The association of HIV-1 and other sexually transmitted diseases, and its relevance to intervention programmes in rural Uganda : a simulation modelling exercise.

Since the heterosexual transmission of HIV may be enhanced in the presence of other sexually transmitted diseases (STDs), high STD prevalences in some African populations may contribute substantially to the HIV epidemic, but the magnitude of this effect is uncertain. A stochastic simulation model, SimulAIDS, was extended, and used to simulate the transmission dynamics of HIV infection and of ulcerative and non-ulcerative STDs in an attempt to mirror the development of the HIV epidemic in a rural population cohort of 10,000 under study by the MRC Programme on AIDS in Uganda. Three scenarios were compared, assuming different STD cofactor effects. Simulation results were most consistent with empirical data for a scenario that assumed enhancing effects on HIV transmission per sexual contact of 100 for ulcerative STDs and S for non-ulcerative STDs in females. A scenario assuming no STD cofactor effects was not consistent with results from the study population. By sampling from the simulated population, it was possible to assess the influence of various factors on associations between HIV and other STDs in observational studies. The most important included type of study design, choice of study sample, prevalence of STDs, misclassification of STDs, period over which STD history is recorded, and sexual behaviour characteristics. Further simulations were conducted to estimate the fraction of HIV infections in this population attributable to the cofactor effect of STDs, and to assess the relative effectiveness of differing intervention strategies. Results were consistent with STDs playing a critical role in establishing an HIV epidemic, their role decreasing as the epidemic progresses. Reducing the incidence of HIV infection in short-term sexual partnerships, through improved STD treatment, increased condom use, and a reduction in one-off sexual encounters, was found to have a substantial impact on HIV incidence in the general population

Disentangling interglacial sea level and global dynamic topography: Analysis of Madagascar

© 2019 Global inventories of stable sea-level markers for the peak of the last interglacial period, Marine Isotopic Stage (MIS) 5e, play a pivotal role in determining sea-level changes and in testing models of glacial isostatic adjustment. Here, we present surveying and radiometric dating results for emergent terraces from northern Madagascar, which is generally regarded as a stable equatorial site. Fossil coral specimens were dated using conventional and open-system corrected uranium series methods. Elevation of the upper (undated) terrace decreases from 33.8 m to 29.5 m over a distance of 35 km. An intermediate terrace has an average radiometric age of 130.7±13.2 ka (i.e. MIS 5e). Its elevation decreases from 9.3 m to 2.8 m over a distance of 80 km. The record of the lowest terrace is fragmentary and consists of beach rock containing rare corals with ages of 1.6–3.8 ka. The spatial gradient of the MIS 5e marker is inconsistent with glacio-isostatic adjustment calculations. Instead, we propose that variable elevations of this marker around Madagascar, and possibly throughout the Indian Ocean, at least partly reflect spatial patterns of dynamic topography generated by sub-plate mantle convection

Training load monitoring in team sports: A novel framework separating physiological and biomechanical load-adaptation pathways

There have been considerable advances in monitoring the training load in running-based team sports in recent years. Novel technologies nowadays offer ample opportunities to continuously monitor the activities of a player. These activities lead to internal biochemical stresses on the various physiological sub-systems. However, they also cause internal mechanical stresses on the various musculoskeletal tissues. Based on the amount and periodization of these stresses, the sub-systems and tissues adapt. So by monitoring external loads one hopes to estimate internal loads to predict adaptation, and this through understanding the load-adaptation pathways. We propose a new theoretical framework in which physiological and biomechanical load-adaptation pathways are considered separately, shedding a new light on some of the previously published evidence. We hope that it can help the various practitioners in this field (trainers, coaches, medical staff, sport scientists) to align their thoughts when considering the value of monitoring load, and that it can help researchers design experiments that can better rationalise training load monitoring for improving performance whilst preventing injury

Reasoning about goal-directed real-time teleo-reactive programs

The teleo-reactive programming model is a high-level approach to developing real-time systems that supports hierarchical composition and durative actions. The model is different from frameworks such as action systems, timed automata and TLA+, and allows programs to be more compact and descriptive of their intended behaviour. Teleo-reactive programs are particularly useful for implementing controllers for autonomous agents that must react robustly to their dynamically changing environments. In this paper, we develop a real-time logic that is based on Duration Calculus and use this logic to formalise the semantics of teleo-reactive programs. We develop rely/guarantee rules that facilitate reasoning about a program and its environment in a compositional manner. We present several theorems for simplifying proofs of teleo-reactive programs and present a partially mechanised method for proving progress properties of goal-directed agents. © 2013 British Computer Society

Estimates of tropical bromoform emissions using an inversion method

Abstract. Bromine plays an important role in ozone chemistry in both the troposphere and stratosphere. When measured by mass, bromoform (CHBr3) is thought to be the largest organic source of bromine to the atmosphere. While seaweed and phytoplankton are known to be dominant sources, the size and the geographical distribution of CHBr3 emissions remains uncertain. Particularly little is known about emissions from the Maritime Continent, which have usually been assumed to be large, and which appear to be especially likely to reach the stratosphere. In this study we aim to reduce this uncertainty by combining the first multi-annual set of CHBr3 measurements from this region, and an inversion process, to investigate systematically the distribution and magnitude of CHBr3 emissions. The novelty of our approach lies in the application of the inversion method to CHBr3. We find that local measurements of a short-lived gas like CHBr3 can be used to constrain emissions from only a relatively small, sub-regional domain. We then obtain detailed estimates of CHBr3 emissions within this area, which appear to be relatively insensitive to the assumptions inherent in the inversion process. We extrapolate this information to produce estimated emissions for the entire tropics (defined as 20° S–20° N) of 225 Gg CHBr3 yr−1. The ocean in the area we base our extrapolations upon is typically somewhat shallower, and more biologically productive, than the tropical average. Despite this, our tropical estimate is lower than most other recent studies, and suggests that CHBr3 emissions in the coastline-rich Maritime Continent may not be stronger than emissions in other parts of the tropics. M. Ashfold thanks the Natural Environment Research Council (NERC) for a research studentship, and is grateful for support through the ERC ACCI project (project number 267760). N. Harris is supported by a NERC Advanced Research Fellowship. This work was supported through the EU SHIVA project, through the NERC OP3 project, and NERC grants NE/F020341/1 and NE/J006246/1. We also acknowledge the Department of Energy and Climate Change for their support in the development of InTEM (contract GA0201). For field site support we thank S.-M. Phang, A. A. Samah and M. S. M. Nadzir of Universiti Malaya, S. Ong and H. E. Ung of Global Satria, Maznorizan Mohamad, L. K. Peng and S. E. Yong of the Malaysian Meteorological Department, the Sabah Foundation, the Danum Valley Field Centre and the Royal Society. This paper constitutes publication no. 613 of the Royal Society South East Asia Rainforest Research Programme.This is the final published version. It first appeared at http://www.atmos-chem-phys.net/14/979/2014/acp-14-979-2014.html

Studying seabird diet through genetic analysis of faeces: a case study on Macaroni Penguins (Eudyptes chrysolophus)

Determination of seabird diet usually relies on the analysis of stomach-content remains obtained through stomach flushing; this technique is both invasive and logistically difficult. We evaluate the usefulness of DNA-based faecal analysis in a dietary study on chick-rearing macaroni penguins (Eudyptes chrysolophus) at Heard Island. Conventional stomach-content data was also collected, allowing comparison of the approaches. Methodology/Principal Findings. Preyspecific PCR tests were used to detect dietary DNA in faecal samples and amplified prey DNA was cloned and sequenced. Of the 88 faecal samples collected, 39 contained detectable DNA from one or more of the prey groups targeted with PCR tests. Euphausiid DNA was most commonly detected in the early (guard) stage of chick-rearing, and detection of DNA from the myctophid fish Krefftichthys anderssoni and amphipods became more common in samples collected in the later (cre`che) stage. These trends followed those observed in the penguins’ stomach contents. In euphausiid-specific clone libraries the proportion of sequences from the two dominant euphausiid prey species (Euphausia vallentini and Thysanoessa macrura) changed over the sampling period; again, this reflected the trend in the stomach content data. Analysis of prey sequences in universal clone libraries revealed a higher diversity of fish prey than identified in the stomachs, but non-fish prey were not well represented. Conclusions/Significance. The present study is one of the first to examine the full breadth of a predator’s diet using DNA based faecal analysis. We discuss methodological difficulties encountered and suggest possible refinements. Overall, the ability of the DNA-based approach to detect temporal variation in the diet of macaroni penguins indicates this non-invasive method will be generally useful for monitoring population-level dietary trends in seabirds

The relationship between whole-body external loading and body-worn accelerometry during team sports movements

Purpose: The aim of this study was to investigate the relationship between whole-body accelerations and body-worn accelerometry during team sports movements. Methods: Twenty male team sport players performed forward running, and anticipated 45° and 90° side-cuts at approach speeds of 2, 3, 4 and 5 m·s-1. Whole-body Centre of Mass (CoM) accelerations were determined from ground reaction forces collected from one foot-ground-contact and segmental accelerations were measured from a commercial GPS/accelerometer unit on the upper trunk. Three higher specification accelerometers were also positioned on the GPS unit, the dorsal aspect of the pelvis, and the shaft of the tibia. Associations between mechanical load variables (peak acceleration, loading rate and impulse) calculated from both CoM accelerations and segmental accelerations were explored using regression analysis. In addition one-dimensional Statistical Parametric Mapping (SPM) was used to explore the relationships between peak segmental accelerations and CoM acceleration profiles during the whole foot-ground-contact. Results: A weak relationship was observed for the investigated mechanical load variables regardless of accelerometer location and task (R2 values across accelerometer locations and tasks: peak acceleration 0.08-0.55, loading rate 0.27-0.59 and impulse 0.02-0.59). Segmental accelerations generally overestimated whole-body mechanical load. SPM analysis showed that peak segmental accelerations were mostly related to CoM accelerations during the first 40-50% of contact phase. Conclusions: Whilst body-worn accelerometry correlates to whole-body loading in team sports movements and can reveal useful estimates concerning loading, these correlations are not strong. Body-worn acclerometry should therefore be used with caution to monitor whole-body mechanical loading in the field

Biomechanical loading during running: can a two mass-spring-damper model be used to evaluate ground reaction forces for high-intensity tasks?

Running impact forces expose the body to biomechanical loads leading to beneficial adaptations, but also risk of injury. High-intensity running tasks, especially, are deemed highly demanding for the musculoskeletal system, but loads experienced during these actions are not well understood. To eventually predict GRF and understand the biomechanical loads experienced during such activities in greater detail, this study aimed to (1) examine the feasibility of using a simple two mass-spring-damper model, based on eight model parameters, to reproduce ground reaction forces (GRFs) for high-intensity running tasks and (2) verify whether the required model parameters were physically meaningful. This model was used to reproduce GRFs for rapid accelerations and decelerations, constant speed running and maximal sprints. GRF profiles and impulses could be reproduced with low to very low errors across tasks, but subtler loading characteristics (impact peaks, loading rate) were modelled less accurately. Moreover, required model parameters varied strongly between trials and had minimal physical meaning. These results show that although a two mass-spring-damper model can be used to reproduce overall GRFs for high-intensity running tasks, the application of this simple model for predicting GRFs in the field and/or understanding the biomechanical demands of training in greater detail is likely limited

Sphaerosiderites as sensitive recorders of non-marine depositional and diagenetic history: Insights from the Lower Cretaceous Wealden Supergroup

Abstract: Waterlogged, reducing soils in modern and ancient wetlands feature distinctive syndepositional to early diagenetic spherical iron carbonate concretions, known as sphaerosiderites. Sphaerosiderites are thought to record pore water elemental chemistry and local palaeoenvironmental conditions, and are widely used in palaeohydrological reconstructions throughout the Phanerozoic. The Lower Cretaceous non‐marine Wealden Supergroup of Southern England, deposited in fluvio‐lacustrine settings, contains abundant well‐preserved sphaerosiderites offering an ideal archive for unravelling the geochemistry of ancient non‐marine environments. Sphaerosiderites were characterised via multiple microanalytical techniques (SEM‐EDS, EPMA, XRD, SIMS), and show morphological and compositional heterogeneity (e.g. concentric zones of variably enriched Mn, Ca or Mg, elemental differences between cores and rims) in well‐preserved sphaerosiderites from the Ashdown and Tunbridge Wells Sand formations. The preservation of primary fabrics, lack of post‐burial cements or extensive alteration suggests these sphaerosiderites record primary palaeoenvironmental conditions. By contrast, in the Wadhurst Clay Formation, sphaerosiderites are recrystallised, potentially reflecting wide scale palaeoenvironmental changes (e.g. marine incursions). New experimental constraints on elemental uptake during siderite growth suggests that rather than reflecting pore water elemental chemistry, the elemental heterogeneity in the Wealden sphaerosiderites reflects complex parameters; variations in pH, cation concentrations, DIC, growth rate and siderite saturation state in groundwaters. At a larger scale, morphological and compositional differences between sphaerosiderites from distinct palaeosol horizons record spatial and temporal variability in local hydrogeochemistry. This suggests that the Weald Basin wetlands of the Lower Cretaceous featured a dynamic and periodically fluctuating groundwater table, where sphaerosiderites growing close to the soil surface responded rapidly to variability in physiochemical conditions, consistent with wet and warm conditions suggested by sedimentological evidence and climate model simulations. Similar morphological and compositional variability noted in other Phanerozoic sphaerosiderites suggests analogous processes operated in ancient wetlands, and that sphaerosiderites could provide a crucial tool to understand wetland dynamics in deep time

The epidemiology of gonorrhoea, chlamydial infection and syphilis in four African cities.

OBJECTIVES: To compare the epidemiology of gonorrhoea, chlamydial infection and syphilis in four cities in sub-Saharan Africa; two with a high prevalence of HIV infection (Kisumu, Kenya and Ndola, Zambia), and two with a relatively low HIV prevalence (Cotonou, Benin and Yaoundé, Cameroon). DESIGN: Cross-sectional study, using standardized methods, including a standardized questionnaire and standardized laboratory tests, in four cities in sub-Saharan Africa. METHODS: In each city, a random sample of about 2000 adults aged 15-49 years was taken. Consenting men and women were interviewed about their socio-demographic characteristics and their sexual behaviour, and were tested for HIV, syphilis, herpes simplex virus type 2 (HSV-2), gonorrhoea, chlamydial infection, and (women only) Trichomonas vaginalis infection. Risk factor analyses were carried out for chlamydial infection and syphilis seroreactivity. RESULTS: The prevalence of gonorrhoea ranged between 0% in men in Kisumu and 2.7% in women in Yaoundé. Men and women in Yaoundé had the highest prevalence of chlamydial infection (5.9 and 9.4%, respectively). In the other cities, the prevalence of chlamydial infection ranged between 1.3% in women in Cotonou and 4.5% in women in Kisumu. In Ndola, the prevalence of syphilis seroreactivity was over 10% in both men and women; it was around 6% in Yaoundé, 3-4% in Kisumu, and 1-2% in Cotonou. Chlamydial infection was associated with rate of partner change for both men and women, and with young age for women. At the population level, the prevalence of chlamydial infection correlated well with reported rates of partner change. Positive syphilis serology was associated with rate of partner change and with HSV-2 infection. The latter association could be due to biological interaction between syphilis and HSV-2 or to residual confounding by sexual behaviour. At the population level, there was no correlation between prevalence of syphilis seroreactivity and reported rates of partner change. CONCLUSION: Differences in prevalence of chlamydial infection could be explained by differences in reported sexual behaviour, but the variations in prevalence of syphilis seroreactivity remained unexplained. More research is needed to better understand the epidemiology of sexually transmitted infections in Africa