bluuebunny/crossref_metadata_2025_split huggingface dataset:
Faster program adaptation through reward attribution inference
Authors: Bauer Tim , Erwig Martin , Fern Alan , Pinto Jervis 
Published: April 2020

In the adaptation-based programming (ABP) paradigm, programs may contain variable parts (function calls, parameter values, etc.) that can be take a number of different values. Programs also contain reward statements with which a programmer can provide feedback about how well a program is performing with respect to achieving its goals (for example, achieving a high score on some scale). By repeatedly running the program, a machine learning component will, guided by the rewards, gradually adjust the automatic choices made in the variable program parts so that they converge toward an optimal strategy.
ABP is a method for semi-automatic program generation in which the choices and rewards offered by programmers allow standard machine-learning techniques to explore a design space defined by the programmer to find an optimal instance of a program template. ABP effectively provides a DSL that allows non-machine-learning experts to exploit machine learning to generate self-optimizing programs.
Unfortunately, in many cases the placement and structuring of choices and rewards can have a detrimental effect on how an optimal solution to a program-generation problem can be found. To address this problem, we have developed a dataflow analysis that computes influence tracks of choices and rewards. This information can be exploited by an augmented machine-learning technique to ignore misleading rewards and to generally attribute rewards better to the choices that have actually influenced them. Moreover, this technique allows us to detect errors in the adaptive program that might arise out of program maintenance. Our evaluation shows that the dataflow analysis can lead to improvements in performance.
L24
Authors: Stanley-Marbell Phillip 
Published: April 2020

Networks of sensors must process large amounts of intermittently-available data in situ. This motivates the investigation of means for achieving high performance when required, but ultra-low-power dissipation when idle. One approach to this challenge is the use of embedded multiprocessor systems, leading to trade-offs between parallelism, performance, energy efficiency, and cost. To evaluate these trade-offs and to gain insight for future system designs, this article presents the design, implementation, and evaluation of a miniature, energy-scalable, 24-processor module,
L24
, for use in embedded sensor systems.

Analytic results and empirical evidence motivating such embedded multiprocessors is provided, and a parallel fixed-point fast Fourier transform implementation is presented. This application is used as a challenging but realistic evaluator of the presented hardware platform. Through a combination of hardware measurements, instruction-level microarchitectural simulation, and analytic modeling, it is demonstrated that the platform provides idle power dissipation over an order of magnitude lower than systems employing a monolithic processor of equivalent performance, while dynamic power dissipation remains competitive.
Taking into account both application computation and interprocessor communication demands, it is shown that there may exist an optimum operating voltage that minimizes either time-to-solution, energy usage, or the energy-delay product. This optimum operating point is formulated analytically, calibrated with system measurements, and evaluated for the hardware platform and application presented.
Software thread integration for instruction-level parallelism
Authors: So Won , Dean Alexander G. 
Published: April 2020

Multimedia applications require a significantly higher level of performance than previous workloads of embedded systems. They have driven digital signal processor (DSP) makers to adopt high-performance architectures like VLIW (Very-Long Instruction Word). Despite many efforts to exploit instruction-level parallelism (ILP) in the application, the speed is a fraction of what it could be, limited by the difficulty of finding enough independent instructions to keep all of the processor's functional units busy.
This article proposes Software Thread Integration (STI) for instruction-level parallelism. STI is a software technique for interleaving multiple threads of control into a single implicitly multithreaded one. We use STI to improve the performance on ILP processors by merging parallel procedures into one, increasing the compiler's scope and hence allowing it to create a more efficient instruction schedule. Assuming the parallel procedures are given, we define a methodology for finding the best performing integrated procedure with a minimum compilation time.
We quantitatively estimate the performance impact of integration, allowing various integration scenarios to be compared and ranked via profitability analysis. During integration of threads, different ILP-improving code transformations are selectively applied according to the control structure and the ILP characteristics of the code, driven by interactions with software pipelining. The estimated profitability is verified and corrected by an iterative compilation approach, compensating for possible estimation inaccuracy. Our modeling methods combined with limited compilation quickly find the best integration scenario without requiring exhaustive integration.
NetKAT
Authors: Anderson Carolyn Jane , Foster Nate , Guha Arjun , Jeannin Jean-Baptiste , Kozen Dexter , Schlesinger Cole , Walker David 
Published: April 2020

Recent years have seen growing interest in high-level languages for programming networks. But the design of these languages has been largely ad hoc, driven more by the needs of applications and the capabilities of network hardware than by foundational principles. The lack of a semantic foundation has left language designers with little guidance in determining how to incorporate new features, and programmers without a means to reason precisely about their code.
This paper presents NetKAT, a new network programming language that is based on a solid mathematical foundation and comes equipped with a sound and complete equational theory. We describe the design of NetKAT, including primitives for filtering, modifying, and transmitting packets; union and sequential composition operators; and a Kleene star operator that iterates programs. We show that NetKAT is an instance of a canonical and well-studied mathematical structure called a Kleene algebra with tests (KAT) and prove that its equational theory is sound and complete with respect to its denotational semantics. Finally, we present practical applications of the equational theory including syntactic techniques for checking reachability, proving non-interference properties that ensure isolation between programs, and establishing the correctness of compilation algorithms.
Counter-factual typing for debugging type errors
Authors: Chen Sheng , Erwig Martin 
Published: April 2020

Changing a program in response to a type error plays an important part in modern software development. However, the generation of good type error messages remains a problem for highly expressive type systems. Existing approaches often suffer from a lack of precision in locating errors and proposing remedies. Specifically, they either fail to locate the source of the type error consistently, or they report too many potential error locations. Moreover, the change suggestions offered are often incorrect. This makes the debugging process tedious and ineffective.
We present an approach to the problem of type debugging that is based on generating and filtering a comprehensive set of type-change suggestions. Specifically, we generate all (program-structure-preserving) type changes that can possibly fix the type error. These suggestions will be ranked and presented to the programmer in an iterative fashion. In some cases we also produce suggestions to change the program. In most situations, this strategy delivers the correct change suggestions quickly, and at the same time never misses any rare suggestions. The computation of the potentially huge set of type-change suggestions is efficient since it is based on a variational type inference algorithm that type checks a program with variations only once, efficiently reusing type information for shared parts.
We have evaluated our method and compared it with previous approaches. Based on a large set of examples drawn from the literature, we have found that our method outperforms other approaches and provides a viable alternative.
Battery transition systems
Authors: Boker Udi , Henzinger Thomas A. , Radhakrishna Arjun 
Published: April 2020

The analysis of the energy consumption of software is an important goal for quantitative formal methods. Current methods, using weighted transition systems or energy games, model the energy source as an ideal resource whose status is characterized by one number, namely the amount of remaining energy. Real batteries, however, exhibit behaviors that can deviate substantially from an ideal energy resource. Based on a discretization of a standard continuous battery model, we introduce {\em battery transition systems}. In this model, a battery is viewed as consisting of two parts -- the available-charge tank and the bound-charge tank. Any charge or discharge is applied to the available-charge tank. Over time, the energy from each tank diffuses to the other tank.
Battery transition systems are infinite state systems that, being not well-structured, fall into no decidable class that is known to us. Nonetheless, we are able to prove that the $\omega$-regular model-checking problem is decidable for battery transition systems. We also present a case study on the verification of control programs for energy-constrained semi-autonomous robots.
Backpack
Authors: Kilpatrick Scott , Dreyer Derek , Peyton Jones Simon , Marlow Simon 
Published: April 2020

Module systems like that of Haskell permit only a weak form of modularity in which module implementations depend directly on other implementations and must be processed in dependency order. Module systems like that of ML, on the other hand, permit a stronger form of modularity in which explicit interfaces express assumptions about dependencies, and each module can be typechecked and reasoned about independently.
In this paper, we present Backpack, a new language for building separately-typecheckable *packages* on top of a weak module system like Haskell's. The design of Backpack is inspired by the MixML module calculus of Rossberg and Dreyer, but differs significantly in detail. Like MixML, Backpack supports explicit interfaces and recursive linking. Unlike MixML, Backpack supports a more flexible applicative semantics of instantiation. Moreover, its design is motivated less by foundational concerns and more by the practical concern of integration into Haskell, which has led us to advocate simplicity---in both the syntax and semantics of Backpack---over raw expressive power. The semantics of Backpack packages is defined by elaboration to sets of Haskell modules and binary interface files, thus showing how Backpack maintains interoperability with Haskell while extending it with separate typechecking. Lastly, although Backpack is geared toward integration into Haskell, its design and semantics are largely agnostic with respect to the details of the underlying core language.
Rapalog-Mediated Repression of Tribbles Pseudokinase 3 Regulates Pre-mRNA Splicing
Authors: Stefanovska Bojana , Vicier Cecile Edith , Dayris Thibault , Ogryzko Vasily , Scott Veronique , Bouakka Ibrahim , Delaloge Suzette , Rocca Anna , Le Saux Olivia , Trédan Olivier , Bachelot Thomas , André Fabrice , Fromigué Olivia 
Published: April 2020

Abstract

Rapalogs have become standard-of-care in patients with metastatic breast, kidney, and neuroendocrine cancers. Nevertheless, tumor escape occurs after several months in most patients, highlighting the need to understand mechanisms of resistance. Using a panel of cancer cell lines, we show that rapalogs downregulate the putative protein kinase TRIB3 (tribbles pseudokinase 3). Blood samples of a small cohort of patients with cancer treated with rapalogs confirmed downregulation of TRIB3. Downregulation of TRIB3 was mediated by LRRFIP1 independently of mTOR and disrupted its interaction with the spliceosome, where it participated in rapalog-induced deregulation of RNA splicing. Conversely, overexpression of TRIB3 in a panel of cancer cell lines abolished the cytotoxic effects of rapalogs. These findings identify TRIB3 as a key component of the spliceosome, whose repression contributes significantly to the mechanism of resistance to rapalog therapy.

Significance:
Independent of mTOR signaling, rapalogs induce cytoxicity by dysregulating spliceosome function via repression of TRIB3, the loss of which may, in the long term, contribute to therapeutic resistance.
Human Epidermal Growth Factor Receptor 2–Positive Breast Cancer Is Associated with Indigenous American Ancestry in Latin American Women
Authors: Marker Katie M. , Zavala Valentina A. , Vidaurre Tatiana , Lott Paul C. , Vásquez Jeannie Navarro , Casavilca-Zambrano Sandro , Calderón Mónica , Abugattas Julio E. , Gómez Henry L. , Fuentes Hugo A. , Picoaga Ruddy Liendo , Cotrina Jose M. , Neciosup Silvia P. , Castañeda Carlos A. , Morante Zaida , Valencia Fernando , Torres Javier , Echeverry Magdalena , Bohórquez Mabel E. , Polanco-Echeverry Guadalupe , Estrada-Florez Ana P. , Serrano-Gómez Silvia J. , Carmona-Valencia Jenny A. , Alvarado-Cabrero Isabel , Sanabria-Salas María Carolina , Velez Alejandro , Donado Jorge , Song Sikai , Cherry Daniel , Tamayo Lizeth I. , Huntsman Scott , Hu Donglei , Ruiz-Cordero Roberto , Balassanian Ronald , Ziv Elad , Zabaleta Jovanny , Carvajal-Carmona Luis , Fejerman Laura 
Published: April 2020

AbstractWomen of Latin American origin in the United States are more likely to be diagnosed with advanced breast cancer and have a higher risk of mortality than non-Hispanic White women. Studies in U.S. Latinas and Latin American women have reported a high incidence of HER2 positive (+) tumors; however, the factors contributing to this observation are unknown. Genome-wide genotype data for 1,312 patients from the Peruvian Genetics and Genomics of Breast Cancer Study (PEGEN-BC) were used to estimate genetic ancestry. We tested the association between HER2 status and genetic ancestry using logistic and multinomial logistic regression models. Findings were replicated in 616 samples from Mexico and Colombia. Average Indigenous American (IA) ancestry differed by subtype. In multivariate models, the odds of having an HER2+ tumor increased by a factor of 1.20 with every 10% increase in IA ancestry proportion (95% CI, 1.07–1.35; P = 0.001). The association between HER2 status and IA ancestry was independently replicated in samples from Mexico and Colombia. Results suggest that the high prevalence of HER2+ tumors in Latinas could be due in part to the presence of population-specific genetic variant(s) affecting HER2 expression in breast cancer.Significance:The positive association between Indigenous American genetic ancestry and HER2+ breast cancer suggests that the high incidence of HER2+ subtypes in Latinas might be due to population and subtype-specific genetic risk variants.
Safety and Feasibility of PARP1/2 Imaging with 18F-PARPi in Patients with Head and Neck Cancer
Authors: Schöder Heiko , França Paula Demétrio De Souza , Nakajima Reiko , Burnazi Eva , Roberts Sheryl , Brand Christian , Grkovski Milan , Mauguen Audrey , Dunphy Mark P. , Ghossein Ronald A. , Lyashchenko Serge K. , Lewis Jason S. , O'Donoghue Joseph A. , Ganly Ian , Patel Snehal G. , Lee Nancy Y. , Reiner Thomas 
Published: April 2020

Abstract

Purpose:
We performed a first-in-human clinical trial. The aim of this study was to determine safety and feasibility of PET imaging with 18F-PARPi in patients with head and neck cancer.

Patients and Methods:
Eleven patients with newly diagnosed or recurrent oral and oropharyngeal cancer were injected with 18F-PARPi (331 ± 42 MBq), and dynamic PET/CT imaging was performed between 0 and 25 minutes postinjection. Static PET/CT scans were obtained at 30, 60, and 120 minutes postinjection. Blood samples for tracer concentration and metabolite analysis were collected. Blood pressure, ECG, oxygen levels, clinical chemistry, and complete blood count were obtained before and after tracer administration.

Results:
18F-PARPi was well-tolerated by all patients without any safety concerns. Of the 11 patients included in the analysis, 18F-PARPi had focal uptake in all primary lesions (n = 10, SUVmax = 2.8 ± 1.2) and all 18F-FDG–positive lymph nodes (n = 34). 18F-PARPi uptake was seen in 18F-FDG–negative lymph nodes of 3 patients (n = 6). Focal uptake of tracer in primary and metastatic lesions was corroborated by CT alone or in combination with 18F-FDG. The overall effective dose with 18F-PARPi PET was 3.9 mSv – 5.2 mSv, contrast was high [SUVmax(lesion)/SUVmax(trapezius muscle) = 4.5] and less variable than 18F-FDG when compared with the genioglossus muscle (1.3 vs. 6.0, P = 0.001).

Conclusions:
Imaging of head and neck cancer with 18F-PARPi is feasible and safe. 18F-PARPi detects primary and metastatic lesions, and retention in tumors is longer than in healthy tissues.
Not So FASt: Tumor Cells Resisting Death Drive CAR T-cell Dysfunction
Authors: Green Michael R. , Neelapu Sattva S. 
Published: April 2020

Abstract

Summary:
In this issue, Singh and colleagues describe a novel tumor-intrinsic mechanism of resistance to chimericantigen receptor (CAR) T-cell therapy targeting CD19 in B-cell malignancies. They show that reduced expression of death receptor genes in the tumors mediates resistance to killing by CAR T cells, leads to progressive CAR T-cell dysfunction, and is associated with unfavorable clinical outcome in patients.
See related article by Singh et al., p. 552.
Characterization, Pathogenesis, and Clinical Implications of Inflammation‐Related Atrial Myopathy as an Important Cause of Atrial Fibrillation
Authors: Packer Milton 
Published: April 2020

Abstract
Historically, atrial fibrillation has been observed in clinical settings of prolonged hemodynamic stress, eg, hypertension and valvular heart disease. However, recently, the most prominent precedents to atrial fibrillation are metabolic diseases that are associated with adipose tissue inflammation (ie, obesity and diabetes mellitus) and systemic inflammatory disorders (ie, rheumatoid arthritis and psoriasis). These patients typically have little evidence of left ventricular hypertrophy or dilatation; instead, imaging reveals abnormalities of the structure or function of the atria, particularly the left atrium, indicative of an atrial myopathy. The left atrium is enlarged, fibrotic and noncompliant, potentially because the predisposing disorder leads to an expansion of epicardial adipose tissue, which transmits proinflammatory mediators to the underlying left atrium. The development of an atrial myopathy not only leads to atrial fibrillation, but also contributes to pulmonary venous hypertension and systemic thromboembolism. These mechanisms explain why disorders of systemic or adipose tissue inflammation are accompanied an increased risk of atrial fibrillation, abnormalities of left atrium geometry and an enhanced risk of stroke. The risk of stroke exceeds that predicted by conventional cardiovascular risk factors or thromboembolism risk scores used to guide the use of anticoagulation, but it is strongly linked to clinical evidence and biomarkers of systemic inflammation.
Thomas Berry and the Reshaping of Catholic Environmentalism
Authors: Graham Mark 
Published: April 2020

Abstract
This article criticizes the so-called “stewardship paradigm,” which forms the theological basis for Catholic environmentalism, and argues that Thomas Berry’s cosmology provides a more theologically palatable platform for developing Catholic environmentalism. The substantive ethical shift emerging from Berry’s cosmology is the displacement of human well-being as the proximate norm for human behavior in favor of promoting biodiversity on planet Earth. In other words, biodiversity is the primary ethical good, and human well-being is secondary.
US Drug Policy and Perpetual War against the Drug Trade in Mexico
Authors: Luna-Monsivais Alberto Omar , del Castillo-Mussot Marcelo , de la Lama García Alfredo , Montemayor Aldrete Jorge Antonio 
Published: April 2020

Abstract
Globalization of drug consumption has generated a highly lucrative market for illegal traffickers. The US launched a worldwide campaign against illicit drug use, forcing many countries to comply with the ‘War on Drugs.’ We describe this historical process as a perpetual war resulting in violence, criminality, forced displacement, and disappearances in Mexico and other countries. For instance, despite economic, political, and military coercion in Mexico, the “drug problem” shows little sign of going away, unless a new approach regarding drug production and trade is adopted.
Adjustments for Wind-Induced Undercatch in Snowfall Measurements Based on Precipitation Intensity
Authors: Colli Matteo , Stagnaro Mattia , Lanza Luca G. , Rasmussen Roy , Thériault Julie M. 
Published: April 2020

AbstractAdjustments for the wind-induced undercatch of snowfall measurements use transfer functions to account for the expected reduction of the collection efficiency with increasing the wind speed for a particular catching-type gauge. Based on field experiments or numerical simulation, collection efficiency curves as a function of wind speed also involve further explanatory variables such as surface air temperature and/or precipitation type. However, while the wind speed or wind speed and temperature approach is generally effective at reducing the measurement bias, it does not significantly reduce the root-mean-square error (RMSE) of the residuals, implying that part of the variance is still unexplained. In this study, we show that using precipitation intensity as the explanatory variable significantly reduces the scatter of the residuals. This is achieved by optimized curve fitting of field measurements from the Marshall Field Site (Colorado, United States), using a nongradient optimization algorithm to ensure optimal binning of experimental data. The analysis of a recent quality-controlled dataset from the Solid Precipitation Intercomparison Experiment (SPICE) campaign of the World Meteorological Organization confirms the scatter reduction, showing that this approach is suitable to a variety of locations and catching-type gauges. Using computational fluid dynamics simulations, we demonstrate that the physical basis of the reduction in RMSE is the correlation of precipitation intensity with the particle size distribution. Overall, these findings could be relevant in operational conditions since the proposed adjustment of precipitation measurements only requires wind sensor and precipitation gauge data.