methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

DNA methylation is a chemical modification of cytosine bases that is pivotal for gene regulation, cellular specification and cancer development. Here, we describe an R package, methylKit, that rapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation and hydroxymethylation sequencing experiments. methylKit includes functions for clustering, sample quality visualization, differential methylation analysis and annotation features, thus automating and simplifying many of the steps for discerning statistically significant bases or regions of DNA methylation. Finally, we demonstrate methylKit on breast cancer data, in which we find statistically significant regions of differential methylation and stratify tumor subtypes. methylKit is available at http://code.google.com/p/methylkit

A randomized controlled trial of a physician-directed treatment program for low-income patients with high blood cholesterol: the Southeast Cholesterol Project

OBJECTIVE: To assess the effectiveness of a cholesterol-lowering intervention designed to facilitate the management of hypercholesterolemia by primary care clinicians. DESIGN: Randomized controlled trial, with randomization of clinician-patient groups. SETTING: Twenty-one community and rural health centers in North Carolina and Virginia. PARTICIPANTS: Primary care clinicians (n = 42, 71% physicians) and the patients they enrolled with high cholesterol (n = 372). Twenty-two clinicians were randomized to give the special intervention (184 patients) and 20 to give usual care (188 patients). Two thirds of participating patients were women, 40% were African American, and 11% were Native American. INTERVENTION: A 90-minute tutorial to train clinicians how to use a structured assessment and treatment program (Food for Heart Program) consisting of a brief dietary assessment and three 5- to 10-minute dietary counseling sessions given by the primary care clinician, referral to a local dietitian if the low-density lipoprotein cholesterol (LDL-C) remained elevated at 4-month follow-up, and a prompt for the clinician to consider lipid-lowering medication based on the LDL-C at 7-month follow-up. MAIN OUTCOME MEASURES: Changes in total and LDL cholesterol at 4-month follow-up and averaged over a 1-year follow-up period (4-, 7-, and 12-month follow-up). RESULTS: At 4-month follow-up, total cholesterol decreased 0.33 mmol/L (12.6 mg/dL) in the intervention group and 0.21 mmol/L (8.3 mg/dL) in the control group: the difference was 0.11 mmol/L (4.2 mg/dL) (90% confidence interval [CI], -0.02 to 0.24 mmol/L [-0.7 to 9.1 mg/dL]). The average reduction during the 1-year follow-up period was 0.09 mmol/L (3.6 mg/dL) greater in the intervention group (90% CI, -0.01 to 0.19 mmol/L [-0.3 to 7.5 mg/dL]). Eight percent of intervention patients were taking lipid-lowering medication at follow-up visits compared with 15% of control patients. In a subgroup analysis restricted to the 89% of returnees who were not taking lipid-lowering medication, the reduction in total cholesterol at 4-month follow-up was 0.14 mmol/L (5.5 mg/dL) greater in the intervention group (95% CI, 0.01 to 0.28 mmol/L [0.3 to 10.7 mg/dL]); averaged over 1 year, it was 0.14 mmol/L (5.3 mg/dL) greater (95% CI, 0.03 to 0.24 mmol/L [1.2 to 9.4 mg/dL]). Changes in LDL-C were similar. CONCLUSIONS: Total cholesterol and LDL-C decreased more in the intervention group than in the control group. Overall, the difference in lipid reduction between groups was modest and of borderline statistical significance; among participants who did not take lipid-lowering medication during follow-up, the difference in lipid reduction between groups was larger. We conclude that primary care clinicians can be trained to give a cholesterol-lowering intervention to low-income patients that results in modest, short-term reductions in total cholesterol and LDL-C

Evidence for Shape Co-existence at medium spin in 76Rb

Four previously known rotational bands in 76Rb have been extended to moderate spins using the Gammasphere and Microball gamma ray and charged particle detector arrays and the 40Ca(40Ca,3pn) reaction at a beam energy of 165 MeV. The properties of two of the negative-parity bands can only readily be interpreted in terms of the highly successful Cranked Nilsson-Strutinsky model calculations if they have the same configuration in terms of the number of g9/2 particles, but they result from different nuclear shapes (one near-oblate and the other near-prolate). These data appear to constitute a unique example of shape co-existing structures at medium spins.Comment: Accepted for publication in Physics Letters

A Peer-reviewed Newspaper About_ Research Values

An interrogation of value and values in contemporary media and digital culture. Publication resulting from research workshop at Brandenburg Center for Media Studies – ZeM, Potsdam, organised in collaboration with Brandenburg Center for Media Studies – ZeM, Potsdam, and transmediale festival for art and digital culture, Berlin

High-Precision Branching Ratio Measurement for the Superallowed + Emitter 74Rb

A high-precision branching-ratio measurement for the superallowed β + decay of 74Rb was performed at the TRIUMF Isotope Separator and Accelerator (ISAC) radioactive ion-beam facility. The scintillating electronpositron tagging array (SCEPTAR), composed of 10 thin plastic scintillators, was used to detect the emitted β particles; the 8π spectrometer, an array of 20 Compton-suppressed HPGe detectors, was used for detecting γ rays that were emitted following Gamow-Teller and nonanalog Fermi β + decays of 74Rb; and the Pentagonal Array of Conversion Electron Spectrometers (PACES), an array of 5 Si(Li) detectors, was employed for measuring β-delayed conversion electrons. Twenty-three excited states were identified in 74Kr following 8.241(4) × 108 detected 74Rb β decays. A total of 58 γ -ray and electron transitions were placed in the decay scheme, allowing the superallowed branching ratio to be determined as B0 = 99.545(31)%. Combined with previous half-life and Q-value measurements, the superallowed branching ratio measured in this work leads to a superallowed f t value of 3082.8(65) s. Comparisons between this superallowed f t value and the world-average-corrected Ft value, as well as the nonanalog Fermi branching ratios determined in this work, provide guidance for theoretical models of the isospin-symmetry-breaking corrections in this mass region.IS

Investigation of excited 0+ states in 160Er populated via the (p, t) two-neutron transfer reaction

Many efforts have been made in nuclear structure physics to interpret the nature of low-lying excited 0+ states in well-deformed rare-earth nuclei. However, one of the difficulties in resolving the nature of these states is that there is a paucity of data. In this work, excited 0+ states in the N = 92 nucleus 160Er were studied via the 162Er(p, t)160Er two-neutron transfer reaction, which is ideal for probing 0+ → 0+ transitions, at the Maier-Leibnitz-Laboratorium in Garching, Germany. Reaction products were momentum-analyzed with a Quadrupole-3-Dipole magnetic spectrograph. The 0+2 state was observed to be strongly populated with 18% of the ground state strength

Testing microscopically derived descriptions of nuclear collectivity : Coulomb excitation of 22Mg

Many-body nuclear theory utilizing microscopic or chiral potentials has developed to the point that collectivity might be studied within a microscopic or ab initio framework without the use of effective charges; for example with the proper evolution of the E2 operator, or alternatively, through the use of an appropriate and manageable subset of particle–hole excitations. We present a precise determination of E2 strength in 22Mg and its mirror 22Ne by Coulomb excitation, allowing for rigorous comparisons with theory. No-core symplectic shell-model calculations were performed and agree with the new B(E2) values while in-medium similarity-renormalization-group calculations consistently underpredict the absolute strength, with the missing strength found to have both isoscalar and isovector components. The discrepancy between two microscopic models demonstrates the sensitivity of E2 strength to the choice of many-body approximation employed

Reorientation-effect measurement of the first 2+ state in 12C : Confirmation of oblate deformation

A Coulomb-excitation reorientation-effect measurement using the TIGRESS γ−ray spectrometer at the TRIUMF/ISAC II facility has permitted the determination of the 〈21 +‖E2ˆ‖21 +〉 diagonal matrix element in 12C from particle−γ coincidence data and state-of-the-art no-core shell model calculations of the nuclear polarizability. The nuclear polarizability for the ground and first-excited (21 +) states in 12C have been calculated using chiral NN N4LO500 and NN+3NF350 interactions, which show convergence and agreement with photo-absorption cross-section data. Predictions show a change in the nuclear polarizability with a substantial increase between the ground state and first excited 21 + state at 4.439 MeV. The polarizability of the 21 + state is introduced into the current and previous Coulomb-excitation reorientation-effect analyses of 12C. Spectroscopic quadrupole moments of QS(21 +)=+0.053(44) eb and QS(21 +)=+0.08(3) eb are determined, respectively, yielding a weighted average of QS(21 +)=+0.071(25) eb, in agreement with recent ab initio calculations. The present measurement confirms that the 21 + state of 12C is oblate and emphasizes the important role played by the nuclear polarizability in Coulomb-excitation studies of light nuclei

An epigenome-wide association study of posttraumatic stress disorder in US veterans implicates several new DNA methylation loci

Background Previous studies using candidate gene and genome-wide approaches have identified epigenetic changes in DNA methylation (DNAm) associated with posttraumatic stress disorder (PTSD). Methods In this study, we performed an EWAS of PTSD in a cohort of Veterans (n = 378 lifetime PTSD cases and 135 controls) from the Translational Research Center for TBI and Stress Disorders (TRACTS) cohort assessed using the Illumina EPIC Methylation BeadChip which assesses DNAm at more than 850,000 sites throughout the genome. Our model included covariates for ancestry, cell heterogeneity, sex, age, and a smoking score based on DNAm at 39 smoking-associated CpGs. We also examined in EPIC-based DNAm data generated from pre-frontal cortex (PFC) tissue from the National PTSD Brain Bank (n = 72). Results The analysis of blood samples yielded one genome-wide significant association with PTSD at cg19534438 in the gene G0S2 (p = 1.19 x 10(-7), p(adj) = 0.048). This association was replicated in an independent PGC-PTSD-EWAS consortium meta-analysis of military cohorts (p = 0.0024). We also observed association with the smoking-related locus cg05575921 in AHRR despite inclusion of a methylation-based smoking score covariate (p = 9.16 x 10(-6)), which replicates a previously observed PGC-PTSD-EWAS association (Smith et al. 2019), and yields evidence consistent with a smoking-independent effect. The top 100 EWAS loci were then examined in the PFC data. One of the blood-based PTSD loci, cg04130728 in CHST11, which was in the top 10 loci in blood, but which was not genome-wide significant, was significantly associated with PTSD in brain tissue (in blood p = 1.19 x 10(-5), p(adj) = 0.60, in brain, p = 0.00032 with the same direction of effect). Gene set enrichment analysis of the top 500 EWAS loci yielded several significant overlapping GO terms involved in pathogen response, including "Response to lipopolysaccharide" (p = 6.97 x 10(-6), p(adj) = 0.042). Conclusions The cross replication observed in independent cohorts is evidence that DNA methylation in peripheral tissue can yield consistent and replicable PTSD associations, and our results also suggest that that some PTSD associations observed in peripheral tissue may mirror associations in the brain.Stress-related psychiatric disorders across the life spa