The Heterogeneity, Distribution, and Environmental Associations of Borrelia burgdorferi Sensu Lato, the Agent of Lyme Borreliosis, in Scotland

Genospecies controls were obtained from the laboratory of Dr. Muriel Cornet at the Institut Pasteur, Paris. We thank Bob Furness for collecting ticks from passerine birds, Steph Vollmer for processing the samples from one site, E. Packer, A. Wiebe, J. Low, E. Stephen, and J. Arthur for help collecting ticks, Kenny Raey for laboratory assistance, and Jackie Potts for statistical advice. Marianne C. James was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) Doctoral Training Grant with CASE support from the Macaulay Development Trust awarded to Alan S. Bowman and Lucy Gilbert. Lucy Gilbert was supported by the Scottish Government’s Rural and Environment Science and Analytical Services Division (RESAS).Peer reviewedPublisher PD

Small RNA-based antiviral defense in the phytopathogenic fungus Colletotrichum higginsianum

Even though the fungal kingdom contains more than 3 million species, little is known about the biological roles of RNA silencing in fungi. The Colletotrichum genus comprises fungal species that are pathogenic for a wide range of crop species worldwide. To investigate the role of RNA silencing in the ascomycete fungus Colletotrichum higginsianum, knock-out mutants affecting genes for three RNA-dependent RNA polymerase (RDR), two Dicer-like (DCL), and two Argonaute (AGO) proteins were generated by targeted gene replacement. No effects were observed on vegetative growth for any mutant strain when grown on complex or minimal media. However, Δdcl1, Δdcl1Δdcl2 double mutant, and Δago1 strains showed severe defects in conidiation and conidia morphology. Total RNA transcripts and small RNA populations were analyzed in parental and mutant strains. The greatest effects on both RNA populations was observed in the Δdcl1, Δdcl1Δdcl2, and Δago1 strains, in which a previously uncharacterized dsRNA mycovirus [termed Colletotrichum higginsianum non-segmented dsRNA virus 1 (ChNRV1)] was derepressed. Phylogenetic analyses clearly showed a close relationship between ChNRV1 and members of the segmented Partitiviridae family, despite the non-segmented nature of the genome. Immunoprecipitation of small RNAs associated with AGO1 showed abundant loading of 5'U-containing viral siRNA. C. higginsianum parental and Δdcl1 mutant strains cured of ChNRV1 revealed that the conidiation and spore morphology defects were primarily caused by ChNRV1. Based on these results, RNA silencing involving ChDCL1 and ChAGO1 in C. higginsianum is proposed to function as an antiviral mechanism

Predictions of the causal entropic principle for environmental conditions of the universe

The causal entropic principle has been proposed as a superior alternative to the anthropic principle for understanding the magnitude of the cosmological constant. In this approach, the probability to create observers is assumed to be proportional to the entropy production \Delta S in a maximal causally connected region -- the causal diamond. We improve on the original treatment by better quantifying the entropy production due to stars, using an analytic model for the star formation history which accurately accounts for changes in cosmological parameters. We calculate the dependence of \Delta S on the density contrast Q=\delta\rho/\rho, and find that our universe is much closer to the most probable value of Q than in the usual anthropic approach and that probabilities are relatively weakly dependent on this amplitude. In addition, we make first estimates of the dependence of \Delta S on the baryon fraction and overall matter abundance. Finally, we also explore the possibility that decays of dark matter, suggested by various observed gamma ray excesses, might produce a comparable amount of entropy to stars.Comment: RevTeX4, 13pp, 10 figures; v2. clarified introduction, added ref

The Metal-Poor Halo of the Andromeda Spiral Galaxy (M31)

We present spectroscopic observations of red giant branch (RGB) stars over a large expanse in the halo of the Andromeda spiral galaxy (M31), acquired with the DEIMOS instrument on the Keck II 10-m telescope. Using a combination of five photometric/spectroscopic diagnostics -- (1) radial velocity, (2) intermediate-width DDO51 photometry, (3) Na I equivalent width (surface gravity sensitive), (4) position in the color-magnitude diagram, and (5) comparison between photometric and spectroscopic [Fe/H] estimates -- we isolate over 250 bona fide M31 bulge and halo RGB stars located in twelve fields ranging from R = 12-165kpc from the center of M31 (47 of these stars are halo members with R > 60 kpc). We derive the photometric and spectroscopic metallicity distribution function of M31 RGB stars in each of these fields. The mean of the resulting M31 spheroid (bulge and halo) metallicity distribution is found to be systematically more metal-poor with increasing radius, shifting from = -0.47+/-0.03 (sigma = 0.39) at R = -0.94+/-0.06 (sigma = 0.60) at R ~ 30 kpc to = -1.26+/-0.10 (sigma = 0.72) at R > 60 kpc, assuming [alpha/Fe] = 0.0. These results indicate the presence of a metal-poor RGB population at large radial distances out to at least R = 160 kpc, thereby supporting our recent discovery of a stellar halo in M31: its halo and bulge (defined as the structural components with R^{-2} power law and de Vaucouleurs R^{1/4} law surface brightness profiles, respectively) are shown to have distinct metallicity distributions. If we assume an alpha-enhancement of [alpha/Fe] = +0.3 for M31's halo, we derive = -1.5+/-0.1 (sigma = 0.7). Therefore, the mean metallicity and metallicity spread of this newly found remote M31 RGB population are similar to those of the Milky Way halo.Comment: Accepted for publication in ApJ on May 4th, 2006 (submitted on Jan 30, 2006). 16 pages, 13 figures, 3 table

Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness.

UnlabelledWe analyzed the 16S rRNA amplicon composition in fecal samples of selected patients during their prolonged stay in an intensive care unit (ICU) and observed the emergence of ultra-low-diversity communities (1 to 4 bacterial taxa) in 30% of the patients. Bacteria associated with the genera Enterococcus and Staphylococcus and the family Enterobacteriaceae comprised the majority of these communities. The composition of cultured species from stool samples correlated to the 16S rRNA analysis and additionally revealed the emergence of Candida albicans and Candida glabrata in ~75% of cases. Four of 14 ICU patients harbored 2-member pathogen communities consisting of one Candida taxon and one bacterial taxon. Bacterial members displayed a high degree of resistance to multiple antibiotics. The virulence potential of the 2-member communities was examined in C. elegans during nutrient deprivation and exposure to opioids in order to mimic local conditions in the gut during critical illness. Under conditions of nutrient deprivation, the bacterial members attenuated the virulence of fungal members, leading to a "commensal lifestyle." However, exposure to opioids led to a breakdown in this commensalism in 2 of the ultra-low-diversity communities. Application of a novel antivirulence agent (phosphate-polyethylene glycol [Pi-PEG]) that creates local phosphate abundance prevented opioid-induced virulence among these pathogen communities, thus rescuing the commensal lifestyle. To conclude, the gut microflora in critically ill patients can consist of ultra-low-diversity communities of multidrug-resistant pathogenic microbes. Local environmental conditions in gut may direct pathogen communities to adapt to either a commensal style or a pathogenic style.ImportanceDuring critical illness, the normal gut microbiota becomes disrupted in response to host physiologic stress and antibiotic treatment. Here we demonstrate that the community structure of the gut microbiota during prolonged critical illness is dramatically changed such that in many cases only two-member pathogen communities remain. Most of these ultra-low-membership communities display low virulence when grouped together (i.e., a commensal lifestyle); individually, however, they can express highly harmful behaviors (i.e., a pathogenic lifestyle). The commensal lifestyle of the whole community can be shifted to a pathogenic one in response to host factors such as opioids that are released during physiologic stress and critical illness. This shift can be prevented by using compounds such as Pi-PEG15-20 that interrupt bacterial virulence expression. Taking the data together, this report characterizes the plasticity seen with respect to the choice between a commensal lifestyle and a pathogenic lifestyle among ultra-low-diversity pathogen communities that predominate in the gut during critical illness and offers novel strategies for prevention of sepsis

Suicide Screening in Primary Care: Use of an Electronic Screener to Assess Suicidality and Improve Provider Follow-Up for Adolescents

Purpose The purpose of this study was to assess the feasibility of using an existing computer decision support system to screen adolescent patients for suicidality and provide follow-up guidance to clinicians in a primary care setting. Predictors of patient endorsement of suicidality and provider documentation of follow-up were examined. Methods A prospective cohort study was conducted to examine the implementation of a CDSS that screened adolescent patients for suicidality and provided follow-up recommendations to providers. The intervention was implemented for patients aged 12–20 years in two primary care clinics in Indianapolis, Indiana. Results The sample included 2,134 adolescent patients (51% female; 60% black; mean age = 14.6 years [standard deviation = 2.1]). Just over 6% of patients screened positive for suicidality. A positive endorsement of suicidality was more common among patients who were female, depressed, and seen by an adolescent−medicine board-certified provider as opposed to general pediatric provider. Providers documented follow-up action for 83% of patients who screened positive for suicidality. Documentation of follow-up action was correlated with clinic site and Hispanic race. The majority of patients who endorsed suicidality (71%) were deemed not actively suicidal after assessment by their provider. Conclusions Incorporating adolescent suicide screening and provider follow-up guidance into an existing computer decision support system in primary care is feasible and well utilized by providers. Female gender and depressive symptoms are consistently associated with suicidality among adolescents, although not all suicidal adolescents are depressed. Universal use of a multi-item suicide screener that assesses recency might more effectively identify suicidal adolescents

Using Color in Machine Vision Systems for Wood Processing

Color information, already shown to be valuable in distinguishing wood surface features, should prove especially useful for future applications of machine vision in the wood products industry. This review provides investigators interested in such applications with the information necessary for understanding the benefits-and associated difficulties-of using color. Various standard color-measurement systems ("color spaces") are discussed. No one system has been completely successful, at least partly because simple physical measurements are difficult to correlate with a human observer's complex perception of color. Color video camera systems, designed with human viewers in mind, have the potential for machine vision applications, but certain system "features" (white balance, gamma or contour correction) could cause problems. Future applications, including detecting and classifying hard-to-identify defects and matching colors of wood components, will require careful choice of lighting geometry and source, camera system, and color space for the purpose at hand

Measurement of [OIII] Emission in Lyman Break Galaxies

Measurements of [OIII] emission in Lyman Break galaxies (LBGs) at z>3 are presented. Four galaxies were observed with narrow-band filters using the Near-IR Camera on the Keck I 10-m telescope. A fifth galaxy was observed spectroscopically during the commissioning of NIRSPEC, the new infrared spectrometer on Keck II. The emission-line spectrum is used to place limits on the metallicity. Comparing these new measurements with others available from the literature, we find that strong oxygen emission in LBGs may suggest sub-solar metallicity for these objects. The [OIII]5007 line is also used to estimate the star formation rate (SFR) of the LBGs. The inferred SFRs are higher than those estimated from the UV continuum, and may be evidence for dust extinction.Comment: 25 pages, including 6 figures. Accepted for publication in Ap

A method for exploratory repeated-measures analysis applied to a breast-cancer screening study

When a model may be fitted separately to each individual statistical unit, inspection of the point estimates may help the statistician to understand between-individual variability and to identify possible relationships. However, some information will be lost in such an approach because estimation uncertainty is disregarded. We present a comparative method for exploratory repeated-measures analysis to complement the point estimates that was motivated by and is demonstrated by analysis of data from the CADET II breast-cancer screening study. The approach helped to flag up some unusual reader behavior, to assess differences in performance, and to identify potential random-effects models for further analysis.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS481 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org