The spectrum of HIV-1 related cancers in South Africa

Despite the high prevalence of infection by the Human Immunodeficiency Virus (HIV) in South Africa, information on its association with cancer is sparse. Our study was carried out to examine the relationship between HIV and a number of cancer types or sites that are common in South Africa. A total of 4,883 subjects, presenting with a cancer or cardiovascular disease at the 3 tertiary referral hospitals in Johannesburg, were interviewed and had blood tested for HIV. Odds ratios associated with HIV infection were calculated by using unconditional logistic regression models for 16 major cancer types where data was available for 50 or more patients. In the comparison group, the prevalence of HIV infection was 8.3% in males and 9.1% in females. Significant excess risks associated with HIV infection were found for Kaposi's sarcoma (OR=21.9, 95% CI=12.5–38.6), non-Hodgkin lymphoma (OR=5.0, 95%CI=2.7–9.5), vulval cancer (OR=4.8, 95%CI=1.9–12.2) and cervical cancer (OR=1.6, 95%CI=1.1–2.3) but not for any of the other major cancer types examined, including Hodgkin disease, multiple myeloma and lung cancer. In Johannesburg, South Africa, HIV infection was associated with significantly increased risks of Kaposi's sarcoma, non-Hodgkin lymphoma and cancers of the cervix and the vulva. The relative risks for Kaposi's sarcoma and non-Hodgkin lymphoma associated with HIV infection were substantially lower than those found in the West.

Robotics for the mining industry

The mining industry is highly suitable for the application of robotics and automation technology since the work is both arduous and dangerous. However, while the industry makes extensive use of mechanisation it has shown a slow uptake of automation. A major cause of this is the complexity of the task, and the limitations of existing automation technology which is predicated on a structured and time invariant working environment. Here we discuss the topic of mining automation from a robotics and computer vision perspective — as a problem in sensor based robot control, an issue which the robotics community has been studying for nearly two decades. We then describe two of our current mining automation projects to demonstrate what is possible for both open-pit and underground mining operations.

Robust sensing for a 3,500 tonne field robot

The mining industry is highly suitable for the application of robotics and automation technology since the work is arduous, dangerous and often repetitive. This paper discusses a robust sensing system developed to find and trade the position of the hoist ropes of a dragline. Draglines are large `walking cranes' used in open-pit coal mining to remove the material covering the coal seam. The rope sensing system developed uses two time-of-flight laser scanners. The finding algorithm uses a novel data association and tracking strategy based on pairing rope data.

Swing load stabilization for mining and construction applications

This paper discusses the issue of sensing and control for stabilizing a swinging load. Our work has focused in particular on the dragline as used for overburden stripping in open-pit coal mining, but many of the principles would also be applicable to construction cranes. Results obtained from experimental work on a full-scale production dragline are presented.

A comparative risk assessment of burden of disease and injury attributable to 67 risk factors and risk factor clusters in 21 regions, 1990–2010: A systematic analysis for the Global Burden of Disease Study 2010

BACKGROUND Quantification of the disease burden caused by different risks informs prevention by providing an account of health loss different to that provided by a disease-by-disease analysis. No complete revision of global disease burden caused by risk factors has been done since a comparative risk assessment in 2000, and no previous analysis has assessed changes in burden attributable to risk factors over time. METHODS We estimated deaths and disability-adjusted life years (DALYs; sum of years lived with disability [YLD] and years of life lost [YLL]) attributable to the independent effects of 67 risk factors and clusters of risk factors for 21 regions in 1990 and 2010. We estimated exposure distributions for each year, region, sex, and age group, and relative risks per unit of exposure by systematically reviewing and synthesising published and unpublished data. We used these estimates, together with estimates of cause-specific deaths and DALYs from the Global Burden of Disease Study 2010, to calculate the burden attributable to each risk factor exposure compared with the theoretical-minimum-risk exposure. We incorporated uncertainty in disease burden, relative risks, and exposures into our estimates of attributable burden. FINDINGS In 2010, the three leading risk factors for global disease burden were high blood pressure (7·0% [95% uncertainty interval 6·2-7·7] of global DALYs), tobacco smoking including second-hand smoke (6·3% [5·5-7·0]), and alcohol use (5·5% [5·0-5·9]). In 1990, the leading risks were childhood underweight (7·9% [6·8-9·4]), household air pollution from solid fuels (HAP; 7·0% [5·6-8·3]), and tobacco smoking including second-hand smoke (6·1% [5·4-6·8]). Dietary risk factors and physical inactivity collectively accounted for 10·0% (95% UI 9·2-10·8) of global DALYs in 2010, with the most prominent dietary risks being diets low in fruits and those high in sodium. Several risks that primarily affect childhood communicable diseases, including unimproved water and sanitation and childhood micronutrient deficiencies, fell in rank between 1990 and 2010, with unimproved water and sanitation accounting for 0·9% (0·4-1·6) of global DALYs in 2010. However, in most of sub-Saharan Africa childhood underweight, HAP, and non-exclusive and discontinued breastfeeding were the leading risks in 2010, while HAP was the leading risk in south Asia. The leading risk factor in Eastern Europe, most of Latin America, and southern sub-Saharan Africa in 2010 was alcohol use; in most of Asia, North Africa and Middle East, and central Europe it was high blood pressure. Despite declines, tobacco smoking including second-hand smoke remained the leading risk in high-income north America and western Europe. High body-mass index has increased globally and it is the leading risk in Australasia and southern Latin America, and also ranks high in other high-income regions, North Africa and Middle East, and Oceania. INTERPRETATION Worldwide, the contribution of different risk factors to disease burden has changed substantially, with a shift away from risks for communicable diseases in children towards those for non-communicable diseases in adults. These changes are related to the ageing population, decreased mortality among children younger than 5 years, changes in cause-of-death composition, and changes in risk factor exposures. New evidence has led to changes in the magnitude of key risks including unimproved water and sanitation, vitamin A and zinc deficiencies, and ambient particulate matter pollution. The extent to which the epidemiological shift has occurred and what the leading risks currently are varies greatly across regions. In much of sub-Saharan Africa, the leading risks are still those associated with poverty and those that affect children.

Raman and infrared spectroscopic study of turquoise minerals

Raman and infrared spectra of three well-defined turquoise samples, CuAl6(PO4)4(OH)8·4H2O, from Lavender Pit, Bisbee, Cochise county, Arizona; Kouroudaiko mine, Faleme river, Senegal and Lynch Station, Virginia were studied, interpreted and compared. Observed Raman and infrared bands were assigned to the stretching and bending vibrations of phosphate tetrahedra, water molecules and hydroxyl ions. Approximate O–H⋯O hydrogen bond lengths were inferred from the Raman and infrared spectra. No Raman and infrared bands attributable to the stretching and bending vibrations of (PO3OH)2− units were observed.

Reconstruction of a multi-vent kimberlite eruption from deposit and host rock characteristics: Jericho kimberlite, Nunavut, Canada

The Jericho kimberlite (173.1. ±. 1.3. Ma) is a small (~. 130. ×. 70. m), multi-vent system that preserves products from deep (>. 1. km?) portions of kimberlite vents. Pit mapping, drill core examination, petrographic study, image analysis of olivine crystals (grain size distributions and shape studies), and compositional and mineralogical studies, are used to reconstruct processes from near-surface magma ascent to kimberlite emplacement and alteration. The Jericho kimberlite formed by multiple eruptions through an Archean granodiorite batholith that was overlain by mid-Devonian limestones ~. 1. km in thickness. Kimberlite magma ascended through granodiorite basement by dyke propagation but ascended through limestone, at least in part, by locally brecciating the host rocks. After the first explosive breakthrough to surface, vent deepening and widening occurred by the erosive forces of the waxing phase of the eruption, by gravitationally induced failures as portions of the vent margins slid into the vent and, in the deeper portions of the vent (>. 1. km), by scaling, as thin slabs burst from the walls into the vent. At currently exposed levels, coherent kimberlite (CK) dykes (<. 40. cm thick) are found to the north and south of the vent complex and represent the earliest preserved in-situ products of Jericho magmatism. Timing of CK emplacement on the eastern side of the vent complex is unclear; some thick CK (15-20. m) may have been emplaced after the central vent was formed. Explosive eruptive products are preserved in four partially overlapping vents that are roughly aligned along strike with the coherent kimberlite dyke. The volcaniclastic kimberlite (VK) facies are massive and poorly sorted, with matrix- to clast-supported textures. The VK facies fragmented by dry, volatile-driven processes and were emplaced by eruption column collapse back into the volcanic vents. The first explosive products, poorly preserved because of partial destruction by later eruptions, are found in the central-east vent and were formed by eruption column collapse after the vent was largely cleared of country rock debris. The next active vent was either the north or south vent. Collapse of the eruption column, linked to a vent widening episode, resulted in coeval avalanching of pipe margin walls into the north vent, forming interstratified lenses of country rock-rich boulder breccias in finer-grained volcaniclastic kimberlite. South vent kimberlite has similar characteristics to kimberlite of the north vent and likely formed by similar processes. The final eruptive phase formed olivine-rich and moderately sorted deposits of the central vent. Better sorting is attributed to recycling of kimberlite debris by multiple eruptions through the unconsolidated volcaniclastic pile and associated collapse events. Post-emplacement alteration varies in intensity, but in all cases, has overprinted the primary groundmass and matrix, in CK and VK, respectively. Erosion has since removed all limestone cover.

Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls

Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed 19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with diseaseIRGM for Crohns disease, HLA for Crohns disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetesalthough in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases. © 2010 Macmillan Publishers Limited. All rights reserved.

A revisit to Pope's cohort analysis

Gulland's [Gulland, J.A., 1965. Estimation of mortality rates. Annex to Arctic Fisheries Working Group Report (meeting in Hamburg, January 1965). ICES. C.M. 1965, Doc. No. 3 (mimeographed)] virtual population analysis (VPA) is commonly used for studying the dynamics of harvested fish populations. However, it necessitates the solving of a nonlinear equation for the instantaneous rate of fishing mortality of the fish in a population. Pope [Pope, J.G., 1972. An investigation of the accuracy of Virtual Population Analysis using cohort analysis. ICNAF Res. Bull. 9, 65-74. Also available in D.H. Cushing (ed.) (1983), Key Papers on Fish Populations, p. 291-301, IRL Press, Oxford, 405 p.] eliminated this necessity in his cohort analysis by approximating its underlying age- and time-dependent population model. His approximation has since become one of the most commonly used age- and time-dependent fish population models in fisheries science. However, some of its properties are not well understood. For example, many assert that it describes the dynamics of a fish population, from which the catch of fish is taken instantaneously in the middle of the year. Such an assertion has never been proven, nor has its implied instantaneous rate of fishing mortality of the fish of a particular age at a particular time been examined, nor has its implied catch equation been derived from a general catch equation. In this paper, we prove this assertion, examine its implied instantaneous rate of fishing mortality of the fish of a particular age at a particular time, derive its implied catch equation from a general catch equation, and comment on how to structure an age- and time-dependent population model to ensure its internal consistency. This work shows that Gulland's (1965) virtual population analysis and Pope's (1972) cohort analysis lie at the opposite end of a continuous spectrum as a general model for a seasonally occurring fishery; Pope's (1972) approximation implies an infinitely large instantaneous rate of fishing mortality of the fish of a particular age at a particular time in a fishing season of zero length; and its implied catch equation has an undefined instantaneous rate of fishing mortality of the fish in a population, but a well-defined cumulative instantaneous rate of fishing mortality of the fish in the population. This work also highlights a need for a more careful treatment of the times of start and end of a fishing season in fish population models.

Laboratory investigation on the effects of overburden pressure, water, and time on slaking induced material property degradation of coal mine spoil

In open-cut strip mining, waste material is placed in-pit to minimise operational mine costs. Slope failures in these spoil piles pose a significant safety risk to personnel, along with a financial risk from loss of equipment and scheduling delays. It has been observed that most spoil pile failures occur when the pit has been previously filled with water and then subsequently dewatered. The failures are often initiated at the base of spoil piles where the material can undergo significant slaking (disintegration) over time due to overburden pressure and water saturation. It is important to understand how the mechanical properties of base spoil material are affected by slaking when designing safe spoil pile slope angles, heights, and dewatering rates. In this study, fresh spoil material collected from a coal mine in Brown Basin Coalfield of Queensland, Australia was subjected to high overburden pressure (0 – 900 kPa) under saturated condition and maintained over a period of time (0 – 6 months) allowing the material to slake. To create the above conditions, laboratory designed pressure chambers were used. Once a spoil sample was slaked under certain overburden pressure over a period of time, it was tested for classification, permeability, and strength properties. Results of this testing program suggested that the slaking of saturated coal mine spoil increase with overburden pressure and the time duration over which the overburden pressure was maintained. Further, it was observed that shear strength and permeability of spoil decreased with increase in spoil slaking.

An operational-level multi-stage mine production timetabling model for optimally synchronising drilling, blasting and excavating operations

This paper proposes a new multi-stage mine production timetabling (MMPT) model to optimise open-pit mine production operations including drilling, blasting and excavating under real-time mining constraints. The MMPT problem is formulated as a mixed integer programming model and can be optimally solved for small-size MMPT instances by IBM ILOG-CPLEX. Due to NP-hardness, an improved shifting-bottleneck-procedure algorithm based on the extended disjunctive graph is developed to solve large-size MMPT instances in an effective and efficient way. Extensive computational experiments are presented to validate the proposed algorithm that is able to efficiently obtain the near-optimal operational timetable of mining equipment units. The advantages are indicated by sensitivity analysis under various real-life scenarios. The proposed MMPT methodology is promising to be implemented as a tool for mining industry because it is straightforwardly modelled as a standard scheduling model, efficiently solved by the heuristic algorithm, and flexibly expanded by adopting additional industrial constraints.

Trial of the Primary Care Practice Improvement Tool: Building organisational performance in Australian general practice and primary health care

Objective: To nationally trial the Primary Care Practice Improvement Tool (PC-PIT), an organisational performance improvement tool previously co-created with Australian primary care practices to increase their focus on relevant quality improvement (QI) activities. Design: The study was conducted from March to December 2015 with volunteer general practices from a range of Australian primary care settings. We used a mixed-methods approach in two parts. Part 1 involved staff in Australian primary care practices assessing how they perceived their practice met (or did not meet) each of the 13 PC-PIT elements of high-performing practices, using a 1–5 Likert scale. In Part 2, two external raters conducted an independent practice visit to independently and objectively assess the subjective practice assessment from Part 1 against objective indicators for the 13 elements, using the same 1–5 Likert scale. Concordance between the raters was determined by comparing their ratings. In-depth interviews conducted during the independent practice visits explored practice managers’ experiences and perceived support and resource needs to undertake organisational improvement in practice. Results: Data were available for 34 general practices participating in Part 1. For Part 2, independent practice visits and the inter-rater comparison were conducted for a purposeful sample of 19 of the 34 practices. Overall concordance between the two raters for each of the assessed elements was excellent. Three practice types across a continuum of higher- to lower-scoring practices were identified, with each using the PC-PIT in a unique way. During the in-depth interviews, practice managers identified benefits of having additional QI tools that relate to the PC-PIT elements. Conclusions: The PC-PIT is an organisational performance tool that is acceptable, valid and relevant to our range of partners and the end users (general practices). Work is continuing with our partners and end users to embed the PC-PIT in existing organisational improvement programs.