Goodness-of-Fit Testing for the Logistic Regression Model when the Estimated Probabilities are Small

The distribution of the Hosmer-Lemeshow chi-square type goodness-of-fit tests (?_g, ?_g) for the logistic regression model are examined via simulations designed to examine their behavior when most of the estimated probabilities are small or are expected to fall in a few deciles. The results of the simulations show statistic ?_g should be used when the two outcome groups (y = 0, 1) are not well separated, Δ≤2, where Δ² is the Mahalanobis distance. Statistic ?_g should be used when Δ ≥ 8. Either statistic may be used when 2 ≦ Δ ≦ 8. All tests should be used with caution when the proportion in the sample with y = 1 is less than 0.1.     

Baculovirus-mediated gene transfer and recombinant protein expression do not interfere with insulin dependent phosphorylation of PKB/Akt in human SHSY-5Y and C3A cells

Background  

Recombinant adenovirus vectors and transfection agents comprising cationic lipids are widely used as gene delivery vehicles for functional expression in cultured cells. Consequently, these tools are utilized to investigate the effects of functional over-expression of proteins on insulin mediated events. However, we have previously reported that cationic lipid reagents cause a state of insulin unresponsiveness in cell cultures. In addition, we have found that cultured cells often do not respond to insulin stimulation following adenovirus treatment. Infection with adenovirus compromises vital functions of the host cell leading to the activation of protein kinases central to insulin signalling, such as protein kinase B/Akt. Therefore, we investigated the effect of adenovirus infection on insulin unresponsiveness by means of Akt activation in cultured cells. Moreover, we investigated the use of baculovirus as a heterologous viral gene delivery vehicle to circumvent these phenomena. Since the finding that baculovirus can efficiently transduce mammalian cells, the applications of this viral system in gene delivery has greatly expanded and one advantage is the virtual absence of cytotoxicity in mammalian cells.     

The wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of G-ending codons

According to Crick's wobble hypothesis, tRNAs with uridine at the wobble position (position 34) recognize A- and G-, but not U- or C-ending codons. However, U in the wobble position is almost always modified, and Salmonella enterica tRNAs containing the modified nucleoside uridine-5-oxyacetic acid (cmo⁵U34) at this position are predicted to recognize U- (but not C-) ending codons, in addition to A- and G-ending codons. We have constructed a set of S. enterica mutants with only the cmo⁵U-containing tRNA left to read all four codons in the proline, alanine, valine, and threonine family codon boxes. From the phenotypes of these mutants, we deduce that the proline, alanine, and valine tRNAs containing cmo⁵U read all four codons including the C-ending codons, while the corresponding threonine tRNA does not. A cmoB mutation, leading to cmo⁵U deficiency in tRNA, was introduced. Monitoring A-site selection rates in vivo revealed that the presence of cmo⁵U34 stimulated the reading of CCU and CCC (Pro), GCU (Ala), and GUC (Val) codons. Unexpectedly, cmo⁵U is critical for efficient decoding of G-ending Pro, Ala, and Val codons. Apparently, whereas G34 pairs with U in mRNA, the reverse pairing (U34-G) requires a modification of U34.     

Shelter Availability,Occupancy, and Residency in Size‐Asymmetric Contests Between Rusty Crayfish,Orconectes rusticus

Contest outcomes are usually determined by differences in resource‐holding potential, the social histories of the combatants, and perceptions of resource value. One aspect of gaining an advantage is the residency effect. Prior occupancy of a particular place can affect the knowledge and motivation of the resident. There could be a tactical advantage in knowing the terrain or an increased willingness to fight to maintain control of a familiar area. In this study, we evaluated the importance of shelter residency effects relative to size differences between rusty crayfish (Orconectes rusticus) as potential competitors for access to shelter. The intensity of any residency effects was manipulated by altering the number of shelters in the arena. Our results suggest that any residency effect is very weak in this system, and if present, may often be masked by the strong and pervasive influence on contest outcome of the relative body sizes of the contestants. We also found that both shelter number and crayfish size asymmetries had strong, independent effects on levels of aggression. Dominance, but not residency status, was a factor in shelter use.     

Occurrence of Anguillicola crassus (Nematoda: Dracunculoidea) in Japanese eels Anguilla japonica from a river and an aquaculture unit in SW Taiwan

The infection by swimbladder nematodes of the genus Anguillicola (Dracunculoidea: Anguillicolidae) was examined in 2 populations of the Japanese eel Anguilla japonica in SW Taiwan. Wild eels from the Kao-Ping river were compared with cultured eels from an adjacent aquaculture unit. Only the cosmopolitan species Anguillicola crassus was present. Among wild eels, prevalence of infection varied between 21 and 62%, and mean intensity between 1.7 and 2.7 for adult worms. Similar intensity values (1.3 to 2.8) were recorded for the larvae. In cultured eels, prevalence as well as mean intensities were higher. In the cultured hosts, mean larval intensities exceeded those of adult worms 2-fold, and maximum larval intensities were 4- to 5-fold higher than in eels from the river. In cultured eels, dead larvae were also more abundant than in wild eels. We conclude that infrapopulations of A. crassus in Japanese eels are regulated by the defense system of this host, intraspecific density-dependent regulation being less likely as the major regulatory mechanism. No influence of the parasite on eel condition was found in either wild or cultured eels, indicating a low or moderate pathogenic effect of A. crassus on this host. This study shows that A. crassus is moderately common in cultured and wild Japanese eels in Taiwan, where the parasite is endemic.     

Towards a computational method for imaging the extracellular potassium concentration during regional ischemia

We investigate the possibility of using body surface potential maps to image the extracellular potassium concentration during regional ischemia. The problem is formulated as an inverse problem based on a linear approximation of the bidomain model, where we minimize the difference between the results of the model and observations of body surface potentials. The minimization problem is solved by a one-shot technique, where the original PDE system, an adjoint problem, and the relation describing the minimum, are solved simultaneously. This formulation of the problem requires the solution of a 5 × 5 system of linear partial differential equations. The performance of the model is investigated by performing tests based on synthetic data. We find that the model will in many cases detect the correct position and approximate size of the ischemic regions, while some cases are more difficult to locate. It is observed that a simple post-processing of the results produces images that are qualitatively very similar to the true solution.     

Flow cytometry for enrichment and titration in massively parallel DNA sequencing

Massively parallel DNA sequencing is revolutionizing genomics research throughout the life sciences. However, the reagent costs and labor requirements in current sequencing protocols are still substantial, although improvements are continuously being made. Here, we demonstrate an effective alternative to existing sample titration protocols for the Roche/454 system using Fluorescence Activated Cell Sorting (FACS) technology to determine the optimal DNA-to-bead ratio prior to large-scale sequencing. Our method, which eliminates the need for the costly pilot sequencing of samples during titration is capable of rapidly providing accurate DNA-to-bead ratios that are not biased by the quantification and sedimentation steps included in current protocols. Moreover, we demonstrate that FACS sorting can be readily used to highly enrich fractions of beads carrying template DNA, with near total elimination of empty beads and no downstream sacrifice of DNA sequencing quality. Automated enrichment by FACS is a simple approach to obtain pure samples for bead-based sequencing systems, and offers an efficient, low-cost alternative to current enrichment protocols.     

Mutations in the Fatty Acid Transport Protein 4 Gene Cause the Ichthyosis Prematurity Syndrome

Ichthyosis prematurity syndrome (IPS) is an autosomal-recessive disorder characterized by premature birth and neonatal asphyxia, followed by a lifelong nonscaly ichthyosis with atopic manifestations. Here we show that the gene encoding the fatty acid transport protein 4 (FATP4) is mutated in individuals with IPS. Fibroblasts derived from a patient with IPS show reduced activity of very long-chain fatty acids (VLCFA)-CoA synthetase and a specific reduction in the incorporation of VLCFA into cellular lipids. The human phenotype is consistent with Fatp4 deficiency in mice that is characterized by a severe skin phenotype, a defective permeability barrier function, and perturbed VLCFA metabolism. Our results further emphasize the importance of fatty acid metabolism for normal epidermal barrier function illustrated by deficiency of a member in the FATP family of proteins.