bluuebunny/crossref_metadata_2025 huggingface dataset:
A GPU‐accelerated Monte Carlo dose calculation platform and its application toward validating an MRI‐guided radiation therapy beam model
Authors: Wang Yuhe , Mazur Thomas R. , Green Olga , Hu Yanle , Li Hua , Rodriguez Vivian , Wooten H. Omar , Yang Deshan , Zhao Tianyu , Mutic Sasa , Li H. Harold
Published: June 2016

Purpose:

The clinical commissioning of IMRT subject to a magnetic field is challenging. The purpose of this work is to develop a GPU‐accelerated Monte Carlo dose calculation platform based on penelope and then use the platform to validate a vendor‐provided MRIdian head model toward quality assurance of clinical IMRT treatment plans subject to a 0.35 T magnetic field.

Methods:

penelope was first translated from fortran to c++ and the result was confirmed to produce equivalent results to the original code. The c++ code was then adapted to cuda in a workflow optimized for GPU architecture. The original code was expanded to include voxelized transport with Woodcock tracking, faster electron/positron propagation in a magnetic field, and several features that make gpenelope highly user‐friendly. Moreover, the vendor‐provided MRIdian head model was incorporated into the code in an effort to apply gpenelope as both an accurate and rapid dose validation system. A set of experimental measurements were performed on the MRIdian system to examine the accuracy of both the head model and gpenelope. Ultimately, gpenelope was applied toward independent validation of patient doses calculated by MRIdian's kmc.

Results:

An acceleration factor of 152 was achieved in comparison to the original single‐thread fortran implementation with the original accuracy being preserved. For 16 treatment plans including stomach (4), lung (2), liver (3), adrenal gland (2), pancreas (2), spleen(1), mediastinum (1), and breast (1), the MRIdian dose calculation engine agrees with gpenelope with a mean gamma passing rate of 99.1% ± 0.6% (2%/2 mm).

Conclusions:

A Monte Carlo simulation platform was developed based on a GPU‐ accelerated version of penelope. This platform was used to validate that both the vendor‐provided head model and fast Monte Carlo engine used by the MRIdian system are accurate in modeling radiation transport in a patient using 2%/2 mm gamma criteria. Future applications of this platform will include dose validation and accumulation, IMRT optimization, and dosimetry system modeling for next generation MR‐IGRT systems.
A hierarchical multimode molecular stress function model for linear polymer melts in extensional flows
Authors: Narimissa Esmaeil , Wagner Manfred H.
Published: June 2016

A novel hierarchical multimode molecular stress function (HMMSF) model for linear polymer melts is proposed, which implements the basic ideas of (i) hierarchical relaxation, (ii) dynamic dilution, and (iii) interchain tube pressure. The capability of this approach is demonstrated in modeling the extensional viscosity data of monodisperse, bidisperse, and polydisperse linear polymer melts. Predictions of the HMMSF model, which are solely based on the linear-viscoelastic relaxation modulus and a single free model parameter, the segmental equilibration time, are compared to elongational viscosity data of monodisperse polystyrene melts and solutions as well as to the elongational viscosity data of a bidisperse blend of two monodisperse polystyrenes, and good agreement between model and experimental data is observed. By using a simplified relation between the Rouse stretch-relaxation times and the relaxation times of the melts, the modeling is extended to the uniaxial, equibiaxial, and planar extensional viscosity data of a high-density polyethylene, the uniaxial and equibiaxial extensional viscosity data of a polydisperse polystyrene, the elongational viscosity data of three high-density polyethylenes, and a linear low-density polyethylene. For polydisperse melts, the modeling is again based exclusively on the linear-viscoelastic relaxation modulus with only one material parameter, the dilution modulus, which quantifies the onset of dynamic dilution.
Need for and Interest in a Sports Nutrition Mobile Device Application Among Division I Collegiate Athletes
Authors: Zuniga Krystle E. , Downey Darcy L. , McCluskey Ryan , Rivers Carley
Published: June 2016

The majority of National Collegiate Athletic Association (NCAA) programs do not have a sports nutritionist, leaving athletes to gather information from resources that vary in reputability. The objective of this study was to identify a need for the development of accessible and reputable resources of nutrition information by assessing the current use of nutrition information resources, dietary habits, and sports nutrition knowledge among Division I collegiate athletes. Seventy-two athletes across eight sports completed questionnaires concerning nutrition resources used, dietary habits, and sports nutrition knowledge. In addition, interest levels in a mobile device application for delivery of nutrition information and tools were assessed. Primary sources for nutrition information included parents and family, athletic trainers (AT), and the internet/media, and athletes felt most comfortable discussing nutrition with parents and family, ATs, and strength and conditioning specialists. Performance on a sports nutrition knowledge questionnaire indicated a general lack of nutrition knowledge, and the high frequency of “unsure” responses suggested a lack of confidence in nutrition knowledge. Athletes conveyed a high likelihood that they would use a mobile device application as a nutrition resource, but were more interested in access to nutrition topics than tools such as a food log. We found that college athletes possess minimal sports nutrition knowledge, obtain nutrition information from nonprofessional resources, and were interested in utilizing a mobile device application as a resource. Further research is needed to explore the feasibility and effectiveness of alternative resources, such as a mobile device application, to deliver nutrition information and improve nutrition knowledge.
Genome Sequence of Hafnia alvei bta3_1, a Bacterium with Antimicrobial Properties Isolated from Honey Bee Gut
Authors: Tian Baoyu , Moran Nancy A.
Published: June 2016

Hafnia alvei
bta3_1, a strain with antibacterial properties, was isolated from honey bee gut and cultured under aerobic and anaerobic conditions. To explore the potential genetic bases of its antibacterial and possible pathogenic properties, the complete genome of this organism was sequenced and analyzed.
Complete Genome Sequence of Soil Fungus Aspergillus terreus (KM017963), a Potent Lovastatin Producer
Authors: Savitha Janakiraman , Bhargavi S. D. , Praveen V. K.
Published: June 2016

We report the complete genome of
Aspergillus terreus
(KM017963), a tropical soil isolate. The genome sequence is 29 Mb, with a G+C content of 51.12%. The genome sequence of
A. terreus
shows the presence of the complete gene cluster responsible for lovastatin (an anti-cholesterol drug) production in a single scaffold (1.16).
Complete Genome and Plasmid Sequences for Rhodococcus fascians D188 and Draft Sequences for
Rhodococcus
Isolates PBTS 1 and PBTS 2
Authors: Stamler Rio A. , Vereecke Danny , Zhang Yucheng , Schilkey Faye , Devitt Nico , Randall Jennifer J.
Published: June 2016

Rhodococcus fascians
, a phytopathogen that alters plant development, inflicts significant losses in plant production around the world. We report here the complete genome sequence of
R. fascians
D188, a well-characterized model isolate, and
Rhodococcus
species PBTS (pistachio bushy top syndrome) 1 and 2, which were shown to be responsible for a disease outbreak in pistachios.
Draft Genome Sequence of Aeribacillus pallidus Strain 8m3, a Thermophilic Hydrocarbon-Oxidizing Bacterium Isolated from the Dagang Oil Field (China)
Authors: Poltaraus Andrey B. , Sokolova Diyana S. , Grouzdev Denis S. , Ivanov Timophey M. , Malakho Sophia G. , Korshunova Alena V. , Rozanov Aleksey S. , Tourova Tatiyana P. , Nazina Tamara N.
Published: June 2016

The draft genome sequence of
Aeribacillus pallidus
strain 8m3, a thermophilic aerobic oil-oxidizing bacterium isolated from production water from the Dagang high-temperature oil field, China, is presented here. The genome is annotated to provide insights into the genomic and phenotypic diversity of the genus
Aeribacillus
.
Genome Sequence of a Novel H14N7 Subtype Influenza A Virus Isolated from a Blue-Winged Teal (
Anas discors
) Harvested in Texas, USA
Authors: Ramey Andrew M. , Reeves Andrew B. , Poulson Rebecca L. , Carter Deborah L. , Davis-Fields Nicholas , Stallknecht David E.
Published: June 2016

We report here the complete genome sequence of a novel H14N7 subtype influenza A virus (IAV) isolated from a blue-winged teal (
Anas discors
) harvested in Texas, USA. The genomic characteristics of this IAV strain with a previously undetected subtype combination suggest recent viral evolution within the New World wild-bird IAV reservoir.
Complete Chloroplast and Mitochondrial Genome Sequences of the Hydrocarbon Oil-Producing Green Microalga
Botryococcus braunii
Race B (Showa)
Authors: Blifernez-Klassen Olga , Wibberg Daniel , Winkler Anika , Blom Jochen , Goesmann Alexander , Kalinowski Jörn , Kruse Olaf
Published: June 2016

The green alga
Botryococcus braunii
is capable of the production and excretion of high quantities of long-chain hydrocarbons and exopolysaccharides. In this study, we present the complete plastid and mitochondrial genomes of the hydrocarbon-producing microalga
Botryococcus braunii
race B (Showa), with a total length of 156,498 and 129,356 bp, respectively.
Draft Genome Sequence of Hydrotalea flava Strain CCUG 51397
T
Authors: Leite Laura Rabelo , Medeiros Julliane Dutra , Fernandes Gabriel Rocha , Araújo Flávio , Pylro Victor Satler , Salim Anna Christina , Volpini Ângela , Oliveira Guilherme , Cuadros-Orellana Sara
Published: June 2016

We report the draft genome sequence of
Hydrotalea flava
CCUG 51397
T
, the type strain of the genus
Hydrotalea
(family
Chitinophagaceae
), isolated from water samples in southern Sweden.
Complete Genome Sequence of Sphingopyxis macrogoltabida Strain 203N (NBRC 111659), a Polyethylene Glycol Degrader
Authors: Ohtsubo Yoshiyuki , Nonoyama Shouta , Nagata Yuji , Numata Mitsuru , Tsuchikane Keiko , Hosoyama Akira , Yamazoe Atsushi , Tsuda Masataka , Fujita Nobuyuki , Kawai Fusako
Published: June 2016

We determined the complete genome sequence of
Sphingopyxis macrogoltabida
strain 203N, a polyethylene glycol degrader. Because the PacBio assembly (285× coverage) seemed to be full of nucleotide-level mismatches, the Newbler assembly of MiSeq mate-pair and paired-end data was used for finishing and the PacBio assembly was used as a reference. The PacBio assembly carried 414 nucleotide mismatches over 5,953,153 bases of the 203N genome.
Complete Coding Sequences of One H9 and Three H7 Low-Pathogenic Influenza Viruses Circulating in Wild Birds in Belgium, 2009 to 2012
Authors: Van Borm Steven , Rosseel Toon , Marché Sylvie , Steensels Mieke , Vangeluwe Didier , Linden Annick , van den Berg Thierry , Lambrecht Bénédicte
Published: June 2016

The complete coding sequences of four avian influenza A viruses (two H7N7, one H7N1, and one H9N2) circulating in wild waterfowl in Belgium from 2009 to 2012 were determined using Illumina sequencing. All viral genome segments represent viruses circulating in the Eurasian wild bird population.
Complete Genome Sequence of Mycobacterium abscessus subsp.
bolletii
Authors: Caverly Lindsay J. , Spilker Theodore , LiPuma John J.
Published: June 2016

We report the complete genome sequence of a
Mycobacterium abscessus
subsp.
bolletii
isolate recovered from a sputum culture from an individual with cystic fibrosis. This sequence is the first completed whole-genome sequence of
M. abscessus
subsp.
bolletii
and adds value to studies of
M. abscessus
complex genomics.
Treatment of severe, refractory and rapidly evolving thrombotic thrombocytopenic purpura
Authors: Acedillo Rey R , Govind Mayur , Kashgary Abdullah , Clark William F
Published: June 2016

A 36-year-old man presented to hospital with gross haematuria and evidence of severe, refractory thrombotic thrombocytopenic purpura. Initial treatment with high-volume plasma exchange therapy and early administration of rituximab failed to achieve a sustained clinical response. His clinical course was complicated by left hemianopsia and despite an urgent splenectomy he developed a large right-sided stroke with malignant cerebral oedema that required an emergent decompressive craniotomy. He also had numerous infectious complications as a consequence of an aggressive immunosuppressive strategy. While the patient did not respond to cyclophosphamide, cyclosporine,N-acetylcysteine, and one course of bortezomib, he eventually responded to a second course of bortezomib. One year later, the patient remains in remission and maintains excellent cognitive function. However, he has not completely recovered from his stroke and continues to participate in rehabilitation for his residual physical deficits.
Response of growth and nitrogen fixation to pod elimination of three annual Medicago species submitted to drought and subsequent recovery
Authors: Sadeghi Hossein , Fakhari Farzaneh
Published: June 2016

This research examined the effect of pod elimination on growth and N2 fixation ability in three annual Medicago species during drought stress and subsequent recovery. This study was carried out as a factorial experiment based on a completely randomized design with four replications. The treatments included annual Medicago species, presence or removal of the pod, and water stress at four levels: 100% (as a control), 80%, 60%, and 40% field capacity (FC) during the period of stress. The results showed that annual Medicago species can be considered as semi-drought tolerant species and their recovery ability from mild and moderate drought stress is relatively good. M. polymorpha performed better and showed higher recovery ability in comparison with other tested species. The results of this study showed that elimination of pods from annual Medicago species before sowing enhanced seedling performance under drought stress. However, the effect of pod elimination showed higher significance on growth parameters than nitrogen fixation. The information from this research would be useful for better understanding the physiological basis of changes in drought resistance, as well as targeted breeding programs, to improve the performance of annual Medicago species under conditions of limited or scarce water supply.
Covariant mutually unbiased bases
Authors: Carmeli Claudio , Schultz Jussi , Toigo Alessandro
Published: June 2016

The connection between maximal sets of mutually unbiased bases (MUBs) in a prime-power dimensional Hilbert space and finite phase-space geometries is well known. In this article, we classify MUBs according to their degree of covariance with respect to the natural symmetries of a finite phase-space, which are the group of its affine symplectic transformations. We prove that there exist maximal sets of MUBs that are covariant with respect to the full group only in odd prime-power dimensional spaces, and in this case, their equivalence class is actually unique. Despite this limitation, we show that in dimension [Formula: see text] covariance can still be achieved by restricting to proper subgroups of the symplectic group, that constitute the finite analogues of the oscillator group. For these subgroups, we explicitly construct the unitary operators yielding the covariance.
Analytic Aharonov–Bohm rings — Currents readout from Zeeman spectrum
Authors: Xiao Mufei , Reyes-Serrato Armando
Published: June 2016

This paper reports the work on the development and analysis of a model for quantum rings in which persistent currents are induced by Aharonov–Bohm (AB) or other similar effects. The model is based on a centric and annual potential profile. The time-independent Schrödinger equation including an external magnetic field and an AB flux is analytically solved. The outputs, namely energy dispersion and wavefunctions, are analyzed in detail. It is shown that the rotation quantum number [Formula: see text] is limited to small numbers, especially in weak confinement, and a conceptual proposal is put forward for acquiring the flux and eventually estimating the persistent currents in a Zeeman spectroscopy. The wavefunctions and electron distributions are numerically studied and compared to one-dimensional (1D) quantum well. It is predicated that the model and its solutions, eigen energy structure and analytic wavefunctions, would be a powerful tool for studying various electric and optical properties of quantum rings.
Evolution in totally constrained models: Schrödinger vs. Heisenberg pictures
Authors: Olmedo Javier
Published: June 2016

We study the relation between two evolution pictures that are currently considered for totally constrained theories. Both descriptions are based on Rovelli’s evolving constants approach, where one identifies a (possibly local) degree of freedom of the system as an internal time. This method is well understood classically in several situations. The purpose of this paper is to further analyze this approach at the quantum level. Concretely, we will compare the (Schrödinger-like) picture where the physical states evolve in time with the (Heisenberg-like) picture in which one defines parametrized observables (or evolving constants of the motion). We will show that in the particular situations considered in this paper (the parametrized relativistic particle and a spatially flat homogeneous and isotropic spacetime coupled to a massless scalar field) both descriptions are equivalent. We will finally comment on possible issues and on the genericness of the equivalence between both pictures.
Charge symmetry breaking effect for 3H and 3He within s-wave approach
Authors: Filikhin I. , Suslov V. M. , Vlahovic B.
Published: June 2016

Three-nucleon systems are considered assuming the neutrons and protons to be distinguishable particles. The configuration space Faddeev equations are exploited to calculate ground state energies of 3H and 3He nuclei within an [Formula: see text]-wave approach applying the Malfliet–Tjon, Tamagaki G3RS and Afnan–Tang ATS3 NN potentials. We modify the potentials by scaling strength parameters to define [Formula: see text], [Formula: see text] and [Formula: see text] singlet components. The scaling parameters are fixed to reproduce experimental scattering lengths. The charge symmetry breaking energy is numerically evaluated. The relation between [Formula: see text], [Formula: see text] and [Formula: see text] singlet potentials is discussed.
Infinite-dimensional Ellentuck spaces and Ramsey-classification theorems
Authors: Dobrinen Natasha
Published: June 2016

We extend the hierarchy of finite-dimensional Ellentuck spaces to infinite dimensions. Using uniform barriers [Formula: see text] on [Formula: see text] as the prototype structures, we construct a class of continuum many topological Ramsey spaces [Formula: see text] which are Ellentuck-like in nature, and form a linearly ordered hierarchy under projections. We prove new Ramsey-classification theorems for equivalence relations on fronts, and hence also on barriers, on the spaces [Formula: see text], extending the Pudlák–Rödl theorem for barriers on the Ellentuck space. The inspiration for these spaces comes from continuing the iterative construction of the forcings [Formula: see text] to the countable transfinite. The [Formula: see text]-closed partial order [Formula: see text] is forcing equivalent to [Formula: see text], which forces a non-p-point ultrafilter [Formula: see text]. This work forms the basis for further work classifying the Rudin–Keisler and Tukey structures for the hierarchy of the generic ultrafilters [Formula: see text].
Smartphone microendoscopy for high resolution fluorescence imaging
Authors: Hong Xiangqian , Nagarajan Vivek K. , Mugler Dale H. , Yu Bing
Published: June 2016

High resolution optical endoscopes are increasingly used in diagnosis of various medical conditions of internal organs, such as the cervix and gastrointestinal (GI) tracts, but they are too expensive for use in resource-poor settings. On the other hand, smartphones with high resolution cameras and Internet access have become more affordable, enabling them to diffuse into most rural areas and developing countries in the past decade. In this paper, we describe a smartphone microendoscope that can take fluorescence images with a spatial resolution of 3.1 [Formula: see text]m. Images collected from ex vivo, in vitro and in vivo samples using the device are also presented. The compact and cost-effective smartphone microendoscope may be envisaged as a powerful tool for detecting pre-cancerous lesions of internal organs in low and middle-income countries (LMICs).
Energy--Performance Trade-Offs via the EP Queue
Authors: Harrison Peter G. , Patel Naresh M. , Knottenbelt William J.
Published: June 2016

We introduce the EP queue -- a significant generalization of the

M
B

/
G
/1 queue that has state-dependent service time probability distributions and incorporates power-up for first arrivals and power-down for idle periods. We derive exact results for the busy-time and response-time distributions. From these, we derive power consumption metrics during nonidle periods and overall response time metrics, which together provide a single measure of the trade-off between energy and performance. We illustrate these trade-offs for some policies and show how numerical results can provide insights into system behavior. The EP queue has application to storage systems, especially hard disks, and other data-center components such as compute servers, networking, and even hyperconverged infrastructure.
Modeling Robot Swarms Using Integrals of Birth-Death Processes
Authors: Khaluf Yara , Dorigo Marco
Published: June 2016

This article investigates the use of the integral of linear birth-death processes in the context of analyzing swarm robotics systems. We show that when a robot swarm can be modeled as a linear birth-death process, well-established results can be used to compute the expected value and/or the distribution of important swarm performance measures, such as the swarm activity time or the swarm energy consumption. We also show how the linear birth-death model can be used to estimate the long-term value of such performance measures and design robot controllers that satisfy constraints on these measures.
Heuristic Evaluation for Novice Programming Systems
Authors: Kölling Michael , McKay Fraser
Published: June 2016

The past few years has seen a proliferation of novice programming tools. The availability of a large number of systems has made it difficult for many users to choose among them. Even for education researchers, comparing the relative quality of these tools, or judging their respective suitability for a given context, is hard in many instances. For designers of such systems, assessing the respective quality of competing design decisions can be equally difficult.

Heuristic evaluation provides a practical method of assessing the quality of alternatives in these situations and of identifying potential problems with existing systems for a given target group or context. Existing sets of heuristics, however, are not specific to the domain of novice programming and thus do not evaluate all aspects of interest to us in this specialised application domain.

In this article, we propose a set of heuristics to be used in heuristic evaluations of novice programming systems. These heuristics have the potential to allow a useful assessment of the quality of a given system with lower cost than full formal user studies and greater precision than the use of existing sets of heuristics. The heuristics are described and discussed in detail. We present an evaluation of the effectiveness of the heuristics that suggests that the new set of heuristics provides additional useful information to designers not obtained with existing heuristics sets.
A Bimodal Scheduler for Coarse-Grained Reconfigurable Arrays
Authors: Theocharis Panagiotis , Sutter Bjorn De
Published: June 2016

Compilers for Course-Grained Reconfigurable Array (CGRA) architectures suffer from long compilation times and code quality levels far below the theoretical upper bounds. This article presents a new scheduler, called the Bimodal Modulo Scheduler (BMS), to map inner loops onto (heterogeneous) CGRAs of the Architecture for Dynamically Reconfigurable Embedded Systems (ADRES) family. BMS significantly outperforms existing schedulers for similar architectures in terms of generated code quality and compilation time. This is achieved by combining new schemes for backtracking with extended and adapted forms of priority functions and cost functions, as described in the article. BMS is evaluated by mapping multimedia and software-defined radio benchmarks onto tuned ADRES instances.
Security Injections@Towson
Authors: Taylor Blair , Kaza Siddharth
Published: June 2016

Despite the critical societal importance of computer security, security is not well integrated into the undergraduate computing curriculum. Security classes and tracks treat security issues as separable topics as opposed to fundamental issues that pervade all aspects of software development. Recently, there has been an increasing focus on security as a cross-cutting concern across the computer science curriculum. The Security Injections@Towson project provides resources and effective strategies to incorporate secure coding in the early programming classes. We describe the development, assessment, and dissemination of more than 40 lab-based security injection modules designed to be injected into courses with minimal impact on the curriculum. We include assessment results from 1,135 students across five diverse institutions demonstrating that the security injections help students retain, comprehend, and apply secure coding concepts in the introductory programming courses.
A Game-Theoretic Approach for Elastic Distributed Data Stream Processing
Authors: Mencagli Gabriele
Published: June 2016

Distributed data stream processing applications are structured as graphs of interconnected modules able to ingest high-speed data and to transform them in order to generate results of interest. Elasticity is one of the most appealing features of stream processing applications. It makes it possible to scale up/down the allocated computing resources on demand in response to fluctuations of the workload. On clouds, this represents a necessary feature to keep the operating cost at affordable levels while accommodating user-defined QoS requirements. In this article, we study this problem from a game-theoretic perspective. The control logic driving elasticity is distributed among local control agents capable of choosing the right amount of resources to use by each module. In a first step, we model the problem as a noncooperative game in which agents pursue their self-interest. We identify the Nash equilibria and we design a distributed procedure to reach the best equilibrium in the Pareto sense. As a second step, we extend the noncooperative formulation with a decentralized incentive-based mechanism in order to promote cooperation by moving the agreement point closer to the system optimum. Simulations confirm the results of our theoretical analysis and the quality of our strategies.
Design and Usability of Interactive User Profiles for Online Health Communities
Authors: Hartzler Andrea L. , Weis Bridget , Cahill Carly , Pratt Wanda , Park Albert , Backonja Uba , McDonald David W.
Published: June 2016

Online health communities provide a rich source of expertise from experienced patients, but uncovering “peer mentors” with shared circumstances is like finding a needle in a haystack—a problem that will escalate as these communities grow and diversify. We investigated interactive health interest profiles (HIPs) that summarize health-related terms extracted from users’ community posts. Through iterative design, we explored practical designs that accommodate differences in users’ community participation in three HIP prototypes:
Text
,
Word Cloud,
and
Timeline
. By comparing prototype usability with patients and design experts, we found that patients accurately used each prototype but completed some tasks faster with the
Timeline HIP
. Despite this advantage, patients preferred the
Text HIP
. Design experts and patients agreed that simple data overviews and granular details with salient cues that invite interactivity are key design considerations for HIPs. Findings offer key design considerations for HIPs that patients find most useful when forging critical connections.
Vehicular Networks
Authors: Silva Fabrício A. , Boukerche Azzedine , Silva Thais R. M. Braga , Ruiz Linnyer B. , Cerqueira Eduardo , Loureiro Antonio A. F.
Published: June 2016

A significant number of promising applications for vehicular ad hoc networks (VANETs) are becoming a reality. Most of these applications require a variety of heterogenous content to be delivered to vehicles and to their on-board users. However, the task of content delivery in such dynamic and large-scale networks is easier said than done. In this article, we propose a classification of content delivery solutions applied to VANETs while highlighting their new characteristics and describing their underlying architectural design. First, the two fundamental building blocks that are part of an entire content delivery system are identified: replica allocation and content delivery. The related solutions are then classified according to their architectural definition. Within each category, solutions are described based on the techniques and strategies that have been adopted. As result, we present an in-depth discussion on the architecture, techniques, and strategies adopted by studies in the literature that tackle problems related to vehicular content delivery networks.
Socializing the Semantic Gap
Authors: Li Xirong , Uricchio Tiberio , Ballan Lamberto , Bertini Marco , Snoek Cees G. M. , Bimbo Alberto Del
Published: June 2016

Where previous reviews on content-based image retrieval emphasize what can be seen in an image to bridge the semantic gap, this survey considers what people tag about an image. A comprehensive treatise of three closely linked problems (i.e., image tag assignment, refinement, and tag-based image retrieval) is presented. While existing works vary in terms of their targeted tasks and methodology, they rely on the key functionality of tag relevance, that is, estimating the relevance of a specific tag with respect to the visual content of a given image and its social context. By analyzing what information a specific method exploits to construct its tag relevance function and how such information is exploited, this article introduces a two-dimensional taxonomy to structure the growing literature, understand the ingredients of the main works, clarify their connections and difference, and recognize their merits and limitations. For a head-to-head comparison with the state of the art, a new experimental protocol is presented, with training sets containing 10,000, 100,000, and 1 million images, and an evaluation on three test sets, contributed by various research groups. Eleven representative works are implemented and evaluated. Putting all this together, the survey aims to provide an overview of the past and foster progress for the near future.
Whirlpool
Authors: Mukkara Anurag , Beckmann Nathan , Sanchez Daniel
Published: June 2016

Cache hierarchies are increasingly non-uniform and difficult to manage. Several techniques, such as scratchpads or reuse hints, use static information about how programs access data to manage the memory hierarchy. Static techniques are effective on regular programs, but because they set fixed policies, they are vulnerable to changes in program behavior or available cache space. Instead, most systems rely on dynamic caching policies that adapt to observed program behavior. Unfortunately, dynamic policies spend significant resources trying to learn how programs use memory, and yet they often perform worse than a static policy. We present Whirlpool, a novel approach that combines static information with dynamic policies to reap the benefits of each. Whirlpool statically classifies data into pools based on how the program uses memory. Whirlpool then uses dynamic policies to tune the cache to each pool. Hence, rather than setting policies statically, Whirlpool uses static analysis to guide dynamic policies. We present both an API that lets programmers specify pools manually and a profiling tool that discovers pools automatically in unmodified binaries.

We evaluate Whirlpool on a state-of-the-art NUCA cache. Whirlpool significantly outperforms prior approaches: on sequential programs, Whirlpool improves performance by up to 38% and reduces data movement energy by up to 53%; on parallel programs, Whirlpool improves performance by up to 67% and reduces data movement energy by up to 2.6x.
True IOMMU Protection from DMA Attacks
Authors: Markuze Alex , Morrison Adam , Tsafrir Dan
Published: June 2016

Malicious I/O devices might compromise the OS using DMAs. The OS therefore utilizes the IOMMU to map and unmap every target buffer right before and after its DMA is processed, thereby restricting DMAs to their designated locations. This usage model, however, is not truly secure for two reasons: (1) it provides protection at page granularity only, whereas DMA buffers can reside on the same page as other data; and (2) it delays DMA buffer unmaps due to performance considerations, creating a vulnerability window in which devices can access in-use memory. We propose that OSes utilize the IOMMU differently, in a manner that eliminates these two flaws. Our new usage model restricts device access to a set of shadow DMA buffers that are never unmapped, and it copies DMAed data to/from these buffers, thus providing sub-page protection while eliminating the aforementioned vulnerability window. Our key insight is that the cost of interacting with, and synchronizing access to the slow IOMMU hardware---required for zero-copy protection against devices---make
copying preferable to zero-copying
.

We implement our model in Linux and evaluate it with standard networking benchmarks utilizing a 40,Gb/s NIC. We demonstrate that despite being more secure than the safest preexisting usage model, our approach provides up to 5x higher throughput. Additionally, whereas it is inherently less scalable than an IOMMU-less (unprotected) system, our approach incurs only 0%--25% performance degradation in comparison.
High-Performance Transactions for Persistent Memories
Authors: Kolli Aasheesh , Pelley Steven , Saidi Ali , Chen Peter M. , Wenisch Thomas F.
Published: June 2016

Emerging non-volatile memory (NVRAM) technologies offer the durability of disk with the byte-addressability of DRAM. These devices will allow software to access persistent data structures directly in NVRAM using processor loads and stores, however, ensuring consistency of persistent data across power failures and crashes is difficult. Atomic, durable transactions are a widely used abstraction to enforce such consistency. Implementing transactions on NVRAM requires the ability to constrain the order of NVRAM writes, for example, to ensure that a transaction's log record is complete before it is marked committed. Since NVRAM write latencies are expected to be high, minimizing these ordering constraints is critical for achieving high performance. Recent work has proposed programming interfaces to express NVRAM write ordering constraints to hardware so that NVRAM writes may be coalesced and reordered while preserving necessary constraints. Unfortunately, a straightforward implementation of transactions under these interfaces imposes unnecessary constraints. We show how to remove these dependencies through a variety of techniques, notably, deferring commit until after locks are released. We present a comprehensive analysis contrasting two transaction designs across three NVRAM programming interfaces, demonstrating up to 2.5x speedup.
LDX
Authors: Kwon Yonghwi , Kim Dohyeong , Sumner William Nick , Kim Kyungtae , Saltaformaggio Brendan , Zhang Xiangyu , Xu Dongyan
Published: June 2016

Causality inference, such as dynamic taint anslysis, has many applications (e.g., information leak detection). It determines whether an event e is causally dependent on a preceding event c during execution. We develop a new causality inference engine LDX. Given an execution, it spawns a slave execution, in which it mutates c and observes whether any change is induced at e. To preclude non-determinism, LDX couples the executions by sharing syscall outcomes. To handle path differences induced by the perturbation, we develop a novel on-the-fly execution alignment scheme that maintains a counter to reflect the progress of execution. The scheme relies on program analysis and compiler transformation. LDX can effectively detect information leak and security attacks with an average overhead of 6.08% while running the master and the slave concurrently on separate CPUs, much lower than existing systems that require instruction level monitoring. Furthermore, it has much better accuracy in causality inference.
CASPAR
Authors: Gangwani Tanmay , Morrison Adam , Torrellas Josep
Published: June 2016

In multicores, performance-critical synchronization is increasingly performed in a
lock-free
manner using atomic instructions such as CAS or LL/SC. However, when many processors synchronize on the same variable, performance can still degrade significantly. Contending writes get serialized, creating a non-scalable condition. Past proposals that build hardware queues of synchronizing processors do not fundamentally solve this problem---at best, they help to
efficiently serialize
the contending writes.

This paper proposes a novel architecture that
breaks
the serialization of hardware queues and enables the queued processors to perform lock-free synchronization
in parallel
. The architecture, called
CASPAR
, is able to (1) execute the CASes in the queued-up processors in parallel through eager forwarding of expected values, and (2) validate the CASes in parallel and dequeue groups of processors at a time. The result is highly-scalable synchronization. We evaluate CASPAR with simulations of a 64-core chip. Compared to existing proposals with hardware queues, CASPAR improves the throughput of kernels by 32% on average, and reduces the execution time of the sections considered in lock-free versions of applications by 47% on average. This makes these sections 2.5x faster than in the original applications.
Proactive Control of Approximate Programs
Authors: Sui Xin , Lenharth Andrew , Fussell Donald S. , Pingali Keshav
Published: June 2016

Approximate computing trades off accuracy of results for resources such as energy or computing time. There is a large and rapidly growing literature on approximate computing that has focused mostly on showing the benefits of approximate computing. However, we know relatively little about how to control approximation in a disciplined way. In this paper, we address the problem of controlling approximation for non-streaming programs that have a set of "knobs" that can be dialed up or down to control the level of approximation of different components in the program. We formulate this control problem as a constrained optimization problem, and describe a system called Capri that uses machine learning to learn cost and error models for the program, and uses these models to determine, for a desired level of approximation, knob settings that optimize metrics such as running time or energy usage. Experimental results with complex benchmarks from different problem domains demonstrate the effectiveness of this approach.
Failure-Atomic Persistent Memory Updates via JUSTDO Logging
Authors: Izraelevitz Joseph , Kelly Terence , Kolli Aasheesh
Published: June 2016

Persistent memory invites applications to manipulate persistent data via load and store instructions. Because failures during updates may destroy transient data (e.g., in CPU registers), preserving data integrity in the presence of failures requires failure-atomic bundles of updates. Prior failure atomicity approaches for persistent memory entail overheads due to logging and CPU cache flushing. Persistent caches can eliminate the need for flushing, but conventional logging remains complex and memory intensive. We present the design and implementation of JUSTDO logging, a new failure atomicity mechanism that greatly reduces the memory footprint of logs, simplifies log management, and enables fast parallel recovery following failure. Crash-injection tests confirm that JUSTDO logging preserves application data integrity and performance evaluations show that it improves throughput 3x or more compared with a state-of-the-art alternative for a spectrum of data-intensive algorithms.
Action of the diaphragm on the rib cage
Authors: Troyer André De , Wilson Theodore A.
Published: June 2016

When the diaphragm contracts, pleural pressure falls, exerting a caudal and inward force on the entire rib cage. However, the diaphragm also exerts forces in the cranial and outward direction on the lower ribs. One of these forces, the “insertional force,” is applied by the muscle at its attachments to the lower ribs. The second, the “appositional force,” is due to the transmission of abdominal pressure to the lower rib cage in the zone of apposition. In the control condition at functional residual capacity, the effects of these two forces on the lower ribs are nearly equal and outweigh the effect of pleural pressure, whereas for the upper ribs, the effect of pleural pressure is greater. The balance between these effects, however, may be altered. When the abdomen is given a mechanical support, the insertional and appositional forces are increased, so that the muscle produces a larger expansion of the lower rib cage and, with it, a smaller retraction of the upper rib cage. In contrast, at higher lung volumes the zone of apposition is decreased, and pleural pressure is the dominant force on the lower ribs as well. Consequently, although the force exerted by the diaphragm on these ribs remains inspiratory, rib displacement is reversed into a caudal-inward displacement. This mechanism likely explains the inspiratory retraction of the lateral walls of the lower rib cage observed in many subjects with chronic obstructive pulmonary disease (Hoover's sign). These observations support the use of a three-compartment, rather than a two-compartment, model to describe chest wall mechanics.
Measurements of Intracellular Ca2+ Content and Phosphatidylserine Exposure in Human Red Blood Cells: Methodological Issues
Authors: Wesseling Mauro C. , Wagner-Britz Lisa , Boukhdoud Fatima , Asanidze Salome , Nguyen Duc Bach , Kaestner Lars , Bernhardt Ingolf
Published: June 2016

Background/Aims: The increase of the intracellular Ca2+ content as well as the exposure of phosphatidylserine (PS) on the outer cell membrane surface after activation of red blood cells (RBCs) by lysophosphatidic acid (LPA) has been investigated by a variety of research groups. Carrying out experiments, which we described in several previous publications, we observed some discrepancies when comparing data obtained by different investigators within our research group and also between batches of LPA. In addition, we found differences comparing the results of double and single labelling experiments (for Ca2+ and PS). Furthermore, the results of PS exposure depended on the fluorescent dye used (annexin V-FITC versus annexin V alexa fluor® 647). Therefore, it seems necessary to investigate these methodological approaches in more detail to be able to quantify results and to compare data obtained by different research groups. Methods: The intracellular Ca2+ content and the PS exposure of RBCs separated from whole blood have been investigated after treatment with LPA (2.5 µM) obtained from three different companies (Sigma-Aldrich, Cayman Chemical Company, and Santa Cruz Biotechnology Inc.). Fluo-4 and x-rhod-1 have been used to detect intracellular Ca2+ content, annexin V alexa fluor® 647 and annexin V-FITC have been used for PS exposure measurements. Both parameters (Ca2+ content, PS exposure) were studied using flow cytometry and fluorescence microscopy. Results: The percentage of RBCs showing increased intracellular Ca2+ content as well as PS exposure changes significantly between different LPA manufacturers as well as on the condition of mixing of LPA with the RBC suspension. Furthermore, the percentage of RBCs showing PS exposure is reduced in double labelling compared to single labelling experiments and depends also on the fluorescent dye used. Finally, data on Ca2+ content are slightly affected whereas PS exposure data are not affected significantly by the measuring method (flow cytometry, fluorescence microscopy). Conclusion: The LPA batch used and the mixing procedure of LPA and the RBC suspension has to be taken into consideration when comparing results of intracellular Ca2+ content and PS exposure of RBCs after LPA activation. In addition, one should consider that the results of single and double labelling experiments might be different depending on the fluorescent dyes used.
Activated Circulating Myeloid-Derived Suppressor Cells in Patients with Dilated Cardiomyopathy
Authors: Zhang Wen-Cai , Wang Yan-Ge , Wei Wen-Hui , Xiong Xin , Liu Kan-Ling , Wang Ding-Hang , Hu Xiao-Fan , Peng Yu-Dong , Wu Jing-Jing , Cheng Long-Xian
Published: June 2016

Background/Aims: Myeloid-derived suppressor cells (MDSCs) are increased in inflammatory and autoimmune disorders. This study aims to evaluate the significance of MDSCs in dilated cardiomyopathy (DCM) patients. Methods: In total, 42 newly hospitalized DCM patients and 39 healthy controls were enrolled in the study. The frequencies of circulating CD14+HLA-DR-/low MDSCs were determined by flow cytometry. Then, the functional properties of MDSCs in suppressing T cell proliferation and interferon-gamma (IFN-γ) production were measured in a co-culture model. Then, mRNA expression levels of various important molecules in peripheral blood mononuclear cells were measured by real time polymerase chain reaction. Furthermore, correlation analyses between MDSC frequencies and cardiac function parameters were also performed. Results: The frequencies of circulating CD14+HLA-DR-/low MDSCs were significantly elevated in DCM patients compared with healthy controls. It showed that MDSCs from DCM patients more effectively suppressed T cell proliferation and IFN-γ production compared with those from healthy controls, which was partially mediated by arginase-1 (Arg-1). In addition, the correlation analysis suggested that MDSC frequencies were negatively correlated with left ventricular ejection fraction (LVEF), while positively with N-terminal pro-brain natriuretic peptide (NT-proBNP) in patients with DCM. Conclusions: Circulating activated MDSCs might play significant immunomodulatory roles in the pathogenesis of DCM.
Classical Presentation of Acute Pyelonephritis in a Case of Brucellosis
Authors: Alfouzan Wadha , Al-Sahali Sara , Sultan Hawra’a , Dhar Rita
Published: June 2016

Although Brucella species is known to affect almost all organs in humans, renal involvement presenting as acute pyelonephritis remains a rare entity in brucellosis. We report the case of a female patient who presented with symptoms of fever with chills, right loin pain and dysuria in the emergency room. Blood cultures drawn at the time of admission grew Brucella spp., but no organisms were isolated from urine culture although urinalysis data was indicative of urinary tract infection. Empiric therapy with piperacillin/tazobactam plus gentamicin relieved her symptoms. However, the treatment was switched to doxycycline plus rifampicin once the blood culture result was obtained.