scholarly journals Memory mapped parallel BAM file access API for high throughput sequence analysis informatics

2021 ◽  
Author(s):  
Timothy A. Pitman ◽  
Xiaomeng Huang ◽  
Gabor T Marth ◽  
Yi Qiao
Keyword(s):  
Sequence Analysis ◽  
Precision Medicine ◽  
High Performance ◽  
Sequencing Data ◽  
Analysis Software ◽  
File Access ◽  
Parallel Data ◽  
Timely Fashion ◽  
New Generation ◽  
Informatics Tools

In precision medicine, genomic data needs to be processed as fast as possible to arrive at treatment decisions in a timely fashion. We developed mmbam, a library to allow sequence analysis informatics software to access raw sequencing data stored in BAM files extremely fast. Taking advantage of memory mapped file access and parallel data processing, we demonstrate that analysis software ported to mmbam consistently outperforms their stock versions. Open source and freely available, we envision that mmbam will enable a new generation of high performance informatics tools for precision medicine.

Macintosh sequence analysis software

1995 ◽  
Vol 3 (3) ◽  
pp. 221-224 ◽  
Author(s):  
Jonathan P. Clewley
Keyword(s):  
Sequence Analysis ◽  
Analysis Software

scholarly journals Review of Functional Treatments for Modified Wood

Coatings ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 327
Author(s):  
Morwenna J. Spear ◽  
Simon F. Curling ◽  
Athanasios Dimitriou ◽  
Graham A. Ormondroyd
Keyword(s):  
High Performance ◽  
Responsive Materials ◽  
Wood Modification ◽  
Wide Range ◽  
Natural Wood ◽  
Impregnation Modification ◽  
New Applications ◽  
New Generation ◽  
Dimensional Instability ◽  
Modified Wood

Wood modification is now widely recognized as offering enhanced properties of wood and overcoming issues such as dimensional instability and biodegradability which affect natural wood. Typical wood modification systems use chemical modification, impregnation modification or thermal modification, and these vary in the properties achieved. As control and understanding of the wood modification systems has progressed, further opportunities have arisen to add extra functionalities to the modified wood. These include UV stabilisation, fire retardancy, or enhanced suitability for paints and coatings. Thus, wood may become a multi-functional material through a series of modifications, treatments or reactions, to create a high-performance material with previously impossible properties. In this paper we review systems that combine the well-established wood modification procedures with secondary techniques or modifications to deliver emerging technologies with multi-functionality. The new applications targeted using this additional functionality are diverse and range from increased electrical conductivity, creation of sensors or responsive materials, improvement of wellbeing in the built environment, and enhanced fire and flame protection. We identified two parallel and connected themes: (1) the functionalisation of modified timber and (2) the modification of timber to provide (multi)-functionality. A wide range of nanotechnology concepts have been harnessed by this new generation of wood modifications and wood treatments. As this field is rapidly expanding, we also include within the review trends from current research in order to gauge the state of the art, and likely direction of travel of the industry.

scholarly journals A study on the numerical modelling of UHPFRC-strengthened members

2018 ◽  
Vol 199 ◽  
pp. 09001
Author(s):  
Renaud Franssen ◽  
Serhan Guner ◽  
Luc Courard ◽  
Boyan Mihaylov
Keyword(s):  
Numerical Modelling ◽  
High Performance ◽  
Concrete Structures ◽  
Concrete Members ◽  
High Durability ◽  
Tension Tests ◽  
The World ◽  
Aging Infrastructure ◽  
New Generation ◽  
Modelling Approach

The maintenance of large aging infrastructure across the world creates serious technical, environmental, and economic challenges. Ultra-high performance fibre-reinforced concretes (UHPFRC) are a new generation of materials with outstanding mechanical properties as well as very high durability due to their extremely low permeability. These properties open new horizons for the sustainable rehabilitation of aging concrete structures. Since UHPFRC is a young and evolving material, codes are still either lacking or incomplete, with recent design provisions proposed in France, Switzerland, Japan, and Australia. However, engineers and public agencies around the world need resources to study, model, and rehabilitate structures using UHPFRC. As an effort to contribute to the efficient use of this promising material, this paper presents a new numerical modelling approach for UHPFRC-strengthened concrete members. The approach is based on the Diverse Embedment Model within the global framework of the Disturbed Stress Field Model, a smeared rotating-crack formulation for 2D modelling of reinforced concrete structures. This study presents an adapted version of the DEM in order to capture the behaviour of UHPFRC by using a small number of input parameters. The model is validated with tension tests from the literature and is then used to model UHPFRC-strengthened elements. The paper will discuss the formulation of the model and will provide validation studies with various tests of beams, columns and walls from the literature. These studies will demonstrate the effectiveness of the proposed modelling approach.

Recent Advances in the Study of Film Cooling on the Gas Turbine Blade

2014 ◽  
Vol 971-973 ◽  
pp. 143-147 ◽  
Author(s):  
Ping Dai ◽  
Shuang Xiu Li
Keyword(s):  
Gas Turbine ◽  
Turbine Blade ◽  
Film Cooling ◽  
Gas Turbines ◽  
High Performance ◽  
Leading Edge ◽  
Development Trend ◽  
Research Progress ◽  
Gas Turbine Blade ◽  
New Generation

The development of a new generation of high performance gas turbine engines requires gas turbines to be operated at very high inlet temperatures, which are much higher than the allowable metal temperatures. Consequently, this necessitates the need for advanced cooling techniques. Among the numerous cooling technologies, the film cooling technology has superior advantages and relatively favorable application prospect. The recent research progress of film cooling techniques for gas turbine blade is reviewed and basic principle of film cooling is also illustrated. Progress on rotor blade and stationary blade of film cooling are introduced. Film cooling development of leading-edge was also generalized. Effect of various factor on cooling effectiveness and effect of the shape of the injection holes on plate film cooling are discussed. In addition, with respect to progress of discharge coefficient is presented. In the last, the future development trend and future investigation direction of film cooling are prospected.

scholarly journals Refinement of metabolite detection in cystic fibrosis sputum reveals heme negatively correlates with lung function

2018 ◽  
Author(s):  
Nathaniel R. Glasser ◽  
Ryan C. Hunter ◽  
Theodore G. Liou ◽  
Dianne K. Newman ◽  
Keyword(s):  
Mass Spectrometry ◽  
Cystic Fibrosis ◽  
Lung Function ◽  
High Performance ◽  
16S Rrna Gene Sequencing ◽  
Initial Study ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Unknown Compound ◽  
Mountain West

SummaryPseudomonas aeruginosalung infections are a leading cause of morbidity and mortality in cystic fibrosis (CF) patients (1, 2). Our laboratory has studied a class of small molecules produced byP. aeruginosaknown as phenazines, including pyocyanin and its biogenic precursor phenazine-1-carboxylic acid (PCA). As phenazines are known virulence factors (3), we and others have explored the possibility of using phenazine concentrations as a marker for disease progression (4–6). Previously, we reported that sputum concentrations of pyocyanin and PCA negatively correlate with lung function in cystic fibrosis patients (6). Our study used high performance liquid chromatography (HPLC) to quantify phenazines by UV–vis absorbance after extraction from lung sputum. Since our initial study, methods for metabolite analysis have advanced considerably, aided in large part by usage of mass spectrometry (LC-MS) and tandem mass spectrometry (LC-MS/MS). Because a more recent study employing LC-MS/MS revealed a surprising decoupling ofP. aeruginosametabolites in sputum and the detection ofP. aeruginosathrough culturing or microbiome profiles (4), we decided to check whether we could reproduce our previous findings by analyzing sputum samples from a different patient cohort with a new LC-MS instrument in our laboratory. Our new samples were provided by the Mountain West CF Consortium Sputum Biomarker study (7). In the course of performing our new analyses, comparison of our old HPLC data to our new LC-MS data led us to realize that the peak previously assigned to PCA instead originates from heme, and the peak assigned to pyocyanin originates from an as-yet unknown compound. This correction only affects the measurements of phenazines in sputum, and we are confident in the phenazine measurements from isolated cultures and the 16S rRNA gene sequencing data from that study (6). Here we outline the basis for our correction and present additional data showing that heme concentration negatively correlates with lung function in cystic fibrosis patients.

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