Article
Computer Science, Artificial Intelligence
Mohammad Ali Manouchehri, Mohammad Sadegh Helfroush, Habibollah Danyali
Summary: This paper introduces a strategy using non-uniform IBM methods to limit rumor propagation, determines user weights through distance-aware IBM, and develops the NU-IBM-Solver method to handle users with different weights. Experimental results show that the method is similar to greedy algorithm in effectiveness but thousands of times faster.
EXPERT SYSTEMS WITH APPLICATIONS
(2022)
Article
Computer Science, Information Systems
Simon Foucart, Deanna Needell, Reese Pathak, Yaniv Plan, Mary Wootters
Summary: The study focuses on the matrix completion problem with deterministic and possibly non-uniform observation patterns. It proposes a debiased projection scheme for recovery from noisy observations and analyzes the error under a suitable weighted metric. The theoretical guarantees upper bound the recovery error and nearly matching lower bounds showcase optimality in several regimes, demonstrating the computational efficiency and accuracy of the approach.
IEEE TRANSACTIONS ON INFORMATION THEORY
(2021)
Article
Multidisciplinary Sciences
Yenchia Feng, Nicholas T. Ouellette
Summary: By studying the mating swarms of non-biting midge Chironomus riparius, we found that the individuals in the swarm do not randomly occupy positions but have a certain internal structure.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Engineering, Electrical & Electronic
Mohammad Elmi, Martin Lee, Kambiz Moez
Summary: This paper presents an ultra-low-power nonuniform sampling scheme using a derivative-based algorithm. The scheme identifies high signal activity by measuring the change in the derivative of the signal above certain threshold values. The proposed system achieves high compression factor and low power consumption for real-world biomedical signals.
IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS I-REGULAR PAPERS
(2023)
Article
Biochemical Research Methods
Johann F. Jadebeck, Axel Theorell, Samuel Leweke, Katharina Noeh
Summary: The C++ library Highly Optimized Polytope Sampling (HOPS) offers efficient and scalable algorithms for sampling convex-constrained models with arbitrary target functions, achieving substantial performance gains for uniform sampling. The utility and ease of integration of non-uniform sampling is demonstrated in a Bayesian inference setting, showcasing interoperability with third-party software.
Article
Engineering, Biomedical
Mahmoud Alipour, Seyed Mohammad Reza Hashemi Gholpayeghani
Summary: The Lempel-Ziv algorithm is used to measure the complexity of a non-linear system. By improving this algorithm, a new non-uniform sampling method for EEG is introduced, which can compress EEG in real-time with a low computational load. The proposed method can achieve a compress ratio of 1.97 without prior knowledge or training, and by ignoring redundant samples, it increases the distinguishability of non-linear features in EEG.
BIOMEDICAL SIGNAL PROCESSING AND CONTROL
(2021)
Article
Mathematics, Applied
Alban Gossard, Frederic de Gournay, Pierre Weiss
Summary: A recent trend in the signal/image processing literature is the optimization of Fourier sampling schemes for specific datasets. This paper explains why choosing optimal non Cartesian Fourier sampling patterns is a difficult nonconvex problem by addressing two optimization issues: the existence of a combinatorial number of spurious minimizers and the vanishing gradient effect for high frequencies. The paper concludes by demonstrating how the use of large datasets and stochastic gradient algorithms with a variable metric can alleviate these issues.
Article
Optics
Weiqiang Lyu, Zhengkai Li, Lingjie Zhang, Huan Tian, Zhenwei Fu, Zhiyao Zhang, Bao Sun, Yali Zhang, Shangjian Zhang, Heping Li, Yong Liu
Summary: A new non-uniform photonic sampling strategy and signal reconstruction algorithm are proposed for digital acquisition of broadband periodic signals at a low sampling rate, reducing sampling number significantly. Simulation results show reconstructed signal information is identical to high-speed uniform photonic sampling.
Article
Engineering, Marine
Chunying Xu, Junwei Hu, Jiawang Chen, Yongqiang Ge, Ruixin Liang
Summary: Sensor placement is crucial in terrain deformation monitoring systems and significantly impacts data collection. To obtain reliable information with minimal sensors, it is essential to follow specific conditions and utilize as few sensors as possible.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2021)
Article
Environmental Sciences
Wanying Cheng, Zhao Li, Liming Yan
Summary: Temperature is the primary factor affecting plant phenology, with spring leaf unfolding dates showing a certain pattern at different latitudes. Despite temperature warming in recent years, the stability of leaf unfolding dates in spring varies across different latitudes.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Engineering, Electrical & Electronic
Ce Yang, Shiyu Su, Mike Shuo-Wei Chen
Summary: This article presents a non-uniform (NU) time approximation filter (TAF) technique for a wireless receiver (RX) to reject unwanted blockers. The proposed technique uses NU sampling (NUS) and a TAF to achieve a flexible and high attenuation filter response without changing passive component values. It also introduces a quad-switch gated integrator to reduce power consumption. The article provides theoretical analysis and a proof-of-concept implementation in the 28-nm CMOS process.
IEEE JOURNAL OF SOLID-STATE CIRCUITS
(2023)
Review
Automation & Control Systems
Xian-Ming Zhang, Qing-Long Han, Xiaohua Ge, Boda Ning, Bao-Lin Zhang
Summary: This paper presents a survey of methods and trends in non-uniform sampled-data control systems. It discusses fundamental issues of both continuous-time and discrete-time sampled-data control systems and elaborates on main methods in both domains. It also examines event-triggered sampling and reviews typical triggering mechanisms in the literature. Furthermore, it provides applications in terms of automated vehicle platoons and islanded microgrids to demonstrate the capability of sampled-data control methods.
ANNUAL REVIEWS IN CONTROL
(2023)
Article
Computer Science, Information Systems
Maria Antonia Maisto, Mario del Prete, Giovanni Leone, Rocco Pierri, Raffaele Solimene
Summary: This study addresses the problem of detecting defective turned-off elements in antenna arrays from near-field measurements. By adopting the warping sampling method, the number of measurements is reduced to positively affect the acquisition time. The performance of this new sampling strategy is compared to the usual half-wavelength sampling, and it is shown that the warping sampling method provides similar performance with fewer data.
Article
Mathematics, Applied
Kateryna Pozharska, Tino Ullrich
Summary: This study investigates the recovery of multivariate functions using a weighted least squares recovery operator from reproducing kernel Hilbert spaces. The results show that this operator yields near-optimal outcomes in various relevant situations. The application of the results provides new recovery guarantees for Sobolev type spaces related to Jacobi type differential operators and multivariate periodic Sobolev type spaces with general smoothness weight.
SIAM JOURNAL ON NUMERICAL ANALYSIS
(2022)
Article
Engineering, Electrical & Electronic
Jiannan Dong, Hongkun Li, Zhenfang Fan, Xinwei Zhao
Summary: In this article, the reconstruction of time-frequency characteristics of sparse multi-band signals using the discrete multi-coset sampling (DMCS) model was addressed. The proposed method involves the utilization of a multi-coset sliding window (MCSW) for locally windowing the discrete multi-coset sampling sequence, leading to optimal time-frequency reconstruction of the original signal. Numerical simulations demonstrated the feasibility of the method, which is significant for sub-Nyquist sampling technique research and development.
IEEE TRANSACTIONS ON VEHICULAR TECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Radoslav Z. Pavlovic, Remy F. Lalisse, Alexandar L. Hansen, Christopher A. Waudby, Zhiquan Lei, Murat Guney, Xiuze Wang, Christopher M. Hadad, Jovica D. Badjic
Summary: The molecular recognition processes of induced fit (IF) and conformational selection (CS) have been shown to play a central role in allosteric regulation in natural systems, where the substrate can either instruct the host to change its shape or the guest can select the optimal fit. A study demonstrated the potential interplay between the two mechanisms, providing insights for designing novel allosteric sequestering agents and chemosensors.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Multidisciplinary Sciences
Elena Plessa, Lien P. Chu, Sammy H. S. Chan, Oliver L. Thomas, Anais M. E. Cassaignau, Christopher A. Waudby, John Christodoulou, Lisa D. Cabrita
Summary: Proteins can fold co-translationally during biosynthesis, with misfolding potentially causing disease. The alpha-1-antitrypsin protein folds under kinetic control, and misfolding may initiate from co-translational structures. Co-translational folding intermediates could drive how some proteins fold under kinetic control, serving as potential therapeutic targets for human disease.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Christopher A. Waudby, Charles Burridge, Lisa D. Cabrita, John Christodoulou
Summary: This article reviews recent progress in understanding the process by which a nascent chain attains its full native stability and how interactions with the nearby ribosome surface can perturb or modulate this process.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Sammy H. S. Chan, Tomasz Wlodarski, Julian O. Streit, Anais M. E. Cassaignau, Lauren F. Woodburn, Minkoo Ahn, Georg Johannes Freiherr von Sass, Christopher A. Waudby, Nediljko Budisa, Lisa D. Cabrita, John Christodoulou
Summary: Translation: We developed a method to label nascent chains and used NMR spectroscopy to detect and measure multiple states during protein synthesis, revealing the role of the ribosome in the folding process.
Article
Multidisciplinary Sciences
Minkoo Ahn, Tomasz Wlodarski, Alkistis Mitropoulou, Sammy H. S. Chan, Haneesh Sidhu, Elena Plessa, Thomas A. Becker, Nediljko Budisa, Christopher A. Waudby, Roland Beckmann, Anais M. E. Cassaignau, Lisa D. Cabrita, John Christodoulou
Summary: The structure and surface of the ribosome exit tunnel modulate the free energy of cotranslational protein folding through variations in protein loops. The shape of the tunnel, dynamic interactions between the ribosome surface and the unfolded nascent chain, and altered exit pathway influence the folding outcome.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Robert Creutznacher, Thorben Maass, Jasmin Dulfer, Clara Feldmann, Veronika Hartmann, Miranda Sophie Lane, Jan Knickmann, Leon Torben Westermann, Lars Thiede, Thomas J. Smith, Charlotte Uetrecht, Alvaro Mallagaray, Christopher A. Waudby, Stefan Taube, Thomas Peters
Summary: The VP1 proteins of murine and human norovirus exhibit distinct behaviors and are differentially regulated by the binding of glycochenodeoxycholic acid.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Radoslav Z. Pavlovic, Lei Zhiquan, Tyler J. Finnegan, Christopher A. Waudby, Xiuze Wang, Vageesha W. Liyana Gunawardana, Xingrong Zhu, Curt M. Wong, Taylor Hamby, Curtis E. Moore, Nicole Hoefer, David W. McComb, Christo S. Sevov, Jovica D. Badjic
Summary: In this study, a synthetic method for incorporating arenes into closed tubes, called capsularenes, is described. Different-sized capsularenes were prepared and characterized using various techniques. The capsularenes showed exceptional properties, indicating their potential for the construction of novel organic electronic devices.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Correction
Multidisciplinary Sciences
Minkoo Ahn, Tomasz Wlodarski, Alkistis Mitropoulou, Sammy H. S. Chan, Haneesh Sidhu, Elena Plessa, Thomas A. Becker, Nediljko Budisa, Christopher A. Waudby, Roland Beckmann, Anais M. E. Cassaignau, Lisa D. Cabrita, John Christodoulou
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Christopher A. Waudby, Saul Alvarez-Teijeiro, E. Josue Ruiz, Simon Suppinger, Nikos Pinotsis, Paul R. Brown, Axel Behrens, John Christodoulou, Anastasia Mylona
Summary: Protein phosphorylation regulates cellular signaling, and the phosphorylation of c-JUN at multiple sites controls various functional states in signal response.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Joseph F. Thole, Christopher A. Waudby, Gary J. Pielak
Summary: The biophysical characterization of protein-protein interactions involving disordered proteins is challenging. Although simplifications can be made, such as measuring the thermodynamics and kinetics using peptides with minimum residues, these methods do not provide a complete understanding of the interactions.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Tinna Palmadottir, Christopher A. Waudby, Katja Bernfur, John Christodoulou, Sara Linse, Anders Malmendal
Summary: In this study, two morphologically distinct α-synuclein fibrils were observed under identical conditions. The two fibrils, A and B, were found to have different surface properties and solubility. Over time, fibrils of morphology A gradually transformed into morphology B.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Radoslav Z. Pavlovic, Tyler J. Finnegan, Anna Metlushko, Alexandar L. Hansen, Christopher A. Waudby, Xiuze Wang, Nicole Hoefer, David W. McComb, Aleksandar Pavic, Nikola Plackic, Jovana Novakovic, Jovana Bradic, Nevena Jeremic, Vladimir Jakovljevic, Biljana Smit, Sanja Matic, Matias A. Alvarez-Saavedra, Ivan Capo, Curtis E. Moore, Samuel I. Stupp, Jovica D. Badjic
Summary: This study describes the preparation, dynamic, and assembly characteristics of a vase-shaped basket and its ability to form an inclusion complex with the anticancer drug mitoxantrone. The results of various measurements indicate that the basket can exist as a dimer, in equilibrium with relaxed and squeezed monomers. The basket can include mitoxantrone in its pocket, forming a stable binary complex. The basket shows nontoxic behavior in vitro and a reduced cytotoxicity in the presence of mitoxantrone.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Multidisciplinary Sciences
Anna C. Papageorgiou, Michaela Pospisilova, Jakub Cibulka, Raghib Ashraf, Christopher A. Waudby, Pavel Kaderavek, Volha Maroz, Karel Kubicek, Zbynek Prokop, Lumir Krejci, Konstantinos Tripsianes
Summary: In this study, the authors propose a three-step charge-driven coacervation model involving dynamic complexes between a positively charged IDR of human RECQ4 and G-quadruplexes. The IDR also interacts with Replication Protein A, implying RECQ4's regulatory role.
NATURE COMMUNICATIONS
(2023)
Meeting Abstract
Biophysics
Julian O. Streit, Ivana V. Bukvin, Charity Hornby, Tomasz Wlodarski, Haneesh Sidhu, Christopher A. Waudby, Lisa D. Cabrita, Anais M. Cassaignau, John Christodoulou
BIOPHYSICAL JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Charles Burridge, Christopher A. Waudby, Tomasz Wlodarski, Anais M. E. Cassaignau, Lisa D. Cabrita, John Christodoulou
Summary: This study used solution-state NMR spectroscopy to measure transverse proton relaxation rates for methyl groups in folded ribosome-nascent chain complexes, revealing interactions between the nascent chain and ribosome surface driven predominantly by electrostatics. By observing changes in these interactions as subsequent domain emerges, the impact on free energy landscapes associated with co-translational folding process can be deduced.