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.     

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.     

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.     

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.     

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.     

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.     

Immunizations for foreign travel.

One of the most important aspects of preparing travelers for destinations throughout the world is providing them with immunizations. Before administering any vaccines, however, a careful health and immunization history and travel itinerary should be obtained in order to determine vaccine indications and contraindications. There are three categories of immunizations for foreign travel. The first category includes immunizations which are routinely recommended whether or not the individual is traveling. Many travelers are due for primary vaccination or boosting against tetanus-diphtheria, measles-mumps-rubella, pneumococcal pneumonia, and influenza, for example, and the pre-travel visit is an ideal time to administer these. The second category are immunizations which might be required by a country as a condition for entry; these are yellow fever and cholera. The final category contains immunizations which are recommended because there is a risk of acquiring a particular disease during travel. Typhoid fever, meningococcal disease, rabies, and hepatitis are some examples. Travelers who are pregnant or who are infected with the human immunodeficiency virus require special consideration. Provision of appropriate immunizations for foreign travel is an important aspect of preventing illness in travelers.     

Three mechanisms and rapid-equilibrium rate equations for a type of reductase reaction

Rapid-equilibrium rate equations for enzyme-catalyzed reactions are especially useful when the mechanism involves a number of pKs, but they are also useful when some reactants have stoichiometric numbers greater than one or hydrogen ions are produced or consumed in the rate-determining step. The pH dependencies of limiting velocities, Michaelis constants, and reaction velocities for the forward reaction are discussed for two examples of reductase reactions of the type mR + O -> products, where R is the reductant and O is the oxidant. For the nitrate reductase reaction (EC 1.9.6.1), m = 2 and two hydrogen ions are consumed. For the nitrite-ferredoxin reductase reaction (EC 1.7.7.1), m = 6 and eight hydrogen ions are consumed. The expressions for the limiting velocities, Michaelis constants, and rate equations for the forward reaction are derived for two ordered mechanisms and the random mechanism. Three Mathematica programs are used to make plots of kinetic parameters as functions of pH and three-dimensional plots of rapid-equilibrium velocities as functions of [O] and [R] for arbitrary sets of input parameters.     

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.     

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.     

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.     

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.     

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.     

DAPI (4',6-diamidino-2-phenylindole) binds differently to DNA and RNA: minor-groove binding at AT sites and intercalation at AU sites.

The interaction of DAPI and propidium with RNA (polyA.polyU) and corresponding DNA (polydA.polydT) sequences has been compared by spectroscopic, kinetic, viscometric, Tm, and molecular modeling methods. Spectral changes of propidium are similar on binding to the AT and AU sequences but are significantly different for binding of DAPI. Spectral changes for DAPI with the DNA sequence are consistent with the expected groove-binding mode. All spectral changes for complexes of propidium with RNA and DNA and for DAPI with RNA, however, are consistent with an intercalation binding mode. When complexed with RNA, for example, DAPI aromatic protons signals shift significantly upfield, and the DAPI UV-visible spectrum shows significantly larger changes than when complexed with DNA. Slopes of log kd (dissociation rate constants) versus-log [Na+] plots are similar for complexes of propidium with RNA and DNA and for the DAPI-RNA complex and are in the range expected for an intercalation complex. The slope for the DAPI-DNA complex, however, is much larger and is in the range expected for a groove-binding complex. Association kinetics results also support an intercalation binding mode for the DAPI-RNA complex. The viscosity of polyA.polyU solutions increases significantly on addition of both propidium and DAPI, again in agreement with an intercalation binding mode for both molecules with RNA. Molecular modeling studies completely support the experimental findings and indicate that DAPI forms a very favorable intercalation complex with RNA. DAPI also forms a very stable complex in the minor groove of AT sequences of DNA, but the stabilizing interactions are considerably reduced in the wide, shallow minor groove of RNA. Modeling studies,thus,indicate that DAPI interaction energetics are more favorable for minor-groove binding in AT sequences but are more favorable for interaction in RNA.     

Bacteriophage and Bacteria in a Flow Reactor

The Levin-Stewart model of bacteriophage predation of bacteria in a chemostat is modified for a flow reactor in which bacteria are motile, phage diffuse, and advection brings fresh nutrient and removes medium, cells and phage. A fixed latent period for phage results in a system of delayed reaction-diffusion equations with non-local nonlinearities. Basic reproductive numbers are obtained for bacteria and for phage which predict survival of each in the bio-reactor. These are expressed in terms of physical and biological parameters. Persistence and extinction results are obtained for both bacteria and phage. Numerical simulations are in general agreement with those for the chemostat model.     

Biotope prioritisation in the Central Apennines (Italy): species rarity and cross-taxon congruence

The conservation status of invertebrates is usually lesser known than that of vertebrates, and strategies to identify biotopes to preserve invertebrate diversity are typically based on a single surrogate taxon, or even on the use of vertebrates as surrogates. Aim of this research is to illustrate a method for biotope prioritisation that can be easily adapted to different animal groups and geographical contexts. A two-step protocol for biotope prioritisation is proposed on the basis of a multidimensional characterisation of species vulnerability. Firstly, species vulnerability is estimated from rarity measures which include geographical range, abundance and biotope specialisation. Then, these values of vulnerability are used to rank biotopes. The method was applied here to the tenebrionid beetles, the butterflies, the birds and the mammals of the Central Apennines, a montane area of high conservation concern for South Europe. This study provides evidence for the importance of including insects in conservation decisions, because vertebrates are poor surrogates for insects. Conservation efforts in the reserves included in the study area are mostly focused on vertebrates, for which woodlands are considered particularly important. However high altitude open biotopes are crucial for both tenebrionids and butterflies, and preservation of such kind of biotopes would be beneficial also for vertebrates. The approach applied here demonstrates that (1) vertebrates are poor surrogates for insects, and (2) measures of species rarity, typically used in vertebrate conservation, can be obtained also for insects, for which a veritable amount of data are hidden in specialised literature and museum collections.     

Multilocus estimation of pairwise relatedness with dominant markers

Estimators for pairwise relatedness designed for dominant markers are derived, based on a genetic model that accounts for the full structure of pairwise relatedness between two individuals at a diploid locus with dominance. They jointly estimate 'relatedness' and 'fraternity', in which case the estimators are inherently multilocus, as at least two loci of differing gene frequency are required. Extensions to cases of zero fraternity and isolation by distance (inbreeding) are also examined. Properties of estimators are examined by simulation and compared to the estimator of Hardy. The most statistical power for pairwise relatedness occurs when roughly half of individuals are the recessive phenotype. Estimation procedures are implemented in the computer program mark.     

Basic strategies for valid cytometry using image analysis

The present review provides a starting point for setting up an image analysis system for quantitative densitometry and absorbance or fluorescence measurements in cell preparations, tissue sections or gels. Guidelines for instrumental settings that are essential for the valid application of image analysis in cytophotometry and cytofluorometry are described. The general principles of the working mechanism of CCD cameras in combination with general methods to improve the behaviour of the cameras are presented. Optimization of illumination of microscopical and macroscopical objects receives special attention because of its importance for valid cytometry. Sources of errors in quantitative measurements are listed and step-by-step charts for tuning the CCD camera, frame grabber and illumination for the optimal use of the systems are described. Suggestions are given for improvement of image arithmetics in difficult imaging situations, such as low fluorescence signals and high absorbance signals. This revised version was published online in November 2006 with corrections to the Cover Date.