bluuebunny/crossref_metadata_2025 huggingface dataset:
Complete Coding Genome Sequences of Uncommon GII.8 Sapovirus Strains Identified in Diarrhea Samples Collected from Peruvian Children
Authors: Kagning Tsinda Emmanuel , Malasao Rungnapa , Furuse Yuki , Gilman Robert H. , Liu Xiaofang , Apaza Sonia , Espetia Susan , Cama Vitaliano , Oshitani Hitoshi , Saito Mayuko
Published: October 2017

We report here two complete coding genome sequences of novel genotype GII.8 sapovirus strains identified in diarrhea samples collected from two Peruvian children. The complete coding genome sequences of both GII.8 variants were determined using the Sanger sequencing method.
Complete Genome Sequences of Cluster A Mycobacteriophages BobSwaget, Fred313, KADY, Lokk, MyraDee, Stagni, and StepMih
Authors: Butela Kristen A. , Gurney Susan M. R. , Hendrickson Heather L. , LeBlanc-Straceski Janine M. , Zimmerman Anastasia M. , Conant Stephanie B. , Freed Nikki E. , Silander Olin K. , Thomson Joshua J. , Berkes Charlotte A. , Bertolez Cristina , Davies Courtney G. , Elinsky Amber , Hanlon Alison J. , Nersesyan Juliette , Patel Payal , Sherwood John , Tieu Ngo Tiffany , Wisniewski Kathryn A. , Yacoo Kathrine , Arendse Paul M. , Bowlen Nathan W. , Cunmulaj Jasmina , Downs Julie L. , Ferrenberg Charlee A. , Gassman Alexandra E. , Gilligan Cody E. R. , Gorkiewicz Emily , Harness Christopher , Huffman Anthony , Jones Christina , Julien Anna , Kupic Alexis E. , Latu Sayonara F. , Manning Thomas J. , Maxwell Danielle ,   Merrimack College SEA-PHAGES Annotators 2016, Meyer Catherine E. , Reardon Madeleine , Slaughter Matthew , Swasey Royce , Tennent Rebecca I. , Torres Victoria , Waller Tamia , Worcester Rachel M. , Yost Brooke L. , Cresawn Steven G. , Garlena Rebecca A. , Jacobs-Sera Deborah , Pope Welkin H. , Russell Daniel A. , Hatfull Graham F. , Kagey Jacob D.
Published: October 2017

Seven mycobacteriophages from distinct geographical locations were isolated, using
Mycobacterium smegmatis
mc
2
155 as the host, and then purified and sequenced. All of the genomes are related to cluster A mycobacteriophages, BobSwaget and Lokk in subcluster A2; Fred313, KADY, Stagni, and StepMih in subcluster A3; and MyraDee in subcluster A18, the first phage to be assigned to that subcluster.
Does the association between leisure activities and survival in old age differ by living arrangement?
Authors: Nilsen Charlotta , Agahi Neda , Shaw Benjamin A
Published: October 2017

Background

Government policies to promote ageing in place have led to a growing frail population living at home in advanced old age, many of whom live alone. Living alone in old age is associated with adverse health outcomes, but we know little about whether it moderates the health impact of other risk and protective factors. Engagement in leisure activities is considered critical to successful ageing. We investigated whether the association between different types of leisure activities and survival in non-institutionalised older adults (aged 76 and above) differs by living arrangement and gender.

Methods

We used the Swedish Panel Study of Living Conditions of the Oldest Old study from 2011 and the Swedish Cause of Death Register (until 30 June 2014) to conduct Cox regression analyses (n=669). Incident mortality was 30.2% during the follow-up period.

Results

Overall level of leisure activity was not significantly associated with survival in either living arrangement, but some specific leisure activities, and associations, were different across gender and living arrangement. More specifically, certain social activities (participation in organisations and having relatives visit) were associated with longer survival, but only in men living alone. In women, most results were statistically non-significant, with the exception of solving crosswords being associated with longer survival in women living with someone.

Conclusion

In order to facilitate engagement with life, interventions focusing on leisure activities in the oldest age groups should take gender and living arrangement into consideration when determining the type of activity most needed.
Investigation of the international comparability of population-based routine hospital data set derived comorbidity scores for patients with lung cancer
Authors: Lüchtenborg Margreet , Morris Eva J A , Tataru Daniela , Coupland Victoria H , Smith Andrew , Milne Roger L , te Marvelde Luc , Baker Deborah , Young Jane , Turner Donna , Nishri Diane , Earle Craig , Shack Lorraine , Gavin Anna , Fitzpatrick Deirdre , Donnelly Conan , Lin Yulan , Møller Bjørn , Brewster David H , Deas Andrew , Huws Dyfed W , White Ceri , Warlow Janet , Rashbass Jem , Peake Michael D
Published: October 2017

Introduction

The International Cancer Benchmarking Partnership (ICBP) identified significant international differences in lung cancer survival. Differing levels of comorbid disease across ICBP countries has been suggested as a potential explanation of this variation but, to date, no studies have quantified its impact. This study investigated whether comparable, robust comorbidity scores can be derived from the different routine population-based cancer data sets available in the ICBP jurisdictions and, if so, use them to quantify international variation in comorbidity and determine its influence on outcome.

Methods

Linked population-based lung cancer registry and hospital discharge data sets were acquired from nine ICBP jurisdictions in Australia, Canada, Norway and the UK providing a study population of 233 981 individuals. For each person in this cohort Charlson, Elixhauser and inpatient bed day Comorbidity Scores were derived relating to the 4–36 months prior to their lung cancer diagnosis. The scores were then compared to assess their validity and feasibility of use in international survival comparisons.

Results

It was feasible to generate the three comorbidity scores for each jurisdiction, which were found to have good content, face and concurrent validity. Predictive validity was limited and there was evidence that the reliability was questionable.

Conclusion

The results presented here indicate that interjurisdictional comparability of recorded comorbidity was limited due to probable differences in coding and hospital admission practices in each area. Before the contribution of comorbidity on international differences in cancer survival can be investigated an internationally harmonised comorbidity index is required.
Microbiomes of the Arctic carnivorous sponges Chondrocladia grandis and Cladorhiza oxeata suggest a specific, but differential involvement of bacterial associates
Authors: Verhoeven Joost T.P. , Dufour Suzanne C.
Published: October 2017

While sponges are generally known to host a wide range of microbial associates, the composition and specificity of the microbial communities in carnivorous sponges are poorly understood. We used 16S rRNA gene data to examine and compare the bacterial communities associated with distinct anatomical regions of two carnivorous sponge species, Chondrocladia grandis and Cladorhiza oxeata, sampled from Baffin Bay and the Gulf of Maine (C. grandis only). The two sponge species hosted distinct bacterial communities, with taxonomic diversity being greater in C. grandis. Some bacterial taxa (including particular oligotypes) were consistently recovered in multiple host individuals from geographically distant sites, suggesting specificity. Within C. grandis, certain bacterial taxa were enriched in particular anatomical regions, suggesting functional roles in carnivorous sponge metabolism or other biological processes. Stable isotope analysis provided no evidence for methanotrophy in the sponges examined, but Gulf of Maine C. grandis might incorporate 13C-depleted carbon via the bacteria-mediated heterotrophic degradation of other hydrocarbons. Overall, our results demonstrate that the carnivorous sponge microbiome appears host species specific and stable, even over large geographical areas. The observed differences in bacterial community composition and diversity between C. grandis and C. oxeata may reflect differences in trophic adaptability, specialization, and overall reliance on associated bacteria.
Direct simulation of random field samples from sparsely measured geotechnical data with consideration of uncertainty in interpretation
Authors: Wang Yu , Zhao Tengyuan , Phoon Kok-Kwang
Published: October 2017

Random field theory has been increasingly used in probabilistic geotechnical analyses over the past few decades, where a random field generator with random field parameters is needed to simulate random field samples (RFSs) of interest. Estimation of random field parameters, particularly correlation functions or correlation length, generally requires extensive measurements. However, the data gathered from site characterizations are usually sparse, particularly for small or medium sized projects. Therefore, it is difficult to provide an accurate estimation on random field parameters, and the random field parameters estimated and subsequently used in RFS generation might contain significant uncertainty. This leads to a challenge of properly simulating RFSs in consideration of such uncertainty. This paper aims to address this challenge by developing a novel random field generator, which is capable of directly generating RFSs from sparse measurements obtained during site characterization and properly accounting for uncertainty associated with interpretation of sparse data. The proposed generator is based on Bayesian compressive sampling (BCS) and Karhunen–Loève (KL) expansion, and it is denoted as BCS–KL generator. The proposed BCS–KL generator is illustrated and validated through both simulated data and 30 sets of cone penetration test data measured throughout the world.
Double averaged turbulence characteristics of alluvial channel with downward seepage
Authors: Sharma Anurag , Kumar Bimlesh
Published: October 2017

Present work evaluates the double averaged turbulence characteristics of the sand bed channel subjected to the downward seepage through permeable bed. Measures of turbulent statistics are observed to increase with the application of downward seepage. The form induced stress in near bed has a reducing effect with no seepage and an increasing effect with seepage. The seepage increases the turbulent kinetic energy and turbulent intensities causing the bed particles to move rapidly. The quadrant analysis suggests that at near bed, the sweep events in flows with seepage are the main bursting events towards the Reynolds stress production, while ejection and sweep events in no seepage flow have almost equal contribution. The increase in sediment transport with seepage is caused by an increase in flow turbulence production and an associated decrease in turbulent kinetic energy dissipation and turbulent diffusion.
Spores of two probiotic Bacillus species enhance cellular immunity in BALB/C mice
Authors: Gong Li , Huang Qin , Fu Aikun , Wu YanPing , Li Yali , Xu Xiaogang , Huang Yi , Yu Dongyou , Li Weifen
Published: October 2017

Previous studies found that Bacillus subtilis BS02 and B. subtilis subsp. natto BS04 isolated in our laboratory could activate the immune response of murine macrophages in vitro. This study aims to investigate the effects of dietary supplementation with Bacillus species spores on the systemic cellular immune response in BALB/C mice. Results showed that both B. subtilis BS02 and B. subtilis natto BS04 enhanced the phagocytic function of the mononuclear phagocyte system (MPS) and the cytotoxicity of natural killer (NK) cells. In addition, B. subtilis BS02 could increase the respiratory burst activity of blood phagocytes. Furthermore, B. subtilis BS02 and B. subtilis natto BS04 increased the percentage of gamma-interferon-producing CD4+ cells and CD8+ T-cells, but only BS04 increased the percentage of CD3+ cells and CD3+ CD4+ cells in splenocytes. However, there were no effects on other subsets of splenic lymphocytes and mitogen-induced splenic lymphocyte proliferation. All data suggested that oral administration of B. subtilis BS02 or B. subtilis natto BS04 could significantly enhance cellular immunity in BALB/C mice by increasing phagocytic activity of MPS and cytotoxic activity of NK cells in a strain-specific manner.
Behaviour of elastic and ultrasonic properties of curium monopnictides
Authors: Tripathy Chinmayee , Singh Devraj , Paikaray Rita
Published: October 2017

The temperature-dependent elastic and ultrasonic properties of curium monopnictides CmPn (Pn = N, P, As, Sb) have been explored in the present investigation. The second- and third-order elastic constants have been calculated using Coulomb and Born–Mayer potentials using lattice and hardness parameters. Mechanical parameters, such as Young’s modulus, bulk modulus, shear modulus, tetragonal modulus, anisotropic factor, and Poisson’s ratio, have been computed with second-order elastic constants. These materials fulfilled the requirement of the Born stability criterion. The toughness or fracture ratio is found to be more than 0.57 in CmPn, which indicates their brittle nature. In addition, the ultrasonic wave velocity, Debye average velocity, Debye temperature, thermal relaxation time, thermal conductivity, acoustic coupling constant, and ultrasonic attenuation have also been computed along ⟨100⟩, ⟨110⟩, ⟨111⟩ directions at room temperature. The results are discussed in correlation with other similar types of the materials.
The molecular basis for an ancient colour mutant in sweet pea (Lathyrus odoratus)
Authors: Xue Xinxin , Cronk Quentin C.B.
Published: October 2017

The classic A1 locus in sweet pea (Lathyrus odoratus) was investigated by Bateson, Punnett, and Saunders in the early 20th century history of Mendelian genetics. The mutation, in the form of the pink and white cultivar ‘Painted Lady’, is known from the 18th century. We show that this locus is associated with a single base pair mutation (332 G/A) in the flavonoid 3′,5′-hydroxylase (F3′5′H) gene. This results in an amino acid change (111 glycine/aspartic acid) in the conserved substrate recognition site 1 of the enzyme. The mutant flower lacks the blue pigment delphinidin and is thus pink and white, rather than purple and blue as in the wild-type. This single amino acid change at a functionally important site appears to convert the enzyme from primary F3′5′H activity to a relatively efficient F3′H, as suggested by heterologous transformation into Arabidopsis PAP1D (a mutant line that produces anthocyanin constitutively).
Uncertainty estimation for a geological model of the Sandstone greenstone belt, Western Australia – insights from integrated geological and geophysical inversion in a Bayesian inference framework
Authors: Wellmann J. Florian , de la Varga Miguel , Murdie Ruth E. , Gessner Klaus , Jessell Mark
Published: October 2017

The spatial relationship between different rock types and relevant structural features is an important aspect in the characterization of ore-forming systems. Our knowledge about this geological architecture is often captured in 3D structural geological models. Multiple methods exist to generate these models, but one important problem remains: structural models often contain significant uncertainties. In recent years, several approaches have been developed to consider uncertainties in geological prior parameters that are used to create these models through the use of stochastic simulation methods. However, a disadvantage of these methods is that there is no guarantee that each simulated model is geologically reasonable – and that it forms a valid representation in the light of additional data (e.g. geophysical measurements). We address these shortcomings here with an approach for the integration of structural geological and geophysical data into a framework that explicitly considers model uncertainties. We combine existing implicit structural modelling methods with novel developments in probabilistic programming in a Bayesian framework. In an application of these concepts to a gold-bearing greenstone belt in Western Australia, we show that we are able to significantly reduce uncertainties in the final model by additional data integration. Although the final question always remains whether a predicted model suite is a suitable representation of accuracy or not, we conclude that our application of a Bayesian framework provides a novel quantitative approach to addressing uncertainty and optimization of model parameters.
Parametrized Adomian Decomposition Method with Optimum Convergence
Authors: Turkyilmazoglu Mustafa
Published: October 2017

The classical Adomian decomposition method frequently used to solve linear and nonlinear algebraic or integro-differential equations of ordinary and partial type is revisited. Rewriting the technique in an elegant form, a parameter so-called as the convergence control parameter, is embedded into the method to control the convergence and the rate of convergence of the method. Besides the constant level curves for determining suitable values, an effective approach for obtaining the best possible convergence control parameter is later devised based on the squared residual error of the studied problem. The optimum Adomian decomposition method is proved to converge to the true solution where the classical Adomian decomposition method fails to converge. When both methods are convergent, the present algorithm is observed to accelerate the rate of convergence. Moreover, the restricted domain of convergent physical solution obtained by the classical Adomian method is shown to be greatly extended to a finer interval by the optimum Adomian decomposition method. The justification of the new scheme is made clear on several mathematical/physical examples selected from the open literature. Finally, an example is provided to demonstrate the better accuracy of the optimum Adomian decomposition method over the recently popular homotopy analysis method.
Tiny-Tail Flash
Authors: Yan Shiqin , Li Huaicheng , Hao Mingzhe , Tong Michael Hao , Sundararaman Swaminathan , Chien Andrew A. , Gunawi Haryadi S.
Published: October 2017

Flash storage has become the mainstream destination for storage users. However, SSDs do not always deliver the performance that users expect. The core culprit of flash performance instability is the well-known garbage collection (GC) process, which causes long delays as the SSD cannot serve (blocks) incoming I/Os, which then induces the long tail latency problem. We present
tt
F
lash
as a solution to this problem.
tt
F
lash
is a “tiny-tail” flash drive (SSD) that eliminates GC-induced tail latencies by circumventing GC-blocked I/Os with four novel strategies: plane-blocking GC, rotating GC, GC-tolerant read, and GC-tolerant flush. These four strategies leverage the timely combination of modern SSD internal technologies such as powerful controllers, parity-based redundancies, and capacitor-backed RAM. Our strategies are dependent on the use of intra-plane copyback operations. Through an extensive evaluation, we show that
tt
F
lash
comes significantly close to a “no-GC” scenario. Specifically, between the 99 and 99.99th percentiles,
tt
F
lash
is only 1.0 to 2.6× slower than the no-GC case, while a base approach suffers from 5–138× GC-induced slowdowns.
The Applied Pi Calculus
Authors: Abadi Martín , Blanchet Bruno , Fournet Cédric
Published: October 2017

We study the interaction of the programming construct “new,” which generates statically scoped names, with communication via messages on channels. This interaction is crucial in security protocols, which are the main motivating examples for our work; it also appears in other programming-language contexts.

We define the applied pi calculus, a simple, general extension of the pi calculus in which values can be formed from names via the application of built-in functions, subject to equations, and be sent as messages. (In contrast, the pure pi calculus lacks built-in functions; its only messages are atomic names.) We develop semantics and proof techniques for this extended language and apply them in reasoning about security protocols.

This article essentially subsumes the conference paper that introduced the applied pi calculus in 2001. It fills gaps, incorporates improvements, and further explains and studies the applied pi calculus. Since 2001, the applied pi calculus has been the basis for much further work, described in many research publications and sometimes embodied in useful software, such as the tool ProVerif, which relies on the applied pi calculus to support the specification and automatic analysis of security protocols. Although this article does not aim to be a complete review of the subject, it benefits from that further work and provides better foundations for some of it. In particular, the applied pi calculus has evolved through its implementation in ProVerif, and the present definition reflects that evolution.
An Efficient Budget Allocation Approach for Quantifying the Impact of Input Uncertainty in Stochastic Simulation
Authors: Yi Yuan , Xie Wei
Published: October 2017

Simulations are often driven by input models estimated from finite real-world data. When we use simulations to assess the performance of a stochastic system, there exist two sources of uncertainty in the performance estimates: input and simulation estimation uncertainty. In this article, we develop a budget allocation approach that can efficiently employ the potentially tight simulation resource to construct a percentile confidence interval quantifying the impact of the input uncertainty on the system performance estimates, while controlling the simulation estimation error. Specifically, nonparametric bootstrap is used to generate samples of input models quantifying both the input distribution family and parameter value uncertainty. Then, the direct simulation is used to propagate the input uncertainty to the output response. Since each simulation run could be computationally expensive, given a tight simulation budget, we propose an efficient budget allocation approach that can balance the finite sampling error introduced by using finite bootstrapped samples to quantify the input uncertainty and the system response estimation error introduced by using finite replications to estimate the system response at each bootstrapped sample. Our approach is theoretically supported, and empirical studies also demonstrate that it has better and more robust performance than direct bootstrapping.
Replicated Computations Results (RCR) Report for “Green Simulation: Reusing the Output of Repeated Experiments”
Authors: Nelson Barry L.
Published: October 2017

“Green Simulation: Reusing the Output of Repeated Experiments” by Feng and Staum describes methods based on likelihood ratio or importance sampling theory for reusing the outputs of simulation experiments at previous parameter settings to augment and improve (by reducing the estimator variance) simulation experiments at new parameter settings. The article presents empirical results for two realistic examples in the area of finance; Matlab code for these examples was made available by the authors. The examples were straightforward to run without extensive knowledge of Matlab, and both experiment and scenario parameters can be altered easily. All experiment results in the article were reproduced.
Declarative Probabilistic Programming with Datalog
Authors: BáRány Vince , Cate Balder Ten , Kimelfeld Benny , Olteanu Dan , Vagena Zografoula
Published: October 2017

Probabilistic programming languages are used for developing statistical models. They typically consist of two components: a specification of a stochastic process (the prior) and a specification of observations that restrict the probability space to a conditional subspace (the posterior). Use cases of such formalisms include the development of algorithms in machine learning and artificial intelligence.

In this article, we establish a probabilistic-programming extension of Datalog that, on the one hand, allows for defining a rich family of statistical models, and on the other hand retains the fundamental properties of declarativity. Our proposed extension provides mechanisms to include common numerical probability functions; in particular, conclusions of rules may contain values drawn from such functions. The semantics of a program is a probability distribution over the possible outcomes of the input database with respect to the program. Observations are naturally incorporated by means of integrity constraints over the extensional and intensional relations. The resulting semantics is robust under different chases and invariant to rewritings that preserve logical equivalence.
Differentially Private K-Means Clustering and a Hybrid Approach to Private Optimization
Authors: Su Dong , Cao Jianneng , Li Ninghui , Bertino Elisa , Lyu Min , Jin Hongxia
Published: October 2017

k
-means clustering is a widely used clustering analysis technique in machine learning. In this article, we study the problem of differentially private
k
-means clustering. Several state-of-the-art methods follow the
single-workload
approach, which adapts an existing machine-learning algorithm by making each step private. However, most of them do not have satisfactory empirical performance. In this work, we develop techniques to analyze the empirical error behaviors of one of the state-of-the-art single-workload approaches, DPLloyd, which is a differentially private version of the Lloyd algorithm for
k
>-means clustering. Based on the analysis, we propose an improvement of DPLloyd. We also propose a new algorithm for
k
-means clustering from the perspective of the
noninteractive
approach, which publishes a synopsis of the input dataset and then runs
k
-means on synthetic data generated from the synopsis. We denote this approach by EUGkM. After analyzing the empirical error behaviors of EUGkM, we further propose a
hybrid
approach that combines our DPLloyd improvement and EUGkM. Results from extensive and systematic experiments support our analysis and demonstrate the effectiveness of the DPLloyd improvement, EUGkM, and the hybrid approach.
Simple, Accurate, Analytical Time Modeling and Optimal Tile Size Selection for GPGPU Stencils
Authors: Prajapati Nirmal , Ranasinghe Waruna , Rajopadhye Sanjay , Andonov Rumen , Djidjev Hristo , Grosser Tobias
Published: October 2017

Stencil computations are an important class of compute and data intensive programs that occur widely in scientific and engineeringapplications. A number of tools use sophisticated tiling, parallelization, and memory mapping strategies, and generate code that relies on vendor-supplied compilers. This code has a number of parameters, such as tile sizes, that are then tuned via empirical exploration.

We develop a model that guides such a choice. Our model is a simple set of analytical functions that predict the execution time of the generated code. It is deliberately optimistic, since tile sizes and, moreover, the optimistic assumptions are intended to enable we are targeting modeling and parameter selections yielding highly tuned codes.

We experimentally validate the model on a number of 2D and 3D stencil codes, and show that the root mean square error in the execution time is less than 10% for the subset of the codes that achieve performance within 20% of the best. Furthermore, based on using our model, we are able to predict tile sizes that achieve a further improvement of 9% on average.
SC-Haskell
Authors: Vollmer Michael , Scott Ryan G. , Musuvathi Madanlal , Newton Ryan R.
Published: October 2017

A core, but often neglected, aspect of a programming language design is its memory (consistency) model. Sequential consistency~(SC) is the most intuitive memory model for programmers as it guarantees sequential composition of instructions and provides a simple abstraction of shared memory as a single global store with atomic read and writes. Unfortunately, SC is widely considered to be impractical due to its associated performance overheads.

Perhaps contrary to popular opinion, this paper demonstrates that SC is achievable with acceptable performance overheads for mainstream languages that minimize mutable shared heap. In particular, we modify the Glasgow Haskell Compiler to insert fences on all writes to shared mutable memory accessed in nonfunctional parts of the program. For a benchmark suite containing 1,279 programs, SC adds a geomean overhead of less than 0.4\% on an x86 machine.

The efficiency of SC arises primarily due to the isolation provided by the Haskell type system between purely functional and thread-local imperative computations on the one hand, and imperative computations on the global heap on the other. We show how to use new programming idioms to further reduce the SC overhead; these create a virtuous cycle of less overhead and even stronger semantic guarantees (static data-race freedom).
Checking Concurrent Data Structures Under the C/C++11 Memory Model
Authors: Ou Peizhao , Demsky Brian
Published: October 2017

Concurrent data structures often provide better performance on multi-core processors but are significantly more difficult to design and test than their sequential counterparts. The C/C++11 standard introduced a weak memory model with support for low-level atomic operations such as compare and swap (CAS). While low-level atomic operations can significantly improve the performance of concurrent data structures, they introduce non-intuitive behaviors that can increase the difficulty of developing code.

In this paper, we develop a correctness model for concurrent data structures that make use of atomic operations. Based on this correctness model, we present CDSSPEC, a specification checker for concurrent data structures under the C/C++11 memory model. We have evaluated CDSSPEC on 10 concurrent data structures, among which CDSSPEC detected 3 known bugs and 93% of the injected bugs.
Pagoda
Authors: Yeh Tsung Tai , Sabne Amit , Sakdhnagool Putt , Eigenmann Rudolf , Rogers Timothy G.
Published: October 2017

Massively multithreaded GPUs achieve high throughput by running thousands of threads in parallel. To fully utilize the hardware, workloads spawn work to the GPU in bulk by launching large tasks, where each task is a kernel that contains thousands of threads that occupy the entire GPU.

GPUs face severe underutilization and their performance benefits vanish if the tasks are narrow, i.e., they contain < 500 threads. Latency-sensitive applications in network, signal, and image processing that generate a large number of tasks with relatively small inputs are examples of such limited parallelism.

This paper presents Pagoda, a runtime system that virtualizes GPU resources, using an OS-like daemon kernel called MasterKernel. Tasks are spawned from the CPU onto Pagoda as they become available, and are scheduled by the MasterKernel at the warp granularity. Experimental results demonstrate that Pagoda achieves a geometric mean speedup of 5.70x over PThreads running on a 20-core CPU, 1.51x over CUDA-HyperQ, and 1.69x over GeMTC, the state-of- the-art runtime GPU task scheduling system.
Groute
Authors: Ben-Nun Tal , Sutton Michael , Pai Sreepathi , Pingali Keshav
Published: October 2017

Nodes with multiple GPUs are becoming the platform of choice for high-performance computing. However, most applications are written using bulk-synchronous programming models, which may not be optimal for irregular algorithms that benefit from low-latency, asynchronous communication. This paper proposes constructs for asynchronous multi-GPU programming, and describes their implementation in a thin runtime environment called Groute. Groute also implements common collective operations and distributed work-lists, enabling the development of irregular applications without substantial programming effort. We demonstrate that this approach achieves state-of-the-art performance and exhibits strong scaling for a suite of irregular applications on 8-GPU and heterogeneous systems, yielding over 7x speedup for some algorithms.
Contention in Structured Concurrency
Authors: Acar Umut A. , Ben-David Naama , Rainey Mike
Published: October 2017

Over the past two decades, many concurrent data structures have been designed and implemented. Nearly all such work analyzes concurrent data structures empirically, omitting asymptotic bounds on their efficiency, partly because of the complexity of the analysis needed, and partly because of the difficulty of obtaining relevant asymptotic bounds: when the analysis takes into account important practical factors, such as contention, it is difficult or even impossible to prove desirable bounds.

In this paper, we show that considering structured concurrency or relaxed concurrency models can enable establishing strong bounds, also for contention. To this end, we first present a dynamic relaxed counter data structure that indicates the non-zero status of the counter. Our data structure extends a recently proposed data structure, called SNZI, allowing our structure to grow dynamically in response to the increasing degree of concurrency in the system.

Using the dynamic SNZI data structure, we then present a concurrent data structure for series-parallel directed acyclic graphs (sp-dags), a key data structure widely used in the implementation of modern parallel programming languages. The key component of sp-dags is an
in-counter
data structure that is an instance of our dynamic SNZI. We analyze the efficiency of our concurrent sp-dags and in-counter data structures under nested-parallel computing paradigm. This paradigm offers a structured model for concurrency. Under this model, we prove that our data structures require amortized

(1) shared memory steps, including contention. We present an implementation and an experimental evaluation that suggests that the sp-dags data structure is practical and can perform well in practice.
Processor-Oblivious Record and Replay
Authors: Utterback Robert , Agrawal Kunal , Lee I-Ting Angelina , Kulkarni Milind
Published: October 2017

Record-and-replay systems are useful tools for debugging non-deterministic parallel programs by first recording an execution and then replaying that execution to produce the same access pattern. Existing record-and-replay systems generally target thread-based execution models, and record the behaviors and interleavings of individual threads. Dynamic multithreaded languages and libraries, such as the Cilk family, OpenMP, TBB, etc., do not have a notion of threads. Instead, these languages provide a processor-oblivious model of programming, where programs expose task-parallelism using high-level constructs such as spawn/sync without regard to the number of threads/cores available to run the program. Thread-based record-and-replay would violate the processor-oblivious nature of these programs, as they incorporate the number of threads into the recorded information, constraining the replayed execution to the same number of threads.

In this paper, we present a processor-oblivious record-and-replay scheme for such languages where record and replay can use different number of processors and both are scheduled using work stealing. We provide theoretical guarantees for our record and replay scheme --- namely that record is optimal for programs with one lock and replay is near-optimal for all cases. In addition, we implemented this scheme in the Cilk Plus runtime system and our evaluation indicates that processor-obliviousness does not cause substantial overheads.
Noise Injection Techniques to Expose Subtle and Unintended Message Races
Authors: Sato Kento , Ahn Dong H. , Laguna Ignacio , Lee Gregory L. , Schulz Martin , Chambreau Christopher M.
Published: October 2017

Debugging intermittently occurring bugs within MPI applications is challenging, and message races, a condition in which two or more sends race to match with a receive, are one of the common root causes. Many debugging tools have been proposed to help programmers resolve them, but their runtime interference perturbs the timing such that subtle races often cannot be reproduced with debugging tools. We present novel noise injection techniques to expose message races even under a tool's control. We first formalize this race problem in the context of non-deterministic parallel applications and use this analysis to determine an effective noise-injection strategy to uncover them. We codified these techniques in NINJA (Noise INJection Agent) that exposes these races without modification to the application. Our evaluations on synthetic cases as well as a real-world bug in Hypre-2.10.1 show that NINJA significantly helps expose races.
Isoefficiency in Practice
Authors: Shudler Sergei , Calotoiu Alexandru , Hoefler Torsten , Wolf Felix
Published: October 2017

Task-based programming offers an elegant way to express units of computation and the dependencies among them, making it easier to distribute the computational load evenly across multiple cores. However, this separation of problem decomposition and parallelism requires a sufficiently large input problem to achieve satisfactory efficiency on a given number of cores. Unfortunately, finding a good match between input size and core count usually requires significant experimentation, which is expensive and sometimes even impractical. In this paper, we propose an automated empirical method for finding the isoefficiency function of a task-based program, binding efficiency, core count, and the input size in one analytical expression. This allows the latter two to be adjusted according to given (realistic) efficiency objectives. Moreover, we not only find (i) the actual isoefficiency function but also (ii) the function one would yield if the program execution was free of resource contention and (iii) an upper bound that could only be reached if the program was able to maintain its average parallelism throughout its execution. The difference between the three helps to explain low efficiency, and in particular, it helps to differentiate between resource contention and structural conflicts related to task dependencies or scheduling. The insights gained can be used to co-design programs and shared system resources.
Grammar-aware Parallelization for Scalable XPath Querying
Authors: Jiang Lin , Zhao Zhijia
Published: October 2017

Semi-structured data emerge in many domains, especially in web analytics and business intelligence. However, querying such data is inherently sequential due to the nested structure of input data. Existing solutions pessimistically enumerate all execution paths to circumvent dependencies, yielding sub-optimal performance and limited scalability.

This paper presents GAP, a parallelization scheme that, for the first time, leverages the grammar of the input data to boost the parallelization efficiency. GAP leverages static analysis to infer feasible execution paths for specific con- texts based on the grammar of the semi-structured data. It can eliminate unnecessary paths without compromising the correctness. In the absence of a pre-defined grammar, GAP switches into a speculative execution mode and takes potentially incomplete grammar extracted either from prior inputs. Together, the dual-mode GAP reduces the execution paths from all paths to a minimum, therefore maximizing the parallelization efficiency and scalability. The benefits of path elimination go beyond reducing extra computation -- it also enables the use of more efficient data structures, which further improves the efficiency. An evaluation on a large set of standard benchmarks with diverse queries shows that GAP yields significant efficiency increase and boosts the speedup of the state-of-the-art from 2.9X to 17.6X on a 20-core ma- chine for a set of 200 queries.
POSTER
Authors: Ramalhete Pedro , Correia Andreia
Published: October 2017

Queues are a widely deployed data structure. They are used extensively in many multi threaded applications, or as a communication mechanism between threads or processes. We propose a new linearizable multi-producer-multi-consumer queue we named Turn queue, with wait-free progress bounded by the number of threads, and with wait-free bounded memory reclamation. Its main characteristics are: a simple algorithm that does no memory allocation apart from creating the node that is placed in the queue, a new wait-free consensus algorithm using only the atomic instruction compare-and-swap (CAS), and is easy to plugin with other algorithms for either enqueue or dequeue methods.
POSTER
Authors: Zhao Yue , Liao Chunhua , Shen Xipeng
Published: October 2017

This paper presents a prototype infrastructure for addressing the barriers for effective accumulation, sharing, and reuse of the various types of knowledge for high performance parallel computing.
POSTER
Authors: Balaji Vignesh , Tirumala Dhruva , Lucia Brandon
Published: October 2017

Synchronization and data movement are the key impediments to an efficient parallel execution. To ensure that data shared by multiple threads remain consistent, the programmer must use synchronization (e.g., mutex locks) to serialize threads' accesses to data. This limits parallelism because it forces threads to sequentially access shared resources. Additionally, systems use cache coherence to ensure that processors always operate on the most up-to-date version of a value even in the presence of private caches. Coherence protocol implementations cause processors to serialize their accesses to shared data, further limiting parallelism and performance.
POSTER
Authors: Moscovici Nurit , Cohen Nachshon , Petrank Erez
Published: October 2017

We propose a design for a fine-grained lock-based skiplist optimized for Graphics Processing Units (GPUs). While GPUs are often used to accelerate streaming parallel computations, it remains a significant challenge to efficiently offload concurrent computations with more complicated data-irregular access and fine-grained synchronization. Natural building blocks for such computations would be concurrent data structures, such as skiplists, which are widely used in general purpose computations. Our design utilizes array-based nodes which are accessed and updated by warp-cooperative functions, thus taking advantage of the fact that GPUs are most efficient when memory accesses are coalesced and execution divergence is minimized. The proposed design has been implemented, and measurements demonstrate improved performance of up to 2.6x over skiplist designs for the GPU existing today.
Flaxseed Consumption Inhibits Chemically Induced Lung Tumorigenesis and Modulates Expression of Phase II Enzymes and Inflammatory Cytokines in A/J Mice
Authors: Chikara Shireen , Mamidi Sujan , Sreedasyam Avinash , Chittem Kishore , Pietrofesa Ralph , Zuppa Athena , Moorthy Ganesh , Dyer Neil , Christofidou-Solomidou Melpo , Reindl Katie M.
Published: October 2017

Flaxseed consumption is associated with reduced oxidative stress and inflammation in lung injury models and has shown anticancer effects for breast and prostate tissues. However, the chemopreventive potential of flaxseed remains unexplored for lung cancer. In this study, we investigated the effect of flaxseed on tobacco smoke carcinogen (NNK)–induced lung tumorigenesis in an A/J mouse model. Mice exposed to NNK were fed a control diet or a 10% flaxseed-supplemented diet for 26 weeks. Flaxseed-fed mice showed reduced lung tumor incidence (78%) and multiplicity, with an average of 2.7 ± 2.3 surface lung tumor nodules and 1.0 ± 0.9 H&E cross-section nodules per lung compared with the control group, which had 100% tumor incidence and an average of 10.2 ± 5.7 surface lung tumor nodules and 3.9 ± 2.6 H&E cross-section nodules per lung. Furthermore, flaxseed-fed mice had a lower incidence of adenocarcinomas compared with control-fed mice. Western blotting performed on normal lung tissues showed flaxseed suppressed phosphorylation (activation) of p-AKT, p-ERK, and p-JNK kinases. RNA-Seq data obtained from normal lung and lung tumors of control and flaxseed-fed mice suggested that flaxseed intake resulted in differential expression of genes involved in inflammation-mediated cytokine signaling (IL1, 6, 8, 9, and 12α), xenobiotic metabolism (several CYPs, GSTs, and UGTs), and signaling pathways (AKT and MAPK) involved in tumor cell proliferation. Together, our results indicate that dietary flaxseed supplementation may be an effective chemoprevention strategy for chemically induced lung carcinogenesis by altering signaling pathways, inflammation, and oxidative stress. Cancer Prev Res; 11(1); 27–37. ©2017 AACR.
Genetic Variants in Metabolic Signaling Pathways and Their Interaction with Lifestyle Factors on Breast Cancer Risk: A Random Survival Forest Analysis
Authors: Jung Su Yon , Papp Jeanette C. , Sobel Eric M. , Zhang Zuo-Feng
Published: October 2017

Genetic variants in the insulin-like growth factor-I (IGF-I)/insulin resistance axis may interact with lifestyle factors, influencing postmenopausal breast cancer risk, but these interrelated pathways are not fully understood. In this study, we examined 54 single-nucleotide polymorphisms (SNP) in genes related to IGF-I/insulin phenotypes and signaling pathways and lifestyle factors in relation to postmenopausal breast cancer, using data from 6,567 postmenopausal women in the Women's Health Initiative Harmonized and Imputed Genome-Wide Association Studies. We used a machine-learning method, two-stage random survival forest analysis. We identified three genetic variants (AKT1 rs2494740, AKT1 rs2494744, and AKT1 rs2498789) and two lifestyle factors [body mass index (BMI) and dietary alcohol intake] as the top five most influential predictors for breast cancer risk. The combination of the three SNPs, BMI, and alcohol consumption (≥1 g/day) significantly increased the risk of breast cancer in a gene and lifestyle dose-dependent manner. Our findings provide insight into gene–lifestyle interactions and will enable researchers to focus on individuals with risk genotypes to promote intervention strategies. These data also suggest potential genetic targets in future intervention/clinical trials for cancer prevention in order to reduce the risk for breast cancer in postmenopausal women. Cancer Prev Res; 11(1); 44–51. ©2017 AACR.
A Novel Application of Structural Equation Modeling Estimates the Association between Oxidative Stress and Colorectal Adenoma
Authors: Eldridge Ronald C. , Goodman Michael , Bostick Roberd M. , Fedirko Veronika , Gross Myron , Thyagarajan Bharat , Flanders W. Dana
Published: October 2017

In vitro evidence implicates oxidative stress in many adverse health conditions, including colorectal neoplasia. In human studies, however, oxidative stress is measured by imperfect biomarkers, which are inconsistently associated with health outcomes. Structural equation modeling (SEM) offers one possible solution by modeling a latent (unobserved) construct from multiple biomarkers. Our goal was to investigate the association of a latent oxidative stress variable with colorectal adenoma. Using SEM, we analyzed pooled data from two cross-sectional studies of colorectal adenoma (n = 526) that measured five plasma biomarkers of oxidative stress and inflammation that comprised the latent oxidative stress variable: F2-isoprostanes (FIP), fluorescent oxidation products (FOP), mitochondrial DNA (MtDNA) copy number, γ-tocopherol (Gtoc), and C-reactive protein (CRP). Higher levels of oxidative stress were associated with colorectal adenoma [OR = 3.23 per SD increase in oxidative stress; 95% confidence interval (CI), 1.28–8.18]. The latent variable estimate was considerably stronger than the associations of adenoma with the individual biomarkers, which were modest and mostly nonsignificant. Risk factors were associated with adenoma via the oxidative stress pathway, particularly overweight and obesity with an OR = 1.50; 95% CI, 1.10–2.81; and OR = 2.95; 95% CI, 1.28–12.45, respectively. Oxidative stress may be positively associated with colorectal adenoma, and important risk factors may act through this mechanism, but the cross-sectional design of the current study precludes observing the directionality of associations. The presence of an adenoma could affect levels of the circulating biomarkers; thus, we should be cautious of strong conclusions until the findings are replicated in a follow-up study. Cancer Prev Res; 11(1); 52–58. ©2017 AACR.