bluuebunny/crossref_metadata_2025 huggingface dataset:
Using Functional Gains for Optimal Sensor Placement in Fluid-Structure Interaction
Authors: Akhtar Imran , Borggaard Jeff , Burns John A. , Zietsman Lizette
Published: July 2010

Functional gains are integral kernels of the standard feedback operator and are useful in control of partial differential equations (PDEs). These functional gains provide physical insight into how the control mechanism is operating. In some cases, these functional gains can provide information about the optimal placement of actuators and sensors. The study is motivated by fluid flow control and focuses on the computation of these functions. However, for practical purposes, one must be able to compute these functions for a wide variety of PDEs. For higher dimensional systems, computing these gains is at least as challenging as the original simulation problem. To reduce the complexity of the governing equations, reduced-order models are often developed by reducing the PDEs to ordinary-differential equations (ODEs). In this study, we use proper orthogonal decomposition (POD)-Galerkin based approach and develop a reduced-order model of a bluff body wake. We solve the incompressible Navier-Stokes equations, simulate the flow past a circular cylinder, and record the snapshots of the flow field. We compute the POD eigenfunctions and project the Navier-Stokes equations onto these few of these eigenfunctions to develop a reduced-order model. Later, we modify the model by introducing a control function simulating suction actuation on the cylinder surface. We linearize the model about the mean flow and apply feedback control to suppress vortex shedding. We then compute the functional gains for the applied control. We identify these gains at various stations in the wake region and suggest optimum locations for the sensors.
Design Optimization of an L-Shaped Extrusion Die
Authors: Yilmaz Oktay , Gunes Hasan , Kirkkopru Kadir
Published: July 2010

It is an important problem in the polymer extrusion of complex profiles to balance the flow at the die exit. In this paper, we employ simulated annealing-kriging meta-algorithm to optimize the geometric parameters of a die channel to obtain a uniform exit velocity distribution. Design variables for our optimization problem involve the suitable geometric parameters for the die design, which are the thickness of the large channel and the length of the narrow channel. Die balance is based on the deviation of the velocity with respect to the average velocity at the die exit. So the cost function for the optimization problem involves the minimization of this deviation. For the design of numerical experiments, we use Latin Hypercube Sampling (LHS) to construct the kriging model. Then, based on the LHS points, the numerical solutions are performed using Polyflow, a commercial software based on the finite element method and is specifically designed to simulate the flow and heat transfer of non-newtonian, viscoelastic fluids. In our simulations, a HDPE (high density polyethylene) is used as extrusion material. Having obtained numerical simulations for N = 60 LHS points in two-dimensional parameter space (t and L), the optimization of these parameters is carried out by Simulated Annealing (SA) method in conjunction with kriging model. We show that kriging model employed in SA algorithm can be used to optimize the die geometry.
Numerical Simulation of Laser Glazing and Laser Deposition Processes Using Coupled Temperature-Displacement FEM Models
Authors: Muci-Ku¨chler Karim H. , Tirukovelluri Prashanth K. , Langerman Michael A.
Published: July 2010

Predicting the changes in the temperature, displacement and stress fields during Laser Powder Deposition (LPD) is of particular importance. To create a FEM model of LPD, it is convenient to consider first Laser Glazing (LG) since it does not involve the addition of material. Once an adequate approach has been identified to model the thermal aspects associated with the effect of the laser, the complexity of adding material can be included. In this paper coupled temperature-displacement FEM models of LG and LPD developed using the commercial FEM code ABAQUS/Standard are presented. In the case of LG, a model based on the sequentially coupled thermo-mechanical theory was used to predict the temperature distribution, deformations and stresses in a rectangular plate on which the laser moved along a straight path. The results for the temperature distribution were validated using Rosenthal’s solution and experiments performed using the same material and processing parameters. For LPD, the model was developed using fully coupled thermo-mechanical theory and it was limited to thin-wall builds deposited on a plate with dimensions comparable to the wall thickness. To add material, new elements were sequentially introduced in the mesh. Qualitatively, the results obtained with the model were promising.
Computational Simulations on Melting Process of Fine Metal Powders With Laser Irradiation Welding
Authors: Takase Kazuyuki , Muramatsu Toshiharu , Shobu Takahisa , Tsukimori Kazuyuki
Published: July 2010

At the commercial use stage in sodium-cooled fast breeder reactors, securing maintenance and repair better than an equal to that of present water-cooled reactors is needed. Especially a repair technology that secures the plant integrity for long-term operation period becomes indispensable in the heat exchanger tubes of the steam generator that form the boundary of sodium and water coolants. Then the present study focused on the standardization of welding technology with a laser. An experimental study regarding the welding of a stainless steel plate with the laser using fine metal powders is being performed. Moreover, a numerical study is performed to simulate the welding of the fine metal powder on the stainless steel plate. The fine metal powder is made of iron, and is heated by the laser beam, and then melts exceeding the melting temperature. This paper reports the computational results of the welding phenomenon of some metal powders which changes from solid to liquid and liquid to solid. The results were compared with the experimental results qualitatively.
Energy Efficiency Improvement in a Coated Paper Line Using a Custom Back Surface Reflector
Authors: Rozzi Jay C. , Phillips Scott D.
Published: July 2010

Paper-drying and coating processes consume significant amounts of energy. A single coated paper line in a New Page Corporation paper-making plant consumes approximately 1.7 MW of electrical power. Because of the poor efficiency of the infrared (IR) dryers used in this application, only 6% to 10% of the input power is utilized for moisture removal; the remainder of the energy input is lost as waste heat. The poor efficiency also impacts the quality of the paper sheet, resulting in poor control of the moisture profile and increased scrap. To address these issues, we developed a Back Surface Reflector (BSR) that captures thermal energy transmitted through the paper sheet and re-radiates it at wavelengths the paper can readily absorb. For coated 70 lb. paper, we demonstrated a 90% increase in the overall efficiency of the moisture removal process and an improvement in the paper quality. In this case, the energy saved in one month is enough to power five households for one year. These benefits translate to reduced energy costs and decreased scrap. In this paper, we will discuss the development of a simplified thermal model of the process, the completed benchtop experiments, and the results of our in-plant testing on a New Page paper line.
Microgrids: A New Approach to Supply-Side Design for Data Centers
Authors: Sharma Ratnesh , Bash Cullen , Marwah Manish , Patel Chandrakant , Christian Tom
Published: July 2010

Growth in IT infrastructure driven by socio-economic demand for services has led to the creation of large data centers. There is a need for cost-effective and sustainable design and management of such data centers. From this perspective, evolutionary changes in the regulatory and operational climate of traditional electrical and energy utilities has created new opportunities for development of data centers with low TCO and environmental footprint. These opportunities primarily exist on developing unique supply-side architectures for delivery of power, water and other resources to service data centers. Concurrent emergence of smaller heat and power generating systems also provides novel options to create solutions that improve the reliability and scalability of supply-side infrastructures in data centers. In this paper we investigate the impact of combined heat and power generation in operation of data centers in reducing TCO and environmental footprint and improving operational reliability. Usage of natural resources like water, fuel is minimized to create a low footprint IT infrastructure. Through use of mix of on-site power generation technologies alongside energy and water storage we create a power, cooling and water microgrid for the data center. Such microgrids are a promising way to capture the significant potential of smaller distributed energy resources to meet growing demands for low footprint IT infrastructures.
Methodology for Energy Assessment and Conservation
Authors: Aulds Brittany , Kozman Theodore , Lee Jim , Tyagi Satish
Published: July 2010

The current state of the economy along with the rising cost of energy has strained the university’s budget. As a result, the university is forced to cut spending. To elude the possibility of layoffs, wage decreases, or tuition increases, the university can cut costs by reducing the amount of energy it is using. In many cases, energy is not being utilized properly; instead it is being wasted unnecessarily. Considerable savings can be obtained by better managing the university’s energy usage. To estimate the potential cost savings, the energy currently being used by the university was determined separately for each building. The numbers of lights in all accessible areas were counted. The presence of computers, fans, refrigerators, microwaves, and heaters in each room was recorded. Furthermore, it was noted whether the lights were on or off and if the room was occupied or not. The assessments revealed a considerable amount of wasted energy. Lights were on in unoccupied rooms. Lights were also observed to be left on for extended periods of time. Computers were on and not being used, and were rarely ever turned off. A number of personal fans, heaters, microwaves, and refrigerators were present in faculty’s offices. To reduce or eliminate the wasted energy created by these findings, recommendations to the university are to install occupancy sensors, set computers to go into sleep mode when they are not in use, close unused computer labs and buildings, and regulate the occurrence of personal energy consuming devices found in offices. All of the suggestions have a rapid simple payback period.
Single-Phase Thermal Transport of Nanofluids in a Minichannel
Authors: Yu Leyuan , Liu Dong
Published: July 2010

As a promising candidate for heat transfer fluids in advanced cooling technologies, nanofluids have been studied extensively in the past decade. Despite the tremendous research efforts, it is still unclear if and how the presence of dispersed nanoparticles alters the thermal transport and leads to enhanced thermal performance of nanofluids. An experimental investigation was conducted to explore the single-phase forced convection of Al2O3-water nanofluids in a circular minichannel with 1.09 mm inner diameter. The Reynolds number studied ranges from approximately 600 to 2300. The friction factor and convective heat transfer coefficient were measured for nanofluids with volume concentrations of up to 2%. The effects of nanoparticle concentration and flow rate on the local and average heat transfer coefficient as well as Nusselt number are examined. It was found that, once the thermophysical properties of the nanofluids are properly accounted for, the established pressure drop and heat transfer correlations can offer satisfactory predictions of the single-phase thermal transport of nanofluids under the experimental conditions considered in this study.
CFD Study of an Evaporative Trickle Bed Reactor
Authors: Strasser Wayne , Svihla Kurt
Published: July 2010

A numerical study was carried out to investigate steady-state and transient phase distribution, evaporation, and thermal runaway in a large-scale high-pressure trickle bed reactor operating in the low interaction regime. The thermal inertia of the catalyst particles proved to be a significant contribution to the overall energy balance. A cooling recycle stream, containing reaction products and a fresh feed, was included via a closed loop calculation. It was found that, as expected, phase distribution in the catalyst bed had a substantial impact production rate; a faulty feed distribution system can cost approximately 20% in overall steady-state product conversion. Grid resolution effects were quantified and were found to have minimal impact on macroscopic measures. Also, most results were insensitive to the extent of the modeled domain and the commercial solver version. In the event that the cooling recycle stream is lost, the external reactor shell temperature can exceed its design intent. It was found that reducing the quantity of fresh reactant feed in this situation can dramatically reduce the potential for vessel damage.
Non-Isothermal Peristaltic Flow of Newtonian Fluids in a Circular Tube
Authors: Yun M. S. , Huynh B. P.
Published: July 2010

Non-isothermal peristaltic flow of Newtonian fluids in a circular tube is investigated numerically, using a commercial Computational Fluid Dynamics (CFD) software package. Simulation is performed over a range of Reynolds-number values, up to 1000. Temperature affects the flow field via fluid viscosity, which is assumed to decrease exponentially with temperature. Other fluid properties are assumed to be constant, and are similar to those of an oil. Allowing for temperature effects alters significantly the flow pattern and reduces pressure change. In the crest region, recirculation appears in non-isothermal flow at a much smaller Reynolds number Re than in isothermal flow. Influence of the Reynolds number itself is also reduced significantly, such that the flow pattern changes very little with increasing Re, in contrast to the isothermal case. Similarly, in non-isothermal flow, flow pattern is unchanged at different flow rate. This is also in contrast to the isothermal situation.
GPU-Accelerated Simulation of Two-Phase Incompressible Fluid Flow Using a Level-Set Method for Interface Capturing
Authors: Kelly Jesse
Published: July 2010

Computational fluid dynamics has seen a surge of popularity as a tool for visual effects animators over the past decade since Stam’s seminal Stable Fluids paper [1]. Complex fluid dynamics simulations can often be prohibitive to run due to the time it takes to perform all of the necessary computations. This project proposes an accelerated two-phase incompressible fluid flow solver implemented on programmable graphics hardware. Modern graphics-processing units (GPUs) are highly parallel computing devices, and in problems with a large potential for parallel computation the GPU may vastly out-perform the CPU. This project will use the potential parallelism in the solution of the Navier-Stokes equations in writing a GPU-accelerated flow solver. NVIDIA’s Compute-Unified-Device-Architecture (CUDA) language will be used to program the parallel portions of the solver. CUDA is a C-like language introduced by the NVIDIA Corporation with the goal of simplifying general-purpose computing on the GPU. CUDA takes advantage of data-parallelism by executing the same or near-same code on different data streams simultaneously, so the algorithms used in the flow solver will be designed to be highly data-parallel. Most finite difference-based fluid solvers for computer graphics applications have used the traditional staggered marker-and-cell (MAC) grid, introduced by Harlow and Welsh [2]. The proposed approach improves upon the programmability of solvers such as these by using a non-staggered (collocated) grid. An efficient technique is implemented to smooth the pressure oscillations that often result from the use of a collocated grid in the simulation of incompressible flows. To be appropriate for visual effects use, a fluid solver must have some means of tracking fluid interfaces in order to have a renderable fluid surface. This project uses the level-set method [3] for interface tracking. The level set is treated as a scalar property, and so its propagation in time is computed using the same transport algorithm used in the main fluid flow solver.
Comment on “Differential Sensitivity to Human Communication in Dogs, Wolves, and Human Infants”
Authors: Fiset Sylvain
Published: July 2010

Topál
et al
. (Reports, 4 September 2009, p. 1269) reported that dogs’ sensitivity to reading and using human signals contributes to the emergence of a spatial perseveration error (the A-not-B error) for locating objects. Here, I argue that the authors’ conclusion was biased by two confounding factors: the use of an atypical A-not-B search task and an inadequate nonsocial condition as a control.
Gamete Recognition in Mice Depends on the Cleavage Status of an Egg’s Zona Pellucida Protein
Authors: Gahlay Gagandeep , Gauthier Lyn , Baibakov Boris , Epifano Olga , Dean Jurrien
Published: July 2010

Getting Gametes Together

Despite decades of research, the molecular basis of sperm-egg recognition in mammals remains unresolved. Models in which a glycan ligand in the zona pellucida (ZP) surrounding ovulated eggs binds to a sperm surface receptor have been widely embraced. A more recent model proposes that the cleavage status of a ZP protein, ZP2, renders the structure of the zona matrix either permissive or nonpermissive for sperm binding.

Gahlay
et al.

(p.
216
) tested predictions of each model by replacing endogenous zona proteins with either a mutant form of ZP2 that could not be cleaved or of ZP3 that lacked O glycan attachment sites. Sperm-egg recognition depended on the cleavage status of ZP2 rather than on glycan ligands released following fertilization.
Predictive Model for Wall-Bounded Turbulent Flow
Authors: Marusic I. , Mathis R. , Hutchins N.
Published: July 2010

Elucidating Turbulent Flow

When needing to mix two fluids rapidly, turbulent flow can be beneficial. However, in most cases, the churning and tumbling motions of a fluid during turbulent flow reduce the efficiency of a device or process. When fluid flows past a solid object, the bulk of the turbulent motion is concentrated at the surface boundary, but it is unclear to what extent these inner motions are influenced by flow far from the boundary.

Marusic
et al.

(p.
193
; see the Perspective by
Adrian
) demonstrate a nonlinear connection between inner-layer motions and the large-scale outer-layer motions in wind tunnel experiments. A simple model was able to describe the relationship mathematically while accurately mapping the experimental data.
Genomic Analysis of Organismal Complexity in the Multicellular Green Alga
Volvox carteri
Authors: Prochnik Simon E. , Umen James , Nedelcu Aurora M. , Hallmann Armin , Miller Stephen M. , Nishii Ichiro , Ferris Patrick , Kuo Alan , Mitros Therese , Fritz-Laylin Lillian K. , Hellsten Uffe , Chapman Jarrod , Simakov Oleg , Rensing Stefan A. , Terry Astrid , Pangilinan Jasmyn , Kapitonov Vladimir , Jurka Jerzy , Salamov Asaf , Shapiro Harris , Schmutz Jeremy , Grimwood Jane , Lindquist Erika , Lucas Susan , Grigoriev Igor V. , Schmitt Rüdiger , Kirk David , Rokhsar Daniel S.
Published: July 2010

Going Multicellular

The volvocine algae include both the unicellular
Chlamydomonas
and the multicellular
Volvox
, which diverged from one another 50 to 200 million years ago.

Prochnik
et al.

(p.
223
) compared the
Volvox
genome with that of
Chlamydomonas
to identify any genomic innovations that might have been associated with the transition to multicellularity. Size changes were observed in several protein families in
Volvox
, but, overall, the
Volvox
genome and predicted proteome were highly similar to those of
Chlamydomonas
. Thus, biological complexity can arise without major changes in genome content or protein domains.
Firefly Synchrony: A Behavioral Strategy to Minimize Visual Clutter
Authors: Moiseff Andrew , Copeland Jonathan
Published: July 2010

Female fireflies are more likely to respond to simulated male flashes that are synchronized than to unsynchronized flashes.
Deepwater Formation in the North Pacific During the Last Glacial Termination
Authors: Okazaki Y. , Timmermann A. , Menviel L. , Harada N. , Abe-Ouchi A. , Chikamoto M. O. , Mouchet A. , Asahi H.
Published: July 2010

Switching Basins

Most of the densest, deepest water at the bottom of the oceans comes from two regions, the North Atlantic and the circum-Antarctic. Have other regions been able to produce significant quantities of deep water in the past? For decades, researchers have looked, with limited success, for evidence of deepwater formation in the North Pacific since the time of the Last Glacial Maximum, about 23,000 years ago.

Okazaki
et al.

(p.
200
) combine published observational evidence from the North Pacific with model simulations to suggest that deep water did form in the North Pacific during the early part of the Last Glacial Termination, between about 17,500 and 15,000 years ago. The switch between deep-water formation in the North Atlantic and the North Pacific is likely to have had an important effect on heat transport and climate.
The View a Decade On
Drawing the Map of Life
Inside the Human Genome Project

by Victor K. McElheny

Basic Books (Perseus Books Group), New York, 2010. 383 pp. $28, C$35.50, £16.99. ISBN 9780465043330.
Authors: Creager Angela N. H.
Published: July 2010

In this account that draws heavily on interviews with key participants, McElheny examines the background, course, and prospects of the Human Genome Project.
Old Gate Gets a New Look
Authors: Weyand Simone , Iwata So
Published: July 2010

A proposed structure for a protein that enables potassium ions to move in and out of cells raises new questions about how its “gate” works.
Universal Access in the Fight Against HIV/AIDS
Authors: Girard Françoise , Ford Nathan , Montaner Julio , Cahn Pedro , Katabira Elly
Published: July 2010

Now is not the time to retreat on global commitments to HIV programs.
Gender Inequities Must Be Addressed in HIV Prevention
Authors: Jewkes Rachel
Published: July 2010

Building gender equity and reducing gender-based violence are vital in the fight against AIDS.
Repressive Transcription
Authors: Guenther Matthew G. , Young Richard A.
Published: July 2010

Chromatin repression is ironically controlled by the initiation of transcription at specific sites in the genome.
Martin Gardner (1914–2010)
Authors: Richards Dana
Published: July 2010

An author of science, philosophy, and games delighted readers with explanations of how math is connected to the larger world
Panel Explores What It'll Take To Keep Universities Strong
Authors: Mervis Jeffrey
Published: July 2010

The National Academies has convened a blue-ribbon committee to recommend ways to keep research universities healthy. But universities are likely to be disappointed if they are hoping that the committee will conclude that money is the solution.
Solar Sensor Grounded on Revamped Satellite Program
Authors: Kintisch Eli
Published: July 2010

Last week's announcement that the first spacecraft of the newly reconfigured program previously known as the National Polar-orbiting Operational Environmental Satellite System wouldn't be able to measure the intensity of sunlight has left U.S. climate scientists feeling out in the cold.
Volvox
Genome Shows It Doesn't Take Much to Be Multicellular
Authors: Pennisi Elizabeth
Published: July 2010

On page
223
of this week's issue of
Science
, a comparison between the genomes of the 2000-cell
Volvox carteri
and a single-celled green alga,
Chlamydomonas reinhardtii
, has revealed surprisingly few differences in their gene makeup.
Broken-Down Icebreakers Hamstring U.S. Science
Authors: Mervis Jeffrey
Published: July 2010

Scientists' access to the polar regions depends on an over-the-hill and increasingly fragile U.S. icebreaking fleet. And the latest breakdown has scientists worried about the fate of future research cruises.
Dream Team Plans a Blitz on Schizophrenia
Authors: Kaiser Jocelyn
Published: July 2010

Three top neuroscientists are betting big money and their scientific careers on a new approach to studying schizophrenia and other psychiatric diseases. With help from philanthropists, they are launching an institute that will look for treatments by probing early brain development for the origins of mental illness.
Will a Midsummer's Nightmare Return?
Authors: Stone Richard
Published: July 2010

In southwestern China, people of all ages have been dropping dead suddenly and inexplicably. After a 5-year pursuit, scientists have nabbed a surprising culprit.
No Opiate Substitutes For the Masses of IDUs
Authors: Cohen Jon
Published: July 2010

Methadone can slow HIV's spread, yet Russia outlaws the drug, and Ukraine, which only recently made it legal, struggles to meet demand.
HIV/AIDS Investigators Few and Far Between
Authors: Cohen Jon
Published: July 2010

The Biomedical Center conducts top-notch studies with foreign collaborators, a surprising rarity in Russia to this day.
HIV-1 Reactivation Induced by the Periodontal Pathogens
Fusobacterium nucleatum
and
Porphyromonas gingivalis
Involves Toll-Like Receptor 4 and 9 Activation in Monocytes/Macrophages
Authors: González Octavio A. , Li Mengtao , Ebersole Jeffrey L. , Huang Chifu B.
Published: July 2010

Although oral coinfections (e.g., periodontal disease) are highly prevalent in human immunodeficiency virus type 1-positive (HIV-1
+
) patients and appear to positively correlate with viral load levels, the potential for oral bacteria to induce HIV-1 reactivation in latently infected cells has received little attention. We showed that HIV-1 long terminal repeat (LTR) promoter activation can be induced by periodontopathogens in monocytes/macrophages; nevertheless, the mechanisms involved in this response remain undetermined. Since Toll-like receptor 2 (TLR2), TLR4, and TLR9 activation have been involved in HIV-1 recrudescence, we sought to determine the role of these TLRs in HIV-1 reactivation induced by the periodontal pathogens
Fusobacterium nucleatum
and
Porphyromonas gingivalis
using BF24 monocytes/macrophages stably transfected with the HIV-1 promoter driving chloramphenicol acetyltransferase (CAT) expression and THP89GFP cells, a model of HIV-1 latency. We demonstrated that TLR9 activation by
F. nucleatum
and TLR2 activation by both bacteria appear to be involved in HIV-1 reactivation; however, TLR4 activation had no effect. Moreover, the autocrine activity of tumor necrosis factor alpha (TNF-α) but not interleukin-1β (IL-1β) produced in response to bacteria could impact viral reactivation. The transcription factors NF-κB and Sp1 appear to be positively regulating HIV-1 reactivation induced by these oral pathogens. These results suggest that oral Gram-negative bacteria (
F. nucleatum and P. gingivalis
) associated with oral and systemic chronic inflammatory disorders enhance HIV-1 reactivation in monocytes/macrophages through TLR2 and TLR9 activation in a mechanism that appears to be transcriptionally regulated. Increased bacterial growth and emergence of these bacteria or their products accompanying chronic oral inflammatory diseases could be risk modifiers for viral replication, systemic immune activation, and AIDS progression in HIV-1
+
patients.
External Quality Assessment for the Determination of Diphtheria Antitoxin in Human Serum
Authors: Di Giovine Paolo , Pinto Antonella , Ölander Rose-Marie , Sesardic Dorothea , Stickings Paul , Berbers Guy , Neal Shona , Efstratiou Androulla , Paberza Ruta , Dauksiene Snieguole , Bujko Marina , Detcheva Antoaneta , Joks Unna , Levent Belkis , von Hunolstein Christina
Published: July 2010

Accurate determination of diphtheria toxin antibodies is of value in determining the rates of immunity within broad populations or the immune status of individuals who may be at risk of infection, by assessing responses to vaccination and immunization schedule efficacy. Here we report the results of an external quality assessment (EQA) study for diphtheria serology, performed within the dedicated surveillance network DIPNET. Twelve national laboratories from 11 European countries participated by testing a standard panel of 150 sera using their current routine method: Vero cell neutralization test (NT), double-antigen enzyme-linked immunosorbent assay (ELISA; DAE), dual double-antigen time-resolved fluorescence immunoassay (dDA-DELFIA), passive hemagglutination assay (PHA), toxin binding inhibition assay (ToBI), and in-house or commercial ELISAs. The objective of the study was not to identify the best assay, as the advantages and drawbacks of methods used were known, but to verify if laboratories using their routine method would have categorized (as negative, equivocal, or positive) a serum sample in the same way. The performance of each laboratory was determined by comparing its results on a quantitative and qualitative basis to NT results from a single reference laboratory, as this test is considered thein vitro“gold standard.” The performance of laboratories using NT was generally very good, while the laboratories’ performance using otherin vitromethods was variable. Laboratories using ELISA and PHA performed less well than those using DAE, dDA-DELFIA, or ToBI. EQA is important for both laboratories that usein vitrononstandardized methods and those that use commercial ELISA kits.
Association of Single Nucleotide Polymorphisms in Cytotoxic T-Lymphocyte Antigen 4 and Susceptibility to Autoimmune Type 1 Diabetes in Tunisians
Authors: Benmansour Jihen , Stayoussef Mouna , Al-Jenaidi Fayza A. , Rajab Mansoor H. , Rayana Chiheb B. , Said Hichem B. , Mahjoub Touhami , Almawi Wassim Y.
Published: July 2010

In addition to HLA and insulin genes, the costimulatory molecule
CTLA-4
gene is a confirmed type 1 diabetes (T1D) susceptibility gene. Previous studies investigated the association of
CTLA-4
genetic variants with the risk of T1D, but with inconclusive findings. Here, we tested the contributions of common
CTLA-4
gene variants to T1D susceptibility in Tunisian patients and control subjects. The study subjects comprised 228 T1D patients (47.8% females) and 193 unrelated healthy controls (45.6% females). Genotyping for
CTLA-4
CT60A/G (rs3087243), +49A/G (rs231775), and −318C/T (rs5742909) was performed by PCR-restriction fragment length polymorphism (RFLP) analysis. The minor-allele frequencies (MAF) for the three
CTLA-4
variants were significantly higher in T1D patients, and significantly higher frequencies of homozygous +49G/G and homozygous CT60G/G genotypes were seen in patients, which was confirmed by univariate regression analysis (taking the homozygous wild type as a reference). Of the eight possible three-locus
CTLA-4
haplotypes (+49A/G, −318C/T, and CT60A/G) identified, multivariate regression analysis confirmed the positive association of ACG (odds ratio [OR], 1.93; 95% confidence interval [CI], 1.26 to 2.94), GCG (OR, 2.40; 95% CI, 1.11 to 5.21), and GTA (OR, 4.67; 95% CI, 1.52 to 14.39) haplotypes with T1D, after confounding variables were adjusted for. Our results indicate that
CTLA-4
gene variants are associated with increased T1D susceptibility in Tunisian patients, further supporting a central role for altered T-cell costimulation in T1D pathogenesis.
Aortic Valve Endocarditis Possibly Caused by a
Haematobacter-
Like Species
Authors: Buscher April , Li Linda , Han Xiang Y. , Trautner Barbara W.
Published: July 2010

Haematobacter
is a newly proposed genus for a group of fastidious Gram-negative aerobic bacilli isolated mostly from blood samples from patients with septicemia. The
Haematobacter
genus currently includes two species,
H. massiliensis
and
H. missouriensis
. We report isolation of a novel
Haematobacter-
like species from the blood of a 65-year-old man who suffered from probable aortic valve endocarditis. The possible causative role was suggested by the monomicrobial culture and the absence of another causative agent in a patient with probable endocarditis by Duke criteria. This fastidious organism could not be identified by routine biochemical tests. Sequencing analysis of the 16S rRNA gene (1,425 bp) best matched the known
Haematobacter
species yet was substantially different with a nucleotide similarity of 96.7%. This strain also reduced nitrate to nitrite, unlike known species. This case is likely the first reported case of endocarditis possibly caused by a
Haematobacter-
like organism.
Should South Africa Be Performing Nucleic Acid Testing on HIV Enzyme-Linked Immunosorbent Assay-Negative Samples?
Authors: Gous Natasha , Scott Lesley , Perovic Olga , Venter Francios , Stevens Wendy
Published: July 2010

The frequency of acute HIV infection (AHI) among HIV-1 enzyme-linked immunosorbent assay (ELISA)-negative samples received from general hospital patient admissions was assessed. Of 3,005 samples pooled for nucleic acid testing, a prevalence of 0.13% was found. Pooled nucleic acid testing may be feasible for low-cost identification of AHI in high-prevalence settings.
Analytical Performance Determination and Clinical Validation of the Novel Roche RealTime Ready Influenza A/H1N1 Detection Set
Authors: Wenzel Jürgen J. , Panning Marcus , Kaul Karen L. , Mangold Kathy A. , Revell Paula A. , Luna Ruth Ann , Zepeda Héctor , Perea Lizbeth , Vazquez-Perez Joel A. , Young Steve , Rodic-Polic Bojana , Eickmann Markus , Drosten Christian , Jilg Wolfgang , Reischl Udo
Published: July 2010

The emergence of a novel pandemic human strain of influenza A (H1N1/09) virus in April 2009 has demonstrated the need for well-validated diagnostic tests that are broadly applicable, rapid, sensitive, and specific. The analytical performance and clinical validity of results generated with the novel Roche RealTime Ready Influenza A/H1N1 Detection Set using the LightCycler 2.0 instrument were characterized. Analytical performance was assessed by processing respiratory samples spiked with H1N1/09 and seasonal influenza A virus, a set of seasonal influenza A virus subtypes, and samples containing common viral and bacterial respiratory pathogens. The clinical validity of results was assessed in comparison to other assays by analyzing 359 specimens at three clinical sites and one reference laboratory. Direct sequencing was used to resolve samples with discrepant results. The assay detected virus concentrations down to <50 RNA copies per reverse transcription (RT)-quantitative PCR (qPCR). Various influenza A virus subtypes were covered. The analytical specificity was 100%. High clinical validity was demonstrated by the 99% positive agreement between seasonal influenza A viruses, 98% positive agreement between H1N1/09 viruses, and 88% agreement between negative results. The analytical sensitivity was compared to those of three other RT-qPCR assays and was found to be equivalent. The novel Roche RealTime Ready Influenza A/H1N1 Detection Set can be utilized on the widely used LightCycler platform. We demonstrate its usefulness for the rapid detection and surveillance of pandemic H1N1/09 influenza A virus infections.
HIV-1 gp120 Determinants Proximal to the CD4 Binding Site Shift Protective Glycans That Are Targeted by Monoclonal Antibody 2G12
Authors: Duenas-Decamp Maria J. , Clapham Paul R.
Published: July 2010

HIV-1 R5 envelopes vary considerably in their capacities to exploit low CD4 levels on macrophages for infection and in their sensitivities to the CD4 binding site (CD4bs) monoclonal antibody (MAb) b12 and the glycan-specific MAb 2G12. Here, we show that nonglycan determinants flanking the CD4 binding loop, which affect exposure of the CD4bs, also modulate 2G12 neutralization. Our data indicate that such residues act via a mechanism that involves shifts in the orientation of proximal glycans, thus modulating the sensitivity of 2G12 neutralization and affecting the overall presentation and structure of the glycan shield.
Different Strains of Theiler's Murine Encephalomyelitis Virus Antagonize Different Sites in the Type I Interferon Pathway
Authors: Stavrou Spyridon , Feng Zongdi , Lemon Stanley M. , Roos Raymond P.
Published: July 2010

The DA strain of Theiler's murine encephalomyelitis virus (TMEV), a member of the
Cardiovirus
genus of the family
Picornaviridae
, causes persistent infection in susceptible mice, associated with restricted expression of viral proteins, and induces a demyelinating disease of the central nervous system. DA-induced demyelinating disease serves as a model of human multiple sclerosis because of similarities in pathology and because host immune responses contribute to pathogenesis in both disorders. In contrast, the GDVII strain of TMEV causes acute lethal encephalitis with no virus persistence. Cardiovirus L is a multifunctional protein that blocks beta interferon (IFN-β) gene transcription. We show that both DA L and GDVII L disrupt IFN-β gene transcription induction by IFN regulatory factor 3 (IRF-3) but do so at different points in the signaling pathway. DA L blocks IFN-β gene transcription downstream of mitochondrial antiviral signaling protein (MAVS) but upstream of IRF-3 activation, while GDVII L acts downstream of IRF-3 activation. Both DA L and GDVII L block IFN-β gene transcription in infected mice; however, IFN-β mRNA is expressed at low levels in the central nervous systems of mice persistently infected with DA. The particular level of IFN-β mRNA expression set by DA L as well as other factors in the IRF-3 pathway may play a role in virus persistence, inflammation, and the restricted expression of viral proteins during the late stage of demyelinating disease.
Dominant Negative Mutants of the Murine Cytomegalovirus M53 Gene Block Nuclear Egress and Inhibit Capsid Maturation
Authors: Popa Mirela , Ruzsics Zsolt , Lötzerich Mark , Dölken Lars , Buser Christopher , Walther Paul , Koszinowski Ulrich H.
Published: July 2010

The alphaherpesvirus proteins UL31 and UL34 and their homologues in other herpesvirus subfamilies cooperate at the nuclear membrane in the export of nascent herpesvirus capsids. We studied the respective betaherpesvirus proteins M53 and M50 in mouse cytomegalovirus (MCMV). Recently, we established a random approach to identify dominant negative (DN) mutants of essential viral genes and isolated DN mutants of M50 (B. Rupp, Z. Ruzsics, C. Buser, B. Adler, P. Walther and U. H. Koszinowski, J. Virol
81:
5508-5517). Here, we report the identification and phenotypic characterization of DN alleles of its partner, M53. While mutations in the middle of the M53 open reading frame (ORF) resulted in DN mutants inhibiting MCMV replication by ∼100-fold, mutations at the C terminus resulted in up to 1,000,000-fold inhibition of virus production. C-terminal DN mutants affected nuclear distribution and steady-state levels of the nuclear egress complex and completely blocked export of viral capsids. In addition, they induced a marked maturation defect of viral capsids, resulting in the accumulation of nuclear capsids with aberrant morphology. This was associated with a two-thirds reduction in the total amount of unit length genomes, indicating an accessory role for M53 in DNA packaging.
Remarkable Lethal G-to-A Mutations in
vif-
Proficient HIV-1 Provirus by Individual APOBEC3 Proteins in Humanized Mice
Authors: Sato Kei , Izumi Taisuke , Misawa Naoko , Kobayashi Tomoko , Yamashita Yoshiki , Ohmichi Masahide , Ito Mamoru , Takaori-Kondo Akifumi , Koyanagi Yoshio
Published: July 2010

Genomic hypermutation of RNA viruses, including human immunodeficiency virus type 1 (HIV-1), can be provoked by intrinsic and extrinsic pressures, which lead to the inhibition of viral replication and/or the progression of viral diversity. Human APOBEC3G was identified as an HIV-1 restriction factor, which edits nascent HIV-1 DNA by inducing G-to-A hypermutations and debilitates the infectivity of
vif
-deficient HIV-1. On the other hand, HIV-1 Vif protein has the robust potential to degrade APOBEC3G protein. Although subsequent investigations have revealed that lines of APOBEC3 family proteins have the capacity to mutate HIV-1 DNA, it remains unclear whether these endogenous APOBEC3s, including APOBEC3G, contribute to mutations of
vif
-proficient HIV-1 provirus
in vivo
and, if so, what is the significance of these mutations. In this study, we use a human hematopoietic stem cell-transplanted humanized mouse (NOG-hCD34 mouse) model and demonstrate the predominant accumulation of G-to-A mutations in
vif
-proficient HIV-1 provirus displaying characteristics of APOBEC3-mediated mutagenesis. Notably, the APOBEC3-associated G-to-A mutation of HIV-1 DNA that leads to the termination of translation was significantly observed. We further provide a novel insight suggesting that HIV-1 G-to-A hypermutation is independently induced by individual APOBEC3 proteins. In contrast to the prominent mutation in intracellular proviral DNA, viral RNA in plasma possessed fewer G-to-A mutations. Taken together, these results provide the evidence indicating that endogenous APOBEC3s are associated with G-to-A mutation of HIV-1 provirus
in vivo
, which can result in the abrogation of HIV-1 infection.
Role of Peroxiredoxin 1 and Peroxiredoxin 4 in Protection of Respiratory Syncytial Virus-Induced Cysteinyl Oxidation of Nuclear Cytoskeletal Proteins
Authors: Jamaluddin Mohammad , Wiktorowicz John E. , Soman Kizhake V. , Boldogh Istvan , Forbus Jeffrey D. , Spratt Heidi , Garofalo Roberto P. , Brasier Allan R.
Published: July 2010

The respiratory epithelium plays a central role in innate immunity by secreting networks of inflammatory mediators in response to respiratory syncytial virus (RSV) infection. Previous proteomic studies focusing on the host cellular response to RSV indicated the existence of a nuclear heat shock response and cytoplasmic depletion of antioxidant proteins in model type II-like airway epithelial cells. Here, we increased the depth of nuclear proteomic interrogation by using fluorescence difference labeling followed by liquid isoelectric focusing prefractionation/two-dimensional gel electrophoresis (2-DE) to identify an additional 41 proteins affected by RSV infection. Surprisingly, we found inducible oligomers and shifts in isoelectric points for peroxiredoxin 1 (Prdx-1), Prdx-3, and Prdx-4 isoforms without changes in their total abundance, indicating that Prdxs were being oxidized in response to RSV. To address the role of Prdx-1 and Prdx-4 in RSV infection, isoforms were selectively knocked down by small interfering RNA (siRNA) transfection. Cells lacking Prdx-1, Prdx-4, or both showed increased levels of reactive oxygen species formation and a higher level of protein carbonylation in response to RSV infection. Using a novel saturation fluorescence labeling 2-DE analysis, we showed that 15 unique proteins had enhanced oxidative modifications of at least >1.2-fold in the Prdx knockdowns in response to RSV, including annexin A2 and desmoplakin. Our results suggest that Prdx-1 and Prdx-4 are essential for preventing RSV-induced oxidative damage in a subset of nuclear intermediate filament and actin binding proteins in epithelial cells.
T Cell Responses Are Required for Protection from Clinical Disease and for Virus Clearance in Severe Acute Respiratory Syndrome Coronavirus-Infected Mice
Authors: Zhao Jincun , Zhao Jingxian , Perlman Stanley
Published: July 2010

A dysregulated innate immune response and exuberant cytokine/chemokine expression are believed to be critical factors in the pathogenesis of severe acute respiratory syndrome (SARS), caused by a coronavirus (SARS-CoV). However, we recently showed that inefficient immune activation and a poor virus-specific T cell response underlie severe disease in SARS-CoV-infected mice. Here, we extend these results to show that virus-specific T cells, in the absence of activation of the innate immune response, were sufficient to significantly enhance survival and diminish clinical disease. We demonstrated that T cells are responsible for virus clearance, as intravenous adoptive transfer of SARS-CoV-immune splenocytes orin vitro-generated T cells to SCID or BALB/c mice enhanced survival and reduced virus titers in the lung. Enhancement of the number of virus-specific CD8 T cells by immunization with SARS-CoV peptide-pulsed dendritic cells also resulted in a robust T cell response, earlier virus clearance, and increased survival. These studies are the first to show that T cells play a crucial role in SARS-CoV clearance and that a suboptimal T cell response contributes to the pathological changes observed in SARS. They also provide a new approach to SARS vaccine design.
Polarographic determination of vitamin C after derivatization with o-phenylenediamine
Authors: Rodrigues José António , Valente Inês Maria , Gonçalves Luís Moreira , Pacheco João Grosso , Barros Aquiles Araújo
Published: July 2010

A differential pulse polarographic (DPP) method has been developed for the determination of ascorbic acid (AA) and dehydroascorbic acid (DHA), the two main forms of Vitamin C. The method consists of the DPP analysis of a quinoxaline obtained by the derivatization of DHA with o-phenylenediamine. Results using the proposed method correlated well with those obtained by two reference methodologies: the common iodometric method and a published chromatographic methodology. It was also used in the study of Vitamin C degradation in fruit juices, showing that it involves an initial oxidation of AA to DHA, followed by hydrolytic degradation of the latter.
Follow the money: How the billions of dollars that flow from smokers in poor nations to companies in rich nations greatly exceed funding for global tobacco control and what might be done about it
Authors: Callard Cynthia
Published: July 2010

The business of selling cigarettes is increasingly concentrated in the hands of five tobacco companies that collectively control almost 90% of the world's cigarette market, four of which are publicly traded corporations. The economic activities of these cigarette manufacturers can be monitored through their reports to shareholders and other public documents. Reports for 2008 show that the revenues of these five companies exceeded $300 billion, of which more than $160 billion was provided to governments as taxes, and that corporate earnings of the four publicly traded companies were over $25 billion, of which $14 billion was retained after corporate income taxes were paid. By contrast, funding for domestic and international tobacco control is not reliably reported. Estimated funding for global tobacco control in 2008, at $240 million, is significantly lower than resources provided to address other high-mortality global health challenges. Tobacco control has not yet benefited from the innovative finance mechanisms that are in place for HIV/AIDS, tuberculosis and malaria. The Framework Convention On Tobacco Control (FCTC) process could be used to redirect some of the earnings from transnational tobacco sales to fund FCTC implementation or other global health efforts.
A HAUSDORFF–YOUNG INEQUALITY FOR LOCALLY COMPACT QUANTUM GROUPS
Authors: COONEY TOM
Published: July 2010

Let G be a locally compact abelian group with dual group Ĝ. The Hausdorff–Young theorem states that if f ∈ Lp(G), where 1 ≤ p ≤ 2, then its Fourier transform [Formula: see text] belongs to Lq(Ĝ) (where (1/p) + (1/q) = 1) and [Formula: see text]. Kunze and Terp extended this to unimodular and locally compact groups, respectively. We further generalize this result to an arbitrary locally compact quantum group 𝔾 by defining a Fourier transform [Formula: see text] and showing that this Fourier transform satisfies the Hausdorff–Young inequality.