scholarly journals stLFRsv: a germline SV analysis pipeline using co-barcoded reads

2020 ◽  
Author(s):  
Junfu Guo ◽  
Chang Shi ◽  
Xi Chen ◽  
Ou Wang ◽  
Ping Liu ◽  
...  
Keyword(s):  
Signal To Noise Ratio ◽  
Complex Structure ◽  
Recall Rate ◽  
Genomic Information ◽  
Signal To Noise ◽  
Analysis Pipeline ◽  
Structure Variation ◽  
Base Level ◽  
Long Reads ◽  
Dna Fragment

AbstractCo-barcoded reads originated from long DNA fragment (mean length larger than 50Kbp) with barcodes, maintain both single base level accuracy and long range genomic information. We propose a pipeline stLFRsv to detect structure variation using co-barcoded reads. stLFRsv identifies abnormally large gaps between co-barcoded reads to detect potential breakpoints and reconstruct complex structure variations. The barcodes enabled co-barcoded reads phasing increases the signal to noise ratio and barcode sharing profiles are used to filter out false positives. We integrate the short reads SV caller smoove for smaller variations with stLFRsv. The integrated pipeline was evaluated on the well characterized genome HG002/NA24385 and obtained precision and recall rate of 74.2% and 22.3% for deletion on the whole genome. stLFR found some large variations not included in the benchmark set and verified by means of long reads or assembly. Our work indicates that co-barcoded reads technology has the potential to improve genome completeness.

scholarly journals stLFRsv: A Germline Structural Variant Analysis Pipeline Using Co-barcoded Reads

2021 ◽  
Vol 12 ◽  
Author(s):  
Junfu Guo ◽  
Chang Shi ◽  
Xi Chen ◽  
Ou Wang ◽  
Ping Liu ◽  
...  
Keyword(s):  
Structural Variation ◽  
Signal To Noise Ratio ◽  
Recall Rate ◽  
Structural Variants ◽  
Analysis Pipeline ◽  
Haplotype Phasing ◽  
Base Level ◽  
Long Reads ◽  
Variant Analysis ◽  
Complex Structural

Co-barcoded reads originating from long DNA fragments (mean length >30 kbp) maintain both single base level accuracy and long-range genomic information. We propose a pipeline, stLFRsv, to detect structural variation using co-barcoded reads. stLFRsv identifies abnormal large gaps between co-barcoded reads to detect potential breakpoints and reconstruct complex structural variants (SVs). Haplotype phasing by co-barcoded reads increases the signal to noise ratio, and barcode sharing profiles are used to filter out false positives. We integrate the short read SV caller smoove for smaller variants with stLFRsv. The integrated pipeline was evaluated on the well-characterized genome HG002/NA24385, and 74.5% precision and a 22.4% recall rate were obtained for deletions. stLFRsv revealed some large variants not included in the benchmark set that were verified by long reads or assembly. For the HG001/NA12878 genome, stLFRsv also achieved the best performance for both resource usage and the detection of large variants. Our work indicates that co-barcoded read technology has the potential to improve genome completeness.

Determination of the Best Emulsion for the Microscopy of Crystals

1981 ◽  
Vol 39 ◽  
pp. 32-33
Author(s):  
David A. Grano ◽  
Kenneth H. Downing
Keyword(s):  
Spatial Frequency ◽  
Information Transfer ◽  
Signal To Noise Ratio ◽  
Experimental Situation ◽  
Photographic Emulsion ◽  
Modulation Transfer ◽  
Signal To Noise ◽  
Frequency Space ◽  
Noise Ratio

The retrieval of high-resolution information from images of biological crystals depends, in part, on the use of the correct photographic emulsion. We have been investigating the information transfer properties of twelve emulsions with a view toward 1) characterizing the emulsions by a few, measurable quantities, and 2) identifying the “best” emulsion of those we have studied for use in any given experimental situation. Because our interests lie in the examination of crystalline specimens, we've chosen to evaluate an emulsion's signal-to-noise ratio (SNR) as a function of spatial frequency and use this as our critereon for determining the best emulsion.The signal-to-noise ratio in frequency space depends on several factors. First, the signal depends on the speed of the emulsion and its modulation transfer function (MTF). By procedures outlined in, MTF's have been found for all the emulsions tested and can be fit by an analytic expression 1/(1+(S/S0)2). Figure 1 shows the experimental data and fitted curve for an emulsion with a better than average MTF. A single parameter, the spatial frequency at which the transfer falls to 50% (S0), characterizes this curve.

Experiments in Bright-Field Imaging with Hollow-Cone Illumination

1981 ◽  
Vol 39 ◽  
pp. 226-227
Author(s):  
W. Kunath ◽  
K. Weiss ◽  
E. Zeitler
Keyword(s):  
Signal To Noise Ratio ◽  
Carbon Support ◽  
Electronic System ◽  
Optic Axis ◽  
Hollow Cone ◽  
Signal To Noise ◽  
Bright Field ◽  
Noise Ratio ◽  
Single Field ◽  
Field Imaging

Bright-field images taken with axial illumination show spurious high contrast patterns which obscure details smaller than 15 ° Hollow-cone illumination (HCI), however, reduces this disturbing granulation by statistical superposition and thus improves the signal-to-noise ratio. In this presentation we report on experiments aimed at selecting the proper amount of tilt and defocus for improvement of the signal-to-noise ratio by means of direct observation of the electron images on a TV monitor.Hollow-cone illumination is implemented in our microscope (single field condenser objective, Cs = .5 mm) by an electronic system which rotates the tilted beam about the optic axis. At low rates of revolution (one turn per second or so) a circular motion of the usual granulation in the image of a carbon support film can be observed on the TV monitor. The size of the granular structures and the radius of their orbits depend on both the conical tilt and defocus.

Correlation averaging of two-dimensional crystals: basic strategy and refinements

1986 ◽  
Vol 44 ◽  
pp. 136-139
Author(s):  
W. Baumeister ◽  
R. Rachel ◽  
R. Guckenberger ◽  
R. Hegerl
Keyword(s):  
Low Dose ◽  
Signal To Noise Ratio ◽  
Real Space ◽  
Fourier Domain ◽  
Two Dimensional ◽  
Signal To Noise ◽  
Unit Cells ◽  
Lateral Displacements ◽  
Established Technique ◽  
Crystalline Array

IntroductionCorrelation averaging (CAV) is meanwhile an established technique in image processing of two-dimensional crystals /1,2/. The basic idea is to detect the real positions of unit cells in a crystalline array by means of correlation functions and to average them by real space superposition of the aligned motifs. The signal-to-noise ratio improves in proportion to the number of motifs included in the average. Unlike filtering in the Fourier domain, CAV corrects for lateral displacements of the unit cells; thus it avoids the loss of resolution entailed by these distortions in the conventional approach. Here we report on some variants of the method, aimed at retrieving a maximum of information from images with very low signal-to-noise ratios (low dose microscopy of unstained or lightly stained specimens) while keeping the procedure economical.

Information capacity and bandwidth limitations in the SEM

1989 ◽  
Vol 47 ◽  
pp. 84-85
Author(s):  
D. C. Joy ◽  
R. D. Bunn
Keyword(s):  
Signal To Noise Ratio ◽  
Critical Dimension ◽  
Information Capacity ◽  
Acquisition Time ◽  
Signal To Noise ◽  
Sem Image ◽  
Probe Size ◽  
Minimum Number ◽  
Noise Ratio ◽  
Signal Channel

The information available from an SEM image is limited both by the inherent signal to noise ratio that characterizes the image and as a result of the transformations that it may undergo as it is passed through the amplifying circuits of the instrument. In applications such as Critical Dimension Metrology it is necessary to be able to quantify these limitations in order to be able to assess the likely precision of any measurement made with the microscope.The information capacity of an SEM signal, defined as the minimum number of bits needed to encode the output signal, depends on the signal to noise ratio of the image - which in turn depends on the probe size and source brightness and acquisition time per pixel - and on the efficiency of the specimen in producing the signal that is being observed. A detailed analysis of the secondary electron case shows that the information capacity C (bits/pixel) of the SEM signal channel could be written as :

Speech Reception in the Presence of Classroom Noise

1979 ◽  
Vol 10 (4) ◽  
pp. 221-230 ◽  
Author(s):  
Veronica Smyth
Keyword(s):  
Signal To Noise Ratio ◽  
Learning Processes ◽  
Speech Discrimination ◽  
Signal To Noise ◽  
Speech Reception ◽  
Monosyllabic Words ◽  
Noise Ratio

Three hundred children from five to 12 years of age were required to discriminate simple, familiar, monosyllabic words under two conditions: 1) quiet, and 2) in the presence of background classroom noise. Of the sample, 45.3% made errors in speech discrimination in the presence of background classroom noise. The effect was most marked in children younger than seven years six months. The results are discussed considering the signal-to-noise ratio and the possible effects of unwanted classroom noise on learning processes.

Effects of Fundamental Frequency Contours on Sentence Recognition in Mandarin-Speaking Children With Cochlear Implants

2020 ◽  
Vol 63 (11) ◽  
pp. 3855-3864
Author(s):  
Wanting Huang ◽  
Lena L. N. Wong ◽  
Fei Chen ◽  
Haihong Liu ◽  
Wei Liang
Keyword(s):  
Cochlear Implants ◽  
Fundamental Frequency ◽  
Signal To Noise Ratio ◽  
Lexical Tone ◽  
Signal To Noise ◽  
Sentence Recognition ◽  
Test Conditions ◽  
Age Appropriate ◽  
F0 Contour ◽  
Appropriate Sentences

Purpose Fundamental frequency (F0) is the primary acoustic cue for lexical tone perception in tonal languages but is processed in a limited way in cochlear implant (CI) systems. The aim of this study was to evaluate the importance of F0 contours in sentence recognition in Mandarin-speaking children with CIs and find out whether it is similar to/different from that in age-matched normal-hearing (NH) peers. Method Age-appropriate sentences, with F0 contours manipulated to be either natural or flattened, were randomly presented to preschool children with CIs and their age-matched peers with NH under three test conditions: in quiet, in white noise, and with competing sentences at 0 dB signal-to-noise ratio. Results The neutralization of F0 contours resulted in a significant reduction in sentence recognition. While this was seen only in noise conditions among NH children, it was observed throughout all test conditions among children with CIs. Moreover, the F0 contour-induced accuracy reduction ratios (i.e., the reduction in sentence recognition resulting from the neutralization of F0 contours compared to the normal F0 condition) were significantly greater in children with CIs than in NH children in all test conditions. Conclusions F0 contours play a major role in sentence recognition in both quiet and noise among pediatric implantees, and the contribution of the F0 contour is even more salient than that in age-matched NH children. These results also suggest that there may be differences between children with CIs and NH children in how F0 contours are processed.

Quantifying the Effects of Background Speech Babble on Preschool Children's Novel Word Learning in a Multisession Paradigm: A Preliminary Study

2020 ◽  
Vol 63 (1) ◽  
pp. 345-356
Author(s):  
Meital Avivi-Reich ◽  
Megan Y. Roberts ◽  
Tina M. Grieco-Calub
Keyword(s):  
Word Learning ◽  
Signal To Noise Ratio ◽  
Preschool Age ◽  
Exposure Condition ◽  
Signal To Noise ◽  
Verbal Recall ◽  
Referent Selection ◽  
Main Effect ◽  
Noise Ratio ◽  
Novel Word Learning

Purpose This study tested the effects of background speech babble on novel word learning in preschool children with a multisession paradigm. Method Eight 3-year-old children were exposed to a total of 8 novel word–object pairs across 2 story books presented digitally. Each story contained 4 novel consonant–vowel–consonant nonwords. Children were exposed to both stories, one in quiet and one in the presence of 4-talker babble presented at 0-dB signal-to-noise ratio. After each story, children's learning was tested with a referent selection task and a verbal recall (naming) task. Children were exposed to and tested on the novel word–object pairs on 5 separate days within a 2-week span. Results A significant main effect of session was found for both referent selection and verbal recall. There was also a significant main effect of exposure condition on referent selection performance, with more referents correctly selected for word–object pairs that were presented in quiet compared to pairs presented in speech babble. Finally, children's verbal recall of novel words was statistically better than baseline performance (i.e., 0%) on Sessions 3–5 for words exposed in quiet, but only on Session 5 for words exposed in speech babble. Conclusions These findings suggest that background speech babble at 0-dB signal-to-noise ratio disrupts novel word learning in preschool-age children. As a result, children may need more time and more exposures of a novel word before they can recognize or verbally recall it.

Selecting the Optimal FM System for Children With Cochlear Implants

2008 ◽  
Vol 18 (1) ◽  
pp. 19-24
Author(s):  
Erin C. Schafer
Keyword(s):  
Speech Recognition ◽  
Cochlear Implants ◽  
Empirical Research ◽  
Background Noise ◽  
Signal To Noise Ratio ◽  
Evidence Based ◽  
Signal To Noise ◽  
Speech Processor ◽  
System Input ◽  
Optimal Type

Children who use cochlear implants experience significant difficulty hearing speech in the presence of background noise, such as in the classroom. To address these difficulties, audiologists often recommend frequency-modulated (FM) systems for children with cochlear implants. The purpose of this article is to examine current empirical research in the area of FM systems and cochlear implants. Discussion topics will include selecting the optimal type of FM receiver, benefits of binaural FM-system input, importance of DAI receiver-gain settings, and effects of speech-processor programming on speech recognition. FM systems significantly improve the signal-to-noise ratio at the child's ear through the use of three types of FM receivers: mounted speakers, desktop speakers, or direct-audio input (DAI). This discussion will aid audiologists in making evidence-based recommendations for children using cochlear implants and FM systems.

A compact guided-wave EMAT with pulsed electromagnet for ferromagnetic tube inspection

2020 ◽  
Vol 64 (1-4) ◽  
pp. 951-958
Author(s):  
Tianhao Liu ◽  
Yu Jin ◽  
Cuixiang Pei ◽  
Jie Han ◽  
Zhenmao Chen
Keyword(s):  
Power Plants ◽  
Signal To Noise Ratio ◽  
Small Diameter ◽  
Performance Testing ◽  
Guided Wave ◽  
High Signal ◽  
Receiver Coil ◽  
Signal To Noise ◽  
Corrosion Defects

Small-diameter tubes that are widely used in petroleum industries and power plants experience corrosion during long-term services. In this paper, a compact inserted guided-wave EMAT with a pulsed electromagnet is proposed for small-diameter tube inspection. The proposed transducer is noncontact, compact with high signal-to-noise ratio and unattractive to ferromagnetic tubes. The proposed EMAT is designed with coils-only configuration, which consists of a pulsed electromagnet and a meander pulser/receiver coil. Both the numerical simulation and experimental results validate its feasibility on generating and receiving L(0,2) mode guided wave. The parameters for driving the proposed EMAT are optimized by performance testing. Finally, feasibility on quantification evaluation for corrosion defects was verified by experiments.

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