bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fair CPU time accounting in CMP+SMT processors
Authors: Luque Carlos , Moreto Miquel , Cazorla Francisco J. , Valero Mateo 
Published: January 2013

Processor architectures combining several paradigms of Thread-Level Parallelism (TLP), such as CMP processors in which each core is SMT, are becoming more and more popular as a way to improve performance at a moderate cost. However, the complex interaction between running tasks in hardware shared resources in multi-TLP architectures introduces complexities when accounting CPU time (or CPU utilization) to tasks. The CPU utilization accounted to a task depends on both the time it runs in the processor and the amount of processor hardware resources it receives. Deploying systems with accurate CPU accounting mechanisms is necessary to increase fairness. Moreover, it will allow users to be fairly charged on a shared data center, facilitating server consolidation in future systems.
In this article we analyze the accuracy and hardware cost of previous CPU accounting mechanisms for pure-CMP and pure-SMT processors and we show that they are not adequate for CMP+SMT processors. Consequently, we propose a new accounting mechanism for CMP+SMT processors which: (1) increases the accuracy of accounted CPU utilization; (2) provides much more stable results over a wide range of processor setups; and (3) does not require tracking all hardware shared resources, significantly reducing its implementation cost. In particular, previous proposals lead to inaccuracies between 21% and 79% when measuring CPU utilization in an 8-core 2-way SMT processor, while our proposal reduces this inaccuracy to less than 5.0%.
PARTANS
Authors: Lutz Thibaut , Fensch Christian , Cole Murray 
Published: January 2013

GPGPUs are a powerful and energy-efficient solution for many problems. For higher performance or larger problems, it is necessary to distribute the problem across multiple GPUs, increasing the already high programming complexity.
In this article, we focus on abstracting the complexity of multi-GPU programming for stencil computation. We show that the best strategy depends not only on the stencil operator, problem size, and GPU, but also on the PCI express layout. This adds nonuniform characteristics to a seemingly homogeneous setup, causing up to 23% performance loss. We address this issue with an autotuner that optimizes the distribution across multiple GPUs.
Template your boilerplate
Authors: Adams Michael D. , DuBuisson Thomas M. 
Published: January 2013

Generic programming allows the concise expression of algorithms that would otherwise require large amounts of handwritten code. A number of such systems have been developed over the years, but a common drawback of these systems is poor runtime performance relative to handwritten, non-generic code. Generic-programming systems vary significantly in this regard, but few consistently match the performance of handwritten code. This poses a dilemma for developers. Generic-programming systems offer concision but cost performance. Handwritten code offers performance but costs concision.
This paper explores the use of Template Haskell to achieve the best of both worlds. It presents a generic-programming system for Haskell that provides both the concision of other generic-programming systems and the efficiency of handwritten code. Our system gives the programmer a high-level, generic-programming interface, but uses Template Haskell to generate efficient, non-generic code that outperforms existing generic-programming systems for Haskell.
This paper presents the results of benchmarking our system against both handwritten code and several other generic-programming systems. In these benchmarks, our system matches the performance of handwritten code while other systems average anywhere from two to twenty times slower.
Dependently typed programming with singletons
Authors: Eisenberg Richard A. , Weirich Stephanie 
Published: January 2013

Haskell programmers have been experimenting with dependent types for at least a decade, using clever encodings that push the limits of the Haskell type system. However, the cleverness of these encodings is also their main drawback. Although the ideas are inspired by dependently typed programs, the code looks significantly different. As a result, GHC implementors have responded with extensions to Haskell's type system, such as GADTs, type families, and datatype promotion. However, there remains a significant difference between programming in Haskell and in full-spectrum dependently typed languages. Haskell enforces a phase separation between runtime values and compile-time types. Therefore, singleton types are necessary to express the dependency between values and types. These singleton types introduce overhead and redundancy for the programmer.
This paper presents the singletons library, which generates the boilerplate code necessary for dependently typed programming using GHC. To compare with full-spectrum languages, we present an extended example based on an Agda interface for safe database access. The paper concludes with a detailed discussion on the current capabilities of GHC for dependently typed programming and suggestions for future extensions to better support this style of programming.
Layout-sensitive language extensibility with SugarHaskell
Authors: Erdweg Sebastian , Rieger Felix , Rendel Tillmann , Ostermann Klaus 
Published: January 2013

Programmers need convenient syntax to write elegant and concise programs. Consequently, the Haskell standard provides syntactic sugar for some scenarios (e.g., do notation for monadic code), authors of Haskell compilers provide syntactic sugar for more scenarios (e.g., arrow notation in GHC), and some Haskell programmers implement preprocessors for their individual needs (e.g., idiom brackets in SHE). But manually written preprocessors cannot scale: They are expensive, error-prone, and not composable. Most researchers and programmers therefore refrain from using the syntactic notations they need in actual Haskell programs, but only use them in documentation or papers. We present a syntactically extensible version of Haskell, SugarHaskell, that empowers ordinary programmers to implement and use custom syntactic sugar.
Building on our previous work on syntactic extensibility for Java, SugarHaskell integrates syntactic extensions as sugar libraries into Haskell's module system. Syntax extensions in SugarHaskell can declare arbitrary context-free and layout-sensitive syntax. SugarHaskell modules are compiled into Haskell modules and further processed by a Haskell compiler. We provide an Eclipse-based IDE for SugarHaskell that is extensible, too, and automatically provides syntax coloring for all syntax extensions imported into a module.
We have validated SugarHaskell with several case studies, including arrow notation (as implemented in GHC) and EBNF as a concise syntax for the declaration of algebraic data types with associated concrete syntax. EBNF declarations also show how to extend the extension mechanism itself: They introduce syntactic sugar for using the declared concrete syntax in other SugarHaskell modules.
Collections of Simultaneously Altered Genes as Biomarkers of Cancer Cell Drug Response
Authors: Masica David L. , Karchin Rachel 
Published: January 2013

Abstract
Computational analysis of cancer pharmacogenomics data has resulted in biomarkers predictive of drug response, but the majority of response is not captured by current methods. Methods typically select single biomarkers or groups of related biomarkers but do not account for response that is strictly dependent on many simultaneous genetic alterations. This shortcoming reflects the combinatorics and multiple-testing problem associated with many-body biologic interactions. We developed a novel approach, Multivariate Organization of Combinatorial Alterations (MOCA), to partially address these challenges. Extending on previous work that accounts for pairwise interactions, the approach rapidly combines many genomic alterations into biomarkers of drug response, using Boolean set operations coupled with optimization; in this framework, the union, intersection, and difference Boolean set operations are proxies of molecular redundancy, synergy, and resistance, respectively. The algorithm is fast, broadly applicable to cancer genomics data, is of immediate use for prioritizing cancer pharmacogenomics experiments, and recovers known clinical findings without bias. Furthermore, the results presented here connect many important, previously isolated observations. Cancer Res; 73(6); 1699–708. ©2012 AACR.
Measles Virus Vaccine–Infected Tumor Cells Induce Tumor Antigen Cross-Presentation by Human Plasmacytoid Dendritic Cells
Authors: Guillerme Jean-Baptiste , Boisgerault Nicolas , Roulois David , Ménager Jérémie , Combredet Chantal , Tangy Frédéric , Fonteneau Jean-François , Gregoire Marc 
Published: January 2013

AbstractPurpose: Plasmacytoid dendritic cells (pDC) are antigen-presenting cells specialized in antiviral response. The measles virus vaccine is proposed as an antitumor agent to target and specifically kill tumor cells without infecting healthy cells.Experimental Design: Here, we investigated, in vitro, the effects of measles virus vaccine–infected tumor cells on the phenotype and functions of human pDC. We studied maturation and tumor antigen cross-presentation by pDC, exposed either to the virus alone, or to measles virus vaccine–infected or UV-irradiated tumor cells.Results: We found that only measles virus vaccine–infected cells induced pDC maturation with a strong production of IFN-α, whereas UV-irradiated tumor cells were unable to activate pDC. This IFN-α production was triggered by the interaction of measles virus vaccine single-stranded RNA (ssRNA) with TLR7. We observed that measles virus vaccine–infected tumor cells were phagocytosed by pDC. Interestingly, we showed cross-presentation of the tumor antigen NYESO-1 to a specific CD8+ T-cell clone when pDC were cocultured with measles virus vaccine–infected tumor cells, whereas pDC were unable to cross-present NYESO-1 after coculture with UV-irradiated tumor cells.Conclusions: Altogether, our results suggest that the use of measles virus vaccine in antitumor virotherapy induces immunogenic tumor cell death, allowing pDC to mature, produce high amounts of IFN-α, and cross-present tumor antigen, thus representing a mode of recruiting these antigen-presenting cells in the immune response. Clin Cancer Res; 19(5); 1147–58. ©2012 AACR.
Phase I Study of Dovitinib (TKI258), an Oral FGFR, VEGFR, and PDGFR Inhibitor, in Advanced or Metastatic Renal Cell Carcinoma
Authors: Angevin Eric , Lopez-Martin Jose A. , Lin Chia-Chi , Gschwend Jürgen E. , Harzstark Andrea , Castellano Daniel , Soria Jean-Charles , Sen Paramita , Chang Julie , Shi Michael , Kay Andrea , Escudier Bernard 
Published: January 2013

Abstract
Purpose: Signaling through the fibroblast growth factor (FGF) pathway may account for tumor resistance to antiangiogenic therapies targeting the VEGF pathway. Here, dovitinib (TKI258), a potent oral inhibitor of FGF receptor, VEGF receptor (VEGFR), and platelet-derived growth factor receptor tyrosine kinases, is studied in a dose escalation trial.
Experimental Design: Patients with advanced or metastatic renal cell carcinoma (RCC) with predominant clear cell histology were treated with oral dovitinib 500 or 600 mg/day (5-days-on/2-days-off schedule).
Results: Twenty heavily pretreated patients (median 3 prior regimens) were enrolled, with 16, 11, and 12 patients having previously received at least 1: VEGFR inhibitor, mTOR inhibitor, and immunotherapy, respectively. Fifteen and 5 patients were treated in 500- and 600-mg cohorts, respectively. Three patients experienced dose-limiting toxicities: grade 2 bradycardia (500 mg), grade 4 hypertensive crisis (600 mg), and grade 3 asthenia with grade 2 nausea and vomiting (600 mg). The most common adverse events related to dovitinib were nausea (75%), diarrhea (70%), vomiting (70%), and asthenia (50%), the majority of which were mild (grade 1 or 2), with grade 3 events 5% or less (except asthenia, 15%) and only one grade 4 event (hypertensive crisis). Two patients achieved a partial response (500 mg), and 12 patients had stable disease, including 2 patients with long lasting disease stabilizations (&gt;1 year) in the 500-mg cohort.
Conclusions: Dovitinib was tolerable and showed antitumor activity at a maximum tolerated dose of 500 mg on a 5-days-on/2-days-off schedule in heavily pretreated RCC patients. Clin Cancer Res; 19(5); 1257–68. ©2012 AACR.
Unexploited Gains From International Diversification: Patterns Of Portfolio Holdings Around The World
Authors: Didier Tatiana , Rigobon Roberto , Schmukler Sergio L. 
Published: January 2013

Abstract
Using unique data on mutual fund portfolios with different investment scopes, we study the extent of international diversification. Mutual funds invest in a surprisingly limited number of stocks—about 100. The number of holdings from a given region declines as the investment scope broadens. Moreover, unexploited gains exist from international diversification. Funds that invest globally could achieve better risk-adjusted returns by adding stocks held by more specialized funds within the same family. These findings are not driven by different sectoral allocations, lack of information or instruments, transaction costs, or different tail risks. Instead, organizational factors might play an important role.
Identification of Long-Range Transported Haze Phenomena and Their Meteorological Features over Northeast Asia
Authors: Jo Hyun-Young , Kim Cheol-Hee 
Published: January 2013

AbstractThis paper presents a technique used to empirically classify operationally defined “haze” days in South Korea from 2000 to 2007 into long-range transported (LRT) and stagnant (STG) haze cases. A total of 547 haze days were classified into these two cases by tracking consecutive 6-day synoptic weather charts and air trajectories. The meteorological features associated with long-range transport of haze were identified by contrasting the values of 35 candidate meteorological parameters corresponding to the two types of haze cases. A suitable subset of synoptic variables was then chosen to diagnose the unique meteorological features of each case. The statistical test showed that geostrophic wind speed, vorticity, vorticity advection at a geopotential height of 850 hPa, and the vertical stability index of the lower atmosphere were indicated as highly effective parameters for distinguishing between the LRT and STG cases. The classification accuracies showed 93.2%, 87.8%, 85.4%, and 84.4% for these four variables, respectively. The STG case was well characterized by negative vorticity, with stable atmospheric stability conditions and weak geostrophic wind speed, that is, ~2.8 m s−1at a geopotential height of 850 hPa, whereas the LRT case had relatively strong geostrophic wind speed, >6 m s−1. For both cases, the location of the anticyclone played an important role in haze occurrence, directly and indirectly. A high pressure system led to stable STG haze with weak ventilation, resulting from upper-atmospheric subsidence. The LRT case was associated with a strong anticyclone that prevailed over southwestern China, maintaining the pressure gradient force that generated the westerly wind that was persistently conducive to downwind long-range transport of haze.
An Ensemble-Based Four-Dimensional Variational Data Assimilation Scheme. Part III: Antarctic Applications with Advanced Research WRF Using Real Data
Authors: Liu Chengsi , Xiao Qingnong 
Published: January 2013

Abstract
A four-dimensional ensemble-based variational data assimilation (4DEnVar) algorithm proposed in Part I of the 4DEnVar series (denoted En4DVar in Part I, but here we refer to it as 4DEnVar according to WMO conference recommendation to differentiate it from En4DVar algorithm using adjoint model) uses a flow-dependent background error covariance calculated from ensemble forecasts and performs 4DVar optimization based on an incremental approach and a preconditioning algorithm. In Part II, the authors evaluated 4DEnVar with observing system simulation experiments (OSSEs) using the Advanced Research Weather Research and Forecasting Model (ARW-WRF, hereafter WRF). The current study extends the 4DEnVar to assimilate real observations for a cyclone in the Antarctic and the Southern Ocean in October 2007. The authors performed an intercomparison of four different WRF variational approaches for the case, including three-dimensional variational data assimilation (3DVar), first guess at the appropriate time (FGAT), and ensemble-based three-dimensional (En3DVar) and four-dimensional (4DEnVar) variational data assimilations. It is found that all data assimilation approaches produce positive impacts in this case. Applying the flow-dependent background error covariance in En3DVar and 4DEnVar yields forecast skills superior to those with the homogeneous and isotropic background error covariance in 3DVar and FGAT. In addition, the authors carried out FGAT and 4DEnVar 3-day cycling and 72-h forecasts. The results show that 4DEnVar produces a better performance in the cyclone prediction. The inflation factor on 4DEnVar can effectively improve the 4DEnVar analysis. The authors also conducted a short period (10-day lifetime of the cyclone in the domain) of analysis/forecast intercomparison experiments using 4DEnVar, FGAT, and 3DVar. The 4DEnVar scheme demonstrates overall superior and robust performance.
Impacts of Assimilating Measurements of Different State Variables with a Simulated Supercell Storm and Three-Dimensional Variational Method
Authors: Ge Guoqing , Gao Jidong , Xue Ming 
Published: January 2013

Abstract
This paper investigates the impacts of assimilating measurements of different state variables, which can be potentially available from various observational platforms, on the cycled analysis and short-range forecast of supercell thunderstorms by performing a set of observing system simulation experiments (OSSEs) using a storm-scale three-dimensional variational data assimilation (3DVAR) method. The control experiments assimilate measurements every 5 min for 90 min. It is found that the assimilation of horizontal wind can reconstruct the storm structure rather accurately. The assimilation of vertical velocity , potential temperature , or water vapor can partially rebuild the thermodynamic and precipitation fields but poorly retrieves the wind fields. The assimilation of rainwater mixing ratio can build up the precipitation fields together with a reasonable cold pool but is unable to properly recover the wind fields. Overall, data have the greatest impact, while have the second largest impact. The impact of is the smallest. The impact of assimilation frequency is examined by comparing results using 1-, 5-, or 10-min assimilation intervals. When is assimilated every 5 or 10 min, the analysis quality can be further improved by the incorporation of additional types of observations. When are assimilated every minute, the benefit from additional types of observations is negligible, except for . It is also found that for , , and measurements, more frequent assimilation leads to more accurate analyses. For and , a 1-min assimilation interval does not produce a better analysis than a 5-min interval.
Continuity of the Bessel wavelet transform on certain Beurling-type function spaces
Authors: Prasad Akhilesh , Mahato Ashutosh , Dixit MM 
Published: January 2013

Abstract
In this paper, continuity of the Bessel wavelet transform of a suitable function ϕ in terms of an appropriate mother wavelet ψ is investigated on certain Beurling-type function spaces.

MSC:46F12, 26A33.
Systems infection biology: a compartmentalized immune network of pig spleen challenged with Haemophilus parasuis
Authors: Zhao Ming , Liu Xiang-dong , Li Xin-yun , Chen Hong-bo , Jin Hui , Zhou Rui , Zhu Meng-jin , Zhao Shu-hong 
Published: January 2013

Abstract

Background
Network biology (systems biology) approaches are useful tools for elucidating the host infection processes that often accompany complex immune networks. Although many studies have recently focused on Haemophilus parasuis, a model of Gram-negative bacterium, little attention has been paid to the host's immune response to infection. In this article, we use network biology to investigate infection with Haemophilus parasuis in an in vivo pig model.

Results
By targeting the spleen immunogenome, we established an expression signature indicative of H. parasuis infection using a PCA/GSEA combined method. We reconstructed the immune network and estimated the network topology parameters that characterize the immunogene expressions in response to H. parasuis infection. The results showed that the immune network of H. parasuis infection is compartmentalized (not globally linked). Statistical analysis revealed that the reconstructed network is scale-free but not small-world. Based on the quantitative topological prioritization, we inferred that the C1R-centered clique might play a vital role in responding to H. parasuis infection.

Conclusions
Here, we provide the first report of reconstruction of the immune network in H. parasuis-infected porcine spleen. The distinguishing feature of our work is the focus on utilizing the immunogenome for a network biology-oriented analysis. Our findings complement and extend the frontiers of knowledge of host infection biology for H. parasuis and also provide a new clue for systems infection biology of Gram-negative bacilli in mammals.
Increased plasma sVCAM-1 is associated with severity in IgA nephropathy
Authors: Zhu Li , Shi Sufang , Liu Lijun , Lv Jicheng , Zhang Hong 
Published: January 2013

Abstract

Background
A considerable proportion of IgAN patients present with histological vasculitic/crescentic lesions in glomeruli, indicating activation of vascular inflammation. Using sVCAM-1, a well-proven marker for endothelial injury under inflammatory processes, we investigated vascular injury and its association with clinical and pathological manifestations in IgAN patients.

Methods
In this study, 327 biopsy-proven IgAN patients and 55 healthy controls were enrolled. The Oxford classification and two variables, Active Crescentic Lesion Percentage (ACLP) and Chronic Glomerular Lesion Percentage (CGLP), were used for evaluating pathological lesions. Human Umbilical Vein Endothelial Cells were treated with 25-400 ug/ml IgA1. sVCAM-1 in plasma and culture supernatant were measured by ELISA.

Results
Plasma sVCAM-1 in IgAN patients was significantly higher than healthy controls. In patients with IgAN, plasma sVCAM-1 was significantly correlated with eGFR, 24h urine protein excretion, tubular atrophy/interstitial fibrosis lesion and ACLP, but not CGLP. Meanwhile, compared to healthy volunteers, IgA1 from IgAN patients showed a tendency to increase the HUVECs supernatant sVCAM-1 expression. And IgA1 induced the sVCAM-1 increasing from HUVECs in time- and dose-dependent manner.

Conclusions
We found increased plasma sVCAM-1 in IgAN patients and its association with severe clinical and pathological manifestations, which might be partly resulted from effect of IgA1 to endothelial cells.