorithm (RPCA), where each server maintains a list of servers, called Unique Node List (UNL) that represents the network for the server, and will not collectively defraud it. The server believes that the network has come to a consensus when members of the UNL come to a consensus on a transaction. In this paper we improve Ripple to achieve better speed, security, last mile connectivity and ease of use. We implement guidelines and automated systems for building and maintaining UNLs for resilience, robustness, improved security, and efficient information propagation. We enhance the system so as to ensure that each server receives information from across the whole network rather than just from the UNL members. We also introduce the paradigm of UNL overlap as a function of information propagation and the trust a server assigns to its own UNL. Our design not only reduces vulnerabilities such as eclipse attacks, but also makes it easier to identify malicious behaviour and entities attempting to fraudulently Double Spend or stall the system. We provide experimental evidence of the benefits of our approach over the current Ripple scheme. We observe ≥ 4.97x and 98.22x in speedup and success rate for information propagation respectively, and ≥ 3.16x and 51.70x in speedup and success rate in consensus.

Keywords: Ripple, Kelips, unique node list, consensus, information propagation

Procedia PDF Downloads 139

Authors: A. Peyvan, D. Li, J. Komperda, F. Mashayek

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Turbulence can be observed in a variety fluid motions in nature and industrial applications. Recent investment in high-speed aircraft and propulsion systems has revitalized fundamental research on turbulent flows. In these systems, capturing chaotic fluid structures with different length and time scales is accomplished through the Direct Numerical Simulation (DNS) approach since it accurately simulates flows down to smallest dissipative scales, i.e., Kolmogorov’s scales. The discontinuous spectral element method (DSEM) is a high-order technique that uses spectral functions for approximating the solution. The DSEM code has been developed by our research group over the course of more than two decades. Recently, the code has been improved to run large cases in the order of billions of solution points. Running big simulations requires a considerable amount of RAM. Therefore, the DSEM code must be highly parallelized and able to start on multiple computational nodes on an HPC cluster with distributed memory. However, some pre-processing procedures, such as determining global element information, creating a global face list, and assigning global partitioning and element connection information of the domain for communication, must be done sequentially with a single processing core. A separate code has been written to perform the pre-processing procedures on a local machine. It stores the minimum amount of information that is required for the DSEM code to start in parallel, extracted from the mesh file, into text files (pre-files). It packs integer type information with a Stream Binary format in pre-files that are portable between machines. The files are generated to ensure fast read performance on different file-systems, such as Lustre and General Parallel File System (GPFS). A new subroutine has been added to the DSEM code to read the startup files using parallel MPI I/O, for Lustre, in a way that each MPI rank acquires its information from the file in parallel. In case of GPFS, in each computational node, a single MPI rank reads data from the file, which is specifically generated for the computational node, and send them to other ranks on the node using point to point non-blocking MPI communication. This way, communication takes place locally on each node and signals do not cross the switches of the cluster. The read subroutine has been tested on Argonne National Laboratory’s Mira (GPFS), National Center for Supercomputing Application’s Blue Waters (Lustre), San Diego Supercomputer Center’s Comet (Lustre), and UIC’s Extreme (Lustre). The tests showed that one file per node is suited for GPFS and parallel MPI I/O is the best choice for Lustre file system. The DSEM code relies on heavily optimized linear algebra operation such as matrix-matrix and matrix-vector products for calculation of the solution in every time-step. For this, the code can either make use of its matrix math library, BLAS, Intel MKL, or ATLAS. This fact and the discontinuous nature of the method makes the DSEM code run efficiently in parallel. The results of weak scaling tests performed on Blue Waters showed a scalable and efficient performance of the code in parallel computing.

Keywords: computational fluid dynamics, direct numerical simulation, spectral element, turbulent flow

Procedia PDF Downloads 131