Fully Automatic Segmentation of Brain Tumor Images using Support Vector Machine Classiffication in Combination with Hierarchical Conditional Random Field Regularization

Delineating brain tumor boundaries from magnetic resonance images is an essential task for the analysis of brain cancer. We propose a fully automatic method for brain tissue segmentation, which combines Support Vector Machine classification using multispectral intensities and textures with subsequent hierarchical regularization based on Conditional Random Fields. The CRF regularization introduces spatial constraints to the powerful SVM classification, which assumes voxels to be independent from their neighbors. The approach first separates healthy and tumor tissue before both regions are subclassified into cerebrospinal fluid, white matter, gray matter and necrotic, active, edema region respectively in a novel hierarchical way. The hierarchical approach adds robustness and speed by allowing to apply different levels of regularization at different stages. The method is fast and tailored to standard clinical acquisition protocols. It was assessed on 10 multispectral patient datasets with results outperforming previous methods in terms of segmentation detail and computation times.

Impaired top-down modulation of saccadic latencies in patients with schizophrenia but not in first-degree relatives

Impaired eye movements have a long history in schizophrenia research and meet the criteria of a reliable biomarker. However, the effects of cognitive load and task difficulty on saccadic latencies (SL) are less understood. Recent studies showed that SL are strongly task dependent: SL are decreased in tasks with higher cognitive demand, and increased in tasks with lower cognitive demand. The present study investigates SL modulation in patients with schizophrenia and their first-degree relatives. A group of 13 patients suffering from ICD-10 schizophrenia, 10 first-degree relatives, and 24 control subjects performed two different types of visual tasks: a color task and a Landolt ring orientation task. We used video-based oculography to measure SL. We found that patients exhibited a similar unspecific SL pattern in the two different tasks, whereas controls and relatives exhibited 20���26% shorter average latencies in the orientation task (higher cognitive demand) compared to the color task (lower cognitive demand). Also, classification performance using support vector machines suggests that relatives should be assigned to the healthy controls and not to the patient group. Therefore, visual processing of different content does not modulate SL in patients with schizophrenia, but modulates SL in the relatives and healthy controls. The results reflect a specific oculomotor attentional dysfunction in patients with schizophrenia that is a potential state marker, possibly caused by impaired top-down disinhibition of the superior colliculus by frontal/prefrontal areas such as the frontal eye fields.

The triplite���triploidite supergroup: structural modulation in wagnerite, discreditation of magniotriplite, and the new mineral hydroxylwagnerite

Electron-microprobe analysis, single-crystal X-ray diffraction with an area detector, and high-resolution transmission electron microscopy show that minerals related to wagnerite, triplite and triploidite, which are monoclinic Mg, Fe and Mn phosphates with the formula Me2+ 2PO4(F,OH), constitute a modulated series based on the average triplite structure. Modulation occurs along b and may be commensurate with (2b periodicity) or incommensurate but generally close to integer values (���3b, ���5b, ���7b, ���9b), i.e. close to polytypic behaviour. As a result, the Mg- and F-dominant minerals magniotriplite and wagnerite can no longer be considered polymorphs of Mg2PO4F, i.e., there is no basis for recognizing them as distinct species. Given that wagnerite has priority (1821 vs. 1951), the name magniotriplite should be discarded in favour of wagnerite. Hydroxylwagnerite, end-member Mg2PO4OH, occurs in pyrope megablasts along with talc, clinochlore, kyanite, rutile and secondary apatite in two samples from lenses of pyrope���kyanite���phengite���quartz-schist within metagranite in the coesite-bearing ultrahigh-pressure metamorphic unit of the Dora-Maira Massif, western Alps, Vallone di Gilba, Val Varaita, Piemonte, Italy. Electron microprobe analyses of holotype hydroxylwagnerite and of the crystal with the lowest F content gave in wt%: P2O5 44.14, 43.99; SiO2 0.28, 0.02; SO3 ���, 0.01; TiO2 0.20, 0.16; Al2O3 0.06, 0.03; MgO 48.82, 49.12; FeO 0.33, 0.48; MnO 0.01, 0.02; CaO 0.12, 0.10; Na2O 0.01, ���; F 5.58, 4.67; H2O (calc) 2.94, 3.36; ���O = F 2.35, 1.97; Sum 100.14, 99.98, corresponding to (Mg1.954Fe0.007Ca0.003Ti0.004Al0.002Na0.001)��=1.971(P1.003Si0.008)��=1.011O4(OH0.526F0.474)��=1 and (Mg1.971Fe0.011Ca0.003Ti0.003Al0.001)��=1.989(P1.002Si0.001)��=1.003O4(OH0.603F0.397)��=1, respectively. Due to the paucity of material, H2O could not be measured, so OH was calculated from the deficit in F assuming stoichiometry, i.e., by assuming F + OH = 1 per formula unit. Holotype hydroxylwagnerite is optically biaxial (+), �� 1.584(1), �� 1.586(1), �� 1.587(1) (589 nm); 2V Z(meas.) = 43(2)��; orientation Y = b. Single-crystal X-ray diffraction gives monoclinic symmetry, space group P21/c, a = 9.646(3) ��, b = 12.7314(16) ��, c = 11.980(4) ��, �� = 108.38(4) , V = 1396.2(8) ��3, Z = 16, i.e., hydroxylwagnerite is the OH-dominant analogue of wagnerite [��-Mg2PO4(OH)] and a high-pressure polymorph of althausite, holtedahlite, and ��- and ��-Mg2PO4(OH). We suggest that the group of minerals related to wagnerite, triplite and triploidite constitutes a triplite���triploidite super-group that can be divided into F-dominant phosphates (triplite group), OH-dominant phosphates (triploidite group), O-dominant phosphates (stan��kite group) and an OH-dominant arsenate (sarkinite). The distinction among the three groups and a potential fourth group is based only on chemical features, i.e., occupancy of anion or cation sites. The structures of these minerals are all based on the average triplite structure, with a modulation controlled by the ratio of Mg, Fe2+, Fe3+ and Mn2+ ionic radii to (O,OH,F) ionic radii.

Space debris attitude simulation - ��OTA (In-Orbit Tumbling Analysis)

Today, there is little knowledge on the attitude state of decommissioned intact objects in Earth orbit. Observational means have advanced in the past years, but are still limited with respect to an accurate estimate of motion vector orientations and magnitude. Especially for the preparation of Active Debris Removal (ADR) missions as planned by ESA���s Clean Space initiative or contingency scenarios for ESA spacecraft like ENVISAT, such knowledge is needed. ESA's ���Debris Attitude Motion Measurements and Modelling��� project (ESA Contract No. 40000112447), led by the Astronomical Institute of the University of Bern (AIUB), addresses this problem. The goal of the project is to achieve a good understanding of the attitude evolution and the considerable internal and external effects which occur. To characterize the attitude state of selected targets in LEO and GTO, multiple observation methods are combined. Optical observations are carried out by AIUB, Satellite Laser Ranging (SLR) is performed by the Space Research Institute of the Austrian Academy of Sciences (IWF) and radar measurements and signal level determination are provided by the Fraunhofer Institute for High Frequency Physics and Radar Techniques (FHR). The In-Orbit Tumbling Analysis tool (��OTA) is a prototype software, currently in development by Hyperschall Technologie G��ttingen GmbH (HTG) within the framework of the project. ��OTA will be a highly modular software tool to perform short-(days), medium-(months) and long-term (years) propagation of the orbit and attitude motion (six degrees-of-freedom) of spacecraft in Earth orbit. The simulation takes into account all relevant acting forces and torques, including aerodynamic drag, solar radiation pressure, gravitational influences of Earth, Sun and Moon, eddy current damping, impulse and momentum transfer from space debris or micro meteoroid impact, as well as the optional definition of particular spacecraft specific influences like tank sloshing, reaction wheel behaviour, magnetic torquer activity and thruster firing. The purpose of ��OTA is to provide high accuracy short-term simulations to support observers and potential ADR missions, as well as medium-and long-term simulations to study the significance of the particular internal and external influences on the attitude, especially damping factors and momentum transfer. The simulation will also enable the investigation of the altitude dependency of the particular external influences. ��OTA's post-processing modules will generate synthetic measurements for observers and for software validation. The validation of the software will be done by cross-calibration with observations and measurements acquired by the project partners.

Search for Event Rate Modulation in XENON100 Electronic Recoil Data

We have searched for periodic variations of the electronic recoil event rate in the (2-6) keV energy range recorded between February 2011 and March 2012 with the XENON100 detector, adding up to 224.6 live days in total. Following a detailed study to establish the stability of the detector and its background contributions during this run, we performed an un-binned profile likelihood analysis to identify any periodicity up to 500 days. We find a global significance of less than 1 sigma for all periods suggesting no statistically significant modulation in the data. While the local significance for an annual modulation is 2.8 sigma, the analysis of a multiple-scatter control sample and the phase of the modulation disfavor a dark matter interpretation. The DAMA/LIBRA annual modulation interpreted as a dark matter signature with axial-vector coupling of WIMPs to electrons is excluded at 4.8 sigma.

Interstellar neutral helium in the heliosphere from Interstellar Boundary Explorer observations. III. Mach number of the flow, velocity vector, and temperature from the first six years of measurements

We analyzed observations of interstellar neutral helium (ISN He) obtained from the Interstellar Boundary Explorer (IBEX) satellite during its first six years of operation. We used a refined version of the ISN He simulation model, presented in the companion paper by Sokol et al. (2015b), along with a sophisticated data correlation and uncertainty system and parameter fitting method, described in the companion paper by Swaczyna et al. We analyzed the entire data set together and the yearly subsets, and found the temperature and velocity vector of ISN He in front of the heliosphere. As seen in the previous studies, the allowable parameters are highly correlated and form a four-dimensional tube in the parameter space. The inflow longitudes obtained from the yearly data subsets show a spread of similar to 6 degrees, with the other parameters varying accordingly along the parameter tube, and the minimum chi(2) value is larger than expected. We found, however, that the Mach number of the ISN He flow shows very little scatter and is thus very tightly constrained. It is in excellent agreement with the original analysis of ISN He observations from IBEX and recent reanalyses of observations from Ulysses. We identify a possible inaccuracy in the Warm Breeze parameters as the likely cause of the scatter in the ISN He parameters obtained from the yearly subsets, and we suppose that another component may exist in the signal or a process that is not accounted for in the current physical model of ISN He in front of the heliosphere. From our analysis, the inflow velocity vector, temperature, and Mach number of the flow are equal to lambda(ISNHe) = 255 degrees.8 +/- 0 degrees.5, beta(ISNHe) = 5 degrees.16 +/- 0 degrees.10, T-ISNHe = 7440 +/- 260 K, nu(SNHe) = 25.8 +/- 0.4 km s(-1), and M-ISNHe = 5.079 +/- 0.028, with uncertainties strongly correlated along the parameter tube.

A versatile toolkit to produce sensitive FRET biosensors to visualize signaling in time and space

Genetically encoded, ratiometric biosensors based on fluorescence resonance energy transfer (FRET) are powerful tools to study the spatiotemporal dynamics of cell signaling. However, many biosensors lack sensitivity. We present a biosensor library that contains circularly permutated mutants for both the donor and acceptor fluorophores, which alter the orientation of the dipoles and thus better accommodate structural constraints imposed by different signaling molecules while maintaining FRET efficiency. Our strategy improved the brightness and dynamic range of preexisting RhoA and extracellular signal-regulated protein kinase (ERK) biosensors. Using the improved RhoA biosensor, we found micrometer-sized zones of RhoA activity at the tip of F-actin bundles in growth cone filopodia during neurite extension, whereas RhoA was globally activated throughout collapsing growth cones. RhoA was also activated in filopodia and protruding membranes at the leading edge of motile fibroblasts. Using the improved ERK biosensor, we simultaneously measured ERK activation dynamics in multiple cells using low-magnification microscopy and performed in vivo FRET imaging in zebrafish. Thus, we provide a construction toolkit consisting of a vector set, which enables facile generation of sensitive biosensors.