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5th IFAC conference on Analysis and Control of Chaotic Systems (CHAOS)

作者： Nakakuki, Takashi Imura, Jun-ichi Kawamata, Ibuki Murata, Satoshi Kyushu Inst Technol Sch Comp Sci & Syst Engn Dept Syst Design & Informat 680-4 Kawazu Iizuka Fukuoka 8208502 Japan Tokyo Inst Technol Dept Mech & Environm Informat Meguro Ku 2-12-1-W8 O Okayama Tokyo 1528552 Japan Tohoku Univ Grad Sch Engn Dept Robot Aoba Ward 6-6-1 Aoba Sendai Miyagi 9808579 Japan

How to construct a reliable deoxyribonucleic acid (dna) circuit is one of the most important issues in the field of molecular programming and computing. Such a circuit frequently suffers from various kinds of unintended binding reactions on account of a lower specificity of the molecular interaction emerging from base complementarity between dna strands, which results in low reliability of the molecular circuit. In this study, we propose a method to quantitatively evaluate the robustness of a dna circuit created by dna strand displacement reactions. the highlight of our method is representing the circuit system contaminated by unintended reactions by a standard form of a disturbed nonlinear system and evaluating the robustness with the L-2 gain by solving the Hamilton-Jacobi inequality. (C) 2018, IFAC (international Federation of Automatic Control) Hosting by Elsevier Ltd. All rights reserved.

关键词： Complex systems Nonlinear circuits Uncertainty Differential equations Robustness

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Multi-Scale Capsule Network for Predicting dna-Protein Binding Sites

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IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021年第5期18卷 1793-1800页

作者： Zhang, Qinhu Yu, Wenbo Han, Kyungsook Nandi, Asoke K. Huang, De-Shuang Tongji Univ Inst Machine Learning & Syst Biol Sch Elect & Informat Engn 4800 Caoan Rd Shanghai 201804 Peoples R China Tongji Univ Sch Life Sci & Technol Siping Rd 1239 Shanghai 200092 Peoples R China Inha Univ Sch Comp Sci & Engn Incheon 21000 South Korea Brunel Univ London Dept Elect & Comp Engn Uxbridge UB8 3PH Middx England

Discovering dna-protein binding sites, also known as motif discovery, is the foundation for further analysis of transcription factors (TFs). Deep learning algorithms such as convolutional neural networks (CNN) have been introduced to motif discovery task and have achieved state-of-art performance. However, due to the limitations of CNN, motif discovery methods based on CNN do not take full advantage of large-scale sequencing data generated by high-throughput sequencing technology. Hence, in this paper we propose multi-scale capsule network architecture (MSC) integrating multi-scale CNN, a variant of CNN able to extract motif features of different lengths, and capsule network, a novel type of artificial neural network architecture aimed at improving CNN. the proposed method is tested on real ChIP-seq datasets and the experimental results show a considerable improvement compared with two well-tested deep learning-based sequence model, DeepBind and Deepsea.

关键词： dna Machine learning Computational modeling Feature extraction Kernel Convolution Bioinformatics Multi-scale capsule network transcription factors binding specificity

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A Novel Autonomous molecular Mechanism Based on Spatially Localized dna Computation 15th

A Novel Autonomous Molecular Mechanism Based on Spatially Lo...

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15th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2020

作者： Wang, Yue Qian, Mengyao Hu, Wenxiao Wang, Luhui Dong, Yafei School of Computer Science Shaanxi Normal University Xi’an Shaanxi710119 China College of Life Science Shaanxi Normal University Xi’an Shaanxi710119 China

ISBN: (纸本)9789811613531

Contemporary dna synthesis technology matures, and the development provides intriguing possibilities for dynamic manipulation of dna self-assembly, which plays a pivotal role in the behavior of designing versatile nanodevices and generating controllable networks. Similarly, in synthetic molecular circuits, the spatially localized architecture furnishes a different strategy, allowing for immobilized dna molecules in close vicinity to each other. Herein, the formal modeling language was utilized to mark the address with a specific sequence of location tags, thus a set of routes were precisely arranged at the nanoscale. Beyond building a collection of separate modules, computer simulations were used to explore further complex assemblies of the building blocks. By orchestrating a series of dna strand displacement operations locally, autonomous movement and addressing operations were realized, completing the group transport and partition storage of dissimilar molecules. the nanodevice gives the dna molecule its mechanical properties and follows an embedded "molecular program". the simulation results of the Visual DSD tool provided qualitative and quantitative proof for the operation of the system. © 2021, Springer Nature Singapore Pte Ltd.

关键词： dna

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An Efficient Fault Recovery Algorithm in Multiprocessor Mixed-Criticality Systems

An Efficient Fault Recovery Algorithm in Multiprocessor Mixe...

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15th IEEE international conference on High Performance computing and Communications (HPCC) /11th IEEE/IFIP international conference on Embedded and Ubiquitous computing (EUC)

作者： Liu, Guangdong Lu, Ying Wang, Shige Univ Nebraska Dept Comp Sci & Engn Lincoln NE 68588 USA Gen Motor Global Res & Dev Elect & Controls Integrat Lab Warren MI USA

ISBN: (纸本)9780769550886

Recent years, there is an increasing interest of integrating mixed-criticality functionalities onto a shared computing platform in automotive, avionics and the control industry. the benefits of such an integration include reduced hardware cost and high computational performance. Also, new challenges appear as a result of the integration since interferences across tasks with different criticalities are introduced and these interferences could potentially lead to catastrophic results. Failures are likely to be more frequent due to the interferences. Hence, it is becoming increasingly important to deal with faults in mixed-criticality systems. Although several approaches have been proposed to handle failures in mixed-criticality systems, they come either with a high cost due to a hardware replication (spatial redundancy) or with a poor utilization due to reexecution (time redundancy). In this paper, we study a scheme that provides fault recovery through task reallocations in response to permanent faults in multiprocessor mixed-criticality systems. We present an algorithm to minimize the number of task reallocations while retaining the promise that the most critical applications continue to meet their deadlines. the performance evaluation of the proposed algorithm is carried out by comparing it with two baseline algorithms. In order to evaluate the performance of algorithms from the perspective of mixed-criticality systems, we choose the state of art metric called ductility to formally measure the effects of deadline misses for tasks with different criticality levels. Under this metric, a high-criticality task is considered more important than all low-criticality tasks combined. the simulation results confirm the effectiveness of our proposed algorithm in both minimizing the number of task reallocations and retaining the promised performance of high-criticality tasks.

关键词： fault recovery multiprocessor mixed-criticality real-time systems task reallocation failure recovery Multiprocessor Religious Missions permanent fault algorithms dna Integration integration

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Accelerating Motif Finding Problem using Grid computing with Enhanced Brute Force

Accelerating Motif Finding Problem using Grid Computing with...

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12th international conference on Advanced Communication Technology (ICACT) - lCT for Green Growth and Sustainable Development

作者： Faheem, H. M. Ain Shams Univ Fac Comp & Informat Sci Comp Syst Dept Cairo Egypt

ISBN: (纸本)9788955191455

Motif finding problem is a major task to understand the mechanisms of gene expression regulation. Motif is generally defined as a recurring pattern in the sequence of nucleotides or amino acids. In the dna sequence, it is usually a short segment that occurs frequently, but not required to be an exact copy for each occurrence. this property of motif makes motif mining very difficult. In fact, motif finding problem is proven to be NP-Complete. Many algorithms fail to solve the well-known challenge problem of finding a motif of length 15 and has at most 4 mutations (15, 4) due to the huge runtime needed. Others fail to distinguish the motif from background sequences. Brute Force is one of the exact algorithms that never fail to find the motif, but it suffers from an intractable running time. In this paper, we present a novel approach to accelerate the motif finding problem using grid computing. As grid computing makes available low-cost high-performance computing (HPC) infrastructures, the best candidates for using such infrastructures are applications that require high computational power, large storage capacity, or fast and high-throughput networking. the nature of motif finding problem is considered one of the perfect scenarios for grid computing. We deployed an enhanced version of the Brute Force;skip-Brute Force running on EUMEDGRID infrastructure (Co-Funded project by the European Commission in the framework of FP6, with the aim of supporting the development of a Grid e-Infrastructure in the Mediterranean Area and promoting the porting of computationally intensive applications on the Grid platform). the idea behind our skip Brute Force algorithm is that it skips all the iterations that will not lead to a correct solution. the message passing programming paradigm is deployed since it assumes a partitioned address space and supports explicit parallelization. Our experimental results showed boosting in the performance without sacrificing the exactness of the Brute F

关键词： Motif findin dna sequence analysis Grid computing

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Controllable dna Nano-Tweezer Technique Based on the Combinatorial Strand Displacement 10th

Controllable DNA Nano-Tweezer Technique Based on the Combina...

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10th international conference on Bio-Inspired computing - theories and Applications (BIC-TA)

作者： Zhang, Xuncai Shen, Chaonan Cui, Guangzhao Wang, Yanfeng Zhengzhou Univ Light Ind Coll Elect & Elect Engn Henan Key Lab Informat Based Elect Appliances Zhengzhou 450002 Henan Peoples R China

ISBN: (纸本)9783662490143;9783662490136

Toehold-mediated strand displacement has great advantage in dna molecular computing. It is widely applied to build the large-scale and complex logic circuits. However, in general, the detection of molecular circuits is achieved by dna double helices with nicked segment. So to some extent it limits the detection method of molecular circuits. Here, we report a strategy implemented by the combinatorial strand displacement technology to control the state of dna nano-tweezer. the distance between the fluorescent dye and the quencher dye is drawn closer because of the closed dna nano-tweezer, inducing the fluorescence signal disappeared in response to the logic gate function. Four logic circuits (AND gate, OR gate, Inhibit gate and XOR gate) are designed in this paper based on the combinatorial strand displacement.

关键词： Combinatorial strand displacement dna nano-tweezer Logic circuits

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Label-Free Fluorescence Detection of Carbohydrate Antigen 15-3 via dna AND Logic Gate Based on Graphene Oxide 15th

Label-Free Fluorescence Detection of Carbohydrate Antigen 15...

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15th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2020

作者： Hu, Wenxiao Wang, Luhui Wang, Yue Qian, Mengyao Dong, Yafei College of Life Science Shaanxi Normal University Xi’an710119 China School of Computer Sciences Shaanxi Normal University Xi’an710119 China

ISBN: (纸本)9789811613531

In this work, we have developed a dna AND logic gate based on graphene oxide (GO) absorbing single dna and G-quadruplex interacting with N-methyl mesoporphyrin IX(NMM) for detecting breast cancer biomarker carbohydrate antigen 15-3 (CA15-3). With CA15-3 and NMM as the two inputs, the fluorescence intensity of the NMM is the output signal. A hairpin dna probe is designed, consisting of CA15-3 aptamer and partly anti-CA15-3 aptamer sequences as a long stem and G-rich sequences as a quadruplex-forming oligomer. In the presence of CA15-3 or NMM alone, there is no significant fluorescence enhancing, and the output of the signal is "0". While in the presence of CA15-3 protein and NMM, the fluorescence signal was dramatically increasing and the output of the signal is "1". this biosensor platform also exhibited good reproducibility, selectivity and showed high sensitivity for CA15-3 protein in a range of 10U/mL-500U/mL with the detection limit of 10U/mL. In addition, the fluorescence dna AND logic gate can successfully be applied to the determination of CA15-3 in spiked human serum. In summary, the proposed fluorescent dna AND logic gate could construct a simple, fast, label-free and highly specific sensing methods for CA15-3. © 2021, Springer Nature Singapore Pte Ltd.

关键词： Antigens

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Practical Aspects of Declarative Languages - 16th international Symposium, PADL 2014, Proceedings

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15th international conference on Verification, Model Checking, and Abstract Interpretation, VMCAI 2014

ISBN: (纸本)9783319041315

the proceedings contain 15 papers. the topics discussed include: partial type signatures for Haskell;abstract modular inference systems and solvers;sunroof: a monadic DSL for generating JavaScript;compiling dna strand displacement reactions using a functional programming language;two applications of the ASP-prolog system: decomposable programs and multi-context systems;towards modeling morality computationally with logic programming;a declarative specification of giant number arithmetic;embedding foreign code;on the correctness and efficiency of lock-free expandable tries for tabled logic programs;typelets - a rule-based evaluation model for dynamic, statically typed user interfaces;expand: towards an extensible pandoc system;and generic generic programming.

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Identification of dna-Binding Proteins via Fuzzy Multiple Kernel Model and Sequence Information 15th

Identification of DNA-Binding Proteins via Fuzzy Multiple Ke...

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15th international conference on Intelligent computing, ICIC 2019

作者： Ding, Yijie Tang, Jijun Guo, Fei School of Electronic and Information Engineering Suzhou University of Science and Technology Suzhou China School of Computer Science and Technology College of Intelligence and Computing Tianjin University No. 135 Yaguan Road Tianjin Haihe Education Park Tianjin China Department of Computer Science and Engineering University of South Carolina Columbia United States

ISBN: (纸本)9783030269685

dna-binding proteins is the molecular basis for understanding the basic processes of life activities. Many diseases are associated with dna binding proteins. the methods of detecting dna-binding proteins are mainly realized by biochemical experiment, which is time consuming and extremely expensive. A lot of computational methods based on Machine Learning (ML) algorithm have been developed to detect dna-binding proteins. In this study, we propose a novel dna-binding proteins model via a Fuzzy Multiple Kernel Support Vector Machine. the multiple features of sequence and evolutionary are extracted and constructed as multiple kernels, respectively. Next, these corresponding kernels are integrated by Multiple Kernel Learning (MKL) algorithm. At last, Fuzzy Support Vector Machine (FSVM) is employed to build an effective dna-binding protein predictor. Comparing with other outstanding methods, our proposed approach achieves good results. the accuracy of our model are 82.98% and 81.70% on PDB1075 (benchmark data set of dna-binding proteins) and PDB186 (independent test set), respectively. Our approach is comparable to previous methods. © 2019, Springer Nature Switzerland AG.

关键词： Learning algorithms

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Point-mutation detection of mitochondrial dna by using microfluidic systems

Point-mutation detection of mitochondrial DNA by using micro...

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15th international conference on Miniaturized Systems for Chemistry and Life Sciences 2011, MicroTAS 2011

作者： Chang, Chen-Min Chiou, Li-Fang Shieh, Dar-Bin Lee, Gwo-Bin Department of Engineering Science Taiwan Institute of Oral Medicine National Cheng Kung University Tainan 701 Taiwan Department of Power Mechanical Engineering National Tsing Hua University Hsinchu 300 Taiwan

ISBN: (纸本)9781618395955

Mitochondrial disorders are a group of complex and heterogeneous diseases that may be caused by molecular defects in mitochondrial genomes. Pathogenic mitochondrial dna (mtdna) mutations are usually present in the heteroplasmic form. the degree of mtdna mutation heteroplasmy varies among different tissues. thus, it is important to detect and quantify the degree of mutation heteroplasmy of mtdna. Currently, more than 100 pathogenic mtdna point-mutations have been documented and new ones are still being extensively explored. Among them, A3243G mutation, which causes the myopathy encephalopathy lactic acidosis and stroke (MELAS) syndrome and diabetes, attracts considerable interest recently. In this study, a new microfluidic system capable of point-mutation detection of mtdna has been demonstrated. the entire process including cell lysis, enzyme digestion, amplification of target fragment of mtdna and optical detection can be automatically performed. Experimental results showed that the point-mutation of mtdna can be successfully detected. Copyright © (2011) by the Chemical and Biological Microsystems Society.

关键词： Microfluidics

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