Gauss quadrature for matrix inverse forms with applications

We present a framework for accelerating a spectrum of machine learning algorithms that require computation of bilinear inverse forms u[superscript T] A[superscript −1]u, where A is a positive definite matrix and u a given vector. Our framework is built on Gauss-type quadrature and easily scales to large, sparse matrices. Further, it allows retrospective computation of lower and upper bounds on u[superscript T] > A[superscript −1]u, which in turn accelerates several algorithms. We prove that these bounds tighten iteratively and converge at a linear (geometric) rate. To our knowledge, ours is the first work to demonstrate these key properties of Gauss-type quadrature, which is a classical and deeply studied topic. We illustrate empirical consequences of our results by using quadrature to accelerate machine learning tasks involving determinantal point processes and submodular optimization, and observe tremendous speedups in several instances.Google (Research Award)National Science Foundation (U.S.) (CAREER Award 1553284

Carbapenemase-Producing Escherichia coli among Humans and Backyard Animals

Background: The rapidly increasing dissemination of carbapenem-resistant Enterobacteriaceae (CRE) in both humans and animals poses a global threat to public health. However, the transmission of CRE between humans and animals has not yet been well studied. Objectives: We investigated the prevalence, risk factors, and drivers of CRE transmission between humans and their backyard animals in rural China. Methods: We conducted a comprehensive sampling strategy in 12 villages in Shandong, China. Using the household [residents and their backyard animals (farm and companion animals)] as a single surveillance unit, we assessed the prevalence of CRE at the household level and examined the factors associated with CRE carriage through a detailed questionnaire. Genetic relationships among human- and animal-derived CRE were assessed using whole-genome sequencing–based molecular methods. Results: A total of 88 New Delhi metallo-β-lactamases –type carbapenem-resistant Escherichia coli (NDM-EC), including 17 from humans, 44 from pigs, 12 from chickens, 1 from cattle, and 2 from dogs, were isolated from 65 of the 746 households examined. The remaining 12 NDM-EC were from flies in the immediate backyard environment. The NDM-EC colonization in households was significantly associated with a) the number of species of backyard animals raised/kept in the same household, and b) the use of human and/or animal feces as fertilizer. Discriminant analysis of principal components (DAPC) revealed that a large proportion of the core genomes of the NDM-EC belonged to strains from hosts other than their own, and several human isolates shared closely related core single-nucleotide polymorphisms and blaNDM genetic contexts with isolates from backyard animals. Conclusions: To our knowledge, we are the first to report evidence of direct transmission of NDM-EC between humans and animals. Given the rise of NDM-EC in community and hospital infections, combating NDM-EC transmission in backyard farm systems is needed. https://doi.org/10.1289/EHP525

Identifying Connectome Module Patterns via New Balanced Multi-Graph Normalized Cut.

Computational tools for the analysis of complex biological networks are lacking in human connectome research. Especially, how to discover the brain network patterns shared by a group of subjects is a challenging computational neuroscience problem. Although some single graph clustering methods can be extended to solve the multi-graph cases, the discovered network patterns are often imbalanced, e.g. isolated points. To address these problems, we propose a novel indicator constrained and balanced multi-graph normalized cut method to identify the connectome module patterns from the connectivity brain networks of the targeted subject group. We evaluated our method by analyzing the weighted fiber connectivity networks

Knockout of the BK β2 subunit abolishes inactivation of BK currents in mouse adrenal chromaffin cells and results in slow-wave burst activity

Rat and mouse adrenal medullary chromaffin cells (CCs) express an inactivating BK current. This inactivation is thought to arise from the assembly of up to four β2 auxiliary subunits (encoded by the kcnmb2 gene) with a tetramer of pore-forming Slo1 α subunits. Although the physiological consequences of inactivation remain unclear, differences in depolarization-evoked firing among CCs have been proposed to arise from the ability of β2 subunits to shift the range of BK channel activation. To investigate the role of BK channels containing β2 subunits, we generated mice in which the gene encoding β2 was deleted (β2 knockout [KO]). Comparison of proteins from wild-type (WT) and β2 KO mice allowed unambiguous demonstration of the presence of β2 subunit in various tissues and its coassembly with the Slo1 α subunit. We compared current properties and cell firing properties of WT and β2 KO CCs in slices and found that β2 KO abolished inactivation, slowed action potential (AP) repolarization, and, during constant current injection, decreased AP firing. These results support the idea that the β2-mediated shift of the BK channel activation range affects repetitive firing and AP properties. Unexpectedly, CCs from β2 KO mice show an increased tendency toward spontaneous burst firing, suggesting that the particular properties of BK channels in the absence of β2 subunits may predispose to burst firing