Geographic predictors of primary multidrug-resistant tuberculosis cases in an endemic area of Lima, Peru.

SETTING: Peru reports among the highest multidrug-resistant tuberculosis (MDR-TB) rates in the Americas, with a growing proportion in previously untreated tuberculosis (TB) cases. The identification of clusters of primary MDR-TB compared with drug-susceptible TB (DS-TB) could help prioritize interventions. OBJECTIVE: To examine the clustering of primary MDR-TB case residences and their proximity to high-risk locations in San Juan de Lurigancho District, Lima, Peru. DESIGN: Enrolled primary MDR-TB and primary DS-TB cases were interviewed and their primary residence was recorded using handheld Global Positioning System devices. Kuldorff's spatial scan statistic was used for cluster detection (SaTScan(TM), v. 9.1.1). Identified clusters were visualized in Quantum Geographic Information Systems software (v1.8.0). The following cluster centers were tested: a health centre with the highest TB and MDR-TB rates (Clinic X), a hospital and two prisons. Using regression analyses, we examined predictors of primary MDR-TB cases. RESULTS: A statistically significant cluster of primary MDR-TB cases was identified within a 2.29 km radius around Clinic X. Proximity to Clinic X remained a significant predictor of primary MDR-TB in adjusted regression analyses. CONCLUSION: We identified a hotspot of primary MDR-TB cases around Clinic X in a TB-endemic area. Causes of this clustering require investigation; targeted interventions for this high-risk area should be considered.

Isolation and characterization of microsatellite markers for Bertholletia excelsa (Lecythidaceae) population genetic analysis.

Seven polymorphic microsatellite markers were developed and validated for Bertholletia excelsa (Brazil nut tree) population genetic studies. This species is a widespread monotypic Amazonian tree with high non-timber economic value. Unfortunately, Brazil nut production is currently less than 25% of historical production levels, because of extensive deforestation. All pairs of primers produced clearly interpretable and polymorphic bands. No linkage disequilibrium was observed in an analysis of 46 individuals from one population, three to seven alleles per locus were observed; the expected heterozygosity ranged from 0.378 to 0.978, with significant heterozygote excess for four loci. An analysis of individuals from two populations showed private alleles at all loci. These primer pairs will be useful for population studies, especially for comparing samples from different parts of the Amazon forest.

Morphological and molecular characteristics do not confirm popular classification of the Brazil nut tree in Acre, Brazil.

In the State of Acre, the Brazil nut tree, Bertholletia excelsa (Lecythidaceae), is classified by the local population into two types according to morphological characteristics, including color and quality of wood, shape of the trunk and crown, and fruit production. We examined the reliability of this classification by comparing morphological and molecular data of four populations of Brazil nut trees from Vale do Rio Acre in the Brazilian Amazon. For the morphological analysis, we evaluated qualitative and quantitative information of the trees, fruits, and seeds. The molecular analysis was performed using RAPD and ISSR markers, with cluster analysis. Significant differences were found between the two types of Brazil nut trees for the characters diameter at breast height, fruit yield, fruit size, and number of seeds per fruit. Despite the significant correlation between the morphological characteristics and the popular classification, we observed all possible combinations of morphological characteristics in both types of Brazil nut trees. In some individuals, the classification did not correspond to any of the characteristics. The results obtained with molecular markers showed that the two locally classified types of Brazil nut trees did not differ genetically, indicating that there is no consistent separation between them.

Diversity and genetic structure among subpopulations of Gossypium mustelinum (Malvaceae).

Gossypium mustelinum is the only cotton species native to Brazil; it is endemic to the semi-arid region of the northeast. The populations are found near perennial and semi-perennial sources of water, such as ponds or pools in intermittent streams. Problems with in situ conservation derive from human interference in its habitat, mainly because of excessive cattle grazing and deforestation. Establishing efficient strategies for in situ conservation requires knowledge of the genetic structure of the populations. We evaluated the structure and genetic variability of populations of G. mustelinum in the Tocó and Capivara Rivers (State of Bahia). Two hundred and eighteen mature G. mustelinum plants were genotyped with SSR markers. The molecular data were used to estimate the allelic frequencies, the heterozygosity, the F statistics, and the genetic distance among the populations and among individuals. We found high genetic diversity among the populations. The FST indexes for each population were also high and strongly correlated with physical distance. The high estimated level of endogamy and the low observed heterozygosity are indicative that the populations reproduce mainly by self-fertilization and crosses between related individuals. Consequently, strategies for in situ preservation should include at least three occurrence sites of G. mustelinum from each population. For ex situ conservation, the collections should include as many sites as possible.

Permanent genetic resources added to molecular ecology resources database 1 October 2012-30 November 2012.

This article documents the addition of 153 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Brassica oleracea, Brycon amazonicus, Dimorphandra wilsonii, Eupallasella percnurus, Helleborus foetidus, Ipomoea purpurea, Phrynops geoffroanus, Prochilodus argenteus, Pyura sp., Sylvia atricapilla, Teratosphaeria suttonii, Trialeurodes vaporariorum and Trypanosoma brucei. These loci were cross-tested on the following species: Dimorphandra coccicinea, Dimorphandra cuprea, Dimorphandra gardneriana, Dimorphandra jorgei, Dimorphandra macrostachya, Dimorphandra mollis, Dimorphandra parviflora and Dimorphandra pennigera.

Development and characterization of DNA microsatellite primers for buriti (Mauritia flexuosa L.f.).

Mauritia flexuosa L. (Arecaceae) is a palm tree species known as buriti that occurs in the Cerrado biome. It is characteristic of the vereda, a typical ecosystem of central Brazil. In this phytophysiognomy, M. flexuosa and other groups of arboreal-herbaceous species develop in open fields with very humid soils. M. flexuosa can be found in forest borders and is a palm tree with a wide distribution in South America (Brazil, Colombia, Venezuela, French Guyana Ecuador, Peru, and Bolivia). The main objectives of this study were to develop simple sequence repeat marker-enriched libraries and to characterize these loci in buriti palm to facilitate future population studies. A total of 40 sequences derived from the microsatellite-enriched libraries were selected for primer design. The optimization results showed that 9 primer pairs could successfully amplify polymorphic target fragments of the expected sizes. The data also show that the described primers can be used in population genetic studies in M. flexuosa to obtain information that will inform conservation and management strategies.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 June 2010 - 31 July 2010.

This article documents the addition of 205 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Bagassa guianensis, Bulweria bulwerii, Camelus bactrianus, Chaenogobius annularis, Creontiades dilutus, Diachasmimorpha tryoni, Dioscorea alata, Euhrychiopsis lecontei, Gmelina arborea, Haliotis discus hannai, Hirtella physophora, Melanaphis sacchari, Munida isos, Thaumastocoris peregrinus and Tuberolachnus salignus. These loci were cross-tested on the following species: Halobaena caerulea, Procellaria aequinoctialis, Oceanodroma monteiroi, Camelus ferus, Creontiades pacificus, Dioscorea rotundata, Dioscorea praehensilis, Dioscorea abyssinica, Dioscorea nummularia, Dioscorea transversa, Dioscorea esculenta, Dioscorea pentaphylla, Dioscorea trifida, Hirtella bicornis, Hirtella glandulosa, Licania alba, Licania canescens, Licania membranaceae, Couepia guianensis and 7 undescribed Thaumastocoris species.

A retrospective, exploratory, secondary analysis of the association between antipsychotic use and mortality in elderly patients with delirium.

BACKGROUND: Delirium, an acute altered level of cognition, is a frequent complication of medical illness in the elderly. Antipsychotic medications (APs) are often used to treat agitation and psychosis in delirium. The goal of this study is to compare mortality in delirious elderly medical inpatients treated with APs with those who did not receive APs. METHOD: 326 elderly hospitalized patients were identified with delirium at an acute care community hospital. A nested case-control analysis was conducted on this cohort. Cases consisted of all patients who died in hospital within eight weeks of admission. Each case was matched for age and severity of illness to patients (controls) alive on the same day post-admission. Conditional logistic regression was used to assess the impact of exposure to AP on mortality. Covariates used for adjustment were the Charlson comorbidity score and the acute physiology score. Odds ratio (OR) and 95% confidence intervals were calculated from the regression coefficients. RESULTS: 111 patients received an AP. A total of 62 patients died, 16 of whom were exposed to an AP. The OR of association between AP use and death was 1.53 (95% C.I, 0.83-2.80) in univariate and 1.61 (95% C.I, 0.88-2.96) in multivariate analysis. CONCLUSION: In elderly medical inpatients with delirium, administration of APs was not associated with a statistically significant increased risk of mortality. Larger studies are needed to clarify the safety of AP medication in elderly patients with delirium.

Cortisol response to a psychosocial stressor in schizophrenia: blunted, delayed, or normal?

BACKGROUND: Patients with schizophrenia may differ from healthy controls by having dysregulated physiological responses to stress. Our objective was to determine the extent to which cortisol reaction can discriminate between controls and schizophrenia patients while controlling for symptom severity, personality, body mass index (BMI) and smoking. METHOD: 30 chronic schizophrenia patients and 30 matched controls underwent a modified version of the Trier Social Stress Test (TSST), consisting of public speaking and mental arithmetic. Heart rate, blood pressure, and salivary cortisol were measured repeatedly throughout the TSST. In addition, participants completed the NEO Personality Inventory (NEO-FFI), and were interviewed with the Brief Psychiatric Rating Scale (BPRS). RESULTS: Both groups had a significant increase in heart rate and mean arterial pressure following the TSST. Results of a logistic regression suggests that patients can be discriminated from controls with a smaller change in cortisol between baseline and 15 min post-TSST, controlling for BMI and severity of positive symptoms. There was a trend for lower overall cortisol secretion in patients. CONCLUSIONS: Despite demonstrable effects of the stressor on cardiac measures, schizophrenia patients tend to have smaller acute cortisol reaction to psychosocial stress. The significance of this conclusion for vulnerability-stress models of schizophrenia is discussed.

Isolation of polymorphic microsatellite markers for the tetraploid Dipteryx odorata, an intensely exploited Amazonian tree species.

Dipteryx odorata is an intensely exploited Amazonian tree legume. Microsatellite markers were developed to study the genetic structure, gene flow and reproductive biology of D. odorata. Eight highly polymorphic microsatellite markers were isolated from enriched repeat libraries screened for microsatellite repeats. An average of 16 alleles and 0.964 phenotype diversity per locus were found in 76 individuals from the Tapajos National Forest, in the state of Pará in the Brazilian Amazon.

Colorectal cancer screening in Canada: results of a national survey.

Canadian guidelines recommend colorectal-cancer (CRC) screening for individuals aged 50 to 74 years. The study objective was to estimate rates of CRC screening according to individual and geographical characteristics, and of adherence to current CRC screening guidelines. Respondents to the 2003 Canadian Community Health Survey Cycle 2.1 (aged >or= 50 years, without past or present CRC) participated. Fecal occult blood test (FOBT) and endoscopy utilization and screening rates were calculated. The sample included 16,747 residents of Newfoundland, Ontario, Saskatchewan and British Columbia. Overall, the FOBT screening rate was 7.7% in the past year, and the endoscopy screening rate was 8.8% in the past 5 years. FOBT screening rates were higher in older and male respondents; endoscopy screening rates were higher in older respondents. Individuals aged 50 to 59 and over 90 years were least likely to have been screened. Approximately 70% of respondents were non-adherent to current CRC screening guidelines. Non-adherence rates were higher in most health regions of British Columbia. National survey data suggest CRC screening in Canada is low; younger persons and residents of British Columbia were least likely to report CRC screening.

Isolation and characterization of microsatellite loci for Hymenaea courbaril and transferability to Hymenaea stigonocarpa, two tropical timber species.

Hymenaea courbaril is a tropical timber species, intensely exploited and found in the Amazon, Atlantic Forest and Brazilian Cerrado biome. Nine highly polymorphic microsatellite loci were developed from a genomic library enriched for AG/TC repeats. In a total of 41 individuals, from two natural populations, seven to 13 alleles per locus were detected and expected heterozygosity ranged from 0.75 to 0.90. Seven loci were effectively transferred to Hymenaea stigonocarpa. High levels of polymorphism make the present primers useful for population genetic studies and are a powerful tool to investigate mating system, gene flow and spatial genetic structure.

Eight variable microsatellite loci for a Neotropical tree, Jacaranda copaia (Aubl.) D.Don (Bignoniaceae).

The Dendrogene Project (Genetic Conservation within Managed Forests in Amazonia) aims to understand the genetic and ecological processes that underpin tree species survival and in particular their response to forest management regimes. As part of the project, we developed eight microsatellite markers for Jacaranda copaia to be used for genetic structure, gene flow and reproductive biology studies. Polymorphism was evaluated using 96 adult trees from the Tapajos National Forest in the Eastern Brazilian Amazon. An average of 22 alleles per locus were detected, with expected heterozygosity ranging from 0.731 to 0.94.

Development of microsatellite markers in Annona crassiflora Mart., a Brazilian Cerrado fruit tree species.

Annona crassiflora Mart. (Annonaceae) is a native fruit species of the region of Brazilian Cerrado with a high agronomic potential, although without any traces of domestication. A set of 10 microsatellite primer pairs was developed from an enriched genome library (TC13). An average of 19.3 alleles per locus was detected. Observed heterozygosity estimates were consistently lower than those obtained for gene diversity, evidencing a departure from Hardy-Weinberg expected proportions. The reported set of markers showed to be highly informative and constitutes a powerful tool for the development of genetic characterization studies in A. crassiflora.

Impact of selective logging on inbreeding and gene dispersal in an Amazonian tree population of Carapa guianensis Aubl.

Selective logging may impact patterns of genetic diversity within populations of harvested forest tree species by increasing distances separating conspecific trees, and modifying physical and biotic features of the forest habitat. We measured levels of gene diversity, inbreeding, pollen dispersal and spatial genetic structure (SGS) of an Amazonian insect-pollinated Carapa guianensis population before and after commercial selective logging. Similar levels of gene diversity and allelic richness were found before and after logging in both the adult and the seed generations. Pre- and post-harvest outcrossing rates were high, and not significantly different from one another. We found no significant levels of biparental inbreeding either before or after logging. Low levels of pollen pool differentiation were found, and the pre- vs. post-harvest difference was not significant. Pollen dispersal distance estimates averaged between 75 m and 265 m before logging, and between 76 m and 268 m after logging, depending on the value of tree density and the dispersal model used. There were weak and similar levels of differentiation of allele frequencies in the adults and in the pollen pool, before and after logging occurred, as well as weak and similar pre- and post-harvest levels of SGS among adult trees. The large neighbourhood sizes estimated suggest high historical levels of gene flow. Overall our results indicate that there is no clear short-term genetic impact of selective logging on this population of C. guianensis.

Dietary patterns and lifestyle factors in the Norwegian EPIC cohort: the Norwegian Women and Cancer (NOWAC) study.

OBJECTIVE: To identify different dietary patterns in Norway using a combination of cluster and factor analysis. DESIGN: Cross-sectional study. SETTING: Nation-wide, population-based study. SUBJECTS: The Norwegian EPIC cohort is a subcohort of the Norwegian Women and Cancer study (NOWAC), and consist 37.226 women aged 41-56 y who answered a food frequency questionnaire (FFQ) in 1998. INTERVENTIONS: The associations among 50 food variables were first investigated by using principal component analysis. Five important factors were found. The five principal components were then used as input in the cluster analysis. Different socioeconomic and lifestyle variables were examined. RESULTS: Six clusters of dietary patterns were found, and were labelled accordingly: 'traditional fish eaters', 'healthy eaters', 'average, less fish, less healthy', 'Western', 'traditional bread eaters', and 'alcohol users'. The traditional fish eaters and the traditional bread eaters were both highly represented in the north and west of Norway and were more likely to be present among persons with lower income and lower education. The healthy and the alcohol drinkers were found mostly in the south and east and were more likely to have higher income. Persons in the alcohol group were more likely to be current smokers. The western group had the highest percentage of three or more persons in the household and the shortest time since last birth, indicating that families with children dominate this group. CONCLUSION: Our data indicate six different dietary patterns in Norway, each with different socio-demographic and lifestyle characteristics. SPONSORSHIP: The Norwegian Cancer Society (E 04038/006).

Evaluation of under- and overreporting of energy intake in the 24-hour diet recalls in the European Prospective Investigation into Cancer and Nutrition (EPIC).

OBJECTIVE: To evaluate under- and overreporting and their determinants in the EPIC 24-hour diet recall (24-HDR) measurements collected in the European Prospective Investigation into Cancer and Nutrition (EPIC). DESIGN: Cross-sectional analysis. 24-HDR measurements were obtained by means of a standardised computerised interview program (EPIC-SOFT). The ratio of reported energy intake (EI) to estimated basal metabolic rate (BMR) was used to ascertain the magnitude, impact and determinants of misreporting. Goldberg's cut-off points were used to identify participants with physiologically extreme low or high energy intake. At the aggregate level the value of 1.55 for physical activity level (PAL) was chosen as reference. At the individual level we used multivariate statistical techniques to identify factors that could explain EI/BMR variability. Analyses were performed by adjusting for weight, height, age at recall, special diet, smoking status, day of recall (weekday vs. weekend day) and physical activity. SETTING: Twenty-seven redefined centres in the 10 countries participating in the EPIC project. SUBJECTS: In total, 35 955 men and women, aged 35-74 years, participating in the nested EPIC calibration sub-studies. RESULTS: While overreporting has only a minor impact, the percentage of subjects identified as extreme underreporters was 13.8% and 10.3% in women and men, respectively. Mean EI/BMR values in men and women were 1.44 and 1.36 including all subjects, and 1.50 and 1.44 after exclusion of misreporters. After exclusion of misreporters, adjusted EI/BMR means were consistently less than 10% different from the expected value of 1.55 for PAL (except for women in Greece and in the UK), with overall differences equal to 4.0% and 7.4% for men and women, respectively. We modelled the probability of being an underreporter in association with several individual characteristics. After adjustment for age, height, special diet, smoking status, day of recall and physical activity at work, logistic regression analyses resulted in an odds ratio (OR) of being an underreporter for the highest vs. the lowest quartile of body mass index (BMI) of 3.52 (95% confidence interval (CI) 2.91-4.26) in men and 4.80 (95% CI 4.11-5.61) in women, indicating that overweight subjects are significantly more likely to underestimate energy intake than subjects in the bottom BMI category. Older people were less likely to underestimate energy intake: ORs were 0.58 (95% CI 0.45-0.77) and 0.74 (95% CI 0.63-0.88) for age (> or =65 years vs. <50 years). Special diet and day of the week showed strong effects. CONCLUSION: EI tends to be underestimated in the vast majority of the EPIC centres, although to varying degrees; at the aggregate level most centres were below the expected reference value of 1.55. Underreporting seems to be more prevalent among women than men in the EPIC calibration sample. The hypothesis that BMI (or weight) and age are causally related to underreporting seems to be confirmed in the present work. This introduces further complexity in the within-group (centre or country) and between-group calibration of dietary questionnaire measurements to deattenuate the diet-disease relationship.

A method to assess predominant energies of exposure in a nuclear research centre--Saclay (France).

A study of dosimetric errors is under way within an international collaborative study of cancer risk among workers in the nuclear industry. The objective is to quantify errors in the estimated photon doses to individual organs used for cancer risk estimation. One source of errors is the response of old dosemeters in workplace exposure conditions. As these conditions are not well known, the International Study must rely on expert estimations. This paper describes a method to assess the proportion of the dose from photons in three energy ranges (< 100, 100-300, > or = 300 keV) using the responses under filters of a multi-element dosemeter. The method was tested on experimental and simulated data and provides a good estimate of the proportion of dose from photons below 100 keV, the most critical for dosemeter response. It was applied to personnel readings in one facility, confirming the experts' estimation. Beyond the International Study, the method has implication for the monitoring and protection of workers.

Making decisions about cancer screening when the guidelines are unclear or conflicting.

OBJECTIVE: Our purpose was to determine the factors involved in the cancer screening decisions of family physicians in situations where the clinical practice guidelines are unclear or conflicting as opposed to when they are clear and uncontroversial. STUDY DESIGN: We analyzed discussions with focus groups using a constant comparative approach. POPULATION: A total of 73 family physicians in active practice participated in 10 focus groups (1 urban group and 1 rural group in each of 5 Canadian provinces). OUTCOME MEASURES: Our main outcome measures were participants' perceptions regarding cancer screening when the guidelines were unclear or conflicting. RESULTS: We propose a model of the determinants of cancer screening decision making with regard to unclear and conflicting guidelines. This model is rooted in the physician-patient relationship, and is an interactive process influenced by patient factors (anxiety, expectations, and family history) and physician factors (perception of guidelines, clinical practice experience, influence of colleagues, distinction between the screening styles of specialists and family physicians, and the amount of time and financial costs involved in performing the maneuver). CONCLUSIONS: Our model is unique, because it is embedded in the physician-patient relationship. Ultimately, a modified model could be used to design interventions to assist with the implementation of preventive services guidelines.