Susceptibility to intestinal infection and diarrhoea in Zambian adults in relation to HIV status and CD4 count.

BACKGROUND: The HIV epidemic in sub-Saharan Africa has had a major impact on infectious disease, and there is currently great interest in the impact of HIV on intestinal barrier function. A three year longitudinal cohort study in a shanty compound in Lusaka, Zambia, carried out before anti-retroviral therapy was widely available, was used to assess the impact of HIV on susceptibility to intestinal infectious disease. We measured the incidence and seasonality of intestinal infection and diarrhoea, aggregation of disease in susceptible individuals, clustering by co-habitation and genetic relatedness, and the disease-to-infection ratio. METHODS: Adults living in a small section of Misisi, Lusaka, were interviewed every two weeks to ascertain the incidence of diarrhoea. Monthly stool samples were analysed for selected pathogens. HIV status and CD4 count were determined annually. RESULTS: HIV seroprevalence was 31% and the prevalence of immunosuppression (CD4 count 200 cells/microL or less) was 10%. Diarrhoea incidence was 1.1 episodes per year and the Incidence Rate Ratio for HIV infection was 2.4 (95%CI 1.7-3.3; p < 0.001). The disease-to-infection ratio was increased at all stages of HIV infection. Aggregation of diarrhoea in susceptible individuals was observed irrespective of immunosuppression, but there was little evidence of clustering by co-habitation or genetic relatedness. There was no evidence of aggregation of asymptomatic infections. CONCLUSION: HIV has an impact on intestinal infection at all stages, with an increased disease-to-infection ratio. The aggregation of disease in susceptible individuals irrespective of CD4 count suggests that this phenomenon is not a function of cell mediated immunity

PlantCV v2: Image analysis software for high-throughput plant phenotyping

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here we present the details and rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning

Algorithm for identifying and separating beats from arterial pulse records

BACKGROUND: This project was designed as an epidemiological aid-selecting tool for a small country health center with the general objective of screening out possible coronary patients. Peripheral artery function can be non-invasively evaluated by impedance plethysmography. Changes in these vessels appear as good predictors of future coronary behavior. Impedance plethysmography detects volume variations after simple occlusive maneuvers that may show indicative modifications in arterial/venous responses. Averaging of a series of pulses is needed and this, in turn, requires proper determination of the beginning and end of each beat. Thus, the objective here is to describe an algorithm to identify and separate out beats from a plethysmographic record. A secondary objective was to compare the output given by human operators against the algorithm. METHODS: The identification algorithm detected the beat's onset and end on the basis of the maximum rising phase, the choice of possible ventricular systolic starting points considering cardiac frequency, and the adjustment of some tolerance values to optimize the behavior. Out of 800 patients in the study, 40 occlusive records (supradiastolic- subsystolic) were randomly selected without any preliminary diagnosis. Radial impedance plethysmographic pulse and standard ECG were recorded digitizing and storing the data. Cardiac frequency was estimated with the Power Density Function and, thereafter, the signal was derived twice, followed by binarization of the first derivative and rectification of the second derivative. The product of the two latter results led to a weighing signal from which the cycles' onsets and ends were established. Weighed and frequency filters are needed along with the pre-establishment of their respective tolerances. Out of the 40 records, 30 seconds strands were randomly chosen to be analyzed by the algorithm and by two operators. Sensitivity and accuracy were calculated by means of the true/false and positive/negative criteria. Synchronization ability was measured through the coefficient of variation and the median value of correlation for each patient. These parameters were assessed by means of Friedman's ANOVA and Kendall Concordance test. RESULTS: Sensitivity was 97% and 91% for the two operators, respectively, while accuracy was cero for both of them. The synchronism variability analysis was significant (p < 0.01) for the two statistics, showing that the algorithm produced the best result. CONCLUSION: The proposed algorithm showed good performance as expressed by its high sensitivity. The correlation analysis demonstrated that, from the synchronism point of view, the algorithm performed the best detection. Patients with marked arrhythmic processes are not good candidates for this kind of analysis. At most, they would be singled out by the algorithm and, thereafter, to be checked by an operator

CMB mapping experiments: a designer's guide

We apply state-of-the art data analysis methods to a number of fictitious CMB mapping experiments, including 1/f noise, distilling the cosmological information from time-ordered data to maps to power spectrum estimates, and find that in all cases, the resulting error bars can we well approximated by simple and intuitive analytic expressions. Using these approximations, we discuss how to maximize the scientific return of CMB mapping experiments given the practical constraints at hand, and our main conclusions are as follows. (1) For a given resolution and sensitivity, it is best to cover a sky area such that the signal-to-noise ratio per resolution element (pixel) is of order unity. (2) It is best to avoid excessively skinny observing regions, narrower than a few degrees. (3) The minimum-variance mapmaking method can reduce the effects of 1/f noise by a substantial factor, but only if the scan pattern is thoroughly interconnected. (4) 1/f noise produces a 1/l contribution to the angular power spectrum for well connected single-beam scanning, as compared to virtually white noise for a two-beam scan pattern such as that of the MAP satellite.Comment: 28 pages, with 13 figures included. Minor revisions to match accepted version. Color figures and links at http://www.sns.ias.edu/~max/strategy.html (faster from the US), from http://www.mpa-garching.mpg.de/~max/strategy.html (faster from Europe) or from [email protected]

Baryon Acoustic Oscillations in the Sloan Digital Sky Survey Data Release 7 Galaxy Sample

The spectroscopic Sloan Digital Sky Survey (SDSS) Data Release 7 (DR7) galaxy sample represents the final set of galaxies observed using the original SDSS target selection criteria. We analyse the clustering of galaxies within this sample, including both the Luminous Red Galaxy (LRG) and Main samples, and also include the 2-degree Field Galaxy Redshift Survey (2dFGRS) data. Baryon Acoustic Oscillations are observed in power spectra measured for different slices in redshift; this allows us to constrain the distance--redshift relation at multiple epochs. We achieve a distance measure at redshift z=0.275, of r_s(z_d)/D_V(0.275)=0.1390+/-0.0037 (2.7% accuracy), where r_s(z_d) is the comoving sound horizon at the baryon drag epoch, D_V(z)=[(1+z)^2D_A^2cz/H(z)]^(1/3), D_A(z) is the angular diameter distance and H(z) is the Hubble parameter. We find an almost independent constraint on the ratio of distances D_V(0.35)/D_V(0.2)=1.736+/-0.065, which is consistent at the 1.1sigma level with the best fit Lambda-CDM model obtained when combining our z=0.275 distance constraint with the WMAP 5-year data. The offset is similar to that found in previous analyses of the SDSS DR5 sample, but the discrepancy is now of lower significance, a change caused by a revised error analysis and a change in the methodology adopted, as well as the addition of more data. Using WMAP5 constraints on Omega_bh^2 and Omega_ch^2, and combining our BAO distance measurements with those from the Union Supernova sample, places a tight constraint on Omega_m=0.286+/-0.018 and H_0 = 68.2+/-2.2km/s/Mpc that is robust to allowing curvature and non-Lambda dark energy. This result is independent of the behaviour of dark energy at redshifts greater than those probed by the BAO and supernova measurements. (abridged)Comment: 22 pages, 16 figures, minor changes to match version published in MNRA

Cosmological Constraints from the Clustering of the Sloan Digital Sky Survey DR7 Luminous Red Galaxies

We present the power spectrum of the reconstructed halo density field derived from a sample of Luminous Red Galaxies (LRGs) from the Sloan Digital Sky Survey Seventh Data Release (DR7). The halo power spectrum has a direct connection to the underlying dark matter power for k <= 0.2 h/Mpc, well into the quasi-linear regime. This enables us to use a factor of ~8 more modes in the cosmological analysis than an analysis with kmax = 0.1 h/Mpc, as was adopted in the SDSS team analysis of the DR4 LRG sample (Tegmark et al. 2006). The observed halo power spectrum for 0.02 < k < 0.2 h/Mpc is well-fit by our model: chi^2 = 39.6 for 40 degrees of freedom for the best fit LCDM model. We find \Omega_m h^2 * (n_s/0.96)^0.13 = 0.141^{+0.009}_{-0.012} for a power law primordial power spectrum with spectral index n_s and \Omega_b h^2 = 0.02265 fixed, consistent with CMB measurements. The halo power spectrum also constrains the ratio of the comoving sound horizon at the baryon-drag epoch to an effective distance to z=0.35: r_s/D_V(0.35) = 0.1097^{+0.0039}_{-0.0042}. Combining the halo power spectrum measurement with the WMAP 5 year results, for the flat LCDM model we find \Omega_m = 0.289 +/- 0.019 and H_0 = 69.4 +/- 1.6 km/s/Mpc. Allowing for massive neutrinos in LCDM, we find \sum m_{\nu} < 0.62 eV at the 95% confidence level. If we instead consider the effective number of relativistic species Neff as a free parameter, we find Neff = 4.8^{+1.8}_{-1.7}. Combining also with the Kowalski et al. (2008) supernova sample, we find \Omega_{tot} = 1.011 +/- 0.009 and w = -0.99 +/- 0.11 for an open cosmology with constant dark energy equation of state w.Comment: 26 pages, 19 figures, submitted to MNRAS. The power spectrum and a module to calculate the likelihoods is publicly available at http://lambda.gsfc.nasa.gov/toolbox/lrgdr/ . v2 fixes abstract formatting issu

Certifications of citizenship: the history, politics and materiality of identity documents in South Asian states and diasporas

Experiences in the post-partition Indian subcontinent refute the conventional expectation that the 'possession of citizenship enables the acquisition of documents certifying it' (Jayal, 2013, 71). Instead, identity papers of various types play a vital part in certifying and authenticating claims to citizenship. This is particularly important in a context where the history of state formation, continuous migration flows and the rise of right-wing majoritarian politics has created an uncertain situation for individuals deemed to be on the ‘margins’ of the state. The papers that constitute this special issue bring together a range of disciplinary perspectives in order to investigate the history, politics and materiality of identity documents, and to dismantle citizenship as an absolute and fixed notion, seeking instead to theorise the very mutable ‘hierarchies’ and ‘degrees’ of citizenship. Collectively they offer a valuable lens onto how migrants, refugees and socio-economically marginal individuals negotiate their relationship with the state, both within South Asia and in South Asian diaspora communities. This introduction examines the wider context of the complex intersections between state-issued identity documents and the nature of citizenship and draws out cross-cutting themes across the papers in this collection

The Real Space Power Spectrum of the PSCz Survey from 0.01 to 300 h/Mpc

We report a measurement of the real space (not redshift space) power spectrum of galaxies over four and a half decades of wavenumber, 0.01 to 300 h/Mpc, from the IRAS Point Source Catalog Redshift Survey (PSCz). Since estimates of power are highly correlated in the nonlinear regime, we also report results for the prewhitened power spectrum, which is less correlated. The inferred bias between optically-selected APM and IRAS-selected PSCz galaxies is about 1.15 at linear scales 1 h/Mpc. The nonlinear power spectrum of PSCz shows a near power-law behaviour to the smallest scales measured, with mild upward curvature in the broad vicinity of 1.5 h/Mpc. Contrary to the prediction of unbiased Dark Matter models, there is no prominent inflection at the linear-nonlinear transition scale, and no turnover at the transition to the stable clustering regime. The nonlinear power spectrum of PSCz requires scale-dependent bias: all Dark Matter models without scale-dependent bias are ruled out with high confidence.Comment: Power spectrum at small scales has changed from original: revised power spectrum takes into account 1.5 arcmin resolution of IRAS. Expanded discussion of the selection function, and of the power spectrum at the smallest scales. 26 pages including 16 embedded PostScript figures. Accepted by MNRAS. Revised data available at http://casa.colorado.edu/~ajsh/pscz

Drawings of very preterm-born children at 5 years of age: a first impression of cognitive and motor development?

INTRODUCTION: The aim of this study was to examine differences in drawing skills between very preterm and term children, and to determine whether very preterm children's cognitive and motor development is reflected in the draw-a-person test (DAP) at age 5. Seventy-two very preterm children (birth weight <1,500 g and/or gestational age <32 weeks) and 60 term children at 5 years of age were compared on the DAP. Cognitive and motor skills of the very preterm children had been assessed four times, at 1/2, 1, 2, and 5 years of age. Very preterm children showed a developmental delay in drawing ability. Structural equation modeling revealed a positive relation between both cognitive as well as motor development and the DAP. CONCLUSION: The DAP could be a crude parameter for evaluating cognitive and motor deficits of very preterm children. A worrisome result should be followed by more standardized tests measuring cognitive and motor skill