Multilocus sequence analysis of phylogroup 1 and 2 oral treponeme strains

More than 75 ‘species-level' phylotypes of spirochete bacteria belonging to the genus Treponema reside within the human oral cavity. The majority of these oral treponeme phylotypes correspond to as-yet uncultivated taxa, or strains of uncertain standing in taxonomy. Here, we analyze phylogenetic and taxonomic relationships between oral treponeme strains using a multilocus sequence analysis (MLSA) scheme based on the highly-conserved 16S rRNA, pyrH, recA and flaA genes. We utilize this MLSA scheme to analyze genetic data from a curated collection of oral treponeme strains (n=71) of diverse geographical origins. This comprises phylogroup 1 (n=23) and phylogroup 2 (n=48) treponeme strains; including all relevant ATCC reference strains. The taxonomy of all strains was confirmed or inferred via the analysis of ca. 1,450 bp 16S rRNA gene sequences using a combination of bioinformatic and phylogenetic approaches. Taxonomic and phylogenetic relationships between the respective treponeme strains were further investigated by analyzing individual and concatenated flaA (1,074 nt), recA (1,377 nt) and pyrH (696 nt) gene sequence datasets. Our data confirmed the species differentiation between Treponema denticola (n=41) and Treponema putidum (n=7) strains. Notably, our results clearly supported the differentiation of the 23 phylogroup 1 treponeme strains into 5 distinct ‘species-level' phylotypes. These respectively corresponded to ‘Treponema vincentii' (n=11), Treponema medium (n=1); ‘Treponema sinensis' (T. sp. IA; n=4); Treponema sp. IB (n=3); and Treponema sp. IC (n=4). In conclusion, our MLSA-based approach can be used to effectively discriminate oral treponeme taxa, confirm taxonomic assignment, and enable the delineation of species boundaries with high confidence.published_or_final_versio

Carbonyl sulfide and carbon disulfide: Large-scale distributions over the western Pacific and emissions from Asia during TRACE-P

An extensive set of carbonyl sulfide (OCS) and carbon disulfide (CS 2) observations were made as part of the NASA Transport and Chemical Evolution over the Pacific (TRACE-P) project, which took place in the early spring 2001. TRACE-P sampling focused on the western Pacific region but in total included the geographic region 110°E to 290°E longitude, 5°N to 50°N latitude, and 0-12 km altitude. Substantial OCS and CS2 enhancements were observed for a great many air masses of Chinese and Japanese origin during TRACE-P. Over the western Pacific, mean mixing ratios of long-lived OCS and shorter-lived CS2 showed a gradual decrease by about 10% and a factor of 5-10, respectively, from the surface to 8-10 km altitude, presumably because land-based sources dominated their distribution during February through April 2001. The highest mean OCS and CS 2 levels (580 and 20 pptv, respectively, based on 2.5° × 2.5° latitude bins) were observed below 2 km near the coast of Asia, at latitudes between 25°N and 35°N, where urban Asian outflow was strongest. Ratios of OCS versus CO for continental SE Asia were much lower compared to Chinese and Japanese signatures and were strongly associated with biomass burning/biofuel emissions. We present a new inventory of anthropogenic Asian emissions (including biomass burning) for OCS and CS2 and compare it to emission estimates based on regional relationships of OCS and CS 2 to CO and CO2. The OCS and CS2 results for the two methods compare well for continental SE Asia and Japan plus Korea and also for Chinese CS2 emissions. However, it appears that the inventory underestimates Chinese emissions of OCS by about 30-100%. This difference may be related to the fact that we did not include natural sources such as wetland emissions in our inventory, although the contributions from such sources are believed to be at a seasonal low during the study period. Uncertainties in OCS emissions from Chinese coal burning, which are poorly characterized, likely contribute to the discrepancy. Copyright 2004 by the American Geophysical Union

First Report of a Fatal Case Associated with EV-D68 Infection in Hong Kong and Emergence of an Interclade Recombinant in China Revealed by Genome Analysis

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Elizabethkingia anophelis bacteremia is associated with clinically significant infections and high mortality

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Determination of Cytomegalovirus Prevalence and Glycoprotein B Genotypes Among Ulcerative Colitis Patients in Ahvaz, Iran

Background: The human cytomegalovirus (HCMV) is a common pathogen which usually remains asymptomatic in the healthy adults; however, it can cause a symptomatic disease in the immunocompromised patients. The risk of infection with HCMV increases in ulcerative colitis (UC) patients as a result of receiving immunosuppressive agents. Objectives: This study aimed to determine the prevalence and the glycoprotein B genotypes of HCMV among the patients with HCMV disease superimposed on an UC flare that required hospitalization in Imam Khomeini Hospital in Ahvaz, Iran, during 2010- 2012. Patients and Methods: In this case-control study, formalin-fixed paraffin-embedded intestinal tissue samples were taken from 98 patients with UC disease including 53 males and 45 females (mean age ± standard deviation, 38.95 ± 17.93) and 67 control patients with noninflammatory disease who were referred to Imam Khomeini Hospital during 2010-2012. Detection of HCMV genome in intestinal samples was carried out by seminested polymerase chain reaction. Glycoprotein B genotypes were determined by sequencing. Results: Among 98 patients with UC, only 12 (12.2%) patients were positive for HCMV genome, while the HCMV genome was not detected in any of the controls. (P = 0.002). The distribution of HCMV gB genotypes in 12 CMV-positive UC patients was as follow: gB1, 11 (91.7%) and gB3, 1 (8.3%). The most prevalent genotype in CMV-positive UC patients was gB1. Conclusions: In this study, high prevalence of 91.7% HCMV gB1 genotype was predominant among HCMV-positive UC patients, which suggests that there might be an association between HCMV gB genotype 1 and UC disease

The Formation and Evolution of the First Massive Black Holes

The first massive astrophysical black holes likely formed at high redshifts (z>10) at the centers of low mass (~10^6 Msun) dark matter concentrations. These black holes grow by mergers and gas accretion, evolve into the population of bright quasars observed at lower redshifts, and eventually leave the supermassive black hole remnants that are ubiquitous at the centers of galaxies in the nearby universe. The astrophysical processes responsible for the formation of the earliest seed black holes are poorly understood. The purpose of this review is threefold: (1) to describe theoretical expectations for the formation and growth of the earliest black holes within the general paradigm of hierarchical cold dark matter cosmologies, (2) to summarize several relevant recent observations that have implications for the formation of the earliest black holes, and (3) to look into the future and assess the power of forthcoming observations to probe the physics of the first active galactic nuclei.Comment: 39 pages, review for "Supermassive Black Holes in the Distant Universe", Ed. A. J. Barger, Kluwer Academic Publisher

Gadoxetate-enhanced dynamic contrast-enhanced MRI for evaluation of liver function and liver fibrosis in preclinical trials

BACKGROUND: To facilitate translational drug development for liver fibrosis, preclinical trials need to be run in parallel with clinical research. Liver function estimation by gadoxetate-enhanced dynamic contrast-enhanced MRI (DCE-MRI) is being established in clinical research, but still rarely used in preclinical trials. We aimed to evaluate feasibility of DCE-MRI indices as translatable biomarkers in a liver fibrosis animal model. METHODS: Liver fibrosis was induced in Sprague-Dawley rats by thioacetamide (200 mg, 150 mg, and saline for the high-dose, low-dose, and control groups, respectively). Subsequently, DCE-MRI was performed to measure: relative liver enhancement at 3-min (RLE-3), RLE-15, initial area-under-the-curve until 3-min (iAUC-3), iAUC-15, and maximum-enhancement (Emax). The correlation coefficients between these MRI indices and the histologic collagen area, indocyanine green retention at 15-min (ICG-R15), and shear wave elastography (SWE) were calculated. Diagnostic performance to diagnose liver fibrosis was also evaluated by receiver-operating-characteristic (ROC) analysis. RESULTS: Animal model was successful in that the collagen area of the liver was the largest in the high-dose group, followed by the low-dose group and control group. The correlation between the DCE-MRI indices and collagen area was high for iAUC-15, Emax, iAUC-3, and RLE-3 but moderate for RLE-15 (r, - 0.81, - 0.81, - 0.78, - 0.80, and - 0.51, respectively). The DCE-MRI indices showed moderate correlation with ICG-R15: the highest for iAUC-15, followed by iAUC-3, RLE-3, Emax, and RLE-15 (r, - 0.65, - 0.63, - 0.62, - 0.58, and - 0.56, respectively). The correlation coefficients between DCE-MRI indices and SWE ranged from - 0.59 to - 0.28. The diagnostic accuracy of RLE-3, iAUC-3, iAUC-15, and Emax was 100% (AUROC 1.000), whereas those of RLE-15 and SWE were relatively low (AUROC 0.777, 0.848, respectively). CONCLUSION: Among the gadoxetate-enhanced DCE-MRI indices, iAUC-15 and iAUC-3 might be bidirectional translatable biomarkers between preclinical and clinical research for evaluating histopathologic liver fibrosis and physiologic liver functions in a non-invasive manner

Magnitude, precision, and realism of depth perception in stereoscopic vision

Our perception of depth is substantially enhanced by the fact that we have binocular vision. This provides us with more precise and accurate estimates of depth and an improved qualitative appreciation of the three-dimensional (3D) shapes and positions of objects. We assessed the link between these quantitative and qualitative aspects of 3D vision. Specifically, we wished to determine whether the realism of apparent depth from binocular cues is associated with the magnitude or precision of perceived depth and the degree of binocular fusion. We presented participants with stereograms containing randomly positioned circles and measured how the magnitude, realism, and precision of depth perception varied with the size of the disparities presented. We found that as the size of the disparity increased, the magnitude of perceived depth increased, while the precision with which observers could make depth discrimination judgments decreased. Beyond an initial increase, depth realism decreased with increasing disparity magnitude. This decrease occurred well below the disparity limit required to ensure comfortable viewing