Improving the Expressiveness of Deep Learning Frameworks with Recursion

Recursive neural networks have widely been used by researchers to handle applications with recursively or hierarchically structured data. However, embedded control flow deep learning frameworks such as TensorFlow, Theano, Caffe2, and MXNet fail to efficiently represent and execute such neural networks, due to lack of support for recursion. In this paper, we add recursion to the programming model of existing frameworks by complementing their design with recursive execution of dataflow graphs as well as additional APIs for recursive definitions. Unlike iterative implementations, which can only understand the topological index of each node in recursive data structures, our recursive implementation is able to exploit the recursive relationships between nodes for efficient execution based on parallel computation. We present an implementation on TensorFlow and evaluation results with various recursive neural network models, showing that our recursive implementation not only conveys the recursive nature of recursive neural networks better than other implementations, but also uses given resources more effectively to reduce training and inference time.Comment: Appeared in EuroSys 2018. 13 pages, 11 figure

Direct observation of DNA target searching and cleavage by CRISPR-Cas12a

Cas12a (also called Cpf1) is a representative type V-A CRISPR effector RNA-guided DNA endonuclease, which provides an alternative to type II CRISPR-Cas9 for genome editing. Previous studies have revealed that Cas12a has unique features distinct from Cas9, but the detailed mechanisms of target searching and DNA cleavage by Cas12a are still unclear. Here, we directly observe this entire process by using single-molecule fluorescence assays to study Cas12a from Acidaminococcus sp. (AsCas12a). We determine that AsCas12a ribonucleoproteins search for their on-target site by a one-dimensional diffusion along elongated DNA molecules and induce cleavage in the two DNA strands in a well-defined order, beginning with the non-target strand. Furthermore, the protospacer-adjacent motif (PAM) for AsCas12a makes only a limited contribution of DNA unwinding during R-loop formation and shows a negligible role in the process of DNA cleavage, in contrast to the Cas9 PAM.

Transient Right Ventricular Dysfunction After Pericardiectomy in Patients With Constrictive Pericarditis

Pericardiectomy is the standard treatment in patients with chronic constrictive pericarditis who have persistent symptoms. However, myocardial atrophy with prolonged pericardial constriction and abrupt increase in venous return can lead to heart failure with volume overload after pericardial decompression, especially in the right ventricle (RV). We experienced a 44 year old male patient who developed transient RV failure after pericardiectomy for constrictive pericarditis. Echocardiography revealed a markedly dilated RV with decreased peak systolic velocity of the tricuspid annulus, suggesting severe RV dysfunction. After treatment with inotropics and diuretics, a follow-up echocardiography revealed an improved systolic function with decreased RV chamber size. This case demonstrates the importance of volume overload and RV dysfunction in patients with constrictive pericarditis undergoing pericardiectomy