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16th international conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2012

作者： Suzuki, Takaaki Terao, Kyohei Suzuki, Hiroyuki Nitta, Yuki Takao, Hidekuni Shimokawa, Fusao Oohira, Fumikazu Hiramaru, Daisuke Kotera, Hidetoshi Kagawa University Japan Kyoto University Japan

ISBN: (纸本)9780979806452

In this study, we propose a simple observation method of the shape and molecular orientation of the chromosomes extracted from the cell for a sample-to-analysis system in clinical diagnosis. the proposed technique is composed of total preparation technique such as cell immobilization, chromosomes extraction, stretching, suspension and analysis using a disposable microchip controlled by centrifugal force only. It is experimentally confirmed that the chip having two kinds of microstructures arranged concentrically on a chip is possible to immobilize cells and stretch chromosomes extracted from the immobilized cells.

关键词： Diagnosis

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Bio-Inspired computing: theories and Applications 1

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丛书名： Communications in Computer and Information Science

1000年

作者： Linqiang Pan Lianghao Li Zhihua Cui Jianghui Cai

ISBN: (数字)9789811912535

ISBN: (纸本)9789811912528

this two-volume set (CCIS 1565 and CCIS 1566) constitutes selected and revised papers from the 16th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2021, held in Taiyuan, China, in December 2021.;the 67 papers presented were thoroughly reviewed and selected from 211 submissions. the papers are organized in the following topical sections: evolutionary computation and swarm intelligence; dna and molecular computing; machine learning and computer vision.

关键词： Image Processing and Computer Vision Artificial Intelligence Computer System Implementation Computer Communication Networks Information Systems and Communication Service Computer Appl. in Social and Behavioral Sciences

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RUDEUS: A Machine Learning Classification System to Study dna-Binding Proteins 16

RUDEUS: A Machine Learning Classification System to Study DN...

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16th international conference on Knowledge Discovery and Information Retrieval, KDIR 2024 as part of 16th international Joint conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management, IC3K 2024

作者： Medina-Ortiz, David Cabas-Mora, Gabriel Moya, Iván Soto-García, Nicole Uribe-Paredes, Roberto Departamento de Ingeniería En Computación Universidad de Magallanes Avenida Bulnes 01855 Punta Arenas Chile Centre for Biotechnology and Bioengineering CeBiB Universidad de Chile Beauchef 851 Santiago Chile

ISBN: (纸本)9789897587160

dna-binding proteins play crucial roles in biological processes such as replication, transcription, packaging, and chromatin remodeling. their study has gained importance across scientific fields, with computational biology complementing traditional methods. While machine learning has advanced bioinformatics, generalizable pipelines for identifying dna-binding proteins and their specific interactions remain scarce. We present RUDEUS, a Python library with hierarchical classification models to identify dna-binding proteins and distinguish between single- and double-stranded dna interactions. RUDEUS integrates protein language models, supervised learning, and Bayesian optimization, achieving 95% precision in dna-binding identification and 89% accuracy in distinguishing interaction types. the library also includes tools for annotating unknown sequences and validating dna-protein interactions through molecular docking. RUDEUS delivers competitive performance and is easily integrated into protein engineering workflows. It is available under the MIT License, with the source code and models available on the Github repository https://***/ProteinEngineering-PESB2/RUDEUS. © 2024 by SCITEPRESS – Science and Technology Publications, Lda.

关键词： Adversarial machine learning

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Physical properties of anticancer drug 6-thioguanine

Physical properties of anticancer drug 6-thioguanine

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16th international conference on Spectroscopy of Molecules and Crystals

作者： Rubin, YV Inst Low Temp Phys & Engn UA-61103 Kharkov Ukraine

ISBN: (纸本)0819454443

6-thioguanine has long been in use as an anticancer drug. In the recent years 6-thioguanine and its derivatives are coming into application as photosensibilizers, luminescence probes, targets for forming photo-crosslinks. To ascertain spectroscopic properties of 6-thioguanine, its UV absorption, low temperature (4.2K) luminescence and circular dichroism spectra were studied in solutions of different polarities. Spectrophotometric titration of 6-thioguanine was carried out in the pH 1-13 interval. the MP2 ab initio method was used to calculate the molecular structure, dipole moments, electronic density distribution, thermodynamic characteristics, UV and IR spectra of some 6-thioguanine tautomers. Based on theoretical calculations and experimental results, a diagram of electronic excited states of 6-thioguanine and a scheme of acid-base and tautomeric equilibrium of 6-thioguanine in the polar solvent were built. Migration of excitation in dna with incorporated 6-thioguanine was investigated. As well, we used 6-thioguanine as a luminescent probe to study structural changes in cryoprotector and dna solutions in the temperature range from 4.2 to 273K. In particular, glassification of the dna hydrate shell in the range of 200K was revealed.

关键词： absorption and luminescence electronic spectra IR-spectra ab initio calculations dna 6-thioguanine molecular and electronic structures

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Practical Aspects of Declarative Languages 1

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丛书名： Lecture Notes in Computer Science

1000年

作者： Matthew Flatt Hai-Feng Guo

ISBN: (数字)9783319041322

ISBN: (纸本)9783319041315

this book constitutes the refereed proceedings of the 16th international Symposium on Practical Aspects of Declarative Languages, PADL 2014, held in SanDiego, CA, USA, in January 2014, co-located with POPL 2014, the 41st Symposium on Principles of programming Languages. the 15 revised papers presented were carefully reviewed and selected from 27 submissions. they cover a wide range of topics related to logic and functional programing, including language support for parallelism and GPUs, constructs and techniques for modularity and extensibility, and applications of declarative programming to document processing and dna simulation.

关键词： programming Languages, Compilers, Interpreters programming Techniques Logics and Meanings of Programs Software Engineering

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A privacy-preserving image retrieval scheme based secure kNN, dna coding and deep hashing

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MULTIMEDIA TOOLS AND APPLICATIONS 2021年第15期80卷 22733-22755页

作者： Cheng, Shu-Li Wang, Lie-Jun Huang, Gao Du, An-Yu Xinjiang Univ Coll Informat Sci & Engn Urumqi 830046 Peoples R China Tsinghua Univ Dept Automat Beijing 100084 Peoples R China

In recent years, information leakage incidents occur frequently. Ciphertext domain search has become a hot spot in multimedia technology and software engineering. therefore, how to mine valuable information safely and effectively is very important. In this paper, we present the CBIR solution and complete the relevant software development. the proposed method not only outsources CBIR services but also avoids privacy leaks. Our main contributions are reflected in two aspects: improving search efficiency and protecting user privacy. For one thing, we propose a novel privacy protection algorithm to encrypt images. For the other thing, we propose an integrated deep hash algorithm to extract the high-level features of images. In the index encryption process, we use secure kNN to encrypt the index. through experimental analysis and argumentation, the proposed privacy protection algorithm has a lower correlation coefficient and a better information entropy. It is secure enough and can resist common types of attacks encountered during data transmission. the proposed secure image retrieval algorithm is tested on two datasets. Compared with the same type of algorithm, the proposed algorithm has better retrieval performance. In short, the privacy reservation scheme guarantees the security and effectiveness of the system.

关键词： Multimedia Privacy protection Deep hash Cloud computing Image encryption Secure kNN

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16th international Euro-Par conference on Parallel Processing, Euro-Par 2010

16th International Euro-Par Conference on Parallel Processin...

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16th international Euro-Par conference on Parallel Processing, Euro-Par 2010

ISBN: (纸本)9783642152764

the proceedings contain 104 papers. the special focus in this conference is on Parallel Processing. the topics include: A parallel implementation of the Jacobi-Davidson eigensolver and its application in a plasma turbulence code;scheduling parallel eigenvalue computations in a quantum chemistry code;Scalable parallelization strategies to accelerate NuFFT data translation on multicores;multicore and Manycore programming;javaSymphony: A programming and execution environment for parallel and distributed many-core architectures;scalable producer-consumer pools based on elimination-diffraction trees;productivity and performance: Improving consumability of hardware transactional memory through a real-world case study;exploiting fine-grained parallelism on cell processors;optimized on-chip-pipelined mergesort on the cell/B.E.;transactional mutex locks;Near-optimal placement of MPI processes on hierarchical NUMA architectures;parallel enumeration of shortest lattice vectors;A parallel GPU algorithm for mutual information based 3D nonrigid image registration;Multi-GPU and multi-CPU parallelization for interactive physics simulations;Long dna sequence comparison on multicore architectures;adaptive fault tolerance for many-core based space-borne computing;Maestro: Data orchestration and tuning for openCL devices;multithreaded Geant4: Semi-automatic transformation into scalable thread-parallel software;parallel exact time series motif discovery;optimized dense matrix multiplication on a many-core architecture;exceptions for algorithmic skeletons;a language-based tuning mechanism for task and pipeline parallelism;A study of a software cache implementation of the OpenMP memory model for multicore and manycore architectures;programming CUDA-based GPuS to simulate two-layer shallow water flows;theory and algorithms for parallel computation;analysis of multi-organization scheduling algorithms;Area-maximizing schedules for series-parallel DAGs;parallel Selection by Regular Sampling;a

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16th international Euro-Par conference on Parallel Processing, Euro-Par 2010

16th International Euro-Par Conference on Parallel Processin...

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16th international Euro-Par conference on Parallel Processing, Euro-Par 2010

ISBN: (纸本)9783642152900

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Tetracycline Intelligent Target-Inducing Logic Gate Based on Triple-Stranded dna Nanoswitch 16th

Tetracycline Intelligent Target-Inducing Logic Gate Based on...

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16th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2021

作者： Xi, Sunfan Wang, Yue Hu, Mengyang Wang, Luhui Cheng, Meng Dong, Yafei College of Life Science Shaanxi Normal University Shaanxi Xi’an710119 China School of Computer Science Shaanxi Normal University Shaanxi Xi’an710119 China

ISBN: (纸本)9789811912559

A previously unreported three-strand dna (ts-dna) non-metal structure with hairpin structure was designed based on a strategy of logic switching and tetracycline (TC) signaling molecule switching. Will target and TC-binding aptamer (TBA) is the combination of body, and its relation with three functional chain dna conformation, with programmable dna sensor signal by FAM input molecule fluorescence emission monitoring. After the combination, the input signal is converted to a fluorescent signal to perform a logical operation. By introducing a novel nanomaterial, graphene oxide (GO), as a signal regulator, the fluorescence response changed by intermolecular interactions is the key to achieving logical calculation. the harm of tetracycline can generally cause kidney damage, ear damage, gastrointestinal adverse reactions, skin allergies, *** tetracycline as a molecular trigger to induce conformational changes in dna, a logical operation target detection method was constructed. In addition, nanoscale devices can be reconfigured and optimized to accommodate additional logical calculations and target detection. © 2022, Springer Nature Singapore Pte Ltd.

关键词： dna

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Nucleosome positioning from tiling microarray data

Nucleosome positioning from tiling microarray data

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16th ISMB conference on Intelligent Systems for molecular Biology

作者： Yassour, Moran Kaplan, Tommy Jaimovich, Ariel Friedman, Nir Hebrew Univ Jerusalem Sch Comp Sci & Engn IL-91904 Jerusalem Israel Hebrew Univ Jerusalem Fac Med Dept Mol Biol & Biotechnol IL-91120 Jerusalem Israel

Motivation: the packaging of dna around nucleosomes in eukaryotic cells plays a crucial role in regulation of gene expression, and other dna-related processes. To better understand the regulatory role of nucleosomes, it is important to pinpoint their position in a high (5-10 bp) resolution. Toward this end, several recent works used dense tiling arrays to map nucleosomes in a high-throughput manner. these data were then parsed and hand-curated, and the positions of nucleosomes were assessed. Results: In this manuscript, we present a fully automated algorithm to analyze such data and predict the exact location of nucleosomes. We introduce a method, based on a probabilistic graphical model, to increase the resolution of our predictions even beyond that of the microarray used. We show how to build such a model and how to compile it into a simple Hidden Markov Model, allowing for a fast and accurate inference of nucleosome positions. We applied our model to nucleosomal data from mid-log yeast cells reported by Yuan et al. and compared our predictions to those of the original paper;to a more recent method that uses five times denser tiling arrays as explained by Lee et al.;and to a curated set of literature-based nucleosome positions. Our results suggest that by applying our algorithm to the same data used by Yuan et al. our fully automated model traced 13% more nucleosomes, and increased the overall accuracy by about 20%. We believe that such an improvement opens the way for a better understanding of the regulatory mechanisms controlling gene expression, and how they are encoded in the dna.

关键词： dna

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