Mitochondria in epithelial ovarian carcinoma exhibit abnormal phenotypes and blunted associations with biobehavioral factors

Malignant tumor cells exhibit mitochondrial alterations and are also influenced by biobehavioral processes, but the intersection of biobehavioral factors and mitochondria in malignant tumors remains unexplored. Here we examined multiple biochemical and molecular markers of mitochondrial content and function in benign tissue and in high-grade epithelial ovarian carcinoma (EOC) in parallel with exploratory analyses of biobehavioral factors. First, analysis of a publicly-available database (n = 1435) showed that gene expression of specific mitochondrial proteins in EOC is associated with survival. Quantifying multiple biochemical and molecular markers of mitochondrial content and function in tissue from 51 patients with benign ovarian masses and 128 patients with high-grade EOC revealed that compared to benign tissue, EOCs exhibit 3.3–8.4-fold higher mitochondrial content and respiratory chain enzymatic activities (P < 0.001) but similar mitochondrial DNA (mtDNA) levels (− 3.1%), documenting abnormal mitochondrial phenotypes in EOC. Mitochondrial respiratory chain activity was also associated with interleukin-6 (IL-6) levels in ascites. In benign tissue, negative biobehavioral factors were inversely correlated with mitochondrial content and respiratory chain activities, whereas positive biobehavioral factors tended to be positively correlated with mitochondrial measures, although effect sizes were small to medium (r = − 0.43 to 0.47). In contrast, serous EOCs showed less pronounced biobehavioral-mitochondrial correlations. These results document abnormal mitochondrial functional phenotypes in EOC and warrant further research on the link between biobehavioral factors and mitochondria in cancer

Measurements of top quark pair relative differential cross-sections with ATLAS in pp collisions at sqrt(s) = 7 TeV

See paper for full list of authors 17 pages plus author list (31 pages total), 5 figures, 5 tables, submitted to European Physical Journal CMeasurements are presented of differential cross-sections for top quark pair production in pp collisions at sqrt(s) = 7 TeV relative to the total inclusive top quark pair production cross-section. A data sample of 2.05/fb recorded by the ATLAS detector at the Large Hadron Collider is used. Relative differential cross-sections are derived as a function of the invariant mass, the transverse momentum and the rapidity of the top quark pair system. Events are selected in the lepton (electron or muon) + jets channel. The background-subtracted differential distributions are corrected for detector effects, normalized tothe total inclusive top quark pair production cross-section and compared to theoretical predictions. The measurement uncertainties range typically between 10% and 20% and are generally dominated by systematic effects. No significant deviations from the Standard Model expectations are observed

Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in Python. 0.13.1

0.13.1 (May 20, 2017) FIX: Make release compatible with conda-forge build process (https://github.com/nipy/nipype/pull/2017) ENH: Update some minimum versions in compliance with Debian Jessie (https://github.com/nipy/nipype/pull/2017) ENH: Circle builds use cached docker layers (https://github.com/nipy/nipype/pull/2017) ENH: Base docker to use FS6 and ANTS 2.2.0 (https://github.com/nipy/nipype/pull/2024) FIX: Mailmap and contributor acknowledgment (https://github.com/nipy/nipype/pull/2017) FIX: Preserve node properties in sub nodes of MapNode (https://github.com/nipy/nipype/pull/2019) FIX: Fix interfaces 3DUnifize, ICA_AROMA, BinaryMaths, RegAverage, BBRegister, AffineInitializer (https://github.com/nipy/nipype/pull/2025, https://github.com/nipy/nipype/pull/2027, https://github.com/nipy/nipype/pull/2036, https://github.com/nipy/nipype/pull/2037, https://github.com/nipy/nipype/pull/2031, https://github.com/nipy/nipype/pull/2010) ENH: Add Anisotropic Power interface (https://github.com/nipy/nipype/pull/2039) FIX: Bayesian estimation in SPM (https://github.com/nipy/nipype/pull/2030) 0.13.0 (May 11, 2017) ENH: Multi-stage recon-all directives (https://github.com/nipy/nipype/pull/1991) FIX: FEAT "folder does not exist" error (https://github.com/nipy/nipype/pull/2000) ENH: Niftyfit interfaces (https://github.com/nipy/nipype/pull/1910) FIX: Define ANTSPATH for BrainExtraction automatically (https://github.com/nipy/nipype/pull/1986) ENH: New trait for imaging files (https://github.com/nipy/nipype/pull/1949) ENH: Niftyseg interfaces (https://github.com/nipy/nipype/pull/1911) ENH: Niftyreg interfaces (https://github.com/nipy/nipype/pull/1913) MRG: Allow more support for CLI (https://github.com/nipy/nipype/pull/1908) ENH: 3dQwarpPlusMinus interface (https://github.com/nipy/nipype/pull/1974) FIX: PY3.6 support (https://github.com/nipy/nipype/pull/1977) FIX: PY3 and stream fixes for MRTrix2TrackVis (https://github.com/nipy/nipype/pull/1804) ENH: More mask options for CompCor interfaces (https://github.com/nipy/nipype/pull/1968 + https://github.com/nipy/nipype/pull/1992) ENH: Additional TOPUP outputs (https://github.com/nipy/nipype/pull/1976) ENH: Additional Eddy flags (https://github.com/nipy/nipype/pull/1967) ENH: ReconAll handlers for less common cases (https://github.com/nipy/nipype/pull/1966) ENH: FreeSurferSource now finds graymid/midthickness surfs (https://github.com/nipy/nipype/pull/1972) ENH: Additional fslmaths dimensional reduction operations (https://github.com/nipy/nipype/pull/1956) ENH: More options for RobustFOV interface (https://github.com/nipy/nipype/pull/1923) ENH: Add MRIsCombine to FreeSurfer utils (https://github.com/nipy/nipype/pull/1948) FIX: Level1Design EV parameter substitution (https://github.com/nipy/nipype/pull/1953) FIX: Dcm2niix outputs can be uncompressed (https://github.com/nipy/nipype/pull/1951) FIX: Ensure build fails in Circle when tests fail (https://github.com/nipy/nipype/pull/1981) ENH: Add interface to antsAffineInitializer (https://github.com/nipy/nipype/pull/1980) ENH: AFNI motion parameter support for FrameWiseDisplacement (https://github.com/nipy/nipype/pull/1840) ENH: Add ANTs KellyKapowski interface (https://github.com/nipy/nipype/pull/1845) FIX: AFNI interface bug setting OMP_NUM_THREADS to 1 (https://github.com/nipy/nipype/pull/1728) FIX: Select Eddy run command at runtime (https://github.com/nipy/nipype/pull/1871) FIX: Increase FLIRT's flexibility with apply_xfm (https://github.com/nipy/nipype/pull/1875) DOC: Update FSL preprocess docstrings (https://github.com/nipy/nipype/pull/1881) ENH: Support GIFTI outputs in SampleToSurface (https://github.com/nipy/nipype/pull/1886) FIX: Configparser differences between PY2 and PY3 (https://github.com/nipy/nipype/pull/1890) ENH: Add mris_expand interface (https://github.com/nipy/nipype/pull/1893) FIX: Split over-eager globs in FreeSurferSource (https://github.com/nipy/nipype/pull/1894) FIX: Store undefined by default so that xor checks don't trip (https://github.com/nipy/nipype/pull/1903) FIX: Gantt chart generator PY3 compatibility (https://github.com/nipy/nipype/pull/1907) FIX: Add DOF and --fsl-dof options to BBRegister (https://github.com/nipy/nipype/pull/1917) ENH: Auto-derive input_names in Function (https://github.com/nipy/nipype/pull/1918) FIX: Minor fixes for NonSteadyStateDetector (https://github.com/nipy/nipype/pull/1926) DOC: Add duecredit references for AFNI and FSL (https://github.com/nipy/nipype/pull/1930) ENH: Added zenodo (https://zenodo.org/) file (https://github.com/nipy/nipype/pull/1924) ENH: Disable symlinks on CIFS filesystems (https://github.com/nipy/nipype/pull/1941) ENH: Sphinx extension to plot workflows (https://github.com/nipy/nipype/pull/1896) ENH: Added non-steady state detector for EPI data (https://github.com/nipy/nipype/pull/1839) ENH: Enable new BBRegister init options for FSv6+ (https://github.com/nipy/nipype/pull/1811) REF: Splits nipype.interfaces.utility into base, csv, and wrappers (https://github.com/nipy/nipype/pull/1828) FIX: Makespec now runs with nipype in current directory (https://github.com/nipy/nipype/pull/1813) FIX: Flexible nifti opening with mmap if Numpy < 1.12.0 (https://github.com/nipy/nipype/pull/1796 + https://github.com/nipy/nipype/pull/1831) ENH: DVARS includes intensity normalization feature - turned on by default (https://github.com/nipy/nipype/pull/1827) FIX: DVARS is correctly using sum of squares instead of standard deviation (https://github.com/nipy/nipype/pull/1827) ENH: Refactoring of nipype.interfaces.utility (https://github.com/nipy/nipype/pull/1828) FIX: CircleCI were failing silently. Some fixes to tests (https://github.com/nipy/nipype/pull/1833) FIX: Issues in Docker image permissions, and docker documentation (https://github.com/nipy/nipype/pull/1825) ENH: Revised all Dockerfiles and automated deployment to Docker Hub from CircleCI (https://github.com/nipy/nipype/pull/1815) ENH: Update ReconAll interface for FreeSurfer v6.0.0 (https://github.com/nipy/nipype/pull/1790) FIX: Cast DVARS float outputs to avoid memmap error (https://github.com/nipy/nipype/pull/1777) FIX: FSL FNIRT intensity mapping files (https://github.com/nipy/nipype/pull/1799) ENH: Additional outputs generated by FSL EDDY (https://github.com/nipy/nipype/pull/1793) TST: Parallelize CircleCI build across 4 containers (https://github.com/nipy/nipype/pull/1769) 0.13.0-rc1 (January 4, 2017) FIX: Compatibility with traits 4.6 (https://github.com/nipy/nipype/pull/1770) FIX: Multiproc deadlock (https://github.com/nipy/nipype/pull/1756) TST: Replace nose and unittest with pytest (https://github.com/nipy/nipype/pull/1722, https://github.com/nipy/nipype/pull/1751) FIX: Semaphore capture using MultiProc plugin (https://github.com/nipy/nipype/pull/1689) REF: Refactor AFNI interfaces (https://github.com/nipy/nipype/pull/1678, https://github.com/nipy/nipype/pull/1680) ENH: Move nipype commands to group command using click (https://github.com/nipy/nipype/pull/1608) FIX: AFNI Retroicor interface fixes (https://github.com/nipy/nipype/pull/1669) FIX: Minor errors after migration to setuptools (https://github.com/nipy/nipype/pull/1671) ENH: Add AFNI 3dNote interface (https://github.com/nipy/nipype/pull/1637) ENH: Abandon distutils, only use setuptools (https://github.com/nipy/nipype/pull/1627) FIX: Minor bugfixes related to unicode literals (https://github.com/nipy/nipype/pull/1656) TST: Automatic retries in travis (https://github.com/nipy/nipype/pull/1659/files) ENH: Add signal extraction interface (https://github.com/nipy/nipype/pull/1647) ENH: Add a DVARS calculation interface (https://github.com/nipy/nipype/pull/1606) ENH: New interface to b0calc of FSL-POSSUM (https://github.com/nipy/nipype/pull/1399) ENH: Add CompCor (https://github.com/nipy/nipype/pull/1599) ENH: Add duecredit entries (https://github.com/nipy/nipype/pull/1466) FIX: Python 3 compatibility fixes (https://github.com/nipy/nipype/pull/1572) REF: Improved PEP8 compliance for fsl interfaces (https://github.com/nipy/nipype/pull/1597) REF: Improved PEP8 compliance for spm interfaces (https://github.com/nipy/nipype/pull/1593) TST: Replaced coveralls with codecov (https://github.com/nipy/nipype/pull/1609) ENH: More BrainSuite interfaces (https://github.com/nipy/nipype/pull/1554) ENH: Convenient load/save of interface inputs (https://github.com/nipy/nipype/pull/1591) ENH: Add a Framewise Displacement calculation interface (https://github.com/nipy/nipype/pull/1604) FIX: Use builtins open and unicode literals for py3 compatibility (https://github.com/nipy/nipype/pull/1572) TST: reduce the size of docker images & use tags for images (https://github.com/nipy/nipype/pull/1564) ENH: Implement missing inputs/outputs in FSL AvScale (https://github.com/nipy/nipype/pull/1563) FIX: Fix symlink test in copyfile (https://github.com/nipy/nipype/pull/1570, https://github.com/nipy/nipype/pull/1586) ENH: Added support for custom job submission check in SLURM (https://github.com/nipy/nipype/pull/1582) ENH: Added ANTs interface CreateJacobianDeterminantImage; replaces deprecated JacobianDeterminant (https://github.com/nipy/nipype/pull/1654