baerhunter: an R package for the discovery and anal-ysis of expressed non-coding regions in bacterial RNA-seq data

Summary: Standard bioinformatics pipelines for the analysis of bacterial transcriptomic data com-monly ignore non-coding but functional elements e.g. small RNAs, long antisense RNAs or untrans-lated regions (UTRs) of mRNA transcripts. The root of this problem is the use of incomplete genome annotation files. Here, we present baerhunter, a coverage-based method implemented in R, that au-tomates the discovery of expressed non-coding RNAs and UTRs from RNA-seq reads mapped to a reference genome. The core algorithm is part of a pipeline that facilitates downstream analysis of both coding and non-coding features. The method is simple, easy to extend and customize and, in limited tests with simulated and real data, compares favourably against the currently most popular alternative. Availability: The baerhunter R package is available from: https://github.com/irilenia/baerhunter Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

A Simple Model for the DNA Denaturation Transition

We study pairs of interacting self-avoiding walks on the 3d simple cubic lattice. They have a common origin and are allowed to overlap only at the same monomer position along the chain. The latter overlaps are indeed favored by an energetic gain. This is inspired by a model introduced long ago by Poland and Sheraga [J. Chem. Phys. {\bf 45}, 1464 (1966)] for the denaturation transition in DNA where, however, self avoidance was not fully taken into account. For both models, there exists a temperature T_m above which the entropic advantage to open up overcomes the energy gained by forming tightly bound two-stranded structures. Numerical simulations of our model indicate that the transition is of first order (the energy density is discontinuous), but the analog of the surface tension vanishes and the scaling laws near the transition point are exactly those of a second order transition with crossover exponent \phi=1. Numerical and exact analytic results show that the transition is second order in modified models where the self-avoidance is partially or completely neglected.Comment: 29 pages, LaTeX, 20 postscript figure

A Review of the fossil record of turtles of the clade Baenidae

The fossil record of the turtle clade Baenidae ranges from the Early Cretaceous (Aptian—Albian) to the Eocene. The group is present throughout North America during the Early Cretaceous, but is restricted to the western portions of the continents in the Late Cretaceous and Paleogene. No credible remains of the clade have been reported outside of North America to date. Baenids were warmadapted freshwater aquatic turtles that supported high levels of diversity at times through niche partitioning, particularly by adapting to a broad range of dietary preferences ranging from omnivorous to molluscivorous. Current phylogenies place Baenidae near the split of crown-group Testudines. Within Baenidae three more inclusive, named clades are recognized: Baenodda, Palatobaeninae and Eubaeninae. A taxonomic review of the group concludes that of 49 named taxa, 30 are nomina valida, 12 are nomina invalida and 7 are nomina dubia

Mesoscopic models for DNA stretching under force: new results and comparison to experiments

Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity. It has been proposed that the first transition, at forces of 60--80 pN, is a transition from B to S-DNA, viewed as a stretched duplex DNA, while the second one, at stronger forces, is a strand peeling resulting in single stranded DNAs (ssDNA), similar to thermal denaturation. But due to experimental conditions these two transitions can overlap, for instance for poly(dA-dT). We derive analytical formula using a coupled discrete worm like chain-Ising model. Our model takes into account bending rigidity, discreteness of the chain, linear and non-linear (for ssDNA) bond stretching. In the limit of zero force, this model simplifies into a coupled model already developed by us for studying thermal DNA melting, establishing a connexion with previous fitting parameter values for denaturation profiles. We find that: (i) ssDNA is fitted, using an analytical formula, over a nanoNewton range with only three free parameters, the contour length, the bending modulus and the monomer size; (ii) a surprisingly good fit on this force range is possible only by choosing a monomer size of 0.2 nm, almost 4 times smaller than the ssDNA nucleobase length; (iii) mesoscopic models are not able to fit B to ssDNA (or S to ss) transitions; (iv) an analytical formula for fitting B to S transitions is derived in the strong force approximation and for long DNAs, which is in excellent agreement with exact transfer matrix calculations; (v) this formula fits perfectly well poly(dG-dC) and $\lambda$-DNA force-extension curves with consistent parameter values; (vi) a coherent picture, where S to ssDNA transitions are much more sensitive to base-pair sequence than the B to S one, emerges.Comment: 14 pages, 9 figure

Magnetogenesis and the dynamics of internal dimensions

The dynamical evolution of internal space-like dimensions breaks the invariance of the Maxwell's equations under Weyl rescaling of the (conformally flat) four-dimensional metric. Depending upon the number and upon the dynamics of internal dimensions large scale magnetic fields can be created. The requirements coming from magnetogenesis together with the other cosmological constraints are examined under the assumption that the internal dimensions either grow or shrink (in conformal time) prior to a radiation dominated epoch. If the internal dimensions are growing the magnitude of the generated magnetic fields can seed the galactic dynamo mechanism.Comment: 27 in RevTex style, four figure

Development of endotoxin tolerance does not influence the response to a challenge with the mucosal live-attenuated influenza vaccine in humans in vivo

Introduction: The effects of bacterial infections on the response to subsequent viral infections are largely unknown. This is important to elucidate to increase insight into the pathophysiology of bacterial and viral co-infections, and to assess whether bacterial infections may influence the course of viral infections. Methods: Healthy male subjects received either bacterial endotoxin [Escherichia coli-derived lipopolysaccharide (LPS), 2 ng/kg, n = 15] or placebo (n = 15) intravenously, followed by intranasal Fluenz (live-attenuated influenza vaccine) 1 week later. Results: LPS administration resulted in increased plasma cytokine levels and development of endotoxin tolerance in vivo and ex vivo, illustrated by attenuated cytokine production upon rechallenge with LPS. Following Fluenz administration, infectivity for the Fluenz A/B strains was similar between the LPS-Fluenz and placebo-Fluenz groups (13/15 subjects in both groups). Also, the Fluenz-induced increase in temperature and IL-6, G-CSF and IP-10 concentrations in nasal wash were similar between both groups. Conclusion: While endotoxemia profoundly attenuates the immune response upon a second LPS challenge, it does not influence the Fluenz-induced immune response. These results suggest immune suppression after bacterial infection does not alter the response to a subsequent viral infection

Light propagation in statistically homogeneous and isotropic universes with general matter content

We derive the relationship of the redshift and the angular diameter distance to the average expansion rate for universes which are statistically homogeneous and isotropic and where the distribution evolves slowly, but which have otherwise arbitrary geometry and matter content. The relevant average expansion rate is selected by the observable redshift and the assumed symmetry properties of the spacetime. We show why light deflection and shear remain small. We write down the evolution equations for the average expansion rate and discuss the validity of the dust approximation.Comment: 42 pages, no figures. v2: Corrected one detail about the angular diameter distance and two typos. No change in result

Effectiveness of sensor-augmented insulin-pump therapy in type 1 diabetes

BACKGROUND: Recently developed technologies for the treatment of type 1 diabetes mellitus include a variety of pumps and pumps with glucose sensors. METHODS: In this 1-year, multicenter, randomized, controlled trial, we compared the efficacy of sensor-augmented pump therapy (pump therapy) with that of a regimen of multiple daily insulin injections (injection therapy) in 485 patients (329 adults and 156 children) with inadequately controlled type 1 diabetes. Patients received recombinant insulin analogues and were supervised by expert clinical teams. The primary end point was the change from the baseline glycated hemoglobin level. RESULTS: At 1 year, the baseline mean glycated hemoglobin level (8.3% in the two study groups) had decreased to 7.5% in the pump-therapy group, as compared with 8.1% in the injection-therapy group (P<0.001). The proportion of patients who reached the glycated hemoglobin target (<7%) was greater in the pump-therapy group than in the injection-therapy group. The rate of severe hypoglycemia in the pump-therapy group (13.31 cases per 100 person-years) did not differ significantly from that in the injection-therapy group (13.48 per 100 person-years, P = 0.58). There was no significant weight gain in either group. CONCLUSIONS: In both adults and children with inadequately controlled type 1 diabetes, sensor-augmented pump therapy resulted in significant improvement in glycated hemoglobin levels, as compared with injection therapy. A significantly greater proportion of both adults and children in the pump-therapy group than in the injection-therapy group reached the target glycated hemoglobin level. (ClinicalTrials.gov number, NCT00417989.

Preembryo Personhood: An Assessment of the President’s Council Arguments

The President’s Council on Bioethics has addressed the moral status of human preembryos in its reports on stem cell research and human therapeutic cloning. Although the Council has been criticized for being hand-picked to favor the right-to-life viewpoint concerning human preembryos, it has embraced the idea that the right-to-life position should be defended in secular terms. This is an important feature of the Council’s work, and it demonstrates a recognition of the need for genuine engagement between opposing sides in the debate over stem cell research. To promote this engagement, the Council has stated in secular terms several arguments for the personhood of human preembryos. This essay presents and critiques those arguments, and it concludes that they are unsuccessful. If the best arguments in support of the personhood of human preembryos have been presented by the Council, then there are no reasonable secular arguments in support of that view