bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient processor support for DRFx, a memory model with exceptions
Authors: Singh Abhayendra , Marino Daniel , Narayanasamy Satish , Millstein Todd , Musuvathi Madan 
Published: October 2012

A longstanding challenge of shared-memory concurrency is to provide a memory model that allows for efficient implementation while providing strong and simple guarantees to programmers. The C++0x and Java memory models admit a wide variety of compiler and hardwareoptimizations and provide sequentially consistent (SC) semantics for data-race-free programs. However, they either do not provide any semantics (C++0x) or provide a hard-to-understand semantics (Java) for racy programs, compromising the safety and debuggability of such programs.
In earlier work we proposed the DRFx memory model, which addresses this problem by dynamically detecting potential violations of SC due to the interaction of compiler or hardware optimizations with data races and halting execution upon detection. In this paper, we present a detailed micro-architecture design for supporting the DRFx memory model, formalize the design and prove its correctness, and evaluate the design using a hardware simulator. We describe a set of DRFx-compliant complexity-effective optimizations which allow us to attain performance close to that of TSO (Total Store Model) and DRF0 while providing strong guarantees for all programs.
Orchestration by approximation
Authors: Farhad Sardar M. , Ko Yousun , Burgstaller Bernd , Scholz Bernhard 
Published: October 2012

We present a novel 2-approximation algorithm for deploying stream graphs on multicore computers and a stream graph transformation that eliminates bottlenecks. The key technical insight is a data rate transfer model that enables the computation of a "closed form", i.e., the data rate transfer function of an actor depending on the arrival rate of the stream program. A combinatorial optimization problem uses the closed form to maximize the throughput of the stream program. Although the problem is inherently NP-hard, we present an efficient and effective 2-approximation algorithm that provides a lower bound on the quality of the solution. We introduce a transformation that uses the closed form to identify and eliminate bottlenecks.
We show experimentally that state-of-the art integer linear programming approaches for orchestrating stream graphs are (1) intractable or at least impractical for larger stream graphs and larger number of processors and (2)our 2-approximation algorithm is highly efficient and its results are close to the optimal solution for a standard set of StreamIt benchmark programs.
Dealing with large hidden constants
Authors: Tazari Siamak , Müller-Hannemann Matthias 
Published: October 2012

We present the first attempt on implementing a highly theoretical polynomial-time approximation scheme (PTAS) with huge hidden constants, namely, the PTAS for Steiner tree in planar graphs by Borradaile, Klein, and Mathieu (2009). Whereas this result, and several other PTAS results of the recent years, are of high theoretical importance, no practical applications or even implementation attempts have been known to date, due to the extremely large constants that are involved in them. We describe techniques on how to circumvent the challenges in implementing such a scheme. With today's limitations on processing power and space, we still have to sacrifice approximation guarantees for improved running times by choosing some parameters empirically. But our experiments show that with our choice of parameters, we do get the desired approximation ratios, suggesting that a much tighter analysis might be possible.
Our computational experiments with benchmark instances from SteinLib and large artificial instances well exceeded our own expectations. We demonstrate that we are able to handle instances with up to a million nodes and several hundreds of terminals in 1.5 hours on a standard PC. On the rectilinear preprocessed instances from SteinLib, we observe a monotonous improvement for smaller values of ϵ, with an average gap below 1% for ϵ = 0.1. We compare our implementation against the well-known batched 1-Steiner heuristic and observe that on very large instances, we are able to produce comparable solutions much faster. We also present a thorough experimental evaluation of the influence of the various parameters of the PTAS and thus obtain a better understanding of their empirical effects.
Brainy
Authors: Jung Changhee , Rus Silvius , Railing Brian P. , Clark Nathan , Pande Santosh 
Published: October 2012

Data structure selection is one of the most critical aspects of developing effective applications. By analyzing data structures' behavior and their interaction with the rest of the application on the underlying architecture, tools can make suggestions for alternative data structures better suited for the program input on which the application runs. Consequently, developers can optimize their data structure usage to make the application conscious of an underlying architecture and a particular program input.
This paper presents the design and evaluation of Brainy, a new program analysis tool that automatically selects the best data structure for a given program and its input on a specific microarchitecture. The data structure's interface functions are instrumented to dynamically monitor how the data structure interacts with the application for a given input. The instrumentation records traces of various runtime characteristics including underlying architecture-specific events. These generated traces are analyzed and fed into an offline model, constructed using machine learning, to select the best data structure. That is, Brainy exploits runtime feedback of data structures to model the situation an application runs on, and selects the best data structure for a given application/input/architecture combination based on the constructed model. The empirical evaluation shows that this technique is highly accurate across several real-world applications with various program input sets on two different state-of-the-art microarchitectures. Consequently, Brainy achieved an average performance improvement of 27% and 33% on both microarchitectures, respectively.
Caisson
Authors: Li Xun , Tiwari Mohit , Oberg Jason K. , Kashyap Vineeth , Chong Frederic T. , Sherwood Timothy , Hardekopf Ben 
Published: October 2012

Information flow is an important security property that must be incorporated from the ground up, including at hardware design time, to provide a formal basis for a system's root of trust. We incorporate insights and techniques from designing information-flow secure programming languages to provide a new perspective on designing secure hardware. We describe a new hardware description language, Caisson, that combines domain-specific abstractions common to hardware design with insights from type-based techniques used in secure programming languages. The proper combination of these elements allows for an expressive, provably-secure HDL that operates at a familiar level of abstraction to the target audience of the language, hardware architects.
We have implemented a compiler for Caisson that translates designs into Verilog and then synthesizes the designs using existing tools. As an example of Caisson's usefulness we have addressed an open problem in secure hardware by creating the first-ever provably information-flow secure processor with micro-architectural features including pipelining and cache. We synthesize the secure processor and empirically compare it in terms of chip area, power consumption, and clock frequency with both a standard (insecure) commercial processor and also a processor augmented at the gate level to dynamically track information flow. Our processor is competitive with the insecure processor and significantly better than dynamic tracking.
Understanding POWER multiprocessors
Authors: Sarkar Susmit , Sewell Peter , Alglave Jade , Maranget Luc , Williams Derek 
Published: October 2012

Exploiting today's multiprocessors requires high-performance and correct concurrent systems code (optimising compilers, language runtimes, OS kernels, etc.), which in turn requires a good understanding of the observable processor behaviour that can be relied on. Unfortunately this critical hardware/software interface is not at all clear for several current multiprocessors.
In this paper we characterise the behaviour of IBM POWER multiprocessors, which have a subtle and highly relaxed memory model (ARM multiprocessors have a very similar architecture in this respect). We have conducted extensive experiments on several generations of processors: POWER G5, 5, 6, and 7. Based on these, on published details of the microarchitectures, and on discussions with IBM staff, we give an abstract-machine semantics that abstracts from most of the implementation detail but explains the behaviour of a range of subtle examples. Our semantics is explained in prose but defined in rigorous machine-processed mathematics; we also confirm that it captures the observable processor behaviour, or the architectural intent, for our examples with an executable checker. While not officially sanctioned by the vendor, we believe that this model gives a reasonable basis for reasoning about current POWER multiprocessors.
Our work should bring new clarity to concurrent systems programming for these architectures, and is a necessary precondition for any analysis or verification. It should also inform the design of languages such as C and C++, where the language memory model is constrained by what can be efficiently compiled to such multiprocessors.
LeakChaser
Authors: Xu Guoqing , Bond Michael D. , Qin Feng , Rountev Atanas 
Published: October 2012

In large programs written in managed languages such as Java and C#, holding unnecessary references often results in memory leaks and bloat, degrading significantly their run-time performance and scalability. Despite the existence of many leak detectors for such languages, these detectors often target low-level objects; as a result, their reports contain many false warnings and lack sufficient semantic information to help diagnose problems. This paper introduces a specification-based technique called LeakChaser that can not only capture precisely the unnecessary references leading to leaks, but also explain, with high-level semantics, why these references become unnecessary.
At the heart of LeakChaser is a three-tier approach that uses varying levels of abstraction to assist programmers with different skill levels and code familiarity to find leaks. At the highest tier of the approach, the programmer only needs to specify the boundaries of coarse-grained activities, referred to as transactions. The tool automatically infers liveness properties of these transactions, by monitoring the execution, in order to find unnecessary references. Diagnosis at this tier can be performed by any programmer after inspecting the APIs and basic modules of a program, without understanding of the detailed implementation of these APIs. At the middle tier, the programmer can introduce application-specific semantic information by specifying properties for the transactions. At the lowest tier of the approach is a liveness checker that does not rely on higher-level semantic information, but rather allows a programmer to assert lifetime relationships for pairs of objects. This task could only be performed by skillful programmers who have a clear understanding of data structures and algorithms in the program.
We have implemented LeakChaser in Jikes RVM and used it to help us diagnose several real-world leaks. The implementation incurs a reasonable overhead for debugging and tuning. Our case studies indicate that the implementation is powerful in guiding programmers with varying code familiarity to find the root causes of several memory leaks---even someone who had not studied a leaking program can quickly find the cause after using LeakChaser's iterative process that infers and checks properties with different levels of semantic information.
Spreadsheet table transformations from examples
Authors: Harris William R. , Gulwani Sumit 
Published: October 2012

Every day, millions of computer end-users need to perform tasks over large, tabular data, yet lack the programming knowledge to do such tasks automatically. In this work, we present an automatic technique that takes from a user an example of how the user needs to transform a table of data, and provides to the user a program that implements the transformation described by the example. In particular, we present a language of programs TableProg that can describe transformations that real users require.We then present an algorithm ProgFromEx that takes an example input and output table, and infers a program in TableProg that implements the transformation described by the example. When the program is applied to the example input, it reproduces the example output. When the program is applied to another, potentially larger, table with a 'similar' layout as the example input table, then the program produces a corresponding table with a layout that is similar to the example output table. A user can apply ProgFromEx interactively, providing multiple small examples to obtain a program that implements the transformation that the user desires. Moreover, ProgFromEx can help identify 'noisy' examples that contain errors.
To evaluate the practicality of TableProg and ProgFromEx, we implemented ProgFromEx as a module for the Microsoft Excel spreadsheet program. We applied the module to automatically implement over 50 table transformations specified by endusers through examples on online Excel help forums. In seconds, ProgFromEx found programs that satisfied the examples and could be applied to larger input tables. This experience demonstrates that TableProg and ProgFromEx can significantly automate the tasks over tabular data that users need to perform.
ALTER
Authors: Udupa Abhishek , Rajan Kaushik , Thies William 
Published: October 2012

For decades, compilers have relied on dependence analysis to determine the legality of their transformations. While this conservative approach has enabled many robust optimizations, when it comes to parallelization there are many opportunities that can only be exploited by changing or re-ordering the dependences in the program.
This paper presents Alter: a system for identifying and enforcing parallelism that violates certain dependences while preserving overall program functionality. Based on programmer annotations, Alter exploits new parallelism in loops by reordering iterations or allowing stale reads. Alter can also infer which annotations are likely to benefit the program by using a test-driven framework.
Our evaluation of Alter demonstrates that it uncovers parallelism that is beyond the reach of existing static and dynamic tools. Across a selection of 12 performance-intensive loops, 9 of which have loop-carried dependences, Alter obtains an average speedup of 2.0x on 4 cores.
Taming wildcards in Java's type system
Authors: Tate Ross , Leung Alan , Lerner Sorin 
Published: October 2012

Wildcards have become an important part of Java's type system since their introduction 7 years ago. Yet there are still many open problems with Java's wildcards. For example, there are no known sound and complete algorithms for subtyping (and consequently type checking) Java wildcards, and in fact subtyping is suspected to be undecidable because wildcards are a form of bounded existential types. Furthermore, some Java types with wildcards have no joins, making inference of type arguments for generic methods particularly difficult. Although there has been progress on these fronts, we have identified significant shortcomings of the current state of the art, along with new problems that have not been addressed.
In this paper, we illustrate how these shortcomings reflect the subtle complexity of the problem domain, and then present major improvements to the current algorithms for wildcards by making slight restrictions on the usage of wildcards. Our survey of existing Java programs suggests that realistic code should already satisfy our restrictions without any modifications. We present a simple algorithm for subtyping which is both sound and complete with our restrictions, an algorithm for lazily joining types with wildcards which addresses some of the shortcomings of prior work, and techniques for improving the Java type system as a whole. Lastly, we describe various extensions to wildcards that would be compatible with our algorithms.
NF-κB Activity Regulates Mesenchymal Stem Cell Accumulation at Tumor Sites
Authors: Uchibori Ryosuke , Tsukahara Tomonori , Mizuguchi Hiroyuki , Saga Yasushi , Urabe Masashi , Mizukami Hiroaki , Kume Akihiro , Ozawa Keiya 
Published: October 2012

Abstract
Mesenchymal stem cells (MSC) accumulate at tumor sites when injected into tumor-bearing mice, perhaps offering cellular vectors for cancer-targeted gene therapy. However, the molecular mechanisms involved in MSC targeting the tumors are presently little understood. We focused on MSC–endothelial cell (EC) adhesion following TNF-α stimulation in an attempt to elucidate these mechanisms. Interestingly, stimulation of MSCs with TNF-α enhanced the adhesion of MSCs to endothelial cells in vitro. This adhesion was partially inhibited by blocking antibodies against vascular cell adhesion molecule-1 (VCAM-1) and very late antigen-4 (VLA-4). It is well known that TNF-α induces VCAM-1 expression via the NF-κB signaling pathway. Parthenolide has an anti-inflammatory activity and suppressed NF-κB activity by inhibition of IκBα phosphorylation after TNF-α stimulation and strongly inhibited TNF-α–induced VCAM-1 expression on MSCs. In vivo imaging using luciferase-expressing MSCs revealed that the bioluminescent signal gradually increased at tumor sites in mice injected with untreated MSCs. In contrast, we observed very weak signals at tumor sites in mice injected with parthenolide-treated MSCs. Our results suggest that NF-κB activity regulates MSC accumulation at tumors, by inducing VCAM-1 and thereby its interaction with tumor vessel endothelial cells. These findings have implications for the ongoing development of efficient MSC-based gene therapies for cancer treatment. Cancer Res; 73(1); 364–72. ©2012 AACR.
Clinicopathological Features of Homologous Recombination–Deficient Epithelial Ovarian Cancers: Sensitivity to PARP Inhibitors, Platinum, and Survival
Authors: Mukhopadhyay Asima , Plummer Elizabeth R. , Elattar Ahmed , Soohoo San , Uzir Bisha , Quinn Jennifer E. , McCluggage W. Glenn , Maxwell Perry , Aneke Harriet , Curtin Nicola J. , Edmondson Richard J. 
Published: October 2012

Abstract
Up to 50% of epithelial ovarian cancers (EOC) display defects in the homologous recombination (HR) pathway. We sought to determine the ramifications of the homologous recombination–deficient (HRD) status on the clinicopathologic features, chemotherapy response, and survival outcomes of patients with EOCs. HR status was determined in primary cultures from ascitic fluid in 50 chemotherapy-naïve patients by a functional RAD51 immunofluorescence assay and correlated with in vitro sensitivity to the PARP inhibitor (PARPi), rucaparib. All patients went on to receive platinum-based chemotherapy; platinum sensitivity, tumor progression, and overall survival were compared prospectively in HR-competent versus HRD patients. Compared with HR-competent patients, the HRD group was predominantly serous with a higher median CA125 at presentation. HRD was associated with higher ex vivo PARPi sensitivity and clinical platinum sensitivity. Median follow-up duration was 14 months; patients in the HRD group had lower tumor progression rates at 6 months, lower overall/disease-specific death rates at 12 months, and higher median survival. We therefore suggest that HRD as predicted by a functional RAD51 assay correlates with in vitro PARPi sensitivity, clinical platinum sensitivity, and improved survival outcome. Cancer Res; 72(22); 5675–82. ©2012 AACR.
Raf Kinase Inhibitor RKIP Inhibits MDA-9/Syntenin-Mediated Metastasis in Melanoma
Authors: Das Swadesh K. , Bhutia Sujit K. , Sokhi Upneet K. , Azab Belal , Su Zhao-zhong , Boukerche Habib , Anwar Talha , Moen Erika L. , Chatterjee Devasis , Pellecchia Maurizio , Sarkar Devanand , Fisher Paul B. 
Published: October 2012

Abstract
Melanoma differentiation associated gene-9 (MDA-9), also known as syntenin, functions as a positive regulator of melanoma progression and metastasis. In contrast, the Raf kinase inhibitor, RKIP, a negative modulator of RAF-stimulated MEKK activation, is strongly downregulated in metastatic melanoma cells. In this study, we explored a hypothesized inverse relationship between MDA-9 and RKIP in melanoma. Tumor array and cell line analyses confirmed an inverse relationship between expression of MDA-9 and RKIP during melanoma progression. We found that MDA-9 transcriptionally downregulated RKIP in support of a suggested cross-talk between these two proteins. Furthermore, MDA-9 and RKIP physically interacted in a manner that correlated with a suppression of FAK and c-Src phosphorylation, crucial steps necessary for MDA-9 to promote FAK/c-Src complex formation and initiate signaling cascades that drive the MDA-9–mediated metastatic phenotype. Finally, ectopic RKIP expression in melanoma cells overrode MDA-9–mediated signaling, inhibiting cell invasion, anchorage-independent growth, and in vivo dissemination of tumor cells. Taken together, these findings establish RKIP as an inhibitor of MDA-9–dependent melanoma metastasis, with potential implications for targeting this process therapeutically. Cancer Res; 72(23); 6217–26. ©2012 AACR.
Methylome Profiling Reveals Distinct Alterations in Phenotypic and Mutational Subgroups of Myeloproliferative Neoplasms
Authors: Nischal Sangeeta , Bhattacharyya Sanchari , Christopeit Maximilian , Yu Yiting , Zhou Li , Bhagat Tushar D. , Sohal Davendra , Will Britta , Mo Yongkai , Suzuki Masako , Pardanani Animesh , McDevitt Michael , Maciejewski Jaroslaw P. , Melnick Ari M. , Greally John M. , Steidl Ulrich , Moliterno Alison , Verma Amit 
Published: October 2012

Abstract
Even though mutations in epigenetic regulators frequently occur in myeloproliferative neoplasms, their effects on the epigenome have not been well studied. Furthermore, even though primary myelofibrosis (PMF) has a markedly worse prognosis than essential thrombocytosis or polycythemia vera, the molecular distinctions between these subgroups are not well elucidated. We conducted the HELP (HpaII tiny fragment enriched by LM-PCR) assay to study genome-wide methylation in polycythemia vera, essential thrombocytosis, and PMF samples compared with healthy controls. We determined that polycythemia vera and essential thrombocytosis are characterized by aberrant promoter hypermethylation, whereas PMF is an epigenetically distinct subgroup characterized by both aberrant hyper- and hypomethylation. Aberrant hypomethylation in PMF was seen to occur in non-CpG island loci, showing further qualitative differences between the disease subgroups. The differentially methylated genes in polycythemia vera and essential thrombocytosis were involved predominantly in cell signaling pathways and were enriched for binding sites of GATA1 and other transcription factors. In contrast, aberrantly methylated genes in PMF were involved in inflammatory pathways and were enriched for NF1, LEF1, and other transcription factors. Within the PMF subgroup, cases with ASXL1 disruptions formed an epigenetically distinct subgroup with relatively increased methylation. Cases of myeloproliferative neoplasms (MPN) with TET2 mutations showed decreased levels of hydroxymethylation and distinct set of hypermethylated genes. In contrast, the JAK2V617F mutation did not drive epigenetic clustering within MPNs. Finally, the significance of aberrant methylation was shown by sensitivity of MPN-derived cell lines to decitabine. These results show epigenetic differences between PMF and polycythemia vera/essential thrombocytosis and reveal methylomic signatures of ASXL1 and TET2 mutations. Cancer Res; 73(3); 1076–85. ©2012 AACR.