Coverage Profiles Research Articles

Selecting Stopping Rules for Confidence Interval Procedures

The sample size decision is crucial to the success of any sampling experiment. More samples imply better confidence and precision in the results, but require higher costs in terms of time, computing power, and money. Analysts often choose sequential stopping rules on an ad hoc basis to obtain confidence intervals with desired properties without requiring large sample sizes. However, the choice of stopping rule can affect the quality of the interval produced in terms of the coverage, precision, and replication cost. This article introduces methods for choosing and evaluating stopping rules for confidence interval procedures. We develop a general framework for assessing the quality of a broad class of stopping rules applied to independent and identically distributed data. We introduce coverage profiles that plot the coverage according to the stopping time and reveal situations when the coverage could be unexpectedly low. Finally, we recommend simple techniques for obtaining acceptable or optimal rules.

Recent FDA approval of sofosbuvir and simeprevir. Implications for current HCV treatment.

Recent FDA approval of sofosbuvir and simeprevir. Implications for current HCV treatment.

A Markov chain approach to simulate Atomic Layer Deposition chemistry and transport inside nanostructured substrates

In this work, we present a new theoretical framework to model the transport and surface chemistry under molecular (Knudsen) flow. Our approach is based on casting the transport inside nanostructures as a single-particle discrete Markov chain process. One of the advantages of this approach is that it allows us to decouple the complexity of the surface chemistry from the transport model, thus allowing its application under general surface chemistry conditions, including atomic layer deposition (ALD) and chemical vapor deposition (CVD). Our model also allows us to determine statistical information of the trajectory of individual molecules, such as the average interaction time or the number of wall collisions for molecules entering the nanostructures as well as to track the relative contributions to thin-film growth of different independent reaction pathways at each point of the feature. This offers a straightforward way of incorporating into ALD simulations non-ideal surface processes, such as parasitic CVD or surface recombination. By studying the asymptotic behavior of the Markov chain process, we were also able to establish a direct link between ballistic models, kinetic Monte Carlo simulations, and continuous models based on the use of the diffusion equation under Knudsen conditions. Finally, we show that, under certain approximations, the coverage profile inside a nanostructure under ALD conditions is controlled by the total exposure, and not by the details of the surface flux dependence with time during the exposure, as long as the reaction probabilities are pressure independent.

Electrostatic spray cabinet evaluation to verify uniform delivery of chemical and biological solutions to pre-chilled meat animal carcasses (2014)

Shiga toxin-producing Escherichia coli (STEC) are a group of bacteria that cause an estimated 265,000 illnesses, 3,600 hospitalizations, and 30 deaths annually in the United States. STEC are frequently associated with raw or undercooked meat products, prompting the beef industry to develop and apply various antimicrobial intervention technologies during processing operations. The application of chemical antimicrobials to carcasses and fabricated cuts using an electrostatic spray (ESS) system (Figure 1) offers several potential advantages for controlling disease-causing pathogens, including enhanced chemical deposition (coverage) profiles, reduced overspray wastage of foodgrade antimicrobials, and reduced water requirements. The objectives of this study were to (1) calibrate an ESS carcass cabinet installed at the Kansas State University Biosecurity Research Institute, (2) test the chemical deposition profile of the ESS cabinet onto a meat carcass using fluorescent dye, and (3) determine if the ESS could be used to uniformly apply a biological inoculum to a carcass to support pathogen-inoculated validation studies of different chemical intervention technologies to support the needs of the beef processing industry.

The Relation of Race and Type of Health Insurance to Long-Term Risk of Mortality Among Lung Cancer Patients in Rural Eastern North Carolina

Black patients with lung cancer have a higher mortality rate than do their white counterparts. Differences in insurance coverage, demographic characteristics, and treatment profiles may explain this disparity. The purpose of this study was to compare the longterm risk of mortality of black lung cancer patients with that of white lung cancer patients, by insurance type. Patients who were diagnosed with lung cancer in Eastern North Carolina and treated at the Leo Jenkins Cancer Center between 2001 and 2010 were included in this study. A Cox regression model was used to compare the risk of mortality of black patients with that of white patients. A total of 2,351 lung cancer patients (717 black and 1,634 white) were treated at the Leo Jenkins Cancer Center during the study period. Independent of age and sex, black patients with lung cancer were observed to die sooner than their white counterparts (hazard ratio = 1.2; 95% confidence interval, 1.04-1.3; P = .0070). However, this difference was not statistically significant after controlling for and stratifying by insurance type. Residual confounding and the misclassification of some variables could have biased estimated study effects. The racial disparity in lung cancer mortality observed in Eastern North Carolina is no longer apparent after health insurance type is accounted for.

Whittaker's plant diversity sampling method

ABSTRACT A nested vegetation sampling method which was developed by R.H. Whittaker for comparison of plant species diversity is described. The species richness of an area of 0.1 ha (1 dunam; 20 × 50 m) is analyzed by a special procedure in which different parameters of diversity such as differential diversity, point diversity, equibility and dominance are recorded. Normal supplementary observations such as plant coverage, growth forms, phenology and vertical foliage profile are added to the sample. By standardization of data collection for diversity samples, different plant communities from different regions of the world can be compared.

Analyzing genome coverage profiles with applications to quality control in metagenomics

Genome coverage, the number of sequencing reads mapped to a position in a genome, is an insightful indicator of irregularities within sequencing experiments. While the average genome coverage is frequently used within algorithms in computational genomics, the complete information available in coverage profiles (i.e. histograms over all coverages) is currently not exploited to its full extent. Thus, biases such as fragmented or erroneous reference genomes often remain unaccounted for. Making this information accessible can improve the quality of sequencing experiments and quantitative analyses. We introduce a framework for fitting mixtures of probability distributions to genome coverage profiles. Besides commonly used distributions, we introduce distributions tailored to account for common artifacts. The mixture models are iteratively fitted based on the Expectation-Maximization algorithm. We introduce use cases with focus on metagenomics and develop new analysis strategies to assess the validity of a reference genome with respect to (meta-) genomic read data. The framework is evaluated on simulated data as well as applied to a large-scale metagenomic study, for which we compute the validity of 75 microbial genomes. The results indicate that the choice and quality of reference genomes is vital for metagenomic analyses and that validation of coverage profiles is crucial to avoid incorrect conclusions. The code is freely available and can be downloaded from http://sourceforge.net/projects/fitgcp/. RenardB@rki.de Supplementary data are available at Bioinformatics online.

FROM BINDING MOTIFS IN CHIP-SEQ DATA TO IMPROVED MODELS OF TRANSCRIPTION FACTOR BINDING SITES

Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) became a method of choice to locate DNA segments bound by different regulatory proteins. ChIP-Seq produces extremely valuable information to study transcriptional regulation. The wet-lab workflow is often supported by downstream computational analysis including construction of models of nucleotide sequences of transcription factor binding sites in DNA, which can be used to detect binding sites in ChIP-Seq data at a single base pair resolution. The most popular TFBS model is represented by positional weight matrix (PWM) with statistically independent positional weights of nucleotides in different columns; such PWMs are constructed from a gapless multiple local alignment of sequences containing experimentally identified TFBSs. Modern high-throughput techniques, including ChIP-Seq, provide enough data for careful training of advanced models containing more parameters than PWM. Yet, many suggested multiparametric models often provide only incremental improvement of TFBS recognition quality comparing to traditional PWMs trained on ChIP-Seq data. We present a novel computational tool, diChIPMunk, that constructs TFBS models as optimal dinucleotide PWMs, thus accounting for correlations between nucleotides neighboring in input sequences. diChIPMunk utilizes many advantages of ChIPMunk, its ancestor algorithm, accounting for ChIP-Seq base coverage profiles ("peak shape") and using the effective subsampling-based core procedure which allows processing of large datasets. We demonstrate that diPWMs constructed by diChIPMunk outperform traditional PWMs constructed by ChIPMunk from the same ChIP-Seq data. Software website: http://autosome.ru/dichipmunk/

Superdiffusive Motion of the Pb Wetting Layer on the Si(111) Surface

Mass transport in the Pb wetting layer on the Si(111) surface is investigated by observing nonequilibrium coverage profile evolution with low energy electron microscopy and microlow energy electron diffraction. Equilibration of an initial coverage step profile occurs by the exchange of mass between oppositely directed steep coverage gradients that each move with unperturbed shape. The bifurcation of the initial profile, the shape of the profile between the two moving edges, and the time dependence of equilibration are all at odds with expectations for classical diffusion behavior. These observations signal a very unusual coverage dependence of diffusion or may even reveal an exceptional collective superdiffusive mechanism.

Multi-Scale Analysis and Elementary Reaction Simulation of SiC-CVD Using CH3SiCl3/H2: I. Effect of Reaction Temperature

Silicon carbide (SiC) films were prepared from methyltrichlorosilane (MTS) and H2 at temperatures ranging from 900 to 1000°C by low-pressure chemical vapor deposition (CVD). Multi-scale analysis was performed on the SiC film growth rate using a growth rate profile for a tubular reactor that was 300 mm long from the inlet to the outlet and a step coverage (SC) profile for micron-sized trenches. The precursor consumption ratio was estimated using a quadrupole mass spectrometer (QMS). These systematic analyses revealed that MTS was not the direct growth species for SiC deposition. We concluded that there were two major growth species controlling the SiC deposition rate. The partial pressures of these species were estimated by SC and growth rate analyses. An elementary reaction simulation was performed to predict the SiC film growth species. A comparison between the elementary reaction simulation results and the multi-scale analysis suggested several chemical species as candidates for the direct growth species. The candidates for the first species, with a low sticking probability of around 10−3, were CH4, C2H4, and C2H2, and candidates for the second species, with a high sticking probability of around 10−1, were CH3, C2H3, and C2H5.

Mechanism of Co Liner as Enhancement Layer for Cu Interconnect Gap-Fill

Cu gap-fill is enhanced by replacing the conventional Ta liner with a Co liner in a 22 nm width interconnect structure. The improvement with Co liner seen at the line-end area is attributed to a better resputtered Cu seed profile, which is thicker and exhibits no agglomeration compared to that on Ta liner. The mechanism of Co offering better Cu seed coverage than Ta was further studied and determined to be associated with its better wetting and higher sticking coefficient with Cu during the resputtering process. Similar gap-fill performance was also demonstrated with a reflow Cu seed process. The initial highly conformal Cu seed coverage profile on Co helps ensure a uniform Cu reflow process within the interconnect structure, therefore providing better top-open dimension for electrochemical plating process compared to reflow Cu seed on Ta.

Structure-Dependent Contact Barrier Effects in Bottom-Contact Organic Thin-Film Transistors

This paper investigates and compares the structure-dependent contact barrier effects on the electrical performance of two bottom-contact (BC) structure (staggered and inverted coplanar) organic thin-film transistors (OTFTs) by numerical simulations. The drain saturation current ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dsat</sub> ) of the staggered device is found to be more sensitive to the variation of the source/drain (S/D) electrode thickness than that of the inverted coplanar one. The inverted coplanar device shows stronger dependence of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dsat</sub> on the contact barrier than the staggered device, and the dependence is also much more affected by the step coverage profile of the semiconductor layer on top of the S/D electrodes. For the inverted coplanar structure OTFTs, a steeper step coverage profile and a lower contact barrier can help to achieve better tolerance of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dsat</sub> to the variations of the contact barrier and step profile, respectively. The gate structure (self-aligned or fully covered) does not show any influence. The study forms a clear understanding of the device-structure-dependent carrier transport mechanisms in BC OTFTs and could also provide important guidelines for optimal device structure design and related process development for BC OTFTs.

Fast-Forward Genetics Identifies Plant CPL Phosphatases as Regulators of miRNA Processing Factor HYL1

MicroRNAs (miRNAs) are processed from primary transcripts that contain partially self-complementary foldbacks. As in animals, the core microprocessor in plants is a Dicer protein, DICER-LIKE1 (DCL1). Processing accuracy and strand selection is greatly enhanced through the RNA binding protein HYPONASTIC LEAVES 1 (HYL1) and the zinc finger protein SERRATE (SE). We have combined a luciferase-based genetic screen with whole-genome sequencing for rapid identification of new regulators of miRNA biogenesis and action. Among the first six mutants analyzed were three alleles of C-TERMINAL DOMAIN PHOSPHATASE-LIKE 1 (CPL1)/FIERY2 (FRY2). In the miRNA processing complex, SE functions as a scaffold to mediate CPL1 interaction with HYL1, which needs to be dephosphorylated for optimal activity. In the absence of CPL1, HYL1 dephosphorylation and hence accurate processing and strand selection from miRNA duplexes are compromised. Our findings thus define a new regulatory step in plant miRNA biogenesis.

Optimizing compilation with preservation of structural code coverage metrics to support software testing

Code-coverage-based testing is a widely-used testing strategy with the aim of providing a meaningful decision criterion for the adequacy of a test suite. Code-coverage-based testing is also mandated for the development of safety-critical applications; for example, the DO178b document requires the application of the modified condition/decision coverage. One critical issue of code-coverage testing is that structural code coverage criteria are typically applied to source code whereas the generated machine code may result in a different code structure because of code optimizations performed by a compiler. In this work, we present the automatic calculation of coverage profiles describing which structural code-coverage criteria are preserved by which code optimization, independently of the concrete test suite. These coverage profiles allow to easily extend compilers with the feature of preserving any given code-coverage criteria by enabling only those code optimizations that preserve it. Furthermore, we describe the integration of these coverage profile into the compiler GCC. With these coverage profiles, we answer the question of how much code optimization is possible without compromising the error-detection likelihood of a given test suite. Experimental results conclude that the performance cost to achieve preservation of structural code coverage in GCC is rather low. Copyright © 2012 John Wiley & Sons, Ltd.

Improving mapping and SNP-calling performance in multiplexed targeted next-generation sequencing

BackgroundCompared to classical genotyping, targeted next-generation sequencing (tNGS) can be custom-designed to interrogate entire genomic regions of interest, in order to detect novel as well as known variants. To bring down the per-sample cost, one approach is to pool barcoded NGS libraries before sample enrichment. Still, we lack a complete understanding of how this multiplexed tNGS approach and the varying performance of the ever-evolving analytical tools can affect the quality of variant discovery. Therefore, we evaluated the impact of different software tools and analytical approaches on the discovery of single nucleotide polymorphisms (SNPs) in multiplexed tNGS data. To generate our own test model, we combined a sequence capture method with NGS in three experimental stages of increasing complexity (E. coli genes, multiplexed E. coli, and multiplexed HapMap BRCA1/2 regions).ResultsWe successfully enriched barcoded NGS libraries instead of genomic DNA, achieving reproducible coverage profiles (Pearson correlation coefficients of up to 0.99) across multiplexed samples, with <10% strand bias. However, the SNP calling quality was substantially affected by the choice of tools and mapping strategy. With the aim of reducing computational requirements, we compared conventional whole-genome mapping and SNP-calling with a new faster approach: target-region mapping with subsequent ‘read-backmapping’ to the whole genome to reduce the false detection rate. Consequently, we developed a combined mapping pipeline, which includes standard tools (BWA, SAMtools, etc.), and tested it on public HiSeq2000 exome data from the 1000 Genomes Project. Our pipeline saved 12 hours of run time per Hiseq2000 exome sample and detected ~5% more SNPs than the conventional whole genome approach. This suggests that more potential novel SNPs may be discovered using both approaches than with just the conventional approach.ConclusionsWe recommend applying our general ‘two-step’ mapping approach for more efficient SNP discovery in tNGS. Our study has also shown the benefit of computing inter-sample SNP-concordances and inspecting read alignments in order to attain more confident results.

NOrMAL: accurate nucleosome positioning using a modified Gaussian mixture model

Motivation: Nucleosomes are the basic elements of chromatin structure. They control the packaging of DNA and play a critical role in gene regulation by allowing physical access to transcription factors. The advent of second-generation sequencing has enabled landmark genome-wide studies of nucleosome positions for several model organisms. Current methods to determine nucleosome positioning first compute an occupancy coverage profile by mapping nucleosome-enriched sequenced reads to a reference genome; then, nucleosomes are placed according to the peaks of the coverage profile. These methods are quite accurate on placing isolated nucleosomes, but they do not properly handle more complex configurations. Also, they can only provide the positions of nucleosomes and their occupancy level, whereas it is very beneficial to supply molecular biologists additional information about nucleosomes like the probability of placement, the size of DNA fragments enriched for nucleosomes and/or whether nucleosomes are well positioned or ‘fuzzy’ in the sequenced cell sample.Results: We address these issues by providing a novel method based on a parametric probabilistic model. An expectation maximization algorithm is used to infer the parameters of the mixture of distributions. We compare the performance of our method on two real datasets against Template Filtering, which is considered the current state-of-the-art. On synthetic data, we show that our method can resolve more accurately complex configurations of nucleosomes, and it is more robust to user-defined parameters. On real data, we show that our method detects a significantly higher number of nucleosomes.Availability: Visit http://www.cs.ucr.edu/~polishkaContact: stelo@cs.ucr.edu or polishka@cs.ucr.edu

SU-E-T-485: Validation of Acuros XB Dose Calculations in SBRT Lung Planning with Monte Carlo Methods.

The Acuros XB (AXB) Advanced Dose algorithm (Varian Medical Systems) represents a dramatic shift in clinical photon dose calculation methodology from pencil-beam superposition/convolution methods. Early studies evaluating the accuracy of the algorithm in lung have found good agreement with both measurement and Monte Carlo based dose calculations. In this study, a dosimetric validation of Acuros is performed for clinical SBRT lung planning cases using Monte Carlo (MC) calculations as a benchmark. MC simulations using BEAMnrc/DOSXYZnrc were carried out for 8 AXB calculated 6/10 MV arc plans delivered on a TrueBeamTM STx linac in high-dose-rate flattening filter free mode. Clinical planning constraints were applied in each case with plans normalized to achieve 95% PTV coverage. Metrics used in the evaluation include: maximum and minimum GTV/PTV dose, PTV isodose coverage, conformity and dose profile comparisons. To understand the impact of moving toward to AXB calculations in SBRT lung planning, calculations using the Analytical Anisotropic Algorithm (AAA) are presented for each plan. For both 6 and 10MV energies, consistent mean GTV dose and PTV isodose coverage was observed for AXB and MC calculations. GTV mean dose was observed to deviate by <2% for all cases. Isodose coverage for MC simulations ranged from 92%-98%. AAA was also in agreement with MC simulations within the GTV to within 2%. AXB and MC maximum and minimum PTV dose differences were larger (up to 9%) but not of clinical concern. In several cases, AXB exhibited a significant improvement in dose calculation accuracy in the lung region surrounding the GTV over AAA, particularly with lung densities < 0.1 g/cc. AcurosXB provides increased accuracy in modelling dose deposition for SBRT lung over AAA and is found to be in good agreement with MC calculations.

Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments

High-throughput sequencing of whole genomes and transcriptomes allows one to generate large amounts of sequence data very rapidly and at a low cost. The goal of most mRNA sequencing studies is to perform the comparison of the expression level between different samples. However, given a broad variety of modern sequencing protocols, platforms and versions thereof, it is not clear to what extent the obtained results are consistent across platforms and laboratories. The comparison of 117 human mRNA and genome high-throughput sequencing experiments performed on the Illumina and SOLiD platforms at 26 institutions all over the world demonstrated high dependency of the gene coverage profiles on the producing laboratory. Gene coverage profiles showed laboratory-specific non-uniformity that survived the 3'-bias correction and mappability normalization, suggesting that there are other yet unknown mRNA-associated biases.

Self‐Limited Reaction‐Diffusion in Nanostructured Substrates: Surface Coverage Dynamics and Analytic Approximations to ALD Saturation Times

AbstractWe present a general model based on a time‐dependent, reaction–diffusion equation to determine the dosing times and coverage profiles in structured substrates during atomic layer deposition (ALD). We first derive expressions comprising a non‐linear diffusion–reaction equation coupled to a surface kinetic equation. In their non‐dimensional forms, these equations show that coverage dynamics during ALD in nanostructured substrates depend only on two non‐dimensional parameters, the Damkoler and precursor excess (number of molecules per surface site in the nanostructure) numbers. Using the assumptions of molecular flow in a circular pore, we derive a general, analytic equation to predict saturation exposure times. To demonstrate the utility of our model, we derive additional expressions incorporating a precursor loss term relevant to predicting exposure times during ozone‐based ALD. Because our model makes no assumptions about the diffusion coefficient or sample geometry, it can easily be adapted to describe a broad range of ALD systems such as trenches and vias, anodized alumina, or aerogels under almost any conditions including molecular, viscous, and transition flow regimes

Conformality of thermal and plasma enhanced atomic layer deposition on a non-woven fibrous substrate

Alumina was deposited on a non-woven polyester fiber substrate using both thermal and plasma enhanced atomic layer deposition (ALD). The textile was confined inside a one dimensional test structure. The coverage of the ALD film on the nonwoven as a function of depth in the test structure was determined by energy dispersive X-ray spectroscopy (EDX). A model is introduced which links the precursor transport in the nonwoven (transmission, reflection and deposition) with the nonwoven properties (density, fiber surface area, density of surface sites). The experimental results are compared to simulations of the coverage profile. It is shown that longer precursor exposure times result in deposition deeper inside the nonwoven. However, the majority of precursor molecules entering the nonwoven leave the test structure without contributing to film growth. ALD from TMA and oxygen plasma had a very limited penetration into the nonwoven because of radical recombination. This effect is relevant for plasma treatment of fibrous materials in general.