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Unraveling the genetic mechanisms of UV radiation resistance in Bacillus through biofilm formation, sporulation, and carotenoid production

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Genomics 2025年第4期117卷 111066页

作者： Prasansah Shrestha Byeollee Kim So-Ra Han Hyun Lee Tae-Jin Oh Department of Life Science and Biochemical Engineering Graduate School SunMoon University Asan 31460 Republic of Korea Bio Big Data-based Chungnam Smart Clean Research Leader Training Program SunMoon University Asan 31460 Republic of Korea Genome-based BioIT Convergence Institute Asan 31460 Republic of Korea. Genome-based BioIT Convergence Institute Asan 31460 Republic of Korea Department of Life Science and Biochemical Engineering Graduate School SunMoon University Asan 31460 Republic of Korea. Division of Computer Science and Engineering SunMoon University Asan 31460 Republic of Korea. Department of Pharmaceutical Engineering and Biotechnology SunMoon University Asan 31460 Republic of Korea. Electronic address: tjoh3782@sunmoon.ac.kr.

Bacillus species are Gram-positive bacteria that are rod-shaped, endospore-forming, and aerobic or facultatively anaerobic. With over 300 recognized species, Bacillus subtilis stands out as a well-studied model organism. The genus's various species exhibit a wide range of physiological capabilities, allowing them to thrive in diverse environmental conditions. Each cell produces a single endospore, which is highly resistant to heat, cold, radiation, desiccation, and disinfectants. Among Bacillus strains, those capable of producing spores, biofilms, and carotenoids demonstrate significant resilience to UV light. This review examines the genes involved in spore formation, biofilm development, and carotenoid synthesis, emphasizing their roles in UV radiation survival. We explore the interconnections between these processes and their combined contribution to UV resistance, focusing on the underlying genetic mechanisms. These insights will benefit researchers studying the genetic basis of UV radiation resistance in Bacillus species. IMPORTANCE: Bacteria employ adaptive strategies in extreme environments through rapid changes in gene expression, altering their phenotype for survival. Bacillus species, for example, defend against UV radiation by making spores, creating biofilms, and producing pigments. During sporulation, sigma factors (σ, σ, σ, and σ) regulate gene expression to adapt to environmental shifts. It has been found that the spores of some species may contain pigments that strongly absorb UV radiation, playing a crucial role in spore UV resistance. UV light penetrates biofilm matrices minimally, mainly affecting surface cells, which produce compounds like mycosporine-like amino acids and carotenoids to shield against UV damage.

关键词： Bacillus Biofilm Carotenoid Spore UV-radiation resistance

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Expanders and right-angled Artin groups

arXiv

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arXiv 2020年

作者： Flores, Ramón Kahrobaei, Delaram Koberda, Thomas Department of Geometry and Topology University of Seville Spain Department of Computer Science University of York United Kingdom New York University Tandon School of Engineering PhD Program in Computer Science CUNY Graduate Center Department of Mathematics University of Virginia CharlottesvilleVA22904 United States

The purpose of this article is to give a characterization of families of expander graphs via right-angled Artin groups. We prove that a sequence of simplicial graphs {Γi}i∈ forms a family of expander graphs if and only if a certain natural mini-max invariant arising from the cup product in the cohomology rings of the groups {A(Γi)}i∈ agrees with the Cheeger constant of the sequence of graphs, thus allowing us to characterize expander graphs via cohomology. This result is proved in the more general framework of vector space expanders, a novel structure consisting of sequences of vector spaces equipped with vector-space-valued bilinear pairings which satisfy a certain mini-max condition. These objects can be considered to be analogues of expander graphs in the realm of linear algebra, with a dictionary being given by the cup product in cohomology, and in this context represent a different approach to expanders that those developed by Lubotzky-Zelmanov and Bourgain-Yehudayoff. Copyright © 2020, The Authors. All rights reserved.

关键词： Vector spaces

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Ubiquitous Flat Bands in a Cr-based Kagome Superconductor

arXiv

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arXiv 2024年

作者： Guo, Yucheng Wang, Zehao Xie, Fang Huang, Yuefei Gao, Bin Oh, Ji Seop Wu, Han Liu, Zhaoyu Ren, Zheng Fang, Yuan Biswas, Ananya Zhang, Yichen Yue, Ziqin Hu, Cheng Jozwiak, Chris Bostwick, Aaron Rotenberg, Eli Hashimoto, Makoto Lu, Donghui Kono, Junichiro Chu, Jiun-Haw Yakobson, Boris I. Birgeneau, Robert J. Si, Qimiao Dai, Pengcheng Yi, Ming Department of Physics and Astronomy Rice University HoustonTX77005 United States Advanced Light Source Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Department of Materials Science and NanoEngineering Rice University HoustonTX77005 United States Department of Physics University of California BerkeleyCA94720 United States Department of Physics University of Washington Washington98105 United States Applied Physics Graduate Program Smalley-Curl Institute Rice University HoustonTX77005 United States Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory Menlo ParkCA94025 United States Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States Smalley-Curl Institute Rice University HoustonTX77005 United States Department of Materials Science and NanoEngineering Rice University HoustonTX77005 United States

In the quest for novel quantum states driven by topology and correlation, kagome lattice materials have garnered significant interest due to their distinctive electronic band structures, featuring flat bands (FBs) arising from the quantum destructive interference of the electronic wave function. The tuning of the FBs to the chemical potential would lead to the possibility of liberating electronic instabilities that lead to emergent electronic orders. Despite extensive studies, direct evidence of FBs tuned to the chemical potential and their participation in emergent electronic orders have been lacking in bulk quantum materials. Here using a combination of Angle-Resolved Photoemission Spectroscopy (ARPES) and Density Functional Theory (DFT), we reveal that the low-energy electronic structure of the recently discovered Cr-based kagome metal superconductor CsCr3Sb5 is dominated by a pervasive FB in close proximity to, and below the Fermi level. A comparative analysis with orbital-projected DFT and polarization dependence measurement uncovers that an orbital-selective renormalization mechanism is needed to reconcile the discrepancy with the DFT calculations, which predict the FB to appear 200 meV above the Fermi level. Furthermore, we observe the FB to shift away from the Fermi level by 20 meV in the low-temperature density wave-ordered phase, highlighting the role of the FB in the emergent electronic order. Our results reveal CsCr3Sb5 to stand out as a promising platform for further exploration into the effects of FBs near the Fermi level on kagome lattices, and their role in emergent orders in bulk quantum materials. © 2024, CC BY.

关键词： Density functional theory

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Radio-transparent dipole antenna based on a metasurface cloak

arXiv

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arXiv 2021年

作者： Soric, Jason Ra'di, Younes Farfan, Diego Alù, Andrea Department of Electrical and Computer Engineering University of Texas at Austin AustinTX78712 United States Photonics Initiative Advanced Science Research Center City University of New York NY10031 United States Physics Program Graduate Center City University of New York NY10016 United States Department of Electrical Engineering City College of the City University of New York NY10031 United States

Antenna technology is at the basis of ubiquitous wireless communication systems and sensors. Radiation is typically sustained by conduction currents flowing around resonant metallic objects that are optimized to enhance efficiency and bandwidth. However, resonant conductors are prone to large scattering of impinging waves, leading to challenges in crowded antenna environments due to blockage and distortion. Metasurface cloaks have been explored in the quest of addressing this challenge by reducing antenna scattering, but with limited performance in terms of bandwidth, footprint and overall scattering reduction. Here we introduce a different route towards radio-transparent antennas, in which the cloak itself acts as the radiating element, drastically reducing the overall footprint while enhancing scattering suppression and bandwidth, without sacrificing other relevant radiation metrics compared to conventional antennas. This technique offers a new application of cloaking technology, with promising features for crowded wireless communication platforms and noninvasive sensing. © 2021, CC BY-NC-ND.

关键词： Bandwidth

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Improved Accuracy of Cardiac Tissue-Level Simulations by Considering Membrane Resistance as a Cellular-Level Optimization Objective

Improved Accuracy of Cardiac Tissue-Level Simulations by Con...

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Annual International Conference of the IEEE engineering in Medicine and Biology Society (EMBC)

作者： E. Pouranbarani L. A. Berg R. S. Oliveira R. W. dos Santos A. Nygren Department of Electrical and Computer Engineering University of Calgary Alberta Canada Department of Computer Science and the Graduate Program of Computational Modeling Federal University of Juiz de Fora Juiz de Fora Brazil Department of Computer Science University of São João del-Rei São João del-Rei Brazil

ISBN: (数字)9781728119908

ISBN: (纸本)9781728119915

Cardiac cellular models are utilized as the building blocks for tissue simulation. One of the imprecisions of conventional cellular modeling, especially when the models are used in tissue-level modeling, stems from the mere consideration of cellular properties (e.g., action potential shape) in parameter tuning of the model. In our previous work, we put forward an accurate framework in which membrane resistance (R m ) reflecting inter-cellular characteristics, i.e., electrotonic effects, was considered alongside cellular features in cellular model fitting. This paper, for the first time, examines the hypothesis that considering R m as an additional optimization objective improves the accuracy of tissue-level modeling. To study this hypothesis, after cellular-level optimization of a well-known model, source-sink mismatch configurations in a 2-dimensional model are investigated. The results demonstrate that including R m in the optimization protocol yields a substantial improvement in the relative error of the critical transition border which is defined as the minimum window size between source and sink that wave propagates. Model developers can utilize the proposed concept during parameter tuning to increase the accuracy of models.

关键词： Mathematical model Optimization Computational modeling Resistance Tuning Fitting Protocols

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Terahertz chiral photonic-crystal cavities with broken time-reversal symmetry

arXiv

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arXiv 2024年

作者： Tay, Fuyang Sanders, Stephen Baydin, Andrey Song, Zhigang Welakuh, Davis M. Alabastri, Alessandro Rokaj, Vasil Dag, Ceren B. Kono, Junichiro Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States Applied Physics Graduate Program Smalley–Curl Institute Rice University HoustonTX77005 United States Smalley–Curl Institute Rice University HoustonTX77005 United States John A. Paulson School of Engineering and Applied Sciences Harvard University CambridgeMA02139 United States Max Planck Institute for The Structure and Dynamics of Matter Luruper Chaussee 149 Hamburg22761 Germany ITAMP Harvard-Smithsonian Center for Astrophysics CambridgeMA02138 United States Department of Physics Harvard University CambridgeMA02138 United States Department of Physics Villanova University VillanovaPA19085 United States Department of Physics and Astronomy Rice University HoustonTX77005 United States Department of Materials Science and NanoEngineering Rice University HoustonTX77005 United States

Strong coupling between matter and vacuum electromagnetic fields in a cavity can induce novel quantum phases in thermal equilibrium via symmetry breaking. Particularly, coupling with circularly polarized fields can break time-reversal symmetry, leading to topological modifications in the band structure. Therefore, chiral optical cavities that host chiral vacuum fields are being sought, especially in the terahertz (THz) frequency range, where various large-oscillator-strength resonances exist. Here, we present a novel approach to achieving THz chiral photonic-crystal cavities (PCCs) with high-quality factors (>400) using a magnetoplasma in a lightly doped semiconductor. Numerical simulations of an optimized structure based on InSb in a small perpendicular magnetic field (∼0.2 T) show chiral cavity resonances with near-perfect ellipticity at the surfaces of the central dielectric layer, where one can place atomically thin materials like monolayer graphene. We theoretically estimate an energy gap on the order of 1 meV in graphene when coupled to our proposed chiral cavity, which is potentially measurable in experiments. These THz chiral PCCs offer a promising platform for exploring new phases in cavity-dressed condensed matter with broken time-reversal symmetry. Copyright © 2024, The Authors. All rights reserved.

关键词： Crystal symmetry

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Design, Implementation and Validation of a Multipurpose Localization Service for Cooperative Multi-UAV Systems

Design, Implementation and Validation of a Multipurpose Loca...

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International Conference on Unmanned Aircraft Systems (ICUAS)

作者： Edison Pignaton de Freitas Luis Antonio L. F. da Costa Carlos Felipe Emygdio de Melo Maik Basso Marcos Rodrigues Vizzotto Mateus Schein Cavalheiro Corrêa Túlio Dapper e Silva Graduate Program in Computer Science Federal University of Rio Grande do Sul Porto Alegre Brazil Graduate Program in Electrical Engineering Federal University of Rio Grande do Sul Porto Alegre Brazil Department of Electric Automation and Energy Federal University of Rio Grande do Sul Porto Alegre Brazil

ISBN: (数字)9781728142784

ISBN: (纸本)9781728142791

Systems composed of groups of Unmanned Aerial Vehicles (UAVs) are emerging as an extension of the usage of single UAVs in a number of applications. Besides of very desirable, the possibility of using multi-UAV systems requires that each UAV in the group has information about the locations of the others, so that the system as a whole can work smoothly, i.e. keeping configured flight formation, without collisions, evenly distributing the tasks, and even authenticating one another so that no malicious node access the group. To support such multi-UAV systems setup, this work reports the proposal of a multipurpose localization service to disseminate positioning information of the UAVs to the group as well as to estimate the positions that are not received due to communication errors. The proposal consists in a complete methodology to setup, test and perform multi-UAV missions, which are firstly planned, setup and tested in a simulated environment, and then performed in the real-world. Design and implementation details of the proposed infrastructure service are presented, along with a complete validation of the proposal, from simulation to the field experiments. The acquired results provide evidence that the proposed service and methodology are efficient to support fleet of UAVs performing cooperative missions.

关键词： Proposals Unmanned aerial vehicles Estimation Task analysis Planning Global Positioning System Control systems

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Macroscopically Self-Aligned and Chiralized Carbon Nanotubes: From Filtration to Innovation

arXiv

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arXiv 2023年

作者： Doumani, Jacques Zahn, Keshav Yu, Shengjie Barrios, Gustavo Rodriguez Sasmal, Somesh Kikuchi, Rikuta Kritzell, T. Elijah Xu, Hongjing Baydin, Andrey Kono, Junichiro Department of Electrical and Computer Engineering Rice University 6100 Main Street HoustonTX77005 United States Applied Physics Graduate Program Smalley–Curl Institute Rice University 6100 Main Street HoustonTX77005 United States Carbon Hub Rice University 6100 Main Street HoustonTX77005 United States Smalley–Curl Institute Rice University 6100 Main Street HoustonTX77005 United States Department of Physics and Astronomy Rice University 6100 Main Street HoustonTX77005 United States Department of Materials Science and NanoEngineering Rice University 6100 Main Street HoustonTX77005 United States

Because of their natural one-dimensional (1D) structure combined with intricate chiral variations, carbon nanotubes (CNTs) exhibit various exceptional physical properties, such as ultrahigh electrical and thermal conductivity, exceptional mechanical strength, and chirality-dependent metallicity. These properties make CNTs highly promising for diverse applications, including field-effect transistors, sensors, photodetectors, and thermoelectric devices. While CNTs excel individually at the nanoscale, their 1D and chiral nature can be lost on a macroscopic scale when they are randomly assembled. Therefore, the alignment and organization of CNTs in macroscopic structures is crucial for harnessing their full potential. In this review, we explore recent advancements in understanding CNT alignment mechanisms, improving CNT aligning methods, and demonstrating macroscopically 1D properties of ordered CNT assemblies. We also focus on a newly discovered class of CNT architectures, combining CNT alignment and twisting mechanisms to create artificial radial and chiral CNT films at wafer scales. Finally, we summarize recent developments related to aligned and chiral CNT films in optoelectronics, highlighting their unique roles in solar cells, thermal emitters, and optical modulators. Copyright © 2023, The Authors. All rights reserved.

关键词： Carbon nanotubes

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Angle-resolved photoemission spectroscopy with an in situ tunable magnetic field

arXiv

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arXiv 2023年

作者： Huang, Jianwei Yue, Ziqin Baydin, Andrey Zhu, Hanyu Nojiri, Hiroyuki Kono, Junichiro He, Yu Yi, Ming Department of Physics and Astronomy Rice University HoustonTX77005 United States Applied Physics Graduate Program Smalley-Curl Institute Rice University HoustonTX77005 United States Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States Smalley–Curl Institute Rice University HoustonTX77005 United States Department of Materials Science and NanoEngineering Rice University HoustonTX77005 United States Institute for Materials Research Tohoku University Katahira 2-1-1 Sendai980-8577 Japan Department of Applied Physics Yale University New HavenCT06511 United States

Angle-resolved photoemission spectroscopy (ARPES) is a powerful tool for probing the momentum-resolved single-particle spectral function of materials. Historically, in situ magnetic fields have been carefully avoided as they are detrimental to the control of photoelectron trajectory during the photoelectron detection process. However, magnetic field is an important experimental knob for both probing and tuning symmetry-breaking phases and electronic topology in quantum materials. In this paper, we introduce an easily implementable method for realizing an in situ tunable magnetic field at the sample position in an ARPES experiment and analyze magnetic field induced artifacts in ARPES data. Specifically, we identified and quantified three distinct extrinsic effects of a magnetic field: Constant energy contour rotation, emission angle contraction, and momentum broadening. We examined these effects in three prototypical quantum materials, i.e., a topological insulator (Bi2Se3), an iron-based superconductor (LiFeAs), and a cuprate superconductor (Pb-Bi2Sr2CuO6+x), and demonstrate the feasibility of ARPES measurements in the presence of a controllable magnetic field. Our studies lay the foundation for the future development of the technique and interpretation of ARPES measurements of field-tunable quantum phases. Copyright © 2023, The Authors. All rights reserved.

关键词： Photoelectrons

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Miscentering of Optical Galaxy Clusters Based on Sunyaev-Zeldovich Counterparts

arXiv

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arXiv 2024年

作者： Ding, Jupiter Dalal, Roohi Sunayama, Tomomi Strauss, Michael A. Oguri, Masamune Okabe, Nobuhiro Hilton, Matt Monteiro-Oliveira, Rogério Sifón, Cristóbal Staggs, Suzanne T. Department of Astrophysical Sciences Princeton University Peyton Hall PrincetonNJ08544 United States CIERA Department of Physics and Astronomy Northwestern University 2145 Sheridan Road EvanstonIL60208 United States Department of Physics and Astronomy University of British Columbia VancouverBC Canada Department of Political Science University of British Columbia VancouverBC Canada Department of Astronomy Steward Observatory University of Arizona TucsonAZ85721 United States Center for Frontier Science Chiba University 1-33 Yayoi-cho Inage-ku Chiba263-8522 Japan Department of Physics Graduate School of Science Chiba University 1-33 Yayoi-Cho Inage-Ku Chiba263-8522 Japan Physics Program Graduate School of Advanced Science and Engineering Hiroshima University Higashi Hiroshima Campus Hiroshima739-8526 Japan Wits Centre for Astrophysics School of Physics University of the Witwatersrand Private Bag 3 Johannesburg2050 South Africa Astrophysics Research Centre School of Mathematics Statistics and Computer Science University of KwaZulu-Natal Westville Campus Durban4041 South Africa Institute of Astronomy and Astrophysics Academia Sinica Taipei10617 Taiwan Instituto de Física Pontificia Universidad Católica de Valparaíso Valparaíso Casilla4059 Chile Joseph Henry Laboratories of Physics Princeton University Jadwin Hall PrincetonNJ08544 United States

The "miscentering effect," i.e., the offset between a galaxy cluster’s optically-defined center and the center of its gravitational potential, is a significant systematic effect on brightest cluster galaxy (BCG) studies and cluster lensing analyses. We perform a cross-match between the optical cluster catalog from the Hyper Suprime-Cam (HSC) Survey S19A Data Release and the Sunyaev-Zeldovich cluster catalog from Data Release 5 of the Atacama Cosmology Telescope (ACT). We obtain a sample of 186 clusters in common in the redshift range 0.1 ≤ z ≤ 1.4 over an area of 469 deg2. By modeling the distribution of centering offsets in this fiducial sample, we find a miscentered fraction (corresponding to clusters offset by more than 330 kpc) of ∼ 25%, a value consistent with previous miscentering studies. We examine the image of each miscentered cluster in our sample and identify one of several reasons to explain the miscentering. Some clusters show significant miscentering for astrophysical reasons, i.e., ongoing cluster mergers. Others are miscentered due to non-astrophysical, systematic effects in the HSC data or the cluster-finding algorithm. After removing all clusters with clear, non-astrophysical causes of miscentering from the sample, we find a considerably smaller miscentered fraction, ∼ 10%. We show that the gravitational lensing signal within 1 Mpc of miscentered clusters is considerably smaller than that of well-centered clusters, and we suggest that the ACT SZ centers are a better estimate of the true cluster potential centroid. Copyright © 2024, The Authors. All rights reserved.

关键词： Cosmology

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