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.

X-ray imaging of soft materials is often difficult because of the low contrast of the components. This particularly applies to frozen hydrated biological cells where the feature of interest can have a similar density to the surroundings. As a consequence, a high dose is often required to achieve the desired resolution. However, the maximum dose that a specimen can tolerate is limited by radiation damage. Results from 3D coherent diffraction imaging (CDI) of frozen hydrated specimens have given resolutions of ∼80 nm compared with the expected resolution of 10 nm predicted from theoretical considerations for identifying a protein embedded in water. Possible explanations for this include the inapplicability of the dose-fractionation theorem, the difficulty of phase determination, an overall object-size dependence on the required fluence and dose, a low contrast within the biological cell, insufficient exposure, and a variety of practical difficulties such as scattering from surrounding material. A recent article [Villaneuva-Perez et al. (2018), Optica, 5, 450–457] concluded that imaging by Compton scattering gave a large dose advantage compared with CDI because of the object-size dependence for CDI. An object-size dependence would severely limit the applicability of CDI and perhaps related coherence-based methods for structural studies. This article specifically includes the overall object size in the analysis of the fluence and dose requirements for coherent imaging in order to investigate whether there is a dependence on object size. The applicability of the dose-fractionation theorem is also discussed. The analysis is extended to absorption-based imaging and imaging by incoherent scattering (Compton) and fluorescence. This article includes analysis of the dose required for imaging specific low-contrast cellular organelles as well as for protein against water. This article concludes that for both absorption-based and coherent diffraction imaging, the dose-fractionation theorem applies and the required dose is independent of the overall size of the object. For incoherent-imaging methods such as Compton scattering, the required dose depends on the X-ray path length through the specimen. For all three types of imaging, the dependence of fluence and dose on a resolution d goes as 1/d4 when imaging uniform-density voxels. The independence of CDI on object size means that there is no advantage for Compton scattering over coherent-based imaging methods. The most optimistic estimate of achievable resolution is 3 nm for imaging protein molecules in water/ice using lensless imaging methods in the water window. However, the attainable resolution depends on a variety of assumptions including the model for radiation damage as a function of resolution, the efficiency of any phase-retrieval process, the actual contrast of the feature of interest within the cell and the definition of resolution itself. There is insufficient observational information available regarding the most appropriate model for radiation damage in frozen hydrated biological material. It is advocated that, in order to compare theory with experiment, standard methods of reporting results covering parameters such as the feature examined (e.g. which cellular organelle), resolution, contrast, depth of the material (for 2D), estimate of noise and dose should be adopted.

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.

A scanning soft X-ray spectromicroscope was recently developed based mainly on the photon-in/photon-out measurement scheme for the investigation of local electronic structures on the surfaces and interfaces of advanced materials under conditions ranging from low vacuum to helium atmosphere. The apparatus was installed at the soft X-ray beamline (BL17SU) at SPring-8. The characteristic features of the apparatus are described in detail. The feasibility of this spectromicroscope was demonstrated using soft X-ray undulator radiation. Here, based on these results, element-specific two-dimensional mapping and micro-XAFS (X-ray absorption fine structure) measurements are reported, as well as the observation of magnetic domain structures from using a reference sample of permalloy micro-dot patterns fabricated on a silicon substrate, with modest spatial resolution (e.g. ∼500 nm). Then, the X-ray radiation dose for Nafion® near the fluorine K-edge is discussed as a typical example of material that is not radiation hardened against a focused X-ray beam, for near future experiments.

The unique diagnostic possibilities of X-ray diffraction, small X-ray scattering and phase-contrast imaging techniques applied with high-intensity coherent X-ray synchrotron and X-ray free-electron laser radiation can only be fully realized if a sufficient dynamic range and/or spatial resolution of the detector is available. In this work, it is demonstrated that the use of lithium fluoride (LiF) as a photoluminescence (PL) imaging detector allows measuring of an X-ray diffraction image with a dynamic range of ∼107 within the sub-micrometre spatial resolution. At the PETRA III facility, the diffraction pattern created behind a circular aperture with a diameter of 5 µm irradiated by a beam with a photon energy of 500 eV was recorded on a LiF crystal. In the diffraction pattern, the accumulated dose was varied from 1.7 × 105 J cm−3 in the central maximum to 2 × 10−2 J cm−3 in the 16th maximum of diffraction fringes. The period of the last fringe was measured with 0.8 µm width. The PL response of the LiF crystal being used as a detector on the irradiation dose of 500 eV photons was evaluated. For the particular model of laser-scanning confocal microscope Carl Zeiss LSM700, used for the readout of the PL signal, the calibration dependencies on the intensity of photopumping (excitation) radiation (λ = 488 nm) and the gain have been obtained.

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.


They found that the molars of fruit-eating species had sharp outer edges that likely allow them to pierce tough fruit skin and pulp... By contrast, the molars of insect-eating species were less complex, possibly because of their smoother shearing surfaces.

The post From chewing tough insects to soft fruit, bat teeth are highly specialized appeared first on Smithsonian Insider.

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National Science Foundation (NSF)-funded researchers from North Carolina State and Elon universities have developed a technique that allows them to remotely control the movement of soft robots, lock them into position for as long as needed and later reconfigure the robots into new shapes. The technique relies on light and magnetic fields. "By engineering the properties of the material, we can control the soft robot's movement remotely; we can get it to hold a given shape; we can then return the robot to its original shape or further modify its movement; and we can do this repeatedly. All of those things are valuable, in terms of this technology's utility in biomedical or aerospace applications," says Joe Tracy, a professor of materials science and engineering at NC State and corresponding author of a paper on the work. In experimental testing, the researchers demonstrated that the soft robots could be used to form "grabbers" for lifting and transporting objects. The soft robots could also be used as cantilevers or folded into "flowers" with petals that bend in different directions. "We are not limited to binary configurations, such as a grabber being either open or closed," says Jessica Liu, first author of the paper and a Ph.D. student at NC State. "We can control the light to ensure that a robot will hold its shape at any point."

Image credit: Jessica A.C. Liu

Emsisoft AntiMalware has become a favorite at BleepingComputer.com.  It's dual scanning engine consists of BitDefender definitions as well as definitions created by Emsisoft,  which when combined, allows for excellent and up-to-date detections. [...]

Will Davidson and his Minecraft creation, modeled off the Santa Cruz Mission; Credit: Steve Henn

Minecraft is a deceptively simple video game. You're dropped into a virtual world, and you get to build things. It's like a digital Lego set, but with infinite pieces.

Its simplicity makes it a big hit with kids, like 10-year old Will Davidson. Last year, Will built a Spanish mission for a school report. He modeled his off the Santa Cruz Mission. "I made a chapel over here," Davidson says. "I also have a bell tower."

After he turned in his report, he added a few things. Like skeleton archers. "And zombies ... and exploding things, and spiders, that try to kill you," he said.

Minecraft is popular with kids because they're free to create almost anything, says Ramin Shokrizade, a game designer.

Also, kids aren't manipulated into clicking buttons to buy add-ons within the game. In other games, designers give players a special power for free at first, then take it away and offer it back at a price.

Zynga, the creator of Farmville, calls this fun pain, according to Shokrizade. "That's the idea that, if you make the consumer uncomfortable enough, and then tell them that for money we'll make you less uncomfortable, then [they] will give us money," he says.

Kids, Shokrizade says, are especially susceptible to this — and Minecraft has a loyal following, in part, because it doesn't do it.

Susan Linn, from the Campaign for a Commercial-Free Childhood, agrees. She says a big reason she likes Minecraft is because after you purchase the game upfront, that's it.

"Parents don't have to worry that their kids are going to be targeted for more marketing," Linn says. "How forward-thinking!"

But Linn is worried. Microsoft bought Mojang, the company that created Minecraft, on Monday for $2.5 billion, and she says that any time a large company spends billions to acquire a smaller company, executives are bound start looking for new ways to get even more money out of it.

Full Text:

National Science Foundation (NSF)-funded researchers from North Carolina State and Elon universities have developed a technique that allows them to remotely control the movement of soft robots, lock them into position for as long as needed and later reconfigure the robots into new shapes. The technique relies on light and magnetic fields. "By engineering the properties of the material, we can control the soft robot's movement remotely; we can get it to hold a given shape; we can then return the robot to its original shape or further modify its movement; and we can do this repeatedly. All of those things are valuable, in terms of this technology's utility in biomedical or aerospace applications," says Joe Tracy, a professor of materials science and engineering at NC State and corresponding author of a paper on the work. In experimental testing, the researchers demonstrated that the soft robots could be used to form "grabbers" for lifting and transporting objects. The soft robots could also be used as cantilevers or folded into "flowers" with petals that bend in different directions. "We are not limited to binary configurations, such as a grabber being either open or closed," says Jessica Liu, first author of the paper and a Ph.D. student at NC State. "We can control the light to ensure that a robot will hold its shape at any point."

Image credit: Jessica A.C. Liu

Celonis, a Germany-based...

Updates for the critical-rated vulnerabilities, which are being actively exploited in the wild, are still weeks away

The post Microsoft warns of two Windows zero‑day flaws appeared first on WeLiveSecurity

Microsoft plugs a security hole that could have enabled attackers to weaponize a GIF in order to hijack Teams accounts and steal data

The post Microsoft Teams flaw could let attackers hijack accounts appeared first on WeLiveSecurity

Microsoft Edge is now giving users the ability to hide those pesky browser notification dialog boxes that are commonly used by web sites to push their content, or even spam, on visitors. [...]

A joint delegation of Microsoft and Veriown Global Holdings met Punjab Chief Minister Captain Amarinder Singh here today to discuss a proposal to launch a pilot project in the state for the promotion of the gadget, to be linked through a tablet, to be provided by the companies for offering services across various sectors, including education and agriculture.

Udupi-based Robosoft was started in 1996 with Apple as its first customer. It is now evolving beyond mobile app development to add advisory capabilities.

Sonata Software announced that its Unified Enterprise Mobility Platform, Halosys, has been enhanced with additional features that boost optimization and usability

And what it looks like in the open-source world.

Maritime ships, which transport around 90 percent of the world’s goods across the seas, generate about 3 percent of global carbon emissions.

The decline in growth rate is likely because enterprises relook at their buying decisions owing to increased focus on profitability, said IDC's report.

Microsoft has seen a huge 775 per cent increase in its Cloud services in regions that have enforced social distancing or 'shelter-in-place orders.

While Amazon Web Services, or AWS, and Microsoft are restructuring some large contracts on a case-by-case basis, according to people familiar with the decisions, smaller companies aren’t receiving the same flexibility.

Google is reportedly in negotiation to acquire enterprise cloud software company D2iQ for over $250 million, the media reported.

Microsoft Corp. said on Friday it would create its first datacentre region in Italy under a $1.5 billion investment plan as the U.S. company expands its cloud computing services to more locations across the world.

Microsoft Corp. said on Friday it would create its first datacentre region in Italy under a $1.5 billion investment plan as the U.S. company expands its cloud computing services to more locations across the world.