Burden of pneumocystis pneumonia in HIV-infected adults in sub-Saharan Africa: protocol for a systematic review

BACKGROUND: Reports from Africa have suggested that pneumocystis pneumonia (PCP) is a less important cause of morbidity than in the developed world. However, more recent studies have shown high seroprevalence rates of P. jirovecii in healthy individuals with HIV as well as high rates of clinical disease in African children. This suggests that PCP may be more common in Africa than was previously recognised. Understanding the contribution of PCP to disease in HIV-infected individuals in sub-Saharan Africa (SSA) has important implications for diagnosis, management and resource allocation. We therefore propose to conduct a systematic review and meta-analysis in order to investigate the burden of PCP in this population.METHODS AND DESIGN:We plan to search electronic databases and reference lists of relevant articles published from 1995 to May 2013 using broad terms for pneumocystis, HIV/AIDS and sub-Saharan Africa. Studies will be included if they provide clear diagnostic criteria for PCP and well-defined study populations or mortality data (denominator). A novel quality score assessment tool has been developed to ensure fidelity to inclusion criteria, minimise risk of selection bias between reviewers and to assess quality of outcome ascertainment. This will be applied to eligible full-text articles. We will extract data using a standardised form and perform descriptive and quantitative analysis to assess PCP prevalence, mortality and case fatality, as well as the quality of included studies. This review protocol has been published in the PROSPERO International Prospective Register of systematic reviews, registration number CRD42013005530.DISCUSSION:Our planned review will contribute to the diagnosis and management of community-acquired pneumonia in HIV-infected individuals in SSA by systematically assessing the burden of PCP in this population. We also describe a novel quality assessment tool that may be applied to other prevalence reviews

Using Remote Data Collection to Identify Bridges and Culverts Susceptible to Blockage During Flooding Events

Debris blockages of transportation-related river and stream crossing structures such as bridges and culverts can cause flooding at lower flow volumes than predicted by floodplain delineations. These types of flooding events contribute to the damage that was observed during both Tropical Storm Irene and the heavy rainfall in the spring and summer of 2013. Flooding occurs (1) when rain falls over a prolonged period of time, (2) when intense rain falls over a short period of time, or (3) when an ice or debris jam reduces the capacity of a crossing structure and causes a river or stream to overflow onto the surrounding area. The focus of this project is on the third type of flooding, specifically due to debris jams at crossing structures – culverts and bridges. Debris jams can also cause riverbank erosion, impede migration of aquatic creatures and adversely impact wildlife habitats. A new approach to mapping potential debris blockages that can produce actionable information in a timely manner at a reasonable cost would be highly valuable to Vermont agencies at many levels of government. The objectives of this project were to pilot test the use of an unmanned aerial vehicle (UAV) to gather stereo imagery of streambeds upstream of crossing structures, and develop a process of rapidly transmitting actionable information about potentially blocking material to stakeholders. A new system was developed in this project to identify potentially obstructing debris using a lightweight, easily deployable UAV. The system was pilot-tested to provide safe, timely, and cost-effective information about potentially blocking material at vulnerable bridges and culverts. A process was also developed and tested for automating detection of these potential obstructions and outputting a data table containing an extracted thumbnail image of each identified obstruction

Burden of pneumocystis pneumonia in HIV-infected adults in sub-Saharan Africa: a systematic review and meta-analysis

Abstract Background Seroprevalence data and clinical studies in children suggest that the burden of pneumocystis pneumonia (PCP) in Africa may be underestimated. We performed a systematic review to determine the prevalence and attributable mortality of PCP amongst HIV-infected adults in sub-Saharan Africa. Methods We searched Pubmed, Web of Science, Africa-Wide: NiPAD and CINAHL, from Jan 1 1995 to June 1 2015, for studies that reported the prevalence, mortality or case fatality of PCP in HIV-infected adults living in sub-Saharan African countries. Prevalence data from individual studies were combined by random-effects meta-analysis according to the Mantel-Haenszel method. Data were stratified by clinical setting, diagnostic method, and study year. Results We included 48 unique study populations comprising 6884 individuals from 18 countries in sub-Saharan Africa. The pooled prevalence of PCP among 6018 patients from all clinical settings was 15 · 4 % (95 % CI 12 · 9–18 · 0), and was highest amongst inpatients, 22 · 4 % (95 % CI 17 · 2–27 · 7). More cases were identified by bronchoalveolar lavage, 21 · 0 % (15 · 0–27 · 0), compared with expectorated, 7 · 7 % (4 · 4–11 · 1), or induced sputum, 11 · 7 % (4 · 9–18 · 4). Polymerase chain reaction (PCR) was used in 14 studies (n = 1686). There was a trend of decreasing PCP prevalence amongst inpatients over time, from 28 % (21–34) in the 1990s to 9 % (8–10) after 2005. The case fatality rate was 18 · 8 % (11 · 0–26 · 5), and PCP accounted for 6 · 5 % (3 · 7–9 · 3) of study deaths. Conclusions PCP is an important opportunistic infection amongst HIV-infected adults in sub-Saharan Africa, particularly amongst patients admitted to hospital. Although prevalence appears to be decreasing, improved access to antiretroviral therapy and non-invasive diagnostics, such as PCR, are needed

Testing Lorentz Invariance with Neutrinos from Ultrahigh Energy Cosmic Ray Interactions

We have previously shown that a very small amount of Lorentz invariance violation (LIV), which suppresses photomeson interactions of ultrahigh energy cosmic rays (UHECRs) with cosmic background radiation (CBR) photons, can produce a spectrum of cosmic rays that is consistent with that currently observed by the Pierre Auger Observatory (PAO) and HiRes experiments. Here, we calculate the corresponding flux of high energy neutrinos generated by the propagation of UHECR protons through the CBR in the presence of LIV. We find that LIV produces a reduction in the flux of the highest energy neutrinos and a reduction in the energy of the peak of the neutrino energy flux spectrum, both depending on the strength of the LIV. Thus, observations of the UHE neutrino spectrum provide a clear test for the existence and amount of LIV at the highest energies. We further discuss the ability of current and future proposed detectors make such observations.Comment: final version to appear in Astroparticle Physic

Distributed clean energy opportunities for US oil refinery operations

The oil and gas industry is increasingly seeking operational improvements to reduce costs and emissions while improving resilience. This study describes techno-economic analysis of opportunities for distributed energy resources that could be integrated to support oil and gas companies’ economic, environmental, and energy resiliency goals. Specifically, the analysis evaluates solar photovoltaics, wind turbines, battery energy storage, landfill gas, biomass, municipal solid waste-to-energy, solar steam for process heat, combined heat and power, and electrolyzers for hydrogen production at two hypothetical refineries, one located in Louisiana and the other in southern California. These technologies could reduce the sites’ consumption of grid electricity and/or natural gas and thus can help reduce emissions. This study employs the ReOPT tool and System Advisor Model to evaluate the techno-economic potential for clean energy technologies to support refineries in achieving energy goals, including energy cost savings, resiliency, and emissions reductions. Results indicate that the associated costs of emissions reductions via several distributed clean energy technologies are competitive with other emissions reduction strategies such as energy efficiency, reducing flaring, direct carbon capture and sequestration, and markets under certain conditions. There are also cost beneficial opportunities for the use of renewable energy for refining, especially for resilience, depending on local conditions such as resources and utility costs

Meeting report : 1st international functional metagenomics workshop May 7–8, 2012, St. Jacobs, Ontario, Canada

This report summarizes the events of the 1st International Functional Metagenomics Workshop. The workshop was held on May 7 and 8 in St. Jacobs, Ontario, Canada and was focused on building a core international functional metagenomics community, exploring strategic research areas, and identifying opportunities for future collaboration and funding. The workshop was initiated by researchers at the University of Waterloo with support from the Ontario Genomics Institute (OGI), Natural Sciences and Engineering Research Council of Canada (NSERC) and the University of Waterloo

The impact of interactions, bars, bulges, and AGN on star formation efficiency in local massive galaxies

Using observations from the GASS and COLD GASS surveys and complementary data from SDSS and GALEX, we investigate the nature of variations in gas depletion time observed across the local massive galaxy population. The large and unbiased COLD GASS sample allows us to assess the relative importance of galaxy interactions, bar instabilities, morphologies and the presence of AGN in regulating star formation efficiency. Both the H2 mass fraction and depletion time vary as a function of the distance of a galaxy from the main sequence in the SFR-M* plane. The longest gas depletion times are found in below-main sequence bulge-dominated galaxies that are either gas-poor, or else on average less efficient than disk-dominated galaxy at converting into stars any cold gas they may have. We find no link between AGN and these long depletion times. The galaxies undergoing mergers or showing signs of morphological disruptions have the shortest molecular gas depletion times, while those hosting strong stellar bars have only marginally higher global star formation efficiencies as compared to matched control samples. Our interpretation is that depletion time variations are caused by changes in the ratio between the gas mass traced by the CO(1-0) observations, and the gas mass in high density star-forming cores, with interactions, mergers and bar instabilities able to locally increase pressure and raise the ratio of efficiently star-forming gas to CO-detected gas. Building a sample representative of the local massive galaxy population, we derive a global Kennicutt-Schmidt relation of slope 1.18+/-0.24, and observe structure within the scatter around this relation, with galaxies having low (high) stellar mass surface densities lying systematically above (below) the mean relation, suggesting that gas surface density is not the only parameter driving the global star formation ability of a galaxy.Comment: 19 pages, 12 figures, accepted for publication in Ap

COLD GASS, an IRAM Legacy Survey of Molecular Gas in Massive Galaxies: II. The non-universality of the Molecular Gas Depletion Timescale

We study the relation between molecular gas and star formation in a volume-limited sample of 222 galaxies from the COLD GASS survey, with measurements of the CO(1-0) line from the IRAM 30m telescope. The galaxies are at redshifts 0.025<z<0.05 and have stellar masses in the range 10.0<log(M*/Msun)<11.5. The IRAM measurements are complemented by deep Arecibo HI observations and homogeneous SDSS and GALEX photometry. A reference sample that includes both UV and far-IR data is used to calibrate our estimates of star formation rates from the seven optical/UV bands. The mean molecular gas depletion timescale, tdep(H2), for all the galaxies in our sample is 1 Gyr, however tdep(H2) increases by a factor of 6 from a value of ~0.5 Gyr for galaxies with stellar masses of 10^10 Msun to ~3 Gyr for galaxies with masses of a few times 10^11 Msun. In contrast, the atomic gas depletion timescale remains contant at a value of around 3 Gyr. This implies that in high mass galaxies, molecular and atomic gas depletion timescales are comparable, but in low mass galaxies, molecular gas is being consumed much more quickly than atomic gas. The strongest dependences of tdep(H2) are on the stellar mass of the galaxy (parameterized as log tdep(H2)= (0.36+/-0.07)(log M* - 10.70)+(9.03+/-0.99)), and on the specific star formation rate. A single tdep(H2) versus sSFR relation is able to fit both "normal" star-forming galaxies in our COLD GASS sample, as well as more extreme starburst galaxies (LIRGs and ULIRGs), which have tdep(H2) < 10^8 yr. Normal galaxies at z=1-2 are displaced with respect to the local galaxy population in the tdep(H2) versus sSFR plane and have molecular gas depletion times that are a factor of 3-5 times longer at a given value of sSFR due to their significantly larger gas fractions.Comment: Accepted for publication in MNRAS. 19 pages, 11 figure