Canonical, Stable, General Mapping using Context Schemes

Motivation: Sequence mapping is the cornerstone of modern genomics. However, most existing sequence mapping algorithms are insufficiently general. Results: We introduce context schemes: a method that allows the unambiguous recognition of a reference base in a query sequence by testing the query for substrings from an algorithmically defined set. Context schemes only map when there is a unique best mapping, and define this criterion uniformly for all reference bases. Mappings under context schemes can also be made stable, so that extension of the query string (e.g. by increasing read length) will not alter the mapping of previously mapped positions. Context schemes are general in several senses. They natively support the detection of arbitrary complex, novel rearrangements relative to the reference. They can scale over orders of magnitude in query sequence length. Finally, they are trivially extensible to more complex reference structures, such as graphs, that incorporate additional variation. We demonstrate empirically the existence of high performance context schemes, and present efficient context scheme mapping algorithms. Availability and Implementation: The software test framework created for this work is available from https://registry.hub.docker.com/u/adamnovak/sequence-graphs/. Contact: [email protected] Supplementary Information: Six supplementary figures and one supplementary section are available with the online version of this article.Comment: Submission for Bioinformatic

Influence of Cylinder Bore Volume on Pressure Pulsations in a Hermetic Reciprocating Compressor

Suction pressure pulsations created when the suction valve opens are caused by unsteady mass flow through the valve exciting acoustic resonances in the suction plenum. These pressure pulsations influence valve dynamics, compressor performance and compressor noise. This paper will show the importance of including the cylinder bore volume in the flow path analysis in order to accurately calculate pressure pulsations. Pressure pulsations will be calculated using Finite Element Method (FEM) calculated impedance transfer matrix method in a quasi-static solution. The method models the impedance of the suction plenum flow path including cylinder bore volume using a static geometry condition just after the suction valve opens. The interaction between the suction plenum, suction valve port geometry, and cylinder bore volume influence acoustic resonances in this system. These resonances cause pressure pulsations that effect valve dynamics. This paper uncouples the dynamics of the suction valve from the pressure pulsation modeling. This was done to specifically look at pressure pulsation created due to refrigerant volume flow through the suction valve and suction plenum acoustic resonances without valve dynamics influencing pressure pulsation. The paper then compares simulated suction plenum pressure pulsations when the valve opens to measured pressure pulsation in a reciprocating residential HVAC compressor with good agreement

Influence of Shell Volume on Pressure Pulsations in a Hermetic Reciprocating Compressor

In a hermetic reciprocating compressor the suction pressure pulsations affect compressor performance and noise. The pressure pulsations are created due to the dynamic flow of refrigerant through the suction valve into the cylinder bore. One dimensional (1D) acoustic method, Finite Element Method (FEM) calculated impedance transfer matrix method, and Computational Fluid Dynamics (CFD) are three commonly used methods to calculate these pressure pulsations. With CFD being used most often to solve this type of analysis; however CFD is often time consuming and requires significant computer resources. In order to solve the pressure pulsation analyses faster, the suction plenum geometry is often simplified by reducing the model size. This simplification could lead to inaccuracies in pressure pulsation modeling. This paper will use the FEM calculated impedance transfer matrix method to analyze a hermetic HVAC reciprocating compressor to show that geometry simplifications could result in poor predictions of pressure pulsation. The FEM calculated impedance transfer matrix method was chosen due to its short solution time and the inherent ability to compare similarities and differences in the plenum’s impedances between the full model which includes volume inside the compressor shell, and a simplified model. This paper will specifically look at the influence of the compressor shell volume on simulating suction pressure pulsations. In the compressor analyzed, the compressor shell volume influences the pressure pulsation at the first compressor speed harmonic. A pressure pulsation at the first harmonic has the greatest influence on the compressor performance. This paper will compare measured pressure pulsations to simulated pressure pulsations. The pressure pulsations are in good agreement when the full model is analyzed but when simplifications are done to the model it fails to provide good agreement

The association of preoperative cardiac stress testing with 30-day death and myocardial infarction among patients undergoing kidney transplantation

BACKGROUND:Although periodic cardiac stress testing is commonly used to screen patients on the waiting list for kidney transplantation for ischemic heart disease, there is little evidence to support this practice. We hypothesized that cardiac stress testing in the 18 months prior to kidney transplantation would not reduce postoperative death, total myocardial infarction (MI) or fatal MI. METHODS:Using the United States Renal Data System, we identified ESRD patients ≥40 years old with primary Medicare insurance who received their first kidney transplant between 7/1/2006 and 11/31/2013. Propensity matching created a 1:1 matched sample of patients with and without stress testing in the 18 months prior to kidney transplantation. The outcomes of interest were death, total (fatal and nonfatal) MI or fatal MI within 30 days of kidney transplantation. RESULTS:In the propensity-matched cohort of 17,304 patients, death within 30 days occurred in 72 of 8,652 (0.83%) patients who underwent stress testing and in 65 of 8,652 (0.75%) patients who did not (OR 1.07; 95% CI: 0.79-1.45; P = 0.66). MI within 30 days occurred in 339 (3.9%) patients who had a stress test and in 333 (3.8%) patients who did not (OR 1.03; 95% CI: 0.89-1.21; P = 0.68). Fatal MI occurred in 17 (0.20%) patients who underwent stress testing and 15 (0.17%) patients who did not (OR 0.97; 95% CI: 0.71-1.32; P = 0.84). CONCLUSION:Stress testing in the 18 months prior to kidney transplantation is not associated with a reduction in death, total MI or fatal MI within 30 days of kidney transplantation

Haplotype-aware graph indexes

The variation graph toolkit (VG) represents genetic variation as a graph. Each path in the graph is a potential haplotype, though most paths are unlikely recombinations of true haplotypes. We augment the VG model with haplotype information to identify which paths are more likely to be correct. For this purpose, we develop a scalable implementation of the graph extension of the positional Burrows-Wheeler transform. We demonstrate the scalability of the new implementation by indexing the 1000 Genomes Project haplotypes. We also develop an algorithm for simplifying variation graphs for k-mer indexing without losing any k-mers in the haplotypes

Scale modeling of dust capture through a flooded-bed dust scrubber integrated within a longwall shearer

Meeting federal dust standards at a longwall mine face is among the more difficult challenges for a longwall mine operator. With recent changes in federal dust regulations requiring lower worker exposure, maintaining compliance has become increasingly difficult. The authors recommend the concept of controlling respirable and float dust, which is inherent in longwall mining, through the application of a flooded-bed dust scrubber to a longwall shearer. A full-scale physical model of a longwall shearer, modified with an integrated flooded-bed scrubber, was designed and fabricated at the University of Kentucky to measure the effects of a flooded-bed scrubber on dust capture at a longwall face. The mockup was transported, assembled, and tested in the longwall dust gallery at the Pittsburgh Research Laboratory of the National Institute for Occupational Safety and Health (NIOSH). Test results indicated a dust reduction of up to 57% in the return airway of the longwall gallery. The test results were validated with Computational Fluid Dynamics (CFD) modeling with a maximum of 9.7% difference in results. The aim of the study was to test the flooded-bed scrubber concept with a longwall shearer on a half-scale model using the CFD modeling technique. The paper discusses the validation of the developed scaling laws through the results of CFD modeling on the full-scale porotype and half-scale model

Haplotype-aware graph indexes.

MOTIVATION: The variation graph toolkit (VG) represents genetic variation as a graph. Although each path in the graph is a potential haplotype, most paths are non-biological, unlikely recombinations of true haplotypes. RESULTS: We augment the VG model with haplotype information to identify which paths are more likely to exist in nature. For this purpose, we develop a scalable implementation of the graph extension of the positional Burrows-Wheeler transform. We demonstrate the scalability of the new implementation by building a whole-genome index of the 5008 haplotypes of the 1000 Genomes Project, and an index of all 108 070 Trans-Omics for Precision Medicine Freeze 5 chromosome 17 haplotypes. We also develop an algorithm for simplifying variation graphs for k-mer indexing without losing any k-mers in the haplotypes. AVAILABILITY AND IMPLEMENTATION: Our software is available at https://github.com/vgteam/vg, https://github.com/jltsiren/gbwt and https://github.com/jltsiren/gcsa2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Challenging Industry to Innovate! How the Government Can Apply Transparency, Collaboration, Unencumbered Communication, and Dynamic Engagement Through Challenge-Based Acquisition

Symposium PresentationApproved for public release; distribution is unlimited

Challenging Industry to Innovate! How the Government Can Apply Transparency, Collaboration, Unencumbered Communication, and Dynamic Engagement Through Challenge-Based Acquisition

Excerpt from the Proceedings of the Nineteenth Annual Acquisition Research SymposiumThe Defense Information Systems Agency (DISA) Telecommunications Advanced Research and Dynamic Spectrum Sharing Systems (TARDyS3) program demanded new ideas and novel approaches for sharing electromagnetic spectrum between the Department of Defense and commercial industry. To solve this problem, DISA created an acquisition structure that focused on building transparency, collaborating, and actively communicating with industry across the entire acquisition. This focus on dynamically engaging vendors and encouraging innovation allowed DISA to rapidly deploy high-quality and user-approved capabilities. Dynamic engagement involves a two-way exchange of ideas, listening to industry by seeking input, and conveying the government’s ideas and motivations to potential vendors, while innovation centricity consists of encouraging vendors to solve problems with unique solutions, providing a framework for future acquisitions. Dynamic engagement, coupled with innovation centricity, powerfully engages the vendor community to solve hard problems. Combining innovation with communication creates a vendor community that is motivated to meet the government’s needs, and it accelerates risk mitigation. Furthermore, it can improve product quality and shortens delivery time lines at a reasonable price. For these reasons, future programs should consider incorporating dynamic engagement and innovation-centric approaches at the core of their acquisition strategies.Approved for public release; distribution is unlimited