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  1. Book ; Online: Electrocatalysis in Fuel Cells

    Shao, Minhua

    2016  

    Size 1 electronic resource (XXX, 658 p.)
    Publisher MDPI - Multidisciplinary Digital Publishing Institute
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT020091568
    ISBN 9783038422341 ; 9783038422198 ; 3038422347 ; 3038422193
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Book ; Online: Random Position Adversarial Patch for Vision Transformers

    Shao, Mingzhen

    2023  

    Abstract: Previous studies have shown the vulnerability of vision transformers to adversarial patches, but these studies all rely on a critical assumption: the attack patches must be perfectly aligned with the patches used for linear projection in vision ... ...

    Abstract Previous studies have shown the vulnerability of vision transformers to adversarial patches, but these studies all rely on a critical assumption: the attack patches must be perfectly aligned with the patches used for linear projection in vision transformers. Due to this stringent requirement, deploying adversarial patches for vision transformers in the physical world becomes impractical, unlike their effectiveness on CNNs. This paper proposes a novel method for generating an adversarial patch (G-Patch) that overcomes the alignment constraint, allowing the patch to launch a targeted attack at any position within the field of view. Specifically, instead of directly optimizing the patch using gradients, we employ a GAN-like structure to generate the adversarial patch. Our experiments show the effectiveness of the adversarial patch in achieving universal attacks on vision transformers, both in digital and physical-world scenarios. Additionally, further analysis reveals that the generated adversarial patch exhibits robustness to brightness restriction, color transfer, and random noise. Real-world attack experiments validate the effectiveness of the G-Patch to launch robust attacks even under some very challenging conditions.
    Keywords Computer Science - Computer Vision and Pattern Recognition
    Publishing date 2023-07-08
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Book ; Online: Brightness-Restricted Adversarial Attack Patch

    Shao, Mingzhen

    2023  

    Abstract: Adversarial attack patches have gained increasing attention due to their practical applicability in physical-world scenarios. However, the bright colors used in attack patches represent a significant drawback, as they can be easily identified by human ... ...

    Abstract Adversarial attack patches have gained increasing attention due to their practical applicability in physical-world scenarios. However, the bright colors used in attack patches represent a significant drawback, as they can be easily identified by human observers. Moreover, even though these attacks have been highly successful in deceiving target networks, which specific features of the attack patch contribute to its success are still unknown. Our paper introduces a brightness-restricted patch (BrPatch) that uses optical characteristics to effectively reduce conspicuousness while preserving image independence. We also conducted an analysis of the impact of various image features (such as color, texture, noise, and size) on the effectiveness of an attack patch in physical-world deployment. Our experiments show that attack patches exhibit strong redundancy to brightness and are resistant to color transfer and noise. Based on our findings, we propose some additional methods to further reduce the conspicuousness of BrPatch. Our findings also explain the robustness of attack patches observed in physical-world scenarios.
    Keywords Computer Science - Computer Vision and Pattern Recognition
    Subject code 006
    Publishing date 2023-07-01
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  4. Article ; Online: Existence of connected and autonomous vehicles in mixed traffic: Impacts on safety and environment.

    Wei, Shanshan / Shao, Minhua

    Traffic injury prevention

    2024  Volume 25, Issue 3, Page(s) 390–399

    Abstract: Objectives: With the growing market penetration of connected and autonomous vehicles (CAVs), the interaction between conventional human-driven vehicles (HDVs) and CAVs will be inevitable. However, the effects of CAVs in mixed traffic streams have not ... ...

    Abstract Objectives: With the growing market penetration of connected and autonomous vehicles (CAVs), the interaction between conventional human-driven vehicles (HDVs) and CAVs will be inevitable. However, the effects of CAVs in mixed traffic streams have not been extensively studied in China. This study aims to quantify the changes in driving characteristics of an HDV while following a CAV compared to following another HDV and investigate the corresponding impact on traffic safety and the environment caused by these changes.
    Methods: Firstly, two scenarios were built on a driving simulation platform. In scenario 1, the driver follows a vehicle programmed to execute the speed profile of the HDV obtained from the Shanghai Naturalistic Driving Study (SH-NDS) project. In scenario 2, the driver follows a vehicle whose speed profile is calibrated according to the Cooperative Adaptive Cruise Control (CACC) follow-along theory. Secondly, the speed, acceleration, and headway of 30 individuals in each following scenario were analyzed. Speed and acceleration volatility (standard deviation, deviation rate) and time-to-collision (TTC) were selected as indexes to assess the safety impact. The emission and fuel consumption models were used to determine the environmental impact after being localized by the parameters.
    Results: HDVs following CAVs exhibit less driving volatility in speed and acceleration, show remarkable improvements in TTC, consume less fuel, and produce fewer emissions on average.
    Conclusions: By introducing CAVs into the road traffic system, traffic operation safety and environmental quality will be improved, with a more stable flow status, lower collision risk, and less air pollution.
    MeSH term(s) Humans ; Automobile Driving ; Accidents, Traffic ; Autonomous Vehicles ; China ; Computer Simulation ; Safety
    Language English
    Publishing date 2024-01-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 2089818-6
    ISSN 1538-957X ; 1538-9588
    ISSN (online) 1538-957X
    ISSN 1538-9588
    DOI 10.1080/15389588.2023.2291337
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6253: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: Calibration methods for a camera with a tilted lens and a three-dimensional laser scanner in the Scheimpflug condition.

    Shao, Mingwei

    Journal of the Optical Society of America. A, Optics, image science, and vision

    2020  Volume 37, Issue 7, Page(s) 1076–1082

    Abstract: A three-dimensional laser scanner has been designed and widely utilized in many fields. The lens plane is tilted according to the Scheimpflug condition and the optical axis is not perpendicular to the charge-coupled device plane. In this case, depth of ... ...

    Abstract A three-dimensional laser scanner has been designed and widely utilized in many fields. The lens plane is tilted according to the Scheimpflug condition and the optical axis is not perpendicular to the charge-coupled device plane. In this case, depth of view can be extended significantly. In this paper, analytical models for a camera with a tilted lens and a laser scanner meeting the Scheimpflug condition are presented. Based on these models, a calibration procedure is detailed. We propose a simple calibration method to determine the intrinsic parameters of a Scheimpflug camera. Meanwhile, two calibration methods for a laser scanner in the Scheimpflug condition are detailed. According to the obtained intrinsic parameters, the laser scanner can be calibrated directly. Moreover, a simple calibration for a three-dimensional laser scanner without the help of a precise positioning system is described. Experimental results show the effectiveness and high measurement accuracy of our calibration methods.
    Language English
    Publishing date 2020-07-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 283633-6
    ISSN 1520-8532 ; 1084-7529 ; 0740-3232
    ISSN (online) 1520-8532
    ISSN 1084-7529 ; 0740-3232
    DOI 10.1364/JOSAA.391906
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.B 2689: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: Transcript assembly and annotations: Bias and adjustment.

    Zhang, Qimin / Shao, Mingfu

    PLoS computational biology

    2023  Volume 19, Issue 12, Page(s) e1011734

    Abstract: Transcript annotations play a critical role in gene expression analysis as they serve as a reference for quantifying isoform-level expression. The two main sources of annotations are RefSeq and Ensembl/GENCODE, but discrepancies between their ... ...

    Abstract Transcript annotations play a critical role in gene expression analysis as they serve as a reference for quantifying isoform-level expression. The two main sources of annotations are RefSeq and Ensembl/GENCODE, but discrepancies between their methodologies and information resources can lead to significant differences. It has been demonstrated that the choice of annotation can have a significant impact on gene expression analysis. Furthermore, transcript assembly is closely linked to annotations, as assembling large-scale available RNA-seq data is an effective data-driven way to construct annotations, and annotations are often served as benchmarks to evaluate the accuracy of assembly methods. However, the influence of different annotations on transcript assembly is not yet fully understood. We investigate the impact of annotations on transcript assembly. Surprisingly, we observe that opposite conclusions can arise when evaluating assemblers with different annotations. To understand this striking phenomenon, we compare the structural similarity of annotations at various levels and find that the primary structural difference across annotations occurs at the intron-chain level. Next, we examine the biotypes of annotated and assembled transcripts and uncover a significant bias towards annotating and assembling transcripts with intron retentions, which explains above the contradictory conclusions. We develop a standalone tool, available at https://github.com/Shao-Group/irtool, that can be combined with an assembler to generate an assembly without intron retentions. We evaluate the performance of such a pipeline and offer guidance to select appropriate assembling tools for different application scenarios.
    MeSH term(s) Molecular Sequence Annotation ; Gene Expression Profiling ; Protein Isoforms/genetics ; RNA-Seq
    Chemical Substances Protein Isoforms
    Language English
    Publishing date 2023-12-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1011734
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: On de novo Bridging Paired-end RNA-seq Data.

    Li, Xiang / Shao, Mingfu

    ArXiv

    2023  

    Abstract: The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced two ends in the ... ...

    Abstract The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced two ends in the absence of the reference genome - a problem here we refer to as de novo bridging. Solving this problem provides longer, more informative RNA-seq reads, and benefits downstream RNA-seq analysis such as transcript assembly, expression quantification, and splicing differential analysis. However, de novo bridging is a challenging and complicated task owing to alternative splicing, transcript noises, and sequencing errors. It remains unclear if the data provides sufficient information for accurate bridging, let alone efficient algorithms that determine the true bridges. Methods have been proposed to bridge paired-end reads in the presence of reference genome (called reference-based bridging), but the algorithms are far away from scaling for de novo bridging as the underlying compacted de Bruijn graph(cdBG) used in the latter task often contains millions of vertices and edges. We designed a new truncated Dijkstra's algorithm for this problem, and proposed a novel algorithm that reuses the shortest path tree to avoid running the truncated Dijkstra's algorithm from scratch for all vertices for further speeding up. These innovative techniques result in scalable algorithms that can bridge all paired-end reads in a cdBG with millions of vertices. Our experiments showed that paired-end RNA-seq reads can be accurately bridged to a large extent. The resulting tool is freely available at https://github.com/Shao-Group/rnabridge-denovo.
    Language English
    Publishing date 2023-03-27
    Publishing country United States
    Document type Preprint
    ISSN 2331-8422
    ISSN (online) 2331-8422
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: On

    Li, Xiang / Shao, Mingfu

    ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine

    2023  Volume 2023

    Abstract: The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced two ends in the ... ...

    Abstract The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced two ends in the absence of the reference genome-a problem here we refer to as
    Language English
    Publishing date 2023-10-04
    Publishing country United States
    Document type Journal Article
    DOI 10.1145/3584371.3612987
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Dynamics and optimal control of a stochastic Zika virus model with spatial diffusion.

    Shao, Minna / Zhao, Hongyong

    Mathematical biosciences and engineering : MBE

    2023  Volume 20, Issue 9, Page(s) 17520–17553

    Abstract: Zika is an infectious disease with multiple transmission routes, which is related to severe congenital disabilities, especially microcephaly, and has attracted worldwide concern. This paper aims to study the dynamic behavior and optimal control of the ... ...

    Abstract Zika is an infectious disease with multiple transmission routes, which is related to severe congenital disabilities, especially microcephaly, and has attracted worldwide concern. This paper aims to study the dynamic behavior and optimal control of the disease. First, we establish a stochastic reaction-diffusion model (SRDM) for Zika virus, including human-mosquito transmission, human-human sexual transmission, and vertical transmission of mosquitoes, and prove the existence, uniqueness, and boundedness of the global positive solution of the model. Then, we discuss the sufficient conditions for disease extinction and the existence of a stationary distribution of positive solutions. After that, three controls, i.e. personal protection, treatment of infected persons, and insecticides for spraying mosquitoes, are incorporated into the model and an optimal control problem of Zika is formulated to minimize the number of infected people, mosquitoes, and control cost. Finally, some numerical simulations are provided to explain and supplement the theoretical results obtained.
    MeSH term(s) Animals ; Humans ; Zika Virus ; Zika Virus Infection/prevention & control ; Communicable Diseases ; Infectious Disease Transmission, Vertical ; Aedes
    Language English
    Publishing date 2023-10-18
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2265126-3
    ISSN 1551-0018 ; 1551-0018
    ISSN (online) 1551-0018
    ISSN 1551-0018
    DOI 10.3934/mbe.2023778
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Transcript Assembly and Annotations: Bias and Adjustment.

    Zhang, Qimin / Shao, Mingfu

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Motivation: Transcript annotations play a critical role in gene expression analysis as they serve as a reference for quantifying isoform-level expression. The two main sources of annotations are RefSeq and Ensembl/GENCODE, but discrepancies between ... ...

    Abstract Motivation: Transcript annotations play a critical role in gene expression analysis as they serve as a reference for quantifying isoform-level expression. The two main sources of annotations are RefSeq and Ensembl/GENCODE, but discrepancies between their methodologies and information resources can lead to significant differences. It has been demonstrated that the choice of annotation can have a significant impact on gene expression analysis. Furthermore, transcript assembly is closely linked to annotations, as assembling large-scale available RNA-seq data is an effective data-driven way to construct annotations, and annotations are often served as benchmarks to evaluate the accuracy of assembly methods. However, the influence of different annotations on transcript assembly is not yet fully understood.
    Results: We investigate the impact of annotations on transcript assembly. We observe that conflicting conclusions can arise when evaluating assemblers with different annotations. To understand this striking phenomenon, we compare the structural similarity of annotations at various levels and find that the primary structural difference across annotations occurs at the intron-chain level. Next, we examine the biotypes of annotated and assembled transcripts and uncover a significant bias towards annotating and assembling transcripts with intron retentions, which explains above the contradictory conclusions. We develop a standalone tool, available at https://github.com/Shao-Group/irtool, that can be combined with an assembler to generate an assembly without intron retentions. We evaluate the performance of such a pipeline and offer guidance to select appropriate assembling tools for different application scenarios.
    Language English
    Publishing date 2023-04-21
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.04.20.537700
    Database MEDical Literature Analysis and Retrieval System OnLINE

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