Applicability of Spectral Decomposition by Varimax-Rotated, Principal Component Analysis to the Surface Biology and Geology (SBG) VNIR Mission Concept

Cyanobacterial and Harmful Algal Blooms (CyanoHABs) are a growing concern in coastal and inland waters. But, spectral interference from multiple constituents in optically complex waters can hamper application of remote sensing using traditional image processing methods. The Kent State University (KSU) spectral decomposition method can be applied to multispectral and hyperspectral remote sensing images (e.g. HICO and the NASA Glenn HSI2) to partition and identify signals related to cyanobacteria, algae, pigment degradation products and suspended sediment in each pixel. Fundamental to the use of remote sensing data is the ability to extract independent signals from correlated hyperspectral VNIR data cubes. The Kent State University varimax-rotated, principal component analysis method (VPCA) is important to integrate into the SBG VNIR mission concept because it provides greater specificity, a software-based SNR boost relative to hardware performance, and can assist with Cal/Val, Modeling and Applications. We present examples of the hyperspectral application of the KSU VPCA method with relevance to SBG. The information extracted by VPCA can be validated spectrally or spatially with laboratory and/or in situ sensors, which capture spatial or time series of information at discrete points within remote sensing images. Comparisons show hyperspectral sensors extract more components than multispectral ones, but more independent information can be extracted from multispectral sensors by VPCA than traditional band ratio approaches. The spectral decomposition method is capable of enhancing the signal to noise ratio (SNR) of the NASA Glenn, second-generation hyperspectral imager by a factor of 7x to 20x, with a spectral reproducibility of 3%. The spectral decomposition method, when compared against existing remote sensing monitoring methods exhibits both greater specificity and a lower detection limit. The method has been validated with multispectral images in Lake Erie to quantify the Microcystis CyanoHAB and from the Indian River Lagoon, Florida to quantify the Brown Tide resulting from A. lagunesnsis. Field operations in the Western Basin of Lake Erie were conducted using a bbe Fluoroprobe to collect vertical profiles and horizontal tows along a transect from the Toledo to the Detroit Lighthouse during coincident satellite overpasses. Extraction of pixel values from the MODIS Aqua sensor yields agreement between in situ field and lab-based measures of cyanobacterial, cryptophyte, diatoms and green algae, suspended sediment and pigment degradation products with R2>0.8

Assessing the Accuracy of Biogenic Content Estimation from Visible Derivative Spectroscopy of Sedimentary Cores from the Western Pacific

AbstractThe biogenic contents of marine sediments, such as carbonate (CaCO3) and organic carbon (TOC), provide important information about past climatic and environmental changes. For sediment cores, such as those found in the marginal seas of the western Pacific, intensive laboratory study takes considerable time and effort. The previous drilling and coring programs have developed nondestructive methods, which require less time and labor, such as those that utilize visible reflectance derivative spectra measured from the surface of sediment samples to estimate downcore biogenic content. Nevertheless, these methods have been shown to be useful only for on-site estimation of downcore samples and are not considered entirely feasible for testing samples collected from regional or larger spatial scales. The present study presents a novel protocol of spectral decomposition utilizing varimax-rotated principal component analysis (VPCA) for estimating biogenic contents of sediment samples at the basin scale. Using two sediment cores from the South China Sea (SCS) separated by 200 kilometers, we evaluated a new protocol by measuring the visible reflectance spectrum and the biogenic content. Based on six VPCA components of first derivative reflectance spectrum measurements and laboratory analyzed biogenic contents of core MD972148, a set of empirical equations for estimating CaCO3, TOC, and opal contents have been established. The equations were tested using data from core MD012396, and the new regression equations provided accurate estimations. Our study demonstrated that our new methods could achieve better estimates due to the improvement of the regression model with a reduced number of independent variables. Further, this study circumvents the limitation of applying empirical equations to sediment cores outside of the calibration range. Our present findings state that with more comprehensive and systematic reflectance spectral data, the new protocol can be used to estimate biogenic content with more regional or spatial precision in future research

Clay Mineral Cycles Identified by Diffuse Spectral Reflectance in Quaternary Sediments From the Northwind Ridge: Implications for Glacial-Interglacial Sedimentation Patterns in the Arctic Ocean

A Quaternary record of fine-grained sediment composition is used to investigate Arctic Ocean climate variability on glacial-interglacial time scales. Diffuse spectral reflectance data from sediment core P1-92AR-P25 from the Northwind Ridge, north of Alaska, demonstrates cyclic variations in mineralogy. Varimax-rotated R-mode factor analysis of down-core data revealed three major mineralogical assemblages, which were then compared with the content of manganese, a proxy for basin ventilation, and thus glacial-interglacial cycles. Results indicate that factor 1, a smectite + chlorite clay assemblage, was delivered to the core site during interglacials, either by fluvial discharge or sea-ice drift from Siberian rivers or inflow from the Bering Sea. Factor 2, an illite + goethite assemblage, is related to glacial periods, and was probably transported from the Laurentide Ice Sheet by icebergs or meltwater. Factor 3, glauconite, might have been sourced from the North Slope region of Alaska during deglacial intervals, or from dolomites associated with Laurentide iceberg-discharge pulses. The observed variations in sediment source and transport mechanisms arise from glacial-interglacial changes in sea level, the size of the terrestrial ice sheets surrounding the Arctic Ocean, the extent of sea-ice cover and altered atmospheric circulation. The reconstructed glacial-interglacial circulation patterns from the Late Quaternary show some similarity with modern circulation changes presumably related to the monthly- to decadally-fluctuating Arctic Oscillation. However, because the Arctic Oscillation operates on much shorter time scales, further research is necessary to better understand the driving mechanism for the changes observed over glacial-interglacial cycles, and the potential role of ocean-atmospheric interaction

Pif1-Family helicases support fork convergence during DNA replication termination in eukaryotes

The convergence of two DNA replication forks creates unique problems during DNA replication termination. In E. coli and SV40, the release of torsional strain by type II topoisomerases is critical for converging replisomes to complete DNA synthesis, but the pathways that mediate fork convergence in eukaryotes are unknown. We studied the convergence of reconstituted yeast replication forks that include all core replisome components and both type I and type II topoisomerases. We found that most converging forks stall at a very late stage, indicating a role for additional factors. We showed that the Pif1 and Rrm3 DNA helicases promote efficient fork convergence and completion of DNA synthesis, even in the absence of type II topoisomerase. Furthermore, Rrm3 and Pif1 are also important for termination of plasmid DNA replication in vivo. These findings identify a eukaryotic pathway for DNA replication termination that is distinct from previously characterized prokaryotic mechanisms

The heterodyne sensing system for the ALPS II search for sub-eV weakly interacting particles

ALPS II, the Any Light Particle Search, is a second-generation Light Shining through a Wall experiment that hunts for axion-like particles. The experiment is currently transitioning from the design and construction phase to the commissioning phase, with science runs expected to start in 2021. ALPS II plans to use two different sensing schemes to confirm the potential detection of axion-like particles or to verify an upper limit on their coupling strength to two photons of $g_{a\gamma\gamma}\leq2\times10^{-11}\text{GeV}^{-1}$. This paper discusses a heterodyne sensing scheme (HET) which will be the first scheme deployed to detect the regenerated light. It presents critical details of the optical layout, the length and alignment sensing scheme, design features to minimize spurious signals from stray light, as well as several control and veto channels specific to HET which are needed to commission and operate the instrument and to calibrate the detector sensitivity.Comment: 12 pages, 5 figure

Data report : spectral reflectance observations from recovered sediments

Sediment spectral reflectance measurements were generated aboard the JOIDES Resolution during Ocean Drilling Program Leg 162 shipboard operations. The large size of the raw data set (over 1.3 gigabytes) and limited computer hard disk storage space precluded detailed analysis of the data at sea, although broad band averages were used as aids in developing splices and determining lithologic boundaries. This data report describes the methods used to collect these data and their shipboard and postcruise processing. These initial results provide the basis for further postcruise research

Environmental control of living symbiotic and asymbiotic foraminifera of the California Current

Plankton tows from the northern California Current constrain biological and physical influences on living planktonic foraminifera. In this region, the dominant factors controlling the size and distribution of symbiotic and asymbiotic species are light and food. Food decreases offshore. Light, needed for symbiont photosynthesis, increases offshore as water turbidity lessens. Asymbiotic foraminifera (e.g., right-coiling Neogloboquadrina pachyderma, Globigerina quinqueloba, and Globigerina bulloides), which survive by grazing, dominate the coastal fauna. The most abundant of these species, right-coiling Neogloboquadrina pachyderma, did not change in size in response to increasing food. Species that benefit from symbiont photosynthesis (Orbulina universa, Neogloboquadrina dutertrei, Globigerinoides ruber, and Globigerinita glutinata) dominate the offshore fauna. Individuals of these species are rare and have smaller shells in turbid waters where light is limited. G. ruber, which is near its thermal tolerance limit of ≈14°C, is the only species to demonstrate a clear temperature response. Although temperature may control a foramimferal species distribution near the limits of its thermal tolerance, food and light appear to provide the primary control under more favorable thermal conditions. We infer that gradients in food and light can result in quantifiable sedimentary patterns related to oceanic productivity through changes in plankton biomass and turbidity.Copyright 1995 by the American Geophysical Union

Automated Quantitative Analysis of a Mouse Model of Chronic Pulmonary Inflammation using Micro X-ray Computed Tomography

Micro-CT has emerged as an excellent tool for in-vivo imaging of the lungs of small laboratory animals. Several studies have shown that it can be used to assess the evolution of pulmonary lung diseases in longitudinal studies. However, most of them rely on non-automatic tools for image analysis, or are merely qualitative. In this article, we present a longitudinal, quantitative study of a mouse model of silica-induced pulmonary inflammation. To automatically assess disease progression, we have devised and validated a lung segmentation method that combines threshold-based segmentation, atlas-based segmentation and level sets. Our volume measurements, based on the automatic segmentations, point at a compensation mechanism which leads to an increase of the healthy lung volume in response to the loss of functional tissue caused by inflammation

Evaluating visible derivative spectroscopy by varimax-rotated, principal component analysis of aerial hyperspectral images from the western basin of Lake Erie

The Kent State University (KSU) spectral decomposition method provides information about the spectral signals present in multispectral and hyperspectral images. Pre-processing steps that enhance signal to noise ratio (SNR) by 7.37–19.04 times, enables extraction of the environmental signals captured by the National Aeronautics and Space Administration (NASA) Glenn Research Center\u27s, second generation, Hyperspectral imager (HSI2) into multiple, independent components. We have accomplished this by pre-processing of Level 1 HSI2 data to remove stripes from the scene, followed by a combination of spectral and spatial smoothing to further increase the SNR and remove non-Lambertian features, such as waves. On average, the residual stochastic noise removed from the HSI2 images by this method is 5.43 ± 1.42%. The method also enables removal of a spectrally coherent residual atmospheric bias of 4.28 ± 0.48%, ascribed to incomplete atmospheric correction. The total noise isolated from signal by the method is thu

Equity Matters: Digital and Online Learning for Students with Disabilities

Equity Matters: Digital and Online Learning for Students with Disabilities presents some preliminary understandings from a number of Center research projects and experiences to inform the various stakeholder groups of the emerging trends, outcomes, challenges, and promising practices in this developing field of practice. Special education was founded on, and continues to operate as, a collaboration among students with disabilities, families, professionals, and policymakers. In addition, the digital education industry’s growing, major influence in this realm of education makes collaboration with this sector critical. The overall goal of this publication is to spark discussion, reflection, and debate, with a focus on enhancing understanding within all participant groups, leading to the design of more responsive systems, practices, and policy to support enhanced outcomes for all learners—especially students with disabilities