bluuebunny/crossref_metadata_2025 huggingface dataset:
Statistical Modeling of Fire Occurrence Using Data from the Tōhoku, Japan Earthquake and Tsunami
Authors: Anderson Dana , Davidson Rachel A. , Himoto Keisuke , Scawthorn Charles
Published: August 2015

In this article, we develop statistical models to predict the number and geographic distribution of fires caused by earthquake ground motion and tsunami inundation in Japan. Using new, uniquely large, and consistent data sets from the 2011 Tōhoku earthquake and tsunami, we fitted three types of models—generalized linear models (GLMs), generalized additive models (GAMs), and boosted regression trees (BRTs). This is the first time the latter two have been used in this application. A simple conceptual framework guided identification of candidate covariates. Models were then compared based on their out‐of‐sample predictive power, goodness of fit to the data, ease of implementation, and relative importance of the framework concepts. For the ground motion data set, we recommend a Poisson GAM; for the tsunami data set, a negative binomial (NB) GLM or NB GAM. The best models generate out‐of‐sample predictions of the total number of ignitions in the region within one or two. Prefecture‐level prediction errors average approximately three. All models demonstrate predictive power far superior to four from the literature that were also tested. A nonlinear relationship is apparent between ignitions and ground motion, so for GLMs, which assume a linear response‐covariate relationship, instrumental intensity was the preferred ground motion covariate because it captures part of that nonlinearity. Measures of commercial exposure were preferred over measures of residential exposure for both ground motion and tsunami ignition models. This may vary in other regions, but nevertheless highlights the value of testing alternative measures for each concept. Models with the best predictive power included two or three covariates.
Epstein–Barr virus encephalitis in a renal transplant recipient manifesting as hemorrhagic, ring‐enhancing mass lesions
Authors: Babik J.M. , Katrak S. , Miller S. , Shah M. , Chin‐Hong P.
Published: August 2015

Epstein–Barr virus (EBV) encephalitis has been infrequently described in immunocompromised patients. Here, we report a unique case of biopsy‐proven EBV encephalitis in a renal transplant recipient presenting with altered mental status, prominent visual disturbances, and hemorrhagic, ring‐enhancing mass lesions on magnetic resonance imaging. The patient was successfully treated with a prolonged course of antivirals. This case illustrates the difficulty in interpretation of cerebrospinal fluid EBV polymerase chain reaction assay, given the lack of specificity in immunocompromised patients.
A genome‐wide survey reveals abundant rice blast R genes in resistant cultivars
Authors: Zhang Xiaohui , Yang Sihai , Wang Jiao , Jia Yanxiao , Huang Ju , Tan Shengjun , Zhong Yan , Wang Ling , Gu Longjiang , Chen Jian‐Qun , Pan Qinghua , Bergelson Joy , Tian Dacheng
Published: August 2015

Plant resistance genes (R genes) harbor tremendous allelic diversity, constituting a robust immune system effective against microbial pathogens. Nevertheless, few functional R genes have been identified for even the best‐studied pathosystems. Does this limited repertoire reflect specificity, with most R genes having been defeated by former pests, or do plants harbor a rich diversity of functional R genes, the composite behavior of which is yet to be characterized? Here, we survey 332 NBS‐LRR genes cloned from five resistant Oryza sativa (rice) cultivars for their ability to confer recognition of 12 rice blast isolates when transformed into susceptible cultivars. Our survey reveals that 48.5% of the 132 NBS‐LRR loci tested contain functional rice blast R genes, with most R genes deriving from multi‐copy clades containing especially diversified loci. Each R gene recognized, on average, 2.42 of the 12 isolates screened. The abundant R genes identified in resistant genomes provide extraordinary redundancy in the ability of host genotypes to recognize particular isolates. If the same is true for other pathogens, many extant NBS‐LRR genes retain functionality. Our success at identifying rice blast R genes also validates a highly efficient cloning and screening strategy.
INDUCER OF CBF EXPRESSION 1 integrates cold signals into FLOWERING LOCUS C‐mediated flowering pathways in Arabidopsis
Authors: Lee Jae‐Hyung , Jung Jae‐Hoon , Park Chung‐Mo
Published: August 2015

Plants constantly monitor changes in photoperiod and temperature throughout the year to synchronize flowering with optimal environmental conditions. In the temperate zones, both photoperiod and temperature fluctuate in a somewhat predictable manner through the seasons, although a transient shift to low temperature is also encountered during changing seasons, such as early spring. Although low temperatures are known to delay flowering by inducing the floral repressor FLOWERING LOCUS C (FLC), it is not fully understood how temperature signals are coordinated with photoperiodic signals in the timing of seasonal flowering. Here, we show that the cold signaling activator INDUCER OF CBF EXPRESSION 1 (ICE1), FLC and the floral promoter SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) constitute an elaborate signaling network that integrates cold signals into flowering pathways. The cold‐activated ICE1 directly induces the gene encoding FLC, which represses SOC1 expression, resulting in delayed flowering. In contrast, under floral promotive conditions, SOC1 inhibits the binding of ICE1 to the promoters of the FLC gene, inducing flowering with a reduction of freezing tolerance. These observations indicate that the ICE1‐FLC‐SOC1 signaling network contributes to the fine‐tuning of flowering during changing seasons.
Transcription factor WRKY46 modulates the development of Arabidopsis lateral roots in osmotic/salt stress conditions via regulation of ABA signaling and auxin homeostasis
Authors: Ding Zhong Jie , Yan Jing Ying , Li Chun Xiao , Li Gui Xin , Wu Yun Rong , Zheng Shao Jian
Published: August 2015

The development of lateral roots (LR) is known to be severely inhibited by salt or osmotic stress. However, the molecular mechanisms underlying LR development in osmotic/salt stress conditions are poorly understood. Here we show that the gene encoding the WRKY transcription factor WRKY46 (WRKY46) is expressed throughout lateral root primordia (LRP) during early LR development and that expression is subsequently restricted to the stele of the mature LR. In osmotic/salt stress conditions, lack of WRKY46 (in loss‐of‐function wrky46 mutants) significantly reduces, while overexpression of WRKY46 enhances, LR development. We also show that exogenous auxin largely restores LR development in wrky46 mutants, and that the auxin transport inhibitor 2,3,5‐triiodobenzoic acid (TIBA) inhibits LR development in both wild‐type (WT; Col‐0) and in a line overexpressing WRKY46 (OV46). Subsequent analysis of abscisic acid (ABA)‐related mutants indicated that WRKY46 expression is down‐regulated by ABA signaling, and up‐regulated by an ABA‐independent signal induced by osmotic/salt stress. Next, we show that expression of the DR5:GUS auxin response reporter is reduced in roots of wrky46 mutants, and that both wrky46 mutants and OV46 display altered root levels of free indole‐3‐acetic acid (IAA) and IAA conjugates. Subsequent RT‐qPCR and ChIP‐qPCR experiments indicated that WRKY46 directly regulates the expression of ABI4 and of genes regulating auxin conjugation. Finally, analysis of wrky46 abi4 double mutant plants confirms that ABI4 acts downstream of WRKY46. In summary, our results demonstrate that WRKY46 contributes to the feedforward inhibition of osmotic/salt stress‐dependent LR inhibition via regulation of ABA signaling and auxin homeostasis.
Sequencing of 15 622 gene‐bearing BACs clarifies the gene‐dense regions of the barley genome
Authors: Muñoz‐Amatriaín María , Lonardi Stefano , Luo MingCheng , Madishetty Kavitha , Svensson Jan T. , Moscou Matthew J. , Wanamaker Steve , Jiang Tao , Kleinhofs Andris , Muehlbauer Gary J. , Wise Roger P. , Stein Nils , Ma Yaqin , Rodriguez Edmundo , Kudrna Dave , Bhat Prasanna R. , Chao Shiaoman , Condamine Pascal , Heinen Shane , Resnik Josh , Wing Rod , Witt Heather N. , Alpert Matthew , Beccuti Marco , Bozdag Serdar , Cordero Francesca , Mirebrahim Hamid , Ounit Rachid , Wu Yonghui , You Frank , Zheng Jie , Simková Hana , Dolezel Jaroslav , Grimwood Jane , Schmutz Jeremy , Duma Denisa , Altschmied Lothar , Blake Tom , Bregitzer Phil , Cooper Laurel , Dilbirligi Muharrem , Falk Anders , Feiz Leila , Graner Andreas , Gustafson Perry , Hayes Patrick M. , Lemaux Peggy , Mammadov Jafar , Close Timothy J.
Published: August 2015

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole‐genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene‐containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical‐mapped gene‐bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene‐enriched BACs and are characterized by high recombination rates, there are also gene‐dense regions with suppressed recombination. We made use of published map‐anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D‐genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley–Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map‐based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene‐dense but low recombination is particularly relevant.
English in television commercials in Belgium, France, Italy, the Netherlands and Spain
Authors: RAEDTS MARIET , DUPRÉ NATALIE , HENDRICKX JEF , DEBRAUWERE SOPHIE
Published: August 2015

This study investigates and compares the use of English in 1,539 prime time television commercials from five European countries: Belgium, France, Italy, Spain and the Netherlands. Our study contributes to the existing body of research by adding two methodological issues. First, we investigate whether results differ depending on which definition of the term ‘English word’ is used (i.e. a strict or a broad definition). Second, we explore which factor best predicts the occurrence and the amount of English used in European television commercials: the advertised product (i.e. culture‐free or culture‐bound) or the country where the commercial is broadcast.
Decoupling the level dependence of the basilar membrane gain and phase in nonlinear cochlea models
Authors: Sisto Renata , Moleti Arturo , Altoè Alessandro
Published: August 2015

In animal experiments, the strong dependence on stimulus level of the basilar membrane gain and tuning is not matched by a corresponding change in the phase slope in the resonant region. Linear models, in which the gain dependence on the stimulus level has to be schematized by explicitly changing the tuning parameters of the resonant model, do not easily match this feature of the experimental data. Nonlinear models predict a phase slope that is relatively decoupled from tuning. In addition, delayed-stiffness and feed-forward models also show a significant intrinsic decoupling between gain and tuning, which helps in matching the experimental data.
Slip pulse and resonance of the Kathmandu basin during the 2015 Gorkha earthquake, Nepal
Authors: Galetzka J. , Melgar D. , Genrich J. F. , Geng J. , Owen S. , Lindsey E. O. , Xu X. , Bock Y. , Avouac J.-P. , Adhikari L. B. , Upreti B. N. , Pratt-Sitaula B. , Bhattarai T. N. , Sitaula B. P. , Moore A. , Hudnut K. W. , Szeliga W. , Normandeau J. , Fend M. , Flouzat M. , Bollinger L. , Shrestha P. , Koirala B. , Gautam U. , Bhatterai M. , Gupta R. , Kandel T. , Timsina C. , Sapkota S. N. , Rajaure S. , Maharjan N.
Published: August 2015

The bigger they are, the harder they fall

The magnitude 7.8 Gorkha earthquake hit Nepal on 25 April 2015. The earthquake killed thousands and caused great damage. Galetzka
et al.
determined how the fault that caused this earthquake ruptured. The rupture showed a smooth slip pulse 20 km wide that moved eastward along the fault over about 6 s. The nature of the rupture limited damage to regular dwellings but generated shaking that collapsed taller structures.

Science
, this issue p.
1091
A self-interfering clock as a “which path” witness
Authors: Margalit Yair , Zhou Zhifan , Machluf Shimon , Rohrlich Daniel , Japha Yonathan , Folman Ron
Published: August 2015

Interfering with time

The interference pattern arising from light or particles passing through a double slit is a simple experiment that belies the subtleties of interpretation when attempting to describe and understand the effect. For example, determining “which path” the light or particles travel can result in the interference pattern disappearing. Margalit
et al.
present a new take on interferometry using time (see the Perspective by Arndt and Brand). A clock—i.e., the internal state of a cold atom condensate—was coherently split and brought back together to interfere. Making one-half of the clock tick at a different rate resulted in a change in the interference pattern, possibly as a consequence of the time being a “which path” witness.

Science
, this issue p.
1205
; see also p.
1168
Complete Genome Sequence of Bacillus megaterium Siphophage Stahl
Authors: Brizendine Ashley M. , Rousseau Simon , Hernandez Adriana C. , Kuty Everett Gabriel F.
Published: August 2015

Stahl is a siphophage active against
Bacillus megaterium
, a Gram-positive bacterium often used as a model system in research and as a protein production strain in industrial applications. Here, we present the complete annotated genome of phage Stahl and describe its major features.
Draft Genome Sequence of Paenibacillus polymyxa Strain Mc5Re-14, an Antagonistic Root Endophyte of
Matricaria chamomilla
Authors: Köberl Martina , White Richard A. , Erschen Sabine , El-Arabi Tarek F. , Jansson Janet K. , Berg Gabriele
Published: August 2015

Paenibacillus polymyxa
strain Mc5Re-14 was isolated from the inner root tissue of
Matricaria chamomilla
(German chamomile). Mc5Re-14 revealed promising
in vitro
antagonistic activity against plant and opportunistic human pathogens. The 6.0-Mb draft genome reveals genes putatively involved in pathogen suppression and direct and indirect plant growth promotion.
Protocol for a randomised controlled trial for Reducing Arthritis Fatigue by clinical Teams (RAFT) using cognitive–behavioural approaches
Authors: Hewlett S , Ambler N , Almeida C , Blair P S , Choy E , Dures E , Hammond A , Hollingworth W , Kirwan J , Plummer Z , Rooke C , Thorn J , Tomkinson K , Pollock J
Published: August 2015

Introduction

Rheumatoid arthritis (RA) fatigue is distressing, leading to unmanageable physical and cognitive exhaustion impacting on health, leisure and work. Group cognitive–behavioural (CB) therapy delivered by a clinical psychologist demonstrated large improvements in fatigue impact. However, few rheumatology teams include a clinical psychologist, therefore, this study aims to examine whether conventional rheumatology teams can reproduce similar results, potentially widening intervention availability.

Methods and analysis

This is a multicentre, randomised, controlled trial of a group CB intervention for RA fatigue self-management, delivered by local rheumatology clinical teams. 7 centres will each recruit 4 consecutive cohorts of 10–16 patients with RA (fatigue severity ≥6/10). After consenting, patients will have baseline assessments, then usual care (fatigue self-management booklet, discussed for 5–6 min), then be randomised into control (no action) or intervention arms. The intervention, Reducing Arthritis Fatigue by clinical Teams (RAFT) will be cofacilitated by two local rheumatology clinicians (eg, nurse/occupational therapist), who will have had brief training in CB approaches, a RAFT manual and materials, and delivered an observed practice course. Groups of 5–8 patients will attend 6×2 h sessions (weeks 1–6) and a 1 hr consolidation session (week 14) addressing different self-management topics and behaviours. The primary outcome is fatigue impact (26 weeks); secondary outcomes are fatigue severity, coping and multidimensional impact, quality of life, clinical and mood status (to week 104). Statistical and health economic analyses will follow a predetermined plan to establish whether the intervention is clinically and cost-effective. Effects of teaching CB skills to clinicians will be evaluated qualitatively.

Ethics and dissemination

Approval was given by an NHS Research Ethics Committee, and participants will provide written informed consent. The copyrighted RAFT package will be freely available. Findings will be submitted to the National Institute for Health and Care Excellence, Clinical Commissioning Groups and all UK rheumatology departments.

Trial registration number

ISRCTN: 52709998; Protocol v3 09.02.2015.
Connexin 43 expression predicts poor progression-free survival in patients with non-muscle invasive urothelial bladder cancer
Authors: Poyet Cédric , Buser Lorenz , Roudnicky Filip , Detmar Michael , Hermanns Thomas , Mannhard Doris , Höhn Andrej , Rüschoff Jan , Zhong Qing , Sulser Tullio , Moch Holger , Wild Peter J
Published: August 2015

Objectives

To evaluate the protein expression of connexin 43 (Cx43) in primary urothelial bladder cancer and test its association with the histopathological characteristics and clinical outcome.

Methods

A tissue microarray containing 348 tissue samples from 174 patients with primary urothelial carcinomas of the bladder was immunohistochemically stained for Cx43. The intensity of staining was semiquantitatively evaluated (score 0, 1+, 2+), and the association with clinicopathological features was assessed. Univariable and multivariable analyses were performed to identify predictors for progression-free survival (PFS).

Results

Membranous Cx43 immunoreactivity was detected in 118 (67.8%) of 174 analysable urothelial carcinomas, of which 31 (17.8%) showed even a strong (score 2+) and mainly homogeneous staining. Strong expression levels of Cx43 (score 2+) were associated with higher tumour grade, multiplicity and increased proliferation (all p<0.05). In the subgroup of patients with stage pTa and pT1 bladder tumours (n=158), strong Cx43 expression (p<0.001), solid growth pattern (p<0.001) and increased Ki-67 proliferation fraction (p<0.05) were significantly associated with shorter PFS in an univariable Cox regression analysis. In multivariable Cox regression models, Cx43 immunoreactivity and histological growth pattern remained highly significant and adverse risk factors for PFS.

Conclusions

The expression levels of Cx43 are frequent in non-muscle invasive bladder cancer (NMIBC), with high expression levels being associated with poor prognosis. Routine assessment of Cx43 expression may improve the identification of high-risk NMIBC.
Fibulin-5 is a tumour suppressor inhibiting cell migration and invasion in ovarian cancer
Authors: Heo Jin Hyung , Song Ji-ye , Jeong Ju-yeong , Kim Gwangil , Kim Tae Heon , Kang Haeyoun , Kwon Ah-young , An Hee Jung
Published: August 2015

Aims

Fibulin-5 is an extracellular matrix (ECM) glycoprotein which has a role in the organisation and stabilisation of ECM structures and regulating cell proliferation and tumourigenesis. Here, the expression of fibulin-5 and its functional effects on the migration and invasion of ovarian cancer cells were assessed.

Methods

Expression of fibulin-5 was detected in 44 ovarian tumour tissues by qRT-PCR, Western blotting and immunohistochemistry. We performed cell migration and invasion assays, and cell cycle analysis in fibulin-5 transfected SKOV3 (SKOV3-FBLN5) cells and the parental SKOV3 cells. We further examined the expression of three tissue inhibitors of metalloproteinases (TIMPs) and seven matrix metalloproteinases (MMPs) by RT-PCR.

Results

mRNA and protein expression of fibulin-5 were down-regulated (0.05-fold and 0.1-fold) in ovarian carcinomas compared with control tissues (p<0.01 and p=0.022). In wound-healing and invasion assays, significantly fewer SKOV3-FBLN5 cells than SKOV3 control cells migrated and invaded (39.1%, p=0.046 and 70%, p=0.03, respectively), which was reversed by siRNA-treatment. Overexpression of fibulin-5 induced G2/M arrest and increased cyclin B1, CDC2 and CDC25C. Expression of TIMP-2 (0.56-fold), MMP-3 (0.43-fold) and MMP-13 (0.18-fold) was lower and MMP-9 expression (2.20-fold) was higher in SKOV3-FBLN5 cells than in control cells.

Conclusions

Fibulin-5 is significantly down-regulated in ovarian carcinoma and acts as a tumour suppressor by inhibiting the migration and invasion of ovarian cancer cells.
Development of an indirect ELISA based on a truncated S protein of the porcine epidemic diarrhea virus
Authors: Li Yufeng , Zheng Fangyuan , Fan Baochao , Muhammad Hassan Mushtaq , Zou Yao , Jiang Ping
Published: August 2015

Porcine epidemic diarrhea (PED) is a highly contagious, enteric disease of swine caused by the porcine epidemic diarrhea virus (PEDV). To find a suitable ELISA method to assess the infection of PEDV and the effectiveness of vaccines, we developed and evaluated an indirect enzyme-linked immunosorbent assay (iELISA) based on a truncated recombinant spike (S) protein expressed in Escherichia coli. The parameters of the iELISA were optimized, and the cutoff value determined as 0.259 by analyzing optical density (OD) values of 80 PEDV negative sera confirmed by western blot. Repeatability tests revealed that the coefficients of variation of positive sera within and between runs were both less than 10%. Cross-reactivity assays demonstrated that iELISA was PEDV-specific. A virus neutralization test with sera of 7 different OD values showed a positive correlation between the OD values and virus neutralization. The results suggest this iELISA is specific, sensitive, and repeatable. Further studies should focus on the relationship between OD values of sera and its virus neutralization.
FlashRelate: extracting relational data from semi-structured spreadsheets using examples
Authors: Barowy Daniel W. , Gulwani Sumit , Hart Ted , Zorn Benjamin
Published: August 2015

With hundreds of millions of users, spreadsheets are one of the most important end-user applications. Spreadsheets are easy to use and allow users great flexibility in storing data. This flexibility comes at a price: users often treat spreadsheets as a poor man's database, leading to creative solutions for storing high-dimensional data. The trouble arises when users need to answer queries with their data. Data manipulation tools make strong assumptions about data layouts and cannot read these ad-hoc databases. Converting data into the appropriate layout requires programming skills or a major investment in manual reformatting. The effect is that a vast amount of real-world data is "locked-in" to a proliferation of one-off formats. We introduce FlashRelate, a synthesis engine that lets ordinary users extract structured relational data from spreadsheets without programming. Instead, users extract data by supplying examples of output relational tuples. FlashRelate uses these examples to synthesize a program in Flare. Flare is a novel extraction language that extends regular expressions with geometric constructs. An interactive user interface on top of FlashRelate lets end users extract data by point-and-click. We demonstrate that correct Flare programs can be synthesized in seconds from a small set of examples for 43 real-world scenarios. Finally, our case study demonstrates FlashRelate's usefulness addressing the widespread problem of data trapped in corporate and government formats.
Improving compiler scalability: optimizing large programs at small price
Authors: Mehta Sanyam , Yew Pen-Chung
Published: August 2015

Compiler scalability is a well known problem: reasoning about the application of useful optimizations over large program scopes consumes too much time and memory during compilation. This problem is exacerbated in polyhedral compilers that use powerful yet costly integer programming algorithms to compose loop optimizations. As a result, the benefits that a polyhedral compiler has to offer to programs such as real scientific applications that contain sequences of loop nests, remain impractical for the common users. In this work, we address this scalability problem in polyhedral compilers. We identify three causes of unscalability, each of which stems from large number of statements and dependences in the program scope. We propose a one-shot solution to the problem by reducing the effective number of statements and dependences as seen by the compiler. We achieve this by representing a sequence of statements in a program by a single super-statement. This set of super-statements exposes the minimum sufficient constraints to the Integer Linear Programming (ILP) solver for finding correct optimizations. We implement our approach in the PLuTo polyhedral compiler and find that it condenses the program statements and program dependences by factors of 4.7x and 6.4x, respectively, averaged over 9 hot regions (ranging from 48 to 121 statements) in 5 real applications. As a result, the improvements in time and memory requirement for compilation are 268x and 20x, respectively, over the latest version of the PLuTo compiler. The final compile times are comparable to the Intel compiler while the performance is 1.92x better on average due to the latter’s conservative approach to loop optimization.
Compositional certified resource bounds
Authors: Carbonneaux Quentin , Hoffmann Jan , Shao Zhong
Published: August 2015

This paper presents a new approach for automatically deriving worst-case resource bounds for C programs. The described technique combines ideas from amortized analysis and abstract interpretation in a unified framework to address four challenges for state-of-the-art techniques: compositionality, user interaction, generation of proof certificates, and scalability. Compositionality is achieved by incorporating the potential method of amortized analysis. It enables the derivation of global whole-program bounds with local derivation rules by naturally tracking size changes of variables in sequenced loops and function calls. The resource consumption of functions is described abstractly and a function call can be analyzed without access to the function body. User interaction is supported with a new mechanism that clearly separates qualitative and quantitative verification. A user can guide the analysis to derive complex non-linear bounds by using auxiliary variables and assertions. The assertions are separately proved using established qualitative techniques such as abstract interpretation or Hoare logic. Proof certificates are automatically generated from the local derivation rules. A soundness proof of the derivation system with respect to a formal cost semantics guarantees the validity of the certificates. Scalability is attained by an efficient reduction of bound inference to a linear optimization problem that can be solved by off-the-shelf LP solvers. The analysis framework is implemented in the publicly-available tool C4B. An experimental evaluation demonstrates the advantages of the new technique with a comparison of C4B with existing tools on challenging micro benchmarks and the analysis of more than 2900 lines of C code from the cBench benchmark suite.
Automatically improving accuracy for floating point expressions
Authors: Panchekha Pavel , Sanchez-Stern Alex , Wilcox James R. , Tatlock Zachary
Published: August 2015

Scientific and engineering applications depend on floating point arithmetic to approximate real arithmetic. This approximation introduces rounding error, which can accumulate to produce unacceptable results. While the numerical methods literature provides techniques to mitigate rounding error, applying these techniques requires manually rearranging expressions and understanding the finer details of floating point arithmetic. We introduce Herbie, a tool which automatically discovers the rewrites experts perform to improve accuracy. Herbie's heuristic search estimates and localizes rounding error using sampled points (rather than static error analysis), applies a database of rules to generate improvements, takes series expansions, and combines improvements for different input regions. We evaluated Herbie on examples from a classic numerical methods textbook, and found that Herbie was able to improve accuracy on each example, some by up to 60 bits, while imposing a median performance overhead of 40%. Colleagues in machine learning have used Herbie to significantly improve the results of a clustering algorithm, and a mathematical library has accepted two patches generated using Herbie.
Finding counterexamples from parsing conflicts
Authors: Isradisaikul Chinawat , Myers Andrew C.
Published: August 2015

Writing a parser remains remarkably painful. Automatic parser generators offer a powerful and systematic way to parse complex grammars, but debugging conflicts in grammars can be time-consuming even for experienced language designers. Better tools for diagnosing parsing conflicts will alleviate this difficulty. This paper proposes a practical algorithm that generates compact, helpful counterexamples for LALR grammars. For each parsing conflict in a grammar, a counterexample demonstrating the conflict is constructed. When the grammar in question is ambiguous, the algorithm usually generates a compact counterexample illustrating the ambiguity. This algorithm has been implemented as an extension to the CUP parser generator. The results from applying this implementation to a diverse collection of faulty grammars show that the algorithm is practical, effective, and suitable for inclusion in other LALR parser generators.
Verification of producer-consumer synchronization in GPU programs
Authors: Sharma Rahul , Bauer Michael , Aiken Alex
Published: August 2015

Previous efforts to formally verify code written for GPUs have focused solely on kernels written within the traditional data-parallel GPU programming model. No previous work has considered the higher performance, but more complex, warp-specialized kernels based on producer-consumer named barriers available on current hardware. In this work we present the first formal operational semantics for named barriers and define what it means for a warp-specialized kernel to be correct. We give algorithms for verifying the correctness of warp-specialized kernels and prove that they are both sound and complete for the most common class of warp-specialized programs. We also present WEFT, a verification tool for checking warp-specialized code. Using WEFT, we discover several non-trivial bugs in production warp-specialized kernels.
Zero-overhead metaprogramming: reflection and metaobject protocols fast and without compromises
Authors: Marr Stefan , Seaton Chris , Ducasse Stéphane
Published: August 2015

Runtime metaprogramming enables many useful applications and is often a convenient solution to solve problems in a generic way, which makes it widely used in frameworks, middleware, and domain-specific languages. However, powerful metaobject protocols are rarely supported and even common concepts such as reflective method invocation or dynamic proxies are not optimized. Solutions proposed in literature either restrict the metaprogramming capabilities or require application or library developers to apply performance improving techniques. For overhead-free runtime metaprogramming, we demonstrate that dispatch chains, a generalized form of polymorphic inline caches common to self-optimizing interpreters, are a simple optimization at the language-implementation level. Our evaluation with self-optimizing interpreters shows that unrestricted metaobject protocols can be realized for the first time without runtime overhead, and that this optimization is applicable for just-in-time compilation of interpreters based on meta-tracing as well as partial evaluation. In this context, we also demonstrate that optimizing common reflective operations can lead to significant performance improvements for existing applications.
Static detection of asymptotic performance bugs in collection traversals
Authors: Olivo Oswaldo , Dillig Isil , Lin Calvin
Published: August 2015

This paper identifies and formalizes a prevalent class of asymptotic performance bugs called redundant traversal bugs and presents a novel static analysis for automatically detecting them. We evaluate our technique by implementing it in a tool called CLARITY and applying it to widely-used software packages such as the Google Core Collections Library, the Apache Common Collections, and the Apache Ant build tool. Across 1.6M lines of Java code, CLARITY finds 92 instances of redundant traversal bugs, including 72 that have never been previously reported, with just 5 false positives. To evaluate the performance impact of these bugs, we manually repair these programs and find that for an input size of 50,000, all repaired programs are at least 2.45 faster than their original code.
Relatively complete counterexamples for higher-order programs
Authors: Nguyễn Phúc C. , Van Horn David
Published: August 2015

In this paper, we study the problem of generating inputs to a higher-order program causing it to error. We first approach the problem in the setting of PCF, a typed, core functional language and contribute the first relatively complete method for constructing counterexamples for PCF programs. The method is relatively complete with respect to a first-order solver over the base types of PCF. In practice, this means an SMT solver can be used for the effective, automated generation of higher-order counterexamples for a large class of programs. We achieve this result by employing a novel form of symbolic execution for higher-order programs. The remarkable aspect of this symbolic execution is that even though symbolic higher-order inputs and values are considered, the path condition remains a first-order formula. Our handling of symbolic function application enables the reconstruction of higher-order counterexamples from this first-order formula. After establishing our main theoretical results, we sketch how to apply the approach to untyped, higher-order, stateful languages with first-class contracts and show how counterexample generation can be used to detect contract violations in this setting. To validate our approach, we implement a tool generating counterexamples for erroneous modules written in Racket.
Tree dependence analysis
Authors: Weijiang Yusheng , Balakrishna Shruthi , Liu Jianqiao , Kulkarni Milind
Published: August 2015

We develop a new framework for analyzing recursive methods that perform traversals over trees, called tree dependence analysis. This analysis translates dependence analysis techniques for regular programs to the irregular space, identifying the structure of dependences within a recursive method that traverses trees. We develop a dependence test that exploits the dependence structure of such programs, and can prove that several locality- and parallelism- enhancing transformations are legal. In addition, we extend our analysis with a novel path-dependent, conditional analysis to refine the dependence test and prove the legality of transformations for a wider range of algorithms. We then use these analyses to show that several common algorithms that manipulate trees recursively are amenable to several locality- and parallelism-enhancing transformations. This work shows that classical dependence analysis techniques, which have largely been confined to nested loops over array data structures, can be extended and translated to work for complex, recursive programs that operate over pointer-based data structures.
Stateless model checking concurrent programs with maximal causality reduction
Authors: Huang Jeff
Published: August 2015

We present maximal causality reduction (MCR), a new technique for stateless model checking. MCR systematically explores the state-space of concurrent programs with a provably minimal number of executions. Each execution corresponds to a distinct maximal causal model extracted from a given execution trace, which captures the largest possible set of causally equivalent executions. Moreover, MCR is embarrassingly parallel by shifting the runtime exploration cost to offline analysis. We have designed and implemented MCR using a constraint-based approach and compared with iterative context bounding (ICB) and dynamic partial order reduction (DPOR) on both benchmarks and real-world programs. MCR reduces the number of executions explored by ICB and ICB+DPOR by orders of magnitude, and significantly improves the scalability, efficiency, and effectiveness of the state-of-the-art for both state-space exploration and bug finding. In our experiments, MCR has also revealed several new data races and null pointer dereference errors in frequently studied real-world programs.
Efficient synthesis of probabilistic programs
Authors: Nori Aditya V. , Ozair Sherjil , Rajamani Sriram K. , Vijaykeerthy Deepak
Published: August 2015

We show how to automatically synthesize probabilistic programs from real-world datasets. Such a synthesis is feasible due to a combination of two techniques: (1) We borrow the idea of ``sketching'' from synthesis of deterministic programs, and allow the programmer to write a skeleton program with ``holes''. Sketches enable the programmer to communicate domain-specific intuition about the structure of the desired program and prune the search space, and (2) we design an efficient Markov Chain Monte Carlo (MCMC) based synthesis algorithm to instantiate the holes in the sketch with program fragments. Our algorithm efficiently synthesizes a probabilistic program that is most consistent with the data. A core difficulty in synthesizing probabilistic programs is computing the likelihood L(P | D) of a candidate program P generating data D. We propose an approximate method to compute likelihoods using mixtures of Gaussian distributions, thereby avoiding expensive computation of integrals. The use of such approximations enables us to speed up evaluation of the likelihood of candidate programs by a factor of 1000, and makes Markov Chain Monte Carlo based search feasible. We have implemented our algorithm in a tool called PSKETCH, and our results are encouraging PSKETCH is able to automatically synthesize 16 non-trivial real-world probabilistic programs.
Monitoring refinement via symbolic reasoning
Authors: Emmi Michael , Enea Constantin , Hamza Jad
Published: August 2015

Efficient implementations of concurrent objects such as semaphores, locks, and atomic collections are essential to modern computing. Programming such objects is error prone: in minimizing the synchronization overhead between concurrent object invocations, one risks the conformance to reference implementations — or in formal terms, one risks violating observational refinement. Precisely testing this refinement even within a single execution is intractable, limiting existing approaches to executions with very few object invocations. We develop scalable and effective algorithms for detecting refinement violations. Our algorithms are founded on incremental, symbolic reasoning, and exploit foundational insights into the refinement-checking problem. Our approach is sound, in that we detect only actual violations, and scales far beyond existing violation-detection algorithms. Empirically, we find that our approach is practically complete, in that we detect the violations arising in actual executions.
Termination and non-termination specification inference
Authors: Le Ton Chanh , Qin Shengchao , Chin Wei-Ngan
Published: August 2015

Techniques for proving termination and non-termination of imperative programs are usually considered as orthogonal mechanisms. In this paper, we propose a novel mechanism that analyzes and proves both program termination and non-termination at the same time. We first introduce the concept of second-order termination constraints and accumulate a set of relational assumptions on them via a Hoare-style verification. We then solve these assumptions with case analysis to determine the (conditional) termination and non- termination scenarios expressed in some specification logic form. In contrast to current approaches, our technique can construct a summary of terminating and non-terminating behaviors for each method. This enables modularity and reuse for our termination and non-termination proving processes. We have tested our tool on sample programs from a recent termination competition, and compared favorably against state-of-the-art termination analyzers.
LaminarIR: compile-time queues for structured streams
Authors: Ko Yousun , Burgstaller Bernd , Scholz Bernhard
Published: August 2015

Stream programming languages employ FIFO (first-in, first-out) semantics to model data channels between producers and consumers. A FIFO data channel stores tokens in a buffer that is accessed indirectly via read- and write-pointers. This indirect token-access decouples a producer’s write-operations from the read-operations of the consumer, thereby making dataflow implicit. For a compiler, indirect token-access obscures data-dependencies, which renders standard optimizations ineffective and impacts stream program performance negatively. In this paper we propose a transformation for structured stream programming languages such as StreamIt that shifts FIFO buffer management from run-time to compile-time and eliminates splitters and joiners, whose task is to distribute and merge streams. To show the effectiveness of our lowering transformation, we have implemented a StreamIt to C compilation framework. We have developed our own intermediate representation (IR) called LaminarIR, which facilitates the transformation. We report on the enabling effect of the LaminarIR on LLVM’s optimizations, which required the conversion of several standard StreamIt benchmarks from static to randomized input, to prevent computation of partial results at compile-time. We conducted our experimental evaluation on the Intel i7-2600K, AMD Opteron 6378, Intel Xeon Phi 3120A and ARM Cortex-A15 platforms. Our LaminarIR reduces data-communication on average by 35.9% and achieves platform-specific speedups between 3.73x and 4.98x over StreamIt. We reduce memory accesses by more than 60% and achieve energy savings of up to 93.6% on the Intel i7-2600K.
Asynchronous programming, analysis and testing with state machines
Authors: Deligiannis Pantazis , Donaldson Alastair F. , Ketema Jeroen , Lal Akash , Thomson Paul
Published: August 2015

Programming efficient asynchronous systems is challenging because it can often be hard to express the design declaratively, or to defend against data races and interleaving-dependent assertion violations. Previous work has only addressed these challenges in isolation, by either designing a new declarative language, a new data race detection tool or a new testing technique. We present P#, a language for high-reliability asynchronous programming co-designed with a static data race analysis and systematic concurrency testing infrastructure. We describe our experience using P# to write several distributed protocols and port an industrial-scale system internal to Microsoft, showing that the combined techniques, by leveraging the design of P#, are effective in finding bugs.
Peer-to-peer affine commitment using bitcoin
Authors: Crary Karl , Sullivan Michael J.
Published: August 2015

The power of linear and affine logic lies in their ability to model state change. However, in a trustless, peer-to-peer setting, it is difficult to force principals to commit to state changes. We show how to solve the peer-to-peer affine commitment problem using a generalization of Bitcoin in which transactions deal in types rather than numbers. This has applications to proof-carrying authorization and mechanically executable contracts. Importantly, our system can be---and is---implemented on top of the existing Bitcoin network, so there is no need to recruit computing power to a new protocol.
Interactive parser synthesis by example
Authors: Leung Alan , Sarracino John , Lerner Sorin
Published: August 2015

Despite decades of research on parsing, the construction of parsers remains a painstaking, manual process prone to subtle bugs and pitfalls. We present a programming-by-example framework called Parsify that is able to synthesize a parser from input/output examples. The user does not write a single line of code. To achieve this, Parsify provides: (a) an iterative algorithm for synthesizing and refining a grammar one example at a time, (b) an interface that provides immediate visual feedback in response to changes in the grammar being refined, and (c) a graphical mechanism for specifying example parse trees using only textual selections. We empirically demonstrate the viability of our approach by using Parsify to construct parsers for source code drawn from Verilog, SQL, Apache, and Tiger.
A formal C memory model supporting integer-pointer casts
Authors: Kang Jeehoon , Hur Chung-Kil , Mansky William , Garbuzov Dmitri , Zdancewic Steve , Vafeiadis Viktor
Published: August 2015

The ISO C standard does not specify the semantics of many valid programs that use non-portable idioms such as integer-pointer casts. Recent efforts at formal definitions and verified implementation of the C language inherit this feature. By adopting high-level abstract memory models, they validate common optimizations. On the other hand, this prevents reasoning about much low-level code relying on the behavior of common implementations, where formal verification has many applications. We present the first formal memory model that allows many common optimizations and fully supports operations on the representation of pointers. All arithmetic operations are well-defined for pointers that have been cast to integers. Crucially, our model is also simple to understand and program with. All our results are fully formalized in Coq.
Verification of a cryptographic primitive: SHA-256 (abstract)
Authors: Appel Andrew W.
Published: August 2015

A full formal machine-checked verification of a C program: the OpenSSL implementation of SHA-256. This is an interactive proof of functional correctness in the Coq proof assistant, using the Verifiable C program logic. Verifiable C is a separation logic for the C language, proved sound w.r.t. the operational semantics for C, connected to the CompCert verified optimizing C compiler.