Evaluation of the effect of stent strut profile on shear stress distribution using statistical moments

Background  

In-stent restenosis rates have been closely linked to the wall shear stress distribution within a stented arterial segment, which in turn is a function of stent design. Unfortunately, evaluation of hemodynamic performance can only be evaluated with long term clinical trials. In this work we introduce a set of metrics, based on statistical moments, that can be used to evaluate the hemodynamic performance of a stent in a standardized way. They are presented in the context of a 2D flow study, which analyzes the impact of different strut profiles on the wall shear stress distribution for stented coronary arteries.     

Preclinical model to test human papillomavirus virus (HPV) capsid vaccines in vivo using infectious HPV/cottontail rabbit papillomavirus chimeric papillomavirus particles

A human papillomavirus (HPV) vaccine consisting of virus-like particles (VLPs) was recently approved for human use. It is generally assumed that VLP vaccines protect by inducing type-specific neutralizing antibodies. Preclinical animal models cannot be used to test for protection against HPV infections due to species restriction. We developed a model using chimeric HPV capsid/cottontail rabbit papillomavirus (CRPV) genome particles to permit the direct testing of HPV VLP vaccines in rabbits. Animals vaccinated with CRPV, HPV type 16 (HPV-16), or HPV-11 VLPs were challenged with both homologous (CRPV capsid) and chimeric (HPV-16 capsid) particles. Strong type-specific protection was observed, demonstrating the potential application of this approach.     

Dry spots and wet spots in the Andean hotspot

Aim To explain the relationship between topography, prevailing winds and precipitation in order to identify regions with contrasting precipitation regimes and then compare floristic similarity among regions in the context of climate change. Location Eastern slope of the tropical Andes, South America. Methods We used information sources in the public domain to identify the relationship between geology, topography, prevailing wind patterns and precipitation. Areas with contrasting precipitation regimes were identified and compared for their floristic similarity. Results We identify spatially separate super‐humid, humid and relatively dry regions on the eastern slope of the Andes and show how they are formed by the interaction of prevailing winds, diurnally varying atmospheric circulations and the local topography of the Andes. One key aspect related to the formation of these climatically distinct regions is the South American low‐level jet (SALLJ), a relatively steady wind gyre that flows pole‐ward along the eastern slopes of the Andes and is part of the gyre associated with the Atlantic trade winds that cross the Amazon Basin. The strongest winds of the SALLJ occur near the ‘elbow of the Andes’ at 18° S. Super‐humid regions with mean annual precipitation greater than 3500 mm, are associated with a ‘favourable’ combination of topography, wind‐flow orientation and local air circulation that favours ascent at certain hours of the day. Much drier regions, with mean annual precipitation less than 1500 mm, are associated with ‘unfavourable’ topographic orientation with respect to the mean winds and areas of reduced cloudiness produced by local breezes that moderate the cloudiness. We show the distribution of satellite‐estimated frequency of cloudiness and offer hypotheses to explain the occurrence of these patterns and to explain regions of anomalously low precipitation in Bolivia and northern Peru. Floristic analysis shows that overall similarity among all circumscribed regions of this study is low; however, similarity among super‐humid and humid regions is greater when compared with similarity among dry regions. Spatially separate areas with humid and super‐humid precipitation regimes show similarity gradients that are correlated with latitude (proximity) and precipitation. Main conclusions The distribution of precipitation on the eastern slope of the Andes is not simply correlated with latitude, as is often assumed, but is the result of the interplay between wind and topography. Understanding the phenomena responsible for producing the observed precipitation patterns is important for mapping and modelling biodiversity, as well as for interpreting both past and future climate scenarios and the impact of climate change on biodiversity. Super‐humid and dry regions have topographic characteristics that contribute to local climatic stability and may represent ancestral refugia for biodiversity; these regions are a conservation priority due to their unique climatic characteristics and the biodiversity associated with those characteristics.     

Success of maximum likelihood phylogeny inference in the four-taxon case

We used simulated data to investigate a number of properties of maximum- likelihood (ML) phylogenetic tree estimation for the case of four taxa. Simulated data were generated under a broad range of conditions, including wide variation in branch lengths, differences in the ratio of transition and transversion substitutions, and the absence of presence of gamma-distributed site-to-site rate variation. Data were analyzed in the ML framework with two different substitution models, and we compared the ability of the two models to reconstruct the correct topology. Although both models were inconsistent for some branch-length combinations in the presence of site-to-site variation, the models were efficient predictors of topology under most simulation conditions. We also examined the performance of the likelihood ratio (LR) test for significant positive interior branch length. This test was found to be misleading under many simulation conditions, rejecting too often under some simulation conditions. Under the null hypothesis of zero length internal branch, LR statistics are assumed to be asymptotically distributed chi 2(1); with limited data, the distribution of LR statistics under the null hypothesis varies from chi 2(1).      

Metabolic engineering of Klebsiella oxytoca M5A1 for ethanol production from xylose and glucose.

The efficient diversion of pyruvate from normal fermentative pathways to ethanol production in Klebsiella oxytoca M5A1 requires the expression of Zymomonas mobilis genes encoding both pyruvate decarboxylase and alcohol dehydrogenase. Final ethanol concentrations obtained with the best recombinant, strain M5A1 (pLOI555), were in excess of 40 g/liter with an efficiency of 0.48 g of ethanol (xylose) and 0.50 g of ethanol (glucose) per g of sugar, as compared with a theoretical maximum of 0.51 g of ethanol per g of sugar. The maximal volumetric productivity per hour for both sugars was 2.0 g/liter. This volumetric productivity with xylose is almost twice that previously obtained with ethanologenic Escherichia coli. Succinate was also produced as a minor product during fermentation.     

Establishment of a doxycycline-regulated cell line with inducible,doubly-stable expression of the wild-type p53 gene from p53-deleted hepatocellular carcinoma cells

p53 is important in the development of hepatocellular carcinoma (HCC) and in therapeutic approaches, but the mechanism whereby it inhibits HCC growth is still unclear. The aim of the present study was to establish a HCC cell system in which p53 levels can be regulated. Full-length wild-type p53 cDNA obtained by PCR was cloned into a retroviral response vector controlled by the tetracycline responsive element (RevTRE-p53). The regulatory vectors RevTet-Off and RevTRE-p53 were transfected into a packaging cell line, PT67. Hep3B cells in which the p53 gene was deleted were infected with RevTet-Off viral particles from the PT67. Three G418-resistant cell clones with high luciferase expression and low background were infected with RevTRE-p53. By screening dozens of RevTRE-p53-infected clones with hygromycin we identified the one with the highest expression of p53 and the lowest background after doxycycline treatment. The results showed that p53 expression in this cell clone could be simply turned on or off by removing or adding doxycycline. Furthermore, it was found that the level of p53 protein was negatively and sensitively related to the doxycycline concentration. In conclusion, we have established a HCC cell line in which p53 expression can be switched on or off and regulated in a dose- and time-dependent manner.     

Detecting substitution-rate heterogeneity among regions of a nucleotide sequence

Likelihood-ratio statistics are proposed to test for heterogeneity in nucleotide substitution rate among regions of a DNA sequence. The tests examine three-sequence phylogenies, and two specific tests are proposed: a test to detect rate heterogeneity among genic regions within a sequence, over all evolutionary lineages; and a test to detect rate heterogeneity among regions in a specific evolutionary lineage. Simulations examine the ability of tests to detect a single region that varies in nucleotide substitution rate relative to the remainder of the sequence. A 50-bp region with a fivefold substitution-rate increase can be detected > or = 90% of the time when it is found in all three lineages of the phylogeny, and a 50-bp region of fivefold rate increase can be detected with approximately 70% power when it is found in only one evolutionary lineage. Simulation also examines the effect of transition- and transversion-rate differences. The tests are applied to published DNA sequences. While the tests are powerful, significant results can be difficult to interpret biologically.      

Monoclonal antibodies against Trypanosoma cruzi neuraminidase reveal enzyme polymorphism, recognize a subset of trypomastigotes, and enhance infection in vitro

The identification and characterization of two murine mAb (TCN-1 and TCN-2) that react with the neuraminidase of Trypanosoma cruzi is reported. The mAb were identified based on their ability to inhibit enzyme activity and recognize neuraminidase in crude enzyme preparations. TCN-1 and TCN-2 recognized Ag in tissue culture trypomastigotes but not in the amastigotes, epimastigotes, or metacyclic trypomastigotes using immunoblot assays and immunofluorescence. In addition, clones Y-H6, MV-13, and Silvio X-10/4 of T. cruzi revealed a unique banding pattern characteristic of each clone. In Silvio X-10/4, the mAb recognized four distinct bands ranging from 121,000 to 203,000 whereas in Y-H6 and MV-13 they identified bands ranging from 138,000 to 222,000. Characterization of neuraminidase by two-dimensional PAGE revealed the polypeptides that make up the enzyme to have isoelectrical points ranging from 6.55 to 7.30. Immunofluorescence and C-mediated lysis assays showed that the mAb reacted with a subset of trypomastigotes representing 28% of the total parasite population. Functional studies showed that the mAb enhanced infection of cultured cells by trypomastigotes. Our experiments confirm previous findings with polyclonal Ab and are in accordance with the hypothesis that neuraminidase modulates infection through a negative control mechanism.