scholarly journals Improved genome inference in the MHC using a population reference graph

2015 ◽  
Vol 47 (6) ◽  
pp. 682-688 ◽  
Author(s):  
Alexander Dilthey ◽  
Charles Cox ◽  
Zamin Iqbal ◽  
Matthew R Nelson ◽  
Gil McVean
Keyword(s):  
Reference Graph

scholarly journals Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Rachel M. Colquhoun ◽  
Michael B. Hall ◽  
Leandro Lima ◽  
Leah W. Roberts ◽  
Kerri M. Malone ◽  
...  
Keyword(s):  
Core Genome ◽  
Graph Structure ◽  
Rare Snps ◽  
Pan Genome ◽  
Nucleotide Resolution ◽  
Reference Bias ◽  
Multiple Samples ◽  
Reference Graph ◽  
Genome Graph ◽  
Better Than

AbstractWe present pandora, a novel pan-genome graph structure and algorithms for identifying variants across the full bacterial pan-genome. As much bacterial adaptability hinges on the accessory genome, methods which analyze SNPs in just the core genome have unsatisfactory limitations. Pandora approximates a sequenced genome as a recombinant of references, detects novel variation and pan-genotypes multiple samples. Using a reference graph of 578 Escherichia coli genomes, we compare 20 diverse isolates. Pandora recovers more rare SNPs than single-reference-based tools, is significantly better than picking the closest RefSeq reference, and provides a stable framework for analyzing diverse samples without reference bias.

scholarly journals Designing Thin 2.5D Parts Optimized for Fused Deposition Modeling

2019 ◽  
pp. 134-164 ◽  
Author(s):  
James I. Novak ◽  
Mark Zer-Ern Liu ◽  
Jennifer Loy
Keyword(s):  
Computer Aided Design ◽  
Fused Deposition Modeling ◽  
Outer Wall ◽  
Fused Deposition ◽  
Design Engineers ◽  
Test Pieces ◽  
New Knowledge ◽  
Deposition Modeling ◽  
Aided Design ◽  
Reference Graph

This chapter builds new knowledge for design engineers adopting fused deposition modeling (FDM) technology as an end manufacturing process, rather than simply as a prototyping process. Based on research into 2.5D printing and its use in real-world additive manufacturing situations, a study featuring 111 test pieces across the range of 0.4-4.0mm in thickness were analyzed in increments of 0.1mm to understand how these attributes affect the quality and print time of the parts and isolate specific dimensions which are optimized for the FDM process. The results revealed optimized zones where the outer wall, inner wall/s, and/or infill are produced as continuous extrusions significantly faster to print than thicknesses falling outside of optimized zones. As a result, a quick reference graph and several equations are presented based on fundamental FDM principles, allowing design engineers to implement optimized wall dimensions in computer-aided design (CAD) rather than leaving print optimization to technicians and manufacturers in the final process parameters.

Determination of Microgram Quantities of Inorganic Boron in Mammalian Specimens

1965 ◽  
Vol 11 (3) ◽  
pp. 378-385 ◽  
Author(s):  
T Konikowski ◽  
Lee E Farr
Keyword(s):  
Cerebrospinal Fluid ◽  
Sulfuric Acid ◽  
Boron Concentration ◽  
Clinical Chemistry ◽  
Mammalian Tissue ◽  
Mammalian Tissues ◽  
Concentrated Sulfuric Acid ◽  
Reference Graph

Abstract A method is presented for estimation of inorganic boron in mammalian tissues, blood, cerebrospinal fluid, and urine. The procedure is simple and rapid, qualifying it particularly to meet needs in clinical chemistry. The mammalian tissues are first enzymatically digested and extracted; then the deproteinized extract is allowed to react with quinalizarin in concentrated sulfuric acid. The intensity of the resultant color is read spectrophotometrically at 620 mµ. The boron concentration in the tissue analyzed is obtained from a standard reference graph for that tissue. The method is applicable to concentrations as low as I µg. of boron per gram of mammalian tissue or fluid.

scholarly journals Influence of spectral solar irradiance on the formation of new particles in the continental boundary layer

2002 ◽  
Vol 2 (5) ◽  
pp. 1317-1350 ◽  
Author(s):  
M. Boy ◽  
M. Kulmala
Keyword(s):  
Solar Irradiance ◽  
Short Wavelength ◽  
Correlation Coefficients ◽  
Spectral Irradiance ◽  
Reference Curve ◽  
Spectral Radiation ◽  
Short Wavelength Range ◽  
Spectral Solar Irradiance ◽  
Reference Graph ◽  
New Particles

Abstract. The relationship between nucleation events and spectral solar irradiance was analysed using two years of data collected at the Station for Measuring Forest Ecosystem-Atmosphere Relations (SMEAR II) in Hyytiälä, Finland. We analysed the data in two different ways. In the first step we calculated ten nanometer average values from the irradiance measurements between 280 and 580 nm and explored if any special wavelengths groups showed higher values on event days compared to a spectral reference curve for all the days for 2 years or to reference curves for every month. The results indicated that short wavelength irradiance between 300 and 340 nm is higher on event days in winter (February and March) compared to the monthly reference graph but quantitative much smaller than in spring or summer. By building the ratio between the average values of different event classes and the yearly reference graph we obtained peaks between 1.17 and 1.6 in the short wavelength range (300--340 nm). In the next step we included number concentrations of particles between 3 and 10 nm and calculated correlation coefficients between the different wavelengths groups and the particles. The results were quite similar to those obtained previously; the highest correlation coefficients were reached for the spectral irradiance groups 3--5 (300--330 nm) with average values for the single event classes around 0.6 and a nearly linear decrease towards higher wavelengths groups by 30%. Both analyses indicate quite clearly that short wavelength irradiance between 300 and 330 or 340 nm is the most important solar spectral radiation for the formation of newly formed aerosols. In the end we introduce a photochemical mechanism as the probable responsible pathway by calculating the production rate of excited oxygen. This mechanism shows in which way short wavelength irradiance can influence the formation of new particles even though the absolute values are one to two magnitudes smaller compared to irradiance between 400 and 500 nm.

scholarly journals Improved genome inference in the MHC using a population reference graph

2014 ◽  
Author(s):  
Alexander Dilthey ◽  
Charles Cox ◽  
Zamin Iqbal ◽  
Matthew R. Nelson ◽  
Gil McVean
Keyword(s):  
Hidden Markov ◽  
Structural Diversity ◽  
Chromosome 6 ◽  
Genome Sequences ◽  
1000 Genomes ◽  
Reference Quality ◽  
Reference Sequences ◽  
Multiple Reference ◽  
Short Indels ◽  
Reference Graph

In humans and many other species, while much is known about the extent and structure of genetic variation, such information is typically not used in assembling novel genomes. Rather, a single reference is used against which to map reads, which can lead to poor characterisation of regions of high sequence or structural diversity. Here, we introduce a population reference graph, which combines multiple reference sequences as well as catalogues of SNPs and short indels. The genomes of novel samples are reconstructed as paths through the graph using an efficient hidden Markov Model, allowing for recombination between different haplotypes and variants. By applying the method to the 4.5Mb extended MHC region on chromosome 6, combining eight assembled haplotypes, sequences of known classical HLA alleles and 87,640 SNP variants from the 1000 Genomes Project, we demonstrate, using simulations, SNP genotyping, short-read and longread data, how the method improves the accuracy of genome inference. Moreover, the analysis reveals regions where the current set of reference sequences is substantially incomplete, particularly within the Class II region, indicating the need for continued development of reference-quality genome sequences.

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