Search results for "Probability."

Diagramme mit ggplot2

2020

Mit dem Zusatzpaket ggplot2 lassen sich die in Kap. 14 vorgestellten Diagrammtypen ebenfalls erstellen. Dabei ist die Herangehensweise eine grundsatzlich andere: Wahrend der Basisumfang von R fur verschiedene Diagrammarten einzelne Funktionen bereitstellt, werden mit ggplot2 alle Diagrammtypen mit einem einheitlichen System erzeugt. Sind Diagramme des Basisumfangs analog zu einer Leinwand, auf der jede Funktion spater nicht mehr anderbare Elemente aufmalt, reprasentiert ggplot2 alle Diagrammelemente explizit in einem Objekt. Erstellte Diagramme lassen sich uber dieses Objekt weiter verandern, an Funktionen ubergeben und speichern.

Dosimetric Impact of Interfractional Variations in Prostate Cancer Radiotherapy—Implications for Imaging Frequency and Treatment Adaptation

2019

Background and purpose: To analyze deviations of the applied from the planned doses on a voxel-by-voxel basis for definitive prostate cancer radiotherapy depending on anatomic variations and imaging frequency. Materials and methods: Daily in-room CT imaging was performed in treatment position for 10 patients with prostate cancer undergoing intensity-modulated radiotherapy (340 fraction CTs). Applied fraction doses were recalculated on daily images, and voxel-wise dose accumulation was performed using a deformable registration algorithm. For weekly imaging, weekly position correction vectors were derived and used to rigidly register daily scans of that week to the planning CT scan prior to d…

Reducing sample size in experiments with animals: historical controls and related strategies

2015

Reducing the number of animal subjects used in biomedical experiments is desirable for ethical and practical reasons. Previous reviews of the benefits of reducing sample sizes have focused on improving experimental designs and methods of statistical analysis, but reducing the size of control groups has been considered rarely. We discuss how the number of current control animals can be reduced, without loss of statistical power, by incorporating information from historical controls, i.e. subjects used as controls in similar previous experiments. Using example data from published reports, we describe how to incorporate information from historical controls under a range of assumptions that mig…

Spectral entropy based neuronal network synchronization analysis based on microelectrode array measurements

2016

Synchrony and asynchrony are essential aspects of the functioning of interconnected neuronal cells and networks. New information on neuronal synchronization can be expected to aid in understanding these systems. Synchronization provides insight in the functional connectivity and the spatial distribution of the information processing in the networks. Synchronization is generally studied with time domain analysis of neuronal events, or using direct frequency spectrum analysis, e.g., in specific frequency bands. However, these methods have their pitfalls. Thus, we have previously proposed a method to analyze temporal changes in the complexity of the frequency of signals originating from differ…

Retract p < 0.005 and propose using JASP, instead

2018

Seeking to address the lack of research reproducibility in science, including psychology and the life sciences, a pragmatic solution has been raised recently:  to use a stricter p < 0.005 standard for statistical significance when claiming evidence of new discoveries. Notwithstanding its potential impact, the proposal has motivated a large mass of authors to dispute it from different philosophical and methodological angles. This article reflects on the original argument and the consequent counterarguments, and concludes with a simpler and better-suited alternative that the authors of the proposal knew about and, perhaps, should have made from their Jeffresian perspective: to use a Bayes …

Longitudinal Investigation into Genetics in the Conservation of Metabolic Phenotypes in Danish and Chinese Twins

2016

Longitudinal twin studies on long term conservation of individual metabolic phenotypes can help to explore the genetic and environmental basis in maintaining metabolic homeostasis and metabolic health. We performed a longitudinal twin study on 12 metabolic phenotypes from Danish twins followed up for 12 years and Chinese twins traced for 7 years. The study covered a relatively large sample of 502 pairs of Danish adult twins with a mean age at intake of 38 years and a total of 181 Chinese adult twin pairs with a mean baseline age of 39.5 years. Bivariate twin models were fitted to the longitudinal measurements taken at two time points (at baseline and follow-up) to estimate the genetic and e…

Informational and linguistic analysis of large genomic sequence collections via efficient Hadoop cluster algorithms

2018

Abstract Motivation Information theoretic and compositional/linguistic analysis of genomes have a central role in bioinformatics, even more so since the associated methodologies are becoming very valuable also for epigenomic and meta-genomic studies. The kernel of those methods is based on the collection of k-mer statistics, i.e. how many times each k-mer in {A,C,G,T}k occurs in a DNA sequence. Although this problem is computationally very simple and efficiently solvable on a conventional computer, the sheer amount of data available now in applications demands to resort to parallel and distributed computing. Indeed, those type of algorithms have been developed to collect k-mer statistics in…

FASTdoop: A versatile and efficient library for the input of FASTA and FASTQ files for MapReduce Hadoop bioinformatics applications

2017

Abstract Summary MapReduce Hadoop bioinformatics applications require the availability of special-purpose routines to manage the input of sequence files. Unfortunately, the Hadoop framework does not provide any built-in support for the most popular sequence file formats like FASTA or BAM. Moreover, the development of these routines is not easy, both because of the diversity of these formats and the need for managing efficiently sequence datasets that may count up to billions of characters. We present FASTdoop, a generic Hadoop library for the management of FASTA and FASTQ files. We show that, with respect to analogous input management routines that have appeared in the Literature, it offers…

Searching events in AFM force-extension curves: A wavelet approach

2016

An algorithm, based on the wavelet scalogram energy, for automatically detecting events in force-extension AFM force spectroscopy experiments is introduced. The events to be detected are characterized by a discontinuity in the signal. It is shown how the wavelet scalogram energy has different decay rates at different points depending on the degree of regularity of the signal, showing faster decay rates at regular points and slower rates at singular points (jumps). It is shown that these differences produce peaks in the scalogram energy plot at the event points. Finally, the algorithm is illustrated in a tether analysis experiment by using it for the detection of events in the AFM force-exte…

2018

Genome-Wide-Association-Studies have become a powerful method to link point mutations (e.g. single nucleotide polymorphisms (SNPs)) to a certain phenotype or a disease. However, their power to detect SNPs associated to polygenic diseases such as Alzheimer's Disease (AD) is limited, since they can only infer the pairwise relation of single SNPs to the phenotype and ignore possible effects of various SNP combinations. The common method to probe these possible complex genetic patterns is to compute a measure called linkage disequilibrium (LD). Despite the fact that several predictive patterns found with LD could successfully be applied to medical diagnosis, this measure still holds several dra…