Sources Of Experimental Noise Research Articles

Phase-selected momentum transport in ultra-cold atoms

We propose a phase selected transport scenario for ultra-cold matter waves subject to pulsed optical lattices in which equally-populated momentum eigenstates with a flipped phase are localized while all other states are transported ballistically. The phenomenon relies on the concepts of quantum resonance and anti-resonance in two optical lattice potentials – one with half the wavelength of the other. We demonstrate the effectiveness of the technique in the presence of likely experimental noise sources, including the non-ideal situation where the momentum components are not all of equal amplitude. We also discuss possible uses for atom interferometric experiments and detail how to observe the phenomenon experimentally by creating an ideal initial state using standard atom-optical procedures.

Imprinted Genes … and the Number Is?

Imprinted Genes … and the Number Is?

De-Noising Single Molecule FRET Trajectories using Wavelent and Bayesian Techniques

Extracting quantitative information from low signal-to-noise single molecule FRET trajectories remains a significant challenge. In particular, biological systems that derive their function from shallowly defined or continua of states are not amenable to recent Markovian analysis algorithms. A method to de-noise single-molecule fluorescence resonance energy (smFRET) trajectories using wavelet detail thresholding and Bayesian inference is presented. Bayesian methods are developed to identify fluorophore photoblinks in the time trajectories. Simulated data are used to quantify the improvement in static and dynamic data analysis. Application of the method to experimental smFRET data shows that it distinguishes photoblinks from large shifts in smFRET efficiency while maintaining the important advantage of an unbiased approach. Known sources of experimental noise are examined and quantified as a means to remove their contributions via soft thresholding of wavelet coefficients. A wavelet decomposition algorithm is described, and thresholds are produced through the knowledge of noise parameters in the discrete-time photon signals. Reconstruction of the signals from thresholded coefficients produces signals that contain noise arising only from unquantifiable parameters. The method is applied to simulated and observed smFRET data, and it is found that the denoised data retain their underlying dynamical properties, but with increased resolution.

Denoising Single-Molecule FRET Trajectories with Wavelets and Bayesian Inference

A method to denoise single-molecule fluorescence resonance energy (smFRET) trajectories using wavelet detail thresholding and Bayesian inference is presented. Bayesian methods are developed to identify fluorophore photoblinks in the time trajectories. Simulated data are used to quantify the improvement in static and dynamic data analysis. Application of the method to experimental smFRET data shows that it distinguishes photoblinks from large shifts in smFRET efficiency while maintaining the important advantage of an unbiased approach. Known sources of experimental noise are examined and quantified as a means to remove their contributions via soft thresholding of wavelet coefficients. A wavelet decomposition algorithm is described, and thresholds are produced through the knowledge of noise parameters in the discrete-time photon signals. Reconstruction of the signals from thresholded coefficients produces signals that contain noise arising only from unquantifiable parameters. The method is applied to simulated and observed smFRET data, and it is found that the denoised data retain their underlying dynamic properties, but with increased resolution.

Modeling Clinically Heterogeneous Presenilin Mutations with Transgenic Drosophila

To assess the potential of Drosophila to analyze clinically graded aspects of human disease, we developed a transgenic fly model to characterize Presenilin (PS) gene mutations that cause early-onset familial Alzheimer's disease (FAD). FAD exhibits a wide range in severity defined by ages of onset from 24 to 65 years . PS FAD mutants have been analyzed in mammalian cell culture, but conflicting data emerged concerning correlations between age of onset and PS biochemical activity . Choosing from over 130 FAD mutations in Presenilin-1, we introduced 14 corresponding mutations at conserved residues in Drosophila Presenilin (Psn) and assessed their biological activity in transgenic flies by using genetic, molecular, and statistical methods. Psn FAD mutant activities were tightly linked to their age-of-onset values, providing evidence that disease severity in humans primarily reflects differences in PS mutant lesions rather than contributions from unlinked genetic or environmental modifiers. Our study establishes a precedent for using transgenic Drosophila to study clinical heterogeneity in human disease.

The relationship between life span and adult body size is highly strain-specific in Drosophila melanogaster

Among mammals, body size and life span tend to vary inversely within species, but the pattern is less clear in invertebrates. Here, we report on survival and weight of male flies from 29 laboratory strains of Drosophila melanogaster. Natural variation in body mass was enhanced by rearing larvae under normal and limited food conditions. Strain, weight, and larval treatment have significant effects on survival, but higher order interactions are also significant, indicating strain specificity. For pooled data the overall relationship between mass and life span is slight, positive, and statistically significant, but mass explains ≤1% of the variation in survival. This result is opposite to the common prediction of an inverse relationship between longevity and body size. Effects of artificially reduced body size vary substantially in both sign and magnitude from strain to strain, though long-lived strains generally retain their enhanced survival characteristics. Within-line regressions of life span on mass also vary dramatically from strain to strain; in Canton-S, the most extreme case, mass explains >40% of the variation in survival. For long-lived ‘O’ lines reared under normal larval conditions, smaller flies live 16% longer than larger flies; the latter are significantly underrepresented in the most advanced age class. We conclude that the body size–life span relationship is highly strain-specific; that inconsistencies in the literature probably reflect real biological variation; and that variation in body size can be a significant source of experimental noise in survival studies.

Bootstrap white matter tractography (BOOT-TRAC)

White matter tractography is a noninvasive method for estimating and visualizing the white matter connectivity patterns in the human brain using diffusion tensor imaging (DTI) data. Sources of experimental noise may induce errors in the measured fiber directions, which will reduce the accuracy of the estimated white matter trajectories. In this study, a statistical nonparametric bootstrap method is described for estimating the dispersion and other errors in white matter tractography results. Prior studies have derived models of tractography error using the signal-to-noise ratio (SNR) and diffusion anisotropy of the DTI data. Tractography errors measured using bootstrap methods were generally consistent with an analytic model of tractography error except in areas where branching was evident. White matter tractography with bootstrap resampling is also applied to estimate the probabilities of connection between brain regions. The approach was used to generate probabilistic connectivity maps between the cerebral peduncles and specific cortical regions.

Effects of underwater noise on migrating gray whales off the coast of California

The potential effects of man-made underwater noises on the behavior of gray whales (Eschrictius robustus) off the Coast of central California were studied during their southern and northern migration in 1983. In January, two shore-based theodolite tracking sites recorded whales' swimming patterns as well as behavioral activities while underwater sounds (production platform, drilling platform, semisubmersible, drillship, helicopter, or killer whale, Orcinus orca) were transmitted from a vessel anchored in the middle of the nearshore migratory pattern. In April and May, when the majority of whales were mother-calf pairs, three theodolite tracking sites recorded swimming patterns, behavior, and respiration times for individuals. Experimental noise sources consisted of either a seismic vessel operating a 40-gun array, a vessel operating a single air gun or a stationary vessel broadcasting either drillship or killer whale sounds. The behavioral measures used to assay disturbance included deflection of normal migratory pattern, speed of travel, individual respiration, synchronizing of mother and calf respiration, and rates of behaviors such as breaching or underwater expiration. [Work was supported by Minerals Management Service.]