Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction.

Oxidation states of individual metal atoms within a metalloprotein can be assigned by examining X-ray absorption edges, which shift to higher energy for progressively more positive valence numbers. Indeed, X-ray crystallography is well suited for such a measurement, owing to its ability to spatially resolve the scattering contributions of individual metal atoms that have distinct electronic environments contributing to protein function. However, as the magnitude of the shift is quite small, about +2 eV per valence state for iron, it has only been possible to measure the effect when performed with monochromated X-ray sources at synchrotron facilities with energy resolutions in the range 2-3 × 10-4 (ΔE/E). This paper tests whether X-ray free-electron laser (XFEL) pulses, which have a broader bandpass (ΔE/E = 3 × 10-3) when used without a monochromator, might also be useful for such studies. The program nanoBragg is used to simulate serial femtosecond crystallography (SFX) diffraction images with sufficient granularity to model the XFEL spectrum, the crystal mosaicity and the wavelength-dependent anomalous scattering factors contributed by two differently charged iron centers in the 110-amino-acid protein, ferredoxin. Bayesian methods are then used to deduce, from the simulated data, the most likely X-ray absorption curves for each metal atom in the protein, which agree well with the curves chosen for the simulation. The data analysis relies critically on the ability to measure the incident spectrum for each pulse, and also on the nanoBragg simulator to predict the size, shape and intensity profile of Bragg spots based on an underlying physical model that includes the absorption curves, which are then modified to produce the best agreement with the simulated data. This inference methodology potentially enables the use of SFX diffraction for the study of metalloenzyme mechanisms and, in general, offers a more detailed approach to Bragg spot data reduction

Sex Differences in Mechanisms of Recovery after Isometric and Dynamic Fatiguing Tasks

Purpose The purpose of this study was to determine whether supraspinal mechanisms contribute to the sex difference in fatigability during and recovery from a dynamic and isometric fatiguing task with the knee extensors. Methods: Transcranial magnetic stimulation and electrical stimulation were used to determine voluntary activation and contractile properties of the knee extensors in 14 men and 17 women (20.8 ± 1.9 yr) after a 1) 60-s sustained, maximal voluntary isometric contraction (MVIC), and 2) dynamic fatiguing task involving 120 maximal voluntary concentric contractions with a 20% MVIC load. Results: There were no differences between men and women in the reduction of maximal torque during the sustained MVIC (54.4% ± 18.9% vs 55.9% ± 11.2%, P = 0.49) or in the decrease in power during the dynamic fatiguing task (14.7% ± 20.1% vs 14.2% ± 18.5%, P = 0.92). However, MVIC torque recovered more quickly for women than men after the sustained MVIC and the dynamic task (P \u3c 0.05). The transcranial magnetic stimulation–elicited superimposed twitch was larger for men than for women during the sustained MVIC and in recovery (immediately post, R0.1: 4.7% ± 3.3% vs 2.4% ± 1.9% MVIC; P = 0.02), with no sex difference after the dynamic task (P = 0.35). The reduction in resting twitch amplitude was larger for men than for women immediately after the dynamic task (37% ± 22% vs 23% ± 18%; P = 0.016) with no sex difference after the sustained MVIC (64% ± 16% vs 67% ± 11%; P = 0.46). Conclusions: Supraspinal fatigue contributed to fatigability of the knee extensors more for men than for women after a maximal isometric task, whereas contractile mechanisms explained the sex difference in torque recovery after the fast-velocity dynamic task. The mechanisms for the sex difference in fatigability are task dependent

Randomized Polypill Crossover Trial in People Aged 50 and Over

PMCID: PMC3399742This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Implementation of low-loss superinductances for quantum circuits

The simultaneous suppression of charge fluctuations and offsets is crucial for preserving quantum coherence in devices exploiting large quantum fluctuations of the superconducting phase. This requires an environment with both extremely low DC and high RF impedance. Such an environment is provided by a superinductance, defined as a zero DC resistance inductance whose impedance exceeds the resistance quantum $R_Q = h/(2e)^2 \simeq 6.5\ \mathrm{k\Omega}$ at frequencies of interest (1 - 10 GHz). In addition, the superinductance must have as little dissipation as possible, and possess a self-resonant frequency well above frequencies of interest. The kinetic inductance of an array of Josephson junctions is an ideal candidate to implement the superinductance provided its phase slip rate is sufficiently low. We successfully implemented such an array using large Josephson junctions ($E_J >> E_C$), and measured internal losses less than 20 ppm, self-resonant frequencies greater than 10 GHz, and phase slip rates less than 1 mHz

Sacramento River Predator Diet Analysis: A Comparative Study

This study examined diets of two predatory fish species, the native Sacramento Pikeminnow (Ptychocheilus grandis) and the introduced Striped Bass (Morone saxatilis), in the Sacramento River, California, USA. Both species have been implicated in native species declines through predation, eliciting our investigation of their diets in the Sacramento River. Sampling occurred between March and November 2017, and was conducted via hook and line on a 35-km reach near Chico, California. Habitat types sampled include engineered structures (water diversions and beam bridges), rip-rapped channel edges, and natural riverbank. Stomach contents were collected via gastric lavage and later processed using visual, gravimetric, and genetic techniques. Diets of Sacramento Pikeminnow and Striped Bass were highly similar as determined through index of relative importance and PERMANOVA modeling. Water temperature was the only variable that significantly affected diet composition. Results reflect similar dietary niches for both species in the Sacramento River

Inter-band magnetoplasmons in mono- and bi-layer graphene

Collective excitations spectrum of Dirac electrons in mono and bilayer graphene in the presence of a uniform magnetic field is investigated. Analytical results for inter-Landau band plasmon spectrum within the self-consistent-field approach are obtained. SdH type oscillations that are a monotonic function of the magnetic field are observed in the plasmon spectrum of both mono- and bi-layer graphene systems. The results presented are also compared with those obtained in conventional 2DEG. The chiral nature of the quasiparticles in mono and bilayer graphene system results in the observation of $\pi$ and $2\pi$ Berry's phase in the SdH- type oscillations in the plasmon spectrum.Comment: 9 pages, 2 figure

Metal-Insulator oscillations in a Two-dimensional Electron-Hole system

The electrical transport properties of a bipolar InAs/GaSb system have been studied in magnetic field. The resistivity oscillates between insulating and metallic behaviour while the quantum Hall effect shows a digital character oscillating from 0 to 1 conducatance quantum e^2/h. The insulating behaviour is attributed to the formation of a total energy gap in the system. A novel looped edge state picture is proposed associated with the appearance of a voltage between Hall probes which is symmetric on magnetic field reversal.Comment: 4 pages, 5 Postscript figures: revised versio

Significant Inter-Test Reliability across Approximate Number System Assessments

The approximate number system (ANS) is the hypothesized cognitive mechanism that allows adults, infants, and animals to enumerate large sets of items approximately. Researchers usually assess the ANS by having subjects compare two sets and indicate which is larger. Accuracy or Weber fraction is taken as an index of the acuity of the system. However, as Clayton et al., (2015) have highlighted, the stimulus parameters used when assessing the ANS vary widely. In particular, the numerical ratio between the pairs, and the way in which non-numerical features are varied often differ radically between studies. Recently, Clayton et al. (2015) found that accuracy measures derived from two commonly used stimulus sets are not significantly correlated. They argue that a lack of inter-test reliability threatens the validity of the ANS construct. Here we apply a recently developed modeling technique to the same data set. The model, by explicitly accounting for the effect of numerical ratio and non-numerical features, produces dependent measures that are less perturbed by stimulus protocol. Contrary to their conclusion we find a significant correlation in Weber fraction across the two stimulus sets. Nevertheless, in agreement with Clayton et al., we find that different protocols do indeed induce differences in numerical acuity and the degree of influence of non-numerical stimulus features. These findings highlight the need for a systematic investigation of how protocol idiosyncrasies affect ANS assessments

Analyzing intramolecular vibrational energy redistribution via the overlap intensity-level velocity correlator

Numerous experimental and theoretical studies have established that intramolecular vibrational energy redistribution (IVR) in isolated molecules has a heirarchical tier structure. The tier structure implies strong correlations between the energy level motions of a quantum system and its intensity-weighted spectrum. A measure, which explicitly accounts for this correaltion, was first introduced by one of us as a sensitive probe of phase space localization. It correlates eigenlevel velocities with the overlap intensities between the eigenstates and some localized state of interest. A semiclassical theory for the correlation is developed for systems that are classically integrable and complements earlier work focusing exclusively on the chaotic case. Application to a model two dimensional effective spectroscopic Hamiltonian shows that the correlation measure can provide information about the terms in the molecular Hamiltonian which play an important role in an energy range of interest and the character of the dynamics. Moreover, the correlation function is capable of highlighting relevant phase space structures including the local resonance features associated with a specific bright state. In addition to being ideally suited for multidimensional systems with a large density of states, the measure can also be used to gain insights into the phase space transport and localization. It is argued that the overlap intensity-level velocity correlation function provides a novel way of studying vibrational energy redistribution in isolated molecules. The correlation function is ideally suited to analyzing the parametric spectra of molecules in external fields.Comment: 16 pages, 13 figures (low resolution

Caveat Emptor Collecting and Processing Pottery in Western Rough Cilicia

This paper furnishes a preliminary assessment of the field and laboratory procedures used to obtain ceramic field data by the participants of Rough Cilicia Archaeological Survey Project in western Rough Cilicia (Gazipasha District, Antalya Province, south coastal Turkey). Between 1996 and 2004 the pedestrian team of the Rough Cilicia Survey conducted pottery collections and otherwise processed field pottery as its principal operation. Through nine consecutive field seasons the pedestrian team identified and processed an aggregate of 7313 sherds. This is a self-archived copy of the paper that was presented in 2004 and published in 2006 as Rauh, Nicolas K., and Richard Rothaus 2006 Caveat emptor: Collecting and processing pottery in Western Rough Cilicia. In Old pottery in a new century: innovating perspectives on Roman pottery studies: atti del convegno internazionale di studi, Catania, 22-24 aprile 2004. Daniele Malfitana, J. Poblome, and John Lund, eds. Pp. 347–362. Monografie dell’Istituto per i beni archeologici e monumentali, 1. Catania: Istituo per Beni Archeologici e monumenti - CNR