Estimating prevalence of injecting drug use in an urban population: limitations of the three-sample estimation procedure.
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Humans↗
Biomedical subjects
R J Hayes
Publications and source records attributed to R J Hayes.
Cooperative binding of the red clover necrotic mosaic virus movement protein to single-stranded nucleic acids.
The movement protein of red clover necrotic mosaic dianthovirus was produced in Escherichia coli using an expression vector. Gel retardation analysis and u.v. cross-linking studies showed that the movement protein bound cooperatively to ssRNA and ssDNA, but not to dsDNA. Binding competition experiments established that the movement protein bound to ssRNA and ssDNA with similar affinities and that the binding was not sequence-specific in the experimental conditions employed. A truncated movement protein lacking the C-terminal 88 amino acids was also shown to bind to ssRNA.
Binding, Competitive↗
Complete replication of a satellite RNA in vitro by a purified RNA-dependent RNA polymerase.
The 334 nucleotide R satellite RNA was used as a template for purified RNA-dependent RNA polymerase (RdRp) from cucumber mosaic virus-infected tobacco plants. The products of the reaction were dsRNA and positive-strand RNA of the same size as the R satellite RNA. Similar products were obtained when T7 RNA polymerase positive-strand transcripts of a cDNA clone of the satellite RNA, designed to have the same 5' and 3' ends as the satellite RNA, were used as templates. The formation of the positive strands demonstrates complete replication of the satellite RNA. A positive-strand transcript with 65 and 255 additional nucleotides at the 5' and 3' ends of the satellite RNA respectively was also utilized as a template by the RdRp, but only dsRNA was formed. However, no products could be detected when the RdRp was programmed with transcripts corresponding to the negative-strand satellite RNA, either with no additional terminal nucleotides or with 24 and 310 additional nucleotides at the 5' and 3' ends respectively.
Base Sequence↗
Case-control studies of severe malaria.
The majority of children infected with Plasmodium falciparum in areas of stable endemicity do not develop severe, life-threatening disease. It is important to identify risk factors for the minority who do. Case-control studies in which children with severe disease are compared with children with non-severe disease and with community controls, avoid some of the ethical and logistical problems inherent in such an undertaking. This paper discusses methodological aspects of case-control studies of severe malaria including case and control definitions, selection of cases and controls, potential risk factors, sample size calculations and analysis. Although specifically concerned with malaria, many of these issues are equally relevant to case-control studies of other infectious and parasitic diseases in a tropical environment.
Case-Control Studies↗
Epidemiological and public health considerations in the design of HIV vaccine trials.
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AIDS Vaccines↗
Complete replication of a eukaryotic virus RNA in vitro by a purified RNA-dependent RNA polymerase.
A soluble RNA-dependent RNA polymerase was isolated from Nicotiana tabacum plants infected with cucumber mosaic virus (CMV), which has a genome of three positive-strand RNA components, 1, 2, and 3. The purified polymerase contained two virus-encoded polypeptides and one host polypeptide. Polymerase activity was completely dependent on addition of CMV RNA as template, and the products of reaction were single-stranded (ss) RNA and double-stranded (ds) RNA, corresponding to RNAs 1, 2, and 3, and a subgenomic RNA (RNA 4) derived from RNA 3. The ratio of ssRNA to dsRNA was about 5:1, and the ssRNA was shown to be predominantly the positive strand. This demonstrates the complete replication of a eukaryotic virus RNA in vitro by a template-dependent RNA polymerase.
Base Sequence↗
Impact of HIV on tuberculosis in Zambia: a cross sectional study.
OBJECTIVE: To examine the contribution of HIV infection to the apparently increasing incidence of tuberculosis in central Africa. DESIGN: Cross sectional study. SETTING: Outpatient clinic in teaching hospital, Lusaka, Zambia. PATIENTS: 346 Adult patients with tuberculosis. RESULTS: Overall, 206 patients (60%; 95% confidence interval 54% to 65%) were positive for HIV: in one or both assays used. The peaks for both tuberculosis and HIV infection were among men aged 25-34 years and women aged 14-24 years. Of patients with confirmed pulmonary tuberculosis, 73/149 (49%; 41% to 57%) were positive for HIV; 67/83 (81%; 70% to 89%) patients with pleural disease and 16/19 (84%; 60% to 97%) patients with pericardial disease were positive. HIV positive patients with positive sputum culture were less likely to have had a positive sputum smear, and their chest x ray films less often showed classic upper zone disease or cavitation. Of 72 patients who fulfilled clinical criteria for AIDS, 17 were negative for HIV. CONCLUSIONS: The high prevalence of HIV in patients with tuberculosis suggests that an epidemic of reactivating tuberculosis is arising in those who are infected with HIV. The redirection of public health priorities towards tuberculosis would focus on a major treatable and preventable complication of the AIDS epidemic.
Adolescent↗
Leptospiral infection: a household serosurvey in urban and rural communities in Barbados and Trinidad.
A longitudinal study of leptospiral agglutinins in subjects five years of age and over was undertaken in Trinidad and Barbados between 1980 and 1982. Households were sampled randomly from one urban and two rural communities on each island, giving a total of 576 eligible individuals in Barbados and 524 in Trinidad. Participants were examined three times at approximately annual intervals. The prevalence of seropositivity at a titre of 1:50 using the microscopic agglutination test was 18.5% in Barbados and 21.9% in Trinidad. Prevalence increased steeply with age in both sexes and was higher in males than females on both islands. There was a marked difference in predominating serogroups on the two islands--Autumnalis (42% of positive cases) predominated in Barbados while Bataviae (29% of positive cases) predominated in Trinidad. Estimates of incidence rates for seroconversion were 2.9% per annum for Barbados and 3.5% per annum for Trinidad. Occupational risk varied between the islands, but in both cases highest seropositivity rates (greater than 50%) were found in outdoor labourers and lowest were found in indoor non-manual workers and urban homeworkers. In Barbados seroprevalence was higher among persons who cleared drains or who had contact with livestock. Lack of an inside toilet was associated with an increase in seropositivity on both islands. There was little evidence of household clustering of seropositive cases.
Adolescent↗
Epidemiological methods to study the interaction between HIV infection and other sexually transmitted diseases.
Numerous studies performed over the past 5 years have indicated an association between HIV infection and other sexually transmitted diseases (STDs), particularly those involving genital ulceration. Such an association may be causal, indicating that STDs increase susceptibility to, or infectivity of, HIV infection or may result, in whole or in part, from the mutual dependence of HIV and STDs on patterns of sexual activity, or from an effect of HIV infection on the clinical course of STDs. In this paper we discuss the issues arising in the design and analysis of studies conducted to investigate this association. A numerical illustration is used to demonstrate non-causal associations that may arise in observational studies due to confounding and misclassification. Published cross-sectional and longitudinal studies are reviewed, and recommendations made for future studies. Special emphasis is given to the use of randomized intervention trials to overcome many of the biases associated with observational studies, and to provide information on the efficacy of intensive STD treatment programmes in reducing the transmission of HIV.
Cross-Sectional Studies↗
Infectious cucumber mosaic virus RNA transcribed in vitro from clones obtained from cDNA amplified using the polymerase chain reaction.
Full-length cDNA to RNA 1, RNA 2 and RNA 3 of cucumber mosaic virus strain Q (CMV-Q) was amplified using the polymerase chain reaction (PCR). The first-strand primer contained a BamHI site and sequences complementary to the 3' terminus of the RNA. The second-strand primers contained a BamHI site, a T7 promoter and sequences corresponding to the 5' terminus of each RNA. After cleavage with BamHI, the PCR products were cloned into the BamHI site of the vector pEMBL9(+). Five clones of each RNA were selected and RNA transcripts were synthesized in vitro from each clone using T7 RNA polymerase. The constructs were designed to allow transcription to initiate precisely at the 5' terminus of each RNA. All the transcripts were found to be infectious when inoculated onto Nicotiana tabacum cv. Samsun plants in sets of three, corresponding to RNA 1, RNA 2 and RNA 3. Of the transcript sets, four induced symptoms indistinguishable from symptoms induced by CMV-Q RNAs. However a fifth transcript set induced much more severe symptoms. Plasmids were also constructed to allow synthesis of transcripts with one or two additional G residues at the 5' terminus of each RNA. Although the yields of such transcripts synthesized in vitro with T7 RNA polymerase were higher, their infectivity was lower than that of those with no additional residues at their 5' termini.
Base Sequence↗
[Estimate of the incidence rates of chronic parasitosis and infections based on the prevalence: Chagas disease in Latin America].
A simple method is described for using prevalence data to estimate the incidence of chronic infections. The incidence rate is estimated as the prevalence rate multiplied by the crude birth rate. The method is applicable to infections which are detectable for life and which have little effect on mortality. Strictly, it is valid only if infection occurs at or shortly after birth, but we show that little error results if infections occur gradually over the first two decades of life. A method of refining the incidence estimate, when age-specific prevalence data are available, is also given. The methods are illustrated using data on Chagas' disease in Latin America.
Age Factors↗
Testing for the random occurrence of sickle cell disease in a study of 100,000 Jamaican newborns.
In a screening programme for sickle cell haemoglobinopathies at a maternity hospital in Kingston, Jamaica, 100,000 newborns were screened with the detection of 315 cases of SS disease, and 201 cases of SC disease. There was no upward or downward trend in the frequency of SS or SC births during the screening programme. The sequence numbers of the SS and SC births were analysed to examine whether these cases were randomly distributed among the 100,000 newborns. The occurrence of SS births seems to accord well with the random model but there was an excess of very long intervals between SC births.
Anemia, Sickle Cell↗
Evaluation of a primary health care programme in The Gambia. II. Its impact on mortality and morbidity in young children.
Mortality and morbidity in children under 5 years of age were measured in 41 villages and hamlets in a rural area of The Gambia for a 1-year period before and for a 3-year period after the introduction of a primary health care (PHC) programme into 15 of the larger villages in the area. Both infant mortality and child mortality rates fell during the post-intervention period but declines were similar in PHC and in non-PHC villages suggesting that factors such as an up-grading of the Farafenni dispensary, improvements in transport and the survey itself may have played an important part in bringing about these changes. Measurements of morbidity showed a lower prevalence of diarrhoea, vomiting or severe cough in PHC villages after the introduction of the PHC programme. Introduction of the PHC programme had no significant effect on nutritional status or on vaccine coverage. Significant improvements in the health of children in the Farafenni study area have taken place during the past 5 years but the PHC programme is probably only one of the factors that have brought about these changes.
Child Health Services↗
Replication of tomato golden mosaic virus DNA B in transgenic plants expressing open reading frames (ORFs) of DNA A: requirement of ORF AL2 for production of single-stranded DNA.
Tomato golden mosaic geminivirus has a genome of two single-stranded (ss) DNA components, A and B. An almost identical 'common' region in DNA A and DNA B is thought to contain sequence elements controlling replication and transcription. Hence investigation of sequences important for DNA replication by in vitro mutagenesis is complicated by possible effects on the transcription of genes for replication proteins. To overcome this problem, transgenic plants expressing open reading frames (ORFs) of DNA A from an enhanced cauliflower mosaic virus 35S RNA promoter were constructed and tested for their ability to support the replication of DNA B and DNA B mutants. The results show that plants transgenic for ORF AL1 are able to support the replication of the double-stranded (ds) forms of DNA B, but that ORF AL2 is required in addition to produce ssDNA B. ORFs AL3, BL1 or BR1 were not required for replication of ds or ssDNA B. To the best of our knowledge this is the first time that essential replication proteins of a geminivirus have been expressed constitutively from a plant genome without giving rise to replicating DNA A molecules, thereby allowing DNA B to replicate alone. Such transgenic plants should enable not only the mutational analysis of sequence elements within the replication origin region, but also the construction of a new generation of vectors for gene amplification in plants, based on a minimal virus replicon.
DNA Probes↗
Stability and expression of bacterial genes in replicating geminivirus vectors in plants.
Bacterial beta-glucuronidase (gus) and neomycin phosphotransferase (neo) genes were introduced into coat protein replacement vectors based on DNA A of tomato golden mosaic virus (TGMV). Recombinant gus and neo vectors up to 1.1 kbp larger than DNA A were shown to replicate stably in transgenic plants containing partial dimers (master copies) of the vectors integrated into their chromosomal DNA in the absence of DNA B. Beta-glucuronidase and neomycin phosphotransferase activities in independently transformed plants were proportional to the copy number of the double-stranded forms of the vector. Deletion analysis has shown that an essential part of the TGMV coat protein promoter, including a TATA box, lies within 76 nt upstream of the initiation codon of the gene. An increase in expression of a neo gene was obtained by replacing this 76 nt sequence by an 800 nt sequence containing a cauliflower mosaic virus 35S RNA promoter with no effect on the ability of the vector to replicate or on its stability in transgenic plants. Systemic infection of plants by agroinoculation with TGMV vectors larger than DNA A in the presence of DNA B resulted in deletions in the vector DNA in some, but not all, plants. Possible reasons for vector instability in systemically infected plants, and vector stability in transgenic plants containing master copies of the vector, are discussed.
Chromosome Deletion↗
Leptospiral infection in school-children from Trinidad and Barbados.
A serological survey for leptospiral agglutinins was undertaken between 1980 and 1983 in over 500 Barbadian and 500 Trinidadian school-children aged 7-14 years. The children were selected randomly from urban and rural schools, and examined three times at approximately annual intervals. A total of 12.5% of the Barbadian children and 9.5% of the Trinidadian children were seropositive at a titre of 50 using the microscopic agglutination test. On both islands, seroprevalence was higher in males than females, the difference being significant in rural schools. There was no evidence of a difference in prevalence between urban and rural schools, or between junior and secondary age-ranges. Analysis of the association of serology with socio-economic and behavioural factors showed a significant association in Trinidad with father's occupation, but most other variables on both islands showed only weak non-significant associations. Fourteen children in Trinidad and three in Barbados seroconverted. Seroconversion in Trinidad occurred at a rate of 1.6% per annum and was significantly associated with livestock contact and with absence of a tapped water supply. In Trinidad, Autumnalis was the most commonly recorded serogroup, but this accounted for less than a quarter of seropositives. In Barbados, Panama accounted for over half the seropositives and was about four times more common than the next most common serogroup, Autumnalis. In Barbados, 39 persons aged 19 or less were hospitalized with leptospirosis between November 1979 and December 1986. Average annual incidence rates were 2.2, 4.9 and 13.3 per 100,000 in the 5-9, 10-14 and 15-19 age-groups, respectively.
Adolescent↗
Iron-deficiency anaemia and its response to oral iron: report of a study in rural Gambian children treated at home by their mothers.
Haematological and iron parameters, measured in 907 children aged from 6 months to 5 years in rural Gambia at the start of the rainy season, differed from those in American reference populations as follows: mean haemoglobin levels were much lower at ages 1 and 2 years and mean levels of mean corpuscular volume (MCV) were lower at all ages (at age 1 year mean haemoglobin was 11.2 g/dl and mean MCV 68.2 fl); in a sample of 249 children randomly selected from the whole study population, mean serum iron levels were similar but mean transferrin saturation and mean serum ferritin levels were lower, especially at ages 1-3 years (at age 1 year mean serum iron was 11.1 mumol/l, mean transferrin saturation 16.9%, and geometric mean serum ferritin 8.8 ng/ml. A total of 213 children (23%) whose haemoglobin and mean corpuscular volume were both less than the 3rd percentile of the reference population received oral iron or placebo from their mothers during the rainy season when malaria transmission is maximal. Mean levels of haemoglobin, mean corpuscular volume, serum iron, transferrin saturation and serum ferritin rose in the iron-treated group and fell in the placebo group at all ages, except under 1 year for serum ferritin, to produce significant differences between the groups by the end of the study. Total iron-binding capacity showed no significant changes during the study. We concluded that oral iron given by the mother during the rainy season can be used to treat iron-deficiency anaemia in Gambian children who would otherwise become more anaemic.
Administration, Oral↗
The effects on malaria of treatment of iron-deficiency anaemia with oral iron in Gambian children.
In order to determine whether giving iron to iron-deficient children increases their susceptibility to malaria, 213 Gambian children aged between 6 months and 5 years with iron-deficiency anaemia were randomized to receive either oral iron or placebo during the rainy season when malaria transmission is maximal. Haematological and iron measurements improved significantly in the group given iron. Regular morbidity surveys showed that fever associated with parasitaemia occurred more frequently in the iron-treated group than in the placebo group. This difference was not significant for all parasitaemias grouped together, but became significant and progressively larger for parasitaemias of ten or more positive fields per 100 high power fields (P less than 0.025), and for parasitaemias of 50 or more positive fields per 100 high power fields (P less than 0.01). Three children in the iron-treated group but none in the placebo group had more than one episode of fever and parasitaemia. Splenomegaly rates rose appreciably during the study in both groups, but in children at age 2 years the splenomegaly rate at the end of the study was significantly greater in the iron-treated group. We concluded that there is a significantly increased risk of fever associated with severe malarial parasitaemia for children with iron-deficiency anaemia given iron during the season of maximal malaria transmission in this part of The Gambia.
Administration, Oral↗