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A virtual positioning system for external beam radiotherapy

Virtual Reality 2023年第3期27卷 2569-2582页

作者： Sung, Wen-Hsu Jiang, Ching-Fen Su, Tai-Sin Sun, Shuh-Ping Department of Physical Therapy and Assistive Technology National Yang Ming Chiao Tung University Taipei Taiwan Graduate Program of Smart Healthcare and Bioinformatics I-Shou University Kaohsiung Taiwan Department of Biomedical Engineering I-Shou University Kaohsiung Taiwan Department of Digital Media Design I-Shou University Kaohsiung Taiwan

In radiation therapy, positioning patients to ensure the accuracy of the setup of a procedure is a routine and labour-intensive process that substantially determines the efficacy of treatment. In this study, we propose a virtual positioning system that can simulate the positioning process with a visible beam path under the broad view of a life-like patient-positioning platform to obviate problems with excessively narrow view. This system integrates image processing, computer graphics, and virtual reality to encompass a 3D treatment target reconstructed from medical images of different modalities in a virtual scene. An innovative evaluation method is further proposed to verify the efficacy of the system using a full-scale 3D solid anthropometric model, and a treatment target showed an accuracy of 99% in calibration and a mean compatibility of 95% with an actual measurement. The proposed virtual positioning system provides a training and education platform for radiation therapy. The methodology through which the system was developed is also disclosed as a promising approach to improve the efficiency and safety of the position verification process for existing systems. © 2023, The Author(s), under exclusive licence to Springer-Verlag London Ltd., part of Springer Nature.

关键词： Radiotherapy

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A phase vocoder without requiring phase unwrapping

IEEJ Transactions on Electronics, Information and Systems

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IEEJ Transactions on Electronics, Information and Systems 2018年第4期138卷 352-359页

作者： Yoneguchi, Ryoichi Murakami, Takahiro Electrical Engineering Program Graduate School of Science and Technology Meiji University 1-1-1 Higashi-mita Tama-ku Kawasaki Kanagawa214-8571 Japan Department of Electronics and Bioinformatics School of Science and Technology Meiji University 1-1-1 Higashi-mita Tama-ku Kawasaki Kanagawa214-8571 Japan

In recent years, a number of algorithms for controlling parameters of an acoustic signal have been realized according as hardware technologies have been developed. A phase vocoder is one of the widely known methods for time scale modification (TSM) and pitch scale modification (PSM). The phase vocoder converts the length and the pitch of the acoustic signal by increasing or decreasing an instantaneous angular frequency. However, due to the phase unwrapping problem that occurs when the instantaneous angular frequency is estimated, the phase vocoder distorts the waveform of the modified signal. In order to alleviate this problem, we present a new algorithm for the phase vocoder. Our method does not encounter the phase unwrapping problem since we directly use the difference of phases between adjacent analysis frames to avoid estimating the instantaneous angular frequency. Moreover, our approach is effective even when the characteristics of the acoustic signal, e.g., a frequency and amplitude, change rapidly. © 2018 The Institute of Electrical Engineers of Japan.

关键词： Acoustic waves

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eXpanda: An integrated platform for network analysis and visualization

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In Silico Biology 2007年第2期7卷 141-144页

作者： Negishi, Yoshiteru Nakamura, Hiroyuki Yachie, Nozomu Saito, Rintaro Tomita, Masaru Institute for Advanced Biosciences Keio University Fujisawa 252-8520 Japan Bioinformatics Program Graduate School of Media and Governance Keio University Fujisawa 252-8520 Japan Department of Environmental Information Keio University Fujisawa 252-8520 Japan

Analysis and visualization of biological networks, such as protein-protein and protein-DNA interactions, are crucially important toward obtaining a thorough understanding of living systems. Here, we present an integrative software platform, eXpanda, which enables an analysis of a very broad range of biological networks, with a special focus on the extraction of characteristic topologies which potentially function as units in the networks. eXpanda is provided as a Perl library which gives full-automatic connections to various biological databases via a Perl programmable interface and can perform topological analysis based on graph theory. The results of these analyses are visualizable by vector graphics. eXpanda is under GNU General Public License. Software package, detailed documentations, source codes, and some sample scripts are downloadable at http://***/expanda/. © 2007 IOS Press. All rights reserved.

关键词： Interactome Network analysis Network visualization Perl library Scalable Vector Graphics (SVG)

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bioinformatics exploration into potential mechanisms of Calamus draco for colorectal cancer treatment 9th

Bioinformatics exploration into potential mechanisms of Cala...

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9th International Conference on Computer Science and Computational Intelligence, ICCSCI 2024

作者： Kenneth, Christian Nirwantono, Rudi Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Biotechnology Department Faculty of Engineering Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Computer Science Program Bina Nusantara University Jakarta11480 Indonesia

As one of the cancer types with the highest incidence rates, colorectal cancer (CRC) would benefit from treatments with fewer side effects and reduced treatment-resistant potential. One of the options is to harness the anti-CRC potential of natural products. Previous studies have shown that Calamus draco exudate, dragon's blood, has anticancer activity in liver cancer and acute myeloid leukemia, but its bioactivity has not been studied in CRC. Here we conduct a bioinformatics study based on network pharmacology to explore the anti-CRC potential and mechanism of C. draco-derived compounds. The bioinformatics pipeline is composed of compound and target collection, biological network evaluation, and enrichment analysis. We found that there are 43 bioactive compounds from C. draco targeting 91 CRC-related targets, of which most compounds target MEN1, PTGS2, and IDH1. Further analyses show that the targets of C. draco are involved in the cellular response to hypoxia. By inhibiting those targets, C. draco bioactive compounds can potentially hinder angiogenesis and increase treatment response efficacy. © 2024 The Authors.

关键词： Lung cancer

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A discretized differential evolution algorithm for the inference of Gene Regulatory Networks

A discretized differential evolution algorithm for the infer...

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Latin America Congress on Computational Intelligence (LA-CCI)

作者： Leandro T. Hattori Heitor S. Lopes Fabrício M. Lopes Graduate Program in Electrical and Computer Engineering (CPGEI) Federal University of Technology Curitiba Paraná Brazil Graduate Program in Bioinformatics (PPGBIOINFO) Federal University of Technology Paraná Brazil

Feature selection is a very important procedure in the pattern recognition research field. Feature selection algorithms are particularly important in the inference of Gene Regulatory Networks (GRNs) from its gene expression profiles, which usually involves data with a large number of variables and small number of observations. This work presents the inference of GRNs from two different feature selection approaches: classical (deterministic) SFS and SFFS search algorithms, and (meta-heuristic) Discretized Differential Evolution (DDE) algorithm. Several Artificial Gene Networks (AGNs) were probabilistically generated for testing. They had different sizes and topologies following three models: Erdös-Rényi uniformly-random, Watts-Strogatz small-world, and Barabási-Albert scale-free. Results confirm that, as the number of candidate predicting genes increase, the performance of the compared methods decrease, revealing the exponential characteristic of the problem. Notwithstanding, for all network sizes and topologies studies, the DDE algorithm achieved better results than the other approaches, especially for GRNs with hubs.

关键词： Inference algorithms Network topology Prediction algorithms Topology bioinformatics Gene expression Entropy

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The effect of visual advanced driver assistance systems on a following human driver in a mixed-Traffic condition 7

The effect of visual advanced driver assistance systems on a...

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7th International Conference on Computer Science and Computational Intelligence, CSCI 2022

作者： Ariansyah, Dedy Pardamean, Bens Caruso, Giandomenico Bioinformatics and Data Science Research Centre Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia Department of Mechanical Engineering Politecnico di Milano Milan 20156 Italy

Rapid development in vehicular technology has caused more automated vehicle control to increase on the roads. Studies showed that driving in mixed traffic with an autonomous vehicle (AV) had a negative impact on the time headway (THW) of conventional vehicles (CVs) (i.e., driven by humans). To address this issue, there is a need to equip CV with visual advanced driver assistance systems (ADASs) that helps the driver maintain safe headway when driving near AVs. This study examines the perception of drivers using visual ADAS and their associated risk while driving behind the AV at constant and varying speeds. The preliminary results showed that while visual ADAS could help drivers keep the safe THW, it could affect drivers' ability to react to emergencies. This implies that visual modality alone might not be sufficient and therefore requires some other feedback or intelligent transport systems to help drivers maintain safe driving in a mixed-Traffic condition. © 2022 Elsevier B.V.. All rights reserved.

关键词： Advanced driver assistance systems

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Toward Learning Factory for Industry 4.0: Virtual Reality (VR) for Learning Human–Robot Collaboration 1

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International Conference on Innovative Technologies in Intelligent Systems and Industrial Applications, CITISIA 2022

作者： Ariansyah, Dedy Colombo, Giorgio Pardamean, Bens Bioinformatics and Data Science Research Centre Bina Nusantara University Jakarta11480 Indonesia Department of Mechanical Engineering Politecnico di Milano Milan20156 Italy Computer Science Department BINUS Graduate Program Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia

ISBN: (数字)9783031290787

ISBN: (纸本)9783031290770

Industry 4.0 will bring not only transformation to the manufacturing technologies but also to the profile of the workforce. Education system should be revised to prepare the future graduates embracing the knowledge of the ongoing revolution. Initiatives on the modification of curriculum and tools to deliver the concepts of Industry 4.0 must be taken. This paper examines limitations of current engineering tools and proposes a virtual reality (VR)-based learning platform to support the teaching and learning activity for Industry 4.0, focusing on the design of Human–robot Collaboration (HRC). The development process began with the identification of the general Intended Learning Outcomes (ILOs) which were extracted from the review of the HRC design issues, followed by the evaluation of the current teaching tool. From these results, the new requirements of the tools to achieve ILOs are redefined. The implementation of the system is demonstrated to show the feasibility of the proposed learning platform. This workflow can serve as initial development of another learning platform for the other innovative concepts that form the building blocks of Industry 4.0. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2023.

关键词： Industry 4.0

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Computational design of combinatorial peptide library for modulating protein-protein interactions

Computational design of combinatorial peptide library for mo...

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10th Pacific Symposium on Biocomputing, PSB 2005

作者： Li, Xiang Liang, Jie Graduate Program in Bioinformatics SEO University of Illinois 851 S. Morgan Street Chicago IL United States Department of Bioengineering SEO University of Illinois 851 S. Morgan Street Chicago IL United States

ISBN: (纸本)9812560467

Screening phage-displayed combinatorial peptide library is an effective approach for discovery of peptide modulators for protein-protein interactions. However, as peptide length increases, the chance of finding active peptides in a finite size library diminishes. To increase the likelihood of finding peptides that bind to a protein, we develop statistical potential for computational construction of biased combinatorial antibody-like peptide libraries. Based on the alpha shapes of antibody- antigen complexes, we developed an empirical pair potential for antigen-antibody interactions that depends on local packing. We validate this potential and show that it can successfully discriminate the native interface peptides from a simulated library of 10,000 random peptides for 34 antigen-antibody complexes. In addition, we show that it can successfully recognize the native binding surface patch among all possible surface patches taken from either the antibody or the antigen for seven antibody-antigen protein complexes contained in the CAPRI (Critical Assessment of Predicted Interactions) dataset. We then develop a Weighted Amino Acid Residue sequence Generator (WAARG) for design of biased peptide library. When compared with a random peptide library, WAARG libraries contain more native-like binding peptides at a significantly smaller size. Our method can be used to construct peptide library for screening of antibody variants with improved specificity and affinity to a target antigen. It can also be used for screening of antibody-like antagonist peptides modulating other protein-protein interactions.

关键词： Peptides

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Discovery Biological Motifs Using Heuristics Approaches

Discovery Biological Motifs Using Heuristics Approaches

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Brazilian Conference on Intelligent Systems (BRACIS)

作者： Jader M. Caldonazzo Garbelini André Yoshiaki Kashiwabara Danilo Sipoli Sanches Graduate Program in Bioinformatics (PPGBIOINFO) Federal University of Technology Cornélio Procópio PR Brazil

ISBN: (纸本)9781509035670

The identification of transcription factors binding sites (TFBS) - also called motifs - in DNA sequences is the first step to understanding how works gene regulation. Recognizing these patterns in the promoter regions of co-expressed genes is a determining key for this. Although there are several algorithms for this purpose, the problem is still far from being solved because of the great diversity of gene expression and the binding sites low specificity. State of the art algorithms have limitations, such as the high number of false positives and low accuracy for Identifying weak motifs. In this article we proposed a new approach based on memetic algorithms (DMMA) for discovery mofifs. The proposed approach was developed using evolutionary computation along with the local search algorithms simulated annealing and variable neighborhood search. To attest the algorithm ability, tests were conducted in four datasets - two real and two synthetic - and the results were compared with other approaches in the literature.

关键词： Sociology Statistics Complexity theory Biology Probability Mathematical model Simulated annealing

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Influence of conformational change of chain unit on the intrinsic negative thermal expansion of polymers

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Chinese Chemical Letters 2021年第4期32卷 1515-1518页

作者： Qiangsheng Sun Ke Jin Yuhui Huang Jia Guo Thanyada Rungrotmongkol Phornphimon Maitarad Changchun Wang State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science Fudan UniversityShanghai 200433.China Biocatalyst and Environmental Biotechnology Research Unit Department of BiochemistryFaculty of Science and Program in Bioinformatics and Computational BiologyGraduate SchoolChulalongkom UniversityBangkok 10330Thailand Research Center of Nano Science and Technology Shanghai UniversityShanghai 200444China

Negative thermal expansion(NTE) behavior has roused wide interest for the control of thermomechanical properties of functional *** NTE behaviors have been found in kinds of compounds,it remains challenging for polymers to achieve intrinsic NTE *** this work,we systematically studied the conformational change of dibenzocyclooctadiene(DBCOD) derivatives between chair(C) and twist-boat(TB) forms based on density-functional theo ry(DFT) calculations,and found clear evidence of the relationship between the structure of DBCOD units and the thermal contraction behavior of the related *** order to obtain the polymer with NTE property,two conditions should be met for the thermal contracting DBCOD related units as follows:(i) the TB conformation can turn into C conformation as the temperature increases,and(ii) the volume of C conformation is smaller than that of TB *** rule should offer a guidance to exploration of the new intrinsic NTE polymers in the future.

关键词： Negative thermal expansion Conformational change Polyarylamides Density-functional theory Dibenzocyclooctadiene

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