bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Human MicrosporidianEncephalitozoon hellemSynthesizes Two Spore Wall Polymorphic Proteins Useful for Epidemiological Studies
Authors: Polonais Valérie , Mazet Muriel , Wawrzyniak Ivan , Texier Catherine , Blot Nicolas , El Alaoui Hicham , Delbac Frédéric 
Published: March 2010

ABSTRACTMicrosporidia are obligate intracellular fungus-related parasites considered as emerging opportunistic human pathogens. Their extracellular infective and resistance stage is a spore surrounded by a unique plasma membrane protected by a thick cell wall consisting of two layers: the electron-lucent inner endospore which contains chitin and protein components and the outer-electron-dense and mainly proteinaceous exospore. We identified the whole sequences of two spore wall proteins in the microsporidian speciesEncephalitozoon hellem, designated EhSWP1a and EhSWP1b. Isolation of the genes encoding these SWP1-like proteins was performed using degenerate oligonucleotides based on the amino acid sequence alignment of the previously reportedEncephalitozoon cuniculiandEncephalitozoon intestinalisSWP1s. Sequences lacking the 5′ and 3′ ends were then identified by PCR and reverse transcription (RT)-PCR amplifications. Theswp1aandswp1bgenes encode proteins of 509 and 533 amino acids, respectively, which present an identical N-terminal domain of 382 residues and a variable C-terminal extension mainly characterized by a 26-amino-acid (aa) deletion/insertion containing glutamate- and lysine-rich repeats. Using polyclonal antibodies raised against recombinant polypeptides, we showed that EhSWP1a and EhSWP1b appear as dithiothreitol (DTT)-soluble bands of 55 and 60 kDa in size, respectively. Immunolocalization experiments by IFA and transmission electron microscopy (TEM) indicated that both proteins are present at the onset of sporogony and are specifically located to the spore wall exospore in mature spores. Analysis of fourE. hellemhuman isolates revealed that the C-terminal regions of both EhSWP1a and EhSWP1b are polymorphic, which is of interest for epidemiological studies.
Intrapulmonary Administration of Leukotriene B4Enhances Pulmonary Host Defense against Pneumococcal Pneumonia
Authors: Mancuso Peter , Lewis Casey , Serezani Carlos Henrique , Goel Deepti , Peters-Golden Marc 
Published: March 2010

ABSTRACTLeukotriene B4(LTB4) is a potent lipid mediator of inflammation formed by the 5-lipoxygenase (5-LO)-catalyzed oxidation of arachidonic acid. We have previously shown that (i) LTB4is generated during infection, (ii) its biosynthesis is essential for optimal antimicrobial host defense, (iii) LT deficiency is associated with clinical states of immunocompromise, and (iv) exogenous LTB4augments antimicrobial functions in phagocytes. Here, we sought to determine whether the administration of LTB4has therapeutic potential in a mouse model of pneumonia. Wild-type and 5-LO knockout mice were challenged withStreptococcus pneumoniaevia the intranasal route, and bacterial burdens, leukocyte counts, and cytokine levels were determined. LTB4was administered via the intraperitoneal, intravenous, and intranasal routes prior to pneumococcal infection and by aerosol 24 h following infection. Leukocytes recovered from mice givenS. pneumoniaeand treated with aerosolized LTB4were evaluated for expression levels of the p47phox subunit of NADPH oxidase. Intrapulmonary but not systemic pretreatment with LTB4significantly reduced the lungS. pneumoniaeburden in wild-type mice. Aerosolized LTB4was effective at improving lung bacterial clearance when administered postinoculation in animals with established infection and exhibited greater potency in 5-LO knockout animals, which also exhibited greater baseline susceptibility. Augmented bacterial clearance in response to LTB4was associated with enhanced monocyte recruitment and leukocyte expression of p47phox. The results of the current study in an animal model serve as a proof of concept for the potential utility of treatment with aerosolized LTB4as an immunostimulatory strategy in patients with bacterial pneumonia.
Heat-Stable Enterotoxin of EnterotoxigenicEscherichia colias a Vaccine Target
Authors: Taxt Arne , Aasland Rein , Sommerfelt Halvor , Nataro James , Puntervoll Pål 
Published: March 2010

ABSTRACTEnterotoxigenicEscherichia coli(ETEC) is responsible for 280 million to 400 million episodes of diarrhea and about 380,000 deaths annually. Epidemiological data suggest that ETEC strains which secrete heat-stable toxin (ST), alone or in combination with heat-labile toxin (LT), induce the most severe disease among children in developing countries. This makes ST an attractive target for inclusion in an ETEC vaccine. ST is released upon colonization of the small intestine and activates the guanylate cyclase C receptor, causing profuse diarrhea. To generate a successful toxoid, ST must be made immunogenic and nontoxic. Due to its small size, ST is nonimmunogenic in its natural form but becomes immunogenic when coupled to an appropriate large-molecular-weight carrier. This has been successfully achieved with several carriers, using either chemical conjugation or recombinant fusion techniques. Coupling of ST to a carrier may reduce toxicity, but further reduction by mutagenesis is desired to obtain a safe vaccine. More than 30 ST mutants with effects on toxicity have been reported. Some of these mutants, however, have lost the ability to elicit neutralizing immune responses to the native toxin. Due to the small size of ST, separating toxicity from antigenicity is a particular challenge that must be met. Another obstacle to vaccine development is possible cross-reactivity between anti-ST antibodies and the endogenous ligands guanylin and uroguanylin, caused by structural similarity to ST. Here we review the molecular and biological properties of ST and discuss strategies for developing an ETEC vaccine that incorporates immunogenic and nontoxic derivatives of the ST toxin.
Application of the “confusion principle” to Sn-based materials as negative electrode materials for Li-ion batteries
Authors: Ferguson P. P. , Dahn J. R. 
Published: March 2010

The “confusion principle” (Greer. Nature, 366, 303 (1993)) is applied to tin-3d transition metals carbon alloys to obtain a nanostructured negative electrode material. Various Sn–TMs–C samples with TMs = Ti, V, Cr, Mn, Fe, Co, Ni, and Cu (all included with same atomic ratios) were prepared by mechanical milling and by mechanical alloying. Each 10-component alloy sample was examined structurally using X-ray diffraction (XRD) and electrochemically using Li/Sn–TM–C cells. The sample Sn10TMs80C10 showed a nanostructured or amorphous-type XRD pattern, which shows the validity of this principle. XRD patterns of samples prepared with higher Sn atomic content showed crystalline features of Sn-based intermetallics. As expected, a very low specific capacity ( [Formula: see text]100 mAh/g) was observed for the sample Sn10TMs80C10. The sample Sn30TMs30C40 had the highest specific capacity (near 400 mAh/g) of the samples prepared. However, features of Sn aggregation were noticed at cycle number 80 of the latter sample, which are normally detrimental to the capacity retention upon further cycling.
FADDEEV–POPOV GHOSTS
Authors: FADDEEV LUDVIG DMITRIEVICH 
Published: March 2010

In the terminology of theoretical physics, the term "ghost" is used to identify an object that has no real physical meaning. The name "Faddeev–Popov ghosts" is given to the fictitious fields that were originally introduced in the construction of a manifestly Lorentz covariant quantization of the Yang–Mills field. Later, these objects acquired more widespread application, including in string theory. The necessity of ghosts is associated with gauge invariance. In gauge invariant theories, one usually has to deal with local fields, whose number exceeds that of physical degrees of freedom. For example in electrodynamics, in order to maintain manifest Lorentz invariance, one uses a four component vector potential Aμ(x), whereas the photon has only two polarizations. Thus, one needs a suitable mechanism in order to get rid of the unphysical degrees of freedom. Introducing fictitious fields, the ghosts, is one way of achieving this goal.
Satin
Authors: Van Nieuwpoort Rob V. , Wrzesińska Gosia , Jacobs Ceriel J. H. , Bal Henri E. 
Published: March 2010

Computational grids have an enormous potential to provide compute power. However, this power remains largely unexploited today for most applications, except trivially parallel programs. Developing parallel grid applications simply is too difficult. Grids introduce several problems not encountered before, mainly due to the highly heterogeneous and dynamic computing and networking environment. Furthermore, failures occur frequently, and resources may be claimed by higher-priority jobs at any time.
In this article, we solve these problems for an important class of applications: divide-and-conquer. We introduce a system called Satin that simplifies the development of parallel grid applications by providing a rich high-level programming model that completely hides communication. All grid issues are transparently handled in the runtime system, not by the programmer. Satin's programming model is based on Java, features spawn-sync primitives and shared objects, and uses asynchronous exceptions and an abort mechanism to support speculative parallelism.
To allow an efficient implementation, Satin consistently exploits the idea that grids are hierarchically structured. Dynamic load-balancing is done with a novel cluster-aware scheduling algorithm that hides the long wide-area latencies by overlapping them with useful local work. Satin's shared object model lets the application define the consistency model it needs. If an application needs only loose consistency, it does not have to pay high performance penalties for wide-area communication and synchronization.
We demonstrate how grid problems such as resource changes and failures can be handled transparently and efficiently. Finally, we show that adaptivity is important in grids. Satin can increase performance considerably by adding and removing compute resources automatically, based on the application's requirements and the utilization of the machines and networks in the grid.
Using an extensive evaluation on real grids with up to 960 cores, we demonstrate that it is possible to provide a simple high-level programming model for divide-and-conquer applications, while achieving excellent performance on grids. At the same time, we show that the divide-and-conquer model scales better on large systems than the master-worker approach, since it has no single central bottleneck.
SherLog
Authors: Yuan Ding , Mai Haohui , Xiong Weiwei , Tan Lin , Zhou Yuanyuan , Pasupathy Shankar 
Published: March 2010

Computer systems often fail due to many factors such as software bugs or administrator errors. Diagnosing such production run failures is an important but challenging task since it is difficult to reproduce them in house due to various reasons: (1) unavailability of users' inputs and file content due to privacy concerns; (2) difficulty in building the exact same execution environment; and (3) non-determinism of concurrent executions on multi-processors.
Therefore, programmers often have to diagnose a production run failure based on logs collected back from customers and the corresponding source code. Such diagnosis requires expert knowledge and is also too time-consuming, tedious to narrow down root causes. To address this problem, we propose a tool, called SherLog, that analyzes source code by leveraging information provided by run-time logs to infer what must or may have happened during the failed production run. It requires neither re-execution of the program nor knowledge on the log's semantics. It infers both control and data value information regarding to the failed execution.

We evaluate SherLog with 8 representative
real world
software failures (6 software bugs and 2 configuration errors) from 7 applications including 3 servers. Information inferred by SherLog are very useful for programmers to diagnose these evaluated failures. Our results also show that SherLog can analyze large server applications such as Apache with thousands of logging messages within only 40 minutes.
An asymmetric distributed shared memory model for heterogeneous parallel systems
Authors: Gelado Isaac , Stone John E. , Cabezas Javier , Patel Sanjay , Navarro Nacho , Hwu Wen-mei W. 
Published: March 2010

Heterogeneous computing combines general purpose CPUs with accelerators to efficiently execute both sequential control-intensive and data-parallel phases of applications. Existing programming models for heterogeneous computing rely on programmers to explicitly manage data transfers between the CPU system memory and accelerator memory.
This paper presents a new programming model for heterogeneous computing, called Asymmetric Distributed Shared Memory (ADSM), that maintains a shared logical memory space for CPUs to access objects in the accelerator physical memory but not vice versa. The asymmetry allows light-weight implementations that avoid common pitfalls of symmetrical distributed shared memory systems. ADSM allows programmers to assign data objects to performance critical methods. When a method is selected for accelerator execution, its associated data objects are allocated within the shared logical memory space, which is hosted in the accelerator physical memory and transparently accessible by the methods executed on CPUs.
We argue that ADSM reduces programming efforts for heterogeneous computing systems and enhances application portability. We present a software implementation of ADSM, called GMAC, on top of CUDA in a GNU/Linux environment. We show that applications written in ADSM and running on top of GMAC achieve performance comparable to their counterparts using programmer-managed data transfers. This paper presents the GMAC system and evaluates different design choices. We further suggest additional architectural support that will likely allow GMAC to achieve higher application performance than the current CUDA model.
Inter-core cooperative TLB for chip multiprocessors
Authors: Bhattacharjee Abhishek , Martonosi Margaret 
Published: March 2010

Translation Lookaside Buffers (TLBs) are commonly employed in modern processor designs and have considerable impact on overall system performance. A number of past works have studied TLB designs to lower access times and miss rates, specifically for uniprocessors. With the growing dominance of chip multiprocessors (CMPs), it is necessary to examine TLB performance in the context of parallel workloads.
This work is the first to present TLB prefetchers that exploit commonality in TLB miss patterns across cores in CMPs. We propose and evaluate two Inter-Core Cooperative (ICC) TLB prefetching mechanisms, assessing their effectiveness at eliminating TLB misses both individually and together. Our results show these approaches require at most modest hardware and can collectively eliminate 19% to 90% of data TLB (D-TLB) misses across the surveyed parallel workloads.
We also compare performance improvements across a range of hardware and software implementation possibilities. We find that while a fully-hardware implementation results in average performance improvements of 8-46% for a range of TLB sizes, a hardware/software approach yields improvements of 4-32%. Overall, our work shows that TLB prefetchers exploiting inter-core correlations can effectively eliminate TLB misses.
Modulation of Internal Gravity Waves in a Multiscale Model for Deep Convection on Mesoscales
Authors: Ruprecht Daniel , Klein Rupert , Majda Andrew J. 
Published: March 2010

AbstractStarting from the conservation laws for mass, momentum, and energy together with a three-species bulk microphysics model, a model for the interaction of internal gravity waves and deep convective hot towers is derived using multiscale asymptotic techniques. From the leading-order equations, a closed model for the large-scale flow is obtained analytically by applying horizontal averages conditioned on the small-scale hot towers. No closure approximations are required besides adopting the asymptotic limit regime on which the analysis is based. The resulting model is an extension of the anelastic equations linearized about a constant background flow. Moist processes enter through the area fraction of saturated regions and through two additional dynamic equations describing the coupled evolution of the conditionally averaged small-scale vertical velocity and buoyancy. A two-way coupling between the large-scale dynamics and these small-scale quantities is obtained: moisture reduces the effective stability for the large-scale flow, and microscale up- and downdrafts define a large-scale averaged potential temperature source term. In turn, large-scale vertical velocities induce small-scale potential temperature fluctuations due to the discrepancy in effective stability between saturated and nonsaturated regions.The dispersion relation and group velocity of the system are analyzed and moisture is found to have several effects: (i) it reduces vertical energy transport by waves, (ii) it increases vertical wavenumbers but decreases the slope at which wave packets travel, (iii) it introduces a new lower horizontal cutoff wavenumber in addition to the well-known high wavenumber cutoff, and (iv) moisture can cause critical layers. Numerical examples reveal the effects of moisture on steady-state and time-dependent mountain waves in the present hot-tower regime.
A Comparative Verification of Localized Aviation Model Output Statistics Program (LAMP) and Numerical Weather Prediction (NWP) Model Forecasts of Ceiling Height and Visibility
Authors: Rudack David E. , Ghirardelli Judy E. 
Published: March 2010

Abstract
In an effort to support aviation forecasting, the National Weather Service’s Meteorological Development Laboratory (MDL) has recently redeveloped the Localized Aviation Model Output Statistics (MOS) Program (LAMP) system. LAMP is designed to run hourly in NWS operations and produce short-range aviation forecast guidance at 1-h projections out to 25 h. This paper compares and contrasts LAMP ceiling height and visibility forecasts with forecasts produced by the 20-km Rapid Update Cycle model (RUC20), the Weather Research and Forecasting Nonhydrostatic Mesoscale Model (WRF-NMM), and the Short-Range Ensemble Forecast system (SREF). RUC20 and WRF-NMM forecasts of continuous ceiling height and visibility were interpolated to stations and converted into categorical forecasts. These interpolated forecasts were also categorized into instrument flight rule (IFR) or lower conditions and verified against LAMP forecasts at stations in the contiguous United States. LAMP and SREF probabilistic forecasts of ceiling height and visibility from LAMP and the SREF system were also verified. This study demonstrates that for the 0000 and 1200 UTC cycles over the contiguous United States, LAMP station-based categorical forecasts of ceiling height, visibility, and IFR conditions or lower are more accurate than the RUC20 and WRF-NMM ceiling height and visibility forecasts interpolated to stations. Moreover, for the 0900 and 2100 UTC forecast cycles and verification periods studied here, LAMP ceiling height and visibility probabilities exhibit better reliability and skill than the SREF system.
Differing effects of HbS and HbC traits on uncomplicated falciparum malaria, anemia, and child growth
Authors: Kreuels Benno , Kreuzberg Christina , Kobbe Robin , Ayim-Akonor Matilda , Apiah-Thompson Peter , Thompson Benedicta , Ehmen Christa , Adjei Samuel , Langefeld Iris , Adjei Ohene , May Jürgen 
Published: March 2010

Abstract
The high prevalence of hemoglobin S (HbS) in Africa and hemoglobin C (HbC) in parts of West Africa is caused by the strong protection against severe falciparum malaria during childhood. Much less is known about the effect of HbS and especially HbC on Plasmodium falciparum infection, uncomplicated malaria, and anemia. A total of 1070 children from the Ashanti Region, Ghana, were enrolled at the age of 3 months and visited monthly until 2 years of age. The effects of the β-globin genotype on the age-dependent incidence of malaria, levels of parasitemia, and hemoglobin as well as physical development were analyzed by population-averaged models. Infants with HbAS were protected from uncomplicated malaria (P < .005) and anemia (P < .001), had lower age-adjusted parasite densities (P < .001), and higher age-adjusted hemoglobin levels compared with children with the HbAA genotype (P = .004). In contrast, HbAC carriers had lower hemoglobin levels (P < .033) and were not protected against malaria or anemia. Notably, infants with HbAS were also significantly protected against stunting compared with carriers of HbAA or HbAC. This indicates differing mechanisms of protection against malaria of HbAS and HbAC and might help to understand why HbC is restricted to distinct areas of West Africa.
A parallel and incremental algorithm for efficient unique signature discovery on DNA databases
Authors: Lee Hsiao Ping , Sheu Tzu-Fang , Tang Chuan Yi 
Published: March 2010

Abstract

Background
DNA signatures are distinct short nucleotide sequences that provide valuable information that is used for various purposes, such as the design of Polymerase Chain Reaction primers and microarray experiments. Biologists usually use a discovery algorithm to find unique signatures from DNA databases, and then apply the signatures to microarray experiments. Such discovery algorithms require to set some input factors, such as signature length l and mismatch tolerance d, which affect the discovery results. However, suggestions about how to select proper factor values are rare, especially when an unfamiliar DNA database is used. In most cases, biologists typically select factor values based on experience, or even by guessing. If the discovered result is unsatisfactory, biologists change the input factors of the algorithm to obtain a new result. This process is repeated until a proper result is obtained. Implicit signatures under the discovery condition (l, d) are defined as the signatures of length ≤ l with mismatch tolerance ≥ d. A discovery algorithm that could discover all implicit signatures, such that those that meet the requirements concerning the results, would be more helpful than one that depends on trial and error. However, existing discovery algorithms do not address the need to discover all implicit signatures.

Results
This work proposes two discovery algorithms - the consecutive multiple discovery (CMD) algorithm and the parallel and incremental signature discovery (PISD) algorithm. The PISD algorithm is designed for efficiently discovering signatures under a certain discovery condition. The algorithm finds new results by using previously discovered results as candidates, rather than by using the whole database. The PISD algorithm further increases discovery efficiency by applying parallel computing. The CMD algorithm is designed to discover implicit signatures efficiently. It uses the PISD algorithm as a kernel routine to discover implicit signatures efficiently under every feasible discovery condition.

Conclusions
The proposed algorithms discover implicit signatures efficiently. The presented CMD algorithm has up to 97% less execution time than typical sequential discovery algorithms in the discovery of implicit signatures in experiments, when eight processing cores are used.