Decoding crystallography from high-resolution electron imaging and diffraction datasets with deep learning.

While machine learning has been making enormous strides in many technical areas, it is still massively underused in transmission electron microscopy. To address this, a convolutional neural network model was developed for reliable classification of crystal structures from small numbers of electron images and diffraction patterns with no preferred orientation. Diffraction data containing 571,340 individual crystals divided among seven families, 32 genera, and 230 space groups were used to train the network. Despite the highly imbalanced dataset, the network narrows down the space groups to the top two with over 70% confidence in the worst case and up to 95% in the common cases. As examples, we benchmarked against alloys to two-dimensional materials to cross-validate our deep-learning model against high-resolution transmission electron images and diffraction patterns. We present this result both as a research tool and deep-learning application for diffraction analysis.

Cr incorporated phase transformation in Y2O3 under ion irradiation.

Under irradiation, chemical species can redistribute in ways not expected from equilibrium behavior. In oxide-dispersed ferritic alloys, the phenomenon of irradiation-induced Cr redistribution at the metal/oxide interfaces has drawn recent attention. Here, the thermal and irradiation stability of the FeCr/Y2O3 interface has been systematically studied. Trilayer thin films of 90 nm Fe - 20 at.% Cr (1st layer)/100 nm Y2O3 (2nd layer)/135 nm Fe - 20 at.% Cr (3rd layer) were deposited on MgO substrates at 500 °C. After irradiation, Cr diffuses towards and enriches the FeCr/Y2O3 interface. Further, correlated with Cr redistributed into the oxide, an amorphous layer is generated at the interface. In the Y2O3 layer, the original cubic phase is observed to transform to the monoclinic phase after irradiation. Meanwhile, nanosized voids, with relatively larger size at interfaces, are also observed in the oxide layer. First-principles calculations reveal that Cr substitution of Y interstitials in Y2O3 containing excess Y interstitials is favored and the irradiation-induced monoclinic phase enhances this process. Our findings provide new insights that may aid in the development of irradiation resistant oxide-dispersed ferritic alloys.

First records of Charadrius semipalmatus, Bonaparte 1825 (Charadriidae) and Gelochelidon nilotica Gmelin 1789 (Sternidae) in the State of Minas Gerais, Brazil.

Around forty bird species habitually reproduce in the Northern Hemisphere during summer, and migrate to the Southern Hemisphere during northern winter. These migrating birds fly together in large or small groups until they have reached the Caribbean, Central American, or Brazilian shores. Charadrius semipalmatus, Bonaparte 1825, is one of these migrating species that uses resting and feeding areas along eastern and western coasts of North and South America, with several records for the Brazilian coast, and very few for the inland country. On November 24, 2011, an individual of this species was observed on the banks of one of the lakes that compose a complex of about 40 temporary lakes within the Karst of Lagoa Santa Environmental Protection Area. On October 29 and 30, 2012 a single individual of Gelochelidon nilotica, Gmelin 1789, was also observed in Sumidouro State Park. We suggest that these specimens have used the Atlantic Ocean migration route, following the São Francisco River Basin, until the karst area. Although highly impacted, the temporary lakes within the Karst of Lagoa Santa still harbor a significant number of bird species, and serve as resting and feeding places for migratory or errant species that are still eliciting new records.

Oxidatively stable nanoporous silicon photocathodes with enhanced onset voltage for photoelectrochemical proton reduction.

Stable and high-performance nanoporous "black silicon" photoelectrodes with electrolessly deposited Pt nanoparticle (NP) catalysts are made with two metal-assisted etching steps. Doubly etched samples exhibit an ∼300 mV positive shift in photocurrent onset for photoelectrochemical proton reduction compared to oxide-free planar Si with identical catalysts. We find that the photocurrent onset voltage of black Si photocathodes prepared from single-crystal planar Si wafers by an Ag-assisted etching process increases in oxidative environments (e.g., aqueous electrolyte) owing to a positive flat-band potential shift caused by surface oxidation. However, within 24 h, the surface oxide layer becomes a kinetic barrier to interfacial charge transfer that inhibits proton reduction. To mitigate this issue, we developed a novel second Pt-assisted etch process that buries the Pt NPs deep into the nanoporous Si surface. This second etch shifts the onset voltage positively, from +0.25 V to +0.4 V versus reversible hydrogen electrode, and reduces the charge-transfer resistance with no performance decrease seen for at least two months. PEC performance was stable owing to Pt NP catalysts that were buried deeply in the photoelectrode by the second etch, below a thick surface layer comprised primarily of amorphous SiO2 along with some degree of remaining crystalline Si as observed by scanning and transmission electron micrographs. Electrochemical impedance studies reveal that the second etch leads to a considerably smaller interfacial charge-transfer resistance than samples without the additional etch, suggesting that burying the Pt NPs improves the interfacial contact to the crystalline silicon surface.

Antidepressant-like effect of Hoodia gordonii in a forced swimming test in mice: evidence for involvement of the monoaminergic system

Hoodia gordonii is a plant species used traditionally in southern Africa to suppress appetite. Recently, it has been associated with a significant increase in blood pressure and pulse rate in women, suggesting sympathomimetic activity. The present study investigated the possible antidepressant-like effects of acute and repeated (15 days) administration of H. gordonii extract (25 and 50 mg/kg, po) to mice exposed to a forced swimming test (FST). Neurochemical analysis of brain monoamines was also carried out to determine the involvement of the monoaminergic system on these effects. Acute administration of H. gordonii decreased the immobility of mice in the FST without accompanying changes in general activity in the open-field test during acute treatment, suggesting an antidepressant-like effect. The anti-immobility effect of H. gordonii was prevented by pretreatment of mice with PCPA [an inhibitor of serotonin (5-HT) synthesis], NAN-190 (a 5-HT1A antagonist), ritanserin (a 5-HT2A/2C antagonist), ondansetron (a 5-HT3A antagonist), prazosin (an α1-adrenoceptor antagonist), SCH23390 (a D1 receptor antagonist), yohimbine (an α2-adrenoceptor antagonist), and sulpiride (a D2 receptor antagonist). A significant increase in 5-HT levels in the striatum was detected after acute administration, while 5-HT, norepinephrine and dopamine were significantly elevated after chronic treatment. Results indicated that H. gordonii possesses antidepressant-like activity in the FST by altering the dopaminergic, serotonergic, and noradrenergic systems.

Antidepressant-like effect of Hoodia gordonii in a forced swimming test in mice: evidence for involvement of the monoaminergic system.

Hoodia gordonii is a plant species used traditionally in southern Africa to suppress appetite. Recently, it has been associated with a significant increase in blood pressure and pulse rate in women, suggesting sympathomimetic activity. The present study investigated the possible antidepressant-like effects of acute and repeated (15 days) administration of H. gordonii extract (25 and 50 mg/kg, po) to mice exposed to a forced swimming test (FST). Neurochemical analysis of brain monoamines was also carried out to determine the involvement of the monoaminergic system on these effects. Acute administration of H. gordonii decreased the immobility of mice in the FST without accompanying changes in general activity in the open-field test during acute treatment, suggesting an antidepressant-like effect. The anti-immobility effect of H. gordonii was prevented by pretreatment of mice with PCPA [an inhibitor of serotonin (5-HT) synthesis], NAN-190 (a 5-HT1A antagonist), ritanserin (a 5-HT2A/2C antagonist), ondansetron (a 5-HT3A antagonist), prazosin (an α1-adrenoceptor antagonist), SCH23390 (a D1 receptor antagonist), yohimbine (an α2-adrenoceptor antagonist), and sulpiride (a D2 receptor antagonist). A significant increase in 5-HT levels in the striatum was detected after acute administration, while 5-HT, norepinephrine and dopamine were significantly elevated after chronic treatment. Results indicated that H. gordonii possesses antidepressant-like activity in the FST by altering the dopaminergic, serotonergic, and noradrenergic systems.

Hidden one-dimensional spin modulation in a three-dimensional metal.

Pressure can transform a transparent material into an opaque one, quench the moments in a magnet and force solids to flow like liquids. At 15 GPa, the pressure found 500 km below the earth's surface, the semiconductors silicon and germanium superconduct. Yet, at this same pressure, we show here that the magnetism in metallic GdSi remains completely robust even as it shrinks by one-seventh of its volume. Non-resonant X-ray magnetic diffraction in a specially designed diamond anvil cell, combined with band structure calculations, reveal the stability of the incommensurate spin density wave, which can be traced to a persistently nested portion of the Fermi surface that becomes increasingly one-dimensional under pressure. A cooperative interaction between nested, itinerant spins and local magnetic moments provides the organizing principle for the modulated magnetic order, salient both for its insights into the role of topology in ordered states and its potential functionality.

Streptozotocin-induced diabetes mellitus affects lysosomal enzymes in rat liver

It has been previously shown that dextran sulfate administered to diabetic rats accumulates in the liver and kidney, and this could be due to a malfunction of the lysosomal digestive pathway. The aim of the present study was to evaluate the expression and activities of lysosomal enzymes that act upon proteins and sulfated polysaccharides in the livers of diabetic rats. Diabetes mellitus was induced by streptozotocin in 26 male Wistar rats (12 weeks old), while 26 age-matched controls received only vehicle. The livers were removed on either the 10th or the 30th day of the disease, weighed, and used to evaluate the activity, expression, and localization of lysosomal enzymes. A 50-60% decrease in the specific activities of cysteine proteases, especially cathepsin B, was observed in streptozotocin-induced diabetes mellitus. Expression (mRNA) of cathepsins B and L was also decreased on the 10th, but not on the 30th day. Sulfatase decreased 30% on the 30th day, while glycosidases did not vary (or presented a transitory and slight decrease). There were no apparent changes in liver morphology, and immunohistochemistry revealed the presence of cathepsin B in hepatocyte granules. The decrease in sulfatase could be responsible for the dextran sulfate build-up in the diabetic liver, since the action of sulfatase precedes glycosidases in the digestive pathway of sulfated polysaccharides. Our findings suggest that the decreased activities of cathepsins resulted from decreased expression of their genes, and not from general lysosomal failure, because the levels of glycosidases were normal in the diabetic liver.

Streptozotocin-induced diabetes mellitus affects lysosomal enzymes in rat liver.

It has been previously shown that dextran sulfate administered to diabetic rats accumulates in the liver and kidney, and this could be due to a malfunction of the lysosomal digestive pathway. The aim of the present study was to evaluate the expression and activities of lysosomal enzymes that act upon proteins and sulfated polysaccharides in the livers of diabetic rats. Diabetes mellitus was induced by streptozotocin in 26 male Wistar rats (12 weeks old), while 26 age-matched controls received only vehicle. The livers were removed on either the 10th or the 30th day of the disease, weighed, and used to evaluate the activity, expression, and localization of lysosomal enzymes. A 50-60% decrease in the specific activities of cysteine proteases, especially cathepsin B, was observed in streptozotocin-induced diabetes mellitus. Expression (mRNA) of cathepsins B and L was also decreased on the 10th, but not on the 30th day. Sulfatase decreased 30% on the 30th day, while glycosidases did not vary (or presented a transitory and slight decrease). There were no apparent changes in liver morphology, and immunohistochemistry revealed the presence of cathepsin B in hepatocyte granules. The decrease in sulfatase could be responsible for the dextran sulfate build-up in the diabetic liver, since the action of sulfatase precedes glycosidases in the digestive pathway of sulfated polysaccharides. Our findings suggest that the decreased activities of cathepsins resulted from decreased expression of their genes, and not from general lysosomal failure, because the levels of glycosidases were normal in the diabetic liver.

Interfacial ferromagnetism in LaNiO3/CaMnO3 superlattices.

We observe interfacial ferromagnetism in superlattices of the paramagnetic metal LaNiO3 and the antiferromagnetic insulator CaMnO3. LaNiO3 exhibits a thickness dependent metal-insulator transition and we find the emergence of ferromagnetism to be coincident with the conducting state of LaNiO3. That is, only superlattices in which the LaNiO3 layers are metallic exhibit ferromagnetism. Using several magnetic probes, we have determined that the ferromagnetism arises in a single unit cell of CaMnO3 at the interface. Together these results suggest that ferromagnetism can be attributed to a double exchange interaction among Mn ions mediated by the adjacent itinerant metal.

Protective effect of Chresta martii extract against indomethacin-induced gastric lesions in mice.

Chresta martii (Asteraceae) is a plant found in the Xingó region (semi-arid area) in Northeastearn Brazil, and is recognized by the local population as a traditional herb used to treat gastric diseases. This is the first report of the chemical composition, acute toxicity, and gastroprotective effect in mice of the hydroalcoholic extract (HAE) from the aerial parts (leaves and flowers) of Chresta martii. Animals received HAE doses from 10 to 2000 mg/kg, i.p. or 50 to 3000 mg/kg, p.o.) and were observed over 48 h for toxicity signs and mortality; sub-chronic toxicity was evaluated through 14 days treatment with once-daily HAE doses (400 mg/kg, p.o.). The gastroprotective effect of HAE was demonstrated on the indomethacin-induced gastric ulcer model after the administration of extracts. Data comparison of ulcer index averages between saline and HAE (100 or 400 mg/kg, p.o.) groups showed significant (P < 0.01) inhibition (71.73 and 76.72 %, respectively) of indomethacin-induced gastric lesions. Histological analyses showed significant (P < 0.05) inhibition of leukocyte migration in HAE-treated groups. A fingerprint of the HAE obtained by HPLC/UV/MS analysis showed major peaks characteristic of sesquiterpene lactones. Compound 1 was isolated and elucidated as a new natural product. Its capacity to prevent leukocyte chemotaxis was demonstrated in vitro, corroborating the pharmacological effects observed for C. martii HAE.

Investigating the electronic structure of fluorite-structured oxide compounds: comparison of experimental EELS with first principles calculations.

Energy loss spectra from fluorite-structured ZrO(2), CeO(2), and UO(2) compounds are compared with theoretical calculations based on density functional theory (DFT) and its extensions, including the use of Hubbard-U corrections (DFT + U) and hybrid functionals. Electron energy loss spectra (EELS) were obtained from each oxide using a scanning transmission electron microscope (STEM). The same spectra were computed within the framework of the full-potential linear augmented plane-wave (FLAPW) method. The theoretical and experimental EEL spectra are compared quantitatively using non-linear least squares peak fitting and a cross-correlation approach, with the best level of agreement between experiment and theory being obtained using the DFT + U and hybrid computational approaches.

Spatial variation in helminth community structure in the red-legged partridge (Alectoris rufa L.): effects of definitive host density.

Parasite community ecology has recently focused on understanding the forces structuring these communities. There are few surveys, however, designed to study the spatial repeatability and predictability of parasite communities at the local scale in one host. The purpose of our study was to address the relationship between infracommunity and component community richness, and to describe spatial variations on the local scale, of helminth parasite communities in an avian host, the red-legged partridge (Alectoris rufta). We sampled 235 wild partridges from 8 separate localities, with different partridge population densities, in the Ciudad Real and Toledo provinces of central Spain, and we determined their overall and intestinal helminth species. We found that habitat variables (mean temperature and land use) were not significantly associated with any component community. The partridge population abundance index was directly correlated with the prevalence and mean intensity of infection but not with component community species richness. There was a curvilinear relationship between infracommunity and component community species richness, as well as negative interspecific associations, for the helminth species assemblage parasitizing the intestine. A nestedness/anti-nestedness pattern, considered as part of a continuum, was associated with prevalence, mean intensity and partridge population abundance index, but not with component community richness. Increases in the partridge population abundance index and the prevalence and mean intensity of infection were associated with increases in helminth community nestedness. Although negative interactions between helminth species could not be ruled out as forces structuring helminth communities, our results suggest that parasite community structure in the red-legged partridge was primarily determined by the extrinsic influence of parasite habitat heterogeneity and its amplification of the differing probabilities of colonization of parasite species.

Diagnostic usefulness of carbohydrate-deficient transferrin for detecting alcohol-related problems in hospitalized patients.

We evaluated the diagnostic usefulness of carbohydrate-deficient transferrin (CDT) for detecting alcohol-related problems (ARP) in hospitalized patients, assessed potential differences according to gender and age, and compared this value to the other screening measures conventionally used, namely the CAGE questionnaire and standard biological markers MCV (mean corpuscular volume) and GGT (gamma-glutamyltransferase). CDT sensitivity for detecting ARP was 70%, specificity 75% and area under the receiver operating characteristic curve 0.76%. Its sensitivity was shown to be lower both in the female group (65 vs 71%) as well as in the younger-age group whereas its specificity was lower in the liver-damaged group (55%). CDT diagnostic value did not exceed that of CAGE (sensitivity 78% and specificity 99%), MCV (sensitivity and specificity 74%) or GGT (sensitivity 82% and specificity 53%) but was better than those of other biochemical measures. We conclude that CDT is an effective biological marker for the detection of ARP among hospitalized patients, but that its diagnostic usefulness does not exceed that of some other alternative measures commonly used.

Effect of epithelial debridement on human cornea proteoglycans.

Corneal transparency is attributed to the regular spacing and diameter of collagen fibrils, and proteoglycans may play a role in fibrillogenesis and matrix assembly. Corneal scar tissue is opaque and this opacity is explained by decreased ultrastructural order that may be related to proteoglycan composition. Thus, the objectives of the present study were to characterize the proteoglycans synthesized by human corneal explants and to investigate the effect of mechanical epithelial debridement. Human corneas unsuitable for transplants were immersed in F-12 culture medium and maintained under tissue culture conditions. The proteoglycans synthesized in 24 h were labeled metabolically by the addition of (35)S-sulfate to the medium. These compounds were extracted by 4 M GuHCl and identified by a combination of agarose gel electrophoresis, enzymatic degradation with protease and mucopolysaccharidases, and immunoblotting. Decorin was identified as the main dermatan sulfate proteoglycan and keratan sulfate proteoglycans were also prominent components. When the glycosaminoglycan side chains were analyzed, only keratan sulfate and dermatan sulfate were detected (approximately 50% each). Nevertheless, when these compounds were (35)S-labeled metabolically, the label in dermatan sulfate was greater than in keratan sulfate, suggesting a lower synthesis rate for keratan sulfate. (35)S-Heparan sulfate also appeared. The removal of the epithelial layer caused a decrease in heparan sulfate labeling and induced the synthesis of dermatan sulfate by the stroma. The increased deposit of dermatan sulfate proteoglycans in the stroma suggests a functional relationship between epithelium and stroma that could be related to the corneal opacity that may appear after epithelial cell debridement.

Effect of epithelial debridement on human cornea proteoglycans

Corneal transparency is attributed to the regular spacing and diameter of collagen fibrils, and proteoglycans may play a role in fibrillogenesis and matrix assembly. Corneal scar tissue is opaque and this opacity is explained by decreased ultrastructural order that may be related to proteoglycan composition. Thus, the objectives of the present study were to characterize the proteoglycans synthesized by human corneal explants and to investigate the effect of mechanical epithelial debridement. Human corneas unsuitable for transplants were immersed in F-12 culture medium and maintained under tissue culture conditions. The proteoglycans synthesized in 24 h were labeled metabolically by the addition of 35S-sulfate to the medium. These compounds were extracted by 4 M GuHCl and identified by a combination of agarose gel electrophoresis, enzymatic degradation with protease and mucopolysaccharidases, and immunoblotting. Decorin was identified as the main dermatan sulfate proteoglycan and keratan sulfate proteoglycans were also prominent components. When the glycosaminoglycan side chains were analyzed, only keratan sulfate and dermatan sulfate were detected (~50 percent each). Nevertheless, when these compounds were 35S-labeled metabolically, the label in dermatan sulfate was greater than in keratan sulfate, suggesting a lower synthesis rate for keratan sulfate. 35S-Heparan sulfate also appeared. The removal of the epithelial layer caused a decrease in heparan sulfate labeling and induced the synthesis of dermatan sulfate by the stroma. The increased deposit of dermatan sulfate proteoglycans in the stroma suggests a functional relationship between epithelium and stroma that could be related to the corneal opacity that may appear after epithelial cell debridement

Preparation and purification of Flavobacterium heparinum chondroitinases AC and B by hydrophobic interaction chromatography.

Flavobacterium heparinum is a soil bacterium that produces several mucopolysaccharidases such as heparinase, heparitinases I and II, and chondroitinases AC, B, C and ABC. The purpose of the present study was to optimize the preparation of F. heparinum chondroitinases, which are very useful tools for the identification and structural characterization of chondroitin and dermatan sulfates. We observed that during the routine procedure for cell disruption (ultrasound, 100 kHz, 5 min) some of the chondroitinase B activity was lost. Using milder conditions (2 min), most of the chondroitinase B and AC protein was solubilized and the enzyme activities were preserved. Tryptic soy broth without glucose was the best culture medium both for bacterial growth and enzyme induction. Chondroitinases AC and B were separated from each other and also from glucuronidases and sulfatases by hydrophobic interaction chromatography on HP Phenyl-Sepharose. A rapid method for screening of the column fractions was also developed based on the metachromatic shift of the color of dimethylmethylene blue.

Preparation and purification of Flavobacterium heparinum chondroitinases AC and B by hydrophobic interaction chromatography

Flavobacterium heparinum is a soil bacterium that produces several mucopolysaccharidases such as heparinase, heparitinases I and II, and chondroitinases AC, B, C and ABC. The purpose of the present study was to optimize the preparation of F. heparinum chondroitinases, which are very useful tools for the identification and structural characterization of chondroitin and dermatan sulfates. We observed that during the routine procedure for cell disruption (ultrasound, 100 kHz, 5 min) some of the chondroitinase B activity was lost. Using milder conditions (2 min), most of the chondroitinase B and AC protein was solubilized and the enzyme activities were preserved. Tryptic soy broth without glucose was the best culture medium both for bacterial growth and enzyme induction. Chondroitinases AC and B were separated from each other and also from glucuronidases and sulfatases by hydrophobic interaction chromatography on HP Phenyl-Sepharose. A rapid method for screening of the column fractions was also developed based on the metachromatic shift of the color of dimethylmethylene blue