Optimal approximate conversions of odds ratios and hazard ratios to risk ratios

Odds ratios approximate risk ratios when the outcome under consideration is rare but can diverge substantially from risk ratios when the outcome is common. In this paper, we derive optimal analytic conversions of odds ratios and hazard ratios to risk ratios that are minimax for the bias ratio when outcome probabilities are specified to fall in any fixed interval. The results for hazard ratios are derived under a proportional hazard assumption for the exposure. For outcome probabilities specified to lie in symmetric intervals centered around 0.5, it is shown that the square-root transformation of the odds ratio is the optimal minimax conversion for the risk ratio. General results for any nonsymmetric interval are given both for odds ratio and for hazard ratio conversions. The results are principally useful when odds ratios or hazard ratios are reported in papers, and the reader does not have access to the data or to information about the overall outcome prevalence.     

REVERSIBILITY IN EVOLUTION: A MAXIMUM LIKELIHOOD APPROACH TO CHARACTER GAIN/LOSS BIAS IN PHYLOGENIES

Statistical methods are used to test the hypothesis that rate of gain is equal to rate of loss for a single character on a cladogram. Ancestral character states are used as input for maximum likelihood (ML) rate estimation. Two markovian models of character evolution are considered: one has equality of rate across branches; the other permits variation in rate according to predetermined weights for branches. ML estimates are derived for both models, and their properties in large and small trees are investigated. Bias and error are significant in small trees. Error is greatest for characters in which rate of gain is low, and is greater for the loss estimate than for the gain estimate. Likelihood ratio (LR) tests of the null hypothesis of equality of gain/loss rate are derived, and their properties investigated. The distribution of -2 log LR is close to χ² with 1 df with as few as 32 taxa. However, the power of the test is low unless the character is evolving rapidly. Methods for increasing power are examined, including selection of rapidly evolving subsets of characters, and pooling across characters. A goodness of fit test is presented to determine if pooling is justified. An example using published restriction site data on the Asteraceae demonstrates significant deviation from the null model in the direction predicted on the basis of the molecular biology of restriction enzyme site recognition, but only for one large subset of the data in which pooling is warranted.     

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.     

The genetic basis of delay discounting and its genetic relationship to alcohol dependence

Delay discounting is steeper for individuals who drink heavily or are alcohol dependent, but the reasons for this are unclear. Given the substantial genetic component for alcohol dependence it is not unreasonable to ask whether discounting and alcohol dependence have a genetic relationship. For there to be a genetic relationship, delay discounting must have a genetic component (heritability). A review of the human and animal literature suggests that this is the case. Other literature examining whether discounting is a correlated phenotype in individuals who are genetically predisposed to drink (family history positive individuals and selected lines of rats and mice) is mixed, suggesting that networks of genes are critical for the relationship to be seen. The identities of the genes in this network are not yet known, but research examining polymorphisms associated with differences in discounting is beginning to address this issue.     

Cell surface proteins and malignant transformation

Many of the altered properties of malignant cells are thought to involve alterations in cell surface functions. In order to understand these alterations it is necessary to know more about the molecular structure of the surface. Methods for analyzing surface proteins are discussed and their application to normal and transformed tissue culture cells are reviewed. A number of surface proteins are observed to be altered by transformation. Most of the alterations are reductions in amounts of particular species, although a few proteins do increase. Evidence concerning the reasons for these alterations and the possible functions of some of the molecules is reviewed. Working hypotheses arising from these data are presented and prospects for understanding the physiological changes in terms of molecular effects are discussed. Particular emphasis is placed on the idea that surface molecules are associated in specific-non-covalent complexes which are important for their functions.     

Integrating conservation and development: effective trade-offs between biodiversity and cost in the selection of protected areas

Strategies are needed for reconciling competing demands at the regional level when areas are to be selected for protection and there are associated costs, possibly equivalent to forgone development opportunties. As an alternative to the fixed scaling (or weighting) of costs and benefits required by cost-benefit analysis, multi-criteria analyses allow the exploration of alternative weightings and a summary trade-off curve to determine preferred solutions. For alternative sets of areas, total cost could be plotted against total represented biodiversity, but a more consistent approach should look at trade-off space at the level of individual areas. For a given weighting, an area is assigned protection if and only if its contribution to total biodiversity, CB, exceeds its equivalent cost, EC (in biodiversity units). Because CB for a given area depends on which other areas are also protected, it can be more or less than EC. Here we develop an iterative strategy for selecting areas, such that, for a given weighting, an area is in the final protected set if and only if its final CB value is greater than its EC value. Sensitivity analysis is used to identify those areas that: (1) are assigned protection even when low weight is given to biodiversity, or (2) are not assigned protection even when high weight is given to biodiversity. This approach is applicable in principle to any surrogate measure for biodiversity; here examples are presented in which environmental data are summarized as an environmental space.     

Stochastic multitype epidemics in a community of households: estimation and form of optimal vaccination schemes

This paper treats a stochastic model for an SIR (susceptible-->infective-->removed) multitype household epidemic. The community is assumed to be closed, individuals are of different types and each individual belongs to a household. Previously obtained probabilistic and inferential results for the model are used to derive the optimal vaccination scheme. By this is meant the scheme that vaccinates the fewest among all vaccination schemes that reduce the threshold parameter below 1. This is done for the situation where all model parameters are known and also for the case where parameters are estimated from an outbreak in the community prior to vaccination. It is shown that the algorithm which chooses vaccines sequentially, at each step selecting the individual which reduces the threshold parameter the most, is not in general an optimal scheme. As a consequence, explicit characterisation of the optimal scheme is only possible in certain special cases. Two different types of vaccine responses, leaky and all-or-nothing, are considered and compared for the problems mentioned above. The methods are illustrated with some numerical examples.     

The prospects of using transgenic insects in biocontrol programs

Methods of biocontrol are widely used for suppression of pests and human disease vectors. One of the key methods is insects sterilization (sterile insect technique--SIT), which currently is accomplished by irradiation. Radiation-exposed insects have reduced fitness so theis competitive abilities are diminished as compared to insects from wild populations. Modern bioengineering is capable of producing transgenic insects with predetermined traits, and by now the schemes for getting sterile insects without exposure to radiation are developed. Another area of modern studies is producing insects that are unable to transmit diseases malaria, for example. In the present review the implementation and perspectives are outlined for replacement of Anopheles wild populations with transgenic mosquitos. The main way for delivering the genetic material to recipient's genome is using transposon-based constructs. The markers of transgenesis are described. The potential danger for the environment of transgenic constructs remobilization and the necessity of their stabilization within the genome are emphasized. The existing methods of stabilization which involve the deletion of transposon terminal inverted repeats are described.     

Covariance between relatives for X-chromosomal loci in a population in disequilibrium

Summary According to Hardy-Weinberg, for a single autosomal locus, a population achieves equilibrium in one generation of random mating if allelic frequency is the same in the sexes, or in two generations if the frequency is not. For a single X-chromosomal locus, however, the approach to equilibrium oscillates and is gradual. Covariances between relatives for autosomal and for X-chromosomal loci are in the literature for a random mating population in equilibrium. Although assumption of equilibrium is defensible for an autosomal locus, it is less defensible for an X-chromosomal locus. Covariances between collateral and between lineal relatives are derived for X-chromosomal loci in a random mating population not in equilibrium. Collateral relatives such as sibs are of the same generation, and lineal relatives such as parent-offspring are of different generations. Coefficient of co-ancestry between relatives, based on identity by descent, was used in this development. Results are applicable to crossbreeding in livestock and poultry, and also to haplo-diploid organisms, such as the honeybee, in which the entire genome is equivalent to being X-chromosomal.Supported in part by the Illinois Agricultural Experiment Station, Hatch Project 35-0367     

Estimation of Bayesian confidence intervals for the product of conditional survival probabilities

A model is derived to estimate the survival probability of a time interval when censorings occur. The time interval is divided into partial intervals in order to obtain the conditional survival probabilities, each of which is a parameter of a Binomial distributed random variable. To allow for the dependence between the events in the different intervals these parameters are transformed. Corresponding a priori density functions are formulated regarding both the Bayesian uniform distribution and the special model. The a posteriori density function is derived for the product of the conditional survival probabilities, and formulae for the BAYE sian confidence interval and the expectation are given. Lower and upper bounds for the confidence interval and the expectation are derived. Some examples are given to compare the results with other methods.     

Tail effects on yaw stability in birds

Bird tails, which are an aerodynamic surface in the horizontal plane, are treated with regard to their effects on yaw stability. Reference is made to wings of very small aspect ratio similar to the values of bird tails in order to identify features which are significant for the aerodynamic yawing moment characteristics due to sideslip. It is shown that there are yawing moments of considerable magnitude for this aspect ratio region. Furthermore, the lift coefficient, which also exerts an influence, is included in the treatment of yaw stability. To show more concretely the addressed effects for birds, the yawing moment characteristics of the wing-tail combination of a pigeon, which is considered as a representative example, are treated in detail. For this purpose, a sophisticated aerodynamic method capable to deal with the mutual flow interactions between the tail and the wing is used to compute results of high precision. The yawing moment characteristics of the pigeon wing-tail combination with respect to the sideslip angle and the lift coefficient are determined, with emphasis placed on the contribution of the tail. It is shown that there is a significant contribution of the tail to yaw stability. The findings of this paper on the contribution of the tail to the yawing moment characteristics are supported by an evaluation of existing experimental data. Furthermore, the physical mechanisms are considered which are the reasons for the stabilizing role of the tail. These effects concern the contribution of the drag acting at the tail to the yawing moment. In addition, it is shown that extended legs and feet, when exposed to the airflow, can contribute to yaw stability.     

Establishing the Minimal Bactericidal Concentration of an Antimicrobial Agent for Planktonic Cells (MBC-P) and Biofilm Cells (MBC-B)

This protocol allows for a direct comparison between planktonic and biofilm resistance for a bacterial strain that can form a biofilm in vitro. Bacteria are inoculated into the wells of a 96-well microtiter plate. In the case of the planktonic assay, serial dilutions of the antimicrobial agent of choice are added to the bacterial suspensions. In the biofilm assay, once inoculated, the bacteria are left to form a biofilm over a set period of time. Unattached cells are removed from the wells, the media is replenished and serial dilutions of the antimicrobial agent of choice are added. After exposure to the antimicrobial agent, the planktonic cells are assayed for growth. For the biofilm assay, the media is refreshed with fresh media lacking the antimicrobial agent and the biofilm cells are left to recover. Biofilm cell viability is assayed after the recovery period. The MBC-P for the antimicrobial agent is defined as the lowest concentration of drug that kills the cells in the planktonic culture.  In contrast, the MBC-B for a strain is determined by exposing preformed biofilms to increasing concentrations of antimicrobial agent for 24 hr. The MBC-B is defined as the lowest concentration of antimicrobial agent that kills the cells in the biofilm.     

On estimating similarity of artificial and real organisms

Summary In this paper, a dissimilarity measure for artificial organisms is proposed. The organisms are simulated in the Framsticks system [10]. Properties of agents are enumerated formally, and the heuristic algorithm for estimating overall phenetic dissimilarity of two agents is described. An example of performance is shown on two selected organisms. Two clustering experiments with interesting results are presented using the UPGMA method. The properties of the measure are then discussed. Computer simulations of complex systems and their characteristics are compared to biological systems, which may bring up ideas for further experiments related to biology.     

New Coleoptera records for New Brunswick, Canada: Kateretidae, Nitidulidae, Cerylonidae, Endomychidae, Coccinellidae, and Latridiidae

We report 20 new species records for the Coleoptera fauna in New Brunswick, Canada, five of which are new records for the Maritime provinces, including one species that is new for Canada. One species of Kateretidae, Kateretes pusillus (Thunberg) is newly recorded for New Brunswick and the Maritime provinces. Stelidota octomaculata (Say), Phenolia grossa (Fabricius), andCryptarcha strigatula Parsons of the family Nitidulidae are added to the faunal list of New Brunswick; the latter species is new to the Maritime provinces. Two species of Cerylonidae, Philothermus glabriculus LeConte and Cerylon unicolor (Ziegler), are reported for the first time for New Brunswick. Philothermus glabriculus is new for the Maritime provinces. Two species of Endomychidae, Hadromychus chandleri Bousquet and Leschen and Danae testacea (Ziegler) are newly recorded for New Brunswick. Three species of Coccinelidae, Stethorus punctum punctum (LeConte), Naemia seriata seriata Melsheimer, and Macronaemia episcopalis (Kirby) are added to the provincial list. Macronaemia episcopalis (Kirby) is a species new to the Maritime provinces. Nine species of Latridiidae, Cartodere nodifer (Westwood), Dienerella ruficollis (Marsham), Enicmus aterrimus Motschulsky, Enicmus fictus Fall, Encimus histrio Jay and Tomlin, Lathridius minutus (Linnaeus), Stephostethus productus Rosenhauer, Corticaria elongata (Gyllenhal), and Corticarina longipennis (LeConte) are newly recorded for New Brunswick. Stephostehus productus is newly recorded from Canada. Collection and habitat data are presented for all these species.     

Models of epidemics and endemicity in genetically variable host populations

A discrete time genetics model is developed for populations that are undergoing selection due to infectious disease. It is assumed that the generation time of the host and infectious agent are non-synchronous and that only the host population is evolving. Two classes of epidemic processes are considered. The first class is for infectious agents that confer immunity following infection, while the second class is for those that do not confer immunity. The necessary and sufficient conditions are found in order for the disease to persist in a stable polymorphic host population. These conditions are shown to depend on the density of susceptibles, the selection coefficients, and the severity and class of the disease process.     

Equilibrium points for nonlinear compartmental models.

Equilibrium points for nonlinear autonomous compartmental models with constant input are discussed. Upper and lower bounds for the steady states are derived. Theorems guaranteeing existence and uniqueness of equilibrium points for a large collection of system are proved. New information relating to mean residence times is developed. Asymptotic results and a section on stability are included. A recursive process is discussed that generates iterates that converge to steady states for certain types of models. An interesting range of models are included as examples. An attempt is made to provide general qualitative theory for such nonlinear compartmental systems.     

Radiation risk in manned space flights

This paper addresses some of the pertinent questions relating to the assessment of radiation risk for humans in space; the paper is not intended as a comprehensive review. The radiation field is briefly summarised and doses to be expected are given based on recent on-board measurements. The problems in adapting terrestrial epidemiological data to the space situation are outlined. Apart from the intrinsic uncertainties in deriving risk factors the specific difficulties are mainly concerned with the effects of energetic charged particles for which no human data exist. The necessity for continuing ground-based research is stressed. Also discussed is whether the principles of radiation protection successfully applied on Earth are really suitable for the space situation or whether they should be replaced by a different approach.     

Why Alcoholics Ought to Compete Equally for Liver Transplants

Some philosophers and physicians have argued that alcoholic patients, who are responsible for their liver failure by virtue of alcoholism, ought to be given lower priority for a transplant when donated livers are being allocated to patients in need of a liver transplant. The primary argument for this proposal, known as the Responsibility Argument, is based on the more general idea that patients who require scarce medical resources should be given lower priority for those resources when they are responsible for needing them and when they are competing with patients who need the same resources through no fault of their own. Since alcoholic patients are responsible for needing a new liver and are in direct competition with other patients who need a new liver through no fault of their own, it follows that alcoholic patients ought to be given lower priority for a transplant. In this article, I argue against the Responsibility Argument by suggesting that in order for it to avoid the force of plausible counter examples, it must be revised to say that patients who are responsible for needing a scarce medical resource due to engaging in behavior that is not socially valuable ought to be given lower priority. I'll then argue that allocating organs according to social value is inconsistent or in tension with liberal neutrality on the good life. Thus, if one is committed to liberal neutrality, one ought to reject the Responsibility Argument.     

Proprioception and Tension Receptors in Crab Limbs: Student Laboratory Exercises

The primary purpose of these procedures is to demonstrate for teaching and research purposes how to record the activity of living primary sensory neurons responsible for proprioception as they are detecting joint position and movement, and muscle tension. Electrical activity from crustacean proprioceptors and tension receptors is recorded by basic neurophysiological instrumentation, and a transducer is used to simultaneously measure force that is generated by stimulating a motor nerve. In addition, we demonstrate how to stain the neurons for a quick assessment of their anatomical arrangement or for permanent fixation. Staining reveals anatomical organization that is representative of chordotonal organs in most crustaceans. Comparing the tension nerve responses to the proprioceptive responses is an effective teaching tool in determining how these sensory neurons are defined functionally and how the anatomy is correlated to the function. Three staining techniques are presented allowing researchers and instructors to choose a method that is ideal for their laboratory.