bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leucine‐rich glioma inactivated 3 promotes HaCaT keratinocyte migration
Authors: Jeong Yun‐Mi , Park Woo‐Jae , Kim Myo‐Kyoung , Baek Kwang Jin , Kwon Nyoun Soo , Yun Hye‐Young , Kim Dong‐Seok 
Published: July 2013

AbstractOur finding that human skin expresses leucine‐rich glioma inactivated 3 (LGI3) raises the question of the function of this cytokine in keratinocytes. We have shown that LGI3 stimulates human HaCaT keratinocyte migration without affecting viability or proliferation. Western blot analysis showed that LGI3 induced focal adhesion kinase activation, Akt phosphorylation, and glycogen synthase kinase 3β (GSK3β) phosphorylation in these cells. Using the scratch wound assay and a modified Boyden chamber, we found that LY294002, a selective phosphatidylinositol 3‐kinase inhibitor, and LiCl, a selective GSK3β inhibitor, abolished LGI3‐induced cell migration. We tested β‐catenin levels after LGI3 treatment because the Akt‐GSK3β pathway regulates β‐catenin accumulation, and β‐catenin promotes cell migration. LGI3 treatment increased β‐catenin protein and nuclear localization, whereas LY294002 prevented LGI3‐induced focal adhesion kinase and Akt activation as well as β‐catenin accumulation. Overall, these data suggest that LGI3 stimulates HaCaT cell migration following β‐catenin accumulation through the Akt pathway.
Gray matter parcellation constrained full brain fiber bundling with diffusion tensor imaging
Authors: Xu Qing , Anderson Adam W. , Gore John C. , Ding Zhaohua 
Published: July 2013

Purpose:Studying white matter fibers from diffusion tensor imaging (DTI) often requires them to be grouped into bundles that correspond to coherent anatomic structures, particularly bundles that connect cortical/subcortical basic units. However, traditional fiber clustering algorithms usually generate bundles with poor anatomic correspondence as they do not incorporate brain anatomic information into the clustering process. On the other hand, image registration‐based bundling methods segment fiber bundles by referring to a coregistered atlas or template with prelabeled anatomic information, but these approaches suffer from the uncertainties introduced from misregistration and fiber tracking errors and thus the resulting bundles usually have poor coherence. In this work, a bundling algorithm is proposed to overcome the above issues.Methods:The proposed algorithm combines clustering‐ and registration‐based approaches so that the bundle coherence and the consistency with brain anatomy are simultaneously achieved. Moreover, based on this framework, a groupwise fiber bundling method is further proposed to leverage a group of DTI data for reducing the effect of the uncertainties in a single DTI data set and improving cross‐subject bundle consistency.Results:Using the Montreal Neurological Institute template, the proposed methods are applied to building a full brain bundle network that connects cortical/subcortical basic units. Based on several proposed metrics, the resulting bundles show promising bundle coherence and anatomic consistency as well as improved cross‐subject consistency for the groupwise bundling.Conclusions:A fiber bundling algorithm has been proposed in this paper to cluster a set of whole brain fibers into coherent bundles that are consistent to the brain anatomy.
Determination of air‐kerma strength for the 192Ir GammaMed iX pulsed‐dose‐rate brachytherapy source
Authors: Riley A. D. , Pike T. L. , Micka J. A. , Fulkerson R. K. , DeWerd L. A. 
Published: July 2013

Purpose:Pulsed‐dose‐rate (PDR) brachytherapy was originally proposed to combine the therapeutic advantages of high‐dose‐rate (HDR) and low‐dose‐rate brachytherapy. Though uncommon in the United States, several facilities employ pulsed‐dose‐rate brachytherapy in Europe and Canada. Currently, there is no air‐kerma strength standard for PDR brachytherapy 192Ir sources traceable to the National Institute of Standards and Technology. Discrepancies in clinical measurements of the air‐kerma strength of the PDR brachytherapy sources using HDR source‐calibrated well chambers warrant further investigation.Methods:In this research, the air‐kerma strength for an192Ir PDR brachytherapy source was compared with the University of Wisconsin Accredited Dosimetry Calibration Laboratory transfer standard well chambers, the seven‐distance technique [B. E. Rasmussen et al., “The air‐kerma strength standard for 192Ir HDR sources,” Med. Phys. 38, – (2011)] 10.1118/1.3656683, and the manufacturer's stated value. Radiochromic film and Monte Carlo techniques were also employed for comparison to the results of the measurements.Results:While the measurements using the seven‐distance technique were within + 0.44% from the manufacturer's determination, there was a + 3.10% difference between the transfer standard well chamber measurements and the manufacturer's stated value. Results showed that the PDR brachytherapy source has geometric and thus radiological qualities that exhibit behaviors similar to a point source model in contrast to a conventional line source model.Conclusions:The resulting effect of the pointlike characteristics of the PDR brachytherapy source likely account for the differences observed between well chamber and in‐air measurements.
Calculation method using Clarkson integration for the physical dose at the center of the spread‐out Bragg peak in carbon‐ion radiotherapy
Authors: Tajiri Minoru , Maeda Takamasa , Koba Yusuke , Isobe Yoshiharu , Kuroiwa Toshitaka , Fukuda Shigekazu , Tanimoto Katsuyuki , Shibayama Koichi 
Published: July 2013

Purpose:In broad‐beam carbon‐ion radiotherapy performed using the heavy‐ion medical accelerator in Chiba, the number of monitor units is determined by measuring the physical dose at the center of the spread‐out Bragg peak (SOBP) for the treatment beam. The total measurement time increases as the number of treatment beams increases, which hinders the treatment of an increased number of patients. Hence, Kusano et al. [Jpn. J. Med. Phys. 23(Suppl. 2), – (2003)] proposed a method to calculate the physical dose at the center of the SOBP for a treatment beam. Based on a recent study, the authors here propose a more accurate calculation method.Methods:The authors measured the physical dose at the center of the SOBP while varying the circular field size and range‐shifter thickness. The authors obtained the physical dose at the center of the SOBP for an irregularly shaped beam using Clarkson integration based on these measurements.Results:The difference between the calculated and measured physical doses at the center of the SOBP varied with a change in the central angle of the sector segment. The differences between the calculated and measured physical doses at the center of the SOBP were within ±1% for all irregularly shaped beams that were used to validate the calculation method.Conclusions:The accuracy of the proposed method depends on both the number of angular intervals used for Clarkson integration and the fineness of the basic data used for calculations: sampling numbers for the field size and thickness of the range shifter. If those parameters are properly chosen, the authors can obtain a calculated monitor unit number with high accuracy sufficient for clinical applications.
Recovery within long-running transactions
Authors: Colombo Christian , Pace Gordon J. 
Published: July 2013

As computer systems continue to grow in complexity, the possibility of failure increases. At the same time, the increase in computer system pervasiveness in day-to-day activities bring along increased expectations on their reliability. This has led to the need for effective and automatic error-recovery techniques to resolve failures. Transactions enable the handling of failure propagation over concurrent systems due to dependencies, restoring the system to the point before the failure occurred. However, in various settings, especially when interacting with the real world, reversal is not possible. The notion of compensations has been long advocated as a way of addressing this issue, through the specification of activities which can be executed to undo partial transactions. Still, there is no accepted standard theory; the literature offers a plethora of distinct formalisms and approaches.In this survey, we review the compensations from a theoretical point of view by (i) giving a historic account of the evolution of compensating transactions; (ii) delineating and describing a number of design options involved; (iii) presenting a number of formalisms found in the literature, exposing similarities and differences; (iv) comparing formal notions of compensation correctness; (v) giving insights regarding the application of compensations in practice; and (vi) discussing current and future research trends in the area.
Learning to detect english and hungarian light verb constructions
Authors: Vincze Veronika , Nagy T. István , Zsibrita János 
Published: July 2013

Light verb constructions consist of a verbal and a nominal component, where the noun preserves its original meaning while the verb has lost it (to some degree). They are syntactically flexible and their meaning can only be partially computed on the basis of the meaning of their parts, thus they require special treatment in natural language processing. For this purpose, the first step is to identify light verb constructions.
In this study, we present our conditional random fields-based tool—called FXTagger—for identifying light verb constructions. The flexibility of the tool is demonstrated on two, typologically different, languages, namely, English and Hungarian. As earlier studies labeled different linguistic phenomena as light verb constructions, we first present a linguistics-based classification of light verb constructions and then show that FXTagger is able to identify different classes of light verb constructions in both languages.
Different types of texts may contain different types of light verb constructions; moreover, the frequency of light verb constructions may differ from domain to domain. Hence we focus on the portability of models trained on different corpora, and we also investigate the effect of simple domain adaptation techniques to reduce the gap between the domains. Our results show that in spite of domain specificities, out-domain data can also contribute to the successful LVC detection in all domains.
GPUDet
Authors: Jooybar Hadi , Fung Wilson W.L. , O'Connor Mike , Devietti Joseph , Aamodt Tor M. 
Published: July 2013

Nondeterminism is a key challenge in developing multithreaded applications. Even with the same input, each execution of a multithreaded program may produce a different output. This behavior complicates debugging and limits one's ability to test for correctness. This non-reproducibility situation is aggravated on massively parallel architectures like graphics processing units (GPUs) with thousands of concurrent threads. We believe providing a deterministic environment to ease debugging and testing of GPU applications is essential to enable a broader class of software to use GPUs.
Many hardware and software techniques have been proposed for providing determinism on general-purpose multi-core processors. However, these techniques are designed for small numbers of threads. Scaling them to thousands of threads on a GPU is a major challenge. This paper proposes a scalable hardware mechanism, GPUDet, to provide determinism in GPU architectures. In this paper we characterize the existing deterministic and nondeterministic aspects of current GPU execution models, and we use these observations to inform GPUDet's design. For example, GPUDet leverages the inherent determinism of the SIMD hardware in GPUs to provide determinism within a wavefront at no cost. GPUDet also exploits the Z-Buffer Unit, an existing GPU hardware unit for graphics rendering, to allow parallel out-of-order memory writes to produce a deterministic output. Other optimizations in GPUDet include deterministic parallel execution of atomic operations and a workgroup-aware algorithm that eliminates unnecessary global synchronizations.
Our simulation results indicate that GPUDet incurs only 2X slowdown on average over a baseline nondeterministic architecture, with runtime overheads as low as 4% for compute-bound applications, despite running GPU kernels with thousands of threads. We also characterize the sources of overhead for deterministic execution on GPUs to provide insights for further optimizations.
Production-run software failure diagnosis via hardware performance counters
Authors: Arulraj Joy , Chang Po-Chun , Jin Guoliang , Lu Shan 
Published: July 2013

Sequential and concurrency bugs are widespread in deployed software. They cause severe failures and huge financial loss during production runs. Tools that diagnose production-run failures with low overhead are needed. The state-of-the-art diagnosis techniques use software instrumentation to sample program properties at run time and use off-line statistical analysis to identify properties most correlated with failures. Although promising, these techniques suffer from high run-time overhead, which is sometimes over 100%, for concurrency-bug failure diagnosis and hence are not suitable for production-run usage.
We present PBI, a system that uses existing hardware performance counters to diagnose production-run failures caused by sequential and concurrency bugs with low overhead. PBI is designed based on several key observations. First, a few widely supported performance counter events can reflect a wide variety of common software bugs and can be monitored by hardware with almost no overhead. Second, the counter overflow interrupt supported by existing hardware and operating systems provides a natural and effective mechanism to conduct event sampling at user level. Third, the noise and non-determinism in interrupt delivery complements well with statistical processing.
We evaluate PBI using 13 real-world concurrency and sequential bugs from representative open-source server, client, and utility programs, and 10 bugs from a widely used software-testing benchmark. Quantitatively, PBI can effectively diagnose failures caused by these bugs with a small overhead that is never higher than 10%. Qualitatively, PBI does not require any change to software and presents a novel use of existing hardware performance counters.
Transparent mutable replay for multicore debugging and patch validation
Authors: Viennot Nicolas , Nair Siddharth , Nieh Jason 
Published: July 2013

We present Dora, a mutable record-replay system which allows a recorded execution of an application to be replayed with a modified version of the application. This feature, not available in previous record-replay systems, enables powerful new functionality. In particular, Dora can help reproduce, diagnose, and fix software bugs by replaying a version of a recorded application that is recompiled with debugging information, reconfigured to produce verbose log output, modified to include additional print statements, or patched to fix a bug.
Dora uses lightweight operating system mechanisms to record an application execution by capturing nondeterministic events to a log without imposing unnecessary timing and ordering constraints. It replays the log using a modified version of the application even in the presence of added, deleted, or modified operations that do not match events in the log. Dora searches for a replay that minimizes differences between the log and the replayed execution of the modified program. If there are no modifications, Dora provides deterministic replay of the unmodified program.
We have implemented a Linux prototype which provides transparent mutable replay without recompiling or relinking applications. We show that Dora is useful for reproducing, diagnosing, and fixing software bugs in real-world applications, including Apache and MySQL. Our results show that Dora (1) captures bugs and replays them with applications modified or reconfigured to produce additional debugging output for root cause diagnosis, (2) captures exploits and replays them with patched applications to validate that the patches successfully eliminate vulnerabilities, (3) records production workloads and replays them with patched applications to validate patches with realistic workloads, and (4) maintains low recording overhead on commodity multicore hardware, making it suitable for production systems.
Computational sprinting on a hardware/software testbed
Authors: Raghavan Arun , Emurian Laurel , Shao Lei , Papaefthymiou Marios , Pipe Kevin P. , Wenisch Thomas F. , Martin Milo M.K. 
Published: July 2013

CMOS scaling trends have led to an inflection point where thermal constraints (especially in mobile devices that employ only passive cooling) preclude sustained operation of all transistors on a chip --- a phenomenon called "dark silicon." Recent research proposed computational sprinting --- exceeding sustainable thermal limits for short intervals --- to improve responsiveness in light of the bursty computation demands of many media-rich interactive mobile applications. Computational sprinting improves responsiveness by activating reserve cores (parallel sprinting) and/or boosting frequency/voltage (frequency sprinting) to power levels that far exceed the system's sustainable cooling capabilities, relying on thermal capacitance to buffer heat.
Prior work analyzed the feasibility of sprinting through modeling and simulation. In this work, we investigate sprinting using a hardware/software testbed. First, we study unabridged sprints, wherein the computation completes before temperature becomes critical, demonstrating a 6.3x responsiveness gain, and a 6% energy efficiency improvement by racing to idle. We then analyze truncated sprints, wherein our software runtime system must intervene to prevent overheating by throttling parallelism and frequency before the computation is complete. To avoid oversubscription penalties (context switching inefficiencies after a truncated parallel sprint), we develop a sprint-aware task-based parallel runtime. We find that maximal-intensity sprinting is not always best, introduce the concept of sprint pacing, and evaluate an adaptive policy for selecting sprint intensity. We report initial results using a phase change heat sink to extend maximum sprint duration. Finally, we demonstrate that a sprint-and-rest operating regime can actually outperform thermally-limited sustained execution.
Verifying security invariants in ExpressOS
Authors: Mai Haohui , Pek Edgar , Xue Hui , King Samuel Talmadge , Madhusudan Parthasarathy 
Published: July 2013

Security for applications running on mobile devices is important. In this paper we present ExpressOS, a new OS for enabling high-assurance applications to run on commodity mobile devices securely. Our main contributions are a new OS architecture and our use of formal methods for proving key security invariants about our implementation. In our use of formal methods, we focus solely on proving that our OS implements our security invariants correctly, rather than striving for full functional correctness, requiring significantly less verification effort while still proving the security relevant aspects of our system.
We built ExpressOS, analyzed its security, and tested its performance. Our evaluation shows that the performance of ExpressOS is comparable to an Android-based system. In one test, we ran the same web browser on ExpressOS and on an Android-based system, and found that ExpressOS adds 16% overhead on average to the page load latency time for nine popular web sites.
Verifying systems rules using rule-directed symbolic execution
Authors: Cui Heming , Hu Gang , Wu Jingyue , Yang Junfeng 
Published: July 2013

Systems code must obey many rules, such as "opened files must be closed." One approach to verifying rules is static analysis, but this technique cannot infer precise runtime effects of code, often emitting many false positives. An alternative is symbolic execution, a technique that verifies program paths over all inputs up to a bounded size. However, when applied to verify rules, existing symbolic execution systems often blindly explore many redundant program paths while missing relevant ones that may contain bugs.
Our key insight is that only a small portion of paths are relevant to rules, and the rest (majority) of paths are irrelevant and do not need to be verified. Based on this insight, we create WOODPECKER, a new symbolic execution system for effectively checking rules on systems programs. It provides a set of builtin checkers for common rules, and an interface for users to easily check new rules. It directs symbolic execution toward the program paths relevant to a checked rule, and soundly prunes redundant paths, exponentially speeding up symbolic execution. It is designed to be heuristic-agnostic, enabling users to leverage existing powerful search heuristics.

Evaluation on 136 systems programs totaling 545K lines of code, including some of the most widely used programs, shows that, with a time limit of typically just one hour for each verification run, WOODPECKER effectively verifies 28.7% of the program and rule combinations over bounded input, whereas an existing symbolic execution system KLEE verifies only 8.5%. For the remaining combinations, WOODPECKER verifies 4.6 times as many relevant paths as KLEE. With a longer time limit, WOODPECKER verifies much more paths than KLEE,
e.g.,
17 times as many with a fourhour limit. WOODPECKER detects 113 rule violations, including 10 serious data loss errors with 2 most serious ones already confirmed by the corresponding developers.
Volition
Authors: Qian Xuehai , Torrellas Josep , Sahelices Benjamin , Qian Depei 
Published: July 2013

Sequential Consistency (SC) is the most intuitive memory model, and SC Violations (SCVs) produce unintuitive, typically incorrect executions. Most prior SCV detection schemes have used data races as proxies for SCVs, which is highly imprecise. Other schemes that have targeted data-race cycles are either too conservative or are designed only for two-processor cycles and snoopy-based systems.
This paper presents Volition, the first hardware scheme that detects SCVs in a relaxed-consistency machine precisely, in a scalable manner, and for an arbitrary number of processors in the cycle. Volition leverages cache coherence protocol transactions to dynamically detect cycles in memory-access orders across threads. When a cycle is about to occur, an exception is triggered. Volition can be used in both directory- and snoopy-based coherence protocols. Our simulations of Volition in a 64-processor multicore with directory-based coherence running SPLASH-2 and Parsec programs shows that Volition induces negligible traffic and execution overhead. In addition, it can detect SCVs with several processors. Volition is suitable for on-the-fly use.