“Fecal microbiome in epidemiologic studies” - Letter

We congratulate Sinha et al. on their recent report (1) comparing fecal sample collection methods for epidemiologic studies of the gut microbiome. These data contribute to the increasing body of literature describing robust methodological frameworks for specimen collection and processing (2, 3). However, their claim that fixation of stool using RNAlater® results in “considerable changes to the microbiome diversity” contrasts with previous findings (2, 3), including those from their earlier reports (4, 5). We have previously demonstrated that self-collected stool stabilized with RNAlater® or other fixatives yields high fidelity and reproducibility in compositional profiling of DNA and RNA from shotgun sequence data, compared to immediately-frozen specimens (3). Additionally, fixation offers several distinct advantages crucial for large-scale population-based studies: a straightforward self-collection procedure; sample stabilization without deep-freezing during shipping, receiving, and processing; and versatility for multiple molecular analyses. The authors’ finding that specimens preserved in RNAlater® had poor correlation with immediately frozen specimens (1) could be explained, for example, by improper fixation resulting from an excess of specimen relative to preservative volume (1–2 g:2.5 ml, compared to the manufacturer-recommended ratio of 1 g:5–10 ml; Thermo Fisher Scientific Inc., Waltham, MA)

Visualization of comparative genomic analyses by BLAST score ratio

BACKGROUND: The first microbial genome sequence, Haemophilus influenzae, was published in 1995. Since then, more than 400 microbial genome sequences have been completed or commenced. This massive influx of data provides the opportunity to obtain biological insights through comparative genomics. However few tools are available for this scale of comparative analysis. RESULTS: The BLAST Score Ratio (BSR) approach, implemented in a Perl script, classifies all putative peptides within three genomes using a measure of similarity based on the ratio of BLAST scores. The output of the BSR analysis enables global visualization of the degree of proteome similarity between all three genomes. Additional output enables the genomic synteny (conserved gene order) between each genome pair to be assessed. Furthermore, we extend this synteny analysis by overlaying BSR data as a color dimension, enabling visualization of the degree of similarity of the peptides being compared. CONCLUSIONS: Combining the degree of similarity, synteny and annotation will allow rapid identification of conserved genomic regions as well as a number of common genomic rearrangements such as insertions, deletions and inversions. The script and example visualizations are available at:

Peritoneal dialysis in children after cardiopulmonary bypass

AbstractObjective: We reviewed 5 years' experience with peritoneal dialysis in children with acute renal failure after cardiac operations. We hypothesized that peritoneal dialysis is safe and effective in children with low-output cardiac failure after cardiac operations. Results: Mortality in these patients with renal failure (n = 32) was 46.9%. Fluid removed by peritoneal dialysis was 48 ± 28 ml/kg per 24 hours. Most complications of peritoneal dialysis were minor, hyperglycemia being the most frequent (53.1%). Peritoneal infection was suspected in 25%. Bowel perforation developed in two patients. None of the complications required early termination of dialysis. Hemodynamics and pulmonary function improved continuously during the study period. Conclusion: The early institution of peritoneal dialysis in acute renal failure and low cardiac output after cardiac operations not only removes fluid, thus easing fluid restriction, but may also improve cardiopulmonary function(J Thorac Cardiovasc Surg 1997;113:64-70

CAPM-based company (mis)valuations

© 2020 The Author(s) 2020. Published by Oxford University Press on behalf of The Society for Financial Studies. All rights reserved. There is a discrepancy between CAPM-implied and realized returns. Using the CAPM in capital budgeting - as recommended in textbooks - should thus have real effects. For instance, low beta projects should be valued more by CAPM users than by the market. We test this hypothesis using M&A data and show that bids for low-beta private targets entail lower bidder returns. We provide further support by testing several ancillary predictions. Our analyses suggest that using the CAPM when valuing targets leads to valuation errors (relative to the market's view) corresponding on average to 12% to 33% of the deal values

The structure of TTHA0988 from Thermus thermophilus, a KipI-KipA homologue incorrectly annotated as allophanate hydrolase

The Thermus thermophilus protein TTHA0988 is a protein of unknown function which represents a fusion of two proteins found almost ubiquitously across the bacterial kingdom. These two proteins perform a role regulating sporulation in Bacillus subtilis, where they are known as KipI and KipA. kipI and kipA genes are usually found immediately adjacent to each other and are often fused to produce a single polypeptide, as is the case with TTHA0988. Here, three crystal forms are reported of TTHA0988, the first structure to be solved from the family of `KipI-KipA fusion' proteins. Comparison of the three forms reveals structural flexibility which can be described as a hinge motion between the `KipI' and `KipA' components. TTHA0988 is annotated in various databases as a putative allophanate hydrolase. However, no such activity could be identified and genetic analysis across species with known allophanate hydrolases indicates that a misannotation has occurred. © 2011, Wiley-Blackwell. The definitive version is available at www3.interscience.wiley.co

The fables of pity: Rousseau, Mandeville and the animal-fable

Copyright @ 2012 Edinburgh University PressPrompted by Derrida’s work on the animal-fable in eighteenth-century debates about political power, this article examines the role played by the fiction of the animal in thinking of pity as either a natural virtue (in Rousseau’s Second Discourse) or as a natural passion (in Mandeville’s The Fable of the Bees). The war of fables between Rousseau and Mandeville – and their hostile reception by Samuel Johnson and Adam Smith – reinforce that the animal-fable illustrates not so much the proper of man as the possibilities and limitations of a moral philosophy that is unable to address the political realities of the state

Making the most othe relic density for dark matter searches at the LHC 14TeV Run

As the LHC continues to search for new weakly interacting particles, it is important to remember that the search is strongly motivated by the existence of dark matter. In view of a possible positive signal, it is essential to ask whether the newly discovered weakly interacting particle can be be assigned the label "dark matter". Within a given set of simplified models and modest working assumptions, we reinterpret the relic abundance bound as a relic abundance range, and compare the parameter space yielding the correct relic abundance with projections of the Run II exclusion regions. Assuming that dark matter is within the reach of the LHC, we also make the comparison with the potential 5\u3c3 discovery regions. Reversing the logic, relic density calculations can be used to optimize dark matter searches by motivating choices of parameters where the LHC can probe most deeply into the dark matter parameter space. In the event that DM is seen outside of the region giving the correct relic abundance, we will learn that either thermal relic DM is ruled out in that model, or the DM-quark coupling is suppressed relative to the DM coupling strength to other SM particles

A Hybrid Technique applied to the Intermediate-Target Optimal Control Problem

The DoD has introduced the concept of Manned-Unmanned Teaming, a subset of which is the loyal wingman. Optimal control techniques have been proposed as a method for rapidly solving the intermediate-target (mid-point constraint) optimal control problem. Initial results using direct orthogonal collocation and a gradient-based method for solving the resulting nonlinear program reveals a tendency to converge to or to get `stuck’ in locally optimal solutions. The literature suggested a hybrid technique in which a particle swarm optimization is used to quickly find a neighborhood of a more globally minimal solution, at which point the algorithm switches to a gradient-based nonlinear programming solver to converge on the globally optimal solution. The work herein applies the hybrid optimization technique to rapidly solve the loyal wingman optimal control problem. After establishing the background and describing the loyal wingman particle swarm optimization algorithm, the problem is solved first using the gradient-based direct orthogonal collocation method, then re-solved using a hybrid approach in which the results of the particle swarm optimization algorithm are used as the initial guess for the gradient-based direct orthogonal collocation method. Results comparing the final trajectory and convergence time, demonstrate the hybrid technique as a reliable method for producing rapid, autonomous, and feasible solutions to the loyal wingman optimal control problem