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Observation of a single protein by ultrafast X-ray diffraction

Light(Science & Applications) 2024年第1期13卷 80-90页

作者： Tomas Ekeberg Dameli Assalauova Johan Bielecki Rebecca Boll Benedikt J.Daurer Lutz A.Eichacker Linda E.Franken Davide E.Galli Luca Gelisio Lars Gumprecht Laura H.Gunn Janos Hajdu Robert Hartmann Dirk Hasse Alexandr Ignatenko Jayanath Koliyadu Olena Kulyk Ruslan Kurta Markus Kuster Wolfgang Lugmayr Jannik Lübke Adrian P.Mancuso Tommaso Mazza Carl Nettelblad Yevheniy Ovcharenko daniel E.Rivas Max Rose Amit K.Samanta Philipp Schmidt Egor Sobolev Nicusor Timneanu Sergey Usenko daniel westphal Tamme Wollweber Lena Worbs Paul Lourdu Xavier Hazem Yousef Kartik Ayyer Henry N.Chapman Jonas A.Sellberg Carolin Seuring Ivan A.Vartanyants Jochen Küpper Michael Meyer Filipe R.N.C.Maia Laboratory of Molecular Biophysics Department of Cell and Molecular BiologyUppsala UniversityHusargatan 3(Box 596)SE-75124 UppsalaSweden Deutsches Electronen-Synchrotron DESY Notkestrasse 8522607 HamburgGermany European XFEL Holzkoppel 422869 SchenefeldGermany Diamond Light Source Harwell Science&Innovation CampusDidcot OX110DEUK University of Stavanger Centre Organelle ResearchRichard-Johnsensgate 44021 StavangerNorway Leibniz Institute for Experimental Virology(HPI) Centre for Structural Systems BiologyNotkestraße 8522607 HamburgGermany Dipartimento di Fisica“Aldo Pontremoli” Universitàdegli Studi di Milanovia Celoria 1620133 MilanoItaly Center for Free-Electron Laser Science DESY22607 HamburgGermany Plant Biology Section School of Integrative Plant ScienceCornell UniversityIthacaNY 14853USA PNSensor GmbH Otto-Hahn-Ring 6D-81739 MünchenGermany Biomedical and X-Ray Physics Department of Applied PhysicsAlbaNova University CenterKTH Royal Institute of TechnologySE-10691 StockholmSweden ELI Beamlines/IoP Institute of Physics AS CR v.v.i.Na Slovance 218221 Prague 8Czech Republic Multi-User CryoEM Facility Centre for Structural Systems BiologyNotkestr.8522607 HamburgGermany University Medical Center Hamburg-Eppendorf(UKE) Martinistrasse 5220246 HamburgGermany The Hamburg Center for Ultrafast Imaging Universität HamburgLuruper Chaussee 14922761 HamburgGermany Department of Physics Universität HamburgLuruper Chaussee 14922761 HamburgGermany Department of Chemistry and Physics La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVIC 3086Australia Division of Scientific Computing Science for Life LaboratoryDepartment of Information TechnologyUppsala UniversityBox 337SE-75105 UppsalaSweden European Molecular Biology Laboratory c/o DESYNotkestrasse 8522607 HamburgGermany Department of Physics and Astronomy Uppsala UniversityBox 516SE-75120 UppsalaSweden Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 14922761 HamburgGe

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired *** was one of the arguments for building X-ray free-electron *** to theory,the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier,and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably *** was first demonstrated on biological samples a decade ago on the giant *** then,a large collaboration has been pushing the limit of the smallest sample that can be *** ability to capture snapshots on the timescale of atomic vibrations,while keeping the sample at room temperature,may allow probing the entire conformational phase space of *** we show the first observation of an X-ray diffraction pattern from a single protein,that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays,and demonstrate that the concept of diffraction before destruction extends to single *** the pattern,it is possible to determine the approximate orientation of the *** experiment demonstrates the feasibility of ultrafast imaging of single proteins,opening the way to single-molecule time-resolved studies on the femtosecond timescale.

关键词： smallest intense ultrafast

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Amyloid-β-induced disruption of axon-initial-segment mitochondria localization:consequences for TAU missorting in Alzheimer's disease pathology

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Neural Regeneration Research 2025年第5期20卷 1407-1408页

作者： daniel Adam Felix Langerscheidt Hans Zempel Institute of Human Genetics University Hospital CologneCologneGermany Center for Molecular Medicine Cologne(CMMC) University of CologneCologneGermany

TAU is a neuronal microtubule-associated protein preferentially located in *** a battery of neurodegenerative diseases termed"tauopathies,"including Alzheimer's disease (AD),TAU is missorted and abnormally phosphorylated,leading to filamentous accumulations of hyperphosphorylated TAU,a pathological hallmark and potential disease driver of AD and related tauopathies (Zempel,2024).

关键词： Alzheimer tau diseases

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Instream coliform gradients in the Holtemme, a small headwater stream in the Elbe River Basin, Northern Germany

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Frontiers of Earth Science 2017年第3期11卷 544-553页

作者： daniel KARTHE Pei-Ying LIN Katja westphal Helmholtz Centre for Environmental Research Magdeburg Germany Department of Geography Gottingen University Germany Institute of Applied Geology Central University Taiwan China

The Holtemme is a small headwater stream in North Germany＇s Elbe River Basin. According to German and European legislation, hygienic monitoring is not mandatory for such water bodies which are neither drinking water sources nor categorized as bathing waters. Consequently, relatively little is known about the occur- rence of-potentially pathogenic- bacteria and viruses in Germany＇s streams and rivers. The Holtemme was selected for a case study because it is relatively well monitored for both chemical water quality and aquatic ecology, but not for hygiene. Originating in the mountains of Harz Nature Park, the 47 km long Holtemme is characterized by a strong longitudinal gradient in chemical water quality, which is related to different land uses and the influx of treated wastewater from two urban areas （Wernigerode and Halberstadt）. Waste water loads received by the Holtemme are comparatively high when compared to similarly small streams. In 2015, total coliform concentrations between more than 200 and 77,010 bacteria per 100 mL, and fecal coliform concentrations between 5 and 24,060 bacteria per I00 mL were observed in the Holtemme＇s main channel. The highest concentrations were typically found below the outlets of the two wastewater treatment plants. The treated wastewater contained total and fecal coliform concentra- tions of up to 200,500 and 83,100 per 100 mL, respectively; however, there were significant temporal variations. While the observed concentrations are unpro- blematic from a legal perspective （because no maximum permissible limits are defined for streams in Germany）, they would exceed the tolerable limits for bathing waters in the EU, indicating moderate to critical pollution limits.

关键词： surface water stream hygine instream coli-forms

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Vascular endothelial growth factor:a double-edged sword in the development of white matter lesions

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Neural Regeneration Research 2025年第1期20卷 191-192页

作者： Narek Manukjan daniel Fulton Zubair Ahmed WMatthijs Blankesteijn Sébastien Foulquier Department of Pharmacology and Toxicology Maastricht UniversityMaastrichtThe Netherlands CARIM-School for Cardiovascular Diseases Maastricht UniversityMaastrichtThe Netherlands Neuroscience and Ophthalmology Institute of Inflammation and AgeingUniversity of BirminghamEdgbastonBirminghamUK Centre for Trauma Sciences Research University of BirminghamEdgbastonBirminghamUK MHeNs-School for Mental Health and Neuroscience Maastricht UniversityMaastrichtThe Netherlands Department of Neurology Maastricht University Medical CenterMaastrichtThe Netherlands

As the population ages,the burden of age-related diseases becomes ***,over 55 million people suffer from dementia worldwide,with Alzheimer’s disease being the most common ***,it is becoming clearer that underlying vascular pathology such as cerebral small vessel disease(cSVD)may be a more detrimental cause for dementia(Cuadrado-Godia et al.,2018).It is estimated that 10%-30%of the elderly population and 35%-90%of all dementia patients exhibit signs of *** term cSVD refers to pathology affecting the small vessels of the brain,which can lead to lacunar cerebral infarcts,enlarged perivascular spaces,and cortical hemorrhages(Cuadrado-Godia et al.,2018).CSVD is often associated with cognitive decline,gait problems,and dementia(Cuadrado-Godia et al.,2018).

关键词： pathology becoming white

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Complement-dependent neuroinflammation in spinal cord injury:from pathology to therapeutic implications

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Neural Regeneration Research 2025年第5期20卷 1324-1335页

作者： Hassan Saad Bachar El Baba Ali Tfaily Firas Kobeissy Juanmarco Gutierrez Gonzalez daniel Refai Gerald R.Rodts Christian Mustroph David Gimbel Jonathan Grossberg daniel L.Barrow Matthew F.Gary Ali M.Alawieh Department of Neurosurgery Emory University School of MedicineAtlantaGAUSA Department of Neurology Yale UniversityNew HavenCTUSA Center for Neurotrauma Multiomics&Biomarkers(CNMB)Morehouse School of MedicineAtlantaGAUSA

Spinal cord injury remains a major cause of disability in young adults,and beyond acute decompression and rehabilitation,there are no pharmacological treatments to limit the progression of injury and optimize recovery in this *** the thorough investigation of the complement system in triggering and propagating cerebral neuroinflammation,a similar role for complement in spinal neuroinflammation is a focus of ongoing *** this work,we survey the current literature investigating the role of complement in spinal cord injury including the sources of complement proteins,triggers of complement activation,and role of effector functions in the *** study relevant data demonstrating the different triggers of complement activation after spinal cord injury including direct binding to cellular debris,and or activation via antibody binding to damage-associated molecular *** effector functions of complement have been implicated in spinal cord injury,and we critically evaluate recent studies on the dual role of complement anaphylatoxins in spinal cord injury while emphasizing the lack of pathophysiological understanding of the role of opsonins in spinal cord *** this pathophysiological review,we systematically review the different translational approaches used in preclinical models of spinal cord injury and discuss the challenges for future translation into human *** review emphasizes the need for future studies to dissect the roles of different complement pathways in the pathology of spinal cord injury,to evaluate the phases of involvement of opsonins and anaphylatoxins,and to study the role of complement in white matter degeneration and regeneration using translational strategies to supplement genetic models.

关键词： complement neuroinflammation neuroplasticity regeneration spinal cord injury targeted therapy

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Regulator of G protein signaling 6 mediates exercise-induced recovery of hippocampal neurogenesis,learning,and memory in a mouse model of Alzheimer’s disease

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Neural Regeneration Research 2025年第10期20卷 2969-2981页

作者： Mackenzie M.Spicer Jianqi Yang daniel Fu Alison N.DeVore Marisol Lauffer Nilufer S.Atasoy Deniz Atasoy Rory A.Fisher Department of Neuroscience and Pharmacology University of Iowa Carver College of MedicineIowa CityIAUSA Iowa Neuroscience Institute University of Iowa Carver College of MedicineIowa CityIAUSA Interdisciplinary Graduate Program in Molecular Medicine University of Iowa Carver College of MedicineIowa CityIAUSA Neural Circuits and Behavior Core University of Iowa Carver College of MedicineIowa CityIAUSA

Hippocampal neuronal loss causes cognitive dysfunction in Alzheimer’s *** hippocampal neurogenesis is reduced in patients with Alzheimer’s *** stimulates adult hippocampal neurogenesis in rodents and improves memory and slows cognitive decline in patients with Alzheimer’s ***,the molecular pathways for exercise-induced adult hippocampal neurogenesis and improved cognition in Alzheimer’s disease are poorly ***,regulator of G protein signaling 6(RGS6)was identified as the mediator of voluntary running-induced adult hippocampal neurogenesis in ***,we generated novel RGS6fl/fl;APP_(SWE) mice and used retroviral approaches to examine the impact of RGS6 deletion from dentate gyrus neuronal progenitor cells on voluntary running-induced adult hippocampal neurogenesis and cognition in an amyloid-based Alzheimer’s disease mouse *** found that voluntary running in APP_(SWE) mice restored their hippocampal cognitive impairments to that of control *** cognitive rescue was abolished by RGS6 deletion in dentate gyrus neuronal progenitor cells,which also abolished running-mediated increases in adult hippocampal *** hippocampal neurogenesis was reduced in sedentary APP_(SWE) mice versus control mice,with basal adult hippocampal neurogenesis reduced by RGS6 deletion in dentate gyrus neural precursor ***6 was expressed in neurons within the dentate gyrus of patients with Alzheimer’s disease with significant loss of these RGS6-expressing ***,RGS6 mediated voluntary running-induced rescue of impaired cognition and adult hippocampal neurogenesis in APP_(SWE) mice,identifying RGS6 in dentate gyrus neural precursor cells as a possible therapeutic target in Alzheimer’s disease.

关键词： adult hippocampal neurogenesis Alzheimer’s disease dentate gyrus exercise learning/memory neural precursor cells regulator of G protein signaling 6(RGS6)

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Gastric polyps are not created equal: Know your enemy

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World Journal of Gastroenterology 2025年第2期31卷 144-146页

作者： Fady daniel Department of Gastroenterology and Hepatology American University of Beirut Medical CenterBeirut 11072020Lebanon

Gastric polyps are commonly detected during upper gastrointestinal *** are most often benign and rarely become ***,adequate knowledge,diagnostic modalities,and management strategies should be the endoscopist’s readily available“weapons”to defeat the potentially malignant“enemies”.This article sheds light on the valuable effort by Costa et al to generate a new classification system of gastric polyps as“good”,“bad”,and“ugly”.This comprehensive overview provides clinicians with a simplified decision-making process.

关键词： Gastric polyps Polypoid subepithelial lesions Early gastric cancer Endoscopic ultrasonography Electronic chromoendoscopy

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Kernel-Based State-Space Kriging for Predictive Control

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IEEE/CAA Journal of Automatica Sinica 2023年第5期10卷 1263-1275页

作者： A.daniel Carnerero daniel R.Ramirez daniel Limon Teodoro Alamo the Department of System Engineering and Automation University of SevilleSevilla 41020Spain the School of Engineering Tokyo Institute of TechnologyTokyo 152-8552Japan Department of System Engineering and Automation University of SevilleSevilla 41020Spain

In this paper, we extend the state-space kriging(SSK) modeling technique presented in a previous work by the authors in order to consider non-autonomous systems. SSK is a data-driven method that computes predictions as linear combinations of past outputs. To model the nonlinear dynamics of the system, we propose the kernel-based state-space kriging(K-SSK), a new version of the SSK where kernel functions are used instead of resorting to considerations about the locality of the data. Also, a Kalman filter can be used to improve the predictions at each time step in the case of noisy measurements. A constrained tracking nonlinear model predictive control(NMPC) scheme using the black-box input-output model obtained by means of the K-SSK prediction method is proposed. Finally, a simulation example and a real experiment are provided in order to assess the performance of the proposed controller.

关键词： Data-driven methods model identification Kernel methods predictive control

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Nanosecond modulation of thermal emission

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Light(Science & Applications) 2019年第1期8卷 574-576页

作者： daniel Wasserman Department of Electrical and Computer Engineering University of Texas AustinAustinTX 78758USA

Femtosecond laser pulses are used to modulate the thermal emission from semiconductor materials at the nanosecond timescale.A visible-frequency laser photoexcites energetic free carriers in intrinsic Si and GaAs *** these free carriers return to equilibrium,they not only emit thermal radiation on a picosecond time scale but also modulate the semiconductor thermal emission on a nanosecond to microsecond time scale,offering a novel route towards ultrafast infrared optical pulses.

关键词： thermal laser Femto

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Space Deformations,Surface Deformations and the Opportunities In-Between

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Journal of Computer Science & Technology 2009年第1期24卷 2-5页

作者： daniel Cohen-Or School of Computer Science Tel-Aviv UniversityIsrael

In recent years we have witnessed a large interest in surface deformation techniques. This has been a reaction that can be attributed to the ability to develop techniques which are detail-preserving. Space deformation techniques, on the other hand, received less attention, but nevertheless they have many advantages over surface-based techniques. This paper explores the potential of these two approaches to deformation and discusses the opportunities that the fusion of the two may lead to.

关键词： space deformation mesh editing digital surfaces

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