Stochastic models of some endemic infections

Stochastic models are established and studied for several endemic infections with demography. Approximations of quasi-stationary distributions and of times to extinction are derived for stochastic versions of SI, SIS, SIR, and SIRS models. The approximations are valid for sufficiently large population sizes. Conditions for validity of the approximations are given for each of the models. These are also conditions for validity of the corresponding deterministic model. It is noted that some deterministic models are unacceptable approximations of the stochastic models for a large range of realistic parameter values.     

Variances and Asymptotic Distributions of Direct Standardized Rates

Formulas for the variance of direct standardized rates are given for three different sampling models. The three models are product multinomial models when population totals are fixed by design, or strata totals are fixed by design, or cell (each population—each stratum) totals are fixed by design. Asymptotic distributions are derived for each model. A discussion on the relevance and use of standardized rates and the need for distribution theory is also provided.     

Enthalpies of transfer for proteins from aqueous to water-alcohol solutions: a test for models of residues exposed to solvent

The enthalpies of transfer of proteins from aqueous solution to alcohol–water solutions are used as probes of solvent-accessible surface for these proteins. Enthalpies of transfer to 10 wt% ethanol solutions are determined calorimetrically for the native proteins ribonuclease A, lysozyme, and ovalbumin. Ribonuclease A and lysozyme are reduced and carboxamidomethylated to produce configurations in which interior residues of the native protein are exposed to the solvent; enthalpies of transfer are determined for these species. These data are then compared with enthalpies of transfer for the constituent amino acids of the proteins. The enthalpies of transfer for the residues are used to generate a maximal enthalpy of transfer that can be compared with the enthalpies of transfer for the reduced, carboxamidomethylated proteins. The residue amino acid enthalpies are coupled with probabilities that each residue is an exterior residue to predict an enthalpy of transfer for the native protein that can be compared with the observed enthalpy. The probabilities developed by Wertz and Scheraga and Lee and Richards, and Chothia are then compared on their ability to predict the native enthalpies of transfer for the protein. The Wertz–Scheraga model gives the better fit of this data in all cases.     

Experience in building a balance model of a lake ecosystem (using the example of subarctic Lake Krivoe)

The principles of balance calculation are presented for aquatic ecosystems. The step-by-step building of the balance model are described for subarctic Lake Krivoe (Karelia, western coast of the White Sea), as are the problems arising during calculations and ways to fix them. The significance of the recall ratio and the primary data reliability of major ecosystem components are specified for building a plausible pattern of energy fluxes in the studied ecosystem. The energy balance models are presented for Lake Krivoe for the productive periods of 2003–2005.     

Linear regression analysis of censored medical costs

This paper deals with the problem of linear regression for medical cost data when some study subjects are not followed for the full duration of interest so that their total costs are unknown. Standard survival analysis techniques are ill-suited to this type of censoring. The familiar normal equations for the least-squares estimation are modified in several ways to properly account for the incompleteness of the data. The resulting estimators are shown to be consistent and asymptotically normal with easily estimated variance-covariance matrices. The proposed methodology can be used when the cost database contains only the total costs for those with complete follow-up. More efficient estimators are available when the cost data are recorded in multiple time intervals. A study on the medical cost for ovarian cancer is presented.     

2 x 2 kappa coefficients: measures of agreement or association

Two general but different contexts in which kappa might be used are defined: agreement and association. Two models, one for agreement and one for utility of association, are defined yielding different kappa coefficients and different sampling theory. Asymptotic results are derived for both models. Small-sample evaluations are presented for the model for agreement.     

New Staphylinidae (Coleoptera) records with new collection data from New Brunswick, and an addition to the fauna of Quebec, Canada: Aleocharinae

Thirty-eight species of Aleocharinae are newly reported from New Brunswick, bringing the total number of species known from the province to 216. Thirty-one of these species are newly recorded for the Maritime provinces, and four of them, Phloeopora oregona Casey, Gyrophaena michigana Seevers, Gyrophaena wisconsinica Seevers, and Tomoglossa decora (Casey), are newly recorded for Canada. Tomoglossa constitutes a new generic record for Canada. Collection and habitat data for all these species are presented and discussed. Color habitus, median lobe of the aedeagus, and male tergite and sternite 8 images are presented for the first time for Phloeopora oregona, and references to illustrations are provided for all other species included in this paper. A color habitus image is presented for Tomoglossa decora.     

New Coleoptera records from New Brunswick, Canada: Stenotrachelidae, Oedemeridae, Meloidae, Myceteridae, Boridae, Pythidae, Pyrochroidae, Anthicidae, and Aderidae

We report 19 new species records for the faunal list of Coleoptera in New Brunswick, Canada, six of which are new records for the Maritime provinces, and one of which is new Canadian record. We also provide the first recent records for five additional species in New Brunswick. One new species of Stenotrachelidae, Cephaloon ungulare LeConte, is added to the New Brunswick faunal list. Additional records are provided for Cephaloon lepturides Newman, as well the first recent record of Nematoplus collaris LeConte. Two species of Oedemeridae, Asclera puncticollis (Say) and Asclera ruficollis (Say), are newly reported for New Brunswick, and additional locality and bionomic data are provided for Calopus angustus LeConte and Ditylus caeruleus (Randall). The records of Ditylus caerulus are the first recent records for the province. Three species of Meloidae, Epicauta pestifera Werner, Lytta sayi LeConte, and Meloe augustcollis Say are reported the first time for New Brunswick; Epicauta pestifera is newly recorded in Canada. Lacconotus punctatus LeConte and the family Mycteridaeis newly recorded for New Brunswick. The first recent records of Borus unicolor Say (Boridae) are reported from the province. One new species of Pythidae, Pytho siedlitzi Blair, and the first recent records of Pytho niger Kirby are added to the faunal list of New Brunswick. Three species of Pyrochroidae are newly reported for the province, including Pedilus canaliculatus (LeConte) and Pedilus elegans (Hentz), which are new for the Maritime provinces. Five species of Anthicidae and the first recent record of Anthicus cervinus LaFerté-Sénectére are newly reported for New Brunswick. Anthicus melancholicus LaFerté-Sénectère, Sapintus pubescens (LaFerté-Sénectère), Notoxus bifasciatus (LeConte), and Stereopalpus rufipes Casey are new to the Maritime provinces faunal list. Ambyderus granularis (LeConte) is removed from the faunal list of the province. Three species of Aderidae, Vanonus huronicus Casey, Zonantes fasciatus (Melsheimer), and Zonantes pallidusWerner, are newly recorded for New Brunswick; Zonantes fasciatus and Vanonus huronicus are new for the Maritime provinces' faunal list. Collection data, bionomic data, and distribution maps are presented for all these species.     

Stochastic theory of population genetics

Stochastic models of population genetics are studied with special reference to the biological interest. Mathematical methods are described for treating some simple models and their modifications aimed at the problems of the molecular evolution. Unified theory for treating different quantities is extensively developed and applied to some typical problems of current interest in genetics. Mathematical methods for treating geographically structured populations are given. Approximation formulae and their accuracy are discussed. Some criteria are given for a structured population to behave almost like a panmictic population of the same total size. Some quantities are shown to be independent of the geographical structure and their dynamics are described.     

Likelihood Under the Mixed Model for Quantitative Traits

Mathematical details of obtaining the likelihood functions for testing hypotheses under the mixed model for quantitative traits are given. Since families are assumed to be chosen by the value of the trait of a particular family member, conditional distributions are required. Algorithms for efficient computation of the likelihood are given.     

Strategies for computer modeling

Modeling is a ubiquitous and often misunderstood enterprise in which data from diverse disciplines are analyzed by techniques from other diverse disciplines in an attempt to confirm or falsify a set of hypotheses about the real world. Guidelines are offered for designing models to match the goals of modeling biological systems. Techniques for the construction and interpretation of models are discussed. The requirements for credibility of models are detailed, and tests are suggested for their validation.     

Linear rank tests for interval-censored data with application to PCB levels in adipose tissue of transformer repair workers

Linear rank statistics are described for testing for differences between groups when the data are interval-censored. The statistics are closely related to those described by Prentice (1978, Biometrika 65, 167-179) for right-censored data. Problems in calculating the statistics are discussed and several approaches to computation including estimation of the efficient rank scores are described. Results from a small simulation study are presented. The methods are applied to data from a study relating tissue levels of PCBs to occupational exposure.     

Wood, bark and stem anatomy of New World species of Gnetum

Quantitative and qualitative data are presented for 11 collections of six species. The wide range of character states for the species is presented in the form of a key to emphasize their potential systematic correlations. Distinctive among these are phcllem characteristics. Fibre-tracheids are newly reported for lianoid Gnetum species. Cells previously thought to be like companion cells in secondary phloem are shown to be uniseriate rays, counterparts to uniseriate xylem rays. Laticifers are abundant in most of the species, and are newly described for secondary tissues of Gnetum. Presence of tyloses in laticifers of two species is apparently a new report for vascular plants. Tori are present in two New World Gnetum species, adding to the report in African species. Perforation plates are simple except near or in primary xylem, where they are simple or foraminate. Torus presence and foraminate perforation plate presence are features more reminiscent of Ephedra and other gymnosperms than of angiosperms. The bark of Gnetum is also very similar to that of Ephedra.     

Comparative biogeography of mammals on islands

Insular faunas of terrestrial mammals and bats are examined on a worldwide basis to test the adequacy of equilibrium and historical legacy models as explanations for species-area relationships. Species numbers of bats on islands conform to predictions from equilibrium theory, whereby recurrent immigrations and extinctions influence species richness. By contrast, species numbers of terrestrial mammals on islands result from a historical legacy of very low immigration rates on oceanic islands (the faunas are colonization-limited) and by the fragmentation of once contiguous continental faunas to form relictual populations, which subsequently undergo extinctions, on landbridge islands (the faunas are extinction-limited). This explanation is supported by several lines of evidence: (1) z values (slopes of species-area curves) are lower for non-volant mammals on oceanic islands than for those on landbridge islands, but are the opposite for bats; (2) z values for non-volant mammals are lower than those for bats on oceanic islands, but are higher than those for bats on landbridge islands; and (3) landbridge island faunas are attenuated mainland faunas, whereas those on oceanic islands are ecologically incomplete. No support is found for alternative hypotheses to explain low species-area slopes for terrestrial mammals on oceanic islands.     

New Coleoptera records from New Brunswick, Canada: Mycetophagidae, Tetratomidae, and Melandryidae

We report 21 new species records for the Coleoptera fauna of New Brunswick, Canada, seven of which are new records for the Maritime provinces. Four species of Mycetophagidae (Litargus didesmus Say, Litargus tetrapilotus LeConte, Mycetophagus punctatus Say, and Mycetophagus quadriguttatus Müller) are newly reported for the province of New Brunswick. Litargus didesmus is newly recorded for the Maritime provinces. Seven species of Tetratomidae are added to the faunal list of New Brunswick: Eustrophus tomentosus Say, Penthe obliquata (Fabricius), and Tetratoma tessellata Melsheimer are new to New Brunswick: Hallomenus serricornis LeConte, Pisenus humeralis Kirby, Synstrophus repandus (Horn), and Tetratoma variegata Casey, which are newly recorded for New Brunswick and the Maritime provinces. Ten additional species of Melandryidae are reported from New Brunswick, of which Orchesia cultriformis Laliberté, Orchesia ovata Laliberté, Phloeotrya fusca (LeConte), Scotochroides antennatus Mank, Spilotus quadripustulatus (Melsheimer), Symphora flavicollis (Haldeman), Symphora rugosa (Haldeman), and Zilora hispida LeConte are new for the province, and Microscapha clavicornis LeConte and Zilora nuda Provancher are newly recorded for the Maritime provinces. In addition, we report numerous additional records for three species of Mycetophagidae and one species of Melandryidae previously recorded from New Brunswick that suggest these species are more widely distributed than previously known. Collection, habitat data, and distribution maps are presented for all these species.     

Method agreement analysis: A review of correct methodology

The correct approach to analyzing method agreement is discussed. Whether we are considering agreement between two measurements on the same samples (repeatability) or two individuals using identical methodology on identical samples (reproducibility) or comparing two methods, appropriate procedures are described, and worked examples are shown. The correct approaches for both categorical and numerical variables are explained. More complex analyses involving a comparison of more than two pairs of data are mentioned and guidance for these analyses given. Simple formulae for calculating the approximate sample size needed for agreement analysis are also given. Examples of good practice from the reproduction literature are cited, and common errors of methodology are indicated.     

Uniform persistence and permanence for non-autonomous semiflows in population biology

Conditions are presented for uniform strong persistence of non-autonomous semiflows, taking uniform weak persistence for granted. Turning the idea of persistence upside down, conditions are derived for non-autonomous semiflows to be point-dissipative. These results are applied to time-heterogeneous models of S-I-R-S type for the spread of infectious childhood diseases. If some of the parameter functions are asymptotically almost periodic, an almost sharp threshold result is obtained for uniform strong endemicity versus extinction in terms of asymptotic time averages. Applications are also presented to scalar retarded functional differential equations modeling one species population growth.     

New data on the spider fauna of Iran (Arachnida: Araneae)

We present the results of some spider surveys that were conducted in different parts of Iran. Faunistic records for 30 species which are new to Iran are presented here. Biogeographic data are provided for each species. Two families, namely Liocranidae and Mimetidae, are recorded for the first time from the country.     

Estimatingdendroctonus frontalis (Coleoptera: Scolytidae) daily infestation dynamics

Summary Mathematical procedures are given to estimate infestation totals and daily life stage arrivals, departures, and mortality ofDendroctonus frontalis Zimmermann for an infested tree in the field. These estimates are based on minimal sample data and are designed to utilize all available information. Daily arrival estimates for larvae, pupae, and callow adults are obtained by indirect analysis without direct observation of these stages. The procedures are applied to 147 infested trees, and the results are transformed to a common time basis to obtain daily expectations by life stage for an “average” tree. These expectations suggest optimal times for field sampling or relative times of sampling when optimal times are missed. Expected daily arrival distributions by life stage for a single egg and a single attacking adult are given. Procedures are given for utilizing collateral information to obtain an infestation total and daily arrival estimates for a boundary life stage. The results of this study are applicable to anyD. frontalis field study, and the procedures given are applicable to any bark inhabiting insect having similar habits.