J Agric Biol Environ Stat

In the estimation of proportions by pooled testing, the MLE is biased, and several methods of correcting the bias have been presented in previous studies. We propose a new estimator based on the bias correction method introduced by Firth (Biometrika 80:27-38, 1993), which uses a modification of the score function, and we provide an easily computable, Newton-Raphson iterative formula for its computation. Our proposed estimator is almost unbiased across a range of problems, and superior to existing methods. We show that for equal pool sizes the new estimator is equivalent to the estimator proposed by Burrows (Phytopathology 77:363-365, 1987). The performance of our estimator is examined using pooled testing problems encountered in plant disease assessment and prevalence estimation of mosquito-borne viruses.CC999999/Intramural CDC HHS/United States2019-01-09T00:00:00Z30636859PMC6325642vault:3136

Sample Size under Inverse Negative Binomial Group Testing for Accuracy in Parameter Estimation

Background:The group testing method has been proposed for the detection and estimation of genetically modified plants (adventitious presence of unwanted transgenic plants, AP). For binary response variables (presence or absence), group testing is efficient when the prevalence is low, so that estimation, detection, and sample size methods have been developed under the binomial model. However, when the event is rare (low prevalence Methodology/Principal Findings: This research proposes three sample size procedures (two computational and one analytic) for estimating prevalence using group testing under inverse (negative) binomial sampling. These methods provide the required number of positive pools (rm), given a pool size (k), for estimating the proportion of AP plants using the Dorfman model and inverse (negative) binomial sampling. We give real and simulated examples to show how to apply these methods and the proposed sample-size formula. The Monte Carlo method was used to study the coverage and level of assurance achieved by the proposed sample sizes. An R program to create other scenarios is given in Appendix S2. Conclusions: The three methods ensure precision in the estimated proportion of AP because they guarantee that the width (W) of the confidence interval (CI) will be equal to, or narrower than, the desired width (v), with a probability of c. With the Monte Carlo study we found that the computational Wald procedure (method 2) produces the more precise sample size (with coverage and assurance levels very close to nominal values) and that the samples size based on the Clopper-Pearson CI (method 1) is conservative (overestimates the sample size); the analytic Wald sample size method we developed (method 3) sometimes underestimated the optimum number of pools

Group testing as a strategy for COVID-19 epidemiological monitoring and community surveillance

International audienceWe propose an analysis and applications of sample pooling to the epidemiologic monitoring of COVID-19. We first introduce a model of the RT-qPCR process used to test for the presence of virus in a sample and construct a statistical model for the viral load in a typical infected individual inspired by large-scale clinical datasets. We then propose a method for the measure of the prevalence in a population, based on group testing, taking into account the increased number of false negatives associated with this method. Finally, we present an application of sample pooling for the prevention of epidemic outbreak in closed connected communities

An Arabidopsis flavonoid transporter is required for anther dehiscence and pollen development

FLOWER FLAVONOID TRANSPORTER (FFT) encodes a multidrug and toxin efflux family transporter in Arabidopsis thaliana. FFT (AtDTX35) is highly transcribed in floral tissues, the transcript being localized to epidermal guard cells, including those of the anthers, stigma, siliques and nectaries. Mutant analysis demonstrates that the absence of FFT transcript affects flavonoid levels in the plant and that the altered flavonoid metabolism has wide-ranging consequences. Root growth, seed development and germination, and pollen development, release and viability are all affected. Spectrometry of mutant versus wild-type flowers shows altered levels of a glycosylated flavonol whereas anthocyanin seems unlikely to be the substrate as previously speculated. Thus, as well as adding FFT to the incompletely described flavonoid transport network, it is found that correct reproductive development in Arabidopsis is perturbed when this particular transporter is missing

Otolith function in human subjects: Perception of motion, reflex eye movements and vision during linear interaural acceleration

The thesis investigates how the otolith organs of the vestibular system, specifically the utricles, assist motion perception and aid visual stabilization, during translational lateral whole-body acceleration. It was found that high gradients of acceleration facilitate the detection of motion and that, for low acceleration gradients, motion perception in normal subjects relies on a 'velocity' threshold detection process. Experiments in patients without vestibular function indicated that, for the stimuli employed, the somatosensory system could be as sensitive to linear motion as the vestibular system. The interaction between the horizontal linear vestibulo-ocular reflex (LVOR) and visual context was characterized in the following experiments. Subjects were accelerated transiently in darkness, or while viewing earth-fixed or head-fixed targets. From onset, the eye velocity response to head translation was enhanced with acceleration level and target proximity, but was only slightly reduced by fixation of head-fixed targets. This suggested that the gain of the LVOR pathway was adjusted before or immediately after motion onset by a parameter depending mainly on viewing distance and less on the knowledge of probable relative target motion. For high relative target velocities, LVORs improved ocular fixation over what would be attained by pursuit alone, although fully compensatory eye movements were not always produced. The LVORs of patients who underwent unilateral vestibular deafferentation suggested that the utricular area generating transaural LVORs is the macular region lateral to the striola. Psychophysical experiments based on a reading task established the functional role of the LVOR for stabilising vision during high-frequency sinusoidal whole-body acceleration. Unlike normal subjects, visual acuity in patients without vestibular function was not better during self-motion than during display oscillation. Finally, the LVOR interaction with canal-ocular reflexes was studied using isolated and combined translational/rotational stimuli. The results showed that, shortly after motion onset, canal stimulation enhances the LVOR evoked by head translation

Interference Mitigation in Large Random Wireless Networks

A central problem in the operation of large wireless networks is how to deal with interference -- the unwanted signals being sent by transmitters that a receiver is not interested in. This thesis looks at ways of combating such interference. In Chapters 1 and 2, we outline the necessary information and communication theory background, including the concept of capacity. We also include an overview of a new set of schemes for dealing with interference known as interference alignment, paying special attention to a channel-state-based strategy called ergodic interference alignment. In Chapter 3, we consider the operation of large regular and random networks by treating interference as background noise. We consider the local performance of a single node, and the global performance of a very large network. In Chapter 4, we use ergodic interference alignment to derive the asymptotic sum-capacity of large random dense networks. These networks are derived from a physical model of node placement where signal strength decays over the distance between transmitters and receivers. (See also arXiv:1002.0235 and arXiv:0907.5165.) In Chapter 5, we look at methods of reducing the long time delays incurred by ergodic interference alignment. We analyse the tradeoff between reducing delay and lowering the communication rate. (See also arXiv:1004.0208.) In Chapter 6, we outline a problem that is equivalent to the problem of pooled group testing for defective items. We then present some new work that uses information theoretic techniques to attack group testing. We introduce for the first time the concept of the group testing channel, which allows for modelling of a wide range of statistical error models for testing. We derive new results on the number of tests required to accurately detect defective items, including when using sequential `adaptive' tests.Comment: PhD thesis, University of Bristol, 201

New Constructions for Competitive and Minimal-Adaptive Group Testing

Group testing (GT) was originally proposed during the World War II in an attempt to minimize the \emph{cost} and \emph{waiting time} in performing identical blood tests of the soldiers for a low-prevalence disease. Formally, the GT problem asks to find $d\ll n$ \emph{defective} elements out of $n$ elements by querying subsets (pools) for the presence of defectives. By the information-theoretic lower bound, essentially $d\log_2 n$ queries are needed in the worst-case. An \emph{adaptive} strategy proceeds sequentially by performing one query at a time, and it can achieve the lower bound. In various applications, nothing is known about $d$ beforehand and a strategy for this scenario is called \emph{competitive}. Such strategies are usually adaptive and achieve query optimality within a constant factor called the \emph{competitive ratio}. In many applications, queries are time-consuming. Therefore, \emph{minimal-adaptive} strategies which run in a small number $s$ of stages of parallel queries are favorable. This work is mainly devoted to the design of minimal-adaptive strategies combined with other demands of both theoretical and practical interest. First we target unknown $d$ and show that actually competitive GT is possible in as few as $2$ stages only. The main ingredient is our randomized estimate of a previously unknown $d$ using nonadaptive queries. In addition, we have developed a systematic approach to obtain optimal competitive ratios for our strategies. When $d$ is a known upper bound, we propose randomized GT strategies which asymptotically achieve query optimality in just $2$, $3$ or $4$ stages depending upon the growth of $d$ versus $n$. Inspired by application settings, such as at American Red Cross, where in most cases GT is applied to small instances, \textit{e.g.}, $n=16$. We extended our study of query-optimal GT strategies to solve a given problem instance with fixed values $n$, $d$ and $s$. We also considered the situation when elements to test cannot be divided physically (electronic devices), thus the pools must be disjoint. For GT with \emph{disjoint} simultaneous pools, we show that $\Theta (sd(n/d)^{1/s})$ tests are sufficient, and also necessary for certain ranges of the parameters

Improving measurements in perimetry for glaucoma

Glaucoma is a leading cause of visual impairment and, if untreated, irreversible blindness. Perimetry is the clinical tool for assessing the functional ‘seeing’ part of the field of view (visual field) and is widely used in the detection and clinical monitoring of glaucoma. These measurements rely on a psychophysical response making them inherently variable. This measurement noise can disguise both disease pathology and progression. The work described in this thesis aims to improve the quality of perimetric measurements. The platform for this is the Moorfields Motion Displacement Test (MMDT), a perimetric test that uses unconventional test stimuli and can be delivered on an ordinary computer monitor. Specifically, this thesis describes efforts to develop novel, mathematically derived, test algorithms, designed to be used with the MMDT. The performance of these new testing methods is assessed using pilot studies involving patients and visually healthy people, computer simulation and interim results from a large prospective clinical study. One of these test algorithms, the Enhanced Suprathreshold Testing Algorithm [ESTA] provides shorter test duration, making it attractive for case-finding and screening for glaucoma, without seemingly negatively affecting diagnostic precision, and has become patented technology. Another bespoke test algorithm (Weighted Binary Search; WEBS) provides a threshold test for the MMDT. The thesis also describes a study examining the resistance of several newer clinical perimetric instruments to the optical artefact of stray light that might be caused by media opacity. This is clinically important because cataract and degraded optical media is a leading cause of false-referral for glaucoma. This work, being the first of its kind, indicates that the MMDT has greater resilience to simulated effects of media opacity compared with other clinically used devices

Practical Concepts of Quality Control

This book aims to provide a concise account of the essential elements of quality control. It is designed to be used as a text for courses on quality control for students of industrial engineering at the advanced undergraduate, or as a reference for researchers in related fields seeking a concise treatment of the key concepts of quality control. It is intended to give a contemporary account of procedures used to design quality models