Automated Grain Boundary Detection for Bright-Field Transmission Electron Microscopy Images via U-Net.

Quantification of microstructures is crucial for understanding processing-structure and structure-property relationships in polycrystalline materials. Delineating grain boundaries in bright-field transmission electron micrographs, however, is challenging due to complex diffraction contrast in images. Conventional edge detection algorithms are inadequate; instead, manual tracing is usually required. This study demonstrates the first successful machine learning approach for grain boundary detection in bright-field transmission electron micrographs. The proposed methodology uses a U-Net convolutional neural network trained on carefully constructed data from bright-field images and hand tracings available from prior studies, combined with targeted postprocessing algorithms to preserve fine features of interest. The image processing pipeline accurately estimates grain boundary positions, avoiding segmentation in regions with intragrain contrast and identifying low-contrast boundaries. Our approach is validated by directly comparing microstructural markers (i.e., grain centroids) identified in U-Net predictions with those identified in hand tracings; furthermore, the grain size distributions obtained from the two techniques show notable overlap when compared using t-test, Kolmogorov-Smirnov test, and Cramér-von Mises test. The technique is then successfully applied to interpret new microstructures having different image characteristics from the training data, with preliminary results from platinum and palladium microstructures presented, highlighting the versatility of our approach for grain boundary identification in bright-field micrographs.

Massive Suppression of Proximity Pairing in Topological (Bi_{1-x}Sb_{x})_{2}Te_{3} Films on Niobium.

Interfacing bulk conducting topological Bi_{2}Se_{3} films with s-wave superconductors initiates strong superconducting order in the nontrivial surface states. However, bulk insulating topological (Bi_{1-x}Sb_{x})_{2}Te_{3} films on bulk Nb instead exhibit a giant attenuation of surface superconductivity, even for films only two layers thick. This massive suppression of proximity pairing is evidenced by ultrahigh-resolution band mappings and by contrasting quantified superconducting gaps with those of heavily n-doped topological Bi_{2}Se_{3}/Nb. The results underscore the limitations of using superconducting proximity effects to realize topological superconductivity in nearly intrinsic systems.

In Situ Strain Tuning of the Dirac Surface States in Bi2Se3 Films.

Elastic strain has the potential for a controlled manipulation of the band gap and spin-polarized Dirac states of topological materials, which can lead to pseudomagnetic field effects, helical flat bands, and topological phase transitions. However, practical realization of these exotic phenomena is challenging and yet to be achieved. Here we show that the Dirac surface states of the topological insulator Bi2Se3 can be reversibly tuned by an externally applied elastic strain. Performing in situ X-ray diffraction and in situ angle-resolved photoemission spectroscopy measurements during tensile testing of epitaxial Bi2Se3 films bonded onto a flexible substrate, we demonstrate elastic strains of up to 2.1% and quantify the resulting changes in the topological surface state. Our study establishes the functional relationship between the lattice and electronic structures of Bi2Se3 and, more generally, demonstrates a new route toward momentum-resolved mapping of strain-induced band structure changes.

Superconducting pairing of topological surface states in bismuth selenide films on niobium.

A topological insulator film coupled to a simple isotropic s-wave superconductor substrate can foster helical pairing of the Dirac fermions associated with the topological surface states. Experimental realization of such a system is exceedingly difficult, however using a novel "flip-chip" technique, we have prepared single-crystalline Bi2Se3 films with predetermined thicknesses in terms of quintuple layers (QLs) on top of Nb substrates fresh from in situ cleavage. Our angle-resolved photoemission spectroscopy (ARPES) measurements of the film surface disclose superconducting gaps and coherence peaks of similar magnitude for both the topological surface states and bulk states. The ARPES spectral map as a function of temperature and film thickness up to 10 QLs reveals key characteristics relevant to the mechanism of coupling between the topological surface states and the superconducting Nb substrate; the effective coupling length is found to be much larger than the decay length of the topological surface states.

Correlating interfacial octahedral rotations with magnetism in (LaMnO3+δ)N/(SrTiO3)N superlattices.

Lattice distortion due to oxygen octahedral rotations have a significant role in mediating the magnetism in oxides, and recently attracts a lot of interests in the study of complex oxides interface. However, the direct experimental evidence for the interrelation between octahedral rotation and magnetism at interface is scarce. Here we demonstrate that interfacial octahedral rotation are closely linked to the strongly modified ferromagnetism in (LaMnO3+δ)N/(SrTiO3)N superlattices. The maximized ferromagnetic moment in the N=6 superlattice is accompanied by a metastable structure (space group Imcm) featuring minimal octahedral rotations (a(-)a(-)c(-), α~4.2°, γ~0.5°). Quenched ferromagnetism for N<4 superlattices is correlated to a substantially enhanced c axis octahedral rotation (a(-)a(-)c(-), α~3.8°, γ~8° for N=2). Monte-Carlo simulation based on double-exchange model qualitatively reproduces the experimental observation, confirming the correlation between octahedral rotation and magnetism. Our study demonstrates that engineering superlattices with controllable interfacial structures can be a feasible new route in realizing functional magnetic materials.

Surrogate matrix and surrogate analyte approaches for definitive quantitation of endogenous biomolecules.

BACKGROUND: Quantitation of biomarkers by LC-MS/MS is complicated by the presence of endogenous analytes. This challenge is most commonly overcome by calibration using an authentic standard spiked into a surrogate matrix devoid of the target analyte. A second approach involves use of a stable-isotope-labeled standard as a surrogate analyte to allow calibration in the actual biological matrix. For both methods, parallelism between calibration standards and the target analyte in biological matrix must be demonstrated in order to ensure accurate quantitation. RESULTS: In this communication, the surrogate matrix and surrogate analyte approaches are compared for the analysis of five amino acids in human plasma: alanine, valine, methionine, leucine and isoleucine. In addition, methodology based on standard addition is introduced, which enables a robust examination of parallelism in both surrogate analyte and surrogate matrix methods prior to formal validation. Results from additional assays are presented to introduce the standard-addition methodology and to highlight the strengths and weaknesses of each approach. CONCLUSION: For the analysis of amino acids in human plasma, comparable precision and accuracy were obtained by the surrogate matrix and surrogate analyte methods. Both assays were well within tolerances prescribed by regulatory guidance for validation of xenobiotic assays. When stable-isotope-labeled standards are readily available, the surrogate analyte approach allows for facile method development. By comparison, the surrogate matrix method requires greater up-front method development; however, this deficit is offset by the long-term advantage of simplified sample analysis.

Effects of a novel mGlu2/3 receptor agonist prodrug, LY2140023 monohydrate, on central monoamine turnover as determined in human and rat cerebrospinal fluid.

RATIONALE: Accumulating evidence suggests that the primary symptoms of schizophrenia may be associated with altered central glutamate transmission. LY2140023 monohydrate is the methionine prodrug of the selective mGlu(2/3) receptor agonist LY404039 and is currently being assessed for the treatment of schizophrenia. OBJECTIVE: The objective of this study was to evaluate the central pharmacological activity of LY2140023 monohydrate in preclinical and clinical studies. METHODS: Effects on neurotransmitter/metabolite concentrations were assessed in male rats following single oral doses of LY2140023 monohydrate (microdiasylates from the prefrontal cortex), single intraperitoneal injection of LY404039 [cerebrospinal fluid (CSF)], or LY2140023 monohydrate dosed once daily for 7 days (CSF). A clinical study in 16 healthy subjects assessed the effects of LY2140023 monohydrate 40 mg orally twice daily for 14 days in lumbar CSF. RESULTS: Rat studies: Acute dosing with LY2140023 monohydrate resulted in significant dose-dependent increases in extracellular concentrations of dihydroxyphenylacetic acid (DOPAC) and homovanillic acid (HVA), but not 5-hydroxyindoleacetic acid (5-HIAA), in the prefrontal cortex. LY2140023 monohydrate dosing for 7 days elevated the concentrations of HVA in CSF, while acutely dosed LY404039 increased the concentrations of DOPAC, HVA, and methoxy-hydroxyphenylglycol (MHPG), but not 5-HIAA. Clinical study: Significant increases were seen for DOPAC, HVA, 5-HIAA, and MHPG in the CSF of subjects receiving LY2140023 monohydrate, but not placebo. CONCLUSIONS: LY2140023 monohydrate and/or LY404039 dosing potently affected dopamine turnover and also significantly affected serotonin turnover in the human and rat central nervous systems. The measurement of biogenic amine metabolites such as DOPAC and HVA may serve as useful biomarkers of LY2140023 monohydrate and/or LY404039 central pharmacodynamic activity.

N-(4-((2-(trifluoromethyl)-3-hydroxy-4-(isobutyryl)phenoxy)methyl)benzyl)-1-methyl-1H-imidazole-4-carboxamide (THIIC), a novel metabotropic glutamate 2 potentiator with potential anxiolytic/antidepressant properties: in vivo profiling suggests a link between behavioral and central nervous system neurochemical changes.

The normalization of excessive glutamatergic neurotransmission through the activation of metabotropic glutamate 2 (mGlu2) receptors may have therapeutic potential in a variety of psychiatric disorders, including anxiety/depression and schizophrenia. Here, we characterize the pharmacological properties of N-(4-((2-(trifluoromethyl)-3-hydroxy-4-(isobutyryl)phenoxy)methyl)benzyl)-1-methyl-1H-imidazole-4-carboxamide (THIIC), a structurally novel, potent, and selective allosteric potentiator of human and rat mGlu2 receptors (EC(50) = 23 and 13 nM, respectively). THIIC produced anxiolytic-like efficacy in the rat stress-induced hyperthermia assay and the mouse stress-induced elevation of cerebellar cGMP and marble-burying assays. THIIC also produced robust activity in three assays that detect antidepressant-like activity, including the mouse forced-swim test, the rat differential reinforcement of low rate 72-s assay, and the rat dominant-submissive test, with a maximal response similar to that of imipramine. Effects of THIIC in the forced-swim test and marble burying were deleted in mGlu2 receptor null mice. Analysis of sleep electroencephalogram (EEG) showed that THIIC had a sleep-promoting profile with increased non-rapid eye movement (REM) and decreased REM sleep. THIIC also decreased the dark phase increase in extracellular histamine in the medial prefrontal cortex and decreased levels of the histamine metabolite tele-methylhistamine (t-MeHA) in rat cerebrospinal fluid. Collectively, these results indicate that the novel mGlu2-positive allosteric modulator THIIC has robust activity in models used to predict anxiolytic/antidepressant efficacy, substantiating, at least with this molecule, differentiation in the biological impact of mGlu2 potentiation versus mGlu2/3 orthosteric agonism. In addition, we provide evidence that sleep EEG and CSF t-MeHA might function as viable biomarker approaches to facilitate the translational development of THIIC and other mGlu2 potentiators.

Analysis of glutamine, glutamate, pyroglutamate, and GABA in cerebrospinal fluid using ion pairing HPLC with positive electrospray LC/MS/MS.

A simple and sensitive method for the separation and quantitation of glutamine, glutamate, pyroglutamate, and gamma-aminobutyric acid (GABA) in cerebrospinal fluid (CSF) is presented. The method utilizes ion pairing with heptafluorobutyric acid (HFBA) to achieve HPLC separation with detection by positive ESI LC/MS/MS. The method does not require extraction or derivatization, utilizes a heavy labeled internal standard for each analyte, and allows for rapid throughput with a 5 min run time. The method was developed with particular attention taken to prevent conversion between analytes known to occur under certain conditions. The lower limit of quantitation is 7.8 ng/ml for all analytes, and the intra-day and inter-day accuracy (%RE) and precision (%R.S.D.) are defined for all analytes. The method was developed as a sensitive, selective, and robust method to investigate the excitatory and inhibitory neurotransmitters (glutamate and GABA) as biomarkers in drug development.

Simultaneous profiling of multiple neurochemical pathways from a single cerebrospinal fluid sample using GC/MS/MS with electron capture detection.

Biogenic amines and amino acids are widely characterized in the pathways representing neurotransmission. Although several analytical methodologies have been used to detect specific target molecules in relevant fluids such as cerebrospinal fluid (CSF), multiple assays must be used to survey the primary pathways involved. This article describes the development of a GC/MS/MS method capable of analyzing up to 43 analytes (representing 20 amino acids and more than seven neurochemical pathways) from a single 50 microl CSF sample. In this procedure, a CSF sample is first treated with acetonitrile to precipitate proteins. The dried sample is then derivatized with a mixture of 2,2,3,3,3-pentafluoro-1-propanol and pentafluoropropionic acetic anhydride to replace all active hydrogen atoms with fluorine-containing groups. Due to the concentration difference between amino acids and neurotransmitters, these two compound classes are analyzed in separate injections of the same derivatized extract. The total run time for each injection is approximately 15-20 min. An essential feature of the method is the use of argon as a reagent gas for electron capture chemical ionization (ECCI), as the use of the more traditional gas (methane) lacked sufficient durability to be considered for use with the present instrumentation. This article describes the development of this method including a detailed investigation of the chemical ionization conditions used. The resultant conditions allow for the profiling of biogenic amines (e.g. serotonin, norepinephrine, and dopamine) in the low picogram per milliliter range.

Current applications of liquid chromatography/mass spectrometry in pharmaceutical discovery after a decade of innovation.

Current drug discovery involves a highly iterative process pertaining to three core disciplines: biology, chemistry, and drug disposition. For most pharmaceutical companies the path to a drug candidate comprises similar stages: target identification, biological screening, lead generation, lead optimization, and candidate selection. Over the past decade, the overall efficiency of drug discovery has been greatly improved by a single instrumental technique, liquid chromatography/mass spectrometry (LC/MS). Transformed by the commercial introduction of the atmospheric pressure ionization interface in the mid-1990s, LC/MS has expanded into almost every area of drug discovery. In many cases, drug discovery workflow has been changed owing to vastly improved efficiency. This review examines recent trends for these three core disciplines and presents seminal examples where LC/MS has altered the current approach to drug discovery.

Synthetically lethal interactions involving loss of the yeast ERG24: the sterol C-14 reductase gene.

ERG2 and ERG24 are yeast sterol biosynthetic genes which are targets of morpholine antifungal compounds. ERG2 and ERG24 encode the C-8 sterol isomerase and the C-14 reductase, respectively. ERG2 is regarded as a non-essential gene but the viability of ERG24 depends on genetic background, type of medium, and CaCl(2) concentration. We demonstrate that erg2 and erg24 mutants are viable in the deletion consortium background but are lethal when combined in the same haploid strain. The erg2erg24 double mutant can be suppressed by mutations in the sphingolipid gene ELO3 but not ELO2. Suppression occurs on rich medium but not on synthetic complete medium. We also demonstrate that the suppressed elo3erg2erg24 does not have a sterol composition markedly different from that of erg24. Further genetic analysis indicates that erg24 combined with mutations in erg6 or erg28 is synthetically lethal but when combined with mutations in erg3 is weakly viable. These results suggest that novel sterol intermediates probably contribute to the synthetic lethality observed in this investigation.

Dap1/PGRMC1 binds and regulates cytochrome P450 enzymes.

Cytochrome P450 enzymes are heme-dependent monoxygenases that play a central role in human physiology. Despite the numerous physiological processes that P450 enzymes impact, the electron donors P450 oxidoreductase and cytochrome b5 are the only proteins known to interact with and modulate the activity of ER microsomal P450s. Here, we report that Dap1/PGRMC1 is required for ER P450 function in yeast and humans. We show that S. pombe Dap1 is a hemoprotein that binds and positively regulates Cyp51A1 and Cyp61A1, two P450s required for sterol biosynthesis. Similarly, loss of human PGRMC1 reduces activity of Cyp51A1, blocking cholesterol synthesis and increasing production of toxic sterol intermediates. PGRMC1 stably binds Cyp51A1 and human P450s from three additional families including Cyp3A4, which metabolizes pharmaceutical compounds. These findings demonstrate that PGRMC1 is required for P450 activity and suggest that interindividual variation in PGRMC1 function may impact multiple biochemical pathways and drug metabolism.

Electronic reconstruction at SrMnO3-LaMnO3 superlattice interfaces.

We use resonant soft-x-ray scattering (RSXS) to study the electronic reconstruction at the interface between the Mott insulator LaMnO3 and the band insulator SrMnO3. Superlattices of these two insulators were shown previously to have both ferromagnetism and metallic tendencies [Koida, Phys. Rev. B 66, 144418 (2002)10.1103/PhysRevB.66.144418]. By studying a judiciously chosen superlattice reflection, we show that the interface density of states exhibits a pronounced peak at the Fermi level, similar to that predicted in related titanate superlattices by Okamoto et al. [Phys. Rev. B 70, 241104(R) (2004)10.1103/PhysRevB.70.241104]. The intensity of this peak correlates with the conductivity and magnetization, suggesting it is the driver of metallic behavior. Our study demonstrates a general strategy for using RSXS to probe the electronic properties of heterostructure interfaces.

Cumulative mutations affecting sterol biosynthesis in the yeast Saccharomyces cerevisiae result in synthetic lethality that is suppressed by alterations in sphingolipid profiles.

UPC2 and ECM22 belong to a Zn(2)-Cys(6) family of fungal transcription factors and have been implicated in the regulation of sterol synthesis in Saccharomyces cerevisiae and Candida albicans. Previous reports suggest that double deletion of these genes in S. cerevisiae is lethal depending on the genetic background of the strain. In this investigation we demonstrate that lethality of upc2Delta ecm22Delta in the S288c genetic background is attributable to a mutation in the HAP1 transcription factor. In addition we demonstrate that strains containing upc2Delta ecm22Delta are also inviable when carrying deletions of ERG6 and ERG28 but not when carrying deletions of ERG3, ERG4, or ERG5. It has previously been demonstrated that UPC2 and ECM22 regulate S. cerevisiae ERG2 and ERG3 and that the erg2Delta upc2Delta ecm22Delta triple mutant is also synthetically lethal. We used transposon mutagenesis to isolate viable suppressors of hap1Delta, erg2Delta, erg6Delta, and erg28Delta in the upc2Delta ecm22Delta genetic background. Mutations in two genes (YND1 and GDA1) encoding apyrases were found to suppress the synthetic lethality of three of these triple mutants but not erg2Delta upc2Delta ecm22Delta. We show that deletion of YND1, like deletion of GDA1, alters the sphingolipid profiles, suggesting that changes in sphingolipids compensate for lethality produced by changes in sterol composition and abundance.

Interactions of two major metabolites of prasugrel, a thienopyridine antiplatelet agent, with the cytochromes P450.

The biotransformation of prasugrel to R-138727 (2-[1-2-cyclopropyl-1-(2-fluorophenyl)-2-oxoethyl]-4-mercapto-3-piperidinylidene]acetic acid) involves rapid deesterification to R-95913 (2-[2-oxo-6,7-dihydrothieno[3,2-c]pyridin-5(4H)-yl]-1-cyclopropyl-2-(2-fluorophenyl)ethanone) followed by cytochrome P450 (P450)-mediated formation of R-138727, the metabolite responsible for platelet aggregation. For identification of the P450s responsible for the formation of the active metabolite, the current studies were conducted with R-95913 as the substrate. Incubations required supplementation with reduced glutathione. Hyperbolic kinetics (K(m) 21-30 microM), consistent with a single enzyme predominating, were observed after incubations with human liver microsomes. Correlation analyses revealed a strong relationship between R-138727 formation and CYP3A-mediated midazolam 1'-hydroxylation (r(2) = 0.98; p < 0.001) in a bank of characterized human liver microsomal samples. The human lymphoblast-expressed enzymes capable of forming R-138727, in rank order of rates, were CYP3A4>CYP2B6>CYP2C19 approximately CYP2C9>CYP2D6. A monoclonal antibody to CYP2B6 and the CYP3A inhibitor ketoconazole substantially inhibited R-138727 formation, whereas inhibitors of CYP2C9 (sulfaphenazole) and CYP2C19 (omeprazole) did not. Scaling of in vitro intrinsic clearance values from expressed enzymes to the whole liver using a relative abundance approach indicated that either CYP3A4 alone or CYP3A4 and CYP2B6 are the major contributors to R-138727 formation. R-95913 and R-138727 were also examined for their ability to inhibit metabolism mediated by five P450s. R-138727 did not inhibit the P450s tested. In vitro, R-95913 inhibited CYP2C9, CYP2C19, CYP2D6, and CYP3A, with K(i) values ranging from 7.2 microM to 82 microM, but did not inhibit CYP1A2. These K(i) values exceed circulating concentrations in humans by 3.8- to 43-fold. Therefore, neither R-95913 nor R-138727 is expected to substantially inhibit the P450-mediated metabolism of coadministered drugs.