Journal of Synchrotron Radiation最新文献_第5页

Application study of infrared free-electron lasers towards the development of amyloidosis therapy. 红外自由电子激光器在淀粉样变治疗发展中的应用研究。

IF 2.5 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2022-09-01 Epub Date: 2022-08-12 DOI: 10.1107/S1600577522007330

Mikiko Jindo, Kazuhiro Nakamura, Hisashi Okumura, Koichi Tsukiyama, Takayasu Kawasaki

{"title":"Application study of infrared free-electron lasers towards the development of amyloidosis therapy.","authors":"Mikiko Jindo, Kazuhiro Nakamura, Hisashi Okumura, Koichi Tsukiyama, Takayasu Kawasaki","doi":"10.1107/S1600577522007330","DOIUrl":"https://doi.org/10.1107/S1600577522007330","url":null,"abstract":"Amyloidosis is known to be caused by the deposition of amyloid fibrils into various biological tissues; effective treatments for the disease are little established today. An infrared free-electron laser (IR-FEL) is an accelerator-based picosecond-pulse laser having tunable infrared wavelengths. In the current study, the irradiation effect of an IR-FEL was tested on an 11-residue peptide (NFLNCYVSGFH) fibril from β2-microglobulin (β2M) with the aim of applying IR-FELs to amyloidosis therapy. Infrared microspectroscopy (IRM) and scanning electron microscopy showed that a fibril of β2M peptide was clearly dissociated by IR-FEL at 6.1 µm (amide I) accompanied by a decrease of the β-sheet and an increase of the α-helix. No dissociative process was recognized at 6.5 µm (amide II) as well as at 5.0 µm (non-specific wavelength). Equilibrium molecular dynamics simulations indicated that the α-helix can exist stably and the probability of forming interchain hydrogen bonds associated with the internal asparagine residue (N4) is notably reduced compared with other amino acids after the β-sheet is dissociated by amide I specific irradiation. This result implies that N4 plays a key role for recombination of hydrogen bonds in the dissociation of the β2M fibril. In addition, the β-sheet was disrupted at temperatures higher than 340 K while the α-helix did not appear even though the fibril was heated up to 363 K as revealed by IRM. The current study gives solid evidence for the laser-mediated conversion from β-sheet to α-helix in amyloid fibrils at the molecular level.","PeriodicalId":17114,"journal":{"name":"Journal of Synchrotron Radiation","volume":"29 Pt 5","pages":"1133-1140"},"PeriodicalIF":2.5,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9455209/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33448936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Beamline simulations using monochromators with high d-spacing crystals. 用高d间距晶体单色仪进行光束线模拟。

IF 2.5 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2022-09-01 Epub Date: 2022-08-12 DOI: 10.1107/S160057752200707X

X J Yu, X Chi, T Smulders, A T S Wee, A Rusydi, M Sanchez Del Rio, M B H Breese

{"title":"Beamline simulations using monochromators with high d-spacing crystals.","authors":"X J Yu, X Chi, T Smulders, A T S Wee, A Rusydi, M Sanchez Del Rio, M B H Breese","doi":"10.1107/S160057752200707X","DOIUrl":"https://doi.org/10.1107/S160057752200707X","url":null,"abstract":"Monochromators for synchrotron radiation beamlines typically use perfect crystals for the hard X-ray regime and gratings for soft X-rays. There is an intermediate range, typically 1-3 keV (tender X-rays), which common perfect crystals have difficulties covering and gratings have low efficiency, although some less common crystals with high d-spacing could be suitable. To evaluate the suitability of these crystals for a particular beamline, it is useful to evaluate the crystals' performance using tools such as ray-tracing. However, simulations for double-crystal monochromators are only available for the most used crystals such as Si, Ge or diamond. Here, an upgrade of the SHADOW ray-tracing code and complementary tools in the OASYS suite are presented to simulate high d-spacing crystals with arbitrary, and sometimes complex, structures such as beryl, YB66, muscovite, etc. Isotropic and anisotropic temperature factors are also considered. The YB66 crystal with 1936 atomic sites in the unit cell is simulated, and its applicability for tender X-ray monochromators is discussed in the context of new low-emittance storage rings.","PeriodicalId":17114,"journal":{"name":"Journal of Synchrotron Radiation","volume":"29 Pt 5","pages":"1157-1166"},"PeriodicalIF":2.5,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9455208/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33449318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multicolor single-analyzer high-energy-resolution XES spectrometer for simultaneous examination of different elements. 多色单分析仪高能量分辨率XES光谱仪，可同时检测不同元素。

IF 2.5 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2022-09-01 Epub Date: 2022-08-12 DOI: 10.1107/S1600577522007561

Antal Mikeházi, Jihad El Guettioui, István B Földes, György Vankó, Zoltán Németh

引用次数: 0

AXEAP: a software package for X-ray emission data analysis using unsupervised machine learning. AXEAP:使用无监督机器学习进行x射线发射数据分析的软件包。

IF 2.5 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2022-09-01 Epub Date: 2022-07-21 DOI: 10.1107/S1600577522006786

In Hui Hwang, Mikhail A Solovyev, Sang Wook Han, Maria K Y Chan, John P Hammonds, Steve M Heald, Shelly D Kelly, Nicholas Schwarz, Xiaoyi Zhang, Cheng Jun Sun

引用次数: 2

3D deep convolutional neural network segmentation model for precipitate and porosity identification in synchrotron X-ray tomograms. 三维深度卷积神经网络分割模型在同步加速器x射线层析成像中的沉淀和孔隙度识别。

IF 2.5 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2022-09-01 Epub Date: 2022-07-29 DOI: 10.1107/S1600577522006816

S Gaudez, M Ben Haj Slama, A Kaestner, M V Upadhyay

{"title":"3D deep convolutional neural network segmentation model for precipitate and porosity identification in synchrotron X-ray tomograms.","authors":"S Gaudez, M Ben Haj Slama, A Kaestner, M V Upadhyay","doi":"10.1107/S1600577522006816","DOIUrl":"https://doi.org/10.1107/S1600577522006816","url":null,"abstract":"New developments at synchrotron beamlines and the ongoing upgrades of synchrotron facilities allow the possibility to study complex structures with a much better spatial and temporal resolution than ever before. However, the downside is that the data collected are also significantly larger (more than several terabytes) than ever before, and post-processing and analyzing these data is very challenging to perform manually. This issue can be solved by employing automated methods such as machine learning, which show significantly improved performance in data processing and image segmentation than manual methods. In this work, a 3D U-net deep convolutional neural network (DCNN) model with four layers and base-8 characteristic features has been developed to segment precipitates and porosities in synchrotron transmission X-ray micrograms. Transmission X-ray microscopy experiments were conducted on micropillars prepared from additively manufactured 316L steel to evaluate precipitate information. After training the 3D U-net DCNN model, it was used on unseen data and the prediction was compared with manual segmentation. A good agreement was found between both segmentations. An ablation study was performed and revealed that the proposed model showed better statistics than other models with lower numbers of layers and/or characteristic features. The proposed model is able to segment several hundreds of gigabytes of data in a few minutes and could be applied to other materials and tomography techniques. The code and the fitted weights are made available with this paper for any interested researcher to use for their needs (https://github.com/manasvupadhyay/erc-gamma-3D-DCNN).","PeriodicalId":17114,"journal":{"name":"Journal of Synchrotron Radiation","volume":"29 Pt 5","pages":"1232-1240"},"PeriodicalIF":2.5,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9455210/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33449326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Highly efficient thermal deformation optimization method for smart-cut mirrors over the entire photon energy range. 智能切割镜在整个光子能量范围内的高效热变形优化方法。

IF 2.4 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2022-09-01 Epub Date: 2022-07-29 DOI: 10.1107/S1600577522007160

Shaofeng Wang, Dongni Zhang, Ming Li, Lidan Gao, Minwei Chen, Fugui Yang, Weifan Sheng

引用次数: 0

High-resolution XEOL spectroscopy setup at the X-ray absorption spectroscopy beamline P65 of PETRA III. PETRA III 的 X 射线吸收光谱光束线 P65 上的高分辨率 XEOL 光谱装置。

IF 2.4 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2022-09-01 Epub Date: 2022-08-11 DOI: 10.1107/S1600577522007287

S Levcenko, R Biller, T Pfeiffelmann, K Ritter, H H Falk, T Wang, S Siebentritt, E Welter, C S Schnohr

引用次数: 0

Pump-probe capabilities at the SPB/SFX instrument of the European XFEL. 欧洲 XFEL 的 SPB/SFX 仪器的泵探能力。

IF 2.4 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2022-09-01 Epub Date: 2022-07-21 DOI: 10.1107/S1600577522006701

Jayanath C P Koliyadu, Romain Letrun, Henry J Kirkwood, Jia Liu, Man Jiang, Moritz Emons, Richard Bean, Valerio Bellucci, Johan Bielecki, Sarlota Birnsteinova, Raphael de Wijn, Thomas Dietze, Juncheng E, Jan Grünert, Daniel Kane, Chan Kim, Yoonhee Kim, Max Lederer, Bradley Manning, Grant Mills, Luis L Morillo, Nadja Reimers, Dimitrios Rompotis, Adam Round, Marcin Sikorski, Cedric M S Takem, Patrik Vagovič, Sandhya Venkatesan, Jinxiong Wang, Ulrike Wegner, Adrian P Mancuso, Tokushi Sato

{"title":"Pump-probe capabilities at the SPB/SFX instrument of the European XFEL.","authors":"Jayanath C P Koliyadu, Romain Letrun, Henry J Kirkwood, Jia Liu, Man Jiang, Moritz Emons, Richard Bean, Valerio Bellucci, Johan Bielecki, Sarlota Birnsteinova, Raphael de Wijn, Thomas Dietze, Juncheng E, Jan Grünert, Daniel Kane, Chan Kim, Yoonhee Kim, Max Lederer, Bradley Manning, Grant Mills, Luis L Morillo, Nadja Reimers, Dimitrios Rompotis, Adam Round, Marcin Sikorski, Cedric M S Takem, Patrik Vagovič, Sandhya Venkatesan, Jinxiong Wang, Ulrike Wegner, Adrian P Mancuso, Tokushi Sato","doi":"10.1107/S1600577522006701","DOIUrl":"10.1107/S1600577522006701","url":null,"abstract":"Pump-probe experiments at X-ray free-electron laser (XFEL) facilities are a powerful tool for studying dynamics at ultrafast and longer timescales. Observing the dynamics in diverse scientific cases requires optical laser systems with a wide range of wavelength, flexible pulse sequences and different pulse durations, especially in the pump source. Here, the pump-probe instrumentation available for measurements at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of the European XFEL is reported. The temporal and spatial stability of this instrumentation is also presented.","PeriodicalId":17114,"journal":{"name":"Journal of Synchrotron Radiation","volume":"29 Pt 5","pages":"1273-1283"},"PeriodicalIF":2.4,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9455201/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33449331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A new Kirkpatrick-Baez-based scanning microscope for the Submicron Resolution X-ray Spectroscopy (SRX) beamline at NSLS-II. 用于 NSLS-II 亚微米分辨率 X 射线光谱学 (SRX) 光束线的基于 Kirkpatrick-Baez 的新型扫描显微镜。

IF 2.4 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2022-09-01 Epub Date: 2022-07-29 DOI: 10.1107/S1600577522007056

E Nazaretski, D S Coburn, W Xu, J Ma, H Xu, R Smith, X Huang, Y Yang, L Huang, M Idir, A Kiss, Y S Chu

引用次数: 0

Fe_0.79Si_0.07B_0.14 metallic glass gaskets for high-pressure research beyond 1 Mbar. 用于 1 Mbar 以上高压研究的 Fe0.79Si0.07B0.14 金属玻璃垫圈。

IF 2.4 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2022-09-01 Epub Date: 2022-08-19 DOI: 10.1107/S1600577522007573

Weiwei Dong, Konstantin Glazyrin, Saiana Khandarkhaeva, Timofey Fedotenko, Jozef Bednarčík, Eran Greenberg, Leonid Dubrovinsky, Natalia Dubrovinskaia, Hanns Peter Liermann

{"title":"Fe0.79Si0.07B0.14 metallic glass gaskets for high-pressure research beyond 1 Mbar.","authors":"Weiwei Dong, Konstantin Glazyrin, Saiana Khandarkhaeva, Timofey Fedotenko, Jozef Bednarčík, Eran Greenberg, Leonid Dubrovinsky, Natalia Dubrovinskaia, Hanns Peter Liermann","doi":"10.1107/S1600577522007573","DOIUrl":"10.1107/S1600577522007573","url":null,"abstract":"A gasket is an important constituent of a diamond anvil cell (DAC) assembly, responsible for the sample chamber stability at extreme conditions for X-ray diffraction studies. In this work, we studied the performance of gaskets made of metallic glass Fe0.79Si0.07B0.14 in a number of high-pressure X-ray diffraction (XRD) experiments in DACs equipped with conventional and toroidal-shape diamond anvils. The experiments were conducted in either axial or radial geometry with X-ray beams of micrometre to sub-micrometre size. We report that Fe0.79Si0.07B0.14 metallic glass gaskets offer a stable sample environment under compression exceeding 1 Mbar in all XRD experiments described here, even in those involving small-molecule gases (e.g. Ne, H2) used as pressure-transmitting media or in those with laser heating in a DAC. Our results emphasize the material's importance for a great number of delicate experiments conducted under extreme conditions. They indicate that the application of Fe0.79Si0.07B0.14 metallic glass gaskets in XRD experiments for both axial and radial geometries substantially improves various aspects of megabar experiments and, in particular, the signal-to-noise ratio in comparison to that with conventional gaskets made of Re, W, steel or other crystalline metals.","PeriodicalId":17114,"journal":{"name":"Journal of Synchrotron Radiation","volume":"29 Pt 5","pages":"1167-1179"},"PeriodicalIF":2.4,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9455203/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33449319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0