bluuebunny/crossref_metadata_2025_split huggingface dataset:
SPIRE
Authors: Jia Ning , Yang Chun , Wang Jing , Tong Dong , Wang Keyi 
Published: August 2013

Dynamic binary translation system must perform an address translation for every execution of indirect branch instructions. The procedure to convert Source binary Program Counter (SPC) address to Translated Program Counter (TPC) address always takes more than 10 instructions, becoming a major source of performance overhead. This paper proposes a novel mechanism called SPc-Indexed REdirecting (SPIRE), which can significantly reduce the indirect branch handling overhead. SPIRE doesn't rely on hash lookup and address mapping table to perform address translation. It reuses the source binary code space to build a SPC-indexed redirecting table. This table can be indexed directly by SPC address without hashing. With SPIRE, the indirect branch can jump to the originally SPC address without address translation. The trampoline residing in the SPC address will redirect the control flow to related code cache. Only 2-6 instructions are needed to handle an indirect branch execution. As part of the source binary would be overwritten, a shadow page mechanism is explored to keep transparency of the corrupt source binary code page. Online profiling is adopted to reduce the memory overhead.
We have implemented SPIRE on an x86 to x86 DBT system, and discussed the implementation issues on different guest and host architectures. The experiments show that, compared with hash lookup mechanism, SPIRE can reduce the performance overhead by 36.2% on average, up to 51.4%, while only 5.6% extra memory is needed.
SPIRE can cooperate with other indirect branch handling mechanisms easily, and we believe the idea of SPIRE can also be applied on other occasions that need address translation.
Improving dynamic binary optimization through early-exit guided code region formation
Authors: Hsu Chun-Chen , Liu Pangfeng , Wu Jan-Jan , Yew Pen-Chung , Hong Ding-Yong , Hsu Wei-Chung , Wang Chien-Min 
Published: August 2013

Most dynamic binary translators (DBT) and optimizers (DBO) target binary traces, i.e. frequently executed paths, as code regions to be translated and optimized. Code region formation is the most important first step in all DBTs and DBOs. The quality of the dynamically formed code regions determines the extent and the types of optimization opportunities that can be exposed to DBTs and DBOs, and thus, determines the ultimate quality of the final optimized code. The Next-Executing-Tail (NET) trace formation method used in HP Dynamo is an early example of such techniques. Many existing trace formation schemes are variants of NET. They work very well for most binary traces, but they also suffer a major problem: the formed traces may contain a large number of early exits that could be branched out during the execution. If this happens frequently, the program execution will spend more time in the slow binary interpreter or in the unoptimized code regions than in the optimized traces in code cache. The benefit of the trace optimization is thus lost. Traces/regions with frequently taken early-exits are called delinquent traces/regions. Our empirical study shows that at least 8 of the 12 SPEC CPU2006 integer benchmarks have delinquent traces.
In this paper, we propose a light-weight region formation technique called Early-Exit Guided Region Formation (EEG) to improve the quality of the formed traces/regions. It iteratively identifies and merges delinquent regions into larger code regions. We have implemented our EEG algorithm in two LLVM-based multi-threaded DBTs targeting ARM and IA32 instruction set architecture (ISA), respectively. Using SPEC CPU2006 benchmark suite with reference inputs, our results show that compared to an NET-variant currently used in QEMU, a state-of-the-art retargetable DBT, EEG can achieve a significant performance improvement of up to 72% (27% on average), and to 49% (23% on average) for IA32 and ARM, respectively.
Superblock compilation and other optimization techniques for a Java-based DBT machine emulator
Authors: Kaufmann Marco , Spallek Rainer G. 
Published: August 2013

Superblock compilation techniques such as control flow graph (CFG) or trace compilation have become a widely adopted approach to increase the performance of dynamically compiling virtual machines even further. While this was shown to be successful for many conventional virtual machines, it did not result in a higher performance for Java-based DBT machine emulators so far. These emulators dynamically translate application binaries of a target machine into Java bytecode, which is then eventually compiled into the native code of the emulating host by the Java Virtual Machine (JVM). Successful superblock compilation techniques for this class of emulators must consider the special requirements that result from the two-stage translation as well as the characteristics of the JVM, such as the inability of most Java JIT compilers to handle large bytecode methods efficiently.
In this paper, we present a superblock compilation approach for a Java-based DBT machine emulator that generates a performance increase of up to 90 percent and of 32 percent on average. The key idea of our design is to provide a large scope over the control flow of target applications across basic block boundaries for the JVM, while still keeping small bytecode methods for the execution units.
In addition, we also present two further optimizations -- interpreter context elimination and program counter elimination -- which increase the emulation performance by 16 percent again. In total, the optimization techniques discussed in this paper provide an average performance gain of 48 percent for the surveyed emulator.
A modular approach to on-stack replacement in LLVM
Authors: Lameed Nurudeen A. , Hendren Laurie J. 
Published: August 2013

On-stack replacement (OSR) is a technique that allows a virtual machine to interrupt running code during the execution of a function/method, to re-optimize the function on-the-fly using an optimizing JIT compiler, and then to resume the interrupted function at the point and state at which it was interrupted. OSR is particularly useful for programs with potentially long-running loops, as it allows dynamic optimization of those loops as soon as they become hot.
This paper presents a modular approach to implementing OSR for the LLVM compiler infrastructure. This is an important step forward because LLVM is gaining popular support, and adding the OSR capability allows compiler developers to develop new dynamic techniques. In particular, it will enable more sophisticated LLVM-based JIT compiler approaches. Indeed, other compiler/VM developers can use our approach because it is a clean modular addition to the standard LLVM distribution. Further, our approach is defined completely at the LLVM-IR level and thus does not require any modifications to the target code generation.
The OSR implementation can be used by different compilers to support a variety of dynamic optimizations. As a demonstration of our OSR approach, we have used it to support dynamic inlining in McVM. McVM is a virtual machine for MATLAB which uses a LLVM-based JIT compiler. MATLAB is a popular dynamic language for scientific and engineering applications that typically manipulate large matrices and often contain long-running loops, and is thus an ideal target for dynamic JIT compilation and OSRs. Using our McVM example, we demonstrate reasonable overheads for our benchmark set, and performance improvements when using it to perform dynamic inlining.
Distributed merge trees
Authors: Morozov Dmitriy , Weber Gunther 
Published: August 2013

Improved simulations and sensors are producing datasets whose increasing complexity exhausts our ability to visualize and comprehend them directly. To cope with this problem, we can detect and extract significant features in the data and use them as the basis for subsequent analysis. Topological methods are valuable in this context because they provide robust and general feature definitions.
As the growth of serial computational power has stalled, data analysis is becoming increasingly dependent on massively parallel machines. To satisfy the computational demand created by complex datasets, algorithms need to effectively utilize these computer architectures. The main strength of topological methods, their emphasis on global information, turns into an obstacle during parallelization.
We present two approaches to alleviate this problem. We develop a distributed representation of the merge tree that avoids computing the global tree on a single processor and lets us parallelize subsequent queries. To account for the increasing number of cores per processor, we develop a new data structure that lets us take advantage of multiple shared-memory cores to parallelize the work on a single node. Finally, we present experiments that illustrate the strengths of our approach as well as help identify future challenges.
Integrative Radiogenomic Profiling of Squamous Cell Lung Cancer
Authors: Abazeed Mohamed E. , Adams Drew J. , Hurov Kristen E. , Tamayo Pablo , Creighton Chad J. , Sonkin Dmitriy , Giacomelli Andrew O. , Du Charles , Fries Daniel F. , Wong Kwok-Kin , Mesirov Jill P. , Loeffler Jay S. , Schreiber Stuart L. , Hammerman Peter S. , Meyerson Matthew 
Published: August 2013

Abstract
Radiotherapy is one of the mainstays of anticancer treatment, but the relationship between the radiosensitivity of cancer cells and their genomic characteristics is still not well defined. Here, we report the development of a high-throughput platform for measuring radiation survival in vitro and its validation in comparison with conventional clonogenic radiation survival analysis. We combined results from this high-throughput assay with genomic parameters in cell lines from squamous cell lung carcinoma, which is standardly treated by radiotherapy, to identify parameters that predict radiation sensitivity. We showed that activation of NFE2L2, a frequent event in lung squamous cancers, confers radiation resistance. An expression-based, in silico screen nominated inhibitors of phosphoinositide 3-kinase (PI3K) as NFE2L2 antagonists. We showed that the selective PI3K inhibitor, NVP-BKM120, both decreased NRF2 protein levels and sensitized NFE2L2 or KEAP1-mutant cells to radiation. We then combined results from this high-throughput assay with single-sample gene set enrichment analysis of gene expression data. The resulting analysis identified pathways implicated in cell survival, genotoxic stress, detoxification, and innate and adaptive immunity as key correlates of radiation sensitivity. The integrative and high-throughput methods shown here for large-scale profiling of radiation survival and genomic features of solid-tumor–derived cell lines should facilitate tumor radiogenomics and the discovery of genotype-selective radiation sensitizers and protective agents. Cancer Res; 73(20); 6289–98. ©2013 AACR.
PARP1 Is Overexpressed in Nasopharyngeal Carcinoma and Its Inhibition Enhances Radiotherapy
Authors: Chow Jeremy P.H. , Man Wing Yu , Mao Mao , Chen Han , Cheung Florence , Nicholls John , Tsao Sai Wah , Li Lung Maria , Poon Randy Y.C. 
Published: August 2013

Abstract
Nasopharyngeal carcinoma is a rare but highly invasive cancer. As options of agents for effective combination chemoradiotherapy for advanced nasopharyngeal carcinoma are limited, novel therapeutic approaches are desperately needed. The ubiquitin ligase CHFR is known to target PARP1 for degradation and is epigenetically inactivated in nasopharyngeal carcinoma. We present evidence that PARP1 protein is indeed overexpressed in nasopharyngeal carcinoma cells in comparison with immortalized normal nasopharyngeal epithelial cells. Tissue microarray analysis also indicated that PARP1 protein is significantly elevated in primary nasopharyngeal carcinoma tissues, with strong correlation with all stages of nasopharyngeal carcinoma development. We found that the PARP inhibitor AZD2281 (olaparib) increased DNA damage, cell-cycle arrest, and apoptosis in nasopharyngeal carcinoma cells challenged with ionizing radiation or temozolomide. Isobologram analysis confirmed that the cytotoxicity triggered by AZD2281 and DNA-damaging agents was synergistic. Finally, AZD2281 also enhanced the tumor-inhibitory effects of ionizing radiation in animal xenograft models. These observations implicate that PARP1 overexpression is an early event in nasopharyngeal carcinoma development and provide a molecular basis of using PARP inhibitors to potentiate treatment of nasopharyngeal carcinoma with radio- and chemotherapy. Mol Cancer Ther; 12(11); 2517–28. ©2013 AACR.
Mixing State of Submicrometer Sea Spray Particles Enriched by Insoluble Species in Bubble-Bursting Experiments
Authors: Park Ji Yeon , Lim Sungil , Park Kihong 
Published: August 2013

Abstract
Measurements of size distribution, hygroscopicity, and volatility of submicrometer sea spray particles produced by the bubble busting of artificial and natural seawater were conducted to determine their mixing state and volume fractions of hygroscopic and nonhygroscopic species or volatile and nonvolatile species. The particles sprayed from artificial seawater having insoluble silica particles were found to be an external mixture of two groups of particles having hygroscopic growth factors (HGFs) of 1.33 (an internal mixture of nonhygroscopic silica particles and hygroscopic salt species) and 1.68 (a similar mixture having more salt species) when the mass ratio of insoluble particles to dissolved salts was higher than 2. For sea spray particles from natural seawater, the external mixing was not significantly observed because of a high concentration of dissolved salts. The HGFs of sea spray particles (80–140 nm) from natural seawater were in the range of 1.70–1.76, which were lower than from pure artificial seawater (1.87), and the HGFs had no change before and after membrane filtration of seawater, suggesting that the sea spray particles from natural seawater contained a significant amount of nonhygroscopic dissolved organic matter in addition to hygroscopic salt species. The volume fraction of the nonhygroscopic species ranged from 20% to 29%, and the highest value was observed for seawater samples from the site where strong biological activity occurred, suggesting that biological materials played an important role in the formation of nonhygroscopic organic matter. Volatility measurements also identified the existence of volatile organic species in single particles from natural seawater, with the volume fraction of volatile species evaporated at 100°C being 4%–5%.
Renegotiating environments to achieve participation: A metasynthesis of qualitative chronic disease research: Restructurer les environnements pour favoriser la participation / Une métasynthèse de la recherche qualitative sur les maladies chroniques
Authors: Hand Carri L. , Wilkins Seanne , Letts Lori J. , Law Mary C. 
Published: August 2013

Background. Qualitative studies describe environmental influences on participation in adults with chronic disease, but translating these findings into practice can be difficult. Purpose. This study sought to synthesize qualitative research findings regarding the influence of environmental factors on participation among adults with chronic disease. Methods. Searching revealed 31 articles that describe the link between environment and participation for adults with osteoarthritis, rheumatoid arthritis, diabetes mellitus, heart disease, cancer, chronic obstructive pulmonary disease, and/or depression. Study findings were analyzed using metasynthesis methods to identify themes. Findings. For adults with chronic disease, renegotiating their environments and occupations to achieve, maintain, or rework their participation involves understanding support processes, being ordinary and able, navigating systems, and navigating physical environments. Implications. Key areas that occupational therapy interventions can target are facilitating constructive collaboration between client and support person, fostering connections with others, recognizing cultural pressure to be ordinary and able, and advocating for supportive policy and practice.
The hegemony of the liberal–secular master narrative in Orhan Pamuk’s Snow
Authors: Ahmet Alver 
Published: August 2013

This work will examine the juxtaposition between political and novelistic intentions that distinguish Orhan Pamuk’s treatment of secularism. While Pamuk’s work can be read as a fierce critique of state-imposed secularism in Turkey, he is simultaneously a great champion of a liberal secularist ideology, on which his texts are based even as they claim to be dialogic and polyphonic. This paper will set out the ways in which Pamuk frames the competing political claims of secularism and Islam – key issues on a global scale as well as in Turkish politics – in order to decipher its implications for the contemporary world and the future. Given Pamuk’s status as a global writer, it is essential that his texts are analysed for their ideological underpinnings, so that any conclusions drawn from them are problematized and seen in a broader context. By analysing Snow, along with a selection of Pamuk’s other novels and writings, this article will explore Pamuk’s view of secularism generally, and specifically its function in Turkish society, and in doing so will draw out the tensions in his case for liberal secularism. In order to do this, it will draw upon some recent critical scholarship on secularism including Ziaudddin Sardar, Talal Asad, Saba Mahmood and T. N. Madan.
Flexor Digitorum Brevis Transfer for Floating Toe Prevention after Weil Osteotomy
Authors: Lee Lydia C. , Charlton Timothy P. , Thordarson David B. 
Published: August 2013

Background: A floating toe deformity occurs in many patients who undergo Weil osteotomies. It is likely caused by the failure of the windlass mechanism in shortening the metatarsal. For patients who require a proximal interphalangeal (PIP) joint arthroplasty or fusion in addition to a Weil osteotomy, the transfer of the flexor digitorum brevis (FDB) tendon to the PIP joint might restore the windlass mechanism and decrease the incidence of floating toes. Methods: Fourteen cadaveric foot specimens were examined to determine the effects of changing metatarsal length as well as tensioning the FDB tendon on the angle of the metatarsophalangeal (MTP) joint as a measure of a floating toe. Results: Shortening and lengthening the second metatarsal resulted in a significant change in MTP angle ( P = .03 and .02, respectively), though there was no clear relationship found between the amount of change in metatarsal length and the change in MTP angle. Transferring the FDB to a PIP arthroplasty site plantarflexed the MTP joint and corrected floating toes; the change in angle was significant compared with the control and shortening groups ( P = .0001 and .002, respectively). Conclusion: This study supports the theory that change in length of the metatarsal, possibly via the windlass mechanism, plays a role in the pathophysiology of the floating toe deformity. Tensioning and transferring the FDB tendon into the PIP joint helped prevent the floating toe deformity in this cadaveric model. Clinical Relevance: Continued research in this subject will help to refine methods of prevention and correction of the floating toe deformity.
Factors shaping effective utilization of health information technology in urban safety-net clinics
Authors: George Sheba , Garth Belinda , Fish Allison , Baker Richard 
Published: August 2013

Urban safety-net clinics are considered prime targets for the adoption of health information technology innovations; however, little is known about their utilization in such safety-net settings. Current scholarship provides limited guidance on the implementation of health information technology into safety-net settings as it typically assumes that adopting institutions have sufficient basic resources. This study addresses this gap by exploring the unique challenges urban resource-poor safety-net clinics must consider when adopting and utilizing health information technology. In-depth interviews (N = 15) were used with key stakeholders (clinic chief executive officers, medical directors, nursing directors, chief financial officers, and information technology directors) from staff at four clinics to explore (a) nonhealth information technology-related clinic needs, (b) how health information technology may provide solutions, and (c) perceptions of and experiences with health information technology. Participants identified several challenges, some of which appear amenable to health information technology solutions. Also identified were requirements for effective utilization of health information technology including physical infrastructural improvements, funding for equipment/training, creation of user groups to share health information technology knowledge/experiences, and specially tailored electronic billing guidelines. We found that despite the potential benefit that can be derived from health information technologies, the unplanned and uninformed introduction of these tools into these settings might actually create more problems than are solved. From these data, we were able to identify a set of factors that should be considered when integrating health information technology into the existing workflows of low-resourced urban safety-net clinics in order to maximize their utilization and enhance the quality of health care in such settings.
Efficacy of Higher Dose 13.3 mg/24 h Rivastigmine Patch on Instrumental Activities of Daily Living in Patients with Mild-to-Moderate Alzheimer's Disease
Authors: Grossberg George , Cummings Jeffrey , Frölich Lutz , Bellelli Giuseppe , Molinuevo José L. , Krahnke Tillmann , Strohmaier Christine 
Published: August 2013

Background: Stabilizing/reducing decline in the ability to perform activities of daily living (ADLs) is important in management of Alzheimer’s disease (AD). Methods: Post hoc analysis of OPtimizing Transdermal Exelon In Mild-to-moderate Alzheimer’s disease (OPTIMA), a double-blind trial comparing 13.3 and 9.5 mg/24 h rivastigmine patch in patients with AD demonstrating functional and cognitive decline with 9.5 mg/24 h patch. Efficacy on Alzheimer’s disease Cooperative Study-instrumental ADL (ADCS-IADL) items, higher level function (HLF), and autonomy factors was assessed. Results: The ADCS-IADL, HLF, and autonomy factors favored 13.3 mg/24 h patch at all time points, reaching significance from weeks 16 to 48, 24 to 48, and 32 to 48, respectively. Higher dose patch demonstrated significantly greater efficacy on 10 of 17 ADCS-IADL items at 1 or more time points ( P < .05 vs 9.5 mg/24 h patch). More adverse events were observed with higher dose patch; study discontinuations were similar between the doses. Conclusions: Greater efficacy of 13.3 versus 9.5 mg/24 h patch on ADL, including autonomy and HLF factors, supports this additional dosing option to prolong patients’ independence.