CellH5: a format for data exchange in high-content screening

Summary: High-throughput microscopy data require a diversity of analytical approaches. However, the construction of workflows that use algorithms from different software packages is difficult owing to a lack of interoperability. To overcome this limitation, we present CellH5, an HDF5 data format for cell-based assays in high-throughput microscopy, which stores high-dimensional image data along with inter-object relations in graphs. CellH5Browser, an interactive gallery image browser, demonstrates the versatility and performance of the file format on live imaging data of dividing human cells. CellH5 provides new opportunities for integrated data analysis by multiple software platforms. Availability: Source code is freely available at www.github.com/cellh5 under the GPL license and at www.bioconductor.org/packages/release/bioc/html/rhdf5.html under the Artistic-2.0 license. Demo datasets and the CellH5Browser are available at www.cellh5.org. A Fiji importer for cellh5 will be released soon. Contact: [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

On the Nature of Small Planets around the Coolest Kepler Stars

We constrain the densities of Earth- to Neptune-size planets around very cool (Te =3660-4660K) Kepler stars by comparing 1202 Keck/HIRES radial velocity measurements of 150 nearby stars to a model based on Kepler candidate planet radii and a power-law mass-radius relation. Our analysis is based on the presumption that the planet populations around the two sets of stars are the same. The model can reproduce the observed distribution of radial velocity variation over a range of parameter values, but, for the expected level of Doppler systematic error, the highest Kolmogorov-Smirnov probabilities occur for a power-law index alpha ~ 4, indicating that rocky-metal planets dominate the planet population in this size range. A single population of gas-rich, low-density planets with alpha = 2 is ruled out unless our Doppler errors are >= 5m/s, i.e., much larger than expected based on observations and stellar chromospheric emission. If small planets are a mix of gamma rocky planets (alpha = 3.85) and 1-gamma gas-rich planets (alpha = 2), then gamma > 0.5 unless Doppler errors are >=4 m/s. Our comparison also suggests that Kepler's detection efficiency relative to ideal calculations is less than unity. One possible source of incompleteness is target stars that are misclassified subgiants or giants, for which the transits of small planets would be impossible to detect. Our results are robust to systematic effects, and plausible errors in the estimated radii of Kepler stars have only moderate impact.Comment: Accepted to the Astrophysical Journa

The impact of a ten-week physical exercise program on health-related quality of life in patients with inflammatory bowel disease: A prospective randomized controlled trial

BACKGROUND Improving health-related quality of life is a primary target of therapy for patients with inflammatory bowel disease. Physical activity has been demonstrated to improve health-related quality of life in several patient populations with chronic disease. There are very few studies investigating the effects of physical activity on health-related quality of life in inflammatory bowel disease. The primary purpose of this study is to investigate the effects of 10 weeks of moderate physical activity on health-related quality of life in patients with inflammatory bowel disease. METHODS Thirty patients with mild to moderate IBD (Crohn's Disease Activity Index (CDAI) \textless220 or Rachmilewitz Index (RI) \textless11) were randomized 1:1 to either supervised moderate-intensity running thrice a week for 10 weeks or a control group who were not prescribed any exercise. Health-related quality of life, symptoms, and inflammation were assessed at baseline and after 10 weeks. RESULTS Participants were 41 ± 14 years (73% female), had a body mass index of 22.8 ± 4.1 kg/m(2), and an average CDAI or RI of 66.8 ± 42.4 and 3.6 ± 3.1. No adverse events occurred during the 10-week training period. Health-related quality of life, reported as IBDQ total score, improved 19% in the intervention group and 8% in the control group. Scores for the IBDQ social sub-scale were significantly improved in the intervention group compared with controls (\textgreekDIBDQsocial = 6.27 ± 5.46 vs. 1.87 ± 4.76, p = 0.023). CONCLUSION Patients suffering from moderately active IBD are capable of performing symptom-free regular endurance exercise. Our data support the assumption that PA is feasible in IBD patients. PA may furthermore improve quality of life through improvements in social well-being, and may, therefore, be a useful adjunct to IBD therapy

Simultaneous Morphological and Flow Imaging Enabled by Megahertz Intravascular Doppler Optical Coherence Tomography

We demonstrate three-dimensional intravascular flow imaging compatible with routine clinical image acquisition workflow by means of megahertz (MHz) intravascular Doppler Optical Coherence Tomography (OCT). The OCT system relies on a 1.1 mm diameter motorized imaging catheter and a 1.5 MHz Fourier Domain Mode Locked (FDML) laser. Using a post processing method to compensate the drift of the FDML laser output, we can resolve the Doppler phase shift between two adjoining OCT A-line datasets. By interpretation of the velocity field as measured around the zero phase shift, the flow direction at specific angles can be qualitatively estimated. Imaging experiments were carried out in phantoms, micro channels, and swine coronary artery in vitro at a speed of 600 frames/s. The MHz wavelength sweep rate of the OCT system allows us to directly investigate flow velocity of up to 37.5 cm/s while computationally expensive phase-unwrapping has to be applied to measure such high speed using conventional OCT system. The MHz sweep rate also enables a volumetric Doppler imaging even with a fast pullback at 40 mm/s. We present the first simultaneously recorded 3D morphological images and Doppler flow profiles. Flow pattern estimation and three-dimensional structural reconstruction of entire coronary artery are achieved using a single OCT pullback dataset

Discovery and Validation of Kepler-452b: A 1.6-Re Super Earth Exoplanet in the Habitable Zone of a G2 Star

We report on the discovery and validation of Kepler-452b, a transiting planet identified by a search through the 4 years of data collected by NASA's Kepler Mission. This possibly rocky 1.63$^{+0.23}_{-0.20}$ R$_\oplus$ planet orbits its G2 host star every 384.843$^{+0.007}_{0.012}$ days, the longest orbital period for a small (R$_p$ < 2 R$_\oplus$) transiting exoplanet to date. The likelihood that this planet has a rocky composition lies between 49% and 62%. The star has an effective temperature of 5757$\pm$85 K and a log g of 4.32$\pm$0.09. At a mean orbital separation of 1.046$^{+0.019}_{-0.015}$ AU, this small planet is well within the optimistic habitable zone of its star (recent Venus/early Mars), experiencing only 10% more flux than Earth receives from the Sun today, and slightly outside the conservative habitable zone (runaway greenhouse/maximum greenhouse). The star is slightly larger and older than the Sun, with a present radius of 1.11$^{+0.15}_{-0.09}$ R$_\odot$ and an estimated age of 6 Gyr. Thus, Kepler-452b has likely always been in the habitable zone and should remain there for another 3 Gyr.Comment: 19 pages, 16 figure

Cornering New Physics in b --> s Transitions

We derive constraints on Wilson coefficients of dimension-six effective operators probing the b --> s transition, using recent improved measurements of the rare decays Bs --> mu+mu-, B --> K mu+mu- and B --> K* mu+mu- and including all relevant observables in inclusive and exclusive decays. We consider operators present in the SM as well as their chirality-flipped counterparts and scalar operators. We find good agreement with the SM expectations. Compared to the situation before winter 2012, we find significantly more stringent constraints on the chirality-flipped coefficients due to complementary constraints from B --> K mu+mu- and B --> K* mu+mu- and due to the LHCb measurement of the angular observable S_3 in the latter decay. We also list the full set of observables sensitive to new physics in the low recoil region of B --> K* mu+mu-.Comment: 18 pages, 6 figures, 4 tables. v3: typos correcte

Thermo-elastic optical coherence tomography

The absorption of nanosecond laser pulses induces rapid thermo-elastic deformation in tissue. A sub-micrometer scale displacement occurs within a few microseconds after the pulse arrival. In this Letter, we investigate the laser-induced thermo-elastic deformation using a 1.5 MHz phase-sensitive optical coherence tomography (OCT) system. A displacement image can be reconstructed, which enables a new modality of phase-sensitive OCT, called thermo-elastic OCT. An analysis of the results shows that the optical absorption is a dominating factor for the displacement. Thermo-elastic OCT is capable of visualizing inclusions that do not appear on the structural OCT image, providing additional tissue type information

Model-independent constraints on new physics in b --> s transitions

We provide a comprehensive model-independent analysis of rare decays involving the b --> s transition to put constraints on dimension-six Delta(F)=1 effective operators. The constraints are derived from all the available up-to-date experimental data from the B-factories, CDF and LHCb. The implications and future prospects for observables in b --> s l+l- and b --> s nu nu transitions in view of improved measurements are also investigated. The present work updates and generalises previous studies providing, at the same time, a useful tool to test the flavour structure of any theory beyond the SM.Comment: 1+39 pages, 12 figures, 3 tables. v2: minor modifications, typos corrected, references added, version to be published in JHE

Planetary Candidates Observed by Kepler. VII. The First Fully Uniform Catalog Based on The Entire 48 Month Dataset (Q1-Q17 DR24)

We present the seventh Kepler planet candidate catalog, which is the first to be based on the entire, uniformly processed, 48 month Kepler dataset. This is the first fully automated catalog, employing robotic vetting procedures to uniformly evaluate every periodic signal detected by the Q1-Q17 Data Release 24 (DR24) Kepler pipeline. While we prioritize uniform vetting over the absolute correctness of individual objects, we find that our robotic vetting is overall comparable to, and in most cases is superior to, the human vetting procedures employed by past catalogs. This catalog is the first to utilize artificial transit injection to evaluate the performance of our vetting procedures and quantify potential biases, which are essential for accurate computation of planetary occurrence rates. With respect to the cumulative Kepler Object of Interest (KOI) catalog, we designate 1,478 new KOIs, of which 402 are dispositioned as planet candidates (PCs). Also, 237 KOIs dispositioned as false positives (FPs) in previous Kepler catalogs have their disposition changed to PC and 118 PCs have their disposition changed to FP. This brings the total number of known KOIs to 8,826 and PCs to 4,696. We compare the Q1-Q17 DR24 KOI catalog to previous KOI catalogs, as well as ancillary Kepler catalogs, finding good agreement between them. We highlight new PCs that are both potentially rocky and potentially in the habitable zone of their host stars, many of which orbit solar-type stars. This work represents significant progress in accurately determining the fraction of Earth-size planets in the habitable zone of Sun-like stars. The full catalog is publicly available at the NASA Exoplanet Archive.Comment: Accepted to the Astrophysical Journal Supplement Series. 30 pages, 9 figures, 7 tables. We make the DR24 robovetter decision code publicly available at http://github.com/JeffLCoughlin/robovetter, with input and output examples provided using the same data as contained in the full paper's table