Relaxed Filter Research Articles

Multi-Target Track Initiation in Heavy Clutter

In the heavy clutter environment, the information capacity is large, the relationships among information are complicated, and track initiation often has a high false alarm rate or missing alarm rate. Obviously, it is a difficult task to get a high-quality track initiation in the limited measurement cycles. This paper studies the multi-target track initiation in heavy clutter. At first, a relaxed logic-based clutter filter algorithm is presented. In the algorithm, the raw measurement is filtered by using the relaxed logic method. We not only design a kind of incremental and adaptive filtering gate, but also add the angle extrapolation based on polynomial extrapolation. The algorithm eliminates most of the clutter and obtains the environment with high detection rate and less clutter. Then, we propose a fuzzy sequential Hough transform-based track initiation algorithm. The algorithm establishes a new meshing rule according to system noise to balance the relationship between the grid granularity and the track initiation quality. And a flexible superposition matrix based on fuzzy clustering is constructed, which avoids the transformation error caused by 0–1 voting method in traditional Hough transform. In addition, the algorithm allows the superposition matrixes of nonadjacent cycles to be associated to overcome the shortcoming that the track can’t be initiated in time when the measurements appear in an intermittent way. And a slope verification method is introduced to detect formation-intensive serial tracks. Last, the sliding window method is employed to feedback the track initiation results timely and confirm the track. Simulation results verify that the proposed algorithms can initiate the tracks accurately in heavy clutter.

Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph

BackgroundDuring the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and frequently mutated by post-mortem chemical modifications. These features decrease read mapping accuracy and increase reference bias, in which reads containing non-reference alleles are less likely to be mapped than those containing reference alleles. Alternative approaches have been developed to replace the linear reference with a variation graph which includes known alternative variants at each genetic locus. Here, we evaluate the use of variation graph software vg to avoid reference bias for aDNA and compare with existing methods.ResultsWe use vg to align simulated and real aDNA samples to a variation graph containing 1000 Genome Project variants and compare with the same data aligned with bwa to the human linear reference genome. Using vg leads to a balanced allelic representation at polymorphic sites, effectively removing reference bias, and more sensitive variant detection in comparison with bwa, especially for insertions and deletions (indels). Alternative approaches that use relaxed bwa parameter settings or filter bwa alignments can also reduce bias but can have lower sensitivity than vg, particularly for indels.ConclusionsOur findings demonstrate that aligning aDNA sequences to variation graphs effectively mitigates the impact of reference bias when analyzing aDNA, while retaining mapping sensitivity and allowing detection of variation, in particular indel variation, that was previously missed.

Down syndrome among primiparae at older maternal age: A test of the relaxed filter hypothesis.

Down syndrome (DS) ranks as one of the most common birth defects in the United States. The relaxed filter hypothesis (RFH) asserts that mothers with no previous children but nearing reproductive senescence reduce fetal selectivity against DS pregnancies in the first trimester given the high probability of having no offspring at all if the DS pregnancy is not carried to term. We test the parity prediction of RFH-specifically, that pregnancies to older mothers with no previous live births show an elevated prevalence of DS above values expected from the separate contributions of older maternal age and primiparity. We retrieved maternal age and parity information on 2,748 DS cases (live, stillborn, or terminated due to anomaly) from the Paris Birth Defects Registry, 1983-2015. We used two waves of the Enquête Fertility Survey (n = 5,460) and counts of stillbirths to calculate total prevalence of DS by maternal age and parity. Primiparous mothers 35+ years show the greatest prevalence of any parity group (9.78 cases per 1,000 deliveries). Tests for additive interaction of primiparity and older maternal age reject the null (relative excess risk due to interaction = 1.01; 95% confidence interval: 0.33, 1.69; null value on additive scale is 0). Relaxed selection may account for 10% of the increase in the prevalence, among older primiparous mothers, of DS detected during or after the 11th week. Future work may hold implications for understanding, among older mothers, the strength of this maternal screen against other defects.

Differential Gene Expression Using RNA Sequencing Profiling in a Reconstituted Airway Epithelium Exposed to Conventional Cigarette Smoke or Electronic Cigarette Aerosols

The use of electronic cigarettes (e-cigarettes) potentially offers a safer alternative to conventional tobacco products. The advance in molecular biology and computational sciences offers new perspective to assess adverse biological responses for product risk assessment by combining omics screens with knowledge-based biological pathways. Our aim was to compare transcriptomic perturbations in MucilAir™, a commercially available lung epithelial tissue, after short repeated exposure to cigarette smoke (3R4F) and e-cigarette (Vype ePen) aerosols. We performed deep RNA sequencing and secreted inflammatory cytokine profiling postexposure. One hundred twenty-three genes were differentially expressed at fold change (FC) >1.5 and p-false discovery rate (pFDR) <0.1 for 3R4F exposure and 0 genes for Vype ePen aerosol exposure. When a relaxed filter pFDR <0.5 and FC >1.5 was applied, 29 genes were identified with e-cigarette aerosol exposure and used for validation of potential candidates by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Gene enrichment analysis was conducted and predicted a response to 3R4F smoke exposure in biological processes involving inflammation and oxidative stress pathways. No enrichment could be performed for Vype ePen aerosol exposure due to the lack of regulated gene candidates at those exposure conditions even after qRT-PCR validation. Of a panel of 33 cytokines screened, 8 were upregulated (FC >1.5 p < 0.05) following 3R4F smoke exposure, which was in agreement with our enrichment analysis. In conclusion, aerosol from the tested e-cigarette caused limited perturbations in gene and inflammatory cytokine expression compared to conventional cigarette smoke, as assessed using next-generation sequencing-based systems biology approaches in 3D commercially available reconstituted lung epithelial tissues.

Evaluating Mendelian nephrotic syndrome genes for evidence for risk alleles or oligogenicity that explain heritability.

More than 30 genes can harbor rare exonic variants sufficient to cause nephrotic syndrome (NS), and the number of genes implicated in monogenic NS continues to grow. However, outside the first year of life, the majority of affected patients, particularly in ancestrally mixed populations, do not have a known monogenic form of NS. Even in those children classified with a monogenic form of NS, there is phenotypic heterogeneity. Thus, we have only discovered a fraction of the heritability of NS-the underlying genetic factors contributing to phenotypic variation. Part of the "missing heritability" for NS has been posited to be explained by patients harboring coding variants across one or more previously implicated NS genes, insufficient to cause NS in a classical Mendelian manner, but that nonetheless have a sufficient impact on protein function to cause disease. However, systematic evaluation in patients with NS for rare or low-frequency risk alleles within single genes, or in combination across genes ("oligogenicity"), has not been reported. To determine whether, compared with a reference population, patients with NS have either a significantly increased burden of protein-altering variants ("risk-alleles"), or a unique combination of them ("oligogenicity"), in a set of 21 genes implicated in Mendelian forms of NS. In 303 patients with NS enrolled in the Nephrotic Syndrome Study Network (NEPTUNE), we performed targeted amplification paired with next-generation sequencing of 21 genes implicated in monogenic NS. We created a high-quality variant call set and compared it with a variant call set of the same genes in a reference population composed of 2,535 individuals from phase 3 of the 1000 Genomes Project. We created both a "stringent" and a "relaxed" pathogenicity-filtering pipeline, applied them to both cohorts, and computed the burden of variants in the entire gene set per cohort, the burden of variants in the entire gene set per individual, the burden of variants within a single gene per cohort, and unique combinations of variants across two or more genes per cohort. With few exceptions when using the relaxed filter, and which are likely the result of confounding by population stratification, NS patients did not have a significantly increased burden of variants in Mendelian NS genes in comparison to a reference cohort, nor was there any evidence for oligogenicity. This was true when using both the relaxed and the stringent variant pathogenicity filter. In our study, there were no significant differences in the burden or particular combinations of low-frequency or rare protein-altering variants in a previously implicated Mendelian NS genes cohort between North American patients with NS and a reference population. Studies in larger independent cohorts or meta-analyses are needed to assess the generalizability of our discoveries and also address whether there is in fact small but significant enrichment of risk alleles or oligogenicity in NS cases that was undetectable with this current sample size. It is still possible that rare protein-altering variants in these genes, insufficient to cause Mendelian disease, still contribute to NS as risk alleles and/or via oligogenicity. However, we suggest that more accurate bioinformatic analyses and the incorporation of functional assays would be necessary to identify bona fide instances of this form of genetic architecture as a contributor to the heritability of NS.

CNV analysis in 169 patients with bladder exstrophy-epispadias complex.

BackgroundThe bladder exstrophy-epispadias complex (BEEC) represents the severe end of the congenital uro-rectal malformation spectrum. Initial studies have implicated rare copy number variations (CNVs), including recurrent duplications of chromosomal region 22q11.21, in BEEC etiology.MethodsTo detect further CNVs, array analysis was performed in 169 BEEC patients. Prior to inclusion, 22q11.21 duplications were excluded using multiplex ligation-dependent probe amplification.ResultsFollowing the application of stringent filter criteria, seven rare CNVs were identified: n = 4, not present in 1307 in-house controls; n = 3, frequency of <0.002 in controls. These CNVs ranged from 1 to 6.08 Mb in size. To identify smaller CNVs, relaxed filter criteria used in the detection of previously reported BEEC associated chromosomal regions were applied. This resulted in the identification of six additional rare CNVs: n = 4, not present in 1307 in-house controls; n = 2, frequency <0.0008 in controls. These CNVs ranged from 0.03–0.08 Mb in size. For 10 of these 13 CNVs, confirmation and segregation analyses were performed (5 of maternal origin; 5 of paternal origin). Interestingly, one female with classic bladder extrophy carried a 1.18 Mb duplication of 22q11.1, a chromosomal region that is associated with cat eye syndrome.ConclusionsA number of rare CNVs were identified in BEEC patients, and these represent candidates for further evaluation. Rare inherited CNVs may constitute modifiers of, or contributors to, multifactorial BEEC phenotypes.

Retinal Fundus Image Enhancement Using the Normalized Convolution and Noise Removing.

Retinal fundus image plays an important role in the diagnosis of retinal related diseases. The detailed information of the retinal fundus image such as small vessels, microaneurysms, and exudates may be in low contrast, and retinal image enhancement usually gives help to analyze diseases related to retinal fundus image. Current image enhancement methods may lead to artificial boundaries, abrupt changes in color levels, and the loss of image detail. In order to avoid these side effects, a new retinal fundus image enhancement method is proposed. First, the original retinal fundus image was processed by the normalized convolution algorithm with a domain transform to obtain an image with the basic information of the background. Then, the image with the basic information of the background was fused with the original retinal fundus image to obtain an enhanced fundus image. Lastly, the fused image was denoised by a two-stage denoising method including the fourth order PDEs and the relaxed median filter. The retinal image databases, including the DRIVE database, the STARE database, and the DIARETDB1 database, were used to evaluate image enhancement effects. The results show that the method can enhance the retinal fundus image prominently. And, different from some other fundus image enhancement methods, the proposed method can directly enhance color images.

Color image denoising using high order iterating model by combining relaxed median filter

为去除基于局部平均曲率的彩色图像去噪模型中作为几何特征而保留下来的斑点，提出了一种改进的迭代算法。采用局部平均曲率作为正则项耦合各个颜色通道，在迭代过程中根据局部统计量检测斑点，并引入松弛中值滤波进行斑点抑制。使用不同特征的图像进行仿真实验，并对峰值信噪比的演化进行分析。实验结果表明，改进的算法在有效消除斑点的同时较好地保护了图像结构，并且提高了计算效率。峰值信噪比提高了2.47%，迭代次数减少了93.66%。

High‐resolution MODIS aerosol retrieval during wildfire events in California for use in exposure assessment

Retrieval of aerosol optical depth (AOD) from the Moderate Resolution Imaging Spectroradiometer (MODIS) using the Collection 5 (C005) algorithm provides large-scale (10 × 10 km) estimates that can be used to predict surface layer concentrations of particulate matter with aerodynamic diameter smaller than 2.5 μm (PM2.5). However, these large-scale estimates are not suitable for identifying intraurban variability of surface PM2.5 concentrations during wildfire events when individual plumes impact populated areas. We demonstrate a method for providing high-resolution (2.5 km) kernel-smoothed estimates of AOD over California during the 2008 northern California fires. The method uses high-resolution surface reflectance ratios of the 0.66 and 2.12 μm channels, a locally derived aerosol optical model characteristic of fresh wildfire plumes, and a relaxed cloud filter. Results show that the AOD derived for the 2008 northern California fires outperformed the standard product in matching observed aerosol optical thickness at three coastal Aerosol Robotic Network sites and routinely explained more than 50% of the variance in hourly surface PM2.5 concentrations observed during the wildfires.

A functional trait approach to fen restoration analysis

AbstractQuestionsEcological restoration has traditionally been evaluated with analyses focused on species identities and abundances. These analyses provide no ecological explanation to why certain species change in abundance. One solution may be a functional trait analysis. We asked whether shifts in functional traits could explain vegetation changes in fens restored through tree cutting and rewetting, and how the functional traits in the restored sites compare to those of the reference site?LocationThree former rich fens in east‐central Sweden.MethodsTree cutting and rewetting were applied in a factorial design, and species and abundance data were recorded for 8 yrs. Abundance data and trait data of canopy height, specific leaf area (SLA) and diaspore mass were used to calculate functional richness (FRic), functional divergence (FDiv), functional dispersion (FDis) and community‐weighted mean (CWM) of functional traits. Data were analysed in a linear mixed effect model for vascular plants and bryophytes jointly, and for vascular plants separately. Results of restoration treatments were compared to data from a reference site.ResultsAmong vascular plants, tree cutting caused a decrease in SLA, as shade‐sensitive species increased. In accordance with the change in SLA, FDis increased. In the joint analysis, tree cutting led to increased FDis, FDiv and FRic, indicating reduced filtering caused by the removal of the shading canopy, which allowed shade‐sensitive species to establish. The comparison to the reference site shows that even after 8 yrs, the restoration treatments have higher trait diversity than the reference site, indicating that the restoration sites have a too relaxed trait filter compared to conditions in an undisturbed fen. Our interpretation is that this is primarily caused by insufficient rewetting (and increased nutrient availability) that allow species of both natural and degraded fen conditions to co‐exist, and which failed to suppress the regrowth of trees.ConclusionsAnalysis of functional diversity improves our understanding of the ecological mechanisms affecting restoration results, and allows comparison among regions and communities with different species composition.

Improvement of nonlinear diffusion equation using relaxed geometric mean filter for low PSNR images

A new method to improve the performance of low PSNR image denoising is presented. The proposed scheme estimates edge gradient from an image that is regularised with a relaxed geometric mean filter. The proposed method consists of two stages; the first stage consists of a second order nonlinear anisotropic diffusion equation with new neighboring structure and the second is a relaxed geometric mean filter, which processes the output of nonlinear anisotropic diffusion equation. The proposed algorithm enjoys the benefit of both nonlinear PDE and relaxed geometric mean filter. In addition, the algorithm will not introduce any artefacts, and preserves image details, sharp corners, curved structures and thin lines. Comparison of the results obtained by the proposed method, with those of other methods, shows that a noticeable improvement in the quality of the denoised images, that were evaluated subjectively and quantitatively, is produced.

A test of maternal human chorionic gonadotropin during pregnancy as an adaptive filter of human gestations

The risk of abnormalities and morbidity among live births increases with advanced maternal age. Explanations for this elevated morbidity invoke several maternal mechanisms. The relaxed filter stringency (RFS) hypothesis asserts that mothers, nearing the end of their reproductive lifespan, reduce the stringency of a screen of offspring quality in utero based on life-history traits of parity and interbirth interval (IBI). A separate line of research implicates human chorionic gonadotropin (hCG) during pregnancy as a signal of offspring quality. We test the RFS hypothesis directly by examining whether the difference in gestational hCG across consecutive live births varies positively with the mother's number of previous live births but inversely with her most recent IBI. We applied multivariable regression methods to a unique dataset of gestational hCG for over 500 000 live births from 2002 to 2007. The difference in gestational hCG across mothers' consecutive live births varies positively with both mothers' parity and IBI. These associations remain similar among older mothers (35+ years). Findings support the RFS hypothesis for the parity expectation but not for the IBI expectation. Further evidence for the RFS hypothesis among contemporary human gestations would have to invoke screening mechanisms other than hCG.

A Comparative Study on Noise Removal of Compound Images using Different Types of Filters

With the advances of information technology, many techniques have been discovered to represent data. A large amount of data is commonly represented by an image. Accuracy of this data representation by an image is another important task in image processing. „Representation of data via a compound image‟ is becoming most popular day by day. So, noise removal is necessary to maintain the quality of the compound images. Noise can be added to the compound images during image acquisition, image capturing or image transmission. Different literature study shows that many filtering techniques are presented to remove noise or improve the quality of the corrupted images. This paper deals with the performance study of Median, Relaxed median, Wiener, Centre weighted median and Averaging filters to remove Salt and pepper, Gaussian and Speckle noise in the compound images. This paper proposes relaxed median filter performs better for compound images. General Terms Image Processing

Despeckling of Oil Spill SAR Images using Fusion Technique

speckle noise due to random interference of electromagnetic waves. The speckle degrades the quality of the oil spill images and makes interpretations, analysis and classifications of SAR images harder. Therefore, some speckle mitigation is necessary prior to the processing of SAR oil spill images. In this paper, some basic speckle reduction filters like Kuan, Lee, Frost, antistrophic diffusion and SRAD filters are used. A New method is proposed for despeckling of SAR oil spill images which combines the frost filter with relaxed median filter. The proposed method gives better results when compared to other methods in terms of statistical parameters like PSNR, MSE, energy and entropy value. The approach can also reduce the computing time compared with other approaches.

Investigation of intermittent air exposure on four-stage and one-stage anaerobic semi-continuous mixed-acid fermentations

This study evaluated anaerobic mixed-acid countercurrent fermentations in both strict S (minimal oxygen) and relaxed R (high oxygen) conditions. In relaxed fermentations, filter solids and liquids were exposed to air for 90min every 56h. The total acid concentrations for four-stage trains were 23.0 (4S) and 22.1 (4R) g/LLiq, and for one-stage trains were 17.2 (1S) and 18.4 (1R) g/LLiq. The strict and relaxed trains had statistically similar exit yields. The strict trains had significantly more high-molecular-weight carboxylic acids. The relaxed trains had slightly higher conversion and slightly lower selectivity, but not significantly. Air exposure had no significant effect on the bacterial profiles of the strict and relaxed fermentations. For all fermentations, the most abundant bacterial genus was Prevotella, a strict anaerobe. This study shows that the mixed-culture community is oxygen tolerant because it maintains fermentation performance during oxygen-induced stress.

An Improved Hybrid Model for Molecular Image Denoising

In this paper an improved hybrid method for removing noise from low SNR molecular images is introduced. The method provides an improvement over the one suggested by Jian Ling and Alan C. Bovik (IEEE Trans. Med. Imaging, 21(4), [2002]). The proposed model consists of two stages. The first stage consists of a fourth order PDE and the second stage is a relaxed median filter, which processes the output of fourth order PDE. The model enjoys the benefit of both nonlinear fourth order PDE and relaxed median filter. Apart from the method suggested by Ling and Bovik, the proposed method will not introduce any staircase effect and preserves fine details, sharp corners, curved structures and thin lines. Experiments were done on molecular images (fluorescence microscopic images) and standard test images and the results shows that the proposed model performs better even at higher levels of noise.

Removing Noise and Preserving Details with Relaxed Median Filters

In this paper, a median based filter called relaxed median filter is proposed. The filter is obtained by relaxing the order statistic for pixel substitution. Noise attenuation properties as well as edge and line preservation are analyzed statistically. The trade-off between noise elimination and detail preservation is widely analyzed. It is shown that relaxed median filters preserve details better than the standard median filter, and remove noise better than other median type filters.