bluuebunny/crossref_metadata_2025 huggingface dataset:
Penile Mondor’s disease after anterolateral retroperitoneal approach for lumbar fracture
Authors: Dobran Mauro , Benigni Roberta , Nasi Davide , Cantoro Daniele
Published: November 2017

This is a rare case of thrombosis of the dorsal vein of the penis (Mondor’s disease) occurred after an anterior-lateral retroperitoneal approach for a vertebral stabilisation in thoracolumbar vertebral fracture. Potential causes are traumatism, neoplasms, excessive sexual activity or abstinence. Although penile Mondor’s disease is a clinical diagnosis, ultrasound imaging is the gold standard to confirm it. In the reported case, 1 week after neurosurgical retroperitoneal procedure of vertebral stabilisation, the patient complained of a painful cord-like mass midshaft of penis. The diagnosis was made by clinical evaluation and ultrasound images. After 2 weeks of therapy with enoxaparin sodium, the patient recovered. The authors report this case evaluating the possible correlation between the anterior-lateral retroperitoneal approach and the development of the rare Mondor’s disease.
Graphics and statistics for cardiology: designing effective tables for presentation and publication
Authors: Boers Maarten
Published: November 2017

Research is of little use if its results are not effectively communicated. Data visualised in tables (and graphs) are key components in any scientific report, but their design leaves much to be desired. This article focuses on table design, following two general principles: clear vision and clear understanding. Clear vision is achieved by maximising the signal to noise ratio. In a table, the signal is the data in the form of numbers, and the noise is the support structure necessary to interpret the numbers. Clear understanding is achieved when the story in the data is told effectively, through organisation of the data and use of text. These principles are illustrated by original and improved tables from recent publications. Two special cases are discussed separately: tables produced by the pharmaceutical industry (in clinical study reports and reports to data safety monitoring boards), and study flow diagrams as proposed by the Consolidated Standards of Reporting Trials and Preferred Reporting Items for Systematic Reviews and Meta-Analyses initiatives.
Added fructose as a principal driver of non-alcoholic fatty liver disease: a public health crisis
Authors: DiNicolantonio James J , Subramonian Ashwin M , O’Keefe James H
Published: November 2017

Fatty liver disease affects up to one out of every two adults in the western world. Data from animal and human studies implicate added sugars (eg, sucrose and high-fructose corn syrup) in the development of fatty liver disease and its consequences. Added fructose in particular, as a component of added sugars, may pose the greatest risk for fatty liver disease. Considering that there is no requirement for added sugars in the diet, dietary guidelines should recommend reducing the intake of added sugars to just 5% of total calories in order to decrease the prevalence of fatty liver disease and its related consequences.
Long and short of optimal stent design
Authors: Watson Timothy , Webster Mark W I , Ormiston John A , Ruygrok Peter N , Stewart James T
Published: November 2017

The ideal stent must fulfil a broad range of technical requirements. Stents must be securely crimped onto the delivery balloon and, in this form, must have a low profile and be sufficiently flexible to facilitate deliverability to the lesion site without distortion or displacement. Following expansion, stents must exert sufficient radial force on the vessel wall to overcome lesion resistance and elastic recoil. To achieve an optimal lumen diameter, the lesion must be uniformly and adequately scaffolded, with minimal tissue prolapse between struts but without compromising side-branch access. Furthermore, the deployed stent must conform to the vessel curvature to minimise vessel distortion, particularly at the stent edges. Radio-opacity is also important to guide safe positioning, adequate deployment and postdilataion and to permit assessment of optimal stent expansion. Equally though, the stent lumen must also be sufficiently visible to allow radiographic assessment of flow dynamics and restenosis. Efforts to optimise one characteristic of stent design may have detrimental effects on another. Thus, currently available stents all reflect a compromise between competing desirable features and have subtle differences in their performance characteristics. Striving to achieve stents with optimal deliverability, conformability and radial strength led to a reduction in longitudinal strength. The importance of this parameter was highlighted by complications occurring in the real-world setting where percutaneous coronary intervention is often undertaken in challenging anatomy. This review focuses on aspects of stent design relevant to longitudinal strength.
Criteria for the recognition of Archean calc-alkaline lamprophyres: examples from the Abitibi Subprovince
Authors: Mathieu Lucie , Bouchard Émile , Guay Francis , Liénard Alizée , Pilote Pierre , Goutier Jean
Published: November 2017

Lamprophyres are minor intrusions with atypical sources and crystallisation sequences. Among lamprophyres, the calc-alkaline (CAL) type on which this study focuses has the least distinctive chemistry and petrology. CAL correspond to small-volume mafic intrusions characterised by the early fractionation of amphibole and (or) biotite. In the Archean Superior Province (Canada), CAL are temporally and spatially related to several gold deposits and may thus be relevant to mineral exploration. This study focuses on several altered and metamorphosed intrusions of the Abitibi and La Grande subprovinces, which were designated lamprophyres based on field observations. Several criteria established from thin sections, whole-rock chemical analyses, and SEM data are applied to the studied rocks to distinguish CAL from other types of magma. As a result, only one of the studied dykes has the morphology, chemistry, and petrology typical of CAL, while the other intrusions are either too altered to be classified or may correspond to metamorphosed and metasomatized gabbro and diorite. This study shows that thin sections and whole-rock chemical analyses are not always sufficient to unequivocally classify an altered and metamorphosed intrusion as a CAL. Also, intrusions as challenging to recognise as CAL should not be used by exploration geologists to prospect for orogenic gold deposits. Much remains to be done to document the distribution and volume represented by lamprophyres in Archean greenstone belts and to confirm their spatial dependence with gold deposits.
Coherent population dynamics associated with sockeye salmon juvenile life history strategies
Authors: Freshwater Cameron , Burke Brian J. , Scheuerell Mark D. , Grant Sue C.H. , Trudel Marc , Juanes Francis
Published: November 2017

Although the importance of diversity to maintaining metapopulation stability is widely recognized, the ecological characteristics that lead to synchronous dynamics within population aggregates are often unclear. We used a constrained dynamic factor analysis to explore patterns of covariance in productivity among 16 Fraser River sockeye salmon (Oncorhynchus nerka) conservation units (CUs). Specifically, we tested whether coherent trends in productivity covaried with five distinct ecological attributes: physical characteristics of nursery lakes, large-scale management interventions, genetic similarity, adult migration phenology, or juvenile migratory traits. The top-ranked model had two trends based on nursery lake characteristics and juvenile migratory traits. One trend represented the dynamics of CUs that rear in nursery lakes prior to ocean entry and undergo relatively rapid marine migrations. The second included a sea-type CU, Harrison River, which enters the marine environment without rearing in a nursery lake and migrates more slowly. The uniform response of lake-type CUs, as well as Harrison River CU’s unique life history, suggests that coherent trends are structured by traits that covary with broad life history type, rather than fine-scale characteristics. Furthermore, we document substantial temporal variability in the strength of synchronous dynamics among Fraser River CUs. Greater synchrony in recent years suggests that the importance of shared regional drivers, relative to local processes, may have increased.
A Low-Noise, Low-Power, Wide Dynamic Range Logarithmic Amplifier for Biomedical Applications
Authors: Sundarasaradula Yuwadee , Thanachayanont Apinunt
Published: November 2017

This paper presents the design and realization of a low-noise, low-power, wide dynamic range CMOS logarithmic amplifier for biomedical applications. The proposed amplifier is based on the true piecewise linear function by using progressive-compression parallel-summation architecture. A DC offset cancellation feedback loop is used to prevent output saturation and deteriorated input sensitivity from inherent DC offset voltages. The proposed logarithmic amplifier was designed and fabricated in a standard 0.18[Formula: see text][Formula: see text]m CMOS technology. The prototype chip includes six limiting amplifier stages and an on-chip bias generator, occupying a die area of 0.027[Formula: see text]mm2. The overall circuit consumes 9.75[Formula: see text][Formula: see text]W from a single 1.5[Formula: see text]V power supply voltage. Measured results showed that the prototype logarithmic amplifier exhibited an 80[Formula: see text]dB input dynamic range (from 10[Formula: see text][Formula: see text]V to 100[Formula: see text]mV), a bandwidth of 4[Formula: see text]Hz–10[Formula: see text]kHz, and a total input-referred noise of 5.52[Formula: see text][Formula: see text]V.
Experimental Demonstration for PAPR Reduction in OFDM System Using Partial-OSLM Technique
Authors: Al-Rayif M. I. , Seleem H. , Ragheb A. , Alshebeili S.
Published: November 2017

Orthogonal frequency division multiplexing (OFDM) modulation is proposed in 4G wireless communication systems, and is under consideration for the next generation 5G systems. This is due to the higher spectral efficiency (SE) and the better immunity to channel distortions. One of the shortcomings in OFDM is its high peak-to-average power ratio (PAPR). Several schemes have been proposed to reduce the PAPR in OFDM systems. This includes clipping, coding, and pre/post-distortion schemes with or without side information. In this paper, we experimentally demonstrate one of the most promising method, to mitigate the effect of PAPR, entitled the partial orthogonal selective mapping (POSLM). The experimental results show a comparable performance with respect to the simulation results in terms of PAPR reduction, power spectral density (PSD), and bit error rate (BER) metrics.
On dimensions supporting a rational projective plane
Authors: Kennard Lee , Su Zhixu
Published: November 2017

A rational projective plane ([Formula: see text]) is a simply connected, smooth, closed manifold [Formula: see text] such that [Formula: see text]. An open problem is to classify the dimensions at which such a manifold exists. The Barge–Sullivan rational surgery realization theorem provides necessary and sufficient conditions that include the Hattori–Stong integrality conditions on the Pontryagin numbers. In this paper, we simplify these conditions and combine them with the signature equation to give a single quadratic residue equation that determines whether a given dimension supports a [Formula: see text]. We then confirm the existence of a [Formula: see text] in two new dimensions and prove several non-existence results using factorization of the numerators of the divided Bernoulli numbers. We also resolve the existence question in the Spin case, and we discuss existence results for the more general class of rational projective spaces.
Managing China-U.S. Relations in the Trump Era: Approaches and Policies
Authors: Yang Jiemian
Published: November 2017

China under the leadership of President Xi Jinping has maintained strategic concentration since the election of President Donald Trump who has shown an anti-establishment approach to domestic and foreign affairs. China adheres to its diplomatic principles of preserving core national interests, making overall strategic agendas, going with the trends of the times, and seeking progress while stabilizing China-U.S. relations. China also attaches great importance to summit diplomacy and has achieved early outcomes through Xi-Trump meetings at both Mar-a-Lago and Hamburg. Nevertheless, China has yet to meet daunting challenges on its road ahead to a more stable, cooperative, and predictable relationship with the United States under President Trump.
A Robotic Diathermy System for Automated Capsulotomy
Authors: Ullrich Franziska , Lussi Jonas , Chatzopoulos Vasileios , Michels Stephan , Petruska Andrew J. , Nelson Bradley J.
Published: November 2017

Background: Cataracts are the leading cause of blindness and are treated surgically. Capsulotomy describes the opening of the lens capsule during this surgery and is most commonly performed by manual tearing, thermal cutting, or laser ablation. This work focuses on the development of a flexible instrument for high precision capsulotomy, whose motion is controlled by a hybrid mechanical-magnetic actuation system. Methods: A flexible instrument with a magnetic tip was directed along a circular path with a hybrid mechanical-magnetic actuation system. The system’s motion control and thermal cutting behavior were tested on ex vivo porcine lenses. Results: Position control of the magnetic tip on a circular path with radius of 2.9[Formula: see text]mm resulted in a relative positioning error of 3% at a motion period of 60[Formula: see text]s. The instrument’s accuracy improves with decreasing speed. A fully automated capsulotomy is achieved on an ex vivo porcine lens capsule by continuously coagulating the tissue under controlled conditions. Conclusions: Robot assisted capsulotomy can be performed with excellent precision in ex vivo conditions.
Empowering Stream Processing through Edge Clouds
Authors: Esteves Sergi , Janssens Nico , Theeten Bart , Veiga Luis
Published: November 2017

CHive is a new streaming analytics platform to run distributed SQL-style queries on edge clouds. However, CHive is currently tightly coupled to a specific stream processing system (SPS), Apache Storm. In this paper we address the decoupling of the CHive query planner and optimizer from the runtime environment, and also extend the latter to support pluggable runtimes through a common API. As runtimes, we currently support Apache Spark and Flink streaming. The fundamental contribution of this paper is to assess the cost of employing interstream parallelism in SPS. Experimental evaluation indicates that we can enable popular SPS to be distributed on edge clouds with stable overhead in terms of throughput
"What's in a name?" going beyond allocation site names in heap analysis
Authors: Kanvar Vini , Khedker Uday P.
Published: November 2017

A points-to analysis computes a sound abstraction of heap memory conventionally using a
name-based
abstraction that summarizes runtime memory by grouping locations using the names of allocation sites: All concrete heap locations allocated by the same statement are grouped together. The locations in the same group are treated alike i.e., a pointer to any one location of the group is assumed to point to every location in the group leading to an over-approximation of points-to relations.

We propose an
access-based
abstraction that partitions each name-based group of locations into equivalence classes at every program point using an additional criterion of the sets of access paths (chains of pointer indirections) reaching the locations in the memory. The intuition is that the locations that are both allocated and accessed alike should be grouped into the same equivalence class. Since the access paths in the memory could reach different locations at different program points, our groupings change flow sensitively unlike the name-based groupings. This creates a more precise view of the memory. Theoretically, it is strictly more precise than the name-based abstraction except in some trivial cases; practically it is far more precise.

Our empirical measurements show the benefits of our tool Access-Based Heap Analyzer (ABHA) on SPEC CPU 2006 and heap manipulating SV-COMP benchmarks. ABHA, which is field-, flow-, and context-sensitive, scales to 20 kLoC and can improve the precision even up to 99% (in terms of the number of aliases). Additionally, ABHA allows any user-defined summarization of an access path to be plugged in; we have implemented and evaluated four summarization techniques. ABHA can also act as a front-end to TVLA, a parametrized shape analyzer, in order to automate its parametrization by generating predicates that capture the program behaviour more accurately.
Type-assisted automatic garbage collection for lock-free data structures
Authors: Yang Albert Mingkun , Wrigstad Tobias
Published: November 2017

We introduce Isolde, an automatic garbage collection scheme designed specifically for managing memory in lock-free data structures, such as stacks, lists, maps and queues. Isolde exists as a plug-in memory manager, designed to sit on-top of another memory manager, and use it's allocator and reclaimer (if exists). Isolde treats a lock-free data structure as a logical heap, isolated from the rest of the program. This allows garbage collection outside of Isolde to take place without affecting the lock-free data structure. Isolde further manages objects allocated on a Isolde heap in a fully concurrent manner, allowing garbage collection to incrementally remove garbage without stopping other threads doing work.
Bridging the gap between memory performance and massive parallelism: the critical role of programming systems innovations (keynote)
Authors: Shen Xipeng
Published: November 2017

This talk examines some trends in the modern developments of memory systems and their relations with the massive parallelism in processors and applications. It then draws on some recent work on GPU to explain the important role of programming systems in bridging the gap; it particularly emphasizes the importance of innovations for enabling better software controllability, more software elasticity, and inter-thread data locality enhancements. The talk further discusses the implications brought to programming systems by the increasingly blurred boundaries among memory, storage, and processing.
Ode on a random urn (functional pearl)
Authors: Lampropoulos Leonidas , Spector-Zabusky Antal , Foner Kenneth
Published: November 2017

We present the urn, a simple tree-based data structure that supports sampling from and updating discrete probability distributions in logarithmic time. We avoid the usual complexity of traditional self-balancing binary search trees by not keeping values in a specific order. Instead, we keep the tree maximally balanced at all times using a single machine word of overhead: its size.

Urns provide an alternative interface for the frequency combinator from the QuickCheck library that allows for asymptotically more efficient sampling from dynamically-updated distributions. They also facilitate backtracking in property-based random testing, and can be applied to such complex examples from the literature as generating well-typed lambda terms or information flow machine states, demonstrating significant speedups.
QuickSpec: a lightweight theory exploration tool for programmers (system demonstration)
Authors: Algehed Maximilian , Claessen Koen , Johansson Moa , Smallbone Nick
Published: November 2017

This document gives the outline of a system demonstration for the QuickSpec theory exploration tool.
Speculate: discovering conditional equations and inequalities about black-box functions by reasoning from test results
Authors: Braquehais Rudy , Runciman Colin
Published: November 2017

This paper presents Speculate, a tool that automatically conjectures laws involving conditional equations and inequalities about Haskell functions. Speculate enumerates expressions involving a given collection of Haskell functions, testing to separate those expressions into apparent equivalence classes. Expressions in the same equivalence class are used to conjecture equations. Representative expressions of different equivalence classes are used to conjecture conditional equations and inequalities. Speculate uses lightweight equational reasoning based on term rewriting to discard redundant laws and to avoid needless testing. Several applications demonstrate the effectiveness of Speculate.
Well-typed music does not sound wrong (experience report)
Authors: Szamozvancev Dmitrij , Gale Michael B.
Published: November 2017

Music description and generation are popular use cases for Haskell, ranging from live coding libraries to automatic harmonisation systems. Some approaches use probabilistic methods, others build on the theory of Western music composition, but there has been little work done on checking the correctness of musical pieces in terms of voice leading, harmony, and structure. Haskell's recent additions to the type-system now enable us to perform such analysis statically.

We present our experience of implementing a type-level model of classical music and an accompanying EDSL which enforce the rules of classical music at compile-time, turning composition mistakes into compiler errors. Along the way, we discuss the strengths and limitations of doing this in Haskell and demonstrate that the type system of the language is fully capable of expressing non-trivial and practical logic specific to a particular domain.
A meta-EDSL for distributed web applications
Authors: Ekblad Anton
Published: November 2017

We present a domain-specific language for constructing and configuring web applications distributed across any number of networked, heterogeneous systems. Our language is embedded in Haskell, provides a common framework for integrating components written in third-party EDSLs, and enables type-safe, access-controlled communication between nodes, as well as effortless sharing and movement of functionality between application components. We give an implementation of our language and demonstrate its applicability by using it to implement several important components of distributed web applications, including RDBMS integration, load balancing, and fine-grained sandboxing of untrusted third party code.

The rising popularity of cloud computing and heterogeneous computer architectures is putting a strain on conventional programming models, which commonly assume that one application executes on one machine, or at best on one out of several identical machines. With our language, we take the first step towards a programming model better suited for a computationally multicultural future.
Streaming irregular arrays
Authors: Clifton-Everest Robert , McDonell Trevor L. , Chakravarty Manuel M. T. , Keller Gabriele
Published: November 2017

Previous work has demonstrated that it is possible to generate efficient and highly parallel code for multicore CPUs and GPUs from combinator-based array languages for a range of applications. That work, however, has been limited to operating on flat, rectangular structures without any facilities for irregularity or nesting.

In this paper, we show that even a limited form of nesting provides substantial benefits both in terms of the expressiveness of the language (increasing modularity and providing support for simple irregular structures) and the portability of the code (increasing portability across resource-constrained devices, such as GPUs). Specifically, we generalise Blelloch's flattening transformation along two lines: (1) we explicitly distinguish between definitely regular and potentially irregular computations; and (2) we handle multidimensional arrays. We demonstrate the utility of this generalisation by an extension of the embedded array language Accelerate to include irregular streams of multidimensional arrays. We discuss code generation, optimisation, and irregular stream scheduling as well as a range of benchmarks on both multicore CPUs and GPUs.
Adaptive lock-free data structures in Haskell: a general method for concurrent implementation swapping
Authors: Chen Chao-Hong , Choudhury Vikraman , Newton Ryan R.
Published: November 2017

A key part of implementing high-level languages is providing built- in and default data structures. Yet selecting good defaults is hard. A mutable data structure’s workload is not known in advance, and it may shift over its lifetime—e.g., between read-heavy and write- heavy, or from heavy contention by multiple threads to single- threaded or low-frequency use. One idea is to switch implementa- tions adaptively, but it is nontrivial to switch the implementation of a concurrent data structure at runtime. Performing the transition requires a concurrent snapshot of data structure contents, which normally demands special engineering in the data structure’s de- sign. However, in this paper we identify and formalize an relevant property of lock-free algorithms. Namely, lock-freedom is su cient to guarantee that freezing memory locations in an arbitrary order will result in a valid snapshot. Several functional languages have data structures that freeze and thaw, transitioning between mutable and immutable, such as Haskell vectors and Clojure transients, but these enable only single-threaded writers. We generalize this approach to augment an arbitrary lock-free data structure with the ability to gradually freeze and optionally transition to a new representation. This aug- mentation doesn’t require changing the algorithm or code for the data structure, only replacing its datatype for mutable references with a freezable variant. In this paper, we present an algorithm for lifting plain to adaptive data and prove that the resulting hy- brid data structure is itself lock-free, linearizable, and simulates the original. We also perform an empirical case study in the context of heating up and cooling down concurrent maps.
Research on Distribution of Flow Field and Simulation of Working Pulsation Based on Rotating-Sleeve Distributing-Flow System
Authors: Zhang Yanjun , Zhang Hongxin , Yang Jingzhou , Zhao Qinghai , Jiang Xiaotian , Cheng Qianchang , Hua Qingsong
Published: November 2017

To solve problems of leakage, vibration, and noise caused by disorders of flow field distribution and working pulsation in the rotating-sleeve distributing-flow system, governing equations of plunger and rotating sleeve and computational fluid dynamics (CFD) model are developed through sliding mesh and dynamic mesh technology to simulate flow field and working pulsation. Simulation results show that the following issues exist: obviously periodic fluctuation and sharp corner in flow pulsation, backward flow when fluid is transformed between discharge and suction, and serious turbulence and large loss in kinetic energy around the damping groove in transitional movements. Pressure in the pump chamber rapidly rises to 2.2 MPa involving over 10% more than nominal pressure when the plunger is at the Top Dead Center (TDC) considering changes about damping groove’s position and flow area in two transitional movements. Shortly pressure overshoot gradually decreases to a normal condition with increasing flow area. Similarly, pressure in the pump chamber instantaneously drops to a saturated vapor pressure −98.9 KPa when the plunger is at the Bottom Dead Center (BDC). With increasing flow area the overshoot gradually increases to the normal condition. This research provides foundations for investigating flow field characteristic and structure optimization of rotating-sleeve distributing-flow system.
Fluid Inclusion and Oxygen Isotope Constraints on the Origin and Hydrothermal Evolution of the Haisugou Porphyry Mo Deposit in the Northern Xilamulun District, NE China
Authors: Shu Qihai , Lai Yong
Published: November 2017

The Haisugou porphyry Mo deposit is located in the northern Xilamulun district, northeastern China. Based on alteration and mineralization styles and crosscutting relationships, the hydrothermal evolution in Haisugou can be divided into three stages: an early potassic alteration stage with no significant metal deposition, a synmineralization sericite-chlorite alteration stage with extensive Mo precipitation, and a postmineralization stage characterized by barren quartz and minor calcite and fluorite. The coexistence of high-salinity brine inclusions with low-salinity inclusions both in potassic alteration stage (~440°C) and locally in the early time of mineralization stage (380–320°C) indicates the occurrence of fluid boiling. The positive correlations between the homogenization temperatures and the salinities of the fluids and the low oxygen isotopic compositions (δ18Ofluid < 3‰) of the syn- to postmineralization quartz together suggest the mixing of magmatic fluids with meteoric water, which dominated the whole mineralization process. The early boiling fluids were not responsible for ore precipitation, whereas the mixing with meteoric water, which resulted in temperature decrease and dilution that significantly reduced the metal solubility, should have played the major role in Mo mineralization. Combined fluid inclusion microthermometry and chlorite geothermometer results reveal that ore deposition mainly occurred between 350 and 290°C in Haisugou.
New Transcriptional Reporters to Quantify and Monitor PPARγ Activity
Authors: Degrelle Séverine A. , Shoaito Hussein , Fournier Thierry
Published: November 2017

The peroxisome-proliferator-activated-receptor-γ (PPARγ) is a member of the nuclear receptor superfamily that plays a critical role in diverse biological processes, including adipogenesis, lipid metabolism, and placental development. To study the activity of PPARγ, we constructed two new reporter genes: a fluorescent GFP-tagged histone-2B (PPRE-H2B-eGFP) and a secreted nanoluciferase (PPRE-pNL1.3[secNluc]). This study demonstrates their usage to monitor PPARγ activity in different cell types and screen for PPARγ’s potential ligands.
Tunable Optical Bistability in One-Dimensional Photonic Crystal with a Nonlinear Defect Coupled by Graphene Sheets
Authors: Zheng Zhiwei , Jiang Leyong , Guo Jun , Dai Xiaoyu , Xiang Yuanjiang
Published: November 2017

The optical bistability in one-dimensional photonic crystal (1DPC) with a nonlinear defect is investigated. It is demonstrated that, by introducing graphene layers into the nonlinear defect, the optical bistability in 1DPC can be changed significantly. The hysteresis threshold increases with the number of graphene monolayers and can be lowered or enhanced by tuning the Fermi energy of graphene. On the other hand, the hysteresis width and the nonlinear lateral shift can also be controlled by varying the Femi energy and the number of graphene monolayers. These results may be useful for controlling the optical bistability and nonlinear lateral shift in 1DPCs.
Electromagnetic Scattering by Multiple Columns Partially Buried in a Ground Plane
Authors: Ren Xin-Cheng , Zhao Ye , Yang Peng-Ju , Zhu Xiao-Min
Published: November 2017

Wideband electromagnetic scattering from multiple objects partially buried beneath rough earth soil surfaces is an important topic during recent years due to its extensive applications in several fields, such as ground remote sensing, ground penetrating radar applications, and target identification. Due to the advantages of finite-difference time-domain (FDTD) method in calculating the wideband electromagnetic scattering from rough surface in the presence of multiple objects, the FDTD method under ultrawideband (UWB) Gaussian pulse wave incidence is utilized in the present study for analyzing the frequency response of rough soil surfaces with periodically distributed multiple rectangular cross-section columns buried partially. In this paper, the dielectric property of the actual land surface is expressed using the four-component model, and the actual rough land surface is simulated utilizing Monte Carlo method with exponential correlation function. The emphasis of the present study is on analyzing the wideband response signatures of composite backscattering coefficient varying with frequency on the basis of extensive numerical simulations, in particular for calculating and discussing in detail the influence of the root-mean-square height and the correlation length of rough soil surface, soil moisture, the length and the width of the rectangular cross-section column, separation distance, burial depth, and tilt angle on the composite backscattering coefficient.
P-MartCancer–Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets
Authors: Webb-Robertson Bobbie-Jo M. , Bramer Lisa M. , Jensen Jeffrey L. , Kobold Markus A. , Stratton Kelly G. , White Amanda M. , Rodland Karin D.
Published: November 2017

P-MartCancer is an interactive web-based software environment that enables statistical analyses of peptide or protein data, quantitated from mass spectrometry–based global proteomics experiments, without requiring in-depth knowledge of statistical programming. P-MartCancer offers a series of statistical modules associated with quality assessment, peptide and protein statistics, protein quantification, and exploratory data analyses driven by the user via customized workflows and interactive visualization. Currently, P-MartCancer offers access and the capability to analyze multiple cancer proteomic datasets generated through the Clinical Proteomics Tumor Analysis Consortium at the peptide, gene, and protein levels. P-MartCancer is deployed as a web service (https://pmart.labworks.org/cptac.html), alternatively available via Docker Hub (https://hub.docker.com/r/pnnl/pmart-web/). Cancer Res; 77(21); e47–50. ©2017 AACR.
Computational Radiomics System to Decode the Radiographic Phenotype
Authors: van Griethuysen Joost J.M. , Fedorov Andriy , Parmar Chintan , Hosny Ahmed , Aucoin Nicole , Narayan Vivek , Beets-Tan Regina G.H. , Fillion-Robin Jean-Christophe , Pieper Steve , Aerts Hugo J.W.L.
Published: November 2017

Radiomics aims to quantify phenotypic characteristics on medical imaging through the use of automated algorithms. Radiomic artificial intelligence (AI) technology, either based on engineered hard-coded algorithms or deep learning methods, can be used to develop noninvasive imaging-based biomarkers. However, lack of standardized algorithm definitions and image processing severely hampers reproducibility and comparability of results. To address this issue, we developed PyRadiomics, a flexible open-source platform capable of extracting a large panel of engineered features from medical images. PyRadiomics is implemented in Python and can be used standalone or using 3D Slicer. Here, we discuss the workflow and architecture of PyRadiomics and demonstrate its application in characterizing lung lesions. Source code, documentation, and examples are publicly available at www.radiomics.io. With this platform, we aim to establish a reference standard for radiomic analyses, provide a tested and maintained resource, and to grow the community of radiomic developers addressing critical needs in cancer research. Cancer Res; 77(21); e104–7. ©2017 AACR.
Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas
Authors: Li Jun , Akbani Rehan , Zhao Wei , Lu Yiling , Weinstein John N. , Mills Gordon B. , Liang Han
Published: November 2017

Reverse-phase protein arrays (RPPA) represent a powerful functional proteomic approach to elucidate cancer-related molecular mechanisms and to develop novel cancer therapies. To facilitate community-based investigation of the large-scale protein expression data generated by this platform, we have developed a user-friendly, open-access bioinformatic resource, The Cancer Proteome Atlas (TCPA, http://tcpaportal.org), which contains two separate web applications. The first one focuses on RPPA data of patient tumors, which contains >8,000 samples of 32 cancer types from The Cancer Genome Atlas and other independent patient cohorts. The second application focuses on the RPPA data of cancer cell lines and contains >650 independent cell lines across 19 lineages. Many of these cell lines have publicly available, high-quality DNA, RNA, and drug screening data. TCPA provides various analytic and visualization modules to help cancer researchers explore these datasets and generate testable hypotheses in an effective and intuitive manner. Cancer Res; 77(21); e51–54. ©2017 AACR.
Dendritic Cells Enhance Polyfunctionality of Adoptively Transferred T Cells That Target Cytomegalovirus in Glioblastoma
Authors: Reap Elizabeth A. , Suryadevara Carter M. , Batich Kristen A. , Sanchez-Perez Luis , Archer Gary E. , Schmittling Robert J. , Norberg Pamela K. , Herndon James E. , Healy Patrick , Congdon Kendra L. , Gedeon Patrick C. , Campbell Olivia C. , Swartz Adam M. , Riccione Katherine A. , Yi John S. , Hossain-Ibrahim Mohammed K. , Saraswathula Anirudh , Nair Smita K. , Dunn-Pirio Anastasie M. , Broome Taylor M. , Weinhold Kent J. , Desjardins Annick , Vlahovic Gordana , McLendon Roger E. , Friedman Allan H. , Friedman Henry S. , Bigner Darell D. , Fecci Peter E. , Mitchell Duane A. , Sampson John H.
Published: November 2017

Median survival for glioblastoma (GBM) remains <15 months. Human cytomegalovirus (CMV) antigens have been identified in GBM but not normal brain, providing an unparalleled opportunity to subvert CMV antigens as tumor-specific immunotherapy targets. A recent trial in recurrent GBM patients demonstrated the potential clinical benefit of adoptive T-cell therapy (ATCT) of CMV phosphoprotein 65 (pp65)–specific T cells. However, ex vivo analyses from this study found no change in the capacity of CMV pp65-specific T cells to gain multiple effector functions or polyfunctionality, which has been associated with superior antitumor efficacy. Previous studies have shown that dendritic cells (DC) could further enhance tumor-specific CD8+ T-cell polyfunctionality in vivo when administered as a vaccine. Therefore, we hypothesized that vaccination with CMV pp65 RNA-loaded DCs would enhance the frequency of polyfunctional CMV pp65-specific CD8+ T cells after ATCT. Here, we report prospective results of a pilot trial in which 22 patients with newly diagnosed GBM were initially enrolled, of which 17 patients were randomized to receive CMV pp65-specific T cells with CMV-DC vaccination (CMV-ATCT-DC) or saline (CMV-ATCT-saline). Patients who received CMV-ATCT-DC vaccination experienced a significant increase in the overall frequencies of IFNγ+, TNFα+, and CCL3+ polyfunctional, CMV-specific CD8+ T cells. These increases in polyfunctional CMV-specific CD8+ T cells correlated (R = 0.7371, P = 0.0369) with overall survival, although we cannot conclude this was causally related. Our data implicate polyfunctional T-cell responses as a potential biomarker for effective antitumor immunotherapy and support a formal assessment of this combination approach in a larger randomized study.

Significance: A randomized pilot trial in patients with GBM implicates polyfunctional T-cell responses as a biomarker for effective antitumor immunotherapy. Cancer Res; 78(1); 256–64. ©2017 AACR.
PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models
Authors: Meehan Terrence F. , Conte Nathalie , Goldstein Theodore , Inghirami Giorgio , Murakami Mark A. , Brabetz Sebastian , Gu Zhiping , Wiser Jeffrey A. , Dunn Patrick , Begley Dale A. , Krupke Debra M. , Bertotti Andrea , Bruna Alejandra , Brush Matthew H. , Byrne Annette T. , Caldas Carlos , Christie Amanda L. , Clark Dominic A. , Dowst Heidi , Dry Jonathan R. , Doroshow James H. , Duchamp Olivier , Evrard Yvonne A. , Ferretti Stephane , Frese Kristopher K. , Goodwin Neal C. , Greenawalt Danielle , Haendel Melissa A. , Hermans Els , Houghton Peter J. , Jonkers Jos , Kemper Kristel , Khor Tin O. , Lewis Michael T. , Lloyd K.C. Kent , Mason Jeremy , Medico Enzo , Neuhauser Steven B. , Olson James M. , Peeper Daniel S. , Rueda Oscar M. , Seong Je Kyung , Trusolino Livio , Vinolo Emilie , Wechsler-Reya Robert J. , Weinstock David M. , Welm Alana , Weroha S. John , Amant Frédéric , Pfister Stefan M. , Kool Marcel , Parkinson Helen , Butte Atul J. , Bult Carol J.
Published: November 2017

Patient-derived tumor xenograft (PDX) mouse models have emerged as an important oncology research platform to study tumor evolution, mechanisms of drug response and resistance, and tailoring chemotherapeutic approaches for individual patients. The lack of robust standards for reporting on PDX models has hampered the ability of researchers to find relevant PDX models and associated data. Here we present the PDX models minimal information standard (PDX-MI) for reporting on the generation, quality assurance, and use of PDX models. PDX-MI defines the minimal information for describing the clinical attributes of a patient's tumor, the processes of implantation and passaging of tumors in a host mouse strain, quality assurance methods, and the use of PDX models in cancer research. Adherence to PDX-MI standards will facilitate accurate search results for oncology models and their associated data across distributed repository databases and promote reproducibility in research studies using these models. Cancer Res; 77(21); e62–66. ©2017 AACR.
NDEx 2.0: A Clearinghouse for Research on Cancer Pathways
Authors: Pratt Dexter , Chen Jing , Pillich Rudolf , Rynkov Vladimir , Gary Aaron , Demchak Barry , Ideker Trey
Published: November 2017

We present NDEx 2.0, the latest release of the Network Data Exchange (NDEx) online data commons (www.ndexbio.org) and the ways in which it can be used to (i) improve the quality and abundance of biological networks relevant to the cancer research community; (ii) provide a medium for collaboration involving networks; and (iii) facilitate the review and dissemination of networks. We describe innovations addressing the challenges of an online data commons: scalability, data integration, data standardization, control of content and format by authors, and decentralized mechanisms for review. The practical use of NDEx is presented in the context of a novel strategy to foster network-oriented communities of interest in cancer research by adapting methods from academic publishing and social media. Cancer Res; 77(21); e58–61. ©2017 AACR.
DeepPhe: A Natural Language Processing System for Extracting Cancer Phenotypes from Clinical Records
Authors: Savova Guergana K. , Tseytlin Eugene , Finan Sean , Castine Melissa , Miller Timothy , Medvedeva Olga , Harris David , Hochheiser Harry , Lin Chen , Chavan Girish , Jacobson Rebecca S.
Published: November 2017

Precise phenotype information is needed to understand the effects of genetic and epigenetic changes on tumor behavior and responsiveness. Extraction and representation of cancer phenotypes is currently mostly performed manually, making it difficult to correlate phenotypic data to genomic data. In addition, genomic data are being produced at an increasingly faster pace, exacerbating the problem. The DeepPhe software enables automated extraction of detailed phenotype information from electronic medical records of cancer patients. The system implements advanced Natural Language Processing and knowledge engineering methods within a flexible modular architecture, and was evaluated using a manually annotated dataset of the University of Pittsburgh Medical Center breast cancer patients. The resulting platform provides critical and missing computational methods for computational phenotyping. Working in tandem with advanced analysis of high-throughput sequencing, these approaches will further accelerate the transition to precision cancer treatment. Cancer Res; 77(21); e115–8. ©2017 AACR.
Platform for Quantitative Evaluation of Spatial Intratumoral Heterogeneity in Multiplexed Fluorescence Images
Authors: Spagnolo Daniel M. , Al-Kofahi Yousef , Zhu Peihong , Lezon Timothy R. , Gough Albert , Stern Andrew M. , Lee Adrian V. , Ginty Fiona , Sarachan Brion , Taylor D. Lansing , Chennubhotla S. Chakra
Published: November 2017

We introduce THRIVE (Tumor Heterogeneity Research Interactive Visualization Environment), an open-source tool developed to assist cancer researchers in interactive hypothesis testing. The focus of this tool is to quantify spatial intratumoral heterogeneity (ITH), and the interactions between different cell phenotypes and noncellular constituents. Specifically, we foresee applications in phenotyping cells within tumor microenvironments, recognizing tumor boundaries, identifying degrees of immune infiltration and epithelial/stromal separation, and identification of heterotypic signaling networks underlying microdomains. The THRIVE platform provides an integrated workflow for analyzing whole-slide immunofluorescence images and tissue microarrays, including algorithms for segmentation, quantification, and heterogeneity analysis. THRIVE promotes flexible deployment, a maintainable code base using open-source libraries, and an extensible framework for customizing algorithms with ease. THRIVE was designed with highly multiplexed immunofluorescence images in mind, and, by providing a platform to efficiently analyze high-dimensional immunofluorescence signals, we hope to advance these data toward mainstream adoption in cancer research. Cancer Res; 77(21); e71–74. ©2017 AACR.
Rapid Intraoperative Diagnosis of Pediatric Brain Tumors Using Stimulated Raman Histology
Authors: Hollon Todd C. , Lewis Spencer , Pandian Balaji , Niknafs Yashar S. , Garrard Mia R. , Garton Hugh , Maher Cormac O. , McFadden Kathryn , Snuderl Matija , Lieberman Andrew P. , Muraszko Karin , Camelo-Piragua Sandra , Orringer Daniel A.
Published: November 2017

Accurate histopathologic diagnosis is essential for providing optimal surgical management of pediatric brain tumors. Current methods for intraoperative histology are time- and labor-intensive and often introduce artifact that limit interpretation. Stimulated Raman histology (SRH) is a novel label-free imaging technique that provides intraoperative histologic images of fresh, unprocessed surgical specimens. Here we evaluate the capacity of SRH for use in the intraoperative diagnosis of pediatric type brain tumors. SRH revealed key diagnostic features in fresh tissue specimens collected from 33 prospectively enrolled pediatric type brain tumor patients, preserving tumor cytology and histoarchitecture in all specimens. We simulated an intraoperative consultation for 25 patients with specimens imaged using both SRH and standard hematoxylin and eosin histology. SRH-based diagnoses achieved near-perfect diagnostic concordance (Cohen's kappa, κ > 0.90) and an accuracy of 92% to 96%. We then developed a quantitative histologic method using SRH images based on rapid image feature extraction. Nuclear density, tumor-associated macrophage infiltration, and nuclear morphology parameters from 3337 SRH fields of view were used to develop and validate a decision-tree machine-learning model. Using SRH image features, our model correctly classified 25 fresh pediatric type surgical specimens into normal versus lesional tissue and low-grade versus high-grade tumors with 100% accuracy. Our results provide insight into how SRH can deliver rapid diagnostic histologic data that could inform the surgical management of pediatric brain tumors.

Significance: A new imaging method simplifies diagnosis and informs decision making during pediatric brain tumor surgery. Cancer Res; 78(1); 278–89. ©2017 AACR.