bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome for Photobiological Hydrogen Production Induced by Sulfur Deprivation in the Green Alga
Chlamydomonas reinhardtii
Authors: Nguyen Anh Vu , Thomas-Hall Skye R. , Malnoë Alizée , Timmins Matthew , Mussgnug Jan H. , Rupprecht Jens , Kruse Olaf , Hankamer Ben , Schenk Peer M. 
Published: August 2008

ABSTRACT

Photobiological hydrogen production using microalgae is being developed into a promising clean fuel stream for the future. In this study, microarray analyses were used to obtain global expression profiles of mRNA abundance in the green alga
Chlamydomonas reinhardtii
at different time points before the onset and during the course of sulfur-depleted hydrogen production. These studies were followed by real-time quantitative reverse transcription-PCR and protein analyses. The present work provides new insights into photosynthesis, sulfur acquisition strategies, and carbon metabolism-related gene expression during sulfur-induced hydrogen production. A general trend toward repression of transcripts encoding photosynthetic genes was observed. In contrast to all other
LHCBM
genes, the abundance of the
LHCBM9
transcript (encoding a major light-harvesting polypeptide) and its protein was strongly elevated throughout the experiment. This suggests a major remodeling of the photosystem II light-harvesting complex as well as an important function of
LHCBM9
under sulfur starvation and photobiological hydrogen production. This paper presents the first global transcriptional analysis of
C. reinhardtii
before, during, and after photobiological hydrogen production under sulfur deprivation.
Shr Is a Broad-Spectrum Surface Receptor That Contributes to Adherence and Virulence in Group A Streptococcus
Authors: Fisher Morly , Huang Ya-Shu , Li Xueru , McIver Kevin S. , Toukoki Chadia , Eichenbaum Zehava 
Published: August 2008

ABSTRACTGroup A streptococcus (GAS) is a common hemolytic pathogen that produces a range of suppurative infections and autoimmune sequelae in humans. Shr is an exported protein in GAS, which binds in vitro to hemoglobin, myoglobin, and the hemoglobin-haptoglobin complex. We previously reported that Shr is found in association with whole GAS cells and in culture supernatant. Here, we demonstrate that cell-associated Shr could not be released from the bacteria by the muralytic enzyme mutanolysin and was instead localized to the membrane. Shr was available, however, on the exterior of GAS, exposed to the extracellular environment. In vitro binding and competition assays demonstrated that in addition to hemoprotein binding, purified Shr specifically interacts with immobilized fibronectin and laminin. The absence of typical fibronectin-binding motifs indicates that a new protein pattern is involved in the binding of Shr to the extracellular matrix. RecombinantLactococcus lactiscells expressing Shr on the bacterial surface gained the ability to bind to immobilized fibronectin, suggesting that Shr can function as an adhesin. The inactivation ofshrresulted in a 40% reduction in the attachment to human epithelial cells in comparison to the parent strain. GAS infection elicited a high titer of Shr antibodies in sera from convalescent mice, demonstrating that Shr is expressed in vivo. Theshrmutant was attenuated for virulence in an intramuscular zebrafish model system. In summary, this study identifies Shr as being a new microbial surface component recognizing adhesive matrix molecules in GAS that mediates attachment to epithelial cells and contributes to the infection process.
Chlamydial Effector Proteins Localized to the Host Cell Cytoplasmic Compartment
Authors: Kleba Betsy , Stephens Richard S. 
Published: August 2008

ABSTRACTDisease-causing microbes utilize various strategies to modify their environment in order to create a favorable location for growth and survival. Gram-negative bacterial pathogens often use specialized secretion systems to translocate effector proteins directly into the cytosol of the eukaryotic cells they infect. These bacterial proteins are responsible for modulating eukaryotic cell functions. Identification of the bacterial effectors has been a critical step toward understanding the molecular basis for the pathogenesis of the bacteria that use them. Chlamydiae are obligate intracellular bacterial pathogens that have a type III secretion system believed to translocate virulence effector proteins into the cytosol of their host cells. Selective permeabilization of the eukaryotic cell membrane was used in conjunction with metabolic labeling of bacterial proteins to identify chlamydial proteins that localize within the cytosol of infected cells. More than 20Chlamydia trachomatisandC. pneumoniaeproteins were detected within the cytoplasmic compartment of infected cells. While a number of cytosolic proteins were shared, others were unique to each species, suggesting that variation among cytosolic chlamydial proteins contributes to the differences in the pathogenesis of the chlamydial species. The spectrum of chlamydial proteins exported differed concomitant with the progress of the developmental cycle. These data confirm that a dynamic relationship exists betweenChlamydiaand its host and that translocation of bacterial proteins into the cytosol is developmentally dependent.
Integrative Conjugative Elements and Related Elements Are Major Contributors to the Genome Diversity ofStreptococcus agalactiae
Authors: Brochet Mathieu , Couvé Elisabeth , Glaser Philippe , Guédon Gérard , Payot Sophie 
Published: August 2008

ABSTRACTThirty-five putative integrative conjugative elements and related elements were identified at 15 locations in the eight sequenced genomes ofStreptococcus agalactiae. Twelve are composite, likely resulting from site-specific accretions. Circular forms were detected for five elements. Macroarray analysis confirmed their high plasticity and wide distribution inS. agalactiae.
Interaction of Penicillin-Binding Protein 2 with Soluble Lytic Transglycosylase B1 inPseudomonas aeruginosa
Authors: Legaree Blaine A. , Clarke Anthony J. 
Published: August 2008

ABSTRACTSoluble lytic transglycosylase B1 fromPseudomonas aeruginosawas coupled to Sepharose and used to immobilize interaction partners from membrane protein extracts. Penicillin-binding protein 2 (PBP2) was identified as a binding partner, suggesting that the two proteins function together in the biosynthesis of peptidoglycan. By use of an engineered truncated derivative, the N-terminal module of PBP2 was found to confer the binding properties.
Deflating the big bang
Authors: Smith Randy , Estan Cristian , Jha Somesh , Kong Shijin 
Published: August 2008

Deep packet inspection is playing an increasingly important role in the design of novel network services. Regular expressions are the language of choice for writing signatures, but standard DFA or NFA representations are unsuitable for high-speed environments, requiring too much memory, too much time, or too much per-flow state. DFAs are fast and can be readily combined, but doing so often leads to state-space explosion. NFAs, while small, require large per-flow state and are slow.
We propose a solution that simultaneously addresses all these problems. We start with a first-principles characterization of state-space explosion and give conditions that eliminate it when satisfied. We show how auxiliary variables can be used to transform automata so that they satisfy these conditions, which we codify in a formal model that augments DFAs with auxiliary variables and simple instructions for manipulating them. Building on this model, we present techniques, inspired by principles used in compiler optimization, that systematically reduce runtime and per-flow state. In our experiments, signature sets from Snort and Cisco Systems achieve state-space reductions of over four orders of magnitude, per-flow state reductions of up to a factor of six, and runtimes that approach DFAs.
Satellitelab
Authors: Dischinger Marcel , Haeberlen Andreas , Beschastnikh Ivan , Gummadi Krishna P. , Saroiu Stefan 
Published: August 2008

Planetary-scale network testbeds like PlanetLab and RON have become indispensable for evaluating prototypes of distributed systems under realistic Internet conditions. However, current testbeds lack the heterogeneity that characterizes the commercial Internet. For example, most testbed nodes are connected to well-provisioned research networks, whereas most Internet nodes are in edge networks.
In this paper, we present the design, implementation, and evaluation of SatelliteLab, a testbed that includes nodes from a diverse set of Internet edge networks. SatelliteLab has a two-tier architecture, in which well-provisioned nodes called planets form the core, and lightweight nodes called satellites connect to the planets from the periphery. The application code of an experiment runs on the planets, whereas the satellites only forward network traffic. Thus, the traffic is subjected to the network conditions of the satellites, which greatly improves the testbed's network heterogeneity. The separation of code execution and traffic forwarding enables satellites to remain lightweight, which lowers the barrier to entry for Internet edge nodes.
Our prototype of SatelliteLab uses PlanetLab nodes as planets and a set of 32 volunteered satellites with diverse network characteristics. These satellites consist of desktops, laptops, and handhelds connected to the Internet via cable, DSL, ISDN, Wi-Fi, Bluetooth, and cellular links. We evaluate SatelliteLab's design, and we demonstrate the benefits of evaluating applications on SatelliteLab.
Taming the torrent
Authors: Choffnes David R. , Bustamante Fabián E. 
Published: August 2008

Peer-to-peer (P2P) systems, which provide a variety of popular services, such as file sharing, video streaming and voice-over-IP, contribute a significant portion of today's Internet traffic. By building overlay networks that are oblivious to the underlying Internet topology and routing, these systems have become one of the greatest traffic-engineering challenges for Internet Service Providers (ISPs) and the source of costly data traffic flows. In an attempt to reduce these operational costs, ISPs have tried to shape, block or otherwise limit P2P traffic, much to the chagrin of their subscribers, who consistently finds ways to eschew these controls or simply switch providers.
In this paper, we present the design, deployment and evaluation of an approach to reducing this costly cross-ISP traffic without sacrificing system performance. Our approach recycles network views gathered at low cost from content distribution networks to drive biased neighbor selection without any path monitoring or probing. Using results collected from a deployment in BitTorrent with over 120,000 users in nearly 3,000 networks, we show that our lightweight approach significantly reduces cross-ISP traffic and, over 33% of the time, it selects peers along paths that are within a single autonomous system (AS). Further, we find that our system locates peers along paths that have two orders of magnitude lower latency and 30% lower loss rates than those picked at random, and that these high-quality paths can lead to significant improvements in transfer rates. In challenged settings where peers are overloaded in terms of available bandwidth, our approach provides 31% average download-rate improvement; in environments with large available bandwidth, it increases download rates by 207% on average (and improves median rates by 883%
Symbol-level network coding for wireless mesh networks
Authors: Katti Sachin , Katabi Dina , Balakrishnan Hari , Medard Muriel 
Published: August 2008

This paper describes MIXIT, a system that improves the throughput of wireless mesh networks. MIXIT exploits a basic property of mesh networks: even when no node receives a packet correctly, any given bit is likely to be received by some node correctly. Instead of insisting on forwarding only correct packets, MIXIT routers use physical layer hints to make their best guess about which bits in a corrupted packet are likely to be correct and forward them to the destination. Even though this approach inevitably lets erroneous bits through, we find that it can achieve high throughput without compromising end-to-end reliability.
The core component of MIXIT is a novel network code that operates on small groups of bits, called symbols. It allows the nodes to opportunistically route groups of bits to their destination with low overhead. MIXIT's network code also incorporates an end-to-end error correction component that the destination uses to correct any errors that might seep through. We have implemented MIXIT on a software radio platform running the Zigbee radio protocol. Our experiments on a 25-node indoor testbed show that MIXIT has a throughput gain of 2.8x over MORE, a state-of-the-art opportunistic routing scheme, and about 3.9x over traditional routing using the ETX metric.
Thermodynamic Consistency of the Anelastic Approximation for a Moist Atmosphere
Authors: Pauluis Olivier 
Published: August 2008

AbstractThe primary goal of this paper is to validate the use of the anelastic approximation for fluids with a complex equation of state such as moist air or seawater. The anelastic approximation is based on a leading-order expansion of the equations of motion for a compressible fluid in terms of density. Its application to atmospheric flows has been based on a dry framework that treats phase transitions as an external energy source. However, cloudy air is more accurately described as a two-phase fluid in which condensed water and water vapor are in thermodynamic equilibrium. Thermodynamic equilibrium reduces to three the number of state variables necessary to describe the thermodynamic state of moist air, and leads to a discontinuity in the partial derivatives of the equation of state at the saturation point. A version of the anelastic approximation for a moist atmosphere is derived here by considering the atmospheric density as a small perturbation from a moist-adiabatic reference profile, and using moist entropy and total water content as prognostic variables, with buoyancy determined from the complete nonlinear equation of state.The key finding of this paper is that this implementation of the anelastic approximation conserves energy. The total energy is equal to the sum of the kinetic energy and the thermodynamic energy. The latter is found to be equal to the sum of the enthalpy and geopotential energy of the parcel. Furthermore, the state relationships between this thermodynamic energy, entropy, and other state variables are the same as those for moist air after replacing the total pressure with the reference state pressure. This guarantees that, as long as the pressure perturbation remains small, the thermodynamic behavior of a fluid under the anelastic approximation is fully consistent with both the first and second laws of thermodynamics.Two implications of this finding are also discussed. First, it is shown that the first and second laws of thermodynamics constrain the vertically integrated buoyancy flux. This is equivalent to deriving the total work performed in a compressible atmosphere from its entropy and energy budgets. Second, it is argued that an anelastic model can be built with temperature or enthalpy as a prognostic variable instead of entropy. The rate of change for this new state variable can be obtained from energy conservation, so that such a model explicitly obeys the first law of thermodynamics. The entropy in this model is equal to the entropy of the parcel evaluated at the reference pressure, and its evolution obeys the second law of thermodynamics.
Aspects of Precipitation Development in Trade Wind Cumulus Revealed by Differential Reflectivity at S Band
Authors: Knight Charles A. , Miller L. Jay , Rilling Robert A. 
Published: August 2008

Abstract
Early radar echo development in trade wind cumulus clouds is studied using the equivalent reflectivity factor Ze combined with the differential reflectivity Zdr. The clouds studied are among the largest of trade wind cumulus, developing significantly positive values of Zdr and attaining at least about a 30-dBZ equivalent reflectivity factor. The measures used for analysis are values calculated for entire constant–elevation angle sweeps through the clouds and entire volume scans—not maximum single-pulse-volume values. The radar echo evolution follows fairly closely the Marshall–Palmer distribution with scatter toward higher values of Zdr especially in the earliest stages of echo intensification, where some of the scatter in the whole-sweep values is caused by size sorting. The data provide no evidence for an important role of ultragiant aerosols (UGA) in initiating coalescence. They are in strong contrast with similar data from a cloud over northern Alabama that do suggest a major role for UGA in producing several-mm-diameter raindrops that dominate its weak, early radar echo.
FcγR-stimulated activation of the NADPH oxidase: phosphoinositide-binding protein p40phox regulates NADPH oxidase activity after enzyme assembly on the phagosome
Authors: Tian Wei , Li Xing Jun , Stull Natalie D. , Ming Wenyu , Suh Chang-Il , Bissonnette Sarah A. , Yaffe Michael B. , Grinstein Sergio , Atkinson Simon J. , Dinauer Mary C. 
Published: August 2008

AbstractThe phagocyte NADPH oxidase generates superoxide for microbial killing, and includes a membrane-bound flavocytochrome b558 and cytosolic p67phox, p47phox, and p40phox subunits that undergo membrane translocation upon cellular activation. The function of p40phox, which binds p67phox in resting cells, is incompletely understood. Recent studies showed that phagocytosis-induced superoxide production is stimulated by p40phox and its binding to phosphatidylinositol-3-phosphate (PI3P), a phosphoinositide enriched in membranes of internalized phagosomes. To better define the role of p40phox in FcγR-induced oxidase activation, we used immunofluorescence and real-time imaging of FcγR-induced phagocytosis. YFP-tagged p67phox and p40phox translocated to granulocyte phagosomes before phagosome internalization and accumulation of a probe for PI3P. p67phox and p47phox accumulation on nascent and internalized phagosomes did not require p40phox or PI3 kinase activity, although superoxide production before and after phagosome sealing was decreased by mutation of the p40phox PI3P-binding domain or wortmannin. Translocation of p40phox to nascent phagosomes required binding to p67phox but not PI3P, although the loss of PI3P binding reduced p40phox retention after phagosome internalization. We conclude that p40phox functions primarily to regulate FcγR-induced NADPH oxidase activity rather than assembly, and stimulates superoxide production via a PI3P signal that increases after phagosome internalization.
Overexpression of TOSO in CLL is triggered by B-cell receptor signaling and associated with progressive disease
Authors: Pallasch Christian Philipp , Schulz Alexandra , Kutsch Nadine , Schwamb Janine , Hagist Susanne , Kashkar Hamid , Ultsch Alfred , Wickenhauser Claudia , Hallek Michael , Wendtner Clemens-Martin 
Published: August 2008

Abstract
Resistance toward apoptotic stimuli mediated by overexpression of antiapoptotic factors or extracellular survival signals is considered to be responsible for accumulation of malignant B cells in chronic lymphocytic leukemia (CLL). TOSO was identified as overexpressed candidate gene in CLL, applying unit-transformation assays of publicly available microarray datasets. Based on CLL samples from 106 patients, TOSO was identified to exhibit elevated relative expression (RE) of 6.8 compared with healthy donor B cells using quantitative real-time polymerase chain reaction (PCR; P = .004). High levels of TOSO expression in CLL correlated with high leukocyte count, advanced Binet stage, previous need for chemotherapy, and unmutated IgVH status. CD38+ CLL subsets harboring proliferative activity showed enhanced TOSO expression. We evaluated functional mechanisms of aberrant TOSO expression and identified TOSO expression significantly induced by B-cell receptor (BCR) stimulation compared with control cells (RE; 8.25 vs 4.86; P = .01). In contrast, CD40L signaling significantly reduced TOSO expression (RE, 2.60; P = .01). In summary, we show that the antiapoptotic factor TOSO is associated with progressive disease and enhanced in the proliferative CD38+ CLL subset. Both association with unmutated IgVH and the specific induction of TOSO via the BCR suggest autoreactive BCR signaling as a key mediator of apoptosis resistance in CLL.
A prospective study of mitochondrial DNA copy number and risk of non-Hodgkin lymphoma
Authors: Lan Qing , Lim Unhee , Liu Chin-San , Weinstein Stephanie J. , Chanock Stephen , Bonner Matthew R. , Virtamo Jarmo , Albanes Demetrius , Rothman Nathaniel 
Published: August 2008

Abstract
Mitochondrial DNA (mtDNA) copy number is increased in patients with chronic lymphocytic leukemia (CLL), in Burkitt lymphoma and Epstein-Barr virus–transformed lymphoblastoid cell lines, and in T cells activated via the T-cell receptor. We hypothesized that having a higher mtDNA copy number in peripheral white blood cell DNA from healthy subjects would be associated with future risk of non-Hodgkin lymphoma (NHL). We analyzed mtDNA copy number in 104 incident male NHL cases and 104 matched controls within the prospective Alpha-Tocopherol, Beta-Carotene (ATBC) Cancer Prevention cohort. There was a dose-response relationship between tertiles of mtDNA copy number and risk of NHL (odds ratio [OR], 95% confidence interval [CI]: 1.0; 1.4 [0.7-2.8]; and 2.4 [1.0-5.5], respectively; Ptrend = .046). The effect was most pronounced for the CLL/small lymphocytic lymphoma (SLL) subtype (OR: 1.0; 3.2 [0.7-15.7]; 14.1 [1.9-103.2]; Ptrend = .009). These results suggest that mtDNA copy number could be associated with the risk of NHL, particularly CLL/SLL.