Split Analysis Methods and Parametric Bootstrapping in Molecular Phylogenetics : Taking a closer look at model adequacy

Even though the size of datasets in molecular analyses increased rapidly during the last years, undetected systematic errors as well as unsolved problems concerning the evaluation of data quality and adequate substitution model selection still persist. This not only hampers the correct analysis of these datasets but leads to undetectable effects in phylogenetic tree reconstruction. Model-based tree reconstruction methods like maximum likelihood estimation and Bayesian inference have become the methods of choice for reconstruction of phylogenetic trees. Although maximum likelihood methods are known to be consistent if all necessary conditions are met, it depends strongly on the quality of the multiple sequence alignment and the ability of the chosen evolutionary model to reflect the underlying historical processes. This thesis addresses the assessment of model adequacy of estimated evolutionary models to multiple sequence alignments in the light of parametric bootstrapping and aims to find new methods for detection of model misspecifications with the help of split analyses. The second chapter focuses on the influence of the number of gamma rate categories used in modelling among-site rate variation when trying to assess model adequacy using an absolute goodness-of-fit test. The analyses of simulated alignments show that the Goldmann-Cox test rejects models which were only approximated by four discrete gamma rate categories for various tree shapes and branch length setups, if they were simulated with a continuous gamma distribution. Increasing the number of discrete rate categories leads to an acceptance of model adequacy for stationary datasets and a correct detection of non-stationarity and inhomogenetity in simulated data. The results illustrate that the application of the proposed Goldmann-Cox test to evaluate model adequacy might be too strict and rigorous with empirical data, in particular for large phylogenomic datasets. Approaches such as the Goldman-Cox test evaluate the absolute fit of data and model but, do not deliver a deeper insight into the structure of the misfit. The third chapter presents the visualisation of overrepresented splits within splits graphs, which provides a good tool for gaining an overview of possible patterns and contradictory signal or noise within datasets. The analysis of these split residuals, observed by comparison to parametric bootstrap datasets based on the estimated models can help to gain a deeper insight into model adequacy. Highly overrepresented splits can give hints whether heterotachy applies or non symmetric substitution processes. The fourth chapter aims to define a new split weighting scheme by formalising aspects like 'contrast of character states' or 'character state homogeneity' within split subsets. Splits which are detected by the proposed SAMS (Splits Analysis MethodS) algorithm are re-evaluated for a more objective and formal split weighting. A comparison of the published and the new approach showed that the developed weighting scheme delivers reasonable results but needs further improvement. The development of a new GUI offers a much more capable tool to perform a split analysis and visualise the results. The shape of a visualised split spectra can indicate, whether a dataset delivers a clear split signal or if there is a lot of noise present

Evaluating deformation behavior of a TBC-System during thermal gradient mechanical fatigue by means of high energy X-ray diffraction

Applications of TBC-systems involve complex thermal mechanical loading pattern including transient thermal gradients across the coated system, which result in multiaxial stresses and stress gradients affecting the damage behavior. In an ongoing research, starting more than 10 years ago, the authors developed laboratory test facilities for evaluating the damage behavior of TBC-systems for gas turbine blades in aeroengines under realistic thermal mechanical loading conditions [1]. Fatigue tests involving thermal gradients have been conducted and damage behavior in dependence of load pattern and pre heat treatment has been intensively investigated on TBC-systems comprising a partially yttria stabilized zirconia (YSZ) topcoat and a MCrAlY bond coat both applied by electron physical vapor deposition (EB-PVD) onto nickel based super alloys serving as substrate [2]. Numerical analyses by means of FE-calculations did provide hypotheses explaining the observed damage behavior [3], but even though the results are plausible they did depend on reasonable assumptions on materials properties since reliable data on the properties of the thin coating layers are still lacking, especially for high temperatures. High energy X-ray diffraction can provide the requested information since it is possible to achieve information on the local deformation processes in each layer with high spatial resolution, and short acquisition times allow for in situ investigation of time dependent deformation processes. A new test facility based on concepts after [1] for cyclic thermal loading of tubular specimens and applying a controlled thermal gradient across the coated specimen’s wall has been developed for implementation into an electro-mechanical test machine at the advanced photon source (APS) at Argonne National Laboratory. A precision positioning rig allows for exact µm-positioning of the entire test machine with respect to the focused X-ray beam, and X-ray diffraction patterns were taken using a 2D detector, giving accurate 360° lattice parameter data [4]. Tests have been performed with varying thermal and mechanical load schemata intending to determine material properties from the respective strain response. The beam energy was 65 keV, and throughout all experiments the beam scanned through the coating layers with a window and step size of 30 µm. Strain data were acquired in plane parallel to the specimen’s length axis and out of plane. Results of the strain data evaluation will be presented and discussed. Exemplary results are: - Elastic properties of the YSZ showed a gradient across the coating thickness reflecting the microstructure gradient of the YSZ resulting from the EB-PVD process. - The YSZ strain was – below the deposition temperature - in plane compressive and out of plane tensile, which is a consequence of (i) the higher thermal expansion coefficient of YSZ with respect to the substrate and (ii) the cylindrical specimen geometry with the YSZ at the outer surface. [1] M. Bartsch, G. Marci, K. Mull, C. Sick, Adv. Eng. Mater. (1999), 1(2), 127–9 [2] M. Bartsch, B. Baufeld, S. Dalkilic, L. Chernova, M. Heinzelmann, Int. J. Fatigue (2008) 30, 211–8 [3] M. T. Hernandez, A. M. Karlsson, M. Bartsch, Surf. Coat. Technol. (2009) 203, 3549–58 [4] S.F. Siddiqui, K. Knipe, A. Manero, C. Meid, J. Wischek, J. Okasinski, J. Almer, A.M. Karlsson, M. Bartsch, S. Raghavan, Review of Scientific Instruments (2013) 84, 08390

Clinical relevance of genetic instability in prostatic cells obtained by prostatic massage in early prostate cancer

We investigated whether genetic lesions such as loss of heterozygosity (LOH) are detected in prostatic cells obtained by prostatic massage during early diagnosis of prostate cancer (CaP) and discussed their clinical relevance. Blood and first urine voided after prostatic massage were collected in 99 patients with total prostate-specific antigen (PSA) between 4 and 10 ng ml−1, prior to prostate biopsies. Presence of prostatic cells was confirmed by quantitative RT–PCR analysis of PSA mRNA. Genomic DNA was analysed for LOH on six chromosomal regions. One or more allelic deletions were found in prostatic fluid from 57 patients analysed, of whom 33 (58%) had CaP. Sensitivity and specificity of LOH detection and PSA free to total ratio <15% for positive biopsy were respectively 86.7 and 44% (P=0.002) for LOH, and 55 and 74% (P=0.006) for PSA ratio <15%. Analysis of LOH obtained from prostatic tumours revealed similar patterns compared to prostatic fluid cells in 86% of cases, confirming its accuracy. The presence of LOH of urinary prostatic cells obtained after prostatic massage is significantly associated with CaP on biopsy and may potentially help to identify a set of patients who are candidates for further prostate biopsies

A cluster randomised control trial to evaluate the effectiveness and cost-effectiveness of the Italian medicines use review (I-MUR) for asthma patients

Background The economic burden of asthma, which relates to the degree of control, is €5 billion annually in Italy. Pharmacists could help improve asthma control, reducing this burden. This study aimed to evaluate the effectiveness and cost-effectiveness of Medicines Use Reviews provided by community pharmacists in asthma. Methods This cluster randomised, multi-centre, controlled trial in adult patients with asthma was conducted in 15 of the 20 regions of Italy between September 2014 and July 2015. After stratification by region, community pharmacists were randomly allocated to group A (trained in and delivered the intervention at baseline) or B (training and delivery 3 months later), using computerised random number generation in blocks of 10. Each recruited up to five patients, with both groups followed for 9 months. The intervention consisted of a systematic, structured face-to-face consultation with a pharmacist, covering asthma symptoms, medicines used, attitude towards medicines and adherence, recording pharmacist-identified pharmaceutical care issues (PCIs). The primary outcome was asthma control, assessed using the Asthma-Control-Test (ACT) score (ACT ≥ 20 represents good control). Secondary outcomes were: number of active ingredients, adherence, cost-effectiveness compared with usual care. Although blinding was not possible for either pharmacists or patients, assessment of outcomes was conducted by researchers blind to group allocation. Results Numbers of pharmacists and patients enrolled were 283 (A = 136; B = 147) and 1263 (A = 600; B = 663), numbers completing were 201 (A = 97; B = 104) and 816 (A = 400; B = 416), respectively. Patients were similar in age and gender and 56.13% (458/816) had poor/partial asthma control. Pharmacists identified 1256 PCIs (mean 1.54/patient), mostly need for education, monitoring and potentially ineffective therapy. Median ACT score at baseline differed between groups (A = 19, B = 18; p < 0.01). Odds ratio for improved asthma control was 1.76 (95% CI 1.33–2.33) and number needed to treat 10 (95% CI 6–28). Number of active ingredients reduced by 7.9% post-intervention (p < 0.01). Adherence improved by 35.4% 3 months post-intervention and 40.0% at 6 months (p < 0.01). The probability of the intervention being more cost-effective than usual care was 100% at 9 months. Conclusions This community pharmacist-based intervention demonstrated both effectiveness and cost-effectiveness. It has since been implemented as the first community pharmacy cognitive service in Italy

Combinations of QT-prolonging drugs: towards disentangling pharmacokinetic and pharmaco-dynamic effects in their potentially additive nature.

Background: Whether arrhythmia risks will increase if drugs with electrocardiographic (ECG) QT-prolonging properties are combined is generally supposed but not well studied. Based on available evidence, the Arizona Center for Education and Research on Therapeutics (AZCERT) classification defines the risk of QT prolongation for exposure to single drugs. We aimed to investigate how combining AZCERT drug categories impacts QT duration and how relative drug exposure affects the extent of pharmacodynamic drug–drug interactions. Methods: In a cohort of 2558 psychiatric inpatients and outpatients, we modeled whether AZCERT class and number of coprescribed QT-prolonging drugs correlates with observed rate-corrected QT duration (QTc) while also considering age, sex, inpatient status, and other QTc-prolonging risk factors. We concurrently considered administered drug doses and pharmacokinetic interactions modulating drug clearance to calculate individual weights of relative exposure with AZCERT drugs. Because QTc duration is concentration-dependent, we estimated individual drug exposure with these drugs and included this information as weights in weighted regression analyses. Results: Drugs attributing a ‘known’ risk for clinical consequences were associated with the largest QTc prolongations. However, the presence of at least two versus one QTc-prolonging drug yielded nonsignificant prolongations [exposure-weighted parameter estimates with 95% confidence intervals for ‘known’ risk drugs + 0.93 ms (–8.88;10.75)]. Estimates for the ‘conditional’ risk class increased upon refinement with relative drug exposure and coadministration of a ‘known’ risk drug as a further risk factor. Conclusions: These observations indicate that indiscriminate combinations of QTc-prolonging drugs do not necessarily result in additive QTc prolongation and suggest that QT prolongation caused by drug combinations strongly depends on the nature of the combination partners and individual drug exposure. Concurrently, it stresses the value of the AZCERT classification also for the risk prediction of combination therapies with QT-prolonging drugs