An efficient algorithm to perform multiple testing in epistasis screening

Background: Research in epistasis or gene-gene interaction detection for human complex traits has grown over the last few years. It has been marked by promising methodological developments, improved translation efforts of statistical epistasis to biological epistasis and attempts to integrate different omics information sources into the epistasis screening to enhance power. The quest for gene-gene interactions poses severe multiple-testing problems. In this context, the maxT algorithm is one technique to control the false-positive rate. However, the memory needed by this algorithm rises linearly with the amount of hypothesis tests. Gene-gene interaction studies will require a memory proportional to the squared number of SNPs. A genome-wide epistasis search would therefore require terabytes of memory. Hence, cache problems are likely to occur, increasing the computation time. In this work we present a new version of maxT, requiring an amount of memory independent from the number of genetic effects to be investigated. This algorithm was implemented in C++ in our epistasis screening software MBMDR-3.0.3. We evaluate the new implementation in terms of memory efficiency and speed using simulated data. The software is illustrated on real-life data for Crohn’s disease. Results: In the case of a binary (affected/unaffected) trait, the parallel workflow of MBMDR-3.0.3 analyzes all gene-gene interactions with a dataset of 100,000 SNPs typed on 1000 individuals within 4 days and 9 hours, using 999 permutations of the trait to assess statistical significance, on a cluster composed of 10 blades, containing each four Quad-Core AMD Opteron(tm) Processor 2352 2.1 GHz. In the case of a continuous trait, a similar run takes 9 days. Our program found 14 SNP-SNP interactions with a multiple-testing corrected p-value of less than 0.05 on real-life Crohn’s disease (CD) data. Conclusions: Our software is the first implementation of the MB-MDR methodology able to solve large-scale SNP-SNP interactions problems within a few days, without using much memory, while adequately controlling the type I error rates. A new implementation to reach genome-wide epistasis screening is under construction. In the context of Crohn’s disease, MBMDR-3.0.3 could identify epistasis involving regions that are well known in the field and could be explained from a biological point of view. This demonstrates the power of our software to find relevant phenotype-genotype higher-order associations.

Les médias et le politique : actes du colloque Le français parlé dans les médias, Lausanne, 1-4 septembre 2009

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Seroepidemiology of herpes simplex virus type 1 and 2 in pregnant women in Switzerland: an obstetric clinic based study.

OBJECTIVE: To assess the seroprevalence of herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) IgG antibodies and the seroincidence of HSV-1 and HSV-2 infections in pregnant women attending the maternity clinic of the University Hospital Lausanne. STUDY DESIGN: Blood samples from 1030 women were taken at the usual pregnancy visit in the first trimester to assess the prevalence rate of IgG antibodies against HSV-1 and HSV-2 using a type-specific assay. A second blood sample was taken 6-8 weeks postpartum from returning women who were seronegative for HSV-2 or HSV-1 to assess the incidence of seroconversion (primary infection). RESULTS: The seroprevalence rates were 79.4% (95% CI: 76.9-81.9) for HSV-1 and 21.2% (18.7-23.7) for HSV-2 in women 14-46 years old. Type-specific serostatus patterns were as follows: 17.3% HSV-1/-2: +/+, 62.1% HSV-1/-2: +/-, 3.9% HSV-1/-2: -/+, 16.7% HSV-1/-2: -/-. Two hundred and sixty five women (59 of the 212 seronegative for HSV-1 (27.8%) and 265 of the 812 seronegative for HSV-2 (32.6%)) returned to the outpatient clinic for the post-delivery check and a second blood sample was obtained. One HSV-1 seroconversion was detected (HSV-1 seroconversion rate 2.4%/100 patient×year (95% CI: 0.06-13.4)) in a patient who had symptoms compatible with primary genital herpes. No HSV-2 seroconversion was detected (HSV-2 seroconversion rate: 0/100 patient×year (97.5% one-sided CI: 0-2)). CONCLUSION: Compared to a previous population-based study, our study results suggest a rise in the prevalence of HSV-2 among pregnant women in Switzerland. The low incidence of seroconversion detected during pregnancy is consistent with the very low reported incidence of neonatal herpes in Switzerland. CONDENSATION: This study in a public hospital in Western Switzerland suggests an increasing prevalence of HSV-2, but a low incidence of primary infections in women of childbearing age.

1,2-Dimethylindole-3-sulfonyl (MIS) as protecting group for the side chain of arginine

The protection of arginine (Arg) side chains is a crucial issue in peptide chemistry because of the propensity of the basic guanidinium group to produce side reactions. Currently, sulfonyl-type protecting groups, such as 2,2,5,7,8-pentamethylchroman (Pmc) and 2,2,4,6,7-pentamethyldihydrobenzofurane (Pbf), are the most widely used for this purpose. Nevertheless, Arg side chain protection remains problematic as a result of the acid stability of these two compounds. This issue is even more relevant in Arg-rich sequences, acid-sensitive peptides and large-scale syntheses. The 1,2-dimethylindole-3-sulfonyl (MIS) group is more acid-labile than Pmc and Pbf and can therefore be a better option for Arg side chain protection. In addition, MIS is compatible with tryptophan-containing peptides.

Chronic kidney disease in type 2 diabetic patients followed-up by primary care physicians in Switzerland: prevalence and prescription of antidiabetic drugs.

QUESTION UNDER STUDY: The aim of this study was to assess the prevalence of chronic kidney disease (CKD) among type 2 diabetic patients in primary care settings in Switzerland, and to analyse the prescription of antidiabetic drugs in CKD according to the prevailing recommendations. METHODS: In this cross-sectional study, each participating physician was asked to introduce anonymously in a web database the data from up to 15 consecutive diabetic patients attending her/his office between December 2013 and June 2014. Demographic, clinical and biochemical data were analysed. CKD was classified with the KDIGO nomenclature based on estimated glomerular filtration rate (eGFR) and urinary albumin/creatinine ratio. RESULTS: A total of 1 359 patients (mean age 66.5 ± 12.4 years) were included by 109 primary care physicians. CKD stages 3a, 3b and 4 were present in 13.9%, 6.1%, and 2.4% of patients, respectively. Only 30.6% of patients had an entry for urinary albumin/creatinine ratio. Among them, 35.6% were in CKD stage A2, and 4.1% in stage A3. Despite prevailing limitations, metformin and sulfonylureas were prescribed in 53.9% and 16.5%, respectively, of patients with advanced CKD (eGFR <30 ml/min). More than a third of patients were on a dipeptidyl-peptidase-4 inhibitor across all CKD stages. Insulin use increased progressively from 26.8% in CKD stage 1-2 to 50% in stage 4. CONCLUSIONS: CKD is frequent in patients with type 2 diabetes attending Swiss primary care practices, with CKD stage 3 and 4 affecting 22.4% of cases. This emphasizes the importance of routine screening of diabetic nephropathy based on both eGFR and urinary albumin/creatinine ratio, the latter being largely underused by primary care physicians. A careful individual drug risk/benefit balance assessment is mandatory to avoid the frequently observed inappropriate prescription of antidiabetic drugs in CKD patients.

Worldwide trends in diabetes since 1980: a pooled analysis of 751 population-based studies with 4.4 million participants.

One of the global targets for non-communicable diseases is to halt, by 2025, the rise in the age-standardised adult prevalence of diabetes at its 2010 levels. We aimed to estimate worldwide trends in diabetes, how likely it is for countries to achieve the global target, and how changes in prevalence, together with population growth and ageing, are affecting the number of adults with diabetes. We pooled data from population-based studies that had collected data on diabetes through measurement of its biomarkers. We used a Bayesian hierarchical model to estimate trends in diabetes prevalence-defined as fasting plasma glucose of 7.0 mmol/L or higher, or history of diagnosis with diabetes, or use of insulin or oral hypoglycaemic drugs-in 200 countries and territories in 21 regions, by sex and from 1980 to 2014. We also calculated the posterior probability of meeting the global diabetes target if post-2000 trends continue. We used data from 751 studies including 4,372,000 adults from 146 of the 200 countries we make estimates for. Global age-standardised diabetes prevalence increased from 4.3% (95% credible interval 2.4-7.0) in 1980 to 9.0% (7.2-11.1) in 2014 in men, and from 5.0% (2.9-7.9) to 7.9% (6.4-9.7) in women. The number of adults with diabetes in the world increased from 108 million in 1980 to 422 million in 2014 (28.5% due to the rise in prevalence, 39.7% due to population growth and ageing, and 31.8% due to interaction of these two factors). Age-standardised adult diabetes prevalence in 2014 was lowest in northwestern Europe, and highest in Polynesia and Micronesia, at nearly 25%, followed by Melanesia and the Middle East and north Africa. Between 1980 and 2014 there was little change in age-standardised diabetes prevalence in adult women in continental western Europe, although crude prevalence rose because of ageing of the population. By contrast, age-standardised adult prevalence rose by 15 percentage points in men and women in Polynesia and Micronesia. In 2014, American Samoa had the highest national prevalence of diabetes (>30% in both sexes), with age-standardised adult prevalence also higher than 25% in some other islands in Polynesia and Micronesia. If post-2000 trends continue, the probability of meeting the global target of halting the rise in the prevalence of diabetes by 2025 at the 2010 level worldwide is lower than 1% for men and is 1% for women. Only nine countries for men and 29 countries for women, mostly in western Europe, have a 50% or higher probability of meeting the global target. Since 1980, age-standardised diabetes prevalence in adults has increased, or at best remained unchanged, in every country. Together with population growth and ageing, this rise has led to a near quadrupling of the number of adults with diabetes worldwide. The burden of diabetes, both in terms of prevalence and number of adults affected, has increased faster in low-income and middle-income countries than in high-income countries. Wellcome Trust.

Síntese de novas fitotoxinas derivadas do 8-oxabiciclo[3.2.1]oct-6-en-3-ona

The [4+3] cycloaddition was utilized in order to prepare 8-oxabicyclo[3.2.1]oct-6-en-3-one (1) derivatives. The correspondent acetonide 6 was converted into several alcohols (11-16). Addition of aryllithium reagents to 6 resulted in 3-(2-fluorophenyl)-6,7-exo-isopropylidenedioxy -8-oxabicyclo[3.2.1]octan-3alpha-ol (11, 72%) and 3-(2,4-dimethoxyphenyl)-6,7-exo-isopropylidenedioxy-8-oxabicyclo[3.2.1]octan -3alpha-ol (16, 20%). The 3-butyl-6,7-exo-isopropylidenedioxy-8-oxabicyclo[3.2.1]octan-3 alpha-ol (15, 56%) was obtained through a Grignard reaction. Reduction of 6 resulted in 6,7-exo-isopropylidenedioxy-8-oxabicyclo[3.2.1]octan-3 beta-ol (7, 62%) and 6,7-exo-isopropylidenedioxy-8-oxabicyclo[3.2.1]octan-3 alpha-ol (8, 20%). The alcohols were treated with thionyl chloride in pyridine, and the corresponding alkenes were obtained with 31-80% yield. The effect of these compounds on the development of radicle and aerial parts of Sorghum bicolor was evaluated.

Desenvolvimento de abordagem objetivando a síntese da 3-desidroxi-4-metoxi-tubastrina

We report the synthesis of amino(2-hydroxy-2-(4-methoxyphenyl)ethylamino)methaniminium (14) as a direct precursor of a tubastrine derivative (3-dehydroxy-4-methoxytubastrine). The synthetic steps involved functional group interconversions starting from 1-(4-methoxyphenyl)ethanone to obtain the guanidine-protected derivative 13. Tentative dehydration of 13 with SiOH-adsorbed CuSO4 resulted in guanidine deprotection only. This was an unexpected result, since there are no reports of CuSO4.SiOH as Boc-deprotecting of guanidines. The product 14 was obtained in five steps and 5.4 % overall yield, and constitutes a direct precursor of 3-dehydroxy-4-methoxytubastrine.

Multisystem Developmental Disorder in Children from 2 to 6 Years Old : A Three Years Follow-Up Study

This research studied children who had been diagnosed with Multisystem Developmental Disorder (MSDD) (NC, 2002) under the Diagnostic Classifications of Mental Health and Developmental Disorders of Infancy and Early Childhood (DC: 0 - 3). They all showed, to a varying degree, difficulties in relating to others, play, affective interaction and severe delay in developing communication skills. Some studies have observed continuity in the diagnosis of autism during the first years of life. The objective of this study is to analyse the development of infants with MSDD whose diagnosis of autism was not confirmed. We also attempted to verify any possible psychomotor developmental differences based on, or related to, the severity and typology (B and C) of the MSDD. To enable us to do this we carried out a 3-year follow-up during which we assessed the infants (n = 15) and their parents. They are 2 - 4 years old. Results showed that type B children did present a greater impairment of psychomotor development in assessment tests. However, we did not observe any correlation between the degree of severity of the initial symptoms and later diagnoses. Conclusion: although our sample is small, we can conclude that there isn’t a clear evolution in the diagnosis, but we have found significant differences in the symptomatology between the type B and C

Síntese de derivados 4-aril-3,4-di-hidrocumarínicos catalisada por NbCl5

Multicomponent reactions between phenols, β-diesters and benzaldehydes for the synthesis of 4-aryl-3,4-dihydrocoumarin derivatives were carried out under mild conditions (room temperature) and presented moderate yields (38-88%) and reasonable reaction times (2-4 days), using niobium pentachloride as a catalyst.

Acoplamento de cloreto de 4-nitrofenildiazônio com nucleófilos alifáticos: experimento integrado de síntese orgânica e cristalografia de raios X

This article describes an undergraduate experiment for the synthesis of p-nitrophenyldiazonium chloride and its coupling with acetylacetone and two enaminones, 4-phenylamino-pent-3-en-2-one and 4-amino-pent-3-en-2-one, in an adaptation of a previously reported synthetic protocol. The azo dyes 4-(E)-phenylamino-3-[(E)-2-(4-nitrophenylazo)]-3-penten-2-one and 4-(E)-amino-3-[(E)-2-(4-nitrophenylazo)]-3-penten-2-one were obtained, and the solid state structure of this latter azo compound was characterized by single crystal X-ray diffraction studies. This two-week integrated laboratory approach involves simple synthetic experiments and microwave chemistry in the organic laboratory plus crystallography analysis, suitable for novice students on undergraduate experimental chemistry courses.

Determinação das energias de ativação para nucleação de precipitados e difusão da prata na liga cu-2%al com adições de prata

As energias de ativação para nucleação de precipitados ricos em prata e de difusão da prata no cobre, em ligas de Cu-2%Al contendo 2, 4, 6, 8, 10 e 12%Ag, em peso, foram determinadas utilizando-se medidas de variação da microdureza com a temperatura e o tempo de envelhecimento. Os resultados indicaram que, com o método utilizado, é possível obter valores para as energias de ativação para nucleação da fase rica em prata e de difusão da prata no cobre bastante próximos daqueles citados na literatura.

Fitotoxicidade de novos álcoois e alquenos derivados do 2alfa,4alfa-dimetil-8-oxabiciclo[3.2.1]oct-6-en-3-ona

A reação de cicloadição [4+3] entre o furano e o cátion oxialílico, gerado in situ a partir da 2,4-dibromopentan-3-ona, forneceu o 2alfa,4alfa-dimetil-8-oxabiciclo[3.2.1]oct-6-en-3-ona (1). A oxidação catalítica do oxabiciclo 1 com tetróxido de ósmio em presença de peróxido de hidrogênio em excesso levou à formação do acetonídeo 10, a partir do qual foram obtidos os álcoois 2, 11-15, com rendimentos de 23-86%. O tratamento dos álcoois 11-13 com cloreto de tionila, em presença de piridina, resultou nos respectivos alquenos 17 (94%), 18 (89%) e 19 (80%). A atividade herbicida dos compostos foi avaliada sobre o desenvolvimento do sistema radicular de Sorghum bicolor L. e Cucumis sativus L., nas concentrações de 100 e 250 ppm.

2. Sinfonie : (Thüringische Sinfonie)

Soitinnus: orkesteri.