A two-wheeler rider was injured on Saturday evening after a hand grinder, that slipped from the hands of a worker engaged in cladding work over Kochi

A simple and robust tool for spatio-temporal overlap of THz and XUV pulses in in-vacuum pump–probe experiments is presented. The technique exploits ultrafast changes of the optical properties in semiconductors (i.e. silicon) driven by ultrashort XUV pulses that are probed by THz pulses. This work demonstrates that this tool can be used for a large range of XUV fluences that are significantly lower than when probing by visible and near-infrared pulses. This tool is mainly targeted at emerging X-ray free-electron laser facilities, but can be utilized also at table-top high-harmonics sources.

A novel sample cell with control of temperature and relative humidity permitted collection of data of excellent quality, enabling unrestrained refinement of all atomic parameters. One of the K atoms in the structure is disordered; very strong anisotropy in three of the four water O atoms indicates partial static disorder, which does not involve the bonded H atoms.

Fragment-based molecular replacement exploits the use of very accurate yet incomplete search models. In the case of the ARCIMBOLDO programs, consistent phase sets produced from the placement and refinement of fragments with Phaser can be combined in order to increase their signal before proceeding to the step of density modification and autotracing with SHELXE. The program ALIXE compares multiple phase sets, evaluating mean phase differences to determine their common origin, and subsequently produces sets of combined phases that group consistent solutions. In this work, its use on different scenarios of very partial molecular-replacement solutions and its performance after the development of a much-optimized set of algorithms are described. The program is available both standalone and integrated within the ARCIMBOLDO programs. ALIXE has been analysed to identify its rate-limiting steps while exploring the best parameterization to improve its performance and make this software efficient enough to work on modest hardware. The algorithm has been parallelized and redesigned to meet the typical landscape of solutions. Analysis of pairwise correlation between the phase sets has also been explored to test whether this would provide additional insight. ALIXE can be used to exhaustively analyse all partial solutions produced or to complement those already selected for expansion, and also to reduce the number of redundant solutions, which is particularly relevant to the case of coiled coils, or to combine partial solutions from different programs. In each case parallelization and optimization to provide speedup makes its use amenable to typical hardware found in crystallography. ARCIMBOLDO_BORGES and ARCIMBOLDO_SHREDDER now call on ALIXE by default.

Propagation-based phase-contrast X-ray imaging is by now a well established imaging technique, which – as a full-field technique – is particularly useful for tomography applications. Since it can be implemented with synchrotron radiation and at laboratory micro-focus sources, it covers a wide range of applications. A limiting factor in its development has been the phase-retrieval step, which was often performed using methods with a limited regime of applicability, typically based on linearization. In this work, a much larger set of algorithms, which covers a wide range of cases (experimental parameters, objects and constraints), is compiled into a single toolbox – the HoloTomoToolbox – which is made publicly available. Importantly, the unified structure of the implemented phase-retrieval functions facilitates their use and performance test on different experimental data.

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.

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.

A software package for Grazing Incident Wide Angle X-ray Scattering (GIWAXS) geared toward weakly ordered materials, including: scattering intensity normalization/uncertainty, scattering pattern indexing, and refractive shift correction.

Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X—H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X—H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (dmin ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.

Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) applied through DiSCaMB software library in the structure refinement against X-ray diffraction data largely improves the X—H bond lengths and make them comparable to the averaged neutron bond lengths.

Tool use by sea otters to break open well-armored food is not necessarily a family matter, according to a new study published this week by […]

The post Tool use by sea otters has little to do with genetic ties: Smithsonian study appeared first on Smithsonian Insider.

Smithsonian scientists have joined NASA and other organizations this summer to do something incredible: launch a spacecraft, the Parker Solar Probe, into space and have […]

The post A solar probe is on its way to touch the sun. The Smithsonian built the tool that will measure the sun without melting appeared first on Smithsonian Insider.

Xian Hu, Salma Jalal, Michael Sheetz, Oddmund Bakke, and Felix Margadant

Despite progress made in confocal microscopy, even fast systems still have insufficient temporal resolution for detailed live cell volume imaging, such as tracking rapid movement of membrane vesicles in three-dimensional space. Depending on the shortfall, this may result in undersampling and/or motion artifacts that ultimately limit the quality of the imaging data. By sacrificing detailed information in the Z-direction, we propose a new imaging modality that involves capturing fast "projections" from the field of depth which shortens imaging time by approximately an order of magnitude as compared to standard volumetric confocal imaging. With faster imaging, radiation exposure to the sample is reduced, resulting in less fluorophore photobleaching and potential photodamage. The implementation minimally requires two synchronized control signals that drive a piezo stage and trigger the camera exposure. The device generating the signals has been tested on spinning disk confocals and instant structured-illumination-microscopy (iSIM) microscopes. Our calibration images show that the approach provides highly repeatable and stable imaging conditions that enable photometric measurements of the acquired data, in both standard live imaging and super-resolution modes.

Björn Eismann, Teresa G. Krieger, Jürgen Beneke, Ruben Bulkescher, Lukas Adam, Holger Erfle, Carl Herrmann, Roland Eils, and Christian Conrad

3D cell cultures enable the in vitro study of dynamic biological processes such as the cell cycle, but their use in high-throughput screens remains impractical with conventional fluorescent microscopy. Here, we present a screening workflow for the automated evaluation of mitotic phenotypes in 3D cell cultures by light-sheet microscopy. After sample preparation by a liquid handling robot, cell spheroids are imaged for 24 hours in toto with a dual-view inverted selective plane illumination microscope (diSPIM) with a much improved signal-to-noise ratio, higher imaging speed, isotropic resolution and reduced light exposure compared to a spinning disc confocal microscope. A dedicated high-content image processing pipeline implements convolutional neural network based phenotype classification. We illustrate the potential of our approach by siRNA knock-down and epigenetic modification of 28 mitotic target genes for assessing their phenotypic role in mitosis. By rendering light-sheet microscopy operational for high-throughput screening applications, this workflow enables target gene characterization or drug candidate evaluation in tissue-like 3D cell culture models.

White-faced capuchin monkeys in Panama’s Coiba National Park habitually use hammer-and-anvil stones to break hermit crab shells, snail shells, coconuts and other food items, according […]

The post Scientists observe stone tool use by Cebus monkeys appeared first on Smithsonian Insider.

If you try to open a text file with UTF-16 or UTF-32 encoding, the Import Tool displays a warning message stating that the encoding is not supported.  If you continue to load the file anyways, it is opened with UTF-8 encoding, and the file may not be displayed or imported as expected.This bug exists in the following release(s):
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Although the federal program that sets fuel economy standards for cars and light-duty trucks has helped reduce U.S. dependence on imported oil and lower emissions of greenhouse gases, changes to the program could further cut the nations petroleum dependence and provide more flexibility to carmakers.

A new report from the National Academies of Sciences, Engineering, and Medicine examines the effects and efficacy of using dispersants in marine oil spill response.

A recent study has demonstrated that it is possible to identify which human pressures, such as fisheries and environmental pollution, are causing changes in Marine and Coastal by combining the trends in different indicators. This approach can be used as a tool for integrated ecosystem assessment and management.

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.

There is a common assumption that plant species are more inclined to thrive in a non-native community than a native one, sometimes becoming 'invasive'. However, this behaviour is likely to be quite unusual and invasive alien plants are actually an important exception, according to a new study. Much can be learned from the population of a species 'at home' and should be included in official assessment criteria.

Populations of organisms that live on the bottom of an aquatic ecosystem, the benthic community, can be assessed to determine the health of the ecosystem. New research explores the many existing methods for assessing benthic communities to ensure that the most appropriate and useful tests are used under the Water Framework Directive (WFD).

Even small areas of semi-natural vegetation, farmlands and abandoned farmlands provide important ecosystem services in urban environments. However, there is widespread loss of these non-urbanised areas (NUAs) owing to poor planning and urban sprawl. A new five-step process has now been developed that can inform effective planning to protect and enhance the value of urban green spaces.

Researchers have created a new Green Option Matrix (GOM) to describe and compare the ever growing number of options to develop green products and processes. The GOM was used to analyse 142 companies belonging to the Dow Jones Sustainability World Index.

An overview of research into ‘nudge’ theory and practices has recently been presented. While there is much evidence to show how humans make decisions, translating these psychological and economic insights into viable policy instruments that encourage behavioural change remains challenging, the authors conclude.

A new tool for mapping the sensitivity of seafloor habitats to fishing activities has been developed. Researchers combined data on the resistance of habitats to damage from fishing practices, and how quickly they are able to recover, to produce a widely applicable tool that can be easily understood by stakeholders and used for different locations.

A new tool to help environmental managers make faster, more evidence-based decisions on how to eradicate alien aquatic species has been developed. The tool is a statistical model based on over 140 management case studies in the scientific literature. Packaged as a user-friendly computer program, it allows different management options to be easily compared.

A team of psychologists, kinesiologists and archaeologists at Indiana University and elsewhere are throwing new light on a longstanding archaeological mystery: the purpose of a large number of spherical stone artifacts found at a major archaeological site in South Africa.

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Even small areas of semi-natural vegetation, farmlands and abandoned farmlands provide important ecosystem services in urban environments. However, there is widespread loss of these non-urbanised areas (NUAs) owing to poor planning and urban sprawl. A new five-step process has now been developed that can inform effective planning to protect and enhance the value of urban green spaces.

Researchers have proposed a new indexing scheme to help decision-makers prioritise brownfield sites for redevelopment. The scheme scores potential sites according to socio-economic, smart growth and environmental dimensions. By giving users the flexibility to emphasise some aspects of development as more important than others, it can be adapted for use in different contexts.

Researchers have developed a prototype system to predict the impact of storms on European coastlines. The MICORE Early Warning System aims to improve civil defence and coastal evacuation plans and could pave the way for an autonomous early warning system to save countless lives and protect infrastructure worldwide.

A free online system for assessing the sustainability of buildings is due to be launched across Europe in July this year. The tool captures scientific complexity whilst being accessible and easy-to-use, its developers say.

Researchers have used a new comprehensive life cycle approach to estimate greenhouse gas (GHG) emissions from road construction. When applied to four projects in Spain, the results suggest improvements could be made in the use and efficiency of off-road machinery, the choice of materials and restoration of ecosystems.

Modern technologies have provided new ways for communities to engage with climate change. This study investigated the role of Internet-based tools in disseminating the findings of a climate change research project in Canada and provides insights on how best to use the Internet to communicate the outcomes of scientific research.

Researchers have developed a new tool to evaluate the economic viability of biogas production from agricultural waste, such as manure and straw. It focused on a co-digestion method where farmers treat several types of waste together, including industrial by-products, such as glycerol.

By using design tools to increase sustainability at every stage of production, researchers have developed a new eco-light. The light, which uses low wattage LEDs and recycled plastic, has a substantially lower environmental impact than the traditional equivalent LED lights.

A new tool for flood simulation and visualisation is accessible for both experts and practitioners, allowing them to collaborate better on flood planning and relief. Among other features, the new system includes 3D simulations, rainfall simulation and water flow data.

Identifying emerging research areas and technologies is important for decision makers, but notoriously difficult to do. This study presents a new way of searching the literature to identify emerging topics, which will help policymakers, industry and funding bodies to make better decisions.

A new oil-spill risk-management system has been developed by researchers, which shows the likely effects of a coastal spill on the environment and economic activities for specific locations. It provides maps of oil-spill risk through a web portal and could help decision makers and emergency-response authorities protect the local environment and businesses through targeted and efficient planning and responses.

A new screening tool to assess the potential seismic risks (earthquake activity) from deep geothermal energy projects has been outlined in a recent study. The tool provides categories of seismicity risk for projects, which are dependent on factors including geological aspects, as well as social concern and location in relation to urban areas.

A new review of the potential uses of visual soil evaluation (VSE) shows how this tool can be used to indicate risks of erosion, compaction, greenhouse gas emission or storage and surface-water run-off. Assessing soils in this way is not only useful for agriculture, but has implications for the wider environment, due to the vital role that soil plays in the provision of ecosystem services, for example as a habitat for biodiversity and as a carbon sink.