Testing the transferability of a coarse-grained model to intrinsically disordered proteins

The intermediate-resolution coarse-grained protein model PLUM [T. Bereau and M. Deserno, J. Chem. Phys., 2009, 130, 235106] is used to simulate small systems of intrinsically disordered proteins involved in biomineralisation. With minor adjustments to reduce bias toward stable secondary structure, the model generates conformational ensembles conforming to structural predictions from atomistic simulation. Without additional structural information as input, the model distinguishes regions of the chain by predicted degree of disorder, manifestation of structure, and involvement in chain dimerisation. The model is also able to distinguish dimerisation behaviour between one intrinsically disordered peptide and a closely related mutant. We contrast this against the poor ability of PLUM to model the S1 quartz-binding peptide

Modules for Experiments in Stellar Astrophysics (MESA): Giant Planets, Oscillations, Rotation, and Massive Stars

We substantially update the capabilities of the open source software package Modules for Experiments in Stellar Astrophysics (MESA), and its one-dimensional stellar evolution module, MESA Star. Improvements in MESA Star's ability to model the evolution of giant planets now extends its applicability down to masses as low as one-tenth that of Jupiter. The dramatic improvement in asteroseismology enabled by the space-based Kepler and CoRoT missions motivates our full coupling of the ADIPLS adiabatic pulsation code with MESA Star. This also motivates a numerical recasting of the Ledoux criterion that is more easily implemented when many nuclei are present at non-negligible abundances. This impacts the way in which MESA Star calculates semi-convective and thermohaline mixing. We exhibit the evolution of 3-8 Msun stars through the end of core He burning, the onset of He thermal pulses, and arrival on the white dwarf cooling sequence. We implement diffusion of angular momentum and chemical abundances that enable calculations of rotating-star models, which we compare thoroughly with earlier work. We introduce a new treatment of radiation-dominated envelopes that allows the uninterrupted evolution of massive stars to core collapse. This enables the generation of new sets of supernovae, long gamma-ray burst, and pair-instability progenitor models. We substantially modify the way in which MESA Star solves the fully coupled stellar structure and composition equations, and we show how this has improved MESA's performance scaling on multi-core processors. Updates to the modules for equation of state, opacity, nuclear reaction rates, and atmospheric boundary conditions are also provided. We describe the MESA Software Development Kit (SDK) that packages all the required components needed to form a unified and maintained build environment for MESA. [Abridged]Comment: Accepted for publication in The ApJ Supplement Series. Extra informations required to reproduce the calculations in this paper are available at http://mesastar.org/results/mesa

Pharmacological Modulation of Noradrenergic Arousal Circuitry Disrupts Functional Connectivity of the Locus Ceruleus in Humans

State-dependent activity of locus ceruleus (LC) neurons has long suggested a role for noradrenergic modulation of arousal. However, in vivo insights into noradrenergic arousal circuitry have been constrained by the fundamental inaccessibility of the human brain for invasive studies. Functional magnetic resonance imaging (fMRI) studies performed during site-specific pharmacological manipulations of arousal levels may be used to study brain arousal circuitry. Dexmedetomidine is an anesthetic that alters the level of arousal by selectively targeting α2 adrenergic receptors on LC neurons, resulting in reduced firing rate and norepinephrine release. Thus, we hypothesized that dexmedetomidine-induced altered arousal would manifest with reduced functional connectivity between the LC and key brain regions involved in the regulation of arousal. To test this hypothesis, we acquired resting-state fMRI data in right-handed healthy volunteers 18–36 years of age (n = 15, 6 males) at baseline, during dexmedetomidine-induced altered arousal, and recovery states. As previously reported, seed-based resting-state fMRI analyses revealed that the LC was functionally connected to a broad network of regions including the reticular formation, basal ganglia, thalamus, posterior cingulate cortex (PCC), precuneus, and cerebellum. Functional connectivity of the LC to only a subset of these regions (PCC, thalamus, and caudate nucleus) covaried with the level of arousal. Functional connectivity of the PCC to the ventral tegmental area/pontine reticular formation and thalamus, in addition to the LC, also covaried with the level of arousal. We propose a framework in which the LC, PCC, thalamus, and basal ganglia comprise a functional arousal circuitry

Gene prediction and verification in a compact genome with numerous small introns

The genomes of clusters of related eukaryotes are now being sequenced at an increasing rate, creating a need for accurate, low-cost annotation of exon–intron structures. In this paper, we demonstrate that reverse transcription-polymerase chain reaction (RT–PCR) and direct sequencing based on predicted gene structures satisfy this need, at least for single-celled eukaryotes. The TWINSCAN gene prediction algorithm was adapted for the fungal pathogen Cryptococcus neoformans by using a precise model of intron lengths in combination with ungapped alignments between the genome sequences of the two closely related Cryptococcus varieties. This approach resulted in ∼60% of known genes being predicted exactly right at every coding base and splice site. When previously unannotated TWINSCAN predictions were tested by RT–PCR and direct sequencing, 75% of targets spanning two predicted introns were amplified and produced high-quality sequence. When targets spanning the complete predicted open reading frame were tested, 72% of them amplified and produced high-quality sequence. We conclude that sequencing a small number of expressed sequence tags (ESTs) to provide training data, running TWINSCAN on an entire genome, and then performing RT–PCR and direct sequencing on all of its predictions would be a cost-effective method for obtaining an experimentally verified genome annotation

An Autonomous Onboard Targeting Algorithm Using Finite Thrust Maneuvers

In earlier investigations, the adaptation and implementation of a modified two-level corrections (or targeting) process as the onboard targeting algorithm for the Trans-Earth Injection phase of Orion is presented. The objective of that targeting algorithm is to generate the times of ignition and magnitudes of the required maneuvers such that the desired state at entry interface is achieved. In an actual onboard flight software implementation, these times of ignition and maneuvers are relayed onto Flight Control for command and execution. Although this process works well when the burn durations or burn arcs are small, this might not be the case during a contingency situation when lower thrust engines are employed to perform the maneuvers. Therefore, a new model for the two-level corrections process is formulated here to accommodate finite burn arcs. This paper presents the development and formulation of the finite burn two-level corrector, used as an onboard targeting algorithm for the Trans-Earth Injection phase of Orion. A performance comparison between the impulsive and finite burn models is also presented. The present formulation ensures all entry constraints are met, without violating the available fuel budget, while allowing for low-thrust scenarios with long burn durations

Polarized Narrow-Line Emission from the Nucleus of NGC 4258

The detection of polarized continuum and line emission from the nucleus of NGC 4258 by Wilkes et al. (1995) provides an intriguing application of the unified model of Seyfert nuclei to a galaxy in which there is known to be an edge-on, rotating disk of molecular gas surrounding the nucleus. Unlike most Seyfert nuclei, however, NGC 4258 has strongly polarized narrow emission lines. To further investigate the origin of the polarized emission, we have obtained spectropolarimetric observations of the NGC 4258 nucleus at the Keck-II telescope. The narrow-line polarizations range from 1.0% for [S II] 6716 to 13.9% for the [O II] 7319,7331 blend, and the position angle of polarization is oriented nearly parallel to the projected plane of the masing disk. A correlation between critical density and degree of polarization is detected for the forbidden lines, indicating that the polarized emission arises from relatively dense (n_e > 10^4 cm^-3) gas. An archival Hubble Space Telescope narrow-band [O III] image shows that the narrow-line region has a compact, nearly unresolved core, implying a FWHM size of <2.5 pc. We discuss the possibility that the polarized emission might arise from the accretion disk itself and become polarized by scattering within the disk atmosphere. A more likely scenario is an obscuring torus or strongly warped disk surrounding the inner portion of a narrow-line region which is strongly stratified in density. The compact size of the narrow-line region implies that the obscuring structure must be smaller than ~2.5 pc in diameter.Comment: To appear in the Astronomical Journal. 13 pages, including 1 table and 4 figures. Uses emulateapj.st

Corneal Refractive Surgery in Patients with History of Optic Neuritis

Purpose The purpose of this study was to evaluate the risk of recurrence of optic neuritis after corneal refractive surgery in patients with a history of optic neuritis and to examine the safety and efficacy of the procedure in this population. Methods This was a retrospective chart review of patients with a history of optic neuritis who underwent laser-assisted in situ keratomileusis (LASIK) or photorefractive keratectomy (PRK) at a single tertiary center from June 1996 to December 2014. Fifteen eyes of 14 patients were included in this study. Visual acuity before and after the surgery was recorded. Patients were followed-up for over five years postoperatively for the recurrence of optic neuritis. Results The average LogMAR best corrected visual acuity (BCVA) preoperatively was 0.12 ± 0.19 (–0.10 to 0.60) and postoperatively was 0.06 ± 0.10 (–0.10 to 0.30). No eyes lost lines of BCVA. The average LogMAR uncorrected distance visual acuity (UDVA) after surgery was 0.12 ± 0.13 (0.00 to 0.48). Twenty-eight percent of patients reached a UDVA of 20/20 or better after refractive surgery. Optic neuritis recurred in 3/15 (20%) eyes and 3/14 patients (21%). Conclusion While corneal refractive procedures appear safe in patients with a history of optic neuritis, our data suggest that their efficacy may be reduced

Relative commutants of strongly self-absorbing C*-algebras

The relative commutant $A'\cap A^{\mathcal{U}}$ of a strongly self-absorbing algebra $A$ is indistinguishable from its ultrapower $A^{\mathcal{U}}$. This applies both to the case when $A$ is the hyperfinite II$_1$ factor and to the case when it is a strongly self-absorbing C*-algebra. In the latter case we prove analogous results for $\ell_\infty(A)/c_0(A)$ and reduced powers corresponding to other filters on $\bf N$. Examples of algebras with approximately inner flip and approximately inner half-flip are provided, showing the optimality of our results. We also prove that strongly self-absorbing algebras are smoothly classifiable, unlike the algebras with approximately inner half-flip.Comment: Some minor correction

The Type Ic Supernova 1994I in M51: Detection of Helium and Spectral Evolution

We present a series of spectra of SN 1994I in M51, starting 1 week prior to maximum brightness. The nebular phase began about 2 months after the explosion; together with the rapid decline of the optical light, this suggests that the ejected mass was small. Although lines of He I in the optical region are weak or absent, consistent with the Type Ic classification, we detect strong He I λ10830 absorption during the first month past maximum. Thus, if SN 1994I is a typical Type Ic supernova, the atmospheres of these objects cannot be completely devoid of helium. The emission-line widths are smaller than predicted by the model of Nomoto and coworkers, in which the iron core of a low-mass carbon-oxygen star collapses. They are, however, larger than in Type Ib supernovae

Developing young people's sense of self and place through sport

Previous research has recognized positive health implications, both physical and mental, as an outcome of participation in leisure pursuits. They provide opportunities for self-expression and stress reduction, as well as an environment in which people can socialize. Leisure activities, specifically sport activities, can play a significant role in young people's identity development. This paper explores the leisure activities in which young people in Adelaide, Australia participate. It examines the role of leisure activities in terms of young people's identity and feelings towards their hometown. This study consisted of semi-structured focus groups conducted with 24 senior high school students, followed by a survey resulting in 226 useable responses. Respondents were aged between 16 and 18 years of age. From the range of activities identified and explored, the results revealed sports activities to have the greatest impact on young people's lives. The results demonstrated that frequency of participation has a significant effect on young people's involvement levels and how they identify with the activity