Performance analysis of a novel pyroelectric device for non-dispersive infra-red CO2 detection

We present the performance characteristics of a digital output thin-film pyroelectric sensor for use in non-dispersive infra-red detection. The single channel pyroelectric sensor device was fitted with band-pass optical filter with a central wavelength of 4.26 μm for the detection of carbon dioxide. The classification reported here is concerned with the stability of the device for long-term measurements, with systematic drift not dominating measurement error even after 10 h operation. Comparative NDIR measurements were made for this novel pyroelectric device using two different optical sources, a standard filament lamp and a black body radiation source, operated at 5 Hz repetition rates. The overall limit of detection for the NDIR sensor was calculated to be 6 and 3 ppm for CO 2 for the filament and blackbody source respectively, when the sensor was temperature stabilised at 35 °C and data was averaged over 110 min. The single shot measurement error was calculated to be 48 and 22 ppm for the lamp and blackbody, respectively, when the sensor temperature was stabilised at 35°C. The response of the detector to increasing temperature was found to exhibit a trend in the signal output directly proportional to the pyroelectric coefficient, this was also evident during flow tests when the flowing gas cooled the device. The result of changing both the concentration of analyte and flow rate is also covered. This is the first time the performance of a fully digital output pyroelectric detector has been reported

Shared genomic outliers across two divergent population clusters of a highly threatened seagrass

The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled genomic approach was employed to obtain SNP data and examine neutral genomic variation and to identify potential outlier loci to assess differentiation across 12 populations across the ∼9,600 km distribution of Z. capensis. Results indicate high clonality and low genomic diversity within meadows, which combined with poor protection throughout its range, increases the vulnerability of this seagrass to further declines or local extinction. Shared variation at outlier loci potentially indicates local adaptation to temperature and precipitation gradients, with Isolation-by-Environment significantly contributing towards shaping spatial variation in Z. capensis. Our results indicate the presence of two population clusters, broadly corresponding to populations on the west and east coasts, with the two lineages shaped only by frequency differences of outlier loci. Notably, ensemble modelling of suitable seagrass habitat provides evidence that the clusters are linked to historical climate refugia around the Last Glacial Maxi-mum. Our work suggests a complex evolutionary history of Z. capensis in southern and eastern Africa that will require more effective protection in order to safeguard this important ecosystem engineer into the future

Lack of Evidence for Changing Virulence of HIV-1 in North America

Background: Several long-term cohort studies and in-vitro fitness assays have resulted in inconsistent reports on changes in HIV-1 virulence, including reports of decreasing, stable, and increasing virulence over the course of the AIDS pandemic. We tested the hypothesis of changing HIV-1 virulence by examining trends in prognostic clinical markers of disease progression from 1984 to 2005 among nearly 400 antiretroviral-naı¨ve participants in the United States Multicenter AIDS Cohort Study (MACS), a longitudinal study of HIV infection in men who have sex with men (MSM). \ud \ud Methodology/Principal Findings:\ud Because clinical AIDS endpoints could not be used (due to antiretroviral therapies and prophylaxis), three prognostic markers of disease progression were used as proxies for HIV-1 virulence: plasma viral RNA load and CD4+ T cell count at ‘‘set point’’ (between ~9 and ~15 months after seroconversion), and rate of CD4 cell decline within three years after seroconversion. We performed multivariate analyses of the association between these markers and seroconversion year, with covariates including MACS site, race/ethnic group, seroconversion age, and CCR5D32 status. No statistically significant association was found between year of seroconversion and ‘‘set point’’ plasma viral load (at ~9 months after seroconversion: slope =20.004 log10\ud copies/mL/year, p = 0.76; at ~15 months: slope =20.005 log10 copies/mL/year, p = 0.71), CD4 cell count after seroconversion (at ~9 months: slope =20.112 cells/mL/year, p = 0.22; at ~15 months: slope =20.047 cells/mL/year, p = 0.64), or rate of CD4 cell decline over the first three years after seroconversion (slope =20.010 cells/ul/yr2, p = 0.88). \ud \ud Conclusions/Significance: The lack of significant trends from 1984 to 2005 in these prognostic markers of HIV disease progression suggests no major change in HIV-1 virulence over the AIDS pandemic in MSM in the US

Nucleosome-mediated cooperativity between transcription factors

Cooperative binding of transcription factors (TFs) to cis-regulatory regions (CRRs) is essential for precision of gene expression in development and other processes. The classical model of cooperativity requires direct interactions between TFs, thus constraining the arrangement of TFs sites in a CRR. On the contrary, genomic and functional studies demonstrate a great deal of flexibility in such arrangements with variable distances, numbers of sites, and identities of the involved TFs. Such flexibility is inconsistent with the cooperativity by direct interactions between TFs. Here we demonstrate that strong cooperativity among non-interacting TFs can be achieved by their competition with nucleosomes. We find that the mechanism of nucleosome-mediated cooperativity is mathematically identical to the Monod-Wyman-Changeux (MWC) model of cooperativity in hemoglobin. This surprising parallel provides deep insights, with parallels between heterotropic regulation of hemoglobin (e.g. Bohr effect) and roles of nucleosome-positioning sequences and chromatin modifications in gene regulation. Characterized mechanism is consistent with numerous experimental results, allows substantial flexibility in and modularity of CRRs, and provides a rationale for a broad range of genomic and evolutionary observations. Striking parallels between cooperativity in hemoglobin and in transcription regulation point at a new design principle that may be used in range of biological systems

Long-Term Kidney Function, Proteinuria, and Associated Risks among HIV-Infected and Uninfected Men in the MACS

Background: Factors affecting kidney function and proteinuria among HIV-positive (HIV+) and HIV-negative (HIV–) persons need better characterization. Methods: We evaluated estimated glomerular filtration rate (eGFR, ml/min per 1.73 m2) changes, proteinuria prevalence (a urine protein-to-creatinine ratio of ≥0.2 at two consecutive visits) and associated factors among HIV+ and HIV− men. Results: There were 917 HIV+ men receiving HAART, 159 HIV+ men not receiving HAART, and 1305 HIV− men seen from October 2003 to September 2014. Median annual eGFR change was −0.5, −0.8% for HIV+ and −0.3% for HIV− men (P < 0.001). Factors significantly (P < 0.05) associated with more than 3% annual eGFR decline were HAART receipt (but no specific antiretroviral drug), age more than 50, hypertension, diabetes, current smoking. Proteinuria existed in 14.9% of visit-pairs among HAART recipients, 5.8% among non-HAART recipients, and 1.9% among HIV− men, and was associated with subsequent annual more than 3% eGFR decline (odds ratio 1.80, P < 0.001). Proteinuria-associated factors also included HAART use (vs. HIV−), age at least 50 (vs. <40), diabetes, hypertension, current smoking, hepatitis C virus-infection (all P < 0.05) and, among HIV+ men, lower CD4+ cell count, didanosine, saquinavir, or nelfinavir use (all P < 0.05). After adjusting for proteinuria, among HAART users, having a detectable HIV RNA, cumulative use of tenofovir disoproxil fumarate, emtricitabine, ritonavir, atazanavir, any protease inhibitor, or fluconazole were associated with more than 3% annual eGFR decline. Conclusion: Longitudinal kidney function decline was associated with HAART use but no individual antiretroviral drug, and traditional kidney disease risks. Proteinuria was nearly seven times more common in HAART-treated men than HIV− men, reflected recent eGFR decline and predicted subsequent eGFR declin