Accurate Profiling of Microbial Communities from Massively Parallel Sequencing using Convex Optimization

We describe the Microbial Community Reconstruction ({\bf MCR}) Problem, which is fundamental for microbiome analysis. In this problem, the goal is to reconstruct the identity and frequency of species comprising a microbial community, using short sequence reads from Massively Parallel Sequencing (MPS) data obtained for specified genomic regions. We formulate the problem mathematically as a convex optimization problem and provide sufficient conditions for identifiability, namely the ability to reconstruct species identity and frequency correctly when the data size (number of reads) grows to infinity. We discuss different metrics for assessing the quality of the reconstructed solution, including a novel phylogenetically-aware metric based on the Mahalanobis distance, and give upper-bounds on the reconstruction error for a finite number of reads under different metrics. We propose a scalable divide-and-conquer algorithm for the problem using convex optimization, which enables us to handle large problems (with $\sim10^6$ species). We show using numerical simulations that for realistic scenarios, where the microbial communities are sparse, our algorithm gives solutions with high accuracy, both in terms of obtaining accurate frequency, and in terms of species phylogenetic resolution.Comment: To appear in SPIRE 1

Lombardi Drawings of Graphs

We introduce the notion of Lombardi graph drawings, named after the American abstract artist Mark Lombardi. In these drawings, edges are represented as circular arcs rather than as line segments or polylines, and the vertices have perfect angular resolution: the edges are equally spaced around each vertex. We describe algorithms for finding Lombardi drawings of regular graphs, graphs of bounded degeneracy, and certain families of planar graphs.Comment: Expanded version of paper appearing in the 18th International Symposium on Graph Drawing (GD 2010). 13 pages, 7 figure

Systematic model behavior of adsorption on flat surfaces

A low density film on a flat surface is described by an expansion involving the first four virial coefficients. The first coefficient (alone) yields the Henry's law regime, while the next three correct for the effects of interactions. The results permit exploration of the idea of universal adsorption behavior, which is compared with experimental data for a number of systems

Charge Transport in one Dimension:Dissipative and Non-Dissipative Space-Charge Limited Currents

We consider charge transport in nanopores where the dielectric constant inside the nanopore is much greater than in the surrounding material, so that the flux of the electric fields due to the charges is almost entirely confined to the nanopore. That means that we may model the electric fields due to charge densities in the nanopore in terms of average properties across the nanopore as solutions of one dimensional Poisson equations. We develop basic equations for an M component system using equations of continuity to relate concentrations to currents, and flux equations relating currents to concentration gradients and conductivities. We then derive simplified scaled versions of the equations. We develop exact solutions for the one component case in a variety of boundary conditions using a Hopf-Cole transformation, Fourier series, and periodic solutions of the Burgers equation. These are compared with a simpler model in which the scaled diffusivity is zero so that all charge motion is driven by the electric field. In this non-dissipative case, recourse to an admissibility condition is utilised to obtain the physically relevant weak solution of a Riemann problem concerning the electric field. It is shown that the admissibility condition is Poynting's theorem.Comment: v2 contains the minor updates and corrections that have been incorporated into the published articl

The solution of Burgers' equation for sinusoidal excitation at the upstream boundary

This paper generates an exact solution to Burgers' nonlinear diffusion equation on a convective stream with sinusoidal excitation applied at the upstream boundary, x =0. The downstream boundary, effectively at x =∞, is assumed to always be far enough ahead of the convective front at x=V s t that no disturbance is felt there. The Hopf-Cole transformation is applied in achieving the analytical solution, but only after integrating the equation and its conditions in x to avoid a nonlinearity in the transformed upstream boundary condition.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42700/1/10665_2006_Article_BF02383570.pd

Effect of pre-cardiac and adult stages of Dirofilaria immitis in pulmonary disease of cats: CBC, bronchial lavage cytology, serology, radiographs, CT images, bronchial reactivity, and histopathology

AbstractA controlled, blind study was conducted to define the initial inflammatory response and lung damage associated with the death of precardiac stages of Dirofilaria immitis in cats as compared to adult heartworm infections and normal cats. Three groups of six cats each were used: UU: uninfected untreated controls; PreS I: infected with 100 D. immitis L3 by subcutaneous injection and treated topically with selamectin 32 and 2 days pre-infection and once monthly for 8 months); IU: infected with 100 D. immitis L3 and left untreated. Peripheral blood, serum, bronchial lavage, and thoracic radiographic images were collected from all cats on Days 0, 70, 110, 168, and 240. CT images were acquired on Days 0, 110, and 240. Cats were euthanized, and necropsies were conducted on Day 240 to determine the presence of heartworms. Bronchial rings were collected for in vitro reactivity. Lung, heart, brain, kidney, and liver tissues were collected for histopathology. Results were compared for changes within each group. Pearson and Spearman correlations were performed for association between histologic, radiographic, serologic, hematologic and bronchoalveolar lavage (BAL) results. Infected cats treated with selamectin did not develop radiographically evident changes throughout the study, were heartworm antibody negative, and were free of adult heartworms and worm fragments at necropsy. Histologic lung scores and CT analysis were not significantly different between PreS I cats and UU controls. Subtle alveolar myofibrosis was noted in isolated areas of several PreS I cats and an eosinophilic BAL cytology was noted on Days 75 and 120. Bronchial ring reactivity was blunted in IU cats but was normal in PreS I and UU cats. The IU cats became antibody positive, and five cats developed adult heartworms. All cats with heartworms were antigen positive at one time point; but one cat was antibody positive, antigen negative, with viable adult females at necropsy. The CT revealed early involvement of all pulmonary arteries and a random pattern of parenchymal disease with severe lesions immediately adjacent to normal areas. Analysis of CT 3D reconstruction and Hounsfield units demonstrated lung disease consistent with restrictive pulmonary fibrosis with an interstitial infiltrate, absence of air trapping, and decrease in total lung volume in Group IU as compared to Groups UU and PreS I. The clinical implications of this study are that cats pretreated with selamectin 1 month before D. immitis L3 infection did not become serologically positive and did not develop pulmonary arterial hypertrophy and myofibrosis

Synthesis and characterisation of HIP Ca0.80Ce0.20ZrTi1.60Cr0.40O7 zirconolite and observations of the ceramic–canister interface

A sample of zirconolite with nominal composition Ca0.80Ce0.20ZrTi1.60Cr0.40O7 was processed via Hot Isostatic Pressing (HIP), with a dwell temperature and pressure of 1320 °C/100 MPa maintained for 4 h. The produced wasteform was characterised by powder XRD, SEM–EDS, Ce L3 and Cr K-edge XANES. A significant portion of the Ce inventory did not fully partition within the zirconolite phase, instead remaining as CeO2 within the microstructure. Inspection of the stainless steel–ceramic interface detailed the presence of an interaction region dominated by a Cr-rich oxide layer. No significant Cr or Fe migration was observed, although a greater concentration of perovskite was observed at the periphery, relative to the bulk ceramic matrix. The X-ray absorption features of Cr remained analogous with Cr3+ accommodation within TiO6 octahedra in the zirconolite matrix. The absorption edge of Ce was comprised of contributions from zirconolite-2M and unincorporated CeO2, with an average oxidation state of Ce3.9+. As zirconolite-2M accounted for > 92 wt% of the overall phase assemblage, it is clear that the dominant oxidation state of Ce in this phase was Ce4+

Sexuality, disability, and reproductive issues through the lifespan

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45558/1/11195_2005_Article_BF01102578.pd

Sensitivity of Space Launch System Buffet Forcing Functions to Buffet Mitigation Options

Time-varying buffet forcing functions arise from unsteady aerodynamic pressures and are one of many load environments, which contribute to the overall loading condition of a launch vehicle during ascent through the atmosphere. The buffet environment is typically highest at transonic conditions and can excite the vehicle dynamic modes of vibration. The vehicle response to these buffet forcing functions may cause high structural bending moments and vibratory environments, which can exceed the capabilities of the structure, or of vehicle components such as payloads and avionics. Vehicle configurations, protuberances, payload fairings, and large changes in stage diameter can trigger undesirable buffet environments. The Space Launch System (SLS) multi-body configuration and its structural dynamic characteristics presented challenges to the load cycle design process with respect to buffet-induced loads and responses. An initial wind-tunnel test of a 3-percent scale SLS rigid buffet model was conducted in 2012 and revealed high buffet environments behind the booster forward attachment protuberance, which contributed to reduced vehicle structural margins. Six buffet mitigation options were explored to alleviate the high buffet environments including modified booster nose cones and fences/strakes on the booster and core. These studies led to a second buffet test program that was conducted in 2014 to assess the ability of the buffet mitigation options to reduce buffet environments on the vehicle. This paper will present comparisons of buffet forcing functions from each of the buffet mitigation options tested, with a focus on sectional forcing function rms levels within regions of the vehicle prone to high buffet environments

The acceleration of the universe and the physics behind it

Using a general classification of dark enegy models in four classes, we discuss the complementarity of cosmological observations to tackle down the physics beyond the acceleration of our universe. We discuss the tests distinguishing the four classes and then focus on the dynamics of the perturbations in the Newtonian regime. We also exhibit explicitely models that have identical predictions for a subset of observations.Comment: 18 pages, 18 figure