MP-PCA denoising of fMRI time-series data can lead to artificial activation "spreading"

MP-PCA denoising has become the method of choice for denoising in MRI since it provides an objective threshold to separate the desired signal from unwanted thermal noise components. In rodents, thermal noise in the coils is an important source of noise that can reduce the accuracy of activation mapping in fMRI. Further confounding this problem, vendor data often contains zero-filling and other effects that may violate MP-PCA assumptions. Here, we develop an approach to denoise vendor data and assess activation "spreading" caused by MP-PCA denoising in rodent task-based fMRI data. Data was obtained from N = 3 mice using conventional multislice and ultrafast acquisitions (1 s and 50 ms temporal resolution, respectively), during visual stimulation. MP-PCA denoising produced SNR gains of 64% and 39% and Fourier spectral amplitude (FSA) increases in BOLD maps of 9% and 7% for multislice and ultrafast data, respectively, when using a small [2 2] denoising window. Larger windows provided higher SNR and FSA gains with increased spatial extent of activation that may or may not represent real activation. Simulations showed that MP-PCA denoising causes activation "spreading" with an increase in false positive rate and smoother functional maps due to local "bleeding" of principal components, and that the optimal denoising window for improved specificity of functional mapping, based on Dice score calculations, depends on the data's tSNR and functional CNR. This "spreading" effect applies also to another recently proposed low-rank denoising method (NORDIC). Our results bode well for dramatically enhancing spatial and/or temporal resolution in future fMRI work, while taking into account the sensitivity/specificity trade-offs of low-rank denoising methods

Stroke and recurrent haemorrhage associated with antithrombotic treatment after gastrointestinal bleeding in patients with atrial fibrillation:nationwide cohort study

Study question What are the risks of all cause mortality, thromboembolism, major bleeding, and recurrent gastrointestinal bleeding associated with restarting antithrombotic treatment after gastrointestinal bleeding in patients with atrial fibrillation? Methods This Danish cohort study (1996-2012) included all patients with atrial fibrillation discharged from hospital after gastrointestinal bleeding while receiving antithrombotic treatment. Restarted treatment regimens were single or combined antithrombotic drugs with oral anticoagulation and antiplatelets. Follow-up started 90 days after discharge to avoid confounding from use of previously prescribed drugs on discharge. Risks of all cause mortality, thromboembolism, major bleeding, and recurrent gastrointestinal bleeding were estimated with competing risks models and time dependent multiple Cox regression models. Study answer and limitations 4602 patients (mean age 78 years) were included. Within two years, 39.9% (95% confidence interval 38.4% to 41.3%, n=1745) of the patients had died, 12.0% (11.0% to 13.0%, n=526) had experienced thromboembolism, 17.7% (16.5% to 18.8%, n=788) major bleeding, and 12.1% (11.1% to 13.1%, n=546) recurrent gastrointestinal bleeding. 27.1% (n=924) of patients did not resume antithrombotic treatment. Compared with non-resumption of treatment, a reduced risk of all cause mortality was found in association with restart of oral anticoagulation (hazard ratio 0.39, 95% confidence interval 0.34 to 0.46), an antiplatelet agent (0.76, 0.68 to 0.86), and oral anticoagulation plus an antiplatelet agent (0.41, 0.32 to 0.52), and a reduced risk of thromboembolism was found in association with restart of oral anticoagulation (0.41, 0.31 to 0.54), an antiplatelet agent (0.76, 0.61 to 0.95), and oral anticoagulation plus an antiplatelet agent (0.54, 0.36 to 0.82). Restarting oral anticoagulation alone was the only regimen with an increased risk of major bleeding (1.37, 1.06 to 1.77) compared with non-resumption of treatment; however, the difference in risk of recurrent gastrointestinal bleeding was not significant between patients who restarted an antithrombotic treatment regimen and those who did not resume treatment. What this study adds Among patients with atrial fibrillation who experience gastrointestinal bleeding while receiving antithrombotic treatment; subsequent restart of oral anticoagulation alone was associated with better outcomes for all cause mortality and thromboembolism compared with patients who did not resume treatment. This was despite an increased longitudinal associated risk of bleeding. Funding, competing interests, data sharing This study was supported by a grant from Boehringer-Ingelheim. Competing interests are available in the full paper on bmj.com. The authors have no additional data to share

Ischemic Stroke Severity and Mortality in Patients With and Without Atrial Fibrillation

Background Our objective was to investigate stroke severity and subsequent rate of mortality among patients with and without atrial fibrillation (AF). Contemporary data on stroke severity and prognosis in patients with AF are lacking. Methods and Results First‐time ischemic stroke patients from the Danish Stroke Registry (January 2005–December 2016) were included in an observational study. Patients with AF were matched 1:1 by sex, age, calendar year, and CHA2DS2‐VASc score with patients without AF. Stroke severity was determined by the Scandinavian Stroke Scale (0–58 points). The rate of death was estimated by Kaplan‐Meier plots and multivariable Cox regression. Among 86 458 identified patients with stroke, 17 205 had AF. After matching, 14 662 patients with AF and 14 662 patients without AF were included (51.8% women; median age, 79.6 years [25th–75th percentile, 71.8–86.0]). More patients with AF had very severe stroke (0–14 points) than patients without AF (13.7% versus 7.9%, P<0.01). The absolute rates of 30‐day and 1‐year mortality were significantly higher for patients with AF (12.1% and 28.4%, respectively) versus patients without AF (8.7% and 21.8%, respectively). This held true in adjusted models for 30‐day mortality (hazard ratio [HR], 1.40 [95% CI, 1.30–1.51]). However, this association became nonsignificant when additionally adjusting for stroke severity (HR, 1.10 [95% CI, 1.00–1.23]). AF was associated with a higher rate of 1‐year mortality (HR, 1.39 [95% CI, 1.32–1.46]), although it was mediated by stroke severity (HR, 1.15 [95% CI, 1.09–1.23], model including stroke severity). Conclusions In a contemporary nationwide cohort of patients with ischemic stroke, patients with AF had more severe strokes and higher mortality than patients without AF. The difference in mortality was mainly driven by stroke severity

Mutations in the potassium channel subunit KCNE1 are associated with early-onset familial atrial fibrillation

<p>Abstract</p> <p>Background</p> <p>Atrial fibrillation (AF) is the most common arrhythmia. The potassium current I_Ksis essential for cardiac repolarization. Gain-of-function mutations in K_V7.1, the pore-forming α-subunit of the I_Kschannel, have been associated with AF. We hypothesized that early-onset lone AF is associated with mutations in the I_Kschannel regulatory subunit KCNE1.</p> <p>Methods</p> <p>In 209 unrelated early-onset lone AF patients (< 40 years) the entire coding sequence of <it>KCNE1 </it>was bidirectionally sequenced. We analyzed the identified KCNE1 mutants electrophysiologically in heterologous expression systems.</p> <p>Results</p> <p>Two non-synonymous mutations G25V and G60D were found in <it>KCNE1 </it>that were not present in the control group (n = 432 alleles) and that have not previously been reported in any publicly available databases or in the exom variant server holding exom data from more than 10.000 alleles. Proband 1 (female, age 45, G25V) had onset of paroxysmal AF at the age of 39 years. Proband 2 (G60D) was diagnosed with lone AF at the age of 33 years. The patient has inherited the mutation from his mother, who also has AF. Both probands had no mutations in genes previously associated with AF. In heterologous expression systems, both mutants showed significant gain-of-function for I_Ksboth with respect to steady-state current levels, kinetic parameters, and heart rate-dependent modulation.</p> <p>Conclusions</p> <p>Mutations in K_V7.1 leading to gain-of-function of I_Kscurrent have previously been described in lone AF, yet this is the first time a mutation in the beta-subunit <it>KCNE1 </it>is associated with the disease. This finding further supports the hypothesis that increased potassium current enhances AF susceptibility.</p