scholarly journals normGAM: an R package to remove systematic biases in genome architecture mapping data

BMC Genomics ◽  
2019 ◽  
Vol 20 (S12) ◽  
Author(s):  
Tong Liu ◽  
Zheng Wang
Keyword(s):  
Fragment Length ◽  
R Package ◽  
Genome Architecture ◽  
Systematic Bias ◽  
Length Bias ◽  
Detection Frequency ◽  
Normalization Methods ◽  
New Type ◽  
Systematic Biases ◽  
Better Than

Abstract Background The genome architecture mapping (GAM) technique can capture genome-wide chromatin interactions. However, besides the known systematic biases in the raw GAM data, we have found a new type of systematic bias. It is necessary to develop and evaluate effective normalization methods to remove all systematic biases in the raw GAM data. Results We have detected a new type of systematic bias, the fragment length bias, in the genome architecture mapping (GAM) data, which is significantly different from the bias of window detection frequency previously mentioned in the paper introducing the GAM method but is similar to the bias of distances between restriction sites existing in raw Hi-C data. We have found that the normalization method (a normalized variant of the linkage disequilibrium) used in the GAM paper is not able to effectively eliminate the new fragment length bias at 1 Mb resolution (slightly better at 30 kb resolution). We have developed an R package named normGAM for eliminating the new fragment length bias together with the other three biases existing in raw GAM data, which are the biases related to window detection frequency, mappability, and GC content. Five normalization methods have been implemented and included in the R package including Knight-Ruiz 2-norm (KR2, newly designed by us), normalized linkage disequilibrium (NLD), vanilla coverage (VC), sequential component normalization (SCN), and iterative correction and eigenvector decomposition (ICE). Conclusions Based on our evaluations, the five normalization methods can eliminate the four biases existing in raw GAM data, with VC and KR2 performing better than the others. We have observed that the KR2-normalized GAM data have a higher correlation with the KR-normalized Hi-C data on the same cell samples indicating that the KR-related methods are better than the others for keeping the consistency between the GAM and Hi-C experiments. Compared with the raw GAM data, the normalized GAM data are more consistent with the normalized distances from the fluorescence in situ hybridization (FISH) experiments. The source code of normGAM can be freely downloaded from http://dna.cs.miami.edu/normGAM/.

scholarly journals OneD: increasing reproducibility of Hi-C Samples with abnormal karyotypes

2017 ◽  
Author(s):  
Enrique Vidal ◽  
François le Dily ◽  
Javier Quilez ◽  
Ralph Stadhouders ◽  
Yasmina Cuartero ◽  
...  
Keyword(s):  
Copy Number ◽  
Large Scale ◽  
Chromosomal Abnormalities ◽  
Three Dimensional ◽  
R Package ◽  
Copy Number Variations ◽  
Normalization Methods ◽  
Alternative Approach ◽  
Systematic Biases ◽  
Biological Differences

AbstractThe three-dimensional conformation of genomes is an essential component of their biological activity. The advent of the Hi-C technology enabled an unprecedented progress in our understanding of genome structures. However, Hi-C is subject to systematic biases that can compromise downstream analyses. Several strategies have been proposed to remove those biases, but the issue of abnormal karyotypes received little attention. Many experiments are performed in cancer cell lines, which typically harbor large-scale copy number variations that create visible defects on the raw Hi-C maps. The consequences of these widespread artifacts on the normalized maps are mostly unexplored. We observed that current normalization methods are not robust to the presence of large-scale copy number variations, potentially obscuring biological differences and enhancing batch effects. To address this issue, we developed an alternative approach designed to take into account chromosomal abnormalities. The method, called OneD, increases reproducibility among replicates of Hi-C samples with abnormal karyotype, outperforming previous methods significantly. On normal karyotypes, OneD fared equally well as state-of-the-art methods, making it a safe choice for Hi-C normalization. OneD is fast and scales well in terms of computing resources for resolutions up to 1 kbp. OneD is implemented as an R package available at http://www.github.com/qenvio/dryhic.

scholarly journals Material Considerations in the Microfabrication of Grating Microstructures for use in a Laser-Powered Linear Accelerator

1986 ◽  
Vol 76 ◽  
Author(s):  
John B. Warren
Keyword(s):  
Linear Accelerator ◽  
Material Selection ◽  
Collaborative Work ◽  
Fused Silica ◽  
Image Analyzer ◽  
Metrological Analysis ◽  
Field Gradients ◽  
New Type ◽  
Specialized Form ◽  
Better Than

ABSTRACTCollaborative work between Brookhaven and Los Alamos National Laboratories is developing a new type of linear accelerator that uses a high-power, picosecond pulse CO2 laser to irradiate a specialized form of grating with a pitch of 10.6 microns. The electromagnetic field that results can be used to accelerate electrons at field gradients of several GeV/m with potential efficiencies much better than current accelerators. The grating must be conductive to minimize resistive losses, be able to withstand high fields without damage, and requires dimensional tolerances in the sub-micron range. These requirements focus attention on grating material selection, microfabrication methods, and metrological methods used for quality control. At present, several types of gratings have been manufactured by reactive ion etching of fused silica in CHF 3/Ar or etching silicon with KOH/H 2O or ethylenediamine-pyrocatechol solutions. Metrological analysis of the gratings has begun with a Tracor Northern 5700 digital image analyzer.

scholarly journals A Multi-User Schedule Method for Non-Orthogonal Multiple Access in 5G Heterogeneous Network

2019 ◽  
Vol 37 (2) ◽  
pp. 337-343
Author(s):  
Yi Xie
Keyword(s):  
Heterogeneous Network ◽  
Network Architecture ◽  
Multiple Access ◽  
Average Rate ◽  
Small Cells ◽  
Fifth Generation ◽  
Scheduling Method ◽  
New Type ◽  
Multiuser Scheduling ◽  
Better Than

Heterogeneous network is supposed to be the dominant network architecture of the fifth generation (5G) cellular network, which means small cells are overlaid on the macrocell. The beamforming (BF) and cell expansion are two important approaches to serve users in small cells. Furthermore, non-orthogonal multiple access (NOMA) is a new type of multiple access multiplexing which improves system performance without taking up extra spectrum resources. Therefore, it becomes one promising technique in 5G. In this paper, NOMA is applied in a 5G heterogeneous network with biased small cells. The BF strategy and the multiuser scheduling method are proposed. The main user in NOMA is scheduled inside the original coverage of the small cell while the side user is chosen from the biased expansion area. The BF strategy that is executed depends on the channel of main user. The multiuser scheduling method is to maximize the rate performance. The proposed method can provide performance benefits. Simulation results show that the proposed methods can be well applied in heterogeneous networks. The achieved performance gain is approximately twice better than traditional OMA and has 10% improvement to the stochastic schedule method. In addition, the average rate of cell edge users is improved.

scholarly journals Improvements on Learning Kernel Extended Dictionary for Face Recognition

2020 ◽  
Vol 34 (4) ◽  
pp. 387-394
Author(s):  
Soodabeh Amanzadeh ◽  
Yahya Forghani ◽  
Javad Mahdavi Chabok
Keyword(s):  
Sparse Representation ◽  
Face Image ◽  
Collaborative Representation ◽  
Training Images ◽  
Input Face ◽  
Proposed Model ◽  
Eigen Values ◽  
New Type ◽  
The Mean ◽  
Better Than

Kernel extended dictionary learning model (KED) is a new type of Sparse Representation for Classification (SRC), which represents the input face image as a linear combination of dictionary set and extended dictionary set to determine the input face image class label. Extended dictionary is created based on the differences between the occluded images and non-occluded training images. There are four defaults to make about KED: (1) Similar weights are assigned to the principle components of occlusion variations in KED model, while the principle components of the occlusion variations have different weights, which are proportional to the principle components Eigen-values. (2) Reconstruction of an occluded image is not possible by combining only non-occluded images and the principle components (or the directions) of occlusion variations, but it requires the mean of occlusion variations. (3) The importance and capability of main dictionary and extended dictionary in reconstructing the input face image is not the same, necessarily. (4) KED Runtime is high. To address these problems or challenges, a novel mathematical model is proposed in this paper. In the proposed model, different weights are assigned to the principle components of occlusion variations; different weights are assigned to the main dictionary and extended dictionary; an occluded image is reconstructed by non-occluded images and the principle components of occlusion variations, and also the mean of occlusion variations; and collaborative representation is used instead of sparse representation to enhance the runtime. Experimental results on CAS-PEAL subsets showed that the runtime and accuracy of the proposed model is about 1% better than that of KED.

Effects of Sintering Process on the Properties of Ti3SiC2/Cu Composite

2012 ◽  
Vol 512-515 ◽  
pp. 377-381 ◽  
Author(s):  
Jin Rong Lu ◽  
Yang Zhou ◽  
Yong Zheng ◽  
Shi Bo Li ◽  
Zhen Ying Huang ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
Vickers Hardness ◽  
Hot Pressing ◽  
Sintering Temperature ◽  
Sintering Process ◽  
Vacuum Sintering ◽  
New Type ◽  
Sintering Conditions ◽  
The Relationship ◽  
Better Than

In this paper, a new type of Ti3SiC2/Cu composites with the volume fractions of 30% Ti3SiC2 particle was prepared by hot pressing and vacuum sintering respectively. The effects of sintering temperature and holding time on the density, resistance and Vickers hardness of Cu-30vol%Ti3SiC2 composite were investigated. The results show that the mechanical properties of the composites prepared by hot pressing are better than that prepared by vacuum sintering. The relative densities of Cu-30vol% Ti3SiC2 composites are rather high in suitable sintering conditions. It achieved 100% for the composites prepared by hot pressing at 930°C for 2h, and 98.4% for the composites prepared by vacuum sintering at 1250°C for 1h. At the same time, the maximum Vickers hardness reached 1735MPa at 900°C by hot pressing. The resistance and Vickers hardness of the composites decreased with an increase in sintering temperature, whereas the density increased. Scanning electron microscope (SEM) and energy-dispersive spectroscopy (EDS) were used to observe the microstructure of the composites. The relationship between microstructure and mechanical properties was discussed.

Experimental Study of Air Distribution Characteristics in Room of Stratum Ventilation under Two Kinds of Air Change Times

2013 ◽  
Vol 409-410 ◽  
pp. 668-672
Author(s):  
Yong Mei Xu ◽  
Jian Tang ◽  
Jun Han ◽  
Chu Qin Lin
Keyword(s):  
Experimental Study ◽  
Thermal Comfort ◽  
Experimental Studies ◽  
Air Distribution ◽  
Distribution Characteristics ◽  
Breathing Zone ◽  
Wind Speeds ◽  
Pollutant Concentrations ◽  
New Type ◽  
Better Than

Aimed at a new type of ventilation - stratum ventilation, air distributions at a breathing-zone in a model office were measured under kinds of air changes, the measure parameters in the experimental studies included temperatures, wind speeds and pollutant concentrations, based on which the thermal comfort at a breathing-zone were studied. Experimental results show that, the temperature, pollutant concentration and wind speeds in a breathing-zone under 5 times air changes are better than those under 6 times air changes. The calculating results of PMV and PPD indicate that the thermal comfort at a breathing-zone under 5 times air changes is better. The experimental study is instructive for the development of the ventilation.

Simulation and Experimental Investigation of a New Type of Combined Seal Structure

2021 ◽  
Vol 143 (5) ◽  
Author(s):  
Jin Li ◽  
Xiaoli Fu ◽  
Shenglin Yan
Keyword(s):  
Numerical Simulation ◽  
Labyrinth Seal ◽  
Internal Resistance ◽  
Leakage Rate ◽  
Geometric Parameters ◽  
Inlet Flow ◽  
New Type ◽  
Leakage Characteristics ◽  
Nozzle Structure ◽  
Better Than

Abstract Based on the study of leakage characteristics of labyrinth seal structure (LSS), a new type of combined seal structure (CSS) consisting of the labyrinth structure and the nozzle structure has been proposed. The sealing characteristics of CSS and LSS are compared by means of numerical simulation and experiments, and the effects of the internal resistance of the device, structural geometric parameters and other factors on the leakage characteristics of CSS are studied. The results illustrate the following conclusions: (a) When the inlet flow is 12 m3/h and the internal resistance of the device is 2000–4000 Pa, the leakage rate of CSS decreases by 30%–40% in comparison with that of LSS, which indicates that the performance of CSS is much better than that of LSS. (b) The leakage rate increases as the internal resistance of the device increases. When the internal resistance of the device increases from 2000 Pa to 8000 Pa, the leakage rate increases from 26% to 72%. (c) When the internal resistance of the device is constant, the larger the inlet flow, the smaller the leakage rate. (d) The choice of nozzle radius in structural geometric parameters is more important for the leakage rate than the tooth height and teeth numbers. When the nozzle radius decreases, ΔPAB (pressure difference between the labyrinth structure and the nozzle structure) and the leakage rate decrease accordingly.

Teleseismic slowness-azimuth station corrections for the International Monitoring System Seismic Network

1999 ◽  
Vol 89 (4) ◽  
pp. 989-1003 ◽  
Author(s):  
István Bondár ◽  
Robert G. North ◽  
Gregory Beall
Keyword(s):  
Monitoring System ◽  
Global Network ◽  
Systematic Bias ◽  
International Monitoring System ◽  
Time Data ◽  
International Monitoring ◽  
Event Location ◽  
Systematic Biases ◽  
Predicted Values ◽  
Test Ban

Abstract The prototype International Data Center (PIDC) in Arlington, Virginia, has been developing and testing software and procedures for use in the verification of the Comprehensive Test Ban Treaty. After three years of operation with a global network of array and three-component stations, it has been possible to characterize various systematic biases of those stations that are designated in the Treaty as part of the International Monitoring System (IMS). These biases include deviations of azimuth and slowness measurements from predicted values, caused largely by lateral heterogeneity. For events recorded by few stations, azimuth and slowness are used in addition to arrival-time data for location by the PIDC. Corrections to teleseismic azimuth and slowness observations have been empirically determined for most IMS stations providing data to the PIDC. Application of these corrections is shown to improve signal association and event location. At some stations an overall systematic bias can be ascribed to local crustal structure or to unreported instrumental problems. The corrections have been applied in routine operation of the PIDC since February 1998.

Desire for amputation of a limb: paraphilia, psychosis, or a new type of identity disorder

2004 ◽  
Vol 35 (6) ◽  
pp. 919-928 ◽  
Author(s):  
MICHAEL B. FIRST
Keyword(s):  
Age At Onset ◽  
Rare Condition ◽  
Negative Consequences ◽  
Structured Interviews ◽  
True Self ◽  
Self Identity ◽  
Risk Of Death ◽  
New Type ◽  
The Subject ◽  
Better Than

Background. The objective of this paper is to describe and conceptualize an unusual and probably rare condition: the intense longstanding desire to have an amputation.Method. Structured interviews were conducted by telephone of 52 subjects (mean age: 48·6, range 23–77 years; 47 male, 4 female, 1 intersexed) self-identified as having had a desire to have an amputation.Results. Seventeen per cent (n=9) had an arm or leg amputated with two-thirds using methods that put the subject at risk of death and one-third enlisting a surgeon to amputate their healthy limb. The most common reported reason for wanting an amputation was the subject's feeling that it would correct a mismatch between the person's anatomy and sense of his or her ‘true’ self (identity). None were delusional. For all but one subject age at onset was during childhood or early adolescence. For those who had psychotherapy or medication there was no change in the intensity of the desire for amputation. The six subjects who had an amputation at their desired site reported that following the amputation they felt better than they ever had and no longer had a desire for an amputation.Conclusions. These preliminary results suggest the existence of an extremely unusual clinically distinct condition characterized by a lifelong desire to have an amputation of a particular limb. The condition is associated with serious negative consequences: amputation attempts, impairment and marked distress. Reflecting similarities between Gender Identity Disorder and this condition, the author suggests that it may be conceptualized as an unusual dysfunction in the development one's fundamental sense of anatomical (body) identity.

Preparation of a New Type of Joint Filler and Study on Adhesion Performance

2014 ◽  
Vol 580-583 ◽  
pp. 674-678
Author(s):  
Xiao Wei Li ◽  
Chuan Sha
Keyword(s):  
Tensile Strength ◽  
Tensile Test ◽  
Concrete Pavement ◽  
Modified Bitumen ◽  
New Type ◽  
Adhesion Performance ◽  
Tensile Experiment ◽  
Better Than

Aiming at a new joint filler for pitch concrete pavement, processing it in different condition of water, determining the tensile strength through tensile experiment, analyzes the effect of adhesion performance from joint filler in water surrounding; does analysis to the adhesion performance of the recurrent tensile test in identical water surroundings.It evidenced that the new joint filler is much less affected in water surronuding than rubber modified bitumen,which is made by CARFCO inUSA,what meas that the new joint filler is much better than rubber modified bitumen on adhesion performance.

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