bluuebunny/crossref_metadata_2025_split huggingface dataset:
DMP
Authors: Devietti Joseph , Lucia Brandon , Ceze Luis , Oskin Mark 
Published: September 2013

Current shared memory multicore and multiprocessor systems are nondeterministic. Each time these systems execute a multithreaded application, even if supplied with the same input, they can produce a different output. This frustrates debugging and limits the ability to properly test multithreaded code, becoming a major stumbling block to the much-needed widespread adoption of parallel programming.
In this paper we make the case for fully deterministic shared memory multiprocessing (DMP). The behavior of an arbitrary multithreaded program on a DMP system is only a function of its inputs. The core idea is to make inter-thread communication fully deterministic. Previous approaches to coping with nondeterminism in multithreaded programs have focused on replay, a technique useful only for debugging. In contrast, while DMP systems are directly useful for debugging by offering repeatability by default, we argue that parallel programs should execute deterministically in the field as well. This has the potential to make testing more assuring and increase the reliability of deployed multithreaded software. We propose a range of approaches to enforcing determinism and discuss their implementation trade-offs. We show that determinism can be provided with little performance cost using our architecture proposals on future hardware, and that software-only approaches can be utilized on existing systems.
Maximum benefit from a minimal HTM
Authors: Hofmann Owen S. , Rossbach Christopher J. , Witchel Emmett 
Published: September 2013

A minimal, bounded hardware transactional memory implementation significantly improves synchronization performance when used in an operating system kernel. We add HTM to Linux 2.4, a kernel with a simple, coarse-grained synchronization structure. The transactional Linux 2.4 kernel can improve performance of user programs by as much as 40% over the non-transactional 2.4 kernel. It closes 68% of the performance gap with the Linux 2.6 kernel, which has had significant engineering effort applied to improve scalability.
We then extend our minimal HTM to a fast, unbounded transactional memory with a novel technique for coordinating hardware transactions and software synchronization. Overflowed transactions run in software, with only a minimal coupling between hardware and software systems. There is no performance penalty for overflow rates of less than 1%. In one instance, at 16 processors and an overflow rate of 4%, performance degrades from an ideal 4.3x to 3.6x.
Mixed-mode multicore reliability
Authors: Wells Philip M. , Chakraborty Koushik , Sohi Gurindar S. 
Published: September 2013

Future processors are expected to observe increasing rates of hardware faults. Using Dual-Modular Redundancy (DMR), two cores of a multicore can be loosely coupled to redundantly execute a single software thread, providing very high coverage from many difference sources of faults. This reliability, however, comes at a high price in terms of per-thread IPC and overall system throughput.
We make the observation that a user may want to run both applications requiring high reliability, such as financial software, and more fault tolerant applications requiring high performance, such as media or web software, on the same machine at the same time. Yet a traditional DMR system must fully operate in redundant mode whenever any application requires high reliability.
This paper proposes a Mixed-Mode Multicore (MMM), which enables most applications, including the system software, to run with high reliability in DMR mode, while applications that need high performance can avoid the penalty of DMR. Though conceptually simple, two key challenges arise: 1) care must be taken to protect reliable applications from any faults occurring to applications running in high performance mode, and 2) the desire to execute additional independent software threads for a performance application complicates the scheduling of computation to cores. After solving these issues, an MMM is shown to improve overall system performance, compared to a traditional DMR system, by approximately 2X when one reliable and one performance application are concurrently executing.
Commutativity analysis for software parallelization
Authors: Aleen Farhana , Clark Nathan 
Published: September 2013

Extracting performance from many-core architectures requires software engineers to create multi-threaded applications, which significantly complicates the already daunting task of software development. One solution to this problem is automatic compile-time parallelization, which can ease the burden on software developers in many situations. Clearly, automatic parallelization in its present form is not suitable for many application domains and new compiler analyses are needed address its shortcomings.
In this paper, we present one such analysis: a new approach for detecting commutative functions. Commutative functions are sections of code that can be executed in any order without affecting the outcome of the application, e.g., inserting elements into a set. Previous research on this topic had one significant limitation, in that the results of a commutative functions must produce identical memory layouts. This prevented previous techniques from detecting functions like malloc, which may return different pointers depending on the order in which it is called, but these differing results do not affect the overall output of the application. Our new commutativity analysis correctly identify these situations to better facilitate automatic parallelization. We demonstrate that this analysis can automatically extract significant amounts of parallelism from many applications, and where it is ineffective it can provide software developers a useful list of functions that may be commutative provided semantic program changes that are not automatable.
Accelerating critical section execution with asymmetric multi-core architectures
Authors: Suleman M. Aater , Mutlu Onur , Qureshi Moinuddin K. , Patt Yale N. 
Published: September 2013

To improve the performance of a single application on Chip Multiprocessors (CMPs), the application must be split into threads which execute concurrently on multiple cores. In multi-threaded applications, critical sections are used to ensure that only one thread accesses shared data at any given time. Critical sections can serialize the execution of threads, which significantly reduces performance and scalability.
This paper proposes Accelerated Critical Sections (ACS), a technique that leverages the high-performance core(s) of an Asymmetric Chip Multiprocessor (ACMP) to accelerate the execution of critical sections. In ACS, selected critical sections are executed by a high-performance core, which can execute the critical section faster than the other, smaller cores. As a result, ACS reduces serialization: it lowers the likelihood of threads waiting for a critical section to finish. Our evaluation on a set of 12 critical-section-intensive workloads shows that ACS reduces the average execution time by 34% compared to an equal-area 32T-core symmetric CMP and by 23% compared to an equal-area ACMP. Moreover, for 7 out of the 12 workloads, ACS improves scalability by increasing the number of threads at which performance saturates.
Producing wrong data without doing anything obviously wrong!
Authors: Mytkowicz Todd , Diwan Amer , Hauswirth Matthias , Sweeney Peter F. 
Published: September 2013

This paper presents a surprising result: changing a seemingly innocuous aspect of an experimental setup can cause a systems researcher to draw wrong conclusions from an experiment. What appears to be an innocuous aspect in the experimental setup may in fact introduce a significant bias in an evaluation. This phenomenon is called measurement bias in the natural and social sciences.
Our results demonstrate that measurement bias is significant and commonplace in computer system evaluation. By significant we mean that measurement bias can lead to a performance analysis that either over-states an effect or even yields an incorrect conclusion. By commonplace we mean that measurement bias occurs in all architectures that we tried (Pentium 4, Core 2, and m5 O3CPU), both compilers that we tried (gcc and Intel's C compiler), and most of the SPEC CPU2006 C programs. Thus, we cannot ignore measurement bias. Nevertheless, in a literature survey of 133 recent papers from ASPLOS, PACT, PLDI, and CGO, we determined that none of the papers with experimental results adequately consider measurement bias.
Inspired by similar problems and their solutions in other sciences, we describe and demonstrate two methods, one for detecting (causal analysis) and one for avoiding (setup randomization) measurement bias.
Dynamic prediction of collection yield for managed runtimes
Authors: Wegiel Michal , Krintz Chandra 
Published: September 2013

The growth in complexity of modern systems makes it increasingly difficult to extract high-performance. The software stacks for such systems typically consist of multiple layers and include managed runtime environments (MREs). In this paper, we investigate techniques to improve cooperation between these layers and the hardware to increase the efficacy of automatic memory management in MREs.
General-purpose MREs commonly implement parallel and/or concurrent garbage collection and employ compaction to eliminate heap fragmentation. Moreover, most systems trigger collection based on the amount of heap a program uses. Our analysis shows that in many cases this strategy leads to ineffective collections that are unable to reclaim sufficient space to justify the incurred cost. To avoid such collections, we exploit the observation that dead objects tend to cluster together and form large, never-referenced, regions in the address space that correlate well with virtual pages that have not recently been referenced by the application. We leverage this correlation to design a new, simple and light-weight, yield predictor that estimates the amount of reclaimable space in the heap using hardware page reference bits. Our predictor allows MREs to avoid low-yield collections and thereby improve resource management.
We integrate this predictor into three state-of-the-art parallel compactors, implemented in the HotSpot JVM, that represent distinct canonical heap layouts. Our empirical evaluation, based on standard Java benchmarks and open-source applications, indicates that inexpensive and accurate yield prediction can improve performance significantly.
Antidiabetic Medications and the Risk of Colorectal Cancer in Patients with Diabetes Mellitus: A Systematic Review and Meta-analysis
Authors: Singh Siddharth , Singh Harkirat , Singh Preet Paul , Murad M. Hassan , Limburg Paul J. 
Published: September 2013

AbstractBackground: Antidiabetic medications (ADM) may modify colorectal cancer risk in patients with diabetes mellitus. We performed a systematic review and meta-analysis, evaluating the effect of metformin, thiazolidinediones (TZD), sulfonylureas, and insulin on colorectal cancer risk in diabetic patients.Methods: We conducted a systematic search of multiple bibliographic databases, up to September 2012, for articles that evaluated exposure to metformin, TZD, sulfonylureas, and insulin, reported colorectal cancer risk in patients with diabetes mellitus, and reported OR or provided data for their estimation. Summary OR estimates with 95% confidence intervals (CI) were estimated using the random-effects model.Results: Fifteen studies reporting 13,871 cases of colorectal cancer in 840,787 patients with diabetes mellitus were included. Meta-analysis of observational studies showed an 11% reduction in colorectal cancer risk associated with metformin use (n = 9 studies; OR, 0.89; 95% CI, 0.81–0.99), whereas TZD use was not associated with colorectal cancer risk (n = 5 studies; OR, 0.96; 95% CI, 0.87–1.05). Conversely, a trend toward higher colorectal cancer risk was observed with sulfonylurea (n = 7 studies; OR, 1.11; 95% CI, 0.97–1.26) and insulin (n = 9 studies; OR, 1.33; 95% CI, 0.91–1.94) use, although these associations were not statistically significant. There was considerable heterogeneity across studies, partly explained by study location and adjustment for concomitant use of other ADMs. Post-hoc analysis of randomized controlled trials did not reveal any significant association between ADM and colorectal cancer risk.Conclusions: Meta-analysis of published studies supports a protective association between metformin use and colorectal cancer risk in patients with diabetes mellitus.Impact: Clinical trials on the chemopreventive effect of metformin against colorectal cancer are warranted. Cancer Epidemiol Biomarkers Prev; 22(12); 2258–68. ©2013 AACR.
Lessons Learned from Radiation Oncology Clinical Trials
Authors: Liu Fei-Fei ,   for the workshop participants, Okunieff Paul , Bernhard Eric J. , Stone Helen B. , Yoo Stephen , Coleman C. Norman , Vikram Bhadrasain , Brown Martin , Buatti John , Guha Chandan 
Published: September 2013

Abstract
A workshop entitled “Lessons Learned from Radiation Oncology Trials” was held on December 7–8, 2011, in Bethesda, MD, to present and discuss some of the recently conducted radiation oncology clinical trials with a focus on those that failed to refute the null hypothesis. The objectives of this workshop were to summarize and examine the questions that these trials provoked, to assess the quality and limitations of the preclinical data that supported the hypotheses underlying these trials, and to consider possible solutions to these challenges for the design of future clinical trials. Several themes emerged from the discussions: (i) opportunities to learn from null-hypothesis trials through tissue and imaging studies; (ii) value of preclinical data supporting the design of combinatorial therapies; (iii) significance of validated biomarkers; (iv) necessity of quality assurance in radiotherapy delivery; (v) conduct of sufficiently powered studies to address the central hypotheses; and (vi) importance of publishing results of the trials regardless of the outcome. The fact that well-designed hypothesis-driven clinical trials produce null or negative results is expected given the limitations of trial design and complexities of cancer biology. It is important to understand the reasons underlying such null results, however, to effectively merge the technologic innovations with the rapidly evolving biology for maximal patient benefit through the design of future clinical trials. Clin Cancer Res; 19(22); 6089–100. ©2013 AACR.
Collagen XV: Exploring Its Structure and Role within the Tumor Microenvironment
Authors: Clementz Anthony George , Harris Ann 
Published: September 2013

Abstract
The extracellular matrix (ECM) is a critical component of stroma-to-cell interactions that subsequently activate intracellular signaling cascades, many of which are associated with tumor invasion and metastasis. The ECM contains a wide range of proteins with multiple functions, including cytokines, cleaved cell-surface receptors, secreted epithelial cell proteins, and structural scaffolding. Fibrillar collagens, abundant in the normal ECM, surround cellular structures and provide structural integrity. However during the initial stages of invasive cancers, the ECM is among the first compartments to be compromised. Also present in the normal ECM is the nonfibrillar collagen XV, which is seen in the basement membrane zone but is lost prior to tumor metastasis in several organs. In contrast, the tumor microenvironment often exhibits increased synthesis of fibrillar collagen I and collagen IV, which are associated with fibrosis. The unique localization of collagen XV and its disappearance prior to tumor invasion suggests a fundamental role in maintaining basement membrane integrity and preventing the migration of tumor cells across this barrier. This review examines the structure of collagen XV, its functional domains, and its involvement in cell-surface receptor–mediated signaling pathways, thus providing further insight into its critical role in the suppression of malignancy. Mol Cancer Res; 11(12); 1481–6. ©2013 AACR.
Novel Small Leucine-Rich Repeat Protein Podocan Is a Negative Regulator of Migration and Proliferation of Smooth Muscle Cells, Modulates Neointima Formation, and Is Expressed in Human Atheroma
Authors: Hutter Randolph , Huang Li , Speidl Walter S. , Giannarelli Chiara , Trubin Paul , Bauriedel Gerhard , Klotman Mary E. , Fuster Valentin , Badimon Juan J. , Klotman Paul E. 
Published: September 2013

Background—
Smooth muscle cell (SMC) migration and proliferation critically influence the clinical course of vascular disease. We tested the effect of the novel small leucine-rich repeat protein podocan on SMC migration and proliferation using a podocan-deficient mouse in combination with a model of arterial injury and aortic explant SMC culture. In addition, we examined the effect of overexpression of the human form of podocan on human SMCs and tested for podocan expression in human atherosclerosis. In all these conditions, we concomitantly evaluated the Wnt-TCF (T-cell factor) pathway.

Methods and Results—

Podocan was strongly and selectively expressed in arteries of wild-type mice after injury. Podocan-deficient mice showed increased arterial lesion formation compared with wild-type littermates in response to injury (
P
<0.05). Also, SMC proliferation was increased in arteries of podocan-deficient mice compared with wild-type (
P
<0.05). In vitro, migration and proliferation were increased in podocan-deficient SMCs and were normalized by transfection with the wild-type podocan gene (
P
<0.05). In addition, upregulation of the Wnt-TCF pathway was found in SMCs of podocan-deficient mice both in vitro and in vivo. On the other hand, podocan overexpression in human SMCs significantly reduced SMC migration and proliferation, inhibiting the Wnt-TCF pathway. Podocan and a Wnt-TCF pathway marker were differently expressed in human coronary restenotic versus primary lesions.

Conclusions—
Podocan appears to be a potent negative regulator of the migration and proliferation of both murine and human SMCs. The lack of podocan results in excessive arterial repair and prolonged SMC proliferation, which likely is mediated by the Wnt-TCF pathway.
Uncertainties in CMIP5 Climate Projections due to Carbon Cycle Feedbacks
Authors: Friedlingstein Pierre , Meinshausen Malte , Arora Vivek K. , Jones Chris D. , Anav Alessandro , Liddicoat Spencer K. , Knutti Reto 
Published: September 2013

Abstract
In the context of phase 5 of the Coupled Model Intercomparison Project, most climate simulations use prescribed atmospheric CO2 concentration and therefore do not interactively include the effect of carbon cycle feedbacks. However, the representative concentration pathway 8.5 (RCP8.5) scenario has additionally been run by earth system models with prescribed CO2 emissions. This paper analyzes the climate projections of 11 earth system models (ESMs) that performed both emission-driven and concentration-driven RCP8.5 simulations. When forced by RCP8.5 CO2 emissions, models simulate a large spread in atmospheric CO2; the simulated 2100 concentrations range between 795 and 1145 ppm. Seven out of the 11 ESMs simulate a larger CO2 (on average by 44 ppm, 985 ± 97 ppm by 2100) and hence higher radiative forcing (by 0.25 W m−2) when driven by CO2 emissions than for the concentration-driven scenarios (941 ppm). However, most of these models already overestimate the present-day CO2, with the present-day biases reasonably well correlated with future atmospheric concentrations’ departure from the prescribed concentration. The uncertainty in CO2 projections is mainly attributable to uncertainties in the response of the land carbon cycle. As a result of simulated higher CO2 concentrations than in the concentration-driven simulations, temperature projections are generally higher when ESMs are driven with CO2 emissions. Global surface temperature change by 2100 (relative to present day) increased by 3.9° ± 0.9°C for the emission-driven simulations compared to 3.7° ± 0.7°C in the concentration-driven simulations. Although the lower ends are comparable in both sets of simulations, the highest climate projections are significantly warmer in the emission-driven simulations because of stronger carbon cycle feedbacks.
Dynamical Reconstruction of Upper-Ocean Conditions in the Last Glacial Maximum Atlantic
Authors: Dail Holly , Wunsch Carl 
Published: September 2013

Abstract
Proxies indicate that the Last Glacial Maximum (LGM) Atlantic Ocean was marked by increased meridional and zonal near sea surface temperature gradients relative to today. Using a least squares fit of a full general circulation and sea ice model to upper-ocean proxy data with specified error estimates, a seasonally varying reconstruction is sought of the Atlantic Ocean state that is consistent with both the known dynamics and the data. With reasonable uncertainty assumptions for the observations and the adjustable (control) variables, a consistent LGM ocean state is found, one not radically different from the modern one. Inferred changes include a strengthening of the easterly and westerly winds, leading to strengthened subtropical and subpolar gyres, and increased upwelling favorable winds off the coast of Africa, leading to particularly cold SSTs in those regions.
Evaluating the Performance of Planetary Boundary Layer and Cloud Microphysical Parameterization Schemes in Convection-Permitting Ensemble Forecasts Using Synthetic GOES-13 Satellite Observations
Authors: Cintineo Rebecca , Otkin Jason A. , Xue Ming , Kong Fanyou 
Published: September 2013

Abstract
In this study, the ability of several cloud microphysical and planetary boundary layer parameterization schemes to accurately simulate cloud characteristics within 4-km grid-spacing ensemble forecasts over the contiguous United States was evaluated through comparison of synthetic Geostationary Operational Environmental Satellite (GOES) infrared brightness temperatures with observations. Four double-moment microphysics schemes and five planetary boundary layer (PBL) schemes were evaluated. Large differences were found in the simulated cloud cover, especially in the upper troposphere, when using different microphysics schemes. Overall, the results revealed that the Milbrandt–Yau and Morrison microphysics schemes tended to produce too much upper-level cloud cover, whereas the Thompson and the Weather Research and Forecasting Model (WRF) double-moment 6-class (WDM6) microphysics schemes did not contain enough high clouds. Smaller differences occurred in the cloud fields when using different PBL schemes, with the greatest spread in the ensemble statistics occurring during and after daily peak heating hours. Results varied somewhat depending upon the verification method employed, which indicates the importance of using a suite of verification tools when evaluating high-resolution model performance. Finally, large differences between the various microphysics and PBL schemes indicate that large uncertainties remain in how these schemes represent subgrid-scale processes.