Segmentation and Estimation for SNP Microarrays: A Bayesian Multiple Change‐Point Approach

Summary High‐density single‐nucleotide polymorphism (SNP) microarrays provide a useful tool for the detection of copy number variants (CNVs). The analysis of such large amounts of data is complicated, especially with regard to determining where copy numbers change and their corresponding values. In this article, we propose a Bayesian multiple change‐point model (BMCP) for segmentation and estimation of SNP microarray data. Segmentation concerns separating a chromosome into regions of equal copy number differences between the sample of interest and some reference, and involves the detection of locations of copy number difference changes. Estimation concerns determining true copy number for each segment. Our approach not only gives posterior estimates for the parameters of interest, namely locations for copy number difference changes and true copy number estimates, but also useful confidence measures. In addition, our algorithm can segment multiple samples simultaneously, and infer both common and rare CNVs across individuals. Finally, for studies of CNVs in tumors, we incorporate an adjustment factor for signal attenuation due to tumor heterogeneity or normal contamination that can improve copy number estimates.     

Microcosm-based Study of the Attenuation of an Acid Mine Drainage-Impacted Site through Biological Sulfate and Iron Reduction

Acid mine drainage is a widespread environmental problem and is characterized by elevated proton, sulfate, and dissolved iron concentrations. To understand the driving forces behind the attenuation of AMD, we compared microcosms using sediment and groundwater collected at Davis Mine, Massachusetts, a site where both generation and attenuation of AMD occur. A shift in key geochemical parameters over time was due to the natural microbial population, which was supported by detailed molecular biology results. The attenuation of AMD was stimulated through amendment with glycerol, with nitrogen and phosphorous, or with algae extract, but not by wood chips, suggesting the addition of different organic electron donors as a bioremediation strategy.     

Attenuation corrected-optical coherence tomography for quantitative assessment of skin wound healing and scar morphology

Imaging the structural modifications of underlying tissues is vital to monitor wound healing. Optical coherence tomography (OCT) images high-resolution sub-surface information, but suffers a loss of intensity with depth, limiting quantification. Hence correcting the attenuation loss is important. We performed swept source-OCT of full-thickness excision wounds for 300 days in mice skin. We used single-scatter attenuation models to determine and correct the attenuation loss in the images. The phantom studies established the correspondence of corrected-OCT intensity (reflectivity) with matrix density and hydration. We histologically validated the corrected-OCT and measured the wound healing rate. We noted two distinct phases of healing—rapid and steady-state. We also detected two compartments in normal scars using corrected OCT that otherwise were not visible in the OCT scans. The OCT reflectivity in the scar compartments corresponded to distinct cell populations, mechanical properties and composition. OCT reflectivity has potential applications in evaluating the therapeutic efficacy of healing and characterizing scars.     

Simultaneous detection of cerebral blood perfusion and cerebral edema using swept‐source optical coherence tomography

The progression of ischemic cerebral edema (CE) is closely related to the level of cerebral blood perfusion (CBP) and affects each other. Simultaneous detection of CBP and CE is helpful in understanding the mechanisms of ischemic CE development. In this article, a wide field of view swept‐source optical coherence tomography system was used to detect CE status and CBP levels simultaneously in middle cerebral artery occlusion rats. Images reflecting these two physiological states can be reconstructed with only one C‐scan. We quantify these two physiological states into four parameters, which contain two vascular parameters (vascular displacement distance and vascular perfusion density) and two edema parameters (optical attenuation coefficient and edema area). The association between the two vascular parameters and the two edema parameters was analyzed. The results show that there is a strong linear relationship between blood flow parameters and edema parameters. This work provides a new option for CE in vivo detection, and is very likely to play an important role in the development of relevant drugs or in selection of treatment options.      

OPTICAL PROPERTIES OF DENSE ALGAL CULTURES OUTDOORS AND THEIR APPLICATION TO REMOTE ESTIMATION OF BIOMASS AND PIGMENT CONCENTRATION IN SPIRULINA PLATENSIS (CYANOBACTERIA)1

Reflectance and vertical attenuation coefficient spectra from 400 to 1100 nm were investigated in detail on dense algal cultures of Spirulina in order to create algorithms for remote estimation of pigment and biomass concentration. Reflectance and the vertical attenuation coefficients were compared with biomass and pigment concentration in outdoor algal cultures. For assessing biomass concentration, the sum of reflectance above the base line from 670 to 950 nm was used. This allows the estimation of biomass with an error of less than 0.06 g·L^?1 For chlorophyll a and phycocyanin estimation, vertical attenuation coefficients at the wavelengths 440 nm (or 676 nm) and 624 nm, respectively, were employed. The developed algorithms were tested by using independent data sets in the range of chlorophyll a from 0.2 to 20mg·L^?1 and biomass from 0.15 to 1.1 g·L^?1. An error of pigment estimation of less than 0.80 mg·L^?1 was achieved. The potential use of the algorithms in algal biotechnology is further discussed.     

Dynamics and ecological significance of daily internal load of phosphorus in shallow Lake Balaton, Hungary

1. As supported by field data, turbidity recorded by light scattering sensors could reliably be converted into concentration of suspended particulate matter (SPM) and coefficient of vertical light attenuation (K_d) in Lake Balaton. 2. Autocorrelation analysis revealed that proper determination of SPM concentration and K_d required daily sampling. To approximate daily rate of resuspension, 15 min or more frequent measurements were needed. Thus, routine monitoring provides very little insight into environmental variability of shallow lakes as habitats for phytoplankton. 3. The internal P load was estimated from daily rate of resuspension and P desorption capacity of sediments. The latter was assumed to be proportionate to the potentially mobile inorganic P content of SPM. A comparison with net primary production and nutrient status of phytoplankton showed that the proposed method of estimating time series of internal P load captured seasonal trends. 4. The daily rate of resuspension was high whereas that of internal P load was low in Lake Balaton relative to other shallow lakes. The latter reflects favourable behaviour of the calcite‐rich sediments. As a consequence, carrying capacity of Basin 1 of Lake Balaton was P‐determined. 5. The timing of external and internal loads was radically different. While the former showed mostly seasonal changes, large pulses characterised the latter. As a consequence, internal load may supply more P to phytoplankton growth during the critical summer months than external load. However, the relative importance of these sources may show substantial interannual variability. 6. Large resuspension events often followed each other during periods of 10–15 days. It has been shown that disturbances in this frequency range are of key importance in maintaining the diversity of phytoplankton. We propose that resuspension can be perceived not only as a disturbance factor but also as a factor that periodically relaxes nutrient stress. The former feature may dominate the instantaneous effect, whereas the latter may determine the persistent effect of resuspension on succession of phytoplankton.