The ongoing coronavirus-led lockdown has given rise to a plethora of possibilities in online higher education, post the pandemic

Like the various stages of the journey of virus, the list of fighters against the pandemic also expanded

Moving the barricades in the sun is their punishment, say police

A 23-year-old man who returned from Abu Dhabi on a repatriation flight, has tested positive for SARS-CoV-2. The district now has two positive recorded

‘State government has failed to protect the people of Delhi from the virus’

The city-based K7 Computing Pvt Ltd, provider of cyber security solutions, has topped the winners list for the Advanced+ Performance Award from AV-Com

The high temporal resolution in data acquisition, possible in the quick-scanning EXAFS (QEXAFS) mode of operation, provides new challenges in efficient data processing methods. Here a new approach is developed that combines an easy to use interactive graphical interface with highly optimized and fully parallelized Python-based routines for extracting, normalizing and interpolating oversampled time-resolved XAS spectra from a raw binary stream of data acquired during operando QEXAFS studies. The programs developed are freely available via a Github repository.

'Surrey swarm' quakes 'not caused by oil extraction'  BBC News

Tsunami warning: Britain could be hit by 30m wave - Professor warns of hazards to Britain  Express.co.uk

Earth's North Magnetic Pole Keeps Drifting towards Siberia, Latest World Magnetic Model Shows | Geophysics, Geoscience  Sci-News.com

'Surrey swarm' earthquakes not caused by nearby oil extraction, study suggests  Science Daily

Researchers Describe Why Earth's Magnetic North Pole Is Straying Away From Canada Towards Siberia  The Digital Wise

Scientists Explain Why Earth’s Magnetic North Pole Is Drifting Away From Canada Towards Siberia  Mashable India

A new scaling program is presented with new features to support multi-sweep workflows and analysis within the DIALS software package.

This article presents an overview of the development of two basic software libraries for image manipulation and data visualization in cryo-EM: emcore and emvis.

The title compound, C24H18FNO3, crystallizes in the monoclinic centrosymmetric space group P21/n and its mol­ecular conformation is stabilized via C—H⋯O intra­molecular inter­actions. The supra­molecular network mainly comprises C—H⋯O, C—H⋯F and C—H⋯π inter­actions, which contribute towards the formation of the crystal structure. The different inter­molecular inter­actions have been further analysed via Hirshfeld surface analysis and fingerprint plots.

Rational structure-based drug design (SBDD) relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process. While SBDD has proven successful for many drug-discovery projects, its application to G protein-coupled receptors (GPCRs) has been limited owing to extreme difficulties with their crystallization. Here, a method is presented for the rapid determination of multiple co-crystal structures for a target GPCR in complex with various ligands, taking advantage of the serial femtosecond crystallography approach, which obviates the need for large crystals and requires only submilligram quantities of purified protein. The method was applied to the human β2-adrenergic receptor, resulting in eight room-temperature co-crystal structures with six different ligands, including previously unreported structures with carvedilol and propranolol. The generality of the proposed method was tested with three other receptors. This approach has the potential to enable SBDD for GPCRs and other difficult-to-crystallize membrane proteins.

The first ab initio aspherical structure refinement against experimental X-ray structure factors for polypeptides and proteins using a fragmentation approach to break up the protein into residues and solvent, thereby speeding up quantum-crystallographic Hirshfeld atom refinement (HAR) calculations, is described. It it found that the geometric and atomic displacement parameters from the new fragHAR method are essentially unchanged from a HAR on the complete unfragmented system when tested on dipeptides, tripeptides and hexapeptides. The largest changes are for the parameters describing H atoms involved in hydrogen-bond interactions, but it is shown that these discrepancies can be removed by including the interacting fragments as a single larger fragment in the fragmentation scheme. Significant speed-ups are observed for the larger systems. Using this approach, it is possible to perform a highly parallelized HAR in reasonable times for large systems. The method has been implemented in the TONTO software.

Single crystals of the m = 8 member of the low-dimensional monophosphate tungsten bronzes (PO2)4(WO3)2m family were grown by chemical vapour transport technique and the high crystalline quality obtained allowed a reinvestigation of the physical and structural properties. Resistivity measurements revealed three anomalies at TC1 = 258 K, TC2 = 245 K and TC3 = 140 K, never observed until now. Parallel X-ray diffraction investigations showed a specific signature associated with three structural transitions, i.e. the appearance of different sets of satellite reflections below TC1, TC2 and TC3. Several harmonics of intense satellite reflections were observed, reflecting the non-sinusoidal nature of the structural modulations and a strong electron–phonon coupling in the material. These transitions could be associated with the formation of three successive unconventional charge density wave states.

Oxidation states of individual metal atoms within a metalloprotein can be assigned by examining X-ray absorption edges, which shift to higher energy for progressively more positive valence numbers. Indeed, X-ray crystallography is well suited for such a measurement, owing to its ability to spatially resolve the scattering contributions of individual metal atoms that have distinct electronic environments contributing to protein function. However, as the magnitude of the shift is quite small, about +2 eV per valence state for iron, it has only been possible to measure the effect when performed with monochromated X-ray sources at synchrotron facilities with energy resolutions in the range 2–3 × 10−4 (ΔE/E). This paper tests whether X-ray free-electron laser (XFEL) pulses, which have a broader bandpass (ΔE/E = 3 × 10−3) when used without a monochromator, might also be useful for such studies. The program nanoBragg is used to simulate serial femtosecond crystallography (SFX) diffraction images with sufficient granularity to model the XFEL spectrum, the crystal mosaicity and the wavelength-dependent anomalous scattering factors contributed by two differently charged iron centers in the 110-amino-acid protein, ferredoxin. Bayesian methods are then used to deduce, from the simulated data, the most likely X-ray absorption curves for each metal atom in the protein, which agree well with the curves chosen for the simulation. The data analysis relies critically on the ability to measure the incident spectrum for each pulse, and also on the nanoBragg simulator to predict the size, shape and intensity profile of Bragg spots based on an underlying physical model that includes the absorption curves, which are then modified to produce the best agreement with the simulated data. This inference methodology potentially enables the use of SFX diffraction for the study of metalloenzyme mechanisms and, in general, offers a more detailed approach to Bragg spot data reduction.

In processing X-ray diffraction data, the intensities obtained from integration of the diffraction images must be corrected for experimental effects in order to place all intensities on a common scale both within and between data collections. Scaling corrects for effects such as changes in sample illumination, absorption and, to some extent, global radiation damage that cause the measured intensities of symmetry-equivalent observations to differ throughout a data set. This necessarily requires a prior evaluation of the point-group symmetry of the crystal. This paper describes and evaluates the scaling algorithms implemented within the DIALS data-processing package and demonstrates the effectiveness and key features of the implementation on example macromolecular crystallographic rotation data. In particular, the scaling algorithms enable new workflows for the scaling of multi-crystal or multi-sweep data sets, providing the analysis required to support current trends towards collecting data from ever-smaller samples. In addition, the implementation of a free-set validation method is discussed, which allows the quantification of the suitability of scaling-model and algorithm choices.

Image-processing software has always been an integral part of structure determination by cryogenic electron microscopy (cryo-EM). Recent advances in hardware and software are recognized as one of the key factors in the so-called cryo-EM resolution revolution. Increasing computational power has opened many possibilities to consider more demanding algorithms, which in turn allow more complex biological problems to be tackled. Moreover, data processing has become more accessible to many experimental groups, with computations that used to last for many days at supercomputing facilities now being performed in hours on personal workstations. All of these advances, together with the rapid expansion of the community, continue to pose challenges and new demands on the software-development side. In this article, the development of emcore and emvis, two basic software libraries for image manipulation and data visualization in cryo-EM, is presented. The main goal is to provide basic functionality organized in modular components that other developers can reuse to implement new algorithms or build graphical applications. An additional aim is to showcase the importance of following established practices in software engineering, with the hope that this could be a first step towards a more standardized way of developing and distributing software in the field.

Synchrotron X-ray diffraction (XRD) measured on the XMaS beamline at the ESRF was used to characterize the alloy composition and crystalline surface corrosion of three copper alloy Tudor artefacts recovered from the undersea wreck of King Henry VIII's warship the Mary Rose. The XRD method adopted has a dynamic range ∼1:105 and allows reflections <0.002% of the height of major reflections in the pattern to be discerned above the background without smoothing. Laboratory XRD, scanning electron microscopy–energy dispersive spectroscopy, synchrotron X-ray fluorescence and X-ray excited optical luminescence–X-ray near-edge absorption structure were used as supporting techniques, and the combination revealed structural and compositional features of importance to both archaeology and conservation. The artefacts were brass links believed to be fragments of chainmail and were excavated from the seabed during 1981 and 1982. Their condition reflects very different treatment just after recovery, viz. complete cleaning and conservation, chemical corrosion inhibition and chloride removal only, and distilled water soaking only (to remove the chlorides). The brass composition has been determined for all three at least in the top 7 µm or so as Cu(73%)Zn(27%) from the lattice constant. Measurement of the peak widths showed significant differences in the crystallite size and microstrain between the three samples. All of the links are found to be almost chloride-free with the main corrosion products being spertiniite, sphalerite, zincite, covellite and chalcocite. The balance of corrosion products between the links reflects the conservation treatment applied to one and points to different corrosion environments for the other two.

GIDVis is a software package based on MATLAB specialized for, but not limited to, the visualization and analysis of grazing-incidence thin-film X-ray diffraction data obtained during sample rotation around the surface normal. GIDVis allows the user to perform detector calibration, data stitching, intensity corrections, standard data evaluation (e.g. cuts and integrations along specific reciprocal-space directions), crystal phase analysis etc. To take full advantage of the measured data in the case of sample rotation, pole figures can easily be calculated from the experimental data for any value of the scattering angle covered. As an example, GIDVis is applied to phase analysis and the evaluation of the epitaxial alignment of pentacene­quinone crystallites on a single-crystalline Au(111) surface.

BornAgain is a free and open-source multi-platform software framework for simulating and fitting X-ray and neutron reflectometry, off-specular scattering, and grazing-incidence small-angle scattering (GISAS). This paper concentrates on GISAS. Support for reflectometry and off-specular scattering has been added more recently, is still under intense development and will be described in a later publication. BornAgain supports neutron polarization and magnetic scattering. Users can define sample and instrument models through Python scripting. A large subset of the functionality is also available through a graphical user interface. This paper describes the software in terms of the realized non-functional and functional requirements. The web site https://www.bornagainproject.org/ provides further documentation.

BEATRIX, is a new tool for performing data analysis of energy-resolved neutron-imaging experiments involving intense fitting procedures of multi-channel spectra. The use of BEATRIX is illustrated for a test specimen, providing spatially resolved 2D maps for residual strains and Bragg edge heights.

For those who think that global warming is a 21st-century phenomenon, Scott Wing, a scientist at the Smithsonian’s National Museum of Natural History, has news about the past.

The post Fossils Show Prehistoric Global Warming appeared first on Smithsonian Insider.

The stars move quickly because they are very close to each other, separated by only about one-fourth the distance from the Earth to the Moon. As a result, they share strong gravitational forces. They were once farther apart but have spiraled closer together over time. Billions of years from now, they will crash together and merge.

The post At 1,500,000 mph, twin stars in the constellation Cancer win speediest orbit award appeared first on Smithsonian Insider.

“We are working as hard as we can to find and identify frogs before the disease reaches them, and to learn more about a disease that has the power to ravage an entire group of organisms,” said Roberto Ibanez, research scientist at STRI and local director of the Panama Amphibian Rescue and Conservation Project.

The post Two new frog species discovered in Panama’s fungal war zone appeared first on Smithsonian Insider.

It seems the stuff of science fiction, but astronomers have found a real-life “Death Star” that shredded a rocky planet and is swallowing the dusty remains.

The post “Death Star” Shreds, Swallows Dwarf Planet appeared first on Smithsonian Insider.

A new computer simulation by Gurtina Besla of the Harvard-Smithsonian Center for Astrophysics and her colleagues now shows that the Magellanic Stream resulted from a past close encounter between two dwarf galaxies rather than effects of the Milky Way.

The post Milky Way sidelined in galactic tug of war appeared first on Smithsonian Insider.

Scientists and local dive operators first noticed coral bleaching in the waters surrounding Isla Colon, in Panama’s Bocas del Toro province in July. Smithsonian staff scientist Nancy Knowlton and colleagues documented an extensive bleaching event in late September.

The post Coral bleaching event caused by warming ocean waters is documented in Panama appeared first on Smithsonian Insider.

The awarded film features STRI marine biologist Héctor M. Guzman diving with a group of five whale sharks while traveling in the Tropical Eastern Pacific. In the video, Guzmán tags a radiotransmitter to one of the sharks in order to follow its voyages.

The post Whale sharks featured in award-winning documentary following the work of Tropical Research Institute’s Héctor Guzman appeared first on Smithsonian Insider.

For more than three decades JoGayle Howard dedicated her life and work to reproducing endangered species.

The post JoGayle Howard, National Zoological Park pioneer in reproductive biology, dies appeared first on Smithsonian Insider.

Now, a new study of hellbenders by scientists at the Smithsonian Conservation Biology Institute will place these amphibians at the center of the conservation of Appalachian salamanders.

The post Will global warming be hell on the hellbender? Smithsonian study aims to find out. appeared first on Smithsonian Insider.

"I nearly fell out of my chair at the telescope when I saw one star change its speed by a staggering 750 miles per second in just a few minutes," said Smithsonian astronomer Warren Brown, lead author of the paper reporting the find.

The post Astronomers find two white-dwarf stars locked in death spiral appeared first on Smithsonian Insider.