bluuebunny/crossref_metadata_2025 huggingface dataset:
The Phallus Tree: A Medieval and Renaissance Phenomenon
Authors: Mattelaer Johan J.
Published: January 2010

Introduction

In the year 2000, an exceptional mural was discovered at a fountain in Massa Marittima, Italy. It depicts a tree with phalluses, which are distributed across all the branches, are disproportionately large and in an aroused state, and include a scrotum.

Methods

Other examples were identified by systematic literature research.

Results

Several other depictions of a phallus tree from the medieval and Renaissance periods exist, for example in manuscripts, as wood carvings, on pilgrimage badges, or frescoes, and were retrieved in Germany, Italy, Belgium, the Netherlands, Turkey, and France.

Discussion and Conclusions

The phallus tree was a well-known phenomenon in Western Europe during the late Middle Ages and the beginning of the Renaissance, and mostly find their roots in the link between infertility and impotence on the one hand, and sorcery and witchcraft on the other.
The Tudor Speakers 1485–1601: Choosing, Status, Work*
Authors: HAWKYARD ALASDAIR
Published: January 2010

During the Tudor period the Speaker was nominated by the crown. The house of commons acquiesced with the crown's nomination, but not entirely passively. There is a body of evidence suggesting that the crown's nominee became the focus of disapprobation once his name became known. What hostility there was to the Speaker‐designate from the mid 16th century was displayed to better effect outside the House than within.
Formulation of a Dry Green Tea‐Apple Product: Study on Antioxidant and Color Stability
Authors: Lavelli Vera , Vantaggi Claudia , Corey Mark , Kerr William
Published: January 2010

ABSTRACT: A dry apple product enriched with green tea (GT) extract was designed as a novel food to deliver relevant amounts of catechins. The target water activity (aw) range between 0.11 and 0.32 was chosen for the GT‐fortified apple, since it corresponds to low water mobility and, consequently, maximum stability of dehydrated apples. The GT‐fortified product and a control dehydrated apple product were stored in air, at 30 °C, and evaluated for color, antioxidant contents (monomeric flavan 3‐ols, total procyanidins, ascorbic acid, chlorogenic acid and dihydrochalcones), ferric reducing/antioxidant power (FRAP), and 2,2‐diphenyl‐1‐(2,4,6‐trinitrophenyl)hydrazyl radical (DPPH) scavenging capacity. After 1 mo of storage at the lowest awlevel (0.11), the GT‐fortified product retained 80 and 100% of the initial contents of the monomeric flavan 3‐ols and total procyanidins, respectively. With increasing awlevel to 0.32, the stability of antioxidants slowly decreased. The addition of GT to the apple product increased the FRAP value and the DPPH scavenging capacity by 3.6‐fold and 4.6‐fold respectively, which remained almost unchanged during storage. The GT‐fortified product was similar in color to commercially available dehydrated apples. Results highlighted some advantages of using dehydrated apples as a target for green tea fortification, which deserve further trials to investigate potential applications for fortification of other dehydrated fruits.
Rheological Behavior of High‐Concentration Sodium Caseinate Dispersions
Authors: Loveday Simon M. , Rao M. Anandha , Creamer Lawrence K. , Singh Harjinder
Published: January 2010

ABSTRACT:  Apparent viscosity and frequency sweep (G′, G″) data for sodium caseinate dispersions with concentrations of approximately 18% to 40% w/w were obtained at 20 °C; colloidal glass behavior was exhibited by dispersions with concentration ≥23% w/w. The high concentrations were obtained by mixing frozen powdered buffer with sodium caseinate in boiling liquid nitrogen, and allowing the mixtures to thaw and hydrate at 4 °C. The low‐temperature G′−G″ crossover seen in temperature scans between 60 and 5 °C was thought to indicate gelation. Temperature scans from 5 to 90 °C revealed gradual decrease in G′ followed by plateau values. In contrast, G″ decreased gradually and did not reach plateau values. Increase in hydrophobicity of the sodium caseinate or a decrease in the effective volume fraction of its aggregates may have contributed to these phenomena. The gelation and end of softening temperatures of the dispersions increased with the concentration of sodium caseinate. From an Eldridge–Ferry plot, the enthalpy of softening was estimated to be 29.6 kJ mol−1.

Practical Application: The results of this study should be useful for creating new products with high concentrations of sodium caseinate.
Innovation and Conflict Management in Work Teams: The Effects of Team Identification and Task and Relationship Conflict
Authors: Desivilya Helena Syna , Somech Anit , Lidgoster Helena
Published: January 2010

The current study attempted to elucidate the mechanisms whereby constructive‐cooperative conflict management (integrating) fosters innovation in work teams. The proposed conceptual model postulated that the positive function of integrating in precipitating innovation is motivated by prosocial team atmosphere as manifested in team identity, the team’s capacity to mitigate the adverse impact of relationship conflict and its capability to maximize the potential gains of task conflict. Specifically, it was hypothesized: (a) integrating would predict innovation. (b) Team identity would be positively related to integrating, and that integrating would mediate the positive relationship between team identity and team innovation. (c) Task conflict would be positively related to integrating whereas relationship conflict would be negatively related to integrating. This research embraced a team‐level perspective and analysis. Seventy‐seven intact work teams from high‐technology companies participated in the study. The findings, by and large, supported the proposed conceptual model, especially the contention that teams’ proclivities with respect to conflict management play a pivotal role in their capacity to function in an innovative manner. A team’s integrating pattern meaningfully predicted team innovation. The mediating effect of the integrating strategy on the relationship between team identity and team innovation was also demonstrated. Finally, relationship conflict was negatively associated with a team’s integrating pattern, while the positive association of task conflict with the cooperative strategy was marginally significant.
Electronic Signatures and Interpersonal Trustworthiness in Online Negotiations
Authors: Kurtzberg Terri R. , Naquin Charles E.
Published: January 2010

Corporate‐mandated signature lines in professional e‐mail messages (i.e., those required and often added automatically by the company’s server) are an increasingly common practice in organizations. This research empirically explores the impact of one such electronic signature upon judgments of interpersonal trustworthiness in online negotiations. Specifically, we compare the impact of what we call the “disclaimer” signature (statements that the e‐mail represents the opinion of the sender and not necessarily the organization) to “non‐disclaimer” signatures (statements of confidentiality.) Findings indicate that negotiators who received such a disclaimer signature tended to judge the sender as less trustworthy and also receive lower objective outcomes than did those who either did not have any statement, or those who had one with different (non‐disclaimer) content.
Prospective contralateral eye study to compare conventional and wavefront‐guided laser in situ keratomileusis
Authors: D’Arcy Fiona , Kirwan Caitriona , Qasem Qasim , O’Keefe Michael
Published: January 2010

Purpose:  To compare outcomes of customized/wavefront guided with conventional ablation in myopic patients with or without astigmatism undergoing laser in situ keratomileusis.

Methods:  A prospective, comparative, contralateral eye study was performed. Sixty‐eight eyes of 34 myopic patients with similar refractive error in both eyes were included. One eye was randomly selected to undergo conventional and the fellow eye customized ablation. Surgery was performed using the Technolas 217z laser (Bausch & Lomb, Surrey, UK). Uncorrected visual acuity, manifest refractive spherical equivalent (MRSE), astigmatism, aberrometry and contrast sensitivity were recorded pre and 3 months postoperatively.

Results:  Mean MRSE treated in the conventional and customized groups were 3.77 ± 1.61 dioptres and −3.83 ± 1.59 dioptres respectively. Three months postoperatively there was no significant difference between the groups in mean MRSE (p = 0.99) or cylinder (p = 0.56). The factor increase in postoperative total higher order aberrations (HOAs) was less in the customized (1.32) compared with the conventional (1.54) treatment group but did not reach statistical significance (p = 0.08). Scotopic contrast sensitivity decreased significantly postoperatively in the conventional but not in the customized treatment group.

Conclusion:  Visual acuity and refractive error outcomes were similar in both treatment group and no patient preference was observed. Customized ablation was associated with a smaller but not statistically significant postoperative increase in HOAs, better preservation of scotopic contrast sensitivity, quicker treatment time and removal of less corneal tissue.
Rapid detection of clonal expansion of T‐cell receptor‐beta gene in patients with HBV using the real‐time PCR with DNA melting curve analysis
Authors: Yang Jie‐Zuan , Li Ming‐Wei , Wang Jian‐Guo , Lu Hai‐Feng , Yao Xin‐Sheng , He Jian‐Qin , Li Lan‐Juan
Published: January 2010

Aim:  The gene melting spectral pattern (GMSP) of PCR products from 24 T‐cell receptor beta chain variable (TCRBV) gene families was developed to determine sequence bias and feature of TCRBV CDR3 gene family.

Methods:  The assay was based on reverse transcript quantitative polymerase chain reaction and their DNA melting curves.

Results:  We discovered that the relatively conserved amino acid sequences X‐Q and X‐G are present in TCRBV CDR3 from patients with HBV. Further, the X of the X‐Q motif is preferentially E (glutamic acid), P (proline) or T (threonine) when accompanied by the BJ2.7, BJ1.5, or BJ2.3, respectively. The frequency of sequence bias in the TCRBV gene family showed a positive correlation with the T cell receptor excision circles (TRECs) content, and an inverse correlation with the HBV DNA loading.

Conclusion:  These results suggest that the GMSP assay could be used to monitor the features of TCRBV gene distribution quickly, and facilitate the further study of HBV‐specific T cell in patients with HBV.
Changing the World by Changing Ourselves: Reflections from a Bunch of BINGOs
Authors: Shutt Cathy
Published: January 2010

This Practice Paper aims to contribute to ongoing reflections and debates taking place among aid practitioners about if, and how, big international NGOs (BINGOs) can be more effective agents of ‘progressive social change’. It summarises a series of conversations that took place among seven members of the Institute of Development Studies Participation Power and Social Change team and staff from eight BINGOs between July 2008 and March 2009.

During the conversations, participants considered how internal and external factors influence the potential of BINGOs to contribute to shifts in power relations; greater realisation of rights; and enhanced economic, political and social justice for poor and vulnerable people. All of this was encapsulated in the term ‘progressive social change’. At the end of the process, participants agreed that there is considerable scope for many BINGOs to pursue a more progressive agenda. They recommended that similar conversations need to continue and branch out, both in topical range and in participants in order to stimulate the kind of reflection and organisational learning required to do so.

This paper includes accounts of discussions, case studies shared by participants, inputs from academic critiques of BINGOs and practical tools to feed into such deliberations. It explores the types of changes that BINGOs are trying to achieve, the approaches they use – their models of change, and challenges and tensions commonly perceived to prevent BINGOs pursuing more radical social change agendas. Provocative questions are raised as a means to help practitioners identify changes that their organisations need to make in order to more actively pursue social, economic and political justice. In some instances inspiring examples from BINGO participants suggest means to do so. References to organisational theory, meeting discussions and BINGO case studies are used to interrogate assumptions about how large complex organisations behave and to identify lessons that may be used to inform efforts to transform BINGOs into more effective agents of progressive social change.
Four beams surface plasmon interference nanoscale lithography for patterning of two-dimensional periodic features
Authors: Sreekanth K. V. , Murukeshan V. M.
Published: January 2010

The interference of multiple counterpropagating surface plasmon waves as a lithography technique to pattern periodic two-dimensional features is proposed and illustrated in this article. The surface plasmons are generated by prism coupling method, by employing a custom made prism layer configuration and with a single exposure. 175nm periodic two-dimensional dot array patterns, with feature size as small as 93nm, have been realized using an exposure radiation of 364nm wavelength.
Photoconduction in silicon rich oxide films obtained by low pressure chemical vapor deposition
Authors: Luna-López J. A. , Aceves-Mijares M. , Carrillo-López J. , Morales-Sánchez A.
Published: January 2010

Photoconduction properties of silicon rich oxide (SRO) thin films were studied under different illumination conditions. In the past, Al/SRO/Si structures showed a high photocurrent in spite of the fact that an opaque Al layer was on the active area. In order to elucidate this observation, new Al/SRO/Si structures were tested, but this time they were also measured horizontally. SRO thin films were deposited on silicon wafers by low pressure chemical vapor deposition technique using SiH4 (silane) and N2O (nitrous oxide) as reactive gases at 700°C. 1%–12% silicon excess was used. Structures with a single SRO layer and with a double layer were fabricated in order to have a barrier to isolate the silicon from the active SRO layer. The results show that all structures have a higher current when light shines on them than when they are in the dark. It is proposed that the photocurrent is produced in the SRO bulk, and an explanation for these observations is given.
How the Shape of an H-Bonded Network Controls Proton-Coupled Water Activation in HONO Formation
Authors: Relph Rachael A. , Guasco Timothy L. , Elliott Ben M. , Kamrath Michael Z. , McCoy Anne B. , Steele Ryan P. , Schofield Daniel P. , Jordan Kenneth D. , Viggiano Albert A. , Ferguson Eldon E. , Johnson Mark A.
Published: January 2010

It's the Network

Numerous reactions of small molecules and ions in the atmosphere take place in the confines of watery aerosols.

Relph
et al.

(p.
308
; see the Perspective by

Siefermann and Abel
)

explored the specific influence of a water cluster's geometry on the transformation of solvated nitrosonium (NO
+
) to nitrous acid (HONO). The reaction involves (O)N–O(H) bond formation with one water molecule, concomitant with proton transfer to additional, surrounding water molecules. Vibrational spectroscopy and theoretical simulations suggest that certain arrangements of the surrounding water network are much more effective than others in accommodating this charge transfer, and thus facilitating the reaction.
Electrocatalytic CO
2
Conversion to Oxalate by a Copper Complex
Authors: Angamuthu Raja , Byers Philip , Lutz Martin , Spek Anthony L. , Bouwman Elisabeth
Published: January 2010

Oxalate from Air

In light of increasing concerns about the consequences of excessive atmospheric carbon dioxide, there is demand for methods to use carbon dioxide in the preparation of more elaborate compounds. Though reactions with hydroxide salts to form carbonates tend to proceed fairly cleanly, reductive processes to form carboxylic acids, esters, and alcohols are often rather unselective.

Angamuthu
et al.

(p.
313
; see the news story by

Service

) discovered that a copper complex exhibited remarkable selectivity in reductively coupling carbon dioxide to form oxalate through coordinative electron transfer, even in the presence of excess oxygen, normally a much more potent electron acceptor. Precipitation of the oxalate as a lithium salt and electrochemical re-reduction of the copper produced a preliminary catalytic cycle, demonstrated through six turnovers.
Unidirectional Airflow in the Lungs of Alligators
Authors: Farmer C. G. , Sanders Kent
Published: January 2010

Alligator Breath

Birds have a unidirectional system of airflow within their lungs that has been attributed to the peculiarities of flight. However,
Farmer and Sanders
(p.
338
) provide evidence that this unidirectional and more or less continuous flow of air also occurs through parts of the alligator lung; in contrast to the tidal, biphasic system in mammals. By analyzing lung and tracheal structures, the similarities of the alligator lungs were compared with those of birds. The data suggest that the unusual properties of bird lungs originated before the divergence of the alligator line from the dinosaur or avian line.
The Genetic Map of
Artemisia annua
L. Identifies Loci Affecting Yield of the Antimalarial Drug Artemisinin
Authors: Graham Ian A. , Besser Katrin , Blumer Susan , Branigan Caroline A. , Czechowski Tomasz , Elias Luisa , Guterman Inna , Harvey David , Isaac Peter G. , Khan Awais M. , Larson Tony R. , Li Yi , Pawson Tanya , Penfield Teresa , Rae Anne M. , Rathbone Deborah A. , Reid Sonja , Ross Joe , Smallwood Margaret F. , Segura Vincent , Townsend Theresa , Vyas Darshna , Winzer Thilo , Bowles Dianna
Published: January 2010

The Art of
Artemisia

As the malaria parasite, which is transmitted through mosquito vectors, develops resistance, previously useful control mechanisms are beginning to fail. Combination therapies based on the plant product artemisinin are a promising alternative.

Graham
et al.

(p.
328
; see the Perspective by

Milhous and Weina

) have now developed a genetic map of the plant
Artemisia annua
from which artemisinin is derived. The results lay the foundation for improving agricultural productivity of this natural product, which is becoming increasingly important in the fight against malaria.
Regulation of Adaptive Immunity by the Innate Immune System
Authors: Iwasaki Akiko , Medzhitov Ruslan
Published: January 2010

Twenty years after the proposal that pattern recognition receptors detect invasion by microbial pathogens, the field of immunology has witnessed several discoveries that have elucidated receptors and signaling pathways of microbial recognition systems and how they control the generation of T and B lymphocyte–mediated immune responses. However, there are still many fundamental questions that remain poorly understood, even though sometimes the answers are assumed to be known. Here, we discuss some of these questions, including the mechanisms by which pathogen-specific innate immune recognition activates antigen-specific adaptive immune responses and the roles of different types of innate immune recognition in host defense from infection and injury.
Zebrafish Behavioral Profiling Links Drugs to Biological Targets and Rest/Wake Regulation
Authors: Rihel Jason , Prober David A. , Arvanites Anthony , Lam Kelvin , Zimmerman Steven , Jang Sumin , Haggarty Stephen J. , Kokel David , Rubin Lee L. , Peterson Randall T. , Schier Alexander F.
Published: January 2010

Behavioral Profiling

The complexity of the brain makes it difficult to predict how a drug will affect behavior without direct testing in live animals.

Rihel
et al.

(p.
348
) developed a high-throughput assay to assess the effects of thousands of drugs on sleep/wake behaviors of zebrafish larvae. The data set reveals a broad conservation of zebrafish and mammalian sleep/wake pharmacology and identifies pathways that regulate sleep. Moreover, the biological targets of poorly characterized small molecules can be predicted by matching their behavioral profiles to those of well-known drugs. Thus, behavioral profiling in zebrafish offers a cost-effective way to characterize neuroactive drugs and to predict biological targets of novel compounds.
Recovering a Humboldtian Legacy
The Passage to Cosmos
Alexander von Humboldt and the Shaping of America

by Laura Dassow Walls

University of Chicago Press, Chicago, 2009. 420 pp. $35, £24. ISBN 9780226871820.
Authors: Rupke Nicolaas A.
Published: January 2010

Wells explores the impact Humboldt had on thought, science, and literature in 19th-century United States.
The NLRP3 Inflammasome: A Sensor for Metabolic Danger?
Authors: Schroder Kate , Zhou Rongbin , Tschopp Jurg
Published: January 2010

Interleukin-1β (IL-1β), reactive oxygen species (ROS), and thioredoxin-interacting protein (TXNIP) are all implicated in the pathogenesis of type 2 diabetes mellitus (T2DM). Here we review mechanisms directing IL-1β production and its pathogenic role in islet dysfunction during chronic hyperglycemia. In doing so, we integrate previously disparate disease-driving mechanisms for IL-1β, ROS, and TXNIP in T2DM into one unifying model in which the NLRP3 inflammasome plays a central role. The NLRP3 inflammasome also drives IL-1β maturation and secretion in another disease of metabolic dysregulation, gout. Thus, we propose that the NLRP3 inflammasome contributes to the pathogenesis of T2DM and gout by functioning as a sensor for metabolic stress.
Green Gold Catalysis
Authors: Christensen Claus Hviid , Nørskov Jens K.
Published: January 2010

High–surface area gold catalysts exhibit promising properties suitable for industrial application.
Ion Chemistry Mediated by Water Networks
Authors: Siefermann Katrin R. , Abel Bernd
Published: January 2010

The reaction of ions such as NO
+
with networks of only a few water molecules has implications for understanding chemistry in the ionosphere.
The Botanical Solution for Malaria
Authors: Milhous Wilbur K. , Weina Peter J.
Published: January 2010

Improved breeding of a plant that produces a major antimalarial compound is now possible based on knowledge of its genetic map.
New Approaches in Immunotherapy
Authors: Thomas Paul G. , Doherty Peter C.
Published: January 2010

The past decade of research on the immune system has seen an incredible expansion of knowledge in the area of innate immunity. Analysis over the preceding years had focused largely on how T and B cells orchestrate immune responses to specific pathogens, and how their memory of these encounters confers long-lasting protection. In contrast to these specific “adaptive” mechanisms, innate immunity is driven by a plethora of proteins produced by a wide range of cells throughout the body, and it provides immediate broad-spectrum responses to foreign invaders. This new understanding of innate immunity is providing insights into host reactions to noninfectious diseases such as cancer, to antigen-independent inflammatory conditions such as periodic fever syndromes, and to the inflammatory modulation of basic cellular metabolic processes. As this special issue on innate immunity points out (p. 283), ongoing research to further characterize this complex response system has great potential for identifying new therapies to treat human disease.
White House Mulls Plan to Broaden Access to Published Papers
Authors: Kaiser Jocelyn
Published: January 2010

Should all papers that result from U.S. taxpayer–funded research be made freely available? The White House science office likes the idea and has asked for input on whether many federal agencies should formally adopt it.
The Little Wasp That Could
Authors: Pennisi Elizabeth
Published: January 2010

The sequencing of the genome of a parasitoid wasp promises to bring wider recognition to these tiny, underappreciated insects that play a crucial role in natural ecosystems and in agriculture.
Fishing for Gold in The Last Frontier State
Authors: Kean Sam
Published: January 2010

A proposed mine at a gargantuan gold and copper deposit leaves some Alaskans fearful that they must choose between two great loves: salmon and mining.
Single Lysophosphatidylcholine Components Exhibit Adjuvant Activities
In Vitro
and
In Vivo
Authors: Bach Guillaume , Perrin-Cocon Laure , Gerossier Estelle , Guironnet-Paquet Aurélie , Lotteau Vincent , Inchauspé Geneviève , Fournillier Anne
Published: January 2010

Improving vaccine immunogenicity by developing new adjuvant formulations has long been a goal of vaccinologists. It has previously been shown that a natural mix of lysophosphatidylcholine (LPC) from chicken eggs promotes mature dendritic cell (DC) generation
in vitro
and primes antigen-specific immune responses in mice. In the present study, we dissected the adjuvant potentials of five individual LPC components found in the chicken egg mixture.
In vitro
analyses of the impact of the individual components on the maturation of human DCs were performed by means of phenotypic analysis, chemokine secretion analysis, and analysis of the ability of mature DC to stimulate T lymphocytes. Two components, C16:0-LPC and C18:0-LPC, were identified to be capable of the upregulation of expression of CD86, HLA-DR, and CD40 on
in vitro
-cultured monocyte-derived DCs from healthy donors. Both induced the release of chemokines to high concentrations (macrophage inflammatory protein 1, monocyte chemoattractant protein 1) or moderate concentrations (interleukin-8 [IL-8], gamma interferon-inducible protein 10). In addition, C16:0-LPC engaged naïve T cells to produce gamma interferon. This suggests that C16:0-LPC and C18:0-LPC have the capacity to promote, at least
in vitro
, a Th1-oriented response. The intravenous injection of C16:0-LPC or C18:0-LPC into mice resulted in the detectable secretion of IL-6 and IL-5 in sera. Both LPC components were tested for their capacities to act as adjuvants for two selected immunogens: the hepatitis B virus surface antigen and the hepatitis C virus NS3 helicase. The secretion of specific IgG1 was observed with either or both C16:0-LPC and C18:0-LPC, depending on the immunogen tested, and was observed at an efficiency comparable to that of alum. These data identify C16:0-LPC and C18:0-LPC as the active components of the LPC natural mixture. Although discrepancies between the results of the
in vitro
and
in vivo
analyses existed, studies with animals suggest that these components can trigger significant and specific humoral-mediated immunity.
Understanding the Molecular Epidemiology of the Footrot Pathogen
Dichelobacter nodosus
To Support Control and Eradication Programs
Authors: Buller N. B. , Ashley P. , Palmer M. , Pitman D. , Richards R. B. , Hampson D. J.
Published: January 2010

The Gram-negative anaerobe
Dichelobacter nodosus
is the primary etiologic agent of ovine footrot. Few studies of the genetic diversity and epidemiology of
D. nodosus
have been done, despite the economic cost and welfare implications of the disease. This study examined a large collection of Australian isolates; 735 isolates from footrot-infected sheep from 247 farms in Western Australia (WA) were tested by pulsed-field gel electrophoresis (PFGE), and a subset of 616 isolates was tested by infrequent restriction site PCR (IRS-PCR). The genetic diversity of WA isolates was compared to that of 61 isolates from three other Australian states. WA isolates were genetically diverse, with 181 molecular types resolved by PFGE, resulting in a simple diversity ratio (SDR) of 1:4 and a Simpson's index of discrimination value (
D
) of 0.98. IRS-PCR resolved 77 molecular types (SDR = 1:8 and
D
= 0.95). The isolates were grouped into 67 clonal groups by PFGE (SDR = 1:11,
D
= 0.90) and 36 clonal groups by IRS-PCR (SDR = 1:17,
D
= 0.87). Despite the high genetic diversity, three common clonal groups predominated in WA and were found in other Australian states. On some farms, molecular type was stable over a number of years, whereas on other farms genetically diverse isolates occurred within a flock of sheep or within a hoof. This study provides a large database from which to appropriately interpret molecular types found in epidemiological investigations and to identify common and unknown types that may compromise footrot eradication or control programs.
Duplex Real-Time Reverse Transcriptase PCR Assays for Rapid Detection and Identification of Pandemic (H1N1) 2009 and Seasonal Influenza A/H1, A/H3, and B Viruses
Authors: Chidlow Glenys , Harnett Gerald , Williams Simon , Levy Avram , Speers David , Smith David W.
Published: January 2010

Reports of a novel influenza virus type A (H1N1), now designated by the World Health Organization as pandemic (H1N1) 2009, emerged from the United States and Mexico in April 2009. The management of the pandemic in Australia required rapid and reliable testing of large numbers of specimens for the novel influenza strain and differentiation from seasonal influenza strains. A real-time reverse transcriptase PCR (RT-PCR) assay for the detection of pandemic (H1N1) 2009 was designed and used with existing real-time RT-PCR assays for seasonal influenza viruses A and B. MS2 coliphage was added to all samples and amplified as a quality control. Three duplex RT-PCR assays, each containing two primer pairs and corresponding 5′ nuclease probes, were initially evaluated on control material and stored samples and showed high sensitivity and specificity. More than 11,000 clinical samples were then tested for influenza A and B matrix gene targets and specific hemagglutinin gene targets for seasonal influenza A/H1, A/H3, and pandemic A (H1N1) 2009. Minimum sensitivities and specificities were 98.8% and 100%, respectively, for pandemic (H1N1) 2009, 81.5% and 98.9% for seasonal A/H1, and 96.3% and 99.6% for A/H3. Automated sample extraction facilitated the rapid processing of samples so that the assays allowed accurate, rapid, and cost-effective screening of large numbers of clinical samples.
Clostridium difficile
Testing in the Clinical Laboratory by Use of Multiple Testing Algorithms
Authors: Novak-Weekley Susan M. , Marlowe Elizabeth M. , Miller John M. , Cumpio Joven , Nomura Jim H. , Vance Paula H. , Weissfeld Alice
Published: January 2010

The incidence of
Clostridium difficile
infection (CDI) has risen almost 3-fold in the United States over the past decade, emphasizing the need for rapid and accurate tests for CDI. The Cepheid Xpert
C. difficile
assay is an integrated, closed, nucleic acid amplification system that automates sample preparation and real-time PCR detection of the toxin B gene (
tcdB
). A total of 432 stool specimens from symptomatic patients were tested by a glutamate dehydrogenase (GDH) assay, a toxin A and B enzyme immunoassay (EIA), the Xpert
C. difficile
assay, and a cell culture cytotoxicity neutralization assay (CCCN). The results of these methods, used individually and in combination, were compared to those of toxigenic culture. Results for the Xpert
C. difficile
assay alone showed a sensitivity, specificity, positive predictive value, and negative predictive value (NPV) of 94.4, 96.3, 84.0, and 98.8%, while the EIA alone gave corresponding values of 58.3, 94.7, 68.9, and 91.9%, respectively. An algorithm using the GDH assay and the EIA (plus the CCCN if the EIA was negative) showed corresponding values of 83.1, 96.7, 83.1, and 96.1%. The Xpert
C. difficile
assay was statistically superior to the EIA (
P
, <0.001 by Fisher's exact test) and to the GDH-EIA-CCCN algorithm (
P
, 0.0363). Combining the GDH and Xpert
C. difficile
assays lowered both the sensitivity and the NPV of the Xpert assay. The GDH-EIA-CCCN procedure required, on average, 2 days to complete testing on GDH-positive results, while testing by the Xpert
C. difficile
assay was completed, on average, in less than 1 h. Xpert
C. difficile
testing yielded the highest sensitivity and NPV, in the least amount of time, of the individual- and multiple-test algorithms evaluated in this study.
Direct Ertapenem Disk Screening Method for Identification of KPC-Producing
Klebsiella pneumoniae
and
Escherichia coli
in Surveillance Swab Specimens
Authors: Lolans Karen , Calvert Karen , Won Sarah , Clark James , Hayden Mary K.
Published: January 2010

Klebsiella pneumoniae
carbapenemase (KPC) production in Gram-negative bacilli is an increasing problem worldwide. Rectal swab surveillance is recommended as a component of infection prevention programs, yet few screening methods are published. We compared detection of KPC-producing
Klebsiella pneumoniae
and
Escherichia coli
in surveillance specimens by 2 methods: (i) inoculation of swabs in tryptic soy broth containing 2 μg/ml imipenem followed by plating to MacConkey agar (MAC) (method 1) and (ii) streaking swabs on MAC onto which a 10-μg ertapenem disk was then placed (method 2). Simulated rectal swab specimens of challenge isolates from a collection of well-characterized
K. pneumoniae
and
E. coli
strains and salvage rectal swab specimens collected from patients at 4 different health care facilities over a 7-month period were tested. The gold-standard comparator was
bla
KPC
PCR testing of isolates. Method 1 detected 4/9 (44%) KPC-positive challenge isolates. By method 2, 9/9 KPC-positive challenge isolates exhibited zones of inhibition of ≤27 mm; all KPC-negative isolates exhibited zones of inhibition greater than 27 mm. The sensitivity and specificity of method 1 for detection of KPC-positive
K. pneumoniae
and
E. coli
in 149 rectal swab specimens were 65.6% (95% confidence interval [CI], 46.8% to 80.8%) and 49.6% (95% CI, 40.3% to 58.9%), respectively. With method 2, a zone diameter of ≤27 mm had a sensitivity of 97.0% (95% CI, 82.5% to 99.8%) and specificity of 90.5% (95% CI, 83.3% to 94.9%) for detection of KPC in rectal swab specimens. Direct ertapenem disk testing is simpler, more sensitive, and more specific than selective broth enrichment with imipenem for detection of KPC-producing
K. pneumoniae
and
E. coli
in surveillance specimens.
Rapid Detection of Methicillin-Resistant
Staphylococcus aureus
(MRSA) in Diverse Clinical Specimens by the BD GeneOhm MRSA Assay and Comparison with Culture
Authors: Lucke Katja , Hombach Michael , Hug Melanie , Pfyffer Gaby E.
Published: January 2010

The efficacy of the BD GeneOhm methicillin-resistant
Staphylococcus aureus
(MRSA) assay was assessed by analyzing nasal swabs and swabs from other body sites for the presence of MRSA in a low-prevalence area. From 681 patients with a high risk for MRSA carriage, 1,601 specimens were collected and transported in Amies agar. After discordant analysis, the sensitivity, specificity, positive predictive value, and negative predictive value of the BD GeneOhm MRSA assay were 84.3%, 99.2%, 88.4%, and 98.9%, respectively, compared to culture.
Real-Time PCR Testing for
mecA
Reduces Vancomycin Usage and Length of Hospitalization for Patients Infected with Methicillin-Sensitive Staphylococci
Authors: Nguyen David T. , Yeh Ellen , Perry Sharon , Luo Robert F. , Pinsky Benjamin A. , Lee Betty P. , Sisodiya Deepak , Baron Ellen Jo , Banaei Niaz
Published: January 2010

Nucleic acid amplification tests (NAATs) have revolutionized infectious disease diagnosis, allowing for the rapid and sensitive identification of pathogens in clinical specimens. Real-time PCR testing for the
mecA
gene (
mecA
PCR), which confers methicillin resistance in staphylococci, has the added potential to reduce antibiotic usage, improve clinical outcomes, lower health care costs, and avoid emergence of drug resistance. A retrospective study was performed to identify patients infected with methicillin-sensitive staphylococcal isolates who were receiving vancomycin treatment when susceptibility results became available. Vancomycin treatment and length of hospitalization were compared in these patients for a 6-month period before and after implementation of
mecA
PCR. Among 65 and 94 patients identified before and after
mecA
PCR, respectively, vancomycin usage (measured in days on therapy) declined from a median of 3 days (range, 1 to 44 days) in the pre-PCR period to 1 day (range, 0 to 18 days) in the post-PCR period (
P
< 0.0001). In total, 38.5% (25/65) of patients were switched to β-lactam therapy in the pre-PCR period, compared to 61.7% (58/94) in the post-PCR period (
P
= 0.004). Patient hospitalization days also declined from a median of 8 days (range, 1 to 47 days) in the pre-PCR period to 5 days (range, 0 to 42 days) in the post-PCR period (
P
= 0.03). Real-time PCR testing for
mecA
is an effective tool for reducing vancomycin usage and length of stay of hospitalized patients infected with methicillin-sensitive staphylococci. In the face of ever-rising health care expenditures in the United States, these findings have important implications for improving outcomes and decreasing costs.
Gut Mucosal FOXP3+Regulatory CD4+T Cells and Nonregulatory CD4+T Cells Are Differentially Affected by Simian Immunodeficiency Virus Infection in Rhesus Macaques
Authors: Allers Kristina , Loddenkemper Christoph , Hofmann Jörg , Unbehaun Anett , Kunkel Désirée , Moos Verena , Kaup Franz-Josef , Stahl-Hennig Christiane , Sauermann Ulrike , Epple Hans-Jörg , Schneider Thomas
Published: January 2010

The gastrointestinal tract represents a major site for human and simian immunodeficiency virus (HIV and SIV) replication and CD4+T-cell depletion. Despite severe depletion of mucosal CD4+T cells, FOXP3+regulatory CD4+T cells (Treg) are highly increased in the gut mucosa of chronically HIV-infected individuals and may contribute to HIV pathogenesis, either by their immunosuppressive function or as a significant target cell population for virus production. Little is known about the susceptibility of mucosal Tregto viral infection and the longitudinal effect of HIV/SIV infection on Tregdynamics. In this study, we determined the level of SIV infection in Tregand nonregulatory CD4+T cells (non-Treg) isolated from the colon of SIV-infected rhesus macaques. The dynamics of mucosal Tregand alterations in the mucosal CD4+T-cell pool were examined longitudinally. Our findings indicate that mucosal Tregwere less susceptible to productive SIV infection than non-Tregand thus were selectively spared from SIV-mediated cell death. In addition to improved survival, local expansion of Tregby SIV-induced proliferation of the mucosal CD4+T-cell pool facilitated the accumulation of mucosal Tregduring the course of infection. High frequency of mucosal Tregin chronic SIV infection was strongly related to a reduction of perforin-expressing cells. In conclusion, this study suggests that mucosal Tregare less affected by productive SIV infection than non-Tregand therefore spared from depletion. Although SIV production is limited in mucosal Treg, Tregaccumulation may indirectly contribute to viral persistence by suppressing antiviral immune responses.
Caspase 9 Is Essential for Herpes Simplex Virus Type 2-Induced Apoptosis in T Cells
Authors: Vanden Oever Michael J. , Han Jin-Young
Published: January 2010

Herpes simplex virus type 2 (HSV-2) induces apoptosis in T cells by a caspase-dependent mechanism. Apoptosis can occur via extrinsic (death receptor) and/or intrinsic (mitochondrial) pathways. Here, we show that the initiator caspase for the intrinsic pathway is activated in T cells following HSV-2 exposure. To determine the respective contributions of intrinsic and extrinsic pathways, we assessed apoptosis in Jurkat cells that are deficient in caspase 8 or Fas-associating protein with death domain (FADD) for the extrinsic pathway and in cells deficient in caspase 9 for the intrinsic pathway. Our results indicate HSV-2-induced apoptosis in T cells occurs via the intrinsic pathway.
Autoexcision of Bacterial Artificial Chromosome Facilitated by Terminal Repeat-Mediated Homologous Recombination: a Novel Approach for Generating Traceless Genetic Mutants of Herpesviruses
Authors: Zhou Fuchun , Li Qiuhua , Wong Scott W. , Gao Shou-Jiang
Published: January 2010

Infectious bacterial artificial chromosomes (BACs) of herpesviruses are powerful tools for genetic manipulation. However, the presence of BAC vector sequence in the viral genomes often causes genetic and phenotypic alterations. While the excision of the BAC vector cassette can be achieved by homologous recombination between extra duplicate viral sequences or loxP site-mediated recombination, these methods either are inefficient or leave a loxP site mark in the viral genome. Here we describe the use of viral intrinsic repeat sequences, which are commonly present in herpesviral genomes, to excise the BAC vector cassette. Using a newly developed
in vitro
transposon-based cloning approach, we obtained an infectious BAC of rhesus rhadinovirus (RRV) strain RRV26-95 with the BAC vector cassette inserted in the terminal repeat (TR) region. We showed that the BAC vector cassette was rapidly excised upon reconstitution in cells predominantly through TR-mediated homologous recombination. Genetic and phenotypic analysis showed that the BAC-excised virus was reversed to wild-type RRV. Using this autoexcisable BAC clone, we successfully generated an RRV mutant with a deletion of Orf50, which encodes a replication and transcription activator (RTA) protein. Together, these results illustrate the usefulness of TR for genetic manipulation of herpesviruses when combined with the novel transposon-based cloning approach.
Structure of Adenovirus Type 21 Knob in Complex with CD46 Reveals Key Differences in Receptor Contacts among Species B Adenoviruses
Authors: Cupelli Karolina , Müller Steffen , Persson B. David , Jost Marco , Arnberg Niklas , Stehle Thilo
Published: January 2010

The complement regulation protein CD46 is the primary attachment receptor for most species B adenoviruses (Ads). However, significant variability exists in sequence and structure among species B Ads in the CD46-binding regions, correlating with differences in affinity. Here, we report a structure-function analysis of the interaction of the species B Ad21 knob with the two N-terminal repeats SCR1 and SCR2 of CD46, CD46-D2. We have determined the structures of the Ad21 knob in its unliganded form as well as in complex with CD46-D2, and we compare the interactions with those observed for the Ad11 knob-CD46-D2 complex. Surface plasmon resonance measurements demonstrate that the affinity of Ad21 knobs for CD46-D2 is 22-fold lower than that of the Ad11 knob. The superposition of the Ad21 and Ad11 knob structures in complex with CD46-D2 reveals a substantially different binding mode, providing an explanation for the weaker binding affinity of the Ad21 knob for its receptor. A critical difference in both complex structures is that a key interaction point, the DG loop, protrudes more in the Ad21 knob than in the Ad11 knob. Therefore, the protruding DG loop does not allow CD46-D2 to approach the core of the Ad21 knob as closely as in the Ad11 knob-CD46-D2 complex. In addition, the engagement of CD46-D2 induces a conformational change in the DG loop in the Ad21 knob but not in the Ad11 knob. Our results contribute to a more profound understanding of the CD46-binding mechanism of species B Ads and have relevance for the design of more efficient gene delivery vectors.
Gastrointestinal Delivery of Baculovirus Displaying Influenza Virus Hemagglutinin Protects Mice against Heterologous H5N1 Infection
Authors: Prabakaran Mookkan , Madhan Selvaraj , Prabhu Nayana , Qiang Jia , Kwang Jimmy
Published: January 2010

The recent outbreaks of influenza A H5N1 virus in birds and humans have necessitated the development of potent H5N1 vaccines. In this study, we evaluated the protective potential of an immediate-early promoter-based baculovirus displaying hemagglutinin (BacHA) against highly pathogenic avian influenza (HPAI) H5N1 virus infection in a mouse model. Gastrointestinal delivery of BacHA significantly enhanced the systemic immune response in terms of HA-specific serum IgG and hemagglutination inhibition (HI) titers. In addition, BacHA vaccine was able to significantly enhance the mucosal IgA level. The inclusion of recombinant cholera toxin B subunit as a mucosal adjuvant along with BacHA vaccine did not influence either the systemic or mucosal immunity. Interestingly, an inactivated form of BacHA was able to induce only a negligible level of immune responses compared to its live counterpart. Microneutralization assay also indicated that live BacHA vaccine was able to induce strong cross-clade neutralization against heterologous H5N1 strains (clade 1.0, clade 2.1, and clade 8.0) compared to the inactivated BacHA. Viral challenge studies showed that live BacHA was able to provide 100% protection against 5 50% mouse lethal doses (MLD
50
) of homologous (clade 2.1) and heterologous (clade 1) H5N1. Moreover, histopathological examinations revealed that mice vaccinated with live BacHA had only minimal bronchitis in lungs and regained their body weight more rapidly postchallenge. Furthermore, immunohistochemistry results demonstrated that the live BacHA was able to transduce and express HA in the intestinal epithelial cells
in vitro
and
in vivo
. We have demonstrated that recombinant baculovirus with a white spot syndrome virus (WSSV) immediate-early promoter 1 (ie1) acted as a vector as well as a protein vaccine and will enable the rapid production of prepandemic and pandemic vaccines without any biosafety concerns.
MicroRNA Expression and Virulence in Pandemic Influenza Virus-Infected Mice
Authors: Li Yu , Chan Eric Y. , Li Jiangning , Ni Chester , Peng Xinxia , Rosenzweig Elizabeth , Tumpey Terrence M. , Katze Michael G.
Published: January 2010

The worst known H1N1 influenza pandemic in history resulted in more than 20 million deaths in 1918 and 1919. Although the underlying mechanism causing the extreme virulence of the 1918 influenza virus is still obscure, our previous functional genomics analyses revealed a correlation between the lethality of the reconstructed 1918 influenza virus (r1918) in mice and a unique gene expression pattern associated with severe immune responses in the lungs. Lately, microRNAs have emerged as a class of crucial regulators for gene expression. To determine whether differential expression of cellular microRNAs plays a role in the host response to r1918 infection, we compared the lung cellular “microRNAome” of mice infected by r1918 virus with that of mice infected by a nonlethal seasonal influenza virus, A/Texas/36/91. We found that a group of microRNAs, including miR-200a and miR-223, were differentially expressed in response to influenza virus infection and that r1918 and A/Texas/36/91 infection induced distinct microRNA expression profiles. Moreover, we observed significant enrichment in the number of predicted cellular target mRNAs whose expression was inversely correlated with the expression of these microRNAs. Intriguingly, gene ontology analysis revealed that many of these mRNAs play roles in immune response and cell death pathways, which are known to be associated with the extreme virulence of r1918. This is the first demonstration that cellular gene expression patterns in influenza virus-infected mice may be attributed in part to microRNA regulation and that such regulation may be a contributing factor to the extreme virulence of the r1918.