Correlated binary regression with covariates specific to each binary observation

Regression methods are considered for the analysis of correlated binary data when each binary observation may have its own covariates. It is argued that binary response models that condition on some or all binary responses in a given "block" are useful for studying certain types of dependencies, but not for the estimation of marginal response probabilities or pairwise correlations. Fully parametric approaches to these latter problems appear to be unduly complicated except in such special cases as the analysis of paired binary data. Hence, a generalized estimating equation approach is advocated for inference on response probabilities and correlations. Illustrations involving both small and large block sizes are provided.     

Vegetation responses to past climatic variation

Vegetation responses to climatic change can be studied retrospectively by utilizing the Quaternary fossil record. There has been controversy over the extent to which major changes in vegetation patterns at the continental scale lag behind the climatic changes that drive them, and to what extent vegetation can ever be said to be in equilibrium with climate. The equilibrium question has no single answer. The predominant mode of vegetation response to climatic change depends on the space and time frame and resolution of the data set in which the response is observed.Vegetation (as observed on particular space and time scales) can be in dynamic equilibrium with climate if its response time is sufficiently fast in relation to the rate of climatic change to which it is observed to be responding. Several processes can be involved in the response: successional, migrational, edaphic, and evolutionary. Successional response times can be deduced from forest succession models. The other processes are less well understood and different ideas exist concerning their rates. According to one hypothesis, migrational lags caused delays of thousands of years in the postglacial dynamics of forest composition. The alternative hypothesis explains these changes as dynamic equilibrium responses to changes in climatic seasonality and climatic anomaly patterns. Neither hypothesis need be universally true; gradient analysis and forest succession models are among the techniques that can be used in inferential tests of these hypotheses for particular space-time regions.Dynamic equilibrium may often be a reasonable approximation for the responses of the broadest continental-scale forest patterns to orbitally induced climatic changes. But as spatial and temporal frames of observation are diminished and resolution increased, biotic processes must eventually come to dominate. At sufficiently fine scales the main observable phenomena are successional responses to natural disturbance events. The late-Quaternary record of vegetation change allows a choice of observation scales and thus provides a continuum of possibilities for study, ranging from long-term dynamic bioclimatology to more conventional vegetation dynamics.I thank Margaret Davis, Honor Prentice, Jim Ritchie, Al Solomon, Geoff Spaulding and Tom Webb for their reviews of earlier drafts. Research supported by a US Department of Energy, Carbon Dioxide Research Division, grant to Brown University and a Swedish Natural Science Research Council grant to the project SlsSimulation of Natural Forest Dynamics.I thank Margaret Davis, Honor Prentice, Jim Ritchie, Al Solomon, Geoff Spaulding and Tom Webb for their reviews of earlier drafts. Research supported by a US Department of Energy, Carbon Dioxide Research Division, grant to Brown University and a Swedish Natural Science Research Council grant to the project SlsSimulation of Natural Forest Dynamics.     

SB subregion of the human major histocompatibility complex: gene organization, allelic polymorphism and expression in transformed cells

The SB region of the human major histocompatibility complex (MHC) has been cloned from cosmid and lambda phage libraries made from the human B-lymphoblastoid cell line Priess (DR4/4, DC4/4, SB3/4). Two alpha genes and two beta genes are encoded in the 100 kb long SB region in the order SB alpha-SB beta-SX alpha-SX beta. The SB alpha and SB beta genes encode the alpha and beta subunits of the SB subset of class II MHC molecules. Both the SX alpha and the SX beta genes are pseudogenes in the haplotype examined. From the isolated clones, the two haplotypes of the Priess cell line, SB3 and SB4, are distinguished by nucleotide sequencing and blot hybridization analyses. Restriction site polymorphisms between the SB3 and SB4 clones were observed only in relatively small regions of the SB beta and SX beta genes. A mouse macrophage cell line was transfected with one of the cosmid clones containing both SB alpha and SB beta genes. Expression of the alpha and beta genes was detected by fluorescene-activated cell sorting (FACS) and two-dimensional gel electrophoresis using SB-specific monoclonal antibodies.     

Serum and Urine Fibrinogen-Fibrin-related Antigen (F.R.-Antigen) Levels in Renal Disease

The concentration of serum fibrinogen-fibrin-related antigen (F.R.-antigen) was measured in a group of 142 patients with various renal disorders, in 38 of whom urine F.R.-antigen was also estimated. Raised serum F.R.-antigen levels were present in 48% of the patients, with no particular preponderance in any diagnostic category apart from acute reversible intrinsic renal failure in which high levels were invariably present. Significantly-raised serum levels were also present in the patients with microangiopathic haemolytic anaemia and in those with the more severe degrees of renal impairment. Urine F.R.-antigen was increased in 34 of the 38 patients. The amount of F.R.-antigen in the urine correlated with the degree of proteinuria but not with the serum F.R.-antigen levels. The evidence relating to intravascular coagulation in renal disease is reviewed, and it is suggested that there is a high incidence of localized fibrinogen or fibrin degradation in the kidney, which is related more to factors such as the presence of uraemia and microangiopathic haemolytic anaemia rather than to the diagnostic category.     

The Distribution of Acidic and Neutral Peptidases in Barley and Wheat Kernels

The activity of barley and wheat peptidases which hydrolyze alpha-N-benzoyl-dl-arginine-p-nitronnilide (BAPA) and alpha-N-benzoyl-l-arginine ethyl ester (BAEE) has been measured in proximal and distal portions of ungerminated grain and in these tissues during 6 and 7 day incubations. The proximal portion of ungerminated barleys contained the major part of both the acidic (BAPA-ase and acidic BAEE-ase) and neutral (neutral BAEE-ase) peptidases. In ungcrminated wheat these acidic and neutral peptidases were nearly evenly distributed between the proximal and dislal portions. Commercial wheat embryo was very high in acidic peptidase but contained no neutral peptidase. During the germination of both wheat and barleys, acidic and neutral peptidase activity in the seedlings increased with time. No such consistent increase was observed for aleurone and starchy endosperm tissue for any of these grains. Aleurone and starchy endosperm tissue incubated in the absence of the proximal portion of the kernel showed reduced peptidase activities.     

Genetic differentiation in Hippocrepis emerus (Leguminosae): allozyme and DNA fingerprint variation in disjunct Scandinavian populations

The structure of genetic variation in disjunct Scandinavian populations of Hippocrepis emerus was studied using allozymes and DNA fingerprinting. Variation in the three native regional populations in Scandinavia was compared with that in a recently introduced population in Sweden. In contrast to the recently introduced population, the native Scandinavian isolates of H. emerus showed high levels of allozyme fixation and low levels of DNA diversity. Variation in allozymes and at DNA fingerprint loci showed closely congruent patterns of geographic variation, with pronounced differentiation between the native Norwegian and Swedish isolates of the species. The structure of genetic variation in native Scandinavian H. emerus is interpreted in terms of historical population bottlenecks and founder events during the species' postglacial immigration into Scandinavia.     

Corresponding patterns of geographic variation among populations ofSilene latifolia (=S. alba =S. pratensis) (Caryophyllaceae)

Morphological and biochemical data were analysed from 30 greenhouse-grown populations of EuropeanSilene latifolia. Six separate character sets (flavones, seed, pollen, capsules, male and female flower morphology) were used in the analyses. There was broad-scale congruence between trends of geographic variation in most character sets, with the populations being assigned to western (or southern and western) and eastern clusters. The eastern and western clusters abut along a transition zone that runs roughly from Belgium to the northern Balkans; this zone represents a region of relatively rapid change and contains populations intermediate between the eastern and western clusters. Variation in flower morphology was weak and discordant with variation in the other character sets. The origin and maintenance of the variation pattern is discussed in terms of migrational history and hybrid zones.     

Effects of low-chloride solutions on action potentials of sheep cadiac purkinje fibers

The rapid repolarization during phase 1 of the action potential of sheep cardiac purkinje fibers has been attributed to a time- and voltage-dependent chloride current. In part, this conclusion was based on experiments that showed a substantial slowing of phase 1 when larger, presumably impermeant, anions were substituted for chloride in tyrode’s solution. We have re- examined the electrical effects of low-chloride solutions. We recorded action potentials of sheep cardiac purkinje fibers in normal tyrode’s solution and in low-chloride solutions made by substituting sodium propionate, acetylglycinate, methylsulfate, or methanesulfonate for the NaCl of Tyrode’s solution. Total calcium was adjusted to keep calcium ion activity of test solutions equal to that of control solutions. Propionate gave qualitatively variable results in preliminary experiments; it was not tested further. Low-chloride solutions made with the other anions gave much more consistent results: phase 1 and the notch that often occurs between phases 1 and 2 were usually unaffected, and the action potential duration usually increased. The only apparent change in the resting potential was a transient 3-6 mV depolarization when low-chloride solution was first admitted to the chamber, and a symmetrical transient hyperpolarization when chloride was returned to normal. If a time- and voltage-dependent chloride current exists in sheep cardiac purkinje fibers, our results suggest that it plays little role in generating phase 1 of the action potential.