Detecting differential usage of exons from RNA-Seq data

RNA-Seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding the regulation of these processes requires comparisons between treatments, tissues or conditions. For the analysis of such experiments, we present _DEXSeq_, a statistical method to test for differential exon usage in RNA-Seq data. _DEXSeq_ employs generalized linear models and offers good detection power and reliable control of false discoveries by taking biological variation into account. An implementation is available as an R/Bioconductor package

Transgendered in Alaska: Navigating the Changing Legal Landscape for Change in Gender Petitions

Background: Detecting intracellular bacterial symbionts can be challenging when they persist at very low densities. Wolbachia, a widespread bacterial endosymbiont of invertebrates, is particularly challenging. Although it persists at high titers in many species, in others its densities are far below the detection limit of classic end-point Polymerase Chain Reaction (PCR). These low-titer infections can be reliably detected by combining PCR with DNA hybridization, but less elaborate strategies based on end-point PCR alone have proven less sensitive or less general. Results: We introduce a multicopy PCR target that allows fast and reliable detection of A-supergroup Wolbachia -even at low infection titers -with standard end-point PCR. The target is a multicopy motif (designated ARM: A-supergroup repeat motif) discovered in the genome of wMel (the Wolbachia in Drosophila melanogaster). ARM is found in at least seven other Wolbachia A-supergroup strains infecting various Drosophila, the wasp Muscidifurax and the tsetse fly Glossina. We demonstrate that end-point PCR targeting ARM can reliably detect both high-and low-titer Wolbachia infections in Drosophila, Glossina and interspecific hybrids. Conclusions: Simple end-point PCR of ARM facilitates detection of low-titer Wolbachia A-supergroup infections. Detecting these infections previously required more elaborate procedures. Our ARM target seems to be a general feature of Wolbachia A-supergroup genomes, unlike other multicopy markers such as insertion sequences (IS)

Real-time tacit bargaining, payoff focality, and coordination complexity: Experimental evidence

We conduct a bargaining experiment where interaction is tacit and payoffs are earned and cumulated in real time. We test hypotheses about the interaction between the focal properties of payoffs and the complexity of coordinating on an intertemporal behavior that achieves them. The general finding is that when a payoff focal outcome requires a complicated coordination scheme bargainers tend to settle on a simpler and sometimes inefficient behavior

Sensor Selection and Random Field Reconstruction for Robust and Cost-effective Heterogeneous Weather Sensor Networks for the Developing World

We address the two fundamental problems of spatial field reconstruction and sensor selection in heterogeneous sensor networks: (i) how to efficiently perform spatial field reconstruction based on measurements obtained simultaneously from networks with both high and low quality sensors; and (ii) how to perform query based sensor set selection with predictive MSE performance guarantee. For the first problem, we developed a low complexity algorithm based on the spatial best linear unbiased estimator (S-BLUE). Next, building on the S-BLUE, we address the second problem, and develop an efficient algorithm for query based sensor set selection with performance guarantee. Our algorithm is based on the Cross Entropy method which solves the combinatorial optimization problem in an efficient manner.Comment: Presented at NIPS 2017 Workshop on Machine Learning for the Developing Worl

Regularity of oscillatory integral operators

In this paper, we establish the global boundedness of oscillatory integral operators on Besov-Lipschitz and Triebel-Lizorkin spaces, with amplitudes in general $S^m_{\rho,\delta}(\mathbb{R}^n)$-classes and non-degenerate phase functions in the class \textart F^k. Our results hold for a wide range of parameters $0\leq\rho\leq1$, $0\leq\delta<1$, $0<p\leq\infty$, $0<q\leq\infty$ and $k>0$. We also provide a sufficient condition for the boundedness of operators with amplitudes in the forbidden class $S^m_{1,1}(\mathbb{R}^n)$ in Triebel-Lizorkin spaces.Comment: arXiv admin note: text overlap with arXiv:2302.0031

Regularity of Fourier integral operators with amplitudes in general H\"ormander classes

We prove the global $L^p$-boundedness of Fourier integral operators that model the parametrices for hyperbolic partial differential equations, with amplitudes in classical H\"ormander classes $S^{m}_{\rho, \delta}(\mathbb{R}^n)$ for parameters $0<\rho\leq 1$, $0\leq \delta<1$. We also consider the regularity of operators with amplitudes in the exotic class $S^{m}_{0, \delta}(\mathbb{R}^n)$, $0\leq \delta< 1$ and the forbidden class $S^{m}_{\rho, 1}(\mathbb{R}^n)$, $0\leq\rho\leq 1.$ Furthermore we show that despite the failure of the $L^2$-boundedness of operators with amplitudes in the forbidden class $S^{0}_{1, 1}(\mathbb{R}^n)$, the operators in question are bounded on Sobolev spaces $H^s(\mathbb{R}^n)$ with $s>0.$ This result extends those of Y. Meyer and E. M. Stein to the setting of Fourier integral operators.Comment: 41 page