Remote sensing of photosynthetic light-use efficiency across two forested biomes: Spatial scaling

Eddy covariance (EC) measurements have greatly advanced our knowledge of carbon exchange in terrestrial ecosystems. However, appropriate techniques are required to upscale these spatially discrete findings globally. Satellite remote sensing provides unique opportunities in this respect, but remote sensing of the photosynthetic light-use efficiency (ε), one of the key components of Gross Primary Production, is challenging. Some progress has been made in recent years using the photochemical reflectance index, a narrow waveband index centered at 531 and 570 nm. The high sensitivity of this index to various extraneous effects such as canopy structure, and the view observer geometry has so far prevented its use at landscape and global scales. One critical aspect of upscaling PRI is the development of generic algorithms to account for structural differences in vegetation. Building on previous work, this study compares the differences in the PRI: ? relationship between a coastal Douglas-fir forest located on Vancouver Island, British Columbia, and a mature Aspen stand located in central Saskatchewan, Canada. Using continuous, tower-based observations acquired from an automated multi-angular spectro-radiometer (AMSPEC II) installed at each site, we demonstrate that PRI can be used to measure ? throughout the vegetation season at the DF-49 stand (r² = 0.91, p < 0.00) as well as the deciduous site (r² = 0.88, p < 0.00). It is further shown that this PRI signal can be also observed from space at both sites using daily observations from the Moderate Resolution Imaging Spectro-radiometer (MODIS) and a multi-angular implementation of atmospheric correction (MAIAC) (r² = 0.54 DF-49; r² = 0.63 SOA; p < 0.00). By implementing a simple hillshade model derived from airborne light detection and ranging (LiDAR) to approximate canopy shadow fractions (α_s), it is further demonstrated that the differences observed in the relationship between PRI and ε at DF-49 and SOA can be attributed largely to differences in α_s. The findings of this study suggest that algorithms used to separate physiological from extraneous effects in PRI reflectance may be more broadly applicable and portable across these two climatically and structurally different biome types, when the differences in canopy structure are known.     

Picbreeder: a case study in collaborative evolutionary exploration of design space

For domains in which fitness is subjective or difficult to express formally, interactive evolutionary computation (IEC) is a natural choice. It is possible that a collaborative process combining feedback from multiple users can improve the quality and quantity of generated artifacts. Picbreeder, a large-scale online experiment in collaborative interactive evolution (CIE), explores this potential. Picbreeder is an online community in which users can evolve and share images, and most importantly, continue evolving others' images. Through this process of branching from other images, and through continually increasing image complexity made possible by the underlying neuroevolution of augmenting topologies (NEAT) algorithm, evolved images proliferate unlike in any other current IEC system. This paper discusses not only the strengths of the Picbreeder approach, but its challenges and shortcomings as well, in the hope that lessons learned will inform the design of future CIE systems.     

RANGE–Robust autonomous navigation in GPS‐denied environments

This paper addresses the problem of autonomous navigation of a micro air vehicle (MAV) in GPS‐denied environments. We present experimental validation and analysis for our system that enables a quadrotor helicopter, equipped with a laser range finder sensor, to autonomously explore and map unstructured and unknown environments. The key challenge for enabling GPS‐denied flight of a MAV is that the system must be able to estimate its position and velocity by sensing unknown environmental structure with sufficient accuracy and low enough latency to stably control the vehicle. Our solution overcomes this challenge in the face of MAV payload limitations imposed on sensing, computational, and communication resources. We first analyze the requirements to achieve fully autonomous quadrotor helicopter flight in GPS‐denied areas, highlighting the differences between ground and air robots that make it difficult to use algorithms developed for ground robots. We report on experiments that validate our solutions to key challenges, namely a multilevel sensing and control hierarchy that incorporates a high‐speed laser scan‐matching algorithm, data fusion filter, high‐level simultaneous localization and mapping, and a goal‐directed exploration module. These experiments illustrate the quadrotor helicopter's ability to accurately and autonomously navigate in a number of large‐scale unknown environments, both indoors and in the urban canyon. The system was further validated in the field by our winning entry in the 2009 International Aerial Robotics Competition, which required the quadrotor to autonomously enter a hazardous unknown environment through a window, explore the indoor structure without GPS, and search for a visual target. © 2011 Wiley Periodicals, Inc.     

Micropatterning of sulfonated polyaniline using a soft lithography based lift-off process

A combination of soft lithography and lift-off processing is presented for the fabrication of sulfonated polyaniline (SPAN) microstructures. A soft lithography based micromolding process was used to pattern sacrificial layers using a thermoplastic polymer. SPAN was then polymerized in situ to coat the patterned substrate. The sacrificial layer was removed by lift-off in an organic solvent, leaving the patterned SPAN on the substrate. This process was performed on several rigid and flexible substrates including glass, silicon, and polyimide. The film thickness and roughness were measured as a function of reaction time using atomic force microscopy. Patterns were also imaged using scanning electron microscopy. This process provides a cost effective and versatile method of patterning SPAN and has potential applications in a number of conducting polymer devices.     

Bug localization using latent Dirichlet allocation

ContextSome recent static techniques for automatic bug localization have been built around modern information retrieval (IR) models such as latent semantic indexing (LSI). Latent Dirichlet allocation (LDA) is a generative statistical model that has significant advantages, in modularity and extensibility, over both LSI and probabilistic LSI (pLSI). Moreover, LDA has been shown effective in topic model based information retrieval. In this paper, we present a static LDA-based technique for automatic bug localization and evaluate its effectiveness.ObjectiveWe evaluate the accuracy and scalability of the LDA-based technique and investigate whether it is suitable for use with open-source software systems of varying size, including those developed using agile methods.MethodWe present five case studies designed to determine the accuracy and scalability of the LDA-based technique, as well as its relationships to software system size and to source code stability. The studies examine over 300 bugs across more than 25 iterations of three software systems.ResultsThe results of the studies show that the LDA-based technique maintains sufficient accuracy across all bugs in a single iteration of a software system and is scalable to a large number of bugs across multiple revisions of two software systems. The results of the studies also indicate that the accuracy of the LDA-based technique is not affected by the size of the subject software system or by the stability of its source code base.ConclusionWe conclude that an effective static technique for automatic bug localization can be built around LDA. We also conclude that there is no significant relationship between the accuracy of the LDA-based technique and the size of the subject software system or the stability of its source code base. Thus, the LDA-based technique is widely applicable.     

A rapid computational filter for predicting the rate of human renal clearance

In silico models that predict the rate of human renal clearance for a diverse set of drugs, that exhibit both active secretion and net re-absorption, have been produced using three statistical approaches. Partial Least Squares (PLS) and Random Forests (RF) have been used to produce continuous models whereas Classification And Regression Trees (CART) has only been used for a classification model. The best models generated from either PLS or RF produce significant models that can predict acids/zwitterions, bases and neutrals with approximate average fold errors of 3, 3 and 4, respectively, for an independent test set that covers oral drug-like property space. These models contain additional information on top of any influence arising from plasma protein binding on the rate of renal clearance. Classification And Regression Trees (CART) has been used to generate a classification tree leading to a simple set of Renal Clearance Rules (RCR) that can be applied to man. The rules are influenced by lipophilicity and ion class and can correctly predict 60% of an independent test set. These percentages increase to 71% and 79% for drugs with renal clearances of < 0.1 ml/min/kg and > 1 ml/min/kg, respectively. As far as the authors are aware these are the first set of models to appear in the literature that predict the rate of human renal clearance and can be used to manipulate molecular properties leading to new drugs that are less likely to fail due to renal clearance.     

A silicone-based microfluidic chip grafted with carboxyl functionalized hyperbranched polyglycerols for selective protein capture

A poly(dimethylsiloxane) (PDMS)-based functional microfluidic device containing a charged matrix of PDMS pillar arrays grafted with hyperbranched polyglycerols (HPGs) was developed. Samples of PDMS were modified with allylamine plasma to form amine groups on the surface prior to the covalent grafting of succinimdyl ester-functionalized HPGs. The anionic functionality of the PDMS channel matrices was developed by altering the number of carboxyl groups present on the HPGs. The grafting of HPGs onto PDMS plates was investigated via contact angle measurement and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), while the grafting of the inside channel was investigated by electroosmotic flow (EOF) measurements. The charge density on grafted HPG was optimized to minimize the nonspecific protein adsorption and increase the selective capture of positively charged proteins. A proof-of-concept device was fabricated on PDMS and demonstrated that the device selectively captures positively charged protein (avidin) from a mixture of bovine serum albumin (BSA)-avidin at pH 7.4 in phosphate buffered saline (PBS). In order to increase the capture efficiency of the proteins in this PDMS-based device, pillar arrays have been fabricated within the channel. As a demonstration, the new device separated two proteins with an avidin capture efficiency of 100 ± 2.95% per 3 min from a 0.02 mg/ml protein solution (avidin:BSA wt ratio: 1:1). This new microfluidic-based device shows a great deal of promise as a tool for protein capture and analysis.     

iLogDemons: A Demons-Based Registration Algorithm for Tracking Incompressible Elastic Biological Tissues

Tracking soft tissues in medical images using non-linear image registration algorithms requires methods that are fast and provide spatial transformations consistent with the biological characteristics of the tissues. LogDemons algorithm is a fast non-linear registration method that computes diffeomorphic transformations parameterised by stationary velocity fields. Although computationally efficient, its use for tissue tracking has been limited because of its ad-hoc Gaussian regularisation, which hampers the implementation of more biologically motivated regularisations. In this work, we improve the logDemons by integrating elasticity and incompressibility for soft-tissue tracking. To that end, a mathematical justification of demons Gaussian regularisation is proposed. Building on this result, we replace the Gaussian smoothing by an efficient elastic-like regulariser based on isotropic differential quadratic forms of vector fields. The registration energy functional is finally minimised under the divergence-free constraint to get incompressible deformations. As the elastic regulariser and the constraint are linear, the method remains computationally tractable and easy to implement. Tests on synthetic incompressible deformations showed that our approach outperforms the original logDemons in terms of elastic incompressible deformation recovery without reducing the image matching accuracy. As an application, we applied the proposed algorithm to estimate 3D myocardium strain on clinical cine MRI of two adult patients. Results showed that incompressibility constraint improves the cardiac motion recovery when compared to the ground truth provided by 3D tagged MRI.     

An assessment of photosynthetic light use efficiency from space: Modeling the atmospheric and directional impacts on PRI reflectance

Estimation of photosynthetic light use efficiency (ε) from satellite observations is an important component of climate change research. The photochemical reflectance index, a narrow waveband index based on the reflectance at 531 and 570 nm, allows sampling of the photosynthetic activity of leaves; upscaling of these measurements to landscape and global scales, however, remains challenging. Only a few studies have used spaceborne observations of PRI so far, and research has largely focused on the MODIS sensor. Its daily global coverage and the capacity to detect a narrow reflectance band at 531 nm make it the best available choice for sensing ε from space. Previous results however, have identified a number of key issues with MODIS-based observations of PRI. First, the differences between the footprint of eddy covariance (EC) measurements and the MODIS footprint, which is determined by the sensor's observation geometry make a direct comparison between both data sources challenging and second, the PRI reflectance bands are affected by atmospheric scattering effects confounding the existing physiological signal. In this study we introduce a new approach for upscaling EC based ε measurements to MODIS. First, EC-measured ε values were “translated” into a tower-level optical PRI signal using AMSPEC, an automated multi-angular, tower-based spectroradiometer instrument. AMSPEC enabled us to adjust tower-measured PRI values to the individual viewing geometry of each MODIS overpass. Second, MODIS data were atmospherically corrected using a Multi-Angle Implementation of Atmospheric Correction (MAIAC) algorithm, which uses a time series approach and an image-based rather than pixel-based processing for simultaneous retrievals of atmospheric aerosol and surface bidirectional reflectance (BRDF). Using this approach, we found a strong relationship between tower-based and spaceborne reflectance measurements (r² = 0.74, p < 0.01) throughout the vegetation period of 2006. Swath (non-gridded) observations yielded stronger correlations than gridded data (r² = 0.58, p < 0.01) both of which included forward and backscatter observations. Spaceborne PRI values were strongly related to canopy shadow fractions and varied with different levels of ε. We conclude that MAIAC-corrected MODIS observations were able to track the site-level physiological changes from space throughout the observation period.