Combining MODIS and Landsat imagery to estimate and map boreal forest cover loss

Estimation of forest cover change is important for boreal forests, one of the most extensive forested biomes, due to its unique role in global timber stock, carbon sequestration and deposition, and high vulnerability to the effects of global climate change. We used time-series data from the MODerate Resolution Imaging Spectroradiometer (MODIS) to produce annual forest cover loss hotspot maps. These maps were used to assign all blocks (18.5 by 18.5 km) partitioning the boreal biome into strata of high, medium and low likelihood of forest cover loss. A stratified random sample of 118 blocks was interpreted for forest cover and forest cover loss using high spatial resolution Landsat imagery from 2000 and 2005. Area of forest cover gross loss from 2000 to 2005 within the boreal biome is estimated to be 1.63% (standard error 0.10%) of the total biome area, and represents a 4.02% reduction in year 2000 forest cover. The proportion of identified forest cover loss relative to regional forest area is much higher in North America than in Eurasia (5.63% to 3.00%). Of the total forest cover loss identified, 58.9% is attributable to wildfires. The MODIS pan-boreal change hotspot estimates reveal significant increases in forest cover loss due to wildfires in 2002 and 2003, with 2003 being the peak year of loss within the 5-year study period. Overall, the precision of the aggregate forest cover loss estimates derived from the Landsat data and the value of the MODIS-derived map displaying the spatial and temporal patterns of forest loss demonstrate the efficacy of this protocol for operational, cost-effective, and timely biome-wide monitoring of gross forest cover loss.     

Evaluating the species energy relationship with the newest measures of ecosystem energy: NDVI versus MODIS primary production

Ecosystem energy has been shown to be a strong correlate with biological diversity at continental scales. Early efforts to characterize this association used the normalized difference vegetation index (NDVI) to represent ecosystem energy. While this spectral vegetation index covaries with measures of ecosystem energy such as net primary production, the covariation is known to degrade in areas of very low vegetation or in areas of dense forest. Two of the new vegetation products from the MODIS sensor, derived by integrating spectral reflectance, climate data, and land cover, are thought to better approximate primary productivity than NDVI. In this study, we determine if the new MODIS derived measures of primary production, gross primary productivity (GPP) and net primary productivity (NPP) better explain variation in bird richness than historically used NDVI. Moreover, we evaluate if the two productivity measures covary more strongly with bird diversity in those vegetation conditions where limitations of NDVI are well recognized.Biodiversity was represented as native landbird species richness derived from the North American Breeding Bird Survey. Analyses included correlation analyses among predictor variables, and univariate regression analyses between each predictor variable and bird species richness. Analyses were done at two levels: for all BBS routes across natural landscapes in North America; and for routes in 10 vegetation classes stratified by vegetated cover along a gradient from bare ground to herbaceous cover to tree cover. We found that NDVI, GPP and NPP were highly correlated and explained similar variation in bird species richness when analyzed for all samples across North America. However, when samples were stratified by vegetated cover, strength of correlation between NDVI and both productivity measures was low for samples with bare ground and for dense forest. The NDVI also explained substantially less variation in bird species richness than the primary production in areas with more bare ground and in areas of dense forest. We conclude that MODIS productivity measures have higher utility in studies of the relationship of species richness and productivity and that MODIS GPP and NPP improve on NDVI, especially for studies with large variation in vegetated cover and density.     

VISIM: Sequential simulation for linear inverse problems

Linear inverse Gaussian problems are traditionally solved using least squares-based inversion. The center of the posterior Gaussian probability distribution is often chosen as the solution to such problems, while the solution is in fact the posterior Gaussian probability distribution itself. We present an algorithm, based on direct sequential simulation, which can be used to efficiently draw samples of the posterior probability distribution for linear inverse problems. There is no Gaussian restriction on the distribution in the model parameter space, as inherent in traditional least squares-based algorithms.As data for linear inverse problems can be seen as weighed linear averages over some volume, block kriging can be used to perform both estimation (i.e. finding the center of the posterior Gaussian pdf) and simulation (drawing samples of the posterior Gaussian pdf). We present the kriging system which we use to implement a flexible GSLIB-based algorithm for solving linear inverse problems.We show how we implement such a simulation program conditioned to linear average data. The program is called VISIM as an acronym for Volume average Integration SIMulation. An effort has been made to make the program efficient, even for larger scale problems, and the computational efficiency and accuracy of the code is investigated.Using a synthetic cross-borehole tomography case study, we show how the program can be used to generate realizations of the a posteriori distributions (i.e. solutions) from a linear tomography problem. Both Gaussian and non-Gaussian a priori model parameter distributions are considered.     

Variational Segmentation of Image Sequences Using Region-Based Active Contours and Deformable Shape Priors

In this paper we address the problem of segmentation in image sequences using region-based active contours and level set methods. We propose a novel method for variational segmentation of image sequences containing nonrigid, moving objects. The method is based on the classical Chan-Vese model augmented with a novel frame-to-frame interaction term, which allow us to update the segmentation result from one image frame to the next using the previous segmentation result as a shape prior. The interaction term is constructed to be pose-invariant and to allow moderate deformations in shape. It is expected to handle the appearance of occlusions which otherwise can make segmentation fail. The performance of the model is illustrated with experiments on synthetic and real image sequences.     

A generalized autocovariance least-squares method for Kalman filter tuning

This paper discusses a method for estimating noise covariances from process data. In linear stochastic state-space representations the true noise covariances are generally unknown in practical applications. Using estimated covariances a Kalman filter can be tuned in order to increase the accuracy of the state estimates. There is a linear relationship between covariances and autocovariance. Therefore, the covariance estimation problem can be stated as a least-squares problem, which can be solved as a symmetric semidefinite least-squares problem. This problem is convex and can be solved efficiently by interior-point methods. A numerical algorithm for solving the symmetric is able to handle systems with mutually correlated process noise and measurement noise.     

Evaluation of a type 1 diabetes serum cohort by SELDI-TOF MS protein profiling

Proteomics analysis of serum from patients with type 1 diabetes (T1D) may lead to novel biomarkers for prediction of disease and for patient monitoring. However, the serum proteome is highly sensitive to sample processing and before proteomics biomarker research serum cohorts should preferably be examined for potential bias between sample groups. SELDI‐TOF MS protein profiling was used for preliminary evaluation of a biological‐bank with 766 serum samples from 270 patients with T1D, collected at 18 different paediatric centers representing 15 countries in Europe and Japan over 2 years (2000–2002). Samples collected 1 (n = 270), 6 (n = 248), and 12 (n = 248) months after T1D diagnosis were grouped across centers and compared. The serum protein profiles varied with collection site and day of analysis; however, markers of sample processing were not systematically different between samples collected at different times after diagnosis. Three members of the apolipoprotein family increased with time in patient serum collected 1, 6, and 12 months after diagnosis (ANOVA, p<0.001). These results support the use of this serum cohort for further proteomic studies and illustrate the potential of high‐throughput MALDI/SELDI‐TOF MS protein profiling for evaluation of serum cohorts before proteomics biomarker research.     

Family psychosocial screening: should we focus on high-risk settings?

The objective of this study was to address the question of whether or not psychosocial screening should be focused on "high-risk" populations. A cross-sectional survey of mothers of young children was conducted in various clinics: 758 in teaching clinics, 444 in private practices, and 202 at a military clinic. The self-administered questionnaire covered demographic factors, problems in mothers family of origin, maternal depression, and substance abuse. Mothers in the teaching clinics were younger and had less education and lower incomes than mothers in private practices, with intermediate levels in the military clinic. However, a substantial proportion of mothers seen in all sites reported psychosocial problems. Approximately 20% of mothers in all sites reported a family history of alcoholism. Positive screens for maternal depression ranged from about 15% to 35%. Binge drinking was reported by 10% to 20% at different sites. Psychosocial problems were common even among families seen in "low-risk" settings. Focusing screening only on high-risk clinics would miss many families with psychosocial problems.     

Model-checking discrete duration calculus

Duration Calculus was introduced in [ZHR91] as a logic to specify and reason about requirements for real-time systems. It is an extension of Interval Temporal Logic [Mos85] where one can reason about integrated constraints over time-dependent and Boolean valued states without explicit mention of absolute time. Several major case studies, e.g. the gas burner system in [RRH93], have shown that Duration Calculus provides a high level of abstraction for both expressing and reasoning about specifications. Using Timed Automata [A1D92] one can express how real-time systems can be constructed at a level of detail which is close to an actual implementation. We consider in the paper the correctness of Timed Automata with respect to Duration Calculus formulae. For a subset of Duration Calculus, we show that one can automatically verify whether a Timed Automaton ? is correct with respect to a formulaD, abbreviated ? ?D, i.e. one can domodel-checking. The subset we consider is expressive enough to formalize the requirements to the gas burner system given in [RRH93]; but only for a discrete time domain. Model-checking is done by reducing the correctness problem ? ?D to the inclusion problem of regular languages.     

Laser-speckle angular-displacement sensor: theoretical and experimental study

A novel, to our knowledge, method for the measurement of angular displacement for arbitrarily shaped objects is presented in which the angular displacement is perpendicular to the optical axis. The method is based on Fourier-transforming the scattered field from a single laser beam that illuminates the target. The angular distribution of the light field at the target is linearly mapped on a linear image sensor placed in the Fourier plane. Measuring this displacement facilitates the determination of the angular displacement of the target. It is demonstrated both theoretically and experimentally that the angular-displacement sensor is insensitive to object shape and target distance if the linear image sensor is placed in the Fourier plane. A straightforward procedure for positioning the image sensor in the Fourier plane is presented. Any transverse or longitudinal movement of the target will give rise to partial speckle decorrelation, but it will not affect the angular measurement. Furthermore, any change in the illuminating wavelength will not affect the angular measurements. Theoretically and experimentally it is shown that the method has a resolution of 0.3 mdeg ( approximately 5 murad) for small angular displacements, and methods for further improvement in resolution is discussed. No special surface treatment is required for surfaces giving rise to fully developed speckle. The effect of partially developed speckle is considered both theoretically and experimentally.     

Automated extraction of DNA from blood and PCR setup using a Tecan Freedom EVO liquid handler for forensic genetic STR typing of reference samples

We have implemented and validated automated protocols for DNA extraction and PCR setup using a Tecan Freedom EVO liquid handler mounted with the Te-MagS magnetic separation device (Tecan, M?nnedorf, Switzerland). The protocols were validated for accredited forensic genetic work according to ISO 17025 using the Qiagen MagAttract DNA Mini M48 kit (Qiagen GmbH, Hilden, Germany) from fresh whole blood and blood from deceased individuals. The workflow was simplified by returning the DNA extracts to the original tubes minimizing the risk of misplacing samples. The tubes that originally contained the samples were washed with MilliQ water before the return of the DNA extracts. The PCR was setup in 96-well microtiter plates. The methods were validated for the kits: AmpF?STR Identifiler, SGM Plus and Yfiler (Applied Biosystems, Foster City, CA), GenePrint FFFL and PowerPlex Y (Promega, Madison, WI). The automated protocols allowed for extraction and addition of PCR master mix of 96 samples within 3.5h. In conclusion, we demonstrated that (1) DNA extraction with magnetic beads and (2) PCR setup for accredited, forensic genetic short tandem repeat typing can be implemented on a simple automated liquid handler leading to the reduction of manual work, and increased quality and throughput.