The CU mobile Solar Occultation Flux instrument: structure functions and emission rates of NH₃, NO₂ and C₂H₆

We describe the University of Colorado mobile Solar Occultation Flux instrument (CU mobile SOF). The instrument consists of a digital mobile solar tracker that is coupled to a Fourier transform spectrometer (FTS) of 0.5 cm−1 resolution and a UV–visible spectrometer (UV–vis) of 0.55 nm resolution. The instrument is used to simultaneously measure the absorption of ammonia (NH3), ethane (C2H6) and nitrogen dioxide (NO2) along the direct solar beam from a moving laboratory. These direct-sun observations provide high photon flux and enable measurements of vertical column densities (VCDs) with geometric air mass factors, high temporal resolution of 2 s and spatial resolution of 5–19 m. It is shown that the instrument line shape (ILS) of the FTS is independent of the azimuth and elevation angle pointing of the solar tracker. Further, collocated measurements next to a high-resolution FTS at the National Center for Atmospheric Research (HR-NCAR-FTS) show that the CU mobile SOF measurements of NH3 and C2H6 are precise and accurate; the VCD error at high signal to noise ratio is 2–7 %. During the Front Range Air Pollution and Photochemistry Experiment (FRAPPE) from 21 July to 3 September 2014 in Colorado, the CU mobile SOF instrument measured median (minimum, maximum) VCDs of 4.3 (0.5, 45)  ×  1016 molecules cm−2 NH3, 0.30 (0.06, 2.23)  ×  1016 molecules cm−2 NO2 and 3.5 (1.5, 7.7)  ×  1016 molecules cm−2 C2H6. All gases were detected in larger 95 % of the spectra recorded in urban, semi-polluted rural and remote rural areas of the Colorado Front Range. We calculate structure functions based on VCDs, which describe the variability of a gas column over distance, and find the largest variability for NH3. The structure functions suggest that currently available satellites resolve about 10 % of the observed NH3 and NO2 VCD variability in the study area. We further quantify the trace gas emission fluxes of NH3 and C2H6 and production rates of NO2 from concentrated animal feeding operations (CAFO) using the mass balance method, i.e., the closed-loop vector integral of the VCD times wind speed along the drive track. Excellent reproducibility is found for NH3 fluxes and also, to a lesser extent, NO2 production rates on 2 consecutive days; for C2H6 the fluxes are affected by variable upwind conditions. Average emission factors were 12.0 and 11.4 gNH3 h−1 head−1 at 30 °C for feedlots with a combined capacity for  ∼  54 000 cattle and a dairy farm of  ∼  7400 cattle; the pooled rate of 11.8 ± 2.0 gNH3 h−1 head−1 is compatible with the upper range of literature values. At this emission rate the NH3 source from cattle in Weld County, CO (535 766 cattle), could be underestimated by a factor of 2–10. CAFO soils are found to be a significant source of NOx. The NOx source accounts for  ∼  1.2 % of the N flux in NH3 and has the potential to add  ∼  10 % to the overall NOx emissions in Weld County and double the NOx source in remote areas. This potential of CAFO to influence ambient NOx concentrations on the regional scale is relevant because O3 formation is NOx sensitive in the Colorado Front Range. Emissions of NH3 and NOx are relevant for the photochemical O3 and secondary aerosol formation

Non-Immunogenicity of Overlapping Gag Peptides Pulsed on Autologous Cells after Vaccination of HIV Infected Individuals

Background: HIV Gag-specific CD4+ and CD8+ T-cell responses are important for HIV immune control. Pulsing overlapping Gag peptides on autologous lymphocytes (OPAL) has proven immunogenic and effective in reducing viral loads in multiple pigtail macaque studies, warranting clinical evaluation. Methodology We performed a phase I, single centre, placebo-controlled, double-blinded and dose-escalating study to evaluate the safety and preliminary immunogenicity of a novel therapeutic vaccine approach ‘OPAL-HIV-Gag(c)’. This vaccine is comprised of 120 15mer peptides, overlapping by 11 amino acids, spanning the HIV Gag C clade sequence proteome, pulsed on white blood cells enriched from whole blood using a closed system, followed by intravenous reinfusion. Patients with undetectable HIV viral loads (<50 copies/ml plasma) on HAART received four administrations at week 0, 4, 8 and 12, and were followed up for 12 weeks post-treatment. Twenty-three people were enrolled in four groups: 12 mg (n = 6), 24 mg (n = 7), 48 mg (n = 2) or matching placebo (n = 8) with 18 immunologically evaluable. T-cell immunogenicity was assessed by IFNγ ELIspot and intracellular cytokine staining (ICS). Results: The OPAL-HIV-Gag(c) peptides were antigenic in vitro in 17/17 subjects. After vaccination with OPAL-HIV-Gag(c), 1/6 subjects at 12 mg and 1/6 subjects at 24 mg dose groups had a 2- and 3-fold increase in ELIspot magnitudes from baseline, respectively, of Gag-specific CD8+ T-cells at week 14, compared to 0/6 subjects in the placebo group. No Gag-specific CD4+ T-cell responses or overall change in Rev, Nef, Tat and CMV specific responses were detected. Marked, transient and self-limiting lymphopenia was observed immediately post-vaccination (4 hours) in OPAL-HIV-Gag(c) but not in placebo recipients, with median fall from 1.72 to 0.67 million lymphocytes/mL for active groups (P<0.001), compared to post-placebo from 1.70 to 1.56 lymphocytes/ml (P = 0.16). Conclusion/Significance Despite strong immunogenicity observed in several Macaca nemestrina studies using this approach, OPAL-HIV-Gag(c) was not significantly immunogenic in humans and improved methods of generating high-frequency Gag-specific T-cell responses are required. Name of Registry ClinicalTrials.gov, Registry number: NCT01123915, URL trial registry database: http://www.clinicaltrials.gov/ct2/results?term=OPAL-HIV-1001&Search=Searc

Identifying barriers to and facilitators of tuberculosis contact investigation in Kampala, Uganda: a behavioral approach

Background: The World Health Organization recommends routine household tuberculosis contact investigation in high-burden countries but adoption has been limited. We sought to identify barriers to and facilitators of TB contact investigation during its introduction in Kampala, Uganda. Methods: We collected cross-sectional qualitative data through focus group discussions and interviews with stakeholders, addressing three core activities of contact investigation: arranging household screening visits through index TB patients, visiting households to screen contacts and refer them to clinics, and evaluating at-risk contacts coming to clinics. We analyzed the data using a validated theory of behavior change, the Capability, Opportunity, and Motivation determine Behavior (COM-B) model, and sought to identify targeted interventions using the related Behavior Change Wheel implementation framework. Results: We led seven focus-group discussions with 61 health-care workers, two with 21 lay health workers (LHWs), and one with four household contacts of newly diagnosed TB patients. We, in addition, performed 32 interviews with household contacts from 14 households of newly diagnosed TB patients. Commonly noted barriers included stigma, limited knowledge about TB among contacts, insufficient time and space in clinics for counselling, mistrust of health-center staff among index patients and contacts, and high travel costs for LHWs and contacts. The most important facilitators identified were the personalized and enabling services provided by LHWs. We identified education, persuasion, enablement, modeling of health-positive behaviors, incentivization, and restructuring of the service environment as relevant intervention functions with potential to alleviate barriers to and enhance facilitators of TB contact investigation. Conclusions: The use of a behavioral theory and a validated implementation framework provided a comprehensive approach for systematically identifying barriers to and facilitators of TB contact investigation. The behavioral determinants identified here may be useful in tailoring interventions to improve implementation of contact investigation in Kampala and other similar urban settings. Electronic supplementary material The online version of this article (doi:10.1186/s13012-017-0561-4) contains supplementary material, which is available to authorized users

Individual Tree Data Standard

It is estimated that 40 million trees in the UK have been surveyed and the data stored in local authority databases. Data for just 1.1 million of these trees are included in the UK’s and world’s largest open-access tree database, Treezilla (https://treezilla.org/). Tree surveys are carried out for different purposes and often to different specifications. Many tree data collection protocols and methods overlap in their recommendations but differences between them make it difficult or impossible to compare, combine, or reuse data. To address these problems in 2019 the COMMUNITREE project partners drafted a new data standard for surveys of individual trees. The steps taken to develop the data standard are described in detail here: https://www.forestresearch.gov.uk/research/quantification-and-valuation-of-benefits-provided-by-urban-trees/individual-tree-data-standard/ . Standardised tree data collection and recording will enable people to easily share their data so that a single dataset can be recycled for many purposes. The Individual Tree Data Standard is a partnership between Forest Research, The Open University, Treework Environmental Practice, Natural Apptitude and was funded by Innovate UK and the Geospatial Commission

Inflation and Dark Energy from spectroscopy at z > 2

The expansion of the Universe is understood to have accelerated during two epochs: in its very first moments during a period of Inflation and much more recently, at z < 1, when Dark Energy is hypothesized to drive cosmic acceleration. The undiscovered mechanisms behind these two epochs represent some of the most important open problems in fundamental physics. The large cosmological volume at 2 < z < 5, together with the ability to efficiently target high-$z$ galaxies with known techniques, enables large gains in the study of Inflation and Dark Energy. A future spectroscopic survey can test the Gaussianity of the initial conditions up to a factor of ~50 better than our current bounds, crossing the crucial theoretical threshold of $\sigma(f_{NL}^{\rm local})$ of order unity that separates single field and multi-field models. Simultaneously, it can measure the fraction of Dark Energy at the percent level up to $z = 5$, thus serving as an unprecedented test of the standard model and opening up a tremendous discovery space

A generalist–specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic range

Polyploidy results from whole-genome duplication and is a unique form of heritable variation with pronounced evolutionary implications. Different ploidy levels, or cytotypes, can exist within a single species, and such systems provide an opportunity to assess how ploidy variation alters phenotypic novelty, adaptability, and fitness, which can, in turn, drive the development of unique ecological niches that promote the coexistence of multiple cytotypes. Switchgrass, Panicum virgatum, is a widespread, perennial C4 grass in North America with multiple naturally occurring cytotypes, primarily tetraploids (4×) and octoploids (8×). Using a combination of genomic, quantitative genetic, landscape, and niche modeling approaches, we detect divergent levels of genetic admixture, evidence of niche differentiation, and differential environmental sensitivity between switchgrass cytotypes. Taken together, these findings support a generalist (8×)–specialist (4×) trade-off. Our results indicate that the 8× represent a unique combination of genetic variation that has allowed the expansion of switchgrass’ ecological niche and thus putatively represents a valuable breeding resource

Marine important bird and biodiversity areas for penguins in Antarctica: Targets for conservation action

Global targets for area-based conservation and management must move beyond threshold-based targets alone and must account for the quality of such areas. In the Southern Ocean around Antarctica, a region where key biodiversity faces unprecedented risks from climate change and where there is a growing demand to extract resources, a number of marine areas have been afforded enhanced conservation or management measures through two adopted marine protected areas (MPAs). However, evidence suggests that additional high quality areas could benefit from a proposed network of MPAs. Penguins offer a particular opportunity to identify high quality areas because these birds, as highly visible central-place foragers, are considered indicator species whose populations reflect the state of the surrounding marine environment. We compiled a comprehensive dataset of the location of penguin colonies and their associated abundance estimates in Antarctica. We then estimated the at-sea distribution of birds based on information derived from tracking data and through the application of a modified foraging radius approach with a density decay function to identify some of the most important marine areas for chick-rearing adult penguins throughout waters surrounding Antarctica following the Important Bird and Biodiversity Area (IBA) framework. Additionally, we assessed how marine IBAs overlapped with the currently adopted and proposed network of key management areas (primarily MPAs), and how the krill fishery likely overlapped with marine IBAs over the past five decades. We identified 63 marine IBAs throughout Antarctic waters and found that were the proposed MPAs to be adopted, the permanent conservation of high quality areas for penguin species would increase by between 49 and 100% depending on the species. Furthermore, our data show that, despite a generally contracting range of operation by the krill fishery in Antarctica over the past five decades, a consistently disproportionate amount of krill is being harvested within marine IBAs compared to the total area in which the fishery operates. Our results support the designation of the proposed MPA network and offer additional guidance as to where decision-makers should act before further perturbation occurs in the Antarctic marine ecosystem

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

Speciation and reactivity of uranium products formed during in situ bioremediation in a shallow alluvial aquifer

In this study, we report the results of in situ U(VI) bioreduction experiments at the Integrated Field Research Challenge site in Rifle, Colorado, USA. Columns filled with sediments were deployed into a groundwater well at the site and, after a period of conditioning with groundwater, were amended with a mixture of groundwater, soluble U(VI), and acetate to stimulate the growth of indigenous microorganisms. Individual reactors were collected as various redox regimes in the column sediments were achieved: (i) during iron reduction, (ii) just after the onset of sulfate reduction, and (iii) later into sulfate reduction. The speciation of U retained in the sediments was studied using X-ray absorption spectroscopy, electron microscopy and chemical extractions. Circa 90% of the total uranium was reduced to U(IV) in each reactor. Noncrystalline U(IV) comprised about two-thirds of the U(IV) pool, across large changes in microbial community structure, redox regime, total uranium accumulation, and reaction time. A significant body of recent research has demonstrated that noncrystalline U(IV) species are more suceptible to remobilization and reoxiation than crystalline U(IV) phases such as uraninite. Our results highlight the importance of considering noncrystalline U(IV) formation across a wide range of aquifer parameters when designing in situ remediation plans