bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Hydrophobic Recovery of Plasma Treated PDMS Microchannels on Surface Tension Driven Flow
Authors: Almutairi Zeyad , Ren Carolyn , Johnson David
Published: March 2011

Surface tension driven flow is used in numerous microfluidic applications. It is considered a passive pumping technique which doesn’t require any external energy, aside from the interfacial surface energy between the fluid and walls. Thus, it is preferred in applications where the goal is fluid and sample transport. In many applications PDMS (Polydimethylsiloxane) is the most adapted material for chip manufacturing in microfluidics. PDMS has several aspects that make it favorable for microfluidic applications. Ease of chip fabrication, cost effectiveness, chemical stability, and good optical properties are features offered by PDMS and desirable for microfluidics. On the other hand, PDMS has some shortcomings. One of importance is that PDMS is naturally hydrophobic. For this reason it is hard to achieve surface tension flow in native PDMS for various fluids used in microfluidics. Thus, native PDMS must be treated to get hydrophilic surface properties. The most used method for altering PDMS properties to a hydrophilic state is by plasma treatment. This treatment has several aspects where it enhances the attachment of PDMS to substrates, it alters the surface from a hydrophobic to a hydrophilic state, and it increases the electrokinetic properties of PDMS. As a result, after plasma treatment surface tension pumping can be achieved in PDMS, unlike native PDMS. However, plasma treatment is not permanent due to the diffusion of non-cured PDMS species to the surface of microchannels, as is well documented in the literature. The change of plasma treated PDMS with time will affect both the electrokinetic and surface tension driven flow. To our knowledge, researchers have quantitatively documented the time effect on plasma treated PDMS microchannels (aging of PDMS) for electrokinetic flow, but not for surface tension driven flow. Therefore, a quantitative examination of the time effect on surface tension driven flow for plasma treated PDMS gives valuable information on both regaining the hydrophobic properties in PDMS and changes in the passive flow conditions. In this work a quantitative study on the hydrophobic recovery for oxygen-plasma treated PDMS and its effects on surface tension flow was examined. The study was performed with a quantitative flow visualization technique (micro particle image velocimetry). It was found that the aging of PDMS will strongly affect surface tension flow of water based solutions in PDMS microchannels. This study gives important information on the effectiveness of surface tension driven flow for oxygen plasma treated PDMS microchannels.
IAEA SSG-2: Deterministic Safety Analysis for NPP
Authors: Dusic M. , D’Auria F. , Petruzzi A. , Dutton L. M. C. , Glaeser H. , Mavko B. , Pelayo F.
Published: March 2011

Regulating safety is a national responsibility. However, radiation risks may transcend national borders, and international cooperation serves to promote and enhance safety globally by exchanging experience and by improving capabilities to control hazards, to prevent accidents, to respond to emergencies and to mitigate any harmful consequences. International safety standards provide support for States in meeting their obligations under general principles of international law, such as those relating to environmental protection. The objective of the Safety Guide SSG-2 “Deterministic Safety Analysis for Nuclear Power Plants (NPP)” is to provide harmonized guidance to designers, operators, regulators and providers of technical support on deterministic safety analysis for nuclear power plants.
Direct patterning of coplanar polyethylene glycol alkylsilane monolayers by deep-ultraviolet photolithography as a general method for high fidelity, long-term cell patterning and culture
Authors: Wilson Kerry , Stancescu Maria , Das Mainak , Rumsey John , Hickman James
Published: March 2011

This manuscript details a general method for patterning coplanar alkylsilane monolayers using deep-ultraviolet photolithography that has broad application for high fidelity patterning of cells of varying phenotype in long-term cultures. A polyethylene glycol monolayer was formed on a silica substrate and then patterned using 193 nm light from an ArF excimer laser. The regions of photoablation were then rederivatized with (3-trimethoxysilyl propyl) diethyltriamine (DETA), yielding high contrast cytophilic islands that promoted cell adhesion and growth. Rat hippocampal neurons, motoneurons, and myoblasts were then cultured in a defined, serum-free medium on the patterned surfaces for periods in excess of 40 days. This approach has been shown to be useful as a general method for the long-term culture of multiple cell types in highly defined spatial patterns and can be used for supporting complex cocultures for creating in vitro models for biological systems.
Effect of ion bombarding energies on photocatalytic TiO2 films growing in a pulsed dual magnetron discharge
Authors: Novák Ondřej , Vlček Jaroslav
Published: March 2011

Photocatalytic crystalline TiO2 films were deposited by a pulsed dc dual magnetron system. The depositions were performed using two unbalanced magnetrons with planar titanium targets of 50 mm diameter in Ar+O2 gas mixtures at a total pressure of 0.9 Pa with oxygen partial pressures ranging from 0.2 to 0.9 Pa. The maximum substrate surface temperature was 160 °C. Both magnetrons operated in the same asymmetric bipolar mode at the repetition frequencies of 100 and 350 kHz with a fixed 50% duty cycle and the average target power densities of 52–74 W cm−2 in the negative voltage phase of the pulses, but the magnetron operations were shifted by a half of the period. Time-averaged energy-resolved mass spectroscopy was performed at a substrate position located 100 mm from the targets. The measured structure of the ion energy distributions was correlated with the distinct pulse phases of the magnetron discharges. A decrease in the energy delivered by fast ions (E≥10 eV) to the unit volume of the growing films, together with possible effects of plasma-chemical processes, during the depositions at the oxygen partial pressures of 0.5–0.75 Pa and the repetition frequency of 350 kHz resulted in a strong predominance of the highly photoactive crystalline anatase phase in the TiO2 films.
Teaching Newton's Laws with the iPod Touch in Conceptual Physics
Authors: Kelly Angela M.
Published: March 2011

One of the greatest challenges in teaching physics is helping students achieve a conceptual understanding of Newton's laws. I find that students fresh from middle school can sometimes recite the laws verbatim (“An object in motion stays in motion…” and “For every action…”), but they rarely demonstrate a working knowledge of how to apply them to observable phenomena. As a firm believer in inquiry-based teaching methods, I like to develop activities where students can experiment and construct understandings based on relevant personal experiences. Consequently, I am always looking for exciting new technologies that can readily demonstrate how physics affects everyday things. In a conceptual physics class designed for ninth-graders, I created a structured activity where students applied Newton's laws to a series of free applications downloaded on iPod Touches. The laws had been introduced during the prior class session with textual descriptions and graphical representations. The course is offered as part of the Enlace Latino Collegiate Society, a weekend enrichment program for middle and high school students in the Bronx. The majority of students had limited or no prior exposure to physics concepts, and many attended high schools where physics was not offered at all.1
Physics Thirst? A Survey of Ninth-Grade Physics Students
Authors: Korsunsky Boris , Huckins Grace
Published: March 2011

In 2008, this magazine ran an article1 describing the results of a survey of the eighth-graders who were about to begin their first physics course at Weston High School. The results helped this coauthor (BK) and his high school colleagues better understand the expectations of the incoming students. It seemed useful, however, to conduct another survey—one that would probe the attitudes and the perceptions of our ninth-graders who were actually taking physics. That survey was conducted in June 2010 by BK and GH (the latter, at the time, was a sophomore enrolled in BK's Advanced Placement® Physics C course).
Helium Speech: An Application of Standing Waves
Authors: Wentworth Christopher D.
Published: March 2011

Taking a breath of helium gas and then speaking or singing to the class is a favorite demonstration for an introductory physics course, as it usually elicits appreciative laughter, which serves to energize the class session. Students will usually report that the helium speech “raises the frequency” of the voice. A more accurate description of the phenomenon requires that we distinguish between the frequencies of sound produced by the larynx and the filtering of those frequencies by the vocal tract. We will describe here an experiment done by introductory physics students that uses helium speech as a context for learning about the human vocal system and as an application of the standing sound-wave concept. Modern acoustic analysis software easily obtained by instructors for student use allows data to be obtained and analyzed quickly.
Special Relativity in Week One: 2) All Clocks Run Slow
Authors: Huggins Elisha
Published: March 2011

In our initial article on teaching special relativity in the first week of an introductory physics course, we used the principle of relativity and Maxwell's theory of light to derive Einstein's second postulate (that the speed of light is the same to all observers).1 In this paper we study thought experiments involving a light pulse clock moving past us with uniform motion at a speed v. Using Einstein's second postulate and the Pythagorean theorem, we see that the light pulse clock runs slow by a factor √1 − v2/c2. We then show that it is a direct consequence of the principle of relativity that all clocks moving by us the same way run slow by precisely the same factor.
Cramster: Friend or Foe?
Authors: Grams Michael
Published: March 2011

Recently when teaching a first-semester calculus-based physics course for engineers, I was perplexed by a particular group of students. These individuals were able to solve nearly every homework problem assigned from the end-of-chapter exercises in our textbook, and in some cases were able to do so using methods that we had not covered in class. However, they were unable to explain the steps in their solutions and when given similar problems on exams they performed very poorly. I became suspicious that these students were submitting homework solutions that were not their own, and a quick Internet search confirmed my fears. These students had been plagiarizing their homework assignments from a website called Cramster (www.cramster.com). In this article I would like to discuss the website, what some of my previous students and fellow educators think about it, and also consider whether or not Cramster could be useful in helping students learn physics.
Teaching the First Law of Thermodynamics via Real-Life Examples
Authors: Chang Wheijen
Published: March 2011

The literature has revealed that many students encounter substantial difficulties in applying the first law of thermodynamics. For example, university students sometimes fail to recognize that heat and work are independent means of energy transfer.1 When discussing adiabatic processes for an ideal gas, few students can correctly refer to the concept of “work” to justify a change in temperature.1 Some students adopt the notion that “collisions between molecules produce heat” to explain the rise in temperature for an adiabatic compression process.2 When explaining processes entailing temperature variation, students tend to adopt the ideal-gas law.1,2 Although most university students have acquired a reasonable grasp of the state-function concept, which is valid for variation of internal energy, they fail to grasp the concept that work depends not only on the states but also the processes. Thus, they are unable to use the first law effectively.3 In order to help students comprehend the meaning, usages, and value of the first law, and to realize that the ideal-gas law itself is insufficient to analyze many real-life examples, this paper introduces four examples, some of which can be demonstrated in the classroom. The examples have been devised and gradually modified over a period of several years based on implementation in a calculus-based introductory physics course. Details of when, how, and why each example is adopted, along with the students' pitfalls, are described below.
Stunt Barbie - A Laboratory Practicum Combining Constant Velocity and Constant Acceleration
Authors: Hertting Scott
Published: March 2011

In preparing to teach the advanced physics course at my high school, I found it useful to work through the end-of-chapter problems in the book1 used by the advanced class. A problem on motion in one dimension involved a stunt woman in free fall from a tree limb onto a horse running beneath her.2 The problem presents a connected learning opportunity for students because it requires the use of the constant velocity model xf = v*t + xi and the constant acceleration model yf = ½* g* t2 + vyi* t + yi (where g = 9.8 m/s/s) to solve it. I named the stunt woman Barbie and created an activity titled “Stunt Barbie.”
The Opaque Projector: The Inverse of the Camera Obscura
Authors: Greenslade Thomas B.
Published: March 2011

Many years ago I was running the standard laboratory experiment on thin lens optics. The source was the usual self-illuminated object mounted on an optical bench, and a converging lens formed a real image on a screen. One of the students sitting near one wall of the darkened lab was having some trouble with the idea of image formation. Her face was lit by the light from a shaded gooseneck lamp, and as she looked at me holding the lens in my hand, the inverted image of her face appeared on a nearby wall. And, the image was in color! Not only was this a classic teaching moment, but I realized that, by chance, we had set up an opaque projector.
Doppler frequency shift of sound apparatus
Authors: Schier Walter
Published: March 2011

A large 1-m diameter rotary table with a semicircular waveguide along its periphery is the basis of the Doppler frequency shift of sound apparatus. A “button” speaker is attached to the outer edge of the rotary table and a microphone pickup is positioned on the wall of the waveguide at its midpoint. At approximate speeds of 25 mph (11 m/s), the velocity measured from the frequency shift between the approaching and receding speaker compared to the velocity measured from the repeat sound pattern agree to within 1%. The microphone output is fed successively to our 10 computer stations.
Roll over, Rover
Authors: Shaw Mike
Published: March 2011

Here's a quick, simple, and inexpensive demonstration of an induced static charge. Everyone has probably demonstrated static induction by first rubbing a balloon across his or her hair or animal fur and then sticking it on a wall, whiteboard, or chalkboard. Now you can add a humorous twist to that golden oldie. You will need two balloons (the type clowns use to make animal shapes), an animal fur friction pad or your hair, and a marking pen. Inflate both balloons to their full length and tie off the openings. Along the center of one balloon, in large letters write the word “Rover.” Allow the ink to dry and you are ready for the demonstration.
Comment on “Global Convergence in the Temperature Sensitivity of Respiration at Ecosystem Level”
Authors: Graf Alexander , Weihermüller Lutz , Huisman Johan A. , Herbst Michael , Vereecken Harry
Published: March 2011

Mahecha
et al
. (Reports, 13 August 2010, p. 838) estimated the temperature sensitivity of ecosystem respiration (
Q
10
) and showed that temperature sensitivity and its site-to-site variability are lower than previously reported. We demonstrate that their
Q
10
value of 1.4 is an underestimate if interpreted as the averaged sensitivities of all ecosystem components, because fast temperature fluctuations penetrate poorly into the soil.
Function of Rhodopsin in Temperature Discrimination in
Drosophila
Authors: Shen Wei L. , Kwon Young , Adegbola Abidemi A. , Luo Junjie , Chess Andrew , Montell Craig
Published: March 2011

The light sensor rhodopsin appears to also function in temperature sensation in the fruit fly.
Impact of Undergraduate Science Course Innovations on Learning
Authors: Ruiz-Primo Maria Araceli , Briggs Derek , Iverson Heidi , Talbot Robert , Shepard Lorrie A.
Published: March 2011

Despite revealing some positive impacts, studies too often suffer from weak design and inadequate reporting.
Co-Residence Patterns in Hunter-Gatherer Societies Show Unique Human Social Structure
Authors: Hill Kim R. , Walker Robert S. , Božičević Miran , Eder James , Headland Thomas , Hewlett Barry , Hurtado A. Magdalena , Marlowe Frank , Wiessner Polly , Wood Brian
Published: March 2011

Individuals in residential groups in contemporary hunter-gatherer societies are unrelated to each other.
A Polarized Epithelium Organized by β- and α-Catenin Predates Cadherin and Metazoan Origins
Authors: Dickinson Daniel J. , Nelson W. James , Weis William I.
Published: March 2011

An epithelium in
Dictyostelium discoideum
suggests convergence between multicellular animals and slime molds.
Organic Aerosol Formation Downwind from the Deepwater Horizon Oil Spill
Authors: de Gouw J. A. , Middlebrook A. M. , Warneke C. , Ahmadov R. , Atlas E. L. , Bahreini R. , Blake D. R. , Brock C. A. , Brioude J. , Fahey D. W. , Fehsenfeld F. C. , Holloway J. S. , Le Henaff M. , Lueb R. A. , McKeen S. A. , Meagher J. F. , Murphy D. M. , Paris C. , Parrish D. D. , Perring A. E. , Pollack I. B. , Ravishankara A. R. , Robinson A. L. , Ryerson T. B. , Schwarz J. P. , Spackman J. R. , Srinivasan A. , Watts L. A.
Published: March 2011

Organic compounds of intermediate volatility play an important role in the formation of secondary organic aerosols.
Positive Supercoiling of Mitotic DNA Drives Decatenation by Topoisomerase II in Eukaryotes
Authors: Baxter J. , Sen N. , Martínez V. López , De Carandini M. E. Monturus , Schvartzman J. B. , Diffley J. F. X. , Aragón L.
Published: March 2011

Positive supercoiling of catenated DNA during cell division induces its enzymic decatenation to allow chromosome segregation.
Aging in the Natural World: Comparative Data Reveal Similar Mortality Patterns Across Primates
Authors: Bronikowski Anne M. , Altmann Jeanne , Brockman Diane K. , Cords Marina , Fedigan Linda M. , Pusey Anne , Stoinski Tara , Morris William F. , Strier Karen B. , Alberts Susan C.
Published: March 2011

Aging patterns in humans fall within the parameters of other primates in natural populations.
The Diamond Within a Silicon Analog of Cyclobutadiene
Authors: Apeloig Yitzhak
Published: March 2011

The distinctive rhombic structure of the central ring of a stable silicon analog of cyclobutadiene provides new insights into antiaromaticity.
A Hopeful Vision of Food in Africa
The New Harvest
Agricultural Innovation in Africa

by Calestous Juma

Oxford University Press, New York, 2010. 296 pp. $99, £60. ISBN 9780199783205. Paper, $19.95, £12.99. ISBN 9780199783199.
Authors: Gollin Douglas
Published: March 2011

Drawing on case studies from Africa and successes in developing countries, Juma describes policy and institutional changes for improving Africa's agricultural output and economies.
China Bets Big on Small Grants, Large Facilities
Authors: Stone Richard
Published: March 2011

The National Natural Sciences Foundation of China, the country's main agency for funding competitive, peer-reviewed research grants, will get 12 billion yuan ($1.83 billion) in 2011—a 17% increase over 2010 and twice its budget just 2 years ago.
Ten Months After
Deepwater Horizon
, Picking Up the Remnants of Health Data
Authors: Reardon Sara
Published: March 2011

On 28 February, after 10 months of hearing anecdotal stories of flulike symptoms, rashes, heat stroke, and stress from cleanup workers in the Gulf of Mexico, the U.S. Department of Health and Human Services launched the long-awaited Gulf Long-term Follow-up Study.
More Negative Data for Link Between Mouse Virus and Human Disease
Authors: Cohen Jon
Published: March 2011

A new finding presented at a conference last week throws cold water on the impassioned debate about the link between a novel mouse retrovirus and prostate cancer and chronic fatigue syndrome in humans.
Price Tags for Planet Missions Force NASA to Lower Its Sights
Authors: Kerr Richard A.
Published: March 2011

Outside consultants estimating planetary science mission costs for the next decade have produced huge numbers for the largest proposed missions, forcing some painful and unprecedented recommendations in the committee's report.
Antibody Responses to a Spore Carbohydrate Antigen as a Marker of Nonfatal Inhalation Anthrax in Rhesus Macaques
Authors: Saile Elke , Boons Geert-Jan , Buskas Therese , Carlson Russell W. , Kannenberg Elmar L. , Barr John R. , Boyer Anne E. , Gallegos-Candela Maribel , Quinn Conrad P.
Published: March 2011

TheBacillus anthracisexosporium protein BclA contains an O-linked antigenic tetrasaccharide whose terminal sugar is known as anthrose (J. M. Daubenspeck et al., J. Biol. Chem. 279:30945–30953, 2004). We hypothesized that serologic responses to anthrose may have diagnostic value in confirming exposure to aerosolizedB. anthracis. We evaluated the serologic responses to a synthetic anthrose-containing trisaccharide (ATS) in a group of five rhesus macaques that survived inhalation anthrax following exposure toB. anthracisAmes spores. Two of five animals (RM2 and RM3) were treated with ciprofloxacin starting at 48 hours postexposure and two (RM4 and RM5) at 72 h postexposure; one animal (RM1) was untreated. Infection was confirmed by blood culture and detection of anthrax toxin lethal factor (LF) in plasma. Anti-ATS IgG responses were determined at 14, 21, 28, and 35 days postexposure, with preexposure serum as a control. All animals, irrespective of ciprofloxacin treatment, mounted a specific, measurable anti-ATS IgG response. The earliest detectable responses were on days 14 (RM1, RM2, and RM5), 21 (RM4), and 28 (RM3). Specificity of the anti-ATS responses was demonstrated by competitive-inhibition enzyme immunoassay (CIEIA), in which a 2-fold (wt/wt) excess of carbohydrate in a bovine serum albumin (BSA) conjugate of the oligosaccharide (ATS-BSA) effected >94% inhibition, whereas a structural analog lacking the 3-hydroxy-3-methyl-butyryl moiety at the C-4" of the anthrosyl residue had no inhibition activity. These data suggest that anti-ATS antibody responses may be used to identify aerosol exposure toB. anthracisspores. The anti-ATS antibody responses were detectable during administration of ciprofloxacin.
Multiple-Locus Variable-Number Tandem-Repeat Analysis Is a Suitable Tool for Differentiation of Mycoplasma hyopneumoniae Strains without Cultivation
Authors: Vranckx K. , Maes D. , Calus D. , Villarreal I. , Pasmans F. , Haesebrouck F.
Published: March 2011

An assay based on multiple-locus variable-number tandem-repeat analysis allowed differentiating and studying diversity and persistence of
Mycoplasma hyopneumoniae
strains in pig herds without prior cultivation. The test had a discriminatory index of >0.99 and was applied reliably to porcine bronchoalveolar lavage fluid and tracheal swabs.
Identification and Genotyping of Enterocytozoon bieneusi in China
Authors: Zhang Xu , Wang Zhaoxia , Su Yan , Liang Xiaoying , Sun Xiaojing , Peng Shuai , Lu Huijun , Jiang Ning , Yin Jigang , Xiang Mei , Chen Qijun
Published: March 2011

In this study, the prevalence of
Enterocytozoon bieneusi
in China was investigated. Twelve genotypes of
E. bieneusi
were identified, of which 10 were novel genotypes. Further, 41.6% of the genotypes were found in both humans and animals. This is the first report of
E. bieneusi
in China.
Clinical Relevance of Multiple Single-Nucleotide Polymorphisms in Pneumocystis jirovecii Pneumonia: Development of a Multiplex PCR-Single-Base-Extension Methodology
Authors: Esteves F. , Gaspar J. , De Sousa B. , Antunes F. , Mansinho K. , Matos O.
Published: March 2011

Pneumocystis jirovecii
pneumonia (PcP) is a major cause of respiratory illness in patients with AIDS. The identification of multiple single-nucleotide polymorphisms (SNPs) at three distinct
P. jirovecii
loci encoding dihydrofolate reductase (
DHFR
), mitochondrial large-subunit rRNA (
mtLSU rRNA
), and superoxide dismutase (
SOD
) was achieved using multiplex-PCR (MPCR) followed by direct sequencing and two single-base extension (SBE) techniques. Four SNPs (
DHFR312
,
mt85
,
SOD215
, and
SOD110
), correlated previously with parameters of disease, were amplified and genotyped simultaneously. The concordance of results between the standard sequencing technique (direct sequencing) and SBE analysis was 96.9% for the acrylamide gel electrophoresis and 98.4% for the capillary electrophoresis. The cross-genetic analysis established several statistical associations among the SNPs studied:
mt85C-SOD110T
,
SOD110T-SOD215C
, and
SOD110C-SOD215T
. These results were confirmed by cluster analysis. Data showed that among the isolates with low to moderate parasite burden, the highest percentages of
DHFR312C
,
mt85C
,
SOD110T
, and
SOD215C
were detected, whereas for high parasite burden cases the highest frequencies were observed among isolates with
DHFR312T
,
mt85T
,
SOD110C
, and
SOD215T
. The polymorphisms studied were shown to be suitable genetic targets potentially correlated with PcP clinical data that can be used as predictors of outcome in further studies to help clinical decision-making in the management of PcP. The MPCR/SBE protocol described for the first time in the present study was shown to be a rapid, highly accurate method for genotyping
P. jirovecii
SNPs encoded by different loci that could be used for epidemiological studies and as an additional procedure for the prognostic classification and diagnosis of PcP.
Automated Identification of Medically Important Bacteria by 16S rRNA Gene Sequencing Using a Novel Comprehensive Database, 16SpathDB
Authors: Woo Patrick C. Y. , Teng Jade L. L. , Yeung Juilian M. Y. , Tse Herman , Lau Susanna K. P. , Yuen Kwok-Yung
Published: March 2011

Despite the increasing use of 16S rRNA gene sequencing, interpretation of 16S rRNA gene sequence results is one of the most difficult problems faced by clinical microbiologists and technicians. To overcome the problems we encountered in the existing databases during 16S rRNA gene sequence interpretation, we built a comprehensive database, 16SpathDB (
http://147.8.74.24/16SpathDB
) based on the 16S rRNA gene sequences of all medically important bacteria listed in the
Manual of Clinical Microbiology
and evaluated its use for automated identification of these bacteria. Among 91 nonduplicated bacterial isolates collected in our clinical microbiology laboratory, 71 (78%) were reported by 16SpathDB as a single bacterial species having >98.0% nucleotide identity with the query sequence, 19 (20.9%) were reported as more than one bacterial species having >98.0% nucleotide identity with the query sequence, and 1 (1.1%) was reported as no match. For the 71 bacterial isolates reported as a single bacterial species, all results were identical to their true identities as determined by a polyphasic approach. For the 19 bacterial isolates reported as more than one bacterial species, all results contained their true identities as determined by a polyphasic approach and all of them had their true identities as the “best match in 16SpathDB.” For the isolate (
Gordonibacter pamelaeae
) reported as no match, the bacterium has never been reported to be associated with human disease and was not included in the
Manual of Clinical Microbiology
. 16SpathDB is an automated, user-friendly, efficient, accurate, and regularly updated database for 16S rRNA gene sequence interpretation in clinical microbiology laboratories.
Assembly of Alphavirus Replication Complexes from RNA and Protein Components in a Novel
trans
-Replication System in Mammalian Cells
Authors: Spuul Pirjo , Balistreri Giuseppe , Hellström Kirsi , Golubtsov Andrey V. , Jokitalo Eija , Ahola Tero
Published: March 2011

For positive-strand RNA viruses, the viral genomic RNA also acts as an mRNA directing the translation of the replicase proteins of the virus. Replication takes place in association with cytoplasmic membranes, which are heavily modified to create specific replication compartments. Here we have expressed by plasmid DNA transfection the large replicase polyprotein of Semliki Forest virus (SFV) in mammalian cells from a nonreplicating mRNA and provided a separate RNA containing the replication signals. The replicase proteins were able to efficiently and specifically replicate the template in
trans
, leading to accumulation of RNA and marker gene products expressed from the template RNA. The replicase proteins and double-stranded RNA replication intermediates localized to structures similar to those seen in SFV-infected cells. Using correlative light electron microscopy (CLEM) with fluorescent marker proteins to relocate those transfected cells, in which active replication was ongoing, abundant membrane modifications, representing the replication complex spherules, were observed both at the plasma membrane and in intracellular endolysosomes. Thus, replication complexes are faithfully assembled and localized in the
trans
-replication system. We demonstrated, using CLEM, that the replication proteins alone or a polymerase-negative polyprotein mutant together with the template did not give rise to spherule formation. Thus, the
trans
-replication system is suitable for cell biological dissection and examination in a mammalian cell environment, and similar systems may be possible for other positive-strand RNA viruses.
Subclinical Brain Injury Caused by H5N1 Influenza Virus Infection
Authors: Shinya Kyoko , Makino Akiko , Hatta Masato , Watanabe Shinji , Kim Jin Hyun , Hatta Yasuko , Gao Peng , Ozawa Makoto , Le Quynh Mai , Kawaoka Yoshihiro
Published: March 2011

Although H5N1 influenza A viruses can cause systemic infection, their neurotropism and long-term effects on the central nervous system (CNS) are not fully understood. We assessed H5N1viral invasion of the CNS and its long-term effects in a ferret model. An H5N1 virus caused nonsuppurative encephalitis, which lasted for 3 months without neurologic signs. Further, another H5N1 virus caused nonsuppurative vasculitis with brain hemorrhage. Three-dimensional analysis of viral distribution in the brain identified the olfactory system as a major route for brain invasion. The efficient growth of virus in the upper respiratory tract may thus facilitate viral brain invasion.
Investigation of Koi Herpesvirus Latency in Koi
Authors: Eide Kathleen E. , Miller-Morgan Tim , Heidel Jerry R. , Kent Michael L. , Bildfell Rob J. , LaPatra Scott , Watson Gregory , Jin Ling
Published: March 2011

Koi herpesvirus (KHV) has recently been classified as a member of the family of
Alloherpesviridae
within the order of
Herpesvirales
. One of the unique features of
Herpesviridae
is latent infection following a primary infection. However, KHV latency has not been recognized. To determine if latency occurs in clinically normal fish from facilities with a history of KHV infection or exposure, the presence of the KHV genome was investigated in healthy koi by PCR and Southern blotting. KHV DNA, but not infectious virus or mRNAs from lytic infection, was detected in white blood cells from investigated koi. Virus shedding was examined via tissue culture and reverse transcription-PCR (RT-PCR) testing of gill mucus and feces from six koi every other day for 1 month. No infectious virus or KHV DNA was detected in fecal secretion or gill swabs, suggesting that neither acute nor persistent infection was present. To determine if KHV latent infections can be reactivated, six koi were subjected to a temperature stress regime. KHV DNA and infectious virus were detected in both gill and fecal swabs by day 8 following temperature stress. KHV DNA was also detectable in brain, spleen, gills, heart, eye, intestine, kidney, liver, and pancreas in euthanized koi 1 month post-temperature stress. Our study suggests that KHV may become latent in leukocytes and other tissues, that it can be reactivated from latency by temperature stress, and that it may be more widespread in the koi population than previously suspected.
Structure and Functional Relevance of a Transcription-Regulating Sequence Involved in Coronavirus Discontinuous RNA Synthesis
Authors: Dufour David , Mateos-Gomez Pedro A. , Enjuanes Luis , Gallego José , Sola Isabel
Published: March 2011

Transmissible gastroenteritis coronavirus (TGEV) genomic RNA transcription generates 5′- and 3′-coterminal subgenomic mRNAs. This process involves a discontinuous step during the synthesis of minus-sense RNA that is modulated by transcription-regulating sequences located at the 3′ end of the leader (TRS-L) and also preceding each viral gene (TRS-Bs). TRSs include a highly conserved core sequence (CS) (5′-CUAAAC-3′) and variable flanking sequences. It has been previously proposed that TRS-Bs act as attenuation or stop signals during the synthesis of minus-sense RNAs. The nascent minus-stranded RNA would then be transferred by a template switch process to the TRS-L, which acts as the acceptor RNA. To study whether the TRS-L is structured and to determine whether this structure has a functional impact on genomic and subgenomic viral RNA synthesis, we have used a combination of nuclear magnetic resonance (NMR) spectroscopy and UV thermal denaturation approaches together with site-directed mutagenesis andin vivotranscriptional analyses. The results indicated that a 36-nucleotide oligomer encompassing the wild-type TRS-L forms a structured hairpin closed by an apical AACUAAA heptaloop. This loop contains most of the CS and is isolated from a nearby internal loop by a short Watson-Crick base-paired stem. TRS-L mutations altering the structure and the stability of the TRS-L hairpin affected replication and transcription, indicating the requirement of a functional RNA hairpin structure in these processes.
Identification of a Human SCARB2 Region That Is Important for Enterovirus 71 Binding and Infection
Authors: Yamayoshi Seiya , Koike Satoshi
Published: March 2011

We previously identified human scavenger receptor class B, member 2 (SCARB2), as a cellular receptor for enterovirus 71 (EV71). Expression of human SCARB2 (hSCARB2) permitted mouse L929 cells to efficiently bind to virions and to produce both viral proteins and progeny viruses upon EV71 infection. Mouse Scarb2 (mScarb2) exhibited 85.8% amino acid identity and 99.9% similarity to hSCARB2. The expression of mScarb2 in L929 cells conferred partial susceptibility. Very few virions bound to mScarb2-expressing cells. The viral titer in L929 cells expressing mScarb2 was approximately 40- to 100-fold lower than that in L929 cells expressing hSCARB2. Using hSCARB2-mScarb2 chimeric mutants, we attempted to map the region that was important for efficient EV71 infection. L929 cells expressing chimeras that carried amino acids 142 to 204 from the human sequence were susceptible to EV71, while chimeras that carried the mouse sequence in this region were not. Moreover, this region was also critical for binding to virions. The determination of this region in hSCARB2 that is important for EV71 binding and infection greatly contributes to the understanding of virus-receptor interactions. Further studies will clarify the early steps of EV71 infection.
A Respiratory Syncytial Virus Replicon That Is Noncytotoxic and Capable of Long-Term Foreign Gene Expression
Authors: Malykhina Olga , Yednak Mark A. , Collins Peter L. , Olivo Paul D. , Peeples Mark E.
Published: March 2011

Respiratory syncytial virus (RSV) infection of most cultured cell lines causes cell-cell fusion and death. Cell fusion is caused by the fusion (F) glycoprotein and is clearly cytopathic, but other aspects of RSV infection may also contribute to cytopathology. To investigate this possibility, we generated an RSV replicon that lacks all three of its glycoprotein genes and so cannot cause cell-cell fusion or virus spread. This replicon includes a green fluorescent protein gene and an antibiotic resistance gene to enable detection and selection of replicon-containing cells. Adaptive mutations in the RSV replicon were not required for replicon maintenance. Cells containing the replicon could be cloned and passaged many times in the absence of antibiotic selection, with 99% or more of the cells retaining the replicon after each cell division. Transient expression of the F and G (attachment) glycoproteins supported the production of virions that could transfer the replicon into most cell lines tested. Since the RSV replicon is not toxic to these cultured cells and does not affect their rate of cell division, none of the 8 internal viral proteins, the viral RNA transcripts, or the host response to these molecules or their activities is cytopathic. However, the level of replicon genome and gene expression is controlled in some manner well below that of complete virus and, as such, might avoid cytotoxicity. RSV replicons could be useful for cytoplasmic gene expression
in vitro
and
in vivo
and for screening for compounds active against the viral polymerase.
Electroporation Enhances Immunogenicity of a DNA Vaccine Expressing Woodchuck Hepatitis Virus Surface Antigen in Woodchucks
Authors: Liu Katherine H. , Ascenzi Mary A. , Bellezza Christine A. , Bezuidenhout Abraham J. , Cote Paul J. , Gonzalez-Aseguinolaza Gloria , Hannaman Drew , Luxembourg Alain , Evans Claire F. , Tennant Bud C. , Menne Stephan
Published: March 2011

The development of therapeutic vaccines for chronic hepatitis B virus (HBV) infection has been hampered by host immune tolerance and the generally low magnitude and inconsistent immune responses to conventional vaccines and proposed new delivery methods. Electroporation (EP) for plasmid DNA (pDNA) vaccine delivery has demonstrated the enhanced immunogenicity of HBV antigens in various animal models. In the present study, the efficiency of the EP-based delivery of pDNA expressing various reporter genes first was evaluated in normal woodchucks, and then the immunogenicity of an analog woodchuck hepatitis virus (WHV) surface antigen (WHsAg) pDNA vaccine was studied in this model. The expression of reporter genes was greatly increased when the cellular uptake of pDNA was facilitated by EP. The EP of WHsAg-pDNA resulted in enhanced, dose-dependent antibody and T-cell responses to WHsAg compared to those of the conventional hypodermic needle injection of WHsAg-pDNA. Although subunit WHsAg protein vaccine elicited higher antibody titers than the DNA vaccine delivered with EP, T-cell response rates were comparable. However, in WHsAg-stimulated mononuclear cell cultures, the mRNA expression of CD4 and CD8 leukocyte surface markers and Th1 cytokines was more frequent and was skewed following DNA vaccination compared to that of protein immunization. Thus, the EP-based vaccination of normal woodchucks with pDNA-WHsAg induced a skew in the Th1/Th2 balance toward Th1 immune responses, which may be considered more appropriate for approaches involving therapeutic vaccines to treat chronic HBV infection.
A Novel Respiratory Model of Infection with Monkeypox Virus in Cynomolgus Macaques
Authors: Goff Arthur J. , Chapman Jennifer , Foster Chad , Wlazlowski Carly , Shamblin Joshua , Lin Kenny , Kreiselmeier Norman , Mucker Eric , Paragas Jason , Lawler James , Hensley Lisa
Published: March 2011

Variola, the causative agent of smallpox, and the related monkeypox virus are both select agents that, if purposefully released, would cause public panic and social disruption. For this reason research continues in the areas of animal model and therapeutic development. Orthopoxviruses show a widely varying degree of host specificity, making development of accurate animal models difficult. In this paper, we demonstrate a novel respiratory infection technique that resulted in “classic” orthopox disease in nonhuman primates and takes the field of research one step closer to a better animal model.
Development of a Glycoprotein D-Expressing Dominant-Negative and Replication-Defective Herpes Simplex Virus 2 (HSV-2) Recombinant Viral Vaccine against HSV-2 Infection in Mice
Authors: Akhrameyeva Natalie V. , Zhang Pengwei , Sugiyama Nao , Behar Samuel M. , Yao Feng
Published: March 2011

Using the T-REx (Invitrogen, California) gene switch technology and a dominant-negative mutant polypeptide of herpes simplex virus 1 (HSV-1)-origin binding protein UL9, we previously constructed a glycoprotein D-expressing replication-defective and dominant-negative HSV-1 recombinant viral vaccine, CJ9-gD, for protection against HSV infection and disease. It was demonstrated that CJ9-gD is avirulent following intracerebral inoculation in mice, cannot establish detectable latent infection following different routes of infection, and offers highly effective protective immunity against primary HSV-1 and HSV-2 infection and disease in mouse and guinea pig models of HSV infections. Given these favorable safety and immunological profiles of CJ9-gD, aiming to maximize levels of HSV-2 glycoprotein D (gD2) expression, we have constructed an ICP0 null mutant-based dominant-negative and replication-defective HSV-2 recombinant, CJ2-gD2, that contains 2 copies of the gD2 gene driven by the tetracycline operator (tetO)-bearing HSV-1 major immediate-early ICP4 promoter. CJ2-gD2 expresses gD2 as efficiently as wild-type HSV-2 infection and can lead to a 150-fold reduction in wild-type HSV-2 viral replication in cells coinfected with CJ2-gD2 and wild-type HSV-2 at the same multiplicity of infection. CJ2-gD2 is avirulent following intracerebral injection and cannot establish a detectable latent infection following subcutaneous (s.c.) immunization. CJ2-gD2 is a more effective vaccine than HSV-1 CJ9-gD and a non-gD2-expressing dominant-negative and replication-defective HSV-2 recombinant in protection against wild-type HSV-2 genital disease. Using recall response, we showed that immunization with CJ2-gD2 elicited strong HSV-2-specific memory CD4+and CD8+T-cell responses. Collectively, given the demonstrated preclinical immunogenicity and its unique safety profiles, CJ2-gD2 represents a new class of HSV-2 replication-defective recombinant viral vaccines in protection against HSV-2 genital infection and disease.
The ZIIR Element of the Epstein-Barr Virus BZLF1 Promoter Plays a Central Role in Establishment and Maintenance of Viral Latency
Authors: Yu Xianming , McCarthy Patrick J. , Lim Hui-Jun , Iempridee Tawin , Kraus Richard J. , Gorlen Daniel A. , Mertz Janet E.
Published: March 2011

The Epstein-Barr virus (EBV)
BZLF1
gene encodes the immediate-early (IE) protein Zta, which plays a central role in regulating the switch between viral latency and lytic replication. A silencing element, ZIIR, is located between the ZID and ZII positive regulatory elements in the
BZLF1
promoter Zp. We report here the phenotypes of variants of EBV strain B95.8 containing base substitution mutations in this ZIIR element. HEK293 cells infected with ZIIR mutant (ZIIRmt) virus produced at least 20-fold more viral IE Zta and Rta and early (E) EAD protein than did cells infected with the parental wild-type (WT) virus, leading to viral DNA replication and production of infectious virus. However, ZIIR mutant virus was 1/10 as efficient as WT virus in establishing proliferating B-cell clones following infection of human primary blood B cells. The ZIIRmt-infected lymphoblastoid cell lines (LCLs) that did grow out exhibited a phenotype similar to the one observed in 293 cells, including marked overproduction of IE and E gene products relative to WT-infected LCLs and lytic replication of the viral genome. Incubation of the ZIIRmt-infected LCLs with the chemical inducer 12-
O
-tetradecanoyl-phorbol-13-acetate (TPA) led to much greater activation of Zp than did the same treatment of WT- or ZVmt-infected LCLs. Furthermore, a protein kinase C (PKC) inhibitor, bis-indolylmaleimide, eliminated this activation by TPA. Thus, we conclude that ZIIR is a potent silencing element of Zp; it plays a key role in establishment and maintenance of EBV latency by inhibiting activation of Zp through the PKC signal transduction pathway.
Sclerosing polidocanol injections or arthroscopic shaving to treat patellar tendinopathy/jumper's knee? A randomised controlled study
Authors: Willberg Lotta , Sunding Kerstin , Forssblad Magnus , Fahlström Martin , Alfredson Håkan
Published: March 2011

Background

Proximal patellar tendinopathy/jumper's knee (PT/JK) is well known to be difficult to treat. Recent studies using an ultrasound and colour Doppler-based treatment approach on the dorsal side of the tendon, sclerosing polidocanol injections and ultrasound-guided arthroscopic shaving, have shown promising clinical results.

Objectives

To compare the clinical effects after treatment with sclerosing polidocanol injections and arthroscopic shaving.

Material and methods

52 patellar tendons (43 men and two women) with ultrasound and colour Doppler-verified diagnosis of PT/JK were randomly assigned to treatment with ultrasound and colour Doppler-guided sclerosing polidocanol injections (group A) or ultrasound and colour Doppler-guided arthroscopic shaving (group B). All patients were involved in patellar tendon loading sports or recreational activities, and had had a long duration of pain symptoms from the proximal patellar tendon. Pain during patellar tendon loading activity, and at rest, before and after treatment (visual analogue scale; VAS), and patient satisfaction with the result of the treatment, was registered.

Results

After treatment, the patients treated with arthroscopic shaving had a significantly lower VAS score at rest and during activity, and were significantly more satisfied compared with the patients in the sclerosing injection group.

Conclusions

Both treatment with ultrasound and colour Doppler-guided sclerosing polidocanol injections and arthroscopic shaving showed good clinical results, but patients treated with arthroscopic shaving had less pain and were more satisfied with the treatment result. Because surgical treatment is a one-stage treatment return to sports was faster in this group.