bluuebunny/crossref_metadata_2025_split huggingface dataset:
Model checking
Authors: Clarke Edmund M. , Emerson E. Allen , Sifakis Joseph 
Published: October 2009

Turing Lecture from the winners of the 2007 ACM A.M. Turing Award.
In 1981, Edmund M. Clarke and E. Allen Emerson, working in the USA, and Joseph Sifakis working independently in France, authored seminal papers that founded what has become the highly successful field of model checking. This verification technology provides an algorithmic means of determining whether an abstract model---representing, for example, a hardware or software design---satisfies a formal specification expressed as a temporal logic (TL) formula. Moreover, if the property does not hold, the method identifies a counterexample execution that shows the source of the problem.
The progression of model checking to the point where it can be successfully used for complex systems has required the development of sophisticated means of coping with what is known as the state explosion problem. Great strides have been made on this problem over the past 28 years by what is now a very large international research community. As a result many major hardware and software companies are beginning to use model checking in practice. Examples of its use include the verification of VLSI circuits, communication protocols, software device drivers, real-time embedded systems, and security algorithms.
The work of Clarke, Emerson, and Sifakis continues to be central to the success of this research area. Their work over the years has led to the creation of new logics for specification, new verification algorithms, and surprising theoretical results. Model checking tools, created by both academic and industrial teams, have resulted in an entirely novel approach to verification and test case generation. This approach, for example, often enables engineers in the electronics industry to design complex systems with considerable assurance regarding the correctness of their initial designs. Model checking promises to have an even greater impact on the hardware and software industries in the future.

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Moshe Y. Vardi, Editor-in-Chief
A concurrent dynamic analysis framework for multicore hardware
Authors: Ha Jungwoo , Arnold Matthew , Blackburn Stephen M. , McKinley Kathryn S. 
Published: October 2009

Software has spent the bounty of Moore's law by solving harder problems and exploiting abstractions, such as high-level languages, virtual machine technology, binary rewriting, and dynamic analysis. Abstractions make programmers more productive and programs more portable, but usually slow them down. Since Moore's law is now delivering multiple cores instead of faster processors, future systems must either bear a relatively higher cost for abstractions or use some cores to help tolerate abstraction costs.
This paper presents the design, implementation, and evaluation of a novel concurrent, configurable dynamic analysis framework that efficiently utilizes multicore cache architectures. It introduces Cache-friendly Asymmetric Buffering (CAB), a lock-free ring-buffer that implements efficient communication between application and analysis threads. We guide the design and implementation of our framework with a model of dynamic analysis overheads. The framework implements exhaustive and sampling event processing and is analysis-neutral. We evaluate the framework with five popular and diverse analyses, and show performance improvements even for lightweight, low-overhead analyses.
Efficient inter-core communication is central to high performance parallel systems and we believe the CAB design gives insight into the subtleties and difficulties of attaining it for dynamic analysis and other parallel software.
Accelerating the creation of customized, language-Specific IDEs in Eclipse
Authors: Charles Philippe , Fuhrer Robert M. , Sutton Stanley M. , Duesterwald Evelyn , Vinju Jurgen 
Published: October 2009

Full-featured integrated development environments have become critical to the adoption of new programming languages. Key to the success of these IDEs is the provision of services tailored to the languages. However, modern IDEs are large and complex, and the cost of constructing one from scratch can be prohibitive. Generators that work from language specifications reduce costs but produce environments that do not fully reflect distinctive language characteristics.
We believe that there is a practical middle ground between these extremes that can be effectively addressed by an open, semi-automated strategy to IDE development. This strategy is to reduce the burden of IDE development as much as possible, especially for internal IDE details, while opening opportunities for significant customizations to IDE services. To reduce the effort needed for customization we provide a combination of frameworks, templates, and generators. We demonstrate an extensible IDE architecture that embodies this strategy, and we show that this architecture can be used to produce customized IDEs, with a moderate amount of effort, for a variety of interesting languages.
Allocation wall
Authors: Zhao Yi , Shi Jin , Zheng Kai , Wang Haichuan , Lin Haibo , Shao Ling 
Published: October 2009

Multi-core processors are widely used in computer systems. As the performance of microprocessors greatly exceeds that of memory, the memory wall becomes a limiting factor. It is important to understand how the large disparity of speed between processor and memory influences the performance and scalability of Java applications on emerging multi-core platforms.
In this paper, we studied two popular Java benchmarks, SPECjbb2005 and SPECjvm2008, on multi-core platforms including Intel Clovertown and AMD Phenom. We focus on the "partially scalable" benchmark programs. With smaller number of CPU cores these programs scale perfectly, but when more cores and software threads are used, the slope of the scalability curve degrades dramatically.
We identified a strong correlation between scalability, object allocation rate and memory bus write traffic in our experiments with our partially scalable programs. We find that these applications allocate large amounts of memory and consume almost all the memory write bandwidth in our hardware platforms. Because the write bandwidth is so limited, we propose the following hypothesis: the scalability and performance is limited by the object allocation on emerging multi-core platforms for those objects-allocation intensive Java applications, as if these applications are running into an "allocation wall".
In order to verify this hypothesis, several experiments are performed, including measuring key architecture level metrics, composing a micro-benchmark program, and studying the effect of modifying some of the "partially scalable" programs. All the experiments strongly suggest the existence of the allocation wall.
Relating Satellite-Observed Cloud Properties from MODIS to Meteorological Conditions for Marine Boundary Layer Clouds
Authors: Zhang Guang J. , Vogelmann Andrew M. , Jensen Michael P. , Collins William D. , Luke Edward P. 
Published: October 2009

Abstract
This study examines 6 yr of cloud properties observed by the Moderate Resolution Imaging Spectroradiometer (MODIS) on board the NASA Terra satellite in five prominent marine boundary layer (MBL) cloud regions (California, Peru, Canary, Angola, and Australia) and investigates their relationships with near-surface meteorological parameters obtained from NCEP reanalyses. About 62 000 independent scenes are used to examine the instantaneous relationships between cloud properties and meteorological parameters that may be used for global climate model (GCM) diagnostics and parameterization. Cloud liquid water path (LWP) generally increases with lower-tropospheric stability (LTS) and lifting condensation level (LCL), whereas cloud drizzle frequency is favored by weak LTS and negligible cold air advection. Cloud fraction (CF) depends strongly on variations in LTS, and to a lesser extent on surface air temperature advection and LCL, although the relationships vary from region to region. The authors propose capturing the effects of these three parameters on CF via their linear combination in terms of a single parameter, the effective lower-tropospheric stability (eLTS). Results indicate that eLTS offers a marked improvement over LTS alone in explaining the median CF variations within the different study regions. A parameterization of CF in terms of eLTS is provided, which produces results that are improved over those of Klein and Hartmann’s LTS-only parameterization. However, the new parameterization may not predict the observed variability correctly, and the authors propose a method that might address this shortcoming via a statistical approach.
Intensification of East Asian Summer Rainfall Interannual Variability in the Twenty-First Century Simulated by 12 CMIP3 Coupled Models
Authors: Lu Riyu , Fu Yuanhai 
Published: October 2009

Abstract
The authors examine the projected change in interannual variability of East Asian summer precipitation and of dominant monsoonal circulation components in the twenty-first century under scenarios A1B and A2 by analyzing the simulated results of 12 Coupled Model Intercomparison Project phase 3 (CMIP3) coupled models. Interannual standard deviation is used to depict the intensity of interannual variability. An evaluation indicates that these models can reasonably reproduce the essential features of the present-day interannual variability in both East Asian rainfall and the rainfall-related circulations.
The models project an enhanced interannual variability of summer rainfall over East Asia in the twenty-first century, under both scenarios A1B and A2. Over the East Asian summer rain belt, 10 of the 12 models under scenario A1B and 9 of the 10 models under scenario A2 show enhanced variability in the twenty-first century relative to the twentieth century. The multimodel ensemble (MME) results in increased ratios of interannual standard deviation of precipitation averaged over this region of about 12% and 19% under scenarios A1B and A2, respectively. Furthermore, it is found that the interannual variability is intensified much more remarkably in comparison with mean precipitation.
Two circulation factors, the western North Pacific subtropical high (WNPSH) and East Asian upper-tropospheric jet (EAJ), which are closely related to the interannual variability of East Asian summer rainfall, are also projected by the models to exhibit enhanced interannual variability in the twenty-first century. This provides more evidence for the enhancement of interannual variability in East Asian summer rainfall and implies intensified interannual variability of the whole East Asian summer monsoon system. On the other hand, the relationships of East Asian rainfall with the WNPSH and EAJ do not exhibit clear changes in the twenty-first century under scenarios A1B and A2, and there are great discrepancies in the changes of the relationships among the individual models.
Forecast Skill and Farmers’ Skills: Seasonal Climate Forecasts and Agricultural Risk Management in the Southeastern United States
Authors: Crane Todd A. , Roncoli Carla , Paz Joel , Breuer Norman , Broad Kenneth , Ingram Keith T. , Hoogenboom Gerrit 
Published: October 2009

AbstractDuring the last 10 yr, research on seasonal climate forecasts as an agricultural risk management tool has pursued three directions: modeling potential impacts and responses, identifying opportunities and constraints, and analyzing risk communication aspects. Most of these approaches tend to frame seasonal climate forecasts as a discrete product with direct and linear effects. In contrast, the authors propose that agricultural management is a performative process, constituted by a combination of planning, experimentation, and improvisation and drawing on a mix of technical expertise, situated knowledge, cumulative experience, and intuitive skill as farmers navigate a myriad of risks in the pursuit of livelihood goals and economic opportunities. This study draws on ethnographic interviews conducted with 38 family farmers in southern Georgia, examining their livelihood goals and social values, strategies for managing risk, and interactions with weather and climate information, specifically their responses to seasonal climate forecasts. Findings highlight the social nature of information processing and risk management, indicating that both material conditions and value-based attitudes bear upon the ways farmers may integrate climate predictions into their agricultural management practices. These insights translate into specific recommendations that will enhance the salience, credibility, and legitimacy of seasonal climate forecasts among farmers and will promote the incorporation of such information into a skillful performance in the face of climate uncertainty.
TGF-β inhibits IL-1β-activated PAR-2 expression through multiple pathways in human primary synovial cells
Authors: Tsai Shin-Han , Sheu Ming-Thau , Liang Yu-Chih , Cheng Hsiu-Tan , Fang Sheng-Shiung , Chen Chien-Ho 
Published: October 2009

AbstractTo investigate the mechanism how Transforming growth factor-β(TGF-β) represses Interleukin-1β (IL-1β)-induced Proteinase-Activated Receptor-2 (PAR-2) expression in human primary synovial cells (hPSCs). Human chondrocytes andhPSCs isolated from cartilages and synovium of Osteoarthritis (OA) patients were cultured with 10% fetal bovine serum media or serum free media before treatment with IL-1β, TGF-β1, or Connective tissue growth factor (CTGF). The expression of PAR-2 was detected using reverse transcriptase-polymerase chain reaction (RT-PCR) and western blotting. Collagen zymography was performed to assess the activity of Matrix metalloproteinases-13 (MMP-13). It was demonstrated that IL-1β induces PAR-2 expression via p38 pathway inhPSCs. This induction can be repressed by TGF-β and was observed to persist for at least 48 hrs, suggesting that TGF-β inhibits PAR-2 expression through multiple pathways. First of all, TGF-β was able to inhibit PAR-2 activity by inhibiting IL-1β-induced p38 signal transduction and secondly the inhibition was also indirectly due to MMP-13 inactivation. Finally, TGF-β was able to induce CTGF, and in turn CTGF represses PAR-2 expression by inhibiting IL-1β-induced phospho-p38 level. TGF-β could prevent OA from progression with the anabolic ability to induce CTGF production to maintain extracellular matrix (ECM) integrity and to down regulate PAR-2 expression, and the anti-catabolic ability to induce Tissue inhibitors of metalloproteinase-3 (TIMP-3) production to inhibit MMPs leading to avoid PAR-2 over-expression. Because IL-1β-induced PAR-2 expressed inhPSCs might play a significantly important role in early phase of OA, PAR-2 repression by exogenous TGF-β or other agents might be an ideal therapeutic target to prevent OA from progression.
Successful establishment of primary small airway cell cultures in human lung transplantation
Authors: Banerjee Balarka , Kicic Anthony , Musk Michael , Sutanto Erika N , Stick Stephen M , Chambers Daniel C 
Published: October 2009

Abstract

Background
The study of small airway diseases such as post-transplant bronchiolitis obliterans syndrome (BOS) is hampered by the difficulty in assessing peripheral airway function either physiologically or directly. Our aims were to develop robust methods for sampling small airway epithelial cells (SAEC) and to establish submerged SAEC cultures for downstream experimentation.

Methods
SAEC were obtained at 62 post-transplant bronchoscopies in 26 patients using radiologically guided bronchial brushings. Submerged cell cultures were established and SAEC lineage was confirmed using expression of clara cell secretory protein (CCSP).

Results
The cell yield for SAEC (0.956 ± 0.063 × 106) was lower than for large airway cells (1.306 ± 0.077 × 106) but did not significantly impact on the culture establishment rate (79.0 ± 5.2% vs. 83.8 ± 4.7% p = 0.49). The presence of BOS significantly compromised culture success (independent of cell yield) for SAEC (odds ratio (95%CI) 0.067 (0.01-0.40)) but not LAEC (0.3 (0.05-1.9)). Established cultures were successfully passaged and expanded.

Conclusion
Primary SAEC can be successfully obtained from human lung transplant recipients and maintained in culture for downstream experimentation. This technique will facilitate the development of primary in vitro models for BOS and other diseases with a small airway component such as asthma, cystic fibrosis and COPD.
Construction of an annotated corpus to support biomedical information extraction
Authors: Thompson Paul , Iqbal Syed A , McNaught John , Ananiadou Sophia 
Published: October 2009

AbstractBackgroundInformation Extraction (IE) is a component of text mining that facilitates knowledge discovery by automatically locating instances of interesting biomedical events from huge document collections. As events are usually centred on verbs and nominalised verbs, understanding the syntactic and semantic behaviour of these words is highly important. Corpora annotated with information concerning this behaviour can constitute a valuable resource in the training of IE components and resources.ResultsWe have defined a new scheme for annotating sentence-bound gene regulation events, centred on both verbs and nominalised verbs. For each event instance, all participants (arguments) in the same sentence are identified and assigned a semantic role from a rich set of 13 roles tailored to biomedical research articles, together with a biological concept type linked to the Gene Regulation Ontology. To our knowledge, our scheme is unique within the biomedical field in terms of the range of event arguments identified. Using the scheme, we have created the Gene Regulation Event Corpus (GREC), consisting of 240 MEDLINE abstracts, in which events relating to gene regulation and expression have been annotated by biologists. A novel method of evaluating various different facets of the annotation task showed that average inter-annotator agreement rates fall within the range of 66% - 90%.ConclusionThe GREC is a unique resource within the biomedical field, in that it annotates not only core relationships between entities, but also a range of other important details about these relationships, e.g., location, temporal, manner and environmental conditions. As such, it is specifically designed to support bio-specific tool and resource development. It has already been used to acquire semantic frames for inclusion within theBioLexicon(a lexical, terminological resource to aid biomedical text mining). Initial experiments have also shown that the corpus may viably be used to train IE components, such as semantic role labellers. The corpus and annotation guidelines are freely available for academic purposes.
A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat
Authors: Gu Yong Q , Ma Yaqin , Huo Naxin , Vogel John P , You Frank M , Lazo Gerard R , Nelson William M , Soderlund Carol , Dvorak Jan , Anderson Olin D , Luo Ming-Cheng 
Published: October 2009

AbstractBackgroundBrachypodium distachyon(Brachypodium) has been recognized as a new model species for comparative and functional genomics of cereal and bioenergy crops because it possesses many biological attributes desirable in a model, such as a small genome size, short stature, self-pollinating habit, and short generation cycle. To maximize the utility ofBrachypodium as a model for basic and applied research it is necessary to develop genomic resources for it. A BAC-based physical map is one of them. A physical map will facilitate analysis of genome structure, comparative genomics, and assembly of the entire genome sequence.ResultsA total of 67,151BrachypodiumBAC clones were fingerprinted with the SNaPshot HICF fingerprinting method and a genome-wide physical map of theBrachypodiumgenome was constructed. The map consisted of 671 contigs and 2,161 clones remained as singletons. The contigs and singletons spanned 414 Mb. A total of 13,970 gene-related sequences were detected in the BAC end sequences (BES). These gene tags aligned 345 contigs with 336 Mb of rice genome sequence, showing thatBrachypodiumand rice genomes are generally highly colinear. Divergent regions were mainly in the rice centromeric regions. A dot-plot ofBrachypodiumcontigs against the rice genome sequences revealed remnants of the whole-genome duplication caused by paleotetraploidy, which were previously found in rice and sorghum.Brachypodiumcontigs were anchored to the wheat deletion bin maps with the BES gene-tags, opening the door toBrachypodium-Triticeae comparative genomics.ConclusionThe construction of theBrachypodiumphysical map, and its comparison with the rice genome sequence demonstrated the utility of the SNaPshot-HICF method in the construction of BAC-based physical maps. The map represents an important genomic resource for the completion ofBrachypodiumgenome sequence and grass comparative genomics. A draft of the physical map and its comparisons with rice and wheat are available athttp://phymap.ucdavis.edu/brachypodium/.
The inhibitory receptor LILRB4 (ILT3) modulates antigen presenting cell phenotype and, along with LILRB2 (ILT4), is upregulated in response to Salmonella infection
Authors: Brown Damien P , Jones Des C , Anderson Katie J , Lapaque Nicolas , Buerki Robin A , Trowsdale John , Allen Rachel L 
Published: October 2009

Abstract

Background
Leukocyte Ig-like receptors (LILR) are a family of innate immune receptors with immunomodulatory functions. High-level expression of the receptors LILRB2 (ILT4) and LILRB4 (ILT3) is a feature of tolerogenic antigen presenting cells and has been observed in cancer and transplant situations. There are relatively few studies regarding these receptors in the context of infection and it is not yet clear how LILRB4 exerts its inhibitory effects.

Results
We studied the effects of LILRB4 ligation on antigen presenting cell phenotype, and the expression of LILRB2 and LILRB4 on Salmonella- infected antigen presenting cells. Ligation of LILRB4 throughout in vitro culture of dendritic cells led to an upregulation of the co-stimulatory protein CD86. Alterations in the production of IL-8 and IL-10 by LILRB4-ligated macrophages were also observed. Infection with Salmonella typhimurium or TLR stimulation with Salmonella components led to an upregulation of LILRB2 and LILRB4.

Conclusion
Our results indicate that the inhibitory effects of LILRB4 do not result from a failure to upregulate co-stimulatory proteins. In addition to the high level expression that can render antigen presenting cells tolerogenic, there may be a role for lower level expression and activity of LILRB2 and LILRB4 in response to TLR signalling during an immune response to bacterial infection.