Subjective speckle suppression for 3D measurement using one-dimensional numerical filtering.

Laser speckle projection is a reliable method to generate statistical illumination patterns for 3D reconstruction purposes as in stereo photogrammetry. This type of pattern has several advantages compared to incoherent methods. However, the biggest disadvantage is given by the coherent noise, the so-called "subjective speckles," developing when a coherently illuminated surface is imaged by a lens system. Some experimental techniques have been published already, being costly in measurement time or leading to loss in light intensity and/or depth of field. In this work we want to present numerical one-dimensional filtering techniques that reduce this kind of noise and increase the performance of 3D reconstruction, while no experimental changes to the classical speckle projection technique have to be made. Therefore, a model describing the expectable contrast reduction is derived, the dependency between filter orientation and setup geometry is investigated, and results from simulations and real experiments are shown. It is found that for small filter sizes the results can be improved independent of the filter, but that in the general case a vertical orientation of the filter towards the setup geometry is most useful.

Multigene testing of moderate-risk genes: be mindful of the missense.

BACKGROUND: Moderate-risk genes have not been extensively studied, and missense substitutions in them are generally returned to patients as variants of uncertain significance lacking clearly defined risk estimates. The fraction of early-onset breast cancer cases carrying moderate-risk genotypes and quantitative methods for flagging variants for further analysis have not been established. METHODS: We evaluated rare missense substitutions identified from a mutation screen of ATM, CHEK2, MRE11A, RAD50, NBN, RAD51, RINT1, XRCC2 and BARD1 in 1297 cases of early-onset breast cancer and 1121 controls via scores from Align-Grantham Variation Grantham Deviation (GVGD), combined annotation dependent depletion (CADD), multivariate analysis of protein polymorphism (MAPP) and PolyPhen-2. We also evaluated subjects by polygenotype from 18 breast cancer risk SNPs. From these analyses, we estimated the fraction of cases and controls that reach a breast cancer OR≥2.5 threshold. RESULTS: Analysis of mutation screening data from the nine genes revealed that 7.5% of cases and 2.4% of controls were carriers of at least one rare variant with an average OR≥2.5. 2.1% of cases and 1.2% of controls had a polygenotype with an average OR≥2.5. CONCLUSIONS: Among early-onset breast cancer cases, 9.6% had a genotype associated with an increased risk sufficient to affect clinical management recommendations. Over two-thirds of variants conferring this level of risk were rare missense substitutions in moderate-risk genes. Placement in the estimated OR≥2.5 group by at least two of these missense analysis programs should be used to prioritise variants for further study. Panel testing often creates more heat than light; quantitative approaches to variant prioritisation and classification may facilitate more efficient clinical classification of variants.

Morphological and molecular variation in the least madtom Noturus hildebrandi (Siluriformes: Ictaluridae), a Mississippi Embayment endemic: evidence for a cryptic lineage in the Hatchie River.

Sheared principal component analysis of 40 morphometric characteristics measured for 146 individuals and relative frequencies of pigmentation patterns scored for 980 individuals of the least madtom Noturus hildebrandi, a diminutive catfish endemic to eastern lowland drainages of the Mississippi Embayment region of North America, suggested a clinal pattern of morphological variation extending across the range from north to south. DNA sequence data representing 90 individuals from the mitochondrial gene cytochrome b (cytb) analysed using Bayesian phylogenetic methods recovered four major haplotype clades, suggestive of a high degree of isolation by drainage. Individual gene trees of cytb and four additional nuclear loci as well as trees based on concatenated datasets of these genes consistently recovered a cryptic lineage of individuals from the Hatchie River drainage that is morphologically indistinguishable from surrounding populations. Gene-tree analyses failed to recover a monophyletic N. hildebrandi with respect to Noturus baileyi. A coalescence-based species tree analysis, however, did recover N. hildebrandi monophyly with high support, suggesting that relationships reflected in individual gene trees and concatenated datasets are in part artefacts of incomplete lineage sorting or an ancient introgressive event. Results are consistent with the hypothesis of an ancient connection between the Hatchie and Tennessee River systems. Current subspecific designations are of limited utility as they reflect morphological variation and are not entirely consistent with phylogeny. Discrepancies between the pattern of variation observed in the morphological and molecular data may be explained by recent local adaptation to individual stream conditions that masks deeper evolutionary divergences.