Retinal cross-section motion correction in three-dimensional retinal optical coherence tomography

Motion correction is an important issue in ophthalmic optical coherence tomography (OCT), and can improve the ability of data sets to reflect the physiological structures of tissues and make visualization and subsequent analysis easier. In this study, we present a novel method to correct the cross-sectional motion artifacts in retinal OCT volumes. Motion along the x-direction (fast-scan direction) is corrected through the normalized cross-correlation algorithm, while axial motion compensation is performed using the polynomial fitting method on the inner segment/outer segment (IS/OS) layer segmented by the shortest path faster algorithm (SPFA). The results of volunteers with central serous chorioretinopathy demonstrate that the proposed method effectively corrects motion artifacts in OCT volumes and may have potential application value in the evaluation of ophthalmic diseases such as diabetic retinopathy, glaucoma and age-related macular degeneration.     

On the identification of mortality hotspots in linear infrastructures

One of the main tasks when dealing with the impacts of infrastructures on wildlife is to identify hotspots of high mortality so one can devise and implement mitigation measures. A common strategy to identify hotspots is to divide an infrastructure into several segments and determine when the number of collisions in a segment is above a given threshold, reflecting a desired significance level that is obtained assuming a probability distribution for the number of collisions, which is often the Poisson distribution. The problem with this approach, when applied to each segment individually, is that the probability of identifying false hotspots (Type I error) is potentially high. The way to solve this problem is to recognize that it requires multiple testing corrections or a Bayesian approach. Here, we apply three different methods that implement the required corrections to the identification of hotspots: (i) the familywise error rate correction, (ii) the false discovery rate, and (iii) a Bayesian hierarchical procedure. We illustrate the application of these methods with data on two bird species collected on a road in Brazil. The proposed methods provide practitioners with procedures that are reliable and simple to use in real situations and, in addition, can reflect a practitioner’s concerns towards identifying false positive or missing true hotspots. Although one may argue that an overly cautionary approach (reducing the probability of type I error) may be beneficial from a biological conservation perspective, it may lead to a waste of resources and, probably worse, it may raise doubts about the methodology adopted and the credibility of those suggesting it.     

Estimation of log‐odds ratio from group testing data using Firth correction

We consider the estimation of the prevalence of a rare disease, and the log‐odds ratio for two specified groups of individuals from group testing data. For a low‐prevalence disease, the maximum likelihood estimate of the log‐odds ratio is severely biased. However, Firth correction to the score function leads to a considerable improvement of the estimator. Also, for a low‐prevalence disease, if the diagnostic test is imperfect, the group testing is found to yield more precise estimate of the log‐odds ratio than the individual testing.     

An automated approach for fringe frequency estimation and removal in infrared spectroscopy and hyperspectral imaging of biological samples

In infrared spectroscopy of thin film samples, interference introduces distortions in spectra, commonly referred to as fringes. Fringes may alter absorbance peak ratios, which hampers the spectral analysis. We have previously introduced extended multiplicative signal correction (EMSC) for fringes correction. In the current article, we provide a robust open-source algorithm for fringe correction in infrared spectroscopy and propose several improvements to the Fringe EMSC model. The suggested algorithm achieves a more precise fringe frequency estimation by mean centering of the measured spectrum and applying a window function prior to the Fourier transform. It selects two frequencies from a user defined number of maxima in the Fourier domain. The improved Fringe EMSC algorithm is validated on two experimental datasets, one of them being a hyperspectral image. Techniques for separating sample spectra from background spectra in hyperspectral images, and techniques to identify spectra affected by fringes are also provided.     

Estimation of Box's ε for low‐ and high‐dimensional repeated measures designs with unequal covariance matrices

We present new inference methods for the analysis of low‐ and high‐dimensional repeated measures data from two‐sample designs that may be unbalanced, the number of repeated measures per subject may be larger than the number of subjects, covariance matrices are not assumed to be spherical, and they can differ between the two samples. In comparison, we demonstrate how crucial it is for the popular Huynh‐Feldt (HF) method to make the restrictive and often unrealistic or unjustifiable assumption of equal covariance matrices. The new method is shown to maintain desired α‐levels better than the well‐known HF correction, as demonstrated in several simulation studies. The proposed test gains power when the number of repeated measures is increased in a manner that is consistent with the alternative. Thus, even increasing the number of measurements on the same subject may lead to an increase in power. Application of the new method is illustrated in detail, using two different real data sets. In one of them, the number of repeated measures per subject is smaller than the sample size, while in the other one, it is larger.     

Improved MR-thermometry during hepatic microwave ablation by correcting for intermittent electromagnetic interference artifacts

MRI-guided microwave ablation (MWA) is a minimally invasive treatment for localized cancer. MR thermometry has been shown to be able to provide vital information for monitoring the procedure in real-time. However, MRI during active MWA can suffer from image quality degradation due to intermittent electromagnetic interference (EMI). A novel approach to correct for EMI-contaminated images is presented here to improve MR thermometry during clinical hepatic MWA. The method was applied to MR-thermometry images acquired during four MR-guided hepatic MWA treatments using a commercially available MRI-configured microwave generator system. During the treatments MR thermometry data acquisition was synchronized to respiratory cycle to minimize the impact of motion. EMI was detected and corrected using uncontaminated k-space data from nearby frames in k-space. Substantially improved temperature and thermal damage maps have been obtained and the treatment zone can be better visualized. Our ex vivo tissue sample study shows the correction introduced minimal errors to the temperature maps and thermal damage maps.     

Diet preferences based on sequence read count: The role of species interaction in tissue bias correction

High-throughput sequencing and metabarcoding techniques provide a unique opportunity to study predator–prey relationships. However, in animal dietary preference studies, how to properly correct tissue bias within the sequence read count and the role of interactions between co-occurring species in metabarcoding mixtures remain largely unknown. In this study, we propose two categories of tissue bias correction indices: sequence read count number per unit tissue (SCN) and its ratio form (SCN ratio). By constructing plant mock communities with different numbers of co-occurring species in metabarcoding mixtures and conducting feeding trails on captive sika deer (Cervus nippon), we demonstrate the features of the SCN and SCN ratio, evaluate their correction effects and assess the role of species interactions during tissue bias correction. Tissue differences between species are defined as the differential ability to generate sequence counts. Our study suggests that pure tissue differences among species without a species interaction is not an optimal correction index for many biomes with limited tissue differences among species. Species interactions in mixtures may amplify tissue differences, which is beneficial for tissue bias correction. However, caution must be taken because varied species interactions among communities may increase the risk of worse correction. Correction effects based on the SCN and SCN ratio are comparable, but the SCN is less influenced by control species than the SCN ratio. Based on our study, several suggestions are provided for future animal diet studies or other high-throughput sequencing studies containing tissue bias.     

Extended multiplicative signal correction for FTIR spectral quality test and pre‐processing of infrared imaging data

Spectral quality control is an important step in the analysis of infrared spectral data, however, often neglected in scientific literature. A frequently used quality test that was originally developed for infrared spectra of bacteria is provided by OPUS software from Bruker Optik GmbH. In this study, the OPUS quality test is applied to a large number of spectra of bacteria, yeasts and moulds and hyperspectral images of microorganisms. It is shown that the use of strict thresholds for parameters of the OPUS quality test leads to discarding too many spectra. A strategy for optimizing parameters thresholds of the OPUS quality test is provided and a novel approach for spectral quality testing based on extended multiplicative signal correction (EMSC) is suggested. For all the data sets considered in our study, the EMSC quality test is shown to be the best among different alternatives of OPUS quality test provided.     

PhosR enables processing and functional analysis of phosphoproteomic data

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