Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant Arabidopsis thaliana and a mutant defective in mRNA methylation (m6A). Here we show that m6A can be mapped in full-length mRNAs transcriptome-wide and reveal the combinatorial diversity of cap-associated transcription start sites, splicing events, poly(A) site choice and poly(A) tail length. Loss of m6A from 3’ untranslated regions is associated with decreased relative transcript abundance and defective RNA 30 end formation. A functional consequence of disrupted m6A is a lengthening of the circadian period. We conclude that nanopore direct RNA sequencing can reveal the complexity of mRNA processing and modification in full-length single molecule reads. These findings can refine Arabidopsis genome annotation. Further, applying this approach to less well-studied species could transform our understanding of what their genomes encode

Tale of two curricula: The performance of 2000 students in introductory electromagnetism

The performance of over 2000 students in introductory calculus-based electromagnetism (E&M) courses at four large research universities was measured using the Brief Electricity and Magnetism Assessment (BEMA). Two different curricula were used at these universities: a traditional E&M curriculum and the Matter & Interactions (M&I) curriculum. At each university, postinstruction BEMA test averages were significantly higher for the M&I curriculum than for the traditional curriculum. The differences in post-test averages cannot be explained by differences in variables such as preinstruction BEMA scores, grade point average, or SAT Reasoning Test (SAT) scores. BEMA performance on categories of items organized by subtopic was also compared at one of the universities; M&I averages were significantly higher in each topic. The results suggest that the M&I curriculum is more effective than the traditional curriculum at teaching E&M concepts to students, possibly because the learning progression in M&I reorganizes and augments the traditional sequence of topics, for example, by increasing early emphasis on the vector field concept and by emphasizing the effects of fields on matter at the microscopic level

Use and Outcomes Associated With Bridging During Anticoagulation Interruptions in Patients With Atrial Fibrillation: Findings From the Outcomes Registry for Better Informed Treatment of Atrial Fibrillation (ORBIT-AF)

BACKGROUND: Temporary interruption of oral anticoagulation for procedures is often required, and some propose using bridging anticoagulation. However, the use and outcomes of bridging during oral anticoagulation interruptions in clinical practice are unknown. METHODS AND RESULTS: The Outcomes Registry for Better Informed Treatment of Atrial Fibrillation (ORBIT-AF) registry is a prospective, observational registry study of US outpatients with atrial fibrillation. We recorded incident temporary interruptions of oral anticoagulation for a procedure, including the use and type of bridging therapy. Outcomes included multivariable-adjusted rates of myocardial infarction, stroke or systemic embolism, major bleeding, cause-specific hospitalization, and death within 30 days. Of 7372 patients treated with oral anticoagulation, 2803 overall interruption events occurred in 2200 patients (30%) at a median follow-up of 2 years. Bridging anticoagulants were used in 24% (n=665), predominantly low-molecular-weight heparin (73%, n=487) and unfractionated heparin (15%, n=97). Bridged patients were more likely to have had prior cerebrovascular events (22% versus 15%; P=0.0003) and mechanical valve replacements (9.6% versus 2.4%; P/=2 in 94% versus 95%; P=0.5). Bleeding events were more common in bridged than nonbridged patients (5.0% versus 1.3%; adjusted odds ratio, 3.84;

Outcomes of Temporary Interruption of Rivaroxaban Compared With Warfarin in Patients With Nonvalvular Atrial Fibrillation

Background During long-term anticoagulation in atrial fibrillation, temporary interruptions (TIs) of therapy are common, but the relationship between patient outcomes and TIs has not been well studied. We sought to determine reasons for TI, the characteristics of patients undergoing TI, and the relationship between anticoagulant and outcomes among patients with TI. Methods and Results In the Rivaroxaban Once Daily, Oral, Direct Factor Xa Inhibition Compared With Vitamin K Antagonism for Prevention of Stroke and Embolism Trial in Atrial Fibrillation (ROCKET AF), a randomized, double-blind, double-dummy study of rivaroxaban and warfarin in nonvalvular atrial fibrillation, baseline characteristics, management, and outcomes, including stroke, non-central nervous system systemic embolism, death, myocardial infarction, and bleeding, were reported in participants who experienced TI (3-30 days) for any reason. The at-risk period for outcomes associated with TI was from TI start to 30 days after resumption of study drug. In 14 236 participants who received at least 1 dose of study drug, 4692 (33%) experienced TI. Participants with TI were similar to the overall ROCKET AF population in regard to baseline clinical characteristics. Only 6% (n=483) of TI incidences involved bridging therapy. Stroke/systemic embolism rates during the at-risk period were similar in rivaroxaban-treated and warfarin-treated participants (0.30% versus 0.41% per 30 days; hazard ratio [confidence interval]=0.74 [0.36-1.50]; P=0.40). Risk of major bleeding during the at-risk period was also similar in rivaroxaban-treated and warfarin-treated participants (0.99% versus 0.79% per 30 days; hazard ratio [confidence interval]=1.26 [0.80-2.00]; P=0.32). Conclusions TI of oral anticoagulation is common and is associated with substantial stroke risks and bleeding risks that were similar among patients treated with rivaroxaban or warfarin. Further investigation is needed to determine the optimal management strategy in patients with atrial fibrillation requiring TI of anticoagulation. Clinical Trial Registration URL: http://www.clinicaltrials.gov. Unique identifier: NCT00403767

Open-source, python-based redevelopment of the ChemShell multiscale QM/MM environment

ChemShell is a scriptable computational chemistry environment with an emphasis on multiscale simulation of complex systems using combined quantum mechanical and molecular mechanical (QM/MM) methods. Motivated by a scientific need to efficiently and accurately model chemical reactions on surfaces and within microporous solids on massively parallel computing systems, we present a major redevelopment of the ChemShell code, which provides a modern platform for advanced QM/MM embedding models. The new version of ChemShell has been re-engineered from the ground up with a new QM/MM driver module, an improved parallelization framework, new interfaces to high performance QM and MM programs, and a user interface written in the Python programming language. The redeveloped package is capable of performing QM/MM calculations on systems of significantly increased size, which we illustrate with benchmarks on zirconium dioxide nanoparticles of over 160,000 atoms

Impact of Regional Systems of Care on Disparities in Care Among Female and Black Patients Presenting With ST‐Segment–Elevation Myocardial Infarction

BACKGROUND: The American Heart Association Mission: Lifeline STEMI (ST-segment-elevation myocardial infarction) Systems Accelerator program, conducted in 16 regions across the United States to improve key care processes, resulted in more patients being treated within national guideline goals (time from first medical contact to device: <90 minutes for direct presenters to hospitals capable of performing percutaneous coronary intervention; <120 minutes for transfers). We examined whether the effort reduced reperfusion disparities in the proportions of female versus male and black versus white patients. METHODS AND RESULTS: In total, 23 809 patients (29.3% female, 82.3% white, and 10.7% black) presented with acute STEMI between July 2012 and March 2014. Change in the proportion of patients treated within guideline goals was compared between sex and race subgroups for patients presenting directly to hospitals capable of performing percutaneous coronary intervention (n=18 267) and patients requiring transfer (n=5542). The intervention was associated with an increase in the proportion of men treated within guideline goals that presented directly (58.7-62.1%, P=0.01) or were transferred (43.3-50.7%, P<0.01). An increase was also seen among white patients who presented directly (57.7-59.9%, P=0.02) or were transferred (43.9-48.8%, P<0.01). There was no change in the proportion of female or black patients treated within guideline goals, including both those presenting directly and transferred. CONCLUSION: The STEMI Systems Accelerator project was associated with an increase in the proportion of patients meeting guideline reperfusion targets for male and white patients but not for female or black patients. Efforts to organize systems of STEMI care should implement additional processes targeting barriers to timely reperfusion among female and black patients

Countermovement Jump and Isometric Strength Test-Retest Reliability in English Premier League Academy Football Players.

To examine the test-retest reliability of countermovement jump (CMJ) and isometric strength testing measures in elite-level under-18 and under-23 academy football players. A total of 36 players performed 3 maximal CMJs and isometric abductor (IABS), adductor (IADS), and posterior chain (IPCS) strength tests on 2 separate test days using dual force plates (CMJ and IPCS) and a portable strength testing device (IABS and IADS). Relative (intraclass correlation coefficient) and absolute (coefficient of variation, standard error of the measurement, and minimal detectable change [MDC%]) reliabilities for 34 CMJ, 10 IABS, 10 IADS, and 11 IPCS measures were analyzed using between-sessions best, mean, and within-session methods. For all methods, relative reliability was good to excellent for all CMJ and all IADS measures and poor to good for all IABS and IPCS measures. Absolute reliability was good (ie, coefficient of variation < 10%) for 27 (best) and 28 (mean) CMJ variables and for 6 (IABS and IADS) and 2 (IPCS) isometric measures. Commonly used CMJ measures (jump height, eccentric duration, and flight-time:contraction-time ratio) had good to excellent relative reliability and an MDC% range of 14.6% to 23.7%. Likewise, commonly used isometric peak force measures for IABS, IADS, and IPCS had good to excellent relative reliability and an MDC% range of 22.2% to 26.4%. Commonly used CMJ and isometric strength measures had good test-retest reliability but might be limited by their MDC%. Rate-of-force-development measures (for all isometric tests) and impulse measures (IPCS) are limited by poor relative and absolute reliability and high MDC%. MDC% statistics should be considered in the context of typical responsiveness

Structural Mechanism of Laforin Function in Glycogen Dephosphorylation and Lafora Disease

Glycogen is the major mammalian glucose storage cache and is critical for energy homeostasis. Glycogen synthesis in neurons must be tightly controlled due to neuronal sensitivity to perturbations in glycogen metabolism. Lafora disease (LD) is a fatal, congenital, neurodegenerative epilepsy. Mutations in the gene encoding the glycogen phosphatase laforin result in hyperphosphorylated glycogen that forms water-insoluble inclusions called Lafora bodies (LBs). LBs induce neuronal apoptosis and are the causative agent of LD. The mechanism of glycogen dephosphorylation by laforin and dysfunction in LD is unknown. We report the crystal structure of laforin bound to phosphoglucan product, revealing its unique integrated tertiary and quaternary structure. Structure-guided mutagenesis combined with biophysical and biochemical analyses reveal the basis for normal function of laforin in glycogen metabolism. Analyses of LD patient mutations define the mechanism by which subsets of mutations disrupt laforin function. These data provide fundamental insights connecting glycogen metabolism to neurodegenerative disease