Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton.

Primers targeting the 16S small subunit ribosomal RNA marker gene, used to characterize bacterial and archaeal communities, have recently been re-evaluated for marine planktonic habitats. To investigate whether primer selection affects the ecological interpretation of bacterioplankton populations and community dynamics, amplicon sequencing with four primer sets targeting several hypervariable regions of the 16S rRNA gene was conducted on both mock communities constructed from cloned 16S rRNA genes and a time-series of DNA samples from the temperate coastal Santa Barbara Channel. Ecological interpretations of community structure (delineation of depth and seasonality, correlations with environmental factors) were similar across primer sets, while population dynamics varied. We observed substantial differences in relative abundances of taxa known to be poorly resolved by some primer sets, such as Thaumarchaeota and SAR11, and unexpected taxa including Roseobacter clades. Though the magnitude of relative abundances of common OTUs differed between primer sets, the relative abundances of the OTUs were nonetheless strongly correlated. We do not endorse one primer set but rather enumerate strengths and weaknesses to facilitate selection appropriate to a system or experimental goal. While 16S rRNA gene primer bias suggests caution in assessing quantitative population dynamics, community dynamics appear robust across studies using different primers

The mPower Study, Parkinson Disease Mobile Data Collected Using Researchkit

Current measures of health and disease are often insensitive, episodic, and subjective. Further, these measures generally are not designed to provide meaningful feedback to individuals. The impact of high-resolution activity data collected from mobile phones is only beginning to be explored. Here we present data from mPower, a clinical observational study about Parkinson disease conducted purely through an iPhone app interface. The study interrogated aspects of this movement disorder through surveys and frequent sensor-based recordings from participants with and without Parkinson disease. Benefitting from large enrollment and repeated measurements on many individuals, these data may help establish baseline variability of real-world activity measurement collected via mobile phones, and ultimately may lead to quantification of the ebbs-and-flows of Parkinson symptoms. App source code for these data collection modules are available through an open source license for use in studies of other conditions. We hope that releasing data contributed by engaged research participants will seed a new community of analysts working collaboratively on understanding mobile health data to advance human health

Limits on the Peculiar Velocities of Two Distant Clusters Using the Kinematic Sunyaev-Zel'dovich Effect

We report millimeter-wavelength observations of the Sunyaev-Zel'dovich (S-Z) effect in two distant galaxy clusters. A relativistically correct analysis of the S-Z data is combined with the results of X-ray observations to determine the radial peculiar velocities v_r of the clusters. We observed Abell 2163 (z=.201) in three mm-wavelength bands centered at 2.1, 1.4, and 1.1 mm. We report a significant detection of the thermal component of the S-Z effect seen as both a decrement in the brightness of the CMB at 2.1 mm, and as an increment at 1.1 mm. Including uncertainties due to the calibration of the instrument, distribution and temperature of the IC gas, and astrophysical confusion, a simultaneous fit to the data in all three bands gives v_r=+490 +1370/-880 km/s at 68% confidence. We observed Abell 1689 (z=.181) in the 2.1 and 1.4 mm bands. Including the same detailed accounting of uncertainty, a simultaneous fit to the data in both bands gives v_r=+170 +815/-630 km/s. The limits on the peculiar velocities of A2163 and A1689 correspond to deviations from the uniform Hubble flow of <= 2-3%.Comment: 21 pages, 13 postscript figures, LaTeX(aaspptwo.sty), ApJ(in press

The Sunyaev-Zel'dovich Infrared Experiment: A Millimeter-wave Receiver for Cluster Cosmology

Measurements of the Sunyaev-Zel'dovich (S-Z) effect towards distant clusters of galaxies can be used to determine the Hubble constant and the radial component of cluster peculiar velocities. Determination of the cluster peculiar velocity requires the separation of the two components of the S-Z effect, which are due to the thermal and bulk velocities of the intracluster plasma. The two components can be separated practically only at millimeter (mm) wavelengths. Measurements of the S-Z effect at mm wavelengths are subject to minimal astrophysical confusion and, therefore, provide an important test of results obtained at longer wavelengths. We describe the instrument used to make the first significant detections of the S-Z effect at millimeter wavelengths. This instrument employs new filter, detector, and readout technologies to produce sensitive measurements of differential sky brightness stable on long time scales. These advances allow drift scan observations which achieve high sensitivity while minimizing common sources of systematic error.Comment: 19 pages, 15 postscript figures, LaTeX(aaspptwo.sty), ApJ(in press

T cell sensitivity to TGF-β is required for the effector function but not the generation of splenic CD8+ regulatory T cells induced via the injection of antigen into the anterior chamber

The introduction of antigen into the anterior chamber (AC) of the eye induces the production of antigen-specific splenic CD8+ regulatory T cells (AC-SPL cells) that suppress a delayed-type hypersensitivity (DTH) reaction in immunized mice. Because the generation of these regulatory T cells is also induced by exposure to transforming growth factor (TGF)-β and antigen or F4/80+ cells exposed to TGF-β and antigen in vitro, we investigated (i) whether these cells are produced in dominant negative receptor for transforming growth factor β receptor type II (dnTGFβRII) or Cbl-b−/− mice whose T cells are resistant to TGF-β, (ii) whether DTH is suppressed by wild type (WT) CD8+ AC-SPL cells in Cbl-b−/− and dnTGFβRII mice and (iii) the effect of antibodies to TGF-β on the suppression of DTH by CD8+ AC-SPL cells. DnTGFβRII immunized and Cbl-b−/− mice produced splenic CD8+ regulatory cells after the intracameral injection of antigen and immunization. The suppression of a DTH reaction by CD8+ AC-SPL cells in WT mice was blocked by the local inclusion of antibodies to TGF-β when WT splenic CD8+ AC-SPL cells were injected into the DTH reaction site. Moreover, the DTH reaction in immunized dnTGFβRII and Cbl-b−/− mice was not suppressed by the transfer of WT CD8+ AC-SPL cells to the site challenged with antigen. In aggregate, these observations suggest that T cell sensitivity to TGF-β is not an obligate requirement for the in vivo induction of CD8+ AC-SPL T cells but the suppression of an in vivo DTH reaction by CD8+ AC-SPL cells is dependent on TGF-β

An iron-oxygen intermediate formed during the catalytic cycle of cysteine dioxygenase

Cysteine dioxygenase is a key enzyme in the breakdown of cysteine, but its mechanism remains controversial. A combination of spectroscopic and computational studies provides the first evidence of a short-lived intermediate in the catalytic cycle. The intermediate decays within 20 ms and has absorption maxima at 500 and 640 nm

Virtual patients design and its effect on clinical reasoning and student experience : a protocol for a randomised factorial multi-centre study

Background Virtual Patients (VPs) are web-based representations of realistic clinical cases. They are proposed as being an optimal method for teaching clinical reasoning skills. International standards exist which define precisely what constitutes a VP. There are multiple design possibilities for VPs, however there is little formal evidence to support individual design features. The purpose of this trial is to explore the effect of two different potentially important design features on clinical reasoning skills and the student experience. These are the branching case pathways (present or absent) and structured clinical reasoning feedback (present or absent). Methods/Design This is a multi-centre randomised 2x2 factorial design study evaluating two independent variables of VP design, branching (present or absent), and structured clinical reasoning feedback (present or absent).The study will be carried out in medical student volunteers in one year group from three university medical schools in the United Kingdom, Warwick, Keele and Birmingham. There are four core musculoskeletal topics. Each case can be designed in four different ways, equating to 16 VPs required for the research. Students will be randomised to four groups, completing the four VP topics in the same order, but with each group exposed to a different VP design sequentially. All students will be exposed to the four designs. Primary outcomes are performance for each case design in a standardized fifteen item clinical reasoning assessment, integrated into each VP, which is identical for each topic. Additionally a 15-item self-reported evaluation is completed for each VP, based on a widely used EViP tool. Student patterns of use of the VPs will be recorded. In one centre, formative clinical and examination performance will be recorded, along with a self reported pre and post-intervention reasoning score, the DTI. Our power calculations indicate a sample size of 112 is required for both primary outcomes

TEF, Vol. 1 No. 1

https://scholarworks.sfasu.edu/tef/1000/thumbnail.jp

DT/T beyond linear theory

The major contribution to the anisotropy of the temperature of the Cosmic Microwave Background (CMB) radiation is believed to come from the interaction of linear density perturbations with the radiation previous to the decoupling time. Assuming a standard thermal history for the gas after recombination, only the gravitational field produced by the linear density perturbations present on a $\Omega\neq 1$ universe can generate anisotropies at low z (these anisotropies would manifest on large angular scales). However, secondary anisotropies are inevitably produced during the nonlinear evolution of matter at late times even in a universe with a standard thermal history. Two effects associated to this nonlinear phase can give rise to new anisotropies: the time-varying gravitational potential of nonlinear structures (Rees-Sciama RS effect) and the inverse Compton scattering of the microwave photons with hot electrons in clusters of galaxies (Sunyaev-Zeldovich SZ effect). These two effects can produce distinct imprints on the CMB temperature anisotropy. We discuss the amplitude of the anisotropies expected and the relevant angular scales in different cosmological scenarios. Future sensitive experiments will be able to probe the CMB anisotropies beyong the first order primary contribution.Comment: plain tex, 16 pages, 3 figures. Proceedings of the Laredo Advance School on Astrophysics "The universe at high-z, large-scale structure and the cosmic microwave background". To be publised by Springer-Verla