khmer: Working with Big Data in Bioinformatics

We introduce design and optimization considerations for the 'khmer' package.Comment: Invited chapter for forthcoming book on Performance of Open Source Application

Alien Registration- Brown, Eric C. (Houlton, Aroostook County)

https://digitalmaine.com/alien_docs/24751/thumbnail.jp

Investigation of mixed element hybrid grid-based CFD methods for rotorcraft flow analysis

Accurate first-principles flow prediction is essential to the design and development of rotorcraft, and while current numerical analysis tools can, in theory, model the complete flow field, in practice the accuracy of these tools is limited by various inherent numerical deficiencies. An approach that combines the first-principles physical modeling capability of CFD schemes with the vortex preservation capabilities of Lagrangian vortex methods has been developed recently that controls the numerical diffusion of the rotor wake in a grid-based solver by employing a vorticity-velocity, rather than primitive variable, formulation. Coupling strategies, including variable exchange protocols are evaluated using several unstructured, structured, and Cartesian-grid Reynolds Averaged Navier-Stokes (RANS)/Euler CFD solvers. Results obtained with the hybrid grid-based solvers illustrate the capability of this hybrid method to resolve vortex-dominated flow fields with lower cell counts than pure RANS/Euler methods

Quantum Seismology

We propose a quantum mechanical method of detecting weak vibrational disturbances inspired by the protocol of entanglement farming. We consider a setup where pairs of atoms in their ground state are successively sent through an optical cavity. It is known that in this way it is possible to drive that cavity toward a stable fixed-point state. Here we study how that fixed-point state depends on the time interval between pairs of atoms and on the distance between the cavity's mirrors. Taking advantage of an extremely precise resonance effect, we find that there are special values of these parameters where the fixed-point state is highly sensitive to perturbations, even harmonic vibrations with frequencies several orders of magnitude below the cavity's natural frequency. We propose that this sensitivity may be useful for high precision metrology.Comment: 10 pages, 5 figures. RevTeX 4.

Influence network linkages across implementation strategy conditions in a randomized controlled trial of two strategies for scaling up evidence-based practices in public youth-serving systems.

BackgroundGiven the importance of influence networks in the implementation of evidence-based practices and interventions, it is unclear whether such networks continue to operate as sources of information and advice when they are segmented and disrupted by randomization to different implementation strategy conditions. The present study examines the linkages across implementation strategy conditions of social influence networks of leaders of youth-serving systems in 12 California counties participating in a randomized controlled trial of community development teams (CDTs) to scale up use of an evidence-based practice.MethodsSemi-structured interviews were conducted with 38 directors, assistant directors, and program managers of county probation, mental health, and child welfare departments. A web-based survey collected additional quantitative data on information and advice networks of study participants. A mixed-methods approach to data analysis was used to create a sociometric data set (n = 176) to examine linkages between treatment and standard conditions.ResultsOf those network members who were affiliated with a county (n = 137), only 6 (4.4%) were directly connected to a member of the opposite implementation strategy condition; 19 (13.9%) were connected by two steps or fewer to a member of the opposite implementation strategy condition; 64 (46.7%) were connected by three or fewer steps to a member of the opposite implementation strategy condition. Most of the indirect steps between individuals who were in different implementation strategy conditions were connections involving a third non-county organizational entity that had an important role in the trial in keeping the implementation strategy conditions separate. When these entities were excluded, the CDT network exhibited fewer components and significantly higher betweenness centralization than did the standard condition network.ConclusionAlthough the integrity of the RCT in this instance was not compromised by study participant influence networks, RCT designs should consider how influence networks may extend beyond boundaries established by the randomization process in implementation studies.Trial registrationNCT00880126

Collaborative Consumption Sport Hosting: Value and Consumption Constraints

Purpose – The purpose of this paper is to find evidence of the benefits and constraints of collaborative consumption experiences by investigating the perceptions of hosts and visitors that attended professional regular season basketball and baseball games in the USA. Design/methodology/approach – Data were collected through four focus groups with 37 total participants, and were analyzed through qualitative content analysis. Findings – The results show that participants in a collaborative consumption experience perceive four types of value: social interaction and belonging, new fandom, travel bucket list experiences, and local and sport knowledge. In addition, the results provide evidence of five consumption constraints related to collaborative consumption: expenses, average experiences, seat location, interpersonal disconnects, and personal risk. The selection of only two sites for the study limited the data triangulation that was possible. This study should be replicated across a wider range of teams and countries to confirm the main findings of the study. Practical implications – Practitioners can use this initial study to better understand the benefits hosts and visitors perceive in the experience, and therefore the kind of experience design that would encourage increased purchases and loyalty. Originality/value – This paper provides qualitative insights into the benefits and detriments of a collaborative consumption sport experience, based on participants’ involvement in an innovative peer-to-peer platform

Mass Inflation in the Loop Black Hole

In classical general relativity the Cauchy horizon within a two-horizon black hole is unstable via a phenomenon known as mass inflation, in which the mass parameter (and the spacetime curvature) of the black hole diverges at the Cauchy horizon. Here we study this effect for loop black holes -- quantum gravitationally corrected black holes from loop quantum gravity -- whose construction alleviates the $r=0$ singularity present in their classical counterparts. We use a simplified model of mass inflation, which makes use of the generalized DTR relation, to conclude that the Cauchy horizon of loop black holes indeed results in a curvature singularity similar to that found in classical black holes. The DTR relation is of particular utility in the loop black hole because it does not directly rely upon Einstein's field equations. We elucidate some of the interesting and counterintuitive properties of the loop black hole, and corroborate our results using an alternate model of mass inflation due to Ori.Comment: Latex 20 pages, 7 figure

Optical Polarization and Spectral Variability in the M87 Jet

During the last decade, M87's jet has been the site of an extraordinary variability event, with one knot (HST-1) increasing by over a factor 100 in brightness. Variability was also seen on timescales of months in the nuclear flux. Here we discuss the optical-UV polarization and spectral variability of these components, which show vastly different behavior. HST-1 shows a highly significant correlation between flux and polarization, with P increasing from $\sim 20$ at minimum to >40% at maximum, while the orientation of its electric vector stayed constant. HST-1's optical-UV spectrum is very hard ($\alpha_{UV-O}\sim0.5$, $F_\nu\propto\nu^{-\alpha}$), and displays "hard lags" during epochs 2004.9-2005.5, including the peak of the flare, with soft lags at later epochs. We interpret the behavior of HST-1 as enhanced particle acceleration in a shock, with cooling from both particle aging and the relaxation of the compression. We set 2$\sigma$ upper limits of $0.5 \delta$ parsecs and 1.02$c$ on the size and advance speed of the flaring region. The slight deviation of the electric vector orientation from the jet PA, makes it likely that on smaller scales the flaring region has either a double or twisted structure. By contrast, the nucleus displays much more rapid variability, with a highly variable electric vector orientation and 'looping' in the $(I,P)$ plane. The nucleus has a much steeper spectrum ($\alpha_{UV-O} \sim 1.5$) but does not show UV-optical spectral variability. Its behavior can be interpreted as either a helical distortion to a steady jet or a shock propagating through a helical jet.Comment: 14 pages, 7 figures, ApJ, in pres