ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry

<p>Abstract</p> <p>Background</p> <p>Since its inception, proteomics has essentially operated in a discovery mode with the goal of identifying and quantifying the maximal number of proteins in a sample. Increasingly, proteomic measurements are also supporting hypothesis-driven studies, in which a predetermined set of proteins is consistently detected and quantified in multiple samples. Selected reaction monitoring (SRM) is a targeted mass spectrometric technique that supports the detection and quantification of specific proteins in complex samples at high sensitivity and reproducibility. Here, we describe ATAQS, an integrated software platform that supports all stages of targeted, SRM-based proteomics experiments including target selection, transition optimization and post acquisition data analysis. This software will significantly facilitate the use of targeted proteomic techniques and contribute to the generation of highly sensitive, reproducible and complete datasets that are particularly critical for the discovery and validation of targets in hypothesis-driven studies in systems biology.</p> <p>Result</p> <p>We introduce a new open source software pipeline, ATAQS (Automated and Targeted Analysis with Quantitative SRM), which consists of a number of modules that collectively support the SRM assay development workflow for targeted proteomic experiments (project management and generation of protein, peptide and transitions and the validation of peptide detection by SRM). ATAQS provides a flexible pipeline for end-users by allowing the workflow to start or end at any point of the pipeline, and for computational biologists, by enabling the easy extension of java algorithm classes for their own algorithm plug-in or connection via an external web site.</p> <p>This integrated system supports all steps in a SRM-based experiment and provides a user-friendly GUI that can be run by any operating system that allows the installation of the Mozilla Firefox web browser.</p> <p>Conclusions</p> <p>Targeted proteomics via SRM is a powerful new technique that enables the reproducible and accurate identification and quantification of sets of proteins of interest. ATAQS is the first open-source software that supports all steps of the targeted proteomics workflow. ATAQS also provides software API (Application Program Interface) documentation that enables the addition of new algorithms to each of the workflow steps. The software, installation guide and sample dataset can be found in <url>http://tools.proteomecenter.org/ATAQS/ATAQS.html</url></p

Social Influence in Televised Election Debates: A Potential Distortion of Democracy

A recent innovation in televised election debates is a continuous response measure (commonly referred to as the “worm”) that allows viewers to track the response of a sample of undecided voters in real-time. A potential danger of presenting such data is that it may prevent people from making independent evaluations. We report an experiment with 150 participants in which we manipulated the worm and superimposed it on a live broadcast of a UK election debate. The majority of viewers were unaware that the worm had been manipulated, and yet we were able to influence their perception of who won the debate, their choice of preferred prime minister, and their voting intentions. We argue that there is an urgent need to reconsider the simultaneous broadcast of average response data with televised election debates

The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation

<p>Abstract</p> <p>Background</p> <p>Crucial foundations of any quantitative systems biology experiment are correct genome and proteome annotations. Protein databases compiled from high quality empirical protein identifications that are in turn based on correct gene models increase the correctness, sensitivity, and quantitative accuracy of systems biology genome-scale experiments.</p> <p>Results</p> <p>In this manuscript, we present the <it>Drosophila melanogaster </it>PeptideAtlas, a fly proteomics and genomics resource of unsurpassed depth. Based on peptide mass spectrometry data collected in our laboratory the portal <url>http://www.drosophila-peptideatlas.org</url> allows querying fly protein data observed with respect to gene model confirmation and splice site verification as well as for the identification of proteotypic peptides suited for targeted proteomics studies. Additionally, the database provides consensus mass spectra for observed peptides along with qualitative and quantitative information about the number of observations of a particular peptide and the sample(s) in which it was observed.</p> <p>Conclusion</p> <p>PeptideAtlas is an open access database for the <it>Drosophila </it>community that has several features and applications that support (1) reduction of the complexity inherently associated with performing targeted proteomic studies, (2) designing and accelerating shotgun proteomics experiments, (3) confirming or questioning gene models, and (4) adjusting gene models such that they are in line with observed <it>Drosophila </it>peptides. While the database consists of proteomic data it is not required that the user is a proteomics expert.</p

Towards Quantum Repeaters with Solid-State Qubits: Spin-Photon Entanglement Generation using Self-Assembled Quantum Dots

In this chapter we review the use of spins in optically-active InAs quantum dots as the key physical building block for constructing a quantum repeater, with a particular focus on recent results demonstrating entanglement between a quantum memory (electron spin qubit) and a flying qubit (polarization- or frequency-encoded photonic qubit). This is a first step towards demonstrating entanglement between distant quantum memories (realized with quantum dots), which in turn is a milestone in the roadmap for building a functional quantum repeater. We also place this experimental work in context by providing an overview of quantum repeaters, their potential uses, and the challenges in implementing them.Comment: 51 pages. Expanded version of a chapter to appear in "Engineering the Atom-Photon Interaction" (Springer-Verlag, 2015; eds. A. Predojevic and M. W. Mitchell

Computational Cancer Biology: An Evolutionary Perspective

ISSN:1553-734XISSN:1553-735

Digital image processing with quantum approaches

Digital image processing with quantum approaches

Widespread range expansions shape latitudinal variation in insect thermal limits

I thank the authors of previous studies on global variation in insect thermal tolerances who have generously provided open access use of their data sets.Peer reviewedPostprin

Incidence and classification of pediatric diffuse parenchymal lung diseases in Germany

<p>Abstract</p> <p>Background</p> <p>Diffuse parenchymal lung diseases (DPLD) in children represent a rare and heterogeneous group of chronic pulmonary disorders. Despite substantial advances in genetics and pathomechanisms, these often lethal diseases are still under-diagnosed. This is due to the fact that (i) the incidence is low, and (ii) clinical presentation, (iii) disease classification and (iv) specific treatment options are largely unknown.</p> <p>Methods</p> <p>Here we systematically assessed the incidence, the presentation, the diagnostic yield and treatments of pediatric DPLD in Germany, using the Surveillance Unit for Rare Paediatric Disorders (ESPED).</p> <p>Results</p> <p>The incidence of DPLD was 1.32 new cases per 1 million of children per year. The majority of these children were diagnosed within the first year of life. Overall survival was 87%. Using centralized data entry and stratification tools, the patients were categorized into an advanced classification system based on diagnostic algorithms, including clinical presentations, genetics and/or histology. Combining molecular and clinical information, this survey provides an etiological overview and specific diagnostic recommendations for children with DPLD.</p> <p>Conclusions</p> <p>Standardized surveys and systematic classifications are valuable tools for the clinical handling of children with DPLD and aim to improve the disease understanding and the prognosis of these rare detrimental lung diseases.</p

Learning to dislike alcohol: conditioning negative implicit attitudes toward alcohol and its effect on drinking behavior

Rationale: Since implicit attitudes toward alcohol play an important role in drinking behavior, a possible way to obtain a behavioral change is changing these implicit attitudes. Objectives: This study examined whether a change in implicit attitudes and in drinking behavior can be achieved via evaluative conditioning. Methods: Participants were randomly assigned to an experimental condition and a control condition. In the experimental condition, participants were subjected to an evaluative conditioning procedure that consistently pairs alcohol-related cues with negative stimuli. In the control condition, alcohol-related cues were consistently paired with neutral stimuli during the evaluative conditioning phase. Implicit attitudes, explicit attitudes, and drinking behavior were measured before and after the evaluative conditioning phase. Results: Following the evaluative conditioning procedure, participants in the experimental condition showed stronger negative implicit attitudes toward alcohol and consumed less alcohol compared to participants in the control condition. However, this effect was only found when the evaluative conditioning task paired alcohol-related cues with general negative pictures, but not when using pictures of frowning faces. Conclusions: These results demonstrate that evaluative conditioning can effectively change implicit attitudes toward alcohol and also suggest that this procedure can be used to change drinking behavior. Hence, evaluative conditioning may be a useful new intervention tool to combat alcohol misuse