Earth's north magnetic pole is heading for Russia  The Independent Barents Observer

Compasses at Greenwich Are About to Do Something Not Observed in Over 300 Years  ScienceAlert

What is a sinkhole and are they caused by bad weather?  expressandstar.com

Isle of Mull earthquake compared to low-flying jet  BBC News

Ripon sinkhole: British Geological Survey says area susceptible to holes  BBC News

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.

Six different rare-earth oxyapatites, including Ca2RE8(SiO4)6O2 (RE = La, Nd, Sm, Eu, or Yb) and NaLa9(SiO4)6O2, were synthesized using solution-based processes followed by cold pressing and sinter­ing. The crystal structures of the synthesized oxyapatites were determined from powder X-ray diffraction (P-XRD) and their chemistries verified with electron probe microanalysis (EPMA). All the oxyapatites were isostructural within the hexa­gonal space group P63/m and showed similar unit-cell parameters. The isolated [SiO4]4− tetra­hedra in each crystal are linked by the cations at the 4f and 6h sites occupied by RE3+ and Ca2+ in Ca2RE8(SiO4)6O2 or La3+ and Na+ in NaLa9(SiO4)6O2. The lattice parameters, cell volumes, and densities of the synthesized oxyapatites fit well to the trendlines calculated from literature values.

From solutions of prehnitene and the ternary halides (SnCl)[MCl4] (M = Al, Ga) in chloro­benzene, the new cationic SnII–π-arene complexes catena-poly[[chlorido­aluminate(III)]-tri-μ-chlorido-4':1κ2Cl,1:2κ4Cl-[(η6-1,2,3,4-tetra­meth­yl­benzene)­tin(II)]-di-μ-chlorido-2:3κ4Cl-[(η6-1,2,3,4-tetra­methyl­benzene)­tin(II)]-di-μ-chlorido-3:4κ4Cl-[chlorido­aluminate(III)]-μ-chlorido-4:1'κ2Cl], [Al2Sn2Cl10(C10H14)2]n, (1) and catena-poly[[chlorido­gallate(III)]-tri-μ-chlor­ido-4':1κ2Cl,1:2κ4Cl-[(η6-1,2,3,4-tetra­methyl­benzene)­tin(II)]-di-μ-chlorido-2:3κ4Cl-[(η6-1,2,3,4-tetra­methyl­benzene)­tin(II)]-di-μ-chlorido-3:4κ4Cl-[chlor­ido­gallate(III)]-μ-chlorido-4:1'κ2Cl], [Ga2Sn2Cl10(C10H14)2]n, (2), were isolated. In these first main-group metal–prehnitene complexes, the distorted η6 arene π-bonding to the tin atoms of the Sn2Cl22+ moieties in the centre of [{1,2,3,4-(CH3)4C6H2}2Sn2Cl2][MCl4]2 repeating units (site symmetry overline{1}) is characterized by: (i) a significant ring slippage of ca 0.4 Å indicated by the dispersion of Sn—C distances [1: 2.881 (2)–3.216 (2) Å; 2: 2.891 (3)–3.214 (3) Å]; (ii) the non-methyl-substituted arene C atoms positioned closest to the SnII central atom; (iii) a pronounced tilt of the plane of the arene ligand against the plane of the central (Sn2Cl2)2+ four-membered ring species [1: 15.59 (11)°, 2: 15.69 (9)°]; (iv) metal–arene bonding of medium strength as illustrated by application of the bond-valence method in an indirect manner, defining the π-arene bonding inter­action of the SnII central atoms as s(SnII—arene) = 2 − Σs(SnII—Cl), that gives s(SnII—arene) = 0.37 and 0.38 valence units for the aluminate and the gallate, respectively, indicating that comparatively strong main-group metal–arene bonding is present and in line with the expectation that [AlCl4]− is the slightly weaker coordinating anion as compared to [GaCl4]−.

The non-porous three-dimensional structure of poly[(μ5-2-amino­benzene-1,4-di­carboxyl­ato)(μ6-oxalato)(oxomium)europium(III)], [Eu(C8H5NO4)(C2O4)(H3O)]n or [EuIII(NH2–BDC)(ox)(H3O)]n (NH2–BDC2− = 2-amino­terephthalate and ox2− = oxalate) is constructed from two-dimensional layers of EuIII–carboxyl­ate–oxalate, which are connected by NH2–BDC2− pillars. The basic structural unit of the layer is an edge-sharing dimer of TPRS-{EuIIIO9}, which is assembled through the ox2− moiety. The intra­layer void is partially occupied by TPR-{EuIIIO6} motifs. Weak C—H⋯O and strong, classical intra­molecular N—H⋯O and inter­molecular O—H⋯O hydrogen-bonding inter­actions, as well as weak π–π stacking inter­actions, affix the organic pillars within the framework. The two-dimensional layer can be simplified to a uninodal 4-connected sql/Shubnikov tetra­gonal plane net with point symbol {44.62}.

After crystallization during ionothermal syntheses in phospho­nium-containing ionic liquids, the structure of (NH4)3Al2(PO4)3 [tri­ammonium dialuminum tris­(phosphate)] was refined on the basis of powder X-ray diffraction data from a synchrotron source. (NH4)3Al2(PO4)3 is a member of the structural family with formula A3Al2(PO4)3, where A is a group 1 element, and of which the NH4, K, and Rb forms were previously known. The NH4 form is isostructural with the K form, and was previously solved from single-crystal X-ray data when the material (SIZ-2) crystallized from a choline-containing eutectic mixture [Cooper et al. (2004). Nature, 430, 1012–1017]. Our independent refinement incorporates NH4 groups and shows that these NH4 groups are hydrogen bonded to framework O atoms present in rings containing 12 T sites in a channel along the c-axis direction. We describe structural details of (NH4)3Al2(PO4)3 and discuss differences with respect to isostructural forms.

The title compound, C20H36O2·CH3OH [systematic name: (3S)-4-[(S)-3-hy­droxy-3-methyl­pent-4-en-1-yl]-3,4a,8,8-tetra­methyl­deca­hydro­naphthalen-3-ol methanol monosolvate], is a methanol solvate of sclareol, a diterpene oil isolated from the medicinally important medicinal herb Salvia sclarea, commonly known as clary sage. It crystallizes in space group P1 (No. 1) with Z' = 2. The sclareol mol­ecule comprises two trans-fused cyclo­hexane rings, each having an equatorially oriented hydroxyl group, and a 3-methyl­pent-1-en-3-ol side chain. In the crystal, Os—H⋯Os, Os—H⋯Om, Om—H⋯Os and Om—H⋯Om (s = sclareol, m = methanol) hydrogen bonds connect neighboring mol­ecules into infinite [010] chains. The title compound exhibits weak anti-leishmanial activity (IC50 = 66.4 ± 1.0 µM ml−1) against standard miltefosine (IC50 = 25.8 ± 0.2 µM ml−1).

N-[(Z)-2-(2H-1,3,2-Benzodioxaborol-2-yl)-2-phenyl­ethen­yl]-N-(propan-2-yl)aniline, C23H22BNO2, contains a C=C bond that is conjugated with a donor and an acceptor group. An analysis that included similar push–pull olefins revealed that bond lengths in their B—C=C—N core units correlate with the perceived acceptor and donor strength of the groups. The two phenyl groups in the mol­ecule are rotated with respect to the plane that contains the BCCN atoms, and are close enough for significant π-stacking. Definite characterization of the title compound demonstrates, for the first time in a reliable way, that hydro­boration of ynamines with borandiol esters is feasible. Compared to olefin hydro­boration with borane, the ynamine substrate is activated enough to undergo reaction with the less active hydro­boration reagent catecholborane.

High-quality single-crystal X-ray diffraction measurements are a prerequisite for obtaining precise and reliable structure data and electron densities. The single crystal should therefore fulfill several conditions, of which a regular defined shape is of particularly high importance for compounds consisting of heavy elements with high X-ray absorption coefficients. The absorption of X-rays passing through a 50 µm-thick LiNbO3 crystal can reduce the transmission of Mo Kα radiation by several tens of percent, which makes an absorption correction of the reflection intensities necessary. In order to reduce ambiguities concerning the shape of a crystal, used for the necessary absorption correction, a method for preparation of regularly shaped single crystals out of large samples is presented and evaluated. This method utilizes a focused ion beam to cut crystals with defined size and shape reproducibly and carefully without splintering. For evaluation, a single-crystal X-ray diffraction study using a laboratory diffractometer is presented, comparing differently prepared LiNbO3 crystals originating from the same macroscopic crystal plate. Results of the data reduction, structure refinement and electron density reconstruction indicate qualitatively similar values for all prepared crystals. Thus, the different preparation techniques have a smaller impact than expected. However, the atomic coordinates, electron densities and atomic charges are supposed to be more reliable since the focused-ion-beam-prepared crystal exhibits the smallest extinction influences. This preparation technique is especially recommended for susceptible samples, for cases where a minimal invasive preparation procedure is needed, and for the preparation of crystals from specific areas, complex material architectures and materials that cannot be prepared with common methods (breaking or grinding).

Among different types of polymorphism, disappearing polymorphism deals with the metastable kinetic form which can not be reproduced after its first isolation. In the world of coordination polymers (CPs) and metal–organic frameworks (MOFs), despite the fact that many types of supramolecular isomerism exist, we are unaware of disappearing supramolecular isomerism akin to disappearing polymorphism. This work reports a MOF with dia topology that could not be reproduced, but subsequent synthesis yielded another supramolecular isomer, a double-pillared-layer MOF. When perylene was added in the same reaction, the disappeared dia MOF reappeared with perylene as a guest in the channels. Interestingly, the photoluminescence of the dia MOF with a perylene guest is dominated by the emission of the guest molecule. The influence of guest molecules on the stabilization of the supramolecular isomers of a MOF opens up a strategy to access MOFs with different structures.

Malaria is a devastating disease caused by a protozoan parasite. It affects over 300 million individuals and results in over 400 000 deaths annually, most of whom are young children under the age of five. Hexokinase, the first enzyme in glucose metabolism, plays an important role in the infection process and represents a promising target for therapeutic intervention. Here, cryo-EM structures of two conformational states of Plasmodium vivax hexokinase (PvHK) are reported at resolutions of ∼3 Å. It is shown that unlike other known hexokinase structures, PvHK displays a unique tetrameric organization (∼220 kDa) that can exist in either open or closed quaternary conformational states. Despite the resemblance of the active site of PvHK to its mammalian counterparts, this tetrameric organization is distinct from that of human hexokinases, providing a foundation for the structure-guided design of parasite-selective antimalarial drugs.

Although the success of molecular-replacement techniques requires the solution of a six-dimensional problem, this is often subdivided into two three-dimensional problems. REMO09 is one of the programs which have adopted this approach. It has been revisited in the light of a new probabilistic approach which is able to directly derive conditional distribution functions without passing through a previous calculation of the joint probability distributions. The conditional distributions take into account various types of prior information: in the rotation step the prior information may concern a non-oriented model molecule alone or together with one or more located model molecules. The formulae thus obtained are used to derive figures of merit for recognizing the correct orientation in the rotation step and the correct location in the translation step. The phases obtained by this new version of REMO09 are used as a starting point for a pipeline which in its first step extends and refines the molecular-replacement phases, and in its second step creates the final electron-density map which is automatically interpreted by CAB, an automatic model-building program for proteins and DNA/RNA structures.

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.

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.

This study demonstrates a new preparation method for single-crystal X-ray diffraction samples using a focused ion beam. The results of the structure determination and electron density maps with differently prepared samples are discussed, to evaluate this new method.

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.

Scientists from the Smithsonian Migratory Bird Center at the National Zoo have taken blood samples from thousands of birds and mosquitoes in an effort to track the progress of the West Nile Virus in the eastern United States. Come along in this video as Smithsonian scientists net birds living in downtown Washington, D.C., extract small amounts of blood, and then release them back into the "wild."

The post Video: Common birds in Washington, D.C. are helping Smithsonian scientists track intensity of the West Nile Virus appeared first on Smithsonian Insider.

Native to Africa and Madagascar, females of the species have a body length of 1.5 inches and a leg span of 4 to 5 inches. Males are tiny in comparison.

The post Females are giants in newly discovered species of golden orb weaver spider appeared first on Smithsonian Insider.

The National Zoo has been awarded a grant from the U.S. Fish and Wildlife Service to establish a captive population of the Virginia big-eared bat at the National Zoo’s Conservation & Research Center near Front Royal, Va. Only 15,000 Virginia big-eared bats remain living in caves in West Virginia, Virginia, Kentucky and North Carolina, and these are threatened by the white-nose syndrome.

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Nearly 100 years ago, scientists detected the first signs of cosmic rays—subatomic particles (mostly protons) that zip through space at nearly the speed of light. […]

The post Telescope array finds new evidence that exploding stars are sources of cosmic rays appeared first on Smithsonian Insider.

The way that massive stars form remains mysterious, in part, because massive stars are rare and tend to spend their youth shrouded by dust and gas and hidden from view.

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Koenig and his colleagues examined an area of space called W5, which lies about 6,500 light-years away toward the constellation Cassiopeia—about 6 trillion miles. Their research indicates the prospects for hypothetical alien life there are disappointing.

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For the first time, astronomers have found a supernova explosion with properties similar to a gamma-ray burst, but without seeing any gamma rays from it.

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A new study published in the Feb. 2 issue of the Proceedings of the National Academy of Sciences indicates that forests in the Eastern United […]

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The results show mergers of two dense stellar remnants are the likely cause of many of the supernovae that have been used to measure the accelerated expansion of the universe.

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Eleven bats remain in the National Zoo’s colony. The initial challenge the team faced was how to feed the animals. Virginia big-eared bats, which are a subspecies of the Townsend’s big-eared bat (Corynorhinuss townsendii), eat while flying.

The post Captive colony of Virginia big-eared bats providing valuable lessons in battle against deadly white-nose syndrome appeared first on Smithsonian Insider.

The science-based study will evaluate elephant welfare along a quality continuum, assessing the impact of zoo management practices by looking at the elephants’ responses to differences in practices among zoos.

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The tiger reserves of Asia could support more than 10,000 wild tigers – three times the current number – if they are managed as large-scale […]

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To honor Harvard-Smithsonian astronomer John Huchra, who passed away in October 2010, his friends and colleagues at the Harvard-Smithsonian Center for Astrophysics have created a […]

The post New interactive World Wide Telescope tour chronicles career of Harvard-Smithsonian astronomer John Huchra appeared first on Smithsonian Insider.


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.

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Smithsonian WILD! a new Web site from the Smithsonian Conservation Biology Institute designed to showcase the use of motion-triggered 'camera traps' by Smithsonian researchers, has been launched at the Web address siwild.si.edu.

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As researchers investigate the impact of the Burmese python in the Everglades, scientists from the Smithsonian Institution, South Florida Natural Resources Center and the University of Florida examined the snake’s predation of the area’s birds. They found that birds, including endangered species, accounted for 25 percent of the python’s diet in the Everglades.

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By compiling and comparing long-term data from stranding records and visual sighting records, both taken from nearly every ocean basin in the world, Pyenson verified that stranding records “faithfully reflect the number of species and the relative abundance” found in live surveys.

The post Stranding records are faithful reflection of live whale and dolphin populations, new study reveals appeared first on Smithsonian Insider.

The National Zoo has received a breeding pair of Asian small-clawed otters at Asia Trail for the first time. Mac, a three-year-old male from the Point Defiance Zoo in Tacoma, Wash., and Smidge, a five-year-old female from the Columbus Zoo in Ohio, arrived in April and are now in their exhibit.

The post Keepers are optimistic about Zoo’s new breeding pair of Asian small-clawed otters appeared first on Smithsonian Insider.

Astronomers have probed into the distant universe and discovered that galaxies display one of two distinct behaviors: they are either awake or asleep, actively forming stars or are not forming any new stars at all.

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A new genetic study by a team of Cuban and American researchers confirms that American crocodiles are hybridizing with wild populations of critically endangered Cuban crocodiles, which may cause a population decline of this species found only in the Cuban Archipelago.

The post Genetic study confirms American crocodiles and critically endangered Cuban crocodiles are hybridizing in the wild appeared first on Smithsonian Insider.

Astronomers using NASA's Chandra X-ray Observatory discovered the first pair of supermassive black holes in a spiral galaxy similar to the Milky Way. Approximately 160 million light years from Earth, the pair is the nearest known such phenomenon.

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