bluuebunny/crossref_metadata_2025 huggingface dataset:
Bacteremia Due to Extended-Spectrum-β-Lactamase-Producing Aeromonas spp. at a Medical Center in Southern Taiwan
Authors: Wu Chi-Jung , Chuang Yin-Ching , Lee Mei-Feng , Lee Chin-Chi , Lee Hsin-Chun , Lee Nan-Yao , Chang Chia-Ming , Chen Po-Lin , Lin Yu-Tzu , Yan Jing-Jou , Ko Wen-Chien
Published: October 2011

Although extended-spectrum-β-lactamase (ESBL)-producing aeromonads have been increasingly reported in recent years, most of them were isolates from case reports or environmental isolates. To investigate the prevalence of ESBL producers among
Aeromonas
blood isolates and the genes encoding ESBLs, consecutive nonduplicate
Aeromonas
blood isolates collected at a medical center in southern Taiwan from March 2004 to December 2008 were studied. The ESBL phenotypes were examined by clavulanate combination disk test and the cefepime-clavulanate ESBL Etest. The presence of ESBL-encoding genes, including
bla
TEM
,
bla
PER
,
bla
CTX-M
, and
bla
SHV
genes, was evaluated by PCR and sequence analysis. The results showed that 4 (2.6%) of 156
Aeromonas
blood isolates, 1
Aeromonas hydrophila
isolate and 3
Aeromonas caviae
isolates, expressed an ESBL-producing phenotype. The ESBL gene in two
A. caviae
isolates was
bla
PER-3
, which was located in both chromosomes and plasmids, as demonstrated by Southern hybridization. Of four patients with ESBL-producing
Aeromonas
bacteremia, two presented with catheter-related phlebitis and the other two with primary bacteremia. Three patients had been treated with initial noncarbapenem β-lactams for 5 to 10 days, and all survived. In conclusion, ESBL producers exist among
Aeromonas
blood isolates, and clinical suspicion of ESBL production should be raised in treating infections due to cefotaxime-resistant
Aeromonas
isolates.
Cyclopropyl Carboxamides, a Chemically Novel Class of Antimalarial Agents Identified in a Phenotypic Screen
Authors: Sanz Laura M. , Jiménez-Díaz M. Belen , Crespo Benigno , De-Cozar Cristina , Almela M. Jesus , Angulo-Barturen Iñigo , Castañeda Pablo , Ibañez Javier , Fernández Esther Pilar , Ferrer Santiago , Herreros Esperanza , Lozano Sonia , Martínez María Santos , Rueda Lourdes , Burrows Jeremy N. , García-Bustos Jose F. , Gamo Francisco-Javier
Published: October 2011

Malaria is one of the deadliest infectious diseases in the world, with the eukaryotic parasite
Plasmodium falciparum
causing the most severe form of the disease. Discovery of new classes of antimalarial drugs has become an urgent task to counteract the increasing problem of drug resistance. Screening directly for compounds able to inhibit parasite growth
in
vitro
is one of the main approaches the malaria research community is now pursuing for the identification of novel antimalarial drug leads. Very recently, thousands of compounds with potent activity against the parasite
P. falciparum
have been identified and information about their molecular descriptors, antiplasmodial potency, and cytotoxicity is publicly available. Now the challenges are how to identify the most promising chemotypes for further development and how best to progress these compounds through a lead optimization program to generate antimalarial drug candidates. We report here the first chemical series to be characterized from one of those screenings, a completely novel chemical class with the generic name cyclopropyl carboxamides that has never before been described as having antimalarial or other pharmacological activities. Cyclopropyl carboxamides are potent inhibitors of drug-sensitive and -resistant strains of
P. falciparum
in
vitro
and show
in
vivo
oral efficacy in malaria mouse models. In the present work, we describe the biological characterization of this chemical family, showing that inhibition of their still unknown target has very favorable pharmacological consequences but the compounds themselves seem to select for resistance at a high frequency.
First Face Composite-Tissue Transplant Recipient Successfully Treated for Cytomegalovirus Infection with Preemptive Valganciclovir Treatment
Authors: BenMarzouk-Hidalgo O. J. , Cordero E. , Gómez-Cía T. , Sánchez M. , González-Padilla J. D. , Infante-Cossio P. , Sicilia-Castro D. , Hernández-Guisado J. M. , Pérez-Romero P.
Published: October 2011

Little is known about cytomegalovirus (CMV) infection after face transplantation, since only two of the 11 cases of face transplantation reported worldwide have documented a CMV infection after transplantation. Herein, we present the first report of a composite-tissue face allotransplant recipient at high risk for CMV infection (D
+
/R
−
[CMV serpositive donor positive/CMV seronegative receptor]) undergoing preemptive treatment. Preemptive treatment was safe and effective for controlling CMV infection and thus promoting early acquisition of a CMV-specific immune response that protected the patient from late-onset CMV disease.
PhoQ Mutations Promote Lipid A Modification and Polymyxin Resistance of Pseudomonas aeruginosa Found in Colistin-Treated Cystic Fibrosis Patients
Authors: Miller Amanda K. , Brannon Mark K. , Stevens Laurel , Johansen Helle Krogh , Selgrade Sara E. , Miller Samuel I. , Høiby Niels , Moskowitz Samuel M.
Published: October 2011

Pseudomonas aeruginosa
can develop resistance to polymyxin and other cationic antimicrobial peptides. Previous work has shown that mutations in the PmrAB and PhoPQ regulatory systems can confer low to moderate levels of polymyxin resistance (MICs of 8 to 64 mg/liter) in laboratory and clinical strains of this organism. To explore the role of PhoPQ in high-level clinical polymyxin resistance,
P. aeruginosa
strains with colistin MICs > 512 mg/liter that had been isolated from cystic fibrosis patients treated with inhaled colistin (polymyxin E) were analyzed. Probable loss-of-function
phoQ
alleles found in these cystic fibrosis strains conferred resistance to polymyxin. Partial and complete suppressor mutations in
phoP
were identified in some cystic fibrosis strains with resistance-conferring
phoQ
mutations, suggesting that additional loci can be involved in polymyxin resistance in
P. aeruginosa
. Disruption of chromosomal
phoQ
in the presence of an intact
phoP
allele stimulated 4-amino-
l
-arabinose addition to lipid A and induced transcription from the promoter of the
pmrH
(
arnB
) operon, consistent with the known role of this lipid A modification in polymyxin resistance. These results indicate that
phoQ
loss-of-function mutations can contribute to high-level polymyxin resistance in clinical strains of
P. aeruginosa
.
Role of the Yersinia pestis Ail Protein in Preventing a Protective Polymorphonuclear Leukocyte Response during Bubonic Plague
Authors: Hinnebusch B. Joseph , Jarrett Clayton O. , Callison Julie A. , Gardner Donald , Buchanan Susan K. , Plano Gregory V.
Published: October 2011

The ability of
Yersinia pestis
to forestall the mammalian innate immune response is a fundamental aspect of plague pathogenesis. In this study, we examined the effect of Ail, a 17-kDa outer membrane protein that protects
Y. pestis
against complement-mediated lysis, on bubonic plague pathogenesis in mice and rats. The
Y. pestis ail
mutant was attenuated for virulence in both rodent models. The attenuation was greater in rats than in mice, which correlates with the ability of normal rat serum, but not mouse serum, to kill
ail
-negative
Y. pestis in vitro
. Intradermal infection with the
ail
mutant resulted in an atypical, subacute form of bubonic plague associated with extensive recruitment of polymorphonuclear leukocytes (PMN or neutrophils) to the site of infection in the draining lymph node and the formation of large purulent abscesses that contained the bacteria. Systemic spread and mortality were greatly attenuated, however, and a productive adaptive immune response was generated after high-dose challenge, as evidenced by high serum antibody levels against
Y. pestis
F1 antigen. The
Y. pestis
Ail protein is an important bubonic plague virulence factor that inhibits the innate immune response, in particular the recruitment of a protective PMN response to the infected lymph node.
Educational level and HIV disease progression before and after the introduction of HAART: a cohort study in 989 HIV seroconverters in Spain
Authors: Monge Susana , Jarrín Inmaculada , Pérez-Hoyos Santiago , Ferreros Inmaculada , García-Olalla Patricia , Muga Roberto , Del Romero Jorge , Belda Josefina , Castilla Jesús , Bolúmar Francisco , Del Amo Julia ,   on behalf of GEMES
Published: October 2011

Objectives

To analyse the effect of educational level on the progression from HIV seroconversion to highly active antiretroviral therapy (HAART) requirement, HAART initiation, AIDS and death from any cause at different periods of the HIV epidemic in Spain.

Methods

Open, prospective, multicentre cohort of HIV seroconverters set up in 1983. The risk of progression was calculated by the multiple decrements method. Effect of educational level was estimated by Fine and Gray model, adjusting for sex, HIV transmission category, age and method to estimate seroconversion. Calendar period was introduced as a variable that could change over time (<1997; 1997–2003; >2003).

Results

Up to 2009, 989 HIV seroconverters with information on educational level were identified. Some 52% and 48% had a low and a high educational level respectively. Persons with higher education had 32% lower risk of death (HR: 0.68; 95% CI 0.45 to 1.03). Regarding progression to AIDS, educational level had no effect in the pre-HAART era (HR: 1.47; 95% CI 0.91 to 2.38), but did show an effect in the period 1997–2003 (HR: 0.58; 95% CI 0.34 to 0.99), which was accentuated after 2004 (HR: 0.26; 95% CI 0.10 to 0.68). No difference was found in time to HAART requirement or initiation.

Conclusions

Results suggest that, despite similar access to HAART, persons with low educational level are at increased risk of HIV disease progression, highlighting the impact of social inequities on health. The availability of more effective treatments over time will strengthen the protective effect of higher education on the development of AIDS.
Prevalence and factors associated with HSV-2 and hepatitis B infections among truck drivers crossing the southern Brazilian border
Authors: Pinho Adriana A , Chinaglia Magda , Lippman Sheri A , Reingold Arthur , Diaz Ricardo Sobhie , Sucupira Maria Cecilia , Page Kimberly , Díaz Juan
Published: October 2011

Objectives

The authors estimate the prevalence of HIV, syphilis, hepatitis B virus (HBV) and herpes simplex virus type-2 (HSV-2) infection and correlates of HBV and HSV-2 infection among truck drivers crossing the southern Brazilian border at Foz do Iguaçu.

Methods

Between October 2003 and March 2005, 1945 truck drivers were sampled while accessing voluntary counselling and testing services; 1833 (94.2%) were tested for HIV (ELISA and confirmatory immunofluorescence assay) and syphilis (non-treponemal (VDRL) and treponemal tests (FTA-ABS)). From these, 799 stored sera were tested for HSV-2 (type-specific ELISA test for detection of IgG) and HBV (core antibodies (anti-HBc) with positives tested for surface antigen (HBsAg)). The authors estimate HIV, syphilis, HSV-2 and HBV prevalence and determine socio-demographic and behavioural correlates of HSV-2 infection and HBV exposure.

Results

HIV prevalence was 0.3% (95% CI 0.1 to 0.6) and syphilis 4.5% (95% CI 3.6 to 5.4). Among those tested for HBV and HSV-2, 32.3% (95% CI 28.9 to 35.6) had serological evidence of exposure to HBV and 26.6% (95% CI 23.5 to 29.7) tested positive for HSV-2. Factors independently associated with HBV exposure included increasing age, Brazilian nationality and unprotected anal sex. Increasing age and reporting an unknown number of lifetime partners were associated with HSV-2 infection.

Conclusions

In this sample of truck drivers in southern Brazil, HIV prevalence was lower than national population estimates; exposure to HBV was higher than population estimates, while per cent positive for HSV-2 was similar to population estimates. The low prevalence of HIV in truck drivers indicates prevention successes; however, future HIV prevention programming should incorporate HBV vaccination and sexually transmitted infection prevention.
CTCF, cohesin, and histone variants: connecting the genome
Authors: Millau Jean-François , Gaudreau Luc
Published: October 2011

During the last decades our view of the genome organization has changed. We moved from a linear view to a looped view of the genome. It is now well established that inter- and intra-connections occur between chromosomes and play a major role in gene regulations. These interconnections are mainly orchestrated by the CTCF protein, which is also known as the “master weaver” of the genome. Recent advances in sequencing and genome-wide studies revealed that CTCF binds to DNA at thousands of sites within the human genome, providing the possibility to form thousands of genomic connection hubs. Strikingly, two histone variants, namely H2A.Z and H3.3, strongly co-localize at CTCF binding sites. In this article, we will review the recent advances in CTCF biology and discuss the role of histone variants H2A.Z and H3.3 at CTCF binding sites.
Competition and coexistence among short-grass grazers in the Hluhluwe-iMfolozi Park, South Africa
Authors: Arsenault Randal , Owen-Smith Norman
Published: October 2011

Coexistence among grazing ungulates has been related to differences in grass height and grassland types selected, underlain by morphological distinctions. Nevertheless, resource competition may arise when smaller species depress grass height below that suitable for larger species, whereas competition may be counteracted by facilitation when larger species increase the extent of high-quality grassland available. We investigated resource-use overlap between white rhinoceros ( Ceratotherium simum (Burchell, 1817)), blue wildebeest ( Connochaetes taurinus (Burchell, 1823)), and Burchell’s zebra (Equus burchelli (Gray, 1824)) in the Hluhluwe-iMfolozi Park in South Africa. We recorded the grassland type favoured, grass species utilized, grass height grazed, and greenness selected during the dry seasons of 2 years. Blue wildebeest shifted their grazing away from lawn grassland in the drier year, whereas Burchell’s zebra favoured lawn grassland only in the relatively wet year. White rhinoceros concentrated their feeding on lawn grassland throughout the dry seasons of both years, and favoured shorter grass than the other two grazers. Species characterizing grazing lawns contributed relatively more to the grass used by white rhinoceros in the drier year. Resource competition was potentially ameliorated by widened availability of lawn grassland promoted by white rhinoceros grazing. This counterbalancing of feeding competition and habitat facilitation enables the coexistence of these grazers despite similar food requirements.
Arctic herbivore diet can be inferred from stable carbon and nitrogen isotopes in C3 plants, faeces, and wool
Authors: Kristensen D.K. , Kristensen E. , Forchhammer M.C. , Michelsen A. , Schmidt N.M.
Published: October 2011

The use of stable isotopes in diet analysis usually relies on the different photosynthetic pathways of C3 and C4 plants, and the resulting difference in carbon isotope signature. In the Arctic, however, plant species are exclusively C3, and carbon isotopes alone are therefore not suitable for studying arctic herbivore diets. In this study, we examined the potential of both stable carbon and nitrogen isotopes to reconstruct the diet of an arctic herbivore, here the muskox ( Ovibos moschatus (Zimmermann, 1780)), in northeast Greenland. The isotope composition of plant communities and functional plant groups was compared with those of muskox faeces and shed wool, as this is a noninvasive approach to obtain dietary information on different temporal scales. Plants with different root mycorrhizal status were found to have different δ15N values, whereas differences in δ13C, as expected, were less distinct. As a result, our examination mainly relied on stable nitrogen isotopes. The interpretation of stable isotopes from faeces was difficult because of the large uncertainty in diet–faeces fractionation, whereas isotope signatures from wool suggested that the muskox summer diet consists of around 80% graminoids and up to 20% willows. In conclusion, the diet composition of an arctic herbivore can indeed be inferred from stable isotopes in arctic areas, despite the lack of C4 plants.
Compact data structure and scalable algorithms for the sparse grid technique
Authors: Murarasu Alin , Weidendorfer Josef , Buse Gerrit , Butnaru Daniel , Pflüger Dirk
Published: October 2011

The sparse grid discretization technique enables a compressed representation of higher-dimensional functions. In its original form, it relies heavily on recursion and complex data structures, thus being far from well-suited for GPUs. In this paper, we describe optimizations that enable us to implement compression and decompression, the crucial sparse grid algorithms for our application, on Nvidia GPUs. The main idea consists of a bijective mapping between the set of points in a multi-dimensional sparse grid and a set of consecutive natural numbers. The resulting data structure consumes a minimum amount of memory. For a 10-dimensional sparse grid with approximately 127 million points, it consumes up to 30 times less memory than trees or hash tables which are typically used. Compared to a sequential CPU implementation, the speedups achieved on GPU are up to 17 for compression and up to 70 for decompression, respectively. We show that the optimizations are also applicable to multicore CPUs.
Cooperative reasoning for preemptive execution
Authors: Yi Jaeheon , Sadowski Caitlin , Flanagan Cormac
Published: October 2011

We propose a cooperative methodology for multithreaded software, where threads use traditional synchronization idioms such as locks, but additionally document each point of potential thread interference with a "yield" annotation. Under this methodology, code between two successive yield annotations forms a serializable transaction that is amenable to sequential reasoning. This methodology reduces the burden of reasoning about thread interleavings by indicating only those interference points that matter. We present experimental results showing that very few yield annotations are required, typically one or two per thousand lines of code. We also present dynamic analysis algorithms for detecting cooperability violations, where thread interference is not documented by a yield, and for yield annotation inference for legacy software.
Transaction communicators
Authors: Luchangco Victor , Marathe Virendra J.
Published: October 2011

In this paper, we propose to extend transactional memory with
transaction communicators
, special objects through which concurrent transactions can communicate: changes by one transaction to a communicator can be seen by concurrent transactions before the first transaction commits. Although isolation of transactions is compromised by such communication, we constrain the effects of this compromise by tracking dependencies among transactions, and preventing any transaction from committing unless every transaction whose changes it saw also commits. In particular, mutually dependent transactions must commit or abort together, and transactions that do not communicate remain isolated. To help programmers synchronize accesses to communicators, we also provide special
communicator-isolating transactions
, which ensure isolation even for accesses to communicators. We propose language features to help programmers express the communicator constructs. We implemented a novel communicators-enabled STM runtime in the Maxine VM. Our preliminary evaluation demonstrates that communicators can be used in diverse settings to improve the performance of transactional programs, and to empower programmers with the ability to safely express within transactions important programming idioms that fundamentally require compromise of transaction isolation (e.g., CSP-style synchronous communication).
Lock-free and scalable multi-version software transactional memory
Authors: Fernandes Sérgio Miguel , Cachopo João
Published: October 2011

Software Transactional Memory (STM) was initially proposed as a lock-free mechanism for concurrency control. Early implementations had efficiency limitations, and soon obstruction-free proposals appeared, to tackle this problem, often simplifying STM implementation. Today, most of the modern and top-performing STMs use blocking designs, relying on locks to ensure an atomic commit operation. This approach has revealed better in practice, in part due to its simplicity. Yet, it may have scalability problems when we move into many-core computers, requiring fine-tuning and careful programming to avoid contention. In this paper we present and discuss the modifications we made to a lock-based multi-version STM in Java, to turn it into a lock-free implementation that we have tested to scale at least up to 192 cores, and which provides results that compete with, and sometimes exceed, some of today's top-performing lock-based implementations. The new lock-free commit algorithm allows write transactions to proceed in parallel, by allowing them to run their validation phase independently of each other, and by resorting to helping from threads that would otherwise be waiting to commit, during the write-back phase. We also present a new garbage collection algorithm to dispose of old unused object versions that allows for asynchronous identification of unnecessary versions, which minimizes its interference with the rest of the transactional system.
The STAPL parallel container framework
Authors: Tanase Gabriel , Buss Antal , Fidel Adam , Harshvardhan  , Papadopoulos Ioannis , Pearce Olga , Smith Timmie , Thomas Nathan , Xu Xiabing , Mourad Nedal , Vu Jeremy , Bianco Mauro , Amato Nancy M. , Rauchwerger Lawrence
Published: October 2011

The Standard Template Adaptive Parallel Library (STAPL) is a parallel programming infrastructure that extends C++ with support for parallelism. It includes a collection of distributed data structures called pContainers that are thread-safe, concurrent objects, i.e., shared objects that provide parallel methods that can be invoked concurrently. In this work, we present the STAPL Parallel Container Framework (PCF), that is designed to facilitate the development of generic parallel containers. We introduce a set of concepts and a methodology for assembling a pContainer from existing sequential or parallel containers, without requiring the programmer to deal with concurrency or data distribution issues. The PCF provides a large number of basic parallel data structures (e.g., pArray, pList, pVector, pMatrix, pGraph, pMap, pSet). The PCF provides a class hierarchy and a composition mechanism that allows users to extend and customize the current container base for improved application expressivity and performance. We evaluate STAPL pContainer performance on a CRAY XT4 massively parallel system and show that pContainer methods, generic pAlgorithms, and different applications provide good scalability on more than 16,000 processors.
QoS aware storage cache management in multi-server environments
Authors: Prabhakar Ramya , Srikantaiah Shekhar , Garg Rajat , Kandemir Mahmut
Published: October 2011

In this paper, we propose a novel two-step approach to the management of the storage caches to provide predictable performance in multi-server storage architectures: (1) An adaptive QoS decomposition and optimization step uses max-flow algorithm to determine the best decomposition of application-level QoS to sub-QoSs such that the application performance is optimized, and (2) A storage cache allocation step uses feedback control theory to allocate shared storage cache space such that the specified QoSs are satisfied throughout the execution.
Time skewing made simple
Authors: Strzodka Robert , Shaheen Mohammed , Pajak Dawid
Published: October 2011

Time skewing and loop tiling has been known for a long time to be a highly beneficial acceleration technique for nested loops especially on bandwidth hungry multi-core processors, but it is little used in practice because efficient implementations utilize complicated code and simple or abstract ones show much smaller gains over naive nested loops. We break this dilemma with an essential time skewing scheme that is both compact and fast.
Active pebbles
Authors: Willcock Jeremiah James , Hoefler Torsten , Edmonds Nicholas Gerard , Lumsdaine Andrew
Published: October 2011

A variety of programming models exist to support large-scale, distributed memory, parallel computation. These programming models have historically targeted coarse-grained applications with natural locality such as those found in a variety of scientific simulations of the physical world. Fine-grained, irregular, and unstructured applications such as those found in biology, social network analysis, and graph theory are less well supported. We propose Active Pebbles, a programming model which allows these applications to be expressed naturally; an accompanying execution model ensures performance and scalability.
Symbolically modeling concurrent MCAPI executions
Authors: Fischer Topher , Mercer Eric , Rungta Neha
Published: October 2011

Improper use of Inter-Process Communication (IPC) within concurrent systems often creates data races which can lead to bugs that are challenging to discover. Techniques that use Satisfiability Modulo Theories (SMT) problems to symbolically model possible executions of concurrent software have recently been proposed for use in the formal verification of software. In this work we describe a new technique for modeling executions of concurrent software that use a message passing API called MCAPI. Our technique uses an execution trace to create an SMT problem that symbolically models all possible concurrent executions and follows the same sequence of conditional branch outcomes as the provided execution trace. We check if there exists a satisfying assignment to the SMT problem with respect to specific safety properties. If such an assignment exists, it provides the conditions that lead to the violation of the property. We show how our method models behaviors of MCAPI applications that are ignored in previously published techniques.
SCRATCH
Authors: Donaldson Alastair F. , Kroening Daniel , Ruemmer Philipp
Published: October 2011

We present the SCRATCH tool, which uses bounded model checking and k-induction to automatically analyse software for multicore processors such as the Cell BE, in order to detect DMA races.
Automatic safety proofs for asynchronous memory operations
Authors: Botincan Matko , Dodds Mike , Donaldson Alastair F. , Parkinson Matthew J.
Published: October 2011

We present a work-in-progress proof system and tool, based on separation logic, for analysing memory safety of multicore programs that use asynchronous memory operations.
Timing analysis for a composable mode switch
Authors: Hang Yin , Hansson Hans
Published: October 2011

Component based software development (CBD) reduces development time and effort by allowing systems to be built from pre-developed reusable components. A classical approach to reduce embedded systems design and run-time complexity is to partition the behavior into a set of major system modes. In supporting system modes in CBD, a key issue is seamless composition of multi-mode components into systems.

In addressing this issue, we have developed a mode switch logic and algorithm for component-based multi-mode systems. In this paper we introduce timing analysis for our composable mode switch.
Provably good task assignment on heterogeneous multiprocessor platforms for a restricted case but with a stronger adversary
Authors: Raravi Gurulingesh , Andersson Björn , Bletsas Konstantinos
Published: October 2011

Consider the problem of scheduling a set of implicit-deadline sporadic tasks to meet all deadlines on a heterogeneous multiprocessor platform. We consider a restricted case where the maximum utilization of any task on any processor in the system is no greater than one. We use an algorithm proposed in [1] (we refer to it as LP-EE) from state-of-the-art for assigning tasks to heterogeneous multi-processor platform and (re-)prove its performance guarantee for this restricted case but for a stronger adversary. We show that if a task set can be scheduled to meet deadlines on a heterogeneous multiprocessor platform by an optimal task assignment scheme that allows task migrations then LP-EE meets deadlines as well with no migrations if given processors twice as fast.
Tracing event chains for holistic response-time analysis of component-based distributed real-time systems
Authors: Mubeen Saad , Mäki-Turja Jukka , Sjödin Mikael
Published: October 2011

In this paper we discuss the problem of tracing event chains (distributed transactions) while extracting an end-to-end timing model from an existing industrial component model, the Rubus Component Model (RCM). RCM supports component-based development of distributed embedded and real-time systems. The purpose of extracting an end-to-end timing model is to perform the holistic response-time analysis of component-based distributed real-time applications modeled with RCM. We present a solution for RCM by introducing special purpose generic components to it. We believe that the solution is also suitable for other component models that use a pipe-and-filter style for component interconnection.
CSE week wants you
Authors: Richardson Debra , Farmer Ruthe , Wilson Cameron
Published: October 2011

Computer Science Education Week (CSEdWeek) is rapidly approaching - December 4--10 2011 - held during the week of Grace Hopper's birthday, December 9, 1906. CSEdWeek is a call to action to raise awareness about computing's societal impact, the richness of computing careers, and the critical need for computer science education. CSEdWeek's goal is to inspire students about this important field, motivate teachers to employ new and better ways to engage students, and provide the public a better understanding of the need for computer science education. CSEdWeek 2010 was a smashing success with over 300 events and activities engaging students, parents, teachers and the computing community around the world. But let's not rehash last year. Rather we're asking how you'll support CSEdWeek 2011?
Learning-based visual saliency computation
Authors: Li Jia
Published: October 2011

With the rapid development of Internet, the amounts of images and videos are now growing explosively, leading to many new challenges on image/video processing. On one hand, the processing capability of computer is limited and the computational resource should be allocated to the important visual information with high priorities. On the other hand, the analysis results given by computer should be consistent with human cognition. To solve these two problems, this thesis will focus on learning-based visual saliency computation and the main objective can be described as predicting, locating and mining the important visual information that is consistent with human cognition. The main contributions of this thesis can be summarized as follows:

Firstly, this thesis presents a probabilistic multi-task learning approach for computing visual saliency by simultaneously integrating the bottom-up and topdown factors. To the best of our knowledge, it is the first approach that explores the problem of visual saliency computation with the multi-task learning algorithm. In our approach, the bottom-up and the top-down factors are considered simultaneously in a probabilistic framework. In this framework, a bottom-up component simulates the low-level processes in human vision system using multi-scale wavelet decomposition; while a top-down component simulates the high-level processes to bias the competition of the input visual stimuli. Moreover, we propose a multi-task learning algorithm to optimize the models and model fusion strategies for various scenes. Extensive experiments on several datasets show that this approach demonstrates high robustness and effectiveness in computing visual saliency.
An architecture for federated video processing and online streaming
Authors: Iqbal Razib
Published: October 2011

Today access to video is available via numerous multimedia enabled devices through a wide variety of network types. What is required is a mechanism to ensure that users can receive different qualities of video proportional to their device capabilities and network conditions. In this thesis, we propose an online adaptive video streaming approach which uses the Peer-to-Peer (P2P) paradigm to not only distribute the content using peers' bandwidth, but also adapt the video using peers' processing power, while taking into account receiver heterogeneity, watermarking, and perceptual encryption.
Postmortem Debugging in Dynamic Environments
Authors: Pacheco David
Published: October 2011

Despite the best efforts of software engineers to produce high-quality software, inevitably some bugs escape even the most rigorous testing process and are first encountered by end users. When this happens, such failures must be understood quickly, the underlying bugs fixed, and deployments patched to avoid another user (or the same one) running into the same problem again. As far back as 1951, the dawn of modern computing, Stanley Gill wrote that "some attention has, therefore, been given to the problem of dealing with mistakes after the programme has been tried and found to fail." Gill went on to describe the first use of "the post-mortem technique" in software, whereby the running program was modified to record important system state as it ran so that the programmer could later understand what happened and why the software failed.
The Course of Fatigue during the First 18 Months after First-Ever Stroke: A Longitudinal Study
Authors: Lerdal Anners , Lee Kathryn A. , Bakken Linda N. , Finset Arnstein , Kim Hesook Suzie
Published: October 2011

Background. Little is known about the course of poststroke fatigue.Objectives. To describe the course of poststroke fatigue in relation to the patient's level of physical functioning, depressive symptoms, and self-reported history of prestroke fatigue.Methods. A longitudinal study using structured face-to-face interviews, questionnaires, and patients' medical records. Data were collected from 95 patients in Norway with first-ever stroke. Fatigue was measured with the Fatigue Severity Scale 7 item version and assessed for change between the acute phase, six, 12, and 18 months after stroke using 2-way ANOVA repeated-measures analyses.Results. The patients' level of fatigue did not change over time. However, those who reported prestroke fatigue showed a relatively high level of fatigue over time in the poststroke period, while patients with no history of pre-stroke fatigue showed a stable course of relatively low fatigue over time.Conclusion. Studies on poststroke fatigue should control for the patient's pre-stroke fatigue level.
Alu in Lynch Syndrome: A Danger SINE?
Authors: Hitchins Megan P. , Burn John
Published: October 2011

Lynch syndrome is a hereditary cancer predisposition syndrome caused by germline loss of a DNA mismatch repair gene. In a significant proportion of cases, loss of function of the MSH2 mismatch repair gene is caused by large heterogeneous deletions involving MSH2 and/or the adjacent EPCAM gene. These deletions usually result from homologous malrecombination events between Alu elements, a family of short interspersed nuclear elements (SINE). Recent recognition that the extent of these deletions influences phenotypic outcome provided new impetus for fine-mapping the breakpoints. In doing so, Pérez-Cabornero and colleagues uncovered new evidence for Alu-mediated ancestral founder deletions within MSH2 in the Spanish Lynch syndrome population (as reported beginning on pages 1546 and 1556 in this issue of the journal). This is the first such finding to date and prompted a revisitation of the role of Alu elements in the causation of Lynch syndrome. Whether Alu density is a danger sign for genomic regions prone to rearrangement and what additional factors may be required to actuate these events remain to be discovered. Cancer Prev Res; 4(10); 1527–30. ©2011 AACR.
Molecular Imaging of Inflammation and Carcinogenesis
Authors: Ostrov David A. , Contag Christopher H.
Published: October 2011

Development of imaging agents that can be used broadly for early detection of neoplasia at various tissue sites and at various stages of disease and that also can assess states of minimal residual disease would have tremendous utility in the diagnosis and management of cancer. In a series of articles culminating with a report in this issue of the journal (beginning on page 1536), Uddin and colleagues show their ability to systemically target the enzyme COX-2 with imaging probes that will serve as agents for early detection, risk assessment, prognosis, and intervention outcome measures. These probes will enable the detection and localization of regions of inflammation and a wide variety of premalignant lesions and cancers, with utility in monitoring the effects of cancer prevention and therapy. Cancer Prev Res; 4(10); 1523–6. ©2011 AACR.
Integrated Brain Diversification along the Early Neuraxes
Authors: Sylvester Jonathan B. , Pottin Karen , Streelman J. Todd
Published: October 2011

Brains develop under the influence of signaling centers that link major dorsal/ventral (DV) and anterior/posterior (AP) axes. Over ontogeny, these ‘developmental neuraxes’ progress from near global signaling gradients into more localized gene expression domains separated by molecular boundaries. Therefore, developmental changes along a neuraxis can have major consequences across the brain, or more precise effects on a specific structure, depending upon the time during ontogeny in which change occurs. It is well known from mammalian systems how evolution has acted later in development, via differential neurogenesis, to reshape the cortex. Recent studies in fishes show how early changes in DV and AP patterning result in divergence of integrated brain regions that ultimately define visual versus olfactory ecotypes. We explore the generality of this trend and suggest that such early developmental differences integrating brain diversification along the neuraxes may be a common theme in vertebrates. Early differences in brain patterning among species imply that adult variation in sensory function and behavior manifests in the embryo.
The Quality of Applied Bone Cement Depends on the Chemical Composition of the Application System
Authors: Proschek D. , Kafchitsas K. , Kurth A.A. , Mattyasovszky S.G. , Betz S. , Ludwig H.R. , Mack M.G.
Published: October 2011

The exothermal reaction of polymethylmethacrylate leads to an extensive interaction between bone cement and the synthetic material of the application system. This chemical reaction changes the structure of the cement and might generate air inclusions. Methods and Materials: Two application systems for bone cement made of polycarbonate (PC) and polypropylene (PP) were evaluated. The application systems were mounted in a testing unit. The testing device injects a defined amount of bone cement with a certain pressure. After the injection procedure a microscopic examination was carried out. Results: There were no differences in the size and the design of the used syringes. Forty procedures were carried out. The time frame for application of the cement was 5 min in the PC group and 9 min in the PP group. There was a remarkable interaction between the plastics and the cement with the appearance of numerous air inclusions in the PC group. Barely any interaction was found in the PP group. Conclusion: Application systems made of PP enable a prolonged application time and a reduced number of air inclusions. Further research, especially on a molecular level as well as material tests on the quality of the applied bone cement, should be carried out.
Amelioration of Albuminuria in ROCK1 Knockout Mice with Streptozotocin-Induced Diabetic Kidney Disease
Authors: Zhou Li , Liu Fei , Huang Xiao R. , Liu Fang , Chen Haiyong , Chung Arther C.K. , Shi Jianjian , Wei Lei , Lan Hui Y. , Fu Ping
Published: October 2011

Background: Although blockade of Rho kinase with pharmacologic inhibitors ameliorates renal fibrosis and diabetic kidney disease (DKD), the underlined mechanisms remain largely unclear. The present study tested the hypothesis that ROCK1 may regulate the early development of albuminuria via the megalin/cubilin-dependent mechanism. Methods: A DKD model was induced in ROCK1 knockout and wild-type mice by streptozotocin (STZ). The effect of deleted ROCK1 on urinary albumin excretion and the expression of megalin/cubilin were examined. In addition, the effect of blocking ROCK activities with an inhibitor (Y-27632) on tubular albumin reabsorption was tested in a normal rat tubular epithelial cell line (NRK52E) under high-glucose conditions. Expression of transforming growth factor (TGF)-β1, interleukin-1β and collagen-1 was also been examined. Results: Urinary albumin excretion was significantly increased in ROCK1 WT mice at 8 weeks after STZ injection. In contrast, mice lacking ROCK1 gene were protected against the development of albuminuria. This was associated with the protection against the loss of megalin/cubilin and an increase in TGF-β1, IL-1β, and fibrosis in the kidney. In vitro, we also found that blockade of Rho kinase with inhibitor Y-27632 prevented high-glucose-induced loss of megalin expression and an increase of TGF-β1, thereby increasing the absorption rate of FITC-labeled albumin by tubular epithelial cells. Conclusion: ROCK1 may play a role in the development of albuminuria in DKD by downregulating the endocytosis receptors complex – megalin/cubilin.
Chronic Thromboembolic Pulmonary Hypertension (CTEPH)
Authors: Pepke-Zaba Joanna , Delcroix Marion , Lang Irene , Mayer Eckhard , Jansa Pavel , Ambroz David , Treacy Carmen , D'Armini Andrea M. , Morsolini Marco , Snijder Repke , Bresser Paul , Torbicki Adam , Kristensen Bent , Lewczuk Jerzy , Simkova Iveta , Barberà Joan A. , de Perrot Marc , Hoeper Marius M. , Gaine Sean , Speich Rudolf , Gomez-Sanchez Miguel A. , Kovacs Gabor , Hamid Abdul Monem , Jaïs Xavier , Simonneau Gérald
Published: October 2011

Background—

Chronic thromboembolic pulmonary hypertension (CTEPH) is often a sequel of venous thromboembolism with fatal natural history; however, many cases can be cured by pulmonary endarterectomy. The clinical characteristics and current management of patients enrolled in an international CTEPH registry was investigated.

Methods and Results—

The international registry included 679 newly diagnosed (≤6 months) consecutive patients with CTEPH, from February 2007 until January 2009. Diagnosis was confirmed by right heart catheterization, ventilation-perfusion lung scintigraphy, computerized tomography, and/or pulmonary angiography. At diagnosis, a median of 14.1 months had passed since first symptoms; 427 patients (62.9%) were considered operable, 247 (36.4%) nonoperable, and 5 (0.7%) had no operability data; 386 patients (56.8%, ranging from 12.0%– 60.9% across countries) underwent surgery. Operable patients did not differ from nonoperable patients relative to symptoms, New York Heart Association class, and hemodynamics. A history of acute pulmonary embolism was reported for 74.8% of patients (77.5% operable, 70.0% nonoperable). Associated conditions included thrombophilic disorder in 31.9% (37.1% operable, 23.5% nonoperable) and splenectomy in 3.4% of patients (1.9% operable, 5.7% nonoperable). At the time of CTEPH diagnosis, 37.7% of patients initiated at least 1 pulmonary arterial hypertension–targeted therapy (28.3% operable, 53.8% nonoperable). Pulmonary endarterectomy was performed with a 4.7% documented mortality rate.

Conclusions—

Despite similarities in clinical presentation, operable and nonoperable CTEPH patients may have distinct associated medical conditions. Operability rates vary considerably across countries, and a substantial number of patients (operable and nonoperable) receive off-label pulmonary arterial hypertension–targeted treatments.
Urokinase-Type Plasminogen Activator Promotes Paracellular Transmigration of Neutrophils Via Mac-1, But Independently of Urokinase-Type Plasminogen Activator Receptor
Authors: Reichel Christoph A. , Uhl Bernd , Lerchenberger Max , Puhr-Westerheide Daniel , Rehberg Markus , Liebl Johanna , Khandoga Andrej , Schmalix Wolfgang , Zahler Stefan , Deindl Elisabeth , Lorenzl Stefan , Declerck Paul J. , Kanse Sandip , Krombach Fritz
Published: October 2011

Background—

Urokinase-type plasminogen activator (uPA) has recently been implicated in the pathogenesis of ischemia-reperfusion (I/R) injury. The underlying mechanisms remain largely unclear.

Methods and Results—

Using in vivo microscopy on the mouse cremaster muscle, I/R-elicited firm adherence and transmigration of neutrophils were found to be significantly diminished in uPA-deficient mice and in mice treated with the uPA inhibitor WX-340, but not in uPA receptor (uPAR)–deficient mice. Interestingly, postischemic leukocyte responses were significantly reduced on blockade of the integrin CD11b/Mac-1, which also serves as uPAR receptor. Using a cell transfer technique, postischemic adherence and transmigration of wild-type leukocytes were significantly decreased in uPA-deficient animals, whereas uPA-deficient leukocytes exhibited a selectively reduced transmigration in wild-type animals. On I/R or stimulation with recombinant uPA, >90% of firmly adherent leukocytes colocalized with CD31-immunoreactive endothelial junctions as detected by in vivo fluorescence microscopy. In a model of hepatic I/R, treatment with WX-340 significantly attenuated postischemic neutrophil infiltration and tissue injury.

Conclusions—

Our data suggest that endothelial uPA promotes intravascular adherence, whereas leukocyte uPA facilitates the subsequent paracellular transmigration of neutrophils during I/R. This process is regulated via CD11b/Mac-1, and does not require uPAR. Pharmacological blockade of uPA interferes with these events and effectively attenuates postischemic tissue injury.