Abstract Massively parallel sequencing has revolutionized many areas of biology, but large amounts DNA in individuals is cost-prohibitive and unnecessary for studies. Genomic complexity reduction techniques such as sequence capture restriction enzyme-based methods enable the analysis more per unit cost. Despite their utility, current have limitations, especially when numbers are analyzed. Here we develop a much improved site-associated (RAD) protocol new method called Rapture (RAD capture)....

The MAPKKK Ste11p functions in three Saccharomyces cerevisiae MAPK cascades [the high osmolarity glycerol (HOG), pheromone response, and pseudohyphal/invasive growth pathways], but its activation response to stimulates only the HOG pathway. To determine what restricts cross-activation of (cross talk), we have studied mutants which pathway is activated by (1 m sorbitol). We found that mutations HOG1 gene, encoding p38-type pathway, PBS2 activating kinase for Hog1p, allowed osmolarity-induced...

The Saccharomyces cerevisiae high osmolarity glycerol (HOG) mitogen-activated protein kinase pathway is required for osmoadaptation and contains two branches that activate a (Hog1) via (Pbs2). We have characterized the roles of common components (Hog1 Pbs2) in upstream (Ste11, Sho1, Ssk1) response to elevated by using whole-genome expression profiling. Several new features HOG were revealed. First, Hog1 functions during gene induction repression, cross talk inhibition, governing regulatory...

Genetic selections were used to find peptides that inhibit biological pathways in budding yeast. The presented inside cells as peptamers, surface loops on a highly expressed and biologically inert carrier protein, catalytically inactive derivative of staphylococcal nuclease. Peptamers inhibited the pheromone signaling pathway, transcriptional silencing, spindle checkpoint isolated. Putative targets for inhibitors identified by combination two-hybrid analysis genetic dissection target...

Two Saccharomyces cerevisiae plasma membrane-spanning proteins, Sho1 and Sln1, function during increased osmolarity to activate a mitogen-activated protein (MAP) kinase cascade. One of these Sho1, utilizes the MAP Ste11 Pbs2. We previously used FUS1 gene pheromone response pathway as reporter monitor cross talk in hog1 mutants. Cross requires Sho1-Ste11 branch HOG pathway, but some residual signaling, which is STE11 dependent, still occurs absence Sho1. These observations led us propose...

The budding yeast Saccharomyces cerevisiae has three cell types (a cells, α and a/α cells), each of which is specified by a unique combination transcriptional regulators. This circuit served as an important model for understanding basic features the combinatorial control transcription specification type. Here, using genome-wide chromatin immunoprecipitation, profiling, phylogenetic comparisons, we describe complete cell-type-specification S . We believe this work represents description...

Abstract Extended laboratory culture and antimicrobial susceptibility testing timelines hinder rapid species identification profiling of bacterial pathogens associated with bovine respiratory disease, the most prevalent cause cattle mortality in United States. Whole-genome sequencing offers a culture-independent alternative to current methods, but requires library reference genomes for comparison. To contribute new genome assemblies evaluate genetic diversity variation resistance genotypes,...

We investigate an alternative solution method to the joint signal-beamformer optimization problem considered in a recent publication devoted this topic. First, we directly demonstrate that problem, which minimizes received noise, interference, and clutter power under minimum variance distortionless response constraint, is generally nonconvex provide insight into nature of nonconvexity. Second, employ theory biquadratic semidefinite relaxations produce relaxed version show be <italic...

Abstract Massively parallel sequencing has revolutionized many areas of biology but large amounts DNA in individuals is cost-prohibitive and unnecessary for studies. Genomic complexity reduction techniques such as sequence capture restriction enzyme-based methods enable the analysis more per unit cost. Despite their utility, current have limitations, especially when numbers are analyzed. Here we develop a much improved site associated (RAD) protocol new method called Rapture ( R AD c apture...

Efforts to taxonomically delineate species are often confounded with conflicting information and subjective interpretation. Advances in genomic methods have resulted a new approach taxonomic identification that stands greatly reduce much of this conflict. This is ideal for complexes, where divergence times recent (evolutionarily) lineages less well defined. The California Roach/Hitch fish complex an excellent example, experiencing convoluted geologic history, diverse habitats, designations...

In waveform-adaptive space-time adaptive processing (STAP), signal-dependent interference can be mitigated through joint filter-signal design. For the common signal-to-interference-plus-noise ratio (SINR) optimality criterion, these designs result in biquadratic problems, which efficiently solved relaxation. this paper, we consider addition of two realistic waveform constraints to process, constant modulus (CM) and similarity constraint (SC), demonstrate that they are both amenable a...

Abstract Forward genetic screens provide a powerful approach for inferring gene function on the basis of phenotypes associated with mutated genes. However, determining causal mutation by traditional mapping and candidate sequencing is often rate-limiting step, especially when analyzing many mutants. We report two genomic approaches more rapidly identity affected genes in Caenorhabditis elegans First, we our use restriction site-associated DNA (RAD) polymorphism markers mutations after...

Matrix perturbation inequalities, such as Weyl's theorem (concerning the singular values) and Davis-Kahan vectors), play essential roles in quantitative science; particular, these bounds have found application data analysis well related areas of engineering computer science. In many situations, is assumed to be random, original matrix has certain structural properties (such having low rank). We show that, this scenario, classical results, Weyl Davis-Kahan, can improved significantly. believe...

Vital for Space Situational Awareness, Initial Orbit Determination (IOD) may be used to initialize object tracking and associate observations with a tracked satellite. Classical IOD algorithms provide only point solution are sensitive noisy measurements certain target-observer geometry. This work examines the ability of Multivariate GPR (MV-GPR) accurately perform quantify associated uncertainty. Given perfect test inputs, MV-GPR performs comparably simpler multitask learning algorithm...

The International Society of Information Fusion (ISIF) Stone Soup project seeks to bring together advances in target tracking through an open-source repository software libraries. Additionally, the ISIF uncertainty reasoning working group provides ontology. This paper demonstrate correspondence between open source and Uncertainty Representation Reasoning Evaluation Framework (URREF) For example, many challenge problems propose a scenario for data fusion techniques solve, from which various...

In order for a closed-loop radar system to adapt properly changing operational conditions, the performance standards and requirements of must be known. Often, these are contained in statements made language, which describe different goals system. this article, we explore use language-based cost functions (LBCFs) encode imprecise language into an objective function, fully adaptive (FAR) can optimize its real time. To enable LBCFs, also propose statement decomposer, takes as inputs yields...

In order to encode additional statistical information in data fusion and transfer learning applications, we introduce a generalized covariance constraint for the matching component analysis (MCA) technique. We provide closed-form solution resulting covariance-generalized optimization problem an algorithm its computation. call technique -- applicable both MCA (CGMCA). also demonstrate via numerical experiments that CGMCA is capable of meaningfully encoding into maps more than MCA.

This paper addresses the problem of using multiple, spatially distributed RF/EO sensors for target tracking. Data from multi-modal is collected at a fusion center, and used to track multiple objects in sensors' field view. Continuous approximations are made resolution range, range rate azimuth terms system parameters such as bandwidth, PRF, EO zoom pointing angle. These create continuous objective function tracking filter's information matrix, search undertaken find that optimize performance...

Sequence homologs are an important source of information about proteins. Amino acid profiles, representing the position-specific mutation probabilities found in a richer encoding biological sequences than individual themselves. However, profile comparisons order magnitude slower sequence comparisons, making profiles impractical for large datasets. Also, because they such rich representation, difficult to visualize. To address these problems, we describe method map probabilistic discrete...

We examine prototypical versions of the probabilistic data association (PDA) filter and joint PDA developed in Soviet Union 1972. These filters, created by Y.S. Achkasov, are previously undiscussed conventional English-language multitarget tracking (MTT) literature, despite being translated into English from their original Russian soon after publication. place this work its appropriate historical context demonstrate equivalence proto-(J)PDA with forms these algorithms, as well discuss areas...

The Ensemble Kalman Filter is a well understood method for highly nonlinear data assimilation applications, where many other state estimators either diverge or become computationally unfeasible. Here, an implementation of the (EnKF) and Square Root (EnSRF) proposed inclusion in International Society Information Fusion (ISIF) affiliated open source Python tracking framework Stone Soup. unique representation system's necessitated novel EnsembleState type, which flexibly encapsulates...