Impact of Collection Volume and DNA Extraction Method on the Detection of Biomarkers and HPV DNA in First-Void Urine

The potential of first-void (FV) urine as a non-invasive liquid biopsy for detection of human papillomavirus (HPV) DNA and other biomarkers has been increasingly recognized over the past decade. In this study, we investigated whether the volume of this initial urine stream has an impact on the analytical performance of biomarkers. In parallel, we evaluated different DNA extraction protocols and introduced an internal control in the urine preservative. Twenty-five women, diagnosed with high-risk HPV, provided three home-collected FV urine samples using three FV urine collection devices (Colli-Pee) with collector tubes that differ in volume (4, 10, 20 mL). Each collector tube was prefilled with Urine Conservation Medium spiked with phocine herpesvirus 1 (PhHV-1) DNA as internal control. Five different DNA extraction protocols were compared, followed by PCR for GAPDH and PhHV-1 (qPCR), HPV DNA, and HBB (HPV-Risk Assay), and ACTB (methylation-specific qPCR). Results showed limited effects of collection volume on human and HPV DNA endpoints. In contrast, significant variations in yield for human endpoints were observed for different DNA extraction methods (p < 0.05). Additionally, the potential of PhHV-1 as internal control to monitor FV urine collection, storage, and processing was demonstrated.     

High angle phase modulated low coherence interferometry for path length resolved Doppler measurements of multiply scattered light

We describe an improved method for coherence domain path length resolved measurements of multiply scattered photons in turbid media. An electro-optic phase modulator sinusoidally modulates the phase in the reference arm of a low coherence fiber optic Mach-Zehnder interferometer, at a high phase modulation angle. For dynamic turbid media this results in Doppler broadened phase modulation interference peaks at the modulation frequency and its multiples. The signal to noise ratio is increased by almost one order or magnitude for large modulation angles and the shape of the spectral peaks resulting from the interference of Doppler shifted sample waves and reference light is not changed. The path length dependent Doppler broadening is compared with the theoretical predictions in the single scattered and diffusive regimes. The experimentally measured optical path lengths are validated with the Monte Carlo technique.     

Inverse Cerenkov acceleration and inverse free-electron laserexperimental results for staged electron laser acceleration

The goal of the staged electron laser acceleration (STELLA) experiment is to demonstrate staging of the laser acceleration process whereby an inverse free electron laser (IFEL) will be used to prebunch the electrons, which are then accelerated in an inverse Cerenkov accelerator (ICA). As preparation for this experiment, a new permanent magnet wiggler for the IFEL was constructed and the ICA system was modified. Both systems have been tested on a new beamline specifically built for STELLA. The improved electron beam (e-beam) with its very low emittance (0.8 mm-mrad normalized) enabled focusing the e-beam to an average radius (1σ) of 65 μm, within the ICA interaction region. This small e-beam focus greatly enhanced the ICA process and resulted in electron energy spectra that have demonstrated the best agreement to date in both overall shape and magnitude with the model predictions. The electron energy spectrum using the new wiggler in the IFEL was also measured. These results will be described as well as future improvements to the STELLA experiment     

Speckles in laser Doppler perfusion imaging

We report on the quantitative influence of speckles in laser Doppler perfusion imaging. The influence of speckles on the signal amplitude and on the Doppler spectrum is demonstrated experimentally for particle suspensions with different scattering levels and various beam widths. It is shown that the type of tissue affects the instrumental response through the effect of lateral light diffusion on the number of speckles involved in the detection process. These effects are largest for narrow beams.     

Path-length distribution and path-length-resolved Doppler measurements of multiply scattered photons by use of low-coherence interferometry

We report first results of measurements by low-coherence Doppler interferometry of the path-length distribution of photons undergoing multiple scattering in a highly turbid medium. We use a Mach-Zehnder interferometer with multimode graded-index fibers and a superluminescent diode as the light source. The path-length distribution is obtained by recording of the heterodyne fluctuations that arise from the Brownian motion of particles in an Intralipid suspension as a function of the optical path length. The experimental path-length distribution is in good agreement with predictions of Monte Carlo simulations. In the heterodyne spectrum, an increase of the mean Doppler frequency with path length is observed.     

Quantum Size Effects in the Size–Temperature Phase Diagram of Gallium: Structural Characterization of Shape‐Shifting Clusters

Finite temperature analysis of cluster structures is used to identify signatures of the low‐temperature polymorphs of gallium, based on the results of first‐principle Born–Oppenheimer molecular dynamics simulations. Pre‐melting structural transitions proceed from either the β‐ and/or the δ‐phase to the γ‐ or δ‐phase, with a size‐ dependent phase progression. We relate the stability of each isomer to the electronic structures of the different phases, giving new insight into the origin of polymorphism in this complicated element.     

Time and spatial correlation measurements in the turbulent wake of a circular cylinder using Laser Doppler Anemometry

The present paper reports Laser Doppler Anemometry (LDA) measurements in the turbulent (R _d =1300) wake of a circular cylinder (d=2 mm). On several typical locations in the wake, at cross-section x/d=125, temporal and lateral space velocity correlations have been measured. Temporal autocorrelation functions were determined from the randomly sampled LDA data by means of the Slotting Technique. The autocorrelation functions which were obtained were too low, the discrepancy giving an indication of the influence of noise in the measurements. The influence of noise generated by the photomultiplier tubes, which appeared to be the most important noise source, could be reduced by a cross-correlation technique. A partly new LDA system for two-point velocity correlation measurements was developed, consisting of an elongated measuring volume and a two-point detection system including a semireflecting mirror to divide the scattered light. The results of this investigation clearly demonstrate that LDA is a powerful tool for measuring time and spatial correlations and related properties of turbulence.     

Development and validation of a comprehensive two-dimensional gas chromatography–mass spectrometry method for the analysis of phytosterol oxidation products in human plasma

Phytosterol oxidation products (POPs) have been suggested to exert adverse biological effects similar to, although less severe than, their cholesterol counterparts. For that reason, their analysis in human plasma is highly relevant. Comprehensive two-dimensional gas chromatography (GC×GC) coupled with time-of-flight mass spectrometry (TOF-MS) has been proven to be an extremely powerful separation technique for the analysis of very low levels of target compounds in complex mixtures including human plasma. Thus, a GC×GC/TOF-MS method was developed and successfully validated for the simultaneous quantification of ten POPs in human plasma. The calibration curves for each compound showed correlation coefficients (R ²) better than 0.99. The detection limits were below 0.1 ng mL⁻¹. The recovery data were between 71.0% and 98.6% (RSDs <10% for all compounds validated). Good results were obtained for within- and between-day repeatability, with most values being below 10%. In addition, non-targeted sterol metabolites were also identified with the method. The concentrations of POPs found in human plasma in the current study are between 0.3 and 4.5 ng mL⁻¹, i.e., 10–100 times lower than the typical values found for cholesterol oxidation products.     

Random walks on simplicial complexes and harmonics

In this paper, we introduce a class of random walks with absorbing states on simplicial complexes. Given a simplicial complex of dimension d, a random walk with an absorbing state is defined which relates to the spectrum of the k‐dimensional Laplacian for 1 ≤ k ≤ d. We study an example of random walks on simplicial complexes in the context of a semi‐supervised learning problem. Specifically, we consider a label propagation algorithm on oriented edges, which applies to a generalization of the partially labelled classification problem on graphs. © 2016 Wiley Periodicals, Inc. Random Struct. Alg., 49, 379–405, 2016