bluuebunny/crossref_metadata_2025 huggingface dataset:
Polyethylenimine Is a Strong Inhibitor of Human Papillomavirus and Cytomegalovirus Infection
Authors: Spoden Gilles A. , Besold Katrin , Krauter Steffi , Plachter Bodo , Hanik Nils , Kilbinger Andreas F. M. , Lambert Carsten , Florin Luise
Published: October 2011

Polyethylenimines are cationic polymers with potential as delivery vectors in gene therapy and with proven antimicrobial activity. However, the antiviral activity of polyethylenimines has not been addressed in detail thus far. We have studied the inhibitory effects of a linear 25-kDa polyethylenimine on infections with human papillomaviruses and human cytomegaloviruses. Preincubation of cells with polyethylenimine blocked primary attachment of both viruses to cells, resulting in a significant reduction of infection. In addition, the dissemination of human cytomegalovirus in culture cells was efficiently reduced by recurrent administration of polyethylenimine. Polyethylenimine concentrations required for inhibition of human papillomavirus and cytomegalovirus did not cause any cytotoxic effects. Polyethylenimines and their derivatives may thus be attractive molecules for the development of antiviral microbicides.
Relationship of
agr
Expression and Function with Virulence and Vancomycin Treatment Outcomes in Experimental Endocarditis Due to Methicillin-Resistant Staphylococcus aureus
Authors: Seidl Kati , Chen Liang , Bayer Arnold S. , Hady Wessam Abdel , Kreiswirth Barry N. , Xiong Yan Q.
Published: October 2011

The accessory gene regulator (
agr
) locus has been shown to be important for virulence in several animal models of
Staphylococcus
aureus
infection. However, the role of
agr
in human infections, and specifically in antibiotic treatment, is controversial. Interestingly,
agr
dysfunction has been associated with reduced vancomycin responses. To systematically investigate the role of
agr
in virulence and treatment outcome in the context of endovascular infection, 10 well-characterized vancomycin-susceptible methicillin-resistant
S. aureus
(MRSA) bloodstream isolates (5
agr-I
[clonal complex 45, or CC45] and 5
agr-II
[CC5]) were studied for (i)
agr
function, (ii) RNAIII transcriptional profiles, (iii)
agr
locus sequences, (iv) intrinsic virulence and responses to vancomycin therapy in an experimental infective endocarditis (IE) model, and (v)
in vivo
RNAIII expression. Significant differences in
agr
function (determined by delta-hemolysin activity) correlated with the time point of RNAIII transcription (earlier RNAIII onset equals increased
agr
function). Unexpectedly, four MRSA strains with strong delta-hemolysin activities exhibited significant resistance to vancomycin treatment in experimental IE. In contrast, five of six MRSA strains with weak or no delta-hemolysin activity were highly susceptible to vancomycin therapy in the IE model.
agr
sequence analyses showed no common single-nucleotide polymorphism predictive of
agr
functionality.
In vivo
RNAIII expression in cardiac vegetations did not correlate with virulence or vancomycin treatment outcomes in the IE model. Inactivation of
agr
in two strains with strong delta-hemolysin activity did not affect virulence or the
in vivo
efficacy of vancomycin. Our findings suggest that
agr
dysfunction does not correlate with vancomycin treatment failures in this experimental IE model in two distinct MRSA genetic backgrounds.
Triple-Combination Antiviral Drug for Pandemic H1N1 Influenza Virus Infection in Critically Ill Patients on Mechanical Ventilation
Authors: Kim Won-Young , Young Suh Gee , Huh Jin Won , Kim Sung-Han , Kim Min-ju , Kim Yun Seong , Kim Hye-Ryoun , Ryu Yon Ju , Han Min Soo , Ko Young Gwan , Chon Gyu Rak , Lee Kwan Ho , Choi Sang-Ho , Hong Sang-Bum ,   for the Korean Society of Critical Care Medicine (KSCCM) H1N1 Collaborative
Published: October 2011

A recentin vitrostudy showed that the three compounds of antiviral drugs with different mechanisms of action (amantadine, ribavirin, and oseltamivir) could result in synergistic antiviral activity against influenza virus. However, no clinical studies have evaluated the efficacy and safety of combination antiviral therapy in patients with severe influenza illness. A total of 245 adult patients who were critically ill with confirmed pandemic influenza A/H1N1 2009 (pH1N1) virus infection and were admitted to one of the intensive care units of 28 hospitals in Korea were reviewed. Patients who required ventilator support and received either triple-combination antiviral drug (TCAD) therapy or oseltamivir monotherapy were analyzed. A total of 127 patients were included in our analysis. Among them, 24 patients received TCAD therapy, and 103 patients received oseltamivir monotherapy. The 14-day mortality was 17% in the TCAD group and 35% in the oseltamivir group (P= 0.08), and the 90-day mortality was 46% in the TCAD group and 59% in the oseltamivir group (P= 0.23). None of the toxicities attributable to antiviral drugs occurred in either group of our study, including hemolytic anemia and hepatic toxicities related to the use of ribavirin. Logistic regression analysis indicated that the odds ratio for the association of TCAD with 90-day mortality was 0.58 (95% confidence interval, 0.24 to 1.42;P= 0.24). Although this study was retrospective and did not provide virologic outcomes, our results suggest that the treatment outcome of the triple combination of amantadine, ribavirin, and oseltamivir was comparable to that of oseltamivir monotherapy.
Plasma Drug Activity Assay for Treatment Optimization in Tuberculosis Patients
Authors: Heysell Scott K. , Mtabho Charles , Mpagama Stellah , Mwaigwisya Solomon , Pholwat Suporn , Ndusilo Norah , Gratz Jean , Aarnoutse Rob E. , Kibiki Gibson S. , Houpt Eric R.
Published: October 2011

Low antituberculosis (TB) drug levels are common, but their clinical significance remains unclear, and methods of measurement are resource intensive. Subjects initiating treatment for sputum smear-positive pulmonary TB were enrolled from Kibong'oto National TB Hospital, Tanzania, and levels of isoniazid, rifampin, ethambutol, and pyrazinamide were measured at the time of typical peak plasma concentration (
C
2 h
). To evaluate the significance of the effect of observed drug levels on
Mycobacterium tuberculosis
growth, a plasma TB drug activity (TDA) assay was developed using the Bactec MGIT system. Time to detection of plasma-cocultured
M. tuberculosis
versus time to detection of control growth was defined as a TDA ratio. TDA assays were later performed using the subject's own
M. tuberculosis
isolate and
C
2 h
plasma from the Tanzanian cohort and compared to drug levels and clinical outcomes. Sixteen subjects with a mean age of 37.8 years ± 10.7 were enrolled. Fourteen (88%) had
C
2 h
rifampin levels and 11 (69%) had isoniazid levels below 90% of the lower limit of the expected range. Plasma spiked with various concentrations of antituberculosis medications found TDA assay results to be unaffected by ethambutol or pyrazinamide. Yet with a range of isoniazid and rifampin concentrations, TDA exhibited a statistically significant correlation with drug level and drug MIC, and a TDA of ∼1.0 indicated the presence of multidrug-resistant TB. In Tanzania, low (≤2.0) TDA was significantly associated with both lower isoniazid and rifampin
C
2 h
levels, and very low (≤1.5) TDA corresponded to a trend toward lack of cure. Study of TDA compared to additional clinical outcomes and as a therapeutic management tool is warranted.
Naturally Acquired Immune Responses to Plasmodium falciparum Sexual Stage Antigens Pfs48/45 and Pfs230 in an Area of Seasonal Transmission
Authors: Ouédraogo André Lin , Roeffen Will , Luty Adrian J. F. , de Vlas Sake J. , Nebie Issa , Ilboudo-Sanogo Edith , Cuzin-Ouattara Nadine , Teleen Karina , Tiono Alfred B. , Sirima Sodiomon Bienvenu , Verhave Jan-Peter , Bousema Teun , Sauerwein Robert
Published: October 2011

Acquisition of immunity to
Plasmodium falciparum
sexual stages is a key determinant for reducing human-mosquito transmission by preventing the fertilization and the development of the parasite in the mosquito midgut. Naturally acquired immunity against sexual stages may therefore form the basis for the development of transmission-blocking vaccines, but studies conducted to date offer little in the way of consistent findings. Here, we describe the acquisition of antigametocyte immune responses in malaria-exposed individuals in Burkina Faso. A total of 719 blood samples were collected in a series of three cross-sectional surveys at the start, peak, and end of the wet season. The seroprevalence of antibodies with specificity for the sexual stage antigens Pfs48/45 and Pfs230 was 2-fold lower (22 to 28%) than that for an asexual blood stage antigen glutamate-rich protein (GLURP) (65%) or for the preerythrocytic stage antigen circumsporozoite protein (CSP) (54%). The youngest children responded at frequencies similar to those for all four antigens but, in contrast with the immune responses to GLURP and CSP that increased with age independently of season and area of residence, there was no evidence for a clear age dependence of responses to Pfs48/45 and Pfs230. Anti-Pfs230 antibodies were most prevalent at the peak of the wet season (
P
< 0.001). Our findings suggest that naturally acquired immunity against Pfs48/45 and Pfs230 is a function of recent exposure rather than of cumulative exposure to gametocytes.
Live Attenuated Shigella dysenteriae Type 1 Vaccine Strains Overexpressing Shiga Toxin B Subunit
Authors: Wu Tao , Grassel Christen , Levine Myron M. , Barry Eileen M.
Published: October 2011

Shigella dysenteriae
serotype 1 (
S. dysenteriae
1) is unique among the
Shigella
species and serotypes in the expression of Shiga toxin which contributes to more severe disease sequelae and the ability to cause explosive outbreaks and pandemics.
S. dysenteriae
1 shares characteristics with other
Shigella
species, including the capability of causing clinical illness with a very low inoculum (10 to 100 CFU) and resistance to multiple antibiotics, underscoring the need for efficacious vaccines and therapeutics. Following the demonstration of the successful attenuating capacity of deletion mutations in the
guaBA
operon in
S. flexneri
2a vaccine strains in clinical studies, we developed a series of
S. dysenteriae
1 vaccine candidates containing the fundamental attenuating mutation in
guaBA.
All strains are devoid of Shiga toxin activity by specific deletion of the gene encoding the StxA subunit, which encodes enzymatic activity. The StxB subunit was overexpressed in several derivatives by either plasmid-based constructs or chromosomal manipulation to include a strong promoter. All strains are attenuated for growth
in vitro
in the HeLa cell assay and for plaque formation and were safe in the Serény test and immunogenic in the guinea pigs. Each strain induced robust serum and mucosal anti-
S. dysenteriae
1 lipopolysaccharide (LPS) responses and protected against wild-type challenge. Two strains engineered to overexpress StxB induced high titers of Shiga toxin neutralizing antibodies. These candidates demonstrate the potential for a live attenuated vaccine to protect against disease caused by
S. dysenteriae
1 and potentially to protect against the toxic effects of other Shiga toxin 1-expressing pathogens.
Low-flow vascular malformations of the head and neck: clinicopathology and image guided therapy
Authors: Love Zachary , Hsu Daniel Pierce
Published: October 2011

Low-flow vascular malformations are congenital lesions secondary to errors in the development of veins, capillaries or lymphatics. The majority of these lesions are sporadic although association with heritable syndromes does occur. Patients with these lesions should be treated and evaluated by a multidisciplinary team comprising medical, radiologic and surgical subspecialties. Percutaneous image guided sclerotherapy is gaining acceptance as a firstline treatment of low-flow vascular malformations.
Insulation of tumor suppressor genes by the nuclear factor CTCF
Authors: Recillas-Targa Félix , de la Rosa-Velázquez Inti A. , Soto-Reyes Ernesto
Published: October 2011

One of the most outstanding nuclear factors, which has chromatin insulator and transcriptional properties and also contribute to genomic organization, is the zinc-finger protein CCCTC-binding factor (CTCF). Among its multiple functions, a growing amount of evidence implicates CTCF in the epigenetic regulation of genes responsible for the control of the cell cycle, and its mis-regulation can lead to aberrant epigenetic silencing of genes involved in cancer development. Detailed studies are now revealing that CTCF can serve as a barrier against the spread of DNA methylation and histone repressive marks over promoter regions of tumor suppressor genes. Moreover, new evidences points out to the capacity of CTCF to be covalently modified, in particular, through poly(ADP-ribosyl)ation with regulatory consequences. An unexplored aspect of CTCF is its intergenic and intragenic distribution in certain loci. Such distribution seems to facilitate the formation of an optimal chromatin structure and the recruitment of chromatin remodelers with the possible incorporation of RNA polymerase II. Therefore, in the context of tumor suppressor genes and cancer development, CTCF appears to play a relevant role by incorporating a combination of mechanisms involved in the protection against epigenetic silencing components and the maintenance of optimal higher-order organization of the corresponding loci.
ATRX in chromatin assembly and genome architecture during development and disease
Authors: Bérubé Nathalie G.
Published: October 2011

The regulation of genome architecture is essential for a variety of fundamental cellular phenomena that underlie the complex orchestration of mammalian development. The ATP-dependent chromatin remodeling protein ATRX is emerging as a key regulatory component of nucleosomal dynamics and higher order chromatin conformation. Here we provide an overview of the role of ATRX at chromatin and during development, and discuss recent studies exposing a repertoire of ATRX functions at heterochromatin, in gene regulation, and during mitosis and meiosis. Exciting new progress on several fronts suggest that ATRX operates in histone variant deposition and in the modulation of higher order chromatin structure. Not surprisingly, dysfunction or absence of ATRX protein has devastating consequences on embryonic development and leads to human disease.
Cohesin: a critical chromatin organizer in mammalian gene regulation
Authors: Chien Richard , Zeng Weihua , Ball Alexander R. , Yokomori Kyoko
Published: October 2011

Cohesins are evolutionarily conserved essential multi-protein complexes that are important for higher-order chromatin organization. They play pivotal roles in the maintenance of genome integrity through mitotic chromosome regulation, DNA repair and replication, as well as gene regulation critical for proper development and cellular differentiation. In this review, we will discuss the multifaceted functions of mammalian cohesins and their apparent functional hierarchy in the cell, with particular focus on their actions in gene regulation and their relevance to human developmental disorders.
Age-related male reproductive effort in two mountain ungulates of contrasting sexual size dimorphism
Authors: Garel M. , Forsyth D.M. , Loison A. , Dubray D. , Jullien J.-M. , Tustin K.G. , Maillard D. , Gaillard J.-M.
Published: October 2011

In polygynous ungulates, the reproductive effort of adult males peaks during a short period in which feeding activities are sacrificed for mating activities. Hence, both fat reserves and body mass are predicted to decline markedly during this period. The decline is also predicted to be greater in fat reserves than in body mass because fat is catabolized before muscle, and to increase with the intensity of sexual selection. In contrast, no specific patterns are expected in females for which late gestation and lactation rather than mating are the energetically most demanding periods. We tested these hypotheses in two mountain ungulates of contrasting sexual size dimorphism (SSD): Himalayan tahr ( Hemitragus jemlahicus (H. Smith, 1826)) (SSD = 123%) and alpine chamois ( Rupicapra rupicapra (L., 1758)) (SSD = 26%). As expected, kidney fat declined more rapidly than body mass in adult males of both species. Kidney fat declined faster in adult male tahr compared with adult male chamois. There was no consistent pattern of changes in body mass or kidney fat in female tahr or female chamois. Our results suggest that adult males of species with strong SSD allocate more energy to mating than males of less dimorphic species.
Factors affecting individual variation in nest-defense intensity in colonially breeding Black-tailed Gulls (Larus crassirostris)
Authors: Kazama Kentaro , Niizuma Yasuaki , Sakamoto Kentaro Q. , Watanuki Yutaka
Published: October 2011

The physiological state of parent birds combined with the value of their clutch may affect the intensity of their nest defense. In colonially breeding birds, nest-defense intensity may also be affected by the behavior of neighbors. We investigated individual variation in the nest-defense intensity among colonial Black-tailed Gulls ( Larus crassirostris Vieillot, 1818) over 2 years. Only 30%–40% of males attacked a decoy of an egg predator (Large-billed Crow ( Corvus macrorhynchos Wagler, 1827)), and the other males and females rarely attacked. Males attacking the decoy had higher levels of plasma testosterone than males that did not attack. Each male’s, but not female’s, nest-defense intensity was consistent throughout the incubation period and also across years. The intensity was not related to egg-laying date, clutch size, or age of offspring. The intensity was likely to be higher when individuals had one or more neighbors, representing higher nest-defense intensity in the year where gulls had larger number of adjacent neighboring nests (5.23 nests), but this trend was not observed in the year where they had smaller number of the neighboring nests (3.73 nests). Thus, in addition to testosterone levels, behavior of neighbors also influences the nest-defense intensity.
Reproduction and denning by urban and rural San Clemente Island foxes (Urocyon littoralis clementae)
Authors: Gould N.P. , Andelt W.F.
Published: October 2011

Island foxes ( Urocyon littoralis (Baird, 1858)) have experienced severe reductions in populations on 4 out of 6 California Channel Islands. Although numbers of foxes on San Clemente Island (SCLI; Urocyon littoralis clementae Merriam, 1903) have remained relatively stable, data on reproductive success in urban and rural areas are necessary to better understand population dynamics of foxes and manage the population if it sustains declines. Determining locations and characteristics of den sites will also assist in minimizing possible impacts of humans on foxes. We found that 10 female foxes produced at least 19 kits during 2008. Female foxes that spent a greater proportion of time within an urban area had greater probability of reproducing compared with foxes that infrequently utilized urban areas. However, these “urban” foxes often selected den sites nearer to roads, which may expose them to increased mortalities. We located 23 den sites on a mean of 17°–18° slopes with 40% having westerly facing aspects. We recommend avoiding human disturbance to these areas from February through June, which may minimize potential impacts on foxes. Our study should provide insight into managing island foxes, especially in respect to urban areas on other Channel Islands.
Food limitation causes female haglids to mate more often
Authors: Judge Kevin A. , De Luca Paul A. , Morris Glenn K.
Published: October 2011

Sexual conflict over mating rate has selected for male adaptations to induce females to mate. These inducements can be either coercive or enticing, and there is a growing realization that males of a given species may employ both tactics simultaneously to acquire mating success. Insects in the genus Cyphoderris Uhler, 1864 (Orthoptera: Haglidae) have a unique breeding system in which females feed on the fleshy hind wings of males during copulation, but as mating proceeds males use a specialized abdominal pinching organ known as a gin trap to hold the female until she copulates with him. Previous research has demonstrated the coercive nature of the gin trap, but evidence for a beneficial effect of hind-wing feeding is lacking. Here we tested whether hind-wing feeding provides material benefits to females by manipulating females’ access to nutrition—food restricted or ad lib food—and then providing females with four opportunities to mate over 8 days. As predicted, food-restricted females were more likely to feed on male hind wings, did more hind-wing damage, and were more likely to copulate with males than females provided ad lib food. We discuss these results in the context of the evolution of polyandry and sexual conflict.
Formal Reasoning about Physical Properties of Security Protocols
Authors: Basin David , Capkun Srdjan , Schaller Patrick , Schmidt Benedikt
Published: October 2011

Traditional security protocols are mainly concerned with authentication and key establishment and rely on predistributed keys and properties of cryptographic operators. In contrast, new application areas are emerging that establish and rely on properties of the physical world. Examples include protocols for secure localization, distance bounding, and secure time synchronization.

We present a formal model for modeling and reasoning about such physical security protocols. Our model extends standard, inductive, trace-based, symbolic approaches with a formalization of physical properties of the environment, namely communication, location, and time. In particular, communication is subject to physical constraints, for example, message transmission takes time determined by the communication medium used and the distance between nodes. All agents, including intruders, are subject to these constraints and this results in a distributed intruder with restricted, but more realistic, communication capabilities than those of the standard Dolev-Yao intruder. We have formalized our model in Isabelle/HOL and have used it to verify protocols for authenticated ranging, distance bounding, broadcast authentication based on delayed key disclosure, and time synchronization.
Programming the memory hierarchy revisited
Authors: Bauer Michael , Clark John , Schkufza Eric , Aiken Alex
Published: October 2011

We describe two novel constructs for programming parallel machines with multi-level memory hierarchies: call-up, which allows a child task to invoke computation on its parent, and spawn, which spawns a dynamically determined number of parallel children until some termination condition in the parent is met. Together we show that these constructs allow applications with irregular parallelism to be programmed in a straightforward manner, and furthermore these constructs complement and can be combined with constructs for expressing regular parallelism. We have implemented spawn and call-up in Sequoia and we present an experimental evaluation on a number of irregular applications.
SpiceC
Authors: Feng Min , Gupta Rajiv , Hu Yi
Published: October 2011

In this paper we present an approach to parallel programming called SpiceC. SpiceC simplifies the task of parallel programming through a combination of an intuitive computation model and SpiceC directives. The SpiceC parallel computation model consists of multiple threads where every thread has a private space for data and all threads share data via a shared space. Each thread performs computations using its private space thus offering isolation which allows for speculative computations. SpiceC provides easy to use SpiceC compiler directives using which the programmers can express different forms of parallelism. It allows developers to express high level constraints on data transfers between spaces while the tedious task of generating the code for the data transfers is performed by the compiler. SpiceC also supports data transfers involving dynamic data structures without help from developers. SpiceC allows developers to create clusters of data to enable parallel data transfers. SpiceC programs are portable across modern chip multiprocessor based machines that may or may not support cache coherence. We have developed implementations of SpiceC for shared memory systems with and without cache coherence. We evaluate our implementation using seven benchmarks of which four are parallelized speculatively. Our compiler generated implementations achieve speedups ranging from 2x to 18x on a 24 core system.
ULCC
Authors: Ding Xiaoning , Wang Kaibo , Zhang Xiaodong
Published: October 2011

Scientific applications face serious performance challenges on multicore processors, one of which is caused by access contention in last level shared caches from multiple running threads. The contention increases the number of long latency memory accesses, and consequently increases application execution times. Optimizing shared cache performance is critical to reduce significantly execution times of multi-threaded programs on multicores. However, there are two unique problems to be solved before implementing cache optimization techniques on multicores at the user level. First, available cache space for each running thread in a last level cache is difficult to predict due to access contention in the shared space, which makes cache conscious algorithms for single cores ineffective on multicores. Second, at the user level, programmers are not able to allocate cache space at will to running threads in the shared cache, thus data sets with strong locality may not be allocated with sufficient cache space, and cache pollution can easily happen. To address these two critical issues, we have designed ULCC (User Level Cache Control), a software runtime library that enables programmers to explicitly manage and optimize last level cache usage by allocating proper cache space for different data sets of different threads. We have implemented ULCC at the user level based on a page-coloring technique for last level cache usage management. By means of multiple case studies on an Intel multicore processor, we show that with ULCC, scientific applications can achieve significant performance improvements by fully exploiting the benefit of cache optimization algorithms and by partitioning the cache space accordingly to protect frequently reused data sets and to avoid cache pollution. Our experiments with various applications show that ULCC can significantly improve application performance by nearly 40%.
ScalaExtrap
Authors: Wu Xing , Mueller Frank
Published: October 2011

Performance modeling for scientific applications is important for assessing potential application performance and systems procurement in high-performance computing (HPC). Recent progress on communication tracing opens up novel opportunities for communication modeling due to its lossless yet scalable trace collection. Estimating the impact of scaling on communication efficiency still remains non-trivial due to execution-time variations and exposure to hardware and software artifacts. This work contributes a fundamentally novel modeling scheme. We synthetically generate the application trace for large numbers of nodes by extrapolation from a set of smaller traces. We devise an innovative approach for topology extrapolation of single program, multiple data (SPMD) codes with stencil or mesh communication. The extrapolated trace can subsequently be (a) replayed to assess communication requirements before porting an application, (b) transformed to auto-generate communication benchmarks for various target platforms, and (c) analyzed to detect communication inefficiencies and scalability limitations. To the best of our knowledge, rapidly obtaining the communication behavior of parallel applications at arbitrary scale with the availability of timed replay, yet without actual execution of the application at this scale is without precedence and has the potential to enable otherwise infeasible system simulation at the exascale level.
Thread contracts for safe parallelism
Authors: Karmani Rajesh K. , Madhusudan P. , Moore Brandon M.
Published: October 2011

We build a framework of thread contracts, called Accord, that allows programmers to annotate their concurrency co-ordination strategies. Accord annotations allow programmers to declaratively specify the parts of memory that a thread may read or write into, and the locks that protect them, reflecting the concurrency co-ordination among threads and the reason why the program is free of data-races. We provide automatic tools to check if the concurrency co-ordination strategy ensures race-freedom, using constraint-solvers (SMT solvers). Hence programmers using Accord can both formally state and prove their co-ordination strategies ensure race freedom. The programmer's implementation of the co-ordination strategy may however be correct or incorrect. We show how the formal Accord contracts allow us to automatically insert runtime assertions that serve to check, during testing, whether the implementation conforms to the contract. Using a large class of data-parallel programs that share memory in intricate ways, we show that natural and simple contracts suffice to document the co-ordination strategy amongst threads, and that the task of showing that the strategy ensures race-freedom can be handled efficiently and automatically by an existing SMT solver (Z3). While co-ordination strategies can be proved race-free in our framework, failure to prove the co-ordination strategy race-free, accompanied by counter-examples produced by the solver, indicates the presence of races. Using such counterexamples, we report hitherto undiscovered data-races that we found in the long-tested applu_l benchmark in the Spec OMP2001 suite.
COREMU
Authors: Wang Zhaoguo , Liu Ran , Chen Yufei , Wu Xi , Chen Haibo , Zhang Weihua , Zang Binyu
Published: October 2011

This paper presents the open-source COREMU, a scalable and portable parallel emulation framework that decouples the complexity of parallelizing full-system emulators from building a mature sequential one. The key observation is that CPU cores and devices in current (and likely future) multiprocessors are loosely-coupled and communicate through well-defined interfaces. Based on this observation, COREMU emulates multiple cores by creating multiple instances of existing sequential emulators, and uses a thin library layer to handle the inter-core and device communication and synchronization, to maintain a consistent view of system resources. COREMU also incorporates lightweight memory transactions, feedback-directed scheduling, lazy code invalidation and adaptive signal control to provide scalable performance. To make COREMU useful in practice, we also provide some preliminary tools and APIs that can help programmers to diagnose performance problems and (concurrency) bugs. A working prototype, which reuses the widely-used QEMU as the sequential emulator, is with only 2500 lines of code (LOCs) changes to QEMU. It currently supports x64 and ARM platforms, and can emulates up to 255 cores running commodity OSes with practical performance, while QEMU cannot scale above 32 cores. A set of performance evaluation against QEMU indicates that, COREMU has negligible uniprocessor emulation overhead, performs and scales significantly better than QEMU. We also show how COREMU could be used to diagnose performance problems and concurrency bugs of both OS kernel and parallel applications.
Evaluating graph coloring on GPUs
Authors: Grosset Andre Vincent Pascal , Zhu Peihong , Liu Shusen , Venkatasubramanian Suresh , Hall Mary
Published: October 2011

This paper evaluates features of graph coloring algorithms implemented on graphics processing units (GPUs), comparing coloring heuristics and thread decompositions. As compared to prior work on graph coloring for other parallel architectures, we find that the large number of cores and relatively high global memory bandwidth of a GPU lead to different strategies for the parallel implementation. Specifically, we find that a simple uniform block partitioning is very effective on GPUs and our parallel coloring heuristics lead to the same or fewer colors than prior approaches for distributed-memory cluster architecture. Our algorithm resolves many coloring conflicts across partitioned blocks on the GPU by iterating through the coloring process, before returning to the CPU to resolve remaining conflicts. With this approach we get as few color (if not fewer) than the best sequential graph coloring algorithm and performance is close to the fastest sequential graph coloring algorithms which have poor color quality.
Automatic formal verification of MPI-based parallel programs
Authors: Siegel Stephen F. , Zirkel Timothy K.
Published: October 2011

The Toolkit for Accurate Scientific Software (TASS) is a suite of tools for the formal verification of MPI-based parallel programs used in computational science. TASS can verify various safety properties as well as compare two programs for functional equivalence. The TASS front end takes an integer
n
≥ 1 and a C/MPI program, and constructs an abstract model of the program with
n
processes. Procedures, structs, (multi-dimensional) arrays, heap-allocated data, pointers, and pointer arithmetic are all representable in a TASS model. The model is then explored using symbolic execution and explicit state space enumeration. A number of techniques are used to reduce the time and memory consumed. A variety of realistic MPI programs have been verified with TASS, including Jacobi iteration and manager-worker type programs, and some subtle defects have been discovered. TASS is written in Java and is available from http://vsl.cis.udel.edu/tass under the Gnu Public License.
Agency theory and consultant management in enterprise resource planning systems implementation
Authors: Basu Vedabrata , Lederer Al
Published: October 2011

Enterprise resource planning (ERP) systems are rapidly becoming the foundations to the decision support systems of many organizations, but have all too often failed to deliver their expected benefits. Most ERP implementation projects are carried out using implementation consultants hired from outside the client firm. The current study treated the consultants as agents and the clients as principals, and applied agency theory to test the consultant-client relationship as a predictor of ERP implementation project success.

A survey collected responses from 192 client project managers who worked on the ERP implementation process in their organizations. Data analysis via structural equation modeling showed that more consultant monitoring predicts less moral hazard (i.e., consultant shirking), that less moral hazard predicts greater ERP project success, and that more monitoring directly predicts such success. However, the analysis failed to support expectations that more pre-qualification efforts (i.e., screening of the consultant) would lead to less adverse selection (i.e., the consultant's misrepresentation of skills) or that less adverse selection would lead to greater ERP success. Surprisingly greater incentive alignment predicted greater moral hazard, thus suggesting the potential of incentives to de-motivate rather than motivate.

This study contributed by extending agency theory to outsourced information systems project implementation. It provided new, validated measures of prequalification efforts, monitoring, incentive alignment, moral hazard, and adverse selection constructs. The findings suggest that future researchers may want to learn more about incentive alignment and its impact, and that information systems project managers may want to monitor more to improve ERP and other large-scale system implementation success.
Architecture, mechanisms and scheduling analysis tool for multicore time- and space-partitioned systems
Authors: Craveiro João , Rufino José , Singhoff Frank
Published: October 2011

Time- and space-partitioned systems (TSP) are a current trend in aerospace. They are employed to integrate a heterogeneous set of functions (different criticalities, real-time requirements, and origins) in a shared computing platform, fulfilling individual partitions' and global real-time properties. Applications are separated into logical partitions, scheduled according to predefined partition scheduling tables (PSTs). In this paper we expose our current work on exploiting multiprocessor/multicore processor platforms to add capacity, flexibility and safety to the current state of the art in TSP systems. We propose architectural evolutions, as well as the development of a schedule analysis and generation tool based on Cheddar. The tool will incorporate and extend real-time scheduling theory results, and be able to analyse the feasibility of PSTs and aid the generation of PSTs from the individual timing requirements of each function.
Partitioned scheduling of parallel real-time tasks on multiprocessor systems
Authors: Fauberteau Frédéric , Midonnet Serge , Qamhieh Manar
Published: October 2011

In this paper, we focus on the scheduling of periodic fork-join real-time tasks on multiprocessor systems. Parallel real-time tasks in the fork-join model have strict parallel segments without laxity. We propose a partitioned scheduling algorithm which increases the laxity of the parallel segments and therefore the schedulability of tasksets of this model. A similar algorithm has been proposed in the literature but it produces job migrations. Our algorithm eliminates the use of job migrations in order to create a portable algorithm that can be implemented on a standard Linux kernel. Results of extensive simulations are provided in order to analyze the schedulability of the proposed algorithm, and to provide comparisons with the other algorithm proposed in the literature.
Exploiting intra-task slack time of load operations for DVFS in hard real-time multi-core systems
Authors: Quiñones Eduardo , Abella Jaume , Cazorla Francisco J. , Valero Mateo
Published: October 2011

Power demand grows much faster than battery capacity in embedded systems. Dynamic voltage and frequency scaling (DVFS) has been shown to be extremely efficient to save energy due to the exponential dependence of power on voltage. However, voltage/frequency cannot be blindly scaled in hard real-time systems because DVFS techniques impact on the execution time, and so potentially on the worst-case execution time (WCET) of tasks.

This paper presents a new DVFS technique for hard real-time systems that measures dynamically the
intra-task slack
existing between the actual execution time of a task and its WCET estimation, and exploits it to perform DVFS guaranteeing that the WCET is not affected. Concretely, our approach exploits the slack available due to contention in the use of shared resources in a multi-core system.
Cyber Security for Smart Grid, Cryptography, and Privacy
Authors: Iyer Swapna
Published: October 2011

The invention of “smart grid” promises to improve the efficiency and reliability of the power system. As smart grid is turning out to be one of the most promising technologies, its security concerns are becoming more crucial. The grid is susceptible to different types of attacks. This paper will focus on these threats and risks especially relating to cyber security. Cyber security is a vital topic, since the smart grid uses high level of computation like the IT. We will also see cryptography and key management techniques that are required to overcome these attacks. Privacy of consumers is another important security concern that this paper will deal with.
Asbestos Induces Reduction of Tumor Immunity
Authors: Kumagai-Takei Naoko , Maeda Megumi , Chen Ying , Matsuzaki Hidenori , Lee Suni , Nishimura Yasumitsu , Hiratsuka Junichi , Otsuki Takemi
Published: October 2011

Asbestos-related cancers such as malignant mesothelioma and lung cancer are an important issue in the world. There are many conflicts concerning economical considerations and medical evidence for these cancers and much confusion regarding details of the pathological mechanisms of asbestos-induced cancers. For example, there is uncertainty concerning the degree of danger of the iron-absent chrysotile compared with iron-containing crocidolite and amosite. However, regarding bad prognosis of mesothelioma, medical approaches to ensure the recognition of the biological effects of asbestos and the pathological mechanisms of asbestos-induced carcinogenesis, as well as clinical trials to detect the early stage of mesothelioma, should result in better preventions and the cure of these malignancies. We have been investigating the immunological effects of asbestos in relation to the reduction of tumor immunity. In this paper, cellular and molecular approaches to clarify the immunological effects of asbestos are described, and all the findings indicate that the reduction of tumor immunity is caused by asbestos exposure and involvement in asbestos-induced cancers. These investigations may not only allow the clear recognition of the biological effects of asbestos, but also present a novel procedure for early detection of previous asbestos exposure and the presence of mesothelioma as well as the chemoprevention of asbestos-related cancers.
Determining Satisfaction with Access and Financial Aspects of Care for Persons Exposed to Libby Amphibole Asbestos: Rural and National Environmental Policy Implications
Authors: Winters Charlene A. , Hill Wade , Kuntz Sandra W. , Weinert Clarann , Rowse Kimberly , Hernandez Tanis , Black Brad
Published: October 2011

Libby, Montana is a Superfund site and epicenter of one of the worst environmental disasters in the USA history in terms of asbestos-related mortality and morbidity. Perceptions of access and financial aspects of care were explored among a national cohort of persons postasbestos exposure and prior to a 2009 Public Health Emergency Declaration. Our findings indicated the Libby cohort was significantly less satisfied with access and financial aspects of care as measured by two PSQ-III scales when compared to an adult, chronically ill patient sample. Participants with higher levels of respiratory morbidity and depression had significantly lower satisfaction scores.
Differentiation Potential of Pancreatic Fibroblastoid Cells/Stellate Cells: Effects of Peroxisome Proliferator-Activated Receptor Gamma Ligands
Authors: Kruse M.-L. , Hopf-Jensen S. , Timke C. , Agricola B. , Sparmann G. , Schmid A. , Sipos B. , Arlt A. , Schäfer H.
Published: October 2011

Pancreatic stellate cells have been investigated mostly for their activation process, supposed to support the development of pancreatic disease. Few studies have been presented on reversal of the activation process in vitro. Thiazolidinediones (TZDs) have been used as antidiabetics and have now been reported to exert antifibrotic activity. We tested effects of natural and synthetic ligands of peroxisome proliferator-activated receptor gamma (PPARγ) on human pancreatic fibroblastoid cells (hPFCs) in search for specificity of action. Ciglitazone, as a prototype of TZDs, was shown to have reversible growth inhibitory effects on human pancreatic fibroblastoid cells/stellate cells. Cells treated with ciglitazone for three days showed enhanced lipid content and induction of proteins involved in lipid metabolism. Collagen synthesis was reduced in hPFC. Interaction of PPARγwith DNA binding sites upon ligand binding was shown by gel shift analysis. These findings point toward a potential for adipocyte differentiation in human pancreatic fibroblastoid cells.
Numerical Investigation of the Internal Flow in a Banki Turbine
Authors: De Andrade Jesús , Curiel Christian , Kenyery Frank , Aguillón Orlando , Vásquez Auristela , Asuaje Miguel
Published: October 2011

The paper refers to the numerical analysis of the internal flow in a hydraulic cross-flow turbine type Banki. A 3D-CFD steady state flow simulation has been performed using ANSYS CFX codes. The simulation includes nozzle, runner, shaft, and casing. The turbine has a specific speed of 63 (metric units), an outside runner diameter of 294 mm. Simulations were carried out using a water-air free surface model and k-εturbulence model. The objectives of this study were to analyze the velocity and pressure fields of the cross-flow within the runner and to characterize its performance for different runner speeds. Absolute flow velocity angles are obtained at runner entrance for simulations with and without the runner. Flow recirculation in the runner interblade passages and shocks of the internal cross-flow cause considerable hydraulic losses by which the efficiency of the turbine decreases significantly. The CFD simulations results were compared with experimental data and were consistent with global performance parameters.
Mineralization and Crop Uptake of Nitrogen from Textile Manufacturing Wastewater Sludge Cake
Authors: McGonigle T. P. , Beauchamp E. G. , Evans L. J. , Wells C. J.
Published: October 2011

Wastewater sewage sludge cake from textile manufacturing was evaluated by soil incubation experiments and a greenhouse experiment for use as a soil amendment to provide crop N. Although the sludge had 96% of N in organic combination, 20% of total sludge N was released to soil as mineral N over 28 days. N mineralization from the sludge was indistinguishable from that seen for alfalfa shoot in parallel incubations. However, nitrification inhibition was seen for the alfalfa amendment. Soil respiration was low for the sludge treatments compared to the alfalfa treatments, suggesting that carbon substrates in the sludge were less easily broken down. A second incubation experiment indicated that fine fragmentation of the sludge is not necessary to ensure mineralization proceeds. In a greenhouse experiment, sludge N was approximately 25% as available toZea maysL. as NH4NO3. The textile manufacturing sludge offered potential to offset N fertilizer requirement.
Macrophage Migration Inhibitory Factor in Fetoplacental Tissues from Preeclamptic Pregnancies with or without Fetal Growth Restriction
Authors: Cardaropoli Simona , Paulesu Luana , Romagnoli Roberta , Ietta Francesca , Marzioni Daniela , Castellucci Mario , Rolfo Alessandro , Vasario Elena , Piccoli Ettore , Todros Tullia
Published: October 2011

The proinflammatory cytokine MIF (macrophage migration inhibitory factor) is involved in physiological and pathological processes in pregnancy. MIF maternal serum levels are increased in preeclampsia (PE). We hypothesize that pregnancy tissues are the source of MIF overexpression in PE. MIF protein was studied in maternal sera, placental tissues, fetal membranes, and umbilical cord of 8 control and 20 PE pregnancies: 10 with normal fetal growth (PE-AGA) and 10 with fetal growth restriction (PE-FGR). MIF levels were significantly higher in PE-AGA membranes than in controls and PE-FGR. In PE-FGR, MIF cord concentrations were higher than in PE-AGA while MIF placental levels were lower than in controls. MIF maternal serum levels were higher in PE, compared to controls, and the difference was mainly due to PE-FGR samples. These data support MIF involvement in PE pathogenesis and suggest that different pregnancy tissues contribute to MIF production in PE with and without fetoplacental compromise.