Review
Biochemistry & Molecular Biology
Gunnar Jeschke
Summary: Labeling techniques such as EPR spectroscopy and single-molecule FRET can accurately measure distances within the range of tens of angstroms, providing valuable information for structural modeling of proteins and protein complexes. However, challenges such as limited restraints, label interference, and balancing fitting quality still need to be addressed for further progress in this field.
Article
Biochemistry & Molecular Biology
Irina Ritsch, Laura Esteban-Hofer, Elisabeth Lehmann, Leonidas Emmanouilidis, Maxim Yulikov, Frederic H-T Allain, Gunnar Jeschke
Summary: The study investigates the impact of deviation of conformational ensemble of intrinsically disordered proteins from random coil on their function, and discusses the quantification of this deviation through distance distributions. By analyzing two proteins, it examines whether deviation from random coil can be detected by distance distributions, and proposes a solution to tackle this issue.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Meteorology & Atmospheric Sciences
Simon T. K. Lang, Andrew Dawson, Michail Diamantakis, Peter Dueben, Samuel Hatfield, Martin Leutbecher, Tim Palmer, Fernando Prates, Christopher D. Roberts, Irina Sandu, Nils Wedi
Summary: Reducing the numerical precision of ECMWF's IFS forecast model from double to single precision results in significant computational savings, allowing for an earlier increase in vertical resolution of operational ensemble forecasts and improving forecast skill for all lead times and the mean model climate. The upgrade to 137 levels harmonises vertical resolution across different types of forecasts and will run operationally at single precision from IFS model cycle 47R2 onwards.
QUARTERLY JOURNAL OF THE ROYAL METEOROLOGICAL SOCIETY
(2021)
Article
Computer Science, Artificial Intelligence
Bin Liu, Konstantinos Blekas, Grigorios Tsoumakas
Summary: Class imbalance is a common challenge in multi-label data, and sampling techniques can be an effective strategy to address it. The imbalance level within the local neighborhood of minority class examples is crucial for performance degradation. The proposed sampling approaches, MLSOL and MLUL, are effective in alleviating the local label imbalance and improving performance on multi-label datasets.
PATTERN RECOGNITION
(2022)
Editorial Material
Hematology
Jose A. Cancelas
Summary: In this study, An et al. introduced a new method to generate rare red blood cell (RBC) reagents for antibody screening. By using a combination of human induced pluripotent stemcell (iPSC) reprogramming and gene editing, the authors engineered RBCs lacking the RH locus and expressing low-prevalence antigenic variants. These Rh-engineered RBCs are compatible with standard laboratory assays and can detect the presence of plasma alloantibodies against low-prevalence allelic variants.
Article
Biochemical Research Methods
Yushuang Liu, Shuping Jin, Hongli Gao, Xue Wang, Congjing Wang, Weifeng Zhou, Bin Yu
Summary: This article proposes a novel method called ML-locMLFE, which can effectively predict the multi-label subcellular localization of proteins and has obvious advantages. By using different feature extraction methods and information processing methods, this method demonstrates good accuracy in predicting the protein localization of diseases such as SARS-CoV-2.
Article
Computer Science, Artificial Intelligence
Jiabin Liu, Zhiquan Qi, Bo Wang, YingJie Tian, Yong Shi
Summary: In this paper, a multi-task pipeline called SELF-LLP is proposed for learning from label proportions (LLP) problem. By leveraging self-supervised learning and self-ensemble strategy, the method makes full use of the information contained in the data and model themselves, leading to improved classification performance and training efficiency.
PATTERN RECOGNITION
(2022)
Article
Physics, Multidisciplinary
Kohei Shiota, Akito Inui, Yuta Hosaka, Ryoga Amano, Yoshichika Onuki, Masato Hedo, Takao Nakama, Daichi Hirobe, Jun-ichiro Ohe, Jun-ichiro Kishine, Hiroshi M. Yamamoto, Hiroaki Shishido, Yoshihiko Togawa
Summary: A spin-polarized state was studied in chiral disilicide crystals NbSi2 and TaSi2 at room temperature without magnetic fields, where long-range spin transport occurred over ten micrometers. The conversion coefficient in the current-voltage characteristics adhered to a sum rule, while a diamagnetic nature suggested itinerant electron spins rather than localized ones were responsible for the spin polarization. In addition, a robust protection of spin polarization was observed in chiral crystals over long distances.
PHYSICAL REVIEW LETTERS
(2021)
Article
Materials Science, Multidisciplinary
O. Prokhnenko, G. Marmorini, S. E. Nikitin, D. Yamamoto, A. Gazizulina, M. Bartkowiak, A. N. Ponomaryov, S. A. Zvyagin, H. Nojiri, I. F. Diaz-Ortega, L. M. Anovitz, A. Kolesnikov, A. Podlesnyak
Summary: The high-field magnetic properties and magnetic order of the gem mineral green dioptase Cu-6[Si6O18] center dot 6H(2)O have been studied through single-crystal neutron diffraction, revealing orientation changes of Cu2+ moments under different magnetic field conditions, and a smooth evolution of the magnetic structure with magnetic field changes, which is in line with a certain model.
Article
Automation & Control Systems
Yi-Bo Wang, Jun-Yi Hang, Min-Ling Zhang
Summary: Multi-label learning aims to assign a set of relevant class labels for an unseen instance by extracting label-specific features.
IEEE-CAA JOURNAL OF AUTOMATICA SINICA
(2022)
Article
Computer Science, Information Systems
Yaojin Lin, Qinghua Hu, Jinghua Liu, Xingquan Zhu, Xindong Wu
Summary: This article proposes a multi-label learning algorithm MULFE, which combines multiple label-specific feature spaces, label correlations, and weighted ensemble principle to achieve the maximum margin multi-label classification goal. Experimental studies on 10 public datasets demonstrate the effectiveness of MULFE in achieving accurate multi-label classification.
ACM TRANSACTIONS ON KNOWLEDGE DISCOVERY FROM DATA
(2022)
Article
Optics
Long-Gang Huang, Xuanchen Zhang, Yanzhen Wang, Zhenxing Hua, Yuanjiang Tang, Yong-Chun Liu
Summary: Spin squeezing is crucial for quantum metrology and quantum information science, but its generation faces challenges due to the lack of squeezing interactions in existing physical systems. In this study, we propose a universal scheme to generate spin squeezing in coupled spin models with collective spin-spin interactions. We can transform the coupled spin interactions into squeezing interactions and achieve extreme squeezing with Heisenberg-limited measurement precision scaling as 1/N for N particles. Only constant and continuous driving fields are required, making it accessible for current realistic experiments. This work greatly expands the systems capable of generating Heisenberg-limited spin squeezing, with broad applications in quantum precision measurement.
Article
Computer Science, Information Systems
Xiaoyan Zhu, Jiaxuan Li, Jingtao Ren, Jiayin Wang, Guangtao Wang
Summary: This study proposes a new method called MLDE for solving the multi-label classification problem. It selects the most competent ensemble of base classifiers to predict each unseen instance, effectively utilizing label correlation and achieving better performance.
INFORMATION SCIENCES
(2023)
Article
Astronomy & Astrophysics
Martin M. Roth, George H. Jacoby, Robin Ciardullo, Brian D. Davis, Owen Chase, Peter M. Weilbacher
Summary: This study explores the potential of the DELF technique using archival MUSE data, demonstrating its superiority in high surface brightness regions of galaxies and validating its effectiveness through data analysis of early-type and late-type spiral galaxies. The technique is capable of producing precise [O iii] photometry out to distances of 40 Mpc under excellent observing conditions, while also discriminating between different emission-line objects. These capabilities make MUSE a valuable tool for measuring PNLF distances beyond traditional methods and constraining the local value of the Hubble constant.
ASTROPHYSICAL JOURNAL
(2021)
Article
Mathematics, Applied
Eda Oktay, Erin Carson
Summary: The study demonstrates that different mixed-precision iterative algorithms for solving linear systems can achieve good balance between performance and accuracy. By combining different precision combinations and algorithms in a multi-stage approach, usability and convergence are further improved.
NUMERICAL LINEAR ALGEBRA WITH APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Lisa M. Pietrek, Lukas S. Stelzl, Gerhard Hummer
Summary: Disordered proteins and nucleic acids are important in cellular function and disease. This review discusses recent advances in computationally exploring the dynamics of flexible biomolecules. While molecular dynamics simulation has improved, large-scale computing resources and validation are needed for simulating full-length disordered biopolymers. Hierarchical chain growth is a computationally efficient alternative that combines chain fragments into detailed biomolecular structures. Applications to neurodegeneration-linked proteins highlight the use of hierarchical chain growth, and connections to AI-based structural modeling are also discussed.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Soeren von Buelow, Mateusz Sikora, Florian E. C. Blanc, Roberto Covino, Gerhard Hummer
Summary: Since the start of the COVID-19 pandemic, the emergence of new variants has hindered the effectiveness of vaccines and made achieving herd immunity difficult. However, through molecular dynamics simulations of a SARS-CoV-2 spike protein model, researchers have found that the accessibility of antibodies to regions beyond the glycan shield can predict mutated positions in important variants like Omicron. This understanding of viral evolution and immune defense can help in predicting future mutation activity and escape from antibody-based immune responses.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Chemistry, Physical
Balazs Fabian, Sebastian Thallmair, Gerhard Hummer
Summary: Artificial temperature gradients were observed in MD simulations of phase-separating ternary lipid mixtures using the Martini 2 force field. This was traced back to insufficiently converged bond length constraints caused by default settings and time steps in the linear constraint solver (LINCS). By optimizing the constraint scaffold of cholesterol with equimomental arrangement of virtual sites, the bond constraint convergence can be accelerated while maintaining the original cholesterol force field and dynamics.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Jakob Tomas Bullerjahn, Soren von Bulow, Maziar Heidari, Jerome Henin, Gerhard Hummer
Summary: In molecular dynamics simulations, the size and shape of the simulation box may vary over time. Unbounded position displacements can occur when rescaling the box by the barostat for particle images far from the origin. This necessitates careful trajectory unwrapping and rewrapping methods for accurate calculations of translational diffusion coefficients.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Multidisciplinary Sciences
Miao Yu, Maziar Heidari, Sofya Mikhaleva, Piau Siong Tan, Sara Mingu, Hao Ruan, Christopher D. Reinkemeier, Agnieszka Obarska-Kosinska, Marc Siggel, Martin Beck, Gerhard Hummer, Edward A. Lemke
Summary: This study investigates the conformation of FG nucleoporin NUP98 inside the mammalian nuclear pore complex. The researchers used synthetic biology and time-resolved fluorescence microscopy to directly probe the structure in live cells and permeabilized cells. They found that the channel provides a "good solvent" environment, allowing the FG domain to adopt expanded conformations and control transport between the nucleus and cytoplasm.
Article
Multidisciplinary Sciences
Alexis Gonzalez, Adriana Covarrubias-Pinto, Ramachandra M. Bhaskara, Marius Glogger, Santosh K. Kuncha, Audrey Xavier, Eric Seemann, Mohit Misra, Marina E. Hoffmann, Bastian Braeuning, Ashwin Balakrishnan, Britta Qualmann, Volker Doetsch, Brenda A. Schulman, Michael M. Kessels, Christian A. Huebner, Mike Heilemann, Gerhard Hummer, Ivan Dikic
Summary: The endoplasmic reticulum (ER) can be remodeled through a selective autophagy pathway called ER-phagy. This study identified that ubiquitination of the ER-phagy receptor FAM134B promotes receptor clustering and binding to LC3B, stimulating ER-phagy. The results reveal the importance of ubiquitination in enhancing ER-phagy and controlling ER remodeling.
Article
Multidisciplinary Sciences
Hector Foronda, Yangxue Fu, Adriana Covarrubias-Pinto, Hartmut T. Bocker, Alexis Gonzalez, Eric Seemann, Patricia Franzka, Andrea Bock, Ramachandra M. M. Bhaskara, Lutz Liebmann, Marina E. E. Hoffmann, Istvan Katona, Nicole Koch, Joachim Weis, Ingo Kurth, Joseph G. G. Gleeson, Fulvio Reggiori, Gerhard Hummer, Michael M. M. Kessels, Britta Qualmann, Muriel Mari, Ivan Dikic, Christian A. A. Huebner
Summary: Membrane-shaping proteins containing reticulon homology domains are crucial for dynamic remodelling of the endoplasmic reticulum (ER). FAM134B is an example of such a protein, which mediates the degradation of ER sheets through a process called selective autophagy (ER-phagy) by binding to LC3 proteins. Mutations in FAM134B result in a neurodegenerative disorder in humans.
Article
Biochemistry & Molecular Biology
Di Wu, Ahmad R. R. Mehdipour, Franziska Finke, Hojjat G. G. Goojani, Roan R. R. Groh, Tamara N. N. Grund, Thomas M. B. Reichhart, Rita Zimmermann, Sonja Welsch, Dirk Bald, Mark Shepherd, Gerhard Hummer, Schara Safarian
Summary: CydDC is a protein transporter responsible for the transport of heme, a redox-active cofactor, from the cytoplasm to the respiratory chain complexes, playing a crucial role in cellular respiration. Through the integrated use of cellular, biochemical, structural and computational methods, the structure and function of CydDC, as well as its mechanism in the functional maturation of cytochrome bd, have been revealed.
NATURE CHEMICAL BIOLOGY
(2023)
Correction
Multidisciplinary Sciences
Rong Zhu, Daniel Canena, Mateusz Sikora, Miriam Klausberger, Hannah Seferovic, Ahmad Reza Mehdipour, Lisa Hain, Elisabeth Laurent, Vanessa Monteil, Gerald Wirnsberger, Ralph Wieneke, Robert Tampe, Nikolaus F. Kienzl, Lukas Mach, Ali Mirazimi, Yoo Jin Oh, Josef M. Penninger, Gerhard Hummer, Peter Hinterdorfer
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Wout Oosterheert, Florian E. C. Blanc, Ankit Roy, Alexander Belyy, Micaela Boiero Sanders, Oliver Hofnagel, Gerhard Hummer, Peter Bieling, Stefan Raunser
Summary: This study reveals the mechanism of inorganic phosphate (Pi) release from actin through a 'molecular backdoor' by combining cryo-EM, molecular-dynamics simulations, and in vitro reconstitution. The backdoor opens transiently through amino acid rearrangements, explaining the rapid release of Pi from the filament end and slow release from internal subunits. The study also finds that a disease-linked actin variant distorts the backdoor arrangement, resulting in accelerated Pi release.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Clara Lettl, Franziska Schindele, Ahmad Reza Mehdipour, Thomas Steiner, Diana Ring, Ruth Brack-Werner, Baerbel Stecher, Wolfgang Eisenreich, Ursula Bilitewski, Gerhard Hummer, Matthias Witschel, Wolfgang Fischer, Rainer Haas
Summary: Respiratory complex I plays an important role in cellular respiration of both eukaryotic cells and bacteria. The inhibition of complex I by mitochondrial complex I inhibitors can selectively kill Helicobacter pylori, a Gram-negative bacterial pathogen, while leaving other bacteria unaffected. The unique composition of the quinone-binding pocket in H. pylori complex I is responsible for this hypersensitivity, suggesting the potential of developing complex I inhibitors as narrow-spectrum antimicrobial agents against H. pylori.
CELL CHEMICAL BIOLOGY
(2023)
Article
Computer Science, Interdisciplinary Applications
Hendrik Jung, Roberto Covino, A. Arjun, Christian Leitold, Christoph Dellago, Peter G. Bolhuis, Gerhard Hummer
Summary: A machine learning algorithm accelerates the sampling of rare assembly events, uncovers their mechanisms, extrapolates them across chemical and thermodynamic space, and condenses the learned assembly mechanisms into a human-interpretable form.
NATURE COMPUTATIONAL SCIENCE
(2023)
Article
Chemistry, Physical
Hyuntae Kim, Balazs Fabian, Gerhard Hummer
Summary: This study highlights the issues of membrane deformation and pressure imbalance in molecular dynamics simulations when using default parameters. The problems are mainly caused by missed nonbonded interactions and unbalanced pressure tensor, which result from improper parameter settings.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Multidisciplinary Sciences
Amir Pandi, David Adam, Amir Zare, Van Tuan Trinh, Stefan L. Schaefer, Marie Burt, Bjorn Klabunde, Elizaveta Bobkova, Manish Kushwaha, Yeganeh Foroughijabbari, Peter Braun, Christoph Spahn, Christian Preusser, Elke Pogge von Strandmann, Helge B. Bode, Heiner von Buttlar, Wilhelm Bertrams, Anna Lena Jung, Frank Abendroth, Bernd Schmeck, Gerhard Hummer, Olalla Vazquez, Tobias J. Erb
Summary: This study demonstrates the potential of using deep learning and cell-free protein synthesis for the rapid and cost-effective production and testing of bioactive peptides. Through computational methods and experimental validation, the authors identified 30 functional peptides, including six with broad-spectrum activity against drug-resistant pathogens.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Alfred W. Bronkhorst, Chop Y. Lee, Martin M. Moeckel, Sabine Ruegenberg, Antonio M. de Jesus Domingues, Sheraz Sadouki, Rossana Piccinno, Tetsutaro Sumiyoshi, Mikiko C. Siomi, Lukas Stelzl, Katja Luck, Rene F. Ketting
Summary: In this study, it was demonstrated that BmGtsf1L, a homolog of Gtsf1, binds to piRNA-loaded BmAgo3 and localizes to specific granules in silkworm cells. The study further identified a binding interface on the BmVreteno-eTudor domain that connects piRNA-loaded BmAgo3 and BmGtsf1L.
