bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptional Profiling of Neisseria meningitidis Interacting with Human Epithelial Cells in a Long-Term
In Vitro
Colonization Model
Authors: Hey Ariann , Li Ming-Shi , Hudson Michael J. , Langford Paul R. , Kroll J. Simon
Published: August 2013

Neisseria meningitidis
is a commensal of humans that can colonize the nasopharyngeal epithelium for weeks to months and occasionally invades to cause life-threatening septicemia and meningitis. Comparatively little is known about meningococcal gene expression during colonization beyond those first few hours. In this study, the transcriptome of adherent serogroup B
N. meningitidis
strain MC58 was determined at intervals during prolonged cocultivation with confluent monolayers of the human respiratory epithelial cell line 16HBE14. At different time points up to 21 days, 7 to 14% of the meningococcal genome was found to be differentially regulated. The transcriptome of adherent meningococci obtained after 4 h of coculture was markedly different from that obtained after prolonged cocultivation (24 h, 96 h, and 21 days). Genes persistently upregulated during prolonged cocultivation included three genes (
hfq
,
misR
/
phoP
, and
lrp
) encoding global regulatory proteins. Many genes encoding known adhesins involved in epithelial adherence were upregulated, including those of a novel locus (spanning
NMB0342
to
NMB0348
[
NMB0342-NMB0348
]) encoding epithelial cell-adhesive function. Sixteen genes (including
porA
,
porB
,
rmpM
, and
fbpA
) encoding proteins previously identified by their immunoreactivity to sera from individuals colonized long term with serogroup B meningococci were also upregulated during prolonged cocultivation, indicating that our system models growth conditions
in vivo
during the commensal state. Surface-expressed proteins downregulated in the nasopharynx (and thus less subject to selection pressure) but upregulated in the bloodstream (and thus vulnerable to antibody-mediated bactericidal activity) should be interesting candidate vaccine antigens, and in this study, three new proteins fulfilling these criteria have been identified: NMB0497, NMB0866, and NMB1882.
MrkD
1P
from Klebsiella pneumoniae Strain IA565 Allows for Coexistence with Pseudomonas aeruginosa and Protection from Protease-Mediated Biofilm Detachment
Authors: Childers Brandon M. , Van Laar Tricia A. , You Tao , Clegg Steven , Leung Kai P.
Published: August 2013

Biofilm formation and persistence are essential components for the continued survival of pathogens inside the host and constitute a major contributor to the development of chronic wounds with resistance to antimicrobial compounds. Understanding these processes is crucial for control of biofilm-mediated disease. Though chronic wound infections are often polymicrobial in nature, much of the research on chronic wound-related microbes has focused on single-species models.
Klebsiella pneumoniae
and
Pseudomonas aeruginosa
are microbes that are often found together in wound isolates and are able to form stable
in vitro
biofilms, despite the antagonistic nature of
P. aeruginosa
with other organisms. Mutants of the
K. pneumoniae
strain IA565 lacking the plasmid-borne
mrkD
1P
gene were less competitive than the wild type in an
in vitro
dual-species biofilm model with
P. aeruginosa
(PAO1). PAO1 spent medium inhibited the formation of biofilm of
mrkD
1P
-deficient mutants and disrupted preestablished biofilms, with no effect on IA565 and no effect on the growth of the wild type or mutants. A screen using a two-allele PAO1 transposon library identified the LasB elastase as the secreted effector involved in biofilm disruption, and a purified version of the protein produced results similar to those with PAO1 spent medium. Various other proteases had a similar effect, suggesting that the disruption of the
mrkD
1P
gene causes sensitivity to general proteolytic effects and indicating a role for MrkD
1P
in protection against host antibiofilm effectors. Our results suggest that MrkD
1P
allows for competition of
K. pneumoniae
with
P. aeruginosa
in a mixed-species biofilm and provides defense against microbial and host-derived proteases.
The Haemophilus ducreyi Fis Protein Is Involved in Controlling Expression of thelspB-lspA2Operon and Other Virulence Factors
Authors: Labandeira-Rey Maria , Dodd Dana A. , Brautigam Chad A. , Fortney Kate R. , Spinola Stanley M. , Hansen Eric J.
Published: August 2013

Expression of thelspB-lspA2operon encoding a virulence-related two-partner secretion system inHaemophilus ducreyi35000HP is directly regulated by the CpxRA regulatory system (M. Labandeira-Rey, J. R. Mock, and E. J. Hansen, Infect. Immun. 77:3402–3411, 2009). In the present study, we show that this secretion system is also regulated by the small nucleoid-associated protein Fis. Inactivation of theH. ducreyi fisgene resulted in a reduction in expression of both theH. ducreyiLspB and LspA2 proteins. DNA microarray experiments showed that aH. ducreyi fisdeletion mutant exhibited altered expression levels of genes encoding other importantH. ducreyivirulence factors, including DsrA and Flp1, suggesting a possible global role for Fis in the control of virulence in this obligate human pathogen. While theH. ducreyiFis protein has a high degree of sequence and structural similarity to the Fis proteins of other bacteria, its temporal pattern of expression was very different from that of enterobacterial Fis proteins. The use of alacZ-based transcriptional reporter provided evidence which indicated that theH. ducreyiFis homolog is a positive regulator ofgyrB, a gene that is negatively regulated by Fis in enteric bacteria. Taken together, the Fis protein expression data and the observed regulatory effects of Fis inH. ducreyisuggest that this small DNA binding protein has a regulatory role inH. ducreyiwhich may differ in substantial ways from that of other Fis proteins.
Secreted Pyomelanin of Legionella pneumophila Promotes Bacterial Iron Uptake and Growth under Iron-Limiting Conditions
Authors: Zheng Huaixin , Chatfield Christa H. , Liles Mark R. , Cianciotto Nicholas P.
Published: August 2013

Iron acquisition is critical to the growth and virulence of
Legionella pneumophila
. Previously, we found that
L. pneumophila
uses both a ferrisiderophore pathway and ferrous iron transport to obtain iron. We now report that two molecules secreted by
L. pneumophila
, homogentisic acid (HGA) and its polymerized variant (HGA-melanin, a pyomelanin), are able to directly mediate the reduction of various ferric iron salts. Furthermore, HGA, synthetic HGA-melanin, and HGA-melanin derived from bacterial supernatants enhanced the ability of
L. pneumophila
and other species of
Legionella
to take up radiolabeled iron. Enhanced iron uptake was not observed with a ferrous iron transport mutant. Thus, HGA and HGA-melanin mediate ferric iron reduction, with the resulting ferrous iron being available to the bacterium for uptake. Upon further testing of
L. pneumophila
culture supernatants, we found that significant amounts of ferric and ferrous iron were associated with secreted HGA-melanin. Importantly, a pyomelanin-containing fraction obtained from a wild-type culture supernatant was able to stimulate the growth of iron-starved legionellae. That the corresponding supernatant fraction obtained from a nonpigmented mutant culture did not stimulate growth demonstrated that HGA-melanin is able to both promote iron uptake and enhance growth under iron-limiting conditions. Indicative of a complementary role in iron acquisition, HGA-melanin levels were inversely related to the levels of siderophore activity. Compatible with a role in the ecology and pathogenesis of
L. pneumophila
, HGA and HGA-melanin were effective at reducing and releasing iron from both insoluble ferric hydroxide and the mammalian iron chelates ferritin and transferrin.
Short-Lived Effector CD8 T Cells Induced by Genetically Attenuated Malaria Parasite Vaccination Express CD11c
Authors: Cooney Laura A. , Gupta Megha , Thomas Sunil , Mikolajczak Sebastian , Choi Kimberly Y. , Gibson Claire , Jang Ihn K. , Danziger Sam , Aitchison John , Gardner Malcolm J. , Kappe Stefan H. I. , Wang Ruobing
Published: August 2013

Vaccination with a single dose of genetically attenuated malaria parasites can induce sterile protection against sporozoite challenge in the rodentPlasmodium yoeliimodel. Protection is dependent on CD8+T cells, involves perforin and gamma interferon (IFN-γ), and is correlated with the expansion of effector memory CD8+T cells in the liver. Here, we have further characterized vaccine-induced changes in the CD8+T cell phenotype and demonstrated significant upregulation of CD11c on CD3+CD8b+T cells in the liver, spleen, and peripheral blood. CD11c+CD8+T cells are predominantly CD11ahiCD44hiCD62L−, indicative of antigen-experienced effector cells. Followingin vitrorestimulation with malaria-infected hepatocytes, CD11c+CD8+T cells expressed inflammatory cytokines and cytotoxicity markers, including IFN-γ, tumor necrosis factor alpha (TNF-α), interleukin-2 (IL-2), perforin, and CD107a. CD11c−CD8+T cells, on the other hand, expressed negligible amounts of all inflammatory cytokines and cytotoxicity markers tested, indicating that CD11c marks multifunctional effector CD8+T cells. Coculture of CD11c+, but not CD11c−, CD8+T cells with sporozoite-infected primary hepatocytes significantly inhibited liver-stage parasite development. Tetramer staining for the immunodominant circumsporozoite protein (CSP)-specific CD8+T cell epitope demonstrated that approximately two-thirds of CSP-specific cells expressed CD11c at the peak of the CD11c+CD8+T cell response, but CD11c expression was lost as the CD8+T cells entered the memory phase. Further analyses showed that CD11c+CD8+T cells are primarily KLRG1+CD127−terminal effectors, whereas all KLRG1−CD127+memory precursor effector cells are CD11c−CD8+T cells. Together, these results suggest that CD11c marks a subset of highly inflammatory, short-lived, antigen-specific effector cells, which may play an important role in eliminating infected hepatocytes.
Neuroanatomical Basis for Acupuncture Point Pc8 in the Rat: Neural Tracing Study with Cholera Toxin Subunit B
Authors: Cui Jing-Jing , Ha Li-Juan , Zhu Xin-Long , Shi Hong , Wang Fu-Chun , Jing Xiang-Hong , Bai Wan-Zhu
Published: August 2013

Objectives

This study was performed to investigate the innervations related to acupuncture point PC8 in rats using a neural tracing technique.

Methods

After 6 μL of 1% cholera toxin subunit B (CTB) was injected into the site between the second and third metacarpal bone in rats, a corresponding site to acupuncture point PC8 in the human body, CTB labelling was examined with immunofluorescence and immunohistochemistry in the dorsal root ganglia (DRG), spinal cord and brainstem.

Results

All CTB labelling appeared on the ipsilateral side of the injection. The labelled sensory neurons distributed from cervical (C)6 to thoracic (T)1 DRG, while the labelled motor neurons were located on the dorsolateral part of the spinal ventral horn ranging from the C6 to T1 segments. In addition, the transganglionically-labelled axonal terminals were found to be dense in the medial part of laminae 3–4 from C6 to the T1 spinal dorsal horn, as far as in the cuneate nucleus.

Conclusions

These results indicate that sensory and motor neurons associated with PC8 distribute in a distinct segmental pattern. The sensory information from PC8 could be transganglionically transported to the spinal dorsal horn and cuneate nucleus.
The efficacy of manual joint mobilisation/manipulation in treatment of lateral ankle sprains: a systematic review
Authors: Loudon Janice K , Reiman Michael P , Sylvain Jonathan
Published: August 2013

Background

Lateral ankle sprains are common and can have detrimental consequences to the athlete. Joint mobilisation/manipulation may limit these outcomes.

Objective

Systematically summarise the effectiveness of manual joint techniques in treatment of lateral ankle sprains.

Methods

This review employed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. A computer-assisted literature search of MEDLINE, CINHAL, EMBASE, OVID and Physiotherapy Evidence Database (PEDro) (January 1966 to March 2013) was used with the following keywords alone and in combination ‘ankle’, ‘sprain’, ‘injuries’, 'lateral’, ‘manual therapy’, and ‘joint mobilisation’. The methodological quality of individual studies was assessed using the PEDro scale.

Results

After screening of titles, abstracts and full articles, eight articles were kept for examination. Three articles achieved a score of 10 of 11 total points; one achieved a score of 9; two articles scored 8; one article scored a 7 and the remaining article scored a 5. Three articles examined joint techniques for acute sprains and the remainder examined subacute/chronic ankle sprains. Outcome measures included were pain level, ankle range of motion, swelling, functional score, stabilometry and gait parameters. The majority of the articles only assessed these outcome measures immediately after treatment. No detrimental effects from the joint techniques were revealed in any of the studies reviewed.

Conclusions

For acute ankle sprains, manual joint mobilisation diminished pain and increased dorsiflexion range of motion. For treatment of subacute/chronic lateral ankle sprains, these techniques improved ankle range-of-motion, decreased pain and improved function.
Ancient boreal forests under the environmental instability of the glacial to postglacial transition in the Great Lakes region (14 000 – 11 000 years BP)
Authors: Panyushkina Irina P. , Leavitt Steven W.
Published: August 2013

Retreat of the Laurentide Ice Sheet 20 000 years ago tremendously altered environmental conditions and opened territory to the boreal spruce forest expansion. However, the details of forest colonization during the rapid climate warming and the adaptation of the newly developed stands to short cooling episodes during the warming and degradation of the ice sheet are not known. Preservation of wood from the glacial to postglacial transition offers the opportunity for examination of high-frequency growth variability in response to hemispheric and local forcings on temperature and hydrology. Here we consider growth of spruce at three sites from the interior of Northern America developed at ca. 13 700, 12 100, and 11 300 calibrated years before present (cal years BP), with well-replicated tree-ring chronologies spanning from 116 to 310 years. The data show at least two generations of trees established at each of the sites promoted by short, warm intervals. The tree mortality was variously affected by both cold conditions and the influence of rising water table and sediment burial. The history of these stands indicates breaks in forest colonization following a century (or two) of successful migrations. Interestingly, the thinning of the spruce forest did not seem to open pioneering opportunities for other tree species at those times.
SCHWARZSCHILD–DE SITTER METRIC AND INERTIAL BELTRAMI COORDINATES
Authors: SUN LI-FENG , YAN MU-LIN , DENG YA , HUANG WEI , HU SEN
Published: August 2013

Under consideration of coordinate conditions, we get the Schwarzschild–Beltrami–de Sitter (S-BdS) metric solution of the Einstein field equations with a cosmological constant Λ. A brief review to the de Sitter invariant special relativity (dS-SR), and de Sitter general relativity (dS-GR, or GR with a Λ) is presented. The Beltrami metric Bμν provides inertial reference frame for the dS-spacetime. By examining the Schwarzschild–de Sitter (S-dS) metric [Formula: see text] existed in literatures since 1918, we find that the existed S-dS metric [Formula: see text] describes some mixing effects of gravity and inertial-force, instead of a pure gravity effect arisen from "solar mass" M in dS-GR. In this paper, we solve the vacuum Einstein equation of dS-GR, with the requirement of gravity-free metric [Formula: see text]. In this way we find S-BdS solution of dS-GR, written in inertial Beltrami coordinates. This is a new form of S-dS metric. Its physical meaning and possible applications are discussed.
PHYSICAL UNCLONABLE FUNCTION HARDWARE KEYS UTILIZING KIRCHHOFF-LAW-JOHNSON-NOISE SECURE KEY EXCHANGE AND NOISE-BASED LOGIC
Authors: KISH LASZLO B. , KWAN CHIMAN
Published: August 2013

Weak unclonable function (PUF) encryption key means that the manufacturer of the hardware can clone the key but not anybody else. Strong unclonable function (PUF) encryption key means that even the manufacturer of the hardware is unable to clone the key. In this paper, first we introduce an "ultra" strong PUF with intrinsic dynamical randomness, which is not only unclonable but also gets renewed to an independent key (with fresh randomness) during each use via the unconditionally secure key exchange. The solution utilizes the Kirchhoff-law-Johnson-noise (KLJN) method for dynamical key renewal and a one-time-pad secure key for the challenge/response process. The secure key is stored in a flash memory on the chip to provide tamper-resistance and nonvolatile storage with zero power requirements in standby mode. Simplified PUF keys are shown: a strong PUF utilizing KLJN protocol during the first run and noise-based logic (NBL) hyperspace vector string verification method for the challenge/response during the rest of its life or until it is re-initialized. Finally, the simplest PUF utilizes NBL without KLJN thus it can be cloned by the manufacturer but not by anybody else.
INVESTMENT ADJUSTMENTS IN PRODUCT MARKET COMPETITION
Authors: SCHÜTTE TINO
Published: August 2013

Situated in the research field of market structure and strategic behavior, a model is developed, which shows the impacts of investment adjustments on product market competition. Placed in a multi-firm multi-product setting, the consequences of decisions to split budgets in: (i) marketing and development activities and (ii) development expenditures into innovative or imitative activities is investigated. The model is validated with empirical data of the pharmaceutical industry, especially the drug market in Germany. An agent-based modeling and simulation approach is used to explain how the freedom of firms to adjust their investment according to an absolute (individual aspiration level) or relative comparison (success of competitors) can change market performance. The results show that investment strategies adjusted to the behavior of direct competitors outperforms adjustments based on individual aspiration levels.
Incorporation of a tricationic subphthalocyanine in an organic photovoltaic device
Authors: Sánchez-Molina Irene , Soriano Alejandra , Claessens Christian G. , Torres Tomás , Bolink Henk J.
Published: August 2013

A new tricationic subphthalocyanine was synthesized and employed as light-harvesting and donor material in an ionic solid state organic photovoltaic cell. The incorporation of ionic dyes in organic photovoltaics aims to take advantage of ionic movement in order to enhance the charge transport properties of these materials. In this preliminary study, we report the results obtained in the fabrication of a partially solution-processed device with a cationic dye, where an effiency of 0.5% was reached.
Overlapping community detection in networks
Authors: Xie Jierui , Kelley Stephen , Szymanski Boleslaw K.
Published: August 2013

This article reviews the state-of-the-art in
overlapping
community detection algorithms, quality measures, and benchmarks. A thorough comparison of different algorithms (a total of fourteen) is provided. In addition to community-level evaluation, we propose a framework for evaluating algorithms' ability to detect overlapping nodes, which helps to assess overdetection and underdetection. After considering community-level detection performance measured by normalized mutual information, the Omega index, and node-level detection performance measured by F-score, we reached the following conclusions. For low overlapping density networks, SLPA, OSLOM, Game, and COPRA offer better performance than the other tested algorithms. For networks with high overlapping density and high overlapping diversity, both SLPA and Game provide relatively stable performance. However, test results also suggest that the detection in such networks is still not yet fully resolved. A common feature observed by various algorithms in real-world networks is the relatively small fraction of overlapping nodes (typically less than 30%), each of which belongs to only 2 or 3 communities.
Near-duplicate video retrieval
Authors: Liu Jiajun , Huang Zi , Cai Hongyun , Shen Heng Tao , Ngo Chong Wah , Wang Wei
Published: August 2013

The exponential growth of online videos, along with increasing user involvement in video-related activities, has been observed as a constant phenomenon during the last decade. User's time spent on video capturing, editing, uploading, searching, and viewing has boosted to an unprecedented level. The massive publishing and sharing of videos has given rise to the existence of an already large amount of near-duplicate content. This imposes urgent demands on near-duplicate video retrieval as a key role in novel tasks such as video search, video copyright protection, video recommendation, and many more. Driven by its significance, near-duplicate video retrieval has recently attracted a lot of attention. As discovered in recent works, latest improvements and progress in near-duplicate video retrieval, as well as related topics including low-level feature extraction, signature generation, and high-dimensional indexing, are employed to assist the process.

As we survey the works in near-duplicate video retrieval, we comparatively investigate existing variants of the definition of near-duplicate video, describe a generic framework, summarize state-of-the-art practices, and explore the emerging trends in this research topic.
A survey of trust in social networks
Authors: Sherchan Wanita , Nepal Surya , Paris Cecile
Published: August 2013

Web-based social networks have become popular as a medium for disseminating information and connecting like-minded people. The public accessibility of such networks with the ability to share opinions, thoughts, information, and experience offers great promise to enterprises and governments. In addition to individuals using such networks to connect to their friends and families, governments and enterprises have started exploiting these platforms for delivering their services to citizens and customers. However, the success of such attempts relies on the level of trust that members have with each other as well as with the service provider. Therefore, trust becomes an essential and important element of a successful social network. In this article, we present the first comprehensive review of social and computer science literature on trust in social networks. We first review the existing definitions of trust and define
social trust
in the context of social networks. We then discuss recent works addressing three aspects of social trust:
trust information collection
,
trust evaluation
, and
trust dissemination
. Finally, we compare and contrast the literature and identify areas for further research in social trust.
Separation of concerns in feature diagram languages
Authors: Hubaux Arnaud , Tun Thein Than , Heymans Patrick
Published: August 2013

The need for flexible customization of large feature-rich software systems, according to requirements of various stakeholders, has become an important problem in software development. Among the many software engineering approaches dealing with variability management, the notion of Software Product Line (SPL) has emerged as a major unifying concept. Drawing from established disciplines of manufacturing, SPL approaches aim to design repertoires of software artifacts, from which customized software systems for specific stakeholder requirements can be developed. A major difficulty SPL approaches attempt to address is the modularization of software artifacts, which reconciles the user's needs for certain features and the development and technical constraints. Towards this end, many SPL approaches use feature diagrams to describe possible configurations of a feature set. There have been several proposals for feature diagram languages with varying degrees of expressiveness, intuitiveness, and precision. However, these feature diagram languages have limited scalability when applied to realistic software systems. This article provides a systematic survey of various concerns of feature diagrams and ways in which concerns have been separated. The survey shows how the uncertainty in the purpose of feature diagram languages creates both conceptual and practical limitations to scalability of those languages.
State-based model slicing
Authors: Androutsopoulos Kelly , Clark David , Harman Mark , Krinke Jens , Tratt Laurence
Published: August 2013

Slicing is a technique, traditionally applied to programs, for extracting the parts of a program that affect the values computed at a statement of interest. In recent years authors have begun to consider slicing at model level. We present a detailed review of existing work on slicing at the level of finite-state-machine-based models. We focus on state-based modeling notations because these have received sufficient attention from the slicing community that there is now a coherent body of hitherto unsurveyed work. We also identify the challenges that state-based slicing presents and how the existing literature has addressed these. We conclude by identifying problems that remain open either because of the challenges involved in addressing them or because the community simply has yet to turn its attention to solving them.
Decentralized resource discovery mechanisms for distributed computing in peer-to-peer environments
Authors: Lazaro Daniel , Marques Joan Manuel , Jorba Josep , Vilajosana Xavier
Published: August 2013

Resource discovery is an important part of distributed computing and resource sharing systems, like grids and utility computing. Because of the increasing importance of decentralized and peer-to-peer environments, characterized by high dynamism and churn, a number of resource discovery mechanisms, mainly based on peer-to-peer techniques, have been presented recently. We present and classify them according to criteria like their topology and the degree of achievement of various common requirements of great importance for the targeted environments, as well as compare their reported performance. These classifications intend to provide an intuitive vision of the strengths and weaknesses of each system.
Digital library initiative
Authors: Tabet Myrna , Kanan Tarek , Alhoori Hamed , Lukesh Susan S. , Thompson Carole , Fox Edward A. , Samaka Mohammed
Published: August 2013

This article presents the first phase of an exciting initiative in the Arabian Gulf State of Qatar that brings together four academic institutions working to develop a digital library infrastructure of people, services, software, hardware, and content related to Qatar. Building on prior work on curricular resources developed for the digital library field and extending them to support Arabic as well as English instruction, educators, librarians, and IT specialists are working with content experts, stakeholders, students, and researchers to identify and preserve Qatar oriented digital library collections and information systems.
Efficient live migration of virtual machines using shared storage
Authors: Jo Changyeon , Gustafsson Erik , Son Jeongseok , Egger Bernhard
Published: August 2013

Live migration of virtual machines (VM) across distinct physical hosts is an important feature of virtualization technology for maintenance, load-balancing and energy reduction, especially so for data centers operators and cluster service providers. Several techniques have been proposed to reduce the downtime of the VM being transferred, often at the expense of the total migration time. In this work, we present a technique to reduce the total time required to migrate a running VM from one host to another while keeping the downtime to a minimum. Based on the observation that modern operating systems use the better part of the physical memory to cache data from secondary storage, our technique tracks the VM's I/O operations to the network-attached storage device and maintains an updated mapping of memory pages that currently reside in identical form on the storage device. During the iterative pre-copy live migration process, instead of transferring those pages from the source to the target host, the memory-to-disk mapping is sent to the target host which then fetches the contents directly from the network-attached storage device. We have implemented our approach into the Xen hypervisor and ran a series of experiments with Linux HVM guests. On average, the presented technique shows a reduction of up over 30% on average of the total transfer time for a series of benchmarks.
Performance potential of optimization phase selection during dynamic JIT compilation
Authors: Jantz Michael R. , Kulkarni Prasad A.
Published: August 2013

Phase selection is the process of customizing the applied set of compiler optimization phases for individual functions or programs to improve performance of generated code. Researchers have recently developed novel feature-vector based heuristic techniques to perform phase selection during online JIT compilation. While these heuristics improve program startup speed, steady-state performance was not seen to benefit over the default fixed single sequence baseline. Unfortunately, it is still not conclusively known whether this lack of steady-state performance gain is due to a failure of existing online phase selection heuristics, or because there is, indeed, little or no speedup to be gained by phase selection in online JIT environments. The goal of this work is to resolve this question, while examining the phase selection related behavior of optimizations, and assessing and improving the effectiveness of existing heuristic solutions.

We conduct experiments to find and understand the potency of the factors that can cause the phase selection problem in JIT compilers. Next, using long-running genetic algorithms we determine that program-wide and method-specific phase selection in the HotSpot JIT compiler can produce ideal steady-state performance gains of up to 15% (4.3% average) and 44% (6.2% average) respectively. We also find that existing state-of-the-art heuristic solutions are unable to realize these performance gains (in our experimental setup), discuss possible causes, and show that exploiting knowledge of optimization phase behavior can help improve such heuristic solutions. Our work develops a robust open-source production-quality framework using the HotSpot JVM to further explore this problem in the future.
Towards verifiable resource accounting for outsourced computation
Authors: Chen Chen , Maniatis Petros , Perrig Adrian , Vasudevan Amit , Sekar Vyas
Published: August 2013

Outsourced computation services should ideally only charge customers for the resources used by their applications. Unfortunately, no verifiable basis for service providers and customers to reconcile resource accounting exists today. This leads to undesirable outcomes for both providers and consumers-providers cannot prove to customers that they really devoted the resources charged, and customers cannot verify that their invoice maps to their actual usage. As a result, many practical and theoretical attacks exist, aimed at charging customers for resources that their applications did not consume. Moreover, providers cannot charge consumers precisely, which causes them to bear the cost of unaccounted resources or pass these costs inefficiently to their customers.

We introduce ALIBI, a first step toward a vision for verifiable resource accounting. ALIBI places a minimal, trusted reference monitor underneath the service provider's software platform. This monitor observes resource allocation to customers' guest virtual machines and reports those observations to customers, for verifiable reconciliation. In this paper, we show that ALIBI efficiently and verifiably tracks guests' memory use and CPU-cycle consumption.
Betweenness centrality
Authors: Prountzos Dimitrios , Pingali Keshav
Published: August 2013

Betweenness centrality is an important metric in the study of social networks, and several algorithms for computing this metric exist in the literature. This paper makes three contributions. First, we show that the problem of computing betweenness centrality can be formulated abstractly in terms of a small set of
operators
that update the graph. Second, we show that existing parallel algorithms for computing betweenness centrality can be viewed as implementations of different schedules for these operators, permitting all these algorithms to be formulated in a single framework. Third, we derive a new asynchronous parallel algorithm for betweenness centrality that (i) works seamlessly for both weighted and unweighted graphs, (ii) can be applied to large graphs, and (iii) is able to extract large amounts of parallelism. We implemented this algorithm and compared it against a number of publicly available implementations of previous algorithms on two different multicore architectures. Our results show that the new algorithm is the best performing one in most cases, particularly for large graphs and large thread counts, and is always competitive against other algorithms.
Ligra
Authors: Shun Julian , Blelloch Guy E.
Published: August 2013

There has been significant recent interest in parallel frameworks for processing graphs due to their applicability in studying social networks, the Web graph, networks in biology, and unstructured meshes in scientific simulation. Due to the desire to process large graphs, these systems have emphasized the ability to run on distributed memory machines. Today, however, a single multicore server can support more than a terabyte of memory, which can fit graphs with tens or even hundreds of billions of edges. Furthermore, for graph algorithms, shared-memory multicores are generally significantly more efficient on a per core, per dollar, and per joule basis than distributed memory systems, and shared-memory algorithms tend to be simpler than their distributed counterparts.

In this paper, we present a lightweight graph processing framework that is specific for shared-memory parallel/multicore machines, which makes graph traversal algorithms easy to write. The framework has two very simple routines, one for mapping over edges and one for mapping over vertices. Our routines can be applied to any subset of the vertices, which makes the framework useful for many graph traversal algorithms that operate on subsets of the vertices. Based on recent ideas used in a very fast algorithm for breadth-first search (BFS), our routines automatically adapt to the density of vertex sets. We implement several algorithms in this framework, including BFS, graph radii estimation, graph connectivity, betweenness centrality, PageRank and single-source shortest paths. Our algorithms expressed using this framework are very simple and concise, and perform almost as well as highly optimized code. Furthermore, they get good speedups on a 40-core machine and are significantly more efficient than previously reported results using graph frameworks on machines with many more cores.
Online-ABFT
Authors: Chen Zizhong
Published: August 2013

Soft errors are one-time events that corrupt the state of a computing system but not its overall functionality. Large supercomputers are especially susceptible to soft errors because of their large number of components. Soft errors can generally be detected offline through the comparison of the final computation results of two duplicated computations, but this approach often introduces significant overhead. This paper presents Online-ABFT, a simple but efficient online soft error detection technique that can detect soft errors in the widely used Krylov subspace iterative methods in the middle of the program execution so that the computation efficiency can be improved through the termination of the corrupted computation in a timely manner soon after a soft error occurs. Based on a simple verification of orthogonality and residual, Online-ABFT is easy to implement and highly efficient. Experimental results demonstrate that, when this online error detection approach is used together with checkpointing, it improves the time to obtain correct results by up to several orders of magnitude over the traditional offline approach.
Scheduling parallel programs by work stealing with private deques
Authors: Acar Umut A. , Chargueraud Arthur , Rainey Mike
Published: August 2013

Work stealing has proven to be an effective method for scheduling parallel programs on multicore computers. To achieve high performance, work stealing distributes tasks between concurrent queues, called deques, which are assigned to each processor. Each processor operates on its deque locally except when performing load balancing via steals. Unfortunately, concurrent deques suffer from two limitations: 1) local deque operations require expensive memory fences in modern weak-memory architectures, 2) they can be very difficult to extend to support various optimizations and flexible forms of task distribution strategies needed many applications, e.g., those that do not fit nicely into the divide-and-conquer, nested data parallel paradigm.

For these reasons, there has been a lot recent interest in implementations of work stealing with non-concurrent deques, where deques remain entirely private to each processor and load balancing is performed via message passing. Private deques eliminate the need for memory fences from local operations and enable the design and implementation of efficient techniques for reducing task-creation overheads and improving task distribution. These advantages, however, come at the cost of communication. It is not known whether work stealing with private deques enjoys the theoretical guarantees of concurrent deques and whether they can be effective in practice.

In this paper, we propose two work-stealing algorithms with private deques and prove that the algorithms guarantee similar theoretical bounds as work stealing with concurrent deques. For the analysis, we use a probabilistic model and consider a new parameter, the branching depth of the computation. We present an implementation of the algorithm as a C++ library and show that it compares well to Cilk on a range of benchmarks. Since our approach relies on private deques, it enables implementing flexible task creation and distribution strategies. As a specific example, we show how to implement task coalescing and steal-half strategies, which can be important in fine-grain, non-divide-and-conquer algorithms such as graph algorithms, and apply them to the depth-first-search problem.
ZOOMM
Authors: Cascaval Calin , Fowler Seth , Montesinos-Ortego Pablo , Piekarski Wayne , Reshadi Mehrdad , Robatmili Behnam , Weber Michael , Bhavsar Vrajesh
Published: August 2013

We explore the challenges in expressing and managing concurrency in browsers on mobile devices. Browsers are complex applications that implement multiple standards, need to support legacy behavior, and are highly dynamic and interactive. We present ZOOMM, a highly concurrent web browser engine prototype and show how concurrency is effectively exploited at different levels: speed up computation performance, preload network resources, and preprocess resources outside the critical path of page loading. On a dual-core Android mobile device we demonstrate that ZOOMM is two times faster than the native WebKit based browser when loading the set of pages defined in the Vellamo benchmark.
Control of FeAl Composition Produced by SPS Reactive Sintering from Mechanically Activated Powder Mixture
Authors: Paris S. , Gaffet E. , Bernard F.
Published: August 2013

The effects of mechanically activated powder mixture (Fe + Al) on the microstructure and the chemical composition of FeAl compound produced by reactive sintering implying an exothermic reaction were studied. Firstly, the characteristics of Fe/Al mechanically activated powder mixtures were investigated in terms of their phase composition and microstructure. The high‐energy milling allowed the formation of micrometric agglomerates composed of nanometric crystallites of iron and aluminum. Three aggregate sizes class A: ϕ < 125 µm, class B: 125 µm≤ϕ < 250 µm, and class C: ϕ ≥ 250 µm were considered. The latter class enhanced the reactivity of powder mixtures due to an increase of interfaces in contact as an analogy to nanostructured multilayer systems. Interrupted SPS experiments were performed on these mixtures to understand the origin of chemical heterogeneities observed after the reactive sintering. Formation of the intermediate phase Fe2Al5 at ~510°C was accompanied by an exothermic reaction and a linear expansion and followed by the formation of small amount of FeAl. The conversion to FeAl was complete at temperatures higher than the melting point of Fe2Al5 (1170°C). Finally, a phase evolution between Fe and Al versus the temperature during the reactive sintering is suggested.
Palmitoylethanolamide: A Natural Body-Own Anti-Inflammatory Agent, Effective and Safe against Influenza and Common Cold
Authors: Keppel Hesselink J. M. , de Boer Tineke , Witkamp Renger F.
Published: August 2013

Palmitoylethanolamide (PEA) is a food component known since 1957. PEA is synthesized and metabolized in animal cells via a number of enzymes and exerts a multitude of physiological functions related to metabolic homeostasis. Research on PEA has been conducted for more than 50 years, and over 350 papers are referenced in PubMed describing the physiological properties of this endogenous modulator and its pharmacological and therapeutical profile. The major focus of PEA research, since the work of the Nobel laureate Levi-Montalcini in 1993, has been neuropathic pain states and mast cell related disorders. However, it is less known that 6 clinical trials in a total of nearly 4000 people were performed and published last century, specifically studying PEA as a therapy for influenza and the common cold. This was done before Levi-Montalcini’s clarification of PEA’s mechanism of action, analyzing the role of PEA as an anti-inflammatory agent. We will review in depth these studies, as the results support the effectiveness and safety of PEA in flu and respiratory infections.
Anemia among HIV-Infected Patients Initiating Antiretroviral Therapy in South Africa: Improvement in Hemoglobin regardless of Degree of Immunosuppression and the Initiating ART Regimen
Authors: Takuva Simbarashe , Maskew Mhairi , Brennan Alana T. , Sanne Ian , MacPhail A. Patrick , Fox Mathew P.
Published: August 2013

Among those with HIV, anemia is a strong risk factor for disease progression and death independent of CD4 count and viral load. Understanding the role of anemia in HIV treatment is critical to developing strategies to reduce morbidity and mortality. We conducted a prospective analysis among 10,259 HIV-infected adults initiating first-line ART between April 2004 and August 2009 in Johannesburg, South Africa. The prevalence of anemia at ART initiation was 25.8%. Mean hemoglobin increased independent of baseline CD4. Females, lower BMI, WHO stage III/IV, lower CD4 count, and zidovudine use were associated with increased risk of developing anemia during follow-up. After initiation of ART, hemoglobin improved, regardless of regimen type and the degree of immunosuppression. Between 0 and 6 months on ART, the magnitude of hemoglobin increase was linearly related to CD4 count. However, between 6 and 24 months on ART, hemoglobin levels showed a sustained overall increase, the magnitude of which was similar regardless of baseline CD4 level. This increase in hemoglobin was seen even among patients on zidovudine containing regimens. Since low hemoglobin is an established adverse prognostic marker, prompt identification of anemia may result in improved morbidity and mortality of patients initiating ART.
Protective Effect of Egyptian Propolis against Rabbit Pasteurellosis
Authors: Nassar Somia A. , Mohamed Amira H. , Soufy Hamdy , Nasr Soad M.
Published: August 2013

The present study was conducted to study the protective effect of ethanolic extract of propolis given subcutaneously (S/C) either alone or in combination with inactivated formalizedPasteurella multocida(P. multocida) vaccine in rabbits challenged with virulentP. multocidastrain. Twenty-eight New-Zealand rabbits, 6–8 weeks old and not vaccinated against pasteurellosis, were randomly divided into four equal groups. Group (1) was kept as nonvaccinated control. Group (2) was injected S/C with propolis. Group (3) was vaccinated (S/C) withP. multocidavaccine only. Group (4) was injected with vaccine mixed with propolis as adjuvant. Groups (2, 3, and 4) received the same doses of propolis and vaccine after 4 weeks as a booster dose. The experiment continued for six weeks during which clinical signs, body weight, and mortality rate were recorded. Blood samples were collected every 2 weeks of treatment for evaluating the erythrogram and biochemical parameters. At the end of six weeks, all groups were subjected to challenge with a virulent strain ofP. multocida. Two weeks later, tissue specimens were collected from different organs for histopathological investigation. Results showed that before challenge all rabbits of different groups were apparently healthy and had good appetite. After challenge, control group (1) showed acute form of the disease, 100% mortality rate, and severe histopathological changes. Rabbits of groups (2 and 3) showed less severe clinical signs, mortality rate, and histopathological changes than control. Rabbits of group (4) were apparently healthy with normal histological picture. In conclusion, an ethanolic extract of propolis injected alone or combined with formalized inactivatedP. multocidavaccine improved general health conditions, liver and kidney functions in addition to reduction of the severity of adverse clinical signs, mortality rates, and histopathological changes associated with challenge of rabbits withP. multocidastrain.
Defining Product Lifecycle Management: A Journey across Features, Definitions, and Concepts
Authors: Corallo Angelo , Latino Maria Elena , Lazoi Mariangela , Lettera Serena , Marra Manuela , Verardi Sabrina
Published: August 2013

Product lifecycle management (PLM) has become more important in companies providing technologies and methodologies to manage data, information, and knowledge along the whole product lifecycle. In recent years, several authors have argued about PLM using a managerial or a technological view. The paper analyses these studies and integrates different author's points of view using focus groups, blogs, and face-to-face meetings in a university community of practice. Three sets of features (i.e., managerial, technological, and collaborative ones) have been used to review the existing definitions shared between academic and industrial ones and to propose an extended PLM definition describing its key concepts. The paper is a useful reference for managers and academics who want to have a clear and critical understanding of PLM using a unique source to collect lines of evidence on several PLM definitions, features, and concepts.
Radiometric Imaging for Monitoring and Surveillance Issues
Authors: Soldovieri Francesco , Natale Antonio , Gorishnyak Vladimir , Pavluchenko Andrey , Denisov Alexander , Chen Lijia
Published: August 2013

This paper deals with the recent advances performed by State Research Center “Iceberg” (SRC) in the field of the passive imaging at millimeter wavelengths. In particular, first the paper describes the design and the realization of two systems working in 3 mm and 8 mm wave bands, respectively. Second, the measurements collected by the two systems are enhanced by means of simple data processing strategies developed by the Institute for Electromagnetic Sensing of the Environment (IREA-CNR).