bluuebunny/crossref_metadata_2025_split huggingface dataset:
HOTL
Authors: Xiang Xiaoya , Ding Chen , Luo Hao , Bao Bin 
Published: July 2013

The locality metrics are many, for example, miss ratio to test performance, data footprint to manage cache sharing, and reuse distance to analyze and optimize a program. It is unclear how different metrics are related, whether one subsumes another, and what combination may represent locality completely.
This paper first derives a set of formulas to convert between five locality metrics and gives the condition for correctness. The transformation is analogous to differentiation and integration used to convert between higher order polynomials. As a result, these metrics can be assigned an order and organized into a hierarchy.
Using the new theory, the paper then develops two techniques: one measures the locality in real time without special hardware support, and the other predicts multicore cache interference without parallel testing. The paper evaluates them using sequential and parallel programs as well as for a parallel mix of sequential programs.
Portable performance on heterogeneous architectures
Authors: Phothilimthana Phitchaya Mangpo , Ansel Jason , Ragan-Kelley Jonathan , Amarasinghe Saman 
Published: July 2013

Trends in both consumer and high performance computing are bringing not only more cores, but also increased heterogeneity among the computational resources within a single machine. In many machines, one of the greatest computational resources is now their graphics coprocessors (GPUs), not just their primary CPUs. But GPU programming and memory models differ dramatically from conventional CPUs, and the relative performance characteristics of the different processors vary widely between machines. Different processors within a system often perform best with different algorithms and memory usage patterns, and achieving the best overall performance may require mapping portions of programs across all types of resources in the machine.
To address the problem of efficiently programming machines with increasingly heterogeneous computational resources, we propose a programming model in which the best mapping of programs to processors and memories is determined empirically. Programs define choices in how their individual algorithms may work, and the compiler generates further choices in how they can map to CPU and GPU processors and memory systems. These choices are given to an empirical autotuning framework that allows the space of possible implementations to be searched at installation time. The rich choice space allows the autotuner to construct poly-algorithms that combine many different algorithmic techniques, using both the CPU and the GPU, to obtain better performance than any one technique alone. Experimental results show that algorithmic changes, and the varied use of both CPUs and GPUs, are necessary to obtain up to a 16.5x speedup over using a single program configuration for all architectures.
DDOS
Authors: Hunt Nicholas , Bergan Tom , Ceze Luis , Gribble Steven D. 
Published: July 2013

Nondeterminism complicates the development and management of distributed systems, and arises from two main sources: the local behavior of each individual node as well as the behavior of the network connecting them. Taming nondeterminism effectively requires dealing with both sources.
This paper proposes DDOS, a system that leverages prior work on deterministic multithreading to offer: 1) space-efficient record/replay of distributed systems; and 2) fully deterministic distributed behavior. Leveraging deterministic behavior at each node makes outgoing messages strictly a function of explicit inputs. This allows us to record the system by logging just message's arrival time, not the contents. Going further, we propose and implement an algorithm that makes all communication between nodes deterministic by scheduling communication onto a global logical timeline.
We implement both algorithms in a system called DDOS and evaluate our system with parallel scientific applications, an HTTP/memcached system and a distributed microbenchmark with a high volume of peer-to-peer communication. Our results show up to two orders of magnitude reduction in log size of record/replay, and that distributed systems can be made deterministic with an order of magnitude of overhead.
Automatic dataflow model extraction from modal real-time stream processing applications
Authors: Geuns Stefan J. , Hausmans Joost P.H.M. , Bekooij Marco J.G. 
Published: July 2013

Many real-time stream processing applications are initially described as a sequential application containing while-loops, which execute for an unknown number of iterations. These modal applications have to be executed in parallel on an MPSoC system in order to meet their real-time throughput constraints. However, no suitable approach exists that can automatically derive a temporal analysis model from a sequential specification containing while- loops with an unknown number of iterations.
This paper introduces an approach to the automatic generation of a Structured Variable-rate Phased Dataflow (SVPDF) model from a sequential specification of a modal application. The real-time requirements of an application can be analyzed despite the presence of while-loops with an unknown number of iterations. It is shown that an algorithm that has a polynomial time computational complexity can be applied on the generated SVPDF model to determine whether a throughput constraint can be met. The enabler for the automatic generation of an SVPDF model is the decoupling of synchronization between tasks that contain different while-loops. A DVB-T radio transceiver illustrates the derivation of the SVPDF model.
Natural proofs for structure, data, and separation
Authors: Qiu Xiaokang , Garg Pranav , Ştefănescu Andrei , Madhusudan Parthasarathy 
Published: July 2013

We propose natural proofs for reasoning with programs that manipulate data-structures against specifications that describe the structure of the heap, the data stored within it, and separation and framing of sub-structures. Natural proofs are a subclass of proofs that are amenable to completely automated reasoning, that provide sound but incomplete procedures, and that capture common reasoning tactics in program verification. We develop a dialect of separation logic over heaps, called Dryad, with recursive definitions that avoids explicit quantification. We develop ways to reason with heaplets using classical logic over the theory of sets, and develop natural proofs for reasoning using proof tactics involving disciplined unfoldings and formula abstractions. Natural proofs are encoded into decidable theories of first-order logic so as to be discharged using SMT solvers.
We also implement the technique and show that a large class of more than 100 correct programs that manipulate data-structures are amenable to full functional correctness using the proposed natural proof method. These programs are drawn from a variety of sources including standard data-structures, the Schorr-Waite algorithm for garbage collection, a large number of low-level C routines from the Glib library and OpenBSD library, the Linux kernel, and routines from a secure verified OS-browser project. Our work is the first that we know of that can handle such a wide range of full functional verification properties of heaps automatically, given pre/post and loop invariant annotations. We believe that this work paves the way for deductive verification technology to be used by programmers who do not (and need not) understand the internals of the underlying logic solvers, significantly increasing their applicability in building reliable systems.
TRANSIT
Authors: Udupa Abhishek , Raghavan Arun , Deshmukh Jyotirmoy V. , Mador-Haim Sela , Martin Milo M.K. , Alur Rajeev 
Published: July 2013

With the maturing of technology for model checking and constraint solving, there is an emerging opportunity to develop programming tools that can transform the way systems are specified. In this paper, we propose a new way to program distributed protocols using concolic snippets. Concolic snippets are sample execution fragments that contain both concrete and symbolic values. The proposed approach allows the programmer to describe the desired system partially using the traditional model of communicating extended finite-state-machines (EFSM), along with high-level invariants and concrete execution fragments. Our synthesis engine completes an EFSM skeleton by inferring guards and updates from the given fragments which is then automatically analyzed using a model checker with respect to the desired invariants. The counterexamples produced by the model checker can then be used by the programmer to add new concrete execution fragments that describe the correct behavior in the specific scenario corresponding to the counterexample.
We describe TRANSIT, a language and prototype implementation of the proposed specification methodology for distributed protocols. Experimental evaluations of TRANSIT to specify cache coherence protocols show that (1) the algorithm for expression inference from concolic snippets can synthesize expressions of size 15 involving typical operators over commonly occurring types, (2) for a classical directory-based protocol, TRANSIT automatically generates, in a few seconds, a complete implementation from a specification consisting of the EFSM structure and a few concrete examples for every transition, and (3) a published partial description of the SGI Origin cache coherence protocol maps directly to symbolic examples and leads to a complete implementation in a few iterations, with the programmer correcting counterexamples resulting from underspecified transitions by adding concrete examples in each iteration.
Translation validation for a verified OS kernel
Authors: Sewell Thomas Arthur Leck , Myreen Magnus O. , Klein Gerwin 
Published: July 2013

We extend the existing formal verification of the seL4 operating system microkernel from 9500 lines of C source code to the binary level. We handle all functions that were part of the previous verification. Like the original verification, we currently omit the assembly routines and volatile accesses used to control system hardware.
More generally, we present an approach for proving refinement between the formal semantics of a program on the C source level and its formal semantics on the binary level, thus checking the validity of compilation, including some optimisations, and linking, and extending static properties proved of the source code to the executable. We make use of recent improvements in SMT solvers to almost fully automate this process.
We handle binaries generated by unmodified gcc 4.5.1 at optimisation level 1, and can handle most of seL4 even at optimisation level 2.
P
Authors: Desai Ankush , Gupta Vivek , Jackson Ethan , Qadeer Shaz , Rajamani Sriram , Zufferey Damien 
Published: July 2013

We describe the design and implementation of P, a domain-specific language to write asynchronous event driven code. P allows the programmer to specify the system as a collection of interacting state machines, which communicate with each other using events. P unifies modeling and programming into one activity for the programmer. Not only can a P program be compiled into executable code, but it can also be tested using model checking techniques. P allows the programmer to specify the environment, used to "close" the system during testing, as nondeterministic ghost machines. Ghost machines are erased during compilation to executable code; a type system ensures that the erasure is semantics preserving.
The P language is designed so that a P program can be checked for responsiveness---the ability to handle every event in a timely manner. By default, a machine needs to handle every event that arrives in every state. But handling every event in every state is impractical. The language provides a notion of deferred events where the programmer can annotate when she wants to delay processing an event. The default safety checker looks for presence of unhandled events. The language also provides default liveness checks that an event cannot be potentially deferred forever.
P was used to implement and verify the core of the USB device driver stack that ships with Microsoft Windows 8. The resulting driver is more reliable and performs better than its prior incarnation (which did not use P); we have more confidence in the robustness of its design due to the language abstractions and verification provided by P.
Mechanisms of Banner Cloud Formation
Authors: Voigt Matthias , Wirth Volkmar 
Published: July 2013

Abstract
Banner clouds are clouds in the lee of steep mountains or sharp ridges. Their formation has previously been hypothesized as due to three different mechanisms: (i) vertical uplift in a lee vortex (which has a horizontal axis), (ii) adiabatic expansion along quasi-horizontal trajectories (the so-called Bernoulli effect), and (iii) a mixing cloud (i.e., condensation through mixing of two unsaturated air masses).
In the present work, these hypotheses are tested and quantitatively evaluated against each other by means of large-eddy simulation. The model setup is chosen such as to represent idealized but prototypical conditions for banner cloud formation. In this setup the lee-vortex mechanism is clearly the dominant mechanism for banner cloud formation. An essential aspect is the pronounced windward–leeward asymmetry in the Lagrangian vertical uplift with a plume of large positive values in the immediate lee of the mountain; this allows the region in the lee to tap moister air from closer to the surface. By comparison, the horizontal pressure perturbation is more than two orders of magnitude smaller than the pressure drop along a trajectory in the rising branch of the lee vortex; the “Bernoulli mechanism” is, therefore, very unlikely to be a primary mechanism. Banner clouds are unlikely to be “mixing clouds” in the strict sense of their definition. However, turbulent mixing may lead to small but nonnegligible moistening of parcels along time-mean trajectories; although not of primary importance, the latter may be considered as a modifying factor to existing banner clouds.
Assimilating AMSU-A Radiances in the TC Core Area with NOAA Operational HWRF (2011) and a Hybrid Data Assimilation System: Danielle (2010)
Authors: Zhang Man , Zupanski Milija , Kim Min-Jeong , Knaff John A. 
Published: July 2013

Abstract
A regional hybrid variational–ensemble data assimilation system (HVEDAS), the maximum likelihood ensemble filter (MLEF), is applied to the 2011 version of the NOAA operational Hurricane Weather Research and Forecasting (HWRF) model to evaluate the impact of direct assimilation of cloud-affected Advanced Microwave Sounding Unit-A (AMSU-A) radiances in tropical cyclone (TC) core areas. The forward components of both the gridpoint statistical interpolation (GSI) analysis system and the Community Radiative Transfer Model (CRTM) are utilized to process and simulate satellite radiances. The central strategies to allow the use of cloud-affected radiances are (i) to augment the control variables to include clouds and (ii) to add the model cloud representations in the observation forward models to simulate the microwave radiances. The cloudy AMSU-A radiance assimilation in Hurricane Danielle's (2010) core area has produced encouraging results with respect to the operational cloud-cleared radiance preprocessing procedures used in this study. Through the use of the HVEDAS, ensemble covariance statistics for a pseudo-AMSU-A observation in Danielle's core area show physically meaningful error covariances and statistical couplings with hydrometeor variables (i.e., the total-column condensate in Ferrier microphysics). The cloudy radiance assimilation in the TC core region (i.e., ASR experiment) consistently reduced the root-mean-square errors of the background departures, and also generally improved the forecasts of Danielle's intensity as well as the quantitative cloud analysis and prediction. It is also indicated that an entropy-based information content quantification process provides a useful metric for evaluating the utility of satellite observations in hybrid data assimilation.
The involvement of CD36 in monocyte activation by antiphospholipid antibodies
Authors: Kato M , Atsumi T , Oku K , Amengual O , Nakagawa H , Fujieda Y , Otomo K , Horita T , Yasuda S , Koike T 
Published: July 2013

Background CD36, known as a scavenger receptor, is a transmembrane glycoprotein expressed on monocytes, platelets and endothelial cells, recognizes multiple ligands, including phosphatidylserine, and regulates atherogenesis and thrombosis. The objective of this study is to investigate the possible involvement of CD36 in the pathophysiology of thrombosis in patients with antiphospholipid syndrome (APS). Methods First, rs3765187, a missense mutation linked to CD36 deficiency, was investigated by TaqMan polymerase chain reaction (PCR) genotyping method in 819 Japanese, including 132 patients with APS, 265 with systemic lupus erythematosus (SLE) in the absence of APS, and 422 healthy subjects. Then, the involvement of CD36 in antiphospholipid antibody (aPL)-induced tissue factor (TF) expression was examined using CD36-null mice or anti-CD36. Purified IgG from patients with APS and a monoclonal phosphatidylserine-dependent antiprothrombin antibody were used in these experiments. TF expression was tested by real-time PCR and flow cytometry. Results Minor allele carrier of rs3765187 was less frequent in patients with APS (3.8% p = 0.032), but not in patients with SLE in the absence of APS (7.9% p = 0.32), compared with healthy subjects (10.2%). The aPL-induced TF expression was significantly suppressed on peritoneal macrophages from CD36-null mice compared to wild type and significantly inhibited by anti-CD36 on human monocytes. Conclusions The gene mutation linked to CD36 deficiency was less frequent in patients with APS. The deficient or suppressed CD36 function significantly reduced aPL-induced TF expression in vitro. Taken together, in a susceptible background CD36 scavenger receptor function may be involved in the thrombotic pathophysiology in patients with APS.
Genome-wide identification and expression analysis of calcium-dependent protein kinase in maize
Authors: Kong Xiangpei , Lv Wei , Jiang Shanshan , Zhang Dan , Cai Guohua , Pan Jiaowen , Li Dequan 
Published: July 2013

Abstract

Background
Calcium-dependent protein kinases (CDPKs) have been shown to play important roles in various physiological processes, including plant growth and development, abiotic and biotic stress responses and plant hormone signaling in plants.

Results
In this study, we performed a bioinformatics analysis of the entire maize genome and identified 40 CDPK genes. Phylogenetic analysis indicated that 40 ZmCPKs can be divided into four groups. Most maize CDPK genes exhibited different expression levels in different tissues and developmental stages. Twelve CDPK genes were selected to respond to various stimuli, including salt, drought and cold, as well as ABA and H2O2. Expression analyses suggested that maize CDPK genes are important components of maize development and multiple transduction pathways.

Conclusion
Here, we present a genome-wide analysis of the CDPK gene family in maize for the first time, and this genomic analysis of maize CDPK genes provides the first step towards a functional study of this gene family in maize.
De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration
Authors: Wu Cheng-Han , Tsai Mong-Hsun , Ho Chia-Chuan , Chen Chien-Yu , Lee Hsuan-Shu 
Published: July 2013

Abstract

Background
Salamanders are unique among vertebrates in their ability to completely regenerate amputated limbs through the mediation of blastema cells located at the stump ends. This regeneration is nerve-dependent because blastema formation and regeneration does not occur after limb denervation. To obtain the genomic information of blastema tissues, de novo transcriptomes from both blastema tissues and denervated stump ends of Ambystoma mexicanum (axolotls) 14 days post-amputation were sequenced and compared using Solexa DNA sequencing.

Results
The sequencing done for this study produced 40,688,892 reads that were assembled into 307,345 transcribed sequences. The N50 of transcribed sequence length was 562 bases. A similarity search with known proteins identified 39,200 different genes to be expressed during limb regeneration with a cut-off E-value exceeding 10-5. We annotated assembled sequences by using gene descriptions, gene ontology, and clusters of orthologous group terms. Targeted searches using these annotations showed that the majority of the genes were in the categories of essential metabolic pathways, transcription factors and conserved signaling pathways, and novel candidate genes for regenerative processes. We discovered and confirmed numerous sequences of the candidate genes by using quantitative polymerase chain reaction and in situ hybridization.

Conclusion
The results of this study demonstrate that de novo transcriptome sequencing allows gene expression analysis in a species lacking genome information and provides the most comprehensive mRNA sequence resources for axolotls. The characterization of the axolotl transcriptome can help elucidate the molecular mechanisms underlying blastema formation during limb regeneration.
Frizzled-8 receptor is activated by the Wnt-2 ligand in non-small cell lung cancer
Authors: Bravo Dawn T , Yang Yi-Lin , Kuchenbecker Kristopher , Hung Ming-Szu , Xu Zhidong , Jablons David M , You Liang 
Published: July 2013

Abstract

Background
Wnt-2 plays an oncogenic role in cancer, but which Frizzled receptor(s) mediates the Wnt-2 signaling pathway in lung cancer remains unclear. We sought to (1) identify and evaluate the activation of Wnt-2 signaling through Frizzled-8 in non-small cell lung cancer, and (2) test whether a novel expression construct dominant negative Wnt-2 (dnhWnt-2) reduces tumor growth in a colony formation assay and in a xenograft mouse model.

Methods
Semi-quantitative RT-PCR was used to identify the expression of Wnt-2 and Frizzled-8 in 50 lung cancer tissues from patients. The TCF reporter assay (TOP/FOP) was used to detect the activation of the Wnt canonical pathway in vitro. A novel dnhWnt-2 construct was designed and used to inhibit activation of Wnt-2 signaling through Frizzled-8 in 293T, 293, A549 and A427 cells and in a xenograft mouse model. Statistical comparisons were made using Student’s t-test.

Results
Among the 50 lung cancer samples, we identified a 91% correlation between the transcriptional increase of Wnt-2 and Frizzled-8 (p<0.05). The Wnt canonical pathway was activated when both Wnt-2 and Frizzled-8 were co-expressed in 293T, 293, A549 and A427 cells. The dnhWnt-2 construct we used inhibited the activation of Wnt-2 signaling in 293T, 293, A549 and A427 cells, and reduced the colony formation of NSCLC cells when β-catenin was present (p<0.05). Inhibition of Wnt-2 activation by the dnhWnt-2 construct further reduced the size and mass of tumors in the xenograft mouse model (p<0.05). The inhibition also decreased the expression of target genes of Wnt signaling in these tumors.

Conclusions
We demonstrated an activation of Wnt-2 signaling via the Frizzled-8 receptor in NSCLC cells. A novel dnhWnt-2 construct significantly inhibits Wnt-2 signaling, reduces colony formation of NSCLC cells in vitro and tumor growth in a xenograft mouse model. The dnhWnt-2 construct may provide a new therapeutic avenue for targeting the Wnt pathway in lung cancer.