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A modified SELEX approach to identify DNA aptamers with binding specificity to the major histocompatibility complex presenting ovalbumin model antigen

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RSC Advances 2023年第46期13卷 32681-32693页

作者： Lin, Yang Chen, Cho-Yi Ku, Yu-Chia Wang, Li-Chin Hung, Chia-Chien Lin, Zhi-Qian Chen, Bing-Hong Hung, Jui-Tse Sun, Yi-Chen Hung, Kai-Feng Department of Medical Research Taipei Veterans General Hospital 201 Section 2 Shi-Pai Road Taipei112 Taiwan Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taipei Taiwan School of Computer Science Georgia Institute of Technology Atlanta GA United States Kang Chiao International School Taipei Taiwan School of Medicine Tzu-Chi University Hualien Taiwan Department of Ophthalmology Taipei Tzu Chi Hospital The Buddhist Tzu Chi Medical Foundation New Taipei City Taiwan Department of Dentistry School of Dentistry National Yang Ming Chiao Tung University Taipei Taiwan

Aptamers have sparked significant interest in cell recognition because of their superior binding specificity and biocompatibility. Cell recognition can be mediated by targeting the major histocompatibility complex (MHC) that presents short peptides derived from intracellular antigens. Although numerous antibodies have demonstrated a specific affinity for the peptide-MHC complex, the number of aptamers that exhibit comparable characteristics is limited. Aptamers are usually selected from large libraries via the Systemic Evolution of Ligands by Exponential Enrichment (SELEX), an iterative process of selection and PCR amplification to enrich a pool of aptamers with high affinity. However, the success rate of aptamer identification is low, possibly due to the presence of complementary sequences or sequences rich in guanine and cytosine that are less accessible for primers. Here, we modified SELEX by employing systemic consecutive selections with minimal PCR amplification. We also modified the analysis by selecting aptamers that were identified in multiple selection rounds rather than those that are highly enriched. Using this approach, we were able to identify two aptamers with binding specificity to cells expressing the ovalbumin alloantigen as a proof of concept. These two aptamers were also discovered among the top 150 abundant candidates, despite not being highly enriched, by performing conventional SELEX. Additionally, we found that highly enriched aptamers tend to contain fractions of the primer sequence and have minimal target affinity. Candidate aptamers are easily missed in the conventional SELEX process. Therefore, our modification for SELEX may facilitate the identification of aptamers for more application in diverse biomedical fields. Significance: we modify the conventional method to improve the efficiency in the identification of the aptamer, a single strand of nucleic acid with binding specificity to the target molecule, showing as a proof of concept that

关键词： Peptides

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RoboDesign1M: A Large-scale Dataset for Robot Design Understanding

arXiv

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arXiv 2025年

作者： Le, Tri Nguyen, Toan Tran, Quang Nguyen, Quang Huang, Baoru Nguyen, Hoan Vu, Minh Nhat Ta, Tung D. Nguyen, Anh FPT Software AI Center Viet Nam Department of Computer Science University of Liverpool United Kingdom University of Information Technology HCMC Viet Nam Automation & Control Institute TU Wien Austria Department of Creative Informatics The University of Tokyo Japan

Robot design is a complex and time-consuming process that requires specialized expertise. Gaining a deeper understanding of robot design data can enable various applications, including automated design generation, retrieving example designs from text, and developing AI-powered design assistants. While recent advancements in foundation models present promising approaches to addressing these challenges, progress in this field is hindered by the lack of large-scale design datasets. In this paper, we introduce RoboDesign1M, a large-scale dataset comprising 1 million samples. Our dataset features multimodal data collected from scientific literature, covering various robotics domains. We propose a semi-automated data collection pipeline, enabling efficient and diverse data acquisition. To assess the effectiveness of RoboDesign1M, we conduct extensive experiments across multiple tasks, including design image generation, visual question answering about designs, and design image retrieval. The results demonstrate that our dataset serves as a challenging new benchmark for design understanding tasks and has the potential to advance research in this field. RoboDesign1M will be released to support further developments in AI-driven robotic design automation. © 2025, CC BY-NC-ND.

关键词： Machine design

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The Effectiveness of a Simplified Model Structure for Crowd Counting

arXiv

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arXiv 2024年

作者： Chen, Lei Gao, Xinghang Chao, Fei Chang, Xiang Lin, Chih-Min Gao, Xingen Lin, Shaopeng Zhang, Hongyi Lin, Juqiang The School of Opto-Electronic and Communication Engineering Xiamen University of Technology Xiamen China The Department of Artificial Intelligence School of Informatics Xiamen University Xiamen China The Department of Computer Science Institute of Mathematics Physics and Computer Science Aberystwyth University Aberystwyth United Kingdom The Department of Electrical Engineering Yuan Ze University Taoyuan City320 Taiwan

In the field of crowd counting research, many recent deep learning based methods have demonstrated robust capabilities for accurately estimating crowd sizes. However, the enhancement in their performance often arises from an increase in the complexity of the model structure. This paper discusses how to construct high-performance crowd counting models using only simple structures. We proposes the Fuss-Free Network (FFNet) that is characterized by its simple and efficieny structure, consisting of only a backbone network and a multi-scale feature fusion structure. The multi-scale feature fusion structure is a simple structure consisting of three branches, each only equipped with a focus transition module, and combines the features from these branches through the concatenation operation. Our proposed crowd counting model is trained and evaluated on four widely used public datasets, and it achieves accuracy that is comparable to that of existing complex models. Furthermore, we conduct a comprehensive evaluation by replacing the existing backbones of various models such as FFNet and CCTrans with different networks, including MobileNet-v3, ConvNeXt-Tiny, and Swin-Transformer-Small. The experimental results further indicate that excellent crowd counting performance can be achieved with the simplied structure proposed by us. Copyright © 2024, The Authors. All rights reserved.

关键词： Complex networks

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A Vision on What Explanations of Autonomous Systems are of Interest to Lawyers

A Vision on What Explanations of Autonomous Systems are of I...

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IEEE International Requirements Engineering Conference Workshops (REW)

作者： Miriam C. Buiten Louise A. Dennis Maike Schwammberger Law School University of St. Gallen St. Gallen Switzerland Department of Computer Science University of Manchester Manchester UK Department of Informatics Karlsruhe Institute of Technology Karlsruhe Germany

As (semi-) autonomous systems become more prevalent, accountability for their actions in legal cases becomes crucial. However, understanding the decision-making process of these complex systems can be challenging. System explainability offers a solution by providing insights into how these systems work. In our research vision, we focus on identifying the types of explanations that lawyers need in litigation involving autonomous systems. With an increase in autonomy, these systems get increasingly complex, with some systems even being “black-” or “grey-box” systems where large amounts of their decision making is obscured. By bridging the gap between technology and the law, we aim to enhance the legal process surrounding autonomous vehicles.

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Accidental Face Recognition and Detection Using Machine Learning

Accidental Face Recognition and Detection Using Machine Lear...

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Advanced Innovations in Smart Cities (ICAISC), International Conference on

作者： Ashish Sharma Piyansh Agrawal Krishan Bhisham Sharma Imed Ben Dhaou Department of Computer Engineering & Applications GLA University Mathura UP India Chitkara University Institute of Engineering and Technology Chitkara University Punjab India Department of Computer Science Hekma School of Engineering Computing and Informatics Dar Al-Hekma University Jeddah Saudi Arabia

The data collected from all the States and Union Territories has been compiled in the Publication, according to the ministry of road transport and roads transport research wing. The total number of accident-related deaths in 2018 was 1,51,417, which is a 2.3 percent increase over 2017. Around 85% of accident-related deaths occur in the 18-60 age range, which is the most productive. Road traffic fatalities not only inflict the relatives of the victims considerable emotional suffering, but they also cost the nation a lot of money. In this data maximum hazard happens due to delayed response of family and friends as they are unknown of the situation of the sight of the accident. Also, several cases remain unreported. Our objective is to reduce this number to make our nation strong and prosper. In this current research we are committed to creating a social network where road accidents can be reported quickly to family and friends, so the delayed response can be reduced. The practice of associating a person with a picture has become increasingly common thanks to the media. However, it is less resistant to retinal and fingerprint scanning. The face detection and recognition module created for the current research is described in this paper. Face detection will be performed using Haar-Cascades, while face identification will be performed using Eigenfaces, Fisher faces, and local binary pattern histograms.

关键词： Resistance Technological innovation Road accidents Social networking (online) Smart cities Face recognition Roads

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Maximum Correntropy Criterion Kalman Filter for Indoor Quadrotor Navigation under Intermittent Measurements

Maximum Correntropy Criterion Kalman Filter for Indoor Quadr...

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Mediterranean Conference on Control and Automation (MED)

作者： Loizos Hadjiloizou Evagoras Makridis Themistoklis Charalambous Kyriakos M. Deliparaschos Department of Intelligent Systems KTH Royal Institute of Technology Stockholm Sweden Department of Electrical and Computer Engineering School of Engineering University of Cyprus Nicosia Cyprus Department of Electrical Engineering and Automation School of Electrical Engineering Aalto University Espoo Finland Electrical and Computer Engineering and Informatics Department Cyprus University of Technology Limassol Cyprus

We present a multisensor fusion framework for the onboard real-time navigation of a quadrotor in an indoor environment. The framework integrates sensor readings from an Inertial Measurement Unit (IMU), a camera-based object detection algorithm, and an Ultra-WideBand (UWB) localisation system. Often the sensor readings are not always readily available, leading to inaccurate pose estimation and hence poor navigation performance. To effectively handle and fuse sensor readings, and accurately estimate the pose of the quadrotor for tracking a predefined trajectory, we design a Maximum Correntropy Criterion Kalman Filter (MCC-KF) that can manage intermittent observations. The MCC-KF is designed to improve the performance of the estimation process when is done with a Kalman Filter (KF), since KFs are likely to degrade dramatically in practical scenarios in which noise is non-Gaussian (especially when the noise is heavy-tailed). To evaluate the performance of the MCC-KF, we compare it with a previously designed Kalman filter by the authors. Through this comparison, we aim to demonstrate the effectiveness of the MCC-KF in handling indoor navigation missions. The simulation results show that our presented framework offers low positioning errors, while effectively handling intermittent sensor measurements.

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Applying unsupervised keyphrase methods on concepts extracted from discharge sheets

arXiv

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arXiv 2023年

作者： Memarzadeh, Hoda Ghadiri, Nasser Samwald, Matthias Shahreza, Maryam Lotfi Department of Electrical and Computer Engineering Isfahan University of Technology Isfahan84156-83111 Iran Institute for Artificial Intelligence Center for Medical Statistics Informatics and Intelligent Systems Medical University of Vienna Vienna Austria Department of Computer Engineering Shahreza Campus University of Isfahan Iran

Clinical notes containing valuable patient information are written by different health care providers with various scientific levels and writing styles. It might be helpful for clinicians and researchers to understand what information is essential when dealing with extensive electronic medical records. Entities recognizing and mapping them to standard terminologies is crucial in reducing ambiguity in processing clinical notes. Although named entity recognition and entity linking are critical steps in clinical natural language processing, they can also result in the production of repetitive and low-value concepts. In other hand, all parts of a clinical text do not share the same importance or content in predicting the patient's condition. As a result, it is necessary to identify the section in which each content is recorded and also to identify key concepts to extract meaning from clinical texts. In this study, these challenges have been addressed by using clinical natural language processing techniques. In addition, in order to identify key concepts, a set of popular unsupervised key phrase extraction methods has been verified and evaluated. Considering that most of the clinical concepts are in the form of multi-word expressions and their accurate identification requires the user to specify n-gram range, we have proposed a shortcut method to preserve the structure of the expression based on TF-IDF. In order to evaluate the pre-processing method and select the concepts, we have designed two types of downstream tasks (multiple and binary classification) using the capabilities of transformer-based models. The obtained results show the superiority of proposed method in combination with SciBERT model, also offer an insight into the efficacy of general extracting essential phrase methods for clinical *** Codes 68P20 Copyright © 2023, The Authors. All rights reserved.

关键词： Medical informatics

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A Queueing-theoretic Analysis of the Performance of a Cloud Computing Infrastructure: Accounting for Task Reneging or Dropping

A Queueing-theoretic Analysis of the Performance of a Cloud ...

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2022 International Conference on Electrical, computer, Communications and Mechatronics Engineering, ICECCME 2022

作者： Kuaban, Godlove Suila Soodan, Bhavneet Singh Kumar, Rakesh Czekalski, Piotr Institute of Theoretical and Applied Informatics Polish Academy of Sciences Baltycka 5 Gliwice44-100 Poland Chandigarh University Department of Mathematics Punjab 140413 India Namibia University of Science and Technology Department of Mathematics and Statistics Namibia Department of Computer Graphics Vision and Digital Systems Silesian University of Technology Akademicka 16 Gliwice44-100 Poland

ISBN: (数字)9781665470957

ISBN: (纸本)9781665470957

Cloud computing has revolutionized the information technology era. It offers high-speed computing, storage, and ICT resources on demand. One of the significant challenges in cloud computing is the impact of impatient users or request (task) reneging. When a request has been compromised, missed its execution deadline, or depends on other rejected ones, it must be removed from the queue without being processed. The reneging or removal of tasks from queues may trigger the reneging or removal of other tasks that depend of them. We refer to this reneging of requests from the load balancing or computing queues as correlated reneging. We presented the performance analysis of a network of queues that constitute a queueing model of a simplified cloud computing infrastructure. We show the relationship between the load, delay, and probability of buffer saturation (blocking probability). It is seen that at about 80% utilization, a small increase in utilization (due to a small increase in the arrival rate Δλ for a fixed service rate μ) results in a sharp increase in the delay experienced by the tasks, and on the probability of task rejection or blocking. © 2022 IEEE.

关键词： Cloud computing

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Graph Burning: Bounds and Hardness

arXiv

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arXiv 2024年

作者： Antony, Dhanyamol Das, Anita Gosavi, Shirish Jacob, Dalu Kulamarva, Shashanka Department of Computer Science and Automation Indian Institute of Science Bengaluru India School of Data Science Indian Institute of Science Education and Research Thiruvananthapuram India Department of Mathematics Manipal Institute of Technology Bengaluru Manipal Academy of Higher Education Manipal India Department of Mathematics Indian Institute of Technology Delhi India School of Informatics Kyoto University Kyoto Japan

For an undirected graph G, graph burning is defined as follows: at step t = 0 all vertices in G are unburned. At each step t ≥ 1, one new unburned vertex is selected to burn until we exhaust all the vertices. If a vertex is burned at step t, then all its unburned neighbors are burned in step t + 1, and the process continues until there are no unburned vertices in G. The burning number of a graph G, denoted by b(G), is the minimum number of steps required to burn all the vertices of G. The Burning Number problem asks whether the burning number of an input graph G is at most k or not. In this paper, we study the Burning Number problem both from an algorithmic and a structural point of view. The Burning Number problem is known to be NP-complete for trees with maximum degree at most three and interval graphs. Here, we prove that this problem is NP-complete even when restricted to connected cubic graphs and connected proper interval graphs. The well-known burning number conjecture asserts that all the vertices of a graph of order n can be burned in ⌈√n ⌉ steps. In line with this conjecture, upper and lower bounds of b(G) are well-studied for various graph classes. Here, we provide an improved upper bound for the burning number of connected Pk-free graphs and show that the bound is tight up to an additive constant 1. Finally, we study two variants of the problem, namely edge burning (only edges are burned) and total burning (both vertices and edges are burned). In particular, we establish their relationship with the burning number problem and evaluate the algorithmic complexity of these *** Codes 05C38, 05C05, 05C85 © 2024, CC BY.

关键词： Undirected graphs

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Zero- Touch Privacy Preserving Provisioning in an Edge-, Fog-, and Cloud Environment

Zero- Touch Privacy Preserving Provisioning in an Edge-, Fog...

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International Conference on Fog and Mobile Edge Computing (FMEC)

作者： Raphael Schermann Simone Bussa Rainer Urian Christian Steger Institute of Technical Informatics Graz University of Technology Graz Austria Department of Control and Computer Engineering Politecnico di Torino Turin Italy Infineon Technologies AG Augsburg Germany

IoT device onboarding, especially in the context of an edge-fog-cloud architecture, still has many challenges to solve. FIDO has already specified a zero-touch onboarding process called FIDO Device Onboarding (FDO) specification. In this paper, we present improvements to the FDO specification regarding performance and privacy. For privacy and security reasons, we show how the URL of the Owner Fog can be hidden from the Rendezvous Server. Further, we replaced the EPID protocol with a promising privacy-preserving protocol called AACKA. We also modified the last phase in the FDO protocol to create a performance improvement.

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