Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis.

Cytosine methylation is important for transposon silencing and epigenetic regulation of endogenous genes, although the extent to which this DNA modification functions to regulate the genome is still unknown. Here we report the first comprehensive DNA methylation map of an entire genome, at 35 base pair resolution, using the flowering plant Arabidopsis thaliana as a model. We find that pericentromeric heterochromatin, repetitive sequences, and regions producing small interfering RNAs are heavily methylated. Unexpectedly, over one-third of expressed genes contain methylation within transcribed regions, whereas only approximately 5% of genes show methylation within promoter regions. Interestingly, genes methylated in transcribed regions are highly expressed and constitutively active, whereas promoter-methylated genes show a greater degree of tissue-specific expression. Whole-genome tiling-array transcriptional profiling of DNA methyltransferase null mutants identified hundreds of genes and intergenic noncoding RNAs with altered expression levels, many of which may be epigenetically controlled by DNA methylation.

Semantic Discriminant mapping for classification and browsing of remote sensing textures and objects

We present a new approach based on Discriminant Analysis to map a high dimensional image feature space onto a subspace which has the following advantages: 1. each dimension corresponds to a semantic likelihood, 2. an efficient and simple multiclass classifier is proposed and 3. it is low dimensional. This mapping is learnt from a given set of labeled images with a class groundtruth. In the new space a classifier is naturally derived which performs as well as a linear SVM. We will show that projecting images in this new space provides a database browsing tool which is meaningful to the user. Results are presented on a remote sensing database with eight classes, made available online. The output semantic space is a low dimensional feature space which opens perspectives for other recognition tasks. © 2005 IEEE.

Mapping forces in a 3D elastic assembly of grains

Our understanding of the elasticity and rheology of disordered materials, such as granular piles, foams, emulsions or dense suspensions relies on improving experimental tools to characterise their behaviour at the particle scale. While 2D observations are now routinely carried out in laboratories, 3D measurements remain a challenge. In this paper, we use a simple model system, a packing of soft elastic spheres, to illustrate the capability of X-ray microtomography to characterise the internal structure and local behaviour of granular systems. Image analysis techniques can resolve grain positions, shapes and contact areas; this is used to investigate the materials microstructure and its evolution upon strain. In addition to morphological measurements, we develop a technique to quantify contact forces and estimate the internal stress tensor. As will be illustrated in this paper, this opens the door to a broad array of static and dynamical measurements in 3D disordered systems. © 2011 Elsevier Ltd. All rights reserved.

BarraCUDA – a Fast Sequence Mapping Software using Graphics Processing Units

High-throughput DNA sequencing (HTS) instruments today are capable of generating millions of sequencing reads in a short period of time, and this represents a serious challenge to current bioinformatics pipeline in processing such an enormous amount of data in a fast and economical fashion. Modern graphics cards are powerful processing units that consist of hundreds of scalar processors in parallel in order to handle the rendering of high-definition graphics in real-time. It is this computational capability that we propose to harness in order to accelerate some of the time-consuming steps in analyzing data generated by the HTS instruments. We have developed BarraCUDA, a novel sequence mapping software that utilizes the parallelism of NVIDIA CUDA graphics cards to map sequencing reads to a particular location on a reference genome. While delivering a similar mapping fidelity as other mainstream programs , BarraCUDA is a magnitude faster in mapping throughput compared to its CPU counterparts. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the mapping throughput. BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the mapping of millions of sequencing reads generated by HTS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available at http://seqbarracuda.sf.net

Community-led resettlement: From a flood affected slum to a new society in Pune, India

This paper describes the resettlement process of a community devastated by annual floods, to newly constructed housing in Pune, India. The relocation from Kamgar Putala slum to a housing society at Hadapsar was organized by a community-led NGO partnership in 2004. The housing development was coordinated by the local NGO Shelter Associates with significant community participation. The housing has been revisited in 2010 to evaluate the sustainability of the resettlement project’s delivery model via stakeholder perception. The process of organizing for resettlement after natural disaster is described along with the implementation and evaluation of the new housing nearly six years after initial occupation. The strong partnership approach overcame a series of political and financial hurdles at various stages of the relocation project. The story of resettling Kamgar Putala is detailed alongside an outline of the current political climate for an alternative slum-upgrading policy in India and Pune. The advantages of an empowered community supported by an influential local NGO demonstrate a commendable team effort which has tackled the threat of floods. The paper highlights the merits of a community-led partnership approach to housing development for achieving sustainable urban development as well as the alleviation of poverty in a developing context.

Cortical thickness mapping to identify focal osteoporosis in patients with hip fracture.

BACKGROUND: Individuals with osteoporosis are predisposed to hip fracture during trips, stumbles or falls, but half of all hip fractures occur in those without generalised osteoporosis. By analysing ordinary clinical CT scans using a novel cortical thickness mapping technique, we discovered patches of markedly thinner bone at fracture-prone regions in the femurs of women with acute hip fracture compared with controls. METHODS: We analysed CT scans from 75 female volunteers with acute fracture and 75 age- and sex-matched controls. We classified the fracture location as femoral neck or trochanteric before creating bone thickness maps of the outer 'cortical' shell of the intact contra-lateral hip. After registration of each bone to an average femur shape and statistical parametric mapping, we were able to visualise and quantify statistically significant foci of thinner cortical bone associated with each fracture type, assuming good symmetry of bone structure between the intact and fractured hip. The technique allowed us to pinpoint systematic differences and display the results on a 3D average femur shape model. FINDINGS: The cortex was generally thinner in femoral neck fracture cases than controls. More striking were several discrete patches of statistically significant thinner bone of up to 30%, which coincided with common sites of fracture initiation (femoral neck or trochanteric). INTERPRETATION: Femoral neck fracture patients had a thumbnail-sized patch of focal osteoporosis at the upper head-neck junction. This region coincided with a weak part of the femur, prone to both spontaneous 'tensile' fractures of the femoral neck, and as a site of crack initiation when falling sideways. Current hip fracture prevention strategies are based on case finding: they involve clinical risk factor estimation to determine the need for single-plane bone density measurement within a standard region of interest (ROI) of the femoral neck. The precise sites of focal osteoporosis that we have identified are overlooked by current 2D bone densitometry methods.

Mapping the global flow of steel: from steelmaking to end-use goods.

Our society is addicted to steel. Global demand for steel has risen to 1.4 billion tonnes a year and is set to at least double by 2050, while the steel industry generates nearly a 10th of the world's energy related CO₂ emissions. Meeting our 2050 climate change targets would require a 75% reduction in CO₂ emissions for every tonne of steel produced and finding credible solutions is proving a challenge. The starting point for understanding the environmental impacts of steel production is to accurately map the global steel supply chain and identify the biggest steel flows where actions can be directed to deliver the largest impact. In this paper we present a map of global steel, which for the first time traces steel flows from steelmaking, through casting, forming, and rolling, to the fabrication of final goods. The diagram reveals the relative scale of steel flows and shows where efforts to improve energy and material efficiency should be focused.

Community-led resettlement: From a flood-affected slum to a new society in Pune, India

This paper describes the resettlement process of a community devastated by annual floods, to newly constructed housing in Pune, India. The relocation from Kamgar Putala slum to a housing society at Hadapsar was organized by a community-led NGO partnership in 2004. The housing development was coordinated by the local NGO Shelter Associates with significant community participation. The housing has been revisited in 2010 to evaluate the sustainability of the resettlement project's delivery model via stakeholder perception. The process of organizing for resettlement after natural disaster is described along with the implementation and evaluation of the new housing nearly six years after initial occupation. The strong partnership approach overcame a series of political and financial hurdles at various stages of the relocation project. The story of resettling Kamgar Putala is detailed alongside an outline of the current political climate for an alternative slum-upgrading policy in India and Pune. The advantages of an empowered community supported by an influential local NGO demonstrate a commendable team effort which has tackled the threat of floods. The paper highlights the merits of a community-led partnership approach to housing development for achieving sustainable urban development as well as the alleviation of poverty in a developing context. © 2011 Taylor & Francis.

Mapping the global flow of aluminum: from liquid aluminum to end-use goods.

Demand for aluminum in final products has increased 30-fold since 1950 to 45 million tonnes per year, with forecasts predicting this exceptional growth to continue so that demand will reach 2-3 times today's levels by 2050. Aluminum production uses 3.5% of global electricity and causes 1% of global CO2 emissions, while meeting a 50% cut in emissions by 2050 against growing demand would require at least a 75% reduction in CO2 emissions per tonne of aluminum produced--a challenging prospect. In this paper we trace the global flows of aluminum from liquid metal to final products, revealing for the first time a complete map of the aluminum system and providing a basis for future study of the emissions abatement potential of material efficiency. The resulting Sankey diagram also draws attention to two key issues. First, around half of all liquid aluminum (~39 Mt) produced each year never reaches a final product, and a detailed discussion of these high yield losses shows significant opportunities for improvement. Second, aluminum recycling, which avoids the high energy costs and emissions of electrolysis, requires signification "dilution" (~ 8 Mt) and "cascade" (~ 6 Mt) flows of higher aluminum grades to make up for the shortfall in scrap supply and to obtain the desired alloy mix, increasing the energy required for recycling.