Improving precision and reducing bias in biological surveys: estimating false-negative error rates

The use of presence/absence data in wildlife management and biological surveys is widespread. There is a growing interest in quantifying the sources of error associated with these data. We show that false-negative errors (failure to record a species when in fact it is present) can have a significant impact on statistical estimation of habitat models using simulated data. Then we introduce an extension of logistic modeling, the zero-inflated binomial (ZIB) model that permits the estimation of the rate of false-negative errors and the correction of estimates of the probability of occurrence for false-negative errors by using repeated. visits to the same site. Our simulations show that even relatively low rates of false negatives bias statistical estimates of habitat effects. The method with three repeated visits eliminates the bias, but estimates are relatively imprecise. Six repeated visits improve precision of estimates to levels comparable to that achieved with conventional statistics in the absence of false-negative errors In general, when error rates are less than or equal to50% greater efficiency is gained by adding more sites, whereas when error rates are >50% it is better to increase the number of repeated visits. We highlight the flexibility of the method with three case studies, clearly demonstrating the effect of false-negative errors for a range of commonly used survey methods.

Use of the EM algorithm to detect QTL affecting multiple-traits in an across half-sib family analysis

QTL detection experiments in livestock species commonly use the half-sib design. Each male is mated to a number of females, each female producing a limited number of progeny. Analysis consists of attempting to detect associations between phenotype and genotype measured on the progeny. When family sizes are limiting experimenters may wish to incorporate as much information as possible into a single analysis. However, combining information across sires is problematic because of incomplete linkage disequilibrium between the markers and the QTL in the population. This study describes formulae for obtaining MLEs via the expectation maximization (EM) algorithm for use in a multiple-trait, multiple-family analysis. A model specifying a QTL with only two alleles, and a common within sire error variance is assumed. Compared to single-family analyses, power can be improved up to fourfold with multi-family analyses. The accuracy and precision of QTL location estimates are also substantially improved. With small family sizes, the multi-family, multi-trait analyses reduce substantially, but not totally remove, biases in QTL effect estimates. In situations where multiple QTL alleles are segregating the multi-family analysis will average out the effects of the different QTL alleles.

Milling quality and protein properties of autumn-sown Chinese wheats evaluated through multi-location trials

Eight milling quality and protein properties of autumn-sown Chinese wheats were investigated using 59 cultivars and advanced lines grown in 14 locations in China from 1995 to 1998. Wide ranges of variability for all traits were observed across genotypes and locations. Genotype, location, year, and their interactions all significantly influenced most of the quality parameters. Kernel hardness, Zeleny sedimentation value, and mixograph development time were predominantly influenced by the effects of genotype. Genotype, location and genotype x location interaction were all important sources of variation for thousand kernel weight, test weight, protein content, and falling number, whereas genotype x location interaction had the largest effect on flour yield. Most of the genotypes were characterized by weak gluten strength with Zeleny sedimentation values less than 40 ml and mixograph development time shorter than 3 min. Eight groups of genotypes were recognized based on the average quality performance, grain hardness and gluten strength were the two parameters that determined the grouping, with contributions from protein content. Genotypes such as Zhongyou 16 and Annong 8903 displayed good milling quality, high grain hardness, protein content and strong gluten strength with high sedimentation value and long mixograph development time. Genotypes such as Lumai 15 and Yumai 18 were characterized by low grain hardness, protein content and weak gluten strength. Genotypes such as Yannong 15 and Chuanmai 24 were characterized by strong gluten strength with high sedimentation value and long mixograph development time, but low grain hardness and protein content lower than 12.3%. Genotypes such as Jingdong 6 and Xi'an 8 had weak gluten strength, but with high grain hardness and protein content higher than 12.2%. Five groups of locations were identified, and protein content and gluten strength were the two parameters that determined the grouping. Beijing, Shijiazhuang, Nanyang, Zhumadian and Nanjing produced wheats with medium to strong gluten strength and medium protein content, although there was still a large variation for most of the traits investigated between the locations. Wheat produced in Yantai was characterized by strong gluten strength, but with low protein content. Jinan, Anyang and Linfen locations produced wheats with medium to weak gluten strength and medium to high protein content. Wheats produced in Yangling, Zhenzhou, and Chengdu were characterized by weak gluten strength with medium to low protein content, whereas wheats produced in Xuzhou and Wuhan were characterized by weak gluten strength with low protein content. Industrial grain quality could be substantially improved through integrating knowledge of geographic genotype distribution with key location variables that affected end-use quality.

Operator quantum error correction

This paper is an expanded and more detailed version of the work [1] in which the Operator Quantum Error Correction formalism was introduced. This is a new scheme for the error correction of quantum operations that incorporates the known techniques - i.e. the standard error correction model, the method of decoherence-free subspaces, and the noiseless subsystem method - as special cases, and relies on a generalized mathematical framework for noiseless subsystems that applies to arbitrary quantum operations. We also discuss a number of examples and introduce the notion of unitarily noiseless subsystems.

Designing for Location-Dependence

This paper proposes a methodological framework for use in designing location-dependent games or experiences. An increasing interest in this genre has given rise to a number of common issues surrounding the design and development of these types of experience. Specifically, the treatment of and approach to the use of location gives rise to particular design considerations. The framework proposed here aims to highlight these and provide designers with tools for use in addressing these.

Logistical aspects of large telemedicine networks. 2: Measurement of network activity

We carried out a retrospective review of the videoconference activity records in a university-run hospital telemedicine studio. Usage records describing videoconferencing activity in the telemedicine studio were compared with the billing records provided by the telecommunications company. During a seven-month period there were 211 entries in the studio log: 108 calls made from the studio and 103 calls made from a far-end location. We found that 103 calls from a total of 195 calls reported by the telecommunications company were recorded in the usage log. The remaining 92 calls were not recorded, probably for one of several reasons, including: failed calls-a large number of unrecorded calls (57%) lasted for less than 2 min (median 1.6 min); origin of videoconference calls-calls may have been recorded incorrectly in the usage diary (i.e. as being initiated from the far end, when actually initiated from the studio); and human error. Our study showed that manual recording of videoconference activity may not accurately reflect the actual activity taking place. Those responsible for recording and analysing videoconference activity, particularly in large telemedicine networks, should do so with care.

Scalable location management for context-aware systems

Location information is commonly used in context-aware applications and pervasive systems. These applications and systems may require knowledge, of the location of users, devices and services. This paper presents a location management system able to gather, process and manage location information from a variety of physical and virtual location sensors. The system scales to the complexity of context-aware applications, to a variety of types and large number of location sensors and clients, and to geographical size of the system. The proposed location management system provides conflict resolution of location information and mechanisms to ensure privacy.