scholarly journals A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Thomas H. A. Ederveen ◽  
Jos P. H. Smits ◽  
Karima Hajo ◽  
Saskia van Schalkwijk ◽  
Tessa A. Kouwenhoven ◽  
...  
Keyword(s):  
Phylogenetic Inference ◽  
Species Level ◽  
Single Locus ◽  
Bioinformatics Pipeline ◽  
Discriminative Ability ◽  
Staphylococcus Capitis ◽  
Complex Microbial Community ◽  
Reference Genomes

AbstractWe present TaxPhlAn, a new method and bioinformatics pipeline for design and analysis of single-locus sequence typing (SLST) markers to type and profile bacteria beyond the species-level in a complex microbial community background. TaxPhlAn can be applied to any group of phylogenetically-related bacteria, provided reference genomes are available. As TaxPhlAn requires the SLST targets identified to fit the phylogenetic pattern as determined through comprehensive evolutionary reconstruction of input genomes, TaxPhlAn allows for the identification and phylogenetic inference of new biodiversity. Here, we present a clinically relevant case study of high-resolution Staphylococcus profiling on skin of atopic dermatitis (AD) patients. We demonstrate that SLST enables profiling of cutaneous Staphylococcus members at (sub)species level and provides higher resolution than current 16S-based techniques. With the higher discriminative ability provided by our approach, we further show that the presence of Staphylococcus capitis on the skin together with Staphylococcus aureus associates with AD disease.

scholarly journals CSMD: a computational subtraction-based microbiome discovery pipeline for species-level characterization of clinical metagenomic samples

2019 ◽  
Author(s):  
Yu Liu ◽  
Paul W Bible ◽  
Bin Zou ◽  
Qiaoxing Liang ◽  
Cong Dong ◽  
...  
Keyword(s):  
Species Level ◽  
Supplementary Information ◽  
Clinical Samples ◽  
Plasma Dna ◽  
Bioinformatics Pipeline ◽  
Microbial Identification ◽  
Reference Databases ◽  
Microbial Dna ◽  
Higher Sensitivity

Abstract Motivation Microbiome analyses of clinical samples with low microbial biomass are challenging because of the very small quantities of microbial DNA relative to the human host, ubiquitous contaminating DNA in sequencing experiments and the large and rapidly growing microbial reference databases. Results We present computational subtraction-based microbiome discovery (CSMD), a bioinformatics pipeline specifically developed to generate accurate species-level microbiome profiles for clinical samples with low microbial loads. CSMD applies strategies for the maximal elimination of host sequences with minimal loss of microbial signal and effectively detects microorganisms present in the sample with minimal false positives using a stepwise convergent solution. CSMD was benchmarked in a comparative evaluation with other classic tools on previously published well-characterized datasets. It showed higher sensitivity and specificity in host sequence removal and higher specificity in microbial identification, which led to more accurate abundance estimation. All these features are integrated into a free and easy-to-use tool. Additionally, CSMD applied to cell-free plasma DNA showed that microbial diversity within these samples is substantially broader than previously believed. Availability and implementation CSMD is freely available at https://github.com/liuyu8721/csmd. Supplementary information Supplementary data are available at Bioinformatics online.

Construction of plastic contact deformation maps on ceramics: a case study on aluminum nitride

1996 ◽  
Vol 54 ◽  
pp. 636-637
Author(s):  
D. L. Callahan
Keyword(s):  
Plastic Deformation ◽  
Aluminum Nitride ◽  
Mechanical Response ◽  
Three Dimensional ◽  
Bright Field Image ◽  
Perfectly Plastic ◽  
Contrast Analysis ◽  
Deformation Patterns

Modern polishing, precision machining and microindentation techniques allow the processing and mechanical characterization of ceramics at nanometric scales and within entirely plastic deformation regimes. The mechanical response of most ceramics to such highly constrained contact is not predictable from macroscopic properties and the microstructural deformation patterns have proven difficult to characterize by the application of any individual technique. In this study, TEM techniques of contrast analysis and CBED are combined with stereographic analysis to construct a three-dimensional microstructure deformation map of the surface of a perfectly plastic microindentation on macroscopically brittle aluminum nitride.The bright field image in Figure 1 shows a lg Vickers microindentation contained within a single AlN grain far from any boundaries. High densities of dislocations are evident, particularly near facet edges but are not individually resolvable. The prominent bend contours also indicate the severity of plastic deformation. Figure 2 is a selected area diffraction pattern covering the entire indentation area.

Integrating The Geophysical Characterization Of Seismic Thin Beds With Stochastic Reservoir Modeling: A Case Study From The Kutei Basin (Offshore Kalimantan, Indonesia)

2011 ◽  
Author(s):  
Giorgio Rocco Cavanna ◽  
Ernesto Caselgrandi ◽  
Elisa Corti ◽  
Alessandro Amato del Monte ◽  
Massimo Fervari ◽  
...  
Keyword(s):  
Reservoir Modeling ◽  
Geophysical Characterization

Failure Analysis of CDM-ESD Damage in a GaAs RFIC

2000 ◽  
Author(s):  
Amy Poe ◽  
Steve Brockett ◽  
Tony Rubalcava
Keyword(s):  
Radio Frequency ◽  
Failure Analysis ◽  
Integrated Circuit ◽  
Production Test ◽  
Analysis Techniques ◽  
Device Model ◽  
Charged Device ◽  
Subsequent Failure

Abstract The intent of this work is to demonstrate the importance of charged device model (CDM) ESD testing and characterization by presenting a case study of a situation in which CDM testing proved invaluable in establishing the reliability of a GaAs radio frequency integrated circuit (RFIC). The problem originated when a sample of passing devices was retested to the final production test. Nine of the 200 sampled devices failed the retest, thus placing the reliability of all of the devices in question. The subsequent failure analysis indicated that the devices failed due to a short on one of two capacitors, bringing into question the reliability of the dielectric. Previous ESD characterization of the part had shown that a certain resistor was likely to fail at thresholds well below the level at which any capacitors were damaged. This paper will discuss the failure analysis techniques which were used and the testing performed to verify the failures were actually due to ESD, and not caused by weak capacitors.

dC/dV and CV Characterization of Gate Resistance Defects in eDRAM Circuits

2013 ◽  
Author(s):  
Sweta Pendyala ◽  
Dave Albert ◽  
Katherine Hawkins ◽  
Michael Tenney
Keyword(s):  
Deep Submicron ◽  
Work Flow ◽  
Localization Technique ◽  
Characterization Techniques ◽  
Capacitance Voltage ◽  
Gate Resistance

Abstract Resistive gate defects are unusual and difficult to detect with conventional techniques [1] especially on advanced devices manufactured with deep submicron SOI technologies. An advanced localization technique such as Scanning Capacitance Imaging is essential for localizing these defects, which can be followed by DC probing, dC/dV, CV (Capacitance-Voltage) measurements to completely characterize the defect. This paper presents a case study demonstrating this work flow of characterization techniques.

Case Study and Fault Modeling for Wrong Redundancy Evaluation on DRAM Devices

2007 ◽  
Author(s):  
Martin Versen ◽  
Dorina Diaconescu ◽  
Jerome Touzel
Keyword(s):  
Failure Mode ◽  
Failure Modes ◽  
Fault Modeling ◽  
Mode Analysis ◽  
Root Cause ◽  
Failure Mode Analysis

Abstract The characterization of failure modes of DRAM is often straight forward if array related hard failures with specific addresses for localization are concerned. The paper presents a case study of a bitline oriented failure mode connected to a redundancy evaluation in the DRAM periphery. The failure mode analysis and fault modeling focus both on the root-cause and on the test aspects of the problem.

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