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Revealing the small proteome of Haloferax volcanii by combining ribosome profling and small-protein optimized mass spectrometry

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MicroLife 2023年第4期4卷 uqad001页

作者： Hadjeras, Lydia Bartel, Jürgen Maier, Lisa-Katharina Maaß, Sandra Vogel, Verena Svensson, Sarah L. Eggenhofer, Florian Gelhausen, Rick Müller, Teresa Alkhnbashi, Omer S. Backofen, Rolf Becher, Dörte Sharma, Cynthia M. Marchfelder, Anita Department of Molecular Infection Biology II Institute of Molecular Infection Biology (IMIB) University of Würzburg Josef-Schneider-Straße 2 / D15 Würzburg 97080 Germany Department of Microbial Proteomics Institute of Microbiology University of Greifswald Felix-Hausdorff-Str. 8 Greifswald 17489 Germany Ulm University Albert-Einstein-Allee 11 Ulm 89081 Germany Bioinformatics Group Department of Computer Science University of Freiburg Georges-Koehler-Allee 106 Freiburg 79110 Germany Information and Computer Science Department King Fahd University of Petroleum and Minerals Dhahran 31261 Saudi Arabia Signalling Research Centres BIOSS and CIBSS University of Freiburg Schaenzlestr. 18 Freiburg 79104 Germany

In contrast to extensively studied prokaryotic 'small' transcriptomes (encompassing all small noncoding RNAs), small proteomes (here defned as including proteins ≤70 aa) are only now entering the limelight. The absence of a complete small protein catalogue in most prokaryotes precludes our understanding of how these molecules affect physiology. So far, archaeal genomes have not yet been analyzed broadly with a dedicated focus on small proteins. Here, we present a combinatorial approach, integrating experimental data from small protein-optimized mass spectrometry (MS) and ribosome profling (Ribo-seq), to generate a high confdence inventory of small proteins in the model archaeon Haloferax volcanii. We demonstrate by MS and Ribo-seq that 67% of the 317 annotated small open reading frames (sORFs) are translated under standard growth conditions. Furthermore, annotation-independent analysis of Ribo-seq data showed ribosomal engagement for 47 novel sORFs in intergenic regions. A total of seven of these were also detected by proteomics, in addition to an eighth novel small protein solely identifed by MS. We also provide independent experimental evidence in vivo for the translation of 12 sORFs (annotated and novel) using epitope tagging and western blotting, underlining the validity of our identifcation scheme. Several novel sORFs are conserved in Haloferax species and might have important functions. Based on our fndings, we conclude that the small proteome of H. volcanii is larger than previously appreciated, and that combining MS with Ribo-seq is a powerful approach for the discovery of novel small protein coding genes in archaea. © The Author(s) 2023.

关键词： archaea Haloferax volcanii mass spectrometry proteomics Ribo-seq ribosome profling small protein small proteome sORF sprotein

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Spontaneous Chirality Flipping in an Orthogonal Spin-Charge Ordered Topological Magnet

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Physical Review X 2024年第1期14卷 011053-011053页

作者： H. Miao J. Bouaziz G. Fabbris W. R. Meier F. Z. Yang H. X. Li C. Nelson E. Vescovo S. Zhang A. D. Christianson H. N. Lee Y. Zhang C. D. Batista S. Blügel Materials Science and Technology Division Oak Ridge National Laboratory Oak Ridge Tennessee 37831 USA Peter Grünberg Institut and Institute for Advanced Simulation Forschungszentrum Jülich and JARA D-52425 Jülich Germany Advanced Photon Source Argonne National Laboratory Argonne Illinois 60439 USA Department of Materials Science and Engineering University of Tennessee Knoxville Tennessee USA Advanced Materials Thrust The Hong Kong University of Science and Technology (Guangzhou) Guangzhou China National Synchrotron Light Source II Brookhaven National Laboratory Upton New York 11973 USA Max-Planck-Institut fur Physik komplexer Systeme Nothnitzer Straße 38 01187 Dresden Germany Department of Physics and Astronomy The University of Tennessee Knoxville Tennessee 37996 USA Min H. Kao Department of Electrical Engineering and Computer Science University of Tennessee Knoxville Tennessee 37996 USA Quantum Condensed Matter Division and Shull-Wollan Center Oak Ridge National Laboratory Oak Ridge Tennessee 37831 USA

The asymmetric distribution of chiral objects with opposite chirality is of great fundamental interest ranging from molecular biology to particle physics. In quantum materials, chiral states can build on inversion-symmetry-breaking lattice structures or emerge from spontaneous magnetic ordering induced by competing interactions. Although the handedness of a chiral state can be changed through external fields, a spontaneous chirality flipping has yet to be discovered. We present experimental evidence of chirality flipping via changing temperature in a topological magnet EuAl4, which features orthogonal spin density waves (SDW) and charge density waves (CDW). Using circular dichroism of Bragg peaks in the resonant magnetic x-ray scattering, we find that the chirality of the helical SDW flips through a first-order phase transition with modified SDW wavelength. Intriguingly, we observe that the CDW couples strongly with the SDW and displays a rare commensurate-to-incommensurate transition at the chirality flipping temperature. Combining with first-principles calculations and angle-resolved photoemission spectroscopy, our results support a Fermi surface origin of the helical SDW with intertwined spin, charge, and lattice degrees of freedom in EuAl4. Our results reveal an unprecedented spontaneous chirality flipping and lay the groundwork for a new functional manipulation of chirality through momentum-dependent spin-charge-lattice interactions.

关键词： Charge density waves Chirality Magnetic order Magnetic texture 3-dimensional systems Electron-correlation calculations X-ray diffraction X-ray magnetic circular dichroism

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Exploring the large-Nc limit with one quark flavour 39

Exploring the large-Nc limit with one quark flavour

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39th International Symposium on Lattice Field Theory, LATTICE 2022

作者： Della Morte, Michele Jäger, Benjamin Martins, Sofie Sannino, Francesco Tsang, J. Tobias Ziegler, Felix P.G. CP3-Origins Dept. of Mathematics and Computer Science University of Southern Denmark Campusvej 55 Odense M5230 Denmark Danish Institute for Advanced Study University of Southern Denmark Campusvej 55 Odense M5230 Denmark CP3-Origins Dept. of Physics Chemistry and Pharmacy University of Southern Denmark Campusvej 55 Odense M5230 Denmark Dipartimento di Fisica "E. Pancini" Università di Napoli Federico II INFN Sezione di Napoli Complesso Universitario di Monte S. Angelo Edificio 6 via Cintia Napoli80126 Italy Department of Theoretical Physics CERN Geneva 231211 Switzerland School of Physics and Astronomy The University of Edinburgh EdinburghEH9 3FD United Kingdom

We use one-flavour QCD (Nc = 3) as a proxy to understand N = 1 SYM. For our simulations, we use tree-level improved Wilson fermions and a Symanzik improved gauge action. The hadron spectrum is obtained by using LapH smearing for different masses and simulation volumes. We also report on our efforts to increase the number of colours in our simulations, where we find that the simulations show increasing topological freezing for larger Nc © Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND 4.0).

关键词： Lattice theory

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Inferring the 3D Standing Spine Posture from 2D Radiographs

arXiv

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arXiv 2020年

作者： Bayat, Amirhossein Sekuboyina, Anjany Paetzold, Johannes C. Payer, Christian Stern, Darko Urschler, Martin Kirschke, Jan S. Menze, Bjoern H. Department of Informatics Technical University of Munich Germany Department of Neuroradiology Klinikum rechts der Isar Germany Institute of Computer Graphics and Vision Graz University of Technology Austria School of Computer Science University of Auckland New Zealand

The treatment of degenerative spinal disorders requires an understanding of the individual spinal anatomy and curvature in 3D. An upright spinal pose (i.e. standing) under natural weight bearing is crucial for such bio-mechanical analysis. 3D volumetric imaging modalities (e.g. CT and MRI) are performed in patients lying down. On the other hand, radiographs are captured in an upright pose, but result in 2D projections. This work aims to integrate the two realms, i.e. it combines the upright spinal curvature from radiographs with the 3D vertebral shape from CT imaging for synthesizing an upright 3D model of spine, loaded naturally. Specifically, we propose a novel neural network architecture working vertebra-wise, termed TransVert, which takes orthogonal 2D radiographs and infers the spine’s 3D posture. We validate our architecture on digitally reconstructed radiographs, achieving a 3D reconstruction Dice of 95.52%, indicating an almost perfect 2D-to-3D domain translation. Deploying our model on clinical radiographs, we successfully synthesise full-3D, upright, patient-specific spine models for the first time. Copyright © 2020, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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Efficient Recovery of Multi-Camera Motion from Two Affine Correspondences

Efficient Recovery of Multi-Camera Motion from Two Affine Co...

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IEEE International Conference on Robotics and Automation (ICRA)

作者： Banglei Guan Ji Zhao Daniel Barath Friedrich Fraundorfer College of Aerospace Science and Engineering National University of Defense Technology China Centre for Machine Perception Czech Technical University Czech Republic Machine Perception Research Laboratory MTA SZTAKI Hungary Institute for Computer Graphics and Vision Graz University of Technology Austria Remote Sensing Technology Institute German Aerospace Center Germany

We propose an efficient method to estimate the relative pose of a multi-camera system from a minimum of two affine correspondences (ACs). Our solution is novel as it computes the 6DOF relative pose by utilizing a first-order rotation approximation. We directly derive a single polynomial based on the constraint between ACs and the generalized camera model. Then a closed-form solution is found analytically and it produces an accurate relative pose estimation efficiently. Benefiting from the low number of exploited correspondences and the speed of the solver, it speeds up robust estimators, e.g. RANSAC, significantly. The proposed method is evaluated both on synthetic data and real-world image sequences from the KITTI benchmark. It is shown that the proposed solver is superior to the state-of-the-art algorithms in terms of accuracy.

关键词： Closed-form solutions Automation Computational modeling Roads Conferences Pose estimation Benchmark testing

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Interplay of Machine Learning and Software Engineering for Quality Estimations

Interplay of Machine Learning and Software Engineering for Q...

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2020 IEEE International Conference on Communications, Computing, Cybersecurity, and Informatics, CCCI 2020

作者： Abubakar, Hamza Obaidat, M.S. Gupta, Aaryan Bhattacharya, Pronaya Tanwar, Sudeep Institute of Technology Nirma University Department of Computer Science and Engineering Ahmedabad Gujarat India College of Computing and Informatics University of Sharjah Sharjah27272 United Arab Emirates King Abdullah II School of Information Technology University of Jordan Amman11942 Jordan University of Science and Technology Beijing Beijing10008 China

ISBN: (纸本)9781728120355

In this era, the agile mindset has innovated the traditional software engineering (SE) process through the integration of DevOps flow engines, scrum iterations, and automation of continuous integration (CI) and continuous deployment (CD) cycles. However, the CI/CD integration requires manual code-revisions and refactoring at large scales. Recently, machine-learning (ML) is employed in SE that allows legacy codes to be highly dynamic, less coupling in related modules, automatic code versioning, and refactoring, with less coupling among related modules. However, over time, ML models tend to become bulky, with increasing monotonic losses during model training. To address this, SE techniques like code revisions are employed over ML codes to allow low-order training losses, that enables seamless and precise workflow structures. Motivated from the aforementioned discussions, the paper presents a systematic review of the close interplay of SE and ML and possible interactions in different applications. Suitable research questions and case studies are presented for possible adoption scenarios that depict the close ML-SE interplay share with each other, with the concluding remarks. The paper forms useful insights for ML engineers, data science practitioners, and SE quality estimators towards the building of efficient and scalable software solutions. © 2020 IEEE.

关键词： Machine learning

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Towards computer-Using Personal Agents

arXiv

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arXiv 2025年

作者： Bonatti, Piero A. Domingue, John Gentile, Anna Lisa Harth, Andreas Hartig, Olaf Hogan, Aidan Hose, Katja Jimenez-Ruiz, Ernesto McGuinness, Deborah L. Sun, Chang Verborgh, Ruben Wright, Jesse University of Naples Federico II Naples Italy Knowledge Media Institute The Open University Milton Keynes United Kingdom IBM Research San JoseCA United States Friedrich-Alexander-Universität Erlangen-Nürnberg Fraunhofer Institute for Integrated Circuits IIS Nürnberg Germany Linköping University Linköping Sweden DCC Universidad de Chile IMFD Santiago Chile TU Wien Vienna Austria City St George’s University of London London United Kingdom Rensselaer Polytechnic Institute TroyNY United States Maastricht University Maastricht Netherlands IDLab ELIS Ghent University imec Ghent Belgium Department of Computer Science University of Oxford Oxford United Kingdom

computer-Using Agents (CUA) enable users to automate increasingly-complex tasks using graphical interfaces such as browsers. As many potential tasks require personal data, we propose computer-Using Personal Agents (CUPAs) that have access to an external repository of the user’s personal data. Compared with CUAs, CUPAs offer users better control of their personal data, the potential to automate more tasks involving personal data, better interoperability with external sources of data, and better capabilities to coordinate with other CUPAs in order to solve collaborative tasks involving the personal data of multiple users. © 2025, CC BY.

关键词： Interoperability

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Automated cross-sectional view selection in CT angiography of aortic dissections with uncertainty awareness and retrospective clinical annotations

arXiv

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arXiv 2021年

作者： Pepe, Antonio Egger, Jan Codari, Marina Willemink, Martin J. Gsaxner, Christina Li, Jianning Roth, Peter M. Mistelbauer, Gabriel Schmalstieg, Dieter Fleischmann, Dominik Graz University of Technology Institute of Computer Graphics and Vision Inffeldgasse 16/II Graz8010 Austria Stanford University School of Medicine 3D and Quantitative Imaging Lab 300 Pasteur Drive StanfordCA94305 United States Laboratory Graz Austria Girardetstraße 2 Essen45131 Germany Otto-von-Guericke University Department of Simulation and Graphics. Universitätsplatz 2 Magdeburg39106 Germany

Objective: Surveillance imaging of chronic aortic diseases, such as dissections, relies on obtaining and comparing cross-sectional diameter measurements at predefined aortic landmarks, over time. Due to a lack of robust tools, the orientation of the cross-sectional planes is defined manually by highly trained operators. We show how manual annotations routinely collected in a clinic can be efficiently used to ease this task, despite the presence of a non-negligible interoperator variability in the measurements. Impact: Ill-posed but repetitive imaging tasks can be eased or automated by leveraging imperfect, retrospective clinical annotations. Methodology: In this work, we combine convolutional neural networks and uncertainty quantification methods to predict the orientation of such cross-sectional planes. We use clinical data randomly processed by 11 operators for training, and test on a smaller set processed by 3 independent operators to assess interoperator variability. Results: Our analysis shows that manual selection of cross-sectional planes is characterized by 95% limits of agreement (LOA) of 10.6◦ and 21.4◦ per angle. Our method showed to decrease static error by 3.57◦ (40.2%) and 4.11◦ (32.8%) against state of the art and LOA by 5.4◦ (49.0%) and 16.0◦ (74.6%) against manual processing. Conclusion: This suggests that pre-existing annotations can be an inexpensive resource in clinics to ease ill-posed and repetitive tasks like cross-section extraction for surveillance of aortic dissections. Copyright © 2021, The Authors. All rights reserved.

关键词： Blood vessels

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A Robust Subtree-Based Authentication Scheme for TMIS Using Chaotic Hash Function

A Robust Subtree-Based Authentication Scheme for TMIS Using ...

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International Conference on computer, Information and Telecommunication Systems (CITS)

作者： Chandrashekhar Meshram Mohammad S. Obaidat Balqies Sadoun Agbotiname Lucky Imoize Vishesh P. Gaikwad Department of Post Graduate Studies and Research in Mathematics Jayawanti Haksar Government Post Graduate College College of Chhindwara University Betul M.P. India King Abdullah II School of Information Technology University of Jordan Amman Jordan University of Science and Technology Beijing Beijing China SRM University SRM Nagar Kattankulathur TN India Amity University Noida UP India College of Engineering Al-Balqa’ Applied University Al-Salt Jordan Department of Electrical and Electronics Engineering Faculty of Engineering University of Lagos Akoka Lagos Nigeria Department of Electrical Engineering and Information Technology Institute of Digital Communication Ruhr University Bochum Germany Department of Computer Science and Engineering Sardar Vallabhbhai National Institute of Technology Surat Gujarat India

ISBN: (数字)9798350359091

ISBN: (纸本)9798350359107

The widespread availability of broadband telecommunication and the relatively affordable cost of vital signs monitoring devices have enabled telemedicine to bring its benefits directly to patients' homes. In contemporary healthcare, Telecare Medicine Information System (TMIS) facilitates remote disease diagnosis, treatment, and healthcare delivery through the capabilities of wireless communication and information technology. To protect patient confidentiality, TMIS must develop robust authentication systems since it operates on the public Internet, which exposes its operations to security vulnerabilities. To ensure patient privacy, we present a novel Subtree-based Authentication technique for TMIS. An evaluation of the proposed scheme reveals that it is resistant to known potential attacks, and offers more security effectiveness and resource efficiency than existing schemes, making it an excellent solution for enhancing the security of TMIS implementations.

关键词： Privacy Chaotic communication Telemedicine Authentication Passwords Internet Security

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Schrödinger's ballot: Quantum Information and the violation of Arrow's impossibility theorem

arXiv

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arXiv 2021年

作者： Sun, Xin He, Feifei Kulicki, Piotr Sopek, Mirek Department of the Foundations of Computer Science John Paul II Catholic University of Lublin Lublin Poland Quantum Blockchains Inc. Pulawy Poland Institute of Logic and Cognition Sun Yat-sen University Guangzhou China MakoLab SA Lodz Poland

In this paper we study Arrow's Impossibility Theorem in the quantum setting. Our work is based on the work of Bao and Halpern [3], in which it is proved that the quantum analogue of Arrow's Impossibility Theorem is not valid. However, we feel unsatisfied about the proof presented in [3]. Moreover, the definition of Quantum Independence of Irrelevant Alternatives (QiiA) in [3] seems not appropriate to us. In this paper, we give a better definition of QiiA, which properly captures the idea of the independence of irrelevant alternatives, and a detailed proof of the violation of Arrow's Impossibility Theorem in the quantum setting with the modified definition. © 2021, CC BY.

关键词： Quantum optics

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