bluuebunny/crossref_metadata_2025 huggingface dataset:
Low temperature growth of high-k Hf–La oxides by remote-plasma atomic layer deposition: Morphology, stoichiometry, and dielectric properties
Authors: Tang Fu , Zhu Chiyu , Smith David J. , Nemanich Robert J.
Published: December 2011

In this work, we investigated the growth of Hf oxide, La oxide, and alloyed Hf–La oxide films using remote-plasma atomic layer deposition at temperatures ranging from ∼80 to ∼250 °C. The relative composition and atomic bonding structure of the film were determined by in situ x ray photoelectron spectroscopy (XPS). Atomic force microscopy and transmission electron microscopy were implemented to characterize the morphology and crystalline structure. The XPS results indicated that for low temperature Hf oxide growth, a significant amount of excess oxygen species was observed in the deposited film. This oxygen could lead to instabilities and adversely affect the function of thin film transistors. The authors established that a He plasma post deposition treatment can partially remove the excess oxygen. In addition, the pure Hf oxide films show a surface morphology with protruding islands over a smooth surface which reflects the crystallized nature of the Hf oxide domains. In order to suppress the crystallization of the Hf oxide and to obtain a smooth morphology, 1–3 cycles of La-oxide were employed between adjacent Hf-oxide cycles. The Hf–La oxide films showed reduced roughness compared with that of the pure Hf oxide film. Carbon residue in the alloyed film is also reduced compared with that of the La oxide film. Finally, the electrical properties of the deposited films were characterized by capacitance-voltage (C-V) and current-voltage (I-V) measurement. The I-V curves show that the alloyed Hf–La oxide films have a higher break down field than that of pure Hf oxide films.
Cause and Effect in Biology Revisited: Is Mayr’s Proximate-Ultimate Dichotomy Still Useful?
Authors: Laland Kevin N. , Sterelny Kim , Odling-Smee John , Hoppitt William , Uller Tobias
Published: December 2011

Fifty years ago, Ernst Mayr published a hugely influential paper on the nature of causation in biology, in which he distinguished between proximate and ultimate causes. Mayr equated proximate causation with immediate factors (for example, physiology) and ultimate causation with evolutionary explanations (for example, natural selection). He argued that proximate and ultimate causes addressed different questions and were not alternatives. Mayr’s account of causation remains widely accepted today, with both positive and negative ramifications. Several current debates in biology (for example, over evolution and development, niche construction, cooperation, and the evolution of language) are linked by a common axis of acceptance/rejection of Mayr’s model of causation. We argue that Mayr’s formulation has acted to stabilize the dominant evolutionary paradigm against change but may now hamper progress in the biological sciences.
Growth of Uniformly Oriented Silica MFI and BEA Zeolite Films on Substrates
Authors: Pham Tung Cao Thanh , Kim Hyun Sung , Yoon Kyung Byung
Published: December 2011

Precise control over synthetic conditions eliminates misalignment of pore channels during the growth of zeolite films.
RIM-Binding Protein, a Central Part of the Active Zone, Is Essential for Neurotransmitter Release
Authors: Liu Karen S. Y. , Siebert Matthias , Mertel Sara , Knoche Elena , Wegener Stephanie , Wichmann Carolin , Matkovic Tanja , Muhammad Karzan , Depner Harald , Mettke Christoph , Bückers Johanna , Hell Stefan W. , Müller Martin , Davis Graeme W. , Schmitz Dietmar , Sigrist Stephan J.
Published: December 2011

Transmitter release at the fly neuromuscular junction is abolished in the absence of a scaffold protein.
High Relatedness Is Necessary and Sufficient to Maintain Multicellularity in
Dictyostelium
Authors: Kuzdzal-Fick Jennie J. , Fox Sara A. , Strassmann Joan E. , Queller David C.
Published: December 2011

Experimental evolution shows that the cooperation of cells in multicellular organisms degrades under low relatedness.
The Molecular Basis of Acid Insensitivity in the African Naked Mole-Rat
Authors: Smith Ewan St. John , Omerbašić Damir , Lechner Stefan G. , Anirudhan Gireesh , Lapatsina Liudmila , Lewin Gary R.
Published: December 2011

Life in a high–carbon dioxide environment has eliminated acid-evoked pain in the naked mole-rat.
Revealing Atom-Radical Reactivity at Low Temperature Through the N + OH Reaction
Authors: Daranlot Julien , Jorfi Mohamed , Xie Changjian , Bergeat Astrid , Costes Michel , Caubet Philippe , Xie Daiqian , Guo Hua , Honvault Pascal , Hickson Kevin M.
Published: December 2011

Rates have been measured for a chemical transformation of interstellar interest in which both reagents are unstable.
Observing the Multiexciton State in Singlet Fission and Ensuing Ultrafast Multielectron Transfer
Authors: Chan Wai-Lun , Ligges Manuel , Jailaubekov Askat , Kaake Loren , Miaja-Avila Luis , Zhu X.-Y.
Published: December 2011

Photoelectron detection reveals a previously elusive, short-lived paired carrier state of interest in solar light harvesting.
Translation Goes Global
Authors: Weiss Robert B. , Atkins John F.
Published: December 2011

An assessment of all ribosomes engaged in protein synthesis expands the view of the potential size of the cellular proteome.
Har Gobind Khorana (1922–2011)
Authors: Caruthers Marvin , Wells Robert
Published: December 2011

The remarkable work of a Nobel laureate saw breakthroughs in chemistry, biochemistry, and genetics.
China Bets on the Variome to Uncover Hereditary Diseases
Authors: HVistendahl Mara
Published: December 2011

China is contributing 3 billion yuan ($470 million) to the Human Variome Project, an international effort to catalog gene variations affecting human health.
Taking a New Shot At a TB Vaccine
Authors: Kupferschmidt Kai
Published: December 2011

Eager to replace the current tuberculosis vaccine, scientists hope to push a slew of promising candidates through clinical trials—if the money can be found.
Role of Universal 16S rRNA Gene PCR and Sequencing in Diagnosis of Prosthetic Joint Infection
Authors: Marín M. , Garcia-Lechuz J. M. , Alonso P. , Villanueva M. , Alcalá L. , Gimeno M. , Cercenado E. , Sánchez-Somolinos M. , Radice C. , Bouza E.
Published: December 2011

The etiological diagnosis of prosthetic joint infection (PJI) requires the isolation of microorganisms from periprosthetic samples. Microbiological cultures often yield false-positive and false-negative results. 16S rRNA gene PCR combined with sequencing (16SPCR) has proven useful for diagnosing various infections. We performed a prospective study to compare the utility of this approach with that of culture to diagnose PJI using intraoperative periprosthetic samples. We analyzed 176 samples from 40 patients with PJI and 321 samples from 82 noninfected patients using conventional culture and 16SPCR. Three statistical studies were undertaken following a previously validated mathematical model: sample-to-sample analysis, calculation of the number of samples to be studied, and calculation of the number of positive samples necessary to diagnose PJI. When only the number of positive samples is taken into consideration, a 16SPCR-positive result in one sample has good specificity and positive predictive value for PJI (specificity, 96.3%; positive predictive value, 91.7%; and likelihood ratio [LR], 22), while 3 positive cultures with the same microorganism are necessary to achieve similar specificity. The best combination of results for 16SPCR was observed when 5 samples were studied and the same microorganism was detected in 2 of them (sensitivity, 94%; specificity, 100%; and LR, 69.62). The results for 5 samples with 2 positive cultures were 96% and 82%, respectively, and the likelihood ratio was 1.06. 16SPCR is more specific and has a better positive predictive value than culture for diagnosis of PJI. A positive 16SPCR result is largely suggestive of PJI, even when few samples are analyzed; however, culture is generally more sensitive.
Performance of Different Mono- and Multiplex Nucleic Acid Amplification Tests on a Multipathogen External Quality Assessment Panel
Authors: Loens K. , van Loon A. M. , Coenjaerts F. , van Aarle Y. , Goossens H. , Wallace P. , Claas E. J. C. , Ieven M.
Published: December 2011

An external quality assessment (EQA) panel consisting of a total of 48 samples in bronchoalveolar lavage (BAL) fluid or transport medium was prepared in collaboration with Quality Control for Molecular Diagnostics (QCMD) (
www.qcmd.org
). The panel was used to assess the proficiency of the three laboratories that would be responsible for examining the 6,000 samples to be collected in the GRACE Network of Excellence (
www.grace-lrti.org
). The main objective was to decide on the best-performing testing approach for the detection of influenza viruses A and B, parainfluenza virus types 1 to 3, respiratory syncytial virus (RSV), human metapneumovirus, coronavirus, rhinovirus, adenovirus,
Chlamydophila pneumoniae
,
Mycoplasma pneumoniae
, and
Legionella pneumophila
by nucleic acid amplification techniques (NAATs). Two approaches were chosen: (i) laboratories testing samples using their in-house procedures for extraction and amplification and (ii) laboratories using their in-house amplification procedures on centrally extracted samples. Furthermore, three commercially available multiplex NAAT tests—the ResPlex (Qiagen GmbH, Hilden, Germany), RespiFinder plus (PathoFinder, Maastricht, The Netherlands), and RespiFinder Smart 21 (PathoFinder) tests—were evaluated by examination of the same EQA panel by the manufacturer. No large differences among the 3 laboratories were noticed when the performances of the assays developed in-house in combination with the in-house extraction procedures were compared. Also, the extraction procedure (central versus local) had little effect on performance. However, large differences in amplification efficacy were found between the commercially available tests; acceptable results were obtained by using the PathoFinder assays.
Development and Validation of a Comparative Genomic Fingerprinting Method for High-Resolution Genotyping of Campylobacter jejuni
Authors: Taboada Eduardo N. , Ross Susan L. , Mutschall Steven K. , MacKinnon Joanne M. , Roberts Michael J. , Buchanan Cody J. , Kruczkiewicz Peter , Jokinen Cassandra C. , Thomas James E. , Nash John H. E. , Gannon Victor P. J. , Marshall Barbara , Pollari Frank , Clark Clifford G.
Published: December 2011

Campylobacter
spp. are a leading cause of bacterial gastroenteritis worldwide. The need for molecular subtyping methods with enhanced discrimination in the context of surveillance- and outbreak-based epidemiologic investigations of
Campylobacter
spp. is critical to our understanding of sources and routes of transmission and the development of mitigation strategies to reduce the incidence of campylobacteriosis. We describe the development and validation of a rapid and high-resolution comparative genomic fingerprinting (CGF) method for
C. jejuni
. A total of 412 isolates from agricultural, environmental, retail, and human clinical sources obtained from the Canadian national integrated enteric pathogen surveillance program (C-EnterNet) were analyzed using a 40-gene assay (CGF40) and multilocus sequence typing (MLST). The significantly higher Simpson's index of diversity (ID) obtained with CGF40 (ID = 0.994) suggests that it has a higher discriminatory power than MLST at both the level of clonal complex (ID = 0.873) and sequence type (ID = 0.935). High Wallace coefficients obtained when CGF40 was used as the primary typing method suggest that CGF and MLST are highly concordant, and we show that isolates with identical MLST profiles are comprised of isolates with distinct but highly similar CGF profiles. The high concordance with MLST coupled with the ability to discriminate between closely related isolates suggests that CFG40 is useful in differentiating highly prevalent sequence types, such as ST21 and ST45. CGF40 is a high-resolution comparative genomics-based method for
C. jejuni
subtyping with high discriminatory power that is also rapid, low cost, and easily deployable for routine epidemiologic surveillance and outbreak investigations.
Prospective Evaluation of Clinical and Biological Markers To Predict the Outcome of Invasive Pulmonary Aspergillosis in Hematological Patients
Authors: Bergeron Anne , Porcher Raphaël , Menotti Jean , Poirot Jean Louis , Chagnon Karine , Vekhoff Anne , Cornet Muriel , Isnard Françoise , Raffoux Emmanuel , Brethon Benoit , Lacroix Claire , Touratier Sophie , Latgé Jean Paul , Bouges-Michel Claire , Tazi Abdellatif , Derouin Francis , Ribaud Patricia , Sulahian Annie
Published: December 2011

Early evaluation of treatment efficacy in invasive aspergillosis (IA), a leading cause of morbidity and mortality in hematological patients, remains a challenge. We conducted a prospective study to evaluate the performance of different markers in predicting the outcome of patients with IA. Both clinical and biological criteria were assessed 7, 14, 21, and 45 days after inclusion in the study, and mortality was assessed at day 60. The association between baseline data and their evolution and the day 45 response to treatment was analyzed. A total of 57 patients (4 with proven, 44 with probable, and 9 with possible aspergillosis according to the revised EORTC/MSG [European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and National Institute of Allergy and Infectious Diseases Mycoses Study Group] definitions) were included. At day 45, 30 patients (53%) were determined to be responders, 25 (44%) were nonresponders, and 2 were not able to be evaluated. Twenty patients died within the 60 days of follow-up. We found that a poor day 45 outcome was associated with patients who had high baseline serum galactomannan (GM) antigen levels and those receiving steroids at the time of IA. A consistently negative serum GM index was associated with a good outcome, and the day 14 clinical evaluation was predictive of the day 45 outcome. No association was found betweenAspergillusantibodies or DNA detection and patients' outcome. We conclude that the GM index value at diagnosis of IA, GM index kinetics, and clinical evaluation at day 14 are good markers for predicting the outcome of patients with IA and should be taken into account for adapting antifungal treatment.
International Circumpolar Surveillance Interlaboratory Quality Control Program for Serotyping Haemophilus influenzae and Serogrouping Neisseria meningitidis, 2005 to 2009
Authors: Tsang Raymond S. W. , Rudolph Karen , Lovgren Marguerite , Bekal Sadjia , Lefebvre Brigitte , Lambertsen Lotte , Zulz Tammy , Bruce Michael
Published: December 2011

The International Circumpolar Surveillance (ICS) program was initiated in 1999 to conduct population-based surveillance for invasive pneumococcal disease in select regions of the Arctic. The program was expanded to include the surveillance of invasive diseases caused by
Neisseria meningitidis
and
Haemophilus influenzae
. An interlaboratory quality control (QC) program to monitor laboratory proficiencies in the serogrouping of
N. meningitidis
and serotyping of
H. influenzae
strains was codeveloped by the Arctic Investigations Program (Anchorage, AK) and the Public Health Agency of Canada National Microbiology Laboratory (Winnipeg, Manitoba, Canada) and introduced into the ICS program in 2005. Other participating laboratories included the Provincial Laboratory for Public Health (Edmonton, Alberta, Canada), Laboratoire Santé Publique du Québec (Sainte-Anne-de-Bellevue, Québec, Canada), and Statens Serum Institut (Copenhagen, Denmark). From 2005 through 2009, 50 isolates (24
N. meningitidis
and 26
H. influenzae
isolates) were distributed among the five participating laboratories. The overall serogroup concordance for
N. meningitidis
strains was 92.3% (96/104), without including three isolates that were found to express both serogroup Y and W135 specificities. Concordant results were obtained for serogroups A, B, C, and Y among all laboratories. Discrepancies were observed most frequently for serogroups W135, X, Z, and 29E. The overall serotype concordance for
H. influenzae
was 98% (125/127 attempts). The two discrepant results involved a serotype c strain and a serotype e strain, and in both cases, the serotypeable
H. influenzae
isolates were misidentified as being nontypeable. These data demonstrate a high degree of concordance for serogroup and serotype determinations of
N. meningitidis
and
H. influenzae
isolates, respectively, among the five laboratories participating in this quality control program.
Identification of Infectious Agents in Onychomycoses by PCR-Terminal Restriction Fragment Length Polymorphism
Authors: Verrier Julie , Pronina Marina , Peter Corinne , Bontems Olympia , Fratti Marina , Salamin Karine , Schürch Stéphanie , Gindro Katia , Wolfender Jean-Luc , Harshman Keith , Monod Michel
Published: December 2011

A fast and reliable assay for the identification of dermatophyte fungi and nondermatophyte fungi (NDF) in onychomycosis is essential, since NDF are especially difficult to cure using standard treatment. Diagnosis is usually based on both direct microscopic examination of nail scrapings and macroscopic and microscopic identification of the infectious fungus in culture assays. In the last decade, PCR assays have been developed for the direct detection of fungi in nail samples. In this study, we describe a PCR-terminal restriction fragment length polymorphism (TRFLP) assay to directly and routinely identify the infecting fungi in nails. Fungal DNA was easily extracted using a commercial kit after dissolving nail fragments in an Na2S solution.Trichophytonspp., as well as 12 NDF, could be unambiguously identified by the specific restriction fragment size of 5′-end-labeled amplified 28S DNA. This assay enables the distinction of different fungal infectious agents and their identification in mixed infections. Infectious agents could be identified in 74% (162/219) of cases in which the culture results were negative. The PCR-TRFLP assay described here is simple and reliable. Furthermore, it has the possibility to be automated and thus routinely applied to the rapid diagnosis of a large number of clinical specimens in dermatology laboratories.
Prevalence and Characterization of Staphylococcus aureus, Including Methicillin-Resistant Staphylococcus aureus, Isolated from Bulk Tank Milk from Minnesota Dairy Farms
Authors: Haran K. P. , Godden S. M. , Boxrud D. , Jawahir S. , Bender J. B. , Sreevatsan S.
Published: December 2011

Staphylococcus aureus
is a common causative agent of bovine mastitis in dairy herds. The emergence of methicillin-resistant
Staphylococcus aureus
(MRSA) in hospitals as well as the community is a significant and costly public health concern.
S. aureus
-related bovine mastitis is a common reason for therapeutic and/or prophylactic use of antibiotics on dairy farms. In this study, herd prevalence of
S. aureus
, including MRSA, was estimated from bulk tank milk (BTM) from Minnesota farms. A total of 150 pooled BTM samples from 50 farms, collected over 3 seasons (spring, summer, and fall of 2009), were assessed. Herd prevalence of methicillin-susceptible
S. aureus
(MSSA) was 84%, while MRSA herd prevalence was 4%. A total of 93 MSSA isolates and 2 MRSA isolates were recovered from 150 BTM samples. Antibiotic susceptibility testing of
S. aureus
isolates showed pansusceptibility in 54 isolates, resistance to a single antibiotic class in 21 isolates, resistance to two antibiotic classes in 13 isolates, and resistance to ≥3 antibiotics classes and thus multidrug resistance in 5 isolates. The two MRSA isolates displayed resistance to β-lactams, cephalosporins, and lincosamides and were multiresistant. Staphylococcal protein A gene (
spa
) typing identified
spa
types t529 and t034 most frequently among methicillin-susceptible isolates, while t121 was observed in MRSA isolates. Seven isolates, including the two MRSA isolates, produced staphylococcal enterotoxins B, C, D, and E on overnight culture. MRSA isolates were further genotyped using multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Of the 2 MRSA isolates, one had a composite genotype profile of MLST ST 5-PFGE USA100-unknown
spa
type, which has been reported among hospital-associated MRSA isolates, while the second isolate carried the MLST ST 8-PFGE USA300-
spa
type t121 genotype, commonly identified among community-associated MRSA isolates. These results suggest that MRSA genotypes associated with hospitals and community can be isolated from milk at very low rates.
How Should Long-Term Tunneled Central Venous Catheters Be Managed in Microbiology Laboratories in Order To Provide an Accurate Diagnosis of Colonization?
Authors: Guembe M. , Martín-Rabadán P. , Echenagusia A. , Camúñez F. , Rodríguez-Rosales G. , Simó G. , Echenagusia M. , Bouza E.
Published: December 2011

Guidelines recommend the roll-plate technique for short-term central venous catheter (CVC) tip cultures. However, the issue of whether the roll-plate technique is better than the sonication method for long-term CVCs remains unresolved. In addition, no data are available for predicting the value of direct Gram staining in anticipating catheter colonization or catheter-related bloodstream infection (CRBSI) in these long-term CVCs. Our objectives were to compare the roll-plate technique and the sonication method and to define the validity values of Gram staining for the prediction of colonization and CRBSI in patients with long-term tunneled CVCs. During the study period, all tunneled CVCs removed at our institution were prospectively and routinely sent to the microbiology laboratory for Gram staining (first) and tip culture (the Maki technique and sonication, in a random order). We received 149 tunneled CVCs, 39 (26.2%) of which were colonized and 11 (7.4%) of which were associated with CRBSI. Overall, the roll-plate method detected 94.9% of the colonized catheters, whereas sonication detected only 43.6% (
P
< 0.001). The validity values of Gram staining for the detection of colonization and CRBSI were as follows: a sensitivity of 35.9% to 60.0%, a specificity of 100% to 94.2%, a positive predictive value of 100% to 42.9%, and a negative predictive value of 81.5% to 97.0%. The roll-plate technique proved to be better than sonication for the detection of bacteria in long-term tunneled CVCs. Gram staining of the tips of tunneled CVCs can anticipate a positive culture and rule out CRBSI. In our opinion, direct Gram staining should be incorporated into routine microbiological assessments of long-term catheter tips.
Detection of Mobile-Genetic-Element Variation between Colonizing and Infecting Hospital-Associated Methicillin-Resistant Staphylococcus aureus Isolates
Authors: McCarthy Alex J. , Breathnach Aodhan S. , Lindsay Jodi A.
Published: December 2011

Whole-genome analysis by 62-strain microarray showed variation in resistance and virulence genes on mobile genetic elements (MGEs) between 40 isolates of methicillin-resistant
Staphylococcus aureus
(MRSA) strain CC22-
SCCmecIV
but also showed (i) detection of two previously unrecognized MRSA transmission events and (ii) that 7/8 patients were infected with a variant of their own colonizing isolate.
Clinical Validation of Multiplex Real-Time PCR Assays for Detection of Bacterial Meningitis Pathogens
Authors: Wang Xin , Theodore M. Jordan , Mair Raydel , Trujillo-Lopez Elizabeth , du Plessis Mignon , Wolter Nicole , Baughman Andrew L. , Hatcher Cynthia , Vuong Jeni , Lott Lisa , von Gottberg Anne , Sacchi Claudio , McDonald J. Matthew , Messonnier Nancy E. , Mayer Leonard W.
Published: December 2011

Neisseria meningitidis
,
Haemophilus influenzae
, and
Streptococcus pneumoniae
are important causes of meningitis and other infections, and rapid, sensitive, and specific laboratory assays are critical for effective public health interventions. Singleplex real-time PCR assays have been developed to detect
N. meningitidis ctrA
,
H. influenzae hpd
, and
S. pneumoniae lytA
and serogroup-specific genes in the
cap
locus for
N. meningitidis
serogroups A, B, C, W135, X, and Y. However, the assay sensitivity for serogroups B, W135, and Y is low. We aimed to improve assay sensitivity and develop multiplex assays to reduce time and cost. New singleplex real-time PCR assays for serogroup B
synD
, W135
synG
, and Y
synF
showed 100% specificity for detecting
N. meningitidis
species, with high sensitivity (serogroup B
synD
, 99% [75/76]; W135
synG
, 97% [38/39]; and Y
synF
, 100% [66/66]). The lower limits of detection (LLD) were 9, 43, and 10 copies/reaction for serogroup B
synD
, W135
synG
, and Y
synF
assays, respectively, a significant improvement compared to results for the previous singleplex assays. We developed three multiplex real-time PCR assays for detection of (i)
N. meningitidis ctrA
,
H. influenzae hpd
, and
S. pneumoniae lytA
(NHS assay); (ii)
N. meningitidis
serogroups A, W135, and X (AWX assay); and (iii)
N. meningitidis
serogroups B, C, and Y (BCY assay). Each multiplex assay was 100% specific for detecting its target organisms or serogroups, and the LLD was similar to that for the singleplex assay. Pairwise comparison of real-time PCR between multiplex and singleplex assays showed that cycle threshold values of the multiplex assay were similar to those for the singleplex assay. There were no substantial differences in sensitivity and specificity between these multiplex and singleplex real-time PCR assays.
Assessment on Experimental Bacterial Biofilms and in Clinical Practice of the Efficacy of Sampling Solutions for Microbiological Testing of Endoscopes
Authors: Aumeran C. , Thibert E. , Chapelle F. A. , Hennequin C. , Lesens O. , Traoré O.
Published: December 2011

Opinions differ on the value of microbiological testing of endoscopes, which varies according to the technique used. We compared the efficacy on bacterial biofilms of sampling solutions used for the surveillance of the contamination of endoscope channels. To compare efficacy, we used an experimental model of a 48-h
Pseudomonas
biofilm grown on endoscope internal tubing. Sampling of this experimental biofilm was performed with a Tween 80-lecithin-based solution, saline, and sterile water. We also performed a randomized prospective study during routine clinical practice in our hospital sampling randomly with two different solutions the endoscopes after reprocessing. Biofilm recovery expressed as a logarithmic ratio of bacteria recovered on bacteria initially present in biofilm was significantly more effective with the Tween 80-lecithin-based solution than with saline solution (
P
= 0.002) and sterile water (
P
= 0.002). There was no significant difference between saline and sterile water. In the randomized clinical study, the rates of endoscopes that were contaminated with the Tween 80-lecithin-based sampling solution and the saline were 8/25 and 1/25, respectively (
P
= 0.02), and the mean numbers of bacteria recovered were 281 and 19 CFU/100 ml (
P
= 0.001), respectively. In conclusion, the efficiency and therefore the value of the monitoring of endoscope reprocessing by microbiological cultures is dependent on the sampling solutions used. A sampling solution with a tensioactive action is more efficient than saline in detecting biofilm contamination of endoscopes.
Sulfonamide Resistance in Isolates of Nocardia spp. from a U.S. Multicenter Survey
Authors: Brown-Elliott Barbara A. , Biehle Jon , Conville Patricia S. , Cohen Samuel , Saubolle Michael , Sussland Den , Wengenack Nancy , Kriel Kimberly , Bridge Linda , McNulty Steven , Vasireddy Ravikiran , Wallace Richard J.
Published: December 2011

Recent reports of increasing
in vitro
sulfonamide resistance in
Nocardia
prompted us to investigate the findings. Despite the reports, there is a paucity of clinical reports of sulfonamide failure in treatment of nocardia disease. We reviewed 552 recent susceptibilities of clinical isolates of
Nocardia
from six major laboratories in the United States, and only 2% of the isolates were found to have resistant MICs of trimethoprim-sulfamethoxazole and/or sulfamethoxazole. We hypothesize that the discrepancies in the apparent sulfonamide resistance between our study and the previous findings may be associated with difficulty in the laboratory interpretation of
in vitro
MICs for trimethoprim-sulfamethoxazole and sulfamethoxazole and the lack of quality controls for
Nocardia
for these agents.
Detection of Favorable Oral Cephalosporin-Clavulanate Interactions by
In Vitro
Disk Approximation Susceptibility Testing of Extended-Spectrum-Beta-Lactamase-Producing Members of the Enterobacteriaceae
Authors: Campbell Jennifer D. , Lewis James S. , McElmeel M. Leticia , Fulcher Letitia C. , Jorgensen James H.
Published: December 2011

Extended-spectrum-beta-lactamase (ESBL)-producing members of the
Enterobacteriaceae
are often resistant to multiple drug classes, making therapy of urinary infections with oral antibiotics difficult. Previously it was shown that amoxicillin-clavulanate can provide clavulanate inhibition of ESBLs and protect an oral cephalosporin present in combination when tested by broth microdilution. This study has shown that disk approximation testing could detect favorable cephalosporin-clavulanate interactions among a group of 101 previously characterized members of the
Enterobacteriaceae
with CTX-M, SHV, or TEM ESBLs.
Balamuthia mandrillaris and Acanthamoeba Amebic Encephalitis with Neurotoxoplasmosis Coinfection in a Patient with Advanced HIV Infection
Authors: Pietrucha-Dilanchian Paula , Chan Joseph C. , Castellano-Sanchez Amilcar , Hirzel Alicia , Laowansiri Panthipa , Tuda Claudio , Visvesvara Govinda S. , Qvarnstrom Yvonne , Ratzan Kenneth R.
Published: December 2011

We describe a patient with advanced HIV infection and
Balamuthia mandrillaris
and
Acanthamoeba
amebic encephalitis with
Toxoplasma gondii
coinfection. A multidisciplinary effort and state-of-the-art diagnostic techniques were required for diagnosis. Our patient is the first reported case of an HIV-infected person with dual
Balamuthia mandrillaris
and
Acanthamoeba
amebic encephalitis with neurotoxoplasmosis coinfection.
Recruitment of the Nuclear Form of Uracil DNA Glycosylase into Virus Particles Participates in the Full Infectivity of HIV-1
Authors: Guenzel Carolin A. , Hérate Cécile , Le Rouzic Erwann , Maidou-Peindara Priscilla , Sadler Holly A. , Rouyez Marie-Christine , Mansky Louis M. , Benichou Serge
Published: December 2011

The HIV-1 Vpr protein participates in the early steps of the virus life cycle by influencing the accuracy of reverse transcription. This role of Vpr was related to the recruitment of the nuclear form of the uracil DNA glycosylase (UNG2) enzyme into virus particles, but several conflicting findings have been reported regarding the role of UNG2 encapsidation on viral infectivity. Here, we report that the catalytic activity of UNG2 was not required for influencing HIV-1 mutation, and this function of UNG2 was mapped within a 60-amino-acid domain located in the N-terminal region of the protein required for direct interaction with the p32 subunit of the replication protein A (RPA) complex. Importantly, enforced recruitment of overexpressed UNG2 into virions resulted in a net increase of virus infectivity, and this positive effect on infectivity was also independent of the UNG2 enzymatic activity. In contrast, virus infectivity and replication, as well as the efficiency of the viral DNA synthesis, were significantly reduced when viruses were produced from cells depleted of either endogenous UNG2 or RPA p32. Taken together, these results demonstrate that incorporation of UNG2 into virions has a positive impact on HIV-1 infectivity and replication and positively influences the reverse transcription process through a nonenzymatic mechanism involving the p32 subunit of the RPA complex.
Inhibition of TANK Binding Kinase 1 by Herpes Simplex Virus 1 Facilitates Productive Infection
Authors: Ma Yijie , Jin Huali , Valyi-Nagy Tibor , Cao Youjia , Yan Zhipeng , He Bin
Published: December 2011

The γ
1
34.5 protein of herpes simplex viruses (HSV) is essential for viral pathogenesis, where it precludes translational arrest mediated by double-stranded-RNA-dependent protein kinase (PKR). Paradoxically, inhibition of PKR alone is not sufficient for HSV to exhibit viral virulence. Here we report that γ
1
34.5 inhibits TANK binding kinase 1 (TBK1) through its amino-terminal sequences, which facilitates viral replication and neuroinvasion. Compared to wild-type virus, the γ
1
34.5 mutant lacking the amino terminus induces stronger antiviral immunity. This parallels a defect of γ
1
34.5 for interacting with TBK1 and reducing phosphorylation of interferon (IFN) regulatory factor 3. This activity is independent of PKR. Although resistant to IFN treatment, the γ
1
34.5 amino-terminal deletion mutant replicates at an intermediate level between replication of wild-type virus and that of the γ
1
34.5 null mutant in TBK1
+/+
cells. However, such impaired viral growth is not observed in TBK1
−/−
cells, indicating that the interaction of γ
1
34.5 with TBK1 dictates HSV infection. Upon corneal infection, this mutant replicates transiently but barely invades the trigeminal ganglia or brain, which is a difference from wild-type virus and the γ
1
34.5 null mutant. Therefore, in addition to PKR, γ
1
34.5 negatively regulates TBK1, which contributes viral replication and spread
in vivo
.
Structure of an Antibody in Complex with Its Mucin Domain Linear Epitope That Is Protective against Ebola Virus
Authors: Olal Daniel , Kuehne Ana I. , Bale Shridhar , Halfmann Peter , Hashiguchi Takao , Fusco Marnie L. , Lee Jeffrey E. , King Liam B. , Kawaoka Yoshihiro , Dye John M. , Saphire Erica Ollmann
Published: December 2011

Antibody 14G7 is protective against lethal Ebola virus challenge and recognizes a distinct linear epitope in the prominent mucin-like domain of the Ebola virus glycoprotein GP. The structure of 14G7 in complex with its linear peptide epitope has now been determined to 2.8 Å. The structure shows that this GP sequence forms a tandem β-hairpin structure that binds deeply into a cleft in the antibody-combining site. A key threonine at the apex of one turn is critical for antibody interaction and is conserved among all Ebola viruses. This work provides further insight into the mechanism of protection by antibodies that target the protruding, highly accessible mucin-like domain of Ebola virus and the structural framework for understanding and characterizing candidate immunotherapeutics.
Viral Interferon Regulatory Factors Are Critical for Delay of the Host Immune Response against Rhesus Macaque Rhadinovirus Infection
Authors: Robinson Bridget A. , O'Connor Megan A. , Li He , Engelmann Flora , Poland Britt , Grant Richard , DeFilippis Victor , Estep Ryan D. , Axthelm Michael K. , Messaoudi Ilhem , Wong Scott W.
Published: December 2011

Kaposi's sarcoma-associated herpesvirus (KSHV) and the closely related gamma-2 herpesvirus rhesus macaque (RM) rhadinovirus (RRV) are the only known viruses to encode viral homologues of the cellular interferon (IFN) regulatory factors (IRFs). Recent characterization of a viral IRF (vIRF) deletion clone of RRV (vIRF-knockout RRV [vIRF-ko RRV]) demonstrated that vIRFs inhibit induction of type I and type II IFNs during RRV infection of peripheral blood mononuclear cells. Because the IFN response is a key component to a host's antiviral defenses, this study has investigated the role of vIRFs in viral replication and the development of the immune response duringin vivoinfection in RMs, the natural host of RRV. Experimental infection of RMs with vIRF-ko RRV resulted in decreased viral loads and diminished B cell hyperplasia, a characteristic pathology during acute RRV infection that often develops into more severe lymphoproliferative disorders in immune-compromised animals, similar to pathologies in KSHV-infected individuals. Moreover,in vivoinfection with vIRF-ko RRV resulted in earlier and sustained production of proinflammatory cytokines and earlier induction of an anti-RRV T cell response compared to wild-type RRV infection. These findings reveal the broad impact that vIRFs have on pathogenesis and the immune responsein vivoand are the first to validate the importance of vIRFs duringde novoinfection in the host.
Intronic Deletions That Disrupt mRNA Splicing of the
tva
Receptor Gene Result in Decreased Susceptibility to Infection by Avian Sarcoma and Leukosis Virus Subgroup A
Authors: Reinišová Markéta , Plachý Jiří , Trejbalová Kateřina , Šenigl Filip , Kučerová Dana , Geryk Josef , Svoboda Jan , Hejnar Jiří
Published: December 2011

The group of closely related avian sarcoma and leukosis viruses (ASLVs) evolved from a common ancestor into multiple subgroups, A to J, with differential host range among galliform species and chicken lines. These subgroups differ in variable parts of their envelope glycoproteins, the major determinants of virus interaction with specific receptor molecules. Three genetic loci,
tva
,
tvb
, and
tvc
, code for single membrane-spanning receptors from diverse protein families that confer susceptibility to the ASLV subgroups. The host range expansion of the ancestral virus might have been driven by gradual evolution of resistance in host cells, and the resistance alleles in all three receptor loci have been identified. Here, we characterized two alleles of the
tva
receptor gene with similar intronic deletions comprising the deduced branch-point signal within the first intron and leading to inefficient splicing of
tva
mRNA. As a result, we observed decreased susceptibility to subgroup A ASLV
in vitro
and
in vivo
. These alleles were independently found in a close-bred line of domestic chicken and Indian red jungle fowl (
Gallus gallus murghi
), suggesting that their prevalence might be much wider in outbred chicken breeds. We identified defective splicing to be a mechanism of resistance to ASLV and conclude that such a type of mutation could play an important role in virus-host coevolution.
Specific Mutation of a Gammaherpesvirus-Expressed Antigen in Response to CD8 T Cell SelectionIn Vivo
Authors: Loh Joy , Popkin Daniel L. , Droit Lindsay , Braaten Douglas C. , Zhao Guoyan , Zhang Xin , Vachharajani Punit , Myers Nancy , Hansen Ted H. , Virgin Herbert W.
Published: December 2011

Herpesviruses are thought to be highly genetically stable, and their use as vaccine vectors has been proposed. However, studies of the human gammaherpesvirus, Epstein-Barr virus, have found viral isolates containing mutations in HLA class I-restricted epitopes. Using murine gammaherpesvirus 68 expressing ovalbumin (OVA), we examined the stability of a gammaherpesvirus antigenic locus under strong CD8 T cell selectionin vivo. OVA-specific CD8 T cells selected viral isolates containing mutations in the OVA locus but minimal alterations in other genomic regions. Thus, a CD8 T cell response to a gammaherpesvirus-expressed antigen that is not essential for replication or pathogenesis can result in selective mutation of that antigenin vivo. This finding may have relevance for the use of herpesvirus vectors for chronic antigen expressionin vivo.
Persistence of Circulating Memory B Cell Clones with Potential for Dengue Virus Disease Enhancement for Decades following Infection
Authors: Smith Scott A. , Zhou Yang , Olivarez Nicholas P. , Broadwater Anne H. , de Silva Aravinda M. , Crowe James E.
Published: December 2011

Symptomatic dengue virus infection ranges in disease severity from an influenza-like illness to life-threatening shock. One model of the mechanism underlying severe disease proposes that weakly neutralizing, dengue serotype cross-reactive antibodies induced during a primary infection facilitate virus entry into Fc receptor-bearing cells during a subsequent secondary infection, increasing viral replication and the release of cytokines and vasoactive mediators, culminating in shock. This process has been termed antibody-dependent enhancement of infection and has significantly hindered vaccine development. Much of our understanding of this process has come from studies using mouse monoclonal antibodies (MAbs); however, antibody responses in mice typically exhibit less complexity than those in humans. A better understanding of the humoral immune response to natural dengue virus infection in humans is sorely needed. Using a high-efficiency human hybridoma technology, we isolated 37 hybridomas secreting human MAbs to dengue viruses from 12 subjects years or even decades following primary or secondary infection. The majority of the human antibodies recovered were broadly cross-reactive, directed against either envelope or premembrane proteins, and capable of enhancement of infectionin vitro; few exhibited serotype-specific binding or potent neutralizing activity. Memory B cells encoding enhancing antibodies predominated in the circulation, even two or more decades following infection. Mapping the epitopes and activity of naturally occurring dengue antibodies should prove valuable in determining whether the enhancing and neutralizing activity of antibodies can be separated. Such principles could be used in the rational design of vaccines that enhance the induction of neutralizing antibodies, while lowering the risk of dengue shock syndrome.
Metagenomic Analysis of the Viral Flora of Pine Marten and European Badger Feces
Authors: van den Brand Judith M. A. , van Leeuwen Marije , Schapendonk Claudia M. , Simon James H. , Haagmans Bart L. , Osterhaus Albert D. M. E. , Smits Saskia L.
Published: December 2011

A thorough understanding of the diversity of viruses in wildlife provides epidemiological baseline information about potential pathogens. Metagenomic analysis of the enteric viral flora revealed a new anellovirus and bocavirus species in pine martens and a new circovirus-like virus and geminivirus-related DNA virus in European badgers. In addition, sequences with homology to viruses from the families
Paramyxo
- and
Picornaviridae
were detected.
Comparative Analysis of Transforming Properties of E6 and E7 from Different Beta Human Papillomavirus Types
Authors: Cornet Iris , Bouvard Véronique , Campo Maria Saveria , Thomas Miranda , Banks Lawrence , Gissmann Lutz , Lamartine Jérôme , Sylla Bakary S. , Accardi Rosita , Tommasino Massimo
Published: December 2011

The cutaneous beta human papillomavirus (beta HPV) types appear to be involved in skin carcinogenesis. However, only a few beta HPVs have been investigated so far. Here, we compared the properties of E6 and E7 oncoproteins from six uncharacterized beta HPVs (14, 22, 23, 24, 36, 49). Only HPV49 E6 and E7 immortalized primary human keratinocytes and efficiently deregulated the p53 and pRb pathways. Furthermore, HPV49 E6, similarly to E6 from the oncogenic HPV16, promoted p53 degradation.
Espirito Santo Virus: a New Birnavirus That Replicates in Insect Cells
Authors: Vancini Ricardo , Paredes Angel , Ribeiro Mariana , Blackburn Kevin , Ferreira Davis , Kononchik Joseph P. , Hernandez Raquel , Brown Dennis
Published: December 2011

Espirito Santo virus (ESV) is a newly discovered virus recovered as contamination in a sample of a virulent strain of dengue-2 virus (strain 44/2), which was recovered from a patient in the state of Espirito Santo, Brazil, and amplified in insect cells. ESV was found to be dependent upon coinfection with a virulent strain of dengue-2 virus and to replicate in C6/36 insect cells but not in mammalian Vero cells. A sequence of the genome has been produced by
de novo
assembly and was not found to match to any known viral sequence. An incomplete match to the nucleotide sequence of the RNA-dependent RNA polymerase from
Drosophila
X virus (DXV), another birnavirus, could be detected. Mass spectrometry analysis of ESV proteins found no matches in the protein data banks. However, peptides recovered by mass spectrometry corresponded to the
de novo
-assembled sequence by BLAST analysis. The composition and three-dimensional structure of ESV are presented, and its sequence is compared to those of other members of the birnavirus family. Although the virus was found to belong to the family
Birnaviridae
, biochemical and sequence information for ESV differed from that of DXV, the representative species of the genus
Entomobirnavirus
. Thus, significant differences underscore the uniqueness of this infectious agent, and its relationship to the coinfecting virus is discussed.
Limited Effects of Bile Acids and Small Heterodimer Partner on Hepatitis B Virus Biosynthesis
In Vivo
Authors: Reese Vanessa C. , Moore David D. , McLachlan Alan
Published: December 2011

Multiple nuclear receptors, including hepatocyte nuclear factor 4α (HNF4α), retinoid X receptor α (RXRα) plus peroxisome proliferator-activated receptor α (PPARα), RXRα plus farnesoid X receptor α (FXRα), liver receptor homolog 1 (LRH1), and estrogen-related receptors (ERRs), have been shown to support efficient viral biosynthesis in nonhepatoma cells in the absence of additional liver-enriched transcription factors. Although HNF4α has been shown to be critical for the developmental expression of hepatitis B virus (HBV) biosynthesis in the liver, the relative importance of the various nuclear receptors capable of supporting viral transcription and replication in the adult
in vivo
has not been clearly established. To investigate the role of the nuclear receptor FXR and the corepressor small heterodimer partner (SHP) in viral biosynthesis
in vivo
, SHP-expressing and SHP-null HBV transgenic mice were fed a bile acid-supplemented diet. The increased FXR activity and SHP expression levels resulting from bile acid treatment did not greatly modulate HBV RNA and DNA synthesis. Therefore, FXR and SHP appear to play a limited role in modulating HBV biosynthesis, suggesting that alternative nuclear receptors are more critical determinants of viral transcription in the HBV transgenic mouse model of chronic viral infection. These observations suggest that hepatic bile acid levels or therapeutic agents targeting FXR may not greatly modulate viremia during natural infection.
Emergence and Dissemination of a Swine H3N2 Reassortant Influenza Virus with 2009 Pandemic H1N1 Genes in Pigs in China
Authors: Fan Xiaohui , Zhu Huachen , Zhou Boping , Smith David K. , Chen Xinchun , Lam Tommy T.-Y. , Poon Leo L. M. , Peiris Malik , Guan Yi
Published: December 2011

The 2009 pandemic influenza virus (pdm/09) has been frequently introduced to pigs and has reassorted with other swine viruses. Recently, H3N2 reassortants with pdm/09-like internal genes were isolated in Guangxi and Hong Kong, China. Genetic and epidemiological analyses suggest that these viruses have circulated in swine for some time. This is the first evidence that swine reassortant viruses with pdm/09-like genes may have become established in the field, altering the landscape of human and swine influenza.