From RNA-seq reads to differential expression results

Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression

Correlation between amygdala BOLD activity and frontal EEG asymmetry during real-time fMRI neurofeedback training in patients with depression

Real-time fMRI neurofeedback (rtfMRI-nf) is an emerging approach for studies and novel treatments of major depressive disorder (MDD). EEG performed simultaneously with an rtfMRI-nf procedure allows an independent evaluation of rtfMRI-nf brain modulation effects. Frontal EEG asymmetry in the alpha band is a widely used measure of emotion and motivation that shows profound changes in depression. However, it has never been directly related to simultaneously acquired fMRI data. We report the first study investigating electrophysiological correlates of the rtfMRI-nf procedure, by combining rtfMRI-nf with simultaneous and passive EEG recordings. In this pilot study, MDD patients in the experimental group (n=13) learned to upregulate BOLD activity of the left amygdala using an rtfMRI-nf during a happy emotion induction task. MDD patients in the control group (n=11) were provided with a sham rtfMRI-nf. Correlations between frontal EEG asymmetry in the upper alpha band and BOLD activity across the brain were examined. Average individual changes in frontal EEG asymmetry during the rtfMRI-nf task for the experimental group showed a significant positive correlation with the MDD patients' depression severity ratings, consistent with an inverse correlation between the depression severity and frontal EEG asymmetry at rest. Temporal correlations between frontal EEG asymmetry and BOLD activity were significantly enhanced, during the rtfMRI-nf task, for the amygdala and many regions associated with emotion regulation. Our findings demonstrate an important link between amygdala BOLD activity and frontal EEG asymmetry. Our EEG asymmetry results suggest that the rtfMRI-nf training targeting the amygdala is beneficial to MDD patients, and that alpha-asymmetry EEG-nf would be compatible with the amygdala rtfMRI-nf. Combination of the two could enhance emotion regulation training and benefit MDD patients.Comment: 28 pages, 16 figures, to appear in NeuroImage: Clinica

Gene ontology analysis for RNA-seq: accounting for selection bias

GOseq is a method for GO analysis of RNA-seq data that takes into account the length bias inherent in RNA-se

One hundred twenty-five concomitant endovascular and open procedures for lower extremity arterial disease

AbstractObjective: Although the results of staged endovascular and open surgical reconstructions have been well documented, the safety and efficacy of concomitant procedures in the operating room are less well defined. Suboptimal performance of endovascular procedures in an operative setting, or inappropriate reliance on endovascular techniques, might theoretically compromise graft patency. We questioned whether late graft thrombosis is frequently attributable to failure at the endovascularly treated site in this setting. Materials and Methods: Between May 1, 1993, and June 30, 2001, we performed 125 concomitant endovascular and open arterial reconstructions (73 primary reconstructions, 52 graft revisions) in 106 patients. Endovascular techniques were used to treat inflow lesions in 72 cases, outflow lesions in 14 cases, both in four cases, and the graft itself in 35 cases. Fifty-five iliac, 18 femoral, 13 popliteal, six tibial, and 35 graft lesions were treated. For primary bypasses, 33 were to the popliteal level (21 prosthetic, 12 autogenous), 19 were to the tibial or pedal arteries (16 autogenous, three prosthetic or composite), and 12 were to the femoral arteries (one autogenous, 11 prosthetic). Nine patch angioplasties (eight femoral, one popliteal) were performed. For graft revisions, endovascular intervention was for inflow in 13 cases, outflow in three cases, both in one case, and of the graft itself in 35 cases. Surgical revisions involved segmental grafts in 33 cases, patch angioplasty in 18 cases, and both in one case. Results: In the primary group, the initial technical success rate of the endovascular procedure was 93% (68/73), with five patients needing open conversion. The 30-day mortality rate was 1.4%, and the morbidity rate was 11.0%. Of the 19 grafts in the primary group that occluded during the follow-up period (mean, 11.9 months), five thromboses could possibly be attributed to failure at the endovascular site. In the revision group, the initial technical success rate of the endovascular procedure was 88% (46/52), with six patients undergoing conversion to open procedure. The 30-day mortality rate was 0%, and the morbidity rate was 15.4%. Of 22 late graft occlusions in the revision group, only three were attributed to failure at the endovascular site. Conclusion: This largest report to date of concomitant lower extremity endovascular and open revascularization procedures shows the approach to be safe. Few late graft occlusions were attributable to failure at the endovascularly treated site. The concomitant approach offers the efficiency and convenience of single stage therapy and allows immediate treatment for inadequate endovascular results or their complications and potential cost savings. (J Vasc Surg 2003;37:316-22.