Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'.

Background: The variety of DNA microarray formats and datasets presently available offers an unprecedented opportunity to perform insightful comparisons of heterogeneous data. Cross-species studies, in particular, have the power of identifying conserved, functionally important molecular processes. Validation of discoveries can now often be performed in readily available public data which frequently requires cross-platform studies.Cross-platform and cross-species analyses require matching probes on different microarray formats. This can be achieved using the information in microarray annotations and additional molecular biology databases, such as orthology databases. Although annotations and other biological information are stored using modern database models ( e. g. relational), they are very often distributed and shared as tables in text files, i.e. flat file databases. This common flat database format thus provides a simple and robust solution to flexibly integrate various sources of information and a basis for the combined analysis of heterogeneous gene expression profiles.Results: We provide annotationTools, a Bioconductor-compliant R package to annotate microarray experiments and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file databases. First, annotationTools contains a specialized set of functions for mining this widely used database format in a systematic manner. It thus offers a straightforward solution for annotating microarray experiments. Second, building on these basic functions and relying on the combination of information from several databases, it provides tools to easily perform cross-species analyses of gene expression data.Here, we present two example applications of annotationTools that are of direct relevance for the analysis of heterogeneous gene expression profiles, namely a cross-platform mapping of probes and a cross-species mapping of orthologous probes using different orthology databases. We also show how to perform an explorative comparison of disease-related transcriptional changes in human patients and in a genetic mouse model.Conclusion: The R package annotationTools provides a simple solution to handle microarray annotation and orthology tables, as well as other flat molecular biology databases. Thereby, it allows easy integration and analysis of heterogeneous microarray experiments across different technological platforms or species.

Tackling self-selection into treatment and self-selection into the sample biases in VAA research

Self‐selection into treatment and self‐selection into the sample are major concerns of VAA research and need to be controlled for if the aim is to deduce causal effects from VAA use in observational data. This paper focuses on the methodological aspects of VAA research and outlines omnipresent endogeneity issues, partly imposed through unobserved factors that affect both whether individuals chose to use VAAs and their electoral behavior. We promote using Heckman selection models and apply various versions of the model to data from the Swiss electorate and smartvote users in order to see to what extent selection biases interfere with the estimated effects of interest.

Improving blood pressure control through pharmacist interventions: a meta-analysis of randomized controlled trials.

BACKGROUND: Control of blood pressure (BP) remains a major challenge in primary care. Innovative interventions to improve BP control are therefore needed. By updating and combining data from 2 previous systematic reviews, we assess the effect of pharmacist interventions on BP and identify potential determinants of heterogeneity. METHODS AND RESULTS: Randomized controlled trials (RCTs) assessing the effect of pharmacist interventions on BP among outpatients with or without diabetes were identified from MEDLINE, EMBASE, CINAHL, and CENTRAL databases. Weighted mean differences in BP were estimated using random effect models. Prediction intervals (PI) were computed to better express uncertainties in the effect estimates. Thirty-nine RCTs were included with 14 224 patients. Pharmacist interventions mainly included patient education, feedback to physician, and medication management. Compared with usual care, pharmacist interventions showed greater reduction in systolic BP (-7.6 mm Hg, 95% CI: -9.0 to -6.3; I(2)=67%) and diastolic BP (-3.9 mm Hg, 95% CI: -5.1 to -2.8; I(2)=83%). The 95% PI ranged from -13.9 to -1.4 mm Hg for systolic BP and from -9.9 to +2.0 mm Hg for diastolic BP. The effect tended to be larger if the intervention was led by the pharmacist and was done at least monthly. CONCLUSIONS: Pharmacist interventions - alone or in collaboration with other healthcare professionals - improved BP management. Nevertheless, pharmacist interventions had differential effects on BP, from very large to modest or no effect; and determinants of heterogeneity could not be identified. Determining the most efficient, cost-effective, and least time-consuming intervention should be addressed with further research.

Impact of pharmacist care in the management of cardiovascular disease risk factors: a systematic review and meta-analysis of randomized trials.

BACKGROUND: Pharmacists may improve the clinical management of major risk factors for cardiovascular disease (CVD) prevention. A systematic review was conducted to determine the impact of pharmacist care on the management of CVD risk factors among outpatients. METHODS: The MEDLINE, EMBASE, CINAHL, and Cochrane Central Register of Controlled Trials databases were searched for randomized controlled trials that involved pharmacist care interventions among outpatients with CVD risk factors. Two reviewers independently abstracted data and classified pharmacists' interventions. Mean changes in blood pressure, total cholesterol, low-density lipoprotein cholesterol, and proportion of smokers were estimated using random effects models. RESULTS: Thirty randomized controlled trials (11 765 patients) were identified. Pharmacist interventions exclusively conducted by a pharmacist or implemented in collaboration with physicians or nurses included patient educational interventions, patient-reminder systems, measurement of CVD risk factors, medication management and feedback to physician, or educational intervention to health care professionals. Pharmacist care was associated with significant reductions in systolic/diastolic blood pressure (19 studies [10 479 patients]; -8.1 mm Hg [95% confidence interval {CI}, -10.2 to -5.9]/-3.8 mm Hg [95% CI,-5.3 to -2.3]); total cholesterol (9 studies [1121 patients]; -17.4 mg/L [95% CI,-25.5 to -9.2]), low-density lipoprotein cholesterol (7 studies [924 patients]; -13.4 mg/L [95% CI,-23.0 to -3.8]), and a reduction in the risk of smoking (2 studies [196 patients]; relative risk, 0.77 [95% CI, 0.67 to 0.89]). While most studies tended to favor pharmacist care compared with usual care, a substantial heterogeneity was observed. CONCLUSION: Pharmacist-directed care or in collaboration with physicians or nurses improve the management of major CVD risk factors in outpatients.

Blood glucose and prognosis in children with presumed severe malaria: is there a threshold for 'hypoglycaemia'?

OBJECTIVES: Hypoglycaemia (glucose <2.2 mmol/l) is a defining feature of severe malaria, but the significance of other levels of blood glucose has not previously been studied in children with severe malaria. METHODS: A prospective study of 437 consecutive children with presumed severe malaria was conducted in Mali. We defined hypoglycaemia as <2.2 mmol/l, low glycaemia as 2.2-4.4 mmol/l and hyperglycaemia as >8.3 mmol/l. Associations between glycaemia and case fatality were analysed for 418 children using logistic regression models and a receiver operator curve (ROC). RESULTS: There was a significant difference between blood glucose levels in children who died (median 4.6 mmol/l) and survivors (median 7.6 mmol/l, P < 0.001). Case fatality declined from 61.5% of the hypoglycaemic children to 46.2% of those with low glycaemia, 13.4% of those with normal glycaemia and 7.6% of those with hyperglycaemia (P < 0.001). Logistic regression showed an adjusted odds ratio (AOR) of 0.75 (0.64-0.88) for case fatality per 1 mmol/l increase in baseline blood glucose. Compared to a normal blood glucose, hypoglycaemia and low glycaemia both significantly increased the odds of death (AOR 11.87, 2.10-67.00; and 5.21, 1.86-14.63, respectively), whereas hyperglycaemia reduced the odds of death (AOR 0.34, 0.13-0.91). The ROC [area under the curve at 0.753 (95% CI 0.684-0.820)] indicated that glycaemia had a moderate predictive value for death and identified an optimal threshold at glycaemia <6.1 mmol/l, (sensitivity 64.5% and specificity 75.1%). CONCLUSIONS: If there is a threshold of blood glucose which defines a worse prognosis, it is at a higher level than the current definition of 2.2 mmol/l.

Generation of reconstituted human plasma-derived secretory-like IgA and IgM and their protective effect on intestinal epithelium

Les muqueuses sont les membranes tapissant les cavités du corps, tel que le tube digestif, et sont en contact direct avec l'environnement extérieur. Ces surfaces subissent de nombreuses agressions pouvant être provoquées par des agents pathogènes (bactéries, toxines ou virus). Cela étant, les muqueuses sont munies de divers mécanismes de protection dont notamment deux protéines-clés permettant de neutraliser les agents pathogènes : les anticorps ou immunoglobulines sécrétoires A (SIgA) et M (SIgM). Ces anticorps sont, d'une part, fabriqués au niveau de la muqueuse sous forme d'IgA et IgM. Lorsqu'ils sont sécrétés dans l'intestin, ils se lient à une protéine appelée pièce sécrétoire et deviennent ainsi SIgA et SïgM. La présence de la pièce sécrétoire est essentielle pour que les anticorps puissent fonctionner au niveau de la muqueuse. D'autre part, ces anticorps sont également fabriqués dans d'autres parties du corps en général et se retrouvent dans le sang sous forme d'IgA et IgM Chez l'homme, des thérapies basées sur l'injection d'anticorps donnent de bons résultats depuis de nombreuses années notamment dans le traitement des infections. Bien qu'un certain nombre d'études ont montré le rôle protecteur des anticorps de type IgA et IgM, ceux-ci ne sont que rarement utilisés dans les thérapies actuelles. La principale raison de cette faible utilisation réside dans la production ou la purification des IgA/IgM ou SIgA/SIgM (la forme active au niveau des muqueuses) qui est difficile à réaliser à large échelle. Ainsi, le but de la thèse était (1) d'étudier la possibilité d'employer des IgA et des IgM provenant du sang humain pour générer des SIgA et SIgM et (2) de voir si ces anticorps reconstitués pouvaient neutraliser certains agents pathogènes au niveau des muqueuses. Tout d'abord, une analyse biochimique des IgA et des IgM issues du sang a été effectuée. Nous avons observé que ces anticorps avaient des caractéristiques similaires aux anticorps naturellement présents au niveau des muqueuses. De plus, nous avons confirmé que ces anticorps pouvaient être associés à une pièce sécrétoire produite en laboratoire pour ainsi donner des SIgA et SIgM reconstituées. Ensuite, la fonctionnalité des anticorps reconstitués a été testée grâce à un modèle de couche unique de cellules intestinales différenciées (monocouches) en laboratoire imitant la paroi de l'intestin. Ces monocouches ont été infectées par une bactérie pathogène, Shigella flexneri, responsable de la shigellose, une maladie qui provoque des diarrhées sanglantes chez l'homme. L'infection des monocouches par les bactéries seules ou combinées aux SIgA et SIgM reconstituées a été analysée. Nous avons observé que les dommages des cellules étaient moins importants lorsque les SIgA étaient présentes. Il apparaît que les SIgA neutralisent les bactéries en se fixant dessus, ce qui provoque leur agrégation, et diminuent l'inflammation des cellules. La protection s'est montrée encore plus efficace avec les SIgM. De plus, nous avons vu que les SIgA et SIgM pouvaient diminuer la sécrétion de facteurs nocifs produits par les bactéries. Utilisant le même modèle des monocouches, la fonctionnalité des IgA issues du sang humain a aussi été testée contre une toxine sécrétée par une bactérie appelée Clostridium diffìcile. Cette bactérie peut être présente naturellement dans l'intestin de personnes saines, cependant elle peut devenir pathogène dans certaines conditions et être à l'origine de diarrhées et d'inflammations de l'intestin via la sécrétion de toxines. Des préparations d'anticorps contenant une certaine proportion de SIgA reconstituées ont amené à une diminution des dommages et de l'inflammation des monocouches causés par la toxine. L'ensemble de ces résultats prometteurs, montrant que des SIgA et SIgM reconstituées peuvent protéger la paroi de l'intestin des infections bactériennes, nous conduisent à approfondir la recherche sur ces anticorps dans des modèles animaux. L'aboutissement de ce type de recherche permettrait de tester, par la suite, l'efficacité sur l'homme de traitements des infections des muqueuses par injection d'anticorps de type SIgA et SIgM reconstituées. Les muqueuses, telle que la muqueuse gastrointestinale, sont des surfaces constamment exposées à l'environnement et leur protection est garantie par une combinaison de barrières mécaniques, physicochimiques et immunologiques. Parmi les divers mécanismes de protection immunologiques, la réponse humorale spécifique joue un rôle prépondérant et est assurée par les immunoglobulines sécrétoires de type A (SIgA) et M (SIgM). Les thérapies basées sur l'administration d'IgG apportent d'importants bénéfices dans le domaine de la santé. Bien que des études sur les animaux aient montré que l'administration par voie muqueuse d'IgA polymérique (plgA) ou SIgA pouvaient protéger des infections, des IgA/SIgA n'ont été utilisées qu'occasionnellement dans les thérapies. De plus, des études précliniques et cliniques ont démontré que l'administration par voie systémique de préparations enrichies en IgM pouvait aussi protéger des infections. Cependant, l'administration par voie muqueuse d'IgM/SIgM purifiées n'a pas été examinée jusqu'à présent. La principale raison est que la purification ou là production des IgA/SIgA et IgM/SIgM est difficile à réaliser à large échelle. Le but de ce travail de thèse était d'examiner la possibilité d'associer des IgA et IgM polyclonals purifiées à partir du plasma humain avec une pièce sécrétoire recombinante humaine afin de générer des SIgA et SIgM reconstituées fonctionnelles. Tout d'abord, une analyse biochimique des IgA et IgM issues du plasma humain a été effectuée par buvardage de western et Chromatographie. Ces molécules avaient des caractéristiques biochimiques similaires à celles des immunoglobulines issues de la muqueuse. L'association entre plgA ou IgM issues du plasma humain et la pièce sécrétoire recombinante humaine a été confirmée, ainsi que la stoechiométrie 1:1 de l'association. Comme dans les conditions physiologiques, cette association permettait de retarder la dégradation des SIgA et SIgM reconstituées exposées à des protéases intestinales. Ensuite, la fonctionnalité et le mode d'action des IgA et IgM issues du plasma humain, ainsi que des SIgA et SIgM reconstituées, ont été explorés grâce à un modèle in vitro de monocouches de cellules intestinales épithéliales polarisées de type Caco-2, qui imite l'épithélium intestinal. Les monocouches ont été infectées par un pathogène entérique, Shigella flexneri, seul ou combiné aux immunoglobulines issues du plasma humain ou aux immunoglobulines sécrétoires reconstituées. Bien que les dommages des monocouches aient été retardés par les plgA et SIgA reconstituées, les IgM et SIgM reconstituées se sont montrées supérieures dans le maintien de l'intégrité des cellules. Une agrégation bactérienne et une diminution de l'inflammation des monocouches ont été observées avec les plgA et SIgA reconstituées. Ces effets étaient augmentés avec les IgM et SIgM reconstituées. De plus, il s'est révélé que les deux types d'immunoglobulines de type sécrétoire reconstituées agissaient directement sur la virulence des bactéries en réduisant leur sécrétion de facteurs de virulence. La fonctionnalité des IgA issues du plasma humain a aussi été testée contre la toxine A de Clostridium difficile grâce au même modèle de monocouches de cellules épithéliales. Nous avons démontré que des préparations enrichies en IgA provenant du plasma humain pouvaient diminuer les dommages et l'inflammation des monocouches induits par la toxine. L'ensemble de ces résultats démontrent que des IgA et IgM de type sécrétoire peuvent être générées à partir d'IgA et IgM issues du plasma humain en les associant à la pièce sécrétoire et que ces molécules protègent l'épithélium intestinal contre des bactéries pathogènes. Ces molécules pourraient dès lors être testées dans des modèles in vivo. Le but final serait de les utiliser chez l'homme à des fins d'immunisation passive dans le traitement de pathologies associées à la muqueuse telles que les infections. - Mucosal surfaces, such as gastrointestinal mucosa, are constantly exposed to the external environment and their protection is ensured by a combination of mechanical, physicochemical and immunological barriers. Among the various immunological defense mechanisms, specific humoral mucosal response plays a crucial role and is mediated by secretory immunoglobulins A (SIgA) and M (SIgM). Immunoglobulin therapy based on the administration of IgG molecules leads important health benefits. Even though animal studies have shown that mucosal application of polymeric IgA (plgA) or SIgA provided protection against infections, IgA/SIgA have been only used occasionally for therapeutic application. Moreover, preclinical and clinical studies have demonstrated that systemic administration of IgM-enriched preparations could also afford protection against infections. Nevertheless, mucosal application of purified IgM/SIgM has not been examined. The main reason is that the purification or production of IgA/SIgA and IgM/SIgM at large scale is difficult to achieve. The aim of this PhD project was to examine the possibility to associate polyclonal human plasma-derived IgA and IgM with recombinant human secretory component (SC) to generate functional secretoiy-like IgA and IgM. First, biochemical analysis of human plasma IgA and IgM was performed by western blotting and chromatography. These molecules exhibited the same biochemical features as mucosa-derived antibodies (Abs). The association between human plasma plgA or IgM and recombinant human SC was confirmed, as well as the 1:1 stoichiometry of association. Similarly to physiological conditions, this association delayed the degradation of secretory-like IgA or IgM by intestinal proteases. Secondly, the function activity and the mode of action of human plasma IgA and IgM, as well as secretory-like IgA and IgM were explored using an in vitro model of polarized intestinal epithelial Caco-2 cell monolayers mimicking intestinal epithelium. Cell monolayers were infected with an enteropathogen, Shigella flexneri, alone or in combination to plasma Abs or secretory-like Abs. Even though plasma plgA and secretoiy-like IgA resulted in a delay of bacteria-induced damages of cell monolayers, plasma IgM and secretory-like IgM were shown to be superior in maintenance of cell integrity. Polymeric IgA and secretory-like IgA induced bacterial aggregation and decreased cell monolayer inflammation, effects further amplified with IgM and secretory-like IgM. In addition, both secretory-like Abs directly impacted on bacterial virulence leading to a reduction in secretion of virulence factors by bacteria. The functionality of human plasma IgA was also tested against Clostridium difficile toxin A using Caco-2 cell monolayers. Human plasma IgA- enriched preparations led to a diminution of cell monolayer damages and a decrease of cellular inflammation induced by the toxin. The sum of these results demonstrates that secretory-like IgA and IgM can be generated from purified human plasma IgA and IgM associated to SC and that these molecules are functional to protect intestinal epithelium from bacterial infections. These molecules could be now tested using in vivo models. The final goal would be to use them by passive immunization in the treatment of mucosa-associated pathologies like infections in humans.

Cross National Contact Strategies

Using paradata gathered from the 11-nation Survey of Health, Ageing and Retirement in Europe (SHARE), this paper examines the impact of the first contact attempt and the first contact properties, respectively, on contact and response efficiency using logistic multilevel models. We find that despite the different sample frames and interviewer compensation structure between countries, there are no considerable country effects with respect to making contact, once interviewer effects are controlled. Moreover, results point to an increased efficiency associated with evenings especially on Sundays, at least on the very first contact attempt. For attempts that result in initial contact, Saturday afternoons are most likely to eventually lead to completed interviews, followed by initial contact on weekdays during the daytime. We hypothesize that this may be due to the SHARE sample being composed of people aged 50 and over.

Symptomatic in-hospital deep vein thrombosis and pulmonary embolism following hip and knee arthroplasty among patients receiving recommended prophylaxis: a systematic review.

CONTEXT: Symptomatic venous thromboembolism (VTE) after total or partial knee arthroplasty (TPKA) and after total or partial hip arthroplasty (TPHA) are proposed patient safety indicators, but its incidence prior to discharge is not defined. OBJECTIVE: To establish a literature-based estimate of symptomatic VTE event rates prior to hospital discharge in patients undergoing TPHA or TPKA. DATA SOURCES: Search of MEDLINE, EMBASE, and the Cochrane Library (1996 to 2011), supplemented by relevant articles. STUDY SELECTION: Reports of incidence of symptomatic postoperative pulmonary embolism or deep vein thrombosis (DVT) before hospital discharge in patients who received VTE prophylaxis with either a low-molecular-weight heparin or a subcutaneous factor Xa inhibitor or oral direct inhibitor of factors Xa or IIa. DATA EXTRACTION AND SYNTHESIS: Meta-analysis of randomized clinical trials and observational studies that reported rates of postoperative symptomatic VTE in patients who received recommended VTE prophylaxis after undergoing TPHA or TPKA. Data were independently extracted by 2 analysts, and pooled incidence rates of VTE, DVT, and pulmonary embolism were estimated using random-effects models. RESULTS: The analysis included 44,844 cases provided by 47 studies. The pooled rates of symptomatic postoperative VTE before hospital discharge were 1.09% (95% CI, 0.85%-1.33%) for patients undergoing TPKA and 0.53% (95% CI, 0.35%-0.70%) for those undergoing TPHA. The pooled rates of symptomatic DVT were 0.63% (95% CI, 0.47%-0.78%) for knee arthroplasty and 0.26% (95% CI, 0.14%-0.37%) for hip arthroplasty. The pooled rates for pulmonary embolism were 0.27% (95% CI, 0.16%-0.38%) for knee arthroplasty and 0.14% (95% CI, 0.07%-0.21%) for hip arthroplasty. There was significant heterogeneity for the pooled incidence rates of symptomatic postoperative VTE in TPKA studies but less heterogeneity for DVT and pulmonary embolism in TPKA studies and for VTE, DVT, and pulmonary embolism in TPHA studies. CONCLUSION: Using current VTE prophylaxis, approximately 1 in 100 patients undergoing TPKA and approximately 1 in 200 patients undergoing TPHA develops symptomatic VTE prior to hospital discharge.

Effectiveness of chronic obstructive pulmonary disease-management programs: systematic review and meta-analysis

BACKGROUND: Disease-management programs may enhance the quality of care provided to patients with chronic diseases, such as chronic obstructive pulmonary disease (COPD). The aim of this systematic review was to assess the effectiveness of COPD disease-management programs. METHODS: We conducted a computerized search of MEDLINE, EMBASE, CINAHL, PsychINFO, and the Cochrane Library (CENTRAL) for studies evaluating interventions meeting our operational definition of disease management: patient education, 2 or more different intervention components, 2 or more health care professionals actively involved in patients' care, and intervention lasting 12 months or more. Programs conducted in hospital only and those targeting patients receiving palliative care were excluded. Two reviewers evaluated 12,749 titles and fully reviewed 139 articles; among these, data from 13 studies were included and extracted. Clinical outcomes considered were all-cause mortality, lung function, exercise capacity (walking distance), health-related quality of life, symptoms, COPD exacerbations, and health care use. A meta-analysis of exercise capacity and all-cause mortality was performed using random-effects models. RESULTS: The studies included were 9 randomized controlled trials, 1 controlled trial, and 3 uncontrolled before-after trials. Results indicate that the disease-management programs studied significantly improved exercise capacity (32.2 m, 95% confidence interval [CI], 4.1-60.3), decreased risk of hospitalization, and moderately improved health-related quality of life. All-cause mortality did not differ between groups (pooled odds ratio 0.84, 95% CI, 0.54-1.40). CONCLUSION: COPD disease-management programs modestly improved exercise capacity, health-related quality of life, and hospital admissions, but not all-cause mortality. Future studies should explore the specific elements or characteristics of these programs that bring the greatest benefit.

Recurrent stroke predictors differ in medically treated patients with pathogenic vs. other PFOs.

OBJECTIVE: To examine predictors of stroke recurrence in patients with a high vs a low likelihood of having an incidental patent foramen ovale (PFO) as defined by the Risk of Paradoxical Embolism (RoPE) score. METHODS: Patients in the RoPE database with cryptogenic stroke (CS) and PFO were classified as having a probable PFO-related stroke (RoPE score of >6, n = 647) and others (RoPE score of ≤6 points, n = 677). We tested 15 clinical, 5 radiologic, and 3 echocardiographic variables for associations with stroke recurrence using Cox survival models with component database as a stratification factor. An interaction with RoPE score was checked for the variables that were significant. RESULTS: Follow-up was available for 92%, 79%, and 57% at 1, 2, and 3 years. Overall, a higher recurrence risk was associated with an index TIA. For all other predictors, effects were significantly different in the 2 RoPE score categories. For the low RoPE score group, but not the high RoPE score group, older age and antiplatelet (vs warfarin) treatment predicted recurrence. Conversely, echocardiographic features (septal hypermobility and a small shunt) and a prior (clinical) stroke/TIA were significant predictors in the high but not low RoPE score group. CONCLUSION: Predictors of recurrence differ when PFO relatedness is classified by the RoPE score, suggesting that patients with CS and PFO form a heterogeneous group with different stroke mechanisms. Echocardiographic features were only associated with recurrence in the high RoPE score group.

Spirometry reference equations for central European populations from school age to old age.

BACKGROUND: Spirometry reference values are important for the interpretation of spirometry results. Reference values should be updated regularly, derived from a population as similar to the population for which they are to be used and span across all ages. Such spirometry reference equations are currently lacking for central European populations. OBJECTIVE: To develop spirometry reference equations for central European populations between 8 and 90 years of age. MATERIALS: We used data collected between January 1993 and December 2010 from a central European population. The data was modelled using "Generalized Additive Models for Location, Scale and Shape" (GAMLSS). RESULTS: The spirometry reference equations were derived from 118'891 individuals consisting of 60'624 (51%) females and 58'267 (49%) males. Altogether, there were 18'211 (15.3%) children under the age of 18 years. CONCLUSION: We developed spirometry reference equations for a central European population between 8 and 90 years of age that can be implemented in a wide range of clinical settings.

Adherence as a predictor of the development of class-specific resistance mutations: the Swiss HIV Cohort Study.

BACKGROUND: Non-adherence is one of the strongest predictors of therapeutic failure in HIV-positive patients. Virologic failure with subsequent emergence of resistance reduces future treatment options and long-term clinical success. METHODS: Prospective observational cohort study including patients starting new class of antiretroviral therapy (ART) between 2003 and 2010. Participants were naïve to ART class and completed ≥1 adherence questionnaire prior to resistance testing. Outcomes were development of any IAS-USA, class-specific, or M184V mutations. Associations between adherence and resistance were estimated using logistic regression models stratified by ART class. RESULTS: Of 314 included individuals, 162 started NNRTI and 152 a PI/r regimen. Adherence was similar between groups with 85% reporting adherence ≥95%. Number of new mutations increased with increasing non-adherence. In NNRTI group, multivariable models indicated a significant linear association in odds of developing IAS-USA (odds ratio (OR) 1.66, 95% confidence interval (CI): 1.04-2.67) or class-specific (OR 1.65, 95% CI: 1.00-2.70) mutations. Levels of drug resistance were considerably lower in PI/r group and adherence was only significantly associated with M184V mutations (OR 8.38, 95% CI: 1.26-55.70). Adherence was significantly associated with HIV RNA in PI/r but not NNRTI regimens. CONCLUSION: Therapies containing PI/r appear more forgiving to incomplete adherence compared with NNRTI regimens, which allow higher levels of resistance, even with adherence above 95%. However, in failing PI/r regimens good adherence may prevent accumulation of further resistance mutations and therefore help to preserve future drug options. In contrast, adherence levels have little impact on NNRTI treatments once the first mutations have emerged.

25-hydroxyvitamin D concentration is inversely associated with serum MMP-9 in a cross-sectional study of African American ESRD patients.

BACKGROUND: Circulating 25-hydroxyvitamin D [25(OH)D] concentration is inversely associated with peripheral arterial disease and hypertension. Vascular remodeling may play a role in this association, however, data relating vitamin D level to specific remodeling biomarkers among ESRD patients is sparse. We tested whether 25(OH)D concentration is associated with markers of vascular remodeling and inflammation in African American ESRD patients.METHODS: We conducted a cross-sectional study among ESRD patients receiving maintenance hemodialysis within Emory University-affiliated outpatient hemodialysis units. Demographic, clinical and dialysis treatment data were collected via direct patient interview and review of patients records at the time of enrollment, and each patient gave blood samples. Associations between 25(OH)D and biomarker concentrations were estimated in univariate analyses using Pearson's correlation coefficients and in multivariate analyses using linear regression models. 25(OH) D concentration was entered in multivariate linear regression models as a continuous variable and binary variable (<15 ng/ml and =15 ng/ml). Adjusted estimate concentrations of biomarkers were compared between 25(OH) D groups using analysis of variance (ANOVA). Finally, results were stratified by vascular access type.RESULTS: Among 91 patients, mean (standard deviation) 25(OH)D concentration was 18.8 (9.6) ng/ml, and was low (<15 ng/ml) in 43% of patients. In univariate analyses, low 25(OH) D was associated with lower serum calcium, higher serum phosphorus, and higher LDL concentrations. 25(OH) D concentration was inversely correlated with MMP-9 concentration (r = -0.29, p = 0.004). In multivariate analyses, MMP-9 concentration remained negatively associated with 25(OH) D concentration (P = 0.03) and anti-inflammatory IL-10 concentration positively correlated with 25(OH) D concentration (P = 0.04).CONCLUSIONS: Plasma MMP-9 and circulating 25(OH) D concentrations are significantly and inversely associated among ESRD patients. This finding may suggest a potential mechanism by which low circulating 25(OH) D functions as a cardiovascular risk factor.

The role of phylogeny in the spatial distributions and assembly of mountain plant communities.

A major challenge in community ecology is a thorough understanding of the processes that govern the assembly and composition of communities in time and space. The growing threat of climate change to the vascular plant biodiversity of fragile ecosystems such as mountains has made it equally imperative to develop comprehensive methodologies to provide insights into how communities are assembled. In this perspective, the primary objective of this PhD thesis is to contribute to the theoretical and methodological development of community ecology, by proposing new solutions to better detect the ecological and evolutionary processes that govern community assembly. As phylogenetic trees provide by far, the most advanced tools to integrate the spatial, ecological and evolutionary dynamics of plant communities, they represent the cornerstone on which this work was based. In this thesis, I proposed new solutions to: (i) reveal trends in community assembly on phylogenies, depicted by the transition of signals at the nodes of the different species and lineages responsible for community assembly, (ii) contribute to evidence the importance of evolutionarily labile traits in the distribution of mountain plant species. More precisely, I demonstrated that phylogenetic and functional compositional turnover in plant communities was driven by climate and human land use gradients mostly influenced by evolutionarily labile traits, (iii) predict and spatially project the phylogenetic structure of communities using species distribution models, to identify the potential distribution of phylogenetic diversity, as well as areas of high evolutionary potential along elevation. The altitudinal setting of the Diablerets mountains (Switzerland) provided an appropriate model for this study. The elevation gradient served as a compression of large latitudinal variations similar to a collection of islands within a single area, and allowed investigations on a large number of plant communities. Overall, this thesis highlights that stochastic and deterministic environmental filtering processes mainly influence the phylogenetic structure of plant communities in mountainous areas. Negative density-dependent processes implied through patterns of phylogenetic overdispersion were only detected at the local scale, whereas environmental filtering implied through phylogenetic clustering was observed at both the regional and local scale. Finally, the integration of indices of phylogenetic community ecology with species distribution models revealed the prospects of providing novel and insightful explanations on the potential distribution of phylogenetic biodiversity in high mountain areas. These results generally demonstrate the usefulness of phylogenies in inferring assembly processes, and are worth considering in the theoretical and methodological development of tools to better understand phylogenetic community structure.

Patient- and therapy-related factors on the wear of denture teeth : results of a clinical trial

OBJECTIVE: When we examined a previously published prospective multi-center clinical trial in which complete denture-wearers were followed over a period of 2 years, we found that about 30% of the variability in the clinical wear data of denture teeth was due to unknown characteristics of the subjects. In the second part of the study, we try to identify which patient- and therapy-related factors may explain some of this variability. METHODS: The clinical wear data of denture teeth at different recall times (6, 12, 18, 24 months) in 89 subjects (at baseline) were correlated with the following parameters, which may all have an influence on the wear of denture teeth: age, gender, bruxism as reported by the subjects, number of prostheses used so far, time since last extraction, smoking, fit of dentures as judged by the subject and the clinician, average denture wearing time and wearing of denture during the night. To evaluate the influence of the different patient- and therapy-related variables, both a univariate analysis (one extra factor to the model) and a multivariate analysis were carried out using linear mixed models with the variable Log mean as the outcome. RESULTS: None of the patient- and therapy-related parameters showed a statistically significant effect on the wear of denture teeth. There was, however, a trend for women to show less wear compared to men and a trend of decreasing wear with increasing age. SIGNIFICANCE: Further research is required to identify the factors which are responsible for the high variability observed between the subjects regarding clinical wear data.