bluuebunny/crossref_metadata_2025_split huggingface dataset:
CompCertELF: verified separate compilation of C programs into ELF object files
Authors: Wang Yuting , Xu Xiangzhe , Wilke Pierre , Shao Zhong 
Published: November 2020

We present CompCertELF, the first extension to CompCert that supports verified compilation from C programs all the way to a standard binary file format, i.e., the ELF object format. Previous work on Stack-Aware CompCert provides a verified compilation chain from C programs to assembly programs with a realistic machine memory model. We build CompCertELF by modifying and extending this compilation chain with a verified assembler which further transforms assembly programs into ELF object files.
CompCert supports large-scale verification via verified separate compilation: C modules can be written and compiled separately, and then linked together to get a target program that refines the semantics of the program linked from the source modules. However, verified separate compilation in CompCert only works for compilation to assembly programs, not to object files. For the latter, the main difficulty is to bridge the two different views of linking: one for CompCert's programs that allows arbitrary shuffling of global definitions by linking and the other for object files that treats blocks of encoded definitions as indivisible units.
We propose a lightweight approach that solves the above problem without any modification to CompCert's framework for verified separate compilation: by introducing a notion of syntactical equivalence between programs and proving the commutativity between syntactical equivalence and the two different kinds of linking, we are able to transit from the more abstract linking operation in CompCert to the more concrete one for ELF object files. By applying this approach to CompCertELF, we obtain the first compiler that supports verified separate compilation of C programs into ELF object files.
A large-scale longitudinal study of flaky tests
Authors: Lam Wing , Winter Stefan , Wei Anjiang , Xie Tao , Marinov Darko , Bell Jonathan 
Published: November 2020

Flaky tests are tests that can non-deterministically pass or fail for the same code version. These tests undermine regression testing efficiency, because developers cannot easily identify whether a test fails due to their recent changes or due to flakiness. Ideally, one would detect flaky tests right when flakiness is introduced, so that developers can then immediately remove the flakiness. Some software organizations, e.g., Mozilla and Netflix, run some tools—detectors—to detect flaky tests as soon as possible. However, detecting flaky tests is costly due to their inherent non-determinism, so even state-of-the-art detectors are often impractical to be used on all tests for each project change. To combat the high cost of applying detectors, these organizations typically run a detector solely on newly added or directly modified tests, i.e., not on unmodified tests or when other changes occur (including changes to the test suite, the code under test, and library dependencies). However, it is unclear how many flaky tests can be detected or missed by applying detectors in only these limited circumstances.
To better understand this problem, we conduct a large-scale longitudinal study of flaky tests to determine when flaky tests become flaky and what changes cause them to become flaky. We apply two state-of-theart detectors to 55 Java projects, identifying a total of 245 flaky tests that can be compiled and run in the code version where each test was added. We find that 75% of flaky tests (184 out of 245) are flaky when added, indicating substantial potential value for developers to run detectors specifically on newly added tests. However, running detectors solely on newly added tests would still miss detecting 25% of flaky tests. The percentage of flaky tests that can be detected does increase to 85% when detectors are run on newly added or directly modified tests. The remaining 15% of flaky tests become flaky due to other changes and can be detected only when detectors are always applied to all tests. Our study is the first to empirically evaluate when tests become flaky and to recommend guidelines for applying detectors in the future.
Foundations of empirical memory consistency testing
Authors: Kirkham Jake , Sorensen Tyler , Tureci Esin , Martonosi Margaret 
Published: November 2020

Modern memory consistency models are complex, and it is difficult to reason about the relaxed behaviors that current systems allow. Programming languages, such as C and OpenCL, offer a memory model interface that developers can use to safely write concurrent applications. This abstraction provides functional portability across any platform that implements the interface, regardless of differences in the underlying systems. This powerful abstraction hinges on the ability of the system to correctly implement the interface. Many techniques for memory consistency model validation use empirical testing, which has been effective at uncovering undocumented behaviors and even finding bugs in trusted compilation schemes. Memory model testing consists of small concurrent unit tests called “litmus tests”. In these tests, certain observations,
including potential bugs
, are exceedingly rare, as they may only be triggered by precise interleaving of system steps in a complex processor, which is probabilistic in nature. Thus, each test must be run many times in order to provide a high level of confidence in its coverage.

In this work, we rigorously investigate empirical memory model testing. In particular, we propose methodologies for navigating complex stressing routines and analyzing large numbers of testing observations. Using these insights, we can more efficiently tune stressing parameters, which can lead to higher confidence results at a faster rate. We emphasize the need for such approaches by performing a meta-study of prior work, which reveals results with low reproducibility and inefficient use of testing time.
Our investigation is presented alongside empirical data. We believe that OpenCL targeting GPUs is a pragmatic choice in this domain as there exists a variety of different platforms to test, from large HPC servers to power-efficient edge devices. The tests presented in the work span 3 GPUs from 3 different vendors. We show that our methodologies are applicable across the GPUs, despite significant variances in the results. Concretely, our results show: lossless speedups of more than 5× in tuning using data peeking; a definition of portable stressing parameters which loses only 12% efficiency when generalized across our domain; a priority order of litmus tests for tuning. We stress test a conformance test suite for the OpenCL 2.0 memory model and discover a bug in Intel’s compiler. Our methods are evaluated on the other two GPUs using mutation testing. We end with recommendations for official memory model conformance tests.
Just-in-time learning for bottom-up enumerative synthesis
Authors: Barke Shraddha , Peleg Hila , Polikarpova Nadia 
Published: November 2020

A key challenge in program synthesis is the astronomical size of the search space the synthesizer has to explore. In response to this challenge, recent work proposed to guide synthesis using learned probabilistic models. Obtaining such a model, however, might be infeasible for a problem domain where no high-quality training data is available. In this work we introduce an alternative approach to guided program synthesis: instead of training a model ahead of time we show how to bootstrap one just in time, during synthesis, by learning from partial solutions encountered along the way. To make the best use of the model, we also propose a new program enumeration algorithm we dub guided bottom-up search, which extends the efficient bottom-up search with guidance from probabilistic models.
We implement this approach in a tool called Probe, which targets problems in the popular syntax-guided synthesis (SyGuS) format. We evaluate Probe on benchmarks from the literature and show that it achieves significant performance gains both over unguided bottom-up search and over a state-of-the-art probability-guided synthesizer, which had been trained on a corpus of existing solutions. Moreover, we show that these performance gains do not come at the cost of solution quality: programs generated by Probe are only slightly more verbose than the shortest solutions and perform no unnecessary case-splitting.
Flow2Vec: value-flow-based precise code embedding
Authors: Sui Yulei , Cheng Xiao , Zhang Guanqin , Wang Haoyu 
Published: November 2020

Code embedding, as an emerging paradigm for source code analysis, has attracted much attention over the past few years. It aims to represent code semantics through distributed vector representations, which can be used to support a variety of program analysis tasks (e.g., code summarization and semantic labeling). However, existing code embedding approaches are intraprocedural, alias-unaware and ignoring the asymmetric transitivity of directed graphs abstracted from source code, thus they are still ineffective in preserving the structural information of code.This paper presents Flow2Vec, a new code embedding approach that precisely preserves interprocedural program dependence (a.k.a value-flows). By approximating the high-order proximity, i.e., the asymmetric transitivity of value-flows, Flow2Vec embeds control-flows and alias-aware data-flows of a program in a low-dimensional vector space. Our value-flow embedding is formulated as matrix multiplication to preserve context-sensitive transitivity through CFL reachability by filtering out infeasible value-flow paths. We have evaluated Flow2Vec using 32 popular open-source projects. Results from our experiments show that Flow2Vec successfully boosts the performance of two recent code embedding approaches codevec and codeseq for two client applications, i.e., code classification and code summarization. For code classification, Flow2Vec improves codevec with an average increase of 21.2%, 20.1% and 20.7% in precision, recall and F1, respectively. For code summarization, Flow2Vec outperforms codeseq by an average of 13.2%, 18.8% and 16.0% in precision, recall and F1, respectively.
Clinical Features and Risk Factors of Active Tuberculosis in Patients with Behçet’s Disease
Authors: Liu Yaxu , Zhang Lifan , Zhou Ziyue , Sun Luxi , Zhou Baotong , Liu Xiaoqing , Zheng Wenjie 
Published: November 2020

To investigate the clinical features and potential risk factors of active tuberculosis (ATB) in Behçet’s disease (BD), we conducted a case-control study on hospitalized BD patients in our institute from 2010 to 2019. BD patients with ATB were enrolled as the case group. The control group was selected by random number sampling from the remaining BD patients, including those with latent tuberculosis infection, previous tuberculosis, or without tuberculosis. Finally, we reviewed 386 BD patients and identified 21 (5.4%) ATB cases, including four (19.0%) microbiologically confirmed and 17 (81.0%) clinically diagnosed. We found that BD patients with ATB were more prone to have systemic symptoms (fever, night sweating, and unexplained weight loss) and/or symptoms related to the infection site. Multivariate logistic regression analysis revealed that

erythrocyte

sedimentation

rate

ESR

>
60

mm/h (

OR
=
13.710

, 95% CI (1.101, 170.702)), increased IgG (

OR
=
1.226

, 95% CI (1.001, 1.502)), and positive T-SPOT.TB (

OR
=
7.793

, 95% CI (1.312, 48.464), for 24-200 SFC/106PBMC;

OR
=
17.705

95% CI (2.503, 125.260), for >200 SFC/106PBMC) were potential risk factors for ATB in BD patients. Our study suggested that when BD patients have systemic symptoms with significantly elevated TB-SPOT, the diagnosis of ATB should be considered.
Clinicopathological and Prognostic Roles of STAT3 and Its Phosphorylation in Glioma
Authors: Liang Bo , Li Shuang-Yang , Gong Hui-Zhi , Wang Ling-Xue , Lu Jia , Zhao Yu-Xiu , Gu Ning 
Published: November 2020

Glioma is defined as a common brain tumor which causes severe disability or death. As many genes are reported to relate with glioma’s occurrence and development, their prognostic and therapeutic value still remains uncertain. This study aimed at investigating the association between STAT3/p-STAT3 and glioma prognosis. Nine studies (12 trials) scored ≥5 on the Newcastle-Ottawa scale were meta-analysed from the Medline, Embase, and Web of Science databases. We found that STAT3/p-STAT3 overexpression in glioma patients was associated with worse overall survival (

hazard

ratio

HR

=
1.40

,

95
%
confidence

interval

CI

=
1.05
~
1.86

,

P
=
0.020

), progression-free survival (

HR
=
2.05

,

95
%
CI
=
1.63
~
2.58

,

P
<
0.001

), and better recurrence-free survival (

HR
=
0.37

,

95
%
CI
=
0.15
~
0.95

,

P
<
0.039

). Subgroup analysis implied that STAT3/p-STAT3 overexpression was associated with worse OS in standard treatment (

HR
=
1.80

,

95
%
CI
=
1.06
~
3.04

,

P
=
0.030

), and in China (

HR
=
2.18

,

95
%
CI
=
1.77
~
2.70

,

P
<
0.001

), and metaregression analysis indicated countries (

P
=
0.001

) may be the source of heterogeneity in our study. In conclusion, we suggested STAT3/p-STAT3 was associated with poor prognosis in patients with glioma, which indicated that STAT3/p-STAT3 might be a valuable prognostic biomarker and a promising therapeutic target for glioma.
MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers
Authors: Schaafsma Evelien , Zhao Yanding , Zhang Lanjing , Li Yong , Cheng Chao 
Published: November 2020

Abstract

c-MYC (MYC) is deregulated in more than 50% of all cancers. While MYC amplification is the most common MYC-deregulating event, many other alterations can increase MYC activity. We thus systematically investigated MYC pathway activity across different tumor types. Using a logistic regression framework, we established tumor type–specific, transcriptomic-based MYC activity scores that can accurately capture MYC activity. We show that MYC activity scores reflect a variety of MYC-regulating mechanisms, including MYCL and/or MYCN amplification, MYC promoter methylation, MYC mRNA expression, lncRNA PVT1 expression, MYC mutations, and viral integrations near the MYC locus. Our MYC activity score incorporates all of these mechanisms, resulting in better prognostic predictions compared with MYC amplification status, MYC promoter methylation, and MYC mRNA expression in several cancer types. In addition, we show that tumor proliferation and immune evasion are likely contributors to this reduction in survival. Finally, we developed a MYC activity signature for liquid tumors in which MYC translocation is commonly observed, suggesting that our approach can be applied to different types of genomic alterations. In conclusion, we developed a MYC activity score that captures MYC pathway activity and is clinically relevant.

Implications:
By using cancer type–specific MYC activity profiles, we were able to assess MYC activity across many more tumor types than previously investigated. The range of different MYC-related alterations captured by our MYC activity score can be used to facilitate the application of future MYC inhibitors and aid physicians to preselect patients for targeted therapy.
A Tumor Suppressor Enhancer ofPTENin T-cell Development and Leukemia
Authors: Tottone Luca , Lancho Olga , Loh Jui-Wan , Singh Amartya , Kimura Shunsuke , Roels Juliette , Kuchmiy Anna , Strubbe Steven , Lawlor Matthew A. , da Silva-Diz Victoria , Luo Shirley , Gachet Stéphanie , García-Prieto Carlos A. , Hagelaar Rico , Esteller Manel , Meijerink Jules P.P. , Soulier Jean , Taghon Tom , Van Vlierberghe Pieter , Mullighan Charles G. , Khiabanian Hossein , Rocha Pedro P. , Herranz Daniel 
Published: November 2020

AbstractLong-range oncogenic enhancers play an important role in cancer. Yet, whether similar regulation of tumor suppressor genes is relevant remains unclear. Loss of expression of PTEN is associated with the pathogenesis of various cancers, including T-cell acute lymphoblastic leukemia (T-ALL). Here, we identify a highly conserved distal enhancer (PE) that interacts with the PTEN promoter in multiple hematopoietic populations, including T cells, and acts as a hub of relevant transcription factors in T-ALL. Consistently, loss of PE leads to reduced PTEN levels in T-ALL cells. Moreover, PE-null mice show reduced Pten levels in thymocytes and accelerated development of NOTCH1-induced T-ALL. Furthermore, secondary loss of PE in established leukemias leads to accelerated progression and a gene expression signature driven by Pten loss. Finally, we uncovered recurrent deletions encompassing PE in T-ALL, which are associated with decreased PTEN levels. Altogether, our results identify PE as the first long-range tumor suppressor enhancer directly implicated in cancer.Significance:Here, we identify a PTEN enhancer that is recurrently deleted in patients with T-ALL. Loss of this enhancer leads to reduced PTEN levels in T cells together with accelerated generation and progression of NOTCH1-induced leukemia in vivo. These results uncover long-range regulation of tumor suppressor genes as a relevant mechanism in cancer.This article is highlighted in the In This Issue feature, p. 1
Ketorolac Use for Pain Management in Trauma Patients With Rib Fractures Does not Increase of Acute Kidney Injury or Incidence of Bleeding
Authors: Torabi Julia , Kaban Jody M. , Lewis Erin , Laikhram Dana , Simon Rachel , DeHaan Skylar , Jureller Michael , Chao Edward , Reddy Srinivas H. , Stone Melvin E. 
Published: November 2020

Introduction Ketorolac is useful in acute pain management to avoid opiate-related complications; however, some surgeons fear associated acute kidney injury (AKI) and bleeding despite a paucity of literature on ketorolac use in trauma patients. We hypothesized that our institution's use of intravenous ketorolac for rib fracture pain management did not increase the incidence of bleeding or AKI. Methods Rib fracture patients aged 15 years and above admitted between January 2016-June 2018 were identified in our trauma registry along with frequency of bleeding events. AKI was defined as ≥ 1.5x increase in serum creatinine from baseline measured on the second day of admission (after 24 hours of resuscitation) or an increase of ≥ .3 mg/dL over a 48-hour period. Patients receiving ketorolac were compared to patients with no ketorolac use. Results Two cohorts of 199 control and 205 ketorolac patients were found to be similar in age, gender, admission systolic blood pressure (SBP), injury severity score, intravenous radiocontrast received, and transfusion requirements. Analysis revealed no difference in frequency of AKI using both definitions (8% vs. 7.3%, P = .79) and (19.6% vs. 15.1%, P = .24), respectively, or bleeding events (2.5% vs. 0%, P = .03). Logistic regression demonstrated that ketorolac use was not an independent predictor for AKI but age and admission SBP < 90 were. Conclusion Use of ketorolac in this cohort of trauma patients with rib fractures did not increase the incidence of AKI or bleeding events.
The Effects of the COVID-19 Pandemic on Trauma Presentations in a Level One Trauma Center
Authors: Devarakonda Aditya K. , Wehrle Chase J. , Chibane Fairouz L. , Drevets Peter D. , Fox Elizabeth D. , Lawson Andrew G. 
Published: November 2020

Background Over 28 million confirmed cases of COVID-19 have been reported to date, resulting in over 900 000 deaths. With an increase in awareness regarding the virus, the behavior of general population has changed dramatically. As activities such as driving and hospital presentation patterns have changed, our study aimed to assess the differences in trauma case variables before and during the COVID-19 pandemic. Methods Trauma data for the period of March 1st-June 15th were compared for the years 2015-2019 (pre-COVID) and 2020 (COVID). The data were analyzed across the following categories: injury severity score, injury mechanism, motor vehicle crashes (MVCs) vs. other blunt injuries, alcohol involvement, and length of hospital stay. Results The median injury severity score pre-COVID and during COVID was 9, representing no change. There was no difference in overall distribution of mechanism of injury; however, there was a significant decrease in the percentage of MVCs pre-COVID (36.39%) vs. COVID (29.6%, P < .05). Alcohol was significantly more likely to be involved in trauma during COVID-19 ( P < .05). The mean hospital stay increased from 3.87-5.4 days during COVID-19 ( P < .05). Discussion We saw similar results to prior studies in terms of there being no change in trauma severity. Our observation that motor vehicle collisions have decreased is consistent with current data showing decreased use of motor vehicles during the pandemic. We also observed an increase in alcohol-related cases which are consistent with the reported changes in alcohol consumption since the pandemic began.
Advanced Practice Providers Utilization Trends in Otolaryngology From 2012 to 2017 in the Medicare Population
Authors: Ge Marshall , Kim Jee‐hong , Smith Stephanie Shintani , Paul Julianna , Park Christine , Su Peiyi , Ference Elisabeth H. 
Published: November 2020

ObjectiveNurse practitioners and physician assistants form a growing advanced practice provider (APP) group. We aim to analyze the trends and types of services provided by APPs in otolaryngology.Study DesignCross‐sectional study.SettingMedicare Provider Utilization and Payment Data: Physician and Other Supplier Public Use Files, 2012‐2017.MethodsThe Medicare database was searched for 13 commonly used otolaryngology‐specific Current Procedural Terminology (CPT) codes, and 10 evaluation and management (E/M) codes were evaluated by provider type. Changes in code utilization were compared between physicians and APPs over time.ResultsFrom 2012 to 2017, there was a 51% increase in the number of otolaryngology APPs, compared to a 2.2% increase in physician providers. APPs increased their share of new and established patient visits from 4% to 7%d 11% to 15%, respectively. There was not a significant difference over time in number of patient visits performed annually per provider according to provider type. The increase in number of APP vs physician providers was significantly greater for every procedure except for balloon sinus dilation and tympanostomy tube placement.ConclusionDue to increasing numbers, APPs are accounting for more patient visits and procedures over time. The physician workforce and the numbers of procedures performed per physician have remained relatively stable from 2012 to 2017. Increasing complexity of patients seen and a broader range of procedures offered by work‐experienced or postgraduate‐trained APPs may further improve access to health care in the face of possible physician shortages.