Mapping of cell nuclei based on contour warping

The dynamics of genome regions are associated to the functional or dysfunctional behaviour of the human cell. In order to study these dynamics it is necessary to remove all perturbations coming from movement and deformation of the nucleus, i.e. the container holding the genome. In literature models have been proposed to cope with the transformations corresponding to nuclear dynamics of healthy cells. However for pathological cells, the nucleus deforms in an apparently random way, making the use of such models a non trivial task. In this paper we propose a mapping of the cell nucleus which is based on the matching of the nuclear contours. The proposed method does not put constraints on the possible shapes nor on the possible deformations, making this method suited for the analysis of pathological nuclei

CMB-S4 Science Book, First Edition

This book lays out the scientific goals to be addressed by the next-generation ground-based cosmic microwave background experiment, CMB-S4, envisioned to consist of dedicated telescopes at the South Pole, the high Chilean Atacama plateau and possibly a northern hemisphere site, all equipped with new superconducting cameras. CMB-S4 will dramatically advance cosmological studies by crossing critical thresholds in the search for the B-mode polarization signature of primordial gravitational waves, in the determination of the number and masses of the neutrinos, in the search for evidence of new light relics, in constraining the nature of dark energy, and in testing general relativity on large scales

COrE (Cosmic Origins Explorer) A White Paper

COrE (Cosmic Origins Explorer) is a fourth-generation full-sky, microwave-band satellite recently proposed to ESA within Cosmic Vision 2015-2025. COrE will provide maps of the microwave sky in polarization and temperature in 15 frequency bands, ranging from 45 GHz to 795 GHz, with an angular resolution ranging from 23 arcmin (45 GHz) and 1.3 arcmin (795 GHz) and sensitivities roughly 10 to 30 times better than PLANCK (depending on the frequency channel). The COrE mission will lead to breakthrough science in a wide range of areas, ranging from primordial cosmology to galactic and extragalactic science. COrE is designed to detect the primordial gravitational waves generated during the epoch of cosmic inflation at more than $3\sigma$ for $r=(T/S)>=10^{-3}$. It will also measure the CMB gravitational lensing deflection power spectrum to the cosmic variance limit on all linear scales, allowing us to probe absolute neutrino masses better than laboratory experiments and down to plausible values suggested by the neutrino oscillation data. COrE will also search for primordial non-Gaussianity with significant improvements over Planck in its ability to constrain the shape (and amplitude) of non-Gaussianity. In the areas of galactic and extragalactic science, in its highest frequency channels COrE will provide maps of the galactic polarized dust emission allowing us to map the galactic magnetic field in areas of diffuse emission not otherwise accessible to probe the initial conditions for star formation. COrE will also map the galactic synchrotron emission thirty times better than PLANCK. This White Paper reviews the COrE science program, our simulations on foreground subtraction, and the proposed instrumental configuration.Comment: 90 pages Latex 15 figures (revised 28 April 2011, references added, minor errors corrected

Appraisal of the environmental sustainability of milk production systems in New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Science in Life Cycle Management at Massey University, Manawatū, New Zealand

Life Cycle Assessment (LCA) plays an important role in the environmental assessment of agricultural product systems, including dairy farming systems. Generally, an LCA study accounts for the comprehensive resource use and environmental emissions associated with the life cycle of a studied product system. The inventoried inputs and outputs are then transformed into different environmental impact categories using science-based environmental cause-effect mechanisms. There are different LCA modelling approaches (e.g. attributional LCA [ALCA] and consequential LCA [CLCA]) that can be used to address different research questions; however, there is currently no consensus on the most appropriate approach and when to use it. These LCA approaches require different types of data and methodological procedures and, therefore, generate different sets of environmental information which may have different implications for decision-making. In the present research, a series of studies utilising different LCA modelling approaches were undertaken of pasture-based dairy farming systems in the Waikato region (the largest dairy region in New Zealand). The purposes of the studies were to: (i) assess the environmental impacts and identify environmental hotspots of current pasture-based dairy farming systems, (ii) compare environmental hotspots between high and low levels of dairy farm intensification, (iii) investigate the environmental impacts of potential alternative farm intensification methods to increase milk productivity, and (iv) assess the environmental impacts of different future intensified dairy farming scenarios. Twelve midpoint impact categories were assessed: Climate Change (CC), Ozone Depletion Potential (ODP), Human Health Toxicity - non-cancer effects (Non-cancer), Human Health Toxicity - cancer effects (Cancer), Particulate Matter (PM), Ionizing Radiation - human health effects (IR), Photochemical Ozone Formation Potential (POFP), Acidification Potential (AP), Terrestrial Eutrophication Potential (TEP), Freshwater Eutrophication Potential (FEP), Marine Eutrophication Potential (MEP) and Ecotoxicity for Aquatic Freshwater (Ecotox). Firstly, the environmental impacts of 53 existing pasture-based dairy farm systems in the Waikato region were assessed using ALCA. The results showed that both the offfarm and on-farm stages made significant contributions to a range of environmental impacts per kg of fat- and protein-corrected milk (FPCM), and the relative contributions of the stages varied across different impact categories. Farms classified as high intensification based on a high level of farm inputs (i.e. stocking rate, level of nitrogen (N) fertiliser and level of brought-in feeds) had higher impact results than low intensification farms for 10 of 12 impact categories. This was driven mainly by the offfarm stage, including production of brought-in feeds, manufacturing of agrichemicals (e.g. fertilisers and pesticides), and transport of off-farm inputs for use on a dairy farm. The exceptions were the environmental indicators PM, POFP, AP and TEP; their results were determined mainly by ammonia emissions from the on-farm activities. Secondly, environmental consequences resulting from meeting a future increase in demand for milk production (i.e. 20% more milk production per hectare relative to that in 2010/11) by using different farm intensification scenarios for dairy farming systems in the Waikato region were assessed using CLCA. In this study, only technologies/flows that were actually affected by use of different intensification options to increase milk production were accounted for. The identified intensification methods were: (i) increased pasture utilisation efficiency, (ii) increased use of N fertiliser to boost on-farm pasture production, and (iii) increased use of brought-in feed (i.e. maize silage). The results showed that improved pasture utilisation efficiency was the most effective intensification option since it resulted in lower environmental impacts than the other two intensification options. The environmental performance between the other two intensification options varied, depending on impact categories (environmental tradeoffs). Thirdly, prospective ALCA was used to assess the environmental impacts of six prospective (future) dairy farming intensification scenarios in the Waikato region, primarily involving increased stocking rate, that were modelled to increase milk production per hectare by 50% in 2025. In this study, prospective (future) average flows that were derived from extrapolation were accounted for. The potential intensification scenarios were: (i) increased animal productivity (increased milk production per cow), (ii) increased use of mixed brought-in feed, (iii) improved pasture utilisation efficiency, (iv) increased use of N fertiliser to boost on-farm pasture production, (v) increased use of brought-in maize silage, and (vi) replacement of total mixed brought-in feed in the second scenario by wheat grain. The results showed that, apart from improved animal productivity which was considered the best option, improved pasture utilisation efficiency was the second environmentally-preferential option compared with other intensification options for pasture-based dairy farming systems in the Waikato region. There were environmental trade-offs between other intensification options. The present research demonstrated that pasture-based dairy farming systems in the Waikato region contribute to a range of environmental impacts. More intensive farming systems not only have increased milk productivity (milk production per hectare) but also increased environmental impacts (per kg FPCM) in most environmental impact categories. Farm intensification options associated with improved farm efficiency (e.g. animal productivity or pasture utilisation efficiency) are promising as they have lower environmental indicator results (per kg FPCM) compared with other intensification methods. Increased use of off-farm inputs (e.g. N fertilisers and brought-in feeds) increases some, and decreases other, environmental indicator results. Therefore, decision-making associated with choice of alternative farm intensification options beyond farm efficiency improvements will require prioritisation between different environmental impacts and/or focusing on the ability of key decision-makers to effect change (for example, by distinguishing between local and global activities contributing to environmental impacts). The present research has shown that different LCA modelling approaches can be used in a sequential manner to maximise the usefulness of environmental assessment. Initially, ALCA (based on current average flows) can be used to identify environmental hotspots in the life cycle of dairy farming systems. This will generate environmental information that can assist in selection of improvement options. Subsequently, the improvement options selected should be evaluated using CLCA (based on marginal flows). This will produce comparative environmental information resulting from implementing the selected improvement options, strategies or policies in relation to a non-implementation scenario, when the wider contribution of co-products is accounted for. Finally, prospective ALCA (based on future average flows) can be used to assess total or net environmental benefits

Prioritizing Content of Interest in Multimedia Data Compression

Image and video compression techniques make data transmission and storage in digital multimedia systems more efficient and feasible for the system's limited storage and bandwidth. Many generic image and video compression techniques such as JPEG and H.264/AVC have been standardized and are now widely adopted. Despite their great success, we observe that these standard compression techniques are not the best solution for data compression in special types of multimedia systems such as microscopy videos and low-power wireless broadcast systems. In these application-specific systems where the content of interest in the multimedia data is known and well-defined, we should re-think the design of a data compression pipeline. We hypothesize that by identifying and prioritizing multimedia data's content of interest, new compression methods can be invented that are far more effective than standard techniques. In this dissertation, a set of new data compression methods based on the idea of prioritizing the content of interest has been proposed for three different kinds of multimedia systems. I will show that the key to designing efficient compression techniques in these three cases is to prioritize the content of interest in the data. The definition of the content of interest of multimedia data depends on the application. First, I show that for microscopy videos, the content of interest is defined as the spatial regions in the video frame with pixels that don't only contain noise. Keeping data in those regions with high quality and throwing out other information yields to a novel microscopy video compression technique. Second, I show that for a Bluetooth low energy beacon based system, practical multimedia data storage and transmission is possible by prioritizing content of interest. I designed custom image compression techniques that preserve edges in a binary image, or foreground regions of a color image of indoor or outdoor objects. Last, I present a new indoor Bluetooth low energy beacon based augmented reality system that integrates a 3D moving object compression method that prioritizes the content of interest.Doctor of Philosoph

Spatial normalization of array-CGH data

BACKGROUND: Array-based comparative genomic hybridization (array-CGH) is a recently developed technique for analyzing changes in DNA copy number. As in all microarray analyses, normalization is required to correct for experimental artifacts while preserving the true biological signal. We investigated various sources of systematic variation in array-CGH data and identified two distinct types of spatial effect of no biological relevance as the predominant experimental artifacts: continuous spatial gradients and local spatial bias. Local spatial bias affects a large proportion of arrays, and has not previously been considered in array-CGH experiments. RESULTS: We show that existing normalization techniques do not correct these spatial effects properly. We therefore developed an automatic method for the spatial normalization of array-CGH data. This method makes it possible to delineate and to eliminate and/or correct areas affected by spatial bias. It is based on the combination of a spatial segmentation algorithm called NEM (Neighborhood Expectation Maximization) and spatial trend estimation. We defined quality criteria for array-CGH data, demonstrating significant improvements in data quality with our method for three data sets coming from two different platforms (198, 175 and 26 BAC-arrays). CONCLUSION: We have designed an automatic algorithm for the spatial normalization of BAC CGH-array data, preventing the misinterpretation of experimental artifacts as biologically relevant outliers in the genomic profile. This algorithm is implemented in the R package MANOR (Micro-Array NORmalization), which is described at and available from the Bioconductor site . It can also be tested on the CAPweb bioinformatics platform at

Observations of Detailed Structure in the Solar Wind at 1 AU with STEREO/HI-2

Heliospheric imagers offer the promise of remote sensing of large-scale structures present in the solar wind. The STEREO/HI-2 imagers, in particular, offer high resolution, very low noise observations of the inner heliosphere but have not yet been exploited to their full potential. This is in part because the signal of interest, Thomson scattered sunlight from free electrons, is ~1000 times fainter than the background visual field in the images, making background subtraction challenging. We have developed a procedure for separating the Thomson-scattered signal from the other background/foreground sources in the HI-2 data. Using only the Level 1 data from STEREO/HI-2, we are able to generate calibrated imaging data of the solar wind with sensitivity of a few times 1e-17 Bsun, compared to the background signal of a few times 1e-13 Bsun. These images reveal detailed spatial structure in CMEs and the solar wind at projected solar distances in excess of 1 AU, at the instrumental motion-blur resolution limit of 1-3 degree. CME features visible in the newly reprocessed data from December 2008 include leading-edge pileup, interior voids, filamentary structure, and rear cusps. "Quiet" solar wind features include V shaped structure centered on the heliospheric current sheet, plasmoids, and "puffs" that correspond to the density fluctuations observed in-situ. We compare many of these structures with in-situ features detected near 1 AU. The reprocessed data demonstrate that it is possible to perform detailed structural analyses of heliospheric features with visible light imagery, at distances from the Sun of at least 1 AU.Comment: Accepted by Astrophysical Journa

Forecasting constraints from the cosmic microwave background on eternal inflation

We forecast the ability of cosmic microwave background (CMB) temperature and polarization datasets to constrain theories of eternal inflation using cosmic bubble collisions. Using the Fisher matrix formalism, we determine both the overall detectability of bubble collisions and the constraints achievable on the fundamental parameters describing the underlying theory. The CMB signatures considered are based on state-of-the-art numerical relativistic simulations of the bubble collision spacetime, evolved using the full temperature and polarization transfer functions. Comparing a theoretical cosmic-variance-limited experiment to the WMAP and Planck satellites, we find that there is no improvement to be gained from future temperature data, that adding polarization improves detectability by approximately 30%, and that cosmic-variance-limited polarization data offer only marginal improvements over Planck. The fundamental parameter constraints achievable depend on the precise values of the tensor-to-scalar ratio and energy density in (negative) spatial curvature. For a tensor-to-scalar ratio of $0.1$ and spatial curvature at the level of $10^{-4}$, using cosmic-variance-limited data it is possible to measure the width of the potential barrier separating the inflating false vacuum from the true vacuum down to $M_{\rm Pl}/500$, and the initial proper distance between colliding bubbles to a factor $\pi/2$ of the false vacuum horizon size (at three sigma). We conclude that very near-future data will have the final word on bubble collisions in the CMB.Comment: 14 pages, 6 figure