bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolutionary Dynamics of Complex Networks of HIV Drug-Resistant Strains: The Case of San Francisco
Authors: Smith Robert J. , Okano Justin T. , Kahn James S. , Bodine Erin N. , Blower Sally
Published: March 2010

Transmission of Drug Resistance

Understanding the dynamics of drug-resistant strains of HIV and the key determinants affecting their evolution and spread is crucial for predicting future effects of drug treatment. Current models can only track one resistant strain, so

Smith?
et al.

(p.
697
, published online 14 January) used empirical data from San Francisco to parameterize models that consider the transmission of single-, double-, and triple-resistant HIV strains. Many people who are infected with a resistant strain are capable of infecting more than one other person; a scenario that could trigger an epidemic wave of drug-resistant virus. At a time when the World Health Organization's strategy for universal testing and treatment is being rolled out, the insights gained from this work are not restricted to HIV transmission and treatment in resource-rich countries, but are widely applicable.
Affinity of Ceftaroline and Other β-Lactams for Penicillin-Binding Proteins from
Staphylococcus aureus
and
Streptococcus pneumoniae
Authors: Kosowska-Shick K. , McGhee P. L. , Appelbaum P. C.
Published: March 2010

We compared the affinities of ceftaroline for all penicillin-binding proteins (PBPs) with those of ceftriaxone and cefotaxime in 6
Staphylococcus aureus
and 7
Streptococcus pneumoniae
isolates with various resistance phenotypes. Ceftaroline MICs were ≤1 μg/ml against all
S. aureus
isolates and were ≤0.25 μg/ml for 4 of 7 isolates of
S. pneumoniae
. Ceftaroline affinities for penicillin-susceptible
S. pneumoniae
strains were in the order PBP2X and -3 > PBP1A, -1B, and -2A > PBP2B, and ceftaroline had ≥4-fold higher 50% inhibitory concentrations (IC
50
s) (0.1 to 4 μg/ml) for PBP2X, -2A, -2B, and -3 than those for the other cephalosporins tested. Among 3 penicillin-resistant
S. pneumoniae
strains, ceftaroline had a high affinity for PBP2X (IC
50
, 0.1 to 1 μg/ml), a primary target for cephalosporin PBP binding activity, and high affinities for PBP2B (IC
50
, 0.5 to 4 μg/ml) and PBP1A (IC
50
, 0.125 to 0.25 μg/ml) as well, both of which are also known as major targets for PBP binding activity of cephalosporins. Ceftaroline PBP affinities in methicillin-susceptible
S. aureus
strains were greater than or equal to those of the 3 other β-lactams tested. Ceftaroline bound to PBP2a in methicillin-resistant
S. aureus
(IC
50
, 0.01 to 1 μg/ml) with up to 256-fold-higher affinity than those of other agents. Ceftaroline demonstrated very good PBP affinity against all
S. aureus
and
S. pneumoniae
strains tested, including resistant isolates.
Combinations of Mutations in the Connection Domain of Human Immunodeficiency Virus Type 1 Reverse Transcriptase: Assessing the Impact on Nucleoside and Nonnucleoside Reverse Transcriptase Inhibitor Resistance
Authors: Gupta Soumi , Fransen Signe , Paxinos Ellen E. , Stawiski Eric , Huang Wei , Petropoulos Christos J.
Published: March 2010

Recent reports have described the effect of mutations in the connection and RNase H domains of reverse transcriptase (RT) on nucleoside and nonnucleoside reverse transcriptase inhibitor (NRTI and NNRTI, respectively) resistance in the presence of thymidine analog resistance mutations (TAMs) and NNRTI mutations (J. H. Brehm, D. Koontz, J. D. Meteer, V. Pathak, N. Sluis-Cremer, and J. W. Mellors, J. Virol. 81:7852-7859, 2007; K. A. Delviks-Frankenberry, G. N. Nikolenko, R. Barr, and V. K. Pathak, J. Virol. 81:6837-6845, 2007; G. N. Nikolenko, K. A. Delviks-Frankenberry, S. Palmer, F. Maldarelli, M. J. Fivash, Jr., J. M. Coffin, and V. K. Pathak, Proc. Natl. Acad. Sci. U. S. A. 104:317-322, 2007; G. N. Nikolenko, S. Palmer, F. Maldarelli, J. W. Mellors, J. M. Coffin, and V. K. Pathak, Proc. Natl. Acad. Sci. U. S. A. 102:2093-2098, 2005; and S. H. Yap, C. W. Sheen, J. Fahey, M. Zanin, D. Tyssen, V. D. Lima, B. Wynhoven, M. Kuiper, N. Sluis-Cremer, P. R. Harrigan, and G. Tachedjian, PLoS Med. 4:e335, 2007). In the present study, novel mutations in the connection domain of RT (T369I/V), first identified in patient-derived viruses, were characterized, and their effects on NNRTI and NNRTI susceptibility were determined. Furthermore, the effect of N348I on NRTI and NNRTI resistance was confirmed. HIV-1 with either N348I or T369I/V demonstrated reduced susceptibility to nevirapine (NVP), efavirenz (EFV), delaviridine (DLV), and zidovudine (ZDV) compared to wild-type HIV-1. However, HIV-1 with T369I and N348I demonstrated 10- to 60-fold resistance to these same drugs. In clinical samples, these two connection domain RT mutations were predominantly observed in viruses containing TAMs and NNRTI mutations and did not alter the susceptible-resistant classifications of these samples. Introduction of T369I, N348I, or T369I/N348I also reduced replication capacity (RC). These observations suggest that it may be of scientific interest to test these mutations against new NNRTI candidates.
Immunization with VAR2CSA-DBL5 Recombinant Protein Elicits Broadly Cross-Reactive Antibodies to Placental
Plasmodium falciparum
-Infected Erythrocytes
Authors: Avril Marion , Cartwright Megan M. , Hathaway Marianne J. , Hommel Mirja , Elliott Salenna R. , Williamson Kathryn , Narum David L. , Duffy Patrick E. , Fried Michal , Beeson James G. , Smith Joseph D.
Published: March 2010

Pregnancy-associated malaria is a severe clinical syndrome associated with the sequestration of
Plasmodium falciparum
-infected erythrocytes in the placenta. Placental binding is mediated by VAR2CSA, a member of the large and diverse
P. falciparum
erythrocyte membrane 1 (PfEMP1) protein family. To better understand if conserved regions in VAR2CSA can be targeted by antibodies, we immunized rabbits with VAR2CSA-DBL1 and -DBL5 recombinant proteins produced in
Pichia pastoris
and developed a panel of seven chondroitin sulfate A (CSA)-binding parasites from diverse geographic origins. Overall, no two parasites in the panel expressed the same VAR2CSA sequence. The DBL1 domains averaged 80% amino acid identity (range, 72 to 89%), and the DBL5 domains averaged 86% amino acid identity (range, 83 to 99%), similar to a broader sampling of VAR2CSA sequences from around the world. Whereas antibodies generated against the VAR2CSA-DBL1 recombinant protein had only limited breadth and reacted with three or four parasites in the panel, immunization with DBL5 recombinant proteins elicited broadly cross-reactive antibodies against all or most parasites in the panel, as well as to fresh clinical isolates from pregnant women. These findings demonstrate that the major PfEMP1 variant expressed by placental isolates exposes strain-transcendent epitopes that can be targeted by vaccination and may have application for pregnancy malaria vaccine development.
Biochemistry of Microbial Degradation of Hexachlorocyclohexane and Prospects for Bioremediation
Authors: Lal Rup , Pandey Gunjan , Sharma Pooja , Kumari Kirti , Malhotra Shweta , Pandey Rinku , Raina Vishakha , Kohler Hans-Peter E. , Holliger Christof , Jackson Colin , Oakeshott John G.
Published: March 2010

Lindane, the γ-isomer of hexachlorocyclohexane (HCH), is a potent insecticide. Purified lindane or unpurified mixtures of this and α-, β-, and δ-isomers of HCH were widely used as commercial insecticides in the last half of the 20th century. Large dumps of unused HCH isomers now constitute a major hazard because of their long residence times in soil and high nontarget toxicities. The major pathway for the aerobic degradation of HCH isomers in soil is the Lin pathway, and variants of this pathway will degrade all four of the HCH isomers although only slowly. Sequence differences in the primary LinA and LinB enzymes in the pathway play a key role in determining their ability to degrade the different isomers. LinA is a dehydrochlorinase, but little is known of its biochemistry. LinB is a hydrolytic dechlorinase that has been heterologously expressed and crystallized, and there is some understanding of the sequence-structure-function relationships underlying its substrate specificity and kinetics, although there are also some significant anomalies. The kinetics of some LinB variants are reported to be slow even for their preferred isomers. It is important to develop a better understanding of the biochemistries of the LinA and LinB variants and to use that knowledge to build better variants, because field trials of some bioremediation strategies based on the Lin pathway have yielded promising results but would not yet achieve economic levels of remediation.
Virulence and Immunomodulatory Roles of Bacterial Outer Membrane Vesicles
Authors: Ellis Terri N. , Kuehn Meta J.
Published: March 2010

Outer membrane (OM) vesicles are ubiquitously produced by Gram-negative bacteria during all stages of bacterial growth. OM vesicles are naturally secreted by both pathogenic and nonpathogenic bacteria. Strong experimental evidence exists to categorize OM vesicle production as a type of Gram-negative bacterial virulence factor. A growing body of data demonstrates an association of active virulence factors and toxins with vesicles, suggesting that they play a role in pathogenesis. One of the most popular and best-studied pathogenic functions for membrane vesicles is to serve as natural vehicles for the intercellular transport of virulence factors and other materials directly into host cells. The production of OM vesicles has been identified as an independent bacterial stress response pathway that is activated when bacteria encounter environmental stress, such as what might be experienced during the colonization of host tissues. Their detection in infected human tissues reinforces this theory. Various other virulence factors are also associated with OM vesicles, including adhesins and degradative enzymes. As a result, OM vesicles are heavily laden with pathogen-associated molecular patterns (PAMPs), virulence factors, and other OM components that can impact the course of infection by having toxigenic effects or by the activation of the innate immune response. However, infected hosts can also benefit from OM vesicle production by stimulating their ability to mount an effective defense. Vesicles display antigens and can elicit potent inflammatory and immune responses. In sum, OM vesicles are likely to play a significant role in the virulence of Gram-negative bacterial pathogens.
CHARGED PARTICLES AND THE ELECTRO-MAGNETIC FIELD IN NONINERTIAL FRAMES OF MINKOWSKI SPACE-TIME I: ADMISSIBLE 3 + 1 SPLITTINGS OF MINKOWSKI SPACE-TIME AND THE NONINERTIAL REST FRAMES
Authors: ALBA DAVID , LUSANNA LUCA
Published: March 2010

By using the 3 + 1 point of view and parametrized Minkowski theories we develop the theory of noninertial frames in Minkowski space-time. The transition from a noninertial frame to another one is a gauge transformation connecting the respective notions of instantaneous three-space (clock synchronization convention) and of the three-coordinates inside them. As a particular case we get the extension of the inertial rest-frame instant form of dynamics to the noninertial rest-frame one. We show that every isolated system can be described as an external decoupled noncovariant canonical center of mass (described by frozen Jacobi data) carrying a pole–dipole structure: the invariant mass and an effective spin. Moreover we identify the constraints eliminating the internal three-center of mass inside the instantaneous three-spaces.

In the case of the isolated system of positive-energy scalar particles with Grassmann-valued electric charges plus the electro-magnetic field, we obtain both Maxwell equations and their Hamiltonian description in noninertial frames. Then by means of a noncovariant decomposition we define the noninertial radiation gauge and we find the form of the noncovariant Coulomb potential. We identify the coordinate-dependent relativistic inertial potentials and we show that they have the correct Newtonian limit.

In the second paper we will study properties of Maxwell equations in noninertial frames like the wrap-up effect and the Faraday rotation in astrophysics. Also the 3 + 1 description without coordinate-singularities of the rotating disk and the Sagnac effect will be given, with added comments on pulsar magnetosphere and on a relativistic extension of the Earth-fixed coordinate system.
Slip rate variations on faults during glacial loading and post-glacial unloading: implications for the viscosity structure of the lithosphere
Authors: Hampel Andrea , Karow Tobias , Maniatis Georgios , Hetzel Ralf
Published: March 2010

Many active faults in extensional and contractional tectonic settings experienced a slip rate increase after the last glacial period when the volume of nearby glaciers and lakes decreased. This post-glacial slip rate increase is caused by transient stresses that are generated by the unloading-induced rebound and superimposed on the tectonic background stress field. As the latter is different for normal and thrust faults, the response to loading and unloading should depend on the fault type. Here we use finite-element models including a fault in rheologically layered lithosphere to explore the conditions under which both normal and thrust faults experience a post-glacial slip rate increase. The results show that a post-glacial slip rate increase occurs on normal faults if the lower crust is stronger than the lithospheric mantle, whereas thrust faults accelerate if the lower crust is weaker than the lithospheric mantle. These findings imply that the response of faults to mass fluctuations on the Earth's surface may provide constraints on the rheological stratification of the lithosphere. We use our results to make predictions on the viscosity structure of the Basin-and-Range Province and northern Scandinavia, where palaeoseismological data document a pronounced increase in seismicity as a result of post-glacial unloading and rebound.
On apatite fission track dating and the Tertiary evolution of West Greenland topography
Authors: Redfield T.F.
Published: March 2010

Combined with geological information, apatite fission track (AFT) data can impose valid thermal and temporal constraints. However, their uncritical interpretation may also lead to unsupported conclusions. Because fission tracks in apatite undergo measurable shortening even at surface temperatures, model artefacts can potentially be mistaken for geological cooling events. This problem can be especially acute when older fanning kinetic models are utilized instead of the newest curvilinear ones. In any circumstances, AFT model results must be interpreted with considerable caution and should rarely be considered to supersede conventional geological wisdom. The possibility that young cooling events are simply artefacts ought always to be entertained. As an example, this study considers AFT data and model results that have been cited to suggest that today's high mountains of West Greenland are erosional remnants of a landmass uplifted during the Neogene. However, in the best of circumstances the AFT data in question are heavily contaminated, and in the worst case they carry virtually no geological meaning. Although geological constraints require the faulted, westward-facing escarpment of West Greenland's Disko region to have been erected after commencement of sea-floor spreading in Baffin Bay, the AFT model-based hypothesis that it was constructed in purely Neogene time remains an unproven speculation.
Influence of pore water chemistry on silica diagenesis: evidence from the interaction of diagenetic reaction zones with polygonal fault systems
Authors: Ireland Mark T. , Goulty Neil R. , Davies Richard J.
Published: March 2010

Three-dimensional seismic data from the NE Atlantic margin have revealed opal-A to opal-CT reaction zones hosted in Oligo-Pliocene strata as bright reflection events that cross-cut stratigraphic reflections. In some areas, the topographic relief at the top of the reaction zone has a remarkable geometry comprising roughly circular flattish regions, spaced 1–3 km apart, separated by networks of steep-sided troughs or ridges with a relief of up to 200 m. Here we show that these topographic structures formed around the upper tips of polygonal faults, and that remnants exist at deeper stratigraphic levels below the opal-A to opal-CT cross-cutting reflection. Furthermore, we deduce that the chemistry of formation water expelled transiently through the polygonal faults must have played a key role in their formation. Within silica-bearing successions, the transformation of opal-A to opal-CT is followed by the transformation of opal-CT to quartz at greater depth. The opal-CT to quartz transformation releases magnesium, which is known to promote opal-A to opal-CT transformation at lower temperatures. Consequently, we suggest that when the opal-A to opal-CT reaction zone nears the top of the polygonal fault system, it advances more rapidly through strata flushed by pore water that is richer in magnesium.
Structural position of high-pressure felsic to intermediate granulites from NE Moldanubian domain (Bohemian Massif)
Authors: Tajčmanová L. , Soejono I. , Konopásek J. , Košler J. , Klötzli U.
Published: March 2010

At the northeastern edge of the Moldanubian Zone, a large body of felsic to intermediate granulite with relics of high-pressure mineral assemblage is exposed within medium-grade paragneisses, micaschists and metagranites. A polyphase tectonic evolution in the study area resulted in three deformation phases (D
1
–D
3
). Peak metamorphic conditions (860–1000 °C and 16 kbar) in granulites are interpreted as reflecting an early stage of the high-grade evolution of the orogenic lower crust. These conditions were followed by exhumation of the orogenic lower crustal block to mid-crustal levels (6–8 kbar). In contrast to this, the study of metamorphic conditions in the surrounding micaschists (660 °C and 8 kbar) shows that these rocks never experienced pressures and temperatures of the orogenic lower crust. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) U–Pb dating of zircon from the granulite yielded a concordia age of 354 ± 7 Ma, whereas the conventional isotope dilution thermal ionization mass spectrometry (ID-TIMS) and LA-ICP-MS dating of xenotime gave identical concordia ages of 336.2 ± 1.2 and 339 ± 3 Ma, respectively. Combination of new structural and petrological results with LA-ICP-MS zircon and xenotime dating leads to development of a well-constrained exhumation model and brings new insights into the behaviour of lower crustal rocks during orogenesis.
Constraints on palaeoenvironments in the Lower Cretaceous Wealden of southern England, from the geochemistry of sphaerosiderites
Authors: Robinson Stuart A. , Scotchman James I. , White Timothy S. , Atkinson Tim C.
Published: March 2010

Sphaerosiderites are millimetre-scale concretions of FeCO
3
that form predominantly in waterlogged environments and are of use in palaeoenvironmental and palaeohydrological studies. We present petrographic, elemental and stable-isotopic (δ
13
C, δ
18
O) data from sphaerosiderites collected from the Lower Cretaceous Wealden sediments of southern England. The sphaerosiderites are composed of very pure FeCO
3
, with only small amounts of Ca, Mg and Mn present, suggesting that they are well preserved and were precipitated from fresh groundwater. δ
13
C values display a relatively large range from about −5 to −30‰ (VPDB). In contrast, δ
18
O values are relatively invariant (1σ = 0.83‰), with an average of −3.01‰ (VPDB). The relationship between carbon and oxygen suggests that the sphaerosiderites faithfully record palaeo-groundwater δ
18
O. Likely δ
18
O values for groundwater were calculated using a published, experimentally derived siderite–water fractionation equation and plausible assumed values for palaeotemperature. The average estimate was −4.9‰ (SMOW). The Wealden sphaerosiderite oxygen-isotope values are comparable with other early Cretaceous data from similar palaeolatitudes but lower than estimated Holocene values for equivalent latitudes. This observation may indicate greater rainfall at 30°N during the Cretaceous relative to the Holocene and also suggests relative stability of palaeoclimatic conditions during the early Cretaceous at this palaeolatitude.
Tracking garbage
Authors: Greengard Samuel
Published: March 2010

Researchers are focusing on the so-called "removal chain" in an attempt to save landfill space, improve recycling rates, and trim the flow of toxic materials into the environment.
Making the case for computing
Authors: Wilson Cameron , Harsha Peter
Published: March 2010

Seeking funding for current and future computing initiatives requires both a strong argument and a broad community of supporters.
GFS
Authors: McKusick Kirk , Quinlan Sean
Published: March 2010

Kirk McKusick and Sean Quinlan discuss the origin and evolution of the Google File System.
Making decisions based on the preferences of multiple agents
Authors: Conitzer Vincent
Published: March 2010

Computer scientists have made great strides in how decision-making mechanisms are used.
Future Tense: The primal cue
Authors: Juels Ari
Published: March 2010

Future Tense, one of the revolving features on this page, presents stories and essays from the intersection of computational science and technological speculation, their boundaries limited only by our ability to imagine what will and could be.

Cybersecurity depends on the human dimension.
Is stickiness profitable for electronic retailers?
Authors: Lin Lin , Hu Paul Jen-Hwa , Sheng Olivia R. Liu , Lee Johnny
Published: March 2010

Introduction

Is stickiness the Holy Grail for e-tailing? In general,
stickiness
refers to the amount of time a person spends on a Web site during a visiting session (such as,
session stickiness
) or over a specified time period (such as,
site stickiness
). Zauberman equates stickiness and "within-site lock-in" and uses it to approximate visitors' loyalty to a Web site. The conventional wisdom suggests that stickiness is crucial and can contribute to e-tailers' bottom lines considerably. However, the direct economic impacts of stickiness have not been duly examined empirically, particularly from the perspective of consumers' within-session visiting behaviors.

E-tailing offers an exciting global virtual channel for marketing and exchanges. According to the U.S. Department of Commerce, the e-retailing industry has grown at a 29% compounded annual rate between 2000 and 2004, amounting to $81 billion in sales in 2005 and projected to reach $144 billion by 2010. Accompanied by this impressive growth is the increasingly fierce market competition that results from greatly reduced search costs, diminished product/service differentiation, and rapidly eroding customer loyalty. To survive and excel in this highly competitive market, e-tailers must be effective in converting their Web site visitors into paying customers. Such conversions are challenging, as manifested by the dismal conversion rate (for example, estimated at 2.3% by e-tailing.com) that is likely to continue to decline.

Stickiness serves as a common indicator of customer loyalty to e-tailers. Accordingly, firms have focused on effective Web site design and business strategies to "lock in" visitors by making their Web sites increasingly sticky. Despite the salient beliefs about the business value of stickiness in e-tailing, empirical evidence of its direct economic impacts is surprisingly limited. Moe and Fader discuss the importance of stickiness for business profits and advocate the use of visiting behaviors to investigate the relationship. Straub et al. also highlight the importance of analyzing prominent visitors' behaviors and particularly suggest the use of click-stream data to examine the effects of essential visiting behaviors on business outcomes, such as online purchases. However, few (if any) studies have examined these effects empirically.

In this study, we use within-session visiting behaviors, recorded by a designated client-side monitoring program, to examine the relationship between stickiness and conversion, an outcome metric directly affecting e-tailers' bottom lines. We respond to the call by Moe and Fader by examining session stickiness through analyses of visitors' within-session behaviors. We measure session stickiness using both visiting session duration and total number of pages accessed during a visiting session. We empirically test whether stickiness significantly affects conversion, and further investigate whether product category moderates the focal stickiness--conversion relationship.
The impact of quasi-equally spaced sensor topologies on signal reconstruction
Authors: Nordio Alessandro , Chiasserini Carla-Fabiana , Viterbo Emanuele
Published: March 2010

A wireless sensor network with randomly deployed nodes can be used to provide an irregular sampling of a physical field of interest. We assume that a sink node collects the data gathered by the sensors and uses a linear filter for the reconstruction of a bandlimited scalar field defined over a
d
-dimensional domain. Sensors' locations are assumed to be known at the sink node, up to a certain position error. We then take the mean square error (MSE) of the reconstructed field as performance metric, and evaluate the effect of both uniform and quasi-equally spaced sensor layouts on the quality of the reconstructed field. We define a parameter that provides a measure of the regularity of the sensors deployment, and, through asymptotic analysis, we derive the MSE in the case of different sensor spatial distributions. For two of them, an approximate closed form expression is obtained. We validate our analysis through numerical results, and we show that an excellent match exists between analysis and simulation even for a small number of sensors.
On link asymmetry and one-way estimation in wireless sensor networks
Authors: Sang Lifeng , Arora Anish , Zhang Hongwei
Published: March 2010

Link asymmetry is one of the unique challenges that wireless sensor networks pose in the design of network protocols. We observe, based on testbed experiments, that a substantial percentage of links are asymmetric, many are even unidirectional. We also find that the reliability of synchronous acknowledgments is considerably higher than that of asynchronous messages. Thus the norm of estimating link quality bidirectionally via asynchronous beacons underestimates the link reliability of asymmetric links. This leads us to investigate how to exploit asymmetric links in order to improve network functions such as convergecast routing in sensor networks via one-way link estimation. We propose a new one-way link metric ETF (for the
expected number of transmissions over forward links
) and present a local procedure for its estimation. We use ETF to identify reliable forward links, and we use dynamic retransmission thresholding for error control. Via experiments on testbeds of CC1000 radios and CC2420 radios (an IEEE 802.15.4-compliant radio), we quantify the performance improvement in ETF as compared with ETX. We also study the performance improvement of ETF over ETX when no special mechanism is employed to discover asymmetric links or to control retransmissions.
Query privacy in wireless sensor networks
Authors: Carbunar Bogdan , Yu Yang , Shi Weidong , Pearce Michael , Vasudevan Venu
Published: March 2010

Existing mechanisms for querying wireless sensor networks leak client interests to the servers performing the queries. The leaks are not only in terms of specific regions of interest but also of client access patterns. In this article we introduce the problem of preserving the privacy of clients querying a wireless sensor network owned by untrusted organizations. We first propose an efficient protocol, SPYC, that ensures full client privacy in settings where the servers providing access to the network are honest-but-curious and whose collaboration does not extend beyond well-defined administrative purposes. Furthermore, we study the same query privacy problem in a setting where servers exhibit malicious behavior or where powerful external attackers have access to sensor network traffic information. In this setting we propose two metrics for quantifying the privacy achieved by a client's query sequence. We then extend SPYC with a suite of practical algorithms, then analyze the privacy and efficiency levels they provide. Our TOSSIM simulations show that the proposed extensions are communication efficient while significantly improving client privacy levels.
Dealing with random and selective attacks in wireless sensor systems
Authors: Ni Jinfeng , Zhou Li , Ravishankar Chinya V.
Published: March 2010

We present a framework for analyzing the effects of random and selective compromises (using order statistics) in sensor networks. We discuss the problem of ensuring data integrity at the source and during transit in sensor networks, and present an analysis of the reliability of reports from mobile collectors. No analysis has appeared in the literature of source integrity for mobile nodes, or of selective attacks in sensor networks. We address transit data integrity by presenting mGKE, a key establishment scheme for general group-based sensor deployments, and present a detailed analytical and experimental comparison of mGKE with current schemes. mGKE outperforms current methods in terms of resilience, connectivity, and memory and communication overhead.
An empirical study of low-power wireless
Authors: Srinivasan Kannan , Dutta Prabal , Tavakoli Arsalan , Levis Philip
Published: March 2010

We present empirical measurements of the packet delivery performance of the latest sensor platforms: Micaz and Telos motes. In this article, we present observations that have implications to a set of common assumptions protocol designers make while designing sensornet protocols—specifically—the MAC and network layer protocols. We first distill these common assumptions in to a conceptual model and show how our observations support or dispute these assumptions. We also present case studies of protocols that do not make these assumptions. Understanding the implications of these observations to the conceptual model can improve future protocol designs.
Low-overhead
F

max

calibration at multiple operating points using delay-sensitivity-based path selection
Authors: Paul Somnath , Mahmoodi Hamid , Bhunia Swarup
Published: March 2010

Maximum operating frequency (
F

max

) of a system often needs to be determined at multiple operating points, defined by voltage and temperatures. Such calibration is important for the speed binning process, where the voltage-frequency (V-
F

max

) relation needs to be accurately determined to sort chips into different bins that can be used for different applications. Moreover, adaptive systems typically require
F

max

calibration at multiple operating points in order to dynamically change operating condition such as supply voltage or body bias for power, temperature, or throughput management. For example, a Dynamic Voltage and Frequency Scaling (DVFS) system requires accurate delay calibration at multiple operating voltages in order to apply the correct operating frequency corresponding to a scaled supply. In this article, we propose a low-overhead design technique that allows efficient characterization of
F

max

at different operating voltages and temperatures. The proposed method selects a set of representative timing paths in a circuit based on their temperature and voltage sensitivities and dynamically configures them into a ring oscillator to compute the critical path delay. Compared to existing
F

max

calibration approaches, the proposed approach provides the following two main advantages: (1) it introduces a delay sensitivity metric to isolate few representative timing paths; (2) it considers actual timing paths instead of critical path replicas, thereby accounting for local within-die delay variations. The all-digital calibration method is robust under process variations and achieves high delay estimation accuracy (> 4% error) at the cost of negligible design overhead (1.7% in delay, 0.3% in power, and 3.5% in die-area).
Modeling and exploiting spatial locality trade-offs in wavelet-based applications under varying resource requirements
Authors: Geelen Bert , Ferentinos Vissarion , Catthoor Francky , Lafruit Gauthier , Verkest Diederik , Lauwereins Rudy , Stouraitis Thanos
Published: March 2010

Future dynamic applications will require new mapping strategies to deliver power-efficient performance. Fully static design-time mappings will not be able to optimally address the unpredictably varying application characteristics and system resource requirements. Instead, the platforms will not only need to be programmable in terms of instruction set processors, but also at least partial reconfigurability will be required, while the applications themselves will need to exploit this increased freedom at runtime to adapt to the dynamism. In this context, it is important for applications to optimally exploit the memory hierarchy under varying memory availability. This article presents an analysis of spatial locality trade-offs in wavelet-based applications, to be used in dynamic execution environments: Depending on the encountered runtime conditions, the execution switches to different memory optimized instantiations or localizations, optimally exploiting temporal and spatial locality under these conditions. This is enabled by systematic mapping guidelines, indicating how the miss-rate behavior of a localization is influenced by a specific execution condition, under which conditions a certain localization is optimal and which miss-rate gains may be obtained by switching to that localization.
Multi-buffer manager
Authors: Cesana Ulpian , He Zhen
Published: March 2010

Embedded devices such as personal digital assistants (PDAs), pocket PCs, palmtops, and handheld PCs are increasingly using flash memory for the permanent storage of databases. Databases achieve their fast data access speeds by using a memory manager that manages data pages in a memory buffer. The buffer manager uses a page replacement policy to evict pages when the memory buffer is full. An eviction of a dirty page will result in a write to flash memory. Unfortunately, writing to flash memory consumes a lot more energy than reading. Much of the previous work in page replacement policies has focused on reducing the number of page reads rather than writes. One of the few existing works to consider the effects of flash memory's hardware constraints for database design is Lee et. al.'s in-page Logging (IPL) approach [Lee and Moon 2007]. They demonstrated IPL significantly outperforms traditional disk-based databases when running on flash memory. However, they do not consider the energy efficiency of their approach in terms of the behavior of the page replacement policy. This article addresses this issue by presenting the Multi-Buffer Manager, which is customized for flash databases that use a logging-based approach for managing updates such as IPL. Extensive experiments show the page replacement policy used plays a pivotal role in the performance of the flash database system. In particular, our Multi-Buffer Manager can reduce energy consumption by up to 40% compared to the state-of-the-art clean first flash-based buffer replacement policy (CFLRU).
Widget identification and modification for web 2.0 access technologies (WIMWAT)
Authors: Chen Alex Q.
Published: March 2010

Rich Internet Applications (RIA) encourage World Wide Web (Web) content to be extracted and remixed from dif-ferent sources, so that presented content can be updated in small chunks, rather than reloading the entire Web page. These concepts change the way Web pages are created and how users interact with them. Hence, these changes will require assistive technologies to adapt to them. We intro-duce the concept of identifying and modifying embedded code within a Web page (widget) during development, so that widgets that are not in an accessible form, and which produce inaccessible content can be modi ed. Our concept can be also applied as an enhancement for screen readers, so that they can provide a preview facility of the types of features provided by the widgets. Currently, we are investi-gating di erent methods for detecting widgets from the Web page's source code. An evaluation of our detection methods has been carried out; this was an attempt to search for two types of widgets from the top twenty Websites. The evalu-ation successfully detected all widgets, suggesting that our identi cation methods are successful, although some false positives were also detected. Since we are in our initial stage, further investigations will be required to re ne our methods, and pursue the observation and modi cation phases required by the project.
Using interactive objects for speech intervention
Authors: Hamidi Foad
Published: March 2010

Technological advances in physical computing and automatic speech recognition (ASR) have made the development of novel solutions for speech intervention possible. I plan to combine an ASR engine with programmable microcontrollers to develop exercises and activities based on interaction with smart objects for helping with speech therapy intervention for children.
Improving vocabulary organization in assistive communication tools
Authors: Nikolova Sonya
Published: March 2010

Navigating a vocabulary consisting of thousands of entries in order to select appropriate words for building communication is challenging for individuals with lexical access impairments like those caused by aphasia. Ineffective vocabulary organization and navigation hurt the usability and adoption of assistive communication tools and ultimately fail to help users engage in practical communication. We have developed a multi-modal visual vocabulary that enables improved navigation and effective word finding by modeling a speaker's "mental lexicon", where words are stored and organized in ways that allow efficient access and retrieval. Due to impaired links in their mental lexicon, people with aphasia have persistent difficulties accessing and retrieving words that express intended concepts. The Visual Vocabulary for Aphasia (ViVA) attempts to compensate for some of these missing or impaired semantic connections by organizing words in a dynamic semantic network where links between words reflect word association measures based on WordNet, human judgments of semantic similarity, and past vocabulary usage.
JavaXCSF
Authors: Stalph Patrick O. , Butz Martin V.
Published: March 2010

Learning Classifier Systems were introduced by John H. Holland and constituted one of the first genetics-based machine learning techniques. The most prominent Learning Classifier System is XCS [3]. XCS can also be used for function approximation, then called XCSF [4]. JavaXCSF is an implementation of the XCSF Learning Classifier System. It is freely available from www.coboslab.psychologie.uni-wuerzburg.de/code/

Based on previous implementations, the code was extended and heavily restructured, resulting in a flexible framework that helps newcomers to understand the basic structure, but also allows developers to realize their own ideas in the XCSF system. For a detailed documentation, please refer to [2].
Pro-Inflammatory Cytokine-Mediated Anemia: Regarding Molecular Mechanisms of Erythropoiesis
Authors: Morceau F. , Dicato M. , Diederich M.
Published: March 2010

Anemia of cancer and chronic inflammatory diseases is a frequent complication affecting quality of life. For cancer patients it represents a particularly bad prognostic. Low level of erythropoietin is considered as one of the causes of anemia in these pathologies. The deficiency in erythropoietin production results from pro-inflammatory cytokines effect. However, few data is available concerning molecular mechanisms involved in cytokine-mediated anemia. Some recent publications have demonstrated the direct effect of pro-inflammatory cytokines on cell differentiation towards erythroid pathway, without erythropoietin defect. This suggested that pro-inflammatory cytokine-mediated signaling pathways affect erythropoietin activity. They could interfere with erythropoietin-mediated signaling pathways, inducing early apoptosis and perturbing the expression and regulation of specific transcription factors involved in the control of erythroid differentiation. In this review we summarize the effect of tumor necrosis factor (TNF)α, TNF-related apoptosis-inducing ligand (TRAIL), and interferon (IFN)-γon erythropoiesis with a particular interest for molecular feature.
Regulation of Gene Expression in Protozoa Parasites
Authors: Gomez Consuelo , Esther Ramirez M. , Calixto-Galvez Mercedes , Medel Olivia , Rodríguez Mario A.
Published: March 2010

Infections with protozoa parasites are associated with high burdens of morbidity and mortality across the developing world. Despite extensive efforts to control the transmission of these parasites, the spread of populations resistant to drugs and the lack of effective vaccines against them contribute to their persistence as major public health problems. Parasites should perform a strict control on the expression of genes involved in their pathogenicity, differentiation, immune evasion, or drug resistance, and the comprehension of the mechanisms implicated in that control could help to develop novel therapeutic strategies. However, until now these mechanisms are poorly understood in protozoa. Recent investigations into gene expression in protozoa parasites suggest that they possess many of the canonical machineries employed by higher eukaryotes for the control of gene expression at transcriptional, posttranscriptional, and epigenetic levels, but they also contain exclusive mechanisms. Here, we review the current understanding about the regulation of gene expression inPlasmodium sp., Trypanosomatids,Entamoeba histolyticaandTrichomonas vaginalis.
Limiting Phase Trajectories and Resonance Energy Transfer in a System of Two Coupled Oscillators
Authors: Manevitch L. I. , Kovaleva A. S. , Manevitch E. L.
Published: March 2010

We study a problem of energy exchange in a system of two coupled oscillators subject to 1 : 1 resonance. Our results exploit the concept of limiting phase trajectories (LPTs). The LPT, associated with full energy transfer, is, in certain sense, an alternative to nonlinear normal modes characterized by conservation of energy. We consider two benchmark examples. As a first example, we construct an LPT and examine the convergence to stationary oscillations for a Duffing oscillator subjected to resonance harmonic excitation. As a second example, we treat resonance oscillations in a system of two nonlinearly coupled oscillators. We demonstrate the reduction of the equations of motion to an equation of a single oscillator. It is shown that the most intense energy exchange and beating arise when motion of the equivalent oscillator is close to an LPT. Damped beating and the convergence to rest in a system with dissipation are demonstrated.
Regulation of Adrenal Aldosterone Production by Serine Protease Prostasin
Authors: Ko Takehiro , Kakizoe Yutaka , Wakida Naoki , Hayata Manabu , Uchimura Kohei , Shiraishi Naoki , Miyoshi Taku , Adachi Masataka , Aritomi Shizuka , Konda Tomoyuki , Tomita Kimio , Kitamura Kenichiro
Published: March 2010

A serine protease prostasin has been demonstrated to have a pivotal role in the activation of the epithelial sodium channel. Systemic administration of adenovirus carrying human prostasin gene in rats resulted in an increase in plasma prostasin and aldosterone levels. However, the mechanism by which the elevation of prostasin levels in the systemic circulation stimulated the plasma aldosterone levels remains unknown. Therefore, we examined if prostasin increases the aldosterone synthesis in a human adrenocortical cell line (H295R cells). Luciferase assay using CYP11B2 promoter revealed that prostasin significantly increased the transcriptional activity of CYP11B2. Prostasin significantly increased both CYP11B2 mRNA expression and aldosterone production in a dose-dependent manner. Surprisingly, treatment with camostat mesilate, a potent prostasin inhibitor, had no effect on the aldosterone synthesis by prostasin and also a protease-dead mutant of prostasin significantly stimulated the aldosterone production. A T-type/L-type calcium channel blocker and a protein kinase C (PKC) inhibitor significantly reduced the aldosterone synthesis by prostasin. Our findings suggest a stimulatory effect of prostasin on the aldosterone synthesis by adrenal gland through the nonproteolytic action and indicate a new role of prostasin in the systemic circulation.
Hormonal Aspects of Ménière’s Disease on the Basis of Clinical and Experimental Studies
Authors: Takeda Taizo , Takeda Setsuko , Kakigi Akinobu , Okada Teruhiko , Nishioka Rie , Taguchi Daizo , Nishimura Masahiko , Nakatani Hiroaki
Published: March 2010

Conclusions: Endolymph homeostasis is thought to be mediated by the vasopressin-aquaporin-2 (VP-AQP2) system in the inner ear. Endolymphatic hydrops, the morphological characteristics of Ménière’s disease (MD), seems to reflect the malregulation of the VP-AQP2 system in inner ear fluid. The elevation of plasma vasopressin (p-VP) level, which is often observed in MD and its related diseases, might be one of the causative factors underlying these diseases. Purpose of Review: Review of the role of the VP-AQP2 system in the inner ear fluid homeostasis and in the formation and development of endolymphatic hydrops. Recent Clinical and Experimental Findings: A clinical survey has revealed that the p-VP level is often elevated in MD and its related diseases and that the increase in the p-VP level was closely linked to vertigo attacks in MD. Experimental studies have revealed that proteins and mRNAs of aquaporin-2 and vasopressin type 2 receptor were expressed in the stria vascularis of the cochlea and the epithelium of the endolymphatic sac, and that the volume of the endolymphatic compartment was mediated by the activity of the VP-AQP2 system in the inner ear.
Modification of Surgical Procedures of Type 1 Tympanoplasty for Non-Cholesteatomatous Chronic Otitis Media
Authors: Kakigi Akinobu , Takeda Taizo , Nakatani Hiroaki , Kozakura Kenichi , Sawada Shoichi , Nishioka Rie , Fukushima Kei , Taguchi Daizo , Matsumoto Noboru
Published: March 2010

Objective: To introduce our modified procedures of type 1 tympanoplasty and to assess their efficacy. Methods: We modified the surgical procedures of type 1 tympanoplasty and have used these procedures since September 1999. The modified points are enlargement of the facial recess approach, no elevation of the posterior meatal skin and the tympanic annulus, and endoaural repair of tympanic membrane perforation. 51 patients with simple chronic otitis media have undergone this modified type 1 tympanoplasty. Postoperative hearing was evaluated according to the criteria proposed by the Otological Society of Japan. Results: The average follow-up period was 15 months (range 6–35). The hearing result was considered successful when the postoperative hearing level satisfied with at least one of three conditions as follows: (1) air-bone gap <15 dB, (2) hearing gain >15 dB, or (3) hearing level >30 dB. The success rate was 94.1%. The average postoperative air-bone gap, hearing gain and hearing level were 3.9, 10.0 and 29.3 dB, respectively. Conclusion: Our modified tympanoplasty is useful to achieve better postoperative hearing results.