In this article, a method is presented to estimate a new local quality measure for 3D cryoEM maps that adopts the form of a `local resolution' type of information. The algorithm (DeepRes) is based on deep-learning 3D feature detection. DeepRes is fully automatic and parameter-free, and avoids the issues of most current methods, such as their insensitivity to enhancements owing to B-factor sharpening (unless the 3D mask is changed), among others, which is an issue that has been virtually neglected in the cryoEM field until now. In this way, DeepRes can be applied to any map, detecting subtle changes in local quality after applying enhancement processes such as isotropic filters or substantially more complex procedures, such as model-based local sharpening, non-model-based methods or denoising, that may be very difficult to follow using current methods. It performs as a human observer expects. The comparison with traditional local resolution indicators is also addressed.

Confidence maps provide complementary information for interpreting cryo-EM densities as they indicate statistical significance with respect to background noise. They can be thresholded by specifying the expected false-discovery rate (FDR), and the displayed volume shows the parts of the map that have the corresponding level of significance. Here, the basic statistical concepts of confidence maps are reviewed and practical guidance is provided for their interpretation and usage inside the CCP-EM suite. Limitations of the approach are discussed and extensions towards other error criteria such as the family-wise error rate are presented. The observed map features can be rendered at a common isosurface threshold, which is particularly beneficial for the interpretation of weak and noisy densities. In the current article, a practical guide is provided to the recommended usage of confidence maps.

Silicon nanowire-based sensors find many applications in micro- and nano-electromechanical systems, thanks to their unique characteristics of flexibility and strength that emerge at the nanoscale. This work is the first study of this class of micro- and nano-fabricated silicon-based structures adopting the scanning X-ray diffraction microscopy technique for mapping the in-plane crystalline strain (∊044) and tilt of a device which includes pillars with suspended nanowires on a substrate. It is shown how the micro- and nanostructures of this new type of nanowire system are influenced by critical steps of the fabrication process, such as electron-beam lithography and deep reactive ion etching. X-ray analysis performed on the 044 reflection shows a very low level of lattice strain (<0.00025 Δd/d) but a significant degree of lattice tilt (up to 0.214°). This work imparts new insights into the crystal structure of micro- and nanomaterial-based sensors, and their relationship with critical steps of the fabrication process.

The sin2ψ and cosα methods are compared via diffracting-grain identification from electron backscatter diffraction maps. Artificial textures created by the X-ray diffraction measurements are plotted and X-ray elastic constants of the diffracting-grain sets are computed.

This article reports conformational polymorphisms of the EF-hand protein MCFD2 which is involved in glycoprotein transport..

In a series of ongoing experiments on Barro Colorado Island in the Panama Canal, Kays and other researchers are using camera traps, radio collars and palm nuts with tracking transmitters attached to them to take a closer look at the nut-hoarding strategies of the agouti.

The post Camera traps & radio collars reveal hoarding strategies of the South American agouti appeared first on Smithsonian Insider.

On the Smithsonian Tropical Research Institute's Barro Colorado Island in the Panama Canal, staff members are taking down a network of seven tall Automated Radio Telemetry System towers used to track animals wearing radio-transmitters. Scientists on the island are switching to GPS and camera trap systems to produce more data with less infrastructure.

The post GPS and camera traps to replace radio antennas in tracking animals on Barro Colorado Island appeared first on Smithsonian Insider.

The genomes of modern birds tell a story of how they emerged and evolved after the mass extinction that wiped out dinosaurs 66 million years […]

The post International team maps ‘big bang’ of bird evolution appeared first on Smithsonian Insider.

For the first time, a team from the Smithsonian Conservation Biology Institute’s (SCBI) Center for Conservation Education and Sustainability collected photo evidence of an Andean […]

The post Scientists Find Andean Bears with Camera Traps In Peru appeared first on Smithsonian Insider.

When astronomers study protoplanetary disks of gas and dust that surround young stars, they sometimes spot a dark gap like the Cassini division in Saturn’s […]

The post Disk Gaps Don’t Always Signal Planets appeared first on Smithsonian Insider.

Could the universe’s earliest stars have formed planets, and if so, what might they have looked like? That was the question Harvard-Smithsonian Center for Astrophysics […]

The post Diamonds are a planet’s best friend? In the early universe, perhaps appeared first on Smithsonian Insider.

A crystallographic indexing algorithm, pinkIndexer, is presented for the analysis of snapshot diffraction patterns. It can be used in a variety of contexts including measurements made with a monochromatic radiation source, a polychromatic source or with radiation of very short wavelength. As such, the algorithm is particularly suited to automated data processing for two emerging measurement techniques for macromolecular structure determination: serial pink-beam X-ray crystallography and serial electron crystallography, which until now lacked reliable programs for analyzing many individual diffraction patterns from crystals of uncorrelated orientation. The algorithm requires approximate knowledge of the unit-cell parameters of the crystal, but not the wavelengths associated with each Bragg spot. The use of pinkIndexer is demonstrated by obtaining 1005 lattices from a published pink-beam serial crystallography data set that had previously yielded 140 indexed lattices. Additionally, in tests on experimental serial crystallography diffraction data recorded with quasi-monochromatic X-rays and with electrons the algorithm indexed more patterns than other programs tested.

Maintaining natural movement of animals that live in the tropical rainforest canopy in South America is important for the health of the ecosystem. As development […]

The post Tremie Gregory uses camera traps to study “bridges” in the rainforest canopy appeared first on Smithsonian Insider.

Linn Meyers (American, b. Washington, D.C., 1968; lives and works in Washington, D.C.) created her largest work, “Our View From Here,” at the Smithsonian’s Hirshhorn […]

The post Linn Meyers “Our View From Here” Time-lapse appeared first on Smithsonian Insider.

Ovarian cancer should not be categorized as a single disease, but rather as a constellation of different cancers involving the ovary, yet questions remain on how and where various ovarian cancers arise, says a new congressionally mandated report from the National Academies of Sciences, Engineering, and Medicine.

Improved understanding of the coupled natural-human coastal system will help promote resilience of coastal communities and ecosystems under rapidly changing environmental conditions and support informed decision-making, says a new report from the National Academies of Sciences, Engineering, and Medicine.

After the San Francisco 49ers beat the Atlanta Falcons for the right to go to the Super Bowl, I tweeted my appreciation of a California team going to the game.  If no local team is in the running (or exists), I'm always glad to root for a Bay Area team that makes it.

My tweet got responses from some Southern Californians who have no interest in supporting a San Francisco team, especially given the Giants' World Series championship.  It goes without saying that many Dodger fans are loathe to support the Giants, under any circumstances. 

Given the historic bad blood between the teams, that's no surprise, but I think it runs even deeper.  The divide between Northern and Southern California is about more than sports, or even water rights.  It's rooted in distinct cultural differences between the two.

However, California has evolved to the point where the bigger cultural divide now might be between coastal and inland regions.  Rural Northern Californians typically dislike San Francisco far more than Angelenos do.  Similarly, inland Southern California residents often see Los Angeles as the prohibitively expensive home of two-hour traffic jams.

Until the Inland Empire or the San Joaquin Valley get major league teams, we won't see that rivalry playing out at a stadium near you.   In the meantime, I'm cheering on the Niners, and my state, on February 3rd.

This content is from Southern California Public Radio. View the original story at SCPR.org.

Although a total of 1.3 per cent of global marine areas is currently within Marine Protection Areas (MPAs), this is far from the Convention of Biodiversity's (CBD) 10 per cent target. Significant progress has been made over the last few years, but a new report suggests there is room for improvement as MPA coverage is very uneven and not all eco-regions and habitats are represented. The report makes several recommendations for maximising the effects of MPAs.

Sustainable consumption and production (SCP) programmes are frameworks to systemically develop sustainability. New research has analysed three national SCP programmes in the UK, Sweden and Finland and concluded that, rather than provide a strong roadmap for sustainability, they tend to be a toolbox of good but scattered initiatives.

Municipal solid waste (MSW) landfills, which consist of everyday consumer items, are potential long-term sources of emissions that could threaten the environment and human health if they are not managed carefully after closure. New research has presented a methodology to estimate future emission levels for closed MSW landfills and the impact of different aftercare strategies.

Geography and ecology are key factors that have influenced the genetic makeup of human groups in southern Africa, according to new research discussed in the journal GENETICS, a publication of the Genetics Society of America. By investigating the ancestries of twenty-two KhoeSan groups, including new samples from the Nama and the ≠Khomani, researchers conclude that the genetic clustering of southern African populations is closely tied to the ecogeography of the Kalahari Desert region.

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A global cropland percentage map and a global field size map have been created for the first time to guide scientists and policymakers interested in global agricultural modelling and assessment. Both maps are for the baseline year 2005 and combined multiple data sets from global, regional and national levels to achieve a high level of accuracy and 1 km2 resolution.

Nearly 85% of residents in central Dublin, Ireland, could be exposed to damaging levels of night-time traffic noise, according to a recent study. The researchers explain how they assessed population exposure to noise and calculate the impacts of several noise reduction measures, providing information that could help EU Member States meet the Environmental Noise Directive’s requirements.

Major roads, railways, airports and industrial areas can be a major source of noise nuisance for local communities. To help city planners and architects determine the most appropriate sound insulation design for the exterior of buildings, Turkish researchers have developed a new method that transforms noise maps into insulation maps.

Researchers in Greece have added a new dimension to noise level mapping by including data on residents’ perception and value of different sounds. This consideration of the experiences of residents in this way could lead to more effective policy implementation.

Digital noise maps developed under the EU’s Environmental Noise Directive (END) are a useful way of assessing traffic noise exposure for local residents, according to a recent Swedish study. The END maps could also be used to standardise noise exposure information in noise and health research.

The thinning of Iceland’s ice caps could be influencing volcanic activity, according to new research. The study developed a model to predict the changes in pressure on magma caused by thinning ice and applied it to the recent activity of two Icelandic volcanoes. The results suggest that the effects of thinning ice may increase volcanic activity in some cases, but reduce it in others.

A recent report has summarised what is currently known about the effects of ocean fertilisation as a climate change mitigation measure. The report highlights gaps in scientific understanding of the long term-effects of large-scale ocean fertilisation activities and raises questions about the effectiveness of the approach and the possibility of unintended impacts.

Glaciers are sensitive indicators of climate change. This study focused on hanging glaciers in the French Alps, where warming is increasing the risk of glaciers collapsing. The authors applied a state-of-the-art numerical model to a particularly hazardous glacier in Mont Blanc to simulate how it will respond to climate change. The results suggest the glacier may become unstable in the current century, posing a risk to the inhabitants of the valley below.

Municipal solid waste (MSW) landfills, which consist of everyday consumer items, are potential long-term sources of emissions that could threaten the environment and human health if they are not managed carefully after closure. New research has presented a methodology to estimate future emission levels for closed MSW landfills and the impact of different aftercare strategies.

Researchers use life-cycle assessment (LCA) as a tool to evaluate the environmental impact of products and technologies across their entire lifetime — from extraction of raw material to end-of-life (disposal or recycling). It is challenging to apply the conventional LCA method to new or emerging technologies, however, due to the sheer quantity of data needed for such studies. This study proposes a screening-to-LCA method that uses available data to systematically evaluate the performance of such technologies, and support the uptake of those that are most environmentally sustainable.

A study of two forest ecosystems in Spain has found that land-cover maps of watersheds, ecosystems hosting key interactions between vegetation, wildlife, and water, are made more accurate by the inclusion of LiDAR data — a type of remote sensing that pulses laser light at a target to measure vertical distances for use in 3D-mapping an environment. This has important implications for ecosystem monitoring, flood mitigation, and forest management, fields in which accurately characterising an environment is key.

A new tool has been developed to map the sensitivity of seabirds to offshore wind farm development. The Seabird Mapping and Sensitivity Tool (SeaMaST), currently for use in English waters, combines information on the sensitivity of seabird species to wind turbines with data on the birds’ distribution. It provides maps that can be used for both the offshore wind farm industry and marine spatial planning.

A new global study on the economics of ecosystem services and biodiversity loss suggests that governments can achieve more resilient economies and receive higher rates of return on their public investment strategies when they recognise and target the value of ecosystem services.

Ecological risk maps showing 'hotspots' of risk to wildlife from single or combined soil pollutants have been developed. These maps can be used to improve risk analysis and stakeholder communications.

Setting cycle and footpaths further back from the road can significantly lower the amount of air pollution that cyclists and pedestrians inhale, suggests new research. While wide gaps are not always practical, the study shows that even small increases in distance could substantially reduce the dose of pollution.

Grey is back in the desert, Myke is excited about a new app, and they both have expectations for WWDC.

Its net debt has improved by about $500 million from start to finish.

Futures in New York fell 2.3 percent Wednesday, after doubling in value from a week ago.

California and the Northeast love wine, Colorado and the Midwest quaff beer.

Dependence on GPS hampers your brain's ability to navigate and can even lead you astray. Don't leave home without a trusty paper map.

No, a state senator cannot single-handedly take down Big Oil. That only happens in Frank Capra movies. In real life, the petroleum giants always get their way.

The catastrophic collapse of the massive West Antarctic Ice Sheet is underway.