scholarly journals Selection Corrected Statistical Inference for Region Detection with High-throughput Assays

2016 ◽  
Author(s):  
Yuval Benjamini ◽  
Jonathan Taylor ◽  
Rafael A. Irizarry
Keyword(s):  
Selection Bias ◽  
Exponential Family ◽  
Common Procedure ◽  
Region Detection ◽  
Population Inference ◽  
Local Selection ◽  
Correlation Structures ◽  
Asymptotic Point ◽  
Confidence Interval Estimates ◽  
Genomic Regions

AbstractScientists use high-dimensional measurement assays to detect and prioritize regions of strong signal in a spatially organized domain. Examples include finding methylation enriched genomic regions using microarrays and identifying active cortical areas using brain-imaging. The most common procedure for detecting potential regions is to group together neighboring sites where the signal passed a threshold. However, one needs to account for the selection bias induced by this opportunistic procedure to avoid diminishing effects when generalizing to a population. In this paper, we present a model and a method that permit population inference for these detected regions. In particular, we provide non-asymptotic point and confidence interval estimates for mean effect in the region, which account for the local selection bias and the non-stationary covariance that is typical of these data. Such summaries allow researchers to better compare regions of different sizes and different correlation structures. Inference is provided within a conditional one-parameter exponential family for each region, with truncations that match the constraints of selection. A secondary screening-and-adjustment step allows pruning the set of detected regions, while controlling the false-coverage rate for the set of regions that are reported. We illustrate the benefits of the method by applying it to detected genomic regions with differing DNA-methylation rates across tissue types. Our method is shown to provide superior power compared to non-parametric approaches.

Exploring homogeneity of correlation structures of gene expression datasets within and between etiological disease categories

2014 ◽  
Vol 13 (6) ◽  
Author(s):  
Victor L. Jong ◽  
Putri W. Novianti ◽  
Kit C.B. Roes ◽  
Marinus J.C. Eijkemans
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Correlation Structure ◽  
Common Procedure ◽  
Correlation Matrices ◽  
Detection Call ◽  
Correlation Structures ◽  
Microarray Datasets ◽  
Acute Myeloid

AbstractThe literature shows that classifiers perform differently across datasets and that correlations within datasets affect the performance of classifiers. The question that arises is whether the correlation structure within datasets differ significantly across diseases. In this study, we evaluated the homogeneity of correlation structures within and between datasets of six etiological disease categories; inflammatory, immune, infectious, degenerative, hereditary and acute myeloid leukemia (AML). We also assessed the effect of filtering; detection call and variance filtering on correlation structures. We downloaded microarray datasets from ArrayExpress for experiments meeting predefined criteria and ended up with 12 datasets for non-cancerous diseases and six for AML. The datasets were preprocessed by a common procedure incorporating platform-specific recommendations and the two filtering methods mentioned above. Homogeneity of correlation matrices between and within datasets of etiological diseases was assessed using the Box’s

scholarly journals Local adaptation and the evolution of inversions on sex chromosomes and autosomes

2018 ◽  
Vol 373 (1757) ◽  
pp. 20170423 ◽  
Author(s):  
Tim Connallon ◽  
Colin Olito ◽  
Ludovic Dutoit ◽  
Homa Papoli ◽  
Filip Ruzicka ◽  
...  
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Evolutionary Dynamics ◽  
Deleterious Mutation ◽  
Local Selection ◽  
Theoretical Predictions ◽  
Elevated Rate ◽  
Genomic Regions ◽  
Spatially Varying ◽  
Spatially Varying Selection

Spatially varying selection with gene flow can favour the evolution of inversions that bind locally adapted alleles together, facilitate local adaptation and ultimately drive genomic divergence between species. Several studies have shown that the rates of spread and establishment of new inversions capturing locally adaptive alleles depend on a suite of evolutionary factors, including the strength of selection for local adaptation, rates of gene flow and recombination, and the deleterious mutation load carried by inversions. Because the balance of these factors is expected to differ between X (or Z) chromosomes and autosomes, opportunities for inversion evolution are likely to systematically differ between these genomic regions, though such scenarios have not been formally modelled. Here, we consider the evolutionary dynamics of X-linked and autosomal inversions in populations evolving at a balance between migration and local selection. We identify three factors that lead to asymmetric rates of X-linked and autosome inversion establishment: (1) sex-biased migration, (2) dominance of locally adapted alleles and (3) chromosome-specific deleterious mutation loads. This theory predicts an elevated rate of fixation, and depressed opportunities for polymorphism, for X-linked inversions. Our survey of data on the genomic distribution of polymorphic and fixed inversions supports both theoretical predictions. This article is part of the theme issue ‘Linking local adaptation with the evolution of sex differences'.

A New Look at the Union Wage Premium during the Early Years of the AFL

ILR Review ◽  
1998 ◽  
Vol 51 (2) ◽  
pp. 253-268 ◽  
Author(s):  
Debbie Mullin
Keyword(s):  
Selection Bias ◽  
Union Wage ◽  
Wage Gap ◽  
The United States ◽  
Wage Premium ◽  
Early Years ◽  
Late Nineteenth Century ◽  
Common Procedure ◽  
Union Wage Premium ◽  
Self Selection

This study provides new evidence showing that the union wage premium in the late nineteenth century in the United States was lower than previously believed. Analysis of wage and productivity data from an 1890 survey of individual workers in Maine yields a 9.2% union-nonunion wage gap, once correction is made for self-selection bias (the disproportionate representation in unions of workers who, because of skills and other attributes, would probably gain above-average wages even in the absence of unions). The author argues that business cycle conditions and distinctive union dynamics can affect the results of analyses that employ the Heckman procedure, a common procedure designed to correct for self-selection bias.

The removal and morphology of intact biofilms from implanted venous access devices

1995 ◽  
Vol 53 ◽  
pp. 1020-1021
Author(s):  
M.A. Gregory ◽  
G.P. Hadley
Keyword(s):  
Patient Selection ◽  
Surgical Oncology ◽  
Venous Access ◽  
Common Procedure ◽  
Indwelling Catheters ◽  
Careful Patient ◽  
Novel Method ◽  
The Subject ◽  
Vascular Catheters ◽  
Venous Access Devices

The insertion of implanted venous access systems for children undergoing prolonged courses of chemotherapy has become a common procedure in pediatric surgical oncology. While not permanently implanted, the devices are expected to remain functional until cure of the primary disease is assured. Despite careful patient selection and standardised insertion and access techniques, some devices fail. The most commonly encountered problems are colonisation of the device with bacteria and catheter occlusion. Both of these difficulties relate to the development of a biofilm within the port and catheter. The morphology and evolution of biofilms in indwelling vascular catheters is the subject of ongoing investigation. To date, however, such investigations have been confined to the examination of fragments of biofilm scraped or sonicated from sections of catheter. This report describes a novel method for the extraction of intact biofilms from indwelling catheters.15 children with Wilm’s tumour and who had received venous implants were studied. Catheters were removed because of infection (n=6) or electively at the end of chemotherapy.

In Reply to ‘No Obvious Impact of NSAIDs on Risk of Kidney Failure: Causal or Another Selection Bias’

2020 ◽  
Vol 76 (5) ◽  
pp. 742-743 ◽  
Author(s):  
Min Zhan ◽  
Rebecca M. Doerfler ◽  
Jeffrey C. Fink
Keyword(s):  
Selection Bias ◽  
Kidney Failure

Recurrence Rate of Lumbar Disc Herniation After Standard Discectomy and Microdiscectomy: A 5-Year Study

2019 ◽  
Vol 12 (2) ◽  
pp. 139-146
Author(s):  
Mladen E. Ovcharov ◽  
Iliya V. Valkov ◽  
Milan N. Mladenovski ◽  
Nikolay V. Vasilev
Keyword(s):  
Recurrence Rate ◽  
Lumbar Disc Herniation ◽  
Disc Herniation ◽  
Lumbar Disc ◽  
Surgical Techniques ◽  
Reoperation Rate ◽  
University Hospital ◽  
Recurrence Rates ◽  
Chi Square ◽  
Common Procedure

Summary Lumbar disc herniation (LDH) is the most common pathology in young people, as well as people of active age. Despite sophisticated and new minimally invasive surgical techniques and approaches, reoperations for recurrent lumbar disc herniation (rLDH) could not be avoided. LDH recurrence rates, reported in different studies, range from 5 to 25%. The purpose of this study was to estimate the recurrence rates of LDH after standard discectomy (SD) and microdiscectomy (MD), and compare them to those reported in the literature. Retrospectively, operative reports for the period 2012-2017 were reviewed on LDH surgeries performed at the Neurosurgery Clinic of Dr Georgi Stranski University Hospital in Pleven. Five hundred eighty-nine single-level lumbar discectomies were performed by one neurosurgeon. The diagnoses of recurrent disc herniation were based on the development of new symptoms and magnetic resonance/computed tomography (MRI/CT) images showing compatible lesions in the same lumbar level as the primary lumbar discectomies. The recurrence rate was determined by using chi-square tests and directional measures. SD was the most common procedure (498 patients) followed by MD (91 patients). The cumulative reoperation rate for rLDH was 7.5%. From a total number of reoperations, 26 were males (59.1%) and 18 were females (40.9%). Reoperation rates were 7.6% and 6.6% after SD and MD respectively. The recurrence rate was not significantly higher for SD. Our recurrence rate was 7.5%, which makes it comparable with the rates of 5-25% reported in the literature.

Improving the Computational Cost for Copied Region Detection in Forensic Images

2016 ◽  
Vol 2 (1) ◽  
pp. 55
Author(s):  
Tu Huynh-Kha ◽  
Thuong Le-Tien ◽  
Synh Ha ◽  
Khoa Huynh-Van
Keyword(s):  
Wavelet Transform ◽  
Euclidean Distance ◽  
Research Work ◽  
Computational Cost ◽  
Correlation Coefficients ◽  
Zernike Moments ◽  
Computational Time ◽  
Discrete Wavelet ◽  
Feature Vectors ◽  
Region Detection

This research work develops a new method to detect the forgery in image by combining the Wavelet transform and modified Zernike Moments (MZMs) in which the features are defined from more pixels than in traditional Zernike Moments. The tested image is firstly converted to grayscale and applied one level Discrete Wavelet Transform (DWT) to reduce the size of image by a half in both sides. The approximation sub-band (LL), which is used for processing, is then divided into overlapping blocks and modified Zernike moments are calculated in each block as feature vectors. More pixels are considered, more sufficient features are extracted. Lexicographical sorting and correlation coefficients computation on feature vectors are next steps to find the similar blocks. The purpose of applying DWT to reduce the dimension of the image before using Zernike moments with updated coefficients is to improve the computational time and increase exactness in detection. Copied or duplicated parts will be detected as traces of copy-move forgery manipulation based on a threshold of correlation coefficients and confirmed exactly from the constraint of Euclidean distance. Comparisons results between proposed method and related ones prove the feasibility and efficiency of the proposed algorithm.

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