Lost in parameter space: A road map for Stacks

PublishedThis is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.1.Restriction site-Associated DNA sequencing (RAD-seq) has become a widely adopted method for genotyping populations of model and non-model organisms. Generating a reliable set of loci for downstream analysis requires appropriate use of bioinformatics software, such as the program stacks. 2.Using three empirical RAD-seq datasets, we demonstrate a method for optimising a de novo assembly of loci using stacks. By iterating values of the program's main parameters and plotting resultant core metrics for visualisation, researchers can gain a much better understanding of their dataset and select an optimal set of parameters; we present the 80% rule as a generally effective method to select the core parameters for stacks. 3.Visualisation of the metrics plotted for the three RAD-seq datasets shows that they differ in the optimal parameters that should be used to maximise the amount of available biological information. We also demonstrate that building loci de novo and then integrating alignment positions is more effective than aligning raw reads directly to a reference genome. 4.Our methods will help the community in honing the analytical skills necessary to accurately assemble a RAD-seq dataset.This work was co-funded by the Environment Agency, Westcountry Rivers Trust and the University of Exeter. Overseas collaboration for the project was made possible by funding from The Genetics Society, Santander and the University of Exeter. Thank you to many RAD-seq workshop participants for invaluable insight and new ideas. We thank Dr Nicolas Rochette for his insights into parameter analysis. Thanks also to Dr Andy King for assistance with the brown trout data molecular work and analysis, and Guy Freeman and Martin Young for the species illustrations. Prof Peter Kille and Dr Luis Cunha, Cardiff School of Biosciences, Cardiff University, kindly provided the reference genome of L. rubellus

Modelling prevalence and incidence of fibrosis and pleural plaques in asbestos-exposed populations for screening and follow-up: a cross-sectional study

<p>Abstract</p> <p>Background</p> <p>CT-Scan is currently under assessment for the screening of asbestos-related diseases. However, to date no consensus exists as to how to select high-risk asbestos-exposed populations suitable for such screening programs. The objective of this study is to select the most relevant exposure variables for the prediction of pleural plaques and asbestosis in order to guide clinicians in their use of CT-Scan.</p> <p>Methods</p> <p>A screening program of non malignant asbestos-related diseases by CT-scan was conducted among asbestos-exposed volunteers in France. Precise assessments of asbestos exposure were obtained by occupational hygiene measurements and a job-exposure matrix. Several parameters were calculated (time since first exposure, duration, intensity and cumulative exposure to asbestos). Predictive parameters of prevalence and incidence were then estimated by standard logistic and a complementary log-log regression models.</p> <p>Results</p> <p>1011 subjects were recruited in this screening program among them 474 (46.9%) presented with pleural plaques and 61 (6.0%) with interstitial changes compatible with asbestosis on CT-scan. Time since first exposure (p < 0.0001) and either cumulative or mean exposure (p < 0.0001) showed independent associations with both pleural plaques and asbestosis prevalence and pleural plaques incidence. Modelling incidence of pleural plaques showed a 0.8% to 2.4% yearly increase for a mean exposure of 1 f/ml.</p> <p>Conclusion</p> <p>Our findings confirmed the role played by time since first exposure and dose but not duration in asbestos-related diseases. We recommend to include these parameters in high-risk populations suitable for screening of these diseases. Short-periodicity of survey of pleural plaques by CT-Scan seemed not to be warranted.</p

Determining the Quantum Expectation Value by Measuring a Single Photon

Quantum mechanics, one of the keystones of modern physics, exhibits several peculiar properties, differentiating it from classical mechanics. One of the most intriguing is that variables might not have definite values. A complete quantum description provides only probabilities for obtaining various eigenvalues of a quantum variable. These and corresponding probabilities specify the expectation value of a physical observable, which is known to be a statistical property of an ensemble of quantum systems. In contrast to this paradigm, we demonstrate a unique method allowing to measure the expectation value of a physical variable on a single particle, namely, the polarisation of a single protected photon. This is the first realisation of quantum protective measurements.Comment: Nature Physics, in press (this version corresponds to the one initially submitted to Nature Physics

A frequentist framework of inductive reasoning

Reacting against the limitation of statistics to decision procedures, R. A. Fisher proposed for inductive reasoning the use of the fiducial distribution, a parameter-space distribution of epistemological probability transferred directly from limiting relative frequencies rather than computed according to the Bayes update rule. The proposal is developed as follows using the confidence measure of a scalar parameter of interest. (With the restriction to one-dimensional parameter space, a confidence measure is essentially a fiducial probability distribution free of complications involving ancillary statistics.) A betting game establishes a sense in which confidence measures are the only reliable inferential probability distributions. The equality between the probabilities encoded in a confidence measure and the coverage rates of the corresponding confidence intervals ensures that the measure's rule for assigning confidence levels to hypotheses is uniquely minimax in the game. Although a confidence measure can be computed without any prior distribution, previous knowledge can be incorporated into confidence-based reasoning. To adjust a p-value or confidence interval for prior information, the confidence measure from the observed data can be combined with one or more independent confidence measures representing previous agent opinion. (The former confidence measure may correspond to a posterior distribution with frequentist matching of coverage probabilities.) The representation of subjective knowledge in terms of confidence measures rather than prior probability distributions preserves approximate frequentist validity.Comment: major revisio

CT scan screening is associated with increased distress among subjects of the APExS

<p>Abstract</p> <p>Background</p> <p>The aim of this study was to assess the psychological consequences of HRCT scan screening in retired asbestos-exposed workers.</p> <p>Methods</p> <p>A HRCT-scan screening program for asbestos-related diseases was carried out in four regions of France. At baseline (T1), subjects filled in self-administered occupational questionnaires. In two of the regions, subjects also received a validated psychological scale, namely the psychological consequences questionnaire (PCQ). The physician was required to provide the subject with the results of the HRCT scan at a final visit. A second assessment of psychological consequences was performed 6 months after the HRCT-scan examination (T2). PCQ scores were compared quantitatively (t-test, general linear model) and qualitatively (chi²-test, logistic regression) to screening results. Multivariate analyses were adjusted for gender, age, smoking, asbestos exposure and counseling.</p> <p>Results</p> <p>Among the 832 subjects included in this psychological impact study, HRCT-scan screening was associated with a significant increase of the psychological score 6 months after the examination relative to baseline values (8.31 to 10.08, p < 0.0001, t-test). This increase concerned patients with an abnormal HRCT-scan result, regardless of the abnormalities, but also patients with normal HRCT-scans after adjustment for age, gender, smoking status, asbestos exposure and counseling visit. The greatest increase was observed for pleural plaques (+3.60; 95%CI [+2.15;+5.06]), which are benign lesions. Detection of isolated pulmonary nodules was also associated with a less marked but nevertheless significant increase of distress (+1.88; 95%CI [+0.34;+3.42]). However, analyses based on logistic regressions only showed a close to significant increase of the proportion of subjects with abnormal PCQ scores at T2 for patients with asbestosis (OR = 1.92; 95%CI [0.97-3.81]) or with two or more diseases (OR = 2.04; 95%CI [0.95-4.37]).</p> <p>Conclusion</p> <p>This study suggests that HRCT-scan screening may be associated with increased distress in asbestos-exposed subjects. If confirmed, these results may have consequences for HRCT-scan screening recommendations.</p

Is informed consent related to success in exercise and diet intervention as evaluated at 12 months? DR's EXTRA study

<p>Abstract</p> <p>Background</p> <p>There is a permanent need to evaluate and develop the ethical quality of scientific research and to widen knowledge about the effects of ethical issues. Therefore we evaluated whether informed consent is related to implementation and success in a lifestyle intervention study with older research participants. There is little empirical research into this topic.</p> <p>Methods</p> <p>The subjects (n = 597) are a subgroup of a random population sample of 1410 men and women aged 57-78 years who are participating in a 4-year randomized controlled intervention trial on the effects of physical exercise and diet on atherosclerosis, endothelial function and cognition. Data were collected in two steps: A questionnaire about informed consent was given to all willing participants (n = 1324) three months after the randomization. Data on implementation and success in the exercise and diet interventions were evaluated at 12 months by intervention-group personnel. The main purpose of the analysis procedure performed in this study was to identify and examine potential correlates for the chosen dependent variables and to generate future hypotheses for testing and confirming the independent determinants for implementation and success. The nature of the analysis protocol is exploratory at this stage.</p> <p>Results</p> <p>About half of the participants (54%) had achieved good results in the intervention. Nearly half of the participants (47%) had added to or improved their own activity in some sector of exercise or diet. Significant associations were found between performance in the interventions and participants' knowledge of the purpose of the study (p < 0.001), and between success in interventions and working status (p = 0.02), and the participants' knowledge of the purpose of the study (p = 0.04).</p> <p>Conclusion</p> <p>The main finding of this study was that those participants who were most aware or had understood the purpose of the study at an early stage had also attained better results at their 12-month intervention evaluation. Therefore, implementation and success in intervention is related to whether subjects receive a sufficient amount and are able to comprehend the information provided i.e. the core principles of informed consent.</p> <p>Trial Registration</p> <p>(ISRCTN 45977199)</p

A Study of D0 --> K0(S) K0(S) X Decay Channels

Using data from the FOCUS experiment (FNAL-E831), we report on the decay of $D^0$ mesons into final states containing more than one $K^0_S$. We present evidence for two Cabibbo favored decay modes, $D^0\to K^0_SK^0_S K^- \pi^+$ and $D^0\to K^0_SK^0_S K^+ \pi^-$, and measure their combined branching fraction relative to $D^0\to \bar{K} ^0\pi^+\pi^-$ to be $\frac{\Gamma(D^0\to K^0_SK^0_SK^{\pm}\pi^{\mp})}{\Gamma(D^0\to \bar{K} ^0\pi^+\pi^-)}$ = 0.0106 $\pm$ 0.0019 $\pm$ 0.0010. Further, we report new measurements of $\frac{\Gamma(D^0\to K^0_SK^0_SK^0_S)}{\Gamma(D^0\to \bar{K} ^0\pi^+\pi^-)}$ = 0.0179 $\pm$ 0.0027 $\pm$ 0.0026, $\frac{\Gamma(D^0\to K^0\bar{K} ^0)}{\Gamma(D^0\to \bar{K} ^0\pi^+\pi^-)}$ = 0.0144 $\pm$ 0.0032 $\pm$ 0.0016, and $\frac{\Gamma(D^0\to K^0_SK^0_S\pi^+\pi^-)}{\Gamma(D^0\to \bar{K} ^0\pi^+\pi^-)}$ = 0.0208 $\pm$ 0.0035 $\pm$ 0.0021 where the first error is statistical and the second is systematic.Comment: 11 pages, 3 figures, typos correcte

Mapping the contribution of β3-containing GABA(A )receptors to volatile and intravenous general anesthetic actions

BACKGROUND: Agents belonging to diverse chemical classes are used clinically as general anesthetics. The molecular targets mediating their actions are however still only poorly defined. Both chemical diversity and substantial differences in the clinical actions of general anesthetics suggest that general anesthetic agents may have distinct pharmacological targets. It was demonstrated previously that the immobilizing action of etomidate and propofol is completely, and the immobilizing action of isoflurane partly mediated, by β3-containing GABA(A )receptors. This was determined by using the β3(N265M) mice, which carry a point mutation known to decrease the actions of general anesthetics at recombinant GABA(A )receptors. In this communication, we analyzed the contribution of β3-containing GABA(A )receptors to the pharmacological actions of isoflurane, etomidate and propofol by means of β3(N265M) mice. RESULTS: Isoflurane decreased core body temperature and heart rate to a smaller degree in β3(N265M) mice than in wild type mice, indicating a minor but significant role of β3-containing GABA(A )receptors in these actions. Prolonged time intervals in the ECG and increased heart rate variability were indistinguishable between genotypes, suggesting no involvement of β3-containing GABA(A )receptors. The anterograde amnesic action of propofol was indistinguishable in β3(N265M) and wild type mice, suggesting that it is independent of β3-containing GABA(A )receptors. The increase of heart rate variability and prolongation of ECG intervals by etomidate and propofol were also less pronounced in β3(N265M) mice than in wild type mice, pointing to a limited involvement of β3-containing GABA(A )receptors in these actions. The lack of etomidate- and propofol-induced immobilization in β3(N265M) mice was also observed in congenic 129X1/SvJ and C57BL/6J backgrounds, indicating that this phenotype is stable across different backgrounds. CONCLUSION: Our results provide evidence for a defined role of β3-containing GABA(A )receptors in mediating some, but not all, of the actions of general anesthetics, and confirm the multisite model of general anesthetic action. This pharmacological separation of anesthetic endpoints also suggests that subtype-selective substances with an improved side-effect profile may be developed

A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms

Background: Summer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. Gene expression atlases are crucial for the identification of genes expressed in different tissues at various plant developmental stages. Here, we present the first comprehensive gene expression atlas for a summer squash cultivar, including transcripts obtained from seeds, shoots, leaf stem, young and developed leaves, male and female flowers, fruits of seven developmental stages, as well as primary and lateral roots. Results: In total, 27,868 genes and 2352 novel transcripts were annotated from these 16 tissues, with over 18,000 genes common to all tissue groups. Of these, 3812 were identified as housekeeping genes, half of which assigned to known gene ontologies. Flowers, seeds, and young fruits had the largest number of specific genes, whilst intermediate-age fruits the fewest. There also were genes that were differentially expressed in the various tissues, the male flower being the tissue with the most differentially expressed genes in pair-wise comparisons with the remaining tissues, and the leaf stem the least. The largest expression change during fruit development was early on, from female flower to fruit two days after pollination. A weighted correlation network analysis performed on the global gene expression dataset assigned 25,413 genes to 24 coexpression groups, and some of these groups exhibited strong tissue specificity. Conclusions: These findings enrich our understanding about the transcriptomic events associated with summer squash development and ripening. This comprehensive gene expression atlas is expected not only to provide a global view of gene expression patterns in all major tissues in C. pepo but to also serve as a valuable resource for functional genomics and gene discovery in Cucurbitaceae

Ability of online drug databases to assist in clinical decision-making with infectious disease therapies

<p>Abstract</p> <p>Background</p> <p>Infectious disease (ID) is a dynamic field with new guidelines being adopted at a rapid rate. Clinical decision support tools (CDSTs) have proven beneficial in selecting treatment options to improve outcomes. However, there is a dearth of information on the abilities of CDSTs, such as drug information databases. This study evaluated online drug information databases when answering infectious disease-specific queries.</p> <p>Methods</p> <p>Eight subscription drug information databases: American Hospital Formulary Service Drug Information (AHFS), Clinical Pharmacology (CP), Epocrates Online Premium (EOP), Facts & Comparisons 4.0 Online (FC), Lexi-Comp (LC), Lexi-Comp with AHFS (LC-AHFS), Micromedex (MM), and PEPID PDC (PPDC) and six freely accessible: DailyMed (DM), DIOne (DIO), Epocrates Online Free (EOF), Internet Drug Index (IDI), Johns Hopkins ABX Guide (JHAG), and Medscape Drug Reference (MDR) were evaluated for their scope (presence of an answer) and completeness (on a 3-point scale) in answering 147 infectious disease-specific questions. Questions were divided among five classifications: antibacterial, antiviral, antifungal, antiparasitic, and vaccination/immunization. Classifications were further divided into categories (e.g., dosage, administration, emerging resistance, synergy, and spectrum of activity). Databases were ranked based on scope and completeness scores. ANOVA and Chi-square were used to determine differences between individual databases and between subscription and free databases.</p> <p>Results</p> <p>Scope scores revealed three discrete tiers of database performance: Tier 1 (82-77%), Tier 2 (73-65%) and Tier 3 (56-41%) which were significantly different from each other (p < 0.05). The top tier performers: MM (82%), MDR (81%), LC-AHFS (81%), AHFS (78%), and CP (77%) answered significantly more questions compared to other databases (p < 0.05). Top databases for completeness were: MM (97%), DM (96%), IDI (95%), and MDR (95%). Subscription databases performed better than free databases in all categories (p = 0.03). Databases suffered from 37 erroneous answers for an overall error rate of 1.8%.</p> <p>Conclusion</p> <p>Drug information databases used in ID practice as CDSTs can be valuable resources. MM, MDR, LC-AHFS, AHFS, and CP were shown to be superior in their scope and completeness of information, and MM, AHFS, and MDR provided no erroneous answers. There is room for improvement in all evaluated databases.</p