Article
Multidisciplinary Sciences
Braulio Gutierrez-Medina
Summary: A direct method for three-dimensional (3D) imaging in bright-field microscopy is reported in this study, which is applicable to label-free samples and utilizes digital image processing filters for optical sectioning. The accuracy and applicability of the method are demonstrated through imaging of fungal, animal tissue, and plant samples and comparison with light-sheet fluorescence microscopy imaging.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Computer Science, Artificial Intelligence
Seyed Jalaleddin Mousavirad, Gerald Schaefer, Huiyu Zhou, Mahshid Helali Moghadam
Summary: Multi-level image thresholding is a widely used method for image segmentation, but it can be time-consuming due to the need for an exhaustive search to find optimal threshold values. In this paper, we evaluate 23 population-based metaheuristics for multi-level image thresholding and compare their performance using various measures. Our experimental results show that recently introduced algorithms may not perform well in this task, while some established algorithms work better.
KNOWLEDGE-BASED SYSTEMS
(2023)
Article
Computer Science, Software Engineering
Wenya Yang, Xiao-Diao Chen, Hui Wang, Xiaoyang Mao
Summary: This paper proposes an adaptive edge detection method called MSCNOGP, which combines multi-scale closest neighbor operator with grid partition technique. The MSCNOGP method can remove noise and small area textures, and improve the precision of the edges. Compared with traditional methods, it achieves the best precision and visual effect.
Article
Optics
Timur E. Gureyev, Harry M. Quiney, Leslie J. Allen
Summary: This paper proposes a method for high-resolution, three-dimensional reconstruction of internal structures of objects. The method can be used with any form of radiation or matter waves, as long as the depth of field is smaller than the thickness of the sample. The paper elucidates the physical optics basis for the method and presents the reconstruction algorithm in detail. A simulated example demonstrates the application of the method to three-dimensional electron transmission imaging.
JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION
(2022)
Article
Computer Science, Information Systems
Pei Niu, Lihui Wang, Bingqing Xie, Marc Robini, Loic Boussel, Phillippe Douek, Yuemin Zhu, Feng Yang
Summary: The study presents a reconstruction method for sCT images by combining multi-energy information, which improves image reconstruction quality and material decomposition accuracy through clustering similar material composition pixels, linear fitting between different energy images, pixel value projection, and combination.
Article
Engineering, Electrical & Electronic
Qianqi Dai, Yibing Li, Tao Jiang, Qian Sun
Summary: A new ground-penetrating radar (GPR) B-scan interpretation model based on the hyperbolic trend is proposed, which includes preprocessing, restricted algebraic distance fitting, clustering, and back-projection algorithms. The effectiveness of the model has been demonstrated on both simulated and real datasets.
IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT
(2022)
Article
Engineering, Multidisciplinary
R. Craig Herndon
Summary: This article discusses the process of determining the Shannon entropy of a signal using the uncertainty space method, including reviewing uncertainty space, presenting the uncertainty envelope, and combining components from uncertainty space and measurement space. It is shown that signal entropy is equivalent to the real-valued digit or binary accuracy of the signal data.
Article
Automation & Control Systems
Pengcheng Jiang, Yu Xue, Ferrante Neri
Summary: Dropout is an effective method for training deep neural networks by deactivating some neurons to mitigate overfitting. This paper proposes a novel approach to guide the dropout rate using an evolutionary algorithm, allowing for more flexibility in training. Experimental results demonstrate that this method consistently outperforms other dropout methods, including state-of-the-art techniques.
ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE
(2023)
Article
Materials Science, Multidisciplinary
Akshay Mehra, Bolton Howes, Ryan Manzuk, Alex Spatzier, Bradley M. Samuels, Adam C. Maloof
Summary: The Grinding, Imaging, Reconstruction Instrument (GIRI) is introduced in this paper for automatically grinding and photographing large-volume samples and segmenting data through image processing technique. Three case studies demonstrate the application of GIRI in addressing questions with significant morphological components.
MICROSCOPY AND MICROANALYSIS
(2022)
Article
Computer Science, Artificial Intelligence
Xingchen Zhang
Summary: This paper proposes a benchmark called MEFB for multi-exposure image fusion, which includes a test set, code library, evaluation metrics, fused images, and software toolkit, filling the gap in benchmarking studies in this field. Extensive experiments using MEFB have been conducted for comprehensive performance evaluation and effective algorithm identification, serving as an effective platform for researchers to compare MEF algorithm performance.
INFORMATION FUSION
(2021)
Article
Computer Science, Software Engineering
Pablo Navarro, J. Ignacio Orlando, Claudio Delrieux, Emmanuel Iarussi
Summary: This paper presents an attempt to obtain a learned descriptor for dense registration in line drawings, using deep learning techniques to design descriptors that can locally match images with significant differences in shape, form, and projection angle. By specifically crafting a data set and training a neural network, the descriptors show correct generalization in unseen hand-drawn sketches by humans.
COMPUTER GRAPHICS FORUM
(2021)
Article
Automation & Control Systems
Zhiyan Zhong, Zhichao Ma
Summary: A novel rapid detection algorithm for impurity defects in FICS images is proposed, achieving accurate identification of film/black backgrounds and impurity defects in high-density FICS images. The algorithm enhances image contrast, weakens texture interferences, and calculates the probability of background feature in the edge region between background and defect.
IEEE TRANSACTIONS ON INDUSTRIAL ELECTRONICS
(2022)
Article
Engineering, Electrical & Electronic
Danyang Wu, Shenfei Pei, Feiping Nie, Rong Wang, Xuelong Li
Summary: This paper proposes a novel Multi-Directional Multi-Label Learning (MDML) model, which captures the relationships between multiple labels using discriminative classifiers and low-rank constraints. Experimental results demonstrate the superiority of this model on popular benchmark datasets.
Article
Computer Science, Artificial Intelligence
Yan Huang, Zihan Zhou, Xiangyu Sai, Yong Xu, Yuexian Zou
Summary: This paper proposes a hierarchical hashing-based multi-source image retrieval method, which can search for clean appearance-alike images from external datasets and apply them to a simplified denoising method to improve image quality.
APPLIED SOFT COMPUTING
(2021)
Article
Automation & Control Systems
Dhruv Khandelwal, Maarten Schoukens, Roland Toth
Summary: In this paper, a system identification methodology is proposed to automatically select parametric model structures from a wide range of dynamic system models based on measured data. The methodology encapsulates the problem of inferring model structures and estimating model parameters within these structures in a bi-level optimization problem. The solution approach is based on genetic programming, and the empirical performance of the proposed techniques is studied using a simulation example.
Article
Cell Biology
Weronika Fic, Rebecca Bastock, Francesco Raimondi, Erinn Los, Yoshiko Inoue, Jennifer L. Gallop, Robert B. Russell, Daniel St Johnston
Summary: The study reveals that RhoGAP19D plays a crucial role in the polarity formation of follicular epithelium in fruit flies, by interacting with alpha-catenin to exclude active Cdc42 from the lateral domain and suppress epithelial invasion.
JOURNAL OF CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Stefano Scaramuzza, Daniel Castano-Diez
Summary: Subtomogram averaging (STA) is a powerful image processing technique used in electron tomography to determine the 3D structure of macromolecular complexes in their native environments. This study introduces a detailed and reproducible processing protocol that covers all aspects of particle picking and alignment in STA, based on the Dynamo software. The protocol also demonstrates how to streamline and automate parts of the processing pipeline for increased throughput.
Article
Biochemistry & Molecular Biology
Pierre De Rossi, Amanda J. Lewis, Johanna Furrer, Laura De Vos, Tomas Demeter, Aurelie Zbinden, Weijia Zhong, Vera Wiersma, Carlo Scialo, Julien Weber, Zhongning Guo, Stefano Scaramuzza, Marta Di Fabrizio, Carolin Boeing, Daniel Castano-Diez, Ashraf Al-Amoudi, Manuela Perez-Berlanga, Tammaryn Lashley, Henning Stahlberg, Magdalini Polymenidou
Summary: Pathological TDP-43 follows a prion-like cascade, but the molecular determinants of this process remain unknown. Different subtypes demonstrate distinct amplification efficiency and timeline when inoculated into cells. The resulting neoaggregates also exhibit subtype-specific characteristics, reflecting the diversity seen in patient pathology.
Article
Biochemistry & Molecular Biology
Marin Matic, Gurdeep Singh, Francesco Carli, Natalia De Oliveira Rosa, Pasquale Miglionico, Lorenzo Magni, J. Silvio Gutkind, Robert B. Russell, Asuka Inoue, Francesco Raimondi
Summary: This study demonstrates that protein language models can encode structural and functional information of GPCR sequences for predicting their signaling and functional repertoire. The researchers developed a machine learning predictor called PRECOGx, which outperforms its predecessor PRECOG in predicting GPCR-transducer couplings and considers all GPCR classes. The study also introduces new functionalities in a webserver, allowing for the projection of input sequences and analysis of sequence and structural determinants responsible for coupling.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Elena Porcellato, Juan Carlos Gonzalez-Sanchez, Constantin Ahlmann-Eltze, Mahmoud Ali Elsakka, Itamar Shapira, Juergen Fritsch, Juan Antonio Navarro, Simon Anders, Robert B. Russell, Felix T. Wieland, Christoph Metzendorf
Summary: Protein S-palmitoylation, a reversible protein modification, plays a crucial role in neuronal diseases and cancer. However, its study in Drosophila melanogaster has been limited. In this study, the palmitoylome of Drosophila S2R+ cells was analyzed, and a method called DHHC-BioID was established to identify client proteins and interaction partners of protein acyl-transferases (PATs). The results showed that S-palmitoylated proteins are conserved between mammals and Drosophila, and DHHC-BioID is a sensitive and specific method for identifying DHHC-PAT client proteins.
Article
Genetics & Heredity
Torsten Schmenger, Gaurav D. Diwan, Gurdeep Singh, Gordana Apic, Robert B. Russell
Summary: The rapid pace of genetic variant discovery is crucial for understanding their impact on biological systems. By studying genetic variants in healthy individuals, we identified potential disease-causing variants that have an impact on biological function. These findings suggest the presence of many relatively common lethal or disease-causing variants in healthy human populations.
NPJ GENOMIC MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Narcis A. Petriman, Marta Loureiro-Lopez, Michael Taschner, Nevin K. Zacharia, Magdalena M. Georgieva, Niels Boegholm, Jiaolong Wang, Andre Mourao, Robert B. Russell, Jens S. Andersen, Esben Lorentzen
Summary: Cilia are essential organelles for cellular functions such as motility, signaling, and sensory reception. In this study, the researchers used Alphafold to model the structure of the IFT-B complex, which is involved in cilium formation. The results provide insights into the assembly and function of the IFT-B complex.
Article
Multidisciplinary Sciences
Carlos Santana-Molina, Valentina Henriques, Damaso Hornero-Mendez, Damien P. Devos, Elena Rivas-Marin
Summary: This study demonstrates that C30 carotenoids are synthesized from squalene in Planctomycetes bacteria, which is the most widespread pathway in prokaryotes. The evolutionary history of carotenoid and squalene amino oxidases is used to propose an evolutionary scenario explaining the origin and diversification of these pathways.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Andrea Zanotti, Joao P. L. Coelho, Dinah Kaylani, Gurdeep Singh, Marina Tauber, Manuel Hitzenberger, Donem Avci, Martin Zacharias, Robert B. Russell, Marius K. Lemberg, Matthias J. Feige
Summary: This study reveals a previously unknown function of the human signal peptidase complex (SPC) as a membrane protein quality control factor. The SPC cleaves membrane proteins at hidden cleavage sites when they fail to fold or assemble correctly, contributing to membrane protein homeostasis and cellular fitness.
Article
Cell Biology
Mariam G. Aslanyan, Cenna Doornbos, Gaurav D. Diwan, Zeinab Anvarian, Tina Beyer, Katrin Junger, Sylvia E. C. van Beersum, Robert B. Russell, Marius Ueffing, Alexander Ludwig, Karsten Boldt, Lotte B. Pedersen, Ronald Roepman
Summary: By studying ubiquitination modifications in cells, we have identified the involvement of ESCRT-dependent clathrin-mediated endocytosis vesicles and caveolae components in ciliary function. These findings contribute to a better understanding of the mechanisms underlying cilia biology in health and disease.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Leticia Ferrelli, Matias L. Pidre, Ruben Garcia-Dominguez, Lucas N. Alberca, DMaria del Saz-Navarro, Carlos Santana-Molina, Damien P. Devos
Summary: Membrane coat proteins play a crucial role in the eukaryotic endomembrane traffic system. Prokaryotes, particularly the Planctomycetes, Verrucomicrobia, and Chlamydiae (PVC) superphylum, also possess proteins with membrane-coat architecture. This study strengthens previous structure predictions for prokaryotic membrane coat-like (MCL) proteins and identifies new MCL proteins in the Planctomycete Gemmata obscuriglobus. The function of these proteins is likely related to membrane manipulation and their abundance is primarily limited to Planctomycetes and Verrucomicrobia.
JOURNAL OF STRUCTURAL BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Fabiola De Marchi, Toni Franjkic, Paride Schito, Tommaso Russo, Jerneja Nimac, Anna A. Chami, Angelica Mele, Lea Vidatic, Jasna Kriz, Jean-Pierre Julien, Gordana Apic, Robert B. Russell, Boris Rogelj, Jason R. Cannon, Marco Baralle, Federica Agosta, Silva Hecimovic, Letizia Mazzini, Emanuele Buratti, Ivana Munitic
Summary: Proteinopathy and neuroinflammation are two main features of neurodegenerative diseases with high heterogeneity. This review focuses on ALS and FTD spectrum disorder, highlighting neuroinflammation and immune imbalance as novel therapeutic targets. Dysregulation of TDP-43 is a common mechanism in most ALS and 50% of FTD patients, leading to altered cellular events. Experimental attempts targeting TDP-43 aggregates and inflammation will be discussed.
Article
Multidisciplinary Sciences
Elena Rivas-Marin, David Moyano-Palazuelo, Valentina Henriques, Enrique Merino, Damien P. Devos
Summary: This study presents a genome-wide analysis of essential gene content in Planctopirus limnophila. The findings indicate that certain genes involved in peptidoglycan synthesis or cell division, which are essential in most bacteria, are not essential for growth under laboratory conditions in this species. Additionally, essential genes likely involved in lipopolysaccharide biosynthesis are identified, supporting the view of Planctomycetes as diderm bacteria. The study also explores the evolutionary stages of essential gene repertoire in Planctomycetes and related phyla.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Grace Mercedes Freke, Tiago Martins, Rosalind Jane Davies, Tina Beyer, Marian Seda, Emma Peskett, Naila Haq, Avishek Prasai, Georg Otto, Jeshmi Jeyabalan Srikaran, Victor Hernandez, Gaurav D. Diwan, Robert B. Russell, Marius Ueffing, Martina Huranova, Karsten Boldt, Philip L. Beales, Dagan Jenkins
Summary: Bardet-Biedl syndrome is a ciliopathy that affects multiple tissues. Research suggests that BBS1 plays a crucial role in suppressing the transition from epithelial cells to mesenchymal cells, and dysregulation of epithelial-to-mesenchymal transition genes may be a predisposing feature of BBS.