While much of the current study on quantum computation employs low-level formalisms such as quantum circuits, several high-level languages/calculi have been recently proposed aiming at structured quantum programming. ...
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While much of the current study on quantum computation employs low-level formalisms such as quantum circuits, several high-level languages/calculi have been recently proposed aiming at structured quantum programming. The current work contributes to the semantical study of such languages by providing interaction-based semantics of a functional quantum programming language;the latter is, much like Selinger and Valiron's, based on linear lambda calculus and equipped with features like the ! modality and recursion. The proposed denotational model is the first one that supports the full features of a quantum functional programming language;we prove adequacy of our semantics. The construction of our model is by a series of existing techniques taken from the semantics of classical computation as well as from process theory. The most notable among them is Girard's Geometry of Interaction (GoI), categorically formulated by Abramsky, Haghverdi and Scott. The mathematical genericity of these techniques-largely due to their categorical formulation-is exploited for our move from classical to quantum. (C) 2016 Elsevier B.V. All rights reserved.
Formal software verification includes specifications, tools, and interactivity with the developer. By combining these key components into a programming language and a familiar programming environment with high automat...
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Formal software verification includes specifications, tools, and interactivity with the developer. By combining these key components into a programming language and a familiar programming environment with high automation, Dafny makes verification more easily accessible to programmers and students.
We propose a language-independent symbolic execution framework. The approach is parameterised by a language definition, which consists of a signature for the syntax and execution infrastructure of the language, a mode...
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We propose a language-independent symbolic execution framework. The approach is parameterised by a language definition, which consists of a signature for the syntax and execution infrastructure of the language, a model interpreting the signature, and rewrite rules for the language's operational semantics. Then, symbolic execution amounts to computing symbolic paths using a derivative operation. We prove that the symbolic execution thus defined has the properties naturally expected from it, meaning that the feasible symbolic executions of a program and the concrete executions of the same program mutually simulate each other. We also show how a coinduction-based extension of symbolic execution can be used for the deductive verification of programs. We show how the proposed symbolic-execution approach, and the coinductive verification technique based on it, can be seamlessly implemented in language definition frameworks based on rewriting such as the K framework. A prototype implementation of our approach has been developed in K. We illustrate it on the symbolic analysis and deductive verification of nontrivial programs. (C) 2016 Elsevier Ltd. All rights reserved.
Letters to the Editor and author responses for previously published Computer articles from Bob Colwell, David Patterson, Jeremy Gibbons, Andreas Stefik, and Stefan Hanenberg.
Letters to the Editor and author responses for previously published Computer articles from Bob Colwell, David Patterson, Jeremy Gibbons, Andreas Stefik, and Stefan Hanenberg.
Real-time deformability cytometry (RT-DC) is a microfluidic technique that allows to capture and evaluate morphology and rheology of up to 1000 cells/s in a constricted channel. The cells are deformed without mec...
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Real-time deformability cytometry (RT-DC) is a microfluidic technique that allows to capture and evaluate morphology and rheology of up to 1000 cells/s in a constricted channel. The cells are deformed without mechanical contact by hydrodynamic forces and are quantified in real-time without the need of additional handling or staining procedures. Segmented pictures of the cells are stored and can be used for further analysis. RT-DC is sensitive to alterations of the cytoskeleton, which allows, e.g., to show differences in cell cycle phases, identify different subpopulations in whole blood and to study mechanical stiffening of cells entering a dormant state. The abundance of the obtainable parameters and the interpretation as mechanical readout is an analytical challenge that needs standardization. Here, we will provide guidelines for measuring and post-processing of RT-DC data. less
The oocytes, embryos, and cell-free lysates of the frog Xenopus laevis have emerged as powerful models for quantitative proteomic experiments. In the accompanying paper (Chapter 13) we describe how to prepare samples ...
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The oocytes, embryos, and cell-free lysates of the frog Xenopus laevis have emerged as powerful models for quantitative proteomic experiments. In the accompanying paper (Chapter 13) we describe how to prepare samples and acquire multiplexed proteomics spectra from those. As an illustrative example we use a 10-stage developmental time series from the egg to stage 35 (just before hatching). Here, we outline how to convert the ~700,000 acquired mass spectra from this time series into protein expression dynamics for ~9000 proteins. We first outline a preliminary quality-control analysis to discover any errors that occurred during sample preparation. We discuss how peptide and protein identification error rates are controlled, and how peptide and protein species are quantified. Our analysis relies on the freely available MaxQuant proteomics pipeline. Finally, we demonstrate how to start interpreting this large dataset by clustering and gene-set enrichment analysis. less
CsrA/RsmA is a RNA-binding protein that functions as a global regulator controlling important processes such as virulence, secondary metabolism, motility, and biofilm formation in diverse bacterial species. The activi...
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CsrA/RsmA is a RNA-binding protein that functions as a global regulator controlling important processes such as virulence, secondary metabolism, motility, and biofilm formation in diverse bacterial species. The activity of CsrA/RsmA is regulated by small RNAs that contain multiple binding sites for the protein. The expression of these noncoding RNAs effectively sequesters the protein and reduces free cellular levels of CsrA/RsmA. While multiple bacterial small RNAs that bind to and regulate CsrA/RsmA levels have been discovered, it is anticipated that there are several such small RNAs that remain undiscovered. To assist in the discovery of these small RNAs, we have developed a bioinformatics approach that combines sequence- and structure-based features to predict small RNA regulators of CsrA/RsmA. This approach analyzes structural motifs in the ensemble of low energy secondary structures of known small RNA regulators of CsrA/RsmA and trains a binary classifier on these features. The proposed machine learning approach leads to several testable predictions for small RNA regulators of CsrA/RsmA, thereby complementing and accelerating experimental efforts aimed at discovery of noncoding RNAs in the CsrA/RsmA pathway. less
In order to execute more advanced computational chemogenomic workflows, it is essential to understand the basic data formats and options for processing them. In this chapter, de facto standards for compound and protei...
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In order to execute more advanced computational chemogenomic workflows, it is essential to understand the basic data formats and options for processing them. In this chapter, de facto standards for compound and protein representation are explained, with procedures for processing them given. A walkthrough demonstrates the step-by-step processes of downloading a ligand–target database, parsing the bioactivity in the database, automatically retrieving its chemical structures and protein sequences from a command line, and finally converting the structures and sequences into representative machine-ready formats. A basic protocol to visualize the parsed database and look for patterns is also given. less
Accurate detection of chromothripsis event is important to study the mechanisms underlying this phenomenon. CTLPScanner (http://***/CTLPScanner/ ) is a web-based tool for identification and annotation o...
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Accurate detection of chromothripsis event is important to study the mechanisms underlying this phenomenon. CTLPScanner (http://***/CTLPScanner/ ) is a web-based tool for identification and annotation of chromothripsis-like pattern (CTLP) in genomic array data. In this chapter, we illustrate the utility of CTLPScanner for screening chromosome pulverization regions and give interpretation of the results. The web interface offers a set of parameters and thresholds for customized screening. We also provide practical recommendations for effective chromothripsis detection. In addition to the user data processing module, CTLPScanner contains more than 50,000 preprocessed oncogenomic arrays, which allow users to explore the presence of chromothripsis signatures from public data resources. less
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