bluuebunny/crossref_metadata_2025_split huggingface dataset:
Call graphs for languages with parametric polymorphism
Authors: Petrashko Dmitry , Ureche Vlad , Lhoták Ondřej , Odersky Martin 
Published: December 2016

The performance of contemporary object oriented languages depends on optimizations such as devirtualization, inlining, and specialization, and these in turn depend on precise call graph analysis. Existing call graph analyses do not take advantage of the information provided by the rich type systems of contemporary languages, in particular generic type arguments. Many existing approaches analyze Java bytecode, in which generic types have been erased. This paper shows that this discarded information is actually very useful as the context in a context-sensitive analysis, where it significantly improves precision and keeps the running time small. Specifically, we propose and evaluate call graph construction algorithms in which the contexts of a method are (i) the type arguments passed to its type parameters, and (ii) the static types of the arguments passed to its term parameters. The use of static types from the caller as context is effective because it allows more precise dispatch of call sites inside the callee.
Our evaluation indicates that the average number of contexts required per method is small. We implement the analysis in the Dotty compiler for Scala, and evaluate it on programs that use the type-parametric Scala collections library and on the Dotty compiler itself. The context-sensitive analysis runs 1.4x faster than a context-insensitive one and discovers 20% more monomorphic call sites at the same time. When applied to method specialization, the imprecision in a context-insensitive call graph would require the average method to be cloned 22 times, whereas the context-sensitive call graph indicates a much more practical 1.00 to 1.50 clones per method.
We applied the proposed analysis to automatically specialize generic methods. The resulting automatic transformation achieves the same performance as state-of-the-art techniques requiring manual annotations, while reducing the size of the generated bytecode by up to 5x.
Hoare-style specifications as correctness conditions for non-linearizable concurrent objects
Authors: Sergey Ilya , Nanevski Aleksandar , Banerjee Anindya , Delbianco Germán Andrés 
Published: December 2016

Designing efficient concurrent objects often requires abandoning the standard specification technique of linearizability in favor of more relaxed correctness conditions. However, the variety of alternatives makes it difficult to choose which condition to employ, and how to compose them when using objects specified by different conditions.
In this work, we propose a uniform alternative in the form of Hoare logic, which can explicitly capture--in the auxiliary state--the interference of environment threads. We demonstrate the expressiveness of our method by verifying a number of concurrent objects and their clients, which have so far been specified only by non-standard conditions of concurrency-aware linearizability, quiescent, and quantitative quiescent consistency. We report on the implementation of the ideas in an existing Coq-based tool, providing the first mechanized proofs for all the examples in the paper.
Directed synthesis of failing concurrent executions
Authors: Samak Malavika , Tripp Omer , Ramanathan Murali Krishna 
Published: December 2016

Detecting concurrency-induced bugs in multithreaded libraries can be challenging due to the intricacies associated with their manifestation. This includes invocation of multiple methods, synthesis of inputs to the methods to reach the failing location, and crafting of thread interleavings that cause the erroneous behavior. Neither fuzzing-based testing techniques nor over-approximate static analyses are well positioned to detect such subtle defects while retaining high accuracy alongside satisfactory coverage.
In this paper, we propose a directed, iterative and scalable testing engine that combines the strengths of static and dynamic analysis to help synthesize concurrent executions to expose complex concurrency-induced bugs. Our engine accepts as input the library, its client (either sequential or concurrent) and a specification of correctness. Then, it iteratively refines the client to generate an execution that can break the input specification. Each step of the iterative process includes statically identifying sub-goals towards the goal of failing the specification, generating a plan toward meeting these goals, and merging of the paths traversed dynamically with the plan computed statically via constraint solving to generate a new client. The engine reports full reproduction scenarios, guaranteed to be true, for the bugs it finds.
We have created a prototype of our approach named MINION. We validated MINION by applying it to well-tested concurrent classes from popular Java libraries, including the latest versions of openjdk and google-guava. We were able to detect 31 real crashes across 10 classes in a total of 23 minutes, including previously unknown bugs. Comparison with three other tools reveals that combined, they report only 9 of the 31 crashes (and no other crashes beyond MINION). This is because several of these bugs manifest under deeply nested path conditions (observed maximum of 11), deep nesting of method invocations (observed maximum of 6) and multiple refinement iterations to generate the crash-inducing client.
A Phase II Randomized Placebo-Controlled Trial of OralN-acetylcysteine for Protection of Melanocytic Nevi against UV-Induced Oxidative StressIn Vivo
Authors: Cassidy Pamela B. , Liu Tong , Florell Scott R. , Honeggar Matthew , Leachman Sancy A. , Boucher Kenneth M. , Grossman Douglas 
Published: December 2016

AbstractOxidative stress plays a role in UV-induced melanoma, which may arise from melanocytic nevi. We investigated whether oral administration of the antioxidant N-acetylcysteine (NAC) could protect nevi from oxidative stress in vivo in the setting of acute UV exposure. The minimal erythemal dose (MED) was determined for 100 patients at increased risk for melanoma. Patients were randomized to receive a single dose (1,200 mg) of NAC or placebo, in double-blind fashion, and then one nevus was irradiated (1–2 MED) using a solar simulator. One day later, the MED was redetermined and the irradiated nevus and a control unirradiated nevus were removed for histologic analysis and examination of biomarkers of NAC metabolism and UV-induced oxidative stress. Increased expression of 8-oxoguanine, thioredoxin reductase-1, and γ-glutamylcysteine synthase modifier subunit were consistently seen in UV-treated compared with unirradiated nevi. However, no significant differences were observed in these UV-induced changes or in the pre- and postintervention MED between those patients receiving NAC versus placebo. Similarly, no significant differences were observed in UV-induced changes between subjects with germline wild-type versus loss-of-function mutations in the melanocortin-1 receptor. Nevi showed similar changes of UV-induced oxidative stress in an open-label post-trial study in 10 patients who received NAC 3 hours before nevus irradiation. Thus, a single oral dose of NAC did not effectively protect nevi from UV-induced oxidative stress under the conditions examined. Cancer Prev Res; 10(1); 36–44. ©2016 AACR.
Low
MT‐CO1
in Monocytes and Microvesicles Is Associated With Outcome in Patients With Coronary Artery Disease
Authors: Holvoet Paul , Vanhaverbeke Maarten , Bloch Katarzyna , Baatsen Pieter , Sinnaeve Peter , Janssens Stefan 
Published: December 2016

Background
Cytochrome oxidase (COX) IV complex regulates energy production in mitochondria. Impaired COX gene expression is related to obesity and type 2 diabetes mellitus, but whether it is directly related to the incidence of cardiovascular events is unknown. We investigated whether COX gene expression in monocytes is predictive for cardiovascular events in coronary artery disease patients. To avoid monocyte isolation from fresh blood, we then aimed to validate our findings in monocyte‐derived microvesicles isolated from plasma.

Methods and Results

We enrolled 142 consecutive patients undergoing diagnostic coronary angiography between June 2010 and January 2011 and followed 67 patients with stable coronary artery disease prospectively for at least 3 years. Twenty‐two patients experienced a new cardiovascular event (32.8%). Circulating CD14
+
monocytes and microvesicles were isolated with magnetic beads, and COX mRNA levels were measured with quantitative polymerase chain reaction, after normalization with 5 validated house‐keeping genes. Patients in the lowest tertile of mitochondrial cytochrome oxidase, subunit I (
MT‐COI
) in monocytes at baseline had a higher risk for developing a new event after adjusting for age, sex, (ex)smoking, body mass index, blood pressure, diabetes mellitus, low‐density lipoprotein– and high‐density lipoprotein–cholesterol, triglycerides, high‐sensitivity C‐reactive protein, interleukin‐6, and number of diseased vessels (harzard ratio [HR], 3.95; 95% CI, 1.63–9.57). Patients in the lowest tertile of
MT‐COI
in monocyte‐specific microvesicles had also a higher risk of developing a new event (adjusted HR, 5.00; 95% CI, 1.77–14).

Conclusions

In the current blinded study, low
MT‐COI
in monocytes of coronary artery disease patients identifies a population at risk for new cardiovascular events. For the first time, we show that signatures in monocyte‐specific microvesicles in plasma have similar predictive properties.
Debating what Lü Dongbin Practiced: Why did the Yuan Daoist Miao Shanshi Denounce the Zhong-Lü Texts?
Authors: Eskildsen Stephen 
Published: December 2016

Miao Shanshi (fl. 1324), in his Chunyang dijun shenhua miaotong ji, a large collection of stories about the legendary immortal Lü Dongbin, denounces as spurious and fallacious the three so-called “Zhong-Lü texts” (Zhong-Lü chuandao ji, Lingbao bifa, and Xishan qunxian huizhen ji) that claim to convey the inner alchemical teachings learned and practiced by Lü Dongbin. So why did Miao Shanshi, who saw himself as a champion of Quanzhen Daoist orthodoxy and defender of Lü Dongbin’s true legacy, so disdain these texts? Clues for answering this question are to be found in the dialogue between Zhongli Quan and Lü Dongbin recorded in the Miaotong ji’s sixth episode. Miao Shanshi’s editorial comments provide further hints as to what he objected to in the Zhong-Lü texts, as well as to how he himself may have arrived at his notion of what Lü Dongbin learned, practiced, and later taught. Attention is here also paid to another work of his, entitled Xuanjiao dagong’an. Miao Shanshi’s inner alchemical methods, which he considered the true teachings of Lü Dongbin, compared to those advocated in the Zhong-Lü texts, are much less complicated and seem to essentially consist of making the mind clear and calm while slowing down one’s breathing. Miao Shanshi (fl. 1324), dénonce dans son Chunyang dijun shenhua miaotong ji (Miaotong ji ; une vaste collection de récits sur l’immortel légendaire Lü Dongbin), les trois textes dits de la tradition “Zhong-Lü” (Zhong-Lü chuandao ji, Lingbao bifa et Xishan qunxian huizhen ji). Il affirme que ces textes réputés exposer les techniques d’alchimie intérieure reçues et pratiquées par Lü Dongbin sont en réalité apocryphes et erronées. Pourquoi Miao Shanshi, qui se présente comme un pilier de l’orthodoxie du taoïsme Quanzhen et un gardien de l’héritage de Lü Dongbin, rejette-t-il ces textes avec autant de virulence ? La réponse se trouve en bonne partie dans le dialogue entre Zhongli Quan et Lü Dongbin exposé dans le 6e épisode du Miaotong ji. Miao Shanshi dans ses commentaires à son propre récit fournit des éléments supplémentaires sur son opposition à ces textes et sur sa propre façon de concevoir ce que fut l’enseignement de Lü Dongbin. La vision de l’orthodoxie défendue par Miao Shanshi est encore analysée dans une autre de ses œuvres, le Xuanjiao dagong’an. L’article conclut que les méthodes d’alchimie intérieure défendues par Miao Shanshi (et qu’il considère comme représentant l’enseignement authentique de Lü Dongbin) sont bien moins complexes techniquement que celles exposées dans les textes Zhong-Lü, et consistent essentiellement à rendre l’esprit clair et calme en ralentissant sa respiration.
The advertisement calls of Quasipaa shini (Ahl, 1930) (Anura: Dicroglossidae)
Authors: KONG SHEN SHEN , ZHENG RONG QUAN , ZHANG QI PENG 
Published: December 2016

The genus Quasipaa (Family Dicroglossidae) is currently composed of 11 species distributed in China and Southeast Asia: Quasipaa acanthophora (Dubois & Ohler 2009), Q. boulengeri (Günther 1889), Q. courtoisi (Angel 1922), Q. delacouri (Angel 1928), Q. exilispinosa (Liu & Hu, 1975), Q. fasciculispina (Inger 1970), Q. jiulongensis (Huang & Liu, 1985), Q. shini (Ahl 1930), Q. spinosa (David 1875), Q. verrucospinosa (Bourret 1937), Q. yei (Chen, Qu & Jiang 2002) (Frost 2016). These species are morphologically similar, and their taxonomy is subject to controversy (Che et al. 2009). Analyses of nuclear and mitochondrial genes suggest the genus likely encompass additional cryptic species (Ye et al. 2013). Bioacoustics has contributed to studies on the taxonomy of the genus (Ye et al. 2013; Shen et al. 2015), however, to date, only the advertisement calls of Q. spinosa are known (Yu & Zheng 2009; Chen et al. 2012; Shen et al. 2015). Here, we describe the advertisement calls of Q. shini, which inhabits streams in the southern part of central China(Guizhou, Hunan, Guangxi and Jiangxi) and is characterized by the presence of keratinized skin spines on the lateral surfaces of the body.
Troubleshooting for bleeding in thoracoscopic anatomic pulmonary resection
Authors: Igai Hitoshi , Kamiyoshihara Mitsuhiro , Ibe Takashi , Kawatani Natsuko , Osawa Fumi , Yoshikawa Ryohei 
Published: December 2016

Introduction The objective of this study was to evaluate intraoperative vessel injury and assess troubleshooting during thoracoscopic anatomic pulmonary resection. Methods Between April 2012 and March 2016, 240 patients underwent thoracoscopic anatomic lung resection, 26 of whom were identified as having massive bleeding intraoperatively. We analyzed the injured vessel and the hemostatic procedure employed, then compared the perioperative outcomes in patients with ( n = 26) and without ( n = 214) vessel injury. In addition, we compared perioperative results based on the period when surgery was performed: early period: April 2012 to March 2014 ( n = 93) or late period: April 2014 to March 2016 ( n = 146). Results The surgical procedures included 20 lobectomies and 6 segmentectomies. One of the 26 patients had vessel injury at 2 points, giving a total of 27 points of injury. Hemostasis was mostly achieved by application of thrombostatic sealant (63.0%). There were no significant differences in the length postoperative hospitalization ( p = 0.67) or morbidity rate ( p = 0.43) between the vessel injury and the no-vessel injury groups. There were no significant differences in the incidence of significant intraoperative bleeding ( p = 0.13) and total blood loss ( p = 0.13) between the early and late periods. Conclusions Application of thrombostatic sealant is one of the useful methods to achieve hemostasis during thoracoscopic anatomic pulmonary resection. Vascular hazards are inherent to a thoracoscopic approach. Therefore, thoracic surgeons should always be concerned about significant intraoperative bleeding and treat it appropriately.
Posterior Meniscal Root Repairs: Outcomes of an Anatomic Transtibial Pull-Out Technique
Authors: LaPrade Robert F. , Matheny Lauren M. , Moulton Samuel G. , James Evan W. , Dean Chase S. 
Published: December 2016

Background: Outcomes after transtibial pull-out repair for posterior meniscal root tears remain underreported, and factors that may affect outcomes are unknown. Purpose/Hypothesis: The purpose of this study was to compare patient-centered outcomes after transtibial pull-out repair for posterior root tears in patients <50 and ≥50 years of age. We hypothesized that improvement in function and activity level at minimum 2-year follow-up would be similar among patients <50 years of age compared with patients ≥50 years and among patients undergoing medial versus lateral root repairs. Study Design: Cohort study; Level of evidence, 3. Methods: Inclusion criteria were patients aged 18 years or older who underwent anatomic transtibial pull-out repair of the medial or lateral posterior meniscus root by a single surgeon. All patients were identified from a data registry consisting of prospectively collected data in a consecutive series. Cohorts were analyzed by age (<50 years [n = 35] vs ≥50 years [n = 15]) and laterality (lateral [n = 15] vs medial [n = 35]). Patients completed a subjective questionnaire preoperatively and at minimum of 2 years postoperatively (Lysholm, Tegner, Western Ontario and McMaster Universities Osteoarthritis Index [WOMAC], 12-Item Short Form Health Survey [SF-12], and patient satisfaction with outcome). Failure was defined as revision meniscal root repair or partial meniscectomy. Results: The analysis included 50 knees in 49 patients (16 females, 33 males; mean age, 38.3 years; mean body mass index, 26.6). Of the 50 knees, 45 were available for analysis. Three of 45 (6.7%) required revision surgery. All failures were in patients <50 years old, and all failures underwent medial root repair. No significant difference in failure was found based on age ( P=.541) or laterality ( P = .544). For age cohorts, Lysholm and WOMAC scores demonstrated significant postoperative improvement. For laterality cohorts, all functional scores significantly improved postoperatively. No significant difference was noted in postoperative Lysholm, WOMAC, SF-12, Tegner, or patient satisfaction scores for the age cohort or the laterality cohort. Conclusion: Outcomes after posterior meniscal root repair significantly improved postoperatively and patient satisfaction was high, regardless of age or meniscal laterality. Patients <50 years had outcomes similar to those of patients ≥50 years, as did patients who underwent medial versus lateral root repair. Transtibial double-tunnel pull-out meniscal root repair provided improvement in function, pain, and activity level, which may aid in delayed progression of knee osteoarthritis.
The Role of Leadership Support for Health Promotion in Employee Wellness Program Participation, Perceived Job Stress, and Health Behaviors
Authors: Hoert Jennifer , Herd Ann M. , Hambrick Marion 
Published: December 2016

Purpose: The purpose of the study was to explore the relationship between leadership support for health promotion and job stress, wellness program participation, and health behaviors. Design: A cross-sectional survey design was used. Setting: Four worksites with a range of wellness programs were selected for this study. Participants: Participants in this study were employees (n = 618) at 4 organizations (bank, private university, wholesale supplier, and public university) in the southeastern United States, each offering an employee wellness program. Response rates in each organization ranged from 3% to 34%. Measures: Leadership support for health promotion was measured with the Leading by Example instrument. Employee participation in wellness activities, job stress, and health behaviors were measured with multi-item scales. Analysis: Correlation/regression analysis and descriptive statistics were used to analyze the relationships among the scaled variables. Results: Employees reporting higher levels of leadership support for health promotion also reported higher levels of wellness activity participation, lower job stress, and greater levels of health behavior ( P = .001). To ascertain the amount of variance in health behaviors accounted for by the other variables in the study, a hierarchical regression analysis revealed a statistically significant model (model F7,523 = 27.28; P = .001), with leadership support for health promotion (β = .19, t = 4.39, P = .001), wellness activity participation (β = .28, t = 6.95, P < .001), and job stress (β = −.27, t = −6.75, P ≤ .001) found to be significant predictors of health behaviors in the model. Exploratory regression analyses by organization revealed the focal variables as significant model predictors for only the 2 larger organizations with well-established wellness programs. Conclusion: Results from the study suggest that employees’ perceptions of organizational leadership support for health promotion are related to their participation in wellness activities, perceived job stress levels, and health behaviors.
Detection of imprinting effects for qualitative traits on X chromosome based on nuclear families
Authors: Zhou Ji-Yuan , You Xiao-Ping , Yang Ran , Fung Wing Kam 
Published: December 2016

Methods for detecting imprinting effects have been developed primarily for autosomal markers. However, no method is available in the literature to test for imprinting effects on X chromosome. Therefore, it is necessary to suggest methods for detecting such imprinting effects. In this article, the parental-asymmetry test on X chromosome (XPAT) is first developed to test for imprinting for qualitative traits in the presence of association, based on family trios each with both parents and their affected daughter. Then, we propose 1-XPAT to deal with parent–daughter pairs, each with one parent and his/her affected daughter. By simultaneously considering family trios and parent–daughter pairs, C-XPAT (the combined test statistic of XPAT and 1-XPAT) is constructed to test for imprinting. Further, we extend the proposed methods to accommodate complete (with both parents) and incomplete (with one parent) nuclear families having multiple daughters of which at least one is affected. Simulation results demonstrate that the proposed methods control the size well, irrespective of the inbreeding coefficient in females being zero or non-zero. By incorporating incomplete nuclear families, C-XPAT is more powerful than XPAT using only complete nuclear families. For practical use, these proposed methods are applied to analyse the rheumatoid arthritis data and Turner’s syndrome data.