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IRIS:A method for predicting in vivo RNA secondary structures using PARIS data

Quantitative Biology 2020年第4期8卷 369-381页

作者： Jianyu Zhou Pan Li Wanwen Zeng Wenxiu Ma Zhipeng Lu Rui Jiang Qiangfeng Cliff Zhang Tao Jiang Bioinformatics Division BNRISTTsinghua UniversityBeijing 100084China Department of Computer Science and Technology Tsinghua UniversityBeijing 100084China MOE Key Laboratory of Bioinformatics Beijing Advanced Innovation Center for Structural BiologyCenter for Synthetic and Systems BiologyTsinghua-Peking Center for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing 100084China College of Software Nankai UniversityTianjin 300071China Department of Statistics University of CaliforniaRiversideCA 92521USA Department of Pharmacology and Pharmaceutical Sciences University of Southern CaliforniaCA 90089USA Department of Automation Tsinghua UniversityBeijing 100084China Department of Computer Science and Engineering University of CaliforniaRiversideCA 92521USA

Background:RNA secondary structures play a pivotal role in posttranscriptional regulation and the functions of non-coding RNAs,yet in vivo RNA secondary structures remain ***(Psoralen Analysis of RNA Interactions and Structures)is a recently developed high-throughput sequencing-based approach that enables direct capture of RNA duplex structures in ***,the existence of incompatible,fuzzy pairing information obstructs the integration of PARIS data with the existing tools for reconstructing RNA secondary structure models at the single-base ***:We introduce IRIS,a method for predicting RNA secondary structure ensembles based on PARIS *** generates a large set of candidate RNA secondary structure models under the guidance of redistributed PARIS reads and then uses a Bayesian model to identify the optimal ensemble,according to both thermodynamic principles and PARIS ***:The predicted RNA structure ensembles by IRIS have been verified based on evolutionary conservation information and consistency with other experimental RNA structural *** is implemented in Python and freely available at http://***:IRIS capitalizes upon PARIS data to improve the prediction of in vivo RNA secondary structure *** expect that IRIS will enhance the application of the PARIS technology and shed more insight on in vivo RNA secondary structures.

关键词： RNA secondary structure PARIS data in vivo structure ensembles incompatible reads

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Influence of Network Speed on Structured Query Language (SQL) Database Data Transmission Performance in an Internet of Things (IoT) Sensing Device on Single Board computers (SBC)

Influence of Network Speed on Structured Query Language (SQL...

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International Conference on Green engineering Technology and Applied Computing 2019, IConGETech2 019 and International Conference on Applied Computing 2019, ICAC 2019

作者： Nor Azhar, A. Nur Ayuni Hasna, S. Roslina, A.H. Fauziah, Z. Rahmah, M. Department of Computer Science Universiti Malaysia Pahang Lebuhraya Tun Razak Gambang Pahang Kuantan26300 Malaysia Department of Computer Systems and Networking Universiti Malaysia Pahang Lebuhraya Tun Razak Gambang Pahang Kuantan26300 Malaysia Department of Software Engineering Universiti Malaysia Pahang Lebuhraya Tun Razak Gambang Pahang Kuantan26300 Malaysia Department of Graphic and Multimedia Technology Faculty of Computer Systems and Software Engineering Universiti Malaysia Pahang Lebuhraya Tun Razak Gambang Pahang Kuantan26300 Malaysia

One of the crucial elements in an Internet of Things (IoT) environment is a database. IoT performance will be at stake if the wrong database is adopted. In this research, three Structured Query Language (SQL) databases were tested against multiple network speeds in an IoT device. Single board computers (SBC) were used as a media of testing instead of an ordinary computer. A controlled wireless sensor network (WSN) was developed with several uniform constants and variable network speeds. A new data transmission rate equation also was proposed and tested. From the result, it was found that not all SQL databases can cater IoT devices. Some of them showed that performance decreased along with network speed. The correlation, between 0.90 and 0.96, proved the strong influence between the research subjects. In addition, file-type database is the best option available for SQL-wise IoT storage. © 2019 Published under licence by IOP Publishing Ltd.

关键词： Internet of things

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Integrating Privacy Enhancing Techniques into Blockchains Using Sidechains

Integrating Privacy Enhancing Techniques into Blockchains Us...

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2019 IEEE Canadian Conference of Electrical and computer engineering, CCECE 2019

作者： Parizi, Reza M. Homayoun, Sajad Yazdinejad, Abbas Dehghantanha, Ali Choo, Kim-Kwang Raymond Department of Software Engineering and Game Development Kennesaw State University GA United States Department of Computer Engineering and Information Technology Shiraz University of Technology Shiraz Iran Faculty of Computer Engineering University of Isfahan Iran School of Computer Science University of Guelph ON Canada Department of Information Systems and Cyber Security University of Texas at San Antonio TX United States

ISBN: (纸本)9781728103198

Blockchains are turning into decentralized computing platforms and are getting worldwide recognition for their unique advantages. There is an emerging trend beyond payments that blockchains could enable a new breed of decentralized applications, and serve as the foundation for Internet's security infrastructure. The immutable nature of the blockchain makes it a winner on security and transparency;it is nearly inconceivable for ledgers to be altered in a way not instantly clear to every single user involved. However, most blockchains fall short in privacy aspects, particularly in data protection. Garlic Routing and Onion Routing are two of major Privacy Enhancing Techniques (PETs) which are popular for anonymization and security. Garlic Routing is a methodology using by I2P Anonymous Network to hide the identity of sender and receiver of data packets by bundling multiple messages into a layered encryption structure. The Onion Routing attempts to provide low-latency Internet-based connections that resist traffic analysis, deanonymization attack, eavesdropping, and other attacks both by outsiders (e.g. Internet routers) and insiders (Onion Routing servers themselves). As there are a few controversies over the rate of resistance of these two techniques to privacy attacks, we propose a PET-Enabled Sidechain (PETES) as a new privacy enhancing technique by integrating Garlic Routing and Onion Routing into a Garlic Onion Routing (GOR) framework suitable to the structure of blockchains. The preliminary proposed GOR aims to improve the privacy of transactions in blockchains via PETES structure. © 2019 IEEE.

关键词： Blockchain

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Green IoT using UAVs in B5G networks: A review of applications and strategies

arXiv

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arXiv 2021年

作者： Alsamhi, Saeed H. Afghah, Fatemeh Sahal, Radhya Hawbani, Ammar Al-Qaness, A.A. Lee, B. Guizani, Mohsen Software Research Institute Athlone Institute of Technology Athlone Ireland IBB University Ibb Yemen School of Informatics Computing and Cyber Systems Northern Arizona University United States Hudaidah University Hudaida Yemen School of Computer Science and Technology University of Science and Technology of China Hefei China State Key Laboratory for Information Engineering in Surveying Mapping and Remote Sensing Wuhan University China Department of Computer Science and Engineering Qatar University Qatar

Recently, Unmanned Aerial Vehicles (UAVs) present a promising advanced technology that can enhance people life quality and smartness of cities dramatically and increase overall economic efficiency. UAVs have attained a significant interest in supporting many applications such as surveillance, agriculture, communication, transportation, pollution monitoring, disaster management, public safety, healthcare, and environmental preservation. Industry 4.0 applications are conceived of intelligent things that can automatically and collaboratively improve beyond 5G (B5G). Therefore, the Internet of Things (IoT) is required to ensure collaboration between the vast multitude of things efficiently anywhere in real-world applications that are monitored in real-time. However, many IoT devices consume a significant amount of energy when transmitting the collected data from surrounding environments. Due to a drone's capability to fly closer to IoT, UAV technology plays a vital role in greening IoT by transmitting collected data to achieve a sustainable, reliable, eco-friendly Industry 4.0. This survey presents an overview of the techniques and strategies proposed recently to achieve green IoT using UAVs infrastructure for a reliable and sustainable smart world. This survey is different from other attempts in terms of concept, focus, and discussion. Finally, various use cases, challenges, and opportunities regarding green IoT using UAVs are presented. © 2021, CC BY.

关键词： Energy efficiency

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COVID-19 pneumonia level detection using deep learning algorithm

TechRxiv

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TechRxiv 2020年

作者： Ghafoor, Kayhan Zrar Ali, Abbas M. Mulahuwaish, Aos Maghdid, Halgurd S. Hussein, Safwan Mawlood Mohammed, Marwan A. Department of Software Engineering Salahaddin University-Erbil Iraq School of Mathematics and Computer Science University of Wolverhampton Wulfruna Street WolverhamptonWV1 1LY United Kingdom Department of Computer Science and Information Systems Saginaw Valley State University University Center 7400 Bay Rd Science East 174 MI48710 United States Department of Software Engineering Faculty of Engineering Koya University Kurdistan Iraq Computer Engineering Department Tishk International University Iraq

The first COVID-19 confirmed case is reported in Wuhan, China and spread across the globe with unprecedented impact on humanity. Since this pandemic requires pervasive diagnosis, it is significant to develop smart, fast and efficient detection technique. To this end, we developed an Artificial Intelligence (AI) engine to classify the lung inflammation level (mild, progressive, severe stage) of the COVID-19 confirmed patient. In particular, the developed model consists of two phases;in the first phase, we calculate the volume and density of lesions and opacities of the CT images of the confirmed COVID-19 patient using Morphological approaches. In the second phase, the second phase classifies the pneumonia level of the confirmed COVID-19 patient. To achieve precise classification of lung inflammation, we use modified Convolution Neural Network (CNN) and k-Nearest Neighbor (kNN). The result of the experiments show that the utilized models can provide the accuracy up to 95.65% and 91.304 % of CNN and kNN respectively. © 2020, CC BY.

关键词： COVID-19

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Performance and energy-aware bi-objective tasks scheduling for cloud data centers

arXiv

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arXiv 2021年

作者： Materwala, Huned Ismail, Leila Intelligent Distributed Computing and Systems Research Laboratory Department of Computer Science and Software Engineering College of Information Technology United Arab Emirates University Al Ain Abu Dhabi15551 United Arab Emirates National Water and Energy Center United Arab Emirates University Al Ain Abu Dhabi United Arab Emirates

Cloud computing enables remote execution of users' tasks. The pervasive adoption of cloud computing in smart cities' services and applications requires timely execution of tasks adhering to Quality of Services (QoS). However, the increasing use of computing servers exacerbates the issues of high energy consumption, operating costs, and environmental pollution. Maximizing the performance and minimizing the energy in a cloud data center is challenging. In this paper, we propose a performance and energy optimization bi-objective algorithm to tradeoff the contradicting performance and energy objectives. An evolutionary algorithm-based multi-objective optimization is for the first time proposed using system performance counters. The performance of the proposed model is evaluated using a realistic cloud dataset in a cloud computing environment. Our experimental results achieve higher performance and lower energy consumption compared to a state-of-the-art algorithm. © 2021, CC BY.

关键词： Energy efficiency

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A novelmethod to improve the retrieved multilingual documents score

A novelmethod to improve the retrieved multilingual document...

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2019 International Conference on computer, Control, Electrical, and Electronics engineering, ICCCEEE 2019

作者： Aboras, Abas Solyman, Aiman Abobieda, Albaraa Yousif, Hajer South China University of Technology School of Software Engineering Guangzhou China International University of Africa Faculty of Computer Studies Khartoum Sudan Sudan University of Science and Technology SUST Department of Computer Systems and Networks Khartoum Sudan

ISBN: (纸本)9781728110066

With an ever-increasing number of resources on the Web, different language resources such as newspapers, magazines, and articles have become available. This demands for an improved technique in the information retrieval to extirpate the communication barrier among languages. Search engines are the cornerstones for informational contents and the link between the two parties of publishing and retrieval of content. Moreover, the search for information is no longer narrowed to users of the native language of the original source. Most of the non-English users such as Arabic speakers are unable to express the terms in their own language. Also, the terminologies written in the native language of the source are acquired from the English language. This challenge drives users to use mixed terms (multilingual terms) to get better results, especially in the scientific domain. This paper attempts to address the problem of documents retrieval using multilingual queries. When users use mixed queries, the results of the multilingual documents will dominate the top of the retrieved documents rather than other relevant documents, and the scores of the mixed documents obtain extra weight values that are not really part of their actual weighting value. This paper proposes a novel method to improve the results of the retrieved documents by adjusting the score of multilingual documents. For experiments, we used a mixed test collection containing mixedlanguage documents (Arabic and English). The results showed that the proposed method led to an enhanced performance in documents retrieval from multilingual queries which made them relevant, effective and accurate thus proving that our approach is more reliable than other traditional approaches. © 2019 IEEE.

关键词： Information retrieval

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A reinforcement-learning-based energy-efficient framework for multi-task video analytics pipeline

arXiv

引用

arXiv 2021年

作者： Zhao, Yingying Dong, Mingzhi Wang, Yujiang Feng, Da Lv, Qin Dick, Robert P. Li, Dongsheng Lu, Tun Gu, Ning Shang, Li School of Computer Science Fudan University Shanghai China Shanghai Key Laboratory of Data Science Fudan University Shanghai China Shanghai Institute of Intelligent Electronics & Systems Shanghai China Department of Computing Imperial College London London United Kingdom Software Service Company Limited Beijing China University of Colorado Boulder BoulderCO United States Department of Electrical Engineering and Computer Science College of Engineering University of Michigan Ann ArborMI United States Microsoft Research Asia Shanghai China School of Computer Science Fudan University Shanghai China

Deep-learning-based video processing has yielded transformative results in recent years. However, the video analytics pipeline is energy-intensive due to high data rates and reliance on complex inference algorithms, which limits its adoption in energy-constrained applications. Motivated by the observation of high and variable spatial redundancy and temporal dynamics in video data streams, we design and evaluate an adaptive-resolution optimization framework to minimize the energy use of multitask video analytics pipelines. Instead of heuristically tuning the input data resolution of individual tasks, our framework utilizes deep reinforcement learning to dynamically govern the input resolution and computation of the entire video analytics pipeline. By monitoring the impact of varying resolution on the quality of high-dimensional video analytics features, hence the accuracy of video analytics results, the proposed end-to-end optimization framework learns the best non-myopic policy for dynamically controlling the resolution of input video streams to globally optimize energy efficiency. Governed by reinforcement learning, optical flow is incorporated into the framework to minimize unnecessary spatio-temporal redundancy that leads to re-computation, while preserving accuracy. The proposed framework is applied to video instance segmentation which is one of the most challenging computer vision tasks, and achieves better energy efficiency than all baseline methods of similar accuracy on the YouTube-VIS dataset. Copyright © 2021, The Authors. All rights reserved.

关键词： Energy efficiency

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A Blockchain-based Framework for Detecting Malicious Mobile Applications in App Stores

A Blockchain-based Framework for Detecting Malicious Mobile ...

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2019 IEEE Canadian Conference of Electrical and computer engineering, CCECE 2019

作者： Homayoun, Sajad Dehghantanha, Ali Parizi, Reza M. Choo, Kim-Kwang Raymond Department of Computer Engineering and Information Technology Shiraz University of Technology Shiraz Iran School of Computer Science University of Guelph ON Canada Department of Software Engineering and Game Development Kennesaw State University MariettaGA30060 United States Department of Information Systems and Cyber Security Department of Electrical and Computer Engineering University of Texas at San Antonio San AntonioTX78249 United States

ISBN: (纸本)9781728103198

The dramatic growth in smartphone malware shows that malicious program developers are shifting from traditional PC systems to smartphone devices. Therefore, security researchers are also moving towards proposing novel antimalware methods to provide adequate protection. This paper proposes a Blockchain-Based Malware Detection Framework (B2MDF) for detecting malicious mobile applications in mobile applications marketplaces (app stores). The framework consists of two internal and external private blockchains forming a dual private blockchain as well as a consortium blockchain for the final decision. The internal private blockchain stores feature blocks extracted by both static and dynamic feature extractors, while the external blockchain stores detection results as blocks for current versions of applications. B2MDF also shares feature blocks with third parties, and this helps antimalware vendors to provide more accurate solutions. © 2019 IEEE.

关键词： Blockchain

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A Model to Measure the Spread Power of Rumors

arXiv

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arXiv 2020年

作者： Jahanbakhsh-Nagadeh, Zoleikha Feizi-Derakhshi, Mohammad-Reza Ramezani, Majid Akan, Taymaz Asgari-Chenaghlu, Meysam Nikzad–Khasmakhi, Narjes Feizi-Derakhshi, Ali-Reza Ranjbar-Khadivi, Mehrdad Zafarani-Moattar, Elnaz Balafar, Mohammad-Ali Computerized Intelligence Systems Laboratory Department of Computer Engineering University of Tabriz Tabriz Iran Department of Computer Engineering Naghadeh Branch Islamic Azad University Naghadeh Iran Department of Computer Science and Research Branch Islamic Azad University Tehran Iran Department of Software Engineering Istanbul Topkapi University Istanbul Turkey Clinical Informatics Louisiana State University Health Sciences Center Shreveport Shreveport United States Department of Computer Engineering Shabestar Branch Islamic Azad University Shabestar Iran Department of Computer Engineering Tabriz Branch Islamic Azad University Tabriz Iran Department of Computer Engineering University of Tabriz Iran

With technologies that have democratized the production and reproduction of information, a significant portion of daily interacted posts in social media has been infected by rumors. Despite the extensive research on rumor detection and verification, so far, the problem of calculating the spread power of rumors has not been considered. To address this research gap, the present study seeks a model to calculate the Spread Power of Rumor (SPR) as the function of content-based features in two categories: False Rumor (FR) and True Rumor (TR). For this purpose, the theory of Allport and Postman will be adopted, which it claims that importance and ambiguity are the key variables in rumor-mongering and the power of rumor. Totally 42 content features in two categories"importance" (28 features) and"ambiguity" (14 features) are introduced to compute SPR. The proposed model is evaluated on two datasets, Twitter and Telegram. The results showed that (i) the spread power of False Rumor documents is rarely more than True Rumors. (ii) there is a significant difference between the SPR means of two groups False Rumor and True Rumor. (iii) SPR as a criterion can have a positive impact on distinguishing False Rumors and True Rumors. © 2020, CC BY.

关键词： Cell proliferation

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