bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tracing compilation by abstract interpretation
Authors: Dissegna Stefano , Logozzo Francesco , Ranzato Francesco 
Published: April 2020

Tracing just-in-time compilation is a popular compilation schema for the efficient implementation of dynamic languages, which is commonly used for JavaScript, Python, and PHP. It relies on two key ideas. First, it monitors the execution of the program to detect so-called hot paths, i.e., the most frequently executed paths. Then, it uses some store information available at runtime to optimize hot paths. The result is a residual program where the optimized hot paths are guarded by sufficient conditions ensuring the equivalence of the optimized path and the original program. The residual program is persistently mutated during its execution, e.g., to add new optimized paths or to merge existing paths. Tracing compilation is thus fundamentally different than traditional static compilation. Nevertheless, despite the remarkable practical success of tracing compilation, very little is known about its theoretical foundations.
We formalize tracing compilation of programs using abstract interpretation. The monitoring (viz., hot path detection) phase corresponds to an abstraction of the trace semantics that captures the most frequent occurrences of sequences of program points together with an abstraction of their corresponding stores, e.g., a type environment. The optimization (viz., residual program generation) phase corresponds to a transform of the original program that preserves its trace semantics up to a given observation as modeled by some abstraction. We provide a generic framework to express dynamic optimizations and to prove them correct. We instantiate it to prove the correctness of dynamic type specialization. We show that our framework is more general than a recent model of tracing compilation introduced in POPL~2011 by Guo and Palsberg (based on operational bisimulations). In our model we can naturally express hot path reentrance and common optimizations like dead-store elimination, which are either excluded or unsound in Guo and Palsberg's framework.
Molecular Imaging of the Tumor Microenvironment Reveals the Relationship between Tumor Oxygenation, Glucose Uptake, and Glycolysis in Pancreatic Ductal Adenocarcinoma
Authors: Yamamoto Kazutoshi , Brender Jeffrey R. , Seki Tomohiro , Kishimoto Shun , Oshima Nobu , Choudhuri Rajani , Adler Stephen S. , Jagoda Elaine M. , Saito Keita , Devasahayam Nallathamby , Choyke Peter L. , Mitchell James B. , Krishna Murali C. 
Published: April 2020

Abstract

Molecular imaging approaches for metabolic and physiologic imaging of tumors have become important for treatment planning and response monitoring. However, the relationship between the physiologic and metabolic aspects of tumors is not fully understood. Here, we developed new hyperpolarized MRI and electron paramagnetic resonance imaging procedures that allow more direct assessment of tumor glycolysis and oxygenation status quantitatively. We investigated the spatial relationship between hypoxia, glucose uptake, and glycolysis in three human pancreatic ductal adenocarcinoma tumor xenografts with differing physiologic and metabolic characteristics. At the bulk tumor level, there was a strong positive correlation between 18F-FDG-PET and lactate production, while pO2 was inversely related to lactate production and 18F-2-fluoro-2-deoxy-D-glucose (18F-FDG) uptake. However, metabolism was not uniform throughout the tumors, and the whole tumor results masked different localizations that became apparent while imaging. 18F-FDG uptake negatively correlated with pO2 in the center of the tumor and positively correlated with pO2 on the periphery. In contrast to pO2 and 18F-FDG uptake, lactate dehydrogenase activity was distributed relatively evenly throughout the tumor. The heterogeneity revealed by each measure suggests a multimodal molecular imaging approach can improve tumor characterization, potentially leading to better prognostics in cancer treatment.

Significance:
Novel multimodal molecular imaging techniques reveal the potential of three interrelated imaging biomarkers to profile the tumor microenvironment and interrelationships of hypoxia, glucose uptake, and glycolysis.
The Influence of Cancer Molecular Subtypes and Treatment on the Mutation Spectrum in Metastatic Breast Cancers
Authors: Verret Benjamin , Sourisseau Tony , Stefanovska Bojana , Mosele Fernanda , Tran-Dien Alicia , André Fabrice 
Published: April 2020

Abstract
Next-generation sequencing has sparked the exploration of cancer genomes, with the aim of discovering the genetic etiology of the disease and proposing rationally designed therapeutic interventions. Driver gene alterations have been comprehensively charted, but the improvement of cancer patient management somewhat lags behind these basic breakthroughs. Recently, large-scale sequencing that focused on metastasis, the main cause of cancer-related deaths, has shed new light on the driving forces at work during disease progression, particularly in breast cancer. Despite a fairly stable pool of driver genetic alterations between early and late disease, a number of therapeutically targetable mutations have been found enriched in metastatic samples. The molecular processes fueling disease progression have been delineated in recent studies and the clonal composition of breast cancer samples can be examined in detail. Here we discuss how these findings may be combined to improve the diagnosis of breast cancer to better select patients at risk, and to identify targeted agents to treat advanced diseases and to design therapeutic strategies exploiting vulnerabilities of cancer cells rooted in their ability to evolve and drive disease progression.
Validating Breast Cancer Risk Prediction Models in the Korean Cancer Prevention Study-II Biobank
Authors: Jee Yon Ho , Gao Chi , Kim Jihye , Park Seho , Jee Sun Ha , Kraft Peter 
Published: April 2020

Abstract

Background:
Risk prediction models may be useful for precision breast cancer screening. We aimed to evaluate the performance of breast cancer risk models developed in European-ancestry studies in a Korean population.

Methods:
We compared discrimination and calibration of three multivariable risk models in a cohort of 77,457 women from the Korean Cancer Prevention Study (KCPS)-II. The first incorporated U.S. breast cancer incidence and mortality rates, U.S. risk factor distributions, and RR estimates from European-ancestry studies. The second recalibrated the first by using Korean incidence and mortality rates and Korean risk factor distributions, while retaining the European-ancestry RR estimates. Finally, we derived a Korea-specific model incorporating the RR estimates from KCPS.

Results:
The U.S. European-ancestry breast cancer risk model was well calibrated among Korean women &lt;50 years [expected/observed = 1.124 (0.989, 1.278)] but markedly overestimated the risk for those ≥50 years [E/O = 2.472 (2.005, 3.049)]. Recalibrating absolute risk estimates using Korean breast cancer rates and risk distributions markedly improved the calibration in women ≥50 [E/O = 1.018 (0.825, 1.255)]. The model incorporating Korean-based RRs had similar but not clearly improved performance relative to the recalibrated model.

Conclusions:
The poor performance of the U.S. European-ancestry breast cancer risk model among older Korean women highlights the importance of tailoring absolute risk models to specific populations. Recalibrating the model using Korean incidence and mortality rates and risk factor distributions greatly improved performance.

Impact:
The data will provide valuable information to plan and evaluate actions against breast cancer focused on primary prevention and early detection in Korean women.
On Global Corporate Control: Review of an Article
Authors: Parry Bruce 
Published: April 2020

Abstract
This article reviews “The network of global corporate control” by Vitali et al. (2011) where the authors use modern network theory to analyze the centralization of global corporate control. Specifically, they calculate how a central core of transnational corporations (TNCs) have control over the total operating revenue of all transnational corporations. They find that out of 43,060 transnational corporations, 737 top shareholders control about 80 percent of the value of all TNCs. This control is centralized in the financial sector and extends to other sectors of the economy, including manufacturing and services. TNCs are more global than ever before. They are in virtually every country of the world and comprise a world capitalist system.
Asian Roboticism: Connecting Mechanized Labor to the Automation of Work
Authors: Bui Long 
Published: April 2020

Abstract
This article reconsiders the present-day automation of work and its transformation of who we are as humans. What has been missing from this important conversation are the social meanings surrounding Asian roboticism or how Asians have already been rendered as “robotic” subjects and labor. Through this racial gendered trope, I assess whether industrial automation will lessen, complicate, or exacerbate this modern archetype. By looking at corporate organizational practices and public media discourse, I believe that Asian roboticism will not simply vanish, but potentially continue to affect the ways such subjects are rendered as exploitable alienated robots without human rights or status.
The Green New Deal: What Makes It Necessary, What It Is, and How We Can Get It
Authors: Davidson Carl 
Published: April 2020

Abstract
This article serves as the content for a slide show presented at the Global Studies Association conference held at Loyola University in Chicago on June 6-8, 2019. The discussion emphasized the importance of establishing The Green New Deal by transitioning away from burning carbon and uranium to stop and reduce CO2 levels, building a Smart Grid, redesigning and rebuilding industries for zero waste, transitioning from agribusiness factory farms to organic, sustainable family-sized farms, redesigning new housing and retrofitting existing stock, increasing innovation and high design for all products and services, and curbing the production of poisons and removing pollutants from human consumption. The link to the presentation is http://ouleft.org/wp-content/uploads/Green-New-Deal-2.pdf.
Gendered Exploitation under Contemporary Capitalism
Authors: Jensen Nick , Dyett Jordan 
Published: April 2020

Abstract
With globalization as a catalyst, hegemonic powers dependent upon neoliberal capitalism continue to exploit resources, locations, and humans for economic benefit. This research explores how states and corporations strategically force already vulnerable populations into further lives of precarity, all to extract surplus value to feed the capitalist machine. Employing World Systems and Decolonial Theory we seek to uncover the paths that corporations take to cut corners, exploit labor, and avoid regulations. Specifically, we will be comparing the evolution of the semiconductor industry in Southeast Asia with the maquiladoras in Mexico to illuminate the methodical exploitation of labor and the earth in the name of economic gain.
Ocean Acidification: A Due Diligence Obligation under the LOSC
Authors: Scott Karen N 
Published: April 2020

Abstract
This article explores the extent to which ocean acidification is adequately addressed by the law of the sea. It will assess the various obligations under Part XII of the 1982 United Nations Convention of the Law of the Sea (LOSC) to prevent, reduce and control pollution of the marine environment, and analyse the extent to which these obligations appropriately address ocean acidification. This article argues that LOSC Parties are subject to a due diligence obligation under Part XII of the Convention to prevent, reduce and control ocean acidification, and that this obligation is not satisfied by simply complying with their obligations under the UN Framework Convention on Climate Change, unless those actions also deliberately address ocean acidification. This article goes on to examine whether and to what extent ocean acidification should be factored into decision-making associated with marine planning, fisheries management and area-based protection under the law of the sea.
Linking Drought Impacts to Drought Severity at the State Level
Authors: Noel Mary , Bathke Deborah , Fuchs Brian , Gutzmer Denise , Haigh Tonya , Hayes Michael , Poděbradská Markéta , Shield Claire , Smith Kelly , Svoboda Mark 
Published: April 2020

AbstractThe U.S. Drought Monitor (USDM), a weekly map depicting severity and spatial extent of drought, is used to communicate about drought in state and federal decision-making, and as a trigger in response policies, including the distribution of hundreds of millions of dollars for agricultural financial relief in the United States annually. An accompanying classification table helps interpret the map and includes a column of possible impacts associated with each level of drought severity. However, the column describing potential drought impacts is generalized for the entire United States. To provide more geographically specific interpretation of drought, state and regionally specific drought impact classification tables were developed by linking impacts chronicled in the Drought Impact Reporter (DIR) to USDM severity levels across the United States and Puerto Rico and identifying recurrent themes at each level. After creating state-level tables of impacts observed for each level of drought, a nationwide survey was administered to drought experts and decision-makers (n = 89), including the USDM authors, to understand whether the tables provided accurate descriptions of drought impacts in their state. Seventy-six percent of respondents indicated the state table was an acceptable or good characterization of drought impacts for their respective state. This classification scheme was created with a reproducible qualitative methodology that used past observations to identify themes in drought impacts across multiple sectors to concisely describe expected impacts at different levels of drought in each state.
Excessive ITCZ but Negative SST Biases in the Tropical Pacific Simulated by CMIP5/6 Models: The Role of the Meridional Pattern of SST Bias
Authors: Zhou Shijie , Huang Gang , Huang Ping 
Published: April 2020

AbstractIn phases 5 and 6 of the state-of-the-art Coupled Model Intercomparison Project (CMIP5 and CMIP6, respectively) models, there is an apparent excessive rainfall bias with a negative SST bias in the tropical Pacific intertropical convergence zone (ITCZ). The regime of the excessive ITCZ but negative SST bias is inconsistent with the common positive rainfall–SST correlation of climate anomalies over the tropics. Using a two-mode model, we decomposed the rainfall bias into two components and found that the surface convergence (SC) bias is the key factor forming the excessive ITCZ bias in the historical runs of 25 CMIP5 models and 23 CMIP6 models. A mixed layer model was further applied to connect the formation of the SC bias with the SST pattern bias. The results suggest that the meridional pattern of the SST bias plays a key role in forming the SC bias. In the CMIP5 and CMIP6 models, the overall negative SST bias has two apparent meridional troughs at around 10°S and 10°N, respectively. The two meridional troughs in the SST bias drive two convergence centers in the SC bias favoring the excessive ITCZ, even though the local SST bias is negative.
Efficacy of intravitreal injection of conbercept on non-proliferative diabetic retinopathy: a retrospective study
Authors: Wang Jing , Jiang Peng-Fei , Liu Min , Kou Ming-Rong , Lei Jia-Ying , Yu Xiao-Ting , Zhao Ying , Wang Hong , Zhang Lin-Na 
Published: April 2020

Objective This study assessed the efficacy of conbercept for patients with non-proliferative diabetic retinopathy (NPDR). Methods In this retrospective clinical study, 54 patients with NPDR (54 eyes) were treated with intravitreal injection of conbercept using a 3+ pro re nata regimen and followed up for 12 months. Best corrected visual acuity (BCVA), central foveal thickness (CFT), area of hard exudate (HE), and number of microaneurysms (MAs) were used as indicators of therapeutic effects. Systemic adverse reactions were recorded to assess safety. Results During the 12-month follow-up period, the mean number of injections was 6.12 ± 1.89 on demand. From baseline to the 12-month follow-up, the BCVA of patients with NPDR increased from 0.71 ± 0.20 logMAR to 0.43 ± 0.16 logMAR, CFT decreased from 424.26 ± 64.89 μm to 269.27 ± 44.79 μm, and the number of MAs declined from 79.53 ± 27.18 to 33.34 ± 16.53. Moreover, the area of HE was significantly reduced after 9 months of treatment. There were no serious systemic adverse events during the follow-up. Conclusions Intravitreal injection of conbercept has a stable and robust effect on patients with NPDR over a 12-month follow-up period. Thus, conbercept is an effective and feasible treatment for NPDR.
Patient-reported outcomes in survivors of childhood hematologic malignancies with hematopoietic stem cell transplant
Authors: Yen Hsiu-Ju , Eissa Hesham M. , Bhatt Neel S. , Huang Sujuan , Ehrhardt Matthew J. , Bhakta Nickhill , Ness Kirsten K. , Krull Kevin R. , Srivastava D. Kumar , Robison Leslie L. , Hudson Melissa M. , Huang I-Chan 
Published: April 2020

Abstract
Patient-reported outcomes among survivors of pediatric hematopoietic stem cell transplant (HSCT) are understudied. We compared symptom prevalence, health-related quality of life (HRQOL), and risk factors in adult survivors of childhood hematologic malignancies treated with HSCT to those treated with conventional therapy and noncancer controls. Survivors of childhood hematologic malignancies (HSCT N = 112 [70% allogeneic, 30% autologous]; conventionally treated N = 1106) and noncancer controls (N = 242) from the St. Jude Lifetime Cohort Study completed surveys assessing 10 symptom domains and SF-36 HRQOL summary scores. Chronic health conditions (CHCs) were validated by clinical assessment. Multivariable logistic regression reveals that compared with noncancer controls, HSCT survivors endorsed a significantly higher symptom prevalence in sensation (OR = 4.7, 95% confidence interval [CI], 2.6-8.4), motor/movement (OR = 4.3, 95% CI, 1.6-11.0), pulmonary (OR = 4.6, 95% CI, 1.8-11.8), and memory domains (OR = 4.8, 95% CI, 2.5-9.2), and poorer physical HRQOL (OR = 6.9, 95% CI, 2.8-17.0). HSCT and conventionally treated survivors had a similar prevalence of all symptom domains and HRQOL (all P &gt; .05); however, HSCT survivors had a significantly higher cumulative prevalence for specific symptoms: double vision (P = .04), very dry eyes (P &lt; .0001), and trouble seeing when wearing glasses (P &lt; .0001). Occurrence of organ-specific CHCs, instead of transplant receipt, was significantly associated with a higher prevalence of all symptom domains (all P &lt; .05) in adult survivors of childhood cancer, except for pain and anxiety domains. This study found that patient-reported outcomes were equally impaired between HSCT and conventionally treated survivors, but poorer in both groups compared with noncancer controls. Poor patient-reported outcomes in all survivors of childhood hematologic malignancies correlated with the presence of CHCs, whether treated with conventional therapy or HSCT.
A systematic review of indicators to assess the sustainability of road infrastructure projects
Authors: Suprayoga Gede B. , Bakker Martha , Witte Patrick , Spit Tejo 
Published: April 2020

Abstract
Background
This study aims to examine to what extent sustainability has been incorporated into assessments of road infrastructure projects. It identifies promising approaches that include indicators reflecting core sustainability criteria, determines criteria that were insufficiently covered as indicators, and develops an integrated indicator set covering all criteria.

Methods
A systematic review was performed to obtain all related papers/reports in two academic databases: Scopus and Web of Sciences. The indicators extracted from papers/reports were first coded, then evaluated by using quantitative and qualitative content analysis.

Results
The project appraisal methods for decision-making is found to be a promising approach, covering more extensive criteria than others. Two criteria – namely adaptation and precaution and intergenerational equity – were hardly ever adopted as indicators. Ten main groups of indicators were extracted to construct an integrated set incorporating all core criteria.

Conclusions
Some criteria appear to have become mainstream, while others deserve attention. The safest choice is to combine methods/tools or to adopt the integrated set developed for exhaustive criteria inclusion.
Visualizing metabolic network dynamics through time-series metabolomic data
Authors: Buchweitz Lea F. , Yurkovich James T. , Blessing Christoph , Kohler Veronika , Schwarzkopf Fabian , King Zachary A. , Yang Laurence , Jóhannsson Freyr , Sigurjónsson Ólafur E. , Rolfsson Óttar , Heinrich Julian , Dräger Andreas 
Published: April 2020

Abstract
Background
New technologies have given rise to an abundance of -omics data, particularly metabolomic data. The scale of these data introduces new challenges for the interpretation and extraction of knowledge, requiring the development of innovative computational visualization methodologies. Here, we present GEM-Vis, an original method for the visualization of time-course metabolomic data within the context of metabolic network maps. We demonstrate the utility of the GEM-Vis method by examining previously published data for two cellular systems—the human platelet and erythrocyte under cold storage for use in transfusion medicine.

Results
The results comprise two animated videos that allow for new insights into the metabolic state of both cell types. In the case study of the platelet metabolome during storage, the new visualization technique elucidates a nicotinamide accumulation that mirrors that of hypoxanthine and might, therefore, reflect similar pathway usage. This visual analysis provides a possible explanation for why the salvage reactions in purine metabolism exhibit lower activity during the first few days of the storage period. The second case study displays drastic changes in specific erythrocyte metabolite pools at different times during storage at different temperatures.

Conclusions
The new visualization technique GEM-Vis introduced in this article constitutes a well-suitable approach for large-scale network exploration and advances hypothesis generation. This method can be applied to any system with data and a metabolic map to promote visualization and understand physiology at the network level. More broadly, we hope that our approach will provide the blueprints for new visualizations of other longitudinal -omics data types. The supplement includes a comprehensive user’s guide and links to a series of tutorial videos that explain how to prepare model and data files, and how to use the software SBMLsimulator in combination with further tools to create similar animations as highlighted in the case studies.