Baseline-free Quantitative Absorption Spectroscopy Based on Cepstral Analysis

The accuracy of quantitative absorption spectroscopy depends on correctly distinguishing molecular absorption signatures in a measured transmission spectrum from the varying intensity or "baseline" of the light source. Baseline correction becomes particularly difficult when the measurement involves complex, broadly absorbing molecules or non-ideal transmission effects such as etalons. We demonstrate a technique that eliminates the need to account for the laser intensity in absorption spectroscopy by converting the measured transmission spectrum of a gas sample to a modified form of the time-domain molecular free induction decay (m-FID) using a cepstral analysis technique developed for audio signal processing. Much of the m-FID signal is temporally separated from and independent of the source intensity, and this portion can be fit directly with a model to determine sample gas properties without correcting for the light source intensity. We validate the new approach in several complex absorption spectroscopy scenarios and discuss its limitations. The technique is applicable to spectra obtained with any absorption spectrometer and provides a fast and accurate approach for analyzing complex spectra

RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank.

SummaryThe Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) resource provides tools for query, analysis and visualization of the 3D structures in the PDB archive. As the mobile Web is starting to surpass desktop and laptop usage, scientists and educators are beginning to integrate mobile devices into their research and teaching. In response, we have developed the RCSB PDB Mobile app for the iOS and Android mobile platforms to enable fast and convenient access to RCSB PDB data and services. Using the app, users from the general public to expert researchers can quickly search and visualize biomolecules, and add personal annotations via the RCSB PDB's integrated MyPDB service.Availability and implementationRCSB PDB Mobile is freely available from the Apple App Store and Google Play (http://www.rcsb.org)

Cosmological perturbations on local systems

We study the effect of cosmological expansion on orbits--galactic, planetary, or atomic--subject to an inverse-square force law. We obtain the laws of motion for gravitational or electrical interactions from general relativity--in particular, we find the gravitational field of a mass distribution in an expanding universe by applying perturbation theory to the Robertson-Walker metric. Cosmological expansion induces an ($\ddot a/a) \vec r$ force where $a(t)$ is the cosmological scale factor. In a locally Newtonian framework, we show that the $(\ddot a/a) \vec r$ term represents the effect of a continuous distribution of cosmological material in Hubble flow, and that the total force on an object, due to the cosmological material plus the matter perturbation, can be represented as the negative gradient of a gravitational potential whose source is the material actually present. We also consider the effect on local dynamics of the cosmological constant. We calculate the perihelion precession of elliptical orbits due to the cosmological constant induced force, and work out a generalized virial relation applicable to gravitationally bound clusters.Comment: 10 page

Discrimination of benign from malignant breast lesions in dense breasts with model-based analysis of regions-of-interest using directional diffusion-weighted images.

BACKGROUND: There is an increasing interest in non-contrast-enhanced magnetic resonance imaging (MRI) for detecting and evaluating breast lesions. We present a methodology utilizing lesion core and periphery region of interest (ROI) features derived from directional diffusion-weighted imaging (DWI) data to evaluate performance in discriminating benign from malignant lesions in dense breasts. METHODS: We accrued 55 dense-breast cases with 69 lesions (31 benign; 38 cancer) at a single institution in a prospective study; cases with ROIs exceeding 7.50 cm RESULTS: The region-growing algorithm for 3D lesion model generation improved inter-observer variability over hand drawn ROIs (DSC: 0.66 vs 0.56 (p \u3c 0.001) with substantial agreement (DSC \u3e 0.8) in 46% vs 13% of cases, respectively (p \u3c 0.001)). The overall classifier improved discrimination over mean ADC, (ROC- area under the curve (AUC): 0.85 vs 0.75 and 0.83 vs 0.74 respectively for the two readers). CONCLUSIONS: A classifier generated from directional DWI information using lesion core and lesion periphery information separately can improve lesion discrimination in dense breasts over mean ADC and should be considered for inclusion in computer-aided diagnosis algorithms. Our model-based ROIs could facilitate standardization of breast MRI computer-aided diagnostics (CADx)

C-Terminal Turn Stability Determines Assembly Differences between Aβ40 and Aβ42

Abstract Oligomerization of the amyloid β-protein (Aβ) is a seminal event in Alzheimer's disease. Aβ42, which is only two amino acids longer than Aβ40, is particularly pathogenic. Why this is so has not been elucidated fully. We report here results of computational and experimental studies revealing a C-terminal turn at Val36-Gly37 in Aβ42 that is not present in Aβ40. The dihedral angles of residues 36 and 37 in an Ile31-Ala42 peptide were consistent with β-turns, and a β-hairpin-like structure was indeed observed that was stabilized by hydrogen bonds and by hydrophobic interactions between residues 31-35 and residues 38-42. In contrast, Aβ(31-40) mainly existed as a statistical coil. To study the system experimentally, we chemically synthesized Aβ peptides containing amino acid substitutions designed to stabilize or destabilize the hairpin. The triple substitution Gly33Val-Val36Pro-Gly38Val ("VPV") facilitated Aβ42 hexamer and nonamer formation, while inhibiting formation of classical amyloid-type fibrils. These assemblies were as toxic as were assemblies from wild-type Aβ42. When substituted into Aβ40, the VPV substitution caused the peptide to oligomerize similarly to Aβ42. The modified Aβ40 was significantly more toxic than Aβ40. The double substitution D-Pro36-L-Pro37 abolished hexamer and dodecamer formation by Aβ42 and produced an oligomer size distribution similar to that of Aβ40. Our data suggest that the Val36-Gly37 turn could be the sine qua non of Aβ42. If true, this structure would be an exceptionally important therapeutic target

Spatially resolved mass flux measurements with dual comb spectroscopy

Providing an accurate, representative sample of mass flux across large open areas for atmospheric studies or the extreme conditions of a hypersonic engine is challenging for traditional intrusive or point-based sensors. Here, we demonstrate that laser absorption spectroscopy with frequency combs can simultaneously measure all of the components of mass flux (velocity, temperature, pressure, and species concentration) with low uncertainty, spatial resolution corresponding to the span of the laser line of sight, and no supplemental sensor readings. The low uncertainty is provided by the broad spectral bandwidth, high resolution, and extremely well-known and controlled frequency axis of stabilized, mode-locked frequency combs. We demonstrate these capabilities in the isolator of a ground-test supersonic propulsion engine at Wright-Patterson Air Force Base. The mass flux measurements are consistent within 3.6% of the facility-level engine air supply values. A vertical scan of the laser beams in the isolator measures the spatially resolved mass flux, which is compared with computational fluid dynamics simulations. A rigorous uncertainty analysis demonstrates a DCS instrument uncertainty of ~0.4%, and total uncertainty (including non-instrument sources) of ~7% for mass flux measurements. These measurements demonstrate DCS as a low-uncertainty mass flux sensor for a variety of applications.Comment: Main Text: 15 pages, 7 figure; Supplement: 6 pages, 4 figures; Submitted to Optic