Calcium-sensing receptor-mediated NLRP3 inflammasome response to calciprotein particles drives inflammation in rheumatoid arthritis

How extracellular calcium can trigger Nlrp3 inflammasome activation has been somewhat controversial and unclear. Here the authors show calciprotein particles are taken up by myeloid cells via calcium-sensing receptor-dependent macropinocytosis in response to high levels of extracellular Ca2+ and this pathway might be critical to inflammatory conditions

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

Polygenic risk scores for prediction of breast cancer and breast cancer subtypes

Abstract Stratification of women according to their risk of breast cancer based on polygenic risk scores (PRSs) could improve screening and prevention strategies. Our aim was to develop PRSs, optimized for prediction of estrogen receptor (ER)-specific disease, from the largest available genome-wide association dataset and to empirically validate the PRSs in prospective studies. The development dataset comprised 94,075 case subjects and 75,017 control subjects of European ancestry from 69 studies, divided into training and validation sets. Samples were genotyped using genome-wide arrays, and single-nucleotide polymorphisms (SNPs) were selected by stepwise regression or lasso penalized regression. The best performing PRSs were validated in an independent test set comprising 11,428 case subjects and 18,323 control subjects from 10 prospective studies and 190,040 women from UK Biobank (3,215 incident breast cancers). For the best PRSs (313 SNPs), the odds ratio for overall disease per 1 standard deviation in ten prospective studies was 1.61 (95%CI: 1.57–1.65) with area under receiver-operator curve (AUC) = 0.630 (95%CI: 0.628–0.651). The lifetime risk of overall breast cancer in the top centile of the PRSs was 32.6%. Compared with women in the middle quintile, those in the highest 1% of risk had 4.37- and 2.78-fold risks, and those in the lowest 1% of risk had 0.16- and 0.27-fold risks, of developing ER-positive and ER-negative disease, respectively. Goodness-of-fit tests indicated that this PRS was well calibrated and predicts disease risk accurately in the tails of the distribution. This PRS is a powerful and reliable predictor of breast cancer risk that may improve breast cancer prevention programs