Reevaluating Syntax-to-Phonology Mapping in Korean: An Optimality-Acoustic Account

This paper offers an optimality-based revision of previous syntax-driven analyses for detennining how prosodic constituency is derived from phrase structure in Korean. Under this revision, syntax-to-phonology mapping constraints (Selkirk 1987) appear to be outranked by a metrical constraint that idealizes minor phonological phrases as binary branching. This analysis accounts not only for data previously discussed in the literature on Korean phrasal phonology, but also for previously problematic data: the acoustic behavior of lax stops in existential expressions of the sort 'father(-NOM) exists'. Taken together, the theoretical discussion and the quantitative acoustic data under investigation reaffirm the notion that determining prosodic structure requires reference not only to syntactic information, but also to phonological conditions that constrain the nature of prosodic units

Human 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 : the catalytic roles of Tyr24 and Asp80

The human enzyme 2′-deoxynucleoside 5′-phosphate N-hydrolase 1 (HsDNPH1) catalyses the hydrolysis of 5-hydroxymethyl-2′-deoxyuridine 5′-phosphate to generate 5-hydroxymethyluracil and 2-deoxyribose-5-phosphate via a covalent 5-phospho-2-deoxyribosylated enzyme intermediate. HsDNPH1 is a promising target for inhibitor development towards anticancer drugs. Here, site-directed mutagenesis of conserved active-site residues, followed by HPLC analysis of the reaction and steady-state kinetics are employed to reveal the importance of each of these residues in catalysis, and the reaction pH-dependence is perturbed by each mutation. Solvent deuterium isotope effects indicate no rate-limiting proton transfers. Crystal structures of D80N-HsDNPH1 in unliganded and substrate-bound states, and of unliganded D80A- and Y24F-HsDNPH1 offer atomic level insights into substrate binding and catalysis. The results reveal a network of hydrogen bonds involving the substrate and the E104-Y24-D80 catalytic triad and are consistent with a proposed mechanism whereby D80 is important for substrate positioning, for helping modulate E104 nucleophilicity, and as the general acid in the first half-reaction. Y24 positions E104 for catalysis and prevents a catalytically disruptive close contact between E104 and D80.Peer reviewe

Snapshots of the reaction coordinate of a thermophilic 2'-deoxyribonucleoside/ribonucleoside transferase

Funding: P.T. is funded by IBioIC (IBioIC 2020-2-1), and C.M.C. is funded by the Wellcome Trust (217078/Z/19/Z). C.M.C. and D.H. are funded by research grants from NuCana plc..Nucleosides are ubiquitous to life and are required for the synthesis of DNA, RNA, and other molecules crucial for cell survival. Despite the notoriously difficult organic synthesis of nucleosides, 2′-deoxynucleoside analogues can interfere with natural DNA replication and repair and are successfully employed as anticancer, antiviral, and antimicrobial compounds. Nucleoside 2′-deoxyribosyltransferase (dNDT) enzymes catalyze transglycosylation via a covalent 2′-deoxyribosylated enzyme intermediate with retention of configuration, having applications in the biocatalytic synthesis of 2′-deoxynucleoside analogues in a single step. Here, we characterize the structure and function of a thermophilic dNDT, the protein from Chroococcidiopsis thermalis (CtNDT). We combined enzyme kinetics with structural and biophysical studies to dissect mechanistic features in the reaction coordinate, leading to product formation. Bell-shaped pH-rate profiles demonstrate activity in a broad pH range of 5.5–9.5, with two very distinct pKa values. A pronounced viscosity effect on the turnover rate indicates a diffusional step, likely product (nucleobase1) release, to be rate-limiting. Temperature studies revealed an extremely curved profile, suggesting a large negative activation heat capacity. We trapped a 2′-fluoro-2′-deoxyarabinosyl-enzyme intermediate by mass spectrometry and determined high-resolution structures of the protein in its unliganded, substrate-bound, ribosylated, 2′-difluoro-2′-deoxyribosylated, and in complex with probable transition-state analogues. We reveal key features underlying (2′-deoxy)ribonucleoside selection, as CtNDT can also use ribonucleosides as substrates, albeit with a lower efficiency. Ribonucleosides are the building blocks of RNA and other key intracellular metabolites participating in energy and metabolism, expanding the scope of use of CtNDT in biocatalysis.Peer reviewe

Human 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 : mechanism of 2'-deoxyuridine 5'-monophosphate hydrolysis

Funding: Industrial Biotechnology Innovation Centre - 2021-01-01.The enzyme 2′-deoxynucleoside 5′-phosphate N-hydrolase 1 (DNPH1) catalyzes the N-ribosidic bond cleavage of 5-hydroxymethyl-2′-deoxyuridine 5′-monophosphate to generate 2-deoxyribose 5-phosphate and 5-hydroxymethyluracil. DNPH1 accepts other 2′-deoxynucleoside 5′-monophosphates as slow-reacting substrates. DNPH1 inhibition is a promising strategy to overcome resistance to and potentiate anticancer poly(ADP-ribose) polymerase inhibitors. We solved the crystal structure of unliganded human DNPH1 and took advantage of the slow reactivity of 2′-deoxyuridine 5′-monophosphate (dUMP) as a substrate to obtain a crystal structure of the DNPH1:dUMP Michaelis complex. In both structures, the carboxylate group of the catalytic Glu residue, proposed to act as a nucleophile in covalent catalysis, forms an apparent low-barrier hydrogen bond with the hydroxyl group of a conserved Tyr residue. The crystal structures are supported by functional data, with liquid chromatography–mass spectrometry analysis showing that DNPH1 incubation with dUMP leads to slow yet complete hydrolysis of the substrate. A direct UV-vis absorbance-based assay allowed characterization of DNPH1 kinetics at low dUMP concentrations. A bell-shaped pH-rate profile indicated that acid–base catalysis is operational and that for maximum kcat/KM, two groups with an average pKa of 6.4 must be deprotonated, while two groups with an average pKa of 8.2 must be protonated. A modestly inverse solvent viscosity effect rules out diffusional processes involved in dUMP binding to and possibly uracil release from the enzyme as rate limiting to kcat/KM. Solvent deuterium isotope effects on kcat/KM and kcat were inverse and unity, respectively. A reaction mechanism for dUMP hydrolysis is proposed.Publisher PDFPeer reviewe

A Volumetric Method for Quantifying Atherosclerosis in Mice by Using MicroCT: Comparison to En Face

Precise quantification of atherosclerotic plaque in preclinical models of atherosclerosis requires the volumetric assessment of the lesion(s) while maintaining in situ architecture. Here we use micro-computed tomography (microCT) to detect ex vivo aortic plaque established in three dyslipidemic mouse models of atherosclerosis. All three models lack the low-density lipoprotein receptor (Ldlr−/−), each differing in plaque severity, allowing the evaluation of different plaque volumes using microCT technology. From clearly identified lesions in the thoracic aorta from each model, we were able to determine plaque volume (0.04–3.1 mm3), intimal surface area (0.5–30 mm2), and maximum plaque (intimal-medial) thickness (0.1–0.7 mm). Further, quantification of aortic volume allowed calculation of vessel occlusion by the plaque. To validate microCT for future preclinical studies, we compared microCT data to intimal surface area (by using en face methodology). Both plaque surface area and plaque volume were in excellent correlation between microCT assessment and en face surface area (r2 = 0.99, p<0.0001 and r2 = 0.95, p<0.0001, respectively). MicroCT also identified internal characteristics of the lipid core and fibrous cap, which were confirmed pathologically as Stary type III-V lesions. These data validate the use of microCT technology to provide a more exact empirical measure of ex vivo plaque volume throughout the entire intact aorta in situ for the quantification of atherosclerosis in preclinical models

An Overview of the Semi-Span Super-Sonic Transport (S4T) Wind-Tunnel Model Program

A summary of computational and experimental aeroelastic (AE) and aeroservoelastic (ASE) results for the Semi-Span Super-Sonic Transport (S4T) wind-tunnel model is presented. A broad range of analyses and multiple AE and ASE wind-tunnel tests of the S4T wind-tunnel model have been performed in support of the ASE element in the Supersonics Program, part of the NASA Fundamental Aeronautics Program. This paper is intended to be an overview of multiple papers that comprise a special S4T technical session. Along those lines, a brief description of the design and hardware of the S4T wind-tunnel model will be presented. Computational results presented include linear and nonlinear aeroelastic analyses, and rapid aeroelastic analyses using CFD-based reduced-order models (ROMs). A brief survey of some of the experimental results from two open-loop and two closed-loop wind-tunnel tests performed at the NASA Langley Transonic Dynamics Tunnel (TDT) will be presented as well

No Conclusive Evidence for Transits of Proxima b in MOST photometry

The analysis of Proxima Centauri's radial velocities recently led Anglada-Escud\'e et al. (2016) to claim the presence of a low mass planet orbiting the Sun's nearest star once every 11.2 days. Although the a-priori probability that Proxima b transits its parent star is just 1.5%, the potential impact of such a discovery would be considerable. Independent of recent radial velocity efforts, we observed Proxima Centauri for 12.5 days in 2014 and 31 days in 2015 with the MOST space telescope. We report here that we cannot make a compelling case that Proxima b transits in our precise photometric time series. Imposing an informative prior on the period and phase, we do detect a candidate signal with the expected depth. However, perturbing the phase prior across 100 evenly spaced intervals reveals one strong false-positive and one weaker instance. We estimate a false-positive rate of at least a few percent and a much higher false-negative rate of 20-40%, likely caused by the very high flare rate of Proxima Centauri. Comparing our candidate signal to HATSouth ground-based photometry reveals that the signal is somewhat, but not conclusively, disfavored (1-2 sigmas) leading us to argue that the signal is most likely spurious. We expect that infrared photometric follow-up could more conclusively test the existence of this candidate signal, owing to the suppression of flare activity and the impressive infrared brightness of the parent star.Comment: Accepted to ApJ. Posterior samples, MOST photometry and HATSouth photometry are all available at https://github.com/CoolWorlds/Proxim

Kepler-432: a red giant interacting with one of its two long period giant planets

We report the discovery of Kepler-432b, a giant planet ($M_b = 5.41^{+0.32}_{-0.18} M_{\rm Jup}, R_b = 1.145^{+0.036}_{-0.039} R_{\rm Jup}$) transiting an evolved star $(M_\star = 1.32^{+0.10}_{-0.07} M_\odot, R_\star = 4.06^{+0.12}_{-0.08} R_\odot)$ with an orbital period of $P_b = 52.501129^{+0.000067}_{-0.000053}$ days. Radial velocities (RVs) reveal that Kepler-432b orbits its parent star with an eccentricity of $e = 0.5134^{+0.0098}_{-0.0089}$, which we also measure independently with asterodensity profiling (AP; $e=0.507^{+0.039}_{-0.114}$), thereby confirming the validity of AP on this particular evolved star. The well-determined planetary properties and unusually large mass also make this planet an important benchmark for theoretical models of super-Jupiter formation. Long-term RV monitoring detected the presence of a non-transiting outer planet (Kepler-432c; $M_c \sin{i_c} = 2.43^{+0.22}_{-0.24} M_{\rm Jup}, P_c = 406.2^{+3.9}_{-2.5}$ days), and adaptive optics imaging revealed a nearby (0\farcs87), faint companion (Kepler-432B) that is a physically bound M dwarf. The host star exhibits high signal-to-noise asteroseismic oscillations, which enable precise measurements of the stellar mass, radius and age. Analysis of the rotational splitting of the oscillation modes additionally reveals the stellar spin axis to be nearly edge-on, which suggests that the stellar spin is likely well-aligned with the orbit of the transiting planet. Despite its long period, the obliquity of the 52.5-day orbit may have been shaped by star-planet interaction in a manner similar to hot Jupiter systems, and we present observational and theoretical evidence to support this scenario. Finally, as a short-period outlier among giant planets orbiting giant stars, study of Kepler-432b may help explain the distribution of massive planets orbiting giant stars interior to 1 AU.Comment: 22 pages, 19 figures, 5 tables. Accepted to ApJ on Jan 24, 2015 (submitted Nov 11, 2014). Updated with minor changes to match published versio

An Overview of Preliminary Computational and Experimental Results for the Semi-Span Super-Sonic Transport (S4T) Wind-Tunnel Model

A summary of computational and experimental aeroelastic and aeroservoelastic (ASE) results for the Semi-Span Super-Sonic Transport (S4T) wind-tunnel model is presented. A broad range of analyses and multiple ASE wind-tunnel tests of the S4T have been performed in support of the ASE element in the Supersonics Program, part of NASA's Fundamental Aeronautics Program. The computational results to be presented include linear aeroelastic and ASE analyses, nonlinear aeroelastic analyses using an aeroelastic CFD code, and rapid aeroelastic analyses using CFD-based reduced-order models (ROMs). Experimental results from two closed-loop wind-tunnel tests performed at NASA Langley's Transonic Dynamics Tunnel (TDT) will be presented as well

CubeSat Active Thermal Control via Microvascular Carbon Fiber Channel Radiator

Small spacecraft rarely have space for any thermal control subsystems and often must perform operations in “burst” mode as a result. The few spacecraft who do have control rely on low-complexity thermal control systems which conduct heat to the bus structure and then radiate the heat away. These simplistic techniques are sufficient for low power missions in Low Earth Orbit (LEO) but are not capable of dumping the heat produced in new mission profiles that are in development. This is due to small spacecraft incorporating increasingly advanced subsystems which have difficult thermal control requirements such as propulsion systems or high-power antennas. The University of Illinois at Urbana-Champaign, in partnership with NASA Ames Research Center, is developing a thermal control system for small spacecraft. This control system uses a deployable radiator panel made from carbon fiber with micro-vascular circulatory system for coolant. This paper is a follow-up on the previous year’s SmallSat conference. A bench prototype of the thermal control subsystem was designed and built. The prototype underwent a range of thermal and vibration tests at NASA Ames. Test results and lessons learned are presented. Moving forward, test conclusions will require some design parameters to be changed and the subsystem will reach TRL 6 by the end of the two-year program