bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seamless Parametrization with Arbitrary Cones for Arbitrary Genus
Authors: Campen Marcel , Shen Hanxiao , Zhou Jiaran , Zorin Denis 
Published: December 2019

Seamless global parametrization of surfaces is a key operation in geometry processing, e.g., for high-quality quad mesh generation. A common approach is to prescribe the parametric domain structure, in particular, the locations of parametrization singularities (cones), and solve a non-convex optimization problem minimizing a distortion measure, with local injectivity imposed through either constraints or barrier terms. In both cases, an initial valid parametrization is essential to serve as a feasible starting point for obtaining an optimized solution. While convexified versions of the constraints eliminate this initialization requirement, they narrow the range of solutions, causing some problem instances that actually do have a solution to become infeasible.
We demonstrate that for arbitrary given sets of topologically admissible parametric cones with prescribed curvature, a global seamless parametrization always exists (with the exception of one well-known case). Importantly, our proof is constructive and directly leads to a general algorithm for computing such parametrizations. Most distinctively, this algorithm is bootstrapped with a convex optimization problem (solving for a conformal map), in tandem with a simple linear equation system (determining a seamless modification of this map). This initial map can then serve as a valid starting point and be optimized for low distortion using existing injectivity preserving methods.
Coq Coq correct! verification of type checking and erasure for Coq, in Coq
Authors: Sozeau Matthieu , Boulier Simon , Forster Yannick , Tabareau Nicolas , Winterhalter Théo 
Published: December 2019

Coq is built around a well-delimited kernel that perfoms typechecking for definitions in a variant of the Calculus of Inductive Constructions (CIC). Although the metatheory of CIC is very stable and reliable, the correctness of its implementation in Coq is less clear. Indeed, implementing an efficient type checker for CIC is a rather complex task, and many parts of the code rely on implicit invariants which can easily be broken by further evolution of the code. Therefore, on average, one critical bug has been found every year in Coq.
This paper presents the first implementation of a type checker for the kernel of Coq (without the module system and template polymorphism), which is proven correct in Coq with respect to its formal specification and axiomatisation of part of its metatheory. Note that because of Gödel's incompleteness theorem, there is no hope to prove completely the correctness of the specification of Coq inside Coq (in particular strong normalisation or canonicity), but it is possible to prove the correctness of the implementation assuming the correctness of the specification, thus moving from a trusted code base (TCB) to a trusted theory base (TTB) paradigm.
Our work is based on the MetaCoq project which provides metaprogramming facilities to work with terms and declarations at the level of this kernel. Our type checker is based on the specification of the typing relation of the Polymorphic, Cumulative Calculus of Inductive Constructions (PCUIC) at the basis of Coq and the verification of a relatively efficient and sound type-checker for it. In addition to the kernel implementation, an essential feature of Coq is the so-called extraction: the production of executable code in functional languages from Coq definitions. We present a verified version of this subtle type-and-proof erasure step, therefore enabling the verified extraction of a safe type-checker for Coq.
Executable formal semantics for the POSIX shell
Authors: Greenberg Michael , Blatt Austin J. 
Published: December 2019

The POSIX shell is a widely deployed, powerful tool for managing computer systems. The shell is the expert’s control panel, a necessary tool for configuring, compiling, installing, maintaining, and deploying systems. Even though it is powerful, critical infrastructure, the POSIX shell is maligned and misunderstood. Its power and its subtlety are a dangerous combination.
We define a formal, mechanized, executable small-step semantics for the POSIX shell, which we call Smoosh. We compared Smoosh against seven other shells that aim for some measure of POSIX compliance (bash, dash, zsh, OSH, mksh, ksh93, and yash). Using three test suites—the POSIX test suite, the Modernish test suite and shell diagnostic, and a test suite of our own device—we found Smoosh’s semantics to be the most conformant to the POSIX standard. Modernish judges Smoosh to have the fewest bugs (just one, from using dash’s parser) and no quirks. To show that our semantics is useful beyond yielding a conformant, executable shell, we also implemented a symbolic stepper to illuminate the subtle behavior of the shell.
Smoosh will serve as a foundation for formal study of the POSIX shell, supporting research on and development of new shells, new tooling for shells, and new shell designs.
Disentanglement in nested-parallel programs
Authors: Westrick Sam , Yadav Rohan , Fluet Matthew , Acar Umut A. 
Published: December 2019

Nested parallelism has proved to be a popular approach for programming the rapidly expanding range of multicore computers. It allows programmers to express parallelism at a high level and relies on a run-time system and a scheduler to deliver efficiency and scalability. As a result, many programming languages and extensions that support nested parallelism have been developed, including in C/C++, Java, Haskell, and ML. Yet, writing efficient and scalable nested parallel programs remains challenging, primarily due to difficult concurrency bugs arising from destructive updates or effects. For decades, researchers have argued that functional programming can simplify writing parallel programs by allowing more control over effects but functional programs continue to underperform in comparison to parallel programs written in lower-level languages. The fundamental difficulty with functional languages is that they have high demand for memory, and this demand only grows with parallelism.
In this paper, we identify a memory property, called disentanglement, of nested-parallel programs, and propose memory management techniques for improved efficiency and scalability. Disentanglement allows for (destructive) effects as long as concurrently executing threads do not gain knowledge of the memory objects allocated by each other. We formally define disentanglement by considering an ML-like higher-order language with mutable references and presenting a dynamic semantics for it that enables reasoning about computation graphs of nested parallel programs. Based on this graph semantics, we formalize a classic correctness property---determinacy race freedom---and prove that it implies disentanglement. This establishes that disentanglement applies to a relatively broad class of parallel programs. We then propose memory management techniques for nested-parallel programs that take advantage of disentanglement for improved efficiency and scalability. We show that these techniques are practical by extending the MLton compiler for Standard ML to support this form of nested parallelism. Our empirical evaluation shows that our techniques are efficient and scale well.
Interaction trees: representing recursive and impure programs in Coq
Authors: Xia Li-yao , Zakowski Yannick , He Paul , Hur Chung-Kil , Malecha Gregory , Pierce Benjamin C. , Zdancewic Steve 
Published: December 2019

Interaction trees
(ITrees) are a general-purpose data structure for representing the behaviors of recursive programs that interact with their environments. A coinductive variant of “free monads,” ITrees are built out of uninterpreted events and their continuations. They support compositional construction of interpreters from
event handlers
, which give meaning to events by defining their semantics as monadic actions. ITrees are expressive enough to represent impure and potentially nonterminating, mutually recursive computations, while admitting a rich equational theory of equivalence up to weak bisimulation. In contrast to other approaches such as relationally specified operational semantics, ITrees are executable via code extraction, making them suitable for debugging, testing, and implementing software artifacts that are amenable to formal verification.

We have implemented ITrees and their associated theory as a Coq library, mechanizing classic domain- and category-theoretic results about program semantics, iteration, monadic structures, and equational reasoning. Although the internals of the library rely heavily on coinductive proofs, the interface hides these details so that clients can use and reason about ITrees without explicit use of Coq’s coinduction tactics.
To showcase the utility of our theory, we prove the termination-sensitive correctness of a compiler from a simple imperative source language to an assembly-like target whose meanings are given in an ITree-based denotational semantics. Unlike previous results using operational techniques, our bisimulation proof follows straightforwardly by structural induction and elementary rewriting via an equational theory of combinators for control-flow graphs.
LncRNA TUG1 mediates ischemic myocardial injury by targeting miR-132-3p/HDAC3 axis
Authors: Su Qiang , Liu Yang , Lv Xiang-Wei , Dai Ri-Xin , Yang Xi-Heng , Kong Bing-Hui 
Published: December 2019

Increased production of reactive oxygen species (ROS) significantly contributed to the pathogenesis of acute myocardial infarction (AMI). Recent studies suggest that hypoxia upregulated the long noncoding RNA taurine upregulated gene 1 (TUG1). In this study, we explored the functional significance and molecular mechanisms of TUG1/miR-132-3p axis in ischemia-challenged cardiomyocytes. In primary cardiomyocytes challenged with H2O2, expressions of miR-132-3p, TUG1, and other target proteins were measured by RT quantitative PCR or Western blot analysis; cell viability by 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide assay; apoptosis by annexin V and propidium iodide staining; the abundance of acetylated H3K9 or histone deacetylase 3 (HDAC3) within the promoter of target genes by chromatin immunoprecipitation; the direct interaction between miR-132-3p and HDAC3 or TUG1 by luciferase reporter assay. The biological significance of miR-132-3p, TUG1, and HDAC3 was assessed using miR-132-3p mimic, siRNA-targeting TUG1 and HDAC3 inhibitor RGF966, respectively, in H2O2-challenged cells in vitro or ischemia-reperfusion (I/R)-induced AMI in vivo. miR-132-3p was downregulated, whereas TUG1 upregulated in H2O2-challenged cardiomyocytes. Overexpressing miR-132-3p or knocking down TUG1 significantly improved viability, inhibited apoptosis, and reduced ROS production in H2O2-stressed cardiomyocytes in vitro and alleviated I/R-induced AMI in vivo. Mechanistically, TUG1 sponged miR-132-3p and upregulated HDAC3, which reduced the acetylation of H3K9 and epigenetically inhibited expressions of antioxidative genes, including Bcl-xL, Prdx2, and Hsp70. The TUG1/miR-132-3p/HDAC3 axis critically regulates ROS production and the pathogenic development of AMI. Targeting TUG1, upregulating miR-132-3p, or inhibiting HDAC3 may benefit AMI treatment. NEW & NOTEWORTHY Increased production of reactive oxygen species (ROS) significantly contributed to the pathogenesis of acute myocardial infarction (AMI). Recent studies suggest that hypoxia upregulated the long noncoding RNA taurine upregulated gene 1 (TUG1). However, the underlying mechanisms remain elusive. In the present study, we reported for the first time that H2O2 or ischemia-reperfusion-induced TUG1, by sponging microRNA 132-3p, activated histone deacetylase 3, which in turn targeted multiple protective genes, stimulated intracellular ROS accumulation, and aggravated the injury of AMI. Our findings might provide some insight to seek new targets for AMI treatment.
Collating The Signs of Benevolent Deeds: Muḥammad Mahdī al-Fāsī’s Commentary on Muḥammad al-Jazūlī’s Dalā’il al-Khayrāt and Its Ottoman Readers
Authors: Burak Guy 
Published: December 2019

AbstractThe article examines the efforts of Muḥammad al-Mahdī al-Fāsī (d. 1605) and his readers in the Ottoman domains to reconstruct an authoritative version of Muḥammad b. Sulaymān b. Abī Bakr al-Jazūlī’s (d. 1465) Dalā’il al-khayrāt. In his commentary on the Dalā’il, al-Fāsī recorded his collation of multiple versions of al-Jazūlī’s work. The commentary and its contribution to a notion of an authoritative and authorial version of Dalā’il al-khayrāt accompanied al-Jazūlī’s text in its journey to the eastern parts of the Islamic world and helped readers there bridge a two-century gap in the transmission of the work. The article studies the manners in which Ottoman readers/reciters of Dalā’il used al-Fāsī’s commentary to create a channel to al-Jazūlī and the divine. In so doing, the article seeks to draw attention to additional functions of the genre of the commentary in the Islamic tradition. Moreover, by focusing on the textual practices of al-Fāsī and his Ottoman readers, the essay argues that the act of collation of the multiple versions of Dalā’il al-khayrāt was in and of itself an ethical act of devotion that manifested the readers’/reciters’ quest for proximity to al-Jazūlī.
A New Approach for Modeling Dissipation due to Breaking in Wind Wave Spectra
Authors: Ardag Dorukhan , Resio Donald T. 
Published: December 2019

AbstractA robust spectral dissipation term for wind waves has long been a goal of detailed-balance spectral modeling and is represented by many different approximations in spectral models of random wave fields. A Monte Carlo approach is employed here to create a random-phase sea surface that is used to simulate the distribution of horizontal surface velocities at the sea surface and to relate these velocities to deep-water wind wave breaking. Results are consistent with many recent studies that show a kinematic-based breaking criterion can provide a consistent depiction of the onset of wave breaking. This criterion is combined with the calculated nonlinear flux rates to estimate a transition point within a spectrum at which a spectrum changes from an f−4 equilibrium-range form to an f−5 region dominated by dissipation, potentially an important factor within several air–sea interaction mechanisms, turbulence at the sea surface, and remote sensing applications. It also has the potential to improve operational modeling capabilities.
The influence of a cooked-fish meal on estimated glomerular filtration rate
Authors: Shah Kezah F , Stevens Paul E , Lamb Edmund J 
Published: December 2019

BackgroundIngestion of cooked meat increases circulating blood creatinine concentration due to conversion of creatine during cooking. This may cause falsely low estimated glomerular filtration rate. National Institute for Health and Care Excellence chronic kidney disease guidelines recommend meat avoidance prior to blood testing for estimated glomerular filtration rate. Fish muscle also contains creatine, but the influence of fish consumption on blood creatinine concentration has not been studied.MethodFour blood samples were collected from each of 20 healthy volunteers: one before and three (at 2, 4 and 20 h) after consuming cooked fish (200 g/person cod, approximately 35 g/person protein). Apart from this meal, for the study duration, subjects were asked to avoid eating meat or fish. Creatinine and cystatin C were measured and estimated glomerular filtration rate (CKD-EPI equations) was calculated.ResultsSerum creatinine concentration (mean) was increased relative to the preprandial concentration (71.8 μmol/L) in all subjects at 2 h (77.3 μmol/L) and in 17/20 subjects at 4 h (75.5 μmol/L) ( P < 0.0001) but was not significantly different from baseline after 20 h (73.6 μmol/L P = 0.1170). Mean cystatin C concentration remained unchanged throughout the study ( P > 0.05). Estimated glomerular filtration rate calculated using the CKD-EPI (creatinine) and CKD-EPI (creatinine and cystatin C) equations demonstrated significant declines at 2 and 4 h ( P < 0.0005), while the CKD-EPI (cystatin C) equation remained unchanged ( P > 0.05).ConclusionCooked fish consumption transiently increases blood creatinine concentration and consequently lowers the estimates of glomerular filtration rate derived from creatinine-based equations. Consideration should be given to avoidance of cooked fish consumption before glomerular filtration rate estimation.
Academic policy advice in consensus-seeking countries: the cases of Belgium and Germany
Authors: Pattyn Valérie , Blum Sonja , Fobé Ellen , Pekar-Milicevic Mirjam , Brans Marleen 
Published: December 2019

Research on policy-advisory systems worldwide has shown that historically dominant sources of advice traditionally located in-house to the government have been increasingly supplemented by other actors and outside knowledge. However, the vast majority of research has concentrated on the anglophone context. Yet, countries with a consensus-seeking, neo-corporatist tradition provide a special case in terms of policy advice and merit more scholarly attention. What counts as evidence in these countries is the expert rationality of institutional representatives. The position and role of academic research in consensus-based systems is unclear, and is the focus of this article. Can we observe commonalities across consensus-style countries, or do differences prevail? We investigate two typical consensus-seeking countries: Belgium and Germany. To examine the supply side of policy advice, the article reviews current evidence regarding their policy-advisory systems. For the demand side, we present insights from a survey among federal ministerial officials. We find common trends between the two cases but their nature and extent are idiosyncratic. In Belgium, the supply of and demand for academic policy advice is comparatively lower, while the German case exhibits more change in the advisory landscape and institutionalisation of the supply of and demand for academic research. Points for practitioners   • Countries with a consensus-seeking, neo-corporatist tradition provide a special case in terms of policy advice.   • The findings suggest that there are common trends but their nature and extent are idiosyncratic.   • In Belgium, the supply of and demand for academic advice is comparatively lower.   • Germany’s policy-advisory landscape exhibits more change and institutionalisation of the supply of and demand for academic research.
Lived Experience: Characteristics of Workers in Alcohol and Other Drug Nongovernment Organizations
Authors: Chapman Janine , Roche Ann M. , Kostadinov Victoria , Duraisingam Vinita , Hodge Sianne 
Published: December 2019

Background: Workers with lived experience of problematic alcohol and other drug (AOD) use are increasingly recognized as integral to the AOD field. However, little is known about the prevalence or characteristics of AOD workers with lived experience across the general AOD workforce, in Australia or internationally. This study aimed to (1) investigate the prevalence of lived experience in AOD workers, (2) build an initial profile of workers with lived experience, (3) identify areas where appropriate support mechanisms may be warranted, and (4) generate recommendations for future work. Method: Nongovernment organization AOD workers from New South Wales, Australia, were invited to participate in a purpose-designed, online survey. Measures included demographic and workforce characteristics, work-related psychosocial factors, and health, quality of life, and AOD use. Descriptive analyses compared responses from workers with and without lived experience on key variables. Results: Two hundred and sixty-eight workers responded. Workers with lived experience comprised 43% of the sample; were more likely to be older; male; identify as lesbian, gay, homosexual, or queer; have lower salary; report discrimination in the workplace; abstain from alcohol; report opioid use; and experience less support outside work. Conclusion: This is the first Australian study to examine the profile of AOD workers with lived experience. Workers with lived experience constituted a substantial proportion of the AOD workforce. Analogous to other countries, comprehensive, appropriately tailored workforce development and support policies are required. Future research should build on these findings by extending to a broader population base, including government workers.
Does trunk muscle training with an oscillating rod improve urinary incontinence after radical prostatectomy? A prospective randomized controlled trial
Authors: Heydenreich Marc , Puta Christian , Gabriel Holger HW , Dietze Andre , Wright Peter , Zermann Dirk-Henrik 
Published: December 2019

Objective: To investigate the effect of a new therapeutic approach, using an oscillating rod to strength the pelvic floor and deep abdominal musculature and to speed up recovery of continence after radical prostatectomy. Design: Prospective randomized controlled clinical trial. Setting: Inpatient uro-oncology rehabilitation clinic. Subjects: Ninety-three (intervention group (IG)) and ninety-one patients (control group (CG)) with urinary incontinence after prostatectomy were examined. Intervention: All patients were randomly allocated to either standard pelvic floor muscle exercises and oscillating rod therapy (IG) or standard pelvic floor muscle exercises and relaxation therapy (CG). Main outcome measures: Urinary incontinence (1- and 24-hour pad test) was assessed, and health-related quality of life (HRQL; Functional Assessment of Cancer Therapy-Prostate (FACT-P) questionnaire) was measured for all patients before and after three weeks of treatment. Results: One hundred and eighty-four patients (mean (SD) age: 64.1 (6.94) years) completed the study. The IG showed a significant reduction in urinary incontinence (1-hour pad test: P = 0.008, 24-hour pad test: P = 0.012) and a significant improvement of HRQL ( P = 0.017) compared with CG. Continence was significantly improved in both groups (1-hour pad test: 22.6–8.5 g (IG) vs. 23.0–18.1 g (CG)/24-hour pad test: 242.9–126.7 g (IG) vs. 237.6–180.9 g (CG)). Conclusion: The study demonstrated that a combination of conventional continence exercises and the new oscillation rod training increased abdominal and pelvic floor musculature and speeded up recovery of continence after radical prostatectomy.