A class of latent Markov models for capture-recapture data allowing for time, heterogeneity, and behavior effects

We propose an extension of the latent class model for the analysis of capture-recapture data which allows us to take into account the effect of a capture on the behavior of a subject with respect to future captures. The approach is based on the assumption that the variable indexing the latent class of a subject follows a Markov chain with transition probabilities depending on the previous capture history. Several constraints are allowed on these transition probabilities and on the parameters of the conditional distribution of the capture configuration given the latent process. We also allow for the presence of discrete explanatory variables, which may affect the parameters of the latent process. To estimate the resulting models, we rely on the conditional maximum likelihood approach and for this aim we outline an EM algorithm. We also give some simple rules for point and interval estimation of the population size. The approach is illustrated by applying it to two data sets concerning small mammal populations.     

Distance-type reaction coordinates for modelling activated processes

A suitably defined distance is the simplest parameter for measuring the difference between two positions, orientations, and/or conformations of a molecular system. Distances also provide a first guess for the reaction coordinates of activated processes. It is shown here that mass-weighted distances possess remarkable mechanical and statistical mechanical properties. They allow us to restrict motions to internal coordinates of a molecule in a simple way where this demand makes sense. Moreover, the computation of free energy changes and rates is facilitated by simple explicit formulae. The numerical treatment of a rate process in a peptide, the ring flip of a phenylalanine, demonstrates the practical application of our results. It also indicates the role of internal friction in macromolecules and the need to consider transmission coefficients.     

Generalization of the variance-covariance method for microdosimetric measurements

Numerical simulations in terms of microdosimetric data for 5-MeV neutrons are utilized to test the twin detector method of microdosimetric measurements in its new, extended form. Three different conditions of measurement are considered: (I) constant dose increments per measurement, (II) fluctuating dose increments per measurement, and (III) fluctuating dose increments combined with slow changes of the dose-rate ratio for the two detectors. Under each of the conditions, large numbers of measurement series are simulated, and the estimation formulae for the mean and the two subsequent moments of the dose-weighted single-event distribution, d(y), are applied. The estimation formulae exist in three different forms: uncorrected formulae that apply to condition I, corrected formulae that are valid also for condition II, and fully corrected formulae that remain applicable under condition III. The results of the simulations indicate the acceptable ranges of doses per measurement interval. It can be seen that all three parameters are obtainable through the twin detector method, and that the fully corrected formulae for the two lower moments are generally applicable. The determination of the third moment is possible only under limited conditions, and the fully corrected formula is not useful in this case, while the corrected formula has some applicability even under condition III. Received: 10 January 1996 / Accepted in revised form: 27 May 1996     

Nestboxes and immigration drive the growth of an urban Peregrine Falcon Falco peregrinus population

Drivers of wildlife population dynamics are generally numerous and interacting. Some of these drivers may impact demographic processes that are difficult to estimate, such as immigration into the focal population. Populations may furthermore be small and subject to demographic stochasticity. All of these factors contribute to blur the causal relationship between past management action and current population trends. The urban Peregrine Falcon Falco peregrinus population in Cape Town, South Africa, increased from three pairs in 1997 to 18 pairs in 2010. Nestboxes were installed over this period to manage the interface between new urban pairs of Falcons and the human users of colonized buildings, and incidentally to improve breeding success. We used integrated population models (IPMs) formally to combine information from a capture–mark–recapture study, monitoring of reproductive success and counts of population size. As all local demographic processes were directly observed, the IPM approach also allowed us to estimate immigration by difference. The provision of nestboxes, as a possible stimulant of population growth, improved breeding success and accounted for an estimated 3–26% of the population increase. The most important driver of growth, however, was immigration. Despite low sample sizes, the IPM approach allowed us to obtain relatively precise estimates of the population‐level impact of nestbox deployment. The goal of conservation interventions is often to increase population size, so the effectiveness of such interventions should ideally be assessed at the population level. IPMs are powerful tools in this context for combining demographic information that may be limited due to small population size or practical constraints on monitoring. Our study quantitatively documented both the immigration process that led to growth of a small population and the effect of a management action that helped the process.     

Generalization of the variance-covariance method for microdosimetric measurements

The variance method of microdosimetric measurements and its extension, the variance-covariance method, permit the determination of an essential parameter of radiation quality, the dose mean event size,y _d. The methods have — among other advantages — the feature that they permit measurements for smaller simulated sites than the conventional single-event technique. It is, therefore, desirable to employ them also for the determination of further moments of the distribution ofy. The formulae for the first three moments are here derived both for the case of constant dose rate and of fluctuating dose rates. A second article will use the same mathematical approach to deduce formulae that remain valid even if there are slow changes of the ratio of dose rates in the two detectors for the variance-covariance method. A third article will explore — in terms of microdosimetric data — the applicability of the formulae.     

Time as an ecological constraint

Conventional approaches to population biology emphasise the roles of climatic conditions, nutrient flow and predation as constraints on population dynamics. We argue here that this focus has obscured the role of time as a crucial constraint on species' abilities to survive in some habitats. Time constraints may be particularly intrusive both for species that live in intensely bonded groups (where the need to devote time to social interaction may ultimately limit the size of group that a species can maintain in a particular habitat) and for taxa that face constraints on the length of the active day. We use a linear programming approach that allows us to specify both how time allocations to different activities are influenced by local environmental and climatic variables and how these in turn limit group size and population density. The linear programming approach identifies the realizable niche space within which a species can maintain coherent groups that are larger than the minimum viable group size (or density). This approach thus allow us to understand better why a given taxon can survive in some habitats but not others, as well as the demographic stress that a population may face. In addition, they also allow us to evaluate the implications of both past and future climate change for a taxon's ability to cope with particular habitats.     

New conversion formulae for light-skinned populations using photovolt and E.E.L. reflectometers

Recent research in Belize revealed that published conversion coefficients for use between the two most commonly used reflectance spectro-photometers were inadequate when applied to dark-skinned populations. New research in Ireland shows that the published conversion coefficients for light-skinned populations are also inadequate. A total of 320 school children from Longford, Ireland were measured for skin reflectances at the upper inner arm site with the Photovolt Model 670 and the E.E.L. Reflectance Spectrophotometers. Six and nine filters respectively were used to sample the visible spectrum. Multiple regression techniques were then used to estimate new conversion coefficients which accurately predict readings for one instrument by using some or all of the measurements from the other. Double cross-validation techniques showed the inadequacy of the old (1967) formulae and the very high accuracy of the new ones. Some problems encountered in this study, but not in the one which produced new formulae for dark-skinned populations, suggest further work may be necessary. Additional independently sampled light-skinned populations have not been measured on both machines, so conclusive cross-validation of the new coefficients must remain tentative. Despite this drawback, the new formulae presented here are almost certainly an improvement over the old ones. These new conversion formulae may allow previously impossible comparisons of worldwide data on similar populations.     

Diachronic analysis of biodiversity: Study of a herbarium “reviewed” by Francesco Cupani (1657–1710) at the end of the 17th century

The subject of this paper is the study of the pre-Linnaean herbarium with the inventory number “VII F1 Hortus Botanicus Catinensis” belonging to the Department of Biological, Geological and Environmental Sciences (University of Catania). The volume examined comprises 186 pages (originally 190) with 1–9 specimens on each sheet. The herbarium samples mainly include angiosperms (386), but a few taxa belonging to gymnosperms (1) and pteridophytes (4) are also present. Unfortunately, some specimens are partially or entirely damaged or even missing; nonetheless, it has been possible to identify most of them. As far as the nomenclature is concerned, we find two kinds of handwriting (of which only that of Cupani can be identified), numerous corrections and/or integrations of the polylogus and different types of ink that were used. These elements allow us to state that we are speaking of a herbarium which was prepared by an unknown person and reviewed by Cupani.     

Orientation and Characteristics of Theropod Trackways from the Las Losas Palaeoichnological Site (La Rioja,Spain)

The Las Losas site (approximately 500 m²) was cleared in July 1998 and revealed 375 theropod dinosaur footprints. Statistical surveys of their biomorphical and morphometrical data are congruent with a continuous morphological transition among the theropod footprints—a transition which does not allow us to differentiate ichnogroups. Certain footprints show a longitudinal groove in their toes. The foot movement of their trackmakers can be inferred from these grooves. There are also, in this outcrop, i) trackways whose ichnites are either regular or anomalous according to the position of crossing, ii) semiplantigrade trackways with digitigrade sections and iii) trackways that cross the footprint site without variation in their footprints. These facts allow us to infer that: i) the substrate hardness was different in different zones at particular moments, and ii) the variation in the regularity and shape of the footprints depended upon the mud conditions at the moment they were made. Three preferential directions of march are shown by the trackways, suggesting different phases of activity.     

A calcium model with random absorption: a stochastic approach.

Absorption of calcium, or any mineral, by the body is subject to the random fluctuations typical of diffusion through membranes. In this paper we consider the absorption of calcium from the gut as a white noise process added to the deterministic model of Sen & Mohr (1990, J. theor. Biol. 142, 179-188). The first two moments for the amount of calcium in the extracellular fluid (ECF) have been derived using the Ito Calculus. A confidence interval for the total amount of calcium in the ECF is constructed. The equations for the first two moments of the fraction of dose calcium in the ECF are also given. Suggestions are made for the collection of experimental data in a form which should be helpful in investigating the magnitude of the stochastic effect.     

Changes in the Asymmetry of Eeg Waves During Voluntary Word Memorization

Study of electroencephalographic (EEG) correlates of psychological processes is becoming an increasingly popular subject, and scientists are gradually abandoning the notion that EEG parameters contain no useful information about the activity in which the subject is engaged. The search for various EEG indices reflecting the characteristics of the work being performed by a subject is being pursued with increasing vigor. The hypothesis behind these studies is that as a person goes about performing some activity, specific changes in neurodynamics take place in various locations in the cerebral cortex and that these changes will be reflected in the corresponding EEG indices. Furthermore, these EEG changes will persist as long as the subject continues what he is doing, but will be especially intense at critical moments during that activity: during the first stages, at moments preceding or accompanying the discovery of an algorithm for solving the given problem, when wrong responses are given, etc.     

Nonparametric analysis of stathmokinesis

The nonparametric analysis of the stathmokinetic experiment presented in this paper is an extension of procedures by Jagers and Staudte. The method allows one to estimate, under very general assumptions, the first two moments of the residence time in successive cell cycle phases. Approximate formulae for the mean square errors of the estimates are derived. Applications include experimental stathmokinetic data for various cell lines, both analyzed and not analyzed previously. Comparison proves that the nonparametric method is very accurate whenever it can be applied. Results of analysis of the stathmokinetic data are also discussed from the viewpoint of the variability of the cell cycle generation time.     

Going beyond limitations of plant functional types when predicting global ecosystem–atmosphere fluxes: exploring the merits of traits‐based approaches

Aim Despite their importance for predicting fluxes to and from terrestrial ecosystems, dynamic global vegetation models have insufficient realism because of their use of plant functional types (PFTs) with constant attributes. Based on recent advances in community ecology, we explore the merits of a traits‐based vegetation model to deal with current shortcomings. Location Global. Methods A research review of current concepts and information, providing a new perspective, supported by quantitative analysis of a global traits database. Results Continuous and process‐based trait–environment relations are central to a traits‐based approach and allow us to directly calculate fluxes based on functional characteristics. By quantifying community assembly concepts, it is possible to predict trait values from environmental drivers, although these relations are still imperfect. Through the quantification of these relations, effects of adaptation and species replacement upon environmental changes are implicitly accounted for. Such functional links also allow direct calculation of fluxes, including those related to feedbacks through the nitrogen and water cycle. Finally, a traits‐based model allows the prediction of new trait combinations and no‐analogue ecosystem functions projected to arise in the near future, which is not feasible in current vegetation models. A separate calculation of ecosystem fluxes and PFT occurrences in traits‐based models allows for flexible vegetation classifications. Main conclusions Given the advantages described above, we argue that traits‐based modelling deserves consideration (although it will not be easy) if one is to aim for better climate projections.     

Comparing Accuracy in an Unpaired Post‐market Device Study with Incomplete Disease Assessment

The sensitivity and specificity of a new medical device are often compared relative to that of an existing device by calculating ratios of sensitivities and specificities. Although it would be ideal for all study subjects to receive the gold standard so true disease status was known for all subjects, it is often not feasible or ethical to obtain disease status for everyone. This paper proposes two unpaired designs where each subject is only administered one of the devices and device results dictate which subjects are to receive disease verification. Estimators of the ratio of accuracy and corresponding confidence intervals are proposed for these designs as well as sample size formulae. Simulation studies are performed to investigate the small sample bias of the estimators and the performance of the variance estimators and sample size formulae. The sample size formulae are applied to the design of a cervical cancer study to compare the accuracy of a new device with the conventional Pap smear.     

The effect on neutral gene flow of selection at a linked locus

The effect on gene flow at a neutral locus of a selective cline at a linked locus is investigated. A diffusion approximation for a two-locus island model is derived in which only one locus is subject to selection. The moments of the stationary distribution are obtained and compared to the corresponding moments from a one-locus, neutral island model. This comparison yields an effective migration rate. The effective migration rate is always less than the actual migration rate, but this effect is seen to be small for weak selection and loose linkage in the case of adult migration. The importance of selection at linked loci to the question of genetic differentiation in a subdivided population is discussed.     

Dynamics of Epidemiological Models

We study the SIS and SIRI epidemic models discussing different approaches to compute the thresholds that determine the appearance of an epidemic disease. The stochastic SIS model is a well known mathematical model, studied in several contexts. Here, we present recursively derivations of the dynamic equations for all the moments and we derive the stationary states of the state variables using the moment closure method. We observe that the steady states give a good approximation of the quasi-stationary states of the SIS model. We present the relation between the SIS stochastic model and the contact process introducing creation and annihilation operators. For the spatial stochastic epidemic reinfection model SIRI, where susceptibles S can become infected I, then recover and remain only partial immune against reinfection R, we present the phase transition lines using the mean field and the pair approximation for the moments. We use a scaling argument that allow us to determine analytically an explicit formula for the phase transition lines in pair approximation.     

Mutation-Selection Balance under Genomic Imprinting at an Autosomal Locus

I model the effect of genomic imprinting on the equilibrium allele frequencies at an autosomal diallelic locus subject to viability selection and mutation. The population size is assumed to be very large; male and female mutation rates may be unequal. Different models examine cases of the inactivation of one gene (with both complete and partial penetrance) and of differential expression of genes according to the parent of origin. In the simplest cases the frequency of the deleterious allele is approximately twice that of a dominant nonimprinting mutant, but considerably less than that of a recessive nonimprinting mutant. Under imprinting, selection and unequal mutation rates interact: other things being equal, male-biased mutation leads to lower mutant frequencies under maternal imprinting and higher frequencies under paternal imprinting. I also model cases where just one allele is imprintable (and the other not). These models allow us to predict the frequency of a failure to imprint in a normally imprinting system, as well as the frequency of imprinting at a standard nonimprinting locus.     

The role of Bacillus anthracis germinant receptors in germination and virulence

Nutrient‐dependent germination of Bacillus anthracis spores is stimulated when receptors located in the inner membrane detect combinations of amino acid and purine nucleoside germinants. B. anthracis produces five distinct germinant receptors, GerH, GerK, GerL, GerS and GerX. Otherwise isogenic mutant strains expressing only one of these receptors were created and tested for germination and virulence. The GerH receptor was necessary and sufficient for wild‐type levels of germination with inosine‐containing germinants in the absence of other receptors. GerK and GerL were sufficient for germination in 50 mM L‐alanine. When mutants were inoculated intratracheally, any receptor, except for GerX, was sufficient to allow for a fully virulent infection. In contrast, when inoculated subcutaneously only the GerH receptor was able to facilitate a fully virulent infection. These results suggest that route of infection determines germinant receptor requirements. A mutant lacking all five germinant receptors was also attenuated and exhibited a severe germination defect in vitro. Together, these data give us a greater understanding of the earliest moments of germination, and provide a more detailed picture of the signals required to stimulate this process.     

Visual competition

Binocular rivalry--the alternations in perception that occur when different images are presented to the two eyes--has been the subject of intensive investigation for more than 160 years. The psychophysical properties of binocular rivalry have been well described, but newer imaging and electrophysiological techniques have not resolved the issue of where in the brain rivalry occurs. The most recent evidence supports a view of rivalry as a series of processes, each of which is implemented by neural mechanisms at different levels of the visual hierarchy. Although unanswered questions remain, this view of rivalry might allow us to resolve some of the controversies and apparent contradictions that have emerged from its study.