Segmenting root systems in X-ray computed tomography images using level sets

The segmentation of plant roots from soil and other growing media in X-ray computed tomography images is needed to effectively study the root system architecture without excavation. However, segmentation is a challenging problem in this context because the root and non-root regions share similar features. In this paper, we describe a method based on level sets and specifically adapted for this segmentation problem. In particular, we deal with the issues of using a level sets approach on large image volumes for root segmentation, and track active regions of the front using an occupancy grid. This method allows for straightforward modifications to a narrow-band algorithm such that excessive forward and backward movements of the front can be avoided, distance map computations in a narrow band context can be done in linear time through modification of Meijster et al.'s distance transform algorithm, and regions of the image volume are iteratively used to estimate distributions for root versus non-root classes. Results are shown of three plant species of different maturity levels, grown in three different media. Our method compares favorably to a state-of-the-art method for root segmentation in X-ray CT image volumes.Comment: 11 page

The Lives of Erich Fromm: Love’s Prophet by Lawrence J. Friedman (2013)

Histor

First CMB Constraints on Direction-Dependent Cosmological Birefringence from WMAP-7

A Chern-Simons coupling of a new scalar field to electromagnetism may give rise to cosmological birefringence, a rotation of the linear polarization of electromagnetic waves as they propagate over cosmological distances. Prior work has sought this rotation, assuming the rotation angle to be uniform across the sky, by looking for the parity-violating TB and EB correlations a uniform rotation produces in the CMB temperature/polarization. However, if the scalar field that gives rise to cosmological birefringence has spatial fluctuations, then the rotation angle may vary across the sky. Here we search for direction-dependent cosmological birefringence in the WMAP-7 data. We report the first CMB constraint on the rotation-angle power spectrum for multipoles between L = 0 and L = 512. We also obtain a 68% confidence-level upper limit of 1 degree on the square root of the quadrupole of a scale-invariant rotation-angle power spectrum.Comment: 14 pages, 12 figures, 4 tables; accepted to PR

"Changing ourselves, changing others" : an analysis of the life stories of participants in a training course for volunteers within a non-governmental organisation in the Eastern Cape Province of South Africa

Gender-based violence has been recognized as a pressing mental health problem that is prevalent within South African society. Non-governmental organizations play a major role in addressing and highlighting the issue. These organizations make use of volunteers in order to assist in meeting their goals. The modernist perspective has been the dominant investigative mode when research into volunteers has been conducted. However, this study has been conducted with an emphasis on narrative. In its use of this constitutionalist and deconstructive perspective, it examines the identity of the research participants within the dominant social and cultural discourses that story their lives. This presents a major challenge to the modernist framework. In examining the life stories of the participants an emergent nature of identity is noted. Through the process of storying their lives and ascribing meaning to their experiences and understandings, the participants engaged in a process of constructing their identity. This research recognizes that identity is both multi-sited and multi-storied. The emphasis on personal agency enables the participants to restory their lives in the light of challenging prevailing discourses. It is in this process of challenge that they reauthor their lives and are in a position to change their own lives and the lives of others

On the complementarity of galaxy clustering with cosmic shear and flux magnification

In this paper, we motivate the use of galaxy clustering measurements using photometric redshift information, including a contribution from flux magnification, as a probe of cosmology. We present cosmological forecasts when clustering data alone is used, and when clustering is combined with a cosmic shear analysis. We consider two types of clustering analysis: firstly, clustering with only redshift auto-correlations in tomographic redshift bins; secondly, using all available redshift bin correlations. Finally, we consider how inferred cosmological parameters may be biased using each analysis when flux magnification is neglected. Results are presented for a Stage III ground-based survey, and a Stage IV space-based survey modelled with photometric redshift errors, and values for the slope of the luminosity function inferred from CFHTLenS catalogues. We find that combining clustering information with shear can improve constraints on cosmological parameters, giving an improvement to a Dark Energy Task Force-like figure of merit by a factor of 1.33 when only auto-correlations in redshift are used for the clustering analysis, rising to 1.52 when cross-correlations in redshift are also included. The addition of galaxy-galaxy lensing gives further improvement, with increases in figure of merit by a factor of 2.82 and 3.7 for each type of clustering analysis respectively. The presence of flux magnification in a clustering analysis does not significantly affect the precision of cosmological constraints when combined with cosmic shear and galaxy-galaxy lensing. However if magnification is neglected, inferred cosmological parameter values are biased, with biases in some cosmological parameters larger than statistical errors. (Abridged)Comment: Accepted by MNRAS, 18 pages, 12 Figures, 3 Table

The Conservation Ecology of Neotropical Tree Cavity Communities in Forest and Agro-Ecosystems in the Alexander Skutch Biological Corridor, Costa Rica

Shade coffee agro-ecosystems with a diversified canopy have been documented to provide quality habitat for a variety of vertebrates. For tree cavity dependent species however, shade coffee may be lacking critical habitat. I chose to investigate whether cavity abundance and the number cavity forming dead trees i.e., snags differed between shade coffee and other disturbed/undisturbed habitats within the Alexander Skutch Biological Corridor (ASBC) in Costa Rica. I also chose to investigate whether artificial tree cavities could be used in ecological restoration projects for cavity-nesting species in agro-ecosystems like shade coffee. To accomplish these tasks, I first conducted a comprehensive survey of tree cavities and snags in 1) primary cloud forest (elevation 1100-1400m), 2) primary middle elevation old-growth rainforest (650-750m), 3) selectively logged secondary middle elevation rainforest (650-700m), and (4) shade coffee (900-1000m) and installed motion-sensor cameras across from selected cavities within each habitat to monitor/compare potential occupancy/use. I then installed artificial tree cavities constructed of bamboo in 3 of the 4 habitats with iButton temperature loggers to test the prediction that shade coffee artificial cavities would have a greater number of occupancy detections due to the low number of cavities in this habitat compared with other habitat types. My findings showed an almost complete absence of snags and tree cavities in shade coffee supporting the hypothesis that shade coffee does not provide habitat for cavity-dependent species. Consistent with my prediction, artificial bamboo tree cavities in shade coffee were occupied/used most relative to the other habitats, further supporting the hypothesis that habitat for cavity-nesting species is limited is this agro-ecosystem. This thesis provides evidence that tree cavity restoration through the use of artificial cavities and a change in the management practices of shade coffee farms should be a priority for those concerned with biodiversity in shade coffee agro-ecosystems. A similar study conducted over a broader geographic range would show whether the lack of available habitat for cavity nesting species in shade coffee is reflected in other areas

Delensing CMB Polarization with External Datasets

One of the primary scientific targets of current and future CMB polarization experiments is the search for a stochastic background of gravity waves in the early universe. As instrumental sensitivity improves, the limiting factor will eventually be B-mode power generated by gravitational lensing, which can be removed through use of so-called delensing algorithms. We forecast prospects for delensing using lensing maps which are obtained externally to CMB polarization: either from large-scale structure observations, or from high-resolution maps of CMB temperature. We conclude that the forecasts in either case are not encouraging, and that significantly delensing large-scale CMB polarization requires high-resolution polarization maps with sufficient sensitivity to measure the lensing B-mode. We also present a simple formalism for including delensing in CMB forecasts which is computationally fast and agrees well with Monte Carlos.Comment: typos correcte