MRBrainS Challenge: Online Evaluation Framework for Brain Image Segmentation in 3T MRI Scans

Many methods have been proposed for tissue segmentation in brain MRI scans. The multitude of methods proposed complicates the choice of one method above others. We have therefore established the MRBrainS online evaluation framework for evaluating (semi) automatic algorithms that segment gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) on 3T brain MRI scans of elderly subjects (65-80 y). Participants apply their algorithms to the provided data, after which their results are evaluated and ranked. Full manual segmentations of GM, WM, and CSF are available for all scans and used as the reference standard. Five datasets are provided for training and fifteen for testing. The evaluated methods are ranked based on their overall performance to segment GM, WM, and CSF and evaluated using three evaluation metrics (Dice, H95, and AVD) and the results are published on the MRBrainS13 website. We present the results of eleven segmentation algorithms that participated in the MRBrainS13 challenge workshop at MICCAI, where the framework was launched, and three commonly used freeware packages: FreeSurfer, FSL, and SPM. The MRBrainS evaluation framework provides an objective and direct comparison of all evaluated algorithms and can aid in selecting the best performing method for the segmentation goal at hand.This study was financially supported by IMDI Grant 104002002 (Brainbox) from ZonMw, the Netherlands Organisation for Health Research and Development, within kind sponsoring by Philips, the University Medical Center Utrecht, and Eindhoven University of Technology. The authors would like to acknowledge the following members of the Utrecht Vascular Cognitive Impairment Study Group who were not included as coauthors of this paper but were involved in the recruitment of study participants and MRI acquisition at the UMC Utrecht (in alphabetical order by department): E. van den Berg, M. Brundel, S. Heringa, and L. J. Kappelle of the Department of Neurology, P. R. Luijten and W. P. Th. M. Mali of the Department of Radiology, and A. Algra and G. E. H. M. Rutten of the Julius Center for Health Sciences and Primary Care. The research of Geert Jan Biessels and the VCI group was financially supported by VIDI Grant 91711384 from ZonMw and by Grant 2010T073 of the Netherlands Heart Foundation. The research of Jeroen de Bresser is financially supported by a research talent fellowship of the University Medical Center Utrecht (Netherlands). The research of Annegreet van Opbroek and Marleen de Bruijne is financially supported by a research grant from NWO (the Netherlands Organisation for Scientific Research). The authors would like to acknowledge MeVis Medical Solutions AG (Bremen, Germany) for providing MeVisLab. Duygu Sarikaya and Liang Zhao acknowledge their Advisor Professor Jason Corso for his guidance. Duygu Sarikaya is supported by NIH 1 R21CA160825-01 and Liang Zhao is partially supported by the China Scholarship Council (CSC).info:eu-repo/semantics/publishedVersio

A Neptune-sized transiting planet closely orbiting a 5–10-million-year-old star

Theories of the formation and early evolution of planetary systems postulate that planets are born in circumstellar disks, and undergo radial migration during and after dissipation of the dust and gas disk from which they formed^1, 2. The precise ages of meteorites indicate that planetesimals—the building blocks of planets—are produced within the first million years of a star’s life^3. Fully formed planets are frequently detected on short orbital periods around mature stars. Some theories suggest that the in situ formation of planets close to their host stars is unlikely and that the existence of such planets is therefore evidence of large-scale migration^4, 5. Other theories posit that planet assembly at small orbital separations may be common^6, 7, 8. Here we report a newly born, transiting planet orbiting its star with a period of 5.4 days. The planet is 50 per cent larger than Neptune, and its mass is less than 3.6 times that of Jupiter (at 99.7 per cent confidence), with a true mass likely to be similar to that of Neptune. The star is 5–10 million years old and has a tenuous dust disk extending outward from about twice the Earth–Sun separation, in addition to the fully formed planet located at less than one-twentieth of the Earth–Sun separation

Effectiveness of classroom based crew resource management training in the intensive care unit: study design of a controlled trial

<p>Abstract</p> <p>Background</p> <p>Crew resource management (CRM) has the potential to enhance patient safety in intensive care units (ICU) by improving the use of non-technical skills. However, CRM evaluation studies in health care are inconclusive with regard to the effect of this training on behaviour and organizational outcomes, due to weak study designs and the scarce use of direct observations. Therefore, the aim of this study is to determine the effectiveness and cost-effectiveness of CRM training on attitude, behaviour and organization after one year, using a multi-method approach and matched control units. The purpose of the present article is to describe the study protocol and the underlying choices of this evaluation study of CRM in the ICU in detail.</p> <p>Methods/Design</p> <p>Six ICUs participated in a paired controlled trial, with one pre-test and two post test measurements (respectively three months and one year after the training). Three ICUs were trained and compared to matched control ICUs. The 2-day classroom-based training was delivered to multidisciplinary groups. Typical CRM topics on the individual, team and organizational level were discussed, such as situational awareness, leadership and communication. All levels of Kirkpatrick's evaluation framework (reaction, learning, behaviour and organisation) were assessed using questionnaires, direct observations, interviews and routine ICU administration data.</p> <p>Discussion</p> <p>It is expected that the CRM training acts as a generic intervention that stimulates specific interventions. Besides effectiveness and cost-effectiveness, the assessment of the barriers and facilitators will provide insight in the implementation process of CRM.</p> <p>Trial registration</p> <p>Netherlands Trial Register (NTR): <a href="http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=1976">NTR1976</a></p

Disease-Associated Mutations That Alter the RNA Structural Ensemble

Genome-wide association studies (GWAS) often identify disease-associated mutations in intergenic and non-coding regions of the genome. Given the high percentage of the human genome that is transcribed, we postulate that for some observed associations the disease phenotype is caused by a structural rearrangement in a regulatory region of the RNA transcript. To identify such mutations, we have performed a genome-wide analysis of all known disease-associated Single Nucleotide Polymorphisms (SNPs) from the Human Gene Mutation Database (HGMD) that map to the untranslated regions (UTRs) of a gene. Rather than using minimum free energy approaches (e.g. mFold), we use a partition function calculation that takes into consideration the ensemble of possible RNA conformations for a given sequence. We identified in the human genome disease-associated SNPs that significantly alter the global conformation of the UTR to which they map. For six disease-states (Hyperferritinemia Cataract Syndrome, β-Thalassemia, Cartilage-Hair Hypoplasia, Retinoblastoma, Chronic Obstructive Pulmonary Disease (COPD), and Hypertension), we identified multiple SNPs in UTRs that alter the mRNA structural ensemble of the associated genes. Using a Boltzmann sampling procedure for sub-optimal RNA structures, we are able to characterize and visualize the nature of the conformational changes induced by the disease-associated mutations in the structural ensemble. We observe in several cases (specifically the 5′ UTRs of FTL and RB1) SNP–induced conformational changes analogous to those observed in bacterial regulatory Riboswitches when specific ligands bind. We propose that the UTR and SNP combinations we identify constitute a “RiboSNitch,” that is a regulatory RNA in which a specific SNP has a structural consequence that results in a disease phenotype. Our SNPfold algorithm can help identify RiboSNitches by leveraging GWAS data and an analysis of the mRNA structural ensemble

Pulsations in main sequence OBAF-type stars

CONTEXT: The third Gaia data release provides photometric time series covering 34 months for about 10 million stars. For many of those stars, a characterisation in Fourier space and their variability classification are also provided. This paper focuses on intermediate- to high-mass (IHM) main sequence pulsators (M ≥  1.3 M⊙) of spectral types O, B, A, or F, known as β Cep, slowly pulsating B (SPB), δ Sct, and γ Dor stars. These stars are often multi-periodic and display low amplitudes, making them challenging targets to analyse with sparse time series. AIMS: We investigate the extent to which the sparse Gaia DR3 data can be used to detect OBAF-type pulsators and discriminate them from other types of variables. We aim to probe the empirical instability strips and compare them with theoretical predictions. The most populated variability class is that of the δ Sct variables. For these stars, we aim to confirm their empirical period-luminosity (PL) relation, and verify the relation between their oscillation amplitude and rotation. METHODS: All datasets used in this analysis are part of the Gaia DR3 data release. The photometric time series were used to perform a Fourier analysis, while the global astrophysical parameters necessary for the empirical instability strips were taken from the Gaia DR3 gspphot tables, and the v sin i data were taken from the Gaia DR3 esphs tables. The δ Sct PL relation was derived using the same photometric parallax method as the one recently used to establish the PL relation for classical Cepheids using Gaia data. RESULTS: We show that for nearby OBAF-type pulsators, the Gaia DR3 data are precise and accurate enough to pinpoint them in the Hertzsprung-Russell (HR) diagram. We find empirical instability strips covering broader regions than theoretically predicted. In particular, our study reveals the presence of fast rotating gravity-mode pulsators outside the strips, as well as the co-existence of rotationally modulated variables inside the strips as reported before in the literature. We derive an extensive period–luminosity relation for δ Sct stars and provide evidence that the relation features different regimes depending on the oscillation period. We demonstrate how stellar rotation attenuates the amplitude of the dominant oscillation mode of δ Sct stars. CONCLUSIONS: The Gaia DR3 time-series photometry already allows for the detection of the dominant (non-)radial oscillation mode in about 100 000 intermediate- and high-mass dwarfs across the entire sky. This detection capability will increase as the time series becomes longer, allowing the additional delivery of frequencies and amplitudes of secondary pulsation modes

Gaia Data Release 3: Mapping the asymmetric disc of the Milky Way

With the most recent Gaia data release the number of sources with complete 6D phase space information (position and velocity) has increased to well over 33 million stars, while stellar astrophysical parameters are provided for more than 470 million sources, in addition to the identification of over 11 million variable stars. Using the astrophysical parameters and variability classifications provided in Gaia DR3, we select various stellar populations to explore and identify non-axisymmetric features in the disc of the Milky Way in both configuration and velocity space. Using more about 580 thousand sources identified as hot OB stars, together with 988 known open clusters younger than 100 million years, we map the spiral structure associated with star formation 4-5 kpc from the Sun. We select over 2800 Classical Cepheids younger than 200 million years, which show spiral features extending as far as 10 kpc from the Sun in the outer disc. We also identify more than 8.7 million sources on the red giant branch (RGB), of which 5.7 million have line-of-sight velocities, allowing the velocity field of the Milky Way to be mapped as far as 8 kpc from the Sun, including the inner disc. The spiral structure revealed by the young populations is consistent with recent results using Gaia EDR3 astrometry and source lists based on near infrared photometry, showing the Local (Orion) arm to be at least 8 kpc long, and an outer arm consistent with what is seen in HI surveys, which seems to be a continuation of the Perseus arm into the third quadrant. Meanwhile, the subset of RGB stars with velocities clearly reveals the large scale kinematic signature of the bar in the inner disc, as well as evidence of streaming motions in the outer disc that might be associated with spiral arms or bar resonances. (abridged

Phylogeography and epidemic history of hepatitis C virus genotype 4 in Africa

HCV genotype 4 is prevalent in many African countries, yet little is known about the genotype׳s epidemic history on the continent. We present a comprehensive study of the molecular epidemiology of genotype 4. To address the deficit of data from the Democratic Republic of the Congo (DRC) we PCR amplified 60 new HCV isolates from the DRC, resulting in 33 core- and 48 NS5B-region sequences. Our data, together with genotype 4 database sequences, were analysed using Bayesian phylogenetic approaches. We find three well-supported intra-genotypic lineages and estimate that the genotype 4 common ancestor existed around 1733 (1650-1805). We show that genotype 4 originated in central Africa and that multiple lineages have been exported to north Africa since ~1850, including subtype 4a which dominates the epidemic in Egypt. We speculate on the causes of the historical intra-continental spread of genotype 4, including population movements during World War 2

Gaia Data Release 3 The extragalactic content⋆

The Gaia Galactic survey mission is designed and optimized to obtain astrometry, photometry, and spectroscopy of nearly two billion stars in our Galaxy. Yet as an all-sky multi-epoch survey, Gaia also observes several million extragalactic objects down to a magnitude of G ∼ 21 mag. Due to the nature of the Gaia onboard-selection algorithms, these are mostly point-source-like objects. Using data provided by the satellite, we have identified quasar and galaxy candidates via supervised machine learning methods, and estimate their redshifts using the low resolution BP/RP spectra. We further characterise the surface brightness profiles of host galaxies of quasars and of galaxies from pre-defined input lists. Here we give an overview of the processing of extragalactic objects, describe the data products in Gaia DR3, and analyse their properties. Two integrated tables contain the main results for a high completeness, but low purity (50−70%), set of 6.6 million candidate quasars and 4.8 million candidate galaxies. We provide queries that select purer sub-samples of these containing 1.9 million probable quasars and 2.9 million probable galaxies (both ∼95% purity). We also use high quality BP/RP spectra of 43 thousand high probability quasars over the redshift range 0.05−4.36 to construct a composite quasar spectrum spanning restframe wavelengths from 72−1000 nm

Gaia Data Release 3: Chemical cartography of the Milky Way

Context. The motion of stars has been used to reveal details of the complex history of the Milky Way, in constant interaction with its environment. Nevertheless, to reconstruct the Galactic history puzzle in its entirety, the chemo-physical characterisation of stars is essential. Previous Gaia data releases were supported by a smaller, heterogeneous, and spatially biased mixture of chemical data from ground-based observations. Aims. Gaia Data Release 3 opens a new era of all-sky spectral analysis of stellar populations thanks to the nearly 5.6 million stars observed by the Radial Velocity Spectrometer (RVS) and parametrised by the GSP-Spec module. In this work, we aim to demonstrate the scientific quality of Gaia’s Milky Way chemical cartography through a chemo-dynamical analysis of disc and halo populations. Methods. Stellar atmospheric parameters and chemical abundances provided by Gaia DR3 spectroscopy are combined with DR3 radial velocities and EDR3 astrometry to analyse the relationships between chemistry and Milky Way structure, stellar kinematics, and orbital parameters. Results. The all-sky Gaia chemical cartography allows a powerful and precise chemo-dynamical view of the Milky Way with unprecedented spatial coverage and statistical robustness. First, it reveals the strong vertical symmetry of the Galaxy and the flared structure of the disc. Second, the observed kinematic disturbances of the disc – seen as phase space correlations – and kinematic or orbital substructures are associated with chemical patterns that favour stars with enhanced metallicities and lower [α/Fe] abundance ratios compared to the median values in the radial distributions. This is detected both for young objects that trace the spiral arms and older populations. Several α, iron-peak elements and at least one heavy element trace the thin and thick disc properties in the solar cylinder. Third, young disc stars show a recent chemical impoverishment in several elements. Fourth, the largest chemo-dynamical sample of open clusters analysed so far shows a steepening of the radial metallicity gradient with age, which is also observed in the young field population. Finally, the Gaia chemical data have the required coverage and precision to unveil galaxy accretion debris and heated disc stars on halo orbits through their [α/Fe] ratio, and to allow the study of the chemo-dynamical properties of globular clusters. Conclusions. Gaia DR3 chemo-dynamical diagnostics open new horizons before the era of ground-based wide-field spectroscopic surveys. They unveil a complex Milky Way that is the outcome of an eventful evolution, shaping it to the present day

Gaia Data Release 3 Exploring and mapping the diffuse interstellar band at 862 nm

Context. Diffuse interstellar bands (DIBs) are common interstellar absorption features in spectroscopic observations but their origins remain unclear. DIBs play an important role in the life cycle of the interstellar medium (ISM) and can also be used to trace Galactic structure. Aims. Here, we demonstrate the capacity of the Gaia-Radial Velocity Spectrometer (RVS) in Gaia DR3 to reveal the spatial distribution of the unknown molecular species responsible for the most prominent DIB at 862 nm in the RVS passband, exploring the Galactic ISM within a few kiloparsecs from the Sun. Methods. The DIBs are measured within the GSP-Spec module using a Gaussian profile fit for cool stars and a Gaussian process for hot stars. In addition to the equivalent widths and their uncertainties, Gaia DR3 provides their characteristic central wavelength, width, and quality flags. Results. We present an extensive sample of 476 117 individual DIB measurements obtained in a homogeneous way covering the entire sky. We compare spatial distributions of the DIB carrier with interstellar reddening and find evidence that DIB carriers are present in a local bubble around the Sun which contains nearly no dust. We characterised the DIB equivalent width with a local density of 0.19 ± 0.04 Å kpc−1 and a scale height of 98.60−8.46+11.10 pc. The latter is smaller than the dust scale height, indicating that DIBs are more concentrated towards the Galactic plane. We determine the rest-frame wavelength with unprecedented precision (λ0 = 8620.86  ± 0.019 Å in air) and reveal a remarkable correspondence between the DIB velocities and the CO gas velocities, suggesting that the 862 nm DIB carrier is related to macro-molecules. Conclusions. We demonstrate the unique capacity of Gaia to trace the spatial structure of the Galactic ISM using the 862 nm DIB