What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual.

BackgroundNext-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficiency and accuracy of alignments, a significant percentage of reads often remain unmapped.ResultsWe generated de novo assemblies of unmapped reads from the DNA and RNA sequencing of the Bos taurus reference individual and identified the closest matching sequence to each contig by alignment to the NCBI non-redundant nucleotide database using BLAST. As expected, many of these contigs represent vertebrate sequence that is absent, incomplete, or misassembled in the UMD3.1 reference assembly. However, numerous additional contigs represent invertebrate species. Most prominent were several species of Spirurid nematodes and a blood-borne parasite, Babesia bigemina. These species are either not present in the US or are not known to infect taurine cattle and the reference animal appears to have been host to unsequenced sister species.ConclusionsWe demonstrate the importance of exploring unmapped reads to ascertain sequences that are either absent or misassembled in the reference assembly and for detecting sequences indicative of parasitic or commensal organisms

An Inversion Method for Measuring Beta in Large Redshift Surveys

A precision method for determining the value of Beta= Omega_m^{0.6}/b, where b is the galaxy bias parameter, is presented. In contrast to other existing techniques that focus on estimating this quantity by measuring distortions in the redshift space galaxy-galaxy correlation function or power spectrum, this method removes the distortions by reconstructing the real space density field and determining the value of Beta that results in a symmetric signal. To remove the distortions, the method modifies the amplitudes of a Fourier plane-wave expansion of the survey data parameterized by Beta. This technique is not dependent on the small-angle/plane-parallel approximation and can make full use of large redshift survey data. It has been tested using simulations with four different cosmologies and returns the value of Beta to +/- 0.031, over a factor of two improvement over existing techniques.Comment: 16 pages including 6 figures Submitted to The Astrophysical Journa

The spread of marine anoxia on the northern Tethys margin during the Paleocene-Eocene Thermal Maximum

Records of the paleoenvironmental changes that occurred during the Paleocene-Eocene Thermal Maximum (PETM) are preserved in sedimentary rocks along the margins of the former Tethys Ocean and Peri-Tethys. This paper presents new geochemical data that constrain paleoproductivity, sediment delivery, and seawater redox conditions, from three sites that were located in the Peri-Tethys region. Trace and major element, iron speciation, and biomarker data indicate that water column anoxia was established during episodes when inputs of land-derived higher plant organic carbon and highly weathered detrital clays and silts became relatively higher. Anoxic conditions are likely to have been initially caused by two primary processes: (i) oxygen consumption by high rates of marine productivity, initially stimulated by the rapid delivery of terrestrially derived organic matter and nutrients, and (ii) phosphorus regeneration from seafloor sediments. The role of the latter process requires further investigation before its influence on the spread of deoxygenated seawater during the PETM can be properly discerned. Other oxygen-forcing processes, such as temperature/salinity-driven water column stratification and/or methane oxidation, are considered to have been relatively less important in the study region. Organic carbon enrichments occur only during the initial stages of the PETM as defined by the negative carbon isotope excursions at each site. The lack of observed terminal stage organic carbon enrichment does not support a link between PETM climate recovery and the sequestration of excess atmospheric CO2 as organic carbon in this region; such a feedback may, however, have been important in the early stages of the PETM

Solitary vortex couples in viscoelastic Couette flow

We report experimental observation of a localized structure, which is of a new type for dissipative systems. It appears as a solitary vortex couple ("diwhirl") in Couette flow with highly elastic polymer solutions. A unique property of the diwhirls is that they are stationary, in contrast to the usual localized wave structures in both Hamiltonian and dissipative systems which are stabilized by wave dispersion. It is also a new object in fluid dynamics - a couple of vortices that build a single entity somewhat similar to a magnetic dipole. The diwhirls arise as a result of a purely elastic instability through a hysteretic transition at negligible Reynolds numbers. It is suggested that the vortex flow is driven by the same forces that cause the Weissenberg effect. The diwhirls have a striking asymmetry between the inflow and outflow, which is also an essential feature of the suggested elastic instability mechanism.Comment: 9 pages (LaTeX), 5 Postscript figures, submitte

Calculation of the Density of States Using Discrete Variable Representation and Toeplitz Matrices

A direct and exact method for calculating the density of states for systems with localized potentials is presented. The method is based on explicit inversion of the operator $E-H$. The operator is written in the discrete variable representation of the Hamiltonian, and the Toeplitz property of the asymptotic part of the obtained {\it infinite} matrix is used. Thus, the problem is reduced to the inversion of a {\it finite} matrix

Urban Dust Microbiome: Impact on Later Atopy and Wheezing

INTRODUCTION: Investigations in urban areas have just begun to explore how the indoor dust microbiome may affect the pathogenesis of asthma and allery. We aimed to investigate the early fungal and bacterial microbiome in house dust with allergic sensitization and wheezing later in childhood. METHODS: Individual dust samples from 189 homes of the LISAplus birth cohort study were collected shortly after birth from living room floors and profiled for fungal and bacterial microbiome. Fungal and bacterial diversity was assessed with terminal restriction fragment length polymorphism (tRFLP) and defined by the Simpson diversity index. Information on wheezing outcomes and co-variates until the age of 10 years was obtained by parental questionnaires. Information on specific allergic sensitization was available at 6 and 10 years. Logistic regression and General Estimation Equation (GEE) models were used to examine the relationship between microbial diversity and health outcomes. RESULTS: Logistic regression analyses revealed a significantly reduced risk of developing sensitization to aero-allergens at 6 years and ever wheezing until the age of 10 years for exposure to higher fungal diversity (adjusted Odds Ratio aOR (95%CI): 0.26 (0.10-0.70)), and 0.42 (0.18-0.96), respectively), in adjusted analyses. The associations were attenuated for the longitudinal analyses (GEE) until the age of 10 years. There was no association between higher exposure to bacterial diversity and the tested health outcomes. CONCLUSION: Higher early exposure to fungal diversity might help to prevent from developing sensitization to aero-allergens in early childhood, but the reasons for attenuated effects in later childhood require further prospective studies

Exponential Metric Fields

The Laser Interferometer Space Antenna (LISA) mission will use advanced technologies to achieve its science goals: the direct detection of gravitational waves, the observation of signals from compact (small and dense) stars as they spiral into black holes, the study of the role of massive black holes in galaxy evolution, the search for gravitational wave emission from the early Universe. The gravitational red-shift, the advance of the perihelion of Mercury, deflection of light and the time delay of radar signals are the classical tests in the first order of General Relativity (GR). However, LISA can possibly test Einstein's theories in the second order and perhaps, it will show some particular feature of non-linearity of gravitational interaction. In the present work we are seeking a method to construct theoretical templates that limit in the first order the tensorial structure of some metric fields, thus the non-linear terms are given by exponential functions of gravitational strength. The Newtonian limit obtained here, in the first order, is equivalent to GR.Comment: Accepted for publication in Astrophysics and Space Science, 17 page

Platelet-Induced Clumping of Plasmodium falciparum–Infected Erythrocytes from Malawian Patients with Cerebral Malaria—Possible Modulation In Vivo by Thrombocytopenia

Platelets may play a role in the pathogenesis of human cerebral malaria (CM), and they have been shown to induce clumping of Plasmodium falciparum–parasitized red blood cells (PRBCs) in vitro. Both thrombocytopenia and platelet-inducedPRBCclumping are associated with severe malaria and, especially, withCM.In the present study, we investigated the occurrence of the clumping phenomenon in patients with CM by isolating and coincubating their plasma and PRBCs ex vivo. Malawian children with CM all had low platelet counts, with the degree of thrombocytopenia directly proportional to the density of parasitemia. Plasma samples obtained from these patients subsequently induced weak PRBC clumping. When the assays were repeated, with the plasma platelet concentrations adjusted to within the physiological range considered to be normal, massive clumping occurred. The results of this study suggest that thrombocytopenia may, through reduction of platelet-mediated clumping of PRBCs, provide a protective mechanism for the host during CM

Flame Enhancement and Quenching in Fluid Flows

We perform direct numerical simulations (DNS) of an advected scalar field which diffuses and reacts according to a nonlinear reaction law. The objective is to study how the bulk burning rate of the reaction is affected by an imposed flow. In particular, we are interested in comparing the numerical results with recently predicted analytical upper and lower bounds. We focus on reaction enhancement and quenching phenomena for two classes of imposed model flows with different geometries: periodic shear flow and cellular flow. We are primarily interested in the fast advection regime. We find that the bulk burning rate v in a shear flow satisfies v ~ a*U+b where U is the typical flow velocity and a is a constant depending on the relationship between the oscillation length scale of the flow and laminar front thickness. For cellular flow, we obtain v ~ U^{1/4}. We also study flame extinction (quenching) for an ignition-type reaction law and compactly supported initial data for the scalar field. We find that in a shear flow the flame of the size W can be typically quenched by a flow with amplitude U ~ alpha*W. The constant alpha depends on the geometry of the flow and tends to infinity if the flow profile has a plateau larger than a critical size. In a cellular flow, we find that the advection strength required for quenching is U ~ W^4 if the cell size is smaller than a critical value.Comment: 14 pages, 20 figures, revtex4, submitted to Combustion Theory and Modellin