The chemical mechanisms of flavin-dependent amine oxidases and the plasticity of the two-his one-carboxylate facial triad in tyrosine hydroxylase

Despite a number of kinetic and spectroscopic studies, the chemical mechanisms of amine oxidation by flavoenzymes remain widely debated. The mechanisms of by Nmethyltryptophan oxidase (MTOX) and tryptophan 2-monooxygenase (TMO) were probed using a combination of pH and primary deuterium, solvent, and 15N kinetic isotope effects. Slow substrates were chosen for these studies; MTOX was characterized with N-methylglycine and TMO was characterized with L-alanine. Primary deuterium kinetic isotope effects of 7.2 and 5.3 were observed for sarcosine oxidation by MTOX and for alanine oxidation by TMO, respectively, independent of the substrate concentration and pH. Monitoring the reduction of flavin spectroscopically revealed no intermediate flavin species with both enzyme-substrate systems. Furthermore, the magnitudes of the 15N kinetic isotope effects observed with both systems suggest that nitrogen rehybridization and C-H bond cleavage are concerted. These results are consistent with both enzymes utilizing a hydride transfer mechanism for amine oxidation. The role of the iron ligands of tyrosine hydroxylase (TyrH) was also investigated. TyrH contains one iron per monomer, which is held by three conserved amino acid residues, two histidines and a glutamate. As a probe of the plasticity of the metal binding site, each of the metal ligands in TyrH was substituted with glutamine, glutamate, or histidine. The resulting proteins were characterized for metal content, catalytic activity, and dopamine binding. The H336E and H336Q enzymes retain substantial catalytic activity. In contrast, the E376Q enzyme retains about 0.4% of the wild-type catalytic activity, and the E376H enzyme has no significant activity. The H331E enzyme oxidizes tetrahydropterin in a tyrosine-independent manner. The position of the charge-transfer absorbance band for the H336E and H336Q enzyme-inhibitor complexes is shifted relative to that of the wild-type enzyme, consistent with the change in the metal ligand. In contrast, the E376H and E376Q enzymes catalyze dopamine oxidation. These results provide a reference point for further structural studies of TyrH and the other aromatic amino acid hydroxylases, and for similar studies of other enzymes containing this ironbinding motif

Intersecting D-Branes on Shift Z2 x Z2 Orientifolds

We investigate Z2 x Z2 orientifolds with group actions involving shifts. A complete classification of possible geometries is presented where also previous work by other authors is included in a unified framework from an intersecting D-brane perspective. In particular, we show that the additional shifts not only determine the topology of the orbifold but also independently the presence of orientifold planes. In the second part, we work out in detail a basis of homological three cycles on shift Z2 x Z2 orientifolds and construct all possible fractional D-branes including rigid ones. A Pati-Salam type model with no open-string moduli in the visible sector is presented.Comment: 36 pages, 4 figures, refs. adde

Measurement of inner wall limiter SOL widths in KSTAR tokamak

https://doi.org/10.1016/j.nme.2016.12.001.Scrape-off layer (SOL) widths λq are presented from the KSTAR tokamak using fast reciprocating Langmuir probe assembly (FRLPA) measurements at the outboard mid-plane (OMP) and the infra-Red (IR) thermography at inboard limiter tiles in moderately elongated (κ = 1.45 – 1.55) L-mode inner wall-limited (IWL) plasmas under experimental conditions such as BT = 2.0 T, PNBI = 1.4 – 1.5 MW, line averaged densities 2.5 – 5.1 × 1019 m−3) and plasma current Ip = 0.4 − 0.7 MA. There is clear evidence for a double exponential structure in q||(r) from the FRLPA such that, for example at Ip = 0.6 MA, a narrow feature, λq,near (=3.5 mm) is found close to the LFCS, followed by a broader width, λq,main (=57.0 mm). Double exponential profiles (λq,near = 1.5 – 2.8 mm, λq,main = 17.0 – 35.0 mm) can be also observed in the IR heat flux mapped to the OMP throughout the range of Ip investigated. In addition, analysis of SOL turbulence statistics obtained with the FRLPA shows high relative fluctuation levels and positively skewed distributions in electron temperature and ion particle flux across the SOL, with both properties increasing for longer distance from the LCFS, as often previously observed in the tokamaks. Interestingly, the fluctuation character expressed in terms of spectral distributions remains unchanged in passing from the narrow to the broad SOL heat flux channel

Agreement Between Experts and an Untrained Crowd for Identifying Dermoscopic Features Using a Gamified App: Reader Feasibility Study

Background Dermoscopy is commonly used for the evaluation of pigmented lesions, but agreement between experts for identification of dermoscopic structures is known to be relatively poor. Expert labeling of medical data is a bottleneck in the development of machine learning (ML) tools, and crowdsourcing has been demonstrated as a cost- and time-efficient method for the annotation of medical images. Objective The aim of this study is to demonstrate that crowdsourcing can be used to label basic dermoscopic structures from images of pigmented lesions with similar reliability to a group of experts. Methods First, we obtained labels of 248 images of melanocytic lesions with 31 dermoscopic “subfeatures” labeled by 20 dermoscopy experts. These were then collapsed into 6 dermoscopic “superfeatures” based on structural similarity, due to low interrater reliability (IRR): dots, globules, lines, network structures, regression structures, and vessels. These images were then used as the gold standard for the crowd study. The commercial platform DiagnosUs was used to obtain annotations from a nonexpert crowd for the presence or absence of the 6 superfeatures in each of the 248 images. We replicated this methodology with a group of 7 dermatologists to allow direct comparison with the nonexpert crowd. The Cohen κ value was used to measure agreement across raters. Results In total, we obtained 139,731 ratings of the 6 dermoscopic superfeatures from the crowd. There was relatively lower agreement for the identification of dots and globules (the median κ values were 0.526 and 0.395, respectively), whereas network structures and vessels showed the highest agreement (the median κ values were 0.581 and 0.798, respectively). This pattern was also seen among the expert raters, who had median κ values of 0.483 and 0.517 for dots and globules, respectively, and 0.758 and 0.790 for network structures and vessels. The median κ values between nonexperts and thresholded average–expert readers were 0.709 for dots, 0.719 for globules, 0.714 for lines, 0.838 for network structures, 0.818 for regression structures, and 0.728 for vessels. Conclusions This study confirmed that IRR for different dermoscopic features varied among a group of experts; a similar pattern was observed in a nonexpert crowd. There was good or excellent agreement for each of the 6 superfeatures between the crowd and the experts, highlighting the similar reliability of the crowd for labeling dermoscopic images. This confirms the feasibility and dependability of using crowdsourcing as a scalable solution to annotate large sets of dermoscopic images, with several potential clinical and educational applications, including the development of novel, explainable ML tools

BioDiVinE: A Framework for Parallel Analysis of Biological Models

In this paper a novel tool BioDiVinEfor parallel analysis of biological models is presented. The tool allows analysis of biological models specified in terms of a set of chemical reactions. Chemical reactions are transformed into a system of multi-affine differential equations. BioDiVinE employs techniques for finite discrete abstraction of the continuous state space. At that level, parallel analysis algorithms based on model checking are provided. In the paper, the key tool features are described and their application is demonstrated by means of a case study

Plasma p-tau181/Aβ1-42 ratio predicts Aβ-PET status and correlates with CSF-p-tau181/Aβ1-42 and future cognitive decline

Background: In Alzheimer\u27s disease (AD), plasma amyloid beta (Aβ)1-42 and phosphorylated tau (p-tau) predict high amyloid status from Aβ positron emission tomography (PET); however, the extent to which combination of these plasma assays can predict remains unknown. Methods: Prototype Simoa assays were used to measure plasma samples from participants who were either cognitively normal (CN) or had mild cognitive impairment (MCI)/AD in the Australian Imaging, Biomarkers and Lifestyle (AIBL) study. Results: The p-tau181/Aβ1-42 ratio showed the best prediction of Aβ-PET across all participants (area under the curve [AUC] = 0.905, 95% confidence interval [CI]: 0.86–0.95) and in CN (AUC = 0.873; 0.80–0.94), and symptomatic (AUC = 0.908; 0.82–1.00) adults. Plasma p-tau181/Aβ1-42 ratio correlated with cerebrospinal fluid (CSF) p-tau181 (Elecsys, Spearman\u27s ρ = 0.74, P \u3c 0.0001) and predicted abnormal CSF Aβ (AUC = 0.816; 0.74–0.89). The p-tau181/Aβ1-42 ratio also predicted future rates of cognitive decline assessed by AIBL Preclinical Alzheimer Cognitive Composite or Clinical Dementia Rating Sum of Boxes (P \u3c 0.0001). Discussion: Plasma p-tau181/Aβ1-42 ratio predicted both Aβ-PET status and cognitive decline, demonstrating potential as both a diagnostic aid and as a screening and prognostic assay for preclinical AD trials