Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.

A single LC-tandem mass spectrometry method for the simultaneous determination of 14 antimalarial drugs and their metabolites in human plasma.

Among the various determinants of treatment response, the achievement of sufficient blood levels is essential for curing malaria. For helping us at improving our current understanding of antimalarial drugs pharmacokinetics, efficacy and toxicity, we have developed a liquid chromatography-tandem mass spectrometry method (LC-MS/MS) requiring 200mul of plasma for the simultaneous determination of 14 antimalarial drugs and their metabolites which are the components of the current first-line combination treatments for malaria (artemether, artesunate, dihydroartemisinin, amodiaquine, N-desethyl-amodiaquine, lumefantrine, desbutyl-lumefantrine, piperaquine, pyronaridine, mefloquine, chloroquine, quinine, pyrimethamine and sulfadoxine). Plasma is purified by a combination of protein precipitation, evaporation and reconstitution in methanol/ammonium formate 20mM (pH 4.0) 1:1. Reverse-phase chromatographic separation of antimalarial drugs is obtained using a gradient elution of 20mM ammonium formate and acetonitrile both containing 0.5% formic acid, followed by rinsing and re-equilibration to the initial solvent composition up to 21min. Analyte quantification, using matrix-matched calibration samples, is performed by electro-spray ionization-triple quadrupole mass spectrometry by selected reaction monitoring detection in the positive mode. The method was validated according to FDA recommendations, including assessment of extraction yield, matrix effect variability, overall process efficiency, standard addition experiments as well as antimalarials short- and long-term stability in plasma. The reactivity of endoperoxide-containing antimalarials in the presence of hemolysis was tested both in vitro and on malaria patients samples. With this method, signal intensity of artemisinin decreased by about 20% in the presence of 0.2% hemolysed red-blood cells in plasma, whereas its derivatives were essentially not affected. The method is precise (inter-day CV%: 3.1-12.6%) and sensitive (lower limits of quantification 0.15-3.0 and 0.75-5ng/ml for basic/neutral antimalarials and artemisinin derivatives, respectively). This is the first broad-range LC-MS/MS assay covering the currently in-use antimalarials. It is an improvement over previous methods in terms of convenience (a single extraction procedure for 14 major antimalarials and metabolites reducing significantly the analytical time), sensitivity, selectivity and throughput. While its main limitation is investment costs for the equipment, plasma samples can be collected in the field and kept at 4 degrees C for up to 48h before storage at -80 degrees C. It is suited to detecting the presence of drug in subjects for screening purposes and quantifying drug exposure after treatment. It may contribute to filling the current knowledge gaps in the pharmacokinetics/pharmacodynamics relationships of antimalarials and better define the therapeutic dose ranges in different patient populations.

Concurrent and simultaneous polydrug use among young Swiss males: use patterns and associations of number of substances used with health issues.

Background: Simultaneous polydrug use (SPU) may represent a greater incremental risk factor for human health than concurrent polydrug use (CPU). However, few studies have examined these patterns of use in relation to health issues, particularly with regard to the number of drugs used. Methods: In the present study, we have analyzed data from a representative sample of 5734 young Swiss males from the Cohort Study on Substance Use Risk Factors. Exposure to drugs (i.e., alcohol, tobacco, cannabis, and 15 other illicit drugs), as well as mental, social and physical factors, were studied through regression analysis. Results: We found that individuals engaging in CPU and SPU followed the known stages of drug use, involving initial experiences with licit drugs (e.g., alcohol and tobacco), followed by use of cannabis and then other illicit drugs. In this regard, two classes of illicit drugs were identified, including first uppers, hallucinogens and sniffed drugs; and then "harder" drugs (ketamine, heroin, and crystal meth), which were only consumed by polydrug users who were already taking numerous drugs. Moreover, we observed an association between the number of drugs used simultaneously and social issues (i.e., social consequences and aggressiveness). In fact, the more often the participants simultaneously used substances, the more likely they were to experience social problems. In contrast, we did not find any relationship between SPU and depression, anxiety, health consequences, or health. Conclusions: We identified some associations with SPU that were independent of CPU. Moreover, we found that the number of concurrently used drugs can be a strong factor associated with mental and physical health, although their simultaneous use may not significantly contribute to this association. Finally, the negative effects related to the use of one substance might be counteracted by the use of an additional substance.

Improving the performance of positive selection inference by filtering unreliable alignment regions.

Errors in the inferred multiple sequence alignment may lead to false prediction of positive selection. Recently, methods for detecting unreliable alignment regions were developed and were shown to accurately identify incorrectly aligned regions. While removing unreliable alignment regions is expected to increase the accuracy of positive selection inference, such filtering may also significantly decrease the power of the test, as positively selected regions are fast evolving, and those same regions are often those that are difficult to align. Here, we used realistic simulations that mimic sequence evolution of HIV-1 genes to test the hypothesis that the performance of positive selection inference using codon models can be improved by removing unreliable alignment regions. Our study shows that the benefit of removing unreliable regions exceeds the loss of power due to the removal of some of the true positively selected sites.

Simultaneous B(0)- and B(1)+-map acquisition for fast localized shim, frequency, and RF power determination in the heart at 3 T.

High-field (>or=3 T) cardiac MRI is challenged by inhomogeneities of both the static magnetic field (B(0)) and the transmit radiofrequency field (B(1)+). The inhomogeneous B fields not only demand improved shimming methods but also impede the correct determination of the zero-order terms, i.e., the local resonance frequency f(0) and the radiofrequency power to generate the intended local B(1)+ field. In this work, dual echo time B(0)-map and dual flip angle B(1)+-map acquisition methods are combined to acquire multislice B(0)- and B(1)+-maps simultaneously covering the entire heart in a single breath hold of 18 heartbeats. A previously proposed excitation pulse shape dependent slice profile correction is tested and applied to reduce systematic errors of the multislice B(1)+-map. Localized higher-order shim correction values including the zero-order terms for frequency f(0) and radiofrequency power can be determined based on the acquired B(0)- and B(1)+-maps. This method has been tested in 7 healthy adult human subjects at 3 T and improved the B(0) field homogeneity (standard deviation) from 60 Hz to 35 Hz and the average B(1)+ field from 77% to 100% of the desired B(1)+ field when compared to more commonly used preparation methods.

Quantitative genetic modeling and inference in the presence of nonignorable missing data.

Natural selection is typically exerted at some specific life stages. If natural selection takes place before a trait can be measured, using conventional models can cause wrong inference about population parameters. When the missing data process relates to the trait of interest, a valid inference requires explicit modeling of the missing process. We propose a joint modeling approach, a shared parameter model, to account for nonrandom missing data. It consists of an animal model for the phenotypic data and a logistic model for the missing process, linked by the additive genetic effects. A Bayesian approach is taken and inference is made using integrated nested Laplace approximations. From a simulation study we find that wrongly assuming that missing data are missing at random can result in severely biased estimates of additive genetic variance. Using real data from a wild population of Swiss barn owls Tyto alba, our model indicates that the missing individuals would display large black spots; and we conclude that genes affecting this trait are already under selection before it is expressed. Our model is a tool to correctly estimate the magnitude of both natural selection and additive genetic variance.

Concurrent versus simultaneous use of alcohol and non-medical use of prescription drugs: is simultaneous use worse for mental, social, and health issues?

Abstract This study investigated the difference between concurrent and simultaneous use of alcohol and non-medical use of prescription drugs (NMUPD) in relation to mental, social, and health issues. The 544 study participants of the Swiss ongoing Cohort Study on Substance Use Risk Factors (C-SURF) had a combined use of alcohol with NMUPD during the previous 12 months. Alcohol-related problems (i.e., dependence and consequences), as well as mental, social, and health concerns (i.e., depression, general mental/physical health, and social/health consequences), were assessed. The simultaneous use of alcohol and NMUPD proved to be a greater risk factor for mental, social, and health issues than concurrent use. This study adds information regarding simultaneous polydrug use, which results in distinct effects compared to concurrent use, including important social, psychosocial, and health-related consequences.

Simultaneous biliary drainage and portal vein embolization before extended hepatectomy for hilar cholangiocarcinoma: preliminary experience.

BACKGROUND: Patients with resectable hilar cholangiocarcinoma often present obstructive jaundice and a small future remnant liver (FRL) ratio. A sequential approach comprising preoperative biliary drainage followed by portal vein embolization (PVE) is usually performed but leads to long preoperative management (6-12 weeks) before patients can undergo resection. To simplify and shorten this phase of liver preparation, we developed a new preoperative approach that involves percutaneous biliary drainage and PVE during the same procedure. We report the outcomes of this combined procedure. METHODS: During 1 year, four patients underwent simultaneous biliary drainage and PVE followed 1 month later by surgical resection of hilar cholangiocarcinoma. Liver volumes were assessed by CT before, and 1, and 3 months after the combined procedure. Serum liver enzymes were assessed before and 1 month after the combined procedure. RESULTS: The combined procedure was feasible in all cases, with no related complications. After the combined procedure, transaminases remained stable or decreased, whereas gamma-glutamyl-transpeptidase, alkaline phosphatase, and bilirubin decreased. During the first month, the left lobe volume increased by +27.9 % (range 19-40.9 %). The FRL ratio increased from 24.9 to 33.2 %. All patients underwent R0 liver resection with a favorable postoperative outcome. The remnant liver volume increased by +132 % (range 78-245 %) between 1 and 3 months. CONCLUSIONS: Simultaneous percutaneous biliary drainage and PVE is feasible. This all-in-one preoperative approach greatly decreases waiting time until surgical resection. These encouraging results warrant further investigation to confirm the safety and to evaluate the reduction in the dropout rate for liver resection in this tumor with poor prognosis.

Simultaneous estimation of indirect and interaction effects using structural equation models

Interaction effects are usually modeled by means of moderated regression analysis. Structural equation models with non-linear constraints make it possible to estimate interaction effects while correcting formeasurement error. From the various specifications, Jöreskog and Yang's(1996, 1998), likely the most parsimonious, has been chosen and further simplified. Up to now, only direct effects have been specified, thus wasting much of the capability of the structural equation approach. This paper presents and discusses an extension of Jöreskog and Yang's specification that can handle direct, indirect and interaction effects simultaneously. The model is illustrated by a study of the effects of an interactive style of use of budgets on both company innovation and performance

Simultaneous infection of human host with genetically distinct isolates of Paracoccidioides brasiliensis

This study is the first report on genetic differences between isolates of Paracoccidioides brasiliensis from a single patient. We describe a simultaneous infection with genetically distinct isolates of P. brasiliensis in a patient with chronic paracoccidioidomycosis. The clinical isolates were obtained from lesions in different anatomical sites and were characterised by random amplified polymorphic DNA (RAPD) analysis. The RAPD technique can be helpful for distinguishing between clinical isolates. Different random primers were used to characterise these clinical isolates. The RAPD patterns allowed for differentiation between isolates and the construction of a phenetic tree, which showed more than 28% genetic variability in this fungal species, opening new possibilities for clinical studies of P. brasiliensis. Based on these results and preliminary clinical findings, we suggest that different genotypes of P. brasiliensis might infect the same patient, inducing the active form of the disease.

Inference of distributional parameters from compositional samples containing nondetects

Low concentrations of elements in geochemical analyses have the peculiarity of beingcompositional data and, for a given level of significance, are likely to be beyond thecapabilities of laboratories to distinguish between minute concentrations and completeabsence, thus preventing laboratories from reporting extremely low concentrations of theanalyte. Instead, what is reported is the detection limit, which is the minimumconcentration that conclusively differentiates between presence and absence of theelement. A spatially distributed exhaustive sample is employed in this study to generateunbiased sub-samples, which are further censored to observe the effect that differentdetection limits and sample sizes have on the inference of population distributionsstarting from geochemical analyses having specimens below detection limit (nondetects).The isometric logratio transformation is used to convert the compositional data in thesimplex to samples in real space, thus allowing the practitioner to properly borrow fromthe large source of statistical techniques valid only in real space. The bootstrap method isused to numerically investigate the reliability of inferring several distributionalparameters employing different forms of imputation for the censored data. The casestudy illustrates that, in general, best results are obtained when imputations are madeusing the distribution best fitting the readings above detection limit and exposes theproblems of other more widely used practices. When the sample is spatially correlated, itis necessary to combine the bootstrap with stochastic simulation

Explaining Fiscal Balances with a Simultaneous Equation Model of Revenue and Expenditure : A Case Study of Swiss Cantons Using Panel Data

Empirical literature on the analysis of the efficiency of measures for reducing persistent government deficits has mainly focused on the direct explanation of deficit. By contrast, this paper aims at modeling government revenue and expenditure within a simultaneous framework and deriving the fiscal balance (surplus or deficit) equation as the difference between the two variables. This setting enables one to not only judge how relevant the explanatory variables are in explaining the fiscal balance but also understand their impact on revenue and/or expenditure. Our empirical results, obtained by using a panel data set on Swiss Cantons for the period 1980-2002, confirm the relevance of the approach followed here, by providing unambiguous evidence of a simultaneous relationship between revenue and expenditure. They also reveal strong dynamic components in revenue, expenditure, and fiscal balance. Among the significant determinants of public fiscal balance we not only find the usual business cycle elements, but also and more importantly institutional factors such as the number of administrative units, and the ease with which people can resort to political (direct democracy) instruments, such as public initiatives and referendum.