A phylogenomics approach to resolving fungal evolution, and phylogenetic method development

Bien que les champignons soient régulièrement utilisés comme modèle d'étude des systèmes eucaryotes, leurs relations phylogénétiques soulèvent encore des questions controversées. Parmi celles-ci, la classification des zygomycètes reste inconsistante. Ils sont potentiellement paraphylétiques, i.e. regroupent de lignées fongiques non directement affiliées. La position phylogénétique du genre Schizosaccharomyces est aussi controversée: appartient-il aux Taphrinomycotina (précédemment connus comme archiascomycetes) comme prédit par l'analyse de gènes nucléaires, ou est-il plutôt relié aux Saccharomycotina (levures bourgeonnantes) tel que le suggère la phylogénie mitochondriale? Une autre question concerne la position phylogénétique des nucléariides, un groupe d'eucaryotes amiboïdes que l'on suppose étroitement relié aux champignons. Des analyses multi-gènes réalisées antérieurement n'ont pu conclure, étant donné le choix d'un nombre réduit de taxons et l'utilisation de six gènes nucléaires seulement. Nous avons abordé ces questions par le biais d'inférences phylogénétiques et tests statistiques appliqués à des assemblages de données phylogénomiques nucléaires et mitochondriales. D'après nos résultats, les zygomycètes sont paraphylétiques (Chapitre 2) bien que le signal phylogénétique issu du jeu de données mitochondriales disponibles est insuffisant pour résoudre l'ordre de cet embranchement avec une confiance statistique significative. Dans le Chapitre 3, nous montrons à l'aide d'un jeu de données nucléaires important (plus de cent protéines) et avec supports statistiques concluants, que le genre Schizosaccharomyces appartient aux Taphrinomycotina. De plus, nous démontrons que le regroupement conflictuel des Schizosaccharomyces avec les Saccharomycotina, venant des données mitochondriales, est le résultat d'un type d'erreur phylogénétique connu: l'attraction des longues branches (ALB), un artéfact menant au regroupement d'espèces dont le taux d'évolution rapide n'est pas représentatif de leur véritable position dans l'arbre phylogénétique. Dans le Chapitre 4, en utilisant encore un important jeu de données nucléaires, nous démontrons avec support statistique significatif que les nucleariides constituent le groupe lié de plus près aux champignons. Nous confirmons aussi la paraphylie des zygomycètes traditionnels tel que suggéré précédemment, avec support statistique significatif, bien que ne pouvant placer tous les membres du groupe avec confiance. Nos résultats remettent en cause des aspects d'une récente reclassification taxonomique des zygomycètes et de leurs voisins, les chytridiomycètes. Contrer ou minimiser les artéfacts phylogénétiques telle l'attraction des longues branches (ALB) constitue une question récurrente majeure. Dans ce sens, nous avons développé une nouvelle méthode (Chapitre 5) qui identifie et élimine dans une séquence les sites présentant une grande variation du taux d'évolution (sites fortement hétérotaches - sites HH); ces sites sont connus comme contribuant significativement au phénomène d'ALB. Notre méthode est basée sur un test de rapport de vraisemblance (likelihood ratio test, LRT). Deux jeux de données publiés précédemment sont utilisés pour démontrer que le retrait graduel des sites HH chez les espèces à évolution accélérée (sensibles à l'ALB) augmente significativement le support pour la topologie « vraie » attendue, et ce, de façon plus efficace comparée à d'autres méthodes publiées de retrait de sites de séquences. Néanmoins, et de façon générale, la manipulation de données préalable à l'analyse est loin d’être idéale. Les développements futurs devront viser l'intégration de l'identification et la pondération des sites HH au processus d'inférence phylogénétique lui-même.

Comparaison des méthodes d'analyse de l'expression différentielle basée sur la dépendance des niveaux d'expression

La technologie des microarrays demeure à ce jour un outil important pour la mesure de l'expression génique. Au-delà de la technologie elle-même, l'analyse des données provenant des microarrays constitue un problème statistique complexe, ce qui explique la myriade de méthodes proposées pour le pré-traitement et en particulier, l'analyse de l'expression différentielle. Toutefois, l'absence de données de calibration ou de méthodologie de comparaison appropriée a empêché l'émergence d'un consensus quant aux méthodes d'analyse optimales. En conséquence, la décision de l'analyste de choisir telle méthode plutôt qu'une autre se fera la plupart du temps de façon subjective, en se basant par exemple sur la facilité d'utilisation, l'accès au logiciel ou la popularité. Ce mémoire présente une approche nouvelle au problème de la comparaison des méthodes d'analyse de l'expression différentielle. Plus de 800 pipelines d'analyse sont appliqués à plus d'une centaine d'expériences sur deux plateformes Affymetrix différentes. La performance de chacun des pipelines est évaluée en calculant le niveau moyen de co-régulation par l'entremise de scores d'enrichissements pour différentes collections de signatures moléculaires. L'approche comparative proposée repose donc sur un ensemble varié de données biologiques pertinentes, ne confond pas la reproductibilité avec l'exactitude et peut facilement être appliquée à de nouvelles méthodes. Parmi les méthodes testées, la supériorité de la sommarisation FARMS et de la statistique de l'expression différentielle TREAT est sans équivoque. De plus, les résultats obtenus quant à la statistique d'expression différentielle corroborent les conclusions d'autres études récentes à propos de l'importance de prendre en compte la grandeur du changement en plus de sa significativité statistique.

Features for detection of Parkinson's disease tremor from local field potentials of the subthalamic nucleus

Deep Brain Stimulation (DBS) is a treatment routinely used to alleviate the symptoms of Parkinson's disease (PD). In this type of treatment, electrical pulses are applied through electrodes implanted into the basal ganglia of the patient. As the symptoms are not permanent in most patients, it is desirable to develop an on-demand stimulator, applying pulses only when onset of the symptoms is detected. This study evaluates a feature set created for the detection of tremor - a cardinal symptom of PD. The designed feature set was based on standard signal features and researched properties of the electrical signals recorded from subthalamic nucleus (STN) within the basal ganglia, which together included temporal, spectral, statistical, autocorrelation and fractal properties. The most characterized tremor related features were selected using statistical testing and backward algorithms then used for classification on unseen patient signals. The spectral features were among the most efficient at detecting tremor, notably spectral bands 3.5-5.5 Hz and 0-1 Hz proved to be highly significant. The classification results for determination of tremor achieved 94% sensitivity with specificity equaling one.

Testando a Existência de Prêmio de Volatilidade em Ações Líquidas da Bovespa

A existência e o sinal do prêmio de volatilidade têm causado controvérsias dentro da literatura especializada. Este trabalho propôs, criticou e aplicou uma nova metodologia com a natalidade de testar estatisticamente a existência do prêmio de volatilidade, com as vantagens de testar para um conjunto de ações, e não para séries individuais, e de não depender de uma forma funcional específica para e relação entre o retorno e a volatilidade esperados. Os resultados da aplicação para um conjunto selecionado de ações negociadas na Bovespa foram favoráveis à existência do prêmio.

Tendência e determinantes do aleitamento materno exclusivo em crianças menores de 6 meses no município de Bauru-SP

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Differential expression analysis for sequence count data via mixtures of negative binomials

The recent advent of Next-generation sequencing technologies has revolutionized the way of analyzing the genome. This innovation allows to get deeper information at a lower cost and in less time, and provides data that are discrete measurements. One of the most important applications with these data is the differential analysis, that is investigating if one gene exhibit a different expression level in correspondence of two (or more) biological conditions (such as disease states, treatments received and so on). As for the statistical analysis, the final aim will be statistical testing and for modeling these data the Negative Binomial distribution is considered the most adequate one especially because it allows for "over dispersion". However, the estimation of the dispersion parameter is a very delicate issue because few information are usually available for estimating it. Many strategies have been proposed, but they often result in procedures based on plug-in estimates, and in this thesis we show that this discrepancy between the estimation and the testing framework can lead to uncontrolled first-type errors. We propose a mixture model that allows each gene to share information with other genes that exhibit similar variability. Afterwards, three consistent statistical tests are developed for differential expression analysis. We show that the proposed method improves the sensitivity of detecting differentially expressed genes with respect to the common procedures, since it is the best one in reaching the nominal value for the first-type error, while keeping elevate power. The method is finally illustrated on prostate cancer RNA-seq data.

Palliative in-patient cancer treatment in an anthroposophic hospital: II. Quality of life during and after stationary treatment, and subjective treatment benefits

BACKGROUND: There is an increasing demand for comprehensive forms of palliative cancer care, meeting physical as well as emotional, cognitive, spiritual and social needs. Therapy programs of anthroposophic hospitals are aimed at improving health and quality of life (QoL) at these levels. However, data on the influence of these programs on QoL of patients with advanced cancer are scarce. PATIENTS AND METHODS: 144 in-patients with advanced epithelial cancers were treated at the anthroposophic Lukas Klinik, Arlesheim, Switzerland. QoL was assessed upon admission, discharge and after 4 months, using 20 functional scales from the questionnaires EORTC QLQ-C30, HADS and SELT-M. Statistical testing was performed with the Wilcoxon signed rank test. At month 4, subjectively perceived benefits from anthroposophic medicine (AM) and conventional cancer therapy (CCT) were assessed by telephone. OBJECTIVE: The aim was to provide an account of global, physical, emotional, cognitive-spiritual and social QoL developments in advanced cancer patients, during and after in-patient AM treatment, and to investigate subjective benefits from AM and CCT. RESULTS: QoL improvements were observed in all 20 dimensions (12 significant). Compared to related studies, improvements were fairly high. At month 4, QoL scores had decreased but were still above baseline in all 20 dimensions. Both AM and CCT were perceived as beneficial. CONCLUSION: Our data provide evidence that in-patient therapy at an anthroposophic hospital can lead to significant QoL improvements, especially in emotional, but also global, physical, cognitive-spiritual and social aspects. Benefits of AM were experienced on the physical, emotional, cognitive- spiritual and social level. Benefits of CCT were tumor-focused.

Datenanalyse. Das Null-Ritual und der Umgang mit Effekten in der Zeitschrift für Sportpsychologie

Ziel dieses Beitrages ist die Analyse der Anwendung empirischer Tests in der deutschsprachigen Sportpsychologie. Die Ergebnisse vergleichbarer Analysen, bspw. in der Psychologie, zeigen, dass zwischen Anforderungen aus Testkonzepten und empirischer Realität Unterschiede existieren, die bislang für die Sportpsychologie nicht beschrieben und bewertet worden sind. Die Jahrgänge 1994–2007 der Zeitschrift für Sportpsychologie (früher psychologie und sport) wurden danach untersucht, ob Forschungsfragen formuliert, welche Stichprobenart gewählt, welches Testkonzept verwendet, welches Signifikanzniveau benutzt und ob statistische Probleme diskutiert wurden. 83 Artikel wurden von zwei unabhängigen Bewertern nach diesen Aspekten kategorisiert. Als Ergebnis ist festzuhalten, dass in der sportpsychologischen Forschung überwiegend eine Mischung aus Fishers Signifikanztesten sowie Neyman-Pearsons-Hypothesentesten zur Anwendung kommt,das sogenannte „Hybrid-Modell” oder „Null-Ritual”. Die Beschreibung der Teststärke ist kaum zu beobachten. Eine zeitliche Analyse der Beiträge zeigt, dass vor allem die Benutzung von Effektgrößen in den letzten Jahren zugenommen hat. Abschließend werden Ansätze zur Verbesserung und der Vereinheitlichung der Anwendung empirischer Tests vorgeschlagen und diskutiert.

Electromyographic activity of back muscles during stochastic whole body vibration

OBJECTIVES: Stochastic resonance whole body vibrations (SR-WBV) may reduce and prevent musculoskeletal problems (MSP). The aim of this study was to evaluate how activities of the lumbar erector spinae (ES) and of the ascending and descending trapezius (TA, TD) change in upright standing position during SR-WBV. METHODS: Nineteen female subjects completed 12 series of 10 seconds of SR-WBV at six different frequencies (2, 4, 6, 8, 10, 12Hz) and two types of "noise"-applications. An assessment at rest had been executed beforehand. Muscle activities were measured with EMG and normalized to the maximum voluntary contraction (MVC%). For statistical testing a three-factorial analysis of variation (ANOVA) was applied. RESULTS: The maximum activity of the respective muscles was 14.5 MVC% for the ES, 4.6 MVC% for the TA (12Hz with "noise" both), and 7.4 MVC% for the TD (10Hz without "noise"). Furthermore, all muscles varied significantly at 6Hz and above (p⋜0.047) compared to the situation at rest. No significant differences were found at SR-WBV with or without "noise". CONCLUSIONS: In general, muscle activity during SR-WBV is reasonably low and comparable to core strength stability exercises, sensorimotor training and "abdominal hollowing" in water. SR-WBV may be a therapeutic option for the relief of MSP.

COMPARISON OF THE ORGANIZATIONAL STRUCTURES AND EFFECTIVENESS OF THE INVESTOR-OWNED AND VOLUNTARY MULTIHOSPITAL SECTORS

Objectives. The central objective of this study was to systematically examine the internal structure of multihospital systems, determining the management principles used and the performance levels achieved in medical care and administrative areas.^ The Universe. The study universe consisted of short-term general American hospitals owned and operated by multihospital corporations. Corporations compared were the investor-owned (for-profit) and the voluntary multihospital systems. The individual hospital was the unit of analysis for the study.^ Theoretical Considerations. The contingency theory, using selected aspects of the classical and human relations schools of thought, seemed well suited to describe multihospital organization and was used in this research.^ The Study Hypotheses. The main null hypotheses generated were that there are no significant differences between the voluntary and the investor-owned multihospital sectors in their (1) hospital structures and (2) patient care and administrative performance levels.^ The Sample. A stratified random sample of 212 hospitals owned by multihospital systems was selected to equally represent the two study sectors. Of the sampled hospitals approached, 90.1% responded.^ The Analysis. Sixteen scales were constructed in conjunction with 16 structural variables developed from the major questions and sub-items of the questionnaire. This was followed by analysis of an additional 7 structural and 24 effectiveness (performance) measures, using frequency distributions. Finally, summary statistics and statistical testing for each variable and sub-items were completed and recorded in 38 tables.^ Study Findings. While it has been argued that there are great differences between the two sectors, this study found that with a few exceptions the null hypotheses of no difference in organizational and operational characteristics of non-profit and for-profit hospitals was accepted. However, there were several significant differences found in the structural variables: functional specialization, and autonomy were significantly higher in the voluntary sector. Only centralization was significantly different in the investor owned. Among the effectiveness measures, occupancy rate, cost of data processing, total manhours worked, F.T.E. ratios, and personnel per occupied bed were significantly higher in the voluntary sector. The findings indicated that both voluntary and for-profit systems were converging toward a common hierarchical corporate management approach. Factors of size and management style may be better descriptors to characterize a specific multihospital group than its profit or nonprofit status. (Abstract shortened with permission of author.) ^

Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution

Estimation of evolutionary distances has always been a major issue in the study of molecular evolution because evolutionary distances are required for estimating the rate of evolution in a gene, the divergence dates between genes or organisms, and the relationships among genes or organisms. Other closely related issues are the estimation of the pattern of nucleotide substitution, the estimation of the degree of rate variation among sites in a DNA sequence, and statistical testing of the molecular clock hypothesis. Mathematical treatments of these problems are considerably simplified by the assumption of a stationary process in which the nucleotide compositions of the sequences under study have remained approximately constant over time, and there now exist fairly extensive studies of stationary models of nucleotide substitution, although some problems remain to be solved. Nonstationary models are much more complex, but significant progress has been recently made by the development of the paralinear and LogDet distances. This paper reviews recent studies on the above issues and reports results on correcting the estimation bias of evolutionary distances, the estimation of the pattern of nucleotide substitution, and the estimation of rate variation among the sites in a sequence.

On the existence of visual technical patterns in the UK stock market

The aim in this paper is to replicate and extend the analysis of visual technical patterns by Lo et al. (2000) using data on the UK market. A non-parametric smoother is used to model a nonlinear trend in stock price series. Technical patterns, such as the 'head-and-shoulders' pattern, that are characterised by a sequence of turning points are identified in the smoothed data. Statistical tests are used to determine whether returns conditioned on the technical patterns are different from random returns and, in an extension to the analysis of Lo et al. (2000), whether they can outperform a market benchmark return. For the stocks in the FTSE 100 and FTSE 250 indices over the period 1986 to 2001, we find that technical patterns occur with different frequencies to each other and in different relativities to the frequencies found in the US market. Our extended statistical testing indicates that UK stock returns are less influenced by technical patterns than was the case for US stock returns.

Mobile Technologies: Expectancy, Usage, and Acceptance of Clinical Staff and Patients at a University Medical Center

BACKGROUND: Despite their increasing popularity, little is known about how users perceive mobile devices such as smartphones and tablet PCs in medical contexts. Available studies are often restricted to evaluating the success of specific interventions and do not adequately cover the users' basic attitudes, for example, their expectations or concerns toward using mobile devices in medical settings. OBJECTIVE: The objective of the study was to obtain a comprehensive picture, both from the perspective of the patients, as well as the doctors, regarding the use and acceptance of mobile devices within medical contexts in general well as the perceived challenges when introducing the technology. METHODS: Doctors working at Hannover Medical School (206/1151, response 17.90%), as well as patients being admitted to this facility (213/279, utilization 76.3%) were surveyed about their acceptance and use of mobile devices in medical settings. Regarding demographics, both samples were representative of the respective study population. GNU R (version 3.1.1) was used for statistical testing. Fisher's exact test, two-sided, alpha=.05 with Monte Carlo approximation, 2000 replicates, was applied to determine dependencies between two variables. RESULTS: The majority of participants already own mobile devices (doctors, 168/206, 81.6%; patients, 110/213, 51.6%). For doctors, use in a professional context does not depend on age (P=.66), professional experience (P=.80), or function (P=.34); gender was a factor (P=.009), and use was more common among male (61/135, 45.2%) than female doctors (17/67, 25%). A correlation between use of mobile devices and age (P=.001) as well as education (P=.002) was seen for patients. Minor differences regarding how mobile devices are perceived in sensitive medical contexts mostly relate to data security, patients are more critical of the devices being used for storing and processing patient data; every fifth patient opposed this, but nevertheless, 4.8% of doctors (10/206) use their devices for this purpose. Both groups voiced only minor concerns about the credibility of the provided content or the technical reliability of the devices. While 8.3% of the doctors (17/206) avoided use during patient contact because they thought patients might be unfamiliar with the devices, (25/213) 11.7% of patients expressed concerns about the technology being too complicated to be used in a health context. CONCLUSIONS: Differences in how patients and doctors perceive the use of mobile devices can be attributed to age and level of education; these factors are often mentioned as contributors of the problems with (mobile) technologies. To fully realize the potential of mobile technologies in a health care context, the needs of both the elderly as well as those who are educationally disadvantaged need to be carefully addressed in all strategies relating to mobile technology in a health context.

Aspirin and extended-release dipyridamole versus clopidogrel for recurrent stroke

Background Recurrent stroke is a frequent, disabling event after ischemic stroke. This study compared the efficacy and safety of two antiplatelet regimens — aspirin plus extendedrelease dipyridamole (ASA–ERDP) versus clopidogrel. Methods In this double-blind, 2-by-2 factorial trial, we randomly assigned patients to receive 25 mg of aspirin plus 200 mg of extended-release dipyridamole twice daily or to receive 75 mg of clopidogrel daily. The primary outcome was first recurrence of stroke. The secondary outcome was a composite of stroke, myocardial infarction, or death from vascular causes. Sequential statistical testing of noninferiority (margin of 1.075), followed by superiority testing, was planned. Results A total of 20,332 patients were followed for a mean of 2.5 years. Recurrent stroke occurred in 916 patients (9.0%) receiving ASA–ERDP and in 898 patients (8.8%) receiving clopidogrel (hazard ratio, 1.01; 95% confidence interval [CI], 0.92 to 1.11). The secondary outcome occurred in 1333 patients (13.1%) in each group (hazard ratio for ASA–ERDP, 0.99; 95% CI, 0.92 to 1.07). There were more major hemorrhagic events among ASA–ERDP recipients (419 [4.1%]) than among clopidogrel recipients (365 [3.6%]) (hazard ratio, 1.15; 95% CI, 1.00 to 1.32), including intracranial hemorrhage (hazard ratio, 1.42; 95% CI, 1.11 to 1.83). The net risk of recurrent stroke or major hemorrhagic event was similar in the two groups (1194 ASA–ERDP recipients [11.7%], vs. 1156 clopidogrel recipients [11.4%]; hazard ratio, 1.03; 95% CI, 0.95 to 1.11). Conclusions The trial did not meet the predefined criteria for noninferiority but showed similar rates of recurrent stroke with ASA–ERDP and with clopidogrel. There is no evidence that either of the two treatments was superior to the other in the prevention of recurrent stroke. (ClinicalTrials.gov number, NCT00153062.)

Outcome Prediction of Consciousness Disorders in the Acute Stage Based on a Complementary Motor Behavioural Tool.

INTRODUCTION: Attaining an accurate diagnosis in the acute phase for severely brain-damaged patients presenting Disorders of Consciousness (DOC) is crucial for prognostic validity; such a diagnosis determines further medical management, in terms of therapeutic choices and end-of-life decisions. However, DOC evaluation based on validated scales, such as the Revised Coma Recovery Scale (CRS-R), can lead to an underestimation of consciousness and to frequent misdiagnoses particularly in cases of cognitive motor dissociation due to other aetiologies. The purpose of this study is to determine the clinical signs that lead to a more accurate consciousness assessment allowing more reliable outcome prediction. METHODS: From the Unit of Acute Neurorehabilitation (University Hospital, Lausanne, Switzerland) between 2011 and 2014, we enrolled 33 DOC patients with a DOC diagnosis according to the CRS-R that had been established within 28 days of brain damage. The first CRS-R assessment established the initial diagnosis of Unresponsive Wakefulness Syndrome (UWS) in 20 patients and a Minimally Consciousness State (MCS) in the remaining13 patients. We clinically evaluated the patients over time using the CRS-R scale and concurrently from the beginning with complementary clinical items of a new observational Motor Behaviour Tool (MBT). Primary endpoint was outcome at unit discharge distinguishing two main classes of patients (DOC patients having emerged from DOC and those remaining in DOC) and 6 subclasses detailing the outcome of UWS and MCS patients, respectively. Based on CRS-R and MBT scores assessed separately and jointly, statistical testing was performed in the acute phase using a non-parametric Mann-Whitney U test; longitudinal CRS-R data were modelled with a Generalized Linear Model. RESULTS: Fifty-five per cent of the UWS patients and 77% of the MCS patients had emerged from DOC. First, statistical prediction of the first CRS-R scores did not permit outcome differentiation between classes; longitudinal regression modelling of the CRS-R data identified distinct outcome evolution, but not earlier than 19 days. Second, the MBT yielded a significant outcome predictability in the acute phase (p<0.02, sensitivity>0.81). Third, a statistical comparison of the CRS-R subscales weighted by MBT became significantly predictive for DOC outcome (p<0.02). DISCUSSION: The association of MBT and CRS-R scoring improves significantly the evaluation of consciousness and the predictability of outcome in the acute phase. Subtle motor behaviour assessment provides accurate insight into the amount and the content of consciousness even in the case of cognitive motor dissociation.