bluuebunny/crossref_metadata_2025 huggingface dataset:
MICROPOLAR FLUID MODEL FOR BLOOD FLOW THROUGH A STENOSED ARTERY
Authors: ASADI H. , JAVAHERDEH K. , RAMEZANI S.
Published: November 2013

Various experimental observations have demonstrated that the classical fluid theory is incapable of explaining many phenomena at micro and nano scales. On the other hand, micropolar fluid dynamics can naturally pick up the physical phenomena at these scales owing to its additional degrees of freedom caused by incorporating the effects of fluid molecules on the continuum. Therefore, one of the aims of this paper is to investigate the applicability of the theory of micropolar fluids to modeling and calculating flows in circular microchannels depending on the geometrical dimension of the flow field. Hence, a finite element formulation for the numerical analysis of micropolar laminar fluid flow is developed. In order to validate the results of the FE formulation, the analytical and exact solution of the micropolar Hagen–Poiseuille flow in a circular microchannel is presented, and an excellent agreement between the results of the analytical solution and those of the FE formulation is observed. It is also shown that the micropolar viscosity and the length scale parameter have significant roles on changing the flow characteristics. Then, the behavior of an incompressible viscous fluid flow such as blood flow in a stenosed artery, having multiple kinds of stenoses, is investigated. The obtained results are compared to the results reported in the literature, and an excellent agreement is observed.
ELASTODYNAMIC STRESS INTENSITY FACTOR FOR A FINITE CRACK IN ELASTIC SOLID UNDER 3D TRANSIENT LOADING OF MODE I
Authors: MENG XIANHONG , BAI ZHAOYU , LI MING
Published: November 2013

In this paper, the three-dimensional dynamic problem for an infinite elastic medium weakened by a crack of infinite length and finite width is analyzed, while the crack surfaces are subjected to mode I transient linear tractions. The integral transform approach is applied to reduce the governing differential equations to a pair of coupled singular integral equations, whose solutions can be obtained with the typical iteration method. The analytical solution of the stress intensity factor when the first wave and the first scattered wave reach the investigated crack tip is obtained. Numerical results are presented for different values of the width-to-longitudinal distance ratio z/l. It is found that the stress intensity factor decreases with the arrival of the first scattered longitudinal wave and increases with the arrival of the first scattered Rayleigh wave and tends to be stable. The static value considering both the first scattered wave and the first wave is about 50% greater than that considering only the first wave, and then the effect of the reflected wave is remarkable and deserves further study.
Acceleration of optical coherence tomography signal processing by multi-graphics processing units
Authors: Li Xiqi , Shi Guohua , Huang Ping , Zhang Yudong
Published: November 2013

A multi-GPU system designed for high-speed, real-time signal processing of optical coherence tomography (OCT) is described herein. For the OCT data sampled in linear wave numbers, the maximum processing rates reached 2.95 MHz for 1024-OCT and 1.96 MHz for 2048-OCT. Data sampled using linear wavelengths were re-sampled using a time-domain interpolation method and zero-padding interpolation method to improve image quality. The maximum processing rates for 1024-OCT reached 2.16 MHz for the time-domain method and 1.26 MHz for the zero-padding method. The maximum processing rates for 2048-OCT reached 1.58 MHz, and 0.68 MHz, respectively. This method is capable of high-speed, real-time processing for OCT systems.
Syn- to post-rift diapirism and minibasins of the Central High Atlas (Morocco): the changing face of a mountain belt
Authors: Saura Eduard , Vergés Jaume , Martín-Martín Juan Diego , Messager Grégoire , Moragas Mar , Razin Philippe , Grélaud Carine , Joussiaume Rémi , Malaval Manon , Homke Stéphane , Hunt David W.
Published: November 2013

The Atlas Mountains are classically regarded as a failed Mesozoic rift arm subject to Alpine inversion, folding and thrusting. Here, we present new integrated structural and sedimentological studies that have revealed numerous Early–Middle Jurassic diapiric ridges and minibasins, characterized by distinctive halokinetic structures. Diachroneity in halokinesis is observed across the Central High Atlas, waning first in the SW during the Early–Middle Jurassic (Jbel Azourki and Tazoult ridges) and continuing to late Middle Jurassic towards the NE (Imilchil region). The halokinetic structures are readily differentiated from the effects of later Alpine deformation, allowing a new picture of the Central High Atlas to emerge. The most pervasive deformation in the Central High Atlas is associated with Early–Middle Jurassic diapirism, whereas the impact of Alpine inversion is mostly focused at the basin margins. This new understanding helps explain previously problematic aspects of the Atlas Mountains, which we now recognize as an exceptionally well exposed natural laboratory for understanding the interactions between halokinesis, tectonics and sedimentation.
Integration of Literature with Heterogeneous Information for Genes Correlation Scoring
Authors: Abate Francesco , Acquaviva Andrea , Ficarra Elisa , Macii Enrico
Published: November 2013

Determining the correlation between biomedical terms is a powerful instrument to help scientist research activity, both to understand experimental results and to design new ones. In particular, a great potential comes from the integration of the many heterogeneous information sources currently available on the Web.

In this article we focus on the correlation between genes and biological processes. In this context, we present a methodology for integrating information from biomedical literature with other heterogeneous types of structured information. In particular, the information sources integrated in this work are PubMed abstracts, pathway databases, and NCI thesaurus definitions. The integration is performed at the semantic analysis level using a customized approach we developed to modulate the impact of the different sources on the correlation score.

We report the results of a study concerning the impact of the information integration on the correlation score and of the user-level parameters we introduced to modulate the impact of pathway data or NCI definitions with respect to biomedical literature information, depending on the context of the search. To evaluate the methodology, we performed correlation measures on six biological processes and nine genes by comparing the results with and without the integration of pathways and NCI definitions.
Life points the way to a new template for chipmaking
Authors: Edwards Chris
Published: November 2013

While significant obstacles remain, researchers are optimistic about using DNA to guide graphene into complex circuit shapes on silicon.
Q&A: Securing the Risk
Authors: Hoffmann Leah
Published: November 2013

Peter G. Neumann views computers and their related issues holistically.
Information technology impact sourcing
Authors: Heeks Richard
Published: November 2013

New ways to contract IT work to base-of-the-pyramid suppliers.
Barrier invariants
Authors: Chong Nathan , Donaldson Alastair F. , Kelly Paul H.J. , Ketema Jeroen , Qadeer Shaz
Published: November 2013

Data-dependent GPU kernels, whose data or control flow are dependent on the input of the program, are difficult to verify because they require reasoning about shared state manipulated by many parallel threads. Existing verification techniques for GPU kernels achieve soundness and scalability by using a two-thread reduction and making the contents of the shared state
nondeterministic
each time threads synchronise at a barrier, to account for all possible thread interactions. This coarse abstraction prohibits verification of data-dependent kernels. We present
barrier invariants
, a novel abstraction technique which allows key properties about the shared state of a kernel to be preserved across barriers during formal reasoning. We have integrated barrier invariants with the GPUVerify tool, and present a detailed case study showing how they can be used to verify three
prefix sum
algorithms, allowing efficient modular verification of a
stream compaction
kernel, a key building block for GPU programming. This analysis goes significantly beyond what is possible using existing verification techniques for GPU kernels.
Combining concern input with program analysis for bloat detection
Authors: Bhattacharya Suparna , Gopinath Kanchi , Nanda Mangala Gowri
Published: November 2013

Framework based software tends to get bloated by accumulating optional features (or
concerns
) just-in-case they are needed. The good news is that such feature bloat need not always cause runtime execution bloat. The bad news is that often enough, only a few statements from an optional concern may cause execution bloat that may result in as much as 50% runtime overhead.

We present a novel technique to analyze the connection between optional concerns and the potential sources of execution bloat induced by them. Our analysis automatically answers questions such as (1) whether a given set of optional concerns could lead to execution bloat and (2) which particular statements are the likely sources of bloat when those concerns are not required. The technique combines coarse grain concern input from an external source with a fine-grained static analysis. Our experimental evaluation highlights the effectiveness of such concern augmented program analysis in execution bloat assessment of ten programs.
Set-based pre-processing for points-to analysis
Authors: Smaragdakis Yannis , Balatsouras George , Kastrinis George
Published: November 2013

We present set-based pre-analysis: a virtually universal optimization technique for flow-insensitive points-to analysis. Points-to analysis computes a static abstraction of how object values flow through a program's variables. Set-based pre-analysis relies on the observation that much of this reasoning can take place at the set level rather than the value level. Computing constraints at the set level results in significant optimization opportunities: we can rewrite the input program into a simplified form with the same essential points-to properties. This rewrite results in removing both local variables and instructions, thus simplifying the subsequent value-based points-to computation. Effectively, set-based pre-analysis puts the program in a normal form optimized for points-to analysis.

Compared to other techniques for off-line optimization of points-to analyses in the literature, the new elements of our approach are the ability to eliminate statements, and not just variables, as well as its modularity: set-based pre-analysis can be performed on the input just once, e.g., allowing the pre-optimization of libraries that are subsequently reused many times and for different analyses. In experiments with Java programs, set-based pre-analysis eliminates 30% of the program's local variables and 30% or more of computed context-sensitive points-to facts, over a wide set of benchmarks and analyses, resulting in a ~20% average speedup (max: 110%, median: 18%).
Taking off the gloves with reference counting Immix
Authors: Shahriyar Rifat , Blackburn Stephen Michael , Yang Xi , McKinley Kathryn S.
Published: November 2013

Despite some clear advantages and recent advances, reference counting remains a poor cousin to high-performance tracing garbage collectors. The advantages of reference counting include a) immediacy of reclamation, b) incrementality, and c) local scope of its operations. After decades of languishing with hopelessly bad performance, recent work narrowed the gap between reference counting and the fastest tracing collectors to within 10%. Though a major advance, this gap remains a substantial barrier to adoption in performance-conscious application domains.

Our work identifies heap organization as the principal source of the remaining performance gap. We present the design, implementation, and analysis of a new collector, RC Immix, that replaces reference counting's traditional free-list heap organization with the line and block heap structure introduced by the Immix collector. The key innovations of RC Immix are 1) to combine traditional reference counts with per-line live object counts to identify reusable memory and 2) to eliminate fragmentation by integrating copying with reference counting of new objects and with backup tracing cycle collection. In RC Immix, reference counting offers efficient collection and the line and block heap organization delivers excellent mutator locality and efficient allocation. With these advances, RC Immix closes the 10% performance gap, matching the performance of a highly tuned production generational collector. By removing the performance barrier, this work transforms reference counting into a serious alternative for meeting high performance objectives for garbage collected languages.
Do developers benefit from generic types?
Authors: Hoppe Michael , Hanenberg Stefan
Published: November 2013

Type systems that permit developers to express themselves more precisely are one of the primary topics in programming language research, as well as in industrial software development. While it seems plausible that an expressive static type system increases developer productivity, there is little empirical evidence for or against this hypothesis. Generic types in Java are an example: as an extension of Java's original type system, some claim that Java 1.5 improves the type system's "expressiveness." Even if this claim is true, there exists little empirical evidence that claimed expressiveness leads to a measurable increase in developer productivity. This paper introduces an experiment where generic types (in comparison to raw types) have been evaluated in three different directions: (1) the documentation impact on undocumented APIs, (2) the time required for fixing type errors, and (3) the extensibility of a generic type hierarchy. The results of the experiment suggest that generic types improve documentation and reduce extensibility -- without revealing a difference in the time required for fixing type errors.
Storage strategies for collections in dynamically typed languages
Authors: Bolz Carl Friedrich , Diekmann Lukas , Tratt Laurence
Published: November 2013

Dynamically typed language implementations often use more memory and execute slower than their statically typed cousins, in part because operations on collections of elements are unoptimised. This paper describes storage strategies, which dynamically optimise collections whose elements are instances of the same primitive type. We implement storage strategies in the PyPy virtual machine, giving a performance increase of 18% on wide-ranging benchmarks of real Python programs. We show that storage strategies are simple to implement, needing only 1500LoC in PyPy, and have applicability to a wide range of virtual machines.
On-the-fly capacity planning
Authors: Mitchell Nick , Sweeney Peter F.
Published: November 2013

When resolving performance problems, a simple histogram of hot call stacks does not cut it, especially given the highly fluid nature of modern deployments. Why bother tuning, when adding a few CPUs via the management console will quickly resolve the problem? The findings of these tools are also presented without any sense of context: e.g. string conversion may be expensive, but only matters if it contributes greatly to the response time of user logins.

Historically, these concerns have been the purview of
capacity planning
. The power of planners lies in their ability to weigh demand versus capacity, and to do so in terms of the important
units of work
in the application (such as user logins). Unfortunately, they rely on measurements of rates and latencies, and both quantities are difficult to obtain. Even if possible, when all is said and done, these planners only relate to the code as a black-box: but, why bother adding CPUs, when easy code changes will fix the problem?

We present a way to do planning
on-the-fly
: with a few call stack samples taken from an already-running system, we predict the benefit of a proposed tuning plan. We accomplish this by simulating the effect of a tuning action upon execution speed and the way it
shifts
resource demand. To identify existing problems, we show how to generate tuning actions automatically, guided by the desire to maximize speedup without needless expense, and that these generated plans may span resource and code changes. We show that it is possible to infer everything needed from these samples alone: levels of resource demand and the units of work in the application. We evaluate our planner on a suite of microbenchmarks and a suite of 15,000 data sets that come from real applications running in the wild.
Instant pickles
Authors: Miller Heather , Haller Philipp , Burmako Eugene , Odersky Martin
Published: November 2013

As more applications migrate to the cloud, and as "big data" edges into even more production environments, the performance and simplicity of exchanging data between compute nodes/devices is increasing in importance. An issue central to distributed programming, yet often under-considered, is serialization or pickling,
i.e.
, persisting runtime objects by converting them into a binary or text representation. Pickler combinators are a popular approach from functional programming; their composability alleviates some of the tedium of writing pickling code by hand, but they don't translate well to object-oriented programming due to qualities like open class hierarchies and subtyping polymorphism. Furthermore, both functional pickler combinators and popular, Java-based serialization frameworks tend to be tied to a specific pickle format, leaving programmers with no choice of how their data is persisted. In this paper, we present object-oriented pickler combinators and a framework for generating them at compile-time, called
scala/pickling
, designed to be the default serialization mechanism of the Scala programming language. The static generation of OO picklers enables significant performance improvements, outperforming Java and Kryo in most of our benchmarks. In addition to high performance and the need for little to no boilerplate, our framework is extensible: using the type class pattern, users can provide both (1) custom, easily interchangeable pickle formats and (2) custom picklers, to override the default behavior of the pickling framework. In benchmarks, we compare scala/pickling with other popular industrial frameworks, and present results on time, memory usage, and size when pickling/unpickling a number of data types used in real-world, large-scale distributed applications and frameworks.
Mtac
Authors: Ziliani Beta , Dreyer Derek , Krishnaswami Neelakantan R. , Nanevski Aleksandar , Vafeiadis Viktor
Published: November 2013

Effective support for custom proof automation is essential for large scale interactive proof development. However, existing languages for automation via *tactics* either (a) provide no way to specify the behavior of tactics within the base logic of the accompanying theorem prover, or (b) rely on advanced type-theoretic machinery that is not easily integrated into established theorem provers.

We present Mtac, a lightweight but powerful extension to Coq that supports dependently-typed tactic programming. Mtac tactics have access to all the features of ordinary Coq programming, as well as a new set of typed tactical primitives. We avoid the need to touch the trusted kernel typechecker of Coq by encapsulating uses of these new tactical primitives in a *monad*, and instrumenting Coq so that it executes monadic tactics during type inference.
A short cut to parallelization theorems
Authors: Morihata Akimasa
Published: November 2013

The third list-homomorphism theorem states that if a function is both
foldr
and
foldl
, it has a divide-and-conquer parallel implementation as well. In this paper, we develop a theory for obtaining such parallelization theorems. The key is a new proof of the third list-homomorphism theorem based on shortcut deforestation. The proof implies that there exists a divide-and-conquer parallel program of the form of
h
(
x
'
merge
'
y
) =
h
1
x
odot
h
2
y
, where
h
is the subject of parallelization,
merge
is the operation of integrating independent substructures,
h
1
and
h
2
are computations applied to substructures, possibly in parallel, and odot merges the results calculated for substructures, if (i)
h
can be specified by two certain forms of iterative programs, and (ii)
merge
can be implemented by a function of a certain polymorphic type. Therefore, when requirement (ii) is fulfilled,
h
has a divide-and-conquer implementation if
h
has two certain forms of implementations. We show that our approach is applicable to structure-consuming operations by catamorphisms (folds), structure-generating operations by anamorphisms (unfolds), and their generalizations called hylomorphisms.
Higher-order functional reactive programming without spacetime leaks
Authors: Krishnaswami Neelakantan R.
Published: November 2013

Functional reactive programming (FRP) is an elegant approach to declaratively specify reactive systems. However, the powerful abstractions of FRP have historically made it difficult to predict and control the resource usage of programs written in this style.

In this paper, we give a new language for higher-order reactive programming. Our language generalizes and simplifies prior type systems for reactive programming, by supporting the use of streams of streams, first-class functions, and higher-order operations. We also support many temporal operations beyond streams, such as terminatable streams, events, and even resumptions with first-class schedulers. Furthermore, our language supports an efficient implementation strategy permitting us to eagerly deallocate old values and statically rule out spacetime leaks, a notorious source of inefficiency in reactive programs. Furthermore, these memory guarantees are achieved without the use of a complex substructural type discipline.

We also show that our implementation strategy of eager deallocation is safe, by showing the soundness of our type system with a novel step-indexed Kripke logical relation.
Exploiting vector instructions with generalized stream fusion
Authors: Mainland Geoffrey , Leshchinskiy Roman , Peyton Jones Simon
Published: November 2013

Stream fusion is a powerful technique for automatically transforming high-level sequence-processing functions into efficient implementations. It has been used to great effect in Haskell libraries for manipulating byte arrays, Unicode text, and unboxed vectors. However, some operations, like vector append, still do not perform well within the standard stream fusion framework. Others, like SIMD computation using the SSE and AVX instructions available on modern x86 chips, do not seem to fit in the framework at all.

In this paper we introduce generalized stream fusion, which solves these issues. The key insight is to bundle together multiple stream representations, each tuned for a particular class of stream consumer. We also describe a stream representation suited for efficient computation with SSE instructions. Our ideas are implemented in modified versions of the GHC compiler and vector library. Benchmarks show that high-level Haskell code written using our compiler and libraries can produce code that is faster than both compiler- and hand-vectorized C.
Optimizing abstract abstract machines
Authors: Glaze Dionna , Labich Nicholas , Might Matthew , Van Horn David
Published: November 2013

The technique of abstracting abstract machines (AAM) provides a systematic approach for deriving computable approximations of evaluators that are easily proved sound. This article contributes a complementary step-by-step process for subsequently going from a naive analyzer derived under the AAM approach, to an efficient and correct implementation. The end result of the process is a two to three order-of-magnitude improvement over the systematically derived analyzer, making it competitive with hand-optimized implementations that compute fundamentally less precise results.
Fun with semirings
Authors: Dolan Stephen
Published: November 2013

Describing a problem using classical linear algebra is a very well-known problem-solving technique. If your question can be formulated as a question about real or complex matrices, then the answer can often be found by standard techniques.

It's less well-known that very similar techniques still apply where instead of real or complex numbers we have a closed semiring, which is a structure with some analogue of addition and multiplication that need not support subtraction or division.

We define a typeclass in Haskell for describing closed semirings, and implement a few functions for manipulating matrices and polynomials over them. We then show how these functions can be used to calculate transitive closures, find shortest or longest or widest paths in a graph, analyse the data flow of imperative programs, optimally pack knapsacks, and perform discrete event simulations, all by just providing an appropriate underlying closed semiring.
Initial validation of non-authoritative data for road assessment
Authors: Schnebele E. , Cervone G. , Waters N.
Published: November 2013

This research proposes a methodology that leverages non-authoritative data to augment flood extent mapping and the evaluation of transportation infrastructure. The novelty of this approach is the application of freely available, non-authoritative data and its integration with established data and methods. Crowdsourced photos and volunteered geographic data are fused together using a geostatistical interpolation to create an estimation of flood damage in New York City following Hurricane Sandy. This damage assessment is utilized to augment an authoritative storm surge map as well as to create a road damage map for the affected region.
Exact and approximate supply bound function for multiprocessor periodic resource model
Authors: Khalilzad Nima Moghaddami , Behnam Moris , Nolte Thomas
Published: November 2013

The Multiprocessor Periodic Resource (MPR) model has been proposed for modeling compositional real-time guarantees of real-time systems which run on a shared multiprocessor hardware. In this paper we extend the MPR model such that the execution of virtual processors (servers) is not assumed to be synchronized i.e., the servers can have different phases. We believe that relaxing the server synchronization requirement provides greater deal of compatibility for implementing such a compositional method on various hardware platforms. We derive the resource supply bound function of the extended MPR model using an algorithm. Furthermore, we suggest an approach to calculate an approximate supply bound function with lower computational complexity for systems where calculating their supply bound function is computationally expensive.
Towards a user-mode approach to partitioned scheduling in the seL4 microkernel
Authors: Åsberg Mikael , Nolte Thomas
Published: November 2013

This paper presents a preliminary study of applying partitioned scheduling in the seL4 microkernel. This microkernel is the first operating system kernel ever to be formally proven for its functional correctness. Even though the kernel is completely verified it still delivers high performance comparable to other L4 kernels. The seL4 kernel implements
isolation
of components in terms of the memory resource and security. However, there is still a missing part when it comes to isolation and that is time partitioning. Time partitioning can be implemented inside the kernel (privileged mode) or in user space (user mode). The latter is done using regular user-space thread(s) and can easily be modified while the other approach requires re-verification of the kernel whenever modifications to the time-partitioning policy is done. On the other hand, having the time-partitioning mechanism in privileged mode would yield better performance. We have implemented time partitioning (partitioned scheduling) in the seL4 user space and we elaborate on its performance in terms of overhead costs.
Virtual execution platforms for mixed-time-criticality systems
Authors: Goossens Kees , Azevedo Arnaldo , Chandrasekar Karthik , Gomony Manil Dev , Goossens Sven , Koedam Martijn , Li Yonghui , Mirzoyan Davit , Molnos Anca , Nejad Ashkan Beyranvand , Nelson Andrew , Sinha Shubhendu
Published: November 2013

Systems on chip (SOC) contain multiple concurrent applications with different time criticality (firm, soft, non real-time). As a result, they are often developed by different teams or companies, with different models of computation (MOC) such as dataflow, Kahn process networks (KPN), or time-triggered (TT). SOC functionality and (real-time) performance is verified after all applications have been integrated.

In this paper we propose the CompSOC platform and design flows that offers
a virtual execution platform per application, to allow independent design, verification, and execution
. We introduce the composability and predictability concepts, why they help, and how they are implemented in the different resources of the CompSOC architecture. We define a design flow that allows real-time cyclo-static dataflow (CSDF) applications to be automatically mapped, verified, and executed. Mapping and analysis of KPN and TT applications is not automated but they do run composably in their allocated virtual platforms.

Although most of the techniques used here have been published in isolation, this paper is the first comprehensive overview of the CompSOC approach. Moreover, three new case studies illustrate all claimed benefits: 1) An example firm-real-time CSDF H.263 decoder is automatically mapped and verified. 2) Applications with different models of computation (CSDF and TT) run composably. 3) Adaptive soft-real-time applications execute composably and can hence be verified independently by simulation.
Natural Variations and Genome-Wide Association Studies in Crop Plants
Authors: Huang Xuehui , Han Bin
Published: November 2013

Natural variants of crops are generated from wild progenitor plants under both natural and human selection. Diverse crops that are able to adapt to various environmental conditions are valuable resources for crop improvements to meet the food demands of the increasing human population. With the completion of reference genome sequences, the advent of high-throughput sequencing technology now enables rapid and accurate resequencing of a large number of crop genomes to detect the genetic basis of phenotypic variations in crops. Comprehensive maps of genome variations facilitate genome-wide association studies of complex traits and functional investigations of evolutionary changes in crops. These advances will greatly accelerate studies on crop designs via genomics-assisted breeding. Here, we first discuss crop genome studies and describe the development of sequencing-based genotyping and genome-wide association studies in crops. We then review sequencing-based crop domestication studies and offer a perspective on genomics-driven crop designs.
New Frontiers in Patient-Reported Outcomes: Adverse Event Reporting, Comparative Effectiveness, and Quality Assessment
Authors: Basch Ethan
Published: November 2013

Patient-reported outcomes (PROs) are data elements directly reported by patients or their surrogates about experiences with care, including symptoms, functional status, or quality of life. PROs have commonly been evaluated in clinical trials for drug and medical device development. Interest is growing in the ability to integrate PROs into additional contexts, particularly product safety evaluation, comparative effectiveness research, and measurement of care quality. This interest reflects a growing focus on patient-centeredness in health care broadly and on provisions of the US Patient Protection and Affordable Care Act of 2010. Multiple initiatives demonstrate the feasibility and value of patient reporting in these areas. Inclusion of PROs in electronic health records and hospital patient portals, as well as longitudinal registries, can facilitate use of these data for multiple analytic purposes as well as enhance delivery of care and patient-provider communication. Challenges include the logistics and cost of implementing PRO programs; missing data, particularly from hard-to-reach and ill patients; and the need for standardization of outcome measures and electronic data representation. These challenges have been surmounted in limited initiatives and now must be translated to larger implementations.
Chimeric Antigen Receptor Therapy for Cancer
Authors: Barrett David M. , Singh Nathan , Porter David L. , Grupp Stephan A. , June Carl H.
Published: November 2013

Improved outcomes for patients with cancer hinge on the development of new targeted therapies with acceptable short-term and long-term toxicity. Progress in basic, preclinical, and clinical arenas spanning cellular immunology, synthetic biology, and cell-processing technologies has paved the way for clinical applications of chimeric antigen receptor–based therapies. This new form of targeted immunotherapy merges the exquisite targeting specificity of monoclonal antibodies with the potent cytotoxicity and long-term persistence provided by cytotoxic T cells. Although this field is still in its infancy, clinical trials have already shown clinically significant antitumor activity in neuroblastoma, chronic lymphocytic leukemia, and B cell lymphoma, and trials targeting a variety of other adult and pediatric malignancies are under way. Ongoing work is focused on identifying optimal tumor targets and on elucidating and manipulating both cell- and host-associated factors to support expansion and persistence of the genetically engineered cells in vivo. The potential to target essentially any tumor-associated cell-surface antigen for which a monoclonal antibody can be made opens up an entirely new arena for targeted therapy of cancer.
DNA Sequencing of Cancer: What Have We Learned?
Authors: Chmielecki Juliann , Meyerson Matthew
Published: November 2013

DNA sequencing has taught us much about the structure of cancer genomes and enabled the discovery of novel genes that drive and maintain tumorigenesis. With the advent and application of next-generation massively parallel sequencing technologies, one can rapidly generate and analyze data from the cellular “-omes”: genomes, exomes, and transcriptomes. This review highlights recent genomic discoveries in signal transduction, metabolism, epigenetic modifications, cell cycle and genome maintenance, RNA processing, and transcription. Additionally, genomic sequencing has revealed the complexity of the cancer genome and has enabled the discovery of functional rearrangements with therapeutic and diagnostic potentials.
Exocytosis and Endocytosis: Modes, Functions, and Coupling Mechanisms
Authors: Wu Ling-Gang , Hamid Edaeni , Shin Wonchul , Chiang Hsueh-Cheng
Published: November 2013

Vesicle exocytosis releases content to mediate many biological events, including synaptic transmission essential for brain functions. Following exocytosis, endocytosis is initiated to retrieve exocytosed vesicles within seconds to minutes. Decades of studies in secretory cells reveal three exocytosis modes coupled to three endocytosis modes: (a) full-collapse fusion, in which vesicles collapse into the plasma membrane, followed by classical endocytosis involving membrane invagination and vesicle reformation; (b) kiss-and-run, in which the fusion pore opens and closes; and (c) compound exocytosis, which involves exocytosis of giant vesicles formed via vesicle-vesicle fusion, followed by bulk endocytosis that retrieves giant vesicles. Here we review these exo- and endocytosis modes and their roles in regulating quantal size and synaptic strength, generating synaptic plasticity, maintaining exocytosis, and clearing release sites for vesicle replenishment. Furthermore, we highlight recent progress in understanding how vesicle endocytosis is initiated and is thus coupled to exocytosis. The emerging model is that calcium influx via voltage-dependent calcium channels at the calcium microdomain triggers endocytosis and controls endocytosis rate; calmodulin and synaptotagmin are the calcium sensors; and the exocytosis machinery, including SNARE proteins (synaptobrevin, SNAP25, and syntaxin), is needed to coinitiate endocytosis, likely to control the amount of endocytosis.
A Systematic Statistical Approach to Evaluating Evidence from Observational Studies
Authors: Madigan David , Stang Paul E. , Berlin Jesse A. , Schuemie Martijn , Overhage J. Marc , Suchard Marc A. , Dumouchel Bill , Hartzema Abraham G. , Ryan Patrick B.
Published: November 2013

Threats to the validity of observational studies on the effects of interventions raise questions about the appropriate role of such studies in decision making. Nonetheless, scholarly journals in fields such as medicine, education, and the social sciences feature many such studies, often with limited exploration of these threats, and the lay press is rife with news stories based on these studies. Consumers of these studies rely on the expertise of the study authors to conduct appropriate analyses, and on the thoroughness of the scientific peer-review process to check the validity, but the introspective and ad hoc nature of the design of these analyses appears to elude any meaningful objective assessment of their performance. Here, we review some of the challenges encountered in observational studies and review an alternative, data-driven approach to observational study design, execution, and analysis. Although much work remains, we believe this research direction shows promise.
X-Ray Magnetic Dichroism in the Cobalt-Doped Indium Tin Oxide from First Principle Calculations
Authors: Antonov V. N. , Bekenov L. V. , Germash L. P. , Plotnikov N. A.
Published: November 2013

The electronic structure of the Co-doped indium tin oxide (ITO) diluted magnetic semiconductors (DMSs) were investigated theoretically from first principles, using the fully relativistic Dirac linear muffin-tin orbital band structure method. The X-ray absorption spectra (XAS) and X-ray magnetic circular dichroism (XMCD) spectra at the Co L3, In M2, Sn M2, and O K edges were investigated theoretically from first principles. The origin of the XMCD spectra in these compounds was examined. The calculated results are compared with available experimental data.
Doxapram Use for Apnoea of Prematurity in Neonatal Intensive Care
Authors: Prins S. A. , Pans S. J. A. , van Weissenbruch M. M. , Walther F. J. , Simons S. H. P.
Published: November 2013

Apnoea of prematurity is treated with noninvasive respiratory therapy and methylxanthines. For therapy unresponsive apnoea doxapram is often prescibed in preterm neonates. The duration, dosage and route of administration of doxapram together with its efficacy was evaluated in two Dutch neonatal intensive care. Outcome concerning short-term safety and neonatal morbidity were evaluated. During 5 years, 122 of 1,501 admitted newborns <32 weeks of gestational age received doxapram. 64.8% of patients did not need intubation after doxapram. 25% of treated neonates were <27 weeks of gestation. A positive response to doxapram therapy on apnoea was associated with longer duration of doxapram usage (P<0.001), lower mean doses (P<0.003), and less days of intensive care (median 33 versus 42 days;P<0.002). No patients died during doxapram therapy. Incidence of necrotizing enterocolitis, intraventricular hemorrhage, periventricular leukomalacia, retinopathy of prematurity, persistent ductus arteriosus, or worsening of pulmonary condition did not increase during doxapram therapy. Doxapram is frequently used for apnoea of prematurity, despite a lack of data on short-term efficacy and long-term safety. Until efficacy and safety are confirmed in prospective trials, doxapram should be used with caution.
Recreational Vehicle Water Tanks as a Possible Source forLegionellaInfections
Authors: Litwin Christine M. , Asebiomo Bankole , Wilson Katherine , Hafez Michael , Stevens Valerie , Fliermans Carl B. , Fields Barry S. , Fisher John F.
Published: November 2013

We investigated recreational vehicle (RV) water reservoirs in response to a case of pneumonia in whichLegionella pneumophilawas cultured both from the patient and a RV reservoir in which he travelled. Water samples processed and cultured at the CDC according to standard protocol were positive forLegionellaspp. in 4/17 (24%) faucets, 1/11 (9%) water tanks from 4/20 (20%) RVs from three different campsites.Legionellaspp. that were isolated includedL. pneumophila(serogroups 1 and 6),L. anisa, L. feeleii, andL. quateriensis. Environmental controls from the potable water of the three campsites were culture-negative. A survey of maintenance practices by the RV users at the campsites revealed that chlorine disinfection of the water tanks was rarely performed. To prevent the possibility ofLegionellainfections, RV owners should implement regular chlorine disinfection of their water tanks and follow the recommended maintenance guidelines according to their owner's manuals.
Coordination Scheme for Restructuring Business Operation of the Single Period Newsvendor Problem
Authors: Chyu Chiuh-Cheng , Huang I-Ping
Published: November 2013

This paper presents a coordination scheme for a single period newsvendor problem when both supplier and retailer of the supply chain agree to change the business operation from a market decision power sharing system (Model 1) to a unique decision maker system (Model 2). The supplier is assumed to be a risk-averse decision maker and he will undertake the product quality risk in both models. Model 1 is game theoretic, where the supplier controls the wholesale price, but the retailer controls the order quantity and market price. The bargaining process ends when the supplier has found a wholesale price that maximizes the value of his sales revenue minus the product quality cost. Model 2 is a centralized system where the supplier possesses all decision powers of the market. In general, Model 2 will generate higher total revenue than Model 1. The aim of this research is to propose a satisfying compromise based on consignment policy to resolve the revenue-sharing conflict in Model 2 due to the additional revenue. An example is provided to illustrate the two models and the proposed coordination scheme, along with managerial insights on the models’ benefits. The impacts of several parameters on the scheme are also presented and discussed.
Biological Activities and Pharmacokinetics of Praeruptorins fromPeucedanumSpecies: A Systematic Review
Authors: Sarkhail Parisa , Shafiee Abbas , Sarkheil Pantea
Published: November 2013

Praeruptorins belonging to the angular-type pyranocoumarins are bioactive constituents that have been isolated from somePeucedanumspecies such asP. praeruptorum, which is used in traditional Chinese medicine for treatment of cold, cough, upper respiratory infections, and so forth. Many reports have demonstrated that the beneficial pharmacological effects ofP. praeruptorumroot on cardiovascular, pulmonary, immune, and nervous system diseases were attributed to the presence of praeruptorins. The aim of this review is to explain the recent efforts of scientists in pharmacological screening of natural and synthetic praeruptorin derivatives, studying the mechanisms of some praeruptorins action, pharmacokinetics, toxicity, and relevant structure-activity relationships. Based on reported data about the pharmacological properties of praeruptorins and semisynthetic derivatives of them, it is hopeful that in the near future more studies focus on the discovery of the new application and therapeutic uses of these bioactive compounds and understanding the specific mechanisms of them. The present discusses the reports on molecular and biological activities of praeruptorins of the genusPeucedanum, from 1976 onwards.
Antigen-Specific Gene Therapy after Immunisation Reduces the Severity of Collagen-Induced Arthritis
Authors: Eneljung Tove , Tengvall Sara , Jirholt Pernilla , Henningsson Louise , Holmdahl Rikard , Gustafsson Kenth , Gjertsson Inger
Published: November 2013

Reestablishment of tolerance induction in rheumatoid arthritis (RA) would be an optimal treatment with few, if any, side effects. However, to develop such a treatment further insights in the immunological mechanisms governing tolerance are needed. We have developed a model of antigen-specific tolerance in collagen type II (CII) induced arthritis (CIA) using lentivirus-based gene therapy. The immunodominant epitope of CII was inserted into a lentivirus vector to achieve expression on the MHC class II molecule and the lentiviral particles were subsequently intravenously injected at different time points during CIA. Injection of lentiviral particles in early phases of CIA, that is, at day 7 or day 26 after CII immunisation, partially prevented development of arthritis, decreased the serum levels of CII-specific IgG antibodies, and enhanced the suppressive function of CII-specific T regulatory cells. When lentiviral particles were injected during manifest arthritis, that is, at day 31 after CII immunisation, the severity of arthritis progression was ameliorated, the levels of CII-specific IgG antibodies decreased and the proportion of T regulatory cells increased. Thus, antigen-specific gene therapy is effective when administered throughout the inflammatory course of arthritis and offers a good model for investigation of the basic mechanisms during tolerance in CIA.
Circularly Polarized Low-Profile Antenna for Radiating Parallel to Ground Plane for RFID Reader Applications
Authors: Lertsakwimarn Kittima , Phongcharoenpanich Chuwong , Fukusako Takeshi
Published: November 2013

This paper presents a low-profile printed antenna with double U-shaped arms radiating circular polarization for the UHF RFID readers. The proposed antenna consists of double U-shaped strip structures and a capacitive feeding line to generate circular polarization. A part of the U-shaped arms is bent by 90° to direct the main beam parallel to the ground plane. From the results,-10 dB|S11|and 3 dB axial ratio of the antenna cover a typical UHF RFID band from 920 MHz to 925 MHz. The bidirectional beam is obtained with the maximum gain of 1.8 dBic in the parallel direction to the ground plane at the 925 MHz. The overall size of the proposed antenna including ground plane is 107 mm × 57 mm × 12.8 mm (0.33λ0× 0.17λ0× 0.04λ0).
Multiobjective Gate Assignment Based on Passenger Walking Distance and Fairness
Authors: Jiang Yu , Zeng Linyan , Luo Yuxiao
Published: November 2013

Passenger walking distance is an important index of the airport service quality. How to shorten the walking distance and balance the airlines' service quality is the focus of much research on airport gate assignment problems. According to the problems of airport passenger service quality, an optimization gate assignment model is established. The gate assignment model is based on minimizing the total walking distance of all passengers and balancing the average walking distance of passengers among different airlines. Lingo is used in the simulation of a large airport gate assignment. Test results show that the optimization model can reduce the average walking distance of passenger effectively, improve the number of flights assigned to gate, balance airline service quality, and enhance the overall service level of airports and airlines. The model provides reference for the airport gate preassignment.