Serial crystallography is a powerful technique in structure determination using many small crystals at X-ray free-electron laser or synchrotron radiation facilities. The large diffraction data volumes require high-throughput software to preprocess the raw images for subsequent analysis. ClickX is a program designated for serial crystallography data preprocessing, capable of rapid data sorting for online feedback and peak-finding refinement by parameter optimization. The graphical user interface (GUI) provides convenient access to various operations such as pattern visualization, statistics plotting and parameter tuning. A batch job module is implemented to facilitate large-data-volume processing. A two-step geometry calibration for single-panel detectors is also integrated into the GUI, where the beam center and detector tilting angles are optimized using an ellipse center shifting method first, then all six parameters, including the photon energy and detector distance, are refined together using a residual minimization method. Implemented in Python, ClickX has good portability and extensibility, so that it can be installed, configured and used on any computing platform that provides a Python interface or common data file format. ClickX has been tested in online analysis at the Pohang Accelerator Laboratory X-ray Free-Electron Laser, Korea, and the Linac Coherent Light Source, USA. It has also been applied in post-experimental data analysis. The source code is available via https://github.com/LiuLab-CSRC/ClickX under a GNU General Public License.

A method for reconstructing the three-dimensional grain structure from data collected with a recently introduced laboratory-based X-ray diffraction contrast tomography system is presented. Diffraction contrast patterns are recorded in Laue-focusing geometry. The diffraction geometry exposes shape information within recorded diffraction spots. In order to yield the three-dimensional crystallographic microstructure, diffraction spots are extracted and fed into a reconstruction scheme. The scheme successively traverses and refines solution space until a reasonable reconstruction is reached. This unique reconstruction approach produces results efficiently and fast for well suited samples.

The examination of anisotropic nanostructures, such as wires, platelets or spikes, inside a transmission electron microscope is normally performed only in plan view. However, intrinsic defects such as growth twin interfaces could occasionally be concealed from direct observation for geometric reasons, leading to superposition. This article presents the shadow-focused ion-beam technique to prepare multiple electron-beam-transparent cross-section specimens of ZnO nanospikes, via a procedure which could be readily extended to other anisotropic structures. In contrast with plan-view data of the same nanospikes, here the viewing direction allows the examination of defects without superposition. By this method, the coexistence of two twin configurations inside the wurtzite-type structure is observed, namely [2 {overline 1} {overline 1} 0]^{ m W}/(0 1 {overline 1} 1) and [2 {overline 1} {overline 1} 0]^{ m W}/(0 1 {overline 1} 3), which were not identified during the plan-view observations owing to superposition of the domains. The defect arrangement could be the result of coalescence twinning of crystalline nuclei formed on the partially molten Zn substrate during the flame-transport synthesis. Three-dimensional defect models of the twin interface structures have been derived and are correlated with the plan-view investigations by simulation.

DatView is a new graphical user interface (GUI) for plotting parameters to explore correlations, identify outliers and export subsets of data. It was designed to simplify and expedite analysis of very large unmerged serial femtosecond crystallography (SFX) data sets composed of indexing results from hundreds of thousands of microcrystal diffraction patterns. However, DatView works with any tabulated data, offering its functionality to many applications outside serial crystallography. In DatView's user-friendly GUI, selections are drawn onto plots and synchronized across all other plots, so correlations between multiple parameters in large multi-parameter data sets can be rapidly identified. It also includes an item viewer for displaying images in the current selection alongside the associated metadata. For serial crystallography data processed by indexamajig from CrystFEL [White, Kirian, Martin, Aquila, Nass, Barty & Chapman (2012). J. Appl. Cryst. 45, 335–341], DatView generates a table of parameters and metadata from stream files and, optionally, the associated HDF5 files. By combining the functionality of several commonly needed tools for SFX in a single GUI that operates on tabulated data, the time needed to load and calculate statistics from large data sets is reduced. This paper describes how DatView facilitates (i) efficient feedback during data collection by examining trends in time, sample position or any parameter, (ii) determination of optimal indexing and integration parameters via the comparison mode, (iii) identification of systematic errors in unmerged SFX data sets, and (iv) sorting and highly flexible data filtering (plot selections, Boolean filters and more), including direct export of subset CrystFEL stream files for further processing.

A sample-injection device has been developed at SPring-8 Angstrom Compact Free-Electron Laser (SACLA) for serial femtosecond crystallography (SFX) at atmospheric pressure. Microcrystals embedded in a highly viscous carrier are stably delivered from a capillary nozzle with the aid of a coaxial gas flow and a suction device. The cartridge-type sample reservoir is easily replaceable and facilitates sample reloading or exchange. The reservoir is positioned in a cooling jacket with a temperature-regulated water flow, which is useful to prevent drastic changes in the sample temperature during data collection. This work demonstrates that the injector successfully worked in SFX of the human A2A adenosine receptor complexed with an antagonist, ZM241385, in lipidic cubic phase and for hen egg-white lysozyme microcrystals in a grease carrier. The injection device has also been applied to many kinds of proteins, not only for static structural analyses but also for dynamics studies using pump–probe techniques.

Serial crystallography, at both synchrotron and X-ray free-electron laser light sources, is becoming increasingly popular. However, the tools in the majority of crystallization laboratories are focused on producing large single crystals by vapour diffusion that fit the cryo-cooled paradigm of modern synchrotron crystallography. This paper presents several case studies and some ideas and strategies on how to perform the conversion from a single crystal grown by vapour diffusion to the many thousands of micro-crystals required for modern serial crystallography grown by batch crystallization. These case studies aim to show (i) how vapour diffusion conditions can be converted into batch by optimizing the length of time crystals take to appear; (ii) how an understanding of the crystallization phase diagram can act as a guide when designing batch crystallization protocols; and (iii) an accessible methodology when attempting to scale batch conditions to larger volumes. These methods are needed to minimize the sample preparation gap between standard rotation crystallography and dedicated serial laboratories, ultimately making serial crystallography more accessible to all crystallographers.

Grazing-incidence small-angle X-ray scattering (GISAXS) coupled with computed tomography (CT) has enabled the visualization of the spatial distribution of nanostructures in thin films. 2D GISAXS images are obtained by scanning along the direction perpendicular to the X-ray beam at each rotation angle. Because the intensities at the q positions contain nanostructural information, the reconstructed CT images individually represent the spatial distributions of this information (e.g. size, shape, surface, characteristic length). These images are reconstructed from the intensities acquired at angular intervals over 180°, but the total measurement time is prolonged. This increase in the radiation dosage can cause damage to the sample. One way to reduce the overall measurement time is to perform a scanning GISAXS measurement along the direction perpendicular to the X-ray beam with a limited interval angle. Using filtered back-projection (FBP), CT images are reconstructed from sinograms with limited interval angles from 3 to 48° (FBP-CT images). However, these images are blurred and have a low image quality. In this study, to optimize the CT image quality, total variation (TV) regularization is introduced to minimize sinogram image noise and artifacts. It is proposed that the TV method can be applied to downsampling of sinograms in order to improve the CT images in comparison with the FBP-CT images.

Microcrystal delivery methods are pivotal in the use of serial femtosecond crystallography (SFX) to resolve the macromolecular structures of proteins. Here, the development of a novel technique and instruments for efficiently delivering microcrystals for SFX are presented. The new method, which relies on a one-dimensional fixed-target system that includes a microcrystal container, consumes an extremely low amount of sample compared with conventional two-dimensional fixed-target techniques at ambient temperature. This novel system can deliver soluble microcrystals without highly viscous carrier media and, moreover, can be used as a microcrystal growth device for SFX. Diffraction data collection utilizing this advanced technique along with a real-time visual servo scan system has been successfully demonstrated for the structure determination of proteinase K microcrystals at 1.85 Å resolution.

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The design and assembly of two 3D-printed holders for high-throughput in meso in situ fixed-target crystallographic data collection are described.

Very asymmetric crystal diffraction was obtained from a finely polished silicon crystal set to reflect in Bragg diffraction at grazing incidence for the (333) reflection. The angle of incidence to achieve Bragg diffraction was varied between 1.08° and 0.33° by changing the X-ray energy from 8.100 to 8.200 keV. Topographic images obtained as the crystal was rocked were used to identify the effects of surface undulations, and the results are compared with dynamical X-ray diffraction calculations made with the Takagi–Taupin equations specialized to a surface having convex or concave features, as reported in an accompanying paper.

An algorithm, based on the matching of q-vectors pairs, is combined with three-dimensional pattern matching using a nearest-neighbors approach to index Laue and monochromatic serial crystallography data recorded on small unit cell samples.

The principles of using the Laue-analyzer as an X-ray optical element for separating two characteristic lines of an X-ray tube are presented.

A detailed theoretical and experimental comparison of dark-field electron holography (DFEH) and high-resolution X-ray diffraction (HRXRD) is performed. Both techniques are being applied to measure elastic strain in an array of transistors and the role of the geometric phase is emphasized.

This work presents the crystal structure determination of two elusive polymorphs of furazidin, an antibacterial agent, employing a combination of crystal structure prediction (CSP) calculations and an NMR crystallography approach. Two previously uncharacterized neat crystal forms, one of which has two symmetry-independent molecules (form I), whereas the other one is a Z' = 1 polymorph (form II), crystallize in P21/c and P1 space groups, respectively, and both are built by different conformers, displaying different intermolecular interactions. It is demonstrated that the usage of either CSP or NMR crystallography alone is insufficient to successfully elucidate the above-mentioned crystal structures, especially in the case of the Z' = 2 polymorph. In addition, cases of serendipitous agreement in terms of 1H or 13C NMR data obtained for the CSP-generated crystal structures different from the ones observed in the laboratory (false-positive matches) are analyzed and described. While for the majority of analyzed crystal structures the obtained agreement with the NMR experiment is indicative of some structural features in common with the experimental structure, the mentioned serendipity observed in exceptional cases points to the necessity of caution when using an NMR crystallography approach in crystal structure determination.

Insights were obtained into the structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV and the phylogeny of the aminotransferase pathway for the biosynthesis of lysine.

In southeastern Greenland, two rivers of ice named Helheim and Kangerdlugssuaq flow in spurts and starts toward the coast. They are much like any other […]

The post Astrophysical Observatory scientists are monitoring the mysterious movements of glaciers appeared first on Smithsonian Insider.

When NASA’s Solar Probe Plus launches before the end of the decade, it will carry a suite of cutting-edge scientific instruments. Only one–the Solar Wind Electrons Alphas and Protons Investigation (SWEAP)–will directly sample the Sun’s outer atmosphere.

The post Center for Astrophysics will play major role in mission to “touch” the Sun appeared first on Smithsonian Insider.

New research by astrophysicist David Kipping has revealed that in some special cases, a star can be weighed directly. Such a star must have a planet orbiting it with a moon orbiting the planet.

The post Harvard-Smithsonian astrophysicist discovers new method to weigh some distant stars appeared first on Smithsonian Insider.

"Physics for the 21st Century," a free, on-line course developed at the Harvard-Smithsonian Center for Astrophysics about current research in physics is now available.

The post Free, online course in physics offered by the Harvard-Smithsonian Center for Astrophysics appeared first on Smithsonian Insider.

Snowflake Study through Photomicrography, 1890 Wilson A. Bentley became fascinated with the crystalline structure of individual snowflakes on his parent’s Vermont farm. By adapting a […]

The post Snowflake Study through Photomicrography, 1890 appeared first on Smithsonian Insider.

The Harvard-Smithsonian Center for Astrophysics has been selected by the National Science Foundation as the recipient of a 12-meter (39-foot) radio antenna designed for submillimeter-wavelength astronomy. The ALMA Vertex Prototype Antenna was one of three antennas built as prototypes for the Atacama Large Millimeter Array, a 66-dish radio observatory currently being constructed in Chile.

The post Harvard-Smithsonian Center for Astrophysics to own and operate ALMA Vertex Prototype Antenna appeared first on Smithsonian Insider.

Humanity's most complex ground-based astronomy observatory, the Atacama Large Millimeter/submillimeter Array (ALMA), has officially opened for astronomers at its 16,500-foot high desert plateau in northern Chile.

The post Center for Astrophysics project gets first look through new ALMA telescope appeared first on Smithsonian Insider.

Imagine a gas giant planet spanning three times more sky than the Moon looming over the molten landscape of a lava world. This alien vista exists in the newly discovered two-planet system of Kepler-36.

The post Close encounters between planetary systems of Kepler-36 stun astrophysicists appeared first on Smithsonian Insider.

The scientists made the spiders exercise by irritating them with a small paint brush and causing them to move around until they became exhausted. Spiders from the group with palps removed were able to travel 300 percent further than spiders with their palps intact.

The post Weight of genitals reduces physical endurance in male orb web spiders, researchers find appeared first on Smithsonian Insider.

The Smithsonian Astrophysical Observatory has been awarded a NASA project to build the Tropospheric Emissions: Monitoring of Pollution (TEMPO) instrument. TEMPO will measure North American air pollution, from Mexico City to the Canadian tar/oil sands, and from the Atlantic to the Pacific, hourly and at high spatial resolution.

The post NASA funds Smithsonian Astrophysical Observatory instrument to track North American air pollution appeared first on Smithsonian Insider.

A fiery explosion on the surface of the Moon, visible to the naked eye, recently surprised NASA astronomers monitoring the Moon for meteorite strikes. Occurring […]

The post A meteorite explodes on the Moon: Q&A with geophysicist Bruce Campbell appeared first on Smithsonian Insider.

The number of new X-ray crystallography-based submissions to the Protein Data Bank appears to be at the beginning of a decline, perhaps signalling an end to the era of the dominance of X-ray crystallography within structural biology. This letter, from the viewpoint of a young structural biologist, applies the Copernican method to the life expectancy of crystallography and asks whether the technique is still the mainstay of structural biology. A study of the rate of Protein Data Bank depositions allows a more nuanced analysis of the fortunes of macromolecular X-ray crystallography and shows that cryo-electron microscopy might now be outcompeting crystallography for new labour and talent, perhaps heralding a change in the landscape of the field.

Now, for the first time, Charles Darwin's life is portrayed pictorially in an illustrated biography in graphic novel-style for all ages to enjoy.

The post “Darwin: A Graphic Biography,” new release from Smithsonian Books appeared first on Smithsonian Insider.

Olga Kopach, Noemi Esteras, Selina Wray, Dmitri A. Rusakov, and Andrey Y. Abramov

Frontotemporal dementia and parkinsonism (FTDP-17) caused by the 10+16 splice-site mutation in the MAPT provides an established platform to model tau-related dementia in vitro. Human iPSC-derived neurons have been shown to recapitulate the neurodevelopmental profile of tau pathology during in vitro corticogenesis as in the adult human brain. However, the neurophysiological phenotype of these cells has remained unknown, leaving unanswered questions over the functional relevance and the gnostic power of this disease model. Here we used electrophysiology to explore the membrane properties and intrinsic excitability of the generated neurons to find that human cells mature by ~150 days of neurogenesis to become compatible with matured cortical neurons. In earlier FTDP-17, neurons, however, exhibited a depolarized resting membrane potential associated with increased resistance and reduced voltage-gated Na⁺- and K⁺-channel-mediated conductance. The Na_v1.6 protein was reduced in FTDP-17. These led to a reduced cell capability of induced firing and changed action potential waveform in FTDP-17. The revealed neuropathology may thus contribute to the clinicopathological profile of the disease. This sheds new light on the significance of human models of dementia in vitro.

Bruce Campbell, of the Center for Earth and Planetary Studies at the Smithsonian's National Air and Space Museum, is at the National Radio Astronomy Observatory in Green Bank, W. Va., to make a radar map of the Moon.

The post Smithsonian geophysicist Bruce Campbell explains his work of making a detailed radar map of the Moon appeared first on Smithsonian Insider.

The post Device at the Smithsonian Environmental Research Center examines how phytoplankton would react if the ozone layer vanished appeared first on Smithsonian Insider.

A short history of the Harvard-Smithsonian Center for Astrophysics

The post Lighthouse of the skies, the Harvard-Smithsonian Center for Astrophysics appeared first on Smithsonian Insider.

Jonathan Coddington, Curator of Spiders at the Smithsonian National Museum of Natural History describes how photography has transformed the study of arachnids.

The post How photography has transformed the study of spiders and their webs appeared first on Smithsonian Insider.

The post Kepler 11: A Six-Planet Sonata by Alex Parker, postdoctoral researcher at the Harvard–Smithsonian Center for Astrophysics appeared first on Smithsonian Insider.

The National Air and Space Museum’s 2014 Trophy Award Winner for Current Achievement goes to the Dawn Flight Team. The Dawn team has successfully performed […]

The post The Dawn Flight Team – 2014 NASM Trophy Winner appeared first on Smithsonian Insider.

Smithsonian plant physiologist Bert Drake has studied one wetland's response to climate change for more than two decades. He gives a tour of the field experiment and explains some of the findings.

The post On the Chesapeake Bay, Smithsonian plant physiologist Bert Drake has been studying one wetland’s response to climate change for more than two decades. appeared first on Smithsonian Insider.

The positional change of nitro­gen-7 of the RNA constituent guanosine to the bridgehead position-5 leads to the base-modified nucleoside 5-aza-7-de­aza­guanosine. Contrary to guanosine, this mol­ecule cannot form Hoogsteen base pairs and the Watson–Crick proton donor site N3—H becomes a proton-acceptor site. This causes changes in nucleobase recognition in nucleic acids and has been used to construct stable `all-purine' DNA and DNA with silver-mediated base pairs. The present work reports the single-crystal X-ray structure of 7-iodo-5-aza-7-de­aza­guanosine, C10H12IN5O5 (1). The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O4'-endo) for the ribose moiety, with an anti­periplanar orientation of the 5'-hy­droxy group. Crystal packing is controlled by inter­actions between nucleobase and sugar moieties. The 7-iodo substituent forms a contact to oxygen-2' of the ribose moiety. Self-pairing of the nucleobases does not take place. A Hirshfeld surface analysis of 1 highlights the contacts of the nucleobase and sugar moiety (O—H⋯O and N—H⋯O). The concept of pK-value differences to evaluate base-pair stability was applied to purine–purine base pairing and stable base pairs were predicted for the construction of `all-purine' RNA. Furthermore, the 7-iodo substituent of 1 was functionalized with benzo­furan to detect motional constraints by fluorescence spectroscopy.

Physical quantities in arbitrary dimensional space can be classified into 41 types using three antisymmetries within the framework of Clifford algebra.

The inversion of X-ray reflectivity to reveal the topography of a one-dimensional interface is evaluated through model calculations.

Source: Streetwise Reports   05/07/2020

Oil and gas technology services and solutions company ION Geophysical Corp. (IO:NYSE) yesterday afternoon announced financial results for Q1/20 ending March 31, 2020.

The firm reported total net revenues of $56.4 million in Q1/20, which represented a 53% increase over $37.0 million in Q1/19. The company advised that the increase was due primarily to an increase in 2D multi-client data library sales.

For Q1/20, the firm additionally reported operating income of $6.3 million, compared to an operating loss of $15.9 million in Q1/19. The company further indicated that in Q1/20, it posted a net loss of $2.3 million, or ($0.16) per share, compared to a net loss of $21.4 million, or ($1.52) per share in Q1/19.

The company's President and CEO Chris Usher commented, "We achieved the best first quarter performance in six years despite challenges from both coronavirus and oil price volatility...Our strong revenues of $56 million generated positive operating income and $23 million in Adjusted EBITDA, and, as a result, we expect our liquidity position to improve as revenues are collected in the second quarter. Our first quarter results reflect the value of our offshore data library and validate the combined effectiveness of our strategic refocus and over $20 million cost reductions. Our team creatively closed a number of large multi-client contracts, some of which were delayed from the fourth quarter, even after E&P market dynamics changed. I remain confident in ION's value proposition to cost-effectively support customers' data-driven decision-making in this lower-for-longer exploration and production environment."

The company indicated that it has maintained a strong liquidity position in the face of energy market turmoil and the COVID-19 situation. The firm stated that as of March 31, 2020, it had total liquidity of $53.8 million, which consisted of $42.7 million in cash and $11.1 million remaining available balance under its $50.0 million revolving credit line.

ION Geophysical Corp. is a technology-focused company headquartered in Houston, Tex. that provides geophysical technology, services and solutions to the global oil and gas industry. Its products and technical services are designed to help oil and gas exploration and production companies obtain images of the earth's subsurface.

ION Geophysical started off the day with a market capitalization of around $25.1 million and an enterprise value of $115.7 million with approximately 15.03 million shares outstanding and a short interest of about 6.40%. IO shares opened more than 100% higher today at $3.37 (+$1.70, +101.80%) over yesterday's $1.67 closing price. The stock has traded between $2.84 to $4.36 per share today and is currently trading at $2.88 (+$1.21, +72.46%).

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( Companies Mentioned: IO:NYSE, )

No single approach -- technical, legal, economic, or educational -- will be sufficient to protect children from online pornography.

To meet the bodys daily energy and nutritional needs while minimizing risk for chronic disease, adults should get 45 percent to 65 percent of their calories from carbohydrates, 20 percent to 35 percent from fat, and 10 percent to 35 percent from protein.

Rates of physical and sexual abuse of children have declined over the last 20 years, but for reasons not fully understood, says a new report from the Institute of Medicine. Yet, reports of psychological and emotional child abuse have risen in the same period, and data vary significantly as to whether child neglect is increasing, decreasing, or remaining constant.

While scientists have made remarkable advancements in astronomy and astrophysics since the beginning of this decade – notably the first detection of gravitational waves and the discovery of distant Earth-like planets – unforeseen constraints have slowed progress toward reaching some of the priorities and goals outlined in the Academies’ 2010 decadal survey of these disciplines, says a new report from the National Academies of Sciences, Engineering, and Medicine.

Given the current state of quantum computing and the significant challenges that still need to be overcome, it is highly unlikely that a quantum computer that can compromise public-key cryptography – a basis for the security of most of today’s computers and networks – will be built within the next decade, says a new report by the National Academies of Sciences, Engineering, and Medicine.

NASA, NSF, and NOAA have made substantial progress in implementing the programs recommended in the 2013 decadal survey on solar and space physics (heliophysics) despite a challenging budgetary landscape, says a new midterm assessment from the National Academies of Sciences, Engineering, and Medicine.