bluuebunny/crossref_metadata_2025_split huggingface dataset:
Halide
Authors: Ragan-Kelley Jonathan , Barnes Connelly , Adams Andrew , Paris Sylvain , Durand Frédo , Amarasinghe Saman 
Published: July 2013

Image processing pipelines combine the challenges of stencil computations and stream programs. They are composed of large graphs of different stencil stages, as well as complex reductions, and stages with global or data-dependent access patterns. Because of their complex structure, the performance difference between a naive implementation of a pipeline and an optimized one is often an order of magnitude. Efficient implementations require optimization of both parallelism and locality, but due to the nature of stencils, there is a fundamental tension between parallelism, locality, and introducing redundant recomputation of shared values.
We present a systematic model of the tradeoff space fundamental to stencil pipelines, a schedule representation which describes concrete points in this space for each stage in an image processing pipeline, and an optimizing compiler for the Halide image processing language that synthesizes high performance implementations from a Halide algorithm and a schedule. Combining this compiler with stochastic search over the space of schedules enables terse, composable programs to achieve state-of-the-art performance on a wide range of real image processing pipelines, and across different hardware architectures, including multicores with SIMD, and heterogeneous CPU+GPU execution. From simple Halide programs written in a few hours, we demonstrate performance up to 5x faster than hand-tuned C, intrinsics, and CUDA implementations optimized by experts over weeks or months, for image processing applications beyond the reach of past automatic compilers.
Machine-verified network controllers
Authors: Guha Arjun , Reitblatt Mark , Foster Nate 
Published: July 2013

In many areas of computing, techniques ranging from testing to formal modeling to full-blown verification have been successfully used to help programmers build reliable systems. But although networks are critical infrastructure, they have largely resisted analysis using formal techniques. Software-defined networking (SDN) is a new network architecture that has the potential to provide a foundation for network reasoning, by standardizing the interfaces used to express network programs and giving them a precise semantics.
This paper describes the design and implementation of the first machine-verified SDN controller. Starting from the foundations, we develop a detailed operational model for OpenFlow (the most popular SDN platform) and formalize it in the Coq proof assistant. We then use this model to develop a verified compiler and run-time system for a high-level network programming language. We identify bugs in existing languages and tools built without formal foundations, and prove that these bugs are absent from our system. Finally, we describe our prototype implementation and our experiences using it to build practical applications.
When polyhedral transformations meet SIMD code generation
Authors: Kong Martin , Veras Richard , Stock Kevin , Franchetti Franz , Pouchet Louis-Noël , Sadayappan P. 
Published: July 2013

Data locality and parallelism are critical optimization objectives for performance on modern multi-core machines. Both coarse-grain parallelism (e.g., multi-core) and fine-grain parallelism (e.g., vector SIMD) must be effectively exploited, but despite decades of progress at both ends, current compiler optimization schemes that attempt to address data locality and both kinds of parallelism often fail at one of the three objectives.
We address this problem by proposing a 3-step framework, which aims for integrated data locality, multi-core parallelism and SIMD execution of programs. We define the concept of vectorizable codelets, with properties tailored to achieve effective SIMD code generation for the codelets. We leverage the power of a modern high-level transformation framework to restructure a program to expose good ISA-independent vectorizable codelets, exploiting multi-dimensional data reuse. Then, we generate ISA-specific customized code for the codelets, using a collection of lower-level SIMD-focused optimizations.
We demonstrate our approach on a collection of numerical kernels that we automatically tile, parallelize and vectorize, exhibiting significant performance improvements over existing compilers.
Automated feedback generation for introductory programming assignments
Authors: Singh Rishabh , Gulwani Sumit , Solar-Lezama Armando 
Published: July 2013

We present a new method for automatically providing feedback for introductory programming problems. In order to use this method, we need a reference implementation of the assignment, and an error model consisting of potential corrections to errors that students might make. Using this information, the system automatically derives minimal corrections to student's incorrect solutions, providing them with a measure of exactly how incorrect a given solution was, as well as feedback about what they did wrong.
We introduce a simple language for describing error models in terms of correction rules, and formally define a rule-directed translation strategy that reduces the problem of finding minimal corrections in an incorrect program to the problem of synthesizing a correct program from a sketch. We have evaluated our system on thousands of real student attempts obtained from the Introduction to Programming course at MIT (6.00) and MITx (6.00x). Our results show that relatively simple error models can correct on average 64% of all incorrect submissions in our benchmark set.
Verifying higher-order programs with the dijkstra monad
Authors: Swamy Nikhil , Weinberger Joel , Schlesinger Cole , Chen Juan , Livshits Benjamin 
Published: July 2013

Modern programming languages, ranging from Haskell and ML, to JavaScript, C# and Java, all make extensive use of higher-order state. This paper advocates a new verification methodology for higher-order stateful programs, based on a new monad of predicate transformers called the Dijkstra monad.
Using the Dijkstra monad has a number of benefits. First, the monad naturally yields a weakest pre-condition calculus. Second, the computed specifications are structurally simpler in several ways, e.g., single-state post-conditions are sufficient (rather than the more complex two-state post-conditions). Finally, the monad can easily be varied to handle features like exceptions and heap invariants, while retaining the same type inference algorithm.
We implement the Dijkstra monad and its type inference algorithm for the F* programming language. Our most extensive case study evaluates the Dijkstra monad and its F* implementation by using it to verify JavaScript programs.
Specifically, we describe a tool chain that translates programs in a subset of JavaScript decorated with assertions and loop invariants to F*. Once in F*, our type inference algorithm computes verification conditions and automatically discharges their proofs using an SMT solver. We use our tools to prove that a core model of the JavaScript runtime in F* respects various invariants and that a suite of JavaScript source programs are free of runtime errors.
Monadic abstract interpreters
Authors: Sergey Ilya , Devriese Dominique , Might Matthew , Midtgaard Jan , Darais David , Clarke Dave , Piessens Frank 
Published: July 2013

Recent developments in the systematic construction of abstract interpreters hinted at the possibility of a broad unification of concepts in static analysis. We deliver that unification by showing context-sensitivity, polyvariance, flow-sensitivity, reachability-pruning, heap-cloning and cardinality-bounding to be independent of any particular semantics. Monads become the unifying agent between these concepts and between semantics. For instance, by plugging the same "context-insensitivity monad" into a monadically-parameterized semantics for Java or for the lambda calculus, it yields the expected context-insensitive analysis.
To achieve this unification, we develop a systematic method for transforming a concrete semantics into a monadically-parameterized abstract machine. Changing the monad changes the behavior of the machine. By changing the monad, we recover a spectrum of machines---from the original concrete semantics to a monovariant, flow- and context-insensitive static analysis with a singly-threaded heap and weak updates.
The monadic parameterization also suggests an abstraction over the ubiquitous monotone fixed-point computation found in static analysis. This abstraction makes it straightforward to instrument an analysis with high-level strategies for improving precision and performance, such as abstract garbage collection and widening.
While the paper itself runs the development for continuation-passing style, our generic implementation replays it for direct-style lambda-calculus and Featherweight Java to support generality.
Tropical–Extratropical Interactions of Intraseasonal Oscillations
Authors: Frederiksen Jorgen S. , Lin Hai 
Published: July 2013

Abstract
Tropical–extratropical interactions of intraseasonal oscillations (ISOs), based on 30 years (1979–2009) of northern winter observations and theory, are compared. The phase relationships between the tropical signal of the leading theoretical ISO for a January 1979 basic state and the development of Pacific–North America (PNA)-like and North Atlantic Oscillation (NAO) teleconnection patterns are found to compare closely with those for the observed Madden–Julian oscillation (MJO). For both observations and theory positive NAO occurs 5–15 days after MJO convection [negative outgoing longwave radiation (OLR) and positive precipitation] and negative upper-troposphere velocity potential ISO anomalies are focused over the central Indian Ocean. The fluxes of wave activity, based on the upper-troposphere streamfunction of the leading theoretical mode, indicate strong tropical–extratropical interactions and have very similar structures to those obtained by H. Lin et al. based on observations of extratropical anomalies associated with MJO convection.
The second leading theoretical ISO mode for January 1979 has quite similar properties to the leading ISO mode but has a longer period of 44.5 days compared with 34.4 days and a more distinct quadrupole streamfunction structure straddling the equator. Theoretical ISO modes for other observed basic states, including January 1988 and the 30-yr average of January 1980–2009, again link the tropical ISO signal with Northern Hemisphere teleconnection patterns, particularly the NAO. The growth rates of ISO modes increase with stronger baroclinicity of the basic-state zonal winds in the main jet streams and, importantly, with increased tropical–extratropical interactions because of stronger meridional winds.
Ocean Waves and Teleconnection Patterns in the Northern Hemisphere
Authors: Shimura Tomoya , Mori Nobuhito , Mase Hajime 
Published: July 2013

Abstract
Understanding long-term, ocean wave climate variability is important to assess climate change impacts on coastal and ocean physics and engineering. Teleconnection patterns can represent wave climate variability in the context of climate change. The objective of this study is to identify how large-scale spatial distributions of wave heights vary on a monthly basis and how they are influenced by various teleconnection patterns using reanalysis datasets. The wave height climate responses to teleconnection patterns in the eastern part of the North Pacific and North Atlantic are more sensible than in the corresponding western parts. The dominant spatial patterns of monthly averaged wave height variability in winter were obtained by empirical orthogonal function analysis. The three dominant patterns in the North Pacific and North Atlantic are similar. It is remarkable that one of the three dominant patterns, a band-shaped pattern, exhibits a strong relation to the teleconnection pattern in each ocean. The band-shaped pattern for the North Pacific was investigated in detail and found to be related to the west Pacific (WP) pattern. Where and how each teleconnection pattern influences wave climate becomes apparent especially during winter.
Inequality estimates for the boundedness of multilinear singular and fractional integral operators
Authors: Zhou Xiaosha , Huang Chuangxia , Hu Haijun , Liu Li 
Published: July 2013

Abstract
In this paper, the inequality of boundedness for the multilinear fractional singular integral operators associated to the weighted Lipschitz functions is estimated. The operators include the Calderón-Zygmund singular integral operator and the fractional integral operator.

MSC:42B20, 42B25.
Mitofusion-2-mediated alleviation of insulin resistance in rats through reduction in lipid intermediate accumulation in skeletal muscle
Authors: Zhang Xuemei , Wang Chao , Song Guangyao , Gan Kexin , Kong Dexian , Nie Qian , Ren Luping 
Published: July 2013

Abstract

Background
Increased lipid accumulation and mitochondrial dysfunction within skeletal muscle have been shown to be strongly associated with insulin resistance. However, the role of mitofusion-2 (MFN2), a key factor in mitochondrial function and energy metabolism, in skeletal muscle lipid intermediate accumulation remains to be elucidated.

Results
A high-fat diet resulted in insulin resistance as well as accumulation of cytosolic lipid intermediates and down-regulation of MFN2 and CPT1 in skeletal muscle in rats, while MFN2 overexpression improved insulin sensitivity and reduced lipid intermediates in muscle, possibly by upregulation of CPT1 expression.

Conclusions
MFN2 overexpression can rescue insulin resistance, possibly by upregulating CPT1 expression leading to reduction in the accumulation of lipid intermediates in skeletal muscle. These observations contribute to the investigations of new diabetes therapies.
Chronic glucolipotoxic conditions in pancreatic islets impair insulin secretion due to dysregulated calcium dynamics, glucose responsiveness and mitochondrial activity
Authors: Somesh Baggavalli P , Verma Mahesh Kumar , Sadasivuni Manoj Kumar , Mammen-Oommen Anup , Biswas Sanghamitra , Shilpa Pavagada C , Reddy Ashok Kumar , Yateesh Aggunda N , Pallavi Puttrevana M , Nethra Siddaraju , Smitha Rachapalli , Neelima Korrapati , Narayanan Usha , Jagannath Madanahalli R 
Published: July 2013

Abstract

Background
In the progression towards diabetes, glucolipotoxicity is one of the main causes of pancreatic beta cell pathology. The aim of this study was to examine the in vitro effects of chronic glucolipotoxic conditions on cellular responses in pancreatic islets, including glucose and fat metabolism, Calcium mobilization, insulin secretion and insulin content.

Results
Exposure of islets to chronic glucolipotoxic conditions decreased glucose stimulated insulin secretion in vitro. Reduced protein levels of Glut2/slc2a2, and decreased glucokinase and pyruvate carboxylase mRNA levels indicated a significant lowering in glucose sensing. Concomitantly, both fatty acid uptake and triglyceride accumulation increased significantly while fatty acid oxidation decreased. This general suppression in glucose metabolism correlated well with a decrease in mitochondrial number and activity, reduction in cellular ATP content and dampening of the TCA cycle. Further, we also observed a decrease in IP3 levels and lower Calcium mobilization in response to glucose. Importantly, chronic glucolipotoxic conditions in vitro decreased insulin gene expression, insulin content, insulin granule docking (to the plasma membrane) and insulin secretion.

Conclusions
Our results present an integrated view of the effects of chronic glucolipotoxic conditions on known and novel signaling events, in vitro, that results in reduced glucose responsiveness and insulin secretion.
Overexpression of peptide deformylase in breast, colon, and lung cancers
Authors: Randhawa Harsharan , Chikara Shireen , Gehring Drew , Yildirim Tuba , Menon Jyotsana , Reindl Katie M 
Published: July 2013

Abstract

Background
Human mitochondrial peptide deformylase (PDF) has been proposed as a novel cancer therapeutic target. However, very little is known about its expression and regulation in human tissues. The purpose of this study was to characterize the expression pattern of PDF in cancerous tissues and to identify mechanisms that regulate its expression.

Methods
The mRNA expression levels of PDF and methionine aminopeptidase 1D (MAP1D), an enzyme involved in a related pathway with PDF, were determined using tissue panels containing cDNA from patients with various types of cancer (breast, colon, kidney, liver, lung, ovarian, prostate, or thyroid) and human cell lines. Protein levels of PDF were also determined in 2 colon cancer patients via western blotting. Colon cancer cells were treated with inhibitors of ERK, Akt, and mTOR signaling pathways and the resulting effects on PDF and MAP1D mRNA levels were determined by qPCR for colon and lung cancer cell lines. Finally, the effects of a PDF inhibitor, actinonin, on the proliferation of breast, colon, and prostate cell lines were determined using the CyQUANT assay.

Results
PDF and MAP1D mRNA levels were elevated in cancer cell lines compared to non-cancer lines. PDF mRNA levels were significantly increased in breast, colon, and lung cancer samples while MAP1D mRNA levels were increased in just colon cancers. The expression of PDF and MAP1D varied with stage in these cancers. Further, PDF protein expression was elevated in colon cancer tissue samples. Inhibition of the MEK/ERK, but not PI3K or mTOR, pathway reduced the expression of PDF and MAP1D in both colon and lung cancer cell lines. Further, inhibition of PDF with actinonin resulted in greater reduction of breast, colon, and prostate cancer cell proliferation than non-cancer cell lines.

Conclusions
This is the first report showing that PDF is over-expressed in breast, colon, and lung cancers, and the first evidence that the MEK/ERK pathway plays a role in regulating the expression of PDF and MAP1D. The over-expression of PDF in several cancers and the inhibition of cancer cell growth by a PDF inhibitor suggest this enzyme may act as an oncogene to promote cancer cell proliferation.
Prothrombin complex concentrate in the reduction of blood loss during orthotopic liver transplantation: PROTON-trial
Authors: Arshad Freeha , Ickx Brigitte , van Beem Rachel T , Polak Wojciech , Grüne Frank , Nevens Frederik , Ilmakunnas Minna , Koivusalo Anna-Maria , Isoniemi Helena , Strengers Paul FW , Groen Henk , Hendriks Herman GD , Lisman Ton , Pirenne Jacques , Porte Robert J 
Published: July 2013

Abstract

Background
In patients with cirrhosis, the synthesis of coagulation factors can fall short, reflected by a prolonged prothrombin time. Although anticoagulants factors are decreased as well, blood loss during orthotopic liver transplantation can still be excessive. Blood loss during orthotopic liver transplantation is currently managed by transfusion of red blood cell concentrates, platelet concentrates, fresh frozen plasma, and fibrinogen concentrate. Transfusion of these products may paradoxically result in an increased bleeding tendency due to aggravated portal hypertension. The hemostatic effect of these products may therefore be overshadowed by bleeding complications due to volume overload.
In contrast to these transfusion products, prothrombin complex concentrate is a low-volume highly purified concentrate, containing the four vitamin K dependent coagulation factors. Previous studies have suggested that administration of prothrombin complex concentrate is an effective method to normalize a prolonged prothrombin time in patients with liver cirrhosis. We aim to investigate whether the pre-operative administration of prothrombin complex concentrate in patients undergoing liver transplantation for end-stage liver cirrhosis, is a safe and effective method to reduce perioperative blood loss and transfusion requirements.

Methods/Design
This is a double blind, multicenter, placebo-controlled randomized trial.
Cirrhotic patients with a prolonged INR (≥1.5) undergoing liver transplantation will be randomized between placebo or prothrombin complex concentrate administration prior to surgery. Demographic, surgical and transfusion data will be recorded. The primary outcome of this study is RBC transfusion requirements.

Discussion
Patients with advanced cirrhosis have reduced plasma levels of both pro- and anticoagulant coagulation proteins. Prothrombin complex concentrate is a low-volume plasma product that contains both procoagulant and anticoagulant proteins and transfusion will not affect the volume status prior to the surgical procedure. We hypothesize that administration of prothrombin complex concentrate will result in a reduction of perioperative blood loss and transfusion requirements. Theoretically, the administration of prothrombin complex concentrate may be associated with a higher risk of thromboembolic complications. Therefore, thromboembolic complications are an important secondary endpoint and the occurrence of this type of complication will be closely monitored during the study.

Trial registration
The trial is registered at http://www.trialregister.nl with number NTR3174. This registry is accepted by the ICMJE.
Antimicrobial activity and rutin identification of honey produced by the stingless bee Melipona compressipes manaosensis and commercial honey
Authors: Pimentel Renah Boanerges de Queiroz , da Costa Cristovão Alves , Albuquerque Patrícia Melchionna , Junior Sergio Duvoisin 
Published: July 2013

Abstract

Background
Honey has been identified as a potential alternative to the widespread use of antibiotics, which are of significant concern considering the emergence of resistant bacteria. In this context, this study aimed to evaluate the antimicrobial activity of honey samples produced by a stingless bee species and by Apis sp. against pathogenic bacteria, as well as to identify the presence of phenolic compounds.

Methods
Honey samples from the stingless bee M. compressipes manaosensis were collected twice, during the dry and rainy seasons. Three commercial honey samples from Apis sp. were also included in this study. Two different assays were performed to evaluate the antibacterial potential of the honey samples: agar-well diffusion and broth macrodilution. Liquid-liquid extraction was used to assess phenolic compounds from honey. HPLC analysis was performed in order to identify rutin and apigenin on honey samples. Chromatograms were recorded at 340 and 290 nm.

Results
Two honey samples were identified as having the highest antimicrobial activity using the agar diffusion method. Honey produced by Melipona compressipes manaosensis inhibited the growth of Staphylococcus aureus, Escherichia coli (0157: H7), Proteus vulgaris, Shigella sonnei and Klebsiella sp. A sample of honey produced by Apis sp. also inhibited the growth of Salmonella paratyphi. The macrodilution technique presented greater sensitivity for the antibacterial testing, since all honey samples showed activity. Flavonoid rutin was identified in the honey sample produced by the stingless bee.

Conclusions
Honey samples tested in this work showed antibacterial activity against Gram-positive and Gram-negative bacteria. The results reported herein highlight the potential of using honey to control bacterial growth.