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Versatile multiplexed super-resolution imaging of nanostructures by Quencher-Exchange-PAINT

Nano Research 2018年第12期11卷 6141-6154页

作者： tobias Lutz Alexander H.Clowsley Ruisheng Lin Stefano Pagliara Lorenzo Di Michele Christian Soeller Living Systems Institute & Biomedical Physics University of ExeterExeter EX44QDUK Cavendish Laboratory University of CambridgeCambridge CB30HEUK

The optical super-resolution technique DNA-PAINT (Point Accumulation Imaging in Nanoscale Topography) provides a flexible way to achieve imaging of nanoscale structures at ∼10-nanometer resolution. In DNA-PAINT, fluorescently labeled DNA “imager” strands bind transiently and with high specificity to complementary target “docking” strands anchored to the structure of interest. The localization of single binding events enables the assembly of a super-resolution image, and this approach effectively circumvents photobleaching. The solution exchange of imager strands is the basis of Exchange-PAINT, which enables multiplexed imaging that avoids chromatic aberrations. Fluid exchange during imaging typically requires specialized chambers or washes, which can disturb the sample. Additionally, diffusional washout of imager strands is slow in thick samples such as biological tissue slices. Here, we introduce Quencher-Exchange-PAINT—a new approach to Exchange-PAINT in regular open-top imaging chambers—which overcomes the comparatively slow imager strand switching via diffusional imager washout. Quencher-Exchange-PAINT uses “quencher” strands, i.e., oligonucleotides that prevent the imager from binding to the targets, to rapidly reduce unwanted single-stranded imager concentrations to negligible levels, decoupled from the absolute imager concentration. The quencher strands contain an effective dye quencher that reduces the fluorescence of quenched imager strands to negligible levels. We characterized Quencher-Exchange-PAINT when applied to synthetic, cellular, and thick tissue samples. Quencher-Exchange-PAINT opens the way for efficient multiplexed imaging of complex nanostructures, e.g., in thick tissues, without the need for washing steps.

关键词： super-resolution microscopy fluorescence imaging DNA nanotechnology DNA-PAINT fluorescence quencher

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Dynamics of Submersible Mussel Rafts in Waves and Current

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China Ocean Engineering 2015年第3期29卷 431-444页

作者： WANG Xin-xin M.Robinson SWIFT tobias DEWHURST Igor TSUKROV Barbaros CELIKKOL Carter NEWELL Center for Ocean Engineering and Mechanical Engineering Department University of New Hampshire Laboratory of Fisheries Engineering Fisheries College Ocean University of China Pemaquid Mussel Farms

To investigate the dynamics of submersible mussel rafts, the finite element program Aqua-FETM, developed by the University of New Hampshire（UNH）, was applied to rafts moored at the surface and submerged. The submerged configuration is used to reduce wave forcing and to avoid contact with floating ice during winters in northern waters. Each raft consists of three pontoons connected by a grid framework. Rafts are intended to support densely spaced mussel ropes hung from the framework. When submerged, the pontoons are flooded, and the raft is held vertically by floats attached by lines. The computer models were developed in Aqua-FE？ to simulate the effects of waves and current. They were validated by comparison with wave tank results by use of a 1/10 scale raft physical model. Comparisons showed good agreement for the important heave（vertical） and pitch（rotational） motions, though there was a tendency towards conservative results for wave and current drag. Full-scale simulations of surface and submerged single raft and two rafts connected in tandem were performed. Submerged raft wave response was found to be reduced relative to that at the surface for both the single and two-raft configurations. In particular, the vertical motion of mussel rope connection points was significantly reduced by submergence, resulting in reduced potential for mussel drop-off. For example, the maximum vertical velocities of mussel rope attachment points in the submerged two raft case were 7%-20% of the corresponding velocities when at the surface.

关键词： mussel raft submersible mussel ropes finite element model waves and current storm response

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Signal pathways and precision therapy of small-cell lung cancer

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Signal Transduction and Targeted Therapy 2022年第7期7卷 2293-2310页

作者： Min Yuan Yu Zhao Hendrik-tobias Arkenau Tongnei Lao Li Chu Qing Xu Department of Oncology Shanghai Tenth People’s HospitalTongji University200072 ShanghaiChina Drug Development Unit Sarah Cannon Research InstituteLondonUK Department of Oncology Centro Medico BO CHIMacaoSARChina Department of Radiation Oncology Fudan University Shanghai Cancer Center200032 ShanghaiChina Present address:Department of Oncology Shanghai Medical CollegeFudan University200032 ShanghaiChina

Small-cell lung cancer(SCLC)encounters up 15%of all lung cancers,and is characterized by a high rate of proliferation,a tendency for early metastasis and generally poor *** of the patients present with distant metastatic disease at the time of clinical diagnosis,and only one-third are eligible for potentially curative ***,investigations into the genomic make-up of SCLC show extensive chromosomal rearrangements,high mutational burden and loss-of-function mutations of several tumor suppressor *** the clinical development of new treatments for SCLC has been limited in recent years,a better understanding of oncogenic driver alterations has found potential novel targets that might be suitable for therapeutic ***,there are six types of potential treatable signaling pathways in SCLC,including signaling pathways targeting the cell cycle and DNA repair,tumor development,cell metabolism,epigenetic regulation,tumor immunity and *** this point,however,there is still a lack of understanding of their role in SCLC tumor biology and the promotion of cancer *** optimizing drug targets,improving drug pharmacology,and identifying potential biomarkers are the main focus and further efforts are required to recognize patients who benefit most from novel therapies in *** review will focus on the current learning on the signaling pathways,the status of immunotherapy,and targeted therapy in SCLC.

关键词： metabolism immunity alterations

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From chip-in-a-lab to lab-on-a-chip:a portable Coulter counter using a modular platform

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Microsystems & Nanoengineering 2018年第1期4卷 57-64页

作者： Stefan Dekker Pelin Kubra Isgor tobias Feijten Loes I.Segerink Mathieu Odijk BIOS Lab on Chip Group MESA+Institute for NanotechnologyUniversity of Twente7500 AE EnschedeNetherlands

The field of microfluidics has been struggling to obtain widespread market *** order to overcome this struggle,a standardized and modular platform is introduced and *** providing easy-to-fabricate modular building blocks which are compatible with mass manufacturing,we decrease the gap from *** standardized blocks are used in combination with an application-specific fluidic circuit *** this board,electrical and fluidic connections are demonstrated by implementing an alternating current Coulter *** multipurpose building block is reusable in many *** this study,it identifies and counts 6 and 11μm *** system is kept in a credit card-sized footprint,as a result of in-house-developed electronics and standardized building *** believe that this easy-to-fabricate,credit card-sized,modular,and standardized prototype brings us closer to clinical and veterinary applications,because it provides an essential stepping stone to fully integrated point-of-care devices.

关键词： sized portable closer

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Ab initio density response and local field factor of warm dense hydrogen

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Matter and Radiation at Extremes 2024年第5期9卷 48-67页

作者： tobias Dornheim Sebastian Schwalbe Panagiotis Tolias Maximilian P.Böhme Zhandos A.Moldabekov Jan Vorberger Center for Advanced Systems Understanding(CASUS) D-02826 GörlitzGermany Helmholtz-Zentrum Dresden-Rossendorf(HZDR) D-01328 DresdenGermany Space and Plasma Physics Royal Institute of Technology(KTH)Stockholm SE-10044Sweden Technische Universität Dresden D-01062 DresdenGermany

We present quasi-exact ab initio path integral Monte Carlo(PIMC)results for the partial static density responses and local field factors of hydrogen in the warm dense matter regime,from solid density conditions to the strongly compressed *** full dynamic treatment of electrons and protons on the same footing allows us to rigorously quantify both electronic and ionic exchange–correlation effects in the system,and to compare the results with those of earlier incomplete models such as the archetypal uniform electron gas or electrons in a fixed ion snapshot potential that do not take into account the interplay between the two *** full electronic density response is highly sensitive to electronic localization around the ions,and our results constitute unambiguous predictions for upcoming X-ray Thomson scattering experiments with hydrogen jets and fusion *** PIMC results are made freely available and can be used directly for a gamut of applications,including inertial confinement fusion calculations and the modeling of dense astrophysical ***,they constitute invaluable benchmark data for approximate but computationally less demanding approaches such as density functional theory or PIMC within the fixed-node approximation.

关键词： local incomplete rigorous

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Pro?ling and Validation of the Circular RNA Repertoire in Adult Murine Hearts

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Genomics, Proteomics & Bioinformatics 2016年第4期14卷 216-223页

作者： tobias Jakobi Lisa F. Czaja-Hasse Richard Reinhardt Christoph Dieterich Section of Bioinformatics and Systems Cardiology Department of Internal Medicine IIIUniversity Hospital Heidelberg 69120 HeidelbergGermany German Centre for Cardiovascular Research(DZHK) Heidelberg/Mannheim.Germany Max Planck-Genome-Centre Cologne 50829 CologneGermany

For several decades, cardiovascular disease has been the leading cause of death throughout all countries. There is a strong genetic component to many disease subtypes （e.g., cardiomyopa- thy） and we are just beginning to understand the relevant genetic factors. Several studies have related RNA splicing to cardiovascular disease and circular RNAs （circRNAs） are an emerging player, circRNAs, which originate through back-splicing events from primary transcripts, are resis- tant to exonucleases and typically not polyadenylated. Initial functional studies show clear phenotypic outcomes for selected circRNAs. We provide, for the first time, a comprehensive catalogue of RNase R-resistant circRNA species for the adult murine heart. This work combines state-of-the-art circle sequencing with our novel DCC software to explore the circRNA landscape of heart tissue. Overall, we identified 575 circRNA species that pass a beta-binomial test for enrichment （false discovery rate of 1%） in the exonuclease-treated sequencing sample. Several circRNAs can be directly attributed to host genes that have been previously described as associated with cardiovascular disease. Further studies of these candidate circRNAs may reveal disease-relevant properties or functions of specific circRNAs.

关键词： Circular RNA circSeq Cardiovascular disease Cardiomyopathy Computational cardiology

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Get it white: color-tunable AC/DC OLEDs

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Light(Science & Applications) 2015年第1期4卷 492-497页

作者： Markus Frobel tobias Schwab Mona Kliem Simone Hofmann Karl Leo Malte C Gather Institute for Applied Photophysics(IAPP) Dresden University of TechnologyD-01069 DresdenGermany School of Physics and Astronomy University of St AndrewsSt Andrews KY169SSUK

Organic light-emitting diodes(OLEDs)have gained considerable attention because of their use of inherently flexible materials and their compatibility with facile roll-to-roll and printing *** addition to high efficiency,flexibility and transparency,reliable color tunability of solid state light sources is a desirable feature in the lighting and display ***,we demonstrate a device concept for highly efficient organic light-emitting devices whose emission color can be easily adjusted from deep-blue through cold-white and warm-white to saturated *** approach exploits the different polarities of the positive and negative half-cycles of an alternating current(AC)driving signal to independently address a fluorescent blue emission unit and a phosphorescent yellow emission unit which are vertically stacked on top of each *** electrode design is optimized for simple fabrication and driving and allows for two-terminal operation by a single *** presented concept for color-tunable OLEDs is compatible with application requirements and versatile in terms of emitter combinations.

关键词： alternating current color mixing color tuning vertical stacking white organic light-emitting devices

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Transfer learning from synthetic data for open-circuit voltage curve reconstruction and state of health estimation of lithium-ion batteries from partial charging segments

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Energy and AI 2024年第3期17卷 80-97页

作者： tobias Hofmann Jacob Hamar Bastian Mager Simon Erhard Jan Philipp Schmidt Chair of Systems Engineering for Electrical Energy Storage University of BayreuthWeiherstraße 26Bayreuth95448BavariaGermany BMW Group Petuelring 130Munich80809BavariaGermany

Data-driven models for battery state estimation require extensive experimental training data,which may not be available or suitable for specific tasks like open-circuit voltage(OCV)reconstruction and subsequent state of health(SOH)*** study addresses this issue by developing a transfer-learning-based OCV reconstruction model using a temporal convolutional long short-term memory(TCN-LSTM)network trained on synthetic data from an automotive nickel cobalt aluminium oxide(NCA)cell generated through a mechanistic model *** data consists of voltage curves at constant temperature,C-rates between C/30 to 1C,and a SOH-range from 70%to 100%.The model is refined via Bayesian optimization and then applied to four use cases with reduced experimental nickel manganese cobalt oxide(NMC)cell training data for higher use *** TL models’performances are compared with models trained solely on experimental data,focusing on different C-rates and voltage *** results demonstrate that the OCV reconstruction mean absolute error(MAE)within the average battery electric vehicle(BEV)home charging window(30%to 85%state of charge(SOC))is less than 22 mV for the first three use cases across all *** SOH estimated from the reconstructed OCV exhibits an mean absolute percentage error(MAPE)below 2.2%for these *** study further investigates the impact of the source domain on TL by incorporating two additional synthetic datasets,a lithium iron phosphate(LFP)cell and an entirely artificial,non-existing,cell,showing that solely the shifting and scaling of gradient changes in the charging curve suffice to transfer knowledge,even between different cell chemistries.A key limitation with respect to extrapolation capability is identified and evidenced in our fourth use case,where the absence of such comprehensive data hindered the TL process.

关键词： Lithium-ion battery State of health estimation Transfer learning OCV curve Partial charging Synthetic data

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Assessing hydrological and provisioning ecosystem services in a case study in Western Central Brazil

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Ecological Processes 2014年第1期3卷 248-262页

作者： Lars Koschke Carsten Lorz Christine Fürst tobias Lehmann Franz Makeschin Department of Soil Science and Site Ecology Dresden University of TechnologyPienner Str.1901737 TharandtGermany Faculty for Woods and Forestry Forest PedologyGeology and Site EcologyHochschuleWeihenstephan-TriesdorfUniversity of Applied SciencesFreisingGermany Center for Development Research Department of Ecology and Natural Resources ManagementUniversity of BonnWalter-Flex-Str.353113 BonnGermany

Introduction:Current land use in the Federal District,Western Central Brazil,causes problems related to the water supply which are linked to the regulation of ecosystem services(ES).In scope of an Integrated Water Resources Management concept,we further developed the web-based planning support tool GISCAME for the Pipiripau river basin case ***:We introduced analyses on ecosystem potentials in the raster-based tool to assess,in a spatially explicit manner,the scenario impact on water purification,sediment retention,water retention,and provision of food and fodder in order to identify potential pathways for conserving water *** demonstrate the method,we assess ES depending on a number of land use/land cover change(LULCC)***:We found that a considerable increase of water purification and sediment retention is difficult to achieve with realistic small scale LULCC,mainly because in areas with a low potential to provide hydrological ES and thus with a high demand for sustainable land use,such as native Savanna(Cerrado)and natural forests(Mata),favorable land uses were often already *** observed synergies in the response of regulating hydrological ES to LULCC but at the same time also trade-offs with provision of food and ***:Our findings suggest that further degradation and loss of Cerrado and Mata must be avoided and their restoration should be promoted in order to safeguard water *** suggest that restoration measures should be focused on arable land located at steep slopes near surface waters to effectively increase hydrological ES through the marginal reduction of provision services.

关键词： services retention provision

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Adhesive wear mechanisms uncovered by atomistic simulations

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Friction 2018年第3期6卷 245-259页

作者： Jean-Fran?ois MOLINARI Ramin AGHABABAEI tobias BRINK Lucas FRéROT Enrico MILANESE Civil Engineering Department Materials Science Department école Polytechnique Fédérale de Lausanne Department of Engineering-Mechanical Engineering Aarhus Universitet

In this review, we discuss our recent advances in modeling adhesive wear mechanisms using coarse-grained atomistic simulations. In particular, we present how a model pair potential reveals the transition from ductile shearing of an asperity to the formation of a debris particle. This transition occurs at a critical junction size, which determines the particle size at its birth. Atomistic simulations also reveal that for nearby asperities, crack shielding mechanisms result in a wear volume proportional to an effective area larger than the real contact area. As the density of microcontacts increases with load, we propose this crack shielding mechanism as a key to understand the transition from mild to severe wear. We conclude with open questions and a road map to incorporate these findings in mesoscale continuum models. Because these mesoscale models allow an accurate statistical representation of rough surfaces, they provide a simple means to interpret classical phenomenological wear models and wear coefficients from physics-based principles.

关键词： adhesive wear molecular dynamics continuum mechanics

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