Redistribution down under—dealing with ill-defined deaths in the Australian Burden of Disease Study

Burden of disease analyses measure the healthy years of life lost due to living with and dying prematurely from disease and injury. It is now the global standard for comparable policy-relevant evidence on the impact of disease, injuries, and risks on a population. The Australian Burden of Disease Study (ABDS), undertaken by the Australian Institute of Health and Welfare, uses Australian-specific data and methods (based on the Global Burden of Disease Study, adjusted to suit the Australian context) to quantify disease burden for Australia. Despite the high quality of deaths registration data in Australia, in burden of disease analyses not all coded causes of death are considered appropriate or valid to estimate years of life lost (YLL). Therefore, these ‘ill-defined deaths’ are redistributed to one or more diseases on the ABDS disease list according to a more probable underlying cause of death. In the latest ABDS, almost 1 in 10 deaths in 2018 was an ill-defined death. Most of these were redistributed to other diseases using one of three methods developed for the Study:

1) direct evidence on more plausible causes of death from data linkage studies or other sources

2) redistribution algorithms based on the distribution of underlying causes of death where the ill-defined cause was recorded as an associated cause of death

3) reassignment of deaths across a specified range of target diseases according to patterns of causes of death observed in the mortality data for the ABDS disease list.

Expert advice was also received on the redistribution of deaths from septicaemia and deaths coded to ICD-10 code X59 Exposure to unspecified factor. Overall, 8.5% of the years of life lost for Australia in 2018 came from ill-defined deaths. These deaths generally followed age-specific all-cause mortality patterns. It is important to consider methods and target diseases when redistributing ill-defined deaths to appropriately quantify their contribution to disease-specific burden.

Autumn destabilization of deep porewater CO2 store in a northern peatland driven by turbulent diffusion

The deep porewater of northern peatlands stores large amounts of carbon dioxide (CO2). This store is viewed as a stable feature in the peatland CO2 cycle. Here, we report large and rapid fluctuations in deep porewater CO2 concentration recurring every autumn over four consecutive years in a boreal peatland. Estimates of the vertical diffusion of heat indicate that CO2 diffusion occurs at the turbulent rather than molecular rate. The weakening of porewater thermal stratification in autumn likely increases turbulent diffusion, thus fostering a rapid diffusion of deeper porewater CO2 towards the surface where net losses occur. This phenomenon periodically decreases the peat porewater CO2 store by between 29 and 90 g C m-2 throughout autumn, which is comparable to the peatland's annual C-sink. Our results establish the need to consider the role of turbulent diffusion in regularly destabilizing the CO2 store in peat porewater.

Inequalities in life expectancy in Australia according to education level: a whole-of-population record linkage study

Background

Life expectancy in Australia is amongst the highest globally, but national estimates mask within-country inequalities. To monitor socioeconomic inequalities in health, many high-income countries routinely report life expectancy by education level. However in Australia, education-related gaps in life expectancy are not routinely reported because, until recently, the data required to produce these estimates have not been available. Using newly linked, whole-of-population data, we estimated education-related inequalities in adult life expectancy in Australia.

Methods

Using data from 2016 Australian Census linked to 2016-17 Death Registrations, we estimated age-sex-education-specific mortality rates and used standard life table methodology to calculate life expectancy. For men and women separately, we estimated absolute (in years) and relative (ratios) differences in life expectancy at ages 25, 45, 65 and 85 years according to education level (measured in five categories, from university qualification [highest] to no formal qualifications [lowest]).

Results

Data came from 14,565,910 Australian residents aged 25 years and older. At each age, those with lower levels of education had lower life expectancies. For men, the gap (highest vs. lowest level of education) was 9.1 (95 %CI: 8.8, 9.4) years at age 25, 7.3 (7.1, 7.5) years at age 45, 4.9 (4.7, 5.1) years at age 65 and 1.9 (1.8, 2.1) years at age 85. For women, the gap was 5.5 (5.1, 5.9) years at age 25, 4.7 (4.4, 5.0) years at age 45, 3.3 (3.1, 3.5) years at 65 and 1.6 (1.4, 1.8) years at age 85. Relative differences (comparing highest education level with each of the other levels) were larger for men than women and increased with age, but overall, revealed a 10–25 % reduction in life expectancy for those with the lowest compared to the highest education level.

Conclusions

Education-related inequalities in life expectancy from age 25 years in Australia are substantial, particularly for men. Those with the lowest education level have a life expectancy equivalent to the national average 15–20 years ago. These vast gaps indicate large potential for further gains in life expectancy at the national level and continuing opportunities to improve health equity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12939-021-01513-3.

67 The Evolution of A Frailty Service

Introduction

In September 2017 our frailty service was started within our medium sized DGH in North Wales. Working with our management team we secured a significant clinical resource including:

We describe how resources, setting and staffing develop over a 2 year period in order to create a service which meets the needs of the local population.

Method

The service has been in a constant state of development since it has been in operation, utilising a PDSA model with regular meetings of clinical and managerial staff to analyse performance.

Results

With each new PDSA cycle the amount of patients reviewed has increased. With the move to AMU we increased the monthly number of patients reviewed from 29 to 172 patients reviewed, 97 of which were discharged directly from the unit.

Conclusion

Using QI methodology our Frailty Service has improved dramatically since its inception. We will continue to analyse how we work to improve patient outcomes and cost effectiveness.

Current forest carbon fixation fuels stream CO2 emissions

Stream CO2 emissions contribute significantly to atmospheric climate forcing. While there are strong indications that groundwater inputs sustain these emissions, the specific biogeochemical pathways and timescales involved in this lateral CO2 export are still obscure. Here, via an extensive radiocarbon (14C) characterisation of CO2 and DOC in stream water and its groundwater sources in an old-growth boreal forest, we demonstrate that the 14C-CO2 is consistently in tune with the current atmospheric 14C-CO2 level and shows little association with the 14C-DOC in the same waters. Our findings thus indicate that stream CO2 emissions act as a shortcut that returns CO2 recently fixed by the forest vegetation to the atmosphere. Our results expose a positive feedback mechanism within the C budget of forested catchments, where stream CO2 emissions will be highly sensitive to changes in forest C allocation patterns associated with climate and land-use changes.

Public health response to an imported case of canine melioidosis

Melioidosis in humans presents variably as fulminant sepsis, pneumonia, skin infection and solid organ abscesses. It is caused by Burkholderia pseudomallei, which in the United States is classified as a select agent, with "potential to pose a severe threat to both human and animal health, to plant health or to animal and plant products" (Federal Select Agent Program, http://www.selectagents.gov/, accessed 22 September 2016). Burkholderia pseudomallei is found in soil and surface water in the tropics, especially South-East Asia and northern Australia, where melioidosis is endemic. Human cases are rare in the United States and are usually associated with travel to endemic areas. Burkholderia pseudomallei can also infect animals. We describe a multijurisdictional public health response to a case of subclinical urinary B. pseudomallei infection in a dog that had been adopted into upstate New York from a shelter in Thailand. Investigation disclosed three human contacts with single, low-risk exposures to the dog's urine at his residence, and 16 human contacts with possible exposure to his urine or culture isolates at a veterinary hospital. Contacts were offered various combinations of symptom/fever monitoring, baseline and repeat B. pseudomallei serologic testing, and antibiotic post-exposure prophylaxis, depending on the nature of their exposure and their personal medical histories. The dog's owner accepted recommendations from public health authorities and veterinary clinicians for humane euthanasia. A number of animal rescue organizations actively facilitate adoptions into the United States of shelter dogs from South-East Asia. This may result in importation of B. pseudomallei into almost any community, with implications for human and animal health.

Mercury Human Exposure in Populations Living Around Lake Tana (Ethiopia)

A survey carried out in Lake Tana in 2015 found that Hg levels in some fish species exceeded internationally accepted safe levels for fish consumption. The current study assesses human exposure to Hg through fish consumption around the Lake Tana. Of particular interest was that a dietary intake of fishes is currently a health risk for Bihar Dar residents and anglers. Hair samples were collected from three different groups: anglers, college students and teachers, and daily laborers. A questionary includes gender, age, weight, activity. Frequency of fish consumption and origin of the eaten fish were completed by each participant. Mercury concentrations in hair were significantly higher (P value <0.05) for anglers (mean ± standard deviation 0.120 ± 0.199 μg/g) than college students (mean ± standard deviation 0.018 ± 0.039 μg/g) or daily workers (mean ± standard deviation 16 ± 9.5 ng/g). Anglers consumed fish more often than daily workers and college group. Moreover, there was also a strong correlation (P value <0.05) between the logarithms of total mercury and age associated with mercury concentration in scalp hair. Mercury concentrations in the hair of men were on average twice the value of the women. Also, users of skin lightening soap on a daily basis had 2.5 times greater mercury in scalp hair than non-users. Despite the different sources of mercury exposure mentioned above, the mercury concentrations of the scalp hair of participants of this study were below levels deemed to pose a threat to health.

Peri-implantitis. Part 3: current modes of management

Peri-implantitis is an inflammatory condition fuelled by the presence of bacteria on the implant surface. As such, in a similar manner to periodontal disease management, the removal of biofilm from the implant surface should result in regression of the disease process. The optimal manner with which this is achieved has yet to be realised. This may be unsurprising due to the relative surface complexity of the implant surface when compared to natural tooth root. Other management strategies include surface decontamination, the removal of implant threads known as implantoplasty, and in severe cases the need to explant. Favourable defects can be reconstructed utilising guided bone regeneration techniques. The current review appraises some of the techniques for the management of peri-implantitis.

Management of sodium hypochlorite extrusion beyond the root apex during root canal treatment: a case report

Sodium hypochlorite (NaOCl) is most commonly used as an irrigating solution in endodontic practice. This paper describes an incident of sodium hypochlorite extrusion past the apex (SHEPA) of the UR3. Management of the condition resulted in hospitalisation of the patient, and intravenous antibiotic and steroid therapy. This case report details the measures that can be employed to reduce the risk of SHEPA and management of its potentially serious complications. The reader should understand the various measures that can be adopted to reduce extrusion of endodontic irrigants beyond the root apex and management following SHEPA.

Problems with the reconciliation of good ecological status and public participation in the Water Framework Directive

The Water Framework Directive (WFD) is an ambitious piece of legislation focused on achieving good ecological status as defined by deviations from reference conditions. Achieving good ecological status depends on collaboration between stakeholders, scientists and the public. However, public participation is restricted to consultations about implementing measures to achieve good ecological status, not in the goal setting. There are multiple, competing interpretations of good ecological status. This study addresses two of the pillars of the WFD, good ecological status and public participation. We argue that these two pillars are currently at odds when defining reference conditions for surface waters, and it is unclear how they can work together in practice. We also contend that there is an intention in the WFD to integrate these two pillars, but there is no legal support for their connection. In a case study of a small boreal lake in Sweden, we show that local people possess a great deal of historical knowledge, which they use to conceptualize reference conditions. Their conceptualizations are compared with fish and water chemistry monitoring by the regulatory authority as well as paleolimnological reconstructions of water quality dating back to the beginning of the 20th century. The knowledge that the local people have corresponds to the historical data available for the lake, particularly with water clarity. We highlight the subjective nature of the concept of 'undisturbed state' to show that it varies depending on values, knowledge and perceptions of lay-people, scientists and relevant authorities. The subjectivity of the concept of undisturbed state promises to be a way of linking the two pillars of the WFD.

Congenital abnormalities at a tertiary center in Jamaica: an 18-month maternal-fetal medicine experience

OBJECTIVE

The objective of this study was to compare outcomes of patients with prenatally versus postnatally diagnosed congenital abnormalities seen during the first 18 months of a recently established MFM unit.

METHODS

Hospital charts of all congenital abnormalities diagnosed between July 2008 and December 2009 were reviewed. Data collected included: maternal demographics, perinatal outcome, neonatal mortality and morbidity as defined in the Radius trial.

RESULTS

Fifty-five pregnancies with 57 anomalous fetuses were identified: 13 (23%) postnatally and 44 (77%) prenatally. Most frequent postnatally diagnosed anomalies were gastrointestinal (33%), central nervous system (CNS) (16%) and cardiac (16%); whereas prenatally diagnosed were CNS (29%) and genitourinary (23%). Mothers postnatally diagnosed had a 12 kg (17%) greater mean weight; 12 (92%) had anomaly scans reported as normal; birth weight and moderate neonatal morbidity were statistically greater (2.8 vs. 2.13 kg, p < 0.02) and (9/12 vs. 11/29, p < 0.03), respectively. Neonatal morbidity was 6.2 times more likely in the postnatally diagnosed group adjusting for birth weight, gestational age and route of delivery [OR (95% CI) 6.2, (1.2-32.4), p = 0.03].

CONCLUSIONS

Most abnormalities were diagnosed prenatally; however, the majority of postnatally diagnosed had false negative anomaly scans and experienced significantly more moderate neonatal morbidity.

Screening for acute HIV infection in South Africa: finding acute and chronic disease

BACKGROUND

The yield of screening for acute HIV infection among general medical patients in resource-scarce settings remains unclear. Our objective was to evaluate the strategy of using pooled HIV plasma RNA to diagnose acute HIV infection in patients with negative or discordant rapid HIV antibody tests in Durban, South Africa.

METHODS

We prospectively enrolled patients with negative or discordant rapid HIV antibody tests from a routine HIV screening programme in an out-patient department in Durban with an HIV prevalence of 48%. Study participants underwent venipuncture for pooled qualitative HIV RNA, and, if this was positive, quantitative RNA, enzyme immunoassay and Western blot (WB). Patients with negative or indeterminate WB and positive quantitative HIV RNA were considered acutely infected. Those with chronic infection (positive RNA and WB) despite negative or discordant rapid HIV tests were considered to have had false negative rapid antibody tests.

RESULTS

Nine hundred and ninety-four participants were enrolled with either negative (n=976) or discordant (n=18) rapid test results. Eleven [1.1%; 95% confidence interval (CI) 0.6-2.0%] had acute HIV infection, and an additional 20 (2.0%; 95% CI 1.3-3.1%) had chronic HIV infection (false negative rapid test).

CONCLUSIONS

One per cent of out-patients with negative or discordant rapid HIV tests in Durban, South Africa had acute HIV infection readily detectable through pooled serum HIV RNA screening. Pooled RNA testing also identified an additional 2% of patients with chronic HIV infection. HIV RNA screening has the potential to identify both acute and chronic HIV infections that are otherwise missed by standard HIV testing algorithms.

The use of MTA in the modern management of teeth affected by dens invaginatus

Dens invaginatus is a dental anomaly that can result in loss of tooth vitality and the need for root canal treatment. The pulpal morphology of these teeth can be complex which makes successful root canal treatment difficult to achieve. To maintain vitality attempts have been made to prophylactically treat these teeth by sealing the invagination with a variety of materials. This paper describes the use of mineral trioxide aggregate (MTA) in both the prophylactic treatment of teeth with minor invaginations and the incorporation of MTA in the final obturation of non-vital teeth with invaginations with grossly atypical morphology.

Dens invaginatus. Part 1: classification, prevalence and aetiology

AIM

To review and discuss the aetiology, prevalence and classification of this dental anomaly together with the morphology of an invagination and the most appropriate nomenclature.

SUMMARY

This review considers the different possible nomenclatures and concludes that dens invaginatus is the most appropriate description. The paper highlights the different reported prevalence figures and concludes that the problem is probably one of the most common of the dental developmental abnormalities with maxillary lateral incisors most commonly affected. The paper suggests that the classification system described by Oehlers (1957a) is probably the most clinically relevant and that the morphological features associated with this problem may increase the risk of pulpal pathology developing and complicate any possible endodontic treatment.

KEY LEARNING POINTS

* The aetiology of dens invaginatus is still unknown, although there is some evidence that it may be genetic in origin. * The problem is probably more prevalent than most clinicians are aware of and this is because of the diagnostic difficulties associated with the anomaly. * The nature of the problem may increase the risk of pulp disease and complicate any root canal treatment.

Testing the steady-state water chemistry model predictions of pre-industrial lake pH with paleolimnological data from northern Sweden

Criteria are needed for distinguishing naturally acid water from that acidified by air pollution, especially in the organic-rich waters of northern Sweden. The Steady-State Water Chemistry Model (SSWC) was augmented to include organic acidity so that it could predict pre-industrial pH in organic-rich waters. The resulting model predictions of pre-industrial ANC and pH were then tested against diatom predictions of pre-industrial pH and alkalinity in 58 lakes from N. Sweden (after alkalinity was converted to ANC using the CBALK method). The SSWC Model's predictions of pre-industrial lake pH in N. Sweden did not correspond well with the diatom predictions, even when accounting for the uncertainty in the diatom model. This was due to the SSWC's sensitivity to short-term fluctuations in contemporary water chemistry. Thus the SSWC Model is not suitable for judging the acidification of individual lakes in areas such as northern Sweden where the degree of chronic acidification is small, or without a good average value of contemporary water chemistry. These results should be considered when assessing the accuracy of critical loads calculated using SSWC.

Targeting of a CD8 T cell env epitope presented by HLA-B*5802 is associated with markers of HIV disease progression and lack of selection pressure

In HIV-infected persons, certain HLA class I alleles are associated with effective control of viremia, while others are associated with rapid disease progression. Among the most divergent clinical outcomes are the relatively good prognosis in HLA-B*5801 expressing persons and poor prognosis with HLA-B*5802. These two alleles differ by only three amino acids in regions involved in HLA-peptide recognition. This study evaluated a cohort of over 1000 persons with chronic HIV clade C virus infection to determine whether clinical outcome differences associated with B*5801 (n = 93) and B*5802 ( n = 259) expression are associated with differences in HIV-1-specific CD8 (+) T cell responses. The overall breadth and magnitude of HIV-1-specific CD8(+) T cell responses were lower in persons expressing B*5802, and epitope presentation by B*5802 contributed significantly less to the overall response as compared to B*5801-restricted CD8 (+) T cells. Moreover, viral load in B*5802-positive persons was higher and CD4 cell counts lower when this allele contributed to the overall CD8 (+) T cell response, which was detected exclusively through a single epitope in Env. In addition, persons heterozygous for B*5802 compared to persons homozygous for other HLA-B alleles had significantly higher viral loads. Viral sequencing revealed strong selection pressure mediated through B*5801-restricted responses but not through B*5802. These data indicate that minor differences in HLA sequence can have a major impact on epitope recognition, and that selective targeting of Env through HLA-B*5802 is at least ineffectual if not actively adverse in the containment of viremia. These results provide experimental evidence that not all epitope-specific responses contribute to immune containment, a better understanding of which is essential to shed light on mechanisms involved in HIV disease progression.

Apexification with mineral trioxide aggregate: an overview of the material and technique

Mineral Trioxide Aggregate (MTA) was introduced as an alternative to traditional materials for the repair of root perforations, pulp-capping and as a retrograde root filling due to its superior biocompatibilty and ability to seal the root canal system. Traditionally, calcium hydroxide has been the material of choice for the apexification of immature permanent teeth but MTA holds significant promise as an alternative to multiple treatments with calcium hydroxide. The paper discusses the use of calcium hydroxide as a traditional apexification material and provides an overview of the composition, properties and applications of Mineral Trioxide Aggregate with emphasis on its use in apexification of immature permanent teeth. A case report is presented to highlight its use.

Modelling the effect of climate change on recovery of acidified freshwaters: relative sensitivity of individual processes in the MAGIC model

The MAGIC model was used to evaluate the relative sensitivity of several possible climate-induced effects on the recovery of soil and surface water from acidification. A common protocol was used at 14 intensively studied sites in Europe and eastern North America. The results show that several of the factors are of only minor importance (increase in pCO(2) in soil air and runoff, for example), several are important at only a few sites (seasalts at near-coastal sites, for example) and several are important at nearly all sites (increased concentrations of organic acids in soil solution and runoff, for example). In addition changes in forest growth and decomposition of soil organic matter are important at forested sites and sites at risk of nitrogen saturation. The trials suggest that in future modelling of recovery from acidification should take into account possible concurrent climate changes and focus specially on the climate-induced changes in organic acids and nitrogen retention.

Association between polymorphisms of the GPX1 gene and second primary tumours after index squamous cell cancer of the head and neck

We investigated the association between genetic polymorphisms in GPX1 gene amongst patients who had index squamous cell carcinoma (SCCHN) and a second primary tumour (SPT) after a primary SCCHN in a case-control study. GPX1 genotypes were determined for 61 patients with SPT and for 259 control subjects by a PCR technique using a fluorescent-labelled primer. Analysis was by an ABI automated fluorescent sequencer. The associations between specific genotypes and the development of SPT were examined by logistic regression. A significant difference was found between the control group and the SPT cases in allele frequencies of GPX1 ALA( *)6 and ALA( *)7 (p(trend)=0.04). These results suggest that polymorphisms in the GPX1 gene may be a marker for SPT development and further studies are indicated.

An assessment of the management of patients on warfarin by general dental practitioners in South West Wales

For anticoagulation therapy, warfarin is used to reduce the risk of thrombo-embolic events in patients with mechanical prosthetic heart valves, certain cardiovascular conditions, deep vein thrombosis (DVT) and hypercoagulable states.(1). The International Normalised Ratio (INR) is used as a measure of anticoagulation and is expressed as a ratio of the patient's prothrombin time (PT) to control prothrombin time. In a person with a normal PT, the INR is approximately 1. The therapeutic range is the value of INR or degree of anticoagulation required to prevent the development of serious thrombo-embolism and is normally maintained between 2.0 and 4.5. It is important to recognize that the INR is only valid for patients on well controlled anticoagulant therapy, ie where the level of anticoagulation is reasonably stable over a moderate length of time.(2).

Modeling surface water critical loads with PROFILE: possibilities and challenges

The critical load concept has become a valuable tool for policymakers in the European negotiations on emission reductions. Despite the international acceptance, ongoing validation of critical load methodology is of the utmost importance to avoid a situation where the calculation results are difficult to defend. In this paper we explore the potential of using the steady state soil chemistry model PROFILE as an alternative to the Steady State Water Chemistry (SSWC) method for calculating critical loads of acidity. The hypothesis is that the uncertainty in prediction of preindustrial leaching of base cations is reduced when soil properties instead of lake chemistry are used as input data. Paleolimnological reconstructions of preindustrial lake chemistry are used to test PROFILE. As PROFILE requires soil data that are not generally available on a catchment level, we used distributions of crucial parameters from soil survey data within the vicinity of five lakes for which paleoecological pH reconstructions were available. An important concern is the characterization of catchment hydrology. A calibration of the "effective" soil depth, needed to give PROFILE predictions that coincided with paleolimnology, suggested that approximately 0.6 m of the total soil depth was hydrologically active in supplying acid neutralizing capacity (ANC) to runoff through weathering. At present, there is insufficient evidence to either recommend or reject the PROFILE model for surface water critical loads. Before such a judgement can be made, the approach presented here has to be tested for other regions, and the definition of catchment hydrology needs to be investigated further.

Ecstasy related periodontitis and mucosal ulceration -- a case report

Methylenedioxymethamphetamine (MDMA) more commonly known as 'Ecstasy' is a widely used recreational drug. The oral and systemic effects associated with its use have been well documented. This paper highlights a previously unreported complication of MDMA use on the oral mucosa. MDMA periodontitis is illustrated with a case report and the local oral and systemic effects of MDMA use outlined.

Molecular characteristics of human immunodeficiency virus type 1 subtype C viruses from KwaZulu-Natal, South Africa: implications for vaccine and antiretroviral control strategies

The KwaZulu-Natal region of South Africa is experiencing an explosive outbreak of human immunodeficiency virus type 1 (HIV-1) subtype C infections. Understanding the genetic diversity of C viruses and the biological consequences of this diversity is important for the design of effective control strategies. We analyzed the protease gene, the first 935 nucleotides of reverse transcriptase, and the C2V5 envelope region of a representative set of 72 treatment-naïve patients from KwaZulu-Natal and correlated the results with amino acid signature and resistance patterns. Phylogenetic analysis revealed multiple clusters or "lineages" of HIV-1 subtype C that segregated with other C viruses from southern Africa. The same pattern was observed for both black and Indian subgroups and for retrospective specimens collected prior to 1990, indicating that multiple sublineages of HIV-1 C have been present in KwaZulu-Natal since the early stages of the epidemic. With the exception of three nonnucleoside reverse transcriptase inhibitor mutations, no primary resistance mutations were identified. Numerous accessory polymorphisms were present in the protease, but none were located at drug-binding or active sites of the enzyme. One frequent polymorphism, I93L, was located near the protease/reverse transcriptase cleavage site. In the envelope, disruption of the glycosylation motif at the beginning of V3 was associated with the presence of an extra protein kinase C phosphorylation site at codon 11. Many polymorphisms were embedded within cytotoxic T lymphocyte or overlapping cytotoxic T-lymphocyte/T-helper epitopes, as defined for subtype B. This work forms a baseline for future studies aimed at understanding the impact of genetic diversity on vaccine efficacy and on natural susceptibility to antiretroviral drugs.

CHEK2 variants in susceptibility to breast cancer and evidence of retention of the wild type allele in tumours

We have recently shown that the CHEK2*1100delC mutation acts as a low penetrance breast cancer susceptibility allele. To investigate if other CHEK2 variants confer an increased risk of breast cancer, we have screened an affected individual with breast cancer from 68 breast cancer families. Five of these individuals were found to harbour germline variants in CHEK2. Three carried the 1100delC variant (4%). One of these three individuals also carried the missense variant, Arg180His. In the other two individuals, missense variants, Arg117Gly and Arg137Gln, were identified. These two missense variants reside within the Forkhead-associated domain of CHEK2, which is important for the function of the expressed protein. None of these missense variants were present in 300 healthy controls. Microdissected tumours with a germline mutation showed loss of the mutant allele suggesting a mechanism for tumorigenesis other than a loss of the wild type allele. This study provides further evidence that sequence variation in CHEK2 is associated with an increased risk of breast cancer, and implies that tumorigenesis in association with CHEK2 mutations does not involve loss of the wild type allele.

Prevalence, incidence, and mother-to-child transmission of HIV-1 in rural South Africa

Simple, robust approaches are needed to monitor prevalence, incidence, and mother-to-child transmission of HIV-1 in rural Africa. We have designed a method that uses antibody and viral RNA testing of dried blood spots obtained from mother-infant pairs attending routine immunisation clinics. In our study, prevalence and incidence of HIV-1 was highest in young women in their late teens and early twenties. In children born to infected mothers, prevalence increased from 14% in infants younger than 6 weeks of age to 24% at 3-6 months. The blood-spot approach is an effective method for surveillance of HIV-1 in women and children, and for early identification of incidence of this infection in women of child-bearing age.

Gram-stain diagnosis of bacterial vaginosis after rupture of membranes

Correlation of the Gram stains prior to and after rupture of the membranes (ROM) and the efficacy of Gram-stain diagnosis for bacterial vaginosis (BV) after membrane rupture has not previously been evaluated. From April 1997 to May 1998, women presenting in labor or for labor induction were invited to participate. Women with ROM prior to hospital presentation or contraindications for vaginal delivery were excluded. A Gram stain of vaginal secretions was obtained prior to and approximately 2 hours after ROM. BV was diagnosed with a Nugent score of 7-10. The Gram stain prior to and after membrane rupture was evaluated using the Spearman correlation coefficient. Population characteristics (n = 91) included maternal age of 15 to 38 years, 45 (49%) nulliparas, 59 (65%) African-Americans, 23 (25%) Hispanics, 7 (8%) Caucasian, and 2 (2%) Asians. Gestational age upon study entry was 35 to 44 weeks. Twenty-one percent (19 of 91) of the study population was diagnosed with BV. Using the Gram stain prior to membrane rupture as the standard, the efficacy of the Gram stain after ROM had a sensitivity of 26%, specificity of 97%, positive predictive value of 71%, and negative predicative value of 83%. Good correlation of pre- and post-membrane rupture Gram stains was demonstrated (r = 0.69). Gram stain may be useful for ruling out BV in the presence of membrane rupture, but is not useful for diagnosing BV due to poor sensitivity.

Comparison of PCR-heteroduplex characterization by automated DNA sequencing and line probe assay for the detection of rifampicin resistance in Mycobacterium tuberculosis isolates from KwaZulu-Natal, South Africa

Progress in understanding the basis of resistance to rifampicin (RifR) has allowed molecular tests for the detection of drug-resistant tuberculosis to be developed. One hundred thirteen strains of Mycobacterium tuberculosis isolated from patients with multidrug resistant tuberculosis (MDR-TB) were investigated for genotypic analysis of RifR by polymerase chain reaction-heteroduplex formation (PCR-HDF) and characterization of mutations by automated DNA sequencing of the rpoB gene. A subset of isolates (22) representative of different mutations as confirmed by sequence analysis were also evaluated by the Line Probe Assay (LiPA). In 106 of the RifR strains, 24 mutations within an 81-bp region of the rpoB gene affecting 13 amino acids were observed. Most isolates (7/8) harboring Leu533 --> Pro codon mutation required minimum inhibitory concentrations (MICs) of < or = 8 microg/ml. There was geographic variation in the frequency of occurrence of particular rpoB mutations, with the Ser531 --> Leu/Trp codon mutation found in 59/113 of isolates. Although there are certain limitations in the use of both the rapid PCR-HDF diagnostic assay and the LiPA for the detection of rifampicin susceptibility of M. tuberculosis, these provide important and convenient tools for identifying and managing patients with MDR-TB.

Identification of amino acid residues of influenza virus nucleoprotein essential for RNA binding

The influenza virus nucleoprotein (NP) is a single-strand-RNA-binding protein associated with genome and antigenome RNA and is one of the four virus proteins necessary for transcription and replication of viral RNA. To better characterize the mechanism by which NP binds RNA, we undertook a physical and mutational analysis of the polypeptide, with the strategy of identifying first the regions in direct contact with RNA, then the classes of amino acids involved, and finally the crucial residues by mutagenesis. Chemical fragmentation and amino acid sequencing of NP that had been UV cross linked to radiolabelled RNA showed that protein-RNA contacts occur throughout the length of the polypeptide. Chemical modification experiments implicated arginine but not lysine residues as important for RNA binding, while RNA-dependent changes in the intrinsic fluorescence spectrum of NP suggested the involvement of tryptophan residues. Supporting these observations, single-codon mutagenesis identified five tryptophan, one phenylalanine, and two arginine residues as essential for high-affinity RNA binding at physiological temperature. In addition, mutants unable to bind RNA in vitro were unable to support virus gene expression in vivo. The mutationally sensitive residues are not localized to any particular region of NP but instead are distributed throughout the protein. Overall, these data are inconsistent with previous models suggesting that the NP-RNA interaction is mediated by a discrete N-terminal domain. Instead, we propose that high-affinity binding of RNA by NP requires the concerted interaction of multiple regions of the protein with RNA and that the individual protein-RNA contacts are mediated by a combination of electrostatic interactions between positively charged residues and the phosphate backbone and planar interactions between aromatic side chains and bases.