18 research outputs found
New Statistical Algorithms for the Analysis of Mass Spectrometry Time-Of-Flight Mass Data with Applications in Clinical Diagnostics
Mass spectrometry (MS) based techniques have emerged as a standard forlarge-scale protein analysis. The ongoing progress in terms of more sensitive
machines and improved data analysis algorithms led to a constant expansion of
its fields of applications. Recently, MS was introduced into clinical proteomics
with the prospect of early disease detection using proteomic pattern matching.
Analyzing biological samples (e.g. blood) by mass spectrometry generates
mass spectra that represent the components (molecules) contained in a
sample as masses and their respective relative concentrations.
In this work, we are interested in those components that are constant within a
group of individuals but differ much between individuals of two distinct groups.
These distinguishing components that dependent on a particular medical condition
are generally called biomarkers. Since not all biomarkers found by the
algorithms are of equal (discriminating) quality we are only interested in a
small biomarker subset that - as a combination - can be used as a
fingerprint for a disease. Once a fingerprint for a particular disease
(or medical condition) is identified, it can be used in clinical diagnostics to
classify unknown spectra.
In this thesis we have developed new algorithms for automatic extraction of
disease specific fingerprints from mass spectrometry data. Special emphasis has
been put on designing highly sensitive methods with respect to signal detection.
Thanks to our statistically based approach our methods are able to
detect signals even below the noise level inherent in data acquired by common MS
machines, such as hormones.
To provide access to these new classes of algorithms to collaborating groups
we have created a web-based analysis platform that provides all necessary
interfaces for data transfer, data analysis and result inspection.
To prove the platform's practical relevance it has been utilized in several
clinical studies two of which are presented in this thesis. In these studies it
could be shown that our platform is superior to commercial systems with respect
to fingerprint identification. As an outcome of these studies several
fingerprints for different cancer types (bladder, kidney, testicle, pancreas,
colon and thyroid) have been detected and validated. The clinical partners in
fact emphasize that these results would be impossible with a less sensitive
analysis tool (such as the currently available systems).
In addition to the issue of reliably finding and handling signals in noise we
faced the problem to handle very large amounts of data, since an average dataset
of an individual is about 2.5 Gigabytes in size and we have data of hundreds to
thousands of persons. To cope with these large datasets, we developed a new
framework for a heterogeneous (quasi) ad-hoc Grid - an infrastructure that
allows to integrate thousands of computing resources (e.g. Desktop Computers,
Computing Clusters or specialized hardware, such as IBM's Cell Processor in a
Playstation 3)
Complexity, Emergent Systems and Complex Biological Systems:\ud Complex Systems Theory and Biodynamics. [Edited book by I.C. Baianu, with listed contributors (2011)]
An overview is presented of System dynamics, the study of the behaviour of complex systems, Dynamical system in mathematics Dynamic programming in computer science and control theory, Complex systems biology, Neurodynamics and Psychodynamics.\u
Bioinformatics
This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here
Investigation of mobile devices usage and mobile augmented reality applications among older people
Mobile devices such as tablets and smartphones have allow users to communicate, entertainment, access information and perform productivity. However, older people are having issues to utilise mobile devices that may affect their quality of life and wellbeing. There are some potentials of mobile Augmented Reality (AR) applications to increase older users mobile usage by enhancing their experience and learning. The study aims to investigate mobile devices potential barriers and influence factors in using mobile devices. It also seeks to understand older people issues in using AR applications
Using MapReduce Streaming for Distributed Life Simulation on the Cloud
Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp
Investigation into the changing colonisation of skin bacteria during isotretinoin treatment for acne vulgaris
Poster presentatio