bluuebunny/crossref_metadata_2025 huggingface dataset:
CORRELATION OF ARTICULAR CARTILAGE THICKNESS MEASUREMENTS MADE WITH MAGNETIC RESONANCE IMAGING, MAGNETIC RESONANCE ARTHROGRAPHY, AND COMPUTED TOMOGRAPHIC ARTHROGRAPHY WITH GROSS ARTICULAR CARTILAGE THICKNESS IN THE EQUINE METACARPOPHALANGEAL JOINT
Authors: Porter Erin G. , Winter Matthew D. , Sheppard Barbara J. , Berry Clifford R. , Hernandez Jorge A.
Published: August 2016

Osteoarthritis of the metacarpophalangeal joint is common cause of lameness in equine athletes, and is hallmarked by articular cartilage damage. An accurate, noninvasive method for measuring cartilage thickness would be beneficial to screen for cartilage injury and allow for prompt initiation of interventional therapy. The objective of this methods comparison study was to compare computed tomographic arthrography (CTA), magnetic resonance imaging (MRI), and magnetic resonance arthrography (MRA) measurements of articular cartilage thickness with gross measurements in the metacarpophalangeal joint of Thoroughbred horses. Fourteen cadaveric, equine thoracic limbs were included. Limbs were excluded from the study if pathology of the metacarpophalangeal articular cartilage was observed with any imaging modality. Articular cartilage thickness was measured in nine regions of the third metacarpal bone and proximal phalanx on sagittal plane MRI sequences. After intra‐articular contrast administration, the measurements were repeated on sagittal plane MRA and sagittal CTA reformations. In an effort to increase cartilage conspicuity, the volume of intra‐articular contrast was increased from 14.5 ml, to maximal distention for the second set of seven limbs. Mean and standard deviation values were calculated, and linear regression analysis was used to determine correlations between gross and imaging measurements of cartilage thickness. This study failed to identify one imaging test that consistently yielded measurements correlating with gross cartilage thickness. Even with the use of intra‐articular contrast, cartilage surfaces were difficult to differentiate in regions where the cartilage surfaces of the proximal phalanx and third metacarpal bone were in close contact with each other.
A mathematical model of absorbing Markov chains to understand the routes of metastasis
Authors: Margarit David HipГіlito , Romanelli Lilia
Published: August 2016

Metastasis is a complex and multi-step stochastic process. The study of the probabilities of generating a tumor from a primary site in another organs is the aim of this work. Based on statistics of National Institute of Cancer of Argentina (INC), a characterization of the routes of metastasis for the principal organs is presented by using Absorbing Markov chains. The metastasis propagation from different primary sites towards secondary and tertiary sites is also shown, emphasizing the relation and analysis about absorbing states.
Small heterodimer partner SHP mediates liver X receptor (LXR)–dependent suppression of inflammatory signaling by promoting LXR SUMOylation specifically in astrocytes
Authors: Lee Jee Hoon , Kim Hyunmi , Park Soo Jung , Woo Joo Hong , Joe Eun-hye , Jou Ilo
Published: August 2016

The transcriptional regulator SHP promotes SUMOylation of the LXR transcriptional factors specifically in astrocytes to limit inflammatory signaling.
Papers of note in
Science
Authors: VanHook Annalisa M.
Published: August 2016

This week’s articles are about virulence of the plague bacterium, resistance to parasite attack, a transcription factor that keeps plants from flowering prematurely, an epigenetic link between in utero nutrition and growth, and a synthetic biological system for tracking a cell’s history.
TNF drives thymocyte development
Authors: Foley John F.
Published: August 2016

The survival and development of single-positive thymocytes in the thymus requires activation of NF-κB signaling by the cytokine TNF.
Activity of Ceftazidime-Avibactam against Clinical and Isogenic Laboratory Pseudomonas aeruginosa Isolates Expressing Combinations of Most Relevant β-Lactam Resistance Mechanisms
Authors: Torrens Gabriel , Cabot Gabriel , Ocampo-Sosa Alain A. , Conejo M. Carmen , Zamorano Laura , Navarro Ferrán , Pascual Álvaro , Martínez-Martínez Luis , Oliver Antonio
Published: August 2016

The activity of ceftazidime-avibactam was compared with that of ceftazidime alone and meropenem against a collection of 190
Pseudomonas aeruginosa
clinical isolates recovered from a multicenter study of bloodstream infections. The addition of avibactam increased ceftazidime susceptibility in the complete collection of strains (64.7% to 91.1%) and particularly among subsets of isolates showing AmpC hyperproduction (10.9% to 76.1%) or multidrug resistance (MDR) profiles (27% to 77.8%). The MICs of ceftazidime-avibactam, in contrast with those of ceftazidime or meropenem, remained at ≤4 μg/ml for a panel of 16
P. aeruginosa
PAO1 isogenic mutants expressing multiple combinations of the most relevant β-lactam resistance mechanisms.
Acanthamoeba castellanii Genotype T4 Stimulates the Production of Interleukin-10 as Well as Proinflammatory Cytokines in THP-1 Cells, Human Peripheral Blood Mononuclear Cells, and Human Monocyte-Derived Macrophages
Authors: Mattana Antonella , Sanna Manuela , Cano Antonella , Delogu Giuseppe , Erre Giuseppe , Roberts Craig W. , Henriquez Fiona L. , Fiori Pier Luigi , Cappuccinelli Piero
Published: August 2016

Free-living amoebae of the genus
Acanthamoeba
can cause severe and chronic infections in humans, mainly localized in immune privileged sites, such as the brain and the eye. Monocytes/macrophages are thought to be involved in
Acanthamoeba
infections, but little is known about how these facultative parasites influence their functions. The aim of this work was to investigate the effects of
Acanthamoeba
on human monocytes/macrophages during the early phase of infection. Here, THP-1 cells, primary human monocytes isolated from peripheral blood, and human monocyte-derived macrophages were either coincubated with trophozoites of a clinical isolate of
Acanthamoeba
(genotype T4) or stimulated with amoeba-derived cell-free conditioned medium. Production of proinflammatory cytokines (tumor necrosis factor alpha [TNF-α], interleukin-6 [IL-6], and IL-12), anti-inflammatory cytokine (IL-10), and chemokine (IL-8) was evaluated at specific hours poststimulation (ranging from 1.5 h to 23 h). We showed that both
Acanthamoeba
trophozoites and soluble amoebic products induce an early anti-inflammatory monocyte-macrophage phenotype, characterized by significant production of IL-10; furthermore, challenge with either trophozoites or their soluble metabolites stimulate both proinflammatory cytokines and chemokine production, suggesting that this protozoan infection results from the early induction of coexisting, opposed immune responses. Results reported in this paper confirm that the production of proinflammatory cytokines and chemokines by monocytes and macrophages can play a role in the development of the inflammatory response during
Acanthamoeba
infections. Furthermore, we demonstrate for the first time that
Acanthamoeba
stimulates IL-10 production in human innate immune cells, which might both promote the immune evasion of
Acanthamoeba
and limit the induced inflammatory response.
Paleomagnetic constraints on the Mesozoic drift of the Lhasa terrane (Tibet) from Gondwana to Eurasia
Authors: Li Zhenyu , Ding Lin , Lippert Peter C. , Song Peiping , Yue Yahui , van Hinsbergen Douwe J.J.
Published: August 2016

The Mesozoic plate tectonic history of Gondwana-derived crustal blocks of the Tibetan Plateau is hotly debated, but so far, paleomagnetic constraints quantifying their paleolatitude drift history remain sparse. Here, we compile existing data published mainly in Chinese literature and provide a new, high-quality, well-dated paleomagnetic pole from the ca. 180 Ma Sangri Group volcanic rocks of the Lhasa terrane that yields a paleolatitude of 3.7°S ± 3.4°. This new pole confirms a trend in the data that suggests that Lhasa drifted away from Gondwana in Late Triassic time, instead of Permian time as widely perceived. A total northward drift of ∼4500 km between ca. 220 and ca. 130 Ma yields an average south-north plate motion rate of 5 cm/yr. Our results are consistent with either an Indian or an Australian provenance of Lhasa.
Remote care of a patient with stroke in rural Trinidad: use of telemedicine to optimise global neurological care
Authors: Reyes Antonio Jose , Ramcharan Kanterpersad
Published: August 2016

We report a patient driven home care system that successfully assisted 24/7 with the management of a 68-year-old woman after a stroke-a global illness. The patient's caregiver and physician used computer devices, smartphones and internet access for information exchange. Patient, caregiver, family and physician satisfaction, coupled with outcome and cost were indictors of quality of care. The novelty of this basic model of teleneurology is characterised by implementing a patient/caregiver driven system designed to improve access to cost-efficient neurological care, which has potential for use in primary, secondary and tertiary levels of healthcare in rural and underserved regions of the world. We suggest involvement of healthcare stakeholders in teleneurology to address this global problem of limited access to neurological care. This model can facilitate the management of neurological diseases, impact on outcome, reduce frequency of consultations and hospitalisations, facilitate teaching of healthcare workers and promote research.
Are schools and alcohol a good mix? A qualitative study of school principals' experiences of adults' alcohol use in Australian secondary schools
Authors: Ward Bernadette M , Buykx Penny , Munro Geoffrey , Wiggers John
Published: August 2016

Objective

Parents, schools and the broader community influence children's socialisation to alcohol. In Australia, the UK and the USA, there have been media reports of adults consuming alcohol at family-focused school events such as fairs and graduations. The aim of this qualitative study was to describe school principals' experiences of adults' use of alcohol at school events, when children are present.

Design/setting/participants

A qualitative study was undertaken. Publicly available lists were used to invite 60 principals from government and Catholic secondary schools in Victoria, Australia. In-depth interviews were conducted and analysed thematically and reported using the Consolidated Criteria for Reporting Qualitative Research guidelines.

Results

14 principals (5 female, 9 male) participated. Most (10) of the participating principals reported adults' use of alcohol at events when students were present. Regarding these events, most principals reported concerns regarding potential harms and responsibility for decision-making about alcohol availability in schools. Some (4) principals believed alcohol should not be present at such events and this was their practice. Half of the participating schools had recently made changes to reduce the availability or management of alcohol at school functions.

Conclusions

The findings confirm the common use of alcohol by adults at school events, the challenges this poses for school principals and suggests consideration needs to be given to identifying strategies for supporting schools and school principals in decision-making regarding the conduct of such events.
Computing partial traces and reduced density matrices
Authors: Maziero Jonas
Published: August 2016

Taking partial traces (PTrs) for computing reduced density matrices, or related functions, is a ubiquitous procedure in the quantum mechanics of composite systems. In this paper, we present a thorough description of this function and analyze the number of elementary operations (ops) needed, under some possible alternative implementations, to compute it on a classical computer. As we note, it is worthwhile doing some analytical developments in order to avoid making null multiplications and sums, what can considerably reduce the ops. For instance, for a bipartite system [Formula: see text] with dimensions [Formula: see text] and [Formula: see text] and for [Formula: see text], while a direct use of PTr definition applied to [Formula: see text] requires [Formula: see text] ops, its optimized implementation entails [Formula: see text] ops. In the sequence, we regard the computation of PTrs for general multipartite systems and describe Fortran code provided to implement it numerically. We also consider the calculation of reduced density matrices via Bloch’s parametrization with generalized Gell Mann’s matrices.
A Tartar approach to periodic homogenization of linear hyperbolic stochastic partial differential equation
Authors: Mohammed Mogtaba , Sango Mamadou
Published: August 2016

This paper deals with the homogenization of a linear hyperbolic stochastic partial differential equation (SPDE) with highly oscillating periodic coefficients. We use Tartar’s method of oscillating test functions and deep probabilistic compactness results due to Prokhorov and Skorokhod. We show that the sequence of solutions of the original problem converges in suitable topologies to the solution of a homogenized linear hyperbolic SPDE with constant coefficients. We also prove the convergence of the associated energies.
Investigations on growth and property of mid-infrared lithium selenoindate single crystals
Authors: Dai Li , Tan Chao , Yan Zhehua , Xu Yuheng
Published: August 2016

Lithium selenoindate (LiInSe2) crystals with high optical quality are successfully grown by small-angle inclined horizontal temperature gradient condensation. In order to evaluate the various characteristics, the powder X-ray diffraction (XRD) spectrum, optical damage resistance ability and Vickers hardness in lithium selenoindate crystals were studied. The growth crystals have orthorhombic nature, a = 6.184 Å, b = 7.092 Å and c = 8.207 Å. The damage thresholds of LiInSe2 crystal with the front face and back face were 224 mW/cm2 and 165 mW/cm2. Also the Vickers hardness number of LiInSe2 crystal was found to be 342.4 kg/mm2.
Thermal Stress Analysis for Bi-modulus Foundation Beam under Nonlinear Temperature Difference
Authors: Gao Jinling , Yao Wenjuan
Published: August 2016

It is shown that many materials in practical engineering have different moduli in tension and compression. Especially, graphene, a magical material with the highest strength, is a kind of bi-modulus material. In this paper, mechanical response of bi-modulus Winkler foundation beam under nonlinear temperature distribution along height of the beam is studied. A new and convenient method, “intersecting line criterion”, is proposed to certify number of neutral axis in foundation beam and governing equation (set) of position of neutral axis is established, which is solved by iteration procedure of Newton’s method in Matlab. Semi-analytical solutions of stress, deflection and bending moment are subsequently obtained. Meanwhile, a finite element calculation procedure for calculating the temperature stress in bi-modulus structures is developed. Return the analytical solution to the result of the same modulus theory, and compare the analytical solution with finite element procedure solution and common finite element software Abaqus simulation solution. It shows that both of semi-analytical solution and calculation procedure proposed are reliable to use. Finally, discrepancies between nonlinear temperature effect and linear temperature and external force effect are discussed, which may supply some suggestions for calculation and optimization of such structures and members.
Loop-oriented array- and field-sensitive pointer analysis for automatic SIMD vectorization
Authors: Sui Yulei , Fan XIaokang , Zhou Hao , Xue Jingling
Published: August 2016

Compiler-based auto-vectorization is a promising solution to automatically generate code that makes efficient use of SIMD processors in high performance platforms and embedded systems. Two main auto-vectorization techniques, superword-level parallelism vectorization (SLP) and loop-level vectorization (LLV), re- quire precise dependence analysis on arrays and structs in order to vectorize isomorphic scalar instructions and/or reduce dynamic dependence checks incurred at runtime. The alias analyses used in modern vectorizing compilers are either intra-procedural (without tracking inter-procedural data-flows) or inter-procedural (by using field-insensitive models, which are too imprecise in handling arrays and structs). This paper pro- poses an inter-procedural Loop-oriented Pointer Analysis, called LPA, for analyzing arrays and structs to support aggressive SLP and LLV optimizations. Unlike field-insensitive solutions that pre- allocate objects for each memory allocation site, our approach uses a fine-grained memory model to generate location sets based on how structs and arrays are accessed. LPA can precisely analyze ar- rays and nested aggregate structures to enable SIMD optimizations for large programs. By separating the location set generation as an independent concern from the rest of the pointer analysis, LPA is designed to reuse easily existing points-to resolution algorithms. We evaluate LPA using SLP and LLV, the two classic vectorization techniques on a set of 20 CPU2000/2006 benchmarks. For SLP, LPA enables it to vectorize a total of 133 more basic blocks, with an average of 12.09 per benchmark, resulting in the best speedup of 2.95% for 173.applu. For LLV, LPA has reduced a total of 319 static bound checks, with an average of 22.79 per benchmark, resulting in the best speedup of 7.18% for 177.mesa.
Generalized cache tiling for dataflow programs
Authors: Domagała Łukasz , van Amstel Duco , Rastello Fabrice
Published: August 2016

The dataflow programming paradigm has facilitated the expression of a great number of algorithmic applications on embedded platforms in a wide variety of applicative domains. Whether it is a Domain Specific Language (DSL) or a more generalistic one, the dataflow paradigm allows to intuitively state the successive steps of an algorithm and link them through data communications. The optimization of cache-memory in this context has been a subject of interest since the early '90s as the reuse and communication of data between the agents of a dataflow program is a key factor in achieving a high-performance implementation within the reduced limits of embedded architectures. In order to improve data reuse among the dataflow agents we propose a modelisation of the communications and data usage within a dataflow program. Aside from providing an estimate of the amount of cache-misses that a given scheduling generates, this model allows us to specify the associated optimization problem in a manner that is identical to loop-nest tiling. Improving on the existing state-of-the-art methods we extend our tiling technique to include non-uniform dependencies on one of the dimensions of the iteration space. When applying the proposed technique to dataflow programs expressed within the StreamIt framework we are able to showcase significant reductions in the number of cache-misses for a majority of test-cases when compared to existing optimizations.
Into the depths of C: elaborating the de facto standards
Authors: Memarian Kayvan , Matthiesen Justus , Lingard James , Nienhuis Kyndylan , Chisnall David , Watson Robert N. M. , Sewell Peter
Published: August 2016

C remains central to our computing infrastructure. It is notionally defined by ISO standards, but in reality the properties of C assumed by systems code and those implemented by compilers have diverged, both from the ISO standards and from each other, and none of these are clearly understood. We make two contributions to help improve this error-prone situation. First, we describe an in-depth analysis of the design space for the semantics of pointers and memory in C as it is used in practice. We articulate many specific questions, build a suite of semantic test cases, gather experimental data from multiple implementations, and survey what C experts believe about the de facto standards. We identify questions where there is a consensus (either following ISO or differing) and where there are conflicts. We apply all this to an experimental C implemented above capability hardware. Second, we describe a formal model, Cerberus, for large parts of C. Cerberus is parameterised on its memory model; it is linkable either with a candidate de facto memory object model, under construction, or with an operational C11 concurrency model; it is defined by elaboration to a much simpler Core language for accessibility, and it is executable as a test oracle on small examples. This should provide a solid basis for discussion of what mainstream C is now: what programmers and analysis tools can assume and what compilers aim to implement. Ultimately we hope it will be a step towards clear, consistent, and accepted semantics for the various use-cases of C.
Living on the edge: rapid-toggling probes with cross-modification on x86
Authors: Chamith Buddhika , Svensson Bo Joel , Dalessandro Luke , Newton Ryan R.
Published: August 2016

Dynamic probe injection is now a widely used method to debug performance in production. Current techniques for dynamic probing of native code, however, rely on an expensive stop-the-world approach: binary changes are made within a safe state of the program---typically in which all the program threads are halted---to ensure that another thread executing the modified code region doesn't step into a partially-modified code. Stop-the-world patching is not scalable. In contrast, low overhead, scalable probes that can be rapidly toggled on and off in-place would open up new use cases for statistical profilers and language implementations, even traditional ahead-of-time, native-code compilers. In this paper we introduce safe cross-modification protocols that mutate x86 code between threads but do not require quiescing threads, resulting in radically lower overheads than existing solutions. A key problem is handling instructions that straddle cache lines. We empirically evaluate existing x86 architectures to derive a safe policy given current processor behavior, and we argue that future architectures should clarify the semantics of instruction fetching to make cheap cross-modification easier and future proof.
Input responsiveness: using canary inputs to dynamically steer approximation
Authors: Laurenzano Michael A. , Hill Parker , Samadi Mehrzad , Mahlke Scott , Mars Jason , Tang Lingjia
Published: August 2016

This paper introduces Input Responsive Approximation (IRA), an approach that uses a canary input — a small program input carefully constructed to capture the intrinsic properties of the original input — to automatically control how program approximation is applied on an input-by-input basis. Motivating this approach is the observation that many of the prior techniques focusing on choosing how to approximate arrive at conservative decisions by discounting substantial differences between inputs when applying approximation. The main challenges in overcoming this limitation lie in making the choice of how to approximate both effectively (e.g., the fastest approximation that meets a particular accuracy target) and rapidly for every input. With IRA, each time the approximate program is run, a canary input is constructed and used dynamically to quickly test a spectrum of approximation alternatives. Based on these runtime tests, the approximation that best fits the desired accuracy constraints is selected and applied to the full input to produce an approximate result. We use IRA to select and parameterize mixes of four approximation techniques from the literature for a range of 13 image processing, machine learning, and data mining applications. Our results demonstrate that IRA significantly outperforms prior approaches, delivering an average of 10.2× speedup over exact execution while minimizing accuracy losses in program outputs.
Higher-order and tuple-based massively-parallel prefix sums
Authors: Maleki Sepideh , Yang Annie , Burtscher Martin
Published: August 2016

Prefix sums are an important parallel primitive, especially in massively-parallel programs. This paper discusses two orthogonal generalizations thereof, which we call higher-order and tuple-based prefix sums. Moreover, it describes and evaluates SAM, a GPU-friendly algorithm for computing prefix sums and other scans that directly supports higher orders and tuple values. Its templated CUDA implementation unifies all of these computations in a single 100-statement kernel. SAM is communication-efficient in the sense that it minimizes main-memory accesses. When computing prefix sums of a million or more values, it outperforms Thrust and CUDPP on both a Titan X and a K40 GPU. On the Titan X, SAM reaches memory-copy speeds for large input sizes, which cannot be surpassed. SAM outperforms CUB, the currently fastest conventional prefix sum implementation, by up to a factor of 2.9 on eighth-order prefix sums and by up to a factor of 2.6 on eight-tuple prefix sums.
Remix: online detection and repair of cache contention for the JVM
Authors: Eizenberg Ariel , Hu Shiliang , Pokam Gilles , Devietti Joseph
Published: August 2016

As ever more computation shifts onto multicore architectures, it is increasingly critical to find effective ways of dealing with multithreaded performance bugs like true and false sharing. Previous approaches to fixing false sharing in unmanaged languages have employed highly-invasive runtime program modifications. We observe that managed language runtimes, with garbage collection and JIT code compilation, present unique opportunities to repair such bugs directly, mirroring the techniques used in manual repairs. We present Remix, a modified version of the Oracle HotSpot JVM which can detect cache contention bugs and repair false sharing at runtime. Remix's detection mechanism leverages recent performance counter improvements on Intel platforms, which allow for precise, unobtrusive monitoring of cache contention at the hardware level. Remix can detect and repair known false sharing issues in the LMAX Disruptor high-performance inter-thread messaging library and the Spring Reactor event-processing framework, automatically providing 1.5-2x speedups over unoptimized code and matching the performance of hand-optimization. Remix also finds a new false sharing bug in SPECjvm2008, and uncovers a true sharing bug in the HotSpot JVM that, when fixed, improves the performance of three NAS Parallel Benchmarks by 7-25x. Remix incurs no statistically-significant performance overhead on other benchmarks that do not exhibit cache contention, making Remix practical for always-on use.
Program synthesis from polymorphic refinement types
Authors: Polikarpova Nadia , Kuraj Ivan , Solar-Lezama Armando
Published: August 2016

We present a method for synthesizing recursive functions that provably satisfy a given specification in the form of a polymorphic refinement type. We observe that such specifications are particularly suitable for program synthesis for two reasons. First, they offer a unique combination of expressive power and decidability, which enables automatic verification—and hence synthesis—of nontrivial programs. Second, a type-based specification for a program can often be effectively decomposed into independent specifications for its components, causing the synthesizer to consider fewer component combinations and leading to a combinatorial reduction in the size of the search space. At the core of our synthesis procedure is a newalgorithm for refinement type checking, which supports specification decomposition. We have evaluated our prototype implementation on a large set of synthesis problems and found that it exceeds the state of the art in terms of both scalability and usability. The tool was able to synthesize more complex programs than those reported in prior work (several sorting algorithms and operations on balanced search trees), as well as most of the benchmarks tackled by existing synthesizers, often starting from a more concise and intuitive user input.
A distributed OpenCL framework using redundant computation and data replication
Authors: Kim Junghyun , Jo Gangwon , Jung Jaehoon , Kim Jungwon , Lee Jaejin
Published: August 2016

Applications written solely in OpenCL or CUDA cannot execute on a cluster as a whole. Most previous approaches that extend these programming models to clusters are based on a common idea: designating a centralized host node and coordinating the other nodes with the host for computation. However, the centralized host node is a serious performance bottleneck when the number of nodes is large. In this paper, we propose a scalable and distributed OpenCL framework called SnuCL-D for large-scale clusters. SnuCL-D's remote device virtualization provides an OpenCL application with an illusion that all compute devices in a cluster are confined in a single node. To reduce the amount of control-message and data communication between nodes, SnuCL-D replicates the OpenCL host program execution and data in each node. We also propose a new OpenCL host API function and a queueing optimization technique that significantly reduce the overhead incurred by the previous centralized approaches. To show the effectiveness of SnuCL-D, we evaluate SnuCL-D with a microbenchmark and eleven benchmark applications on a large-scale CPU cluster and a medium-scale GPU cluster.
Coverage-directed differential testing of JVM implementations
Authors: Chen Yuting , Su Ting , Sun Chengnian , Su Zhendong , Zhao Jianjun
Published: August 2016

Java virtual machine (JVM) is a core technology, whose reliability is critical. Testing JVM implementations requires painstaking effort in designing test classfiles (*.class) along with their test oracles. An alternative is to employ binary fuzzing to differentially test JVMs by blindly mutating seeding classfiles and then executing the resulting mutants on different JVM binaries for revealing inconsistent behaviors. However, this blind approach is not cost effective in practice because most of the mutants are invalid and redundant. This paper tackles this challenge by introducing classfuzz, a coverage-directed fuzzing approach that focuses on representative classfiles for differential testing of JVMs’ startup processes. Our core insight is to (1) mutate seeding classfiles using a set of predefined mutation operators (mutators) and employ Markov Chain Monte Carlo (MCMC) sampling to guide mutator selection, and (2) execute the mutants on a reference JVM implementation and use coverage uniqueness as a discipline for accepting representative ones. The accepted classfiles are used as inputs to differentially test different JVM implementations and find defects. We have implemented classfuzz and conducted an extensive evaluation of it against existing fuzz testing algorithms. Our evaluation results show that classfuzz can enhance the ratio of discrepancy-triggering classfiles from 1.7% to 11.9%. We have also reported 62 JVM discrepancies, along with the test classfiles, to JVM developers. Many of our reported issues have already been confirmed as JVM defects, and some even match recent clarifications and changes to the Java SE 8 edition of the JVM specification.
MapReduce program synthesis
Authors: Smith Calvin , Albarghouthi Aws
Published: August 2016

By abstracting away the complexity of distributed systems, large-scale data processing platforms—MapReduce, Hadoop, Spark, Dryad, etc.—have provided developers with simple means for harnessing the power of the cloud. In this paper, we ask whether we can automatically synthesize MapReduce-style distributed programs from input–output examples. Our ultimate goal is to enable end users to specify large-scale data analyses through the simple interface of examples. We thus present a new algorithm and tool for synthesizing programs composed of efficient data-parallel operations that can execute on cloud computing infrastructure. We evaluate our tool on a range of real-world big-data analysis tasks and general computations. Our results demonstrate the efficiency of our approach and the small number of examples it requires to synthesize correct, scalable programs.
Lightweight computation tree tracing for lazy functional languages
Authors: Faddegon Maarten , Chitil Olaf
Published: August 2016

A computation tree of a program execution describes computations of functions and their dependencies. A computation tree describes how a program works and is at the heart of algorithmic debugging. To generate a computation tree, existing algorithmic debuggers either use a complex implementation or yield a less informative approximation. We present a method for lazy functional languages that requires only a simple tracing library to generate a detailed computation tree. With our algorithmic debugger a programmer can debug any Haskell program by only importing our library and annotating suspected functions.
FlexVec: auto-vectorization for irregular loops
Authors: Baghsorkhi Sara S. , Vasudevan Nalini , Wu Youfeng
Published: August 2016

Traditional vectorization techniques build a dependence graph with distance and direction information to determine whether a loop is vectorizable. Since vectorization reorders the execution of instructions across iterations, in general instructions involved in a strongly connected component (SCC) are deemed not vectorizable unless the SCC can be eliminated using techniques such as scalar expansion or privatization. Therefore, traditional vectorization techniques are limited in their ability to efficiently handle loops with dynamic cross-iteration dependencies or complex control flow interweaved within the dependence cycles. When potential dependencies do not occur very often, the end-result is under utilization of the SIMD hardware. In this paper, we propose FlexVec architecture that combines new vector instructions with novel code generation techniques to dynamically adjusts vector length for loop statements affected by cross-iteration dependencies that happen at runtime. We have designed and implemented FlexVec's new ISA as extensions to the recently released AVX-512 ISA. We have evaluated the performance improvements enabled by FlexVec vectorization for 11 C/C++ SPEC 2006 benchmarks and 7 real applications with AVX-512 vectorization as baseline. We show that FlexVec vectorization technique produces a Geomean speedup of 9% for SPEC 2006 and a Geomean speedup of 11% for 7 real applications.
A design and verification methodology for secure isolated regions
Authors: Sinha Rohit , Costa Manuel , Lal Akash , Lopes Nuno P. , Rajamani Sriram , Seshia Sanjit A. , Vaswani Kapil
Published: August 2016

Hardware support for isolated execution (such as Intel SGX) enables development of applications that keep their code and data confidential even while running in a hostile or compromised host. However, automatically verifying that such applications satisfy confidentiality remains challenging. We present a methodology for designing such applications in a way that enables certifying their confidentiality. Our methodology consists of forcing the application to communicate with the external world through a narrow interface, compiling it with runtime checks that aid verification, and linking it with a small runtime that implements the narrow interface. The runtime includes services such as secure communication channels and memory management. We formalize this restriction on the application as Information Release Confinement (IRC), and we show that it allows us to decompose the task of proving confidentiality into (a) one-time, human-assisted functional verification of the runtime to ensure that it does not leak secrets, (b) automatic verification of the application's machine code to ensure that it satisfies IRC and does not directly read or corrupt the runtime's internal state. We present /CONFIDENTIAL: a verifier for IRC that is modular, automatic, and keeps our compiler out of the trusted computing base. Our evaluation suggests that the methodology scales to real-world applications.
Types from data: making structured data first-class citizens in F#
Authors: Petricek Tomas , Guerra Gustavo , Syme Don
Published: August 2016

Most modern applications interact with external services and access data in structured formats such as XML, JSON and CSV. Static type systems do not understand such formats, often making data access more cumbersome. Should we give up and leave the messy world of external data to dynamic typing and runtime checks? Of course, not! We present F# Data, a library that integrates external structured data into F#. As most real-world data does not come with an explicit schema, we develop a shape inference algorithm that infers a shape from representative sample documents. We then integrate the inferred shape into the F# type system using type providers. We formalize the process and prove a relative type soundness theorem. Our library significantly reduces the amount of data access code and it provides additional safety guarantees when contrasted with the widely used weakly typed techniques.
Just-in-time static type checking for dynamic languages
Authors: Ren Brianna M. , Foster Jeffrey S.
Published: August 2016

Dynamic languages such as Ruby, Python, and JavaScript have many compelling benefits, but the lack of static types means subtle errors can remain latent in code for a long time. While many researchers have developed various systems to bring some of the benefits of static types to dynamic languages, prior approaches have trouble dealing with metaprogramming, which generates code as the program executes. In this paper, we propose Hummingbird, a new system that uses a novel technique, just-in-time static type checking, to type check Ruby code even in the presence of metaprogramming. In Hummingbird, method type signatures are gathered dynamically at run-time, as those methods are created. When a method is called, Hummingbird statically type checks the method body against current type signatures. Thus, Hummingbird provides thorough static checks on a per-method basis, while also allowing arbitrarily complex metaprogramming. For performance, Hummingbird memoizes the static type checking pass, invalidating cached checks only if necessary. We formalize Hummingbird using a core, Ruby-like language and prove it sound. To evaluate Hummingbird, we applied it to six apps, including three that use Ruby on Rails, a powerful framework that relies heavily on metaprogramming. We found that all apps typecheck successfully using Hummingbird, and that Hummingbird's performance overhead is reasonable. We applied Hummingbird to earlier versions of one Rails app and found several type errors that had been introduced and then fixed. Lastly, we demonstrate using Hummingbird in Rails development mode to typecheck an app as live updates are applied to it.
On the complexity and performance of parsing with derivatives
Authors: Adams Michael D. , Hollenbeck Celeste , Might Matthew
Published: August 2016

Current algorithms for context-free parsing inflict a trade-off between ease of understanding, ease of implementation, theoretical complexity, and practical performance. No algorithm achieves all of these properties simultaneously. Might et al. introduced parsing with derivatives, which handles arbitrary context-free grammars while being both easy to understand and simple to implement. Despite much initial enthusiasm and a multitude of independent implementations, its worst-case complexity has never been proven to be better than exponential. In fact, high-level arguments claiming it is fundamentally exponential have been advanced and even accepted as part of the folklore. Performance ended up being sluggish in practice, and this sluggishness was taken as informal evidence of exponentiality. In this paper, we reexamine the performance of parsing with derivatives. We have discovered that it is not exponential but, in fact, cubic. Moreover, simple (though perhaps not obvious) modifications to the implementation by Might et al. lead to an implementation that is not only easy to understand but also highly performant in practice.
A Life in Evolutionary Anthropology
Authors: Jolly Clifford J.
Published: August 2016

I am delighted to contribute this career piece, although there are many other aged physical anthropologists who are more distinguished! I have tried to avoid duplicating another retrospective rumination ( Jolly 2009 ) while describing personal academic experiences over the past 60 years or so. This is not a CV; I have concentrated on my main research themes, omitting some academic byways, teaching, textbooks, and edited volumes. The account is punctuated with opinionated comments, mostly on physical anthropology, but sometimes, rashly, on other anthropological specialties. It begins early, because my professional interests have deep roots, and finishes with a speculation about the future of physical anthropology, and anthropology in general, in the coming genomic age.
Decolonizing Archaeological Thought in South America
Authors: Haber Alejandro
Published: August 2016

Decolonizing archaeological thought in South America happens through three paths: (a) a critical approach to the ways archaeology contributes to coloniality, (b) a criticism of the mechanisms by which coloniality informs archaeology, and (c) a varied exposure of archaeology to subaltern (that is, non-hegemonic and counter-hegemonic) knowledge. These three paths are sometimes taken together and sometimes alone, and the diverse pieces of thought reviewed herein provide examples of each. South America as a locus for the enunciation of archaeological theory opens the epistemic range of the discipline to include indigenous and African-descendant communities' theories of history and materiality. Ongoing research prefigures future trends in decolonizing archaeological thought around issues of land, memory, and knowledge.
Red Clump Stars
Authors: Girardi Léo
Published: August 2016

Low-mass stars in their core-helium-burning stage define the sharpest feature present in the color-magnitude diagrams of nearby galaxy systems: the red clump (RC). This feature has given rise to a series of methods aimed at measuring the distributions of stellar distances and extinctions, especially in the Magellanic Clouds and Milky Way Bulge. Because the RC is easily recognizable within the data of large spectroscopic and asteroseismic surveys, it is a useful probe of stellar densities, kinematics, and chemical abundances across the Milky Way disk; it can be applied up to larger distances than that allowed by dwarfs; and it has better accuracy than is possible with other kinds of giants. Here, we discuss the reasons for the RC narrowness in several sets of observational data, its fine structure, and the presence of systematic changes in the RC properties as regards age, metallicity, and the observed passband. These factors set the limits on the validity and accuracy of several RC methods defined in the literature.
Metabolism and the Control of Cell Fate Decisions and Stem Cell Renewal
Authors: Ito Kyoko , Ito Keisuke
Published: August 2016

Although the stem cells of various tissues remain in the quiescent state to maintain their undifferentiated state, they also undergo cell divisions as required, and if necessary, even a single stem cell is able to provide for lifelong tissue homeostasis. Stem cell populations are precisely controlled by the balance between their symmetric and asymmetric divisions, with their division patterns determined by whether the daughter cells involved retain their self-renewal capacities. Recent studies have reported that metabolic pathways and the distribution of mitochondria are regulators of the division balance of stem cells and that metabolic defects can shift division balance toward symmetric commitment, which leads to stem cell exhaustion. It has also been observed that in asymmetric division, old mitochondria, which are central metabolic organelles, are segregated to the daughter cell fated to cell differentiation, whereas in symmetric division, young and old mitochondria are equally distributed between both daughter cells. Thus, metabolism and mitochondrial biology play important roles in stem cell fate decisions. As these decisions directly affect tissue homeostasis, understanding their regulatory mechanisms in the context of cellular metabolism is critical.
The Phyllosphere: Microbial Jungle at the Plant–Climate Interface
Authors: Vacher Corinne , Hampe Arndt , Porté Annabel J. , Sauer Ursula , Compant Stéphane , Morris Cindy E.
Published: August 2016

The surface of plant leaves, or the phyllosphere, harbors hyperdiverse microbial communities. These communities mediate foliar functional traits, influence plant fitness, and contribute to several ecosystem functions, including nutrient and water cycling. In this review, we briefly recall the history of phyllosphere research and present the features of this microbial habitat. Adopting a recent framework for evolutionary community ecology, we then review evidence for each of the four major processes shaping phyllosphere microbial communities: dispersal, evolutionary diversification, selection, and drift. We show how these processes are influenced by the host plant, the surrounding atmospheric conditions, and microbial interactions. Rapidly growing evidence indicates that phyllosphere microbial communities are altered by global change, with potential cascading effects on plant performance, plant evolution, and ecosystem functioning. We propose future avenues for phyllosphere research aimed at improving plant adaptation and ecosystem resilience to environmental changes.
From Topographic Internal Gravity Waves to Turbulence
Authors: Sarkar S. , Scotti A.
Published: August 2016

Internal gravity waves are a key process linking the large-scale mechanical forcing of the oceans to small-scale turbulence and mixing. In this review, we focus on internal waves generated by barotropic tidal flow over topography. We review progress made in the past decade toward understanding the different processes that can lead to turbulence during the generation, propagation, and reflection of internal waves and how these processes affect mixing. We consider different modeling strategies and new tools that have been developed. Simulation results, the wealth of observational material collected during large-scale experiments, and new laboratory data reveal how the cascade of energy from tidal flow to turbulence occurs through a host of nonlinear processes, including intensified boundary flows, wave breaking, wave-wave interactions, and the instability of high-mode internal wave beams. The roles of various nondimensional parameters involving the ocean state, roughness geometry, and tidal forcing are described.
Anisotropic Particles in Turbulence
Authors: Voth Greg A. , Soldati Alfredo
Published: August 2016

Anisotropic particles are common in many industrial and natural turbulent flows. When these particles are small and neutrally buoyant, they follow Lagrangian trajectories while exhibiting rich orientational dynamics from the coupling of their rotation to the velocity gradients of the turbulence field. This system has proven to be a fascinating application of the fundamental properties of velocity gradients in turbulence. When particles are not neutrally buoyant, they experience preferential concentration and very different preferential alignment than neutrally buoyant tracer particles. A vast proportion of the parameter range of anisotropic particles in turbulence is still unexplored, with most existing research focusing on the simple foundational cases of axisymmetric ellipsoids at low concentrations in homogeneous isotropic turbulence and in turbulent channel flow. Numerical simulations and experiments have recently developed a fairly comprehensive picture of alignment and rotation in these cases, and they provide an essential foundation for addressing more complex problems of practical importance. Macroscopic effects of nonspherical particle dynamics include preferential concentration in coherent structures and drag reduction by fiber suspensions. We review the models used to describe nonspherical particle motion, along with numerical and experimental methods for measuring particle dynamics.