bluuebunny/crossref_metadata_2025 huggingface dataset:
An Analysis of Description Logic Augmented with Domain Rules for the Development of Product Models
Authors: Fiorentini Xenia , Rachuri Sudarsan , Suh Hyowon , Lee Jaehyun , Sriram Ram D.
Published: June 2010

The languages and logical formalisms developed by information scientists and logicians concentrate on the theory of languages and logical theorem proving. These languages, when used by domain experts to represent their domain of discourse, most often have issues related to the level of expressiveness and need specific extensions. In this paper, we first analyze the requirements for the development of structured knowledge representation models for manufacturing products. We then explore how these requirements can be satisfied through the levels of logical formalisms and expressivity of a structured knowledge representation model. We report our analysis of description logic (DL) and domain-specific rules with respect to the requirements by giving an example of a product ontology developed with ontology web language-description logic (OWL) and augmented with semantic web rule language (SWRL) rules. Clearly, increasing the expressivity of a product ontology also improves that of domain-specific rules, but there exits the usual tradeoff between the expressivity of languages and the complexity of their reasoning tasks. We present a case study of an electromechanical product to validate the analysis and further show how the OWL-DL reasoner together with the rule engine can enable reasoning about the product ontology. We finally discuss the open issues such as capabilities and limitations related to the usage of DL, OWL, and SWRL for product modeling.
Process Signature Modeling for Tolerance Analysis
Authors: Ascione R. , Polini W. , Semeraro Q.
Published: June 2010

Many well-known approaches exist in the literature for tolerance analysis. All the methods proposed in the literature consider the dimensional and the geometric tolerances applied to some critical points (contact points among profiles belonging to couples of parts) on the surface of the assembly components. These points are generally considered uncorrelated since the nominal surface is considered. Therefore, the methods proposed in the literature do not consider the actual surface due to a manufacturing process. Every manufacturing process leaves on the surface a signature, i.e., a systematic pattern that characterizes all the features machined with that process. The aim of the present work is to investigate the effects of considering the manufacturing signature in solving a tolerance stack-up function. A case study involving three parts has been defined and solved by means of a method of the literature, the variational method, with and without considering the correlation among the points of the same surface due to the manufacturing signature. This work represents a first step toward the integration of the design and the manufacturing in a concurrent engineering approach.
Purinergic Signaling: A Fundamental Mechanism in Neutrophil Activation
Authors: Chen Yu , Yao Yongli , Sumi Yuka , Li Andrew , To Uyen Kim , Elkhal Abdallah , Inoue Yoshiaki , Woehrle Tobias , Zhang Qin , Hauser Carl , Junger Wolfgang G.
Published: June 2010

Neutrophil activation by infectious and inflammatory signals requires ATP release and its feedback through purinergic receptors.
Initiator for Coated Pit Assembly
Authors: Hurtley Stella M.
Published: June 2010

Membrane-sculpting proteins nucleate clathrin-coated pits during endocytosis.
Sepsis Protection
Authors: Mueller Kristen L.
Published: June 2010

Blockade of an enzyme that promotes inflammation results in protection from lethal sepsis.
In Vitro
Antifungal Activities of Bis(Alkylpyridinium)Alkane Compounds against Pathogenic Yeasts and Molds
Authors: Chen Sharon C.-A. , Biswas Chayanika , Bartley Robyn , Widmer Fred , Pantarat Namfon , Obando Daniel , Djordjevic Julianne T. , Ellis David H. , Jolliffe Katrina A. , Sorrell Tania C.
Published: June 2010

Ten bis(alkylpyridinium)alkane compounds were tested for antifungal activity against 19 species (26 isolates) of yeasts and molds. We then determined the MICs and minimum fungicidal concentrations (MFCs) of four of the most active compounds (compounds 1, 4, 5, and 8) against 80
Candida
and 20 cryptococcal isolates, in comparison with the MICs of amphotericin B, fluconazole, itraconazole, voriconazole, posaconazole, and caspofungin, using Clinical Laboratory and Standards Institutes broth microdulition M27-A3 (yeasts) or M38-A2 (filamentous fungi) susceptibility protocols. The compounds were more potent against
Candida
and
Cryptococcus
spp. (MIC range, 0.74 to 27.9 μg/ml) than molds (0.74 to 59.7 μg/ml). MICs against
Exophiala
were 0.37 to 5.9 μg/ml and as low as 1.48 μg/ml for
Scedosporium
but ≥25 μg/ml for zygomycetes,
Aspergillus
, and
Fusarium
spp. Compounds 1, 4, 5, and 8 exhibited good fungicidal activity against
Candida
and
Cryptococcus
, except for
Candida parapsilosis
(MICs of >44 μg/ml). Geometric mean (GM) MICs were similar to those of amphotericin B and lower than or comparable to fluconazole GM MICs but 10- to 100-fold greater than those for the other azoles. GM MICs against
Candida glabrata
were <1 μg/ml, significantly lower than fluconazole GM MICs (
P
< 0.001) and similar to those of itraconazole, posaconazole, and voriconazole (GM MIC range of 0.4 to 1.23 μg/ml). The GM MIC of compound 4 against
Candida guilliermondii
was lower than that of fluconazole (1.69 μg/ml versus 7.48 μg/ml;
P
= 0.012). MICs against
Cryptococcus neoformans
and
Cryptococcus gattii
were similar to those of fluconazole. The GM MIC of compound 4 was significantly higher for
C. neoformans
(3.83 μg/ml versus 1.81 μg/ml for
C. gattii
;
P
= 0.015). This study has identified clinically relevant
in vitro
antifungal activities of novel bisalkypyridinium alkane compounds.
Phagolysosomal Integrity Is Generally Maintained afterStaphylococcus aureusInvasion of Nonprofessional Phagocytes but Is Modulated by Strain 6850
Authors: Lâm Thiên-Trí , Giese Bernd , Chikkaballi Deepak , Kühn Anika , Wolber Wanja , Pané-Farré Jan , Schäfer Daniel , Engelmann Susanne , Fraunholz Martin , Sinha Bhanu
Published: June 2010

Staphylococcus aureusis a major cause of a variety of both local and systemic infections. It can invade human host cells, a process that may account for disseminated and recurrent infections.S. aureuspostinvasion events in nonprofessional phagocytes are only partially understood. While morphological data suggest a phagosomal escape, there is a lack of corroborating functional data. Using a combination of pH determination and morphological techniques, we have tested the integrity ofStaphylococcus-containing phagosomes in 293 (HEK-293), HeLa, and EA.hy926 cells over time. Rapid acidification ofS. aureus-containing phagosomes occurred and was sustained for up to 24 h. AllS. aureusstrains tested displayed equally sustained intraphagosomal pH levels without exhibiting any correlation with pH level and hemolytic activity. The membrane morphology of the phagosomal compartment was heterogeneous, even under conditions where acidic pH was fully maintained, an observation incompatible with phagolysosomal membrane destruction. As an exception,S. aureusstrain 6850 showed a reduced phagosomal acidification signal 6 h after invasion. Additionally, only strain 6850 failed to localize to LAMP-1-positive vesicles in HeLa cells, although this was observed only rarely. Several other strongly beta-hemolytic strains did not modulate phagolysosomal pH, suggesting thatS. aureusα-toxin and β-toxin are not sufficient for this process. Taken together, our data suggest thatS. aureus-containing phagolysosomes generally remain functionally intact in nonprofessional phagocytes, thereby contrasting with transmission electron micrographic results.
Atypia in fine needle aspirates of breast lesions
Authors: Tran Phuong Viet The , Lui Philip C W , Yu Alex M C , Vinh Pham The , Chau Helen H L , Ma Tony K F , Tan Puay-Hoon , Tse Gary M
Published: June 2010

Background

The atypical category is controversial in fine needle aspiration cytology (FNAC) of the breast; most are benign, but a significant number are malignant. To date, no morphological criterion has been found to be consistent in predicting malignancy.

Aims

To evaluate specific cytological parameters and assess their usefulness in predicting histological outcome in a cohort of atypical breast FNAC, in order to establish a set of objective criteria in defining ‘high risk’ atypical breast FNAC.

Methods

A retrospective review of 98 cases of atypical breast FNAC with histological correlation was undertaken. The cytological preparations were evaluated for cellularity, percentage of epithelial cell cluster and single epithelial cells, nuclear atypia, nucleus:cytoplasm ratio, percentage of bipolar nuclei, and the presence of stromal fragments, histiocytes and necrosis.

Results

66 of 98 cases (67.35%) showed benign histology and 32 cases (32.65%) showed malignant histology. Compared with the malignant group, the benign group had significantly lower patient age (p=0.05), higher bipolar nuclei (p<0.0001), less degree of nuclear pleomorphism (p<0.0001), lower nucleus:cytoplasm ratio (p<0.0001), lower cellularity (p=0.05) and less necrosis (p<0.001). There was no difference in the percentage of epithelial clusters and single cells, or the presence of stromal fragments and histiocytes.

Conclusions

The presence of nuclear pleomorphism, high nucleus:cytoplasm ratio, epithelial cell atypia, low number of bipolar nuclei and necrosis are useful parameters to predict malignancy in atypical FNAC of the breast. Assessment of these factors in atypical FNAC may be helpful in predicting cancer risk and subsequent management decision making.
Small cell carcinomas in gastrointestinal tract: immunohistochemical and clinicopathological features
Authors: Li Anna Fen-Yau , Li Alice Chia-Heng , Hsu Chih-Yi , Li Win-Yin , Hsu Han-Shui , Chen Jeou-Yuan
Published: June 2010

Aims

To test the incidence of the expression of the immunohistochemical markers that aid diagnosis of gastrointestinal tract small cell carcinoma (GI-SmCC) and to evaluate the incidence of mixed endocrine–exocrine carcinomas in GI-SmCC.

Methods

Immunohistochemical studies of three antibodies against epithelial markers (CK8, AE1/AE3, EMA), four neuroendocrine differentiation markers (synaptophysin (Syn), neuron specific enolase (NSE), neuronal cell adhesion molecules (CD56), chromogranin A (CgA)), and a transcription factor (thyroid transcription factor 1 (TTF-1)) were performed. The incidence of non-endocrine carcinoma component was evaluated in 42 GI-SmCCs (11 in the oesophagus, 15 in the stomach, 15 in the colon, and 1 in the small intestine).

Results

The percentages of GI-SmCC with positive immunoreactivity were: CK8 92.9%, AE1/AE3 76.2%, EMA 71.4%, Syn 100%, NSE 100%, CD56 90.5%, CgA 61.9%, TTF-1 21.4%. The low molecular weight cytokeratin CK8 is more commonly expressed in GI-SmCC than is the expression of AE1/AE3 or EMA. Synaptophysin and NSE are expressed in all GI-SmCCs studied. Non-endocrine carcinoma components were demonstrated in 8 patients (4 in the oesophagus and 4 in the stomach).

Conclusion

In detecting GI-SmCC, epithelial marker CK8 is more sensitive than AE1/AE3 or EMA, and neuroendocrine differentiation markers synaptophysin and NSE are the most useful markers. TTF-1 positivity is not uncommon in GI-SmCC, but cases with negative TTF-1 staining may indicate an extra-pulmonary primary. Non-endocrine carcinoma components were demonstrated in about 30% of oesophagus and stomach SmCC; the neoplasms should be diagnosed as mixed endocrine–exocrine carcinoma.
Relation between newspaper coverage of ‘light’ cigarette litigation and beliefs about ‘lights’ among American adolescents and young adults: the impact on risk perceptions and quitting intentions
Authors: Dunlop Sally M , Romer Daniel
Published: June 2010

Aim

To investigate the impact of newspaper use in a year of increased coverage of litigation against the tobacco industry on youths' beliefs about the health risks of ‘light’ cigarettes, and examine relations between inaccurate beliefs about ‘lights’, perceptions of risk and intentions to quit smoking.

Participants

The data come from the 2004 National Annenberg Survey of Youth, a representative random digit dial telephone survey of youths aged 14–22 years in the USA (n=1501; current smokers, n=305; ‘lights’ smokers, n=112).

Design

All youths were asked about newspaper use and beliefs regarding ‘light’ cigarettes (riskiness, addictiveness, ease of quitting). Smokers reported on risk perceptions and quitting intentions. We also examined changes in newspaper coverage related to ‘lights’ from January 2001 to April 2004.

Results

Newspaper coverage related to ‘lights’ increased in the first months of 2003, and continued into 2004. Logistic regression analyses suggest that ‘lights’ smokers with lower levels of newspaper use were most likely to hold inaccurate beliefs about ‘lights’ (OR=5.93, 95% CI 1.48 to 23.77). Smokers of ‘lights’ with inaccurate beliefs were less likely to perceive their smoking as risky (OR=0.29, 95% CI 0.11 to 0.87), and smokers with inaccurate beliefs were less likely to have strong quitting intentions (OR=0.52, 95% CI 0.28 to 0.96).

Conclusions

Inaccurate beliefs about the risks of ‘lights’ were negatively related to youth smokers' perceptions of risk and intentions to quit smoking. News coverage surrounding the tobacco industry's failure to disclose these risks might help reduce these inaccurate, and potentially dangerous, beliefs.
Public support in England for raising the price of cigarettes to fund tobacco control activities: Figure 1
Authors: Gardner Benjamin , West Robert
Published: June 2010

Objective

Increasing the price of cigarettes reduces consumption, with a global price elasticity of approximately −0.4. In the UK where the cost of cigarettes is already relatively high, there is an issue surrounding public acceptance of further price rises ahead of the inflation rate. Previous research suggests that price increases may be supported where funds are dedicated to tobacco control. This study assessed public support in England for such a policy.

Methods

A cross-sectional household survey was conducted in England between August 2008 and January 2009. A representative sample of 8736 respondents aged 16+, of whom 1900 (22%) were cigarette smokers at the time of the survey, was recruited. The primary outcome measure was support for a 20p (4%) price increase on a pack of cigarettes with proceeds going to fund tobacco control activities.

Results

6216 participants (71%), including half (47%) of current cigarette smokers, indicated that they would support a 20p price increase if funds were dedicated to tobacco control activities. Levels of support among smokers were similar across the social gradient and gender. Younger smokers were more likely to support the increase. Smokers who smoked 0–10 cigarettes per day were more supportive of the increase than heavier smokers.

Conclusions

There is broad public support for raising the cost of cigarettes with funds being used for tobacco control activities. The absence of a social gradient among smokers concurs with other research showing that more disadvantaged smokers are as engaged with tobacco control objectives as more affluent smokers.
WALKING DYNAMICS FROM STRING DUALS
Authors: NÚÑEZ CARLOS , PAPADIMITRIOU IOANNIS , PIAI MAURIZIO
Published: June 2010

Within the context of a string-theory dual to [Formula: see text] gauge theories with gauge group SU (Nc) and large Nc, we identify a class of solutions to the background equations for which a suitably defined dual of the gauge coupling exhibits the features of a walking theory. We find evidence for three distinct, dynamically generated scales, characterizing walking, symmetry breaking and confinement, and we put them in correspondence with field theory by an analysis of the operators driving the flow.
Decoupled lifeguards
Authors: Ruwase Olatunji , Chen Shimin , Gibbons Phillip B. , Mowry Todd C.
Published: June 2010

Dynamic correctness checking tools (a.k.a. lifeguards) can detect a wide array of correctness issues, such as memory, security, and concurrency misbehavior, in unmodified executables at run time. However, lifeguards that are implemented using dynamic binary instrumentation (DBI) often slow down the monitored application by 10-50X, while proposals that replace DBI with hardware still see 3-8X slowdowns. The remaining overhead is the cost of performing the lifeguard analysis itself. In this paper, we explore compiler optimization techniques to reduce this overhead.

The lifeguard software is typically structured as a set of event-driven handlers, where the events are individual instructions in the monitored application's dynamic instruction stream. We propose to
decouple
the lifeguard checking code from the application that it is monitoring so that the lifeguard analysis can be invoked at the granularity of
hot paths
in the monitored application. In this way, we are able to find many more opportunities for eliminating redundant work in the lifeguard analysis, even starting with well-optimized applications and hand-tuned lifeguard handlers. Experimental results with two lifeguard frameworks - one DBI-based and one hardware-assisted - show significant reduction in monitoring overhead.
Supporting speculative parallelization in the presence of dynamic data structures
Authors: Tian Chen , Feng Min , Gupta Rajiv
Published: June 2010

The availability of multicore processors has led to significant interest in compiler techniques for speculative parallelization of sequential programs. Isolation of speculative state from non-speculative state forms the basis of such speculative techniques as this separation enables recovery from misspeculations. In our prior work on CorD [35,36] we showed that for array and scalar variable based programs copying of data between speculative and non-speculative memory can be highly optimized to support state separation that yields significant speedups on multicore machines available today. However, we observe that in context of heap-intensive programs that operate on linked dynamic data structures, state separation based speculative parallelization poses many challenges. The copying of data structures from non-speculative to speculative state (copy-in operation) can be very expensive due to the large sizes of dynamic data structures. The copying of updated data structures from speculative state to non-speculative state (copy-out operation) is made complex due to the changes in the shape and size of the dynamic data structure made by the speculative computation. In addition, we must contend with the need to translate pointers internal to dynamic data structures between their non-speculative and speculative memory addresses. In this paper we develop an augmented design for the representation of dynamic data structures such that all of the above operations can be performed efficiently. Our experiments demonstrate significant speedups on a real machine for a set of programs that make extensive use of heap based dynamic data structures.
Cache topology aware computation mapping for multicores
Authors: Kandemir Mahmut , Yemliha Taylan , Muralidhara SaiPrashanth , Srikantaiah Shekhar , Irwin Mary Jane , Zhnag Yuanrui
Published: June 2010

The main contribution of this paper is a compiler based, cache topology aware code optimization scheme for emerging multicore systems. This scheme distributes the iterations of a loop to be executed in parallel across the cores of a target multicore machine and schedules the iterations assigned to each core. Our goal is to improve the utilization of the on-chip multi-layer cache hierarchy and to maximize overall application performance. We evaluate our cache topology aware approach using a set of twelve applications and three different commercial multicore machines. In addition, to study some of our experimental parameters in detail and to explore future multicore machines (with higher core counts and deeper on-chip cache hierarchies), we also conduct a simulation based study. The results collected from our experiments with three Intel multicore machines show that the proposed compiler-based approach is very effective in enhancing performance. In addition, our simulation results indicate that optimizing for the on-chip cache hierarchy will be even more important in future multicores with increasing numbers of cores and cache levels.
Bringing extensibility to verified compilers
Authors: Tatlock Zachary , Lerner Sorin
Published: June 2010

Verified compilers, such as Leroy's CompCert, are accompanied by a fully checked correctness proof. Both the compiler and proof are often constructed with an interactive proof assistant. This technique provides a strong, end-to-end correctness guarantee on top of a small trusted computing base. Unfortunately, these compilers are also challenging to extend since each additional transformation must be proven correct in full formal detail.

At the other end of the spectrum, techniques for compiler correctness based on a domain-specific language for writing optimizations, such as Lerner's Rhodium and Cobalt, make the compiler easy to extend: the correctness of additional transformations can be checked completely automatically. Unfortunately, these systems provide a weaker guarantee since their end-to-end correctness has not been proven fully formally.

We present an approach for compiler correctness that provides the best of both worlds by bridging the gap between compiler verification and compiler extensibility. In particular, we have extended Leroy's CompCert compiler with an execution engine for optimizations written in a domain specific and proved that this execution engine preserves program semantics, using the Coq proof assistant. We present our CompCert extension, XCert, including the details of its execution engine and proof of correctness in Coq. Furthermore, we report on the important lessons learned for making the proof development manageable.
Finding low-utility data structures
Authors: Xu Guoqing , Mitchell Nick , Arnold Matthew , Rountev Atanas , Schonberg Edith , Sevitsky Gary
Published: June 2010

Many opportunities for easy, big-win, program optimizations are missed by compilers. This is especially true in highly layered Java applications. Often at the heart of these missed optimization opportunities lie computations that, with great expense, produce data values that have little impact on the program's final output. Constructing a new date formatter to format every date, or populating a large set full of expensively constructed structures only to check its size: these involve costs that are out of line with the benefits gained. This disparity between the formation costs and accrued benefits of data structures is at the heart of much runtime bloat.

We introduce a run-time analysis to discover these
low-utility
data structures. The analysis employs dynamic thin slicing, which naturally associates costs with value flows rather than raw data flows. It constructs a model of the incremental, hop-to-hop, costs and benefits of each data structure. The analysis then identifies suspicious structures based on imbalances of its incremental costs and benefits. To decrease the memory requirements of slicing, we introduce
abstract dynamic thin slicing
, which performs thin slicing over bounded abstract domains. We have modified the IBM J9 commercial JVM to implement this approach.

We demonstrate two client analyses: one that finds objects that are expensive to construct but are not necessary for the forward execution, and second that pinpoints ultimately-dead values. We have successfully applied them to large-scale and long-running Java applications. We show that these analyses are effective at detecting operations that have unbalanced costs and benefits.
A context-free markup language for semi-structured text
Authors: Xi Qian , Walker David
Published: June 2010

An
ad hoc data format
is any nonstandard, semi-structured data format for which robust data processing tools are not easily available. In this paper, we present ANNE, a new kind of markup language designed to help users generate documentation and data processing tools for ad hoc text data. More specifically, given a new ad hoc data source, an ANNE programmer edits the document to add a number of simple annotations, which serve to specify its syntactic structure. Annotations include elements that specify constants, optional data, alternatives, enumerations, sequences, tabular data, and recursive patterns. The ANNE system uses a combination of user annotations and the raw data itself to extract a context-free grammar from the document. This context-free grammar can then be used to parse the data and transform it into an XML parse tree, which may be viewed through a browser for analysis or debugging purposes. In addition, the ANNE system generates a PADS/ML description, which may be saved as lasting documentation of the data format or compiled into a host of useful data processing tools.

In addition to designing and implementing ANNE, we have devised a semantic theory for the core elements of the language. This semantic theory describes the editing process, which translates a raw, unannotated text document into an annotated document, and the grammar extraction process, which generates a context-free grammar from an annotated document. We also present an alternative characterization of system behavior by drawing upon ideas from the field of relevance logic. This secondary characterization, which we call
relevance analysis
, specifies a direct relationship between unannotated documents and the context-free grammars that our system can generate from them. Relevance analysis allows us to prove important theorems concerning the expressiveness and utility of our system.
Printing floating-point numbers quickly and accurately with integers
Authors: Loitsch Florian
Published: June 2010

We present algorithms for accurately converting floating-point numbers to decimal representation. They are fast (up to 4 times faster than commonly used algorithms that use high-precision integers) and correct: any printed number will evaluate to the same number, when read again.

Our algorithms are fast, because they require only fixed-size integer arithmetic. The sole requirement for the integer type is that it has at least two more bits than the significand of the floating-point number. Hence, for IEEE 754 double-precision numbers (having a 53-bit significand) an integer type with 55 bits is sufficient. Moreover we show how to exploit additional bits to improve the generated output.

We present three algorithms with different properties: the first algorithm is the most basic one, and does not take advantage of any extra bits. It simply shows how to perform the binary-to-decimal transformation with the minimal number of bits. Our second algorithm improves on the first one by using the additional bits to produce a shorter (often the shortest) result.

Finally we propose a third version that can be used when the shortest output is a requirement. The last algorithm either produces optimal decimal representations (with respect to shortness and rounding) or rejects its input. For IEEE 754 double-precision numbers and 64-bit integers roughly 99.4% of all numbers can be processed efficiently. The remaining 0.6% are rejected and need to be printed by a slower complete algorithm.
Lock elision for read-only critical sections in Java
Authors: Nakaike Takuya , Michael Maged M.
Published: June 2010

It is not uncommon in parallel workloads to encounter shared data structures with read-mostly access patterns, where operations that update data are infrequent and most operations are read-only. Typically, data consistency is guaranteed using mutual exclusion or read-write locks. The cost of atomic update of lock variables result in high overheads and high cache coherence traffic under active sharing, thus slowing down single thread performance and limiting scalability.

In this paper, we present
SOLERO (Software Optimistic Lock Elision for Read-Only critical sections)
, a new lock implementation called for optimizing read-only critical sections in Java based on sequential locks. SOLERO is compatible with the conventional lock implementation of Java. However, unlike the conventional implementation, only critical sections that may write data or have side effects need to update lock variables, while read-only critical sections need only read lock variables without writing them. Each writing critical section changes the lock value to a new value. Hence, a read-only critical section is guaranteed to be consistent if the lock is free and its value does not change from the beginning to the end of the read-only critical section.

Using Java workloads including SPECjbb2005 and the HashMap and TreeMap Java classes, we evaluate the performance impact of applying SOLERO to read-mostly locks. Our experimental results show performance improvements across the board, often substantial, in both single thread speed and scalability over the conventional lock implementation (mutual exclusion) and read-write locks. SOLERO improves the performance of SPECjbb2005 by 3-5% on single and multiple threads. The results using the HashMap and TreeMap benchmarks show that SOLERO outperforms the conventional lock implementation and read-write locks by substantial multiples on multi-threads.
Smooth interpretation
Authors: Chaudhuri Swarat , Solar-Lezama Armando
Published: June 2010

We presentsmooth interpretation, a method to systematically approximate numerical imperative programs by smooth mathematical functions. This approximation facilitates the use of numerical search techniques like gradient descent for program analysis and synthesis. The method extends to programs the notion ofGaussian smoothing, a popular signal-processing technique that filters out noise and discontinuities from a signal by taking its convolution with a Gaussian function.

In our setting, Gaussian smoothing executes a program according to a probabilistic semantics; the execution of programPon an inputxafter Gaussian smoothing can be summarized as follows: (1) Apply a Gaussian perturbation tox-- the perturbed input is a random variable following a normal distribution with meanx. (2) Compute and return theexpected outputofPon this perturbed input. Computing the expectation explicitly would require the execution ofPon all possible inputs, but smooth interpretation bypasses this requirement by using a form of symbolic execution to approximate the effect of Gaussian smoothing onP. The result is an efficient but approximate implementation of Gaussian smoothing of programs.

Smooth interpretation has the effect of attenuating features of a program that impede numerical searches of its input space -- for example, discontinuities resulting from conditional branches are replaced by continuous transitions. We apply smooth interpretation to the problem of synthesizing values of numerical control parameters in embedded control applications. This problem is naturally formulated as one of numerical optimization: the goal is to find parameter values that minimize the error between the resulting program and a programmer-provided behavioral specification. Solving this problem by directly applying numerical optimization techniques is often impractical due to the discontinuities in the error function. By eliminating these discontinuities, smooth interpretation makes it possible to search the parameter space efficiently by means of simple gradient descent. Our experiments demonstrate the value of this strategy in synthesizing parameters for several challenging programs, including models of an automated gear shift and a PID controller.
Complete functional synthesis
Authors: Kuncak Viktor , Mayer Mikaël , Piskac Ruzica , Suter Philippe
Published: June 2010

Synthesis of program fragments from specifications can make programs easier to write and easier to reason about. To integrate synthesis into programming languages, synthesis algorithms should behave in a predictable way - they should succeed for a well-defined class of specifications. They should also support unbounded data types such as numbers and data structures. We propose to generalize decision procedures into predictable and complete synthesis procedures. Such procedures are guaranteed to find code that satisfies the specification if such code exists. Moreover, we identify conditions under which synthesis will statically decide whether the solution is guaranteed to exist, and whether it is unique. We demonstrate our approach by starting from decision procedures for linear arithmetic and data structures and transforming them into synthesis procedures. We establish results on the size and the efficiency of the synthesized code. We show that such procedures are useful as a language extension with implicit value definitions, and we show how to extend a compiler to support such definitions. Our constructs provide the benefits of synthesis to programmers, without requiring them to learn new concepts or give up a deterministic execution model.
MemSAT
Authors: Torlak Emina , Vaziri Mandana , Dolby Julian
Published: June 2010

Memory models are hard to reason about due to their complexity, which stems from the need to strike a balance between ease-of-programming and allowing compiler and hardware optimizations. In this paper, we present an automated tool, MemSAT, that helps in debugging and reasoning about memory models. Given an axiomatic specification of a memory model and a multi-threaded test program containing assertions, MemSAT outputs a trace of the program in which both the assertions and the memory model axioms are satisfied, if one can be found. The tool is fully automatic and is based on a SAT solver. If it cannot find a trace, it outputs a minimal subset of the memory model and program constraints that are unsatisfiable. We used MemSAT to check several existing memory models against their published test cases, including the current Java Memory Model by Manson et al. and a revised version of it by Sevcik and Aspinall. We found subtle discrepancies between what was expected and the actual results of test programs.
Type-preserving compilation of end-to-end verification of security enforcement
Authors: Chen Juan , Chugh Ravi , Swamy Nikhil
Published: June 2010

A number of programming languages use rich type systems to verify security properties of code. Some of these languages are meant for source programming, but programs written in these languages are compiled without explicit security proofs, limiting their utility in settings where proofs are necessary, e.g., proof-carrying authorization. Others languages do include explicit proofs, but these are generally lambda calculi not intended for source programming, that must be further compiled to an executable form. A language suitable for source programming backed by a compiler that enables end-to-end verification is missing.

In this paper, we present a type-preserving compiler that translates programs written in FINE, a source-level functional language with dependent refinements and affine types, to DCIL, a new extension of the .NET Common Intermediate Language. FINE is type checked using an external SMT solver to reduce the proof burden on source programmers. We extract explicit LCF-style proof terms from the solver and carry these proof terms in the compilation to DCIL, thereby removing the solver from the trusted computing base. Explicit proofs enable DCIL to be used in a number of important scenarios, including the verification of mobile code, proof-carrying authorization, and evidence-based auditing. We report on our experience using FINE to build reference monitors for several applications, ranging from a plugin-based email client to a conference management server.
Mixing type checking and symbolic execution
Authors: Khoo Yit Phang , Chang Bor-Yuh Evan , Foster Jeffrey S.
Published: June 2010

Static analysis designers must carefully balance precision and efficiency. In our experience, many static analysis tools are built around an elegant, core algorithm, but that algorithm is then extensively tweaked to add just enough precision for the coding idioms seen in practice, without sacrificing too much efficiency. There are several downsides to adding precision in this way: the tool's implementation becomes much more complicated; it can be hard for an end-user to interpret the tool's results; and as software systems vary tremendously in their coding styles, it may require significant algorithmic engineering to enhance a tool to perform well in a particular software domain.

In this paper, we present Mix, a novel system that mixes type checking and symbolic execution. The key aspect of our approach is that these analyses are applied independently on disjoint parts of the program, in an off-the-shelf manner. At the boundaries between nested type checked and symbolically executed code regions, we use special mix rules to communicate information between the off-the-shelf systems. The resulting mixture is a provably sound analysis that is more precise than type checking alone and more efficient than exclusive symbolic execution. In addition, we also describe a prototype implementation, Mixy, for C. Mixy checks for potential null dereferences by mixing a null/non-null type qualifier inference system with a symbolic executor.
Evaluating iterative optimization across 1000 datasets
Authors: Chen Yang , Huang Yuanjie , Eeckhout Lieven , Fursin Grigori , Peng Liang , Temam Olivier , Wu Chengyong
Published: June 2010

While iterative optimization has become a popular compiler optimization approach, it is based on a premise which has never been truly evaluated: that it is possible to learn the best compiler optimizations across data sets. Up to now, most iterative optimization studies find the best optimizations through repeated runs on the same data set. Only a handful of studies have attempted to exercise iterative optimization on a few tens of data sets.

In this paper, we truly put iterative compilation to the test for the first time by evaluating its effectiveness across a large number of data sets. We therefore compose KDataSets, a data set suite with 1000 data sets for 32 programs, which we release to the public. We characterize the diversity of KDataSets, and subsequently use it to evaluate iterative optimization.We demonstrate that it is possible to derive a robust iterative optimization strategy across data sets: for all 32 programs, we find that there exists at least one combination of compiler optimizations that achieves 86% or more of the best possible speedup across
all
data sets using Intel's ICC (83% for GNU's GCC). This optimal combination is program-specific and yields speedups up to 1.71 on ICC and 2.23 on GCC over the highest optimization level (-fast and -O3, respectively). This finding makes the task of optimizing programs across data sets much easier than previously anticipated, and it paves the way for the practical and reliable usage of iterative optimization. Finally, we derive pre-shipping and post-shipping optimization strategies for software vendors.
Generative fixation
Authors: Burjorjee Keki M.
Published: June 2010

Simple genetic algorithms have been used in a wide range of engineering and scientific fields to quickly procure useful solutions to poorly understood optimization problems. Unfortunately, despite the routine use of these algorithms for over three decades, their remarkable adaptive capacity has not been adequately accounted for. In my dissertation, I develop, submit, and support the
generative fixation hypothesis
---a unified explanation for the adaptive capacity of the simple genetic algorithm.
Caveolin-1-ablated mice survive in cold by nonshivering thermogenesis despite desensitized adrenergic responsiveness
Authors: Mattsson Charlotte L. , Csikasz Robert I. , Shabalina Irina G. , Nedergaard Jan , Cannon Barbara
Published: June 2010

Caveolin-1 (Cav1)-ablated mice display impaired lipolysis in white adipose tissue. They also seem to have an impairment in brown adipose tissue function, implying that Cav1-ablated mice could encounter problems in surviving longer periods in cold temperatures. To investigate this, Cav1-ablated mice and wild-type mice were transferred to cold temperatures for extended periods of time, and parameters related to metabolism and thermogenesis were investigated. Unexpectedly, the Cav1-ablated mice survived in the cold. There were no differences between Cav1-ablated and wild-type mice with regard to food intake, in behavior related to shivering, or in body temperature. The Cav1-ablated mice had a halved total fat content independently of acclimation temperature. There was no difference in brown adipose tissue uncoupling protein-1 (UCP1) protein amount, and isolated brown fat mitochondria were thermogenically competent but displayed 30% higher thermogenic capacity. However, the β3-adrenergic receptor amount was reduced by about one-third in the Cav1-ablated mice at all acclimation temperatures. Principally in accordance with this, a higher than standard dose of norepinephrine was needed to obtain full norepinephrine-induced thermogenesis in the Cav1-ablated mice; the higher dose was also needed for the Cav1-ablated mice to be able to utilize fat as a substrate for thermogenesis. In conclusion, the ablation of Cav1 impairs brown adipose tissue function by a desensitization of the adrenergic response; however, the desensitization is not evident in the animal as it is overcome physiologically, and Cav1-ablated mice can therefore survive in prolonged cold by nonshivering thermogenesis.
“Lantern‐Shaped” Platinum(III) Complexes with Axially Bound 9‐Ethylguanine or 1‐Methylcytosine (L) of General Formula [Pt2{HN=C(But)O}4L2](NO3) 2
Authors: Pacifico Concetta , Intini Francesco Paolo , Nushi Fiorentin , Natile Giovanni
Published: June 2010

The synthesis, NMR characterization, and X‐ray crystallography of “lantern‐shaped” platinum(III) complexes with four pivaloamidate bridging ligands and two 9‐ethylguanines (9‐EtG) or 1‐methylcytosines (1‐MeC) in axial positions are reported: cis-N2O2‐[Pt2{HN=C(But)O}4(9‐EtG)2](NO3)2 and cis‐N2O2‐[Pt2{HN=C(But)O}4(1‐MeC)2](NO3)2. The last complex is, to the best of our knowledge, the first dinuclear compound of platinum(III) with axially bound 1‐MeC.
Laparo-Endoscopic Single-Site Surgery for Radical and Cytoreductive Nephrectomy, Renal Vein Thrombectomy, and Partial Nephrectomy: A Prospective Pilot Evaluation
Authors: Derweesh Ithaar H. , Silberstein Jonathan L. , Bazzi Wassim , Kopp Ryan , Downs Tracy M. , Kane Christopher J.
Published: June 2010

Introduction. Laparo-endoscopic single-site surgery (LESS) may diminish morbidity of laparoscopic surgery. We prospectively evaluated feasibility and outcomes of LESS-Radical Nephrectomy (LESS-RN) and Partial Nephrectomy (LESS-PN). Methods. 10 patients underwent LESS-RN (6) and LESS-PN (4) between 2/2009-5/2009. LESS-RN included 2 with renal vein thrombectomy, one of which was also cytoreductive. Transperitoneal LESS access was obtained by periumbilical incision. Patient/tumor characteristics, oncologic, and quality of life (QoL) outcomes were analyzed. Results. 3 Men/7 Women (mean age 58.7 years, median follow-up 9.8 months) underwent LESS. 9/10 cases were completed successfully. All had negative margins. Mean operative time was 161 minutes, estimated blood loss was 125 mL, and incision size was 4.4 cm. Median tumor size for LESS-RN and -PN was 5.0 and 1.7 cm (). Median LESS-PN ischemia time was 24 minutes; mean preoperative/postoperative creatinine were 0.7/0.8 mg/dL (). Mean pain score at discharge was 1.3. Mean preoperative, 3-, and 6-month postoperative SF-36 QoL Score was 73.8, 74.4 and 77.1 (). All patients are currently alive. Conclusions. LESS-RN, renal vein thrombectomy, and PN are technically feasible and safe while maintaining adherence to oncologic principles, with excellent QoL preservation and low discharge pain scores. Further study is requisite.
pH‐Potentiometric Investigation towards Chelating Tendencies of p‐Hydroquinone and Phenol Iminodiacetate Copper(II) Complexes
Authors: Stylianou Marios , Keramidas Anastasios D. , Drouza Chryssoula
Published: June 2010

Copper ions in the active sites of several proteins/enzymes interact with phenols and quinones, and this interaction is associated to the reactivity of the enzymes. In this study the speciation of the Cu2+ with iminodiacetic phenolate/hydroquinonate ligands has been examined by pH‐potentiometry. The results reveal that the iminodiacetic phenol ligand forms mononuclear complexes with Cu2+ at acidic and alkaline pHs, and a binuclear Ophenolate‐bridged complex at pH range from 7 to 8.5. The binucleating hydroquinone ligand forms only 2 : 1 metal to ligand complexes in solution. The pK values of the protonation of the phenolate oxygen of the two ligands are reduced about 2 units after complexation with the metal ion and are close to the pK values for the copper‐interacting tyrosine phenol oxygen in copper enzymes.
Clinical Relevance of KRAS in Human Cancers
Authors: Jančík Sylwia , Drábek Jiří , Radzioch Danuta , Hajdúch Marián
Published: June 2010

TheKRASgene (Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) is an oncogene that encodes a small GTPase transductor protein called KRAS. KRAS is involved in the regulation of cell division as a result of its ability to relay external signals to the cell nucleus. Activating mutations in theKRASgene impair the ability of the KRAS protein to switch between active and inactive states, leading to cell transformation and increased resistance to chemotherapy and biological therapies targeting epidermal growth factor receptors. This review highlights some of the features of theKRASgene and the KRAS protein and summarizes current knowledge of the mechanism ofKRASgene regulation. It also underlines the importance of activating mutations in theKRASgene in relation to carcinogenesis and their importance as diagnostic biomarkers, providing clues regarding human cancer patients' prognosis and indicating potential therapeutic approaches.
Features of Recent Codon Evolution: A Comparative Polymorphism-Fixation Study
Authors: Zhao Zhongming , Jiang Cizhong
Published: June 2010

Features of amino-acid and codon changes can provide us important insights on protein evolution. So far, investigators have often examined mutation patterns at either interspecies fixed substitution or intraspecies nucleotide polymorphism level, but not both. Here, we performed a unique analysis of a combined set of intra-species polymorphisms and inter-species substitutions in human codons. Strong difference in mutational pattern was found at codon positions 1, 2, and 3 between the polymorphism and fixation data. Fixation had strong bias towards increasing the rarest codons but decreasing the most frequently used codons, suggesting that codon equilibrium has not been reached yet. We detected strong CpG effect on CG-containing codons and subsequent suppression by fixation. Finally, we detected the signature of purifying selection against A∣U dinucleotides at synonymous dicodon boundaries. Overall, fixation process could effectively and quickly correct the volatile changes introduced by polymorphisms so that codon changes could be gradual and directional and that codon composition could be kept relatively stable during evolution.
Evolution of Statistic Moments of 2D-Distributions of Biological Liquid Crystal Net Mueller Matrix Elements in the Process of Their Birefringent Structure Changes
Authors: Ushenko A. G. , Misevich I. Z. , Istratiy V. , Bachyns'ka I. , Peresunko A. P. , Numan Omar Kamal , Moiysuk T. G.
Published: June 2010

This research is aimed to investigate the reliability of Mueller-matrix differentiation of birefringence change of optically thick layers of biological liquid crystals at the early stages of the change in their physiological state. This is performed by measuring the set of skewness and kurtosis values of Mueller matrix image of the phase element M44 in various points of the object under investigation.