Rigidity analysis of HIV-1 protease

We present a rigidity analysis on a large number of X-ray crystal structures of the enzyme HIV-1 protease using the 'pebble game' algorithm of the software FIRST. We find that although the rigidity profile remains similar across a comprehensive set of high resolution structures, the profile changes significantly in the presence of an inhibitor. Our study shows that the action of the inhibitors is to restrict the flexibility of the beta-hairpin flaps which allow access to the active site. The results are discussed in the context of full molecular dynamics simulations as well as data from NMR experiments.Comment: 4 pages, 3 figures. Conference proceedings for CMMP conference 2010 which was held at the University of Warwic

An online intervention for carers to manage behavioral symptoms in motor neuron disease (MiNDToolkit): A randomized parallel multi-center feasibility trial

Background: Evidence on management of behavioral symptoms in motor neuron disease (MND) is lacking. The MiNDToolkit, an online psychoeducational platform, supports carers dealing with behavioral symptoms (BehSymp). The study objectives were to ascertain recruitment and retention rates, carer and healthcare professional (HCP) use of the platform, and completion of online assessments, to inform a full-scale trial. Design: Randomized, parallel, multi-center, feasibility trial. Setting: England and Wales, across diverse MND services; recruitment from July/21 to November/22; last participant follow-up in March/23. Participants: Carers of people with motor neuron disease (PwMND) with BehSymp, recruited through MND services. After confirming eligibility, participants completed screening and baseline assessments online via the MiNDToolkit platform and were randomized centrally in a 1:1 ratio to MiNDToolkit or control. Intervention: MiNDToolkit offered tailored modules to carers for the 3-month study period. Carers in the intervention group could receive additional support from MiNDToolkit trained HCPs. The control group was offered access to the intervention at the end of the study. Data were collected on platform usage and psychosocial variables. Main outcomes: One hundred and fifty-one carers from 11 sites were invited to join the study (letter, face-to-face); 30 were screened; 29 were randomized. Fifteen people were allocated to the control arm; 14 to intervention. Carers were mostly female; median age for was 62.5 (IQR: 58, 68; intervention) and 57 (IQR: 56, 70; controls). Study retention was high (24/29 = 82.76%); carers engaged with the platform on average 14 times (median (IQR):14.0 (10.0, 18.5)) during the study period. Conclusion: The MiNDToolkit study was feasible and well accepted by carers and trained HCPs. A definitive trial is warranted

A single-particle characterization of a mobile Versatile Aerosol Concentration Enrichment System for exposure studies

BACKGROUND: An Aerosol Time-of-Flight Mass Spectrometer (ATOFMS) was used to investigate the size and chemical composition of fine concentrated ambient particles (CAPs) in the size range 0.2–2.6 μm produced by a Versatile Aerosol Concentration Enrichment System (VACES) contained within the Mobile Ambient Particle Concentrator Exposure Laboratory (MAPCEL). The data were collected during a study of human exposure to CAPs, in Edinburgh (UK), in February-March 2004. The air flow prior to, and post, concentration in the VACES was sampled in turn into the ATOFMS, which provides simultaneous size and positive and negative mass spectral data on individual fine particles. RESULTS: The particle size distribution was unaltered by the concentrator over the size range 0.2–2.6 μm, with an average enrichment factor during this study of ~5 (after dilution of the final air stream). The mass spectra from single particles were objectively grouped into 20 clusters using the multivariate K-means algorithm and then further grouped manually, according to similarity in composition and time sequence, into 8 main clusters. The particle ensemble was dominated by pure and reacted sea salt and other coarse inorganic dusts (as a consequence of the prevailing maritime-source climatology during the study), with relatively minor contributions from carbonaceous and secondary material. Very minor variations in particle composition were noted pre- and post-particle concentration, but overall there was no evidence of any significant change in particle composition. CONCLUSION: These results confirm, via single particle analysis, the preservation of the size distribution and chemical composition of fine ambient PM in the size range 0.2–2.6 μm after passage through the VACES concentration instrumentation

The influence of residential and workday population mobility on exposure to air pollution in the UK

Traditional approaches of quantifying population-level exposure to air pollution assume that concentrations of air pollutants at the residential address of the study population are representative for overall exposure. This introduces potential bias in the quantification of human health effects. Our study combines new UK Census data comprising information on workday population densities, with high spatio-temporal resolution air pollution concentration fields from the WRF-EMEP4UK atmospheric chemistry transport model, to derive more realistic estimates of population exposure to NO2, PM2.5 and O3. We explicitly allocated workday exposures for weekdays between 8:00 am and 6:00 pm. Our analyses covered all of the UK at 1 km spatial resolution. Taking workday location into account had the most pronounced impact on potential exposure to NO2, with an estimated 0.3 μg m−3 (equivalent to 2%) increase in population-weighted annual exposure to NO2 across the whole UK population. Population-weighted exposure to PM2.5 and O3 increased and decreased by 0.3%, respectively, reflecting the different atmospheric processes contributing to the spatio-temporal distributions of these pollutants. We also illustrate how our modelling approach can be utilised to quantify individual-level exposure variations due to modelled time-activity patterns for a number of virtual individuals living and working in different locations in three example cities. Changes in annual-mean estimates of NO2 exposure for these individuals were considerably higher than for the total UK population average when including their workday location. Conducting model-based evaluations as described here may contribute to improving representativeness in studies that use small, portable, automatic sensors to estimate personal exposure to air pollution

Cooperation and Contagion in Web-Based, Networked Public Goods Experiments

A longstanding idea in the literature on human cooperation is that cooperation should be reinforced when conditional cooperators are more likely to interact. In the context of social networks, this idea implies that cooperation should fare better in highly clustered networks such as cliques than in networks with low clustering such as random networks. To test this hypothesis, we conducted a series of web-based experiments, in which 24 individuals played a local public goods game arranged on one of five network topologies that varied between disconnected cliques and a random regular graph. In contrast with previous theoretical work, we found that network topology had no significant effect on average contributions. This result implies either that individuals are not conditional cooperators, or else that cooperation does not benefit from positive reinforcement between connected neighbors. We then tested both of these possibilities in two subsequent series of experiments in which artificial seed players were introduced, making either full or zero contributions. First, we found that although players did generally behave like conditional cooperators, they were as likely to decrease their contributions in response to low contributing neighbors as they were to increase their contributions in response to high contributing neighbors. Second, we found that positive effects of cooperation were contagious only to direct neighbors in the network. In total we report on 113 human subjects experiments, highlighting the speed, flexibility, and cost-effectiveness of web-based experiments over those conducted in physical labs

The sensitivities of emissions reductions for the mitigation of UK PM_2.5

The reduction of ambient concentrations of fine particulate matter (PM2.5) is a key objective for air pollution control policies in the UK and elsewhere. Long-term exposure to PM2.5 has been identified as a major contributor to adverse human health effects in epidemiological studies and underpins ambient PM2.5 legislation. As a range of emission sources and atmospheric chemistry transport processes contribute to PM2.5 concentrations, atmospheric chemistry transport models are an essential tool to assess emissions control effectiveness. The EMEP4UK atmospheric chemistry transport model was used to investigate the impact of reductions in UK anthropogenic emissions of primary PM2.5, NH3, NOx, SOx or non-methane VOC on surface concentrations of PM2.5 in the UK for a recent year (2010) and for a future current legislation emission (CLE) scenario (2030). In general, the sensitivity to UK mitigation is rather small. A 30 % reduction in UK emissions of any one of the above components yields (for the 2010 simulation) a maximum reduction in PM2.5 in any given location of  ∼  0.6 µg m−3 (equivalent to  ∼  6 % of the modelled PM2.5). On average across the UK, the sensitivity of PM2.5 concentrations to a 30 % reduction in UK emissions of individual contributing components, for both the 2010 and 2030 CLE baselines, increases in the order NMVOC, NOx, SOx, NH3 and primary PM2.5; however there are strong spatial differences in the PM2.5 sensitivities across the UK. Consequently, the sensitivity of PM2.5 to individual component emissions reductions varies between area and population weighting. Reductions in NH3 have the greatest effect on area-weighted PM2.5. A full UK population weighting places greater emphasis on reductions of primary PM2.5 emissions, which is simulated to be the most effective single-component control on PM2.5 for the 2030 scenario. An important conclusion is that weighting corresponding to the average exposure indicator metric (using data from the 45 model grids containing a monitor whose measurements are used to calculate the UK AEI) further increases the emphasis on the effectiveness of primary PM2.5 emissions reductions (and of NOx emissions reductions) relative to the effectiveness of NH3 emissions reductions. Reductions in primary PM2.5 have the largest impact on the AEI in both 2010 and the 2030 CLE scenario. The summation of the modelled reductions to the UK PM2.5 AEI from 30 % reductions in UK emissions of primary PM2.5, NH3, SOx, NOx and VOC totals 1.17 and 0.82 µg m−3 for the 2010 and 2030 CLE simulations, respectively (not accounting for non-linearity)

A Policy Maker’s Guide to Designing Payments for Ecosystem Services

Over the past five years, there has been increasing interest around the globe in payment schemes for the provision of ecosystem services, such as water purification, carbon sequestration, flood control, etc. Written for an Asian Development Bank project in China, this report provides a user-friendly guide to designing payments for the provision of ecosystem services. Part I explains the different types of ecosystem services, different ways of assessing their value, and why they are traditionally under-protected by law and policy. This is followed by an analysis of when payments for services are a preferable approach to other policy instruments. Part II explains the design issues underlying payments for services. These include identification of the service as well as potential buyers and sellers, the level of service needed, payment timing, payment type, and risk allocation. Part II contains a detailed analysis of the different types of payment mechanisms, ranging from general subsidy and certification to mitigation and offset payments. Part III explores the challenges to designing a payment scheme. These include the ability to monitor service provision, secure property rights, perverse incentives, supporting institutions, and poverty alleviation

Implementation and evaluation of updated photolysis rates in the EMEP MSC-W chemical transport model using Cloud-J v7.3e

The present work describes the implementation of the state of the art Cloud-J v7.3 photolysis rate calculation code in the EMEP MSC-W chemistry-transport model. Cloud-J calculates photolysis rates and accounts for cloud and aerosol optical properties at model run time, replacing the old system based on tabulated values. The performance of Cloud-J is evaluated against aerial photolysis rate observations made over the Pacific Ocean and against surface observations from three measurement sites in Europe. Numerical experiments are performed to investigate the sensitivity of the calculated photolysis rates to the spatial and temporal model resolution, input meteorology model, simulated ozone column, and cloud effect parameterization. These experiments indicate that the calculated photolysis rates are most sensitive to the choice of input meteorology model and cloud effect parameterization while also showing that surface ozone photolysis rates can vary by up to 20 % due to daily variations in total ozone column. Further analysis investigates the impact of Cloud-J on the oxidizing capacity of the troposphere, aerosol–photolysis interactions, and surface air quality predictions. Results find that the annual mean mass-weighted tropospheric hydroxyl concentration is increased by 26 %, while the photolytic impact of aerosols is mostly limited to large tropical biomass-burning regions. Overall, Cloud-J represents a major improvement over the tabulated system, leading to improved model performance for predicting carbon monoxide and daily maximum ozone surface concentrations

Simulating secondary organic aerosol from missing diesel-related intermediate-volatility organic compound emissions during the Clean Air for London (ClearfLo) campaign

We present high-resolution (5g kmg × g 5g km) atmospheric chemical transport model (ACTM) simulations of the impact of newly estimated traffic-related emissions on secondary organic aerosol (SOA) formation over the UK for 2012. Our simulations include additional diesel-related intermediate-volatility organic compound (IVOC) emissions derived directly from comprehensive field measurements at an urban background site in London during the 2012 Clean Air for London (ClearfLo) campaign. Our IVOC emissions are added proportionally to VOC emissions, as opposed to proportionally to primary organic aerosol (POA) as has been done by previous ACTM studies seeking to simulate the effects of these missing emissions. Modelled concentrations are evaluated against hourly and daily measurements of organic aerosol (OA) components derived from aerosol mass spectrometer (AMS) measurements also made during the ClearfLo campaign at three sites in the London area. According to the model simulations, diesel-related IVOCs can explain on average ∼30g % of the annual SOA in and around London. Furthermore, the 90th percentile of modelled daily SOA concentrations for the whole year is 3.8g μg-3, constituting a notable addition to total particulate matter. More measurements of these precursors (currently not included in official emissions inventories) is recommended. During the period of concurrent measurements, SOA concentrations at the Detling rural background location east of London were greater than at the central London location. The model shows that this was caused by an intense pollution plume with a strong gradient of imported SOA passing over the rural location. This demonstrates the value of modelling for supporting the interpretation of measurements taken at different sites or for short durations