bluuebunny/crossref_metadata_2025_split huggingface dataset:
Static analysis with demand-driven value refinement
Authors: Stein Benno , Nielsen Benjamin Barslev , Chang Bor-Yuh Evan , Møller Anders 
Published: October 2019

Static analysis tools for JavaScript must strike a delicate balance, achieving the level of precision required by the most complex features of target programs without incurring prohibitively high analysis time. For example, reasoning about dynamic property accesses sometimes requires precise relational information connecting the object, the dynamically-computed property name, and the property value. Even a minor precision loss at such critical program locations can result in a proliferation of spurious dataflow that renders the analysis results useless.
We present a technique by which a conventional non-relational static dataflow analysis can be combined soundly with a value refinement mechanism to increase precision on demand at critical locations. Crucially, our technique is able to incorporate relational information from the value refinement mechanism into the non-relational domain of the dataflow analysis.
We demonstrate the feasibility of this approach by extending an existing JavaScript static analysis with a demand-driven value refinement mechanism that relies on backwards abstract interpretation. Our evaluation finds that precise analysis of widely used JavaScript utility libraries depends heavily on the precision at a small number of critical locations that can be identified heuristically, and that backwards abstract interpretation is an effective mechanism to provide that precision on demand.
Getafix: learning to fix bugs automatically
Authors: Bader Johannes , Scott Andrew , Pradel Michael , Chandra Satish 
Published: October 2019

Static analyzers help find bugs early by warning about recurring bug categories. While fixing these bugs still remains a mostly manual task in practice, we observe that fixes for a specific bug category often are repetitive. This paper addresses the problem of automatically fixing instances of common bugs by learning from past fixes. We present Getafix, an approach that produces human-like fixes while being fast enough to suggest fixes in time proportional to the amount of time needed to obtain static analysis results in the first place.
Getafix is based on a novel hierarchical clustering algorithm that summarizes fix patterns into a hierarchy ranging from general to specific patterns. Instead of an expensive exploration of a potentially large space of candidate fixes, Getafix uses a simple yet effective ranking technique that uses the context of a code change to select the most appropriate fix for a given bug.
Our evaluation applies Getafix to 1,268 bug fixes for six bug categories reported by popular static analyzers for Java, including null dereferences, incorrect API calls, and misuses of particular language constructs. The approach predicts exactly the human-written fix as the top-most suggestion between 12% and 91% of the time, depending on the bug category. The top-5 suggestions contain fixes for 526 of the 1,268 bugs. Moreover, we report on deploying the approach within Facebook, where it contributes to the reliability of software used by billions of people. To the best of our knowledge, Getafix is the first industrially-deployed automated bug-fixing tool that learns fix patterns from past, human-written fixes to produce human-like fixes.
Specifying concurrent programs in separation logic: morphisms and simulations
Authors: Nanevski Aleksandar , Banerjee Anindya , Delbianco Germán Andrés , Fábregas Ignacio 
Published: October 2019

In addition to pre- and postconditions, program specifications in recent separation logics for concurrency have employed an algebraic structure of
resources
—a form of state transition systems—to describe the state-based program invariants that must be preserved, and to record the permissible atomic changes to program state. In this paper we introduce a novel notion of
resource morphism
, i.e. structure-preserving function on resources, and show how to effectively integrate it into separation logic, using an associated notion of morphism-specific
simulation
. We apply morphisms and simulations to programs verified under one resource, to compositionally adapt them to operate under another resource, thus facilitating proof reuse.
Ryū revisited: printf floating point conversion
Authors: Adams Ulf 
Published: October 2019

Ryū Printf is a new algorithm to convert floating-point numbers to decimal strings according to the printf %f, %e, and %g formats: %f generates ‘full’ output (integer part of the input, dot, configurable number of digits), %e generates scientific output (one leading digit, dot, configurable number of digits, exponent), and %g generates the shorter of the two. Ryū Printf is based on the Ryū algorithm, which converts binary floating-point numbers to the shortest equivalent decimal floating-point representation. We provide quantitative evidence that Ryū Printf is between 3.8 and 55 times faster than existing printf implementations.
Furthermore, we show that both Ryū and Ryū Printf generalize to arbitrary number bases. This finding implies the existence of a fast algorithm to convert from base-10 to base-2, as long as the maximum precision of the input is known a priori.
Coverage guided, property based testing
Authors: Lampropoulos Leonidas , Hicks Michael , Pierce Benjamin C. 
Published: October 2019

Property-based random testing, exemplified by frameworks such as Haskell's QuickCheck, works by testing an executable predicate (a property) on a stream of randomly generated inputs. Property testing works very well in many cases, but not always. Some properties are conditioned on the input satisfying demanding semantic invariants that are not consequences of its syntactic structure---e.g., that an input list must be sorted or have no duplicates. Most randomly generated inputs fail to satisfy properties with such sparse preconditions, and so are simply discarded. As a result, much of the target system may go untested.
We address this issue with a novel technique called coverage guided, property based testing (CGPT). Our approach is inspired by the related area of coverage guided fuzzing, exemplified by tools like AFL. Rather than just generating a fresh random input at each iteration, CGPT can also produce new inputs by mutating previous ones using type-aware, generic mutator operators. The target program is instrumented to track which control flow branches are executed during a run and inputs whose runs expand control-flow coverage are retained for future mutations. This means that, when sparse conditions in the target are satisfied and new coverage is observed, the input that triggered them will be retained and used as a springboard to go further.
We have implemented CGPT as an extension to the QuickChick property testing tool for Coq programs; we call our implementation FuzzChick. We evaluate FuzzChick on two Coq developments for abstract machines that aim to enforce flavors of noninterference, which has a (very) sparse precondition. We systematically inject bugs in the machines' checking rules and use FuzzChick to look for counterexamples to the claim that they satisfy a standard noninterference property. We find that vanilla QuickChick almost always fails to find any bugs after a long period of time, as does an earlier proposal for combining property testing and fuzzing. In contrast, FuzzChick often finds them within seconds to minutes. Moreover, FuzzChick is almost fully automatic; although highly tuned, hand-written generators can find the bugs faster, they require substantial amounts of insight and manual effort.
Detecting nondeterministic payment bugs in Ethereum smart contracts
Authors: Wang Shuai , Zhang Chengyu , Su Zhendong 
Published: October 2019

The term “smart contracts” has become ubiquitous to describe an enormous number of programs uploaded to the popular Ethereum blockchain system. Despite rapid growth of the smart contract ecosystem, errors and exploitations have been constantly reported from online contract systems, which has put financial stability at risk with losses totaling millions of US dollars. Most existing research focuses on pinpointing specific types of vulnerabilities using known patterns. However, due to the lack of awareness of the inherent nondeterminism in the Ethereum blockchain system and how it affects the funds transfer of smart contracts, there can be unknown vulnerabilities that may be exploited by attackers to access numerous online smart contracts.
In this paper, we introduce a methodical approach to understanding the inherent nondeterminism in the Ethereum blockchain system and its (unwanted) influence on contract payments. We show that our new focus on nondeterminism-related smart contract payment bugs captures the root causes of many common vulnerabilities without relying on any known patterns and also encompasses recently disclosed issues that are not handled by existing research. To do so, we introduce techniques to systematically model components in the contract execution context and to expose various nondeterministic factors that are not yet fully understood. We further study how these nondeterministic factors impact contract funds transfer using information flow tracking. The technical challenge of detecting nondeterministic payments lies in discovering the contract global variables subtly affected by read-write hazards because of unpredictable transaction scheduling and external callee behavior. We show how to augment and instrument a contract program into a representation that simulates the execution of a large subset of the contract behavior. The instrumented code is then analyzed to flag nondeterministic global variables using off-the-shelf model checkers.
We implement the proposed techniques as a practical tool named NPChecker (Nondeterministic Payment Checker) and evaluate it on 30K online contracts (3,075 distinct) collected from the Ethereum mainnet. NPChecker has successfully detected nondeterministic payments in 1,111 online contracts with reasonable cost. Further investigation reports high precision of NPChecker (only four false positives in a manual study of 50 contracts). We also show that NPChecker unveils contracts vulnerable to recently-disclosed attack vectors. NPChecker can identify all six new vulnerabilities or variants of common smart contract vulnerabilities that are missed by existing research relying on a “contract vulnerability checklist.”
Characterization of urea transport mechanisms in the intestinal tract of growing pigs
Authors: Krone Jack E. C. , Agyekum Atta K. , ter Borgh Miriam , Hamonic Kimberley , Penner Gregory B. , Columbus Daniel A. 
Published: October 2019

Pigs are capable of nitrogen salvage via urea recycling, which involves the movement of urea in the gastrointestinal tract. Aquaporins (AQP) and urea transporter B (UT-B) are involved in urea recycling in ruminants; however, their contribution to urea flux in the intestinal tract of the pig is not known. The objective of this study was to characterize the presence and relative contribution of known urea transporters to urea flux in the growing pig. Intestinal tissue samples (duodenum, jejunum, ileum, cecum, and colon) were obtained from nine barrows (50.8 ± 0.9 kg) and analyzed for mRNA abundance of UT-B and AQP-3, -7, and -10. Immediately after tissue collection, samples from the jejunum and cecum were placed in Ussing chambers for analysis of the serosal-to-mucosal urea flux ( Jsm-urea) with no inhibition or when incubated in the presence of phloretin to inhibit UT-B-mediated transport, NiCl2 to inhibit AQP-mediated transport, or both inhibitors. UT-B expression was greatest ( P < 0.05) in the cecum, whereas AQP-3, -7, and -10 expression was greatest ( P < 0.05) in the jejunum. The Jsm-urea was greater in the cecum than the jejunum (67.8 . 42.7 ± 5.01 µmol·cm−2·h−1; P < 0.05), confirming the capacity for urea recycling in the gut in pigs; however, flux rate was not influenced ( P > 0.05) by urea transporter inhibitors. The results of this study suggest that, although known urea transporters are expressed in the gastrointestinal tract of pigs, they may not play a significant functional role in transepithelial urea transport. NEW & NOTEWORTHY We characterized the location and contribution of known urea transporters to urea flux in the pig. Aquaporins are located throughout the intestinal tract, and urea transporter B is expressed only in the cecum. Urea flux occurred in both the jejunum and cecum. Transporter inhibitors had no affect on urea flux, suggesting that their contribution to urea transport in the intestinal tract is limited. Further work is required to determine which factors contribute to urea flux in swine.
IL8 Expression Is Associated with Prostate Cancer Aggressiveness and Androgen Receptor Loss in Primary and Metastatic Prostate Cancer
Authors: Maynard Janielle P. , Ertunc Onur , Kulac Ibrahim , Baena-Del Valle Javier A. , De Marzo Angelo M. , Sfanos Karen S. 
Published: October 2019

Abstract

Chronic inflammation and African ancestry are implicated in prostate cancer aggressiveness, and inflammation-related genes are more highly expressed in prostate cancer in African American men. IL8 secretion is also implicated in prostate cancer progression and castration resistance. We used RNA in situ hybridization to localize IL1β, IL6, IL8, and IL10 mRNA in low- and high-grade prostate cancer from African American and European American men. IL8 was the most abundantly expressed and the only interleukin detected in tumor cells. We further interrogated IL8 expression in primary and metastatic prostate cancer tissue microarrays and both androgen-dependent and castration-resistant patient-derived xenografts (PDX). IL8 was significantly increased in both tumor and benign regions of higher grade cases (ISUP Grade Group 4–5), but there was no difference between races. We determined that IL8 expression in prostate cancer cell lines, distant metastases, and PDX lines was associated with androgen receptor (AR) loss, but not castration resistance. Reciprocal IL8 and AR expression was also observed in high IL8-expressing atrophy lesions with simultaneous AR downregulation. Finally, we show that IL8 is likely repressed by AR binding to the IL8 promoter and is inducible in prostate cancer cells stimulated with lipopolysaccharide only in cells with AR loss. Likewise, AR knockdown in androgen-dependent cells induced IL8 expression, further demonstrating that AR represses IL8 expression. In conclusion, IL8 expression in the tumor microenvironment is associated with aggressive prostate cancer and with AR loss in metastatic disease.

Implications:
IL8 expression is repressed by AR and is associated with prostate cancer aggressiveness and AR loss in metastatic disease.
Annulohypoxylon sp. FPYF3050 produces volatile organic compounds against the pine wood nematode, Bursaphelenchus xylophilus
Authors: Li Hongchang , Dou Guiming , Gao Mengge , Ren Fei , Li Ruhua , Zhang Xingyao , Yan Dong-Hui 
Published: October 2019

Summary
Natural volatiles released by the fungus, Annulohypoxylon sp. FPYF3050, were evaluated against the pine wood nematode (PWN), Bursaphelenchus xylophilus. Our results showed that volatile organic compounds (VOCs) caused 64.1 and 58.4% mortality of second-stage juveniles (J2) and mixed-stages (eggs, J2, third- and fourth-stage juveniles, and adults) of populations of PWN, but no inhibitive effects were detected on nematode eggs in the experiment. Analysis of the gases within the Petri plate by gas chromatography-mass spectrometry (GC-MS) showed a yield of an unique volatile with dominant 1,8-cineole in 77.4% relative area (RA) after 72 h treatment of nematodes with Annulohypoxylon sp. FPYF3050 and Botrytis cinerea. The commercial 1,8-cineole at concentrations of 2, 5, 10 and 15 μl ml−1 was applied to examine nematicidal activity. The results showed that 1,8-cineole had a 40-100% inhibition on the nematode eggs during 48 h treatment, more than 82.9% mortality of J2 after 24 h, 48 h and 96 h, and 18.7-91.9% mortality of the mixed-stage population, depending on the period after exposure. This result indicates that 1,8-cineole in the volatile gas emissions of Annulohypoxylon sp. FPYF3050 may play a crucial inhibitory effect on the pine wood nematode The nematicidal volatile gas from fungi may provide a useful biocontrol agent for controlling B. xylophilus.
More Than “Multiple Jeopardy”: Navigating the Legal System as a British-Muslim-Woman-Litigant-in-Person
Authors: Bi Suriyah 
Published: October 2019

Abstract
Against the backdrop of rising Islamophobia and a deficit in the literature of Muslim experiences of resistance to discrimination through the legal action, in this article, I employ an auto-ethnographic methodological approach to critically reflect on my journey from classroom to courtroom, as a British Muslim woman of colour and litigant-in-person. While threading in excerpts of legal documents from the case, I highlight that: (a) as Muslims we must resist in ways acceptable to gate-keepers of the law, who are largely white and middle-class and unaware of the embodied realities of the inequality that minorities in Britain experience; (b) the law fails to take account of the “context” in which discrimination(s) takes place, as a result of which legal logic(s) and methodologies in cases of religious discrimination are flawed; (c) a religio-social capital operates against Muslims, negating positive social capital(s) such as education, and which, in the social penalties Muslims experience, accumulates greater weight than other intersecting subjectivity markers such as race, class, ethnicity, and gender. I contrast King’s theory of “multiple jeopardy” with my embodied experience of discrimination and inequality, which I demonstrate using the model of the glass Rubik’s cube.
Taking steps towards deinstitutionalizing mental health care within a low and middle-income country: A cross-sectional study of service user needs in the Republic of Moldova
Authors: Frasch Jona J , Petrea Ionela , Chihai Jana , Smit Filip , Oud Matthijs , Shields-Zeeman Laura 
Published: October 2019

Aim: The current research was conducted in the context of an ongoing reform of mental health services in the Republic of Moldova since 2014, where efforts have been devoted to creating community-based mental health services. This article presents a snapshot of the needs of mental health service users in the Republic of Moldova and helps to understand how and with which services their needs can be addressed. Methods: This cross-sectional study compared the levels of needs (CANSAS scale), quality of life (EQ-5D 3L), mental health status (MINI for psychotic disorders) and functioning (WHO-DAS) among mental health service users in the psychiatric hospital in Chisinau, Moldova. All service users resided in districts where community mental health services were being developed. Correlations between quality of life, functioning and unmet need were explored. Results: Of 83 participants, one third had a psychotic or a mood disorder. On average, participants reported needs in 9.41 domains ( SD = 4.41), of which 4.29 were unmet ( SD = 3.63). Most unmet needs related to intimacy and relation to others. The level of functioning and quality of life were reported. We found strong, negative associations between the number of unmet needs and level of functioning, as well as the quality of life. We also found that higher functioning levels were positively associated with higher quality of life. Conclusion: There were a high number of unmet needs among this inpatient population, particularly social needs and service-related needs. A continuum of inpatient and outpatient care and individual treatment plans can help address the different needs of different patients. Individual treatment plans for patients and the choice of the appropriate treatment for patients could be guided by an assessment of service users’ (unmet) needs of care and level of functioning.
Age-Standardized Mortality of Persons on Probation, in Jail, or in State Prison and the General Population, 2001-2012
Authors: Wildeman Christopher , Goldman Alyssa W. , Wang Emily A. 
Published: October 2019

Objectives: The number of adults in the United States being held on probation—persons convicted of crimes and serving their sentence in the community rather than in a correctional facility—approached 4 million at the end of 2016 and continues to grow, yet little is known about the health and well-being of this population. We compared the standardized mortality ratios of persons on probation in the United States with persons in jail, persons in state prison, and the general US population. Methods: We used administrative data from 2001-2012 from the Bureau of Justice Statistics and the Centers for Disease Control and Prevention WONDER database and indirect standardization techniques to compare the mortality rates of persons on probation in 15 states with the mortality rates of persons in jail, persons in state prison, and the general US population. We applied the age-specific mortality rates of 3 populations (general US population, persons in jail, and persons in state prison) to the age distribution of persons on probation to estimate standardized mortality ratios. Results: Persons on probation died at a rate 3.42 times higher than persons in jail, 2.81 times higher than persons in state prison, and 2.10 times higher than the general US population, after standardizing the age distribution of persons on probation relative to the other 3 groups. Conclusions: Public health interventions should target persons on probation, who have received less attention from the public health community than persons serving sentences in jails and prisons.
Effect of teriparatide on quality of life in patients with postmenopausal osteoporosis: a retrospective cohort study
Authors: Yang Tiansong , Feng Chuwen , Qu Yuanyuan , Wang Qingyong , Yang Yan , Wang Bo , Sun Zhongren , Bao Shengyong 
Published: October 2019

Objective To evaluate the effect of teriparatide on life quality in patients with postmenopausal osteoporosis. Methods Patients treated from January 2014 to December 2016 were retrospectively included. Patients were divided into two groups according the treatment received. Those in the teriparatide treatment group were followed up for 24 months, and patients in the control group received calcium supplements and vitamin D. Scores for back pain using a visual analog scale (VAS) and score of the Oswestry Disability Index (ODI) and 36-item Short Form Health Survey of life quality (SF-36) were evaluated at 3, 6, 12, and 24 months and compared between the groups. Results In total, 126 patients were included in the teriparatide treatment group and 127 in the control group. There were no significant differences between the groups concerning body mass index, bone density, VAS back pain score, ODI, and SF-36 life quality scores at baseline. At 3, 6, 12, and 24 months’ follow-up, VAS scores were significantly lower in the treatment group than in controls; ODI and SF-36 scores were significantly higher in the treatment group than in the control group. Conclusion Teriparatide can significantly decrease pain and increase mobility and life quality in patients with postmenopausal osteoporosis.