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Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes

Genomics, Proteomics & Bioinformatics 2024年第3期22卷 29-41页

作者： Fei Qi Junjie Chen Yue Chen Jianfeng Sun Yiting Lin Zipeng Chen philipp Kapranov State Key Laboratory of Cellular Stress Biology School of Life SciencesFaculty of Medicine and Life SciencesXiamen UniversityXiamen 361102China Institute of Genomics School of MedicineHuaqiao UniversityXiamen 361021China Botnar Research Centre University of OxfordOxfordOX37LDUnited Kingdom

Accurate identification of the correct,biologically relevant RNA structures is critical to understanding various aspects of RNA biology since proper folding represents the key to the functionality of all types of RNA molecules and plays pivotal roles in many essential biological ***,a plethora of approaches have been developed to predict,identify,or solve RNA structures based on various computational,molecular,genetic,chemical,or physicochemical *** computational approaches hold distinct advantages over all other strategies in terms of the ease of implementation,time,speed,cost,and throughput,but they strongly underperform in terms of accuracy that significantly limits their broader ***,the advantages of these methods led to a steady development of multiple in silico RNA secondary structure prediction approaches including recent deep learning-based ***,we compared the accuracy of predictions of biologically relevant secondary structures of dozens of self-cleaving ribozyme sequences using seven in silico RNA folding prediction tools with tasks of varying *** found that while many programs performed well in relatively simple tasks,their performance varied significantly in more complex RNA folding ***,in general,a modern deep learning method outperformed the other programs in the complex tasks in predicting the RNA secondary structures,at least based on the specific class of sequences tested,suggesting that it may represent the future of RNA structure prediction algorithms.

关键词： RNA secondary structure RNA secondary structure prediction Ribozyme Deep learning Pseudoknot

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Preprotein Import into Chloroplasts via the Toc and Tic Complexes Is Regulated by Redox Signals in Pisum sativum

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Molecular Plant 2009年第6期2卷 1181-1197页

作者： Anna Stengel J. philipp Benz Bob B. Buchanan Jurgen Soil Bettina Bolter Munich Center for Integrated Protein Science CiPS^M Ludwig-Maximilians-Universitat Munchen Feodor-Lynen-Strasse 25 D-81377 Munich Germany Department of Biology I Botany Ludwig-Maximilians-Universitat Munchen Groβhaderner Strasse 2-4 D-82152 Planegg-Martinsried Germany Department of Plant and Microbial Biology University of California 411 Koshland Hall Berkeley CA 94720 USA

The import of nuclear-encoded preproteins is necessary to maintain chloroplast function. The recognition and transfer of most precursor proteins across the chloroplast envelopes are facilitated by two membrane-inserted protein complexes, the translocons of the chloroplast outer and inner envelope （Toc and Tic complexes, respectively）. Several signals have been invoked to regulate the import of preproteins. In our study, we were interested in redox-based import regulation mediated by two signals： regulation based on thiols and on the metabolic NADP＋/NADPH ratio. We sought to identify the proteins participating in the regulation of these transport pathways and to characterize the preprotein subgroups whose import is redox-dependent. Our results provide evidence that the formation and reduction of disulfide bridges in the Toc receptors and Toc translocation channel have a strong influence on import yield of all tested preproteins that depend on the Toc complex for translocation. Furthermore, the metabolic NADP＋/NADPH ratio influences not only the composition of the Tic complex, but also the import efficiency of most, but not all, preproteins tested. Thus, several Tic subcomplexes appear to participate in the translocation of different preprotein subgroups, and the redox-active compo- nents of these complexes likely play a role in regulating transport.

关键词： Metabolic regulation molecular transport transport processes/kinetics chloroplast biology protein targeting.

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The Impact of Sleep-Wake Behaviour on Tennis Match Performance in Junior State Grade Tennis Players

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Journal of Science in Sport and Exercise 2023年第2期5卷 156-166页

作者： Mitchell Turner philipp Beranek Ian C.Dunican Travis Cruickshank School of Medical and Health Sciences Edith Cowan University270 Joondalup DrivePerthWA 6027Australia Centre for Sleep Science School of Human SciencesThe University of Western AustraliaPerthWA 6009Australia Centre for Precision Health School of Medical and Health SciencesEdith Cowan UniversityPerthAustralia Perron Institute for Neurological and Translational Sciences PerthAustralia

Purpose To date,no study has investigated the extent to which sleep-wake behaviour(SWB)influences match performance in junior tennis *** study aimed to assess the influence of SWB for the week and night before on match performance,particularly match analytics and *** This study recruited 10 junior state grade tennis players who wore an actigraphy device and completed a sleep diary for the week before their match on two separate occasions throughout their competition *** wore a global positioning system device to track their movement during matches,and an experienced tennis coach recorded players'match *** This study showed that the sleep fragmentation index was significantly lower the week before matches in females who had won than those who had ***,the sleep fragmentation index was significantly lower the night before a given match than the week *** sleep fragmentation index and sleep latency significantly influenced match performance in junior tennis *** percentage of second serves points won differed between match wins and losses for male players,while winners and forced errors differed for female *** These findings provide a detailed profile of tennis match play in junior state grade *** individual differences,reduced restlessness the night before a match coincides with increased match performance.

关键词： Sleep fragmentation Tennis analytics Global positioning system Sleep quality Sleep duration

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Remote heart rate measurement using low-cost RGB face video： a technical literature review

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Frontiers of Computer Science 2018年第5期12卷 858-872页

作者： philipp V. ROUAST Marc T. P. ADAM Raymond CHIONG David CORNFORTH Ewa LUX Institute of Information Systems and Marketing Karlsruhe Institute of Technology Karlsruhe 76133 Germany School of Electrical Engineering and Computing The University of Newcastle Callaghan NSW 2308 Australia

Remote photoplethysmography （rPPG） allows remote measurement of the heart rate using low-cost RGB imaging equipment. In this study, we review the development of the field of rPPG since its emergence in 2008. We also classify existing rPPG approaches and derive a framework that provides an overview of modular steps. Based on this framework, practitioners can use our classification to design algorithms for an rPPG approach that suits their specific needs. Researchers can use the reviewed and classified algorithms as a starting point to improve particular features of an rPPG algorithm.

关键词： affective computing heart rate measurement remote non-contact camera-based photoplethysmography

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The impact of having an oxygen-rich microporous surface in carbon electrodes for high-power aqueous supercapacitors

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Journal of Energy Chemistry 2021年第2期30卷 36-48,I0002页

作者： Servann Herou Maria Crespo Ribadeneyr philipp Schlee Hui Luo Liviu Cristian Tanase Christine Roβberg Magdalena Titirici Chemical Engineering Department Imperial College LondonImperial College RdKensingtonLondon SW72AZUK National Institute of Materials Physics Atomiştilor 405A077125 Măgurele–IlfovRomania Fraunhofer-Zentrum für Chemisch-Biotechnologische Prozesse CBP Am Haupttor06237 LeunaGermany

The growth of electrical transportation is crucially important to mitigate rising climate change concerns regarding materials *** are high-power devices,particularly suitable for public transportation since they can easily store breaking energy due to their high-rate charging ***,they can function with two carbon electrodes,which is an advantage due to the abundance of carbon in biomass and other waste materials(i.e.,plastic waste).Newly developed supercapacitive nanocarbons display extremely narrow micropores(100 kW kg^(-1)),using fourty times less activating agent than traditionnal chemically activated *** also demonstrate that the affinity between the carbon and the electrolyte is of paramount importance to maintain rapid ionic diffusion in narrow ***,this facile synthesis method shows that low-cost and bio-based free-standing electrode materials with reliable supercapacitive performances can be used in electrochemistry.

关键词： Porous carbon materials Lignin Supercapacitors Oxygen groups

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Long-term follow-up of liver alveolar echinococcosis using echinococcosis multilocularis ultrasound classification

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World Journal of Gastroenterology 2021年第40期27卷 6939-6950页

作者： Jasmin Schuhbaur Melissa Schweizer Jana philipp Julian Schmidberger Patrycja Schlingeloff Wolfgang Kratzer Department of Internal Medicine I University Hospital UlmUlm 89081Germany

BACKGROUND When Echinococcus multilocularis infects humans as a false intermediate host,alveolar echinococcosis(AE)usually manifests primarily intrahepatically and is initially *** the disease remains undiagnosed and untreated,progressive growth occurs,reminiscent of malignant *** only curative therapy is complete resection,which is limited to localised stages,and palliative drug therapy is used ***,early diagnosis and reliable detection of AE lesions are *** this reason,abdominal ultrasonography,as the most common primary imaging for AE,relies on classification *** To investigate how hepatic AE lesion sonomorphology changes over time in the Echinococcosis Multilocularis Ulm Classification(EMUC)-ultrasound(US)*** Based on data from Germany’s national echinococcosis database,we evaluated clinical and US imaging data for 59 patients according to the AE case definition in our preliminary retrospective longitudinal *** had to be at least two liver sonographies≥6 mo apart,≥1 hepatic AE lesion,and complete documentation in all US *** minimum interval between two separately evaluated US examinations was 4 *** AE reference lesion was the largest hepatic AE lesion at the time of the first US *** classify the sonomorphologic pattern,we used *** addition to classifying the findings of the original US examiner,all reference lesions at each examination time point were assigned EMUC-US patterns in a blinded fashion by two investigators experienced in US *** analysis was performed using SAS version 9.4(SAS Institute Inc.,Cary,NC,United Stated).P values<0.05 were considered statistically *** The preliminary study included 59 patients,38(64.5%)women and 21(35.6%)*** mean age at initial diagnosis was 59.9±16.9 *** the time of initial ultrasonography,a hailstorm pattern was present in 42.4%(25/59)of cases,a hemangioma-like pat

关键词： Alveolar echinococcosis Echinococcus multilocularis Ultrasonography Sonomorphology Pattern change

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Up to 70 THz bandwidth from an implanted Ge photoconductive antenna excited by a femtosecond Er:fibre laser

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Light(Science & Applications) 2020年第1期9卷 1716-1722页

作者： Abhishek Singh Alexej Pashkin Stephan Winnerl Malte Welsch Cornelius Beckh philipp Sulzer Alfred Leitenstorfer Manfred Helm Harald Schneider Institute of Ion Beam Physics and Materials Research Helmholtz-Zentrum Dresden-Rossendorf01328 DresdenGermany Cfaed and Institute of Applied Physics TU Dresden01062 DresdenGermany Department of Physics and Center for Applied Photonics University of Konstanz78457 KonstanzGermany

Phase-stable electromagnetic pulses in the THz frequency range offer several unique capabilities in time-resolved ***,the diversity of their application is limited by the covered spectral *** particular,the upper frequency limit of photoconductive emitters-the most widespread technique in THz spectroscopy-reaches only up to 7 THz in the regular transmission mode due to absorption by infrared-active optical ***,we present ultrabroadband(extending up to 70 THz)THz emission from an Au-implanted Ge emitter that is compatible with mode-locked fibre lasers operating at wavelengths of 1.1 and 1.55μm with pulse repetition rates of 10 and 20 MHz,*** result opens up the possibility for the development of compact THz photonic devices operating up to multi-THz frequencies that are compatible with Si CMOS technology.

关键词： antenna emitter fibre

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Retinal microvascular signs and recurrent vascular events in patients with TIA or minor stroke

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Stroke & Vascular Neurology 2023年第5期8卷 379-386,I0001-I0007页

作者： philipp Klyscz Thomas Ihl Inga Laumeier Maureen Steinicke Matthias Endres Georg Michelson Heinrich J Audebert Neurology Charité-Universitätsmedizin BerlinBerlinGermany Center for Stroke Research Berlin Charité-Universitätsmedizin BerlinBerlinGermany Berlin Institute of Health BerlinGermany Excellence Cluster NeuroCure Charité-Universitätsmedizin BerlinBerlinGermany German Center for Neurodegenerative Diseases partner site BerlinGermany German Center for Cardiovascular Research partner site BerlinGermany Ophthalmology Friedrich-Alexander-Universität Erlangen-Nürnberg Medizinische FakultätErlangenGermany Talkingeyes&More GmbH ErlangenGermany

Background and purpose Retinal pathologies are an independent risk factor for ischaemic stroke,but research on the predictive value of retinal abnormalities for recurrent vascular events in patients with prior stroke is *** investigated the association of retinal pathologies with subsequent vascular *** In a substudy of the Intensified secondary prevention intending a reduction of recurrent events in TIA and minor stroke patients(INSPiRE-TMS)trial,we enrolled patients with recent transient ischaemic attack(TIA)or minor stroke with at least one modifiable risk *** outcome was the composite of subsequent vascular *** photographs were taken at baseline and categorised into three different fundus groups by a telemedically linked *** 722 patients participated in the current study and 109 major vascular events *** multivariable adjustments,we did not find a significant association between fundus categories and risk for subsequent vascular events(HRs for moderate vascular retinopathy and vascular retinopathy with vessel rarefaction in comparison to no vascular retinopathy 1.03(95%CI 0.64 to 1.67),p=0.905 and 1.17(95%CI 0.62 to 2.20),p=0.626).In a selective post hoc analysis in patients with diabetes mellitus and hypertension,patients with vascular retinopathy with vessel rarefaction had a higher risk for recurrent stroke(HR 24.14(95%CI 2.74 to 212.50),p=0.004).Conclusions Retinal changes did not predict major subsequent vascular events in patients with recent TIA or minor *** studies are needed to examine the utility of fundus photography in assessing the risk of stroke recurrence in patients with diabetes mellitus and hypertension.

关键词： patients Retinal prevention

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The Contribution of the Gravitational Propagation Delay to Orbital and Center of Mass Motions

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Journal of Modern Physics 2016年第14期7卷 1909-1932页

作者： philipp Kornreich 1090 Wien Austria King of Prussia PA USA

Recent measurements have shown that gravitational waves and thus the gravitational interaction propagate with the speed of light. The propagation delay of the gravitational interaction in orbiting systems couples the orbital and center of mass motions. This causes the orbits to spiral out and the center of mass to accelerate. It is one of a number of small effects modifying the Kepler orbits. The calculations show that the analytical describable expansion of the semimajor axis started at a time that is less than the age of the systems. This could be caused by a collision of a system component in the past. The effect of this propagation delay on the motion of the Earth Moon and the Brown Dwarf 569Bab binary star system is analyzed. These systems were chosen because a considerable amount of measured astronomical data is available. The calculated results are in excellent agreement with the measured data. In galaxies, too, the energy transfer from the orbit of the star cloud to the center of mass motion causes the galaxies to ac-celerate. If galaxies are considered to be molecules of the universe, then the acceleration of the galaxies will cause the molecular gas to heat and expand. Alternatively, the loss in orbital internal energy of the galaxies should be included in the mass and energy in the calculation of the expanding Universe.

关键词： Propagation Delay Gravitation Gravitational Waves Orbits Center of Mass Newtonian Mechanics

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Intelligent indoor metasurface robotics

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National Science Review 2023年第8期10卷 20-32页

作者： Hanting Zhao Shengguo Hu Hongrui Zhang Zhuo Wang Hao Dong philipp del Hougne Tie Jun Cui Lianlin Li State Key Laboratory of Advanced Optical Communication Systems and Networks School of Electronics Peking University Center on Frontiers of Computing Studies School of Computer Science Peking University The French National Centre for Scientific Research(CNRS) University of Rennes 4. State Key Laboratory of Millimeter WavesSoutheast University

Intelligent indoor robotics is expected to rapidly gain importance in crucial areas of our modern society such as at-home health care and factories. Yet, existing mobile robots are limited in their ability to perceive and respond to dynamically evolving complex indoor environments because of their inherently limited sensing and computing resources that are, moreover, traded off against their cruise time and payload. To address these formidable challenges, here we propose intelligent indoor metasurface robotics(I2MR),where all sensing and computing are relegated to a centralized robotic brain endowed with microwave perception; and I2MR’s limbs(motorized vehicles, airborne drones, etc.) merely execute the wirelessly received instructions from the brain. The key aspect of our concept is the centralized use of a computation-enabled programmable metasurface that can flexibly mold microwave propagation in the indoor wireless environment, including a sensing and localization modality based on configurational diversity and a communication modality to establish a preferential high-capacity wireless link between the I2MR’s brain and limbs. The metasurface-enhanced microwave perception is capable of realizing low-latency and high-resolution three-dimensional imaging of humans, even around corners and behind thick concrete walls, which is the basis for action decisions of the I2MR’s brain. I2MR is thus endowed with real-time and full-context awareness of its operating indoor environment. We implement, experimentally, a proof-of-principle demonstration at ～2.4 GHz, in which I2MR provides health-care assistance to a human inhabitant. The presented strategy opens a new avenue for the conception of smart and wirelessly networked indoor robotics.

关键词： intelligent metasurfaces intelligent robotics edge devices IoT 6G

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