Motion Correction Resolved for MRI via Multi-Tasking: A Simultaneous Reconstruction and Registration Approach

The prolonged time required to form an MR image continues to impose different challenges at both theoretical and clinical levels. With this motivation in mind, this work addresses a central topic in MRI, which is how to correct the motion problem, through a new multitask optimisation framework. The significance is that by tackling the reconstruction and registration tasks simultaneously and jointly one can exploit their strong correlation reducing error propagations and resulting in a significant motion correction. The clinical potentials of our approach are reflected in having higher image quality with fewer artefacts whilst keeping fine details. We evaluate our approach through a set of quantitative and qualitative experimental results

Rethinking efficiency: Growth curves as a proxy for inputs and impacts in finishing beef systems

Quantifying and improving efficiency within beef systems is essential for economic and environmental sustainability. The industry standard for assessing efficiency is liveweight gain per day, however, this metric is limited in that it values each day of a growing animal's life as equally costly, despite the increasing maintenance requirements, inputs, and emissions associated with increasing liveweight. Quantifying the area under the growth curve (AUC) considers both time and liveweight as a cost and therefore may hold potential as a better estimate of cost, impact, and efficiency in beef systems. Liveweight data was taken from 439 finishing beef cattle split across three herds grazing on different pastures, known as ‘farmlets’. Analysis was conducted in three parts: [1] Validation of AUC as a proxy for costs using data from a sub-set of 87 animals that had been part of a previous life cycle assessment (LCA) study in which dry matter intake (DMI), methane emissions (CH4), and nitrous oxide emissions (N2O) were calculated. [2] Calculation of AUC relative to liveweight gain (LWG AUC−1) and comparison of that metric against the industry standard of liveweight gain per day (LWG day−1). [3] Assessment of how LWG AUC−1 varied with breed, sex, and management. When comparing to LCA results, AUC correlated significantly with DMI (r = 0.886), CH4 (r = 0.788) and N2O (r = 0.575) emissions. Over the full dataset, there was a negative non-linear relationship between LWG AUC−1 and slaughter age (r = −0.809). There was a significant difference in LWG AUC−1 between breeds (p = 0.046) and farmlets (p = 0.028), but not sex (p = 0.388). LWG AUC−1 has the potential to act as a proxy for feed intake and emissions. In that regard it is superior to LWG day−1, whilst requiring no additional data. Results highlighted the decreasing efficiency of beef cattle over time and the potential benefits of earlier slaughter. The use of LWG AUC−1 could allow farmers to improve their understanding of efficiency within their herds, aiding informed management decision making

MIUSCAT: extended MILES spectral coverage. I. Stellar populations synthesis models

We extend the spectral range of our stellar population synthesis models based on the MILES and CaT empirical stellar spectral libraries. For this purpose we combine these two libraries with the Indo-U.S. to construct composite stellar spectra to feed our models. The spectral energy distributions (SEDs) computed with these models and the originally published models are combined to construct composite SEDs for single-age, single-metallicity stellar populations (SSPs) covering the range 3465 - 9469\AA at moderately high, and uniform, resolution (FWHM=2.51\AA). The colours derived from these SSP SEDs provide good fits to Galactic globular cluster data. We find that the colours involving redder filters are very sensitive to the IMF, as well as a number of features and molecular bands throughout the spectra. To illustrate the potential use of these models we focus on the NaI doublet at 8200 \AA and with the aid of the newly synthesized SSP model SEDs we define a new IMF-sensitive index that is based on this feature, which overcomes various limitations from previous index definitions for low velocity dispersion stellar systems. We propose an index-index diagram based on this feature and the neighboring CaII triplet at 8600 \AA, to constrain the IMF if the age and [Na/Fe] abundance are known. Finally we also show a survey-oriented spectrophotometric application which evidences the accurate flux calibration of these models for carrying out reliable spectral fitting techniques. These models are available through our user-friendly website.Comment: 16 pages, 17 figures, 2 tables; MNRAS in press. Model predictions available at our website: http://miles.iac.e

Multi-tasking to Correct: Motion-Compensated MRI via Joint Reconstruction and Registration

This work addresses a central topic in Magnetic Resonance Imaging (MRI) which is the motion-correction problem in a joint reconstruction and registration framework. From a set of multiple MR acquisitions corrupted by motion, we aim at - jointly - reconstructing a single motion-free corrected image and retrieving the physiological dynamics through the deformation maps. To this purpose, we propose a novel variational model. First, we introduce an $L^2$ fidelity term, which intertwines reconstruction and registration along with the weighted total variation. Second, we introduce an additional regulariser which is based on the hyperelasticity principles to allow large and smooth deformations. We demonstrate through numerical results that this combination creates synergies in our complex variational approach resulting in higher quality reconstructions and a good estimate of the breathing dynamics. We also show that our joint model outperforms in terms of contrast, detail and blurring artefacts, a sequential approach.Cambridge Cancer Centre, CMIH and CCIMI, University of Cambridge

The scale of population structure in Arabidopsis thaliana

The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales

Comparison of the welfare of beef cattle in housed and grazing systems: hormones, health and behaviour

Animal welfare encompasses all aspects of an animal's life and the interactions between animals. Consequently, welfare must be measured across a variety of factors that consider aspects such as health, behaviour and mental state. Decisions regarding housing and grazing are central to farm management. In this study, two beef cattle systems and their herds were compared from weaning to slaughter across numerous indicators. One herd (‘HH’) were continuously housed, the other (‘HG’) were housed only during winter. Inspections of animals were conducted to assess body condition, cleanliness, diarrhoea, hairlessness, nasal discharge and ocular discharge. Hair and nasal mucus samples were taken for quantification of cortisol and serotonin. Qualitative behaviour assessments (QBA) were also conducted and performance monitored. Physical health indicators were similar between herds with the exception of nasal discharge which was more prevalent in HH (P < 0.001). During winter, QBA yielded differences between herds over PC1 (arousal) (P = 0.032), but not PC2 (mood) (P = 0.139). Through summer, there was a strong difference across both PC1 (P < 0.001) and PC2 (P = 0.002), with HG exhibiting more positive behaviour. A difference was found in hair cortisol levels, with the greatest concentrations observed in HG (P = 0.011), however such a pattern was not seen for nasal mucus cortisol or for serotonin. Overall, providing summer grazing (HG) appeared to afford welfare benefits to the cattle as shown with more positive QBA assessments, but also slightly better health indicators, notwithstanding the higher levels of cortisol in that group

Criteria for effective zero-deforestation commitments

Zero-deforestation commitments are a type of voluntary sustainability initiative that companies adopt to signal their intention to reduce or eliminate deforestation associated with commodities that they produce, trade, and/or sell. Because each company defines its own zero-deforestation commitment goals and implementation mechanisms, commitment content varies widely. This creates challenges for the assessment of commitment implementation or effectiveness. Here, we develop criteria to assess the potential effectiveness of zero-deforestation commitments at reducing deforestation within a company supply chain, regionally, and globally. We apply these criteria to evaluate 52 zero-deforestation commitments made by companies identified by Forest 500 as having high deforestation risk. While our assessment indicates that existing commitments converge with several criteria for effectiveness, they fall short in a few key ways. First, they cover just a small share of the global market for deforestation-risk commodities, which means that their global impact is likely to be small. Second, biome-wide implementation is only achieved in the Brazilian Amazon. Outside this region, implementation occurs mainly through certification programs, which are not adopted by all producers and lack third-party near-real time deforestation monitoring. Additionally, around half of all commitments include zero-net deforestation targets and future implementation deadlines, both of which are design elements that may reduce effectiveness. Zero-net targets allow promises of future reforestation to compensate for current forest loss, while future implementation deadlines allow for preemptive clearing. To increase the likelihood that commitments will lead to reduced deforestation across all scales, more companies should adopt zero-gross deforestation targets with immediate implementation deadlines and clear sanction-based implementation mechanisms in biomes with high risk of forest to commodity conversion.ISSN:0959-3780ISSN:1872-949

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways

Motivation: Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions

Transmission pathways for sporadic Shiga-toxin producing E. coli infections: A systematic review and meta-analysis

Background: Shiga-toxin E. coli infections remain a public health concern because of the severity of the gastrointestinal illness and associated complications. Transmission pathways are typically elucidated from outbreaks, with foodborne transmission the primary source. However, most STEC cases are sporadic. This systematic review aimed to identify the most common pathways for sporadic STEC transmission and quantify their importance. Methods: We systematically reviewed epidemiological studies of sporadic (non-outbreak) STEC cases that investigated potential risk factors. Searches were run in Medline, EMBASE, and Scopus. Included studies needed to confirm STEC infection and investigate ≥20 cases. Results: 31 studies were included, of which 25 were case-control or case-case studies. 62.5% found consumption of undercooked/raw meat associated with STEC infection while 70.4% found contact with animals or their environment a risk factor. Random-effects meta-analysis provided pooled odds ratios and population attributable fraction (PAF). The PAF was 19% for undercooked/raw meat, followed by person to person transmission at 15%. Contact with animals and visiting farm environments had PAFs of 14% and 12% respectively. Conclusions: Out of potential sources for STEC exposure, undercooked meat and contact with animals and their environment were the most frequently found transmission routes. Decreasing the chances of acquiring the bacteria by these methods would additionally cut down on the other major transmission route, person-to-person spread