bluuebunny/crossref_metadata_2025 huggingface dataset:
Dosimetric accuracy of a deterministic radiation transport based brachytherapy treatment planning system. Part II: Monte Carlo and experimental verification of a multiple source dwell position plan employing a shielded applicator
Authors: Petrokokkinos L. , Zourari K. , Pantelis E. , Moutsatsos A. , Karaiskos P. , Sakelliou L. , Seimenis I. , Georgiou E. , Papagiannis P.
Published: April 2011

Purpose:

The aim of this work is the dosimetric validation of a deterministic radiation transport based treatment planning system (BRACHYVISION™ v. 8.8, referred to as TPS in the following) for multiple source dwell position brachytherapy applications employing a shielded applicator in homogeneous water geometries.

Methods:

TPS calculations for an irradiation plan employing seven VS2000 high dose rate (HDR) source dwell positions and a partially shielded applicator (GM11004380) were compared to corresponding Monte Carlo (MC) simulation results, as well as experimental results obtained using the VIP polymer gel–magnetic resonance imaging three‐dimensional dosimetry method with a custom made phantom.

Results:

TPS and MC dose distributions were found in agreement which is mainly within ±2%. Considerable differences between TPS and MC results (greater than 2%) were observed at points in the penumbra of the shields (i.e., close to the edges of the “shielded” segment of the geometries). These differences were experimentally verified and therefore attributed to the TPS. Apart from these regions, experimental and TPS dose distributions were found in agreement within 2 mm distance to agreement and 5% dose difference criteria. As shown in this work, these results mark a significant improvement relative to dosimetry algorithms that disregard the presence of the shielded applicator since the use of the latter leads to dosimetry errors on the order of 20%–30% at the edge of the “unshielded” segment of the geometry and even 2%–6% at points corresponding to the potential location of the target volume in clinical applications using the applicator (points in the unshielded segment at short distances from the applicator).

Conclusions:

Results of this work attest the capability of the TPS to accurately account for the scatter conditions and the increased attenuation involved in HDR brachytherapy applications employing multiple source dwell positions and partially shielded applicators.
Protein Tyrosine Kinase Wee1B Is Essential for Metaphase II Exit in Mouse Oocytes
Authors: Oh Jeong Su , Susor Andrej , Conti Marco
Published: April 2011

Cyclin degradation is not the only mechanism that controls the exit of mouse oocytes from meiosis.
The Impact of Comet Shoemaker-Levy 9 Sends Ripples Through the Rings of Jupiter
Authors: Showalter Mark R. , Hedman Matthew M. , Burns Joseph A.
Published: April 2011

Spacecraft observations show that Saturn’s and Jupiter’s rings preserve records of recent interplanetary debris collisions.
Effect of exercise-induced dehydration on time-trial exercise performance: a meta-analysis
Authors: Goulet Eric D B
Published: April 2011

Objective

To use the meta-analytical procedures to determine the magnitude of the effect of exercise-induced dehydration (EID) upon time-trial (TT) exercise performance.

Methods

Studies were located via database searches and cross-referencing. TT performance outcomes were converted to mean percentage changes in power output. Random-effects model meta-regressions, analogue to the ANOVA and weighted mean effect summaries were used to delineate the effect of the EID-associated body weight (BW) loss on TT performance.

Results

Five research articles, all using cycling TTs, were included, producing 13 effect estimates and representing 39 subjects. The mean ambient temperature, relative humidity, exercise intensity and duration of the exercise trials were 26.0±6.7°C, 61±9%, 68±14% of VO2max and 86±34 min, respectively. The effect of EID (mean BW loss of 2.20±1.0%) during self-paced exercise conditions was to produce a non-significant increase in endurance performance of 0.06±2.72% (p=0.94), compared with the maintenance of euhydration (mean BW loss of 0.44±0.48%). Meta-regression analyses revealed a statistically significant relationship between the percentage changes in power output and exercise intensity and duration, but not with the EID-associated percentage changes in BW loss. Drinking according to the dictate of thirst was associated with an increase in TT performance compared with a rate of drinking below (+5.2±4.6%, p=0.01) or above (+2.4±5.0%, p=0.40) thirst. The probability that drinking to thirst confers a real and meaningful advantage on TT performances conducted under field conditions compared with a rate of drinking below and above thirst sensation is of the order of 98% and 62%, respectively.

Conclusions

(1) Compared with euhydration, EID (up to 4% BW loss) does not alter cycling performances during out-of-door exercise conditions; (2) exercise intensity and duration have a much greater impact on cycling TT performances than EID and; (3) relying on thirst sensation to gauge the need for fluid replacement maximises cycling TT performances.
Teleradiology: practicalities and implications
Authors: Johnson Victoria
Published: April 2011

As digital imaging and improved telecommunications become more widely available in the UK, specialist services such as teleradiology are set to become more accessible to veterinary practice, offering a number of advantages in terms of advanced patient care and greater collaboration between veterinary colleagues. In this article, Victoria Johnson describes the concept of teleradiology, discusses the practicalities of incorporating this technology in practice, and considers the implications for standards of good practice in veterinary medicine.
Republished paper: The WHO patient safety curriculum guide for medical schools
Authors: Walton Merrilyn , Woodward Helen , Van Staalduinen Samantha , Lemer C , Greaves F , Noble D , Ellis B , Donaldson L , Barraclough B ,   Expert Group convened by the World Alliance of Patient Safety, as Expert Lead for the Sub-Programme
Published: April 2011

Background

The urgent need for patient safety education for healthcare students has been recognised by many accreditation bodies, but to date there has been sporadic attention to undergraduate/graduate medical programmes. Medical students themselves have identified quality and safety of care as an important area of instruction; as future doctors and healthcare leaders, they must be prepared to practise safe healthcare. Medical education has yet to fully embrace patient safety concepts and principles into existing medical curricula. Universities are continuing to produce graduate doctors lacking in the patient safety knowledge, skills and behaviours thought necessary to deliver safe care. A significant challenge is that patient safety is still a relatively new concept and area of study; thus, many medical educators are unfamiliar with the literature and unsure how to integrate patient safety learning into existing curriculum.

Design

To address this gap and provide a foothold for medical schools all around the world, the WHO's World Alliance for Patient Safety sponsored the development of a patient safety curriculum guide for medical students. The WHO Patient Safety Curriculum Guide  for Medical Schools adopts a ‘one-stop-shop’ approach in that it includes a teacher's manual providing a step-by-step guide for teachers new to patient safety learning as well as a comprehensive curriculum on the main patient safety areas. This paper establishes the need for patient safety education of medical students, describes the development of the WHO Patient Safety Curriculum Guide for Medical Schools and outlines the content of the Guide.
Assessment of the sedative effects of buprenorphine administered with 10 μg/kg detomidine in horses
Authors: Love E. J. , Taylor P. M. , Murrell J. , Whay H. R. , Waterman‐Pearson A. E.
Published: April 2011

The aim of this randomised, observer‐blinded, crossover study was to compare the effects of six treatments, administered intravenously to six horses: saline and saline (S/S); detomidine and saline (D/S); detomidine and 5 µg/kg buprenorphine (D/B5); detomidine and 7.5 µg/kg buprenorphine (D/B7.5); detomidine and 10 µg/kg buprenorphine (D/B10); and detomidine and 25 µg/kg butorphanol (D/BUT). The detomidine dose was 10 µg/kg for all treatments in which it was included. Sedation was subjectively assessed and recorded on a visual analogue scale. Peak sedation, duration of sedation and the area under the curve (AUC) for sedation scores were investigated using a univariate general linear model with post‐hoc Tukey tests (P<0.05). Peak sedation and duration of sedation were statistically significantly different between treatments (P<0.001). No sedation was apparent after administration of S/S. The AUC was significantly different between treatments (P=0.010), with S/S being significantly different from D/S, D/BUT, D/B5 and D/B7.5, but not D/B10 (P=0.051).
EFFECTS OF SURFACE-MODIFIED GATE INSULATOR ON THE ELECTRICAL CHARACTERISTICS OF ORGANIC THIN-FILM TRANSISTORS
Authors: ZHU WENQING , CHEN LING , LIU XIANG , BAI YU , WEI BIN , JIANG XUEYIN , ZHANG ZHILIN
Published: April 2011

The performance of organic thin film transistors (OTFTs) strongly depends on the surface states of the gate insulator. Top-contact (TC) OTFTs with modified gate insulator were demonstrated in this paper. The modified gate insulator layers consisted of SiO 2 as the gate insulator and OTS (octadecyltrichlorosilane) or PMMA (Poly (methyl methacylate)) as the modified layer. The devices with the modified layer had field-effect mobility larger than 10-3 cm 2/ Vs , which was twice that of the untreated OTFT. The on/off current ratio was increased one order of magnitude and reached more than 104. The leakage current was decreased from 10-9 A to 10-10 A. The results demonstrate that using modified gate insulators can obviously improve the performance of the OTFTs.
SUPERSOLID PHASE IN ONE-DIMENSIONAL BOSE–HUBBARD MODEL WITH EXTENDED RANGE INTERACTIONS: DMRG AND FIELD THEORETIC STUDY AT DIFFERENT DENSITIES
Authors: KUMAR MANORANJAN , SARKAR SUJIT , RAMASESHA S.
Published: April 2011

We use the Density Matrix Renormalization Group and the Abelian bosonization method to study the effect of density on quantum phases of one-dimensional extended Bose–Hubbard model. We predict the existence of supersolid phase and also other quantum phases for this system. We have analyzed the role of extended range interaction parameters on solitonic phase near half-filling. We discuss the effects of dimerization in nearest neighbor hopping and interaction as well as next nearest neighbor interaction on the plateau phase at half-filling.
SPECTRAL FUNCTION OF A d-p HUBBARD MODEL
Authors: CALEGARI E. J. , MAGALHAES S. G.
Published: April 2011

This work investigates a d-p Hubbard model by the n-pole approximation in the hole-doped regime. In particular, the spectral function A(ω, k) is analyzed varying the filling, the local Coulomb interaction and the d-p hybridization. It should be remarked that the original n-pole approximation (Phys. Rev.184, 451 1969) has been improved in order to include adequately the k-dependence of the important correlation function 〈Sj·Si〉 present in the poles of the Green's functions. It has been verified that the topology of the Fermi surface (defined by A(ω = 0, k)) is deeply affected by the doping, the strength of the Coulomb interaction and also by the hybridization. Particularly, in the underdoped regime, the spectral function A(ω = 0, k) presents very low intensity close to the antinodal points (0, ±π) and (±π, 0). Such a behavior produces an anomalous Fermi surface (pockets) with pseudogaps in the region of the antinodal points. On the other hand, if the d-p hybridization is enhanced sufficiently, such pseudogaps vanish. It is precisely the correlation function 〈Sj·Si〉, present in the poles of the Green's functions, plays an important role in the underdoped situation. In fact, antiferromagnetic correlations coming from 〈Sj·Si〉 strongly modify the quasiparticle band structure. This is the ultimate source of anomalies in the Fermi surface in the present approach.
DEPOSITION OF WIDE BAND GAP DLC FILMS USING R.F. PECVD AT VERY LOW POWER
Authors: BARHAI P. K. , SHARMA RISHI , NAYAK B. B.
Published: April 2011

Wide band gap diamond-like carbon films (DLCs) are deposited on silicon (1 0 0) substrates using capacitive coupled radio frequency plasma-enhanced chemical vapor deposition (R.F. PECVD) technique. The deposition of films is carried out at a constant pressure (~5×10-2 mbar ) using acetylene precursor diluted with argon at constant R.F. power of 5 W. Raman spectroscopy of deposited DLC films shows broad G peak near 1550 cm-1 and a weak D peak near 1320 cm1. FTIR plot of DLC films shows a peak near 2900 cm-1 corresponding to C–H stretching mode and peaks below 2000 cm-1 corresponding to C–C modes and C–H bending modes. Maximum hardness of the deposited films is found to be ~15 GPa. Band gap of the DLC films is ~3.5 eV. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) pictures show that the deposited films are amorphous. Deposition mechanism of wide band gap DLC film is explained on the basis of subplantation model.
EFFECT OF PROCESSING CONDITIONS ON DIELECTRIC PROPERTIES OF CaCu3Ti4O12 CERAMICS
Authors: KASHYAP RAMAN , THAKUR O. P. , MEHRA N. C. , TANDON R. P.
Published: April 2011

Samples of CaCu 3 Ti 4 O 12 (CCTO) ceramics were prepared by solid state reaction method. X-ray diffraction analysis confirmed single phase formation for the powder calcined at 1173 K. Sintering was done at different temperatures viz. 1348 K, 1373 K and 1398 K with a fixed heating rate of 3 K/min. Detailed study of dielectric properties was carried out for the CCTO samples sintered at 1373 K for different duration of holding times (2 h and 10 h). It is found that dielectric properties are sensitive to both sintering time and temperature. With increasing sintering time from 2 h to 10 h dielectric constant increases from ∼2.1 × 104 to ∼2.5 × 104 measured at 1 kHz at room temperature. Impedance spectroscopy has been used for separating out of grain and grain boundary contributions to the overall electrical properties.
THE REALIZATION OF TERAHERTZ BAND-GAP FROM InAs/GaSb TYPE II SUPERLATTICES
Authors: LI L. L. , DONG H. M. , XU W. , SHI Y. L.
Published: April 2011

We demonstrate theoretically that terahertz (THz) fundamental band-gap between the electron mini-band in the InAs layer and the heavy-hole mini-band in the GaSb layer can be realized in InAs/GaSb -based type II superlattices (SLs). The THz band-gap can be tuned by varying the widths of the InAs/GaSb layers. The presence of such band-gap can result in a strong cut-off on optical absorption at THz frequencies. For typical sample structures, the THz cut-off of the optical absorption depends sensitively on temperature and a sharper cut-off can be observed at relatively high temperatures. This study is pertinent to the application of InAs/GaSb type II SLs as THz photodetectors.
A COMPARISON OF PRICING KERNELS FOR GARCH OPTION PRICING WITH GENERALIZED HYPERBOLIC DISTRIBUTIONS
Authors: BADESCU ALEXANDRU , ELLIOTT ROBERT J. , KULPERGER REG , MIETTINEN JARKKO , SIU TAK KUEN
Published: April 2011

Under discrete-time GARCH models markets are incomplete so there is more than one price kernel for valuing contingent claims. This motivates the quest for selecting an appropriate price kernel. Different methods have been proposed for the choice of a price kernel. Some of them can be justified by economic equilibrium arguments. This paper studies risk-neutral dynamics of various classes of Generalized Hyperbolic GARCH models arising from different price kernels. We discuss the properties of these dynamics and show that for some special cases, some pricing kernels considered here lead to similar risk neutral GARCH dynamics. Real data examples for pricing European options on the S&P 500 index emphasize the importance of the choice of a price kernel.
SOLVABILITY AND NUMERICAL SIMULATION OF BSDEs RELATED TO BSPDEs WITH APPLICATIONS TO UTILITY MAXIMIZATION
Authors: IMKELLER PETER , RÉVEILLAC ANTHONY , ZHANG JIANING
Published: April 2011

In this paper we study BSDEs arising from a special class of backward stochastic partial differential equations (BSPDEs) that is intimately related to utility maximization problems with respect to arbitrary utility functions. After providing existence and uniqueness we discuss the numerical realizability. Then we study utility maximization problems on incomplete financial markets whose dynamics are governed by continuous semimartingales. Adapting standard methods that solve the utility maximization problem using BSDEs, we give solutions for the portfolio optimization problem which involve the delivery of a liability at maturity. We illustrate our study by numerical simulations for selected examples. As a byproduct we prove existence of a solution to a very particular quadratic growth BSDE with unbounded terminal condition. This complements results on this topic obtained in Briand and Hu (2006, 2008) and Briand et al. (2007).
The Effects of Twitter in an Online Learning Environment
Authors: Rath Logan
Published: April 2011

If educators adopt Twitter as part of the online learning environment, can it be successfully leveraged inside and outside the classroom? With little preexisting research, it is important to understand the implications of combining social networking with class participation.
Achieving Data Consistency by Contextualization in Web-Based Collaborative Applications
Authors: Shen Haifeng , Sun Chengzheng
Published: April 2011

Recent years have witnessed the emergence and rapid development of collaborative Web-based applications exemplified by Web-based office productivity applications. One major challenge in building these applications is maintaining data consistency while meeting the requirements of fast local response, total work preservation, unconstrained interaction, and customizable collaboration mode. These requirements are important in determining users’ experiences in interaction and collaboration, and in meeting users’ diverse needs under complex and dynamic collaboration and networking environments; but none of existing solutions is able to meet all of them. In this article, we present a data consistency maintenance solution capable of meeting these requirements for collaborative Web-based applications. Major technical contributions include an efficient sequence-based operation transformation control algorithm based on the concept of contextualization, an operation broadcast protocol for supporting a variety of collaboration modes, an operation replaying algorithm for ensuring fast local response and efficient remote operation replay, and a set of communication protocols for managing the integrity of collaborative Web-based sessions. The proposed solution has been implemented in a prototype collaborative Web-based editor WRACE and the correctness of the solution is formally verified in the article.
Novelty and Diversity in Top-N Recommendation -- Analysis and Evaluation
Authors: Hurley Neil , Zhang Mi
Published: April 2011

For recommender systems that base their product rankings primarily on a measure of similarity between items and the user query, it can often happen that products on the recommendation list are highly similar to each other and lack diversity. In this article we argue that the motivation of diversity research is to increase the probability of retrieving unusual or novel items which are relevant to the user and introduce a methodology to evaluate their performance in terms of novel item retrieval. Moreover, noting that the retrieval of a set of items matching a user query is a common problem across many applications of information retrieval, we formulate the trade-off between diversity and matching quality as a binary optimization problem, with an input control parameter allowing explicit tuning of this trade-off. We study solution strategies to the optimization problem and demonstrate the importance of the control parameter in obtaining desired system performance. The methods are evaluated for collaborative recommendation using two datasets and case-based recommendation using a synthetic dataset constructed from the public-domain Travel dataset.
An efficient fault detection algorithm for NAND flash memory
Authors: Kuo Tei-Wei , Huang Po-Chun , Chang Yuan-Hao , Ko Chia-Ling , Hsueh Chih-Wen
Published: April 2011

As flash memory gains its momentum in the storage market of embedded systems, existing fault detection algorithms face serious challenges due to the special characteristics of NAND flash memory and the rapid degradation of its reliability. This research proposes an efficient fault detection algorithm to detect the faults of NAND flash memory in a systematic way. Through the analysis of the testing time, the efficiency of the proposed algorithm is also evaluated and proved to be feasible.
Using simulation to design extremescale applications and architectures
Authors: Janssen Curtis L. , Adalsteinsson Helgi , Kenny Joseph P.
Published: April 2011

A key problem facing application developers is that they are expected to utilize extreme levels of parallelism soon after delivery of future leadership class machines, but developing applications capable of exposing sufficient concurrency is a time consuming process requiring experimentation. At the same time, due to the expense of building and operating an exascale machine, it will be necessary to apply tighter engineering margins to their design. Simple metrics such as the computation-communication ratio will not sufficiently specify machine requirements. Simulation fills this gap, allowing the study of extreme-scale architectures with the explicit inclusion of the complex interactions between the various hardware and software components, and can be used for correctness-checking as well as performance estimation. The simulator we discuss in this paper can be driven by reading trace files, typically generated by an actual application that has been run on real hardware, or by using a skeleton application. The skeleton application is designed to have the control flow of a real application, but with expensive computations and large data transfers replaced by discrete events for which the timings are determined by models. Using skeleton applications, we can predict application performance at levels of parallelism unobtainable on any current computational platform. The skeleton application can be modified to experiment with different communication strategies and programming models. Since the machine being simulated is in our control, we can experiment with different network topologies, routing algorithms, bandwidths, latencies, failure modes, core-to-node ratios, etc. In this paper, we use the Structural Simulation Toolkit macroscale components for coarse-grained simulation to illustrate the exploration of alternative programming models at extreme scale.
Benchmarking and modelling of POWER7, Westmere, BG/P, and GPUs
Authors: Herdman J. A. , Gaudin W. P. , Turland D. , Hammond S. D.
Published: April 2011

This paper introduces an industry strength, multi-purpose, benchmark: Shamrock. Developed at the Atomic Weapons Establishment (AWE), Shamrock is a two dimensional (2D) structured hydrocode; one of its aims is to assess the impacts of a change in hardware, and (in conjunction with a larger HPC Benchmark Suite) to provide guidance in procurement of future systems.

A suitable test problem is described and executed on a local, high-end, workstation for a range of compilers and MPI implementations. Based on these observations, specific configurations are subsequently built and executed on a selection of HPC architectures, including Intel's Nehalem and Westmere micro architectures, IBM's POWER-5, POWER-6, POWER-7, BlueGene/L, BlueGene/P, and AMD's Opteron chip set. Comparisons are made between these architectures, for the Shamrock benchmark, and relative compute resources are specified that deliver similar time to solution, along with their associated power budgets.

Additionally, performance comparisons are made for a port of the benchmark to a Nehalem based cluster, accelerated with Tesla C1060 GPUs, with details of the port, and extrapolations to possible performance of the GPU.
Performance characteristics of hybrid MPI/OpenMP implementations of NAS parallel benchmarks SP and BT on large-scale multicore supercomputers
Authors: Wu Xingfu , Taylor Valerie
Published: April 2011

The NAS Parallel Benchmarks (NPB) are well-known applications with the fixed algorithms for evaluating parallel systems and tools. Multicore supercomputers provide a natural programming paradigm for hybrid programs, whereby OpenMP can be used with the data sharing with the multicores that comprise a node and MPI can be used with the communication between nodes. In this paper, we use SP and BT benchmarks of MPI NPB 3.3 as a basis for a comparative approach to implement hybrid MPI/OpenMP versions of SP and BT. In particular, we can compare the performance of the hybrid SP and BT with the MPI counterparts on large-scale multicore supercomputers. Our performance results indicate that the hybrid SP outperforms the MPI SP by up to 20.76%, and the hybrid BT outperforms the MPI BT by up to 8.58% on up to 10,000 cores on BlueGene/P at Argonne National Laboratory and Jaguar (Cray XT4/5) at Oak Ridge National Laboratory. We also use performance tools and MPI trace libraries available on these supercomputers to further investigate the performance characteristics of the hybrid SP and BT.
A framework for architecture-level power, area, and thermal simulation and its application to network-on-chip design exploration
Authors: Hsieh Ming-yu , Rodrigues Arun , Riesen Rolf , Thompson Kevin , Song William
Published: April 2011

We describe the integrated power, area and thermal modeling framework in the Structural Simulation Toolkit (SST) for large-scale high performance computer simulation. It integrates various power and thermal modeling tools and computes run-time energy dissipation for core, network on chip, memory controller and shared cache. It also has functionality to update the leakage power as temperature changes.

We illustrate the utilization of the framework by applying it to explore interconnect options in manycore systems with consideration of temperature variation and leakage feedback. We compare power, energy-delay-area product (EDAP), and energy-delay product (EDP) of four manycore configurations-1 core, 2 cores, 4 cores and 8 cores per cluster. Results from simulation with or without consideration of temperature variation both show that the 4-core per cluster configuration has the best EDAP and EDP. Even so, considering temperature variation increases total power dissipation. We demonstrate the importance of considering temperature variation in the design ow. With this power, area and thermal modeling capability, SST can be used for hardware/software co-design of future Exascale systems.
Preliminary design examination of the ParalleX system from a software and hardware perspective
Authors: Tabbal Alexandre , Anderson Matthew , Brodowicz Maciej , Kaiser Hartmut , Sterling Thomas
Published: April 2011

Exascale systems, expected to emerge by the end of the next decade, will require the exploitation of billion-way parallelism at multiple hierarchical levels in order to achieve the desired sustained performance. While traditional approaches to performance evaluation involve measurements of existing applications on the available platforms, such a methodology is obviously unsuitable for architectures still at the brainstorming stage. The prediction of the future machine performance is an important factor driving the design of both the execution hardware and software environment. A good way to start assessing the performance is to identify the factors challenging the scalability of parallel applications. We believe the root cause of these challenges is the incoherent coupling between the current enabling technologies, such as Non-Uniform Memory Access of present multicore nodes equipped with optional hardware accelerators and the decades older execution model, i.e., Communicating Sequential Processes (CSP). Supercomputing is in the midst of a much needed phase change and the High-Performance Computing community is slowly realizing the necessity for a new design dogma, as affirmed in the preliminary Exascale studies. In this paper, we present an overview of the ParalleX execution model and its complementary design efforts at the software and hardware levels, while including power draw of the system as the resource of utmost importance. Since the interplay of hardware and software environment is quickly becoming one of the dominant factors in the design of well integrated, energy efficient, large-scale systems, we also explore the implications of the ParalleX model on the organization of parallel computing architectures. We also present scaling and performance results for an adaptive mesh refinement application developed using a ParalleX-compliant runtime system implementation, HPX.
On cross-validation and stacking
Authors: Perlich Claudia , Świrszcz Grzegorz
Published: April 2011

A number of times when using cross-validation (CV) while trying to do classification/probability estimation we have observed surprisingly low AUC's on real data with very few positive examples. AUC is the area under the ROC and measures the ranking ability and corresponds to the probability that a positive example receives a higher model score than a negative example. Intuition seems to suggest that no reasonable methodology should ever result in a model with an AUC significantly below 0.5. The focus of this paper is not on the estimator properties of CV (bias/variance/significance), but rather on the properties of the 'holdout' predictions based on which the CV performance of a model is calculated. We show that CV creates predictions that have an 'inverse' ranking with AUC well below 0.25 using features that were initially entirely unpredictive and models that can only perform monotonic transformations. In the extreme, combining CV with bagging (repeated averaging of out-of-sample predictions) generates 'holdout' predictions with perfectly opposite rankings on random data. While this would raise immediate suspicion upon inspection, we would like to caution the data mining community against using CV for stacking or in currently popular ensemble methods. They can reverse the predictions by assigning negative weights and produce in the end a model that appears to have close to perfect predictability while in reality the data was random.
Computation in large-scale scientific and internet data applications is a focus of MMDS 2010
Authors: Mahoney Michael W.
Published: April 2011

A report is provided for the ACM SIGKDD community about the 2010 Workshop on Algorithms for Modern Massive Data Sets (MMDS 2010), its origin in MMDS 2006 and MMDS 2008, and future directions for this interdisciplinary research area.
Topic-based social network analysis for virtual communities of interests in the dark web
Authors: L'Huillier Gaston , Alvarez Hector , Ríos Sebastián A. , Aguilera Felipe
Published: April 2011

The study of extremist groups and their interaction is a crucial task in order to maintain homeland security and peace. Tools such as social networks analysis and text mining have contributed to their understanding in order to develop counter-terrorism applications. This work addresses the topic-based community key-members extraction problem, for which our method combines both text mining and social network analysis techniques. This is achieved by first applying latent Dirichlet allocation to build two topic-based social networks in online forums: one social network oriented towards the thread creator point-of-view, and the other is oriented towards the repliers of the overall forum. Then, by using different network analysis measures, topic-based key members are evaluated using as benchmark a social network built a plain representation of the network of posts. Experiments were successfully performed using an English language based forum available in the Dark Web portal.
Fully decentralized computation of aggregates over data streams
Authors: Becchetti Luca , Bordino Ilaria , Leonardi Stefano , Rosen Adi
Published: April 2011

In several emerging applications, data is collected in massive streams at several distributed points of observation. A basic and challenging task is to allow every node to monitor a neighbourhood of interest by issuing continuous aggregate queries on the streams observed in its vicinity. This class of algorithms is fully decentralized and diffusive in nature: collecting all data at few central nodes of the network is unfeasible in networks of low capability devices or in the presence of massive data sets.

The main difficulty in designing diffusive algorithms is to cope with duplicate detections. These arise both from the observation of the same event at several nodes of the network and/or receipt of the same aggregated information along multiple paths of diffusion. In this paper, we consider fully decentralized algorithms that answer locally continuous aggregate queries on the number of distinct events, total number of events and the second frequency moment in the scenario outlined above. The proposed algorithms use in the worst case or on realistic distributions sublinear space at every node. We also propose strategies that minimize the communication needed to update the aggregates when new events are observed. We experimentally evaluate for the efficiency and accuracy of our algorithms on realistic simulated scenarios.
Colonic microbiota alters host susceptibility to infectious colitis by modulating inflammation, redox status, and ion transporter gene expression
Authors: Ghosh S. , Dai C. , Brown K. , Rajendiran E. , Makarenko S. , Baker J. , Ma C. , Halder S. , Montero M. , Ionescu V. A. , Klegeris A. , Vallance B. A. , Gibson D. L.
Published: April 2011

Individuals vary in their resistance to enteric infections. The role of the intestinal microbiota in altering susceptibility to enteric infection is relatively unknown. Previous studies have identified that C3H/HeOuJ mice suffer 100% mortality during Citrobacter rodentium-induced colitis, whereas C57BL/6 mice recover from infection. The basis for their differences in susceptibility is unclear and has been mainly attributed to differences in host genetics. This study investigated the role of the intestinal microbiota in altering susceptibility to C. rodentium-induced colitis. When the feces of C57BL/6 mice were gavaged into antibiotic treated C3H/HeOuJ mice, the C57BL/6 microflora led to a complete reversal in mortality patterns where 100% of the C3H/HeOuJ mice survived infection. This protection corresponded with reduced colonic pathology and less systemic pathogen load and was associated with increased inflammatory and redox responses with reduced epithelial cell death. C3H/HeOuJ mice are normally susceptible to infection-induced dehydration due to defective expression of colonic ion transporters such as Dra, CA IV, and CA I; expression of these genes was normalized when C3H/HeOuJ mice were colonized with the C57BL/6 microflora. Together, these data reveal that the colonic microbiota play a critical role in protecting against intestinal infection by inducing proinflammatory and prooxidant responses that control pathogen load as well as ion transporter gene expression previously shown to prevent fatal dehydration. Protection of mice from lethal colitis was associated with higher levels of bacteria from Bacteroidetes. This study reveals that the microbiota is sufficient to overcome inherent genetic susceptibility patterns in C3H/HeOuJ mice that cause mortality during C. rodentium infection.
Sympathetic activation by the cold pressor test does not increase the muscle force generation capacity
Authors: Roatta Silvestro , Farina Dario
Published: April 2011

A positive inotropic action by the sympathetic nervous system on skeletal muscles has been observed and investigated in animal and in vitro studies. This action provided a theoretical basis for the putative ergogenic action of catecholamines and adrenergic agonists, although there is no clear evidence of this effect in humans. The aim of this study was to investigate the occurrence of inotropic effects associated to physiological sympathetic activation in healthy subjects. The muscle force capacity was investigated in the tibialis anterior ( n = 9 subjects) and in the soleus ( n = 9) muscles electrically stimulated with single pulses and double pulses with variable interspike interval (4–1,000 ms) and short pulse trains (frequency: 5–14 Hz) before, during, and after sympathetic activation by the cold pressor test (CPT). CPT significantly decreased by 10.4 ± 7.2 and 10.6 ± 4.4% the force produced by single and double pulse stimulation, respectively, and produced smaller decreases in the force obtained by train stimulation in the tibialis anterior, while no significant changes were observed in either type of contraction in the soleus muscle. CPT failed to induce any increase in the force capacity of the investigated muscles. The prevalent decrease in force evidenced in this study supports the concept that the weakening sympathetic action on type I fiber, already shown to occur in humans, prevails over the putative potentiating action.
Dietary nitrate supplementation enhances exercise performance in peripheral arterial disease
Authors: Kenjale Aarti A. , Ham Katherine L. , Stabler Thomas , Robbins Jennifer L. , Johnson Johanna L. , VanBruggen Mitch , Privette Grayson , Yim Eunji , Kraus William E. , Allen Jason D.
Published: April 2011

Peripheral arterial disease (PAD) results in a failure to adequately supply blood and oxygen (O2) to working tissues and presents as claudication pain during walking. Nitric oxide (NO) bioavailability is essential for vascular health and function. Plasma nitrite (NO2−) is a marker of vascular NO production but may also be a protected circulating “source” that can be converted to NO during hypoxic conditions, possibly aiding perfusion. We hypothesized that dietary supplementation of inorganic nitrate in the form of beetroot (BR) juice would increase plasma NO2−concentration, increase exercise tolerance, and decrease gastrocnemius fractional O2extraction, compared with placebo (PL). This was a randomized, open-label, crossover study. At each visit, subjects ( n = 8) underwent resting blood draws, followed by consumption of 500 ml BR or PL and subsequent blood draws prior to, during, and following a maximal cardiopulmonary exercise (CPX) test. Gastrocnemius oxygenation during the CPX was measured by near-infrared spectroscopy. There were no changes from rest for [NO2−] (152 ± 72 nM) following PL. BR increased plasma [NO2−] after 3 h (943 ± 826 nM; P ≤ 0.01). Subjects walked 18% longer before the onset of claudication pain (183 ± 84 s vs. 215 ± 99 s; P ≤ 0.01) and had a 17% longer peak walking time (467 ± 223 s vs. 533 ± 233 s; P ≤ 0.05) following BR vs. PL. Gastrocnemius tissue fractional O2extraction was lower during exercise following BR (7.3 ± 6.2 vs. 10.4 ± 6.1 arbitrary units; P ≤ 0.01). Diastolic blood pressure was lower in the BR group at rest and during CPX testing ( P ≤ 0.05). These findings support the hypothesis that NO2−-related NO signaling increases peripheral tissue oxygenation in areas of hypoxia and increases exercise tolerance in PAD.
Continuous monitoring of absolute cerebral blood flow by near-infrared spectroscopy during global and focal temporary vessel occlusion
Authors: Cooper Joel A. , Tichauer Kenneth M. , Boulton Melfort , Elliott Jonathan , Diop Mamadou , Arango Miguel , Lee Ting-Yim , St. Lawrence Keith
Published: April 2011

Treatment of intracranial aneurysms by surgical clipping carries a risk of intraoperative ischemia, caused mainly by prolonged temporary occlusion of cerebral arteries. The objective of this study was to develop a near-infrared spectroscopy (NIRS) technique for continuous monitoring of cerebral blood flow (CBF) during surgery. With this approach, cerebral hemodynamics prior to clipping are measured by a bolus-tracking method that uses indocyanine green as an intravascular contrast agent. The baseline hemodynamic measurements are then used to convert the continuous Hb difference (HbD) signal (HbD = oxyhemoglobin − deoxyhemoglobin) acquired during vessel occlusion to units of CBF. To validate the approach, HbD signal changes, along with the corresponding CBF changes, were measured in pigs following occlusion of the common carotid arteries or a middle cerebral artery. For both occlusion models, the predicted CBF change derived from the HbD signal strongly correlated with the measured change in CBF. Linear regression of the predicted and measured CBF changes resulted in a slope of 0.962 ( R2 = 0.909) following carotid occlusion and 0.939 ( R2 = 0.907) following middle cerebral artery occlusion. These results suggest that calibrating the HbD signal by baseline hemodynamic measurements provides a clinically feasible method of monitoring CBF changes during neurosurgery.
Diagnosis of Prostate Cancer Using Differentially Expressed Genes in Stroma
Authors: Jia Zhenyu , Wang Yipeng , Sawyers Anne , Yao Huazhen , Rahmatpanah Farahnaz , Xia Xiao-Qin , Xu Qiang , Pio Rebecca , Turan Tolga , Koziol James A. , Goodison Steve , Carpenter Philip , Wang-Rodriguez Jessica , Simoneau Anne , Meyskens Frank , Sutton Manuel , Lernhardt Waldemar , Beach Thomas , Monforte Joseph , McClelland Michael , Mercola Dan
Published: April 2011

More than one million prostate biopsies are performed in the United States every year. A failure to find cancer is not definitive in a significant percentage of patients due to the presence of equivocal structures or continuing clinical suspicion. We have identified gene expression changes in stroma that can detect tumor nearby. We compared gene expression profiles of 13 biopsies containing stroma near tumor and 15 biopsies from volunteers without prostate cancer. About 3,800 significant expression changes were found and thereafter filtered using independent expression profiles to eliminate possible age-related genes and genes expressed at detectable levels in tumor cells. A stroma-specific classifier for nearby tumor was constructed on the basis of 114 candidate genes and tested on 364 independent samples including 243 tumor-bearing samples and 121 nontumor samples (normal biopsies, normal autopsies, remote stroma, as well as stroma within a few millimeters of tumor). The classifier predicted the tumor status of patients using tumor-free samples with an average accuracy of 97% (sensitivity = 98% and specificity = 88%) whereas classifiers trained with sets of 100 randomly generated genes had no diagnostic value. These results indicate that the prostate cancer microenvironment exhibits reproducible changes useful for categorizing the presence of tumor in patients when a prostate sample is derived from near the tumor but does not contain any recognizable tumor. Cancer Res; 71(7); 2476–87. ©2011 AACR.
Epigenetic Silencing of MicroRNA-203 Dysregulates ABL1 Expression and Drives Helicobacter-Associated Gastric Lymphomagenesis
Authors: Craig Vanessa J. , Cogliatti Sergio B. , Rehrauer Hubert , Wündisch Thomas , Müller Anne
Published: April 2011

Gastric B-cell lymphoma of mucosa-associated lymphoid tissue (MALT lymphoma) develops in the chronically inflamed mucosa of patients infected with the bacterial pathogen Helicobacter pylori. Here we use patient material, primary gastric lymphoma cell cultures, and a preclinical model of the disease to examine the role of microRNA (miRNA)-mediated posttranscriptional regulation—focusing in particular on miR-203 and its target ABL1—in gastric MALT lymphomagenesis. Microarray-based miRNA expression profiling revealed a strong downregulation of the putative tumor suppressor miRNA miR-203 in human MALT lymphoma samples, which resulted from extensive promoter hypermethylation of the miR-203 locus and coincided with the dysregulation of the miR-203 target ABL1 in lymphoma biopsies compared with matched adjacent normal material from the same patients. Treatment of lymphoma B cells with demethylating agents led to increased miR-203 expression and the concomitant downregulation of ABL1, confirming the epigenetic regulation of this miRNA. Ectopic reexpression of miR-203 by transfection of a human lymphoma cell line or lentiviral transduction of explanted primary MALT lymphoma cells was sufficient to prevent tumor cell proliferation in vitro. Similarly, the treatment of primary MALT lymphoma cells with the ABL inhibitors imatinib and dasatinib prevented tumor cell growth. Finally, we show that the treatment of tumor-bearing mice with imatinib induces MALT lymphoma regression in a preclinical model of the disease, implicating ABL1 in MALT lymphoma progression. In summary, our results show that the transformation from gastritis to MALT lymphoma is epigenetically regulated by miR-203 promoter methylation and identify ABL1 as a novel target for the treatment of this malignancy. Cancer Res; 71(10); 3616–24. ©2011 AACR.
Congenital Ichthyosis in Severe Type II Gaucher Disease with a Homozygous Null Mutation
Authors: Haverkaemper Sabine , Marquardt Thorsten , Hausser Ingrid , Timme Katharina , Kuehn Thomas , Hertzberg Christoph , Rossi Rainer
Published: April 2011

This paper describes a neonate with type II Gaucher disease. The phenotype was unusually severe with congenital ichthyosis, hepatosplenomegaly, muscular hypotonia, myoclonus and respiratory failure. Electron microscopy of the skin revealed lamellar body contents in the stratum corneum interstices, appearances considered to be typical of type II Gaucher disease. The baby died from respiratory failure 1 month postpartum having made no neurological progress. Molecular analysis identified a previously not reported homozygous null mutation, c.1505G→A of the β-glucocerebrosidase gene.
Delayed Asthmatic Response to Bronchial Challenge with Allergen-Mediators, Eicosanoids, Eosinophil and Neutrophil Constituents in the Blood and Urine
Authors: Pelikan Zdenek
Published: April 2011

Background: In patients with allergic bronchial asthma, different immunologic mechanisms may participate and lead to different types of asthmatic response to allergen challenge, such as immediate/early (IAR/EAR), late (LAR) or delayed asthmatic response (DYAR). Objectives: In 55 of 397 asthmatics, DYAR has been recorded (p < 0.001) and confirmed by repeated bronchial challenge with the same allergen (p < 0.001). DYAR began between 26 and 32 h, reached a maximum between 32 and 48 h and resolved within 56 h after the challenge. DYAR was associated with various clinical symptoms and diagnostic parameters having diverged from those recorded during the IARs/EARs and LARs. Methods: In 25 of 55 patients, repeated DYAR has been supplemented with the recording of leukotriene B4 (LTB4), LTC4, LTE4, prostaglandin D2 (PGD2), PGE2, PGF2α, thromboxane B2, lipoxin A4, eosinophil cationic protein, eosinophil-derived neurotoxin/eosinophil protein X, eosinophilic peroxidase, myeloperoxidase, histamine and tryptase in peripheral blood, and of LTC4, thromboxane B2, eosinophil-derived neurotoxin and 9α,11β-PGF2 in urine, before and up to 72 h after the bronchial allergen challenge, by means of enzyme-linked immunoassay (ELISA/EIA) or ImmunoCAP. Results: DYAR was accompanied by a significant increase in the plasma concentrations of LTB4 (p < 0.05) and myeloperoxidase (p < 0.05) at 24, 36 and 48 h after the challenge, whereas the plasma/serum or urine concentrations of the other factors did not demonstrate any significant changes (p > 0.05). Conclusions: These results would indicate an active and prominent involvement of neutrophils, in addition to the previously demonstrated role of the Th1 lymphocytes, in the clinical DYAR.