Explore the vast range of titles available.

Cryo-electron microscopy is a popular method for the determination of protein structures; however, identifying a sufficient number of particles for analysis can take months of manual effort. Current computational approaches find many false positives and require ad hoc postprocessing, especially for unusually shaped particles. To address these shortcomings, we develop Topaz, an efficient and accurate particle-picking pipeline using neural networks trained with a general-purpose positive-unlabeled learning method. This framework enables particle detection models to be trained with few sparsely labeled particles and no labeled negatives. Topaz retrieves many more real particles than conventional picking methods while maintaining low false-positive rates, is capable of picking challenging unusually shaped proteins (for example, small, non-globular and asymmetric particles), produces more representative particle sets and does not require post hoc curation. We demonstrate the performance of Topaz on two difficult datasets and three conventional datasets. Topaz is modular, standalone, free and open source (http://topaz.csail.mit.edu).

The Miocene rhyolites of the Spor Mountain Formation host Earth's largest beryllium deposit, which produced 85% of the world's beryllium in 2010. The fresh lava is extremely enriched in Be (up to 75 ppm in matrix glass). We have examined the rhyolite to better understand the Be enrichment. The Spor Mountain rhyolite contains ∼40% quartz, ∼40% sanidine, ∼10% biotite, and ∼10% plagioclase, along with accessory fluorite, columbite, euxenite, fergusonite, monazite, thorite, and zircon. Two types of rhyolite are present within the Spor Mountain Formation, a less-evolved magma (1150 ppm Rb, 42 ppm Be, 0.7 wt% F in glass) and a more-evolved magma (1710 ppm Rb, 75 ppm Be, 1.6 wt% F in glass). Eruption temperatures estimated using two-feldspar (Elkins and Grove 1990; Putirka 2008; Benisek et al. 2010), plagioclase-liquid and alkali feldspar-liquid (Putirka 2008), Ti-in-quartz (Thomas et al. 2010, 2015; Huang and Audetat 2012), biotite (Righter and Carmichael 1996), and zircon saturation (Boehnke et al. 2013) geothermometers converge on 718 °C for the less-evolved magma and 682 °C for the more-evolved magma. Using the Ti-in-Qz equation of Huang and Audetat (2012), the pre-eruptive pressure of the Spor Mountain rhyolite system is estimated to be about 2 kbar at 700 °C. Water content of the rhyolite melt was less than <5 wt%, based on the co-crystallization of all four major mineral phases at 700 °C, and the magma was water undersaturated (Webster et al. 1987). Viscosity of the rhyolite was about 106.2 Pa·s for the less-evolved rhyolite and 105.8 Pa·s for the more-evolved rhyolite. Fluorine lowered the melt viscosity, though not by a large amount (less than 0.5 log units at 1.6 wt% F). Partition coefficients for Be and other trace elements were determined for biotite, sanidine, plagioclase, and quartz from laser ablation-inductively coupled plasma-mass spectrometry analyses. Partition coefficients for trace elements in feldspars from the Spor Mountain rhyolite are generally higher than for feldspars from other silicic magmas and lower for biotite. The enrichment of beryllium in the Spor Mountain rhyolite was aided by its high incompatibility in the major mineral phases, with a bulk partition coefficient <0.1. Trace element models using the measured partition coefficients are inconsistent with accumulation of increments of melt formed by different degrees of partial melting and cannot explain the great depletion of compatible elements. Rather, the trace element abundances and Nd and Sr isotopic compositions are consistent with derivation of rhyolite by ∼25% partial melting of crust hybridized with mantle-derived components, followed by extensive fractional crystallization (75%). The combination of these magmatic processes set the stage for the formation of a world-class beryllium deposit.

This paper presents a study of a newly discovered pollucite-lepidolite-albite granite (PLAG) in the Himalayan leucogranite belt, which marks the first occurrence of pollucite, a major cesium silicate mineral, in the Himalayan orogenic belt (China). The rock appears at the northern part of the Gyirong pluton, coexisting with the tourmaline-bearing two-mica granite (TMG). Primary rare-metal minerals include lepidolite (Li), spodumene (Li), pollucite (Cs), cassiterite (Sn), and microlite (Ta). Micas, mainly lithian muscovite to lepidolite, contain 4.07 wt.% Li 2 O and 0.76 wt.% Rb 2 O on average. The average Li 2 O content of the spodumene is 7.95 wt.%. Pollucite not only has an average Cs 2 O content of 34 wt.%, but also has an elevated Rb 2 O content of about 0.16 wt.%. Notably, this granite attains industrial grades for rare metals, specifically with Li 2 O, Rb 2 O, and Cs 2 O contents of 0.49–1.19 wt.%, 0.12–0.24 wt.%, and 0.69–2.33 wt.%, respectively. Dating results of magmatic accessory cassiterite and monazite indicated that the PLAG was formed at 19–18 Ma, slightly later than the TMG (22–20 Ma) of the Gyirong pluton. Thus, these two types of granites may form within the same magmatic system considering their pulsating intrusive contact, formation ages, and whole-rock and mineral chemical compositions. Furthermore, the abundant presence of pollucite suggests that the PLAG experienced high degrees of magmatic fractionation. In comparison to the Pusila spodumene pegmatite in the Himalaya and the Yashan topaz-lepidolite granite in Jiangxi, South China, the Gyirong PLAG exhibits different whole-rock and mineral compositions, resulting from differences in source materials and fractionation processes. Notably, the difference in fluorine (F) content may determine the degree of rare-metal element enrichment. The discovery of Gyirong PLAG highlights multiple stages and types of rare-metal mineralization in the Himalayan leucogranite belt, which is controlled by the South Tibetan Detachment System. The Cs-bearing geyserite deposit exposed along the Yarlung-Zangbo River, together with Himalayan leucogranites, constitutes two systems of rare-metal elements migration and enrichment. These two systems reflect the interaction among Earth systems across time and space, emphasizing how the Himalayan orogeny controls mineralization. As a result, the Himalayan leucogranite belt has considerable prospecting potential for cesium and rubidium resources and may be a crucial area for future exploration and resource utilization.

We present results of calibration-free laser-induced breakdown spectroscopy (CF-LIBS) and energy-dispersive X-ray (EDX) analysis of natural colorless topaz crystal of local Pakistani origin. Topaz plasma was produced in the ambient air using a nanosecond laser pulse of width 5 ns and wavelength 532 nm. For the purpose of detection of maximum possible constituent elements within the Topaz sample, the laser fluences were varied, ranging 19.6–37.6 J·cm−2 and optical emission from the plasma was recorded within the spectral range of 250–870 nm. The spectrum obtained has shown the presence of seven elements viz. Al, Si, F, O, H, Na and N. Results shows that the fluorine was detected at laser fluence higher than 35 J·cm−2 and plasma temperature of >1 eV. Al and Si were found as the major compositional elements in topaz crystals. The ratios of concentrations of Al and Si were found as 1.55 and 1.59 estimated by CF-LIBS and EDX, respectively. Furthermore, no impurity was found in the investigated colorless topaz samples.

The total aboveground biomass production, nutritional status, bearing and branching behaviors of the central leader and one year old shoots of young apple trees have been analyzed. The shoots were further characterized according to the length, shoot demography, and the production of terminal and lateral flowers. All the characteristics are described in connection with nitrogen supply and cultivar. Nitrogen represents one of the major macronutrients involved in the growth and development of the fruit trees. The understanding of the effect of nitrogen supply for flower bud formation can be further improved by detailed analyses of tree architecture. While the biomass production was cultivar specific, the trees within particular cultivar were characterized by almost similar growth with respect to the nitrogen supply. Cultivar ´Rubinola´ exhibited similar branching pattern, but higher vigor than ´Topaz´. As a result of higher apical dominance, ´Rubinola´ produced higher proportion of long shoots, but a lower quality of short shoots than ´Topaz´. Consequently, cultivar ´Rubinola´ produced only few terminal flowers on short shoots and lateral flowers dominantly in the distal zone, while ´Topaz´ was characterized by intensive terminal flowering, but the lateral flowers were more abundant in the median zone. Even a lower dose of spring nitrogen improved the flower bud formation on both terminal and lateral positions extending the flowering zone on one-year-old shoots. This further changed the branching and bearing behavior of the apple trees, which particularly allows to optimize their fertilization management. However, this effect appears to be further regulated by mechanism connected with apical dominance.

Topaz is a kind of mineral with variable composition and a common gemstone variety. Because of its wide distribution and rich colors, it has attracted the attention of scholars around the world. In this paper, the composition, spectral, and gemological characteristics of yellow topaz were systematically characterized, and the dark inclusions inside the samples were discussed and analyzed. The results show that the yellow topaz has a glassy luster, transparent, with a refractive index of 1.609–1.617 and a birefringence of 0.008. The topaz sample has columnar crystal shape and a typical rhomboid cross section. The infrared spectral characteristic absorption peaks of yellow topaz mainly appear near 3649, 3426, 950, 628, 550, and 457 cm−1. The characteristic absorption peaks for Raman spectra are mainly at 937, 404, and 267 cm−1. The UV-vis spectra of all samples only had strong absorption bands in the range of 200–300 nm. The results of XRF and EMPA showed that the contents of Al2O3 and SiO2 in the samples were 52.79 (wt%) and 29.55 (wt%), respectively, and it was reasonable to speculate that the chromogenic element of the yellow color was iron. The inclusions in yellow topaz samples are mainly fluid inclusions, healing cracks, and albite. This paper has enriched the gemological characteristics of topaz and can provide theoretical data for the research and marketization of topaz.

In this study, we concentrate on the seismic signature of subducted sediments and suggest the formation of the L‐discontinuity beneath the ancient craton related to migrated sediment dehydration. We first determined the single‐crystal elasticity of topaz, the product of sediment dehydration, at high pressures and temperatures by Brillouin scattering. Using the derived elastic parameters, we establish the velocity and density profiles of subducted sediments in the upper mantle. According to our modeling results, 8.5–17.5 vol.% sediments intruding into the upper mantle will induce a 2%–4% low‐VS anomaly at 210–260 km. Meanwhile, continuous heating will lead to the dehydration of phengite in sediments. The dehydration of this amount sediments can generate a 3%–6% ISS with negative Clapeyron slopes, satisfying the observed L‐discontinuity in northern Finland and northern America without the anisotropy changes but accompanied by low‐velocity anomalies. Our study thus provides new insights into the origin of the L‐discontinuity. Plain Language Summary The origin of the global seismic discontinuities in the Earth's mantle has been well understood, but the formation mechanism of some local seismic discontinuities is still vague. Lehmann discontinuity (L‐discontinuity) is one of the regional discontinuities in the upper mantle with a 2%–6% impendence contrast (ISS) and negative Clapeyron slope. However, the deformation mechanism changes of olivine cannot explain the formation of the L‐discontinuity without the anisotropy changes. Here, we emphasize the significance of the migration and dehydration of the subducted sediments in the origin of the L‐discontinuity beneath the ancient craton. We determined the single‐crystal elasticity of topaz, the product of the sediment dehydration, and then investigated the seismic signature of subducted sediments. Our modeling results indicated that ∼17.5 vol.% sediments intruding into the upper mantle would lead to ∼4% low‐VS anomalies at 210–260 km. After the continuous heating, these intruding sediments would dehydrate by the reaction with the negative Clapeyron slopes, thus producing significant ISS. Therefore, the migration and dehydration of the subducted sediments can reasonably interpret the seismic characteristics of the L‐discontinuity beneath the cratonic regions such as northern Finland and northern America. Our results deepen the understanding of the origin of the L‐discontinuity. Key Points Single‐crystal elasticity of topaz under high pressure and temperature has been investigated by Brillouin scattering The obtained elasticity parameters are used to model the density and velocity profiles of the subducted sediments We suggest the formation of the L‐discontinuity beneath the ancient craton related to migrated sediment dehydration

Topaz is frequently subjected to heat treatment and irradiation to enhance colour, particularly to produce the market’s most preferred salmon pink and sky blue varieties. However, an insufficient description of these processes can lead to fraudulent practices. This experimental and forensic mineralogical and gemmological study investigates eighteen heat-treated topaz samples from Ouro Preto (OP) and Caraí (CA), Brazil, using electron microanalysis, LA-ICP-MS, Raman, and optical absorption spectroscopy before and after heat treatment at various temperatures. The most significant optical changes were observed at 300 °C when the CA sample lost its colour from sky blue to colourless, while OP samples retained their imperial orange colour up to 500 °C before transitioning to pink at 700 °C. Chemically, the CA samples are rich in F (> 1.8 apfu ) with low trace element concentration (Fe ≤ 125 ppm, Ge ≤ 153 ppm), falling to the pegmatite and greisen field of topaz origin. The OP samples contain less F (1.4–1.5 apfu ) but higher trace element contents (Cr up to 204 ppm, Ti up to 115 ppm, Fe, Mn, Ge < 64 ppm), consistent with a hydrothermal origin. Raman spectra show no significant inter-sample variation, but their luminescence spectra feature strong differences: Mn acts as the luminophore in CA samples, while Cr 3+ centers dominate in OP samples. The optical absorption spectra reveal distinct thermal responses. The OP samples heated to temperatures ≥ 500 °C developed new absorption bands at 530–532 nm, consequently resulting in a visible pink colour. On the other hand, the CA spectra exhibit strong absorption in the NIR region; the unheated sample has a broad absorption band at 634 nm, responsible for the sky-blue colour of topaz. Heating ≥ 300 °C eliminates the transmission window in the blue to cyan regions, removing blue colouration. These thermal-optical signatures serve as indicators of heat treatment in topaz declared from these two localities. Moreover, the combination of spectroscopic methods, which we successfully applied in recognizing heat treatment on the studied samples, provides a systematic approach for identifying treatment in topaz and potentially other gemstones.

A study of the cathodoluminescence (CL) properties of imperial topaz from Ouro Preto region (Minas Gerais state, Brazil) and its relation with trace-element composition was conducted, using scanning electron microscope cathodoluminescence (SEM-CL), optical microscope cathodoluminescence (OM-CL), cathodoluminescence-spectrometry (CL-spectrometry), electron microprobe analysis (EMPA), laser ablation inductively-coupled plasma mass spectrometry (LA-ICP-MS) and Raman spectrometry. Each analytical technique allowed characterization of the imperial topaz fingerprint. SEM-CL panchromatic images show different crystal growth and resorption events in imperial topaz crystals. Colour CL images indicate only blue to violet emissions. The CL-spectra indicate a broad emission band with low intensity peak at ∼417 nm and a broad emission band with high intensity and major peaks at 685, 698, 711 and 733 nm. The EMPA indicates high OH content, in which the OH/(OH + F) ratio ranges between 0.35-0.43 (0.72 ≤ OH ≤ 0.86 apfu). High Cu and Zn concentrations (LA-ICP-MS) were measured in the high luminescence areas of SEM-CL images, suggesting both elements as CL-activators in imperial topaz. Raman and CL-spectra indicate high Cr concentrations, corroborated by EMPA and LA-ICP-MS results. The high Cr caused strong luminescence intensities that enabled their superimposition over the OH stretching mode (∼3650 cm-1) of topaz in all Raman spectra. Among trace elements, the concentrations of Ti, V, Cr, Mn, Fe, Cu, Zn, Ga and Ge provide the fingerprint of imperial topaz.