bluuebunny/crossref_metadata_2025 huggingface dataset:
CD8+T Cells Specific for a Malaria Cytoplasmic Antigen Form Clusters around Infected Hepatocytes and Are Protective at the Liver Stage of Infection
Authors: Kimura Kazumi , Kimura Daisuke , Matsushima Yoshifumi , Miyakoda Mana , Honma Kiri , Yuda Masao , Yui Katsuyuki
Published: July 2013

FollowingAnophelesmosquito-mediated introduction into a human host,Plasmodiumparasites infect hepatocytes and undergo intensive replication. Accumulating evidence indicates that CD8+T cells induced by immunization with attenuatedPlasmodiumsporozoites can confer sterile immunity at the liver stage of infection; however, the mechanisms underlying this protection are not clearly understood. To address this, we generated recombinantPlasmodium bergheiANKA expressing a fusion protein of an ovalbumin epitope and green fluorescent protein in the cytoplasm of the parasite. We have shown that the ovalbumin epitope is presented by infected liver cells in a manner dependent on a transporter associated with antigen processing and becomes a target of specific CD8+T cells from the T cell receptor transgenic mouse line OT-I, leading to protection at the liver stage ofPlasmodiuminfection. We visualized the interaction between OT-I cells and infected hepatocytes by intravital imaging using two-photon microscopy. OT-I cells formed clusters around infected hepatocytes, leading to the elimination of the intrahepatic parasites and subsequent formation of large clusters of OT-I cells in the liver. Gamma interferon expressed in CD8+T cells was dispensable for this protective response. Additionally, we found that polyclonal ovalbumin-specific memory CD8+T cells induced byde novoimmunization were able to confer sterile protection, although the threshold frequency of the protection was relatively high. These studies revealed a novel mechanism of specific CD8+T cell-mediated protective immunity and demonstrated that proteins expressed in the cytoplasm ofPlasmodiumparasites can become targets of specific CD8+T cells during liver-stage infection.
Dissection of the Role of Pili and Type 2 and 3 Secretion Systems in Adherence and Biofilm Formation of an Atypical Enteropathogenic Escherichia coli Strain
Authors: Hernandes Rodrigo T. , De la Cruz Miguel A. , Yamamoto Denise , Girón Jorge A. , Gomes Tânia A. T.
Published: July 2013

Atypical enteropathogenic
Escherichia coli
(aEPEC) strains are diarrheal pathogens that lack bundle-forming pilus production but possess the virulence-associated locus of enterocyte effacement. aEPEC strain 1551-2 produces localized adherence (LA) on HeLa cells; however, its isogenic intimin (
eae
) mutant produces a diffuse-adherence (DA) pattern. In this study, we aimed to identify the DA-associated adhesin of the 1551-2
eae
mutant. Electron microscopy of 1551-2 identified rigid rod-like pili composed of an 18-kDa protein, which was identified as the major pilin subunit of type 1 pilus (T1P) by mass spectrometry analysis. Deletion of
fimA
in 1551-2 affected biofilm formation but had no effect on adherence properties. Analysis of secreted proteins in supernatants of this strain identified a 150-kDa protein corresponding to SslE, a type 2 secreted protein that was recently reported to be involved in biofilm formation of rabbit and human EPEC strains. However, neither adherence nor biofilm formation was affected in a 1551-2
sslE
mutant. We then investigated the role of the EspA filament associated with the type 3 secretion system (T3SS) in DA by generating a double
eae espA
mutant. This strain was no longer adherent, strongly suggesting that the T3SS translocon is the DA adhesin. In agreement with these results, specific anti-EspA antibodies blocked adherence of the 1551-2
eae
mutant. Our data support a role for intimin in LA, for the T3SS translocon in DA, and for T1P in biofilm formation, all of which may act in concert to facilitate host intestinal colonization by aEPEC strains.
Helicobacter pylori Infection in a Pig Model Is Dominated by Th1 and Cytotoxic CD8+T Cell Responses
Authors: Kronsteiner Barbara , Bassaganya-Riera Josep , Philipson Casandra , Viladomiu Monica , Carbo Adria , Pedragosa Mireia , Vento Salvador , Hontecillas Raquel
Published: July 2013

Helicobacter pyloriinfection is the leading cause for peptic ulcer disease and gastric adenocarcinoma. Mucosal T cell responses play an important role in mediatingH. pylori-related gastric immunopathology. While induced regulatory T (iTreg) cells are required for chronic colonization without disease, T helper 1 (Th1) effector responses are associated with lower bacterial loads at the expense of gastric pathology. Pigs were inoculated with eitherH. pyloristrain SS1 or J99. Phenotypic and functional changes in peripheral blood mononuclear cell (PBMC) populations were monitored weekly, and mucosal immune responses and bacterial loads were assessed up to 2 months postinfection. BothH. pyloristrains elicited a Th1 response characterized by increased percentages of CD4+Tbet+cells and elevated gamma interferon (IFN-γ) mRNA in PBMCs. A subset of CD8+T cells expressing Tbet and CD16 increased following infection. Moreover, a significant increase in perforin and granzyme mRNA expression was observed in PBMCs of infected pigs, indicating a predominant cytotoxic immune response. Infiltration of B cells, myeloid cells, T cells expressing Treg- and Th17-associated transcription factors, and cytotoxic T cells was found in the gastric lamina propria of both infected groups. Interestingly, based on bacterial reisolation data, strain SS1 showed greater capacity to colonize and/or persist in the gastric mucosa than did strain J99. This novel pig model of infection closely mimics human gastric pathology and presents a suitable avenue for studying effector and regulatory responses towardH. pyloridescribed in humans.
Development of Severe Pathology in Immunized Pregnant Mice Challenged with Lethal Malaria Parasites
Authors: Mineo Shoichiro , Niikura Mamoru , Inoue Shin-Ichi , Kuroda Masahiko , Kobayashi Fumie
Published: July 2013

Pregnant women are highly susceptible to malaria infection because of their low immunity and are at increased risk of maternal illness or death, in addition to spontaneous abortion, stillbirth, premature delivery, and low birth weight. However, the detailed pathogenesis of maternal malaria remains unclear. In this study, we evaluated a mouse model that shows similar severe pathological features of pregnant women duringPlasmodium falciparuminfection and investigated the pathogenesis of maternal malaria. Pregnant mice immunized by infection with an attenuated parasite,Plasmodium bergheiXAT, were more susceptible to virulentP. bergheiNK65 challenge/infection than were nonpregnant mice and showed high levels of parasitemia and a poor pregnancy outcome associated with placental pathology, such as accumulation of parasitized red blood cells, in the late phase of pregnancy. Notably, the pregnant immune mice challenged/infected withP. bergheiNK65 developed liver injury associated with microvesicular fatty infiltration in late pregnancy. The pathological features were similar to acute fatty liver of pregnancy. Higher levels of gamma interferon and nitric oxide (NO) were found in plasma from pregnant immune mice infected withP. bergheiNK65 than in plasma from nonpregnant mice. These findings suggest that development of liver injury and placental pathology in pregnant immune mice challenged/infected withP. bergheiNK65 is accompanied by enhanced production of proinflammatory cytokines.
Propriospinal myoclonus: is it always psychogenic?
Authors: Verma Rajesh , Praharaj Heramba Narayan , Raut Tushar Premraj , Rai Dheeraj
Published: July 2013

Propriospinal myoclonus (PSM) is a rare type of movement disorder in which the myoclonic jerks are present or intensified in supine position. Arising from a thoracic or abdominal generator, the movements propagate rostrocaudally as per the spinospinal conduction velocity. Routine neuroimaging and electrophysiology being normal in most instances, it is frequently interpreted as psychogenic. We present a case of PSM which will throw ample light on the pathophysiology, approach and dilemmas in treatment.
The sad truth about the SADPERSONS Scale: an evaluation of its clinical utility in self-harm patients
Authors: Saunders Kate , Brand Fiona , Lascelles Karen , Hawton Keith
Published: July 2013

Background

The SADPERSONS Scale is commonly used as a screening tool for suicide risk in those who have self-harmed. It is also used to determine psychiatric treatment needs in those presenting to emergency departments. To date, there have been relatively few studies exploring the utility of SADPERSONS in this context.

Objectives

To determine whether the SADPERSONS Scale accurately predicts psychiatric hospital admission, psychiatric aftercare and repetition of self-harm at presentation to the emergency department following self-harm.

Methods

SADPERSONS scores were recorded for 126 consecutive admissions to a general hospital emergency department. Clinical management outcomes following assessment were recorded, including psychiatric hospital admission, community psychiatric aftercare and repetition of self-harm in the following 6 months.

Results

Psychiatric hospital admission was required in five cases (4.0%) and community psychiatric aftercare in 70 (55.5%). 31 patients (24.6%) repeated self-harm. While the specificity of the SADPERSONS scores was greater than 90% for all outcomes, sensitivity for admission was only 2.0%, for community aftercare was 5.8% and for repetition of self-harm in the following 6 months was just 6.6%.

Conclusions

For the purposes of suicide prevention, a low false negative rate is essential. SADPERSONS failed to identify the majority of those either requiring psychiatric admission or community psychiatric aftercare, or to predict repetition of self-harm. The scale should not be used to screen self-harm patients presenting to general hospitals. Greater emphasis should be placed on clinical assessment which takes account of the individual and dynamic nature of risk assessment.
Stir-Fried White Pepper Can Treat Diarrhea in Infants and Children Efficiently: A Randomized Controlled Trial
Authors: Jin Cheng-Qiang , Jia Yan-Xia , Dong Hai-Xin , Zhou Jian-Wei , Sun Guang-Fei , Zhang Yu-Yan , Zhao Qing , Zheng Bi-Ying
Published: July 2013

We evaluated the efficacy and safety of stir-fried white pepper in the treatment of infant and children diarrhea. This was a randomized trial conducted in the pediatric emergency department of the hospital affiliated to Jining Medical College. One hundred seventy four patients were selected from outpatients from 2011 to 2012. Participants were randomly assigned to treatment with stir-fried white pepper (n = 88) or montmorillonite powder (n = 86). The proportions of chronic diarrhea patients (n = 52) showing success of treatment were similar for both groups. There were great differences between the two groups in acute diarrhea (n = 62) and persistent diarrhea (n = 60), and the cure rate of stir-fried white pepper was higher than montmorillonite powder in both groups. The prescription of stir-fried white pepper significantly decreased the frequency of diarrhea in infants and children under 2.5 years with diarrhea compared to treatment with montmorillonite powder, especially for the patients with acute diarrhea or persistent diarrhea.
Hypoglycemic Activities of Commonly-Used Traditional Chinese Herbs
Authors: Feng Shengbao , Song Lixia , Liu Yuancai , Lai Fuli , Zuo Gang , He Guangyuan , Chen Mingjie , Huang Dejian
Published: July 2013

The α-amylase and α-glucosidase inhibition activity of 92 Traditional Chinese Medicinal (TCM) herbs, which are permitted to be used as food ingredients, were evaluated using the high throughput assay developed in our laboratory. Among these herbs, twenty-seven of them possessed significant α-amylase inhibition activities ranging from 2.4 to 349.2 μmol AE/g (AE = acarbose equivalent) with inhibition concentrations at 50% inhibition (IC50) from 16.0 to 2342.2 μg/mL, respectively. In addition, they showed α-glucosidase inhibition activities ranging from 0.5 to 31.6 μmolAE/g (IC50 from 49.0 to 3385.5 μg/mL). The extracts of Rhizoma fagopyri dibotryis (Jīnqiáomài), Rosa rugosa (Méiguīhuā), Caulis polygoni multiflori (Shǒuwūténg), Fructus amomi (Shārén), Rhizoma alpiniae officinarum (Gāoliángjiāng), Folium ginkgo (Yínxìngyè) and Cortex cinnamomi (Ròuguì) showed the better inhibitory activities against both α-amylase and α-glucosidase. Our results illustrated that these food grade herbs are potent natural hypoglycemic agents and can be used as active ingredients for low glycemic index food production or TCM herbal formulations for controlling hyperglycemia.
Antiviral Activity ofFolium IsatidisDerived ExtractsIn VitroandIn Vivo
Authors: Deng You-Ping , Liu Yuan-Yuan , Liu Zhao , Li Jin , Zhao Ling-Min , Xiao Hong , Ding Xiao-Hua , Yang Zhan-Qiu
Published: July 2013

Folium isatidis is a native Chinese herbaceous plant widely used for medicinal purposes for thousands of years. However, few studies have focused on the leaves of Isatis indigotica. In this report, we isolated a series of four fractions (I–IV) from Folium isatidis and explored the antiviral activity of each tested extract. The extracts were active against a panel of RNA and DNA viruses in vitro, namely influenza A virus (IAV), coxsackie virus B3 (CVB3), respiratory syncytial virus (RSV), and adenovirus type 7 (Ad-7). Oral administration of 200 mg/kg/d of fraction III in mice exerted strong antiviral effects in viral replication, accompanied by prolonged survival rate, attenuated lung tissue damage as well as significant reductions in pulmonary virus titers and lung index. Our results provide the first biochemical evidence that Folium isatidis and its extracts could be used as potential antiviral agent in the postexposure prophylaxis for multiple viral infections.
SEMILEPTONIC DECAY OF Bc MESON INTO $c\bar c$ STATES IN A QCD POTENTIAL MODEL
Authors: PATHAK KRISHNA KINGKAR , CHOUDHURY D. K.
Published: July 2013

The slope and curvature of Isgur–Wise function for Bc meson is computed in a QCD potential model in two different approaches of choosing the perturbative term of the Cornell potential. Based on heavy quark effective theory the exclusive semileptonic decay rates of Bc meson into the [Formula: see text] states are exploited. Spin symmetry breaking effects are ignored up to a particular point and the form factors are connected with Isgur–Wise function for other kinematic point since the recoil momentum of [Formula: see text] from Bc is small due to its heavy mass.
ON THE CONSISTENCY OF QUANTUM HADRO-DYNAMICS
Authors: CENNI R.
Published: July 2013

We explore the consistency of the Quantum Hadro-Dynamics (QHD), namely the Serot and Walecka model, paying attention to its renormalizabilty, the stability of the vacuum and the possible occurrence of a σ-ω condensate. We find that the QHD is not renormalizable as it is usually described, but the true way of formulate it, via the Stueckelberg Lagrangian, alters the formulation of the model in the vacuum but leaves the results in the medium unchanged. Further, we find that the stability of the vacuum imposes a constrain over the parameters of the σ self-interaction while stability against σ condensation at the mean field level imposes a constraint on the coupling constant, namely gσ<8.828 that is kF = 207.2 MeV/c, significantly below the standard value of QHD.
PSEUDOSPIN AND SPIN SYMMETRY OF DIRAC-GENERALIZED YUKAWA PROBLEMS WITH A COULOMB-LIKE TENSOR INTERACTION VIA SUSYQM
Authors: IKOT AKPAN N. , MAGHSOODI ELHAM , ZARRINKAMAR SABER , SALEHI N. , HASSANABADI HASSAN
Published: July 2013

We investigated the approximate solutions of the Dirac equation for the generalized Yukawa types I and II under the framework of pseudospin and spin symmetry limits. We obtained the energy eigenvalues and the corresponding wave functions using the supersymmetry method. Closed form of the energy eigenvalues are obtained for any spin-orbit coupling term κ. We also discuss the energy eigenvalues of the Dirac equation for some well-known potentials such as Yukawa, inversely quadratic Yukawa, new Yukawa, Mie-type and Coulomb potentials which are the special cases of the generalized Yukawa potentials.
FUSION OF MULTISPECTRAL AND PANCHROMATIC IMAGES BASED ON THE NONSUBSAMPLED CONTOURLET TRANSFORM
Authors: JIJI C. V. , UNNI RAVI KRISHNAN
Published: July 2013

This paper proposes two different methods for fusing multispectral (MS) and panchromatic (PAN) satellite images using the nonsubsampled contourlet transform (NSCT). The NSCT decomposes the images into several directional subbands at flexible resolutions. The finer subbands of the MS image decomposition, which represent the high frequency details, are modified with the subbands from PAN image. The inverse transform gives a high resolution MS representation of the given low resolution MS image. The paper also proposes the use of the parameters mean structural similarity index measure (MSSIM) and edge stability mean square error (ESMSE) to measure the quality of the fused image, in addition to standard parameters like correlation coefficient, PSNR, RASE and ERGAS. Experiments show that the proposed methods outperform standard fusion techniques in terms of both visual quality and quantitative error measures. The fused images obtained using the proposed methods show good structural similarity and better edge stability as the contourlet transform very well extracts the oriented edge details from the high resolution PAN image.
ANALYSIS OF LIMIT CYCLES RESPONSE ON PARAMETRIC NOISE IN ONE-DIMENSIONAL DISCRETE-TIME SYSTEMS
Authors: BASHKIRTSEVA IRINA
Published: July 2013

We study cycles of the discrete-time nonlinear dynamical system under parametric random disturbances. A dynamics of deviations of the random solutions from the deterministic cycle is analyzed with the help of first approximation linear systems. A closed system for second moments of these deviations is obtained and explicit formulas for the stable periodic solution are given. Constructive abilities of our mathematical technique are demonstrated for parametrical analysis of stochastically forced periodic regimes in the Ricker population model with Allee effect. A threshold noise intensity corresponding to the onset of stochastic extinction is estimated.
ALMOST ADJACENT IDEALS IN TWO-DIMENSIONAL MUHLY RATIONAL SINGULARITIES
Authors: VAN LIERDE V.
Published: July 2013

Let (R, m) be a two-dimensional Muhly rational singularity, i.e. the residue field R/m is algebraically closed and the associated graded ring is an integrally closed domain. The goal of this paper is to use immediate quadratic transforms and degree coefficients to investigate complete ideals that are almost adjacent to m, i.e. [Formula: see text].
A methodology to characterize fractured reservoirs constrained by statistical geological analysis and production: a real field case study
Authors: Delorme Matthieu , Oliveira Mota Rosane , Khvoenkova Nina , Fourno André , Nœtinger Benoit
Published: July 2013

In the oil industry, complex workflow is used to match or predict fluid production. The large uncertainty of the data can lead to large variability of the simulation results, notably because of the strongly heterogeneous nature of fluid flows. The particular case of naturally fractured reservoirs is well known to be especially difficult to match.

This paper presents a method to improve an initial geological analysis, carried out in 2008, through the integration of hydrodynamic data in the fractured reservoir model. Dynamic data such as production information, production logging tools and well tests are used to determine fractures properties by calibrating the fluid flow or reservoir pressure measured at wells. The approach, applied to a real field case, respects both the statistical geological analysis and the dynamic analysis of the production history. Using this methodology the geological structural model based on static characterization are preserved and available.

In the study we analysed uncertainties and, in respecting the initial geological model, we prove the presence of compartmentalization in the reservoir by matching 1 year of production and three well tests. Both analytical and numerical flow simulations were used at different scales for time and space: near the well and on the whole reservoir.
Detailed mapping, three-dimensional modelling and upscaling of a mixed-influence delta system, Mitchell River delta, Gulf of Carpentaria, Australia
Authors: Massey T. A. , Fernie A. J. , Ainsworth R. B. , Nanson R. A. , Vakarelov B. K.
Published: July 2013

Data from satellite imagery, field measurements and analogues were used to construct a three-dimensional (3D) geocellular facies model of the Mitchell River Delta, Australia; a modern mixed-influence delta system. Detailed mapping identified 16 different facies elements and classified the delta as tide dominated, fluvially influenced and wave affected. The 3D model was subjected to varying degrees of upscaling of the horizontal and vertical dimensions and allowed comparison of volume and connectivity changes throughout. The upscaling process, to coarser grid cells up to 100 m horizontally and 4 m vertically, created false compartmentalization of facies bodies and significant changes in facies bulk volumes. The vertically upscaled models produced greater changes when compared to the horizontally upscaled models. Key changes in reservoir facies connectivity and bulk volume due to upscaling are associated with the facies architecture, including the elongate and thin morphology of beach ridge and channel facies in this mixed-influence delta system. Recognition of the defining reservoir features and incorporation into reservoir modelling methodology can improve volumetric estimation and allow for better predictions of reservoir connectivity in ancient delta systems.
The value of design rationale information
Authors: Falessi Davide , Briand Lionel C. , Cantone Giovanni , Capilla Rafael , Kruchten Philippe
Published: July 2013

A complete and detailed (full) Design Rationale Documentation (DRD) could support many software development activities, such as an impact analysis or a major redesign. However, this is typically too onerous for systematic industrial use as it is not cost effective to write, maintain, or read. The key idea investigated in this article is that DRD should be developed only to the extent required to support activities particularly difficult to execute or in need of significant improvement in a particular context. The aim of this article is to empirically investigate the customization of the DRD by documenting only the information items that will probably be required for executing an activity. This customization strategy relies on the hypothesis that the value of a specific DRD information item depends on its category (e.g., assumptions, related requirements, etc.) and on the activity it is meant to support. We investigate this hypothesis through two controlled experiments involving a total of 75 master students as experimental subjects. Results show that the value of a DRD information item significantly depends on its category and, within a given category, on the activity it supports. Furthermore, on average among activities, documenting only the information items that have been required at least half of the time (i.e., the information that will probably be required in the future) leads to a customized DRD containing about half the information items of a full documentation. We expect that such a significant reduction in DRD information should mitigate the effects of some inhibitors that currently prevent practitioners from documenting design decision rationale.
Enabledness-based program abstractions for behavior validation
Authors: Caso Guido De , Braberman Victor , Garbervetsky Diego , Uchitel Sebastian
Published: July 2013

Code artifacts that have nontrivial requirements with respect to the ordering in which their methods or procedures ought to be called are common and appear, for instance, in the form of API implementations and objects. This work addresses the problem of validating if API implementations provide their intended behavior when descriptions of this behavior are informal, partial, or nonexistent. The proposed approach addresses this problem by generating abstract behavior models which resemble typestates. These models are statically computed and encode all admissible sequences of method calls. The level of abstraction at which such models are constructed has shown to be useful for validating code artifacts and identifying findings which led to the discovery of bugs, adjustment of the requirements expected by the engineer to the requirements implicit in the code, and the improvement of available documentation.
Use case and task models
Authors: Sinnig Daniel , Chalin Patrice , Khendek Ferhat
Published: July 2013

User Interface (UI) development methods are poorly integrated with standard software engineering practice. The differences in terms of artifacts involved, development philosophies, and lifecycles can often result in inconsistent system and UI specifications leading to duplication of effort and increased maintenance costs. To address such shortcomings, we propose an integrated development methodology for use case and task models. Use cases are generally used to capture functional requirements whereas task models specify the detailed user interactions with the UI. Our methodology can assist practitioners in developing software processes which allow these two kinds of artifacts to be developed in a codependent and integrated manner. We present our methodology, describe its semantic foundations along with a set of formal conformance relations, and introduce an automated verification tool.
Dependent Type Theory for Verification of Information Flow and Access Control Policies
Authors: Nanevski Aleksandar , Banerjee Anindya , Garg Deepak
Published: July 2013

Dedicated to the memory of John C. Reynolds (1935--2013).

We present Relational Hoare Type Theory (RHTT), a novel language and verification system capable of expressing and verifying rich information flow and access control policies via dependent types. We show that a number of security policies which have been formalized separately in the literature can all be expressed in RHTT using only standard type-theoretic constructions such as monads, higher-order functions, abstract types, abstract predicates, and modules. Example security policies include conditional declassification, information erasure, and state-dependent information flow and access control. RHTT can reason about such policies in the presence of dynamic memory allocation, deallocation, pointer aliasing and arithmetic.
Efficient Identification of Linchpin Vertices in Dependence Clusters
Authors: Binkley David , Gold Nicolas , Harman Mark , Islam Syed , Krinke Jens , Li Zheng
Published: July 2013

Several authors have found evidence of large dependence clusters in the source code of a diverse range of systems, domains, and programming languages. This raises the question of how we might efficiently locate the fragments of code that give rise to large dependence clusters. We introduce an algorithm for the identification of
linchpin
vertices, which hold together large dependence clusters, and prove correctness properties for the algorithm’s primary innovations. We also report the results of an empirical study concerning the reduction in analysis time that our algorithm yields over its predecessor using a collection of 38 programs containing almost half a million lines of code. Our empirical findings indicate improvements of almost two orders of magnitude, making it possible to process larger programs for which it would have previously been impractical.
Virtualizable hardware/software design infrastructure for dynamically partially reconfigurable systems
Authors: Huang Chun-Hsian , Hsiung Pao-Ann
Published: July 2013

In most existing works, reconfigurable hardware modules are still managed as conventional hardware devices. Further, the software reconfiguration overhead incurred by loading corresponding device drivers into the kernel of an operating system has been overlooked until now. As a result, the enhancement of system performance and the utilization of reconfigurable hardware modules are still quite limited. This work proposes a virtualizable hardware/software design infrastructure (VDI) for dynamically partially reconfigurable systems. Besides the gate-level hardware virtualization provided by the partial reconfiguration technology, VDI supports the device-level hardware virtualization. In VDI, a reconfigurable hardware module can be virtualized such that it can be accessed efficiently by multiple applications in an interleaving way. A Hot-Plugin Connector (HPC) replaces the conventional device driver, such that it not only assists the device-level hardware virtualization but can also be reused across different hardware modules. To facilitate hardware/software communication and to enhance system scalability, the proposed VDI is realized as a hierarchical design framework. User-designed reconfigurable hardware modules can be easily integrated into VDI, and are then executed as
hardware tasks
in an operating system for reconfigurable systems (OS4RS). A dynamically partially reconfigurable network security system was designed using VDI, which demonstrated a higher utilization of reconfigurable hardware modules and a reduction by up to 12.83% of the processing time required by using the conventional method in a dynamically partially reconfigurable system.
Efficient online learning for multitask feature selection
Authors: Yang Haiqin , Lyu Michael R. , King Irwin
Published: July 2013

Learning explanatory features across multiple related tasks, or MultiTask Feature Selection (MTFS), is an important problem in the applications of data mining, machine learning, and bioinformatics. Previous MTFS methods fulfill this task by batch-mode training. This makes them inefficient when data come sequentially or when the number of training data is so large that they cannot be loaded into the memory simultaneously. In order to tackle these problems, we propose a novel online learning framework to solve the MTFS problem. A main advantage of the online algorithm is its efficiency in both time complexity and memory cost. The weights of the MTFS models at each iteration can be updated by closed-form solutions based on the average of previous subgradients. This yields the worst-case bounds of the time complexity and memory cost at each iteration, both in the order ofO(d×Q), wheredis the number of feature dimensions andQis the number of tasks. Moreover, we provide theoretical analysis for the average regret of the online learning algorithms, which also guarantees the convergence rate of the algorithms. Finally, we conduct detailed experiments to show the characteristics and merits of the online learning algorithms in solving several MTFS problems.
Exploiting fisher and fukunaga-koontz transforms in chernoff dimensionality reduction
Authors: Peng Jing , Seetharaman Guna , Fan Wei , Varde Aparna
Published: July 2013

Knowledge discovery from big data demands effective representation of data. However, big data are often characterized by high dimensionality, which makes knowledge discovery more difficult. Many techniques for dimensionality reudction have been proposed, including well-known Fisher's Linear Discriminant Analysis (LDA). However, the Fisher criterion is incapable of dealing with heteroscedasticity in the data. A technique based on the Chernoff criterion for linear dimensionality reduction has been proposed that is capable of exploiting heteroscedastic information in the data. While the Chernoff criterion has been shown to outperform the Fisher's, a clear understanding of its exact behavior is lacking. In this article, we show precisely what can be expected from the Chernoff criterion. In particular, we show that the Chernoff criterion exploits the Fisher and Fukunaga-Koontz transforms in computing its linear discriminants. Furthermore, we show that a recently proposed decomposition of the data space into four subspaces is incomplete. We provide arguments on how to best enrich the decomposition of the data space in order to account for heteroscedasticity in the data. Finally, we provide experimental results validating our theoretical analysis.
Continuous real-world inputs can open up alternative accelerator designs
Authors: Belhadj Bilel , Joubert Antoine , Li Zheng , Héliot Rodolphe , Temam Olivier
Published: July 2013

Motivated by energy constraints, future heterogeneous multi-cores may contain a variety of accelerators, each targeting a subset of the application spectrum. Beyond energy, the growing number of faults steers accelerator research towards fault-tolerant accelerators.

In this article, we investigate a fault-tolerant and energy-efficient accelerator for signal processing applications. We depart from traditional designs by introducing an accelerator which relies on
unary coding
, a concept which is well adapted to the continuous real-world inputs of signal processing applications. Unary coding enables a number of atypical micro-architecture choices which bring down area cost and energy; moreover, unary coding provides graceful output degradation as the amount of transient faults increases.

We introduce a configurable hybrid digital/analog micro-architecture capable of implementing a broad set of signal processing applications based on these concepts, together with a back-end optimizer which takes advantage of the special nature of these applications. For a set of five signal applications, we explore the different design tradeoffs and obtain an accelerator with an area cost of 1.63
mm
2
. On average, this accelerator requires only 2.3% of the energy of an Atom-like core to implement similar tasks. We then evaluate the accelerator resilience to transient faults, and its ability to trade accuracy for energy savings.
ArchShield
Authors: Nair Prashant J. , Kim Dae-Hyun , Qureshi Moinuddin K.
Published: July 2013

DRAM scaling has been the prime driver for increasing the capacity of main memory system over the past three decades. Unfortunately, scaling DRAM to smaller technology nodes has become challenging due to the inherent difficulty in designing smaller geometries, coupled with the problems of device variation and leakage. Future DRAM devices are likely to experience significantly high error-rates. Techniques that can tolerate errors efficiently can enable DRAM to scale to smaller technology nodes. However, existing techniques such as row/column sparing and ECC become prohibitive at high error-rates.

To develop cost-effective solutions for tolerating high error-rates, this paper advocates a cross-layer approach. Rather than hiding the faulty cell information within the DRAM chips, we expose it to the architectural level. We propose
ArchShield
, an architectural framework that employs runtime testing to identify faulty DRAM cells. ArchShield tolerates these faults using two components, a
Fault Map
that keeps information about faulty words in a cache line, and
Selective Word-Level Replication (SWLR)
that replicates faulty words for error resilience. Both Fault Map and SWLR are integrated in reserved area in DRAM memory. Our evaluations with 8GB DRAM DIMM show that ArchShield can efficiently tolerate error-rates as higher as 10
−4
(100x higher than ECC alone), causes less than 2% performance degradation, and still maintains 1-bit error tolerance against soft errors.
Secure I/O device sharing among virtual machines on multiple hosts
Authors: Tu Cheng-Chun , Lee Chao-tang , Chiueh Tzi-cker
Published: July 2013

Virtualization allows flexible mappings between physical resources and virtual entities, and improves allocation efficiency and agility. Unfortunately, most existing virtualization technologies are limited to resources in a single host. This paper presents the design, implementation and evaluation of a multi-host I/O device virtualization system called
Ladon
, which enables I/O devices to be shared among virtual machines running on multiple hosts in a secure and efficient way. Specifically,
Ladon
uses a PCIe network to connect multiple servers with PCIe devices and allows VMs running on these servers to directly interact with these PCIe devices without interfering with one another. Through an evaluation of a fully operational
Ladon
prototype, we show that there is no throughput and latency penalty of the multi-host I/O virtualization enabled by
Ladon
compared to those of the existing single-host I/O virtualization technology.
Quantum rotations
Authors: Kudrow Daniel , Bier Kenneth , Deng Zhaoxia , Franklin Diana , Tomita Yu , Brown Kenneth R. , Chong Frederic T.
Published: July 2013

Work in quantum computer architecture has focused on communication, layout and fault tolerance, largely driven by Shor's factorization algorithm. For the first time, we study a larger range of benchmarks and find that another critical issue is the generation of code sequences for quantum rotation operations. Specifically, quantum algorithms require arbitrary rotation angles, while quantum technologies and error correction codes provide only for discrete angles and operators. A sequence of quantum machine instructions must be generated to approximate the arbitrary rotation to the required precision.

While previous work has focused exclusively on static compilation, we find that some applications require dynamic code generation and explore the advantages and disadvantages of static and dynamic approaches. We find that static code generation can, in some cases, lead to a terabyte of machine code to support required rotations. We also find that some rotation angles are unknown until run time, requiring dynamic code generation. Dynamic code generation, however, exhibits significant trade-offs in terms of time overhead versus code size. Furthermore, dynamic code generation will be performed on classical (non-quantum) computing resources, which may or may not have a clock speed advantage over the target quantum technology. For example, operations on trapped ions run at kilohertz speeds, but superconducting qubits run at gigahertz speeds.

We introduce a new method for compiling arbitrary rotations dynamically, designed to minimize compilation time. The new method reduces compilation time by up to five orders of magnitude while increasing code size by one order of magnitude.

We explore the design space formed by these trade-offs of dynamic versus static code generation, code quality, and quantum technology. We introduce several techniques to provide smoother trade-offs for dynamic code generation and evaluate the viability of options in the design space.
AC-DIMM
Authors: Guo Qing , Guo Xiaochen , Patel Ravi , Ipek Engin , Friedman Eby G.
Published: July 2013

With technology scaling, on-chip power dissipation and off-chip memory bandwidth have become significant performance bottlenecks in virtually all computer systems, from mobile devices to supercomputers. An effective way of improving performance in the face of bandwidth and power limitations is to rely on associative memory systems. Recent work on a PCM-based, associative TCAM accelerator shows that associative search capability can reduce both off-chip bandwidth demand and overall system energy. Unfortunately, previously proposed resistive TCAM accelerators have limited flexibility: only a restricted (albeit important) class of applications can benefit from a TCAM accelerator, and the implementation is confined to resistive memory technologies with a high dynamic range (

R
High
/R
Low

), such as PCM.

This work proposes AC-DIMM, a flexible, high-performance associative compute engine built on a DDR3-compatible memory module. AC-DIMM addresses the limited flexibility of previous resistive TCAM accelerators by combining two powerful capabilities---associative search and processing in memory. Generality is improved by augmenting a TCAM system with a set of integrated, user programmable microcontrollers that operate directly on search results, and by architecting the system such that key-value pairs can be co-located in the same TCAM row. A new, bit-serial TCAM array is proposed, which enables the system to be implemented using STT-MRAM. AC-DIMM achieves a 4.2X speedup and a 6.5X energy reduction over a conventional RAM-based system on a set of 13 evaluated applications.
WeeFence
Authors: Duan Yuelu , Muzahid Abdullah , Torrellas Josep
Published: July 2013

Although fences are designed for low-overhead concurrency coordination, they can be expensive in current machines. If fences were largely free, faster fine-grained concurrent algorithms could be devised, and compilers could guarantee Sequential Consistency (SC) at little cost.

In this paper, we present
WeeFence
(or
WFence
for short), a fence that is very cheap because it allows post-fence accesses to skip it. Such accesses can typically complete and retire before the pre-fence writes have drained from the write buffer. Only when an incorrect reordering of accesses is about to happen, does the hardware stall to prevent it. In the paper, we present the WFence design for TSO, and compare it to a conventional fence with speculation for 8-processor multicore simulations. We run parallel kernels that contain explicit fences and parallel applications that do not. For the kernels, WFence eliminates nearly all of the fence stall, reducing the kernels' execution time by an average of 11%. For the applications, a conservative compiler algorithm places fences in the code to guarantee SC. In this case, on average, WFences reduce the resulting fence overhead from 38% of the applications' execution time to 2% (in a centralized WFence design), or from 36% to 5% (in a distributed WFence design).
Robust architectural support for transactional memory in the power architecture
Authors: Cain Harold W. , Michael Maged M. , Frey Brad , May Cathy , Williams Derek , Le Hung
Published: July 2013

On the twentieth anniversary of the original publication [10], following ten years of intense activity in the research literature, hardware support for transactional memory (TM) has finally become a commercial reality, with HTM-enabled chips currently or soon-to-be available from many hardware vendors. In this paper we describe architectural support for TM added to a future version of the Power ISA™. Two imperatives drove the development: the desire to complement our weakly-consistent memory model with a more friendly interface to simplify the development and porting of multithreaded applications, and the need for robustness beyond that of some early implementations. In the process of commercializing the feature, we had to resolve some previously unexplored interactions between TM and existing features of the ISA, for example translation shootdown, interrupt handling, atomic read-modify-write primitives, and our weakly consistent memory model. We describe these interactions, the overall architecture, and discuss the motivation and rationale for our choices of architectural semantics, beyond what is typically found in reference manuals.
Cooperative boosting
Authors: Paul Indrani , Manne Srilatha , Arora Manish , Bircher W. Lloyd , Yalamanchili Sudhakar
Published: July 2013

This paper examines the interaction between thermal management techniques and power boosting in a state-of-the-art heterogeneous processor consisting of a set of CPU and GPU cores. We show that for classes of applications that utilize both the CPU and the GPU, modern boost algorithms that greedily seek to convert thermal headroom into performance can interact with thermal coupling effects between the CPU and the GPU to degrade performance. We first examine the causes of this behavior and explain the interaction between thermal coupling, performance coupling, and workload behavior. Then we propose a dynamic power-management approach called cooperative boosting (CB) to allocate power dynamically between CPU and GPU in a manner that balances thermal coupling against the needs of performance coupling to optimize performance under a given thermal constraint. Through real hardware-based measurements, we evaluate CB against a state-of-the-practice boost algorithm and show that overall application performance and power savings increase by 10% and 8% (up to 52% and 34%), respectively, resulting in average energy efficiency improvement of 25% (up to 76%) over a wide range of benchmarks.
Orchestrated scheduling and prefetching for GPGPUs
Authors: Jog Adwait , Kayiran Onur , Mishra Asit K. , Kandemir Mahmut T. , Mutlu Onur , Iyer Ravishankar , Das Chita R.
Published: July 2013

In this paper, we present techniques that coordinate the thread scheduling and prefetching decisions in a General Purpose Graphics Processing Unit (GPGPU) architecture to better tolerate long memory latencies. We demonstrate that existing warp scheduling policies in GPGPU architectures are unable to effectively incorporate data prefetching. The main reason is that they schedule consecutive warps, which are likely to access nearby cache blocks and thus prefetch accurately for one another, back-to-back in consecutive cycles. This either 1) causes prefetches to be generated by a warp too close to the time their corresponding addresses are actually demanded by another warp, or 2) requires sophisticated prefetcher designs to correctly predict the addresses required by a future "far-ahead" warp while executing the current warp.

We propose a new
prefetch-aware
warp scheduling policy that overcomes these problems. The key idea is to separate in time the scheduling of consecutive warps such that they are not executed back-to-back. We show that this policy not only enables a simple prefetcher to be effective in tolerating memory latencies but also improves memory bank parallelism, even when prefetching is not employed. Experimental evaluations across a diverse set of applications on a 30-core simulated GPGPU platform demonstrate that the prefetch-aware warp scheduler provides 25% and 7% average performance improvement over baselines that employ prefetching in conjunction with, respectively, the commonly-employed round-robin scheduler or the recently-proposed two-level warp scheduler. Moreover, when prefetching is not employed, the prefetch-aware warp scheduler provides higher performance than both of these baseline schedulers as it better exploits memory bank parallelism.
Reducing memory access latency with asymmetric DRAM bank organizations
Authors: Son Young Hoon , Seongil O. , Ro Yuhwan , Lee Jae W. , Ahn Jung Ho
Published: July 2013

DRAM has been a de facto standard for main memory, and advances in process technology have led to a rapid increase in its capacity and bandwidth. In contrast, its random access latency has remained relatively stagnant, as it is still around 100 CPU clock cycles. Modern computer systems rely on caches or other latency tolerance techniques to lower the average access latency. However, not all applications have ample parallelism or locality that would help hide or reduce the latency. Moreover, applications' demands for memory space continue to grow, while the capacity gap between last-level caches and main memory is unlikely to shrink. Consequently, reducing the main-memory latency is important for application performance. Unfortunately, previous proposals have not adequately addressed this problem, as they have focused only on improving the bandwidth and capacity or reduced the latency at the cost of significant area overhead.

We propose asymmetric DRAM bank organizations to reduce the average main-memory access latency. We first analyze the access and cycle times of a modern DRAM device to identify key delay components for latency reduction. Then we reorganize a subset of DRAM banks to reduce their access and cycle times by half with low area overhead. By synergistically combining these reorganized DRAM banks with support for non-uniform bank accesses, we introduce a novel DRAM bank organization with center high-aspect-ratio mats called CHARM. Experiments on a simulated chip-multiprocessor system show that CHARM improves both the instructions per cycle and system-wide energy-delay product up to 21% and 32%, respectively, with only a 3% increase in die area.