Two-part permutation tests for DNA methylation and microarray data

BACKGROUND: One important application of microarray experiments is to identify differentially expressed genes. Often, small and negative expression levels were clipped-off to be equal to an arbitrarily chosen cutoff value before a statistical test is carried out. Then, there are two types of data: truncated values and original observations. The truncated values are not just another point on the continuum of possible values and, therefore, it is appropriate to combine two statistical tests in a two-part model rather than using standard statistical methods. A similar situation occurs when DNA methylation data are investigated. In that case, there are null values (undetectable methylation) and observed positive values. For these data, we propose a two-part permutation test. RESULTS: The proposed permutation test leads to smaller p-values in comparison to the original two-part test. We found this for both DNA methylation data and microarray data. With a simulation study we confirmed this result and could show that the two-part permutation test is, on average, more powerful. The new test also reduces, without any loss of power, to a standard test when there are no null or truncated values. CONCLUSION: The two-part permutation test can be used in routine analyses since it reduces to a standard test when there are positive values only. Further advantages of the new test are that it opens the possibility to use other test statistics to construct the two-part test and that it avoids the use of any asymptotic distribution. The latter advantage is particularly important for the analysis of microarrays since sample sizes are usually small

Parametric methods outperformed non-parametric methods in comparisons of discrete numerical variables

<p>Abstract</p> <p>Background</p> <p>The number of events per individual is a widely reported variable in medical research papers. Such variables are the most common representation of the general variable type called discrete numerical. There is currently no consensus on how to compare and present such variables, and recommendations are lacking. The objective of this paper is to present recommendations for analysis and presentation of results for discrete numerical variables.</p> <p>Methods</p> <p>Two simulation studies were used to investigate the performance of hypothesis tests and confidence interval methods for variables with outcomes {0, 1, 2}, {0, 1, 2, 3}, {0, 1, 2, 3, 4}, and {0, 1, 2, 3, 4, 5}, using the difference between the means as an effect measure.</p> <p>Results</p> <p>The Welch U test (the T test with adjustment for unequal variances) and its associated confidence interval performed well for almost all situations considered. The Brunner-Munzel test also performed well, except for small sample sizes (10 in each group). The ordinary T test, the Wilcoxon-Mann-Whitney test, the percentile bootstrap interval, and the bootstrap-<it>t </it>interval did not perform satisfactorily.</p> <p>Conclusions</p> <p>The difference between the means is an appropriate effect measure for comparing two independent discrete numerical variables that has both lower and upper bounds. To analyze this problem, we encourage more frequent use of parametric hypothesis tests and confidence intervals.</p

Relevance-shifted tests for high dimensional data with small sample sizes

[no abstract

Proceedings of the BEST EN Think Tank XVI: Corporate Responsibility in Tourism: standards practices and policies

BEST EN is an international consortium of educators committed to the development and dissemination of knowledge in the field of sustainable tourism. The organization's annual Think Tank brings together academics and industry representatives from around the world to discuss a particular theme related to sustainable tourism in order to move research and education in this specific field forward. We are pleased to present the proceedings of the BEST Education Network (BESTEN) Think Tank XVI entitled Corporate Responsibility in Tourism – Standards Practices and Policies. The event was held in Berlin-Eberswalde, July 12-15, 2016, in conjunction with the ZENAT Centre for Sustainable Tourism, Eberswalde University for Sustainable Development, Eberswalde, considered one of Germany's greenest universities. The concept of corporate responsibility in tourism is a challenging one; it is subject to much critical debate, especially with regard to finding an appropriate balance between the different dimensions of standards, practices and policies. The proceedings present work by academics and practitioners worldwide, conducted on various aspects of corporate responsibility in tourism. They include abstracts and papers accepted by the scientific committee following a double blind peer review process

Advances in Forensic Genetics

The book has 25 articles about the status and new directions in forensic genetics. Approximately half of the articles are invited reviews, and the remaining articles deal with new forensic genetic methods. The articles cover aspects such as sampling DNA evidence at the scene of a crime; DNA transfer when handling evidence material and how to avoid DNA contamination of items, laboratory, etc.; identification of body fluids and tissues with RNA; forensic microbiome analysis with molecular biology methods as a supplement to the examination of human DNA; forensic DNA phenotyping for predicting visible traits such as eye, hair, and skin colour; new ancestry informative DNA markers for estimating ethnic origin; new genetic genealogy methods for identifying distant relatives that cannot be identified with conventional forensic DNA typing; sensitive DNA methods, including single-cell DNA analysis and other highly specialised and sensitive methods to examine ancient DNA from unidentified victims of war; forensic animal genetics; genetics of visible traits in dogs; statistical tools for interpreting forensic DNA analyses, including the most used IT tools for forensic STR-typing and DNA sequencing; haploid markers (Y-chromosome and mitochondria DNA); inference of ethnic origin; a comprehensive logical framework for the interpretation of forensic genetic DNA data; and an overview of the ethical aspects of modern forensic genetics

Proceedings der 11. Internationalen Tagung Wirtschaftsinformatik (WI2013) - Band 1

The two volumes represent the proceedings of the 11th International Conference on Wirtschaftsinformatik WI2013 (Business Information Systems). They include 118 papers from ten research tracks, a general track and the Student Consortium. The selection of all submissions was subject to a double blind procedure with three reviews for each paper and an overall acceptance rate of 25 percent. The WI2013 was organized at the University of Leipzig between February 27th and March 1st, 2013 and followed the main themes Innovation, Integration and Individualization.:Track 1: Individualization and Consumerization Track 2: Integrated Systems in Manufacturing Industries Track 3: Integrated Systems in Service Industries Track 4: Innovations and Business Models Track 5: Information and Knowledge ManagementDie zweibändigen Tagungsbände zur 11. Internationalen Tagung Wirtschaftsinformatik (WI2013) enthalten 118 Forschungsbeiträge aus zehn thematischen Tracks der Wirtschaftsinformatik, einem General Track sowie einem Student Consortium. Die Selektion der Artikel erfolgte nach einem Double-Blind-Verfahren mit jeweils drei Gutachten und führte zu einer Annahmequote von 25%. Die WI2013 hat vom 27.02. - 01.03.2013 unter den Leitthemen Innovation, Integration und Individualisierung an der Universität Leipzig stattgefunden.:Track 1: Individualization and Consumerization Track 2: Integrated Systems in Manufacturing Industries Track 3: Integrated Systems in Service Industries Track 4: Innovations and Business Models Track 5: Information and Knowledge Managemen

Religion, liberalism and the social question in the Habsburg hinterland : the Catholic Church in Upper Austria, 1850-1914

This dissertation focuses on the diocese of Linz in the Habsburg Monarchy during the second half of the nineteenth century, examining how the Roman Catholic Church and its priests adapted to and confronted the broad set of modernizing forces that were shaping the world around them against the backdrop of rising Ultramontanism within the Church. The study is divided into three sections. The first section explores the structural and ideological transformation of the Catholic Church in Upper Austria in this period. With a focus on the clergy, it examines the changing networks and structures of religious life; it investigates how the diocese changed under the watch of Bishop Franz Josef Rudigier (1853-1884) and Franz Maria Doppelbauer (1889-1908), and also under the influence of Ultramontanism. The second section examines the confrontation with liberalism. It begins in the 1850s, exploring how two events - the building of a general hospital in Linz and the burial of a prominent Protestant in a small town - inform our understanding of the dynamics of Catholic-liberal conflict in 1850s Austria. Next it turns to the height of the Austrian Kulturkampf between 1867 and 1875, exploring, how liberals and Catholic-conservatives presented a social vision that used the active exclusion of the 'other' to define itself. The third section shifts from liberalism to socialism, and from a study of the rise of Ultramontanism to that of Ultramontanism in practice. Examining Catholic responses to the social question, the study argues that Ultramontanism created its own internal set of contradictions when converted into policy, especially after the publication of the 1891 encyclical Rerum Novarum. Instead of bringing the different elements together within the Church, the encyclical had the opposite effect; each group began to interpret the document in different ways and to act accordingly, effectively demolishing the image of Catholic unity that existed around Ultramontanism

The impact of mathematics teaching efficacy on teachers’ pedagogical practices

This study explores the pedagogical practices of 167 Year 4 and 160 Year 8 New Zealand mathematics teachers who have different levels of mathematics teaching efficacy. Using data from the National Monitoring Study of Student Achievement 2013, the teacher questionnaire items believed to be the indicators of mathematics teaching efficacy were selected, represented by six items such as “I feel confident about teaching maths”. Then, low, mid, and high efficacious teachers were identified and compared to see how they differed with respect to their teaching profile and the frequency they used effective pedagogies when teaching mathematics (italicised below) (Anthony &amp; Walshaw, 2007). Twenty eight percent of Year 4 and 41% of Year 8 teachers had high mathematics teaching efficacy. Compared with the other teachers, teachers with high mathematics teaching efficacy were better able to provide an ethic of care in their classroom, they more frequently arranged their classrooms for learning to enable students to collaborate, and more frequently expected their students to communicate their thinking and debate ideas with others. They more frequently provided students with worthwhile mathematical tasks, they more frequently provided opportunities for their students to build on their own thinking, and to explore how new learning linked to or changed what they already knew. They more frequently expected their students to make mathematical connections by reflecting on their learning, to use multiple representations, and use ideas and skills from different curriculum areas