The Experts below are selected from a list of 327 Experts worldwide ranked by ideXlab platform
Andrew B. Herr - One of the best experts on this subject based on the ideXlab platform.
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functional consequences of b repeat sequence variation in the staphylococcal biofilm protein aap deciphering the Assembly Code
Biochemical Journal, 2017Co-Authors: Catherine L. Shelton, Deborah G. Conrady, Andrew B. HerrAbstract:Staphylococcus epidermidis is an opportunistic pathogen that can form robust biofilms that render the bacteria resistant to antibiotic action and immune responses. Intercellular adhesion in S. epidermidis biofilms is mediated by the cell wall-associated Accumulation-Associated Protein (Aap), via zinc-mediated self-Assembly of its B-repeat region. This region contains up to 17 nearly-identical sequence repeats, with each repeat assumed to be functionally equivalent. However, Aap B-repeats exist as two subtypes, defined by a cluster of consensus or variant amino acids. These variable residues are positioned near the zinc-binding (and dimerization) site and the stability determinant for the B-repeat fold. We have characterized four B-repeat constructs to assess the functional relevance of the two Aap B-repeat subtypes. Analytical ultracentrifugation experiments demonstrated that constructs with the variant sequence show reduced or absent Zn2+-induced dimerization. Likewise, circular dichroism thermal denaturation experiments showed that the variant sequence could significantly stabilize the fold, depending on its location within the construct. Crystal structures of three of the constructs revealed that the side chains from the variant sequence form an extensive bonding network that can stabilize the fold. Furthermore, altered distribution of charged residues between consensus and variant sequences changes the electrostatic potential in the vicinity of the Zn2+ binding site, providing a mechanistic explanation for the loss of zinc-induced dimerization in the variant constructs. These data suggest an Assembly Code that defines preferred oligomerization modes of the B-repeat region of Aap and a slip-grip model for initial contact and firm intercellular adhesion during biofilm formation.
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Functional consequences of B-repeat sequence variation in the staphylococcal biofilm protein Aap: deciphering the Assembly Code.
The Biochemical journal, 2016Co-Authors: Catherine L. Shelton, Deborah G. Conrady, Andrew B. HerrAbstract:Staphylococcus epidermidis is an opportunistic pathogen that can form robust biofilms that render the bacteria resistant to antibiotic action and immune responses. Intercellular adhesion in S. epidermidis biofilms is mediated by the cell wall-associated accumulation-associated protein (Aap), via zinc-mediated self-Assembly of its B-repeat region. This region contains up to 17 nearly identical sequence repeats, with each repeat assumed to be functionally equivalent. However, Aap B-repeats exist as two subtypes, defined by a cluster of consensus or variant amino acids. These variable residues are positioned near the zinc-binding (and dimerization) site and the stability determinant for the B-repeat fold. We have characterized four B-repeat constructs to assess the functional relevance of the two Aap B-repeat subtypes. Analytical ultracentrifugation experiments demonstrated that constructs with the variant sequence show reduced or absent Zn2+-induced dimerization. Likewise, circular dichroism thermal denaturation experiments showed that the variant sequence could significantly stabilize the fold, depending on its location within the construct. Crystal structures of three of the constructs revealed that the side chains from the variant sequence form an extensive bonding network that can stabilize the fold. Furthermore, altered distribution of charged residues between consensus and variant sequences changes the electrostatic potential in the vicinity of the Zn2+-binding site, providing a mechanistic explanation for the loss of zinc-induced dimerization in the variant constructs. These data suggest an Assembly Code that defines preferred oligomerization modes of the B-repeat region of Aap and a slip-grip model for initial contact followed by firm intercellular adhesion during biofilm formation.
W C Newman - One of the best experts on this subject based on the ideXlab platform.
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direct synthesis of optimized dsp Assembly Code from signal flow block diagrams
International Conference on Acoustics Speech and Signal Processing, 1992Co-Authors: D B Powell, Edward A Lee, W C NewmanAbstract:Block diagrams with signal flow semantics have proven their utility in system simulation and algorithm development. They can also be used as high-level languages for real-time system implementation and design. An approach to synthesizing optimized Assembly Code for programmable DSPs from block diagrams is described. The extensible block library defines Code segments in a meta-Assembly language that uses the syntax of the Assembly Code of the target processor, but symbolically references registers and memory. An optimizing Code generator compiles these segments together, allocates registers and memory, and inserts data movement instructions as needed to produce optimized Assembly Code. In exchange for target-processor dependence in both the Code generator and the block library, the system produces Assembly Code that can closely match the efficiency of hand-written Code. >
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ICASSP - Direct synthesis of optimized DSP Assembly Code from signal flow block diagrams
[Proceedings] ICASSP-92: 1992 IEEE International Conference on Acoustics Speech and Signal Processing, 1992Co-Authors: D B Powell, Edward A Lee, W C NewmanAbstract:Block diagrams with signal flow semantics have proven their utility in system simulation and algorithm development. They can also be used as high-level languages for real-time system implementation and design. An approach to synthesizing optimized Assembly Code for programmable DSPs from block diagrams is described. The extensible block library defines Code segments in a meta-Assembly language that uses the syntax of the Assembly Code of the target processor, but symbolically references registers and memory. An optimizing Code generator compiles these segments together, allocates registers and memory, and inserts data movement instructions as needed to produce optimized Assembly Code. In exchange for target-processor dependence in both the Code generator and the block library, the system produces Assembly Code that can closely match the efficiency of hand-written Code. >
Catherine L. Shelton - One of the best experts on this subject based on the ideXlab platform.
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functional consequences of b repeat sequence variation in the staphylococcal biofilm protein aap deciphering the Assembly Code
Biochemical Journal, 2017Co-Authors: Catherine L. Shelton, Deborah G. Conrady, Andrew B. HerrAbstract:Staphylococcus epidermidis is an opportunistic pathogen that can form robust biofilms that render the bacteria resistant to antibiotic action and immune responses. Intercellular adhesion in S. epidermidis biofilms is mediated by the cell wall-associated Accumulation-Associated Protein (Aap), via zinc-mediated self-Assembly of its B-repeat region. This region contains up to 17 nearly-identical sequence repeats, with each repeat assumed to be functionally equivalent. However, Aap B-repeats exist as two subtypes, defined by a cluster of consensus or variant amino acids. These variable residues are positioned near the zinc-binding (and dimerization) site and the stability determinant for the B-repeat fold. We have characterized four B-repeat constructs to assess the functional relevance of the two Aap B-repeat subtypes. Analytical ultracentrifugation experiments demonstrated that constructs with the variant sequence show reduced or absent Zn2+-induced dimerization. Likewise, circular dichroism thermal denaturation experiments showed that the variant sequence could significantly stabilize the fold, depending on its location within the construct. Crystal structures of three of the constructs revealed that the side chains from the variant sequence form an extensive bonding network that can stabilize the fold. Furthermore, altered distribution of charged residues between consensus and variant sequences changes the electrostatic potential in the vicinity of the Zn2+ binding site, providing a mechanistic explanation for the loss of zinc-induced dimerization in the variant constructs. These data suggest an Assembly Code that defines preferred oligomerization modes of the B-repeat region of Aap and a slip-grip model for initial contact and firm intercellular adhesion during biofilm formation.
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Functional consequences of B-repeat sequence variation in the staphylococcal biofilm protein Aap: deciphering the Assembly Code.
The Biochemical journal, 2016Co-Authors: Catherine L. Shelton, Deborah G. Conrady, Andrew B. HerrAbstract:Staphylococcus epidermidis is an opportunistic pathogen that can form robust biofilms that render the bacteria resistant to antibiotic action and immune responses. Intercellular adhesion in S. epidermidis biofilms is mediated by the cell wall-associated accumulation-associated protein (Aap), via zinc-mediated self-Assembly of its B-repeat region. This region contains up to 17 nearly identical sequence repeats, with each repeat assumed to be functionally equivalent. However, Aap B-repeats exist as two subtypes, defined by a cluster of consensus or variant amino acids. These variable residues are positioned near the zinc-binding (and dimerization) site and the stability determinant for the B-repeat fold. We have characterized four B-repeat constructs to assess the functional relevance of the two Aap B-repeat subtypes. Analytical ultracentrifugation experiments demonstrated that constructs with the variant sequence show reduced or absent Zn2+-induced dimerization. Likewise, circular dichroism thermal denaturation experiments showed that the variant sequence could significantly stabilize the fold, depending on its location within the construct. Crystal structures of three of the constructs revealed that the side chains from the variant sequence form an extensive bonding network that can stabilize the fold. Furthermore, altered distribution of charged residues between consensus and variant sequences changes the electrostatic potential in the vicinity of the Zn2+-binding site, providing a mechanistic explanation for the loss of zinc-induced dimerization in the variant constructs. These data suggest an Assembly Code that defines preferred oligomerization modes of the B-repeat region of Aap and a slip-grip model for initial contact followed by firm intercellular adhesion during biofilm formation.
Zhong Shao - One of the best experts on this subject based on the ideXlab platform.
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Modular verification of Assembly Code with stack-based control abstractions
ACM SIGPLAN Notices, 2006Co-Authors: Xinyu Feng, Zhong Shao, Alexander Vaynberg, Sen XiangAbstract:Runtime stacks are critical components of any modern software--they are used to implement powerful control structures such as function call/return, stack cutting and unwinding, coroutines, and thread context switch. Stack operations, however, are very hard to reason about: there are no known formal specifications for certifying C-style setjmp/longjmp, stack cutting and unwinding, or weak continuations (in C--). In many proof-carrying Code (PCC) systems, return Code pointers and exception handlers are treated as general first-class functions (as in continuation-passing style) even though both should have more limited scopes.In this paper we show that stack-based control abstractions follow a much simpler pattern than general first-class Code pointers. We present a simple but flexible Hoare-style framework for modular verification of Assembly Code with all kinds of stackbased control abstractions, including function call/return, tail call, setjmp/longjmp, weak continuation, stack cutting, stack unwinding, multi-return function call, coroutines, and thread context switch. Instead of presenting a specific logic for each control structure, we develop all reasoning systems as instances of a generic framework. This allows program modules and their proofs developed in different PCC systems to be linked together. Our system is fully mechanized. We give the complete soundness proof and a full verification of several examples in the Coq proof assistant.
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verification of safety properties for concurrent Assembly Code
International Conference on Functional Programming, 2004Co-Authors: Zhong ShaoAbstract:Concurrency, as a useful feature of many modern programming languages and systems, is generally hard to reason about. Although existing work has explored the verification of concurrent programs using high-level languages and calculi, the verification of concurrent Assembly Code remains an open problem, largely due to the lack of abstraction at a low-level. Nevertheless, it is sometimes necessary to reason about Assembly Code or machine executables so as to achieve higher assurance.In this paper, we propose a logic-based "type" system for the static verification of concurrent Assembly programs, applying the "invariance proof" technique for verifying general safety properties and the "assume-guarantee" paradigm for decomposition. In particular, we introduce a notion of "local guarantee" for the thread-modular verification in a non-preemptive setting.Our system is fully mechanized. Its soundness has been verified using the Coq proof assistant. A safety proof of a program is semi-automatically constructed with help of Coq, allowing the verification of even undecidable safety properties. We demonstrate the usage of our system using three examples, addressing mutual exclusion, deadlock freedom, and partial correctness respectively.
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ICFP - Verification of safety properties for concurrent Assembly Code
Proceedings of the ninth ACM SIGPLAN international conference on Functional programming - ICFP '04, 2004Co-Authors: Zhong ShaoAbstract:Concurrency, as a useful feature of many modern programming languages and systems, is generally hard to reason about. Although existing work has explored the verification of concurrent programs using high-level languages and calculi, the verification of concurrent Assembly Code remains an open problem, largely due to the lack of abstraction at a low-level. Nevertheless, it is sometimes necessary to reason about Assembly Code or machine executables so as to achieve higher assurance.In this paper, we propose a logic-based "type" system for the static verification of concurrent Assembly programs, applying the "invariance proof" technique for verifying general safety properties and the "assume-guarantee" paradigm for decomposition. In particular, we introduce a notion of "local guarantee" for the thread-modular verification in a non-preemptive setting.Our system is fully mechanized. Its soundness has been verified using the Coq proof assistant. A safety proof of a program is semi-automatically constructed with help of Coq, allowing the verification of even undecidable safety properties. We demonstrate the usage of our system using three examples, addressing mutual exclusion, deadlock freedom, and partial correctness respectively.
Stefan Kowalewski - One of the best experts on this subject based on the ideXlab platform.
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WESS - Stack bounds analysis for microcontroller Assembly Code
Proceedings of the 4th Workshop on Embedded Systems Security - WESS '09, 2009Co-Authors: Jorg Brauer, Thomas Reinbacher, Bastian Schlich, Stefan KowalewskiAbstract:An important criterion for correctness of embedded software is stack safety, which requires that the stack must never overflow. This paper presents a static analysis for Assembly Code that determines upper and lower bounds of the stack. These bounds serve two purposes. First, they can be used to verify stack safety. Second, they can be used to increase the precision of several other static analyses, which are used in the context of model checking. Interrupts play an important role in embedded software, but they are a major challenge for the static analysis of stack bounds. In different micro--controller architectures, the handling of interrupts varies. In some architectures, interrupt handlers are executed atomically, while in others, they are interruptible. Therefore, we applied this analysis to two different microcontrollers, namely the ATMEL ATmega16 and the Intel MCS-51. In a case study, we show the applicability and efficiency of this analysis.
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application of static analyses for state space reduction to microcontroller Assembly Code
Formal Methods for Industrial Critical Systems, 2007Co-Authors: Bastian Schlich, Jann Loll, Stefan KowalewskiAbstract:This paper describes how static analyses can be applied tomicrocontroller Assembly Code to tackle the state explosion problem arisingfrom explicit state model checking. It presents difficulties, which occurwhen trying to apply static analyses to microcontroller AssemblyCode, caused by, for example, interrupts, hardware dependency, recursions,and indirect control. Enhancements of two reduction techniques(namely Dead Variable Reduction and Path Reduction) and their underlyingstatic analyses are detailed, which make these techniques applicableto microcontroller Assembly Code. A short case study is presented inwhich five programs are used to demonstrate the state space reductionsthat can be achieved using these two techniques.
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FMICS - Application of static analyses for state space reduction to microcontroller Assembly Code
Formal Methods for Industrial Critical Systems, 1Co-Authors: Bastian Schlich, Jann Loll, Stefan KowalewskiAbstract:This paper describes how static analyses can be applied tomicrocontroller Assembly Code to tackle the state explosion problem arisingfrom explicit state model checking. It presents difficulties, which occurwhen trying to apply static analyses to microcontroller AssemblyCode, caused by, for example, interrupts, hardware dependency, recursions,and indirect control. Enhancements of two reduction techniques(namely Dead Variable Reduction and Path Reduction) and their underlyingstatic analyses are detailed, which make these techniques applicableto microcontroller Assembly Code. A short case study is presented inwhich five programs are used to demonstrate the state space reductionsthat can be achieved using these two techniques.
