Mesoscale numerical analysis of the historical November 1982 heavy precipitation event over Andorra (Eastern Pyrenees)

From 6 to 8 November 1982 one of the most catastrophic flash-flood events was recorded in the Eastern Pyrenees affecting Andorra and also France and Spain with rainfall accumulations exceeding 400 mm in 24 h, 44 fatalities and widespread damage. This paper aims to exhaustively document this heavy precipitation event and examines mesoscale simulations performed by the French Meso-NH non-hydrostatic atmospheric model. Large-scale simulations show the slow-evolving synoptic environment favourable for the development of a deep Atlantic cyclone which induced a strong southerly flow over the Eastern Pyrenees. From the evolution of the synoptic pattern four distinct phases have been identified during the event. The mesoscale analysis presents the second and the third phase as the most intense in terms of rainfall accumulations and highlights the interaction of the moist and conditionally unstable flows with the mountains. The presence of a SW low level jet (30 m s-1) around 1500 m also had a crucial role on focusing the precipitation over the exposed south slopes of the Eastern Pyrenees. Backward trajectories based on Eulerian on-line passive tracers indicate that the orographic uplift was the main forcing mechanism which triggered and maintained the precipitating systems more than 30 h over the Pyrenees. The moisture of the feeding flow mainly came from the Atlantic Ocean (7-9 g kg-1) and the role of the Mediterranean as a local moisture source was very limited (2-3 g kg-1) due to the high initial water vapour content of the parcels and the rapid passage over the basin along the Spanish Mediterranean coast (less than 12 h).

Exploratory Factor Analysis of the contents and styles of irrational thoughts assessed by "The Attitudes and Beliefs Inventory"

The factor structure of a back translated Spanish version (Lega, Caballo and Ellis, 2002) of the Attitudes and Beliefs Inventory (ABI) (Burgess, 1990) is analyzed in a sample of 250 university students.The Spanish version of the ABI is a 48-items self-report inventory using a 5-point Likert scale that assesses rational and irrational attitudes and beliefs. 24-items cover two dimensions of irrationality: a) areas of content (3 subscales), and b) styles of thinking (4 subscales).An Exploratory Factor Analysis (Parallel Analysis with Unweighted Least Squares method and Promin rotation) was performed with the FACTOR 9.20 software (Lorenzo-Seva and Ferrando, 2013).The results reproduced the main four styles of irrational thinking in relation with the three specific contents of irrational beliefs. However, two factors showed a complex configuration with important cross-loadings of different items in content and style. More analyses are needed to review the specific content and style of such items.

Computational analysis of the genetic and environmental contributions to disease-related human phenotypes: From predicting adverse lipid response of HIV patients receiving antiretroviral therapy to genome-wide association studies of cardiovascular and lipid related disorders

Genetic variants influence the risk to develop certain diseases or give rise to differences in drug response. Recent progresses in cost-effective, high-throughput genome-wide techniques, such as microarrays measuring Single Nucleotide Polymorphisms (SNPs), have facilitated genotyping of large clinical and population cohorts. Combining the massive genotypic data with measurements of phenotypic traits allows for the determination of genetic differences that explain, at least in part, the phenotypic variations within a population. So far, models combining the most significant variants can only explain a small fraction of the variance, indicating the limitations of current models. In particular, researchers have only begun to address the possibility of interactions between genotypes and the environment. Elucidating the contributions of such interactions is a difficult task because of the large number of genetic as well as possible environmental factors.In this thesis, I worked on several projects within this context. My first and main project was the identification of possible SNP-environment interactions, where the phenotypes were serum lipid levels of patients from the Swiss HIV Cohort Study (SHCS) treated with antiretroviral therapy. Here the genotypes consisted of a limited set of SNPs in candidate genes relevant for lipid transport and metabolism. The environmental variables were the specific combinations of drugs given to each patient over the treatment period. My work explored bioinformatic and statistical approaches to relate patients' lipid responses to these SNPs, drugs and, importantly, their interactions. The goal of this project was to improve our understanding and to explore the possibility of predicting dyslipidemia, a well-known adverse drug reaction of antiretroviral therapy. Specifically, I quantified how much of the variance in lipid profiles could be explained by the host genetic variants, the administered drugs and SNP-drug interactions and assessed the predictive power of these features on lipid responses. Using cross-validation stratified by patients, we could not validate our hypothesis that models that select a subset of SNP-drug interactions in a principled way have better predictive power than the control models using "random" subsets. Nevertheless, all models tested containing SNP and/or drug terms, exhibited significant predictive power (as compared to a random predictor) and explained a sizable proportion of variance, in the patient stratified cross-validation context. Importantly, the model containing stepwise selected SNP terms showed higher capacity to predict triglyceride levels than a model containing randomly selected SNPs. Dyslipidemia is a complex trait for which many factors remain to be discovered, thus missing from the data, and possibly explaining the limitations of our analysis. In particular, the interactions of drugs with SNPs selected from the set of candidate genes likely have small effect sizes which we were unable to detect in a sample of the present size (<800 patients).In the second part of my thesis, I performed genome-wide association studies within the Cohorte Lausannoise (CoLaus). I have been involved in several international projects to identify SNPs that are associated with various traits, such as serum calcium, body mass index, two-hour glucose levels, as well as metabolic syndrome and its components. These phenotypes are all related to major human health issues, such as cardiovascular disease. I applied statistical methods to detect new variants associated with these phenotypes, contributing to the identification of new genetic loci that may lead to new insights into the genetic basis of these traits. This kind of research will lead to a better understanding of the mechanisms underlying these pathologies, a better evaluation of disease risk, the identification of new therapeutic leads and may ultimately lead to the realization of "personalized" medicine.

From geriatric service to primary care: a retrospective pharmaceutical analysis of the medical prescription

Introduction The population of elderly persons is increasing andnegative outcomes due to polymedication are frequent. Discrepanciesin information about medication are frequent when older persons aretransitioning from hospital to home, increasing the risk of hospitalreadmission. The aims of this study were a) to determine discrepanciesin medical regimen indicated in two official discharge documents(DS = discharge summary, DP=discharge prescription); b) to characterizethe pharmacotherapy prescribed in older patients dischargedfrom a geriatric service.Materials & Methods Elderly patients (N=230) discharged from thegeriatric service (CHUV, Lausanne) over a 6-month period (January toJune 2009) were selected. Community pharmacists compared DS andDP to identify discrepancies including (a) drugs' name; (b) schedule ofadministration, dosage, frequency, prn prescription, treatment durationand galenic formulation. Beers' criteria were applied to identifypotentially inappropriate drugs and a descriptive analysis of drug costs,prescription profiles and generics were also performed.Results On average, patients were 82 ± 7 years old and stayed23.0 ± 11.6 days in the geriatric service. The delay between the datesof patient's discharge with the DP and the sending of the DS to hisgeneral physician averaged 14.0 ± 7.5 days (range 1-55). The DPhad an average of 10.0 ± 3.3 drugs (range 2-19). 77% of patients hadat least one discrepancy. A drug was missing on the DS in 57.8% ofpatients and 19.6% had a missing prn prescription. Among the 2312drugs prescribed, 3% belonged to Beers' list. They were prescribed to61 patients (26.5%), with 6 patients cumulating two Beers' potentiallyinappropriate drugs in their treatment. Analgesics (85% of thepatients), anticoagulants (80%), mineral supplements (77%), laxatives(52%) and antihypertensives (46%) were the drug classes most frequentlyprescribed. Mean costs of treatment as per DP was160.4 ± 179.4 Euros. Generic prescription represented more than 5%of the costs for 3 therapeutic classes (cholesterol-lowering agents(64%), antihypertensives (50%) and antidepressants (47%)).Discussion & Conclusion The high discrepancy rate between medicationlisted in the DP and the DS highlights a need for safetyimprovement. Potential benefits are expected from reinforced pharmacist-physician collaboration in transition from hospital to primarycare. In addition, even though Beers' criteria are questionable, thedrugs prescribed in this already fragile population, and the potentialopportunities of economical optimizations, are advocating thedevelopment and the scientific evaluation of a structured advancedcollaborative pharmacy practice service. This foresees improvedeffectiveness, safety and efficiency in the medication management ofelderly persons.

Time consumption analysis of the mechanized cut-to-length harvesting system

[Abstract]

Quantitative morphometry analysis of the fetal brain using clinical MR imaging

In vivo fetal magnetic resonance imaging provides aunique approach for the study of early human braindevelopment [1]. In utero cerebral morphometry couldpotentially be used as a marker of the cerebralmaturation and help to distinguish between normal andabnormal development in ambiguous situations. However,this quantitative approach is a major challenge becauseof the movement of the fetus inside the amniotic cavity,the poor spatial resolution provided by very fast MRIsequences and the partial volume effect. Extensiveefforts are made to deal with the reconstruction ofhigh-resolution 3D fetal volumes based on severalacquisitions with lower resolution [2,3,4]. Frameworkswere developed for the segmentation of specific regionsof the fetal brain such as posterior fossa, brainstem orgerminal matrix [5,6], or for the entire brain tissue[7,8], applying the Expectation-Maximization MarkovRandom Field (EM-MRF) framework. However, many of theseprevious works focused on the young fetus (i.e. before 24weeks) and use anatomical atlas priors to segment thedifferent tissue or regions. As most of the gyraldevelopment takes place after the 24th week, acomprehensive and clinically meaningful study of thefetal brain should not dismiss the third trimester ofgestation. To cope with the rapidly changing appearanceof the developing brain, some authors proposed a dynamicatlas [8]. To our opinion, this approach however faces arisk of circularity: each brain will be analyzed /deformed using the template of its biological age,potentially biasing the effective developmental delay.Here, we expand our previous work [9] to proposepost-processing pipeline without prior that allow acomprehensive set of morphometric measurement devoted toclinical application. Data set & Methods: Prenatal MRimaging was performed with a 1-T system (GE MedicalSystems, Milwaukee) using single shot fast spin echo(ssFSE) sequences (TR 7000 ms, TE 180 ms, FOV 40 x 40 cm,slice thickness 5.4mm, in plane spatial resolution1.09mm). For each fetus, 6 axial volumes shifted by 1 mmwere acquired under motherâeuro?s sedation (about 1min pervolume). First, each volume is segmentedsemi-automatically using region-growing algorithms toextract fetal brain from surrounding maternal tissues.Inhomogeneity intensity correction [10] and linearintensity normalization are then performed. Brain tissues(CSF, GM and WM) are then segmented based on thelow-resolution volumes as presented in [9]. Ahigh-resolution image with isotropic voxel size of 1.09mm is created as proposed in [2] and using B-splines forthe scattered data interpolation [11]. Basal gangliasegmentation is performed using a levet setimplementation on the high-resolution volume [12]. Theresulting white matter image is then binarized and givenas an input in FreeSurfer software(http://surfer.nmr.mgh.harvard.edu) to providetopologically accurate three-dimensional reconstructionsof the fetal brain according to the local intensitygradient. References: [1] Guibaud, Prenatal Diagnosis29(4) (2009). [2] Rousseau, Acad. Rad. 13(9), 2006. [3]Jiang, IEEE TMI 2007. [4] Warfield IADB, MICCAI 2009. [5]Claude, IEEE Trans. Bio. Eng. 51(4) 2004. [6] Habas,MICCAI 2008. [7] Bertelsen, ISMRM 2009. [8] Habas,Neuroimage 53(2) 2010. [9] Bach Cuadra, IADB, MICCAI2009. [10] Styner, IEEE TMI 19(39 (2000). [11] Lee, IEEETrans. Visual. And Comp. Graph. 3(3), 1997. [12] BachCuadra, ISMRM 2010.

RiskDiff: A web tool for the analysis of the difference due to risk and demographic factors for incidence or mortality data.

Background Analysing the observed differences for incidence or mortality of a particular disease between two different situations (such as time points, geographical areas, gender or other social characteristics) can be useful both for scientific or administrative purposes. From an epidemiological and public health point of view, it is of great interest to assess the effect of demographic factors in these observed differences in order to elucidate the effect of the risk of developing a disease or dying from it. The method proposed by Bashir and Estève, which splits the observed variation into three components: risk, population structure and population size is a common choice at practice. Results A web-based application, called RiskDiff has been implemented (available at http://rht.iconcologia.net/riskdiff.htm webcite), to perform this kind of statistical analyses, providing text and graphical summaries. Code from the implemented functions in R is also provided. An application to cancer mortality data from Catalonia is used for illustration. Conclusions Combining epidemiological with demographical factors is crucial for analysing incidence or mortality from a disease, especially if the population pyramids show substantial differences. The tool implemented may serve to promote and divulgate the use of this method to give advice for epidemiologic interpretation and decision making in public health.

Cross-scale analysis of the region effect on vascular plant species diversity in southern and northern European mountain ranges.

Background: The divergent glacial histories of southern and northern Europe affect present-day species diversity at coarse-grained scales in these two regions, but do these effects also penetrate to the more fine-grained scales of local communities?Methodology/Principal Findings: We carried out a cross-scale analysis to address this question for vascular plants in two mountain regions, the Alps in southern Europe and the Scandes in northern Europe, using environmentally paired vegetation plots in the two regions (n = 403 in each region) to quantify four diversity components: (i) total number of species occurring in a region (total gamma-diversity), (ii) number of species that could occur in a target plot after environmental filtering (habitat-specific gamma-diversity), (iii) pair-wise species compositional turnover between plots (plot-to-plot beta-diversity) and (iv) number of species present per plot (plot gamma-diversity). We found strong region effects on total gamma-diversity, habitat-specific gamma-diversity and plot-to-plot beta-diversity, with a greater diversity in the Alps even towards distances smaller than 50 m between plots. In contrast, there was a slightly greater plot alpha-diversity in the Scandes, but with a tendency towards contrasting region effects on high and low soil-acidity plots.Conclusions/Significance: We conclude that there are strong regional differences between coarse-grained (landscape- to regional-scale) diversity components of the flora in the Alps and the Scandes mountain ranges,but that these differences do not necessarily penetrate to the finest-grained (plot-scale) diversity component, at least not on acidic soils. Because different processes can lead to a similar pattern, we discuss the consistency of our results with Quaternary history and other divergent features between the two regions such as habitat connectivity, selection for vagility and environmental differences not accounted for in our analyses

Comparative analysis of the transcriptome across distant species.

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.

Meta-analysis of the effects of MI training on clinicians' behavior.

MI-based interventions are widely used with a number of different clinical populations and their efficacy has been well established. However, the clinicians' training has not traditionally been the focus of empirical investigations. We conducted a meta-analytic review of clinicians' MI-training and MI-skills findings. Fifteen studies were included, involving 715 clinicians. Pre-post training effect sizes were calculated (13 studies) as well as group contrast effect sizes (7 studies). Pre-post training comparisons showed medium to large ES of MI training, which are maintained over a short period of time. When compared to a control group, our results also suggested higher MI proficiency in the professionals trained in MI than in nontrained ones (medium ES). However, this estimate of ES may be affected by a publication bias and therefore, should be considered with caution. Methodological limitations and potential sources of heterogeneity of the studies included in this meta-analysis are discussed.

Heat Transfer Analysis of the EPR Core Catcher Test Facility Volley

Uusi EPR-reaktorikonsepti on suunniteltu selviytymään tapauksista, joissa reaktorinsydän sulaa ja sula puhkaisee paineastian. Suojarakennuksen sisälle on suunniteltu alue, jolle sula passiivisesti kerätään, pidätetään ja jäähdytetään. Alueelle laaditaan valurautaelementeistä ns.sydänsieppari, joka tulvitetaan vedellä. Sydänsulan tuottama jälkilämpö siirtyyveteen, mistä se poistetaan suojarakennuksen jälkilämmönpoistojärjestelmän kautta. Suuri osa lämmöstä poistuu sydänsulasta sen yläpuolella olevaan veteen, mutta lämmönsiirron tehostamiseksi myös sydänsiepparin alapuolelle on sijoitettu vedellä täytettävät jäähdytyskanavat. Jotta sydänsiepparin toiminta voitaisiin todentaa, on Lappeenrannan Teknillisellä Yliopistolla rakennettu Volley-koelaitteisto tätä tarkoitusta varten. Koelaitteisto koostuu kahdesta täysimittaisesta valuraudasta tehdystä jäähdytyskanavasta. Sydänsulan tuottamaa jälkilämpöä simuloidaan koelaitteistossa sähkövastuksilla. Tässä työssä kuvataan simulaatioiden suorittaminen ja vertaillaan saatuja arvoja mittaustuloksiin. Työ keskittyy sydänsiepparista jäähdytyskanaviin tapahtuvan lämmönsiirron teoriaan jamekanismeihin. Työssä esitetään kolme erilaista korrelaatiota lämmönsiirtokertoimille allaskiehumisen tapauksessa. Nämä korrelaatiot soveltuvat erityisesti tapauksiin, joissa vain muutamia mittausparametreja on tiedossa. Työn toinen osa onVolley 04 -kokeiden simulointi. Ensin käytettyä simulointitapaa on kelpoistettuvertaamalla tuloksia Volley 04 ja 05 -kokeisiin, joissa koetta voitiin jatkaa tasapainotilaan ja joissa jäähdytteen käyttäytyminen jäähdytyskanavassa on tallennettu myös videokameralla. Näiden simulaatioiden tulokset ovat hyvin samanlaisiakuin mittaustulokset. Korkeammilla lämmitystehoilla kokeissa esiintyi vesi-iskuja, jotka rikkoivat videoinnin mahdollistavia ikkunoita. Tämän johdosta osassa Volley 04 -kokeita ikkunat peitettiin metallilevyillä. Joitakin kokeita jouduttiin keskeyttämään laitteiston suurten lämpöjännitysten johdosta. Tällaisten testien simulaatiot eivät ole yksinkertaisia suorittaa. Veden pinnan korkeudesta ei ole visuaalista havaintoa. Myöskään jäähdytteen tasapainotilanlämpötiloista ei ole tarkkaa tietoa, mutta joitakin oletuksia voidaan tehdä samoilla parametreilla tehtyjen Volley 05 -kokeiden perusteella. Mittaustulokset Volley 04 ja 05 -kokeista, jotka on videoitu ja voitu ajaa tasapainotilaan saakka, antoivat simulaatioiden kanssa hyvin samankaltaisia lämpötilojen arvoja. Keskeytettyjen kokeiden ekstrapolointi tasapainotilaan ei onnistunut kovin hyvin. Kokeet jouduttiin keskeyttämään niin paljon ennen termohydraulista tasapainoa, ettei tasapainotilan reunaehtoja voitu ennustaa. Videonauhoituksen puuttuessa ei veden pinnan korkeudesta saatu lisätietoa. Tuloksista voidaan lähinnä esittää arvioita siitä, mitä suuruusluokkaa mittapisteiden lämpötilat tulevat olemaan. Nämä lämpötilat ovat kuitenkin selvästi alle sydänsiepparissa käytettävän valuraudan sulamislämpötilan. Joten simulaatioiden perusteella voidaan sanoa, etteivät jäähdytyskanavien rakenteet sula, mikäli niissä on pienikin jäähdytevirtaus, eikä useampia kuin muutama vierekkäinen kanava ole täysin kuivana.

Market Opportunity Analysis of the Finnish Mineral Wool Market

Tutkimuksen tarkoituksena on tutkia markkinamahdollisuuksia Suomeneristevillamarkkinoilla. Tutkimuksessa on sekä teoreettinen, että käytännön osuus. Teoreettisessa osiossa luodaan pohja empiiriselle tutkimukselle tutkimalla markkinamahdollisuusanalyysin eri komponenttien sisältöä. Empiirisessä osiossa haastatellaan markkinoiden suurimpia asiakkaita, jotka vastaavat valtaosasta markkinoiden ostovolyymista. Näiden haastattelujen pohjalta pyritään löytämään ne mahdollisuudet mitä eristevillamarkkinoilla on. Tutkimus osoittaa, että markkinamahdollisuusanalyysin eri komponentit ovat tiiviissä keskinäisessä suhteessa. Kattavalla tutkimuksella kyetään osoittamaan eri mahdollisuuksia markkinoilla. Empiirisessä osiossa kyetään osoittamaan, että Suomen eristevillamarkkinoilla on mahdollisuuksia uudelle toimittajalle. Tutkimuksessa esitetään myös joitakin toimenpide-ehdotuksia näiden havaittujen mahdollisuuksien hyödyntämiseksi.

Pseudoachondroplasia and multiple epiphyseal dysplasia: a 7-year comprehensive analysis of the known disease genes identify novel and recurrent mutations and provides an accurate assessment of their relative contribution.

Pseudoachondroplasia (PSACH) and multiple epiphyseal dysplasia (MED) are relatively common skeletal dysplasias resulting in short-limbed dwarfism, joint pain, and stiffness. PSACH and the largest proportion of autosomal dominant MED (AD-MED) results from mutations in cartilage oligomeric matrix protein (COMP); however, AD-MED is genetically heterogenous and can also result from mutations in matrilin-3 (MATN3) and type IX collagen (COL9A1, COL9A2, and COL9A3). In contrast, autosomal recessive MED (rMED) appears to result exclusively from mutations in sulphate transporter solute carrier family 26 (SLC26A2). The diagnosis of PSACH and MED can be difficult for the nonexpert due to various complications and similarities with other related diseases and often mutation analysis is requested to either confirm or exclude the diagnosis. Since 2003, the European Skeletal Dysplasia Network (ESDN) has used an on-line review system to efficiently diagnose cases referred to the network prior to mutation analysis. In this study, we present the molecular findings in 130 patients referred to ESDN, which includes the identification of novel and recurrent mutations in over 100 patients. Furthermore, this study provides the first indication of the relative contribution of each gene and confirms that they account for the majority of PSACH and MED.

'Herbal' but potentially hazardous: an analysis of the constituents and smoke emissions of tobacco-free waterpipe products and the air quality in the cafes where they are served

BACKGROUND: There are limited data on the composition and smoke emissions of 'herbal' shisha products and the air quality of establishments where they are smoked. METHODS: Three studies of 'herbal' shisha were conducted: (1) samples of 'herbal' shisha products were chemically analysed; (2) 'herbal' and tobacco shisha were burned in a waterpipe smoking machine and main and sidestream smoke analysed by standard methods and (3) the air quality of six waterpipe cafes was assessed by measurement of CO, particulate and nicotine vapour content. RESULTS: We found considerable variation in heavy metal content between the three products sampled, one being particularly high in lead, chromium, nickel and arsenic. A similar pattern emerged for polycyclic aromatic hydrocarbons. Smoke emission analyses indicated that toxic byproducts produced by the combustion of 'herbal' shisha were equivalent or greater than those produced by tobacco shisha. The results of our air quality assessment demonstrated that mean PM2.5 levels and CO content were significantly higher in waterpipe establishments compared to a casino where cigarette smoking was permitted. Nicotine vapour was detected in one of the waterpipe cafes. CONCLUSIONS: 'Herbal' shisha products tested contained toxic trace metals and PAHs levels equivalent to, or in excess of, that found in cigarettes. Their mainstream and sidestream smoke emissions contained carcinogens equivalent to, or in excess of, those of tobacco products. The content of the air in the waterpipe cafes tested was potentially hazardous. These data, in aggregate, suggest that smoking 'herbal' shisha may well be dangerous to health.