bluuebunny/crossref_metadata_2025 huggingface dataset:
B cell gene signature with massive intrahepatic production of antibodies to hepatitis B core antigen in hepatitis B virus–associated acute liver failure
Authors: Farci Patrizia , Diaz Giacomo , Chen Zhaochun , Govindarajan Sugantha , Tice Ashley , Agulto Liane , Pittaluga Stefania , Boon Denali , Yu Claro , Engle Ronald E. , Haas Mark , Simon Richard , Purcell Robert H. , Zamboni Fausto
Published: April 2010

Hepatitis B virus (HBV)-associated acute liver failure (ALF) is a dramatic clinical syndrome due to a sudden loss of hepatic cells leading to multiorgan failure. The mechanisms whereby HBV induces ALF are unknown. Here, we show that liver tissue collected at the time of liver transplantation in two patients with HBV-associated ALF is characterized by an overwhelming B cell response apparently centered in the liver with massive accumulation of plasma cells secreting IgG and IgM, accompanied by complement deposition. We demonstrate that the molecular target of these antibodies is the hepatitis B core antigen (HBcAg); that these anti-bodies display a restricted variable heavy chain (V
H
) repertoire and lack somatic mutations; and that these two unrelated individuals with ALF use an identical predominant V
H
gene with unmutated variable domain (
IGHV1-3
) for both IgG and IgM anti-HBc antibodies, indicating that HBcAg is the target of a germline human V
H
gene. These data suggest that humoral immunity may exert a primary role in the pathogenesis of HBV-associated ALF.
Structure of the 70S ribosome bound to release factor 2 and a substrate analog provides insights into catalysis of peptide release
Authors: Jin Hong , Kelley Ann C. , Loakes David , Ramakrishnan V.
Published: April 2010

We report the crystal structure of release factor 2 bound to ribosome with an aminoacyl tRNA substrate analog at the ribosomal P site, at 3.1 Å resolution. The structure shows that upon stop-codon recognition, the universally conserved GGQ motif packs tightly into the peptidyl transferase center. Nucleotide A2602 of 23S rRNA, implicated in peptide release, packs with the GGQ motif in release factor 2. The ribose of A76 of the peptidyl-tRNA adopts the C2′-endo conformation, and the 2′ hydroxyl of A76 is within hydrogen-bond distance of the 2′ hydroxyl of A2451. The structure suggests how a catalytic water can be coordinated in the peptidyl transferase center and, together with previous biochemical and computational data, suggests a model for how the ester bond between the peptidyl tRNA and the nascent peptide is hydrolyzed.
β-Arrestin–dependent activation of Ca2+/calmodulin kinase II after β1–adrenergic receptor stimulation
Authors: Mangmool Supachoke , Shukla Arun K. , Rockman Howard A.
Published: April 2010

Ca2+/calmodulin kinase II (CaMKII) plays an important role in cardiac contractility and the development of heart failure. Although stimulation of β1–adrenergic receptors (ARs) leads to an increase in CaMKII activity, the molecular mechanism by which β1-ARs activate CaMKII is not completely understood. In this study, we show the requirement for the β1-AR regulatory protein β-arrestin as a scaffold for both CaMKII and Epac (exchange protein directly activated by cAMP). Stimulation of β1-ARs induces the formation of a β-arrestin–CaMKII–Epac1 complex, allowing its recruitment to the plasma membrane, whereby interaction with cAMP leads to CaMKII activation. β-Arrestin binding to the carboxyl-terminal tail of β1-ARs promotes a conformational change within β-arrestin that allows CaMKII and Epac to remain in a stable complex with the receptor. The essential role for β-arrestin and identification of the molecular mechanism by which only β1-ARs and not β2-ARs activate CaMKII significantly advances our understanding of this important cellular pathway.
LET-99 inhibits lateral posterior pulling forces during asymmetric spindle elongation in C. elegans embryos
Authors: Krueger Lori E. , Wu Jui-Ching , Tsou Meng-Fu Bryan , Rose Lesilee S.
Published: April 2010

Cortical pulling on astral microtubules positions the mitotic spindle in response to PAR polarity cues and G protein signaling in many systems. In Caenorhabditis elegans single-cell embryos, posterior spindle displacement depends on Gα and its regulators GPR-1/2 and LIN-5. GPR-1/2 and LIN-5 are necessary for cortical pulling forces and become enriched at the posterior cortex, which suggests that higher forces act on the posterior spindle pole compared with the anterior pole. However, the precise distribution of cortical forces and how they are regulated remains to be determined. Using spindle severing, single centrosome assays, and centrosome fragmentation, we show that both the anterior and posterior cortices generate more pulling force than the lateral–posterior region. Lateral inhibition depends on LET-99, which inhibits GPR-1/2 localization to produce a bipolar GPR-1/2 pattern. Thus, rather than two domains of cortical force, there are three. We propose that the attenuation of lateral forces prevents counterproductive pulling, resulting in a higher net force toward the posterior that contributes to spindle elongation and displacement.
Heterogeneity and hierarchy within the most primitive hematopoietic stem cell compartment
Authors: Morita Yohei , Ema Hideo , Nakauchi Hiromitsu
Published: April 2010

Hematopoietic stem cells (HSCs) have been extensively characterized based on functional definitions determined by experimental transplantation into lethally irradiated mice. In mice, HSCs are heterogeneous with regard to self-renewal potential, in vitro colony-forming activity, and in vivo behavior. We attempted prospective isolation of HSC subsets with distinct properties among CD34−/low c-Kit+Sca-1+Lin− (CD34−KSL) cells. CD34−KSL cells were divided, based on CD150 expression, into three fractions: CD150high, CD150med, and CD150neg cells. Compared with the other two fractions, CD150high cells were significantly enriched in HSCs, with great self-renewal potential. In vitro colony assays revealed that decreased expression of CD150 was associated with reduced erythroblast/megakaryocyte differentiation potential. All three fractions were regenerated only from CD150high cells in recipient mice. Using single-cell transplantation studies, we found that a fraction of CD150high cells displayed latent and barely detectable myeloid engraftment in primary-recipient mice but progressive and multilineage reconstitution in secondary-recipient mice. These findings highlight the complexity and hierarchy of reconstitution capability, even among HSCs in the most primitive compartment.
Activating and inhibitory functions for the histone lysine methyltransferase G9a in T helper cell differentiation and function
Authors: Lehnertz Bernhard , Northrop Jeffrey P. , Antignano Frann , Burrows Kyle , Hadidi Sima , Mullaly Sarah C. , Rossi Fabio M.V. , Zaph Colby
Published: April 2010

Accumulating evidence suggests that the regulation of gene expression by histone lysine methylation is crucial for several biological processes. The histone lysine methyltransferase G9a is responsible for the majority of dimethylation of histone H3 at lysine 9 (H3K9me2) and is required for the efficient repression of developmentally regulated genes during embryonic stem cell differentiation. However, whether G9a plays a similar role in adult cells is still unclear. We identify a critical role for G9a in CD4+ T helper (Th) cell differentiation and function. G9a-deficient Th cells are specifically impaired in their induction of Th2 lineage-specific cytokines IL-4, IL-5, and IL-13 and fail to protect against infection with the intestinal helminth Trichuris muris. Furthermore, G9a-deficient Th cells are characterised by the increased expression of IL-17A, which is associated with a loss of H3K9me2 at the Il17a locus. Collectively, our results establish unpredicted and complex roles for G9a in regulating gene expression during lineage commitment in adult CD4+ T cells.
A CoD-based reduction algorithm for designing stationary control policies on Boolean networks
Authors: Ghaffari Noushin , Ivanov Ivan , Qian Xiaoning , Dougherty Edward R.
Published: April 2010

Motivation: Gene regulatory networks serve as models from which to derive therapeutic intervention strategies, in particular, stationary control policies over time that shift the probability mass of the steady state distribution (SSD) away from states associated with undesirable phenotypes. Derivation of control policies is hindered by the high-dimensional state spaces associated with gene regulatory networks. Hence, network reduction is a fundamental issue for intervention.

Results: The network model that has been most used for the study of intervention in gene regulatory networks is the probabilistic Boolean network (PBN), which is a collection of constituent Boolean networks (BNs) with perturbation. In this article, we propose an algorithm that reduces a BN with perturbation, designs a control policy on the reduced network and then induces that policy to the original network. The coefficient of determination (CoD) is used to choose a gene for deletion, and a reduction mapping is used to rewire the remaining genes. This CoD-reduction procedure is used to construct a reduced network, then either the previously proposed mean first-passage time (MFPT) or SSD stationary control policy is designed on the reduced network, and these policies are induced to the original network. The efficacy of the overall algorithm is demonstrated on networks of 10 genes or less, where it is possible to compare the steady state shifts of the induced and original policies (because the latter can be derived), and by applying it to a 17-gene gastrointestinal network where it is shown that there is substantial beneficial steady state shift.

Availability: The code for the algorithms is available at: http://gsp.tamu.edu/Publications/supplementary/ghaffari10a/ Please Contact Noushin Ghaffari at nghaffari@tamu.edu for further questions.

Contact:  edward@ece.tamu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
MLJ Reviews
Authors: Liskin‐Gasparro Judith E.
Published: April 2010

Books reviewed in this article:

Achiba, Machiko. Learning to Request in a Second Language: A Study of Child Interlanguage Pragmatics.

Blyth, Carl. (Ed.). The Sociolinguistics of Foreign‐Language Classrooms.

Bongartz, Christiane. Noun Combination in Interlanguage: Typology Effects in Complex Determiner Phrases.

Brown, James Dean, & Thom Hudson. Criterion‐Referenced Language Testing.

Cohen, Andrew D., R. Michael Paige, Barbara Kappler, Margaret Dem‐Messie, Susan J. Weaver, Julie C. Chia, & James P. Lassegard.

Dickins, James, Sándor Hervey, & Ian Higgins. Thinking Arabic Translation: A Course in Translation Method (Arabic to English).

Dickins, James, Sándor Hervey, & Ian Higgins. Thinking Arabic Translation: Tutor's Handbook.

Doherty, Monika. Language Processing in Discourse: A Key to Felicitous Translation.

Hunston, Susan. Corpora in Applied Linguistics.

Jie Mei Yu, Catherine, & X. Jie Yang. Tingli: Chinese Listening Comprehension, Beginner.

Jie Mei Yu, Catherine, & X. Jie Yang. Tingli: Chinese Listening Comprehension, Intermediate.

Paige, R. Michael, Andrew D. Cohen, Barbara Kappler, Julie C. Chia, & James P. Lassegard. Maximizing Study Abroad: A Students' Guide to Strategies for Language and Culture Learning and Use.

Paige, R. Michael, Andrew D. Cohen, Barbara Kappler, Julie C. Chia, & James P. Lassegard. A Program Professionals' Guide.

Sandrock, Paul. Planning Curriculum for Learning World Languages.

Smyth, Sarah, & Elena Crosbie. RUS': A Comprehensive Course in Russian.

Smyth, Sarah, & Elena Crosbie. RUS': A Comprehensive Course in Russian.

Stevenson, Anna, & Georges Pilard. Harrap's Business Dictionary English‐French/ French‐English

Tannen, Deborah, & James E. Alatis. (Eds.). Georgetown University Round Table on Languages and Linguistics 2001. Linguistics, Language, and the Real World: Discourse and Beyond.

Trappes‐Lomax, Hugh, & Gibson Ferguson. (Eds.). Language in Language Teacher Education.

Vanpatten, Bill. From Input to Output: A Teacher's Guide to Second Language Acquisition.

Wray, Alison. Formulaic Language and the Lexicon.

Yip, Moira. Tone.

Zagona, Karen. The Syntax of Spanish.

Zamel, Vivian, & Ruth Spack. Enriching ESOL Pedagogy: Readings and Activities for Engagement, Reflection, and Inquiry.
Direct endosomal acidification by the outwardly rectifying CLC‐5 Cl−/H+ exchanger
Authors: Smith Andrew J. , Lippiat Jonathan D.
Published: April 2010

The voltage‐gated Cl− channel (CLC) family comprises cell surface Cl− channels and intracellular Cl−/H+ exchangers. CLCs in organelle membranes are thought to assist acidification by providing a passive chloride conductance that electrically counterbalances H+ accumulation. Following recent descriptions of Cl−/H+ exchange activity in endosomal CLCs we have re‐evaluated their role. We expressed human CLC‐5 in HEK293 cells, recorded currents under a range of Cl− and H+ gradients by whole‐cell patch clamp, and examined the contribution of CLC‐5 to endosomal acidification using a targeted pH‐sensitive fluorescent protein. We found that CLC‐5 only conducted outward currents, corresponding to Cl− flux into the cytoplasm and H+ from the cytoplasm. Inward currents were never observed, despite the range of intracellular and extracellular Cl− concentrations and pH used. Endosomal acidification in HEK293 cells was prevented by 25 μm bafilomycin‐A1, an inhibitor of vacuolar‐type H+‐ATPase (v‐ATPase), which actively pumps H+ into the endosomal lumen. Overexpression of CLC‐5 in HEK293 cells conferred an additional bafilomycin‐insensitive component to endosomal acidification. This effect was abolished by making mutations in CLC‐5 that remove H+ transport, which result in either no current (E268A) or bidirectional Cl− flux (E211A). Endosomal acidification in a proximal tubule cell line was partially sensitive to inhibition of v‐ATPase by bafilomycin‐A1. Furthermore, in the presence of bafilomycin‐A1, acidification was significantly reduced and nearly fully ablated by partial and near‐complete knockdown of endogenous CLC‐5 by siRNA. These data suggest that CLC‐5 is directly involved in endosomal acidification by exchanging endosomal Cl− for H+.
Visualizing voltage dynamics in zebrafish heart
Authors: Tsutsui Hidekazu , Higashijima Shin‐ichi , Miyawaki Atsushi , Okamura Yasushi
Published: April 2010

The zebrafish heart provides a useful vertebrate cardiovascular model with outstanding advantages, including genetic manipulatability, optical accessibility and rapid development. In addition, an emerging topic in cardiotoxicity assay and drug discovery is its use in phenotype‐based chemical screening. Here, we report a technique that allows non‐invasive voltage mapping in beating heart using a genetically encoded probe for transmembrane potential. Application of the anti‐allergy compound astemizole resulted in aberrant propagation of excitation, which accounted for a lack of ventricular contraction. This optical method will provide new opportunities in broad areas of physiological, developmental and pharmacological cardiovascular research.
Comparison of the Flow Field of a Swirl Stabilized Premixed Burner in an Annular and a Single Burner Combustion Chamber
Authors: Fanaca D. , Alemela P. R. , Hirsch C. , Sattelmayer T.
Published: April 2010

An experimental investigation of the flow field of a 12 burner annular combustor and a single burner combustor with the same burner was performed. It has revealed the aerodynamic effect, which causes the discrepancies in the flame transfer function behavior measured at the same operating conditions in the single and the annular combustion chambers. The results have shown significant differences in the flow field. In particular, it is seen that for the investigated system in the annular combustor a free swirling jet flow forms, while in the single burner configuration, a swirling wall jet flow regime exists. In this paper, we discuss the physical mechanism and show how to generalize an earlier finding, which identified a critical confinement value for a given swirler. We propose a new correlation for coswirling burners, which explains the changes found for the investigated system. It compares also well with the experimental data from other burner geometries. The correlation should allow to design single burner tests as to match the annular combustor flow regime.
Experimental and FEA Scratch of Magnetic Storage Thin-Film Disks to Correlate Magnetic Signal Degradation With Permanent Deformation
Authors: Katta Raja R. , Polycarpou Andreas A. , Lee Sung-Chang , Suk Mike
Published: April 2010

Scratch-related magnetic signal degradation can occur during magnetic storage hard disk drive operations when the read-write heads contact the spinning multilayer disks. To investigate this phenomenon, controlled nanoscratch experiments were performed on perpendicular magnetic recording media using various indenters of different radii of curvature. Various loading conditions were used to cause permanent scratches that were measured using atomic force microscopy. The nanoscratch experiments were simulated using finite element analysis (FEA) that included the detailed nanometer scale thin-film multilayer mechanical properties. The permanently deformed field in the subsurface magnetic recording layer was extracted from the FEA results. The residual scratch widths measured on the surface of the magnetic storage disk were directly compared with the residual subsurface widths of the region on the magnetic recording layer, where extensive permanent lateral deformation was present. It was found that the subsurface widths of the deformed regions were significantly larger than the surface scratch widths. Thus, subsurface thin-film layers, such as the magnetic recording layer, could be damaged without observable damage to the protective top surface carbon overcoat. The exact location and extent of damage to the magnetic recording layer depends on the scratch load, size of scratch tip, and the friction at the interface. Such permanent deformation in magnetic recording layer could lead to demagnetization, which has been reported in the literature.
Influence of Wear on the Performance of Multirecess Hydrostatic Journal Bearing Operating With Micropolar Lubricant
Authors: Nicodemus E. Rajasekhar , Sharma Satish C.
Published: April 2010

The objective of the present work is to study theoretically the influence of wear on the performance of four-pocket capillary-compensated hydrostatic journal bearing operating with micropolar lubricant. In the present study, the lubricant containing additives and contaminants is modeled as micropolar fluid. The modified Reynolds equation for micropolar lubricant is solved using finite element method along with capillary restrictor flow equation as a constraint together with appropriate boundary conditions. The performance characteristics of a capillary-compensated four-pocket worn hydrostatic journal bearing operating with micropolar lubricant have been presented for a wide range of values of nondimensional external load, wear depth parameter, and micropolar parameters. The simulated results have also been presented for two different loading arrangements. In arrangement I, the load line acts through centers of the pockets, whereas in arrangement II, the load line bisects the land between two pockets. The simulated results suggest that a bearing lubricated with lubricant having higher micropolar effect has better static and dynamic performance characteristics as compared with Newtonian lubricant but the bearing lubricated with lubricant having higher micropolar effect is predominantly affected by the wear vis a vis static characteristics parameters as compared with Newtonian lubricant for both loading arrangements. However, in the case of stiffness and damping coefficients, loading arrangement II shows a significant higher enhancement in the value of direct stiffness and damping coefficients in z-direction due to micropolar effect as compared with load arrangement I. And also, the effect of wear on stiffness and damping coefficients in z-direction for bearing operating with micropolar lubricant is of same order as Newtonian lubricant for the loading arrangement II. A similar behavior is observed for the case of stiffness and damping coefficients in x-direction for loading arrangement I.
Partial Slip Contact Analysis on Three-Dimensional Elastic Layered Half Space
Authors: Wang Zhan-Jiang , Wang Wen-Zhong , Wang Hui , Zhu Dong , Hu Yuan-Zhong
Published: April 2010

An elastic contact model for three-dimensional layered or coated materials under coupled normal and tangential loads, with consideration of partial slip effects, has been developed in this paper. The response functions for calculating the displacements and stresses were determined in the frequency domain by using the Papkovich–Neuber potentials. The partial slip contact problem was solved by a numerical procedure based on the conjugate Gradient method and fast Fourier transform technique. The contact pressure, surface shear tractions, stick ratios, rigid body displacements, and subsurface stresses are analyzed under different conditions with variations in the material properties and coating thickness. Results show that stiffer coatings tend to decrease the stick ratios and the rigid ball tangential displacements in comparison to those with compliant coatings under the same contact conditions. For stiffer coatings, the values of the von Mises stress and compressive surface stress increase and the positions of maximum von Mises stress move up to the surface; meanwhile, the distributions of the compressive stress become asymmetric due to the action of the tangential load.
Analytical Model of Bump-Type Foil Bearings Using a Link-Spring Structure and a Finite-Element Shell Model
Authors: Feng Kai , Kaneko Shigehiko
Published: April 2010

A complete analytical model of bump-type foil bearings taking into consideration the effects of four factors, i.e., the elasticity of bump foil, the interaction forces between bumps, the friction forces at the contact surfaces, and the local deflection of top foil, is presented in this investigation. Each bump is simplified to two rigid links and a horizontally spaced spring, the stiffness of which is determined from Castigliano’s theorem. The interaction forces and the friction forces are coupled with the flexibility of bumps through the horizontal elementary spring. The local deflection of the top foil is described using a finite-element shell model and added to the film thickness to predict the air pressure with Reynolds’ equation. The bump deflections of a strip with ten bumps calculated using the presented model under different load distributions are consistent with the published results. Moreover, the predicted bearing load and film thickness obtained from a foil bearing with a bump circumferential extend of 360 deg also agree very well with the experimental data, especially for predictions with a proper selection of radial clearance (preload of foil structure) and friction coefficients. In addition, the radial clearance and friction force variations in the foil bearing are noted to significantly change the performance of the foil bearing. The predictions demonstrate that the radial clearance of the foil bearing has an optimum value for the maximum load capacity.
Revisiting the Cattaneo–Mindlin Concept of Interfacial Slip in Tangentially Loaded Compliant Bodies
Authors: Etsion Izhak
Published: April 2010

The Cattaneo–Mindlin concept of interfacial slip in tangentially loaded compliant bodies is revisited and its basic simplifying assumptions are critically examined. It is shown that these assumptions, which, in the absence of modern numerical techniques, were essential in 1949 to enable an elegant quantitative solution of the basic problem of presliding between contacting bodies, may be nonphysical. An alternative approach to the same problem that is based on treating sliding inception as a failure mode involving material plastic yield is discussed. This alternative approach was suggested even before 1949 but for the same lack of modern numerical techniques could only be promoted qualitatively. Some recent theoretical models, which are based on this earlier alternative approach, and in which the simplifying assumptions of the Cattaneo–Mindlin concept were completely relaxed, are described along with their experimental verification. It is shown that the presliding problem between contacting bodies can be accurately solved by these models using realistic physical assumptions and failure criterion.
Contact potentials in Casimir force setups: An experimental analysis
Authors: de Man S. , Heeck K. , Wijngaarden R. J. , Iannuzzi D.
Published: April 2010

The authors present an extensive study of the contact potential difference, V0, between a gold coated sphere and a gold coated plate kept in air at submicron separation. The data confirm that in ambient conditions, V0 depends on both time and separation. They discuss the origin of the time dependence of V0 and elaborate on its functional dependence on separation, d. The data strongly support a log(d) hypothesis but also show that in air this description is not quite complete. These effects might have important implications in the realm of Casimir force experiments.
Aligned dense single-walled carbon nanotube beams and cantilevers for nanoelectromechanical systems applications
Authors: Lu Miao , Jang Min-Woo , Campbell Stephen A. , Cui Tianhong
Published: April 2010

A processable approach to fabricate suspended and aligned single-walled carbon nanotube (SWNT) beams and cantilevers is presented in this article. Suspended dense SWNT membranes were aligned and deposited by a controlled dielectrophoresis process. A gallium focused ion beam at 30 keV and 50 pA with an optimized dose bombarded the SWNT membranes to prepare them for suspended nanoscale beams and cantilevers. To demonstrate the application of this process to nanoelectromechanical systems (NEMS), an SWNT switch was realized with a pull-in voltage of ∼7.8 V. Accordingly, the fabrication process of SWNT beams and cantilevers is believed to be very promising for prototyping of many NEMS devices such as switches, resonators, and biosensors.
Molecular-beam epitaxy growth of site-controlled InAs/GaAs quantum dots defined by soft photocurable nanoimprint lithography
Authors: Cheng Chien-Chia , Meneou K. , Cheng K. Y.
Published: April 2010

Molecular-beam epitaxy grown InAs site-controlled quantum dots (SCQDs) have been demonstrated on GaAs substrates patterned with a dense array of 100 nm square nanopores in 200 nm pitch by soft photocurable nanoimprint lithography. The effects of different growth parameters, including GaAs buffer-layer thickness and arsenic overpressure, on SCQD formation are investigated. The buffer-layer thickness is found to be an influential factor affecting homogeneous quantum dot (QD) formation under a certain pore depth. After GaAs buffer-layer deposition with a suitable thickness, a single QD has been achieved in each patterned nanopore. Under an optimal arsenic overpressure, more uniformly distributed SCQDs have also been shown, confirmed by a narrower photoluminescence linewidth. Strong room-temperature photoluminescence indicates a high optical-quality QD layer on a defect-free interface.
The TGF-β Signal Transduction Pathway
Authors: Thatcher Jack D.
Published: April 2010

Animated lessons depict canonical TGF-β pathways.
Striking Species Difference in the Contribution of Concentrative Nucleoside Transporter 2 to Nucleoside Uptake between Mouse and Rat Hepatocytes
Authors: Furihata Tomomi , Fukuchi Yukina , Iikura Minami , Hashizume Misato , Miyajima Atsushi , Nagai Miki , Chiba Kan
Published: April 2010

Concentrative nucleoside transporter 2 (CNT2) (encoded by theSLC28A2gene) transports various antiviral or antitumor purine nucleoside analogs to be involved in their pharmacokinetics and pharmacological actions. The results of our study showed that mouse hepatocytes hardly expressed CNT2 mRNA and no CNT2-dependent nucleoside uptake was observed, while rat hepatocytes exhibited high CNT2-dependent nucleoside uptake activity levels with abundant CNT2 mRNA expression. We concluded that CNT2 contributes considerably to nucleoside uptake in rat hepatocytes but not in mouse hepatocytes.
Exploring the Contribution of Candidate Genes to Artemisinin Resistance in
Plasmodium falciparum
Authors: Imwong Mallika , Dondorp Arjen M. , Nosten Francois , Yi Poravuth , Mungthin Mathirut , Hanchana Sarun , Das Debashish , Phyo Aung Phae , Lwin Khin Maung , Pukrittayakamee Sasithon , Lee Sue J. , Saisung Suwannee , Koecharoen Kitti , Nguon Chea , Day Nicholas P. J. , Socheat Duong , White Nicholas J.
Published: April 2010

The reduced
in vivo
sensitivity of
Plasmodium falciparum
has recently been confirmed in western Cambodia. Identifying molecular markers for artemisinin resistance is essential for monitoring the spread of the resistant phenotype and identifying the mechanisms of resistance. Four candidate genes, including the
P. falciparum mdr1
(
pfmdr1
) gene, the
P. falciparum
ATPase6
(
pfATPase6
) gene, the 6-kb mitochondrial genome, and
ubp-1
, encoding a deubiquitinating enzyme, of artemisinin-resistant
P. falciparum
strains from western Cambodia were examined and compared to those of sensitive strains from northwestern Thailand, where the artemisinins are still very effective. The artemisinin-resistant phenotype did not correlate with
pfmdr1
amplification or mutations (full-length sequencing), mutations in
pfATPase6
(full-length sequencing) or the 6-kb mitochondrial genome (full-length sequencing), or
ubp-1
mutations at positions 739 and 770. The
P. falciparum
CRT K76T mutation was present in all isolates from both study sites. The
pfmdr1
copy numbers in western Cambodia were significantly lower in parasite samples obtained in 2007 than in those obtained in 2005, coinciding with a local change in drug policy replacing artesunate-mefloquine with dihydroartemisinin-piperaquine. Artemisinin resistance in western Cambodia is not linked to candidate genes, as was suggested by earlier studies.
Antifungal Susceptibility Profile of Human-Pathogenic Species of
Lichtheimia
Authors: Alastruey-Izquierdo Ana , Cuesta Isabel , Walther Grit , Cuenca-Estrella Manuel , Rodriguez-Tudela Juan Luis
Published: April 2010

Forty-four isolates belonging to human pathogenic species of
Lichtheimia
were tested against nine antifungal agents by using the EUCAST methodology. No remarkable differences were found between the clinical species, although
L. ramosa
showed slightly higher MICs for all drugs. Amphotericin B was the most active drug. Among azole drugs, posaconazole had the best activity
in vitro
and voriconazole was inactive. Echinocandins showed activity for some isolates, suggesting a potential role in combination therapy.
Use of Plasma Procalcitonin Levels as an Adjunct to Clinical Microbiology
Authors: Gilbert David N.
Published: April 2010

Procalcitonin (PCT) is synthesized by a large number of tissues and organs in response to invasion by pathogenic bacteria, fungi, and some parasites. Current PCT assays are rapid, specific, and of sufficient sensitivity to detect increases in PCT serum levels within 4 to 6 h of initiation of infection. Clinically, PCT levels may help in decisions regarding the need for empirical antibiotic therapy, “source control” of infection, and duration of antibiotic therapy. The addition of PCT levels to bacterial culture and viral detection results can assist with the separation of colonization and invasion by pathogenic bacteria.
RECONSTRUCTION OF DYNAMIC PET IMAGES USING ACCURATE SYSTEM POINT SPREAD FUNCTION MODELING: EFFECTS ON PARAMETRIC IMAGES
Authors: D'AMBROSIO D. , FIACCHI G. , MARENGO M. , BOSCHI S. , FANTI S. , SPINELLI A. E.
Published: April 2010

Quantitative analysis of positron emission tomography (PET) dynamic images allows to estimate physiological parameters such as glucose metabolic rate (GMR), perfusion, and cardiac output (CO). However, several physical effects such as photon attenuation, scatter and partial volume can reduce the accuracy of parameter estimation. The main goal of this work was to improve small animal PET image quality by introducing system point spread function (PSF) in the reconstruction scheme and to evaluate the effect of partial volume correction (PVC) on physiological parameter estimation. Images reconstructed respectively using constant and spatially variant (SV) PSFs and no PSF modeling was compared. The proposed algorithms were tested on simulated and real phantoms and mice images. Results show that the SV-PSF-based reconstruction method provides a significant contrast improvement of small animals PET cardiac images and, thus, the effects of PVC on physiological parameters were evaluated using such algorithm. Simulations show that the proposed PVC method reduces errors with respect to the true values for parametric images of GMR and perfusion. A reduction of CO percentage error with respect to the original value was also obtained using the SF-PSF approach. In conclusion, SV-PSF reconstruction method provides a more accurate estimation of several physiological parameters obtained from a dynamic PET scan.
PIV MEASUREMENTS AND NUMERICAL VALIDATION OF END-TO-SIDE ANASTOMOSIS
Authors: OWIDA AMAL , DO HUNG , YANG WILLIAM , MORSI YOS S.
Published: April 2010

In this article, particle image velocimetry (PIV) technique was used to determine the instantaneous velocity fields inside a model of end-to-side anastomosis under various physiological flow conditions. Using ANSYS software, a three-dimensional (3D) computational model at the peak systolic blood flow was simulated. The numerical and experimental results were presented and discussed in terms of velocity fields at various locations along the graft and the host artery. The numerical results were then compared with the experimental data and a large difference was found, which was attributed to the imperfection of manufacturing the glass model and measurements error associated with PIV. The findings indicated in general that the analysis at peak systole, steady flow could help in providing essential quantitative information of the hemodynamics in anastomotic artery.
SEMINUMERICAL MODEL TO STUDY TEMPERATURE DISTRIBUTION IN PERIPHERAL LAYERS OF ELLIPTICAL AND TAPERED SHAPED HUMAN LIMBS
Authors: AGRAWAL MAMTA , ADLAKHA NEERU , PARDASANI KAMALRAJ
Published: April 2010

In this article, a seminumerical approach has been developed to study temperature distribution in peripheral layers of tapered shaped human limbs, which are elliptical in shape. The model is three-dimensional which incorporates the important biophysical parameters such as blood mass flow rate, thermal conductivity and rate of metabolic heat generation. Appropriate boundary conditions have been framed using biophysical conditions. The finite element method has been employed along radial and angular directions and Fourier series method along axial direction to obtain temperature profiles in the region. The results have been used to study relationships among various physical and physiological parameters. MATLAB 7.0 has been used to simulate the model and obtain numerical results.
Ads-portal domains
Authors: Almishari Mishari , Yang Xiaowei
Published: April 2010

An ads-portal domain refers to a Web domain that shows only advertisements, served by a third-party advertisement syndication service, in the form of ads listing. We develop a machine-learning-based classifier to identify ads-portal domains, which has 96% accuracy. We use this classifier to measure the prevalence of ads-portal domains on the Internet. Surprisingly, 28.3/25% of the (two-level) *.
com
/*.
net
web domains are ads-portal domains. Also, 41/39.8% of *.
com
/*.
net
ads-portal domains are typos of well-known domains, also known as typo-squatting domains. In addition, we use the classifier along with DNS trace files to estimate how often Internet users visit ads-portal domains. It turns out that ∼5% of the two-level *.
com
, *.
net
, *.
org
, *.
biz
and *.
info
web domains on the traces are ads-portal domains and ∼50% of these accessed ads-portal domains are typos. These numbers show that ads-portal domains and typo-squatting ads-portal domains are prevalent on the Internet and successful in attracting many visits. Our classifier represents a step towards better categorizing the web documents. It can also be helpful to search engines ranking algorithms, helpful in identifying web spams that redirects to ads-portal domains, and used to discourage access to typo-squatting ads-portal domains.
How to make progress in computing education
Authors: Wilson Cameron , Guzdial Mark
Published: April 2010

Improving the research base for computing education requires securing competitive funding commitments.
Can IT lean against the wind?
Authors: Beck Roman
Published: April 2010

Lessons from the global financial crisis.
Beyond total capture
Authors: Sellen Abigail J. , Whittaker Steve
Published: April 2010

Rather than try to capture everything, system design should focus on the psychological basis of human memory.
Censored exploration and the dark pool problem
Authors: Ganchev Kuzman , Nevmyvaka Yuriy , Kearns Michael , Vaughan Jennifer Wortman
Published: April 2010

Dark pools are a recent type of stock exchange in which information about outstanding orders is deliberately hidden in order to minimize the market impact of large-volume trades. The success and proliferation of dark pools have created challenging and interesting problems in algorithmic trading---in particular, the problem of optimizing the allocation of a large trade over multiple competing dark pools. In this work, we formalize this optimization as a problem of multi-venue exploration from censored data, and provide a provably efficient and near-optimal algorithm for its solution. Our algorithm and its analysis have much in common with well-studied algorithms for managing the exploration--exploitation trade-off in reinforcement learning. We also provide an extensive experimental evaluation of our algorithm using dark pool execution data from a large brokerage.
Automatic program repair with evolutionary computation
Authors: Weimer Westley , Forrest Stephanie , Le Goues Claire , Nguyen ThanhVu
Published: April 2010

There are many methods for detecting and mitigating software errors but few generic methods for automatically repairing errors once they are discovered. This paper highlights recent work combining program analysis methods with evolutionary computation to automatically repair bugs in off-the-shelf legacy C programs. The method takes as input the buggy C source code, a failed test case that demonstrates the bug, and a small number of other test cases that encode the required functionality of the program. The repair procedure does not rely on formal specifications, making it applicable to a wide range of extant software for which formal specifications rarely exist.
Cloud-TM
Authors: Romano Paolo , Rodrigues Luis , Carvalho Nuno , Cachopo Joäo
Published: April 2010

One of the main challenges to harness the potential of Cloud computing is the design of programming models that simplify the development of large-scale parallel applications and that allow ordinary programmers to take full advantage of the computing power and the storage provided by the Cloud, both of which made available, on demand, in a pay-only-forwhat-you-use pricing model.

In this paper, we discuss the use of the Transactional Memory programming model in the context of the cloud computing paradigm, which we refer to as Cloud-TM. We identify where existing Distributed Transactional Memory platforms still fail to meet the requirements of the cloud and of its users, and we point several open research problems whose solution we deem as essential to materialize the Cloud-TM vision.
A unified execution model for cloud computing
Authors: Van Hensbergen Eric , Evans Noah Paul , Stanley-Marbell Phillip
Published: April 2010

This article presents the design goals and architecture for a unified execution model (UEM) for cloud computing and clusters. The UEM combines interfaces for logical provisioning and distributed command execution with integrated mechanisms for establishing and maintaining communication, synchronization, and control. In this paper, the UEM architecture is described, and an existing application which could benefit from its facilities is used to illustrate its value.
LBSN 2009 Workshop Report
Authors: Xie Xing
Published: April 2010

Social networking services have become extremely popular in recent years, especially among young people. However, they are still rooted in the virtual world. People usually need to sit behind a desktop computer to upload photos, write blogs and communicate with friends. The development of wireless networks and location sensing technologies have made it easier to track and share personal location information on the fly. By adding the location dimension, we can bring social networking back from the virtual world into real life and allow real-life experiences to be shared in a more convenient way. We define Location Based Social Networks (LBSN) as social network services where people can track and share location related information with each other, via either mobile or desktop computers. As location is one of the most important aspects for people's everyday lives, many novel application scenarios can be supported by LBSN. For example, we can collect and share more trustworthy location recommendations within LBSN and use them to rank interesting locations, discover new places, people and activities.
Highlights from GIR 2010
Authors: Purves Ross , Clough Paul , Jones Chris
Published: April 2010

GIR'10 had a new format this year for the 6
th
in a series of workshops on Geographic Information Retrieval -- unlike previous occasions where the workshop was hosted by either ACM SIGIR or CIKM, it was held independently at the University of Zurich, with a two day format allowing more time for discussion and presentations. The workshop was held in cooperation with ACM SIGSPATIAL, a relationship which we look forward to continuing and developing in the future. A total of 13 long and 11 short papers were accepted for presentation after review by the programme committee, and the proceedings can be found online in the ACM Digital Library.
Welcome to SIGSPATIAL Australia
Authors: Zhou Xiaofang
Published: April 2010

Australia has a long history of research excellence and technological innovation in spatial database systems, geographical information systems, and their advanced applications. In early December 2009, eleven members of our community got together and submitted an application for forming an ACM SIGSPATIAL chapter in Australia. The application was officially chartered by ACM on 23 December 2009. ACM SIGSPATIAL Australia Chapter is the second and the most recent chapter for SIGSPATIAL, following the formation of the Chinese Chapter in October 2009.
Precursor Lesions of High-Grade Serous Ovarian Carcinoma: Morphological and Molecular Characteristics
Authors: Gross Amy L. , Kurman Robert J. , Vang Russell , Shih Ie-Ming , Visvanathan Kala
Published: April 2010

The lack of proven screening tools for early detection and the high mortality of ovarian serous carcinoma (OSC), particularly high grade, have focused attention on identifying putative precursor lesions with distinct morphological and molecular characteristics. The finding of occult invasive and intraepithelial fallopian tube carcinomas in prophylactically removed specimens from asymptomatic high-risk BRCA 1/2-mutation carriers supports the notion of an origin for OSC in the fallopian tube. The intraepithelial carcinomas have been referred to as serous intraepithelial carcinomas (STICs) but our own findings (unpublished data) and recent reports have drawn attention to a spectrum of changes that fall short of STICs that we have designated serous tubal intraepithelial lesions (STILs).
Robotic Vision with the Conformal Camera: Modeling Perisaccadic Perception
Authors: Turski Jacek
Published: April 2010

Humans make about 3 saccades per second at the eyeball's speed of 700 deg/sec to reposition the high-acuity fovea on the targets of interest to build up understanding of a scene. The brain's visuosaccadic circuitry uses the oculomotor command of each impending saccade to shift receptive fields (RFs) to cortical locations before the eyes take them there, giving a continuous and stable view of the world. We have developed a model for image representation based on projective Fourier transform (PFT) intended for robotic vision, which may efficiently process visual information during the motion of a camera with silicon retina that resembles saccadic eye movements. Here, the related neuroscience background is presented, effectiveness of the conformal camera's non-Euclidean geometry in intermediate-level vision is discussed, and the algorithmic steps in modeling perisaccadic perception with PFT are proposed. Our modeling utilizes basic properties of PFT. First, PFT is computable by FFT in complex logarithmic coordinates that also approximate the retinotopy. Second, the shift of RFs in retinotopic (logarithmic) coordinates is modeled by the shift property of discrete Fourier transform. The perisaccadic mislocalization observed by human subjects in laboratory experiments is the consequence of the fact that RFs' shifts are in logarithmic coordinates.
Genetic Immunization with CDR3-Based Fusion Vaccine Confers Protection and Long-Term Tumor-Free Survival in a Mouse Model of Lymphoma
Authors: Iurescia Sandra , Fioretti Daniela , Pierimarchi Pasquale , Signori Emanuela , Zonfrillo Manuela , Tonon Giancarlo , Fazio Vito M. , Rinaldi Monica
Published: April 2010

Therapeutic vaccination against idiotype is a promising strategy for immunotherapy of B-cell malignancies. We have previously shown that CDR3-based DNA immunization can induce immune response against lymphoma and explored this strategy to provide protection in a murine B-cell lymphoma model. Here we performed vaccination employing as immunogen a naked DNA fusion product. The DNA vaccine was generated following fusion of a sequence derived from tetanus toxin fragment C to the epitope. Induction of tumor-specific immunity as well as ability to inhibit growth of the aggressive 38C13 lymphoma and to prolong survival of vaccinated mice has been tested. We determined that DNA fusion vaccine induced immune response, elicited a strong protective antitumor immunity, and ensured almost complete long-term tumor-free survival of vaccinated mice. Our results show that CDR3-based DNA fusion vaccines hold promise for vaccination against lymphoma.
Comparative Study on Two Commercial Strains ofSaccharomyces cerevisiaefor Optimum Ethanol Production on Industrial Scale
Authors: Mukhtar K. , Asgher M. , Afghan S. , Hussain K. , Zia-ul-Hussnain S.
Published: April 2010

Two commercial strains of Saccharomyces cerevisiae, Saf-Instant (Baker's yeast) and Ethanol red (Mutant) were compared for ethanol production during hot summer season, using molasses diluted up to 6- Brix containing 4%-5% sugars. The yeasts were then propagated in fermentation vessels to study the effects of yeast cell count and varying concentrations of Urea, DAP, inoculum size and Lactrol (Antibiotic). Continuous circulation of mash was maintained for 24 hours and after this fermenter was allowed to stay for a period of 16 hours to give time for maximum conversion of sugars into ethanol. Saccharomyces cerevisiae strain (Saf-instant) with cell concentration of 400 millions/mL at molasses sugar level of 13%–15% (pH , Temp. ), inoculum size of 25% (v/v), urea concentration, 150 ppm, DAP, 53.4 ppm and Lactrol,150 ppm supported maximum ethanol production (8.8%) with  L ethanol per tone molasses (96.5% yield), and had significantly lower concentrations of byproducts. By selecting higher ethanol yielding yeast strain and optimizing the fermentation parameters both yield and economics of the fermentation process can be improved.