A step-by-step tutorial to use HierFstat to analyse populations hierarchically structured at multiple levels.

The populations of parasites and infectious agents are most of the time structured in complex hierarchy that lies beyond the classical nested design described by Wright's F-statistics (F(IS), F(ST) and F(IT)). In this note we propose a user-friendly step-by-step notice for using recent software (HierFstat) that computes and test fixation indices for any hierarchical structure. We add some tricks and tips for some special data kind (haploid, single locus), some other procedure (bootstrap over loci) and how to handle crossed factors.

Protocol of the COSMIN study: consensus-based standards for the selection of health measurement instruments

Background: Choosing an adequate measurement instrument depends on the proposed use of the instrument, the concept to be measured, the measurement properties (e.g. internal consistency, reproducibility, content and construct validity, responsiveness, and interpretability), the requirements, the burden for subjects, and costs of the available instruments. As far as measurement properties are concerned, there are no sufficiently specific standards for the evaluation of measurement properties of instruments to measure health status, and also no explicit criteria for what constitutes good measurement properties. In this paper we describe the protocol for the COSMIN study, the objective of which is to develop a checklist that contains COnsensus-based Standards for the selection of health Measurement INstruments, including explicit criteria for satisfying these standards. We will focus on evaluative health related patient-reported outcomes (HR-PROs), i.e. patient-reported health measurement instruments used in a longitudinal design as an outcome measure, excluding health care related PROs, such as satisfaction with care or adherence. The COSMIN standards will be made available in the form of an easily applicable checklist.Method: An international Delphi study will be performed to reach consensus on which and how measurement properties should be assessed, and on criteria for good measurement properties. Two sources of input will be used for the Delphi study: (1) a systematic review of properties, standards and criteria of measurement properties found in systematic reviews of measurement instruments, and (2) an additional literature search of methodological articles presenting a comprehensive checklist of standards and criteria. The Delphi study will consist of four (written) Delphi rounds, with approximately 30 expert panel members with different backgrounds in clinical medicine, biostatistics, psychology, and epidemiology. The final checklist will subsequently be field-tested by assessing the inter-rater reproducibility of the checklist.Discussion: Since the study will mainly be anonymous, problems that are commonly encountered in face-to-face group meetings, such as the dominance of certain persons in the communication process, will be avoided. By performing a Delphi study and involving many experts, the likelihood that the checklist will have sufficient credibility to be accepted and implemented will increase.

The interface between oral and systemic health: the need for more collaboration.

The focus of this review is to highlight the need for improved communication between medical and dental professionals in order to deliver more effective care to patients. The need for communication is increasingly required to capitalise on recent advances in the biological sciences and in medicine for the management of patients with chronic diseases. Improvements in longevity have resulted in populations with increasing special oral-care needs, including those who have cancer of the head and neck, those who are immunocompromised due to HIV/AIDS, advanced age, residence in long-term care facilities or the presence of life-long conditions, and those who are receiving long-term prescription medications for chronic conditions (e.g., anti-hypertensives, anticoagulants, immunosuppressants, antidepressants). These medications can cause adverse reactions in the oral cavity, such as xerostomia and ulceration. Patients with xerostomia are at increased risk of tooth decay, periodontal disease and infection. The ideal management of such individuals should involve the collaborative efforts of physicians, nurses, dentists and dental hygienists, thus optimising treatment and minimising secondary complications deriving from the oral cavity.

The relation of body mass index and abdominal adiposity with dyslipidemia in 27 general populations of the WHO MONICA Project.

The association between adiposity measures and dyslipidemia has seldom been assessed in a multipopulational setting. 27 populations from Europe, Australia, New Zealand and Canada (WHO MONICA project) using health surveys conducted between 1990 and 1997 in adults aged 35-64 years (n = 40,480). Dyslipidemia was defined as the total/HDL cholesterol ratio >6 (men) and >5 (women). Overall prevalence of dyslipidemia was 25% in men and 23% in women. Logistic regression showed that dyslipidemia was strongly associated with body mass index (BMI) in men and with waist circumference (WC) in women, after adjusting for region, age and smoking. Among normal-weight men and women (BMI<25 kg/m(2)), an increase in the odds for being dyslipidemic was observed between lowest and highest WC quartiles (OR = 3.6, p < 0.001). Among obese men (BMI ≥ 30), the corresponding increase was smaller (OR = 1.2, p = 0.036). A similar weakening was observed among women. Classification tree analysis was performed to assign subjects into classes of risk for dyslipidemia. BMI thresholds (25.4 and 29.2 kg/m(2)) in men and WC thresholds (81.7 and 92.6 cm) in women came out at first stages. High WC (>84.8 cm) in normal-weight men, menopause in women and regular smoking further defined subgroups at increased risk. standard categories of BMI and WC, or their combinations, do not lead to optimal risk stratification for dyslipidemia in middle-age adults. Sex-specific adaptations are necessary, in particular by taking into account abdominal obesity in normal-weight men, post-menopausal age in women and regular smoking in both sexes.

Systematic review of meaning in life assessment instruments.

BACKGROUND: The construct of "meaning in life" (MiL) has raised the interest of clinicians working in psycho-oncology and end-of-life care. It has become a topic of scientific investigation where diverse assessment approaches have been applied. Aims: We present a comprehensive systematic review of existing MiL assessment instruments. METHODS: Electronic searches of articles published in English peer-reviewed journals were performed in Psycinfo, Medline, Embase and Cinahl. Instruments are appraised with regard to ten measurement properties. RESULTS: In total, 59 nomothetic and idiographic MiL instruments were identified. Most instruments were developed in North America and meet basic psychometric criteria. They assess presence of and search for MiL, crisis and sources of MiL, meaning making, meaningful activity, MiL in the context of illness, breadth, depth, and other structural indicators. These aspects are largely consistent with existing MiL definitions. Nine out of 59 instruments included cancer populations in test development. CONCLUSIONS: This overview of available instruments underscores the complexity of the construct and might assist researchers to select an appropriate instrument for their research needs. Finally, it points to the need for more integrative theorizing and research on MiL. Copyright © 2012 John Wiley & Sons, Ltd.

Impact of biocontrol strain Pseudomonas fluorescens CHA0 on rhizosphere bacteria isolated from barley (Hordeum vulgare L.) with special reference to Cytophaga-like bacteria.

AIMS: To assess the impact of the biocontrol strain Pseudomonas fluorescens CHA0 on a collection of barley rhizosphere bacteria using an agar plate inhibition assay and a plant microcosm, focusing on a CHA0-sensitive member of the Cytophaga-like bacteria (CLB). METHODS AND RESULTS: The effect of strain CHA0 on a collection of barley rhizosphere bacteria, in particular CLB and fluorescent pseudomonads sampled during a growth season, was assessed by a growth inhibition assay. On average, 85% of the bacteria were sensitive in the May sample, while the effect was reduced to around 68% in the July and August samples. In the May sample, around 95% of the CLB and around 45% of the fluorescent pseudomonads were sensitive to strain CHA0. The proportion of CHA0-sensitive CLB and fluorescent pseudomonad isolates decreased during the plant growth season, i.e. in the July and August samples. A particularly sensitive CLB isolate, CLB23, was selected, exposed to strain CHA0 (wild type) and its genetically modified derivatives in the rhizosphere of barley grown in gnotobiotic soil microcosms. Two dry-stress periods were imposed during the experiment. Derivatives of strain CHA0 included antibiotic or exopolysaccharide (EPS) overproducing strains and a dry-stress-sensitive mutant. Despite their inhibitory activity against CLB23 in vitro, neither wild-type strain CHA0, nor any of its derivatives, had a major effect on culturable and total cell numbers of CLB23 during the 23-day microcosm experiment. Populations of all inoculants declined during the two dry-stress periods, with soil water contents below 5% and plants reaching the wilting point, but they recovered after re-wetting the soil. Survival of the dry-stress-sensitive mutant of CHA0 was most affected by the dry periods; however, this did not result in an increased population density of CLB23. CONCLUSIONS: CLB comprise a large fraction of barley rhizosphere bacteria that are sensitive to the biocontrol pseudomonad CHA0 in vitro. However, in plant microcosm experiments with varying soil humidity conditions, CHA0 or its derivatives had no major impact on the survival of the highly sensitive CLB strain, CLB23, during two dry-stress periods and a re-wetting period; all co-existed well in the rhizosphere of barley plants. SIGNIFICANCE AND IMPACT OF THE STUDY: Results indicate a lack of interaction between the biocontrol pseudomonad CHA0 and a sensitive CLB when the complexity increases from agar plate assays to plant microcosm experiments. This suggests the occurrence of low levels of antibiotic production and/or that the two bacterial genera occupy different niches in the rhizosphere.

Molecular epidemiology and evolution of HIV-1 in Portugal and portuguese speaking african countries

The aims of this thesis were to better characterize HIV-1 diversity in Portugal, Angola, Mozambique and Cape Verde and to investigate the origin and epidemiological history of HIV-1 in these countries. The impact of these issues in diagnosis, disease progression and susceptibility to ARV therapy was also investigated. Finally, the nature, dynamics and prevalence of transmitted drug resistance (TDR) was determined in untreated HIV-1 infected patients. In Angola, practically all HIV-1 genetic forms were found, including almost all subtypes, untypable (U) strains, CRFs and URFs. Recombinants (first and second generation) were present in 47.1% of the patients. HIV/AIDS epidemic in Angola probably started in 1961, the major cause being the independence war, subsequently spreading to Portugal. In Maputo, 81% of the patients were infected with subtype C viruses. Subtype G, U and recombinants such as CRF37_cpx, were also present. The results suggest that HIV-1 epidemic in Mozambique is evolving rapidly in genetic complexity. In Cape Verde, where HIV-1 and HIV-2 co-circulate, subtype G is the prevailed subtype. Subtypes B, C, F1, U, CRF02_AG and other recombinant strains were also found. HIV-2 isolates belonged to group A, some being closely related to the original ROD isolate. In all three countries numerous new polymorphisms were identified in the RT and PR of HIV-1 viruses. Mutations conferring resistance to the NRTIs or NNRTIs were found in isolates from 2 (2%) patients from Angola, 4 (6%) from Mozambique and 3 (12%) from Cape Verde. None of the isolates containing TDR mutations would be fully sensitive to the standard first-line therapeutic regimens used in these countries. Close surveillance in treated and untreated populations will be crucial to prevent further transmission of drug resistant strains and maximize the efficacy of ARV therapy. In Portugal, investigation of a seronegative case infection with rapid progression to AIDS and death revealed that the patient was infected with a CRF14_BG-like R5-tropic strain selectively transmitted by his seropositive sexual partner. The results suggest a massive infection with a highly aggressive CRF14_BG like strain and/or the presence of an unidentified immunological problem that prevented the formation of HIV-1-specific antibodies. Near full-length genomic sequences obtained from three unrelated patients enabled the first molecular and phylogenomic characterization of CRF14_BG from Portugal; all sequences were strongly related with CRF14_BG Spanish isolates. The mean date of origin of CRF14_BG was estimated to be 1992. We propose that CRF14_BG emerged in Portugal in the early 1990s, spread to Spain in late 1990s as a consequence of IDUs migration and then to the rest of Europe. Most CRF14_BG strains were predicted to use CXCR4 and were associated with rapid CD4 depletion and disease progression. Finally, we provide evidence suggesting that the X4 tropism of CRF14_BG may have resulted from convergent evolution of the V3 loop possibly driven by an effective escape from neutralizing antibody response.

Epidémiologie et prévention du mélanome cutané en Suisse. [Epidemiology and prevention of melanoma in Switzerland].

[Quintessence] - L'incidence du mélanome malin augmente rapidement depuis plus de 50 ans. - La Suisse, avec 1700 nouveaux cas diagnostiqués par an, est, avec la Norvège, le pays d'Europe le plus touché par le mélanome. - Des différences régionales sont récemment apparues avec une incidence plus élevée dans les cantons romands. - Les changements observés en Suisse dans l'attitude et le comportement face au soleil sont trop récents et modestes pour influencer l'incidence. - La détection précoce effectuée depuis près de 20 ans a permis d'augmenter la survie et le taux de mélanomes fins sans toutefois altérer l'incidence des lésions épaisses. - La mortalité associée au mélanome malin a récemment diminué, d'abord chez les femmes. L'efficacité de la prévention devrait se confirmer à terme si les efforts entrepris se poursuivent. [Auteurs] [Summary] - The incidence of malignant melanoma has steadily increased in Caucasian populations over the last 50 years. - With some 1700 new cases per year, Switzerland has, with Norway, the highest rate of melanoma in Europe. - Regional differences within Switzerland are emerging, with a higher incidence in western (French-speaking) cantons. - Observed changes in sun protection attitudes and knowledge in the Swiss population have yet to impact on the incidence trend. - Early detection, as pursued since the mid-1980s in Switzerland, has led to a substantial increase in survival and rates of thin melanoma, without major change in rates of thick melanoma. - Mortality from melanoma has recently decreased, initially in women. The effectiveness of prevention campaigns should eventually be confirmed if current efforts persist. [Authors]

Random measurement error and regression dilution bias.

Summary points: - The bias introduced by random measurement error will be different depending on whether the error is in an exposure variable (risk factor) or outcome variable (disease) - Random measurement error in an exposure variable will bias the estimates of regression slope coefficients towards the null - Random measurement error in an outcome variable will instead increase the standard error of the estimates and widen the corresponding confidence intervals, making results less likely to be statistically significant - Increasing sample size will help minimise the impact of measurement error in an outcome variable but will only make estimates more precisely wrong when the error is in an exposure variable

European society of hypertension position paper on ambulatory blood pressure monitoring.

Ambulatory blood pressure monitoring (ABPM) is being used increasingly in both clinical practice and hypertension research. Although there are many guidelines that emphasize the indications for ABPM, there is no comprehensive guideline dealing with all aspects of the technique. It was agreed at a consensus meeting on ABPM in Milan in 2011 that the 34 attendees should prepare a comprehensive position paper on the scientific evidence for ABPM.This position paper considers the historical background, the advantages and limitations of ABPM, the threshold levels for practice, and the cost-effectiveness of the technique. It examines the need for selecting an appropriate device, the accuracy of devices, the additional information and indices that ABPM devices may provide, and the software requirements.At a practical level, the paper details the requirements for using ABPM in clinical practice, editing considerations, the number of measurements required, and the circumstances, such as obesity and arrhythmias, when particular care needs to be taken when using ABPM.The clinical indications for ABPM, among which white-coat phenomena, masked hypertension, and nocturnal hypertension appear to be prominent, are outlined in detail along with special considerations that apply in certain clinical circumstances, such as childhood, the elderly and pregnancy, and in cardiovascular illness, examples being stroke and chronic renal disease, and the place of home measurement of blood pressure in relation to ABPM is appraised.The role of ABPM in research circumstances, such as pharmacological trials and in the prediction of outcome in epidemiological studies is examined and finally the implementation of ABPM in practice is considered in relation to the issue of reimbursement in different countries, the provision of the technique by primary care practices, hospital clinics and pharmacies, and the growing role of registries of ABPM in many countries.

Mesure de la pression artérielle et dépistage de l'hypertension chez l'enfant. [Blood pressure measurement and screening of hypertension in children].

Children with elevated blood pressure are at risk of being hypertensive in adulthood and of developing complications such as ventricular hypertrophy. Obesity is a cause of hypertension. Because the prevalence of obesity is increasing, some authors argue that the systematic screening for hypertension in children and adolescents is justified for early prevention and treatment. Sex, age and height all influence children's blood pressure. When elevated blood pressure is identified, complementary investigations and treatment might be necessary. However, due to the difficulties of obtaining a valid estimate of blood pressure, to the moderate tracking of blood pressure from childhood to adulthood, and the rarity of hypertension cases in childhood, the usefulness of systematic screening of hypertension during childhood is still controversial. Un enfant dont la pression artérielle est élevée a un risque accru d'être hypertendu à l'âge adulte et de présenter des complications telles que l'hypertrophie ventriculaire gauche. L'augmentation de la prévalence de l'obésité justifierait selon certains auteurs le dépistage systématique de l'hypertension dès le plus jeune âge afin d'instaurer des mesures préventives ou curatives précoces. Les normes de pression dépendent du sexe, de l'âge et de la taille de l'enfant. En cas de pression élevée, des investigations complémentaires, voire un traitement, peuvent être indiqués. Au vu des difficultés pour obtenir une mesure fiable, des incertitudes entachant la valeur pronostique d'une pression artérielle élevée et de la rareté des cas d'hypertension, il n'y a pas de consensus sur l'utilité du dépistage systématique de l'hypertension durant l'enfance.

Genome-wide association analysis of blood-pressure traits in African-ancestry individuals reveals common associated genes in African and non-African populations.

High blood pressure (BP) is more prevalent and contributes to more severe manifestations of cardiovascular disease (CVD) in African Americans than in any other United States ethnic group. Several small African-ancestry (AA) BP genome-wide association studies (GWASs) have been published, but their findings have failed to replicate to date. We report on a large AA BP GWAS meta-analysis that includes 29,378 individuals from 19 discovery cohorts and subsequent replication in additional samples of AA (n = 10,386), European ancestry (EA) (n = 69,395), and East Asian ancestry (n = 19,601). Five loci (EVX1-HOXA, ULK4, RSPO3, PLEKHG1, and SOX6) reached genome-wide significance (p < 1.0 × 10(-8)) for either systolic or diastolic BP in a transethnic meta-analysis after correction for multiple testing. Three of these BP loci (EVX1-HOXA, RSPO3, and PLEKHG1) lack previous associations with BP. We also identified one independent signal in a known BP locus (SOX6) and provide evidence for fine mapping in four additional validated BP loci. We also demonstrate that validated EA BP GWAS loci, considered jointly, show significant effects in AA samples. Consequently, these findings suggest that BP loci might have universal effects across studied populations, demonstrating that multiethnic samples are an essential component in identifying, fine mapping, and understanding their trait variability.

Understanding and meeting the needs of the older population: a global challenge.

BACKGROUND: In the past century, there has been a significant rise in life expectancy in almost all regions of the world, contributing to an increasingly older population. The aging of the population, in conjunction with urbanization and industrialization, has resulted in an important epidemiological transition marked by a widespread increase in the prevalence of chronic diseases and their sequelae. Current trends suggest that the transition will have a greater impact on developing countries compared to developed countries. An adequate response to the transition requires a strong emphasis on primary prevention and adequate resource allocation.

Prevalence of obesity in children in north-east Italy.

This study was performed to analyse the prevalence of obesity in children living in six different areas of the north-east of Italy. The study included 1523 children (749 male, 774 female), divided into four age categories (4, 8, 10, 12 +/- 0.5 years of age, respectively). The physical characteristics of the children were measured by trained and standardized examiners. In accordance with the guidelines on the Italian Consensus Conference on Obesity (Rome, 4-6 June 1991), a child was defined as obese when his weight was higher than 120% of the weight predicted for height, as calculated from the Tanner's tables. On average, the prevalence of obesity was higher in males than in females (15.7% vs. 11%). The highest prevalence was seen in 10-year-old males (23.4%). The prevalence increased with age both in males (4 years = 3.6%, 8 years = 11.2%, 10 years = 23.4%, 12 years = 17.3%) and in females (4 years = 2%, 8 years = 13.3%, 10 years = 12.7%, 12 years = 11.9%). This tendency was maintained when calculating the obesity prevalence by other methods, such as BMI, triceps skinfold and fat mass, although the magnitude of the prevalence was different depending on the criteria used to define it. A consensus on more precise criteria to define obesity is needed for a better diagnosis of obesity in childhood and to allow a more reliable measurement and comparison of the prevalence of obesity among populations.

Group 4: Career development for diverse and underserved populations

Globalization and diverse populations due to migration imply that counselors are expected to deliver career services to populations from a large array of cultural settings. Moreover, individuals belonging to minority or non-dominant groups may be underserved or misserved, thus decreasing their chances of finding employment opportunities through career counseling. To develop specific interventions minority or non-dominant groups, it seems important to understand their strength and weaknesses. These strengths and weaknesses will be presented in terms of risk and resilience factors, such as low future orientation and social support respectively. In the last two decades, several authors have made contributions to adapt and improve career services in order to best meet these minority groups' needs. A review of this literature identified thirteen keys to effective practice. For example, one key is to take responsibility for one's own biases and prejudices. Nonetheless, some underserved groups remain difficult to identify. Comparing some basic national demographic data with data from our counseling centers may be helpful in this context in identifying specific groups and assessing needs. One solution, in order to promote social justice across (all) cultural groups, is to encourage multiculturalism in both career counseling and society as a whole. A more inclusive society would allow each person in a minority or non-dominant group to contribute more effectively to the development and growth of this society.