Generalized linear mixture models for handling nonignorable dropouts in longitudinal studies

This paper presents a method for analysing longitudinal data when there are dropouts. In particular, we develop a simple method based on generalized linear mixture models for handling nonignorable dropouts for a variety of discrete and continuous outcomes. Statistical inference for the model parameters is based on a generalized estimating equations (GEE) approach (Liang and Zeger, 1986). The proposed method yields estimates of the model parameters that are valid when nonresponse is nonignorable under a variety of assumptions concerning the dropout process. Furthermore, the proposed method can be implemented using widely available statistical software. Finally, an example using data from a clinical trial of contracepting women is used to illustrate the methodology.     

Neuronal differentiation and growth control of neuro-2a cells after retroviral gene delivery of connexin43

Given the roles proposed for gap junctional intercellular communication in neuronal differentiation and growth control, we examined the effects of connexin43 (Cx43) expression in a neuroblastoma cell line. A vesicular stomatitis virus G protein (VSVG)-pseudotyped retrovector was engineered to co-express the green fluorescent protein (GFP) and Cx43 in the communication-deficient neuro-2a (N2a) cell line. The 293 GPG packaging cell line was used to produce VSVG-pseudotyped retrovectors coding for GFP, Cx43, or chimeric Cx43.GFP fusion protein. The titer of viral supernatant, as measured by flow cytometry for GFP fluorescence, was approximately 2.0 x 10(7) colony form units (CFU)/ml and was free of replication-competent retroviruses. After a 7-day treatment with retinoic acid (20 microm), N2a transformants (N2a-Cx43 and N2a-Cx43.GFP) maintained the expression of Cx43 and Cx43.GFP. Expression of both constructs resulted in functional coupling, as evidenced by electrophysiological and dye-injection analysis. Suppression of cell growth correlated with expression of both Cx43 or Cx43.GFP and retinoic acid treatment. Based on morphology and immunocytochemistry for neurofilament, no difference was observed in the differentiation of N2a cells compared with cells expressing Cx43 constructs. In conclusion, constitutive expression of Cx43 in N2a cells does not alter retinoic acid-induced neuronal differentiation but does enhance growth inhibition.     

A novel assay to demonstrate an intersection of the exocytic and endocytic pathways at early endosomes

The mechanism of transport of membrane proteins from the trans-Golgi to the cell surface is still poorly understood. Previous studies suggested that basolateral membrane proteins, such as the transferrin receptor and the asialoglycoprotein receptor H1, take an indirect route to the plasma membrane via an intracellular, most likely endosomal intermediate. To define this compartment we developed a biochemical assay based on the very definition of endosomes. The assay is based on internalizing anti-H1 antibodies via the endocytic cycle of the receptor itself. Internalized antibody formed immune complexes with newly synthesized H1, which had been pulse-labeled with [(35)S]sulfate and chased out of the trans-Golgi for a period of time that was insufficient for H1 to reach the surface. Hence, antibody capture occurred intracellularly. Double-immunofluorescence labeling demonstrated that antibody-containing compartments also contained transferrin and thus corresponded to early and recycling endosomes. The results therefore demonstrate an intracellular intersection of the exocytic and endocytic pathways with implications for basolateral sorting.     

Family-based tests of association and linkage that use unaffected sibs, covariates, and interactions

We extend the methodology for family-based tests of association and linkage to allow for both variation in the phenotypes of subjects and incorporation of covariates into general-score tests of association. We use standard association models for a phenotype and any number of predictors. We then construct a score statistic, using likelihoods for the distribution of phenotype, given genotype. The distribution of the score is computed as a function of offspring genotypes, conditional on parental genotypes and trait values for offspring and parents. This approach provides a natural extension of the transmission/disequilibrium test to any phenotype and to multiple genes or environmental factors and allows the study of gene-gene and gene-environment interaction. When the trait varies among subjects or when covariates are included in the association model, the score statistic depends on one or more nuisance parameters. We suggest two approaches for obtaining parameter estimates: (1) choosing the estimate that minimizes the variance of the test statistic and (2) maximizing the statistic over a nuisance parameter and using a corrected P value. We apply our methods to a sample of families with attention-deficit/hyperactivity disorder and provide examples of how covariates and gene-environment and gene-gene interactions can be incorporated.     

Effect of water clarity on the distribution of marine birds in nearshore waters of Monterey Bay, California

ABSTRACT.   The distribution of marine birds relative to water clarity was examined in the nearshore waters of Monterey Bay, California. I conducted nine at-sea surveys in 1999 and 2000 and simultaneously recorded water clarity and the density of five taxa of marine birds. Among plunge-divers, Forster's Terns ( Sterna forsteri ) occurred more frequently than expected over turbid water (<2.5 m Secchi depth) and, among pursuit-diving species, Brandt's Cormorants ( Phalacrocorax penicillatus ) occurred most often in the clearest water available (>5 m Secchi depth). Turbidity in Monterey Bay may be caused by suspended organic matter, including phytoplankton, during summer and fall. Forster's Tern may prefer such areas because small fish are likely to occur near this potential food source. Brandt's Cormorants probably rely on vision to catch fish near the bottom and turbid water may reduce available light and limit visual acuity. The distribution of Brown Pelicans (Pelecanus occidentalis ), Western/Clark's Grebes (Aechmophorus occidentalis/clarkii ), and Marbled Murrelets ( Brachyramphus marmoratus ) did not appear to be influenced by turbidity levels, indicating that some seabirds use marine habitats with a wide range of water clarities.     

Gap junctions assemble in the presence of cytoskeletal inhibitors, but enhanced assembly requires microtubules

The role of cytoskeletal elements in gap junction (GJ) assembly has been studied using Novikoff hepatoma cells treated with cytochalasin B (CB) to disrupt actin filaments or with colchicine or nocodazole to disrupt microtubules. After 60 min of cell reaggregation, freeze-fracture was used to evaluate quantitatively the "initiation," "maturation," and "growth" phases of GJ assembly. The development of junctional permeability to fluorescent dyes was also analyzed. The only effects of CB on the structure or permeability of the developing junctions involved an elongation of GJ aggregates and a small decrease in formation plaque areas. Colchicine (but not the inactive form, lumicolchicine) prevented the enhancement of GJ growth by cholesterol, but its effect on basal growth was equivocal. Nocodazole inhibited the growth of GJ, even under basal conditions, without an effect on initiation. Nocodazole also blocked the forskolin-enhanced increase in the growth of GJs and, in living MDCK cells, reduced the movement of transport intermediates containing green fluorescent protein-tagged connexin43. Thus, neither actin filaments nor microtubules appear to restrict GJ assembly by anchoring intramembrane GJ proteins, nor are they absolutely required for functional GJs to form. However, microtubules are necessary for enhanced GJ growth and likely for facilitating connexin trafficking under basal conditions.     

Identification of a novel neuropathogenic Theiler's murine encephalomyelitis virus

Theiler's murine encephalitis viruses (TMEV) are divided into two subgroups based on their neurovirulence. Persistent strains resemble Theiler's original viruses (referred to as the TO subgroup), which largely induce a subclinical polioencephalomyelitis during the acute phase of the disease and can persist in the spinal cord of susceptible animals, inducing a chronic demyelinating disease. In contrast, members of the neurovirulent subgroup cause an acute encephalitis characterized by the rapid onset of paralysis and death within days following intracranial inoculation. We report herein the characterization of a novel neurovirulent strain of TMEV, identified using pyrosequencing technology and referred to as NIHE. Complete coverage of the NIHE viral genome was obtained, and it shares <90% nucleotide sequence identity to known TMEV strains irrespective of subgroup, with the greatest sequence variability being observed in genes encoding the leader and capsid proteins. The histopathological analysis of infected brain and spinal cord demonstrate inflammatory lesions and neuronal necrosis during acute infection with no evidence of viral persistence or chronic disease. Intriguingly, genetic analysis indicates the putative expression of the L protein, considered a hallmark of strains within the persistent subgroup. Thus, the identification and characterization of a novel neurovirulent TMEV strain sharing features previously associated with both subgroups will lead to a deeper understanding of the evolution of TMEV strains and new insights into the determinants of neurovirulence.     

IL-1beta stimulates rat cardiac fibroblast migration via MAP kinase pathways

The pro-inflammatory cytokines interleukin-1beta (IL-1beta), interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-alpha) are elevated following acute myocardial infarction (MI) and have been implicated in the pathophysiology of cardiac disease progression. The cardiac fibroblast represents an important effector cell target for cytokine actions. In particular, cytokine-directed cardiac fibroblast migration is likely to impact both myocardial repair following acute MI and pathological myocardial remodeling in the progression to heart failure. In the present study, we examined the migratory response of neonatal rat cardiac fibroblasts to pro-inflammatory cytokines using modified Boyden chamber assays. On the basis of the knowledge of migration in other cell types, we hypothesized that members of the mitogen-activated protein kinase (MAPK) family may regulate this process. This possibility was addressed with the use of immunoblot detection of active phosphorylated MAPK species and pharmacological inhibitors for individual members of the MAPK cascades. IL-1beta stimulated robust and concentration-dependent increases in migration (maximum, 20-fold over control cells). TNF-alpha had lesser effect (fourfold increase over control). IL-6 did not induce migration. Activation of all three MAPK subfamilies (extracellular signal-regulated kinases, c-Jun NH(2)-terminal kinases, and p38) was shown to occur in response to cytokine stimulation. Fibroblast migration was attenuated by pharmacological inhibition of each MAPK subfamily. Understanding the regulation of cardiac fibroblast migration may provide insights in the search for therapies aimed at enhancing the functional nature of the remodeling process.