Unbiased Shape Compactness for Segmentation

We propose to constrain segmentation functionals with a dimensionless, unbiased and position-independent shape compactness prior, which we solve efficiently with an alternating direction method of multipliers (ADMM). Involving a squared sum of pairwise potentials, our prior results in a challenging high-order optimization problem, which involves dense (fully connected) graphs. We split the problem into a sequence of easier sub-problems, each performed efficiently at each iteration: (i) a sparse-matrix inversion based on Woodbury identity, (ii) a closed-form solution of a cubic equation and (iii) a graph-cut update of a sub-modular pairwise sub-problem with a sparse graph. We deploy our prior in an energy minimization, in conjunction with a supervised classifier term based on CNNs and standard regularization constraints. We demonstrate the usefulness of our energy in several medical applications. In particular, we report comprehensive evaluations of our fully automated algorithm over 40 subjects, showing a competitive performance for the challenging task of abdominal aorta segmentation in MRI.Comment: Accepted at MICCAI 201

Auslander-Buchweitz approximation theory for triangulated categories

We introduce and develop an analogous of the Auslander-Buchweitz approximation theory (see \cite{AB}) in the context of triangulated categories, by using a version of relative homology in this setting. We also prove several results concerning relative homological algebra in a triangulated category \T, which are based on the behavior of certain subcategories under finiteness of resolutions and vanishing of Hom-spaces. For example: we establish the existence of preenvelopes (and precovers) in certain triangulated subcategories of \T. The results resemble various constructions and results of Auslander and Buchweitz, and are concentrated in exploring the structure of a triangulated category \T equipped with a pair (\X,\omega), where \X is closed under extensions and $\omega$ is a weak-cogenerator in \X, usually under additional conditions. This reduces, among other things, to the existence of distinguished triangles enjoying special properties, and the behavior of (suitably defined) (co)resolutions, projective or injective dimension of objects of \T and the formation of orthogonal subcategories. Finally, some relationships with the Rouquier's dimension in triangulated categories is discussed.Comment: To appear at: Appl. Categor. Struct. (2011); 22 page

The Effect of Surface Roughness on the Contact Line and Splashing Dynamics of Impacting Droplets

Whether a droplet splashes upon impact onto a solid is known to depend not only on the fluid properties and its speed, but also on the substrate characteristics. Past research has shown that splashing is heavily influenced by the substrate roughness. Indeed, in this manuscript, we demonstrate that splashing is ruled by the surface roughness, the splashing ratio, and the dynamic contact angle. Experiments consist of water and ethanol droplets impacting onto solid substrates with varying degrees of roughness. High speed imaging is used to extract the dynamic contact angle as a function of the spreading speed for these impacting droplets. During the spreading phase, the dynamic contact angle achieves an asymptotic maximum value, which depends on the substrate roughness and the liquid properties. We found that this maximum dynamic contact angle, together with the liquid properties, the ratio of the peak to peak roughness and the surface feature mean width, determines the splashing to no-splashing threshold. In addition, these parameters consistently differentiate the splashing behaviour of impacts onto smooth hydrophilic, hydrophobic and superhydrophobic surfaces

The Role of the Dynamic Contact Angle on Splashing

In this letter we study the splashing behaviour of droplets upon impact onto a variety of substrates with different wetting properties, ranging from hydrophilic to super-hydrophobic surfaces. In particular, we study the effects of the dynamic contact angle on splashing. The experimental approach uses high-speed imaging and image analysis to recover the apparent contact angle as a function of the spreading speed. Our results show that neither the Capillary number nor the so-called splashing parameter are appropriate to characterise the splashing behaviour under these circumstances. However, we show that the maximum dynamic advancing contact angle and the splashing ratio β adequately characterise the splashing behaviour

Large emissions from floodplain trees close the Amazon methane budget

Wetlands are the largest global source of atmospheric methane (CH4), a potent greenhouse gas. However, methane emission inventories from the Amazon floodplain, the largest natural geographic source of CH4 in the tropics, consistently underestimate the atmospheric burden of CH4 determined via remote sensing and inversion modelling, pointing to a major gap in our understanding of the contribution of these ecosystems to CH4 emissions. Here we report CH4 fluxes from the stems of 2,357 individual Amazonian floodplain trees from 13 locations across the central Amazon basin. We find that escape of soil gas through wetland trees is the dominant source of regional CH4 emissions. Methane fluxes from Amazon tree stems were up to 200 times larger than emissions reported for temperate wet forests6 and tropical peat swamp forests, representing the largest non-ebullitive wetland fluxes observed. Emissions from trees had an average stable carbon isotope value (δ13C) of −66.2 ± 6.4 per mil, consistent with a soil biogenic origin. We estimate that floodplain trees emit 15.1 ± 1.8 to 21.2 ± 2.5 teragrams of CH4 a year, in addition to the 20.5 ± 5.3 teragrams a year emitted regionally from other sources. Furthermore, we provide a ‘top-down’ regional estimate of CH4 emissions of 42.7 ± 5.6 teragrams of CH4 a year for the Amazon basin, based on regular vertical lower-troposphere CH4 profiles covering the period 2010–2013. We find close agreement between our ‘top-down’ and combined ‘bottom-up’ estimates, indicating that large CH4 emissions from trees adapted to permanent or seasonal inundation can account for the emission source that is required to close the Amazon CH4 budget. Our findings demonstrate the importance of tree stem surfaces in mediating approximately half of all wetland CH4 emissions in the Amazon floodplain, a region that represents up to one-third of the global wetland CH4 source when trees are combined with other emission sources

Master regulators of FGFR2 signalling and breast cancer risk.

The fibroblast growth factor receptor 2 (FGFR2) locus has been consistently identified as a breast cancer risk locus in independent genome-wide association studies. However, the molecular mechanisms underlying FGFR2-mediated risk are still unknown. Using model systems we show that FGFR2-regulated genes are preferentially linked to breast cancer risk loci in expression quantitative trait loci analysis, supporting the concept that risk genes cluster in pathways. Using a network derived from 2,000 transcriptional profiles we identify SPDEF, ERα, FOXA1, GATA3 and PTTG1 as master regulators of fibroblast growth factor receptor 2 signalling, and show that ERα occupancy responds to fibroblast growth factor receptor 2 signalling. Our results indicate that ERα, FOXA1 and GATA3 contribute to the regulation of breast cancer susceptibility genes, which is consistent with the effects of anti-oestrogen treatment in breast cancer prevention, and suggest that fibroblast growth factor receptor 2 signalling has an important role in mediating breast cancer risk.This is the final version of the article. It was originally published in Nature Communications here: http://www.nature.com/ncomms/2013/130917/ncomms3464/full/ncomms3464.html

Dioxin Toxicity In Vivo Results from an Increase in the Dioxin-Independent Transcriptional Activity of the Aryl Hydrocarbon Receptor

The Aryl hydrocarbon receptor (Ahr) is the nuclear receptor mediating the toxicity of dioxins -widespread and persistent pollutants whose toxic effects include tumor promotion, teratogenesis, wasting syndrome and chloracne. Elimination of Ahr in mice eliminates dioxin toxicity but also produces adverse effects, some seemingly unrelated to dioxin. Thus the relationship between the toxic and dioxin-independent functions of Ahr is not clear, which hampers understanding and treatment of dioxin toxicity. Here we develop a Drosophila model to show that dioxin actually increases the in vivo dioxin-independent activity of Ahr. This hyperactivation resembles the effects caused by an increase in the amount of its dimerisation partner Ahr nuclear translocator (Arnt) and entails an increased transcriptional potency of Ahr, in addition to the previously described effect on nuclear translocation. Thus the two apparently different functions of Ahr, dioxin-mediated and dioxin-independent, are in fact two different levels (hyperactivated and basal, respectively) of a single function

Relationship between length of exposure to trauma and mental illness in the police

Introduction: The activities of the police are considered high risk, because they are exposed to high levels of physical and emotional stress. These work activities can contribute to the emergence of psychiatric disorders that affect their readiness in responding to threats and safety of their actions. Our aim was to conduct a systematic literature review to identify studies that evaluated the time that police officers may be deployed without developing a mental illness. Materials and Methods: Articles published until May 2016 in The MEDLINE (PubMed), Cochrane Library, PsycINFO, and Lilacs databases were searched. In addition, a manual search in the gray literature (theses and dissertations) was also conducted. Several combinations of indexed terms were used in the search of electronic databases, including terms referring to trauma exposure, intervention, and population. There were no restrictions on date and language of the publications. Two reviewers independently assessed studies for eligibility and quality. Disagreements were resolved after consultations with a third reviewer. Results: Of 905 selected studies, 13 studies evaluated deployment duration and the incidence of mental illness. Studies were excluded because they addressed the prevalence of mental illness but did not relate it to deployment duration or because the studied sample was not the target population of the present study. Studies have shown that a longer deployment time is associated with increased incidence of mental illness. Our analysis of the 13 identified studies indicated the existence of an association between exposure to deployment and mental illness onset. Conclusion: These findings will be useful to inform and guide future studies conducted in Brazil and worldwide

LEMUR: Large European Module for solar Ultraviolet Research. European contribution to JAXA's Solar-C mission

Understanding the solar outer atmosphere requires concerted, simultaneous solar observations from the visible to the vacuum ultraviolet (VUV) and soft X-rays, at high spatial resolution (between 0.1" and 0.3"), at high temporal resolution (on the order of 10 s, i.e., the time scale of chromospheric dynamics), with a wide temperature coverage (0.01 MK to 20 MK, from the chromosphere to the flaring corona), and the capability of measuring magnetic fields through spectropolarimetry at visible and near-infrared wavelengths. Simultaneous spectroscopic measurements sampling the entire temperature range are particularly important. These requirements are fulfilled by the Japanese Solar-C mission (Plan B), composed of a spacecraft in a geosynchronous orbit with a payload providing a significant improvement of imaging and spectropolarimetric capabilities in the UV, visible, and near-infrared with respect to what is available today and foreseen in the near future. The Large European Module for solar Ultraviolet Research (LEMUR), described in this paper, is a large VUV telescope feeding a scientific payload of high-resolution imaging spectrographs and cameras. LEMUR consists of two major components: a VUV solar telescope with a 30 cm diameter mirror and a focal length of 3.6 m, and a focal-plane package composed of VUV spectrometers covering six carefully chosen wavelength ranges between 17 and 127 nm. The LEMUR slit covers 280" on the Sun with 0.14" per pixel sampling. In addition, LEMUR is capable of measuring mass flows velocities (line shifts) down to 2 km/s or better. LEMUR has been proposed to ESA as the European contribution to the Solar C mission.Comment: 35 pages, 14 figures. To appear on Experimental Astronom

Fluids in cosmology

We review the role of fluids in cosmology by first introducing them in General Relativity and then by applying them to a FRW Universe's model. We describe how relativistic and non-relativistic components evolve in the background dynamics. We also introduce scalar fields to show that they are able to yield an inflationary dynamics at very early times (inflation) and late times (quintessence). Then, we proceed to study the thermodynamical properties of the fluids and, lastly, its perturbed kinematics. We make emphasis in the constrictions of parameters by recent cosmological probes.Comment: 34 pages, 4 figures, version accepted as invited review to the book "Computational and Experimental Fluid Mechanics with Applications to Physics, Engineering and the Environment". Version 2: typos corrected and references expande