Control and Filtering for Discrete Linear Repetitive Processes with H infty and ell 2--ell infty Performance

Repetitive processes are characterized by a series of sweeps, termed passes, through a set of dynamics defined over a finite duration known as the pass length. On each pass an output, termed the pass profile, is produced which acts as a forcing function on, and hence contributes to, the dynamics of the next pass profile. This can lead to oscillations which increase in amplitude in the pass to pass direction and cannot be controlled by standard control laws. Here we give new results on the design of physically based control laws for the sub-class of so-called discrete linear repetitive processes which arise in applications areas such as iterative learning control. The main contribution is to show how control law design can be undertaken within the framework of a general robust filtering problem with guaranteed levels of performance. In particular, we develop algorithms for the design of an H? and $\ell_{2}–\ell_{\infty}$ dynamic output feedback controller and filter which guarantees that the resulting controlled (filtering error) process, respectively, is stable along the pass and has prescribed disturbance attenuation performance as measured by $H_{\infty}$ and $\ell_{2}$–$\ell_{\infty}$ norms

Using Ontology Fingerprints to evaluate genome-wide association study results

We describe an approach to characterize genes or phenotypes via ontology fingerprints which are composed of Gene Ontology (GO) terms overrepresented among those PubMed abstracts linked to the genes or phenotypes. We then quantify the biological relevance between genes and phenotypes by comparing their ontology fingerprints to calculate a similarity score. We validated this approach by correctly identifying genes belong to their biological pathways with high accuracy, and applied this approach to evaluate GWA study by ranking genes associated with the lipid concentrations in plasma as well as to prioritize genes within linkage disequilibrium (LD) block. We found that the genes with highest scores were: ABCA1, LPL, and CETP for HDL; LDLR, APOE and APOB for LDL; and LPL, APOA1 and APOB for triglyceride. In addition, we identified some top ranked genes linking to lipid metabolism from the literature even in cases where such knowledge was not reflected in current annotation of these genes. These results demonstrate that ontology fingerprints can be used effectively to prioritize genes from GWA studies for experimental validation

The NMDA receptor functions independently and as an LRP1 co-receptor to promote Schwann cell survival and migration

NMDA Receptors (NMDA-Rs) are ionotropic glutamate receptors, which associate with LDL Receptor-related Protein-1 (LRP1) to trigger cell-signaling in response to protein ligands in neurons. Herein, we demonstrate for the first time that the NMDA-R is expressed by rat Schwann cells (SCs) and functions independently and with LRP1 to regulate SC physiology. The NR1 and NR2b NMDA-R subunits were expressed by cultured SCs and up-regulated in sciatic nerves following crush injury. The ability of LRP1 ligands to activate ERK1/2 and promote SC migration required the NMDA-R. NR1 gene-silencing compromised SC survival. Injection of the LRP1 ligands, tissue-type plasminogen activator (tPA) or MMP9-PEX, into crush-injured sciatic nerves, activated ERK1/2 in SCs in vivo and the response was blocked by systemic treatment with the NMDA-R inhibitor, MK801. tPA was unique amongst the LRP1 ligands examined because tPA activated cell-signaling and promoted SC migration by interacting with the NMDA-R independently of LRP1, albeit with delayed kinetics. These results define the NMDA-R as a SC signaling receptor for protein ligands and a major regulator of SC physiology, which may be particularly important in PNS injury

miComplete: weighted quality evaluation of assembled microbial genomes

Metagenomics and single-cell genomics have revolutionized the study of microorganisms, increasing our knowledge of microbial genomic diversity by orders of magnitude. A major issue pertaining to metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) is to estimate their completeness and redundancy. Most approaches rely on counting conserved gene markers. In miComplete, we introduce a weighting strategy, where we normalize the presence/absence of markers by their median distance to the next marker in a set of complete reference genomes. This approach alleviates biases introduced by the presence/absence of shorter DNA pieces containing many markers, e.g. ribosomal protein operons.miComplete is written in Python 3 and released under GPLv3. Source code and documentation are available at https://bitbucket.org/evolegiolab/micomplete.Supplementary data are available at Bioinformatics online

Schubert Polynomials for the affine Grassmannian of the symplectic group

We study the Schubert calculus of the affine Grassmannian Gr of the symplectic group. The integral homology and cohomology rings of Gr are identified with dual Hopf algebras of symmetric functions, defined in terms of Schur's P and Q-functions. An explicit combinatorial description is obtained for the Schubert basis of the cohomology of Gr, and this is extended to a definition of the affine type C Stanley symmetric functions. A homology Pieri rule is also given for the product of a special Schubert class with an arbitrary one.Comment: 45 page

A Geometrical Test of the Cosmological Energy Contents Using the Lyman-alpha Forest

In this Letter we explore a version of the test of cosmological geometry proposed by Alcock and Paczynski (1979), using observations of the Lyman-alpha forest in the spectra of close quasar pairs. By comparing the correlations in absorption in one quasar spectrum with correlations between the spectra of neighboring quasars one can determine the relation of the redshift distance scale to the angle distance scale at the redshift of the absorbers, $z \sim 2 - 4$. Since this relationship depends on the parameters of the cosmological model, these parameters may be determined using the Lyman-alpha forest. While this test is relatively insensitive to the density parameter $\Omega_m$ in a dust-dominated universe, it is more sensitive to the presence of a matter component with large negative pressure (such as a cosmological constant $\Lambda$) and its equation of state. With only 25 pairs of quasar spectra at angular separations $0.5' - 2'$, one can discriminate between an $\Omega_m = 0.3$ open universe ($\Lambda=0$) and an $\Omega_m = 0.3$ flat ($\Lambda$-dominated) universe at the $4-\sigma$ level. The S/N can be enhanced by considering quasar pairs at smaller angular separations, but requires proper modeling of nonlinear redshift space distortions. Here the correlations and redshift space distortions are modeled using linear theory.Comment: 13 pages, 2 ps figures, submitted to ApJ

Systematic and Stochastic Variations in Pulsar Dispersion Measures

We analyze deterministic and random temporal variations in dispersion measure (DM) from the full three-dimensional velocities of pulsars with respect to the solar system, combined with electron-density variations on a wide range of length scales. Previous treatments have largely ignored the pulsar's changing distance while favoring interpretations involving the change in sky position from transverse motion. Linear trends in pulsar DMs seen over 5-10~year timescales may signify sizable DM gradients in the interstellar medium (ISM) sampled by the changing direction of the line of sight to the pulsar. We show that motions parallel to the line of sight can also account for linear trends, for the apparent excess of DM variance over that extrapolated from scintillation measurements, and for the apparent non-Kolmogorov scalings of DM structure functions inferred in some cases. Pulsar motions through atomic gas may produce bow-shock ionized gas that also contributes to DM variations. We discuss possible causes of periodic or quasi-periodic changes in DM, including seasonal changes in the ionosphere, annual variation of the solar elongation angle, structure in the heliosphere-ISM boundary, and substructure in the ISM. We assess the solar cycle's role on the amplitude of ionospheric and solar-wind variations. Interstellar refraction can produce cyclic timing variations from the error in transforming arrival times to the solar system barycenter. We apply our methods to DM time series and DM gradient measurements in the literature and assess consistency with a Kolmogorov medium. Finally, we discuss the implications of DM modeling in precision pulsar timing experiments.Comment: 24 pages, 17 figures, published in Ap