bluuebunny/crossref_metadata_2025 huggingface dataset:
Impairment of Host Defense against Disseminated Candidiasis in Mice Overexpressing GATA-3
Authors: Haraguchi Norihiro , Ishii Yukio , Morishima Yuko , Yoh Keigyou , Matsuno Yosuke , Kikuchi Norihiro , Sakamoto Tohru , Takahashi Satoru , Hizawa Nobuyuki
Published: March 2010

Candidaspecies are the most common source of nosocomial invasive fungal infections. Previous studies have indicated that T-helper immune response is the critical host factor for susceptibility toCandidainfection. The transcription factor GATA-3 is known as the master regulator for T-helper type 2 (Th2) differentiation. We therefore investigated the role of GATA-3 in the host defense against systemicCandidainfection using GATA-3-overexpressing transgenic mice. The survival of GATA-3-overexpressing mice afterCandidainfection was significantly lower than that of wild-type mice.Candidaoutgrowth was significantly increased in the kidneys of GATA-3-overexpressing mice, compared with wild-type mice. The levels of various Th2 cytokines, including interleukin-4 (IL-4), IL-5, and IL-13, were significantly higher while the level of Th1 cytokine gamma interferon was significantly lower in the splenocytes of GATA-3-overexpressing mice afterCandidainfection. Recruitment of macrophages into the peritoneal cavity in response toCandidainfection and their phagocytic activity were significantly lower in GATA-3-overexpressing mice than in wild-type mice. Exogenous administration of gamma interferon to GATA-3-overexpressing mice significantly reducedCandidaoutgrowth in the kidney and thus increased the survival rate. Administration of gamma interferon also increased the recruitment of macrophages into the peritoneal cavity in response toCandidainfection. These results indicate that overexpression of GATA-3 modulates macrophage antifungal activity and thus enhances the susceptibility to systemicCandidainfection, possibly by reducing the production of gamma interferon in response toCandidainfection.
Rapid Identification of Bacteria from Positive Blood Culture Bottles by Use of Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry Fingerprinting
Authors: Christner Martin , Rohde Holger , Wolters Manuel , Sobottka Ingo , Wegscheider Karl , Aepfelbacher Martin
Published: March 2010

Early and adequate antimicrobial therapy has been shown to improve the clinical outcome in bloodstream infections (BSI). To provide rapid pathogen identification for targeted treatment, we applied matrix-assisted laser desorption-ionization time of flight (MALDI-TOF) mass spectrometry fingerprinting to bacteria directly recovered from blood culture bottles. A total of 304 aerobic and anaerobic blood cultures, reported positive by a Bactec 9240 system, were subjected in parallel to differential centrifugation with subsequent mass spectrometry fingerprinting and reference identification using established microbiological methods. A representative spectrum of bloodstream pathogens was recovered from 277 samples that grew a single bacterial isolate. Species identification by direct mass spectrometry fingerprinting matched reference identification in 95% of these samples and worked equally well for aerobic and anaerobic culture bottles. Application of commonly used score cutoffs to classify the fingerprinting results led to an identification rate of 87%. Mismatching mostly resulted from insufficient bacterial numbers and preferentially occurred with Gram-positive samples. The respective spectra showed low concordance to database references and were effectively rejected by score thresholds. Spiking experiments and examination of the respective study samples even suggested applicability of the method to mixed cultures. With turnaround times around 100 min, the approach allowed for reliable pathogen identification at the day of blood culture positivity, providing treatment-relevant information within the critical phase of septic illness.
Production of Infectious Hepatitis C Virus by Using RNA Polymerase I-Mediated Transcription
Authors: Masaki Takahiro , Suzuki Ryosuke , Saeed Mohsan , Mori Ken-ichi , Matsuda Mami , Aizaki Hideki , Ishii Koji , Maki Noboru , Miyamura Tatsuo , Matsuura Yoshiharu , Wakita Takaji , Suzuki Tetsuro
Published: March 2010

In this study, we used an RNA polymerase I (Pol I) transcription system for development of a reverse genetics protocol to produce hepatitis C virus (HCV), which is an uncapped positive-strand RNA virus. Transfection with a plasmid harboring HCV JFH-1 full-length cDNA flanked by a Pol I promoter and Pol I terminator yielded an unspliced RNA with no additional sequences at either end, resulting in efficient RNA replication within the cytoplasm and subsequent production of infectious virions. Using this technology, we developed a simple replicontrans-packaging system, in which transient transfection of two plasmids enables examination of viral genome replication and virion assembly as two separate steps. In addition, we established a stable cell line that constitutively produces HCV with a low mutation frequency of the viral genome. The effects of inhibitors of N-linked glycosylation on HCV production were evaluated using this cell line, and the results suggest that certain step(s), such as virion assembly, intracellular trafficking, and secretion, are potentially up- and downregulated according to modifications of HCV envelope protein glycans. This Pol I-based HCV expression system will be beneficial for a high-throughput antiviral screening and vaccine discovery programs.
Circumstances in which colonoscopy misses cancer: Table 1
Authors: Rabeneck Linda , Paszat Lawrence F
Published: March 2010

Colonoscopy is associated with a varying risk of missing colorectal cancer (CRC). The objective of this paper was to review the existing evidence that indicates when colonoscopy may miss cancer in usual clinical practice and to provide information that would be helpful to endoscopists in their daily practice. CRC is diagnosed within 3 years in about 5% of persons with CRC who undergo colonoscopy in whom the cancer is not detected. Future research should be directed at disentangling the relative contributions of tumour biology and colonoscopy quality in explaining this result. When consent is obtained for colonoscopy, patients must be informed of the small risk that a cancer may not be detected. Steps that can be taken to address colonoscopy quality include formal training in colonoscopy and polypectomy technique, coupled with maintenance of skills by performing at least 300 colonoscopies per year. The use of split dose bowel preparation is advised. Colonoscopy should be completed to the caecum with documentation of landmarks (ileocaecal valve; appendiceal orifice). Careful colonoscopy technique includes examining the proximal sides of flexures and folds, washing and suctioning debris and ensuring adequate colonic distension. Caecal intubation and adenoma detection rates should be reported and reviewed. Lesions should be completely removed at polypectomy and attention given to appropriate surveillance.
Discharge of metals from the St. Lawrence River
Authors: Yeats P. A. , Bewers J. M.
Published: March 2010

The concentrations of dissolved and total Al, Fe, Mn, Co, Ni, Cu, Zn, and Cd in St. Lawrence River water have been measured on a monthly basis over a 2 year period. Riverine suspended particulate matter was also analyzed for nondetrital Mg, Ca, Si, Al, Fe, Mn, Co, Ni, Cu, Zn, and Cd and detrital Mg, Ca, Si, Al, Fe, and Mn. Variability in the concentration of dissolved metals is unrelated to changes in water flow or suspended load. Particulate Al, Fe, Mn, and Zn concentrations are related to water flow. The metal/aluminum ratios of particulate Mn, Cu, Zn, and Cd are elevated with respect to crustal rocks or coastal marine sediments, with the enrichment occurring in the nondetrital, or weak acid soluble, fraction.Annual dissolved metal discharges and nondetrital and total particulate metal discharges that take into account monthly variations in metal concentrations have been calculated for the St. Lawrence River. These discharges have been used to estimate global annual river discharges of metals to the ocean. The calculated discharges are compared with estimates based upon other rivers. The importance of nondetrital particulate metal fluxes is emphasized.
Manganiferous garnet underlying the Bousquet gold orebody, Quebec: metamorphosed manganese sediment as a guide to gold ore
Authors: Valliant R. I. , Barnett R. L.
Published: March 2010

Garnet–quartz–muscovite rock stratigraphically underlies a volcanogenic pyritic gold orebody within Bousquet Township, Abitibi greenstone belt, Quebec. Garnet constitutes only 3% of the rock within muscovite-rich layers near its east and west ends whereas the rock contains 12% of garnet near its center. Trails of quartz, carbonate, and sulphide inclusions and parallel bands of an ultrafine black opaque mineral produce a layered appearance in the garnet. Garnet consists of 25% MnO and is zoned with maximum MnO content at its center. Furthermore, MnO content is greatest in garnet near the center and stratigraphic top of the rock and decreases systematically to the east, west, and stratigraphic base. Pb, Zn, and Ba exhibit similar enrichment trends from stratigraphic base to top of the rock; however Ba remains abundant in the overlying orebody.The interpretation is that the garnet rock was a primary Mn-rich sediment that accumulated near a sea-floor hydrothermal vent. By analogy with modern hydrothermal Mn deposits, the garnets are believed to be metamorphosed equivalents of Archean manganese nodules. The spatial relationship of the garnet rock to gold ore, the increase in MnO/FeO in garnet toward ore, and the large areal extent of the rock indicate its usefulness in exploration for gold mineralization.
Relict ice-scour marks and late phases of Lake Agassiz in northernmost Manitoba
Authors: Dredge L. A.
Published: March 2010

In northern Manitoba, intersecting grooves 300–1800 m long are ice-scour marks created by the dragging of iceberg keels along rises in the bed of a glacial lake whose water plane was at about 305 m asl. The lake was bounded by glacial ice on its northern and eastern margins. The occurrence of scours on topographic divides indicates that a single extensive lake, thought to be a northern extremity of Lake Agassiz, occupied the area as far north as Seal River at the time the ice scours were formed. The lake extended as far west as Sprott Lake and eastwards into the Hudson Bay Lowlands into an area later occupied by Tyrrell Sea. The preservation of the scour marks suggests that the lake drained suddenly.Ice-scour marks are easily recognized on air photographs and provide a means of identifying areas that have been inundated by glacial lakes. Scours in emerged marine sediment are generally obliterated by littoral processes.
Timing of arrival of the Avalon Zone in the northeastern Appalachians: a new look at the Straddling Granite
Authors: Elias Peter N. , Strong D. F.
Published: March 2010

The "Straddling Granite" was previously thought to straddle the Hermitage Bay – Dover fault system, which marks the boundary between the Avalon and Gander Zones of eastern Newfoundland, and hence to fix the earliest juxtaposition of these two zones before 504 ± 12 Ma. More detailed investigation shows that these rocks are divisible into two distinct geochemical suites, the Indian Point Granite to the west and the Hardy's Cove intrusive suite to the east. Of the samples that provided the 504 Ma isochron, five were obtained from the Hardy's Cove suite and one from within the fault zone; hence the isochron must be taken as representing only a typical date for plutonic rocks within the Avalon Zone. The Indian Point Granite intrudes the Gaultois Granite, dated at 350 ± 18 Ma, and is thus considerably younger than the Hardy's Cove suite. These observations now allow for juxtaposition of the Avalon and Gander Zones to have been as late as Early Carboniferous.
Late Wisconsinan ice-flow reconstruction for the central Great Lakes region
Authors: Dworkin Stephen Irving , Larson Grahame J. , Monaghan G. William
Published: March 2010

Late Wisconsinan tills from the lower peninsula of Michigan can be differentiated with respect to the Lake Michigan, Saginaw, and Huron–Erie lobes on the basis of their heavy-mineral assemblages. Using discriminant analysis, the heavy-mineral assemblages can also be associated with specific source areas on the Canadian Shield. These associations suggest that (1) the Lake Michigan Lobe flowed southwestward across a region north of Lake Huron and then into southwestern Michigan; (2) the Saginaw Lobe flowed southwestward across a region northwest of Georgian Bay and then into south-central Michigan; and (3) the Huron–Erie Lobe flowed southwestward across a region north of Georgian Bay and then southward into southeastern Michigan.Comparison of the heavy-mineral assemblages of tills from southeastern Michigan with those from younger tills just south of Lake Huron indicates that a significant westward shift in source area occurred during the retreat of the Huron–Erie Lobe from southeastern Michigan.
Discrete phase space - II: The second quantization of free relativistic wave fields
Authors: Das A.
Published: March 2010

The Klein–Gordon equation, the Maxwell equation, and the Dirac equation are presented as partial difference equations in the eight-dimensional covariant discrete phase space. These equations are also furnished as difference-differential equations in the arena of discrete phase space and continuous time. The scalar field and electromagnetic fields are quantized with commutation relations. The spin-1/2 field is quantized with anti-commutation relations. Moreover, the total momentum, energy and charge of these free relativisitic quantized fields in the discrete phase space and continuous time are computed exactly. The results agree completely with those computed from the relativisitic fields defined on the space-time continuum.
Grey solitons and soliton interaction of higher nonlinear Schrödinger equation
Authors: Li Qiu-Yan , Li Zai-Dong , He Peng-Bin , Song Wei-Wei , Fu Guangsheng
Published: March 2010

In this paper, the higher nonlinear Schrödinger equation is solved by the Hirota method. As an example, the exact grey one- and two-soliton solutions in explicit forms are generated analytically under the continuous-wave background. The results reveal that the velocity of the grey soliton is clearly affected by the higher order effects, yet the grey soliton propagates without any change in their shape and intensity. The higher order term and the phase velocity play the important role for the maximum valley of grey soliton, i.e., the intensity of grey soliton. For the black soliton, the velocity of soliton is determined only by the higher order effects. The analysis of the asymptotic behavior of a two grey soliton solution shows the collision is elastic.
Magnetpolaron effect on the D– center at the hetero-interface of III–V crystals
Authors: Zhang Xiao-Yan , Fan Guo-Liang
Published: March 2010

A theoretical study of the negative-donor center (D–) at the hetero-interface in a magnetic field is presented. The energy of a spin triplet state (p-like) of the D– center is calculated by a variational approach. The polaron correction to the D–state is discussed within second-order perturbation theory. Numerical results are produced for the heterostructure of some III–V crystals. We find that the polaron correction is very important and the contribution of the polaron is not negligible.
SCHWINGER MECHANISM FOR GLUON PAIR PRODUCTION IN THE PRESENCE OF ARBITRARY TIME DEPENDENT CHROMOELECTRIC FIELD IN ARBITRARY GAUGE
Authors: NAYAK GOURANGA C.
Published: March 2010

We study the nonperturbative gluon pair production from arbitrary time dependent chromoelectric field Ea(t) with arbitrary color index a = 1, 2,…, 8 via Schwinger mechanism in arbitrary covariant background gauge α. We show that the probability of nonperturbative gluon pair production per unit time per unit volume per unit transverse momentum [Formula: see text] is independent of gauge fixing parameter α. Hence the result obtained in the Feynman–'t Hooft gauge, α = 1, is the correct gauge invariant and gauge parameter α independent result.
META-STABLE BRANE CONFIGURATIONS BY DUALIZING THE TWO GAUGE GROUPS
Authors: AHN CHANGHYUN
Published: March 2010

We consider the [Formula: see text] supersymmetric gauge theories with product gauge groups. The two kinds of D6-branes in the electric theory are both displaced and rotated respectively where these deformations are interpreted as the mass terms and quartic terms for the two kinds of flavors. Then we apply the Seiberg dual to the whole gauge group factors by moving the branes and obtain the corresponding dual gauge theories. By analyzing the magnetic superpotentials consisting of an interaction term between a magnetic meson field and dual matters as well as the above deformations for each gauge group, we present the type IIA nonsupersymmetric meta-stable brane configurations.
HISTORY OF SUPERSYMMETRIC EXTENSIONS OF THE STANDARD MODEL
Authors: RODRIGUEZ M. C.
Published: March 2010

We recall the many obstacles which seemed, long ago, to prevent supersymmetry from possibly being a fundamental symmetry of Nature. We also present their solutions, leading to the construction of the supersymmetric extensions of the Standard Model. Finally we discuss briefly the early experimental searches for supersymmetry.
A NOTE ON THE ANALOGY BETWEEN SUPERFLUIDS AND COSMOLOGY
Authors: NADDEO A. , SCELZA G.
Published: March 2010

A new analogy between superfluid systems and cosmology is here presented, which relies strongly on the following ingredient: the back-reaction of the vacuum to the quanta of sound waves. We show how the presence of thermal phonons, the excitations above the quantum vacuum for T > 0, enable us to deduce an hydrodynamical equation formally similar to the one obtained for a perfect fluid in a Universe obeying the Friedmann–Robertson–Walker metric.
RIEMANN THETA FUNCTIONS SOLUTIONS WITH RATIONAL CHARACTERISTICS FOR (2+1)-DIMENSIONAL SINH-GORDON EQUATION
Authors: FENG YANG , ZHANG HONG-QING
Published: March 2010

In this letter, we use the Riemann theta functions with rational characteristics and the Hirota bilinear method to construct quasi-periodic wave solutions for (2+1)-dimensional sinh-Gordon equation. This method not only conveniently obtains quasi-periodic solutions of nonlinear equations, but also directly gets the explicit expressions of frequencies, wave numbers, phase and amplitudes for the waves.
HEAT CONDUCTION IN DIELECTRIC ATOMIC CHAINS WITH ON-SITE POTENTIAL
Authors: LI JIN-XING , LIU FEI , CHEN TAO
Published: March 2010

Heat conduction in dielectric atomic chains with on-site potential were studied by means of FKM formalism. Using numerical simulation we found that the on-site potential plays an important role in quantum thermal transport. As special cases, the "Fourier-like behavior" J ∝ 1/N was obtained also for different boundary conditions. The influence of boundaries can be regulated by the coupling strength coefficient of the on-site potential.
THE STRUCTURE OF PHONOLOGICAL NETWORKS ACROSS MULTIPLE LANGUAGES
Authors: ARBESMAN SAMUEL , STROGATZ STEVEN H. , VITEVITCH MICHAEL S.
Published: March 2010

The network characteristics based on the phonological similarities in the lexicons of several languages were examined. These languages differed widely in their history and linguistic structure, but commonalities in the network characteristics were observed. These networks were also found to be different from other networks studied in the literature. The properties of these networks suggest explanations for various aspects of linguistic processing and hint at deeper organization within the human language.
DISPERSION RELATIONS FOR COLD PLASMA AROUND THE HORIZON OF SCHWARZSCHILD–DE SITTER BLACK HOLE
Authors: HASAN M. KHAYRUL
Published: March 2010

In this paper, we investigate the wave properties of cold plasma in the vicinity of Schawarzchild–de Sitter black hole horizon using 3 + 1 formalism. The general relativistic magnetohydrodynamical equations are formulated for this space–time with the use of Rindler coordinates. We consider both the rotating and nonrotating surroundings with magnetized and nonmagnetized plasmas. Linear perturbation and Fourier analysis techniques are applied by introducing simple harmonic waves. We derive complex dispersion relation from the determinant of Fourier analyzed equations for each case which provides real and complex values of the wave number. From the wave number we determine the phase and group velocities, the refractive index etc., which are used to discuss the characteristics of the waves around the event horizon.
THE BSSN FORMULATION IS A PARTIALLY CONSTRAINED EVOLUTION SYSTEM
Authors: GENTLE ADRIAN P.
Published: March 2010

It is shown that the BSSN formulation of the Einstein equations, which forms the basis of most simulations in numerical relativity, explicitly uses the momentum constraints to evolve the conformal connection coefficients.
QUANTUM GRAVITATIONAL CORRECTIONS TO THE HYDROGEN ATOM AND HARMONIC OSCILLATOR
Authors: MAZIASHVILI MICHAEL , SILAGADZE ZURAB
Published: March 2010

It is shown that the rate of corrections to the hydrogen atom and harmonic oscillator energy levels due to the profound quantum gravitational effect of space–time dimension running/reduction coincides well with those obtained by means of minimum-length-deformed quantum mechanics. The rate of corrections is pretty much the same within the accuracy with which we can judge the quantum gravitational corrections at all. Such a convergence of results makes the concept of space–time dimension running more appreciable. As a remarkable distinction, the energy shift due to dimension reduction has the opposite sign as compared with the correction obtained by means of minimum-length-modified quantum mechanics. Therefore, the sign of total quantum gravitational correction remains somewhat obscure.
IMPACT OF CROSS-BORDER MIGRATION ON DISEASE EPIDEMICS: CASE OF THEP. FALCIPARUMANDP. VIVAXMALARIA EPIDEMIC ALONG THE THAI-MYANMAR BORDER
Authors: PONGSUMPUN PUNTANI , TANG I-MING
Published: March 2010

The transmission of Plasmodium falciparum and Plasmodium vivax malaria in a mixed population of Thais and migrant Burmese living along the Thai-Myanmar border is studied through a mathematical model. The population is separated into two groups: Thai and Burmese. Each population in turn is divided into susceptible, infected, recovered and in case of vivax infection, a dormant subclass. The model is then modified to allow for some of the Burmese (given as a fraction P) to be infectious when they enter into Thailand. The behaviour of the modified model is obtained using a standard dynamical analysis. A new basic reproduction number is obtained. Numerical simulations of the modified model show that when P ≠ 0 and the same set of parameter values used in the initial model are used, the Thai population will be in the epidemic state. In other words, the repeated introduction of infectious Burmese (no matter how small of a number) will result in a malaria epidemic among the Thais irregardless of the public health practice undertaken by the Thai government. In the presence of the infected Burmese, the Thai government would have to increase the facilitites to treat the people who are infected by the malaria.
STOCHASTIC MODELING WITH MONTE CARLO OF OBESITY POPULATION
Authors: GONZÁLEZ-PARRA GILBERTO , ARENAS ABRAHAM J. , SANTONJA F.-J.
Published: March 2010

In this paper, we investigate the dynamics of a mathematical model of obesity population within fluctuating social environment. A stochastic differential equation model is constructed by perturbing two social related parameters of the deterministic model with white noise terms characterized by Gaussian distribution having zero mean and unit spectral density. In order to compute the numerical solution of the stochastic models Euler-Maruyama numerical method is used. Confidence intervals for the overweight and obesity childhood population are computed using Monte Carlo method. Analysis of the numerical results reveals that small perturbations on the parameters are not a major driving force for dynamical transitions from the underlying deterministic model. In addition, numerical results indicate a close relationship between the amplitude of the fluctuation of the social environment parameters and the variability of forecasts for the incidence of the obesity in the population.
A CONTROL THEORY APPROACH TO CANCER REMISSION AIDED BY AN OPTIMAL THERAPY
Authors: CHAKRABARTY SIDDHARTHA P. , BANERJEE SANDIP
Published: March 2010

The mathematical model depicting cancer remission as presented by Banerjee and Sarkar1is reinvestigated here. Mathematical tools from control theory have been used to analyze and determine how an optimal external treatment of Adaptive Cellular Immunotherapy and interleukin-2 can result in more effective remission of malignant tumors while minimizing any adverse affect on the immune response.
MODELING BIOLOGICAL CONTROL OF ALGAL BLOOM IN A LAKE CAUSED BY DISCHARGE OF NUTRIENTS
Authors: GHOSH MINI
Published: March 2010

This paper proposes and analyzes a nonlinear model for the biological control of algal bloom in a lake. Algal bloom often occurs in a lake due to excessive flow of nutrients from domestic drainage, industrial and agricultural waste, and this causes the decrease in the concentration of dissolved oxygen in the lake. Hence, it threatens the survival of other species of the ecosystem indirectly, and it is also responsible for the degradation of water quality in the lake because of less oxygen content.

In this work we study biological control which means the introduction of predatory fish, i.e. the release of algae-eating fish into the lake to control the rapid growth of algae. We formulate our model by assuming Michaelis-Menten type ratio-dependent prey-predator interaction. The equilibrium of the mathematical model is found and also the stability is discussed in detail. It is observed that the positive equilibria is locally asymptotically stable under certain conditions on the parameters. Also the system is simulated for various sets of parameters and it is found that system may oscillate for some realistic set of parameters. In fact we found that the parameter m, which is the half saturation constant, is very sensitive and with the decrease in this parameter steady state solution of the system changes to stable oscillation. On the practical side, it means that the method of biological control by introducing predatory fish is not always beneficial because outcome of this method depends upon the actual value of the parameter. Here we get the paradox of biological control, which says that it is not possible to have low level of steady state equilibrium of prey population.
Computer Usage by Children with Down Syndrome
Authors: Feng Jinjuan , Lazar Jonathan , Kumin Libby , Ozok Ant
Published: March 2010

Children with Down syndrome, like neurotypical children, are growing up with extensive exposure to computer technology. Computers and computer-related devices have the potential to help these children in education, career development, and independent living. Our understanding of computer usage by this population is quite limited. Most of the software, games, and Web sites that children with Down syndrome interact with are designed without consideration of their special needs, making the applications less effective or completely inaccessible. We conducted a large-scale survey that collected computer usage information from the parents of approximately six hundred children with Down syndrome. This article reports the text responses collected in the survey and is intended as a step towards understanding the difficulties children with Down syndrome experience while using computers. The relationship between the age and the specific type of difficulties, as well as related design challenges are also reported. A number of potential research directions and hypotheses are identified for future studies. Due to limitations in survey methodology, the findings need to be further validated through hypothesis-driven, empirical studies.
Dynamic filtering
Authors: Harris Tim , Tomic Saša , Cristal Adrián , Unsal Osman
Published: March 2010

This paper introduces a new abstraction to accelerate the read-barriers and write-barriers used by language runtime systems. We exploit the fact that, dynamically, many barrier executions perform checks but no real work -- e.g., in generational garbage collection (GC), frequent checks are needed to detect the creation of inter-generational references, even though such references occur rarely in many workloads. We introduce a form of dynamic filtering that identifies redundant checks by (i) recording checks that have recently been executed, and (ii) detecting when a barrier is repeating one of these checks. We show how this technique can be applied to a variety of algorithms for GC, transactional memory, and language-based security. By supporting dynamic filtering in the instruction set, we show that the fast-paths of these barriers can be streamlined, reducing the impact on the quality of surrounding code. We show how we accelerate the barriers used for generational GC and transactional memory in the Bartok research compiler. With a 2048-entry filter, dynamic filtering eliminates almost all the overhead of the GC write-barriers. Dynamic filtering eliminates around half the overhead of STM over a non-synchronized baseline -- even when used with an STM that is already designed for low overhead, and which employs static analyses to avoid redundant operations.
Decoupling contention management from scheduling
Authors: Johnson F. Ryan , Stoica Radu , Ailamaki Anastasia , Mowry Todd C.
Published: March 2010

Many parallel applications exhibit unpredictable communication between threads, leading to contention for shared objects. The choice of contention management strategy impacts strongly the performance and scalability of these applications: spinning provides maximum performance but wastes significant processor resources, while blocking-based approaches conserve processor resources but introduce high overheads on the critical path of computation. Under situations of high or changing load, the operating system complicates matters further with arbitrary scheduling decisions which often preempt lock holders, leading to long serialization delays until the preempted thread resumes execution.

We observe that contention management is orthogonal to the problems of scheduling and load management and propose to decouple them so each may be solved independently and effectively. To this end, we propose a load control mechanism which manages the number of active threads in the system separately from any contention which may exist. By isolating contention management from damaging interactions with the OS scheduler, we combine the efficiency of spinning with the robustness of blocking. The proposed load control mechanism results in stable, high performance for both lightly and heavily loaded systems, requires no special privileges or modifications at the OS level, and can be implemented as a library which benefits existing code.
Analyzing multicore dumps to facilitate concurrency bug reproduction
Authors: Weeratunge Dasarath , Zhang Xiangyu , Jagannathan Suresh
Published: March 2010

Debugging concurrent programs is difficult. This is primarily because the inherent non-determinism that arises because of scheduler interleavings makes it hard to easily reproduce bugs that may manifest only under certain interleavings. The problem is exacerbated in multi-core environments where there are multiple schedulers, one for each core. In this paper, we propose a reproduction technique for concurrent programs that execute on multi-core platforms. Our technique performs a lightweight analysis of a failing execution that occurs in a multi-core environment, and uses the result of the analysis to enable reproduction of the bug in a single-core system, under the control of a deterministic scheduler.

More specifically, our approach automatically identifies the execution point in the re-execution that corresponds to the failure point. It does so by analyzing the failure core dump and leveraging a technique called
execution indexing
that identifies a related point in the re-execution. By generating a core dump at this point, and comparing the differences betwen the two dumps, we are able to guide a search algorithm to efficiently generate a failure inducing schedule. Our experiments show that our technique is highly effective and has reasonable overhead.
Characterizing processor thermal behavior
Authors: Mesa-Martinez Francisco Javier , Ardestani Ehsan K. , Renau Jose
Published: March 2010

Temperature is a dominant factor in the performance, reliability, and leakage power consumption of modern processors. As a result, increasing numbers of researchers evaluate thermal characteristics in their proposals. In this paper, we measure a real processor focusing on its thermal characterization executing diverse workloads.

Our results show that in real designs, thermal transients operate at larger scales than their performance and power counterparts. Conventional thermal simulation methodologies based on profile-based simulation or statistical sampling, such as Simpoint, tend to explore very limited execution spans. Short simulation times can lead to reduced matchings between performance and thermal phases. To illustrate these issues we characterize and classify from a thermal standpoint SPEC00 and SPEC06 applications, which are traditionally used in the evaluation of architectural proposals. This paper concludes with a list of recommendations regarding thermal modeling considerations based on our experimental insights.
Micro-pages
Authors: Sudan Kshitij , Chatterjee Niladrish , Nellans David , Awasthi Manu , Balasubramonian Rajeev , Davis Al
Published: March 2010

Power consumption and DRAM latencies are serious concerns in modern chip-multiprocessor (CMP or multi-core) based compute systems. The management of the DRAM row buffer can significantly impact both power consumption and latency. Modern DRAM systems read data from cell arrays and populate a row buffer as large as 8 KB on a memory request. But only a small fraction of these bits are ever returned back to the CPU. This ends up wasting energy and time to read (and subsequently write back) bits which are used rarely. Traditionally, an open-page policy has been used for uni-processor systems and it has worked well because of spatial and temporal locality in the access stream. In future multi-core processors, the possibly independent access streams of each core are interleaved, thus destroying the available locality and significantly under-utilizing the contents of the row buffer. In this work, we attempt to improve row-buffer utilization for future multi-core systems.

The schemes presented here are motivated by our observations that a large number of accesses within heavily accessed OS pages are to small, contiguous "chunks" of cache blocks. Thus, the co-location of chunks (from different OS pages) in a row-buffer will improve the overall utilization of the row buffer contents, and consequently reduce memory energy consumption and access time. Such co-location can be achieved in many ways, notably involving a reduction in OS page size and software or hardware assisted migration of data within DRAM. We explore these mechanisms and discuss the trade-offs involved along with energy and performance improvements from each scheme. On average, for applications with room for improvement, our best performing scheme increases performance by 9% (max. 18%) and reduces memory energy consumption by 15% (max. 70%).
Power routing
Authors: Pelley Steven , Meisner David , Zandevakili Pooya , Wenisch Thomas F. , Underwood Jack
Published: March 2010

Data center power infrastructure incurs massive capital costs, which typically exceed energy costs over the life of the facility. To squeeze maximum value from the infrastructure, researchers have proposed over-subscribing power circuits, relying on the observation that peak loads are rare. To ensure availability, these proposals employ power capping, which throttles server performance during utilization spikes to enforce safe power budgets. However, because budgets must be enforced locally -- at each power distribution unit (PDU) -- local utilization spikes may force throttling even when power delivery capacity is available elsewhere. Moreover, the need to maintain reserve capacity for fault tolerance on power delivery paths magnifies the impact of utilization spikes.

In this paper, we develop mechanisms to better utilize installed power infrastructure, reducing reserve capacity margins and avoiding performance throttling. Unlike conventional high-availability data centers, where collocated servers share identical primary and secondary power feeds, we reorganize power feeds to create shuffled power distribution topologies. Shuffled topologies spread secondary power feeds over numerous PDUs, reducing reserve capacity requirements to tolerate a single PDU failure. Second, we propose Power Routing, which schedules IT load dynamically across redundant power feeds to: (1) shift slack to servers with growing power demands, and (2) balance power draw across AC phases to reduce heating and improve electrical stability. We describe efficient heuristics for scheduling servers to PDUs (an NP-complete problem). Using data collected from nearly 1000 servers in three production facilities, we demonstrate that these mechanisms can reduce the required power infrastructure capacity relative to conventional high-availability data centers by 32% without performance degradation.
COMPASS
Authors: Woo Dong Hyuk , Lee Hsien-Hsin S.
Published: March 2010

A traditional fixed-function graphics accelerator has evolved into a programmable general-purpose graphics processing unit over the last few years. These powerful computing cores are mainly used for accelerating graphics applications or enabling low-cost scientific computing. To further reduce the cost and form factor, an emerging trend is to integrate GPU along with the memory controllers onto the same die with the processor cores. However, given such a system-on-chip, the GPU, while occupying a substantial part of the silicon, will sit idle and contribute nothing to the overall system performance when running non-graphics workloads or applications lack of data-level parallelism. In this paper, we propose COMPASS, a compute shader-assisted data prefetching scheme, to leverage the GPU resource for improving single-threaded performance on an integrated system. By harnessing the GPU shader cores with very lightweight architectural support, COMPASS can emulate the functionality of a hardware-based prefetcher using the idle GPU and successfully improve the memory performance of single-thread applications. Moreover, thanks to its flexibility and programmability, one can implement the best performing prefetch scheme to improve each specific application as demonstrated in this paper. With COMPASS, we envision that a future application vendor can provide a custom-designed COMPASS shader bundled with its software to be loaded at runtime to optimize the performance. Our simulation results show that COMPASS can improve the single-thread performance of memory-intensive applications by 68% on average.
Orthrus
Authors: Huang Ruirui , Deng Daniel Y. , Suh G. Edward
Published: March 2010

This paper proposes an efficient hardware/software system that significantly enhances software security through diversified replication on multi-cores. Recent studies show that a large class of software attacks can be detected by running multiple versions of a program simultaneously and checking the consistency of their behaviors. However, execution of multiple replicas incurs significant overheads on today's computing platforms, especially with fine-grained comparisons necessary for high security. Orthrus exploits similarities in automatically generated replicas to enable simultaneous execution of those replicas with minimal overheads; the architecture reduces memory and bandwidth overheads by compressing multiple memory spaces together, and additional power consumption and silicon area by eliminating redundant computations. Utilizing the hardware architecture, Orthrus implements a fine-grained memory layout diversification with the LLVM compiler and can detect corruptions in both pointers and critical data. Experiments indicate that the Orthrus architecture incurs minimal overheads and provides a protection against a broad range of attacks.
Shoestring
Authors: Feng Shuguang , Gupta Shantanu , Ansari Amin , Mahlke Scott
Published: March 2010

Aggressive technology scaling provides designers with an ever increasing budget of cheaper and faster transistors. Unfortunately, this trend is accompanied by a decline in individual device reliability as transistors become increasingly susceptible to soft errors. We are quickly approaching a new era where resilience to soft errors is no longer a luxury that can be reserved for just processors in high-reliability, mission-critical domains. Even processors used in mainstream computing will soon require protection. However, due to tighter profit margins, reliable operation for these devices must come at little or no cost. This paper presents Shoestring, a minimally invasive software solution that provides high soft error coverage with very little overhead, enabling its deployment even in commodity processors with "shoestring" reliability budgets. Leveraging intelligent analysis at compile time, and exploiting low-cost, symptom-based error detection, Shoestring is able to focus its efforts on protecting statistically-vulnerable portions of program code. Shoestring effectively applies instruction duplication to protect only those segments of code that, when subjected to a soft error, are likely to result in user-visible faults without first exhibiting symptomatic behavior. Shoestring is able to recover from an additional 33.9% of soft errors that are undetected by a symptom-only approach, achieving an overall user-visible failure rate of 1.6%. This reliability improvement comes at a modest performance overhead of 15.8%.
A power-efficient all-optical on-chip interconnect using wavelength-based oblivious routing
Authors: Kirman Nevin , Martínez José F.
Published: March 2010

We present an all-optical approach to constructing data networks on chip that combines the following key features: (1) Wavelength-based routing, where the route followed by a packet depends solely on the wavelength of its carrier signal, and not on information either contained in the packet or traveling along with it. (2) Oblivious routing, by which the wavelength (and thus the route) employed to connect a source-destination pair is invariant for that pair, and does not depend on ongoing transmissions by other nodes, thereby simplifying design and operation. And (3) passive optical wavelength routers, whose routing pattern is set at design time, which allows for area and power optimizations not generally available to solutions that use dynamic routing. Compared to prior proposals, our evaluation shows that our solution is significantly more power efficient at a similar level of performance.
A real system evaluation of hardware atomicity for software speculation
Authors: Neelakantam Naveen , Ditzel David R. , Zilles Craig
Published: March 2010

In this paper we evaluate the atomic region compiler abstraction by incorporating it into a commercial system. We find that atomic regions are simple and intuitive to integrate into an x86 binary-translation system. Furthermore, doing so trivially enables additional optimization opportunities beyond that achievable by a high-performance dynamic optimizer, which already implements superblocks.

We show that atomic regions can suffer from severe performance penalties if misspeculations are left uncontrolled, but that a simple software control mechanism is sufficient to reign in all detrimental side-effects. We evaluate using full reference runs of the SPEC CPU2000 integer benchmarks and find that atomic regions enable up to a 9% (3% on average) improvement beyond the performance of a tuned product.

These performance improvements are achieved without any negative side effects. Performance side effects such as code bloat are absent with atomic regions; in fact, static code size is reduced. The hardware necessary is synergistic with other needs and was already available on the commercial product used in our evaluation. Finally, the software complexity is minimal as a single developer was able to incorporate atomic regions into a sophisticated 300,000 line code base in three months, despite never having seen the translator source code beforehand.
Respec
Authors: Lee Dongyoon , Wester Benjamin , Veeraraghavan Kaushik , Narayanasamy Satish , Chen Peter M. , Flinn Jason
Published: March 2010

Deterministic replay systems record and reproduce the execution of a hardware or software system. While it is well known how to replay uniprocessor systems, replaying shared memory multiprocessor systems at low overhead on commodity hardware is still an open problem. This paper presents Respec, a new way to support deterministic replay of shared memory multithreaded programs on commodity multiprocessor hardware. Respec targets online replay in which the recorded and replayed processes execute concurrently.

Respec uses two strategies to reduce overhead while still ensuring correctness: speculative logging and externally deterministic replay. Speculative logging optimistically logs less information about shared memory dependencies than is needed to guarantee deterministic replay, then recovers and retries if the replayed process diverges from the recorded process. Externally deterministic replay relaxes the degree to which the two executions must match by requiring only their system output and final program states match. We show that the combination of these two techniques results in low recording and replay overhead for the common case of data-race-free execution intervals and still ensures correct replay for execution intervals that have data races.

We modified the Linux kernel to implement our techniques. Our software system adds on average about 18% overhead to the execution time for recording and replaying programs with two threads and 55% overhead for programs with four threads.
Addressing shared resource contention in multicore processors via scheduling
Authors: Zhuravlev Sergey , Blagodurov Sergey , Fedorova Alexandra
Published: March 2010

Contention for shared resources on multicore processors remains an unsolved problem in existing systems despite significant research efforts dedicated to this problem in the past. Previous solutions focused primarily on hardware techniques and software page coloring to mitigate this problem. Our goal is to investigate how and to what extent contention for shared resource can be mitigated via thread scheduling. Scheduling is an attractive tool, because it does not require extra hardware and is relatively easy to integrate into the system. Our study is the first to provide a comprehensive analysis of contention-mitigating techniques that use only scheduling. The most difficult part of the problem is to find a classification scheme for threads, which would determine how they affect each other when competing for shared resources. We provide a comprehensive analysis of such classification schemes using a newly proposed methodology that enables to evaluate these schemes separately from the scheduling algorithm itself and to compare them to the optimal. As a result of this analysis we discovered a classification scheme that addresses not only contention for cache space, but contention for other shared resources, such as the memory controller, memory bus and prefetching hardware. To show the applicability of our analysis we design a new scheduling algorithm, which we prototype at user level, and demonstrate that it performs within 2\% of the optimal. We also conclude that the highest impact of contention-aware scheduling techniques is not in improving performance of a workload as a whole but in improving quality of service or performance isolation for individual applications.