bluuebunny/crossref_metadata_2025 huggingface dataset:
Laboratory pentacene and parylene evaporation systems for fabricating organic thin film devices
Authors: Jia Zhang , Lee Vincent W. , Hsu Yu-Jen , Kymissis Ioannis
Published: March 2011

We have developed inexpensive and automated physical vapor deposition and chemical vapor deposition systems for processing pentacene and parylene, respectively for laboratory research purpose. The systems are automated with LABVIEW control software. Only a regulated DC power supply is needed and the silicon control rectifier and the complications associated with the inductance of step-down transformers are eliminated. The integration of the systems with a glovebox opens up a range of new applications.
Involvement of an ATP-Dependent Protease, PA0779/AsrA, in Inducing Heat Shock in Response to Tobramycin in Pseudomonas aeruginosa
Authors: Kindrachuk Kristen N. , Fernández Lucía , Bains Manjeet , Hancock Robert E. W.
Published: March 2011

The adaptive resistance of
Pseudomonas aeruginosa
to aminoglycosides is known to occur during chronic lung infections in cystic fibrosis patients in response to nonlethal concentrations of aminoglycosides. Not only is it difficult to achieve high levels of drug throughout the dehydrated mucus in the lung, but also steep oxygen gradients exist across the mucus layer, further reducing the bactericidal activity of aminoglycosides. In this study, microarray analysis was utilized to examine the gene responses of
P. aeruginosa
to lethal, inhibitory, and subinhibitory concentrations of tobramycin under aerobic and anaerobic conditions. While prolonged exposure to subinhibitory concentrations of tobramycin caused increased levels of expression predominantly of the efflux pump genes
mexXY
, the greatest increases in gene expression levels in response to lethal concentrations of tobramycin involved a number of heat shock genes and the PA0779 gene (renamed here
asrA
), encoding an alternate Lon protease. Microarray analysis of an
asrA
::
luxCDABE
transposon mutant revealed that the induction of heat shock genes in response to tobramycin in this mutant was significantly decreased compared to that in the parent strain. The level of expression of
asrA
was induced from an arabinose-inducible promoter to 35-fold greater than wild-type expression levels in the absence of tobramycin, and this overexpression alone caused an increased expression of the heat shock genes, as determined by quantitative PCR (qPCR). This overexpression of
asrA
conferred short-term protection against lethal levels (4 μg/ml) of tobramycin but did not affect the tobramycin MIC. The RpoH heat shock sigma factor was found to be involved in the regulation of
asrA
in response to both heat shock and tobramycin at the posttranscriptional level. The results of this work suggest that the tobramycin concentration has a significant impact on the gene expression of
P. aeruginosa
, with lethal concentrations resulting in immediate adaptations conferring short-term protection, such as the induction of the heat shock response, and with subinhibitory concentrations leading to more sustainable long-term protection mechanisms, such as increased efflux.
Tomatidine Inhibits Replication of Staphylococcus aureus Small-Colony Variants in Cystic Fibrosis Airway Epithelial Cells
Authors: Mitchell Gabriel , Gattuso Mariza , Grondin Gilles , Marsault Éric , Bouarab Kamal , Malouin François
Published: March 2011

Small-colony variants (SCVs) often are associated with chronic
Staphylococcus aureus
infections, such as those encountered by cystic fibrosis (CF) patients. We report here that tomatidine, the aglycon form of the plant secondary metabolite tomatine, has a potent growth inhibitory activity against SCVs (MIC of 0.12 μg/ml), whereas the growth of normal
S. aureus
strains was not significantly altered by tomatidine (MIC, >16 μg/ml). The specific action of tomatidine was bacteriostatic for SCVs and was clearly associated with their dysfunctional electron transport system, as the presence of the electron transport inhibitor 4-hydroxy-2-heptylquinoline-
N
-oxide (HQNO) caused normal
S. aureus
strains to become susceptible to tomatidine. Inversely, the complementation of SCVs' respiratory deficiency conferred resistance to tomatidine. Tomatidine provoked a general reduction of macromolecular biosynthesis but more specifically affected the incorporation of radiolabeled leucine in proteins of HQNO-treated
S. aureus
at a concentration corresponding to the MIC against SCVs. Furthermore, tomatidine inhibited the intracellular replication of a clinical SCV in polarized CF-like epithelial cells. Our results suggest that tomatidine eventually will find some use in combination therapy with other traditional antibiotics to eliminate persistent forms of
S. aureus
.
Molecular Mechanisms of Chlorhexidine Tolerance in Burkholderia cenocepacia Biofilms
Authors: Coenye Tom , Van Acker Heleen , Peeters Elke , Sass Andrea , Buroni Silvia , Riccardi Giovanna , Mahenthiralingam Eshwar
Published: March 2011

The high tolerance of biofilm-grown
Burkholderia cepacia
complex bacteria against antimicrobial agents presents considerable problems for the treatment of infected cystic fibrosis patients and the implementation of infection control guidelines. In the present study, we analyzed the tolerance of planktonic and sessile
Burkholderia cenocepacia
J2315 cultures and examined the transcriptional response of sessile cells to treatment with chlorhexidine. At low (0.0005%) and high (0.05%) concentrations, chlorhexidine had a similar effect on both populations, but at intermediate concentrations (0.015%) the antimicrobial activity was more pronounced in planktonic cultures. The exposure of sessile cells to chlorhexidine resulted in an upregulation of the transcription of 469 (6.56%) and the downregulation of 257 (3.59%) protein-coding genes. A major group of upregulated genes in the treated biofilms encoded membrane-related and regulatory proteins. In addition, several genes coding for drug resistance determinants also were upregulated. The phenotypic analysis of RND (resistance-nodulation-division) efflux pump mutants suggests the presence of lifestyle-specific chlorhexidine tolerance mechanisms; efflux system RND-4 (BCAL2820-BCAL2822) was more responsible for chlorhexidine tolerance in planktonic cells, while other systems (RND-3 [BCAL1672-BCAL1676] and RND-9 [BCAM1945-BCAM1947]) were linked to resistance in sessile cells. After sessile cell exposure, multiple genes encoding chemotaxis and motility-related proteins were upregulated in concert with the downregulation of an adhesin-encoding gene (BCAM2143), suggesting that sessile cells tried to escape the biofilm. We also observed the differential expression of 19 genes carying putative small RNA molecules, indicating a novel role for these regulatory elements in chlorhexidine tolerance.
AmpG Inactivation Restores Susceptibility of Pan-β-Lactam-Resistant Pseudomonas aeruginosa Clinical Strains
Authors: Zamorano Laura , Reeve Thomas M. , Juan Carlos , Moyá Bartolomé , Cabot Gabriel , Vocadlo David J. , Mark Brian L. , Oliver Antonio
Published: March 2011

Constitutive AmpC hyperproduction is the most frequent mechanism of resistance to the weak AmpC inducers antipseudomonal penicillins and cephalosporins. Previously, we demonstrated that inhibition of the β-
N
-acetylglucosaminidase NagZ prevents and reverts this mechanism of resistance, which is caused by
ampD
and/or
dacB
(PBP4) mutations in
Pseudomonas aeruginosa
. In this work, we compared NagZ with a second candidate target, the AmpG permease for GlcNAc-1,6-anhydromuropeptides, for their ability to block AmpC expression pathways. Inactivation of
nagZ
or
ampG
fully restored the susceptibility and basal
ampC
expression of
ampD
or
dacB
laboratory mutants and impaired the emergence of one-step ceftazidime-resistant mutants in population analysis experiments. Nevertheless, only
ampG
inactivation fully blocked
ampC
induction, reducing the MICs of the potent AmpC inducer imipenem from 2 to 0.38 μg/ml. Moreover, through population analysis and characterization of laboratory mutants, we showed that
ampG
inactivation minimized the impact on resistance of the carbapenem porin OprD, reducing the MIC of imipenem for a PAO1 OprD mutant from >32 to 0.5 μg/ml. AmpG and NagZ targets were additionally evaluated in three clinical isolates that are pan-β-lactam resistant due to AmpC hyperproduction, OprD inactivation, and overexpression of several efflux pumps. A marked increase in susceptibility to ceftazidime and piperacillin-tazobactam was observed in both cases, while only
ampG
inactivation fully restored wild-type imipenem susceptibility. Susceptibility to meropenem, cefepime, and aztreonam was also enhanced, although to a lower extent due to the high impact of efflux pumps on the activity of these antibiotics. Thus, our results suggest that development of small-molecule inhibitors of AmpG could provide an excellent strategy to overcome the relevant mechanisms of resistance (OprD inactivation plus AmpC induction) to imipenem, the only currently available β-lactam not significantly affected by
P. aeruginosa
major efflux pumps.
Advance directives and older people: ethical challenges in the promotion of advance directives in New Zealand
Authors: Malpas Phillipa J
Published: March 2011

In New Zealand an advance directive can be either an oral statement or a written document. Such directives give individuals the opportunity to make choices about future medical treatment in the event they are cognitively impaired or otherwise unable to make their preferences known. All consumers of health care have the right to make an advance directive in accordance with the common law. When we consider New Zealand's rapidly ageing population, the fact that more people now live with and die of chronic rather than acute conditions, the importance given to respecting autonomous decision-making, increasing numbers of individuals who require long-term residential care, and financial pressures in the allocation of medical resources, there would seem to be a number of compelling reasons to encourage individuals to write or verbalise an advance directive. Indeed the promotion of advance directives is encouraged. However, caution should be exercised in promoting advance directives to older people, especially in light of several factors: ageist attitudes and stereotypes towards them, challenges in the primary healthcare setting, and the way in which advance directives are currently focused and formulated. This paper considers some of the specific challenges that need to be addressed if the promotion of advance directives are to improve outcomes of patient treatment and care near the end of life.
Mortality from non-malignant respiratory diseases among workers in the Norwegian silicon carbide industry: associations with dust exposure
Authors: Bugge Merete Drevvatne , Føreland Solveig , Kjærheim Kristina , Eduard Wijnand , Martinsen Jan Ivar , Kjuus Helge
Published: March 2011

Objectives

Increased mortality from asthma, chronic bronchitis and emphysema has previously been reported among workers in the silicon carbide (SiC) industry. The objective of the present study was to evaluate the influence of specific exposure factors on mortality from obstructive lung diseases (OLD), using a newly revised job-exposure matrix.

Materials and methods

1687 long-term workers employed in 1913–2003 in the Norwegian SiC industry were characterised with respect to cumulative exposure to quartz, cristobalite, SiC particles and SiC fibres. Standardised mortality ratios (SMRs) for underlying causes of death, 1951–2007, were calculated stratified by category of cumulative exposure, and Poisson regression analyses of OLD were performed using cumulative exposure variables.

Results

An increased total mortality (SMR 1.1, 95% CI 1.0 to 1.2) and increased mortality from cancer, non-malignant respiratory diseases and external factors, were observed. The SMR of OLD was increased at the highest level of cumulative exposure to all investigated exposure factors. In the internal analyses, a twofold increased risk of OLD was observed with increasing levels of cumulative exposure to SiC particles. In a multivariate model, SiC particles showed the most stable increased risk estimate when controlled for other exposure factors, among workers with less than 15 years of employment. Among workers with more than 15 years of employment, crystalline silica, primarily cristobalite, seemed to be the most important exposure factor.

Conclusion

Exposure to SiC and crystalline silica may contribute to OLD development among SiC industry workers in different time windows, and possibly through different mechanisms.
Prognosis of acute kidney injury in dogs using RIFLE (Risk, Injury, Failure, Loss and End‐stage renal failure)‐like criteria
Authors: Lee Y‐J. , Chang C‐C. , Chan J. P‐W. , Hsu W‐L. , Lin K‐W. , Wong M‐L.
Published: March 2011

A retrospective case‐series study evaluated the prognosis of 853 dogs with acute kidney injury (AKI) based on the RIFLE (Risk, Injury, Failure, Loss and End‐stage renal failure) criteria, derived from human medicine. The 30‐day mortality of dogs with AKI in each class was found to be 23.8 per cent (40 of 168) dogs for Risk, 41.0 per cent (107 of 261) dogs for Injury and 78.5 per cent (333 of 424) dogs for Failure. Using the dogs in the Risk class as the reference, the mortality of dogs in either the Injury or Failure class was significantly higher than that of dogs in the Risk class (P<0.05). The longest median survival time was observed in the Risk class (nine days) and the shortest median survival time was observed in the Failure class (three days). Using a multiple logistic regression model, a new score that simultaneously considered RIFLE class, diarrhoea status and serum phosphorus level was calculated to predict prognosis. Evaluation using the area under the receiver‐operating characteristic curve (AUROC) indicated that the new scoring method (AUROC 0.80) was a better prognostic indicator than using RIFLE criteria alone (AUROC 0.73).
Identifying nonproportionality of fishery-independent survey data to estimate population trends and assess recovery potential for cusk (Brosme brosme)
Authors: Davies Trevor D. , Jonsen Ian D.
Published: March 2011

Cusk ( Brosme brosme ) was designated as “threatened” by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) in 2003, based on an estimated 93% decline between 1970 and 2001 from the Fisheries and Oceans Canada (DFO) Scotian Shelf summer bottom trawl survey index. We combined this index with a fishery-dependent longline index in a Bayesian surplus production state-space model to estimate population trends and the recovery potential of western Scotian Shelf cusk. We tested for index nonproportionality using a power curve function in the observation model and identified potential hyperdepletion for cusk in the trawl survey index. We estimate a 59% decline in cusk biomass between 1970 and 2001, and a 64% decline from 1970 to 2007. Although population projections indicate the current landing limit should lead to population recovery, robustness tests suggest the biomass projections and recovery time lines are overly optimistic. Simulations showed that incorporating multiple indices increases power to recapture model parameters and failure to account for index nonproportionality results in biased parameter estimates. We suggest that nonproportionality of fishery-independent indices must be considered when determining the population status of data-poor species.
STRUCTURAL, ELECTRONIC, OPTICAL AND THERMODYNAMIC PROPERTIES OF PbS, PbSe AND THEIR TERNARY ALLOY PbS1-xSex
Authors: LABIDI M. , MERADJI H. , GHEMID S. , LABIDI S. , EL HAJ HASSAN F.
Published: March 2011

On the basis of ab initio calculations employing density functional theory (DFT), we investigate the structural, electronic, optical and thermodynamic properties of two binaries: PbS and PbSe in rock-salt structures. In addition, several compositions with various ordered structures of PbS 1-x Se x alloys were studied. The calculations were performed using the full potential linearized augmented plane wave (FP-LAPW) method within the generalized gradient approximation (GGA). Various quantities, such as equilibrium lattice constants, bulk modulus, band structures and refractive index for all Se -concentrations are presented. The microscopic origins of the gap bowing were explained by using the approach of Zunger and coworkers. On the other hand, the thermodynamic stability of these alloys was investigated by calculating the excess enthalpy of mixing ΔHm as well as the phase diagram.
SPIN TRANSPORT FOR A QUANTUM WIRE WITH WEAK DRESSELHAUS SPIN-ORBIT COUPLING
Authors: FU XI , CHEN ZESHUN , ZHONG FENG , KONG YONGHONG
Published: March 2011

We investigate theoretically the electron transport properties of a quantum wire (QW) non-adiabatically connected to two normal leads with weak Dresselhaus spin-orbit coupling (DSOC). Using the scattering matrix method and Landauer–Büttiker formula within the effective free-electron approximation, we have calculated the spin-dependent conductances G↑/↓ and spin polarization Pz of a hard-wall potential confined QW. It is demonstrated that regardless of the existence of DSOC G↑/↓ and Pz present oscillation structures near the subband edges of QW, and the number of quantized conductance plateaus is determined by the number of propagation modes in two leads. Moreover, the DSOC induces splitting of spin-up and spin-down conductance plateaus as well as the existence of spin polarization (Pz ≠ 0), and the enhancement of Dresselhaus strength destroys the conductance plateaus for the wide QW case. The above results indicate that the spin-dependent conductances and Pz are strongly dependent on the Dresselhaus strength which is the physical basis for spin transistor.
APPLICATION OF AN EMPIRICAL GROWTH MODEL AND MULTIPLE IMPUTATION IN HARD DISK DRIVE FIELD RETURN PREDICTION
Authors: ZHANG SHAOANG , SUN FENG-BIN , GOUGH ROSS
Published: March 2011

Appropriate model assumption and robust model estimation are critical for accurate hard disk drive (HDD) field return prediction. Parametric distribution models that are conventionally used in HDD reliability analyses do not describe well HDD field survival. A biological growth model, Bertalanfy-Richards growth model, is introduced in this paper to model HDD field survival within warranty period. A nonparametric multiple missing value imputation approach is used to improve model estimation when not enough observations of field returns are available at early stage of product life. Tests of the model and the missing value imputation approach using actual HDD field survival data suggest they perform well in describing and predicting HDD warranty field returns.
ITERATIVE SHAPE REFINEMENT IN AAM
Authors: SU YA , GAO XINBO
Published: March 2011

Active appearance model (AAM) is a powerful model to describe deformable objects in terms of shape and texture. It models the shape and the texture variations linearly and independently and has been widely applied to pattern recognition. However, there are two problems in the model building procedure. On the one hand, much shape information is lost from the shape model because only the sparse landmarks manually labeled are taken into account. On the other hand, the high-dimensional texture has too much nonlinearity. It is resulted from the structure information left by the shape model. In this paper, we propose a shape refinement framework to account for the problems. Firstly, the texture complexity of the shape model is obtained statistically. Then, the shape model is refined based on the texture complexity. Finally, the texture model is rebuilt based on the texture complexity according to the refined shape model. This is an iterative procedure which gradually improves the shape model and reduces the nonlinear of the texture model. As a result, both the complexity and the computational cost of AAM are reduced. Experimental results show that the proposed method greatly improves the accuracy and efficiency of AAM.
INFINITE HILBERT CLASS FIELD TOWERS FROM GALOIS REPRESENTATIONS
Authors: JOSHI KIRTI , MCLEMAN CAMERON
Published: March 2011

We investigate class field towers of number fields obtained as fixed fields of modular representations of the absolute Galois group of the rational numbers. First, for each k ∈ {12, 16, 18, 20, 22, 26}, we give explicit rational primes ℓ such that the fixed field of the mod-ℓ representation attached to the unique normalized cusp eigenform of weight k on SL2(ℤ) has an infinite class field tower. Further, under a conjecture of Hardy and Littlewood, we prove the existence of infinitely many cyclotomic fields of prime conductor, providing infinitely many such primes ℓ for each k in the list. Finally, given a non-CM curve E/ℚ, we show that there exists an integer ME such that the fixed field of the representation attached to the n-division points of E has an infinite class field tower for a set of integers n of density one among integers coprime to ME.
A PRECISE DESCRIPTION OF THE p-ADIC VALUATION OF THE NUMBER OF ALTERNATING SIGN MATRICES
Authors: HEUBERGER CLEMENS , PRODINGER HELMUT
Published: March 2011

Following Sun and Moll ([4]), we study vp(T(N)), the p-adic valuation of the counting function of the alternating sign matrices. We find an exact analytic expression for it that exhibits the fluctuating behavior, by means of Fourier coefficients. The method is the Mellin–Perron technique, which is familiar in the analysis of the sum-of-digits function and related quantities.
GAUSS AND KLOOSTERMAN SUMS OVER RESIDUE RINGS OF ALGEBRAIC INTEGERS
Authors: GURAK S.
Published: March 2011

Let K be a field of degree n over Q, the field of rational numbers, with ring of integers O. Fix an integer m > 1, say with [Formula: see text] as a product of distinct prime powers, and let χ be a numerical character modulo m of conductor f(χ). Set ζm = exp (2πi/m) and let M be any ideal of O satisfying Tr M ⊆ mZ and N(1 + M) ⊆ 1 + f(χ)Z, where Tr and N are the trace and norm maps for K/Q. Then the Gauss sum [Formula: see text] is well-defined. If in addition N(1 + M) ⊆ 1 + mZ, then the Kloosterman sums [Formula: see text] are well-defined for any numerical character η ( mod m). The computation of GM(χ) and RM(η, z) is shown to reduce to their determination for m = pr, a power of a prime p, where M is comprised solely of ideals of K lying above p. In this setting we first explicitly determine GM(χ) for m = pr (r > 1) generalizing Mauclaire's classical result for K = Q. Relying on the recent evaluation of Kloosterman sums for prime powers in p-adic fields, we then proceed to compute the Kloosterman sums RM(η, z) here for m = pr (r > 1) when o(η) | p -1. This determination generalizes Salie's result in the classical case K = Q with o(η) = 1 or 2.
TUNING THE RESONANT FREQUENCIES OF FLEXURE MODE FLEXOELECTRIC PIEZOELECTRIC COMPOSITES
Authors: CHU BAOJIN , ZHU WENYI , CHU MINGJIN , LI NAN , CROSS L. ERIC
Published: March 2011

The newly developed flexure mode flexoelectric composites have extremely high direct piezoelectric response around mechanical resonant frequency. Methods of tuning the resonant frequencies of the composites were studied in this paper. The resonant frequencies can be adjusted by changing dimensions of ferroelectric ceramic bars in the composites or by adding an additional mass on the composites. Design of flexure mode composites with multiple resonant frequencies was also studied.
SYNTHESIS OF CoFe2O4/Pb(Zr0.53Ti0.47)O3 MULTIFERROIC COMPOSITE THICK FILMS BY LOW-SINTERING-TEMPERATURE SCREEN PRINTING METHOD
Authors: CHEN W. , HUANG C. X. , YAN T. S. , ZHU W. , LI Z. P. , CHEN X. F. , TAN O. K.
Published: March 2011

CoFe 2 O 4/ Pb ( Zr 0.53 Ti 0.47) O 3 (abbreviated as CFO/PZT) multiferroic composite thick films were successfully fabricated on alumina substrate with gold bottom electrode by screen printing method at a low-sintering temperature. The processing included the modification and dispersion of ferromagnetic CFO powder and ferroelectric PZT powder, the preparation of uniform pastes, and the selection of proper annealing temperature for composite thick films. Transmission electron microscopic pictures (TEM) indicated the submicron meter of particles size for both CFO and PZT particles. After annealing at 900°C for 1 h in air, tape test confirmed the quality of multiferroic thick films as well as pure CFO and PZT films. X-ray diffraction (XRD) showed a coexistence of CFO and PZT phases; furthermore, a smooth surface was observed through scanning electron microscopic (SEM) pictures along with the sharp cross-sectional picture, indicative of 100 μm of film thickness. Ferromagnetic and ferroelectric properties were observed in CFO/PZT films simultaneously at room temperature. Compared with the reported CFO/PZT multiferrroic thin films, the present ferromagnetic property was closing to that of the chemical sol-gel synthesized film and even that from the physical pulsed laser deposition technique. However, the ferroelectric property showed a degenerated behavior, possible reasons for this was discussed and further optimization was also proposed for the potential multifunctional application.
Scientists, engineers, and computer science; industry and research groups
Authors: Guzdial Mark , Linden Greg
Published: March 2011

The
Communications
Web site, http://cacm.acm.org, features more than a dozen bloggers in the BLOG@CACM community. In each issue of
Communications
, we'll publish selected posts or excerpts.

twitter

Follow us on Twitter at http://twitter.com/blogCACM

http://cacm.acm.org/blogs/blog-cacm

Mark Guzdial discusses what scientists and engineers should know about computer science, such as Alan Kay's "Triple Whammy." Greg Linden writes about industry's different approaches to research and how to organize researchers in a company.
A program greater than the sum of its parts
Authors: Chubin Daryl E. , Johnson Roosevelt Y.
Published: March 2011

Changing the trajectory of participation in computing for students at various stages of development.
Testable system administration
Authors: Burgess Mark
Published: March 2011

Models of determinism are changing IT management.
The informatics philharmonic
Authors: Raphael Christopher
Published: March 2011

A system for musical accompaniment is presented in which a computer-driven orchestra follows and learns from a soloist in a concerto-like setting. The system is decomposed into three modules: The first computes a real-time score match using a hidden Markov model; the second generates the output audio by phase-vocoding a preexisting audio recording; the third provides a link between these two, by predicting future timing evolution using a Kalman Filter--like model. Several examples are presented showing the system in action in diverse musical settings. Connections with machine learning are highlighted, showing current weaknesses and new possible directions.
Puzzled: Solutions and sources
Authors: Winkler Peter
Published: March 2011

Last month (February 2011, p. 112) we posted a trio of brainteasers, including one as yet unsolved, concerning partitions of Ms. Feldman's fifth-grade class. Here, we offer solutions to at least two of them. How did you do?
The Internet electorate
Authors: Garrett R. Kelly , Danziger James N.
Published: March 2011

The 2008 U.S. presidential election demonstrated the Internet is a major source of political information and expression.
Modeling and simulation of pedestrian behaviors in crowded places
Authors: Koh Wee Lit , Zhou Suiping
Published: March 2011

Pedestrian simulation has many applications in computer games, military simulations, and animation systems. A realistic pedestrian simulation requires a realistic pedestrian behavioral model that takes into account the various behavioral aspects of a real pedestrian. In this article, we describe our work on such a model, which aims to generate human-like pedestrian behaviors. To this end, various important factors in a real-pedestrian's decision-making process are considered in our model. These factors include a pedestrian's sensory attention, memory, and navigational behaviors. In particular, a two-level navigation model is proposed to generate realistic navigational behavior. As a result, our pedestrian model is able to generate various realistic behaviors such as overtaking, waiting, side-stepping and lane-forming in a crowded area. The simulated pedestrians are also able to navigate through complex environment, given an abstract map of the environment.
Efficient incremental code update for sensor networks
Authors: Panta Rajesh Krishna , Bagchi Saurabh , Midkiff Samuel P.
Published: March 2011

Wireless reprogramming of sensor nodes is an essential requirement for long-lived networks since software functionality needs to be changed over time. During reprogramming, the number of radio transmissions should be minimized, since reprogramming time and energy depend chiefly on the number of radio transmissions. In this article, we present a multihop incremental reprogramming protocol called Zephyr that transfers the
delta
between old and new software versions, and lets the sensor nodes rebuild the new software using the received delta and the old software. Zephyr reduces the delta size by using application-level modifications to mitigate the effects of function shifts. Then it compares the two binary images at the byte level to generate a small delta, that is then sent over the wireless network to all the nodes. For the wide range of software change cases that we used as benchmarks, Zephyr transfers 1.83 to 1987 times less traffic through the network than Deluge (the standard nonincremental reprogramming protocol for TinyOS) and 1.14 to 49 times less traffic than an existing incremental reprogramming protocol by Jeong and Culler [2004].
A fuzzy algorithm for dynamically adaptive multimedia streaming
Authors: Bagchi Susmit
Published: March 2011

The QoS-aware delivery model of multimedia is an interesting research area. The wireless networking systems connecting mobile clients and media servers have created the paradigm of mobile multimedia. In mobile multimedia systems, the media delivery model has to maintain two diagonally opposite objectives, such as maintaining QoS of playback and saving energy consumption of the mobile devices. The traditional pull, push, and the hybrid push-pull models of media delivery are not completely suitable to offer consistent QoS of playback while saving the energy consumptions at mobile devices. This article proposes a novel multimedia delivery system based on the Fuzzy Adaptive Buffering (FAB) algorithm using pull model. The FAB algorithm employs a fuzzy inference technique and dynamically adapts to the execution environments. The experimental results illustrate that the FAB algorithm successfully adapts to dynamic execution contexts while maintaining playback-QoS and saving the energy consumption of the mobile clients by keeping the data prefetching thread in the sleeping mode from 31.44% to 97.4% of streaming time depending on the execution environments.
Challenges and opportunities for efficient computing with FAWN
Authors: Vasudevan Vijay , Andersen David G. , Kaminsky Michael , Franklin Jason , Kozuch Michael A. , Moraru Iulian , Pillai Padmanabhan , Tan Lawrence
Published: March 2011

This paper presents the architecture and motivation for a clusterbased, many-core computing architecture for energy-efficient, dataintensive computing. FAWN, a Fast Array of Wimpy Nodes, consists of a large number of slower but efficient nodes coupled with low-power storage. We present the computing trends that motivate a FAWN-like approach, for CPU, memory, and storage. We follow with a set of microbenchmarks to explore under what workloads these FAWN nodes perform well (or perform poorly), and briefly examine scenarios in which both code and algorithms may need to be re-designed or optimized to perform well on an efficient platform. We conclude with an outline of the longer-term implications of FAWN that lead us to select a tightly integrated stacked chip and-memory architecture for future FAWN development.
Light-weight communications on Intel's single-chip cloud computer processor
Authors: van der Wijngaart Rob F. , Mattson Timothy G. , Haas Werner
Published: March 2011

Many-core chips are changing the way high-performance computing systems are built and programmed. As it is becoming increasingly difficult to maintain cache coherence across many cores, manufacturers are exploring designs that do not feature any cache coherence between cores. Communications on such chips are naturally implemented using message passing, which makes them resemble clusters, but with an important difference. Special hardware can be provided that supports very fast on-chip communications, reducing latency and increasing bandwidth. We present one such chip, the Single-Chip Cloud Computer (SCC). This is an experimental processor, created by Intel Labs. We describe two communication libraries available on SCC: RCCE and Rckmb. RCCE is a light-weight, minimal library for writing message passing parallel applications. Rckmb provides the data link layer for running network services such as TCP/IP. Both utilize SCC's non-cache-coherent shared memory for transferring data between cores without needing to go off-chip. In this paper we describe the design and implementation of RCCE and Rckmb. To compare their performance, we consider simple benchmarks run with RCCE, and MPI over TCP/IP.
Controlling Mass Transport in Microfluidic Devices
Authors: Kuo Jason S. , Chiu Daniel T.
Published: March 2011

Microfluidic platforms offer exquisite capabilities in controlling mass transport for biological studies. In this review, we focus on recent developments in manipulating chemical concentrations at the microscale. Some techniques prevent or accelerate mixing, whereas others shape the concentration gradients of chemical and biological molecules. We also highlight several in vitro biological studies in the areas of organ engineering, cancer, and blood coagulation that have benefited from accurate control of mass transfer.
Monolithic Phases for Ion Chromatography
Authors: Nordborg Anna , Hilder Emily F. , Haddad Paul R.
Published: March 2011

Monolithic media are continuing to increase in popularity in chromatographic applications, and the ongoing use of commercially available materials in ion chromatography (IC) has made monoliths a viable alternative to packed-bed columns for routine use. We discuss different strategies for the synthesis of polymeric and silica monoliths with ion-exchange functionality, such as direct incorporation of ion-exchange functionality during monolith preparation and different postpolymerization alterations such as grafting and coating. The formulations and strategies presented are focused on materials intended for use in IC. We also discuss strategies for materials characterization, with emphasis on nondestructive techniques for the characterization of monolith surface functionality, especially those with applicability to in situ analysis. Finally, we describe selected IC applications of polymeric and silica monoliths published from 2008 to 2010.
Transport and Sensing in Nanofluidic Devices
Authors: Zhou Kaimeng , Perry John M. , Jacobson Stephen C.
Published: March 2011

Ion transport and sensing in nanofluidic devices are receiving a great deal of attention because of their unique transport properties and potential analytical applications. Some aspects of microscale transport transfer directly to the nanoscale, but nanofluidic systems can be significantly influenced by phenomena such as double-layer overlap, surface charge, ion-current rectification, diffusion, and entropic forces, which are either insignificant or absent in larger microchannels. Micro- and nanofabrication techniques create features with a wide range of well-defined geometries and dimensions in synthetic and solid-state substrates. Moreover, these techniques permit coupling of multiple nano- and microscale elements, which can execute various functions. We discuss basic nanofluidic architectures, material transport properties through single and multiple nanochannels, and characterization of single particles by resistive-pulse sensing.
Small-Volume Nuclear Magnetic Resonance Spectroscopy
Authors: Fratila Raluca M. , Velders Aldrik H.
Published: March 2011

Nuclear magnetic resonance (NMR) spectroscopy is one of the most information-rich analytical techniques available. However, it is also inherently insensitive, and this drawback precludes the application of NMR spectroscopy to mass- and volume-limited samples. We review a particular approach to increase the sensitivity of NMR experiments, namely the use of miniaturized coils. When the size of the coil is reduced, the sample volume can be brought down to the nanoliter range. We compare the main coil geometries (solenoidal, planar, and microslot/stripline) and discuss their applications to the analysis of mass-limited samples. We also provide an overview of the hyphenation of microcoil NMR spectroscopy to separation techniques and of the integration with lab-on-a-chip devices and microreactors.
Technologies for Micromanipulating, Imaging, and Phenotyping Small Invertebrates and Vertebrates
Authors: Yanik Mehmet Fatih , Rohde Christopher B. , Pardo-Martin Carlos
Published: March 2011

Small multicellular model organisms such as the invertebrate nematode C. elegans and the vertebrate zebrafish provide unique opportunities for both basic science and pharmaceutical discovery. In recent years, there have been significant breakthroughs in technologies to manipulate and image these organisms for a variety of purposes ranging from behavioral studies of neuronal circuits to high-throughput screening. Here, we review these advancements with a particular focus on the optically transparent model organisms C. elegans and zebrafish.
In Vitro Models of Traumatic Brain Injury
Authors: Morrison Barclay , Elkin Benjamin S. , Dollé Jean-Pierre , Yarmush Martin L.
Published: March 2011

In vitro models of traumatic brain injury (TBI) are helping elucidate the pathobiological mechanisms responsible for dysfunction and delayed cell death after mechanical stimulation of the brain. Researchers have identified compounds that have the potential to break the chain of molecular events set in motion by traumatic injury. Ultimately, the utility of in vitro models in identifying novel therapeutics will be determined by how closely the in vitro cascades recapitulate the sequence of cellular events that play out in vivo after TBI. Herein, the major in vitro models are reviewed, and a discussion of the physical injury mechanisms and culture preparations is employed. A comparison between the efficacy of compounds tested in vitro and in vivo is presented as a critical evaluation of the fidelity of in vitro models to the complex pathobiology that is TBI. We conclude that in vitro models were greater than 88% predictive of in vivo results.
In Vivo Delivery of RNAi with Lipid-Based Nanoparticles
Authors: Huang Leaf , Liu Yang
Published: March 2011

RNA interference (RNAi) technology represents a fundamentally new category of treatments for human disease by addressing targets that are traditionally considered undruggable with existing medicines. The major challenge for RNAi-based therapy is the delivery system that meets human therapeutic needs. Therefore, engineering vectors with good delivery efficiency and safety profile is an intense area of research. Lipid-based nanoparticles for RNAi have yielded successful advances in vivo and to an extent in clinical trials. In this review, we discuss the barriers in developing lipid-based nanoparticles for in vivo RNAi and different strategies to overcome them. Rational designs that address safety concerns and ensure effective delivery will aid the translation of engineered lipid-based nanoparticles toward the clinic in the foreseeable future.
Chemical Strategies for Stem Cell Biology and Regenerative Medicine
Authors: Zhu Saiyong , Wei Wanguo , Ding Sheng
Published: March 2011

Stem cell technology holds great promises for the cures of devastating diseases, injuries, aging, and even cancers as it is applied in regenerative medicine. Recent breakthroughs in the development of induced pluripotent stem cell techniques and efficient differentiation strategies have generated tremendous enthusiasm and efforts to explore the therapeutic potential of stem cells. Small molecules, which target specific signaling pathways and/or proteins, have been demonstrated to be particularly valuable for manipulating cell fate, state, and function. Such small molecules not only are useful in generating desired cell types in vitro for various applications but also could be further developed as conventional therapeutics to stimulate patients' endogenous cells to repair and regenerate in vivo. Here, we focus on recent progress in the use of small molecules in stem cell biology and regenerative medicine.
Current Status of Developments and Applications of Micro-CT
Authors: Ritman Erik L.
Published: March 2011

Use of microscopic computed-tomography (micro-CT) scanning continues to grow in biomedical research. Laboratory-based micro-CT scanners, laboratory-based nano-CT scanners, and integrated micro-CT/SPECT and micro-CT/PET scanners are now manufactured for “turn-key” operation by a number of commercial vendors. In recent years a number of technical developments in X-ray sources and X-ray imaging arrays have broadened the utility of micro-CT. Of particular interest are photon-counting and energy-resolving detector arrays. These are being explored to maximize micro-CT image grayscale dynamic range and to further increase image contrast by utilizing the unique spectral attenuation characteristics of individual chemical elements. X-ray phase-shift images may increase contrast resolution and reduce radiation exposure. Although radiation exposure is becoming a concern with the drive for increased spatial and temporal resolution, especially for longitudinal studies, gated scans and limited scan-data-set reconstruction algorithms show great potential for keeping radiation exposure to a minimum.
Physiologic Cardiovascular Strain and Intrinsic Wave Imaging
Authors: Konofagou Elisa , Lee Wei-Ning , Luo Jianwen , Provost Jean , Vappou Jonathan
Published: March 2011

Cardiovascular disease remains the primary killer worldwide. The heart, essentially an electrically driven mechanical pump, alters its mechanical and electrical properties to compensate for loss of normal mechanical and electrical function. The same adjustment also is performed in the vessels, which constantly adapt their properties to accommodate mechanical and geometrical changes related to aging or disease. Real-time, quantitative assessment of cardiac contractility, conduction, and vascular function before the specialist can visually detect it could be feasible. This new physiologic data could open up interactive therapy regimens that are currently not considered. The eventual goal of this technology is to provide a specific method for estimating the position and severity of contraction defects in cardiac infarcts or angina. This would improve care and outcomes as well as detect stiffness changes and overcome the current global measurement limitations in the progression of vascular disease, at little more cost or risk than that of a clinical ultrasound.
Multiscale Cancer Modeling
Authors: Deisboeck Thomas S. , Wang Zhihui , Macklin Paul , Cristini Vittorio
Published: March 2011

Simulating cancer behavior across multiple biological scales in space and time, i.e., multiscale cancer modeling, is increasingly being recognized as a powerful tool to refine hypotheses, focus experiments, and enable more accurate predictions. A growing number of examples illustrate the value of this approach in providing quantitative insights in the initiation, progression, and treatment of cancer. In this review, we introduce the most recent and important multiscale cancer modeling works that have successfully established a mechanistic link between different biological scales. Biophysical, biochemical, and biomechanical factors are considered in these models. We also discuss innovative, cutting-edge modeling methods that are moving predictive multiscale cancer modeling toward clinical application. Furthermore, because the development of multiscale cancer models requires a new level of collaboration among scientists from a variety of fields such as biology, medicine, physics, mathematics, engineering, and computer science, an innovative Web-based infrastructure is needed to support this growing community.
Nonthrombogenic Approaches to Cardiovascular Bioengineering
Authors: Li Song , Henry Jeffrey J.D.
Published: March 2011

Cardiovascular devices such as vascular grafts, stents, and heart valves have been widely used to treat cardiovascular diseases. The failure of these devices is usually initiated by the formation of thrombus and neointima on the device surfaces. Antithrombogenic surface modifications have been employed to improve the performance of these devices. In addition to biochemical modifications, tissue engineering approaches hold the promise to fabricate nonthrombogenic biological substitutes for cardiovascular tissues and devices. Endothelial cells (ECs) and stem cells have been used to cover blood-contacting surfaces. Furthermore, for tissue-engineered vascularized tissues and organs, a nonthrombogenic vascular network is essential for mass transfer and the integration of functional tissues and organs into the host upon transplantation. This review discusses the advances in antithrombogenic approaches for surface modifications and cardiovascular tissue engineering.
SAXS Studies of Ion–Nucleic Acid Interactions
Authors: Pollack Lois
Published: March 2011

Positively charged ions, atoms, or molecules compensate the high negative charge of the nucleic acid backbone. Their presence is critical to the biological function of DNA and RNA. This review focuses on experimental studies probing (a) interactions between small ions and nucleic acids and (b) ion-mediated interactions between nucleic acid duplexes. Experimental results on these simple model systems can be compared with specific theoretical models to validate their predictions. Small angle X-ray scattering (SAXS) provides unique insight into these interactions. Anomalous SAXS reports the spatial correlations of condensed (e.g., locally concentrated) counterions to individual DNA or RNA duplexes. SAXS very effectively reports interactions between nucleic acid helices, which range from strongly repulsive to strongly attractive depending on the ionic species present. The sign and strength of interparticle interactions are easily deduced from dramatic changes in the scattering profiles of interacting duplexes.
Molecular Mechanisms of Ubiquitin-Dependent Membrane Traffic
Authors: Hurley James H. , Stenmark Harald
Published: March 2011

Over the past 14 years, ubiquitination has emerged as a centrally important mechanism governing the subcellular trafficking of proteins. Ubiquitination, interaction with sorting factors that contain ubiquitin-binding domains, and deubiquitination govern the itineraries of cargo proteins that include yeast carboxypeptidase S, the epithelial sodium channel ENaC, and epidermal growth factor receptor. The molecular structures and mechanisms of the paradigmatic HECT and RING domain ubiquitin ligases, of JAMM- and USP-domain-deubiquitinating enzymes, and of numerous ubiquitin-binding domains involved in these pathways have been worked out in recent years and are described.