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An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing

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Scientific Reports 2023年第1期13卷 1-12页

作者： Ramos-Mandujano, Gerardo Grünberg, Raik Zhang, Yingzi Bi, Chongwei Guzmán-Vega, Francisco J. Shuaib, Muhammad Gorchakov, Rodion V. Xu, Jinna Tehseen, Muhammad Takahashi, Masateru Takahashi, Etsuko Dada, Ashraf Ahmad, Adeel Nazir Hamdan, Samir M. Pain, Arnab Arold, Stefan T. Li, Mo Stem Cell and Regeneration Laboratory Bioscience Program Biological and Environmental Science and Engineering Division (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia Structural Biology and Engineering Computational Biology Research Center. Biological and Environmental Science and Engineering Division (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia Pathogen Genomics Laboratory Bioscience Program Biological and Environmental Science and Engineering (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia Health Safety and Environment Department King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia Laboratory of DNA Replication and Recombination Bioscience Program Biological and Environmental Science and Engineering Division (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia Department of Pathology and Laboratory Medicine King Faisal Specialist Hospital and Research Center Jeddah Saudi Arabia College of Medicine Al Faisal University Riyadh Saudi Arabia KAUST Health King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia Bioengineering Program Biological and Environmental Science and Engineering Division (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia

The COVID-19 pandemic, caused by SARS-CoV-2, has emphasized the necessity for scalable diagnostic workflows using locally produced reagents and basic laboratory equipment with minimal dependence on global supply chains. We introduce an open-source automated platform for high-throughput RNA extraction and pathogen diagnosis, which uses reagents almost entirely produced in-house. This platform integrates our methods for self-manufacturing magnetic nanoparticles and qRT-PCR reagents-both of which have received regulatory approval for clinical use–with an in-house, open-source robotic extraction protocol. It also incorporates our "Nanopore Sequencing of Isothermal Rapid Viral Amplification for Near Real-time Analysis" (NIRVANA) technology, designed for tracking SARS-CoV-2 mutations and variants. The platform exhibits high reproducibility and consistency without cross-contamination, and its limit of detection, sensitivity, and specificity are comparable to commercial assays. Automated NIRVANA effectively identifies circulating SARS-CoV-2 variants. Our in-house, cost-effective reagents, automated diagnostic workflows, and portable genomic surveillance strategies provide a scalable and rapid solution for COVID-19 diagnosis and variant tracking, essential for current and future pandemic responses. © 2023, The Author(s).

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Low [O/Fe] Ratio in a Luminous Galaxy at the Early Cosmic Epoch (z > 10): Signature of Short Delay Time or Bright Hypernovae/Pair-Instability Supernovae?

arXiv

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arXiv 2024年

作者： Nakane, Minami Ouchi, Masami Nakajima, Kimihiko Harikane, Yuichi Tominaga, Nozomu Takahashi, Koh Kashino, Daichi Yanagisawa, Hiroto Watanabe, Kuria Nomoto, Ken'ichi Isobe, Yuki Nishigaki, Moka Ishigaki, Miho N. Ono, Yoshiaki Takeda, Yui Institute for Cosmic Ray Research The University of Tokyo 5-1-5 Kashiwanoha Kashiwa Chiba 277-8582 Japan Department of Physics Graduate School of Science The University of Tokyo 7-3-1 Hongo Bunkyo Tokyo113-0033 Japan National Astronomical Observatory of Japan 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Osawa 2-21-1 Mitaka Tokyo181-8588 Japan University of Tokyo Kashiwa Chiba277-8583 Japan Astronomical Science Program Graduate Institute for Advanced Studies SOKENDAI 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Department of Physics Faculty of Science and Engineering Konan University 8-9-1 Okamoto Kobe Hyogo658-8501 Japan Waseda Research Institute for Science and Engineering Faculty of Science and Engineering Waseda University 3-4-1 Okubo Shinjuku Tokyo169-8555 Japan

We present an [O/Fe] ratio of a luminous galaxy GN-z11 at z = 10.60 derived with the deep public JWST/NIRSpec data. We fit the medium-resolution grating (G140M, G235M, and G395M) data with the model spectra consisting of BPASS-stellar and Cloudy-nebular spectra in the rest-frame UV wavelength ranges with Fe absorption lines, carefully masking out the other emission and absorption lines in the same manner as previous studies conducted for lower redshift (z ∼ 2 − 6) galaxies with oxygen abundance measurements. We obtain an Fe-rich abundance ratio [O/Fe] = −0.37+0.−04322, which is confirmed with the independent deep prism data as well as by the classic 1978 index method. This [O/Fe] measurement is lower than measured for star-forming galaxies at z ∼ 2−3. Because z = 10.60 is an early epoch after the Big Bang (∼ 430 Myr) and first star formation (likely ∼ 200 Myr), it is difficult to produce Fe by Type Ia supernovae (SNeIa) requiring sufficient delay time for white-dwarf formation and gas accretion. The Fe-rich abundance ratio in GN-z11 suggests that the delay time is short, or that the major Fe enrichment is not accomplished by SNeIa but bright hypernovae (BrHNe) and/or pair-instability supernovae (PISNe), where the yield models of BrHNe and PISNe explain Fe, Ne, and O abundance ratios of GN-z11. The [O/Fe] measurement is not too low to rule out the connection between GN-z11 and globular clusters (GCs) previously suggested by the nitrogen abundance, but rather supports the connection with a GC population at high [N/O] if a metal dilution process exists. © 2024, CC BY.

关键词： White dwarfs

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Manipulating Fano coupling in an opto-thermoelectric field

arXiv

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arXiv 2024年

作者： Lin, Linhan Lepeshov, Sergey Krasnok, Alex Huang, Yu Jiang, Taizhi Peng, Xiaolei Korgel, Brian A. Alu, Andrea Zheng, Yuebing State Key Laboratory of Precision Measurement Technology and Instruments Department of Precision Instrument Tsinghua University Beijing100084 China Department of Electrical and Photonics Engineering DTU Electro Technical University of Denmark Building 343 Kgs. LyngbyDK-2800 Denmark Department of Electrical and Computer Engineering Florida International University MiamiFL33174 United States School of Physics and Electronics Hunan University Changsha410082 China Mc Ketta Department of Chemical Engineering The University of Texas at Austin AustinTX78712 United States Materials Science & Engineering Program Texas Materials Institute The University of Texas at Austin AustinTX78712 United States Department of Electrical and Computer Engineering The University of Texas at Austin AustinTX78712 United States Advanced Science Research Center City University of New York New YorkNY10031 United States Physics Program Graduate Center City University of New York NY10016 United States Walker Department of Mechanical Engineering The University of Texas at Austin AustinTX78712 United States

Fano resonances in photonics arise from the coupling and interference between two resonant modes in structures with broken symmetry. They feature an uneven and narrow and tunable lineshape, and are ideally suited for optical spectroscopy. Many Fano resonance structures have been suggested in nanophotonics over the last ten years, but reconfigurability and tailored design remain challenging. Herein, we propose an all-optical "pick-and-place" approach aimed at assemble Fano metamolecules of various geometries and compositions in a reconfigurable manner. We study their coupling behavior by in-situ dark-field scattering spectroscopy. Driven by a light-directed opto-thermoelectric field, silicon nanoparticles with high quality-factor Mie resonances (discrete states) and low-loss BaTiO3 nanoparticles (continuum states) are assembled into all-dielectric heterodimers, where distinct Fano resonances are observed. The Fano parameter can be adjusted by changing the resonant frequency of the discrete states or the light polarization. We also show tunable coupling strength and multiple Fano resonances by altering the number of continuum states and discrete states in dielectric heterooligomers. Our work offers a general design rule for Fano resonance and an all-optical platform for controlling Fano coupling on demand. Copyright © 2024, The Authors. All rights reserved.

关键词： Light polarization

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The Role of Heterogeneity in Autonomous Perimeter Defense Problems

arXiv

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arXiv 2022年

作者： Adler, Aviv Mickelin, Oscar Ramachandran, K. Sukhatme, Gaurav S. Karaman, Sertac Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA United States Program in Applied and Computational Mathematics Princeton University Princeton NJ08544 United States Department of Computer Science University of Southern California Los AngelesCA90089 United States Department of Aeronautics and Astronautics Massachusetts Institute of Technology CambridgeMA02139 United States

When is heterogeneity in the composition of an autonomous robotic team beneficial and when is it detrimental? We investigate and answer this question in the context of a minimally viable model that examines the role of heterogeneous speeds in perimeter defense problems, where defenders share a total allocated speed budget. We consider two distinct problem settings and develop strategies based on dynamic programming and on local interaction rules. We present a theoretical analysis of both approaches and our results are extensively validated using simulations. Interestingly, our results demonstrate that the viability of heterogeneous teams depends on the amount of information available to the defenders. Moreover, our results suggest a universality property: across a wide range of problem parameters the optimal ratio of the speeds of the defenders remains nearly constant. Copyright © 2022, The Authors. All rights reserved.

关键词： Dynamic programming

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Novel synthesis of nickel-based bimetallic compounds using ammonium tetrafluoroborate and ammonium bifluoride as structure directing agents for energy storage application

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Journal of Energy Storage 2024年 75卷

作者： Kuo, Tsung-Rong Yu, You Zher Lee, Pin-Yan Wu, Chung-Hsien Chen, Hung-Ming Husain, Sadang Kongvarhodom, Chutima Ho, Kuo-Chuan Lin, Lu-Yin International PhD Program in Biomedical Engineering College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan Graduate Institute of Nanomedicine and Medical Engineering College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan Department of Chemical Engineering and Biotechnology National Taipei University of Technology Taipei Taiwan Department of Chemical Engineering National Taiwan University Taipei Taiwan Gingen Technology Co. LTD. Rm. 7 10F. No.189 Sec. 2 Keelung Rd. Xinyi Dist. Taipei11054 Taiwan Department of Physics Faculty of Mathematics and Natural Science Lambung Mangkurat University Banjarmasin70124 Indonesia Department of Chemical Engineering King Mongkut's University of Technology Thonburi 126 Pracha-u-thit Toong-kru Bangkok10140 Thailand

Nickel-based compounds are widely applied as the active material for energy storage devices, owing to high theoretical capacity and easy-fabricated process. Bimetallic compounds having multiple redox states can provide abundant redox reactions for charge storage. Structure directing agent (SDA) can promote the preferable growth of active materials and to enhance energy storage abilities. In this work, NH4BF4 and NH4HF2 are firstly used as SDA to synthesize nickel-based compounds along with 2-methylmidozole in the one-step solution process for energy storage applications. The bimetallic compounds are synthesized by incorporating Al, Mn, Co, Cu and Zn salts in the precursor solution including the Ni salt. The system with Al, Cu or Zn possesses single metal compound and barely nickel compound. Mn and Co-incorporated systems present clear bimetallic components with nickel hydroxide. The highest specific capacitance (CF) of 1336.3 F/g (297.0 mAh/g) are achieved at 20 mV/s for the NiCo-based electrode, owing to the bimetallic feature and favorable two-dimensional sheet-like structures. An energy storage device is assembled using the NiCo-based compound and reduced graphene oxide electrodes. The maximum energy density of 10.5 Wh/kg at 0.3 kW/kg, and the CF retention of 78.5% and Coulombic efficiency of 85.2% are achieved after 10,000 times charge/discharge cycles. © 2023 Elsevier Ltd

关键词： Energy storage

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Active Massive Black Hole Found in the Young Star-Forming Dwarf Galaxy SBS 0335-052E

arXiv

引用

arXiv 2023年

作者： Hatano, Shun Ouchi, Masami Nakajima, Kimihiko Kawaguchi, Toshihiro Kokubo, Mitsuru Kikuta, Satoshi Tominaga, Nozomu Xu, Yi Watanabe, Kuria Harikane, Yuichi Isobe, Yuki Matsumoto, Akinori Nishigaki, Moka Ono, Yoshiaki Onodera, Masato Sugahara, Yuma Umeda, Hiroya Zhang, Yechi National Astronomical Observatory of Japan Osawa 2-21-1 Mitaka Tokyo181-8588 Japan Department of Astronomical Science The Graduate University for Advanced Studies SOKENDAI 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Institute for Cosmic Ray Research The University of Tokyo 5-1-5 Kashiwanoha Chiba Kashiwa277-8582 Japan University of Tokyo Chiba Kashiwa277-8583 Japan Department of Economics Management and Information Science Onomichi City University Hisayamada 1600-2 Hiroshima Onomichi722-8506 Japan Astronomical Science Program Graduate Institute for Advanced Studies SOKENDAI 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Department of Physics Faculty of Science and Engineering Konan University 8-9-1 Okamoto Hyogo Kobe658-8501 Japan Department of Astronomy Graduate School of Science The University of Tokyo 7-3-1 Hongo Bunkyo Tokyo113-0033 Japan Department of Physics Graduate School of Science The University of Tokyo 7-3-1 Hongo Bunkyo Tokyo113-0033 Japan 650 North A’ohoku Place HiloHI96720 United States Waseda Research Institute for Science and Engineering Faculty of Science and Engineering Waseda University 3-4-1 Okubo Shinjuku Tokyo169-8555 Japan

Since the late 20th century, young star-forming dwarf galaxies with extremely low heavy-element abundances have been identified in the local universe1–3. Such a population of galaxies, represented by SBS 0335-052E, is intensively studied as a laboratory of galaxy formation, and interpreted as galaxies with hard emission and energetic outflows driven by massive stars2, 4, 5. Here we report the temporal flux variability of SBS 0335-052E in 3 − 4 µm bands on timescale of months to years with dimming and brightening up to 50% over 12 years. This is a clear signature of dust torus emission of an active massive black hole in SBS 0335-052E. The deep optical spectrum reveals a very broad component with 1.24 (±0.01) × 104 km s−1 in Hα emission, suggesting emission originated from broad line regions around the massive black hole. The black hole mass is estimated to be ∼ 100 thousand solar masses from the spectral energy distribution. This is the first example of the massive black hole existence in a long-considered young star-forming dwarf galaxy. Copyright © 2023, The Authors. All rights reserved.

关键词： Galaxies

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Large spontaneous Hall effect with flexible domain control in an antiferromagnetic material TaMnP

arXiv

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arXiv 2024年

作者： Kotegawa, Hisashi Nakamura, Akira Huyen, Vu Thi Ngoc Arai, Yuki Tou, Hideki Sugawara, Hitoshi Hayashi, Junichi Takeda, Keiki Tabata, Chihiro Kaneko, Koji Kodama, Katsuaki Suzuki, Michi-To Department of Physics Kobe University Hyogo Kobe657-8501 Japan Center for Computational Materials Science Institute for Materials Research Tohoku University Miyagi Sendai980-8577 Japan Muroran Institute of Technology Hokkaido Muroran050-8585 Japan Materials Sciences Research Center Japan Atomic Energy Agency Tokai319-1195 Japan Advanced Science Research Center Japan Atomic Energy Agency Tokai319-1195 Japan Center for Spintronics Research Network Graduate School of Engineering Science Osaka University Osaka Toyonaka560-8531 Japan

Antiferromagnets without parity-time (PT) symmetry offer novel perspectives in the field of functional magnetic materials. Among them, those with ferromagnetic-like responses are promising candidates for future applications such as antiferromagnetic (AF) memory;however, examples showing large effects are extremely limited. In this study, we show that the orthorhombic system TaMnP exhibits a large anomalous Hall conductivity (AHC) ∼ 360 − 370 Ω−1cm−1 in spite of the small net magnetization ∼ 10−2 µB/Mn. Our neutron scattering experiment and the observation of the AH effect indicated that a magnetic structure of TaMnP was dominated by an AF component represented by B3g with the propagation vector q = 0. Furthermore, we confirmed that the obtained AHC is among the largest observed in AF materials at zero fields. Additionally, our first-principles calculations revealed that the spin-orbit interaction originating in the nonmagnetic Ta-5d electrons significantly contributes to enhancing Berry curvatures in the momentum space. We found that the magnetic fields along all the crystal axes triggered the AF domain switching, indicating the possibility of controlling the AF domain using the small net magnetization, which is symmetrically different. Copyright © 2024, The Authors. All rights reserved.

关键词： Antiferromagnetism

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Correction: Reconsidering invasion history of common land snails in Japan through genome-wide analyses

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Biological Invasions 2023年第11期25卷 3551-3552页

作者： Hirano, Takahiro Yamazaki, Daishi Ito, Shun Sato, Mitsuhiko P. Matsuo, Ayumi Saito, Takumi Nishi, Hirotaka Ye, Bin Dong, Zhengzhong Van Tu, Do Shau-Hwai, Aileen Tan Suyama, Yoshihisa Chiba, Satoshi Center for Northeast Asian Studies Tohoku University Sendai Japan Graduate School of Life Sciences Tohoku University Sendai Japan Biology Program Faculty of Science University of the Ryukyus Okinawa Japan Faculty of Agriculture and Marine Science Kochi University Nankoku Japan Department of Environmental Science Faculty of Science Toho University Funabashi Japan Kazusa DNA Research Institute Kisarazu Japan Kawatabi Field Science Center Graduate School of Agricultural Science Tohoku University Osaki Japan Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic Toyohashi Museum of Natural History Toyohashi Japan Institute of Biomedical and Health Engineering Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen China Agricultural Experiment Station Zhejiang University Hangzhou China Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam Graduate University of Science and Technology Vietnam Academy of Science and Technology Hanoi Vietnam School of Biological Sciences Universiti Sains Malaysia Penang Malaysia Centre for Marine and Coastal Studies Universiti Sains Malaysia Penang Malaysia

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Interfacial Layer Materials with a Truxene Core for Dopant-Free NiOx-Based Inverted Perovskite Solar Cells

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Small 2024年第33期20卷 e2310939页

作者： Ramanujam, Rajarathinam Hsu, Hsiang-Lin Shi, Zhong-En Lung, Chien-Yu Lee, Chin-Han Wubie, Gebremariam Zebene Chen, Chih-Ping Sun, Shih-Sheng Institute of Chemistry Academia Sinica Nankang Taipei11529 Taiwan Taiwan International Graduate Program Sustainable Chemical Science and Technology Academia Sinica Nankang Taipei11529 Taiwan Department of Applied Chemistry National Yang Ming Chiao Tung University Hsinchu30050 Taiwan Department of Materials Engineering Ming Chi University of Technology 84 Gunjuan Road Taishan New Taipei City24301 Taiwan College of Engineering and Center for Sustainability and Energy Technologies Chang Gung University Taoyuan33302 Taiwan

Nickel oxide (NiOx) is commonly used as a holetransporting material (HTM) in p-i-n perovskite solar cells. However, the weak chemical interaction between the NiOx and CH3NH3PbI3 (MAPbI3) interface results in poor crystallinity, ineffective hole extraction, and enhanced carrier recombination, which are the leading causes for the limited stability and power conversion efficiency (PCE). Herein, two HTMs, TRUX-D1 (N2,N7,N12-tris(9,9-dimethyl-9H-fluoren-2-yl)-5,5,10,10,15,15-hexaheptyl-N2,N7,N12-tris(4-methoxyphenyl)-10,15-dihydro-5H-diindeno[1,2-a:1′,2′-c]fluorene-2,7,12-triamine) and TRUX-D2 (5,5,10,10,15,15-hexaheptyl-N2,N7,N12-tris(4-methoxyphenyl)-N2,N7,N12-tris(10-methyl-10H-phenothiazin-3-yl)-10,15-dihydro-5H-diindeno[1,2-a:1′,2′-c]fluorene-2,7,12-triamine), are designed with a rigid planar C3 symmetry truxene core integrated with electron-donating amino groups at peripheral positions. The TRUX-D molecules are employed as effective interfacial layer (IFL) materials between the NiOx and MAPbI3 interface. The incorporation of truxene-based IFLs improves the quality of perovskite crystallinity, minimizes nonradiative recombination, and accelerates charge extraction which has been confirmed by various characterization techniques. As a result, the TRUX-D1 exhibits a maximum PCE of up to 20.8% with an impressive long-term stability. The unencapsulated device retains 98% of their initial performance following 210 days of aging in a glove box and 75.5% for the device after 80 days under ambient air condition with humidity over 40% at 25 °C. © 2024 Wiley-VCH GmbH.

关键词： Passivation

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Nucleon isovector couplings in Nf = 2 + 1 lattice QCD at the physical point

arXiv

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arXiv 2022年

作者： Tsuji, Ryutaro Tsukamoto, Natsuki Aoki, Yasumichi Ishikawa, Ken-Ichi Kuramashi, Yoshinobu Sasaki, Shoichi Shintani, Eigo Yamazaki, Takeshi Department of Physics Tohoku University Sendai980-8578 Japan RIKEN Center for Computational Science Kobe650-0047 Japan Core of Research for the Energetic Universe Graduate School of Advanced Science and Engineering Hiroshima University Higashi-Hiroshima739-8526 Japan Center for Computational Sciences University of Tsukuba Ibaraki Tsukuba305-8577 Japan Faculty of Pure and Applied Sciences University of Tsukuba Ibaraki Tsukuba305-8571 Japan

We present results for the scalar and tensor isovector-couplings (gS and gT) of the nucleon measured at the physical point (Mπ = 135 MeV) with a single lattice spacing of 0.085 fm in 2+1 flavor QCD. Our calculations are carried out with two ensembles of gauge configurations generated by the PACS Collaboration with nonperturbatively O(a) improved Wilson quark action and Iwasaki gauge action on (10.9 fm)4 and (5.5 fm)4 lattices, where the finite-size effect on the nucleon mass was not shown at the level of the statistical precision less than 0.5%. We compute the nucleon three-point correlation functions in the vector, axial, scalar, and tensor channels. We confirm that our previous result of the nucleon axial coupling on the large spatial volume of (10.9 fm)4 has no finite-size effect at the level of the statistical precision of 1.9%. For the renormalization, we first renormalize gS and gT nonperturbatively using the RI/SMOM(γµ) scheme, a variant of Rome-Southampton RI/MOM scheme with reduced systematic errors, as the intermediate scheme. We evaluate our final results at the renormalization scale of 2 GeV in the MS scheme through matching procedure between the RI/SMOM(γµ) and MS schemes with the help of perturbation theory, and then obtain gS = 0.927(83)stat(22)syst and gT = 1.036(6)stat(20)syst Copyright © 2022, The Authors. All rights reserved.

关键词： Tensors

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