bluuebunny/crossref_metadata_2025 huggingface dataset:
Comorbidity and outcomes in traumatic brain injury: protocol for a systematic review on functional status and risk of death
Authors: Mollayeva Tatyana , Xiong Chen , Hanafy Sara , Chan Vincy , Hu Zheng Jing , Sutton Mitchell , Escobar Michael , Colantonio Angela
Published: October 2017

Introduction

Reports on the association between comorbidity and functional status and risk of death in patients with traumatic brain injury (TBI) have been inconsistent; it is currently unknown which additional clinical entities (comorbidities) have an adverse influence on the evolution of outcomes across the lifespan of men and women with TBI. The current protocol outlines a strategy for a systematic review of the current evidence examining the impact of comorbidity on functional status and early-term and late-term mortality, taking into account known risk factors of these adverse outcomes (ie, demographic (age and sex) and injury-related characteristics).

Methods and analysis

A comprehensive search strategy for TBI prognosis, functional (cognitive and physical) status and mortality studies has been developed in collaboration with a medical information specialist of the large rehabilitation teaching hospital. All peer-reviewed English language studies with longitudinal design in adults with TBI of any severity, published from May 1997 to April 2017, found through Medline, Central, Embase, Scopus, PsycINFO and bibliographies of identified articles, will be considered eligible. Study quality will be assessed using published guidelines.

Ethics and dissemination

The authors will publish findings from this review in a peer-reviewed scientific journal(s) and present the results at national and international conferences. This work aims to understand how comorbidity may contribute to adverse outcomes in TBI, to inform risk stratification of patients and guide the management of brain injury acutely and at the chronic stages postinjury on a population level.

PROSPERO registration number

CRD42017070033.
Phosphate replacement in the critically ill: potential implications for military patients
Authors: Coulden A E , Rickard L J , Crooks N , Arora N
Published: October 2017

Background

Severe hypophosphataemia in the intensive care unit (ICU) setting has been widely associated with adverse clinical outcomes across multiple organ systems, as well as increased mortality. However, the clinical significance of mild or moderate hypophosphataemia remains uncertain. This can lead to heterogeneous phosphate replacement protocols across different institutions. The aim of this study was to assess the significance of mild and moderate hypophosphataemia on clinical outcomes across several organ systems.

Method

All patients over a 3-week period in our ICU were retrospectively analysed with admission serum phosphate compared with subsequent clinical outcomes after admission. Low serum phosphate (0.3–1.0 mmol/L), according to local protocol, was compared with normal serum phosphate (>1.0 mmol/L).

Results

Of the 72 patients admitted to intensive therapy unit during this period, 14/72 (19%) had phosphate levels deemed low (<1.0 mmol/L) and received phosphate supplementation. No significant difference was found between groups in terms of cardiac arrhythmias (p=0.55), capillary blood glucose (p=0.08) and serum lactate (p=0.32). Low phosphate (0.3–1.0 mmol/L) was not associated with increased likelihood of requiring ventilation. Platelet count was significantly lower in the low phosphate group (p=0.008).

Conclusion

In our study, mild and moderate hypophosphataemia was not associated with adverse clinical outcome across most organ systems analysed. Given the current evidence and results of this study, we would suggest that there is a trend towards over-replacement of phosphate, representing a potential clinical safety issue as well as clear financial implications.
Sacral dural arteriovenous fistulas: a diagnostic and therapeutic challenge – single-centre experience of 13 cases and review of the literature
Authors: Gioppo Andrea , Faragò Giuseppe , Giannitto Caterina , Caputi Luigi , Saladino Andrea , Acerbi Francesco , Ciceri Elisa
Published: October 2017

Background

Sacral dural arteriovenous fistulas (DAVFs) are rare vascular abnormalities of the spine characterised by slowly progressive symptoms that can mimic different myelopathy disorders.

Object

To report our single Institution experience with sacral DAVFs.

Methods

We retrospectively reviewed the clinical records of patients admitted from 1 January 2006 to 31 December 2016 with a diagnosis of sacral DAVFs, treated by endovascular embolisation or surgical clipping. Clinical presentation, imaging characteristics, treatment results and follow-up were analysed.

Results

We identify 13 patients with sacral DAVFs supplied by lateral sacral arteries. Clinical presentation was characterised by different degrees of motor weakness and sphincter disturbances. In all patients, spinal MRI showed spinal cord hyperintensities with enhancement and prominent perimedullary vessels. Selective internal iliac angiography was mandatory to identify the exact location of the fistula. A complete embolisation was achieved in eight patients performing a single endovascular embolisation and in three patients performing a single surgical disconnection: two patients required combined procedures. Follow-up imaging showed a complete resolution of the spinal cord hyperintensities in 81% of patients and a reduction of the intramedullary enhancement in 91%. Gait improvement was observed in 73% of patients, while remaining stable in 27%. Sphincter disturbances improved in 36% of patients and remained stable in 64%.

Conclusion

Awareness of sacral location of DAVFs is critical because standard spinal angiography will not identify sacral supplies, unless internal iliac arteries are properly examined. In our experience, the endovascular treatment show results comparable to surgery when the fistula point is correctly disconnected.
Routinely collected health data to study inherited heart disease: a systematic review (2000–2016)
Authors: Blanch Bianca , Sweeting Joanna , Semsarian Christopher , Ingles Jodie
Published: October 2017

Objective

Our understanding of inherited heart disease is predominantly based on retrospective specialised clinic cohorts, which have inherent selection bias. Population-based routinely collected data can provide insight into unbiased, large-scale patterns of treatment and care but may be limited by the granularity of clinical information available. We sought to synthesise the global literature to determine whether we can identify patients with inherited heart diseases using routinely collected health data.

Methods

Medline, Embase, CINAHL, PreMEDLINE and Google Scholar citation databases were searched for relevant articles published between 1 January 2000 and 31 October 2016.

Results

A total of 5641 titles/abstracts were screened and 46 full-text articles were retrieved. Twelve peer-reviewed, English-language manuscripts met our inclusion criteria. Studies predominantly focused on Marfan syndrome (41%) or hypertrophic cardiomyopathy (29%). All studies used International Classification of Disease diagnosis codes to define inherited heart disease populations; three studies also used procedure codes. Nine of the 17 definitions for inherited heart disease were repeated across studies.

Conclusions

Inherited heart disease populations can be identified using routinely collected health data, though challenges relate to existing diagnosis codes. This is an underutilised resource with the potential to inform patterns of care, patient outcomes and overall disease burden.
Quantitation of nonspecific protein adsorption at solid–liquid interfaces for single-cell proteomics
Authors: Lee Man Chung Gilbert , Sun Bingyun
Published: October 2017

Protein nonspecific adsorption that occurred at the solid–liquid interface has been subjected to intense physical and chemical characterizations due to its crucial role in a wide range of applications, including food and pharmaceutical industries, medical implants, biosensing, and so on. Protein-adsorption caused sample loss has largely hindered the studies of single-cell proteomics; the prevention of such loss requires the understanding of protein–surface adsorption at the proteome level, in which the competitive adsorption of thousands and millions of proteins with vast dynamic range occurs. To this end, we feel the necessity to review current methodologies on their potentials to characterize — more specifically to quantify — the proteome-wide adsorption. We hope this effort can help advancing single-cell proteomics and trace proteomics.
Three problems with the conventional delta-model for biomass sampling data, and a computationally efficient alternative
Authors: Thorson James T.
Published: October 2017

Ecologists often analyse biomass sampling data that result in many zeros, where remaining samples can take any positive real number. Samples are often analysed using a “delta-model” that combines two separate generalized linear models, GLMs (for encounter probability and positive catch rates), or less often using a compound Poisson-gamma (CPG) distribution that is computationally expensive. I discuss three theoretical problems with the conventional delta-model: difficulty interpreting covariates for encounter probability, the assumed independence of the two GLMs, and the biologically implausible form when eliminating covariates for either GLM. I then derive an alternative “Poisson-link model” that solves these problems. To illustrate, I use biomass samples for 113 fish populations to show that the Poisson-link model improves fit (and decreases residual spatial variation) for >80% of populations relative to the conventional delta-model. A simulation experiment illustrates that CPG and Poisson-link models estimate covariate effects that are similar and biologically interpretable. I therefore recommend the Poisson-link model as a useful alternative to the conventional delta-model with similar properties to the CPG distribution.
NONLINEAR ANALYSIS OF CORONARY ARTERY DISEASE, MYOCARDIAL INFARCTION, AND NORMAL ECG SIGNALS
Authors: HAGIWARA YUKI , FAUST OLIVER
Published: October 2017

In this study, we analyze nonlinear feature extraction methods in terms of their ability to support the diagnosis of coronary artery disease (CAD) and myocardial infarction (MI). The nonlinear features were extracted from electrocardiogram (ECG) signals that were measured from CAD patients, MI patients as well as normal controls.

We tested 34 recurrence quantification analysis (RQA) features, 14 bispectrum, and 136 cumulant features. The features were extracted from 10,546 normal, 41,545 CAD, and 40,182 MI heart beats. The feature quality was assessed with Student’s [Formula: see text]-test and the [Formula: see text]-value was used for feature ranking.

We found that nonlinear features can effectively represent the physiological realities of the human heart.
ADAPTIVE UNSCENTED KALMAN FILTER FOR ONLINE SOFT TISSUES CHARACTERIZATION
Authors: SHIN JAEHYUN , ZHONG YONGMIN , SMITH JULIAN , GU CHENGFAN
Published: October 2017

Online soft tissue characterization is important for robotic-assisted minimally invasive surgery to achieve precise and stable robotic control with haptic feedback. This paper presents a new adaptive unscented Kalman filter based on the nonlinear Hunt–Crossley model for online soft tissue characterization without requiring the characteristics of system noise. This filter incorporates the concept of Sage windowing in the traditional unscented Kalman filter to adaptively estimate system noise covariance using predicted residuals within a time window. In order to account for the inherent relationship between the current and previous states of soft tissue deformation involved in robotic-assisted surgery and improve the estimation performance, a recursive estimation of system noise covariance is further constructed by introducing a fading scaling factor to control the contributions between noise covariance estimations at current and previous time points. The proposed adaptive unscented Kalman filter overcomes the limitation of the traditional unscented Kalman filter in requiring the characteristics of system noise. Simulations and comparisons show the efficacy of the suggested nonlinear adaptive unscented Kalman filter for online soft tissue characterization.
INDIVIDUALIZED SURGICAL GUIDANCE FOR MANDIBULAR RECONSTRUCTION USING 3D FEA/PRINTING TECHNOLOGIES
Authors: CHEN YADONG , GONG TIANXING , SUN BOXUAN , SHANG DEHAO
Published: October 2017

The state-of-the-art surgery makes it possible to transfer tissue from donor site to recipient sites for reconstruction. In particular, free fibula becomes one of the common methods to repair mandibular (i.e., lower jawbone) defects. To guide one individual surgery, the 3D printing and finite element analysis (FEA) technologies have been employed in this study. The personalized model of titanium plate with screws was designed on the basis of computed tomography data with the help of the reverse engineering technology and 3D computational model via the PRO/E software. In order to refine the model, FEA results were used to guide the operation plan. Finally, the 3D-printed scaffold was used in the surgery. In conclusion, 3D printing technology and FEA for mandibular reconstruction surgery guidance can achieve good matches among fibula, human mandible and titanium plates, restore mandible functions, reduce the operation time and improve the success rate of surgery. Furthermore, this technology gives more freedom for physicians to discuss surgical plans with patients.
ALGORITHM FOR THE DETECTION OF CONGESTIVE HEART FAILURE INDEX
Authors: KANG YI DA , ZHUO DEMING , FOO RUI EN ANNE , LIM CHOO MIN , FAUST OLIVER , HAGIWARA YUKI
Published: October 2017

This study documents our efforts to provide computer support for the diagnosis of congestive heart failure (CHF). That computer support takes the form of an index value. A high index value indicates a low probability of CHF, and an index value below a threshold of 25.6 suggests a high probability of CHF. To create that index, we have designed a sophisticated algorithm chain which takes electrocardiogram signals as input. The signals are pre-processed before they are sent to a range of nonlinear feature extraction algorithms. The top 10 feature extraction methods were used to create the CHF index. By using objective feature extraction algorithms, we avoid the problem of inter- and intra-observer variability. We observed that the nonlinear feature extraction methods reflect the nature of the human heart very well. That observation is based on the fact that the nonlinear features achieved low [Formula: see text]-values and high feature ranking criterion scores.
Skip blocks: reusing execution history to accelerate web scripts
Authors: Chasins Sarah , Bodik Rastislav
Published: October 2017

With more and more web scripting languages on offer, programmers have access to increasing language support for web scraping tasks. However, in our experiences collaborating with data scientists, we learned that two issues still plague long-running scraping scripts: i) When a network or website goes down mid-scrape, recovery sometimes requires restarting from the beginning, which users find frustratingly slow. ii) Websites do not offer atomic snapshots of their databases; they update their content so frequently that output data is cluttered with slight variations of the same information —
e.g.
, a tweet from profile 1 that is retweeted on profile 2 and scraped from both profiles, once with 52 responses then later with 53 responses.

We introduce the
skip block
, a language construct that addresses both of these disparate problems. Programmers write lightweight annotations to indicate when the current object can be considered equivalent to a previously scraped object and direct the program to skip over the scraping actions in the block. The construct is hierarchical, so programs can skip over long or short script segments, allowing adaptive reuse of prior work. After network and server failures, skip blocks accelerate failure recovery by 7.9x on average. Even scripts that do not encounter failures benefit; because sites display redundant objects, skipping over them accelerates scraping by up to 2.1x. For longitudinal scraping tasks that aim to fetch only new objects, the second run exhibits an average speedup of 5.2x. Our small user study reveals that programmers can quickly produce skip block annotations.
Virtual machine warmup blows hot and cold
Authors: Barrett Edd , Bolz-Tereick Carl Friedrich , Killick Rebecca , Mount Sarah , Tratt Laurence
Published: October 2017

Virtual Machines (VMs) with Just-In-Time (JIT) compilers are traditionally thought to execute programs in two phases: the initial warmup phase determines which parts of a program would most benefit from dynamic compilation, before JIT compiling those parts into machine code; subsequently the program is said to be at a steady state of peak performance. Measurement methodologies almost always discard data collected during the warmup phase such that reported measurements focus entirely on peak performance. We introduce a fully automated statistical approach, based on changepoint analysis, which allows us to determine if a program has reached a steady state and, if so, whether that represents peak performance or not. Using this, we show that even when run in the most controlled of circumstances, small, deterministic, widely studied microbenchmarks often fail to reach a steady state of peak performance on a variety of common VMs. Repeating our experiment on 3 different machines, we found that at most 43.5% of  pairs consistently reach a steady state of peak performance.
Sound gradual typing: only mostly dead
Authors: Bauman Spenser , Bolz-Tereick Carl Friedrich , Siek Jeremy , Tobin-Hochstadt Sam
Published: October 2017

While gradual typing has proven itself attractive to programmers, many systems have avoided sound gradual typing due to the run time overhead of enforcement. In the context of sound gradual typing, both anecdotal and systematic evidence has suggested that run time costs are quite high, and often unacceptable, casting doubt on the viability of soundness as an approach.

We show that these overheads are not fundamental, and that with appropriate improvements,
just-in-time compilers can greatly reduce the overhead of sound gradual typing
. Our study takes benchmarks published in a recent paper on gradual typing performance in Typed Racket (Takikawa et al., POPL 2016) and evaluates them using a experimental tracing JIT compiler for Racket, called Pycket. On typical benchmarks, Pycket is able to eliminate more than 90% of the gradual typing overhead. While our current results are not the final word in optimizing gradual typing, we show that the situation is not dire, and where more work is needed.

Pycket's performance comes from several sources, which we detail and measure individually. First, we apply a sophisticated tracing JIT compiler and optimizer, automatically generated in Pycket using the RPython framework originally created for PyPy. Second, we focus our optimization efforts on the challenges posed by run time checks, implemented in Racket by
chaperones and impersonators
. We introduce representation improvements, including a novel use of
hidden classes
to optimize these data structures.
Sound gradual typing is nominally alive and well
Authors: Muehlboeck Fabian , Tate Ross
Published: October 2017

Recent research has identified significant performance hurdles that sound gradual typing needs to overcome. These performance hurdles stem from the fact that the run-time checks gradual type systems insert into code can cause significant overhead. We propose that designing a type system for a gradually typed language hand in hand with its implementation from scratch is a possible way around these and several other hurdles on the way to efficient sound gradual typing. Such a design process also highlights the type-system restrictions required for efficient composition with gradual typing. We formalize the core of a nominal object-oriented language that fulfills a variety of desirable properties for gradually typed languages, and present evidence that an implementation of this language suffers minimal overhead even in adversarial benchmarks identified in earlier work.
SQLizer: query synthesis from natural language
Authors: Yaghmazadeh Navid , Wang Yuepeng , Dillig Isil , Dillig Thomas
Published: October 2017

This paper presents a new technique for automatically synthesizing SQL queries from natural language (NL). At the core of our technique is a new NL-based program synthesis methodology that combines semantic parsing techniques from the NLP community with type-directed program synthesis and automated program repair. Starting with a program sketch obtained using standard parsing techniques, our approach involves an iterative refinement loop that alternates between probabilistic type inhabitation and automated sketch repair. We use the proposed idea to build an end-to-end system called SQLIZER that can synthesize SQL queries from natural language. Our method is fully automated, works for any database without requiring additional customization, and does not require users to know the underlying database schema. We evaluate our approach on over 450 natural language queries concerning three different databases, namely MAS, IMDB, and YELP. Our experiments show that the desired query is ranked within the top 5 candidates in close to 90% of the cases and that SQLIZER outperforms NALIR, a state-of-the-art tool that won a best paper award at VLDB'14.
Efficient logging in non-volatile memory by exploiting coherency protocols
Authors: Cohen Nachshon , Friedman Michal , Larus James R.
Published: October 2017

Non-volatile memory technologies such as PCM, ReRAM and STT-RAM allow data to be saved to persistent storage significantly faster than hard drives or SSDs. Many of the use cases for non-volatile memory requires persistent logging since it enables a set of operations to execute in an atomic manner. However, a logging protocol must handle reordering, which causes a write to reach the non-volatile memory before a previous write operation.

In this paper, we show that reordering results from two parts of the system: the out-of-order execution in the CPU and the cache coherence protocol. By carefully considering the properties of these reorderings, we present a logging protocol that requires only one round trip to non-volatile memory while avoiding expensive computations, thus increasing performance. We also show how the logging protocol can be extended to building a durable set (hash map) that also requires a single round trip to non-volatile memory for inserting, updating, or deleting operations.
Monadic composition for deterministic, parallel batch processing
Authors: Scott Ryan G. , Navarro Leija Omar S. , Devietti Joseph , Newton Ryan R.
Published: October 2017

Achieving determinism on real software systems remains difficult. Even a batch-processing job, whose task is to map input bits to output bits, risks nondeterminism from thread scheduling, system calls, CPU instructions, and leakage of environmental information such as date or CPU model. In this work, we present a system for achieving low-overhead deterministic execution of batch-processing programs that read and write the file system—turning them into pure functions on files.

We allow multi-process executions where a permissions system prevents races on the file system. Process separation enables different processes to enforce permissions and enforce determinism using distinct mechanisms. Our prototype, DetFlow, allows a statically-typed coordinator process to use shared-memory parallelism, as well as invoking process-trees of sandboxed legacy binaries. DetFlow currently implements the coordinator as a Haskell program with a restricted I/O type for its main function: a new monad we call DetIO. Legacy binaries launched by the coordinator run concurrently, but internally each process schedules threads sequentially, allowing dynamic determinism-enforcement with predictably low overhead.

We evaluate DetFlow by applying it to bioinformatics data pipelines and software build systems. DetFlow enables determinizing these data-processing workflows by porting a small amount of code to become a statically-typed coordinator. This hybrid approach of static and dynamic determinism enforcement permits freedom where possible but restrictions where necessary.
TreeFuser: a framework for analyzing and fusing general recursive tree traversals
Authors: Sakka Laith , Sundararajah Kirshanthan , Kulkarni Milind
Published: October 2017

Series of traversals of tree structures arise in numerous contexts: abstract syntax tree traversals in compiler passes, rendering traversals of the DOM in web browsers, kd-tree traversals in computational simulation codes. In each of these settings, a tree is traversed multiple times to compute various values and modify various portions of the tree. While it is relatively easy to write these traversals as separate small updates to the tree, for efficiency reasons, traversals are often manually fused to reduce the number of times that each portion of the tree is traversed: by performing multiple operations on the tree simultaneously, each node of the tree can be visited fewer times, increasing opportunities for optimization and decreasing cache pressure and other overheads. This fusion process is often done manually, requiring careful understanding of how each of traversals of the tree interact. This paper presents an automatic approach to traversal fusion: tree traversals can be written independently, and then our framework analyzes the dependences between the traversals to determine how they can be fused to reduce the number of visits to each node in the tree. A critical aspect of our framework is that it exploits two opportunities to increase the amount of fusion: i) it automatically integrates code motion, and ii) it supports partial fusion, where portions of one traversal can be fused with another, allowing for a reduction in node visits without requiring that two traversals be fully fused. We implement our framework in Clang, and show across several case studies that we can successfully fuse complex tree traversals, reducing the overall number of traversals and substantially improving locality and performance.
The tensor algebra compiler
Authors: Kjolstad Fredrik , Kamil Shoaib , Chou Stephen , Lugato David , Amarasinghe Saman
Published: October 2017

Tensor algebra is a powerful tool with applications in machine learning, data analytics, engineering and the physical sciences. Tensors are often sparse and compound operations must frequently be computed in a single kernel for performance and to save memory. Programmers are left to write kernels for every operation of interest, with different mixes of dense and sparse tensors in different formats. The combinations are infinite, which makes it impossible to manually implement and optimize them all. This paper introduces the first compiler technique to automatically generate kernels for any compound tensor algebra operation on dense and sparse tensors. The technique is implemented in a C++ library called taco. Its performance is competitive with best-in-class hand-optimized kernels in popular libraries, while supporting far more tensor operations.
Exploiting implicit beliefs to resolve sparse usage problem in usage-based specification mining
Authors: Khairunnesa Samantha Syeda , Nguyen Hoan Anh , Nguyen Tien N. , Rajan Hridesh
Published: October 2017

Frameworks and libraries provide application programming interfaces (APIs) that serve as building blocks in modern software development. As APIs present the opportunity of increased productivity, it also calls for correct use to avoid buggy code. The usage-based specification mining technique has shown great promise in solving this problem through a data-driven approach. These techniques leverage the use of the API in large corpora to understand the recurring usages of the APIs and infer behavioral specifications (preconditions and postconditions) from such usages. A challenge for such technique is thus inference in the presence of insufficient usages, in terms of both frequency and richness. We refer to this as a "sparse usage problem." This paper presents the first technique to solve the sparse usage problem in usage-based precondition mining. Our key insight is to leverage implicit beliefs to overcome sparse usage. An implicit belief (IB) is the knowledge implicitly derived from the fact about the code. An IB about a program is known implicitly to a programmer via the language's constructs and semantics, and thus not explicitly written or specified in the code. The technical underpinnings of our new precondition mining approach include a technique to analyze the data and control flow in the program leading to API calls to infer preconditions that are implicitly present in the code corpus, a catalog of 35 code elements in total that can be used to derive implicit beliefs from a program, and empirical evaluation of all of these ideas. We have analyzed over 350 millions lines of code and 7 libraries that suffer from the sparse usage problem. Our approach realizes 6 implicit beliefs and we have observed that adding single-level context sensitivity can further improve the result of usage based precondition mining. The result shows that we achieve overall 60% in precision and 69% in recall and the accuracy is relatively improved by 32% in precision and 78% in recall compared to base usage-based mining approach for these libraries.
A model for reasoning about JavaScript promises
Authors: Madsen Magnus , Lhoták Ondřej , Tip Frank
Published: October 2017

In JavaScript programs, asynchrony arises in situations such as web-based user-interfaces, communicating with servers through HTTP requests, and non-blocking I/O. Event-based programming is the most popular approach for managing asynchrony, but suffers from problems such as lost events and event races, and results in code that is hard to understand and debug. Recently, ECMAScript 6 has added support for promises, an alternative mechanism for managing asynchrony that enables programmers to chain asynchronous computations while supporting proper error handling. However, promises are complex and error-prone in their own right, so programmers would benefit from techniques that can reason about the correctness of promise-based code.

Since the ECMAScript 6 specification is informal and intended for implementers of JavaScript engines, it does not provide a suitable basis for formal reasoning. This paper presents λ

p

, a core calculus that captures the essence of ECMAScript 6 promises. Based on λ

p

, we introduce the promise graph, a program representation that can assist programmers with debugging of promise-based code. We then report on a case study in which we investigate how the promise graph can be helpful for debugging errors related to promises in code fragments posted to the StackOverflow website.
A verified messaging system
Authors: Mansky William , Appel Andrew W. , Nogin Aleksey
Published: October 2017

We present a concurrent-read exclusive-write buffer system with strong correctness and security properties. Our motivating application for this system is the distribution of sensor values in a multicomponent vehicle-control system, where some components are unverified and possibly malicious, and other components are vehicle-control-critical and must be verified. Valid participants are guaranteed correct communication (i.e., the writer is always able to write to an unused buffer, and readers always read the most recently published value), while invalid readers or writers cannot compromise the correctness or liveness of valid participants. There is only one writer, all operations are wait-free, and there is no extra process or thread mediating communication. We prove the correctness of the system with valid participants by formally verifying a C implementation of the system in Coq, using the Verified Software Toolchain extended with an atomic exchange operation. The result is the first C-level mechanized verification of a nonblocking communication protocol.
Who guards the guards? formal validation of the Arm v8-m architecture specification
Authors: Reid Alastair
Published: October 2017

Software and hardware are increasingly being formally verified against specifications, but how can we verify the specifications themselves? This paper explores what it means to formally verify a specification. We solve three challenges: (1) How to create a secondary, higher-level specification that can be effectively reviewed by processor designers who are not experts in formal verification; (2) How to avoid common-mode failures between the specifications; and (3) How to automatically verify the two specifications against each other.

One of the most important specifications for software verification is the processor specification since it defines the behaviour of machine code and of hardware protection features used by operating systems. We demonstrate our approach on ARM's v8-M Processor Specification, which is intended to improve the security of Internet of Things devices. Thus, we focus on establishing the security guarantees the architecture is intended to provide. Despite the fact that the ARM v8-M specification had previously been extensively tested, we found twelve bugs (including two security bugs) that have all been fixed by ARM.
Type test scripts for TypeScript testing
Authors: Kristensen Erik Krogh , Møller Anders
Published: October 2017

TypeScript applications often use untyped JavaScript libraries. To support static type checking of such applications, the typed APIs of the libraries are expressed as separate declaration files. This raises the challenge of checking that the declaration files are correct with respect to the library implementations. Previous work has shown that mismatches are frequent and cause TypeScript's type checker to misguide the programmers by rejecting correct applications and accepting incorrect ones.

This paper shows how feedback-directed random testing, which is an automated testing technique that has mostly been used for testing Java libraries, can be adapted to effectively detect such type mismatches. Given a JavaScript library with a TypeScript declaration file, our tool TSTEST generates a "type test script", which is an application that interacts with the library and tests that it behaves according to the type declarations. Compared to alternative solutions that involve static analysis, this approach finds significantly more mismatches in a large collection of real-world JavaScript libraries with TypeScript declaration files, and with fewer false positives. It also has the advantage that reported mismatches are easily reproducible with concrete executions, which aids diagnosis and debugging.
Transforming programs and tests in tandem for fault localization
Authors: Li Xia , Zhang Lingming
Published: October 2017

Localizing failure-inducing code is essential for software debugging. Manual fault localization can be quite tedious, error-prone, and time-consuming. Therefore, a huge body of research e orts have been dedicated to automated fault localization. Spectrum-based fault localization, the most intensively studied fault localization approach based on test execution information, may have limited effectiveness, since a code element executed by a failed tests may not necessarily have impact on the test outcome and cause the test failure. To bridge the gap, mutation-based fault localization has been proposed to transform the programs under test to check the impact of each code element for better fault localization. However, there are limited studies on the effectiveness of mutation-based fault localization on sufficient number of real bugs. In this paper, we perform an extensive study to compare mutation-based fault localization techniques with various state-of-the-art spectrum-based fault localization techniques on 357 real bugs from the Defects4J benchmark suite. The study results firstly demonstrate the effectiveness of mutation-based fault localization, as well as revealing a number of guidelines for further improving mutation-based fault localization. Based on the learnt guidelines, we further transform test outputs/messages and test code to obtain various mutation information. Then, we propose TraPT, an automated Learning-to-Rank technique to fully explore the obtained mutation information for effective fault localization. The experimental results show that TraPT localizes 65.12% and 94.52% more bugs within Top-1 than state-of-the-art mutation and spectrum based techniques when using the default setting of LIBSVM.
How type errors were fixed and what students did?
Authors: Wu Baijun , Chen Sheng
Published: October 2017

Providing better supports for debugging type errors has been an active research area in the last three decades. Numerous approaches from different perspectives have been developed. Most approaches work well under certain conditions only, for example, when type errors are caused by single leaves and when type annotations are correct. However, the research community is still unaware of which conditions hold in practice and what the real debugging situations look like. We address this problem with a study of 3 program data sets, which were written in different years, using different compilers, and were of diverse sizes. They include more than 55,000 programs, among which more than 2,700 are ill typed. We investigated all the ill-typed programs, and our results indicate that current error debugging support is far from sufficient in practice since only about 35% of all type errors were caused by single leaves. In addition, type annotations cannot always be trusted in error debuggers since about 30% of the time type errors were caused by wrong type annotations. Our study also provides many insights about the debugging behaviors of students in functional programming, which could be exploited for developing more effective error debuggers.
Verifying distributed programs via canonical sequentialization
Authors: Bakst Alexander , Gleissenthall Klaus v. , Kıcı Rami Gökhan , Jhala Ranjit
Published: October 2017

We introduce canonical sequentialization, a new approach to verifying unbounded, asynchronous, message-passing programs at compile-time. Our approach builds upon the following observation: due the combinatorial explosion in complexity, programmers do not reason about their systems by case-splitting over all the possible execution orders. Instead, correct programs tend to be well-structured so that the programmer can reason about a small number of representative executions, which we call the program’s canonical sequentialization. We have implemented our approach in a tool called Brisk that synthesizes canonical sequentializations for programs written in Haskell, and evaluated it on a wide variety of distributed systems including benchmarks from the literature and implementations of MapReduce, two-phase commit, and a version of the Disco distributed file-system. We show that unlike model checking, which gets prohibitively slow with just 10 processes Brisk verifies the unbounded versions of the benchmarks in tens of milliseconds, yielding the first concurrency verification tool that is fast enough to be integrated into a design-implement-check cycle.
From the National Surveillance State to the Cybersurveillance State
Authors: Hu Margaret
Published: October 2017

This article anchors the phenomenon of bureaucratized cybersurveillance around the concept of the National Surveillance State, a theory attributed to Professor Jack Balkin of Yale Law School and Professor Sanford Levinson of the University of Texas School of Law. Pursuant to the theory of the National Surveillance State, because of the routinized and administrative nature of government-led surveillance, normalized mass surveillance is viewed as justified under crime and counterterrorism policy rationales. This article contends that the Cybersurveillance State is the successor to the National Surveillance State. The Cybersurveillance State harnesses technologies that fuse biometric and biographic data for risk assessment, embedding bureaucratized biometric cybersurveillance within the Administrative State. In ways that are largely invisible, the Cybersurveillance State constructs digital avatars for administrative governance objectives and targets digital data deemed suspicious. Consequently, constitutional violations stemming from cybersurveillance systems will be increasingly difficult to identify and challenge.
Muscle α-adrenergic responsiveness during exercise and ATP-induced vasodilation in chronic obstructive pulmonary disease patients
Authors: Iepsen U. W. , Munch G. W. , Ryrsø C. K. , Secher N. H. , Lange P. , Thaning P. , Pedersen B. K. , Mortensen S. P.
Published: October 2017

Sympathetic vasoconstriction is blunted in exercising muscle (functional sympatholysis) but becomes attenuated with age. We tested the hypothesis that functional sympatholysis is further impaired in chronic obstructive pulmonary disease (COPD) patients. We determined leg blood flow and calculated leg vascular conductance (LVC) during 1) femoral-arterial Tyramine infusion (evokes endogenous norepinephrine release, 1 µmol·min−1·kg leg mass−1), 2) one-legged knee extensor exercise with and without Tyramine infusion [10 W and 20% of maximal workload (WLmax)], 3) ATP (0.05 µmol·min−1·kg leg mass−1) and Tyramine infusion, and 4) incremental ATP infusions (0.05, 0.3, and 3.0 µmol·min−1·kg leg mass−1). We included 10 patients with moderate to severe COPD and 8 age-matched healthy control subjects. Overall, leg blood flow and LVC were lower in COPD patients during exercise ( P < 0.05). Tyramine reduced LVC in both groups at 10-W exercise (COPD: −3 ± 1 ml·min−1·mmHg−1and controls: −3 ± 1 ml·min−1·mmHg−1, P < 0.05) and 20% WLmax(COPD: −4 ± 1 ml·min−1·mmHg−1and controls: −3 ± 1 ml·min−1·mmHg−1, P < 0.05) with no difference between groups. Incremental ATP infusions induced dose-dependent vasodilation with no difference between groups, and, in addition, the vasoconstrictor response to Tyramine infused together with ATP was not different between groups (COPD: −0.03 ± 0.01 l·min−1·kg leg mass−1vs. controls: −0.04 ± 0.01 l·min−1·kg leg mass−1, P > 0.05). Compared with age-matched healthy control subjects, the vasodilatory response to ATP is intact in COPD patients and their ability to blunt sympathetic vasoconstriction (functional sympatholysis) as evaluated by intra-arterial Tyramine during exercise or ATP infusion is maintained.

NEW & NOTEWORTHY The ability to blunt sympathetic vasoconstriction in exercising muscle and ATP-induced dilation in chronic obstructive pulmonary disease patients remains unexplored. Chronic obstructive pulmonary disease patients demonstrated similar sympathetic vasoconstriction in response to intra-arterial Tyramine during exercise and ATP-induced vasodilation compared with age-matched healthy control subjects.
The ALPPS Approach for Colorectal Liver Metastases: Impact of KRAS Mutation Status in Survival
Authors: Serenari Matteo , Alvarez Fernando Andres , Ardiles Victoria , de Santibañes Martin , Pekolj Juan , de Santibañes Eduardo
Published: October 2017

Background/Aims: Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations influence survival after hepatectomy for colorectal liver metastases (CRLM). However, their prognostic significance has never been evaluated in patients who undergo Associating Liver Partition and Portal vein occlusion for Staged hepatectomy (ALPPS). Methods: Between June 2011 and March 2016, 26 patients underwent ALPPS for CRLM. Complications were classified according to the Clavien-Dindo classification. Bi- and multivariate cox analyses were performed to evaluate variables potentially associated with survival. Results: Overall, morbidity grade ≥3a and 90-day mortality were 38.5 and 0%, respectively. The median follow-up from the time of discharge was 21.5 months (interquartile range 9.6-35.6). One- and 3-year overall survival (OS) was 83.4 and 48.9%, respectively. Patients with mutated (MT) KRAS had a median OS of 15.3 vs. 38.3 months for those with wild-type (WT) KRAS (p < 0.0001). Median disease-free survival was 7.9, 5.6 vs. 12.3 months for MT and WT KRAS, respectively (p = 0.023). KRAS mutation was found to be an independent risk factor for OS (hazard ratio 7.15, 95% CI 1.50-34.11; p = 0.014). Conclusion: KRAS mutation is an independent predictor of poor survival after ALPPS. This finding will help to optimize patient selection, both avoiding futile surgical indication and maximizing the benefit for patients with extensive disease who are otherwise subjected to high-risk aggressive surgery.
The Landscape of Circulating Tumor Cell Research in the Context of Epithelial-Mesenchymal Transition
Authors: Markiewicz Aleksandra , Żaczek Anna J.
Published: October 2017

The metastatic spread of cancer accounts for the vast majority of cancer-related deaths. It is mediated by tumor cells circulating in blood (called circulating tumor cells, CTCs), which escaped from their established niches. CTCs give a unique opportunity to look into the metastatic cascade and to study the molecular processes supporting the spread of tumor cells throughout the body. As current therapies are not sufficiently effective in treating metastatic disease, it is important to determine cellular and molecular features of cancer cells that “seed” new tumors in distant organs at early stages. In this review we focus on the role of the epithelial-mesenchymal transition program in providing a survival advantage to metastasizing tumor cells, especially CTCs, and put it in the context of clinical findings.
Survey Results of the Expert Meeting on Laparoscopic Living Donor Hepatectomy and Literature Review
Authors: Cho Jai Young , Han Ho-Seong , Kaneko Hironori , Wakabayashi Go , Okajima Hideaki , Uemoto Shinji , Soubrane Olivier , Yong Chee-Chien , Chen Chao-Long , Cheung Tan To , Belli Giulio , Kubo Shoji , Wu Yao-Ming , Chen Kuo-Hsin , Troisi Roberto I. , Kwon Choon Hyuck David , Suh Kyung-Suk , Soin Arvinder S. , Kim Ki-Hun , Cherqui Daniel
Published: October 2017

Background: Because laparoscopic donor surgery has been successful in pediatric living donor liver transplantation, its application is expanding to right hepatectomy. However, there is no consensus on the indications for laparoscopic donor hepatectomy or on the details of the surgical technique. Objective: To evaluate the current status of laparoscopic donor hepatectomy and to summarize the expert opinion on it. Methods: Before the expert meeting on September 8, 2016, in Seoul, Korea, a survey was undertaken from expert liver surgeons from around the world. Results: Fifteen of 17 (88.2%) surgeons responded to the survey. The selection criteria for laparoscopic donor surgery are stricter than for open surgery in terms of the anatomy, remnant liver volume, and recipient's condition. There is no consensus on the instruments or equipment used. A literature review of laparoscopic donor hepatectomy showed that the use of this method is increasing and the short-term outcomes are similar to those of open surgery. Conclusions: This survey and literature review show that laparoscopic donor hepatectomy is performed by experienced surgeons in selected cases, and that its incidence is increasing worldwide.