bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting the speech reception threshold of cochlear implant listeners using an envelope-correlation based measure
Authors: Yousefian Nima , Loizou Philipos C.
Published: November 2012

A modulation-based index is proposed for predicting speech intelligibility by cochlear implant (CI) listeners. The input to the proposed index are speech envelopes extracted using the individual CI user's daily strategy, and as such, this approach incorporates information about the number of active electrodes, shape of the compression function and electrical dynamic range. High correlation (r = 0.96) was achieved with the proposed index when evaluated with speech-reception thresholds (SRTs) obtained by CI users in steady and speech-masker conditions. This outcome suggests that the information contained in electrodograms seems to be sufficient for reliably predicting CI user's performance in noise. The proposed index can be used by clinicians to optimize the selection of fitting parameters of individual CI users for better performance in noise.
Non-contact acoustic trapping in circular cross-section glass capillaries: A numerical study
Authors: Gralinski Ian , Alan Tuncay , Neild Adrian
Published: November 2012

Ultrasonic particle manipulation has many applications in microfluidic systems. Such manipulation is achievable by establishing an ultrasonic standing wave in fluid filled micromachined chambers. In this work, the focus is on analyzing the trapping potential of water filled capillary tubes actuated ultrasonically. The curved walls necessitate the use of a finite element modeling approach. Multiple arrangements of the piezoelectric transducers were studied along with the effects of changing the capillary and piezoelectric transducer thicknesses. Additionally, different modes of driving the piezoelectric transducers were investigated. It was found that positioning four piezoelectric transducers equally spaced around the capillary tube provided the best force potential field for trapping polystyrene spheres in the center of the capillary.
Short-term acoustic forecasting via artificial neural networks for neonatal intensive care units
Authors: Young Jason , Macke Christopher J. , Tsoukalas Lefteri H.
Published: November 2012

Noise levels in hospitals, especially neonatal intensive care units (NICUs), have become of great concern for hospital designers. This paper details an artificial neural network (ANN) approach to forecasting the sound loads in NICUs. The ANN is used to learn the relationship between past, present, and future noise levels. By training the ANN with data specific to the location and device used to measure the sound, the ANN is able to produce reasonable predictions of noise levels in the NICU. Best case results show average absolute errors of 5.06 ± 4.04 % when used to predict the noise levels one hour ahead, which correspond to 2.53 dBA ± 2.02 dBA. The ANN has the tendency to overpredict during periods of stability and underpredict during large transients. This forecasting algorithm could be of use in any application where prediction and prevention of harmful noise levels are of the utmost concern.
Disentangling preference ratings of concert hall acoustics using subjective sensory profiles
Authors: Lokki Tapio , Pätynen Jukka , Kuusinen Antti , Tervo Sakari
Published: November 2012

Subjective evaluation of acoustics was studied by recording nine concert halls with a simulated symphony orchestra on a seat 12 m from the orchestra. The recorded music was spatially reproduced for subjective listening tests and individual vocabulary profiling. In addition, the preferences of the assessors and objective parameters were gathered. The results show that concert halls were discriminated using perceptual characteristics, such as Envelopment/Loudness, Reverberance, Bassiness, Proximity, Definition, and Clarity. With these perceptual dimensions the preference ratings can be explained. Seventeen assessors were divided into two groups based on their preferences. The first group preferred concert halls with relatively intimate sound, in which it is quite easy to hear individual instruments and melody lines. In contrast, the second group preferred a louder and more reverberant sound with good envelopment and strong bass. Even though all halls were recorded exactly at the same distance, the preference is best explained with subjective Proximity and with Bassiness, Envelopment, and Loudness to some extent. Neither the preferences nor the subjective ratings could be fully explained by objective parameters (ISO3382-1:2009), although some correlations were found.
Broadband sparse-array blind deconvolution using frequency-difference beamforming
Authors: Abadi Shima H. , Song H. C. , Dowling David R.
Published: November 2012

Synthetic time reversal (STR) is a technique for blind deconvolution of receiving-array recordings of sound from an unknown source in an unknown multipath environment. It relies on generic features of multipath sound propagation. In prior studies, the pivotal ingredient for STR, an estimate of the source-signal's phase (as a function of frequency ω), was generated from conventional beamforming of the received-signal Fourier transforms, Pj(ω), 1 ≤ j ≤ N, where N is the number of array elements. This paper describes how STR is implemented even when the receiving-array elements are many wavelengths apart and conventional beamforming is inadequate. Here, the source-signal's phase is estimated by beamforming Pj*(ω1)Pj(ω2) at the difference frequency ω2 − ω1. This extension of STR is tested with broadband signal pulses (11–19 kHz) and a vertical 16-element receiving array having a 3.75-m-spacing between elements using simple propagation simulations and measured results from the FAF06 experiment involving 2.2 km of down slope propagation from 46 to 92 m water depth. The cross-correlation coefficient between the source-broadcast and STR-reconstructed-signal waveforms for the simulations and experiments are 98% and 91%–92%, respectively. In addition, frequency-difference beamforming can be used to determine signal-path-arrival angles that conventional beamforming cannot.
In-plane motions of the stapes in human ears
Authors: Lauxmann M. , Eiber A. , Heckeler C. , Ihrle S. , Chatzimichalis M. , Huber A. , Sim J. H.
Published: November 2012

The piston-like (translation normal to the footplate) and rocking-like (rotation along the long and short axes of the footplate) are generally accepted as motion components of the human stapes. It has been of issue whether in-plane motions, i.e., transversal movements of the footplate in the oval window, are comparable to these motion components. In order to quantify the in-plane motions the motion at nine points on the medial footplate was measured in five temporal bones with the cochlea drained using a three-dimensional (3D) laser Doppler vibrometer. It was found that the stapes shows in-plane movements up to 19.1 ± 8.7% of the piston-like motion. By considering possible methodological errors, i.e., the effects of the applied reflective glass beads and of alignment of the 3D laser Doppler system, such value was reduced to be about 7.4 ± 3.1%. Further, the in-plane motions became minimal ( ≈ 4.2 ± 1.4% of the piston-like motion) in another plane, which was anatomically within the footplate. That plane was shifted to the lateral direction by 118 μm, which was near the middle of the footplate, and rotated by 4.7° with respect to the medial footplate plane.
In situ source levels of mulloway (Argyrosomus japonicus) calls
Authors: Parsons Miles J. G. , McCauley Robert D. , Mackie Michael C. , Siwabessy Paulus J. , Duncan Alec J.
Published: November 2012

Mulloway (Argyrosomus japonicus) in Mosman Bay, Western Australia produce three call categories associated with spawning behavior. The determination of call source levels and their contribution to overall recorded sound pressure levels is a significant step towards estimating numbers of calling fish within the detection range of a hydrophone. The source levels and ambient noise also provide significant information on the impacts anthropogenic activity may have on the detection of A. japonicus calls. An array of four hydrophones was deployed to record and locate individual fish from call arrival-time differences. Successive A. japonicus calls produced samples at various ranges between 1 and 100 m from one of the array hydrophones. The three-dimensional localization of calls, together with removal of ambient noise, allowed the determination of source levels for each call category using observed trends in propagation losses and interference. Mean source levels (at 1 m from the hydrophone) of the three call categories were calculated as 163 ± 16 dB re 1 μPa for Category 1 calls (short call of 2–5 pulses); 172 ± 4 dB re 1 μPa for Category 2 calls (long calls of 11–32 pulses); and 157 ± 5 dB re 1 μPa for Category 3 calls (series of successive calls of 1–4 pulses, increasing in call rate).
Brown meagre vocalization rate increases during repetitive boat noise exposures: A possible case of vocal compensation
Authors: Picciulin Marta , Sebastianutto Linda , Codarin Antonio , Calcagno Giuliana , Ferrero Enrico A.
Published: November 2012

This study investigated whether or not boat noise causes variations in brown meagre (Sciaena umbra) vocalizations recorded in a nearshore Mediterranean marine reserve. Six nocturnal experimental sessions were carried out from June to September 2009. In each of them, a recreational boat passed over vocalizing fish 6 times with 1 boat passage every 10 min. For this purpose three different boats were used in random order: an 8.5-m cabin-cruiser (CC), a 5-m fiberglass boat (FB), and a 7-m inflatable boat (INF). In situ continuous acoustic recordings were collected using a self-standing sonobuoy. Because boat noise levels largely exceeded both background noise and S. umbra vocalizations in the species' hearing frequency range, masking of acoustic communication was assumed. Although no immediate effect was observed during a single boat passage, the S. umbra mean pulse rate increased over multiple boat passages in the experimental condition but not in the control condition, excluding that the observed effect was due to a natural rise in fish vocalizations. The observed vocal enhancement may result either from an increased density of callers or from an increased number of pulses/sounds produced by already acoustically active individuals, as a form of vocal compensation. These two explanations are discussed.
A prediction of the minke whale (Balaenoptera acutorostrata) middle-ear transfer function
Authors: Tubelli Andrew A. , Zosuls Aleks , Ketten Darlene R. , Yamato Maya , Mountain David C.
Published: November 2012

The lack of baleen whale (Cetacea Mysticeti) audiograms impedes the assessment of the impacts of anthropogenic noise on these animals. Estimates of audiograms, which are difficult to obtain behaviorally or electrophysiologically for baleen whales, can be made by simulating the audiogram as a series of components representing the outer, middle, and inner ear (Rosowski, 1991; Ruggero and Temchin, 2002). The middle-ear portion of the system can be represented by the middle-ear transfer function (METF), a measure of the transmission of acoustic energy from the external ear to the cochlea. An anatomically accurate finite element model of the minke whale (Balaenoptera acutorostrata) middle ear was developed to predict the METF for a mysticete species. The elastic moduli of the auditory ossicles were measured by using nanoindentation. Other mechanical properties were estimated from experimental stiffness measurements or from published values. The METF predicted a best frequency range between approximately 30 Hz and 7.5 kHz or between 100 Hz and 25 kHz depending on stimulation location. Parametric analysis found that the most sensitive parameters are the elastic moduli of the glove finger and joints and the Rayleigh damping stiffness coefficient β. The predicted hearing range matches well with the vocalization range.
Effects of encapsulation damping on the excitation threshold for subharmonic generation from contrast microbubbles
Authors: Katiyar Amit , Sarkar Kausik
Published: November 2012

A recent study [Katiyar and Sarkar (2011). J. Acoust. Soc. Am. 130, 3137–3147] showed that in contrast to the analytical result for free bubbles, the minimum threshold for subharmonic generation for contrast microbubbles does not necessarily occur at twice the resonance frequency. Here increased damping—either due to the small radius or the encapsulation—is shown to shift the minimum threshold away from twice the resonance frequency. Free bubbles as well as four models of the contrast agent encapsulation are investigated varying the surface dilatational viscosity. Encapsulation properties are determined using measured attenuation data for a commercial contrast agent. For sufficiently small damping, models predict two minima for the threshold curve—one at twice the resonance frequency being lower than the other at resonance frequency—in accord with the classical analytical result. However, increased damping damps the bubble response more at twice the resonance than at resonance, leading to a flattening of the threshold curve and a gradual shift of the absolute minimum from twice the resonance frequency toward the resonance frequency. The deviation from the classical result stems from the fact that the perturbation analysis employed to obtain it assumes small damping, not always applicable for contrast microbubbles.
Understanding the structure of humpback whale songs (L)
Authors: Mercado Eduardo , Handel Stephen
Published: November 2012

Structured sound sequences produced by humpback whales are described in the literature as hierarchically organized songs. Despite the prevalence of such descriptions, there is no direct evidence that humpback songs are hierarchically structured. It is suggested here that songs may instead be heterarchically structured, in which case traditional approaches to analyzing songs may obscure their organizational and acoustical features. An alternative framework for characterizing patterns within songs is presented, derived from models of humpback whale sound production, that characterizes rhythmic and sequential regularities in the sound sequences produced by singing whales in terms of interacting cycles of breathing and internal air recirculation.
Moments of click-evoked otoacoustic emissions in human ears: Group delay and spread, instantaneous frequency and bandwidth
Authors: Keefe Douglas H.
Published: November 2012

A click-evoked otoacoustic emission (CEOAE) has group delay and spread as first- and second-order temporal moments varying over frequency, and instantaneous frequency and bandwidth as first- and second-order spectral moments varying over time. Energy-smoothed moments were calculated from a CEOAE database over 0.5–15 kHz bandwidth and 0.25–20 ms duration. Group delay and instantaneous frequency were calculated without phase unwrapping using a coherence synchrony measure that accurately classified ears with hearing loss. CEOAE moment measurements were repeatable in individual ears. Group delays were similar for CEOAEs and stimulus-frequency OAEs. Group spread is a frequency-specific measure of temporal spread in an emission, related to spatial spread across tonotopic generation sites along the cochlea. In normal ears, group delay and spread increased with frequency and decreased with level. A direct measure of cochlear tuning above 4 kHz was analyzed using instantaneous frequency and bandwidth. Synchronized spontaneous OAEs were present in most ears below 4 kHz, and confounded interpretation of moments. In ears with sensorineural hearing loss, group delay and spread varied with audiometric classification and amount of hearing loss; group delay differed between older males and females. CEOAE moments reveal clinically relevant information on cochlear tuning in ears with normal and impaired hearing.
Bateman in Nature: Predation on Offspring Reduces the Potential for Sexual Selection
Authors: Byers John , Dunn Stacey
Published: November 2012

Sexual Versus Natural Selection

In a 1948 experiment with
Drosophila
, Angus Bateman showed that sexual selection is strongest in males (versus females) because the number of mates they obtain is correlated with the number of offspring they produce. This relationship between mate number and offspring number has since become known as the Bateman slope, but there has been much debate concerning whether such a relationship can be expected in nature. Using a 30-year data set collected from a closed population of pronghorn antelope in Montana,
Byers and Dunn
(p.
802
; see the Perspective by

Wade

) show that the relationship between mate number and offspring number indeed provides an opportunity for strong sexual selection in this polygynous and dimorphic species—however, environmental effects can make such selection null. In years when coyote predation on newborn fawns was high, sexual selection could not operate and reproductive success was instead determined by natural selection.
Comment on “Glacial Survival of Boreal Trees in Northern Scandinavia”
Authors: Birks Hilary H. , Giesecke Thomas , Hewitt Godfrey M. , Tzedakis Polychronis C. , Bakke Jostein , Birks H. John B.
Published: November 2012

Parducci
et al
. (Reports, 2 March 2012, p. 1083) fail to present convincing evidence for glacial survival of
Pinus
and
Picea
in northern Scandinavia. Their methodology does not exclude contamination. Additionally, they should consider the lack of suitable habitats, the apparent extinction of both taxa after deglacial warming, and alternative hypotheses for the distribution of the
Picea
genetic marker haplotype A.
Polarity-Switching Top Coats Enable Orientation of Sub–10-nm Block Copolymer Domains
Authors: Bates Christopher M. , Seshimo Takehiro , Maher Michael J. , Durand William J. , Cushen Julia D. , Dean Leon M. , Blachut Gregory , Ellison Christopher J. , Willson C. Grant
Published: November 2012

Thermally Transforming Thin Films

Nanoscale features can be created by the phase separation that occurs in block copolymers that join together polymer segments with different wetting properties. For applications such as lithography, it is useful to generate small features and to orient them through simple processing steps. Top-layer coatings should be able to help drive alignment, but it is difficult to coat a layer that also has strong enough interactions to influence assembly.

Bates
et al.

(p.
775
) developed a water-soluble polymer that can top-coat lamellaforming block copolymers and that transforms during thermal annealing into a neutral wetting layer that helps drive the formation of vertically oriented lamellae.
Lifting Reality Off

Measurement
by Paul Lockhart

Harvard University Press, Cambridge, MA, 2012. 415 pp. $29.95, £20, €27. ISBN 9780674057555.
Authors: Finegold Brie
Published: November 2012

Lockhart exposes readers to the beauty and excitement of math as it feels to him.
Constraints on Sexual Selection
Authors: Wade Michael J.
Published: November 2012

Sexual selection in pronghorns is determined both by variance in mate numbers among males and by viability of the young.
Picturing Nature and Empire
Visible Empire
Botanical Expeditions and Visual Culture in the Hispanic Enlightenment

by Daniela Bleichmar

University of Chicago Press, Chicago, 2012. 298 pp. $55, £35.50. ISBN 9780226058535.
Authors: Smith Pamela H.
Published: November 2012

Bleichmar discusses the importance of some 12,000 botanical illustrations that flowed from explorations of the Spanish empire in the half century after 1759.
Did Pulses of Climate Change Drive the Rise and Fall of the Maya?
Authors: Pringle Heather
Published: November 2012

An international research team has produced the best climate record yet of Maya times: a subannual reconstruction of rainfall in the Maya heartland that extends back 2000 years.
Listeria monocytogenes-Derived Listeriolysin O Has Pathogen-Associated Molecular Pattern-Like Properties Independent of Its Hemolytic Ability
Authors: Wallecha Anu , Wood Laurence , Pan Zhen-Kun , Maciag Paulo C. , Shahabi Vafa , Paterson Yvonne
Published: November 2012

There is a constant need for improved adjuvants to augment the induction of immune responses against tumor-associated antigens (TAA) during immunotherapy. Previous studies have established that listeriolysin O (LLO), a cholesterol-dependent cytolysin derived from
Listeria monocytogenes
, exhibits multifaceted effects to boost the stimulation of immune responses to a variety of antigens. However, the direct ability of LLO as an adjuvant and whether it acts as a pathogen-associated molecular pattern (PAMP) have not been demonstrated. In this paper, we show that a detoxified, nonhemolytic form of LLO (dtLLO) is an effective adjuvant in tumor immunotherapy and may activate innate and cellular immune responses by acting as a PAMP. Our investigation of the adjuvant activity demonstrates that dtLLO, either fused to or administered as a mixture with a human papillomavirus type 16 (HPV-16) E7 recombinant protein, can augment antitumor immune responses and facilitate tumor eradication. Further mechanistic studies using bone marrow-derived dendritic cells suggest that dtLLO acts as a PAMP by stimulating production of proinflammatory cytokines and inducing maturation of antigen-presenting cells (APC). We propose that dtLLO is an effective adjuvant for tumor immunotherapy, and likely for other therapeutic settings.
Public Health Value of Next-Generation DNA Sequencing of Enterohemorrhagic Escherichia coli Isolates from an Outbreak
Authors: Underwood Anthony P. , Dallman Tim , Thomson Nicholas R. , Williams Michaela , Harker Katy , Perry Neil , Adak Bob , Willshaw Geraldine , Cheasty Tom , Green Jonathan , Dougan Gordon , Parkhill Julian , Wain John
Published: November 2012

In 2009, an outbreak of enterohemorrhagic
Escherichia coli
(EHEC) on an open farm infected 93 persons, and approximately 22% of these individuals developed hemolytic-uremic syndrome (HUS). Genome sequencing was used to investigate outbreak-derived animal and human EHEC isolates. Phylogeny based on the whole-genome sequence was used to place outbreak isolates in the context of the overall
E. coli
species and the O157:H7 sequence type 11 (ST11) subgroup. Four informative single nucleotide polymorphisms (SNPs) were identified and used to design an assay to type 122 other outbreak isolates. The SNP phylogeny demonstrated that the outbreak strain was from a lineage distinct from previously reported O157:H7 ST11 EHEC and was not a member of the hypervirulent clade 8. The strain harbored determinants for two Stx2 verotoxins and other putative virulence factors. When linked to the epidemiological information, the sequence data indicate that gross contamination of a single outbreak strain occurred across the farm prior to the first clinical report of HUS. The most likely explanation for these results is that a single successful strain of EHEC spread from a single introduction through the farm by clonal expansion and that contamination of the environment (including the possible colonization of several animals) led ultimately to human cases.
Comparative Drug Resistance of Mycobacterium abscessus and M. chelonae Isolates from Patients with and without Cystic Fibrosis in the United Kingdom
Authors: Broda Agnieszka , Jebbari Heather , Beaton Kate , Mitchell Sarah , Drobniewski Francis
Published: November 2012

The isolation of rapidly growing mycobacteria (RGM), particularly
Mycobacterium abscessus
, from individuals with cystic fibrosis (CF) is associated with poor clinical outcome due to broad drug resistance and the difficulty of eradicating the organisms. Susceptibility testing is recommended to guide therapy. A disc diffusion method is used in the United Kingdom, whereas in the United States, the CLSI (Clinical and Laboratory Standards Institute) recommends the broth dilution method. The purpose of this study was to investigate whether the two methods produced comparable drug resistance profiles and to test the hypotheses that the disc diffusion method overscores resistance and that isolates of
M. abscessus
/
M. chelonae
from CF patients are more likely than those from non-CF patients to show drug resistance, as a result of CF patients' greater exposure to antibiotic therapy. A total of 82 isolates (58
M. abscessus
and 24
M. chelonae
isolates) were tested blindly against 15 antimicrobials by broth dilution and the disc diffusion method. Isolates tested by the broth microdilution showed high levels of resistance; susceptibility to amikacin, clarithromycin, tobramycin (only in
M. chelonae
), and cefoxitin (only in
M. abscessus
) was shown. Tigecycline results varied widely depending on which breakpoint was used. Agreement between methods for a few drugs (e.g., cefoxitin and amikacin) was poor. Although there were drug resistance differences between CF and non-CF isolates, these did not reach statistical significance. The CLSI method provided more robust breakpoints, standardization, and reproducibility. An analysis of the implementation of the CLSI method demonstrated ease of use and similar drug resistance findings for the two species.
Impact of Strain Typing Methods on Assessment of Relationship between Paired Nares and Wound Isolates of Methicillin-Resistant Staphylococcus aureus
Authors: Clarridge Jill E. , Harrington Amanda T. , Roberts Marilyn C. , Soge Olusegun O. , Maquelin Kees
Published: November 2012

The anterior nares are the site of choice for the Veterans Administration methicillin-resistant
Staphylococcus aureus
(MRSA) surveillance program; however, a correlation between nares colonization and concomitant wound infections has not been well established. The purpose of this study was 3-fold: to determine the relatedness of MRSA isolates from 40 paired wound and nares specimens by four different strain typing methods, to determine concordance of typing methods, and to establish a baseline of MRSA types at this medical center. Isolates were typed by repetitive PCR (rep-PCR) (DiversiLab System; DL) and SpectraCell Raman analysis (SCRA) (commercially available methods that can be performed within a clinical lab), pulsed-field gel electrophoresis (PFGE), and an antibiotic susceptibility profile (AB). Whole-genome optical mapping (WGM) (OpGen, Inc.) was performed on selected isolates. All methods agreed that 26 pairs were indistinguishable and four pairs were different. Discrepant results were as follows: 4 where only SCRA was discordant, 3 where only AB was discordant, 2 where both DL and AB were discordant, and 1 where both DL and SCRA were discordant. All WGM agreed with PFGE. After discrepancy resolution, 80% of the pairs were indistinguishable and 20% were different. A total of 56% of nares results were nonpredictive if negative nares and positive wound cultures are included. Methods agreed 85 to 93% of the time; however, congruence of isolates to a clade was lower. Baseline analysis of types showed that 15 pairs were unique to single patients (30 strains, 38%; 47% of the matching pairs). Twenty-five strains (30%) represented a single clade identical by PFGE, SCRA, and DL, decreasing specificity. Typing method and institutional type frequency are important in assessing MRSA strain relatedness.
Failure of PCR-Based IS
6110
Analysis To Detect Vertebral Spondylodiscitis Caused by Mycobacterium bovis
Authors: Steensels Deborah , Fauville-Dufaux Maryse , Boie Johan , De Beenhouwer Hans
Published: November 2012

Mycobacterium bovis
is responsible for a zoonosis originating in cattle. We report a case of a man with vertebral spondylodiscitis caused by
Mycobacterium bovis
. Diagnosis was complicated because of the lack of IS
6110
. These strains are rare, but microbiologists should be aware of their existence.
Molecular Characterization of Methicillin-Sensitive Staphylococcus aureus Isolates from Bacteremic Patients in a Norwegian University Hospital
Authors: Blomfeldt Anita , Aamot Hege Vangstein , Eskesen Arne N. , Müller Fredrik , Monecke Stefan
Published: November 2012

Staphylococcus aureus
bacteremia is common in both nosocomial and community settings, and the pathogenicity of the microbe depends upon a large repertoire of virulence factors.
S. aureus
bacteremia isolates (
n
= 126) were characterized using DNA microarrays. Clonal complexes 5, 8, 15, 30, and 45 accounted for 74.6% of the isolates. We identified geographical differences in dominating clones and toxin gene profiles. One isolate was methicillin resistant. Potential associations between age and genotype were detected.
Quantitative Fecal Lactoferrin in Toxin-Positive and Toxin-Negative Clostridium difficile Specimens
Authors: LaSala P. Rocco , Ekhmimi Tariq , Hill A. Kate , Farooqi Imran , Perrotta Peter L.
Published: November 2012

Quantitative fecal lactoferrin was measured in 112 patients tested for toxigenic
Clostridium difficile
using glutamate dehydrogenase (GDH) and toxin immunoassays combined with
tcdB
PCR. Lactoferrin levels were higher in the GDH-positive/toxin-positive group (79 μg/ml) than in the GDH-positive/toxin-negative/PCR-positive (21 μg/ml) and the GDH-negative groups (13 μg/ml). Differences in fecal lactoferrin levels suggest variable presence or severity of
C. difficile
infection among toxin-positive and toxin-negative patients.
Pathogenic Potential of Bacillus cereus Strains as Revealed by Phenotypic Analysis
Authors: Kamar Rita , Gohar Michel , Jéhanno Isabelle , Réjasse Agnès , Kallassy Mireille , Lereclus Didier , Sanchis Vincent , Ramarao Nalini
Published: November 2012

The
Bacillus cereus
pathogenic spectrum ranges from strains used as probiotics to human-lethal strains. However, prediction of the pathogenic potential of a strain remains difficult. Here, we show that food poisoning and clinical strains can be differentiated from harmless strains on the basis of host colonization phenotypes.
Self-Collection of Foam Nasal Swabs for Respiratory Virus Detection by PCR among Immunocompetent Subjects and Hematopoietic Cell Transplant Recipients
Authors: Campbell Angela P. , Kuypers Jane , Englund Janet A. , Guthrie Katherine A. , Corey Lawrence , Boeckh Michael
Published: November 2012

Self-collected foam nasal swabs (NS) obtained after instillation of saline spray were compared with nasal washes from immunocompetent subjects during 146 upper respiratory infections (URIs); the sensitivities for reverse transcription (RT)-PCR respiratory virus detection were 95% and 88%, respectively (
P
= 0.06). The sensitivities from NS collected with and without saline spray during 142 URIs from immunocompetent subjects were 96% and 86% (
P
= 0.004), respectively, and those from 140 URI samples from hematopoietic cell transplantation recipients were 88% and 85% (
P
= 0.56), respectively.
Carbapenem Disks on MacConkey Agar in Screening Methods for Detection of Carbapenem-Resistant Gram-Negative Rods in Stools
Authors: Blackburn Julie , Tsimiklis Catherine , Lavergne Valéry , Pilotte Josée , Grenier Sophie , Gilbert Andrée , Lefebvre Brigitte , Domingo Marc-Christian , Tremblay Cécile , Bourgault Anne-Marie
Published: November 2012

Direct plating of simulated stool specimens on MacConkey agar (MCA) with 10-μg ertapenem, meropenem, and imipenem disks allowed the establishment of optimal zone diameters for the screening of carbapenem-resistant Gram-negative rods (CRGNR) of ≤24 mm (ertapenem), ≤34 mm (meropenem), and ≤32 mm (imipenem).
Repeated Exposure to Trace Amounts of Woodchuck Hepadnavirus Induces Molecularly Evident Infection and Virus-Specific T Cell Response in the Absence of Serological Infection Markers and Hepatitis
Authors: Gujar Shashi A. , Mulrooney-Cousins Patricia M. , Michalak Tomasz I.
Published: November 2012

Exposure to multiple small doses of hepatitis B virus (HBV) is a frequent occurrence in high-risk groups, including close relatives of infected individuals, primary care givers, and intravenous drug users. It remains uncertain whether such repeated contact may culminate in a symptomatic infection coinciding with hepatitis in individuals not immunoprotected. In this study, we evaluated consequences of multiple exposures to small, liver-nonpathogenic amounts of infectious hepadnavirus in the woodchuck model of hepatitis B. Virus-naïve animals were intravenously injected with 6 weekly doses of 110 DNase digestion-protected virions of woodchuck hepatitis virus (WHV), injected again with 6 weekly 110-virion doses after 7.5 months, and then challenged or not with a liver-pathogenic dose of 1.1 × 10
6
virions of the same inoculum. The data revealed that two rounds of such repeated exposure did not result in serologically evident infection or hepatitis. However, a low-level WHV DNA-positive infection accompanied by a WHV-specific T cell response in the absence of antiviral antibody reactivity was established. The kinetics of the virus-specific and mitogen-induced (generalized) T cell responses and the inability to induce immunoprotection against challenge with a large, liver-pathogenic virus dose were closely comparable to those previously reported for occult infection initiated by a single liver-nonpathogenic dose of WHV. Thus, repeated exposures to small quantities of hepadnavirus induce molecularly evident but serologically silent infection that does not culminate in hepatitis or generate immune protection. The findings imply that the HBV-specific T cell response encountered in the absence of serological markers of infection likely reflects ongoing occult infection.
Viral Genome Methylation Differentially Affects the Ability of BZLF1 versus BRLF1 To Activate Epstein-Barr Virus Lytic Gene Expression and Viral Replication
Authors: Wille Coral K. , Nawandar Dhananjay M. , Panfil Amanda R. , Ko Michelle M. , Hagemeier Stacy R. , Kenney Shannon C.
Published: November 2012

The Epstein-Barr virus (EBV) immediate-early proteins BZLF1 and BRLF1 can both induce lytic EBV reactivation when overexpressed in latently infected cells. Although EBV genome methylation is required for BZLF1-mediated activation of lytic gene expression, the effect of viral genome methylation on BRLF1-mediated viral reactivation has not been well studied. Here, we have compared the effect of viral DNA methylation on BZLF1- versus BRLF1-mediated activation of lytic EBV gene transcription and viral genome replication. We show that most early lytic viral promoters are preferentially activated by BZLF1 in the methylated form, while methylation decreases the ability of BRLF1 to activate most early lytic promoters, as well as the BLRF2 late viral promoter. Moreover, methylation of bacmid constructs containing the EBV genome enhances BZLF1-mediated, but decreases BRLF1-mediated, early lytic gene expression. Methylation of viral promoter DNA does not affect BRLF1 binding to a variety of different CpG-containing BRLF1 binding motifs (RREs)
in vitro
or
in vivo
. However, BRLF1 preferentially induces H3K9 histone acetylation of unmethylated promoters
in vivo
. The methylated and unmethylated forms of an oriLyt-containing plasmid replicate with similar efficiency when transfected into EBV-positive cells that express the essential viral replication proteins in
trans
. Most importantly, we demonstrate that lytic viral gene expression and replication can be induced by BRLF1, but not BZLF1, expression in an EBV-positive telomerase-immortalized epithelial cell line (NOKs-Akata) in which lytic viral gene promoters remain largely unmethylated. These results suggest that the unmethylated form of the EBV genome can undergo viral reactivation and replication in a BRLF1-dependent manner.
The Adenoviral Oncogene E1A-13S Interacts with a Specific Isoform of the Tumor Suppressor PML To Enhance Viral Transcription
Authors: Berscheminski Julia , Groitl Peter , Dobner Thomas , Wimmer Peter , Schreiner Sabrina
Published: November 2012

PML nuclear bodies (PML NBs), also called ND10, are matrix-bound nuclear structures that have been implicated in a variety of functions, including DNA repair, transcriptional regulation, protein degradation, and tumor suppression. These domains are also known for their potential to mediate an intracellular defense mechanism against many virus types. This is likely why they are targeted and subsequently manipulated by numerous viral proteins. Paradoxically, the genomes of various DNA viruses become associated with PML NBs, and initial sites of viral transcription/replication centers are often juxtaposed to these domains. The question is why viruses start their transcription and replication next to their supposed antagonists. Here, we report that PML NBs are targeted by the adenoviral (Ad) transactivator protein E1A-13S. Alternatively spliced E1A isoforms (E1A-12S and E1A-13S) are the first proteins expressed upon Ad infection. E1A-13S is essential for activating viral transcription in the early phase of infection. Coimmunoprecipitation assays showed that E1A-13S preferentially interacts with only one (PML-II) of at least six nuclear human PML isoforms. Deletion mapping located the interaction site within E1A conserved region 3 (CR3), which was previously described as the transcription factor binding region of E1A-13S. Indeed, cooperation with PML-II enhanced E1A-mediated transcriptional activation, while deleting the SUMO-interacting motif (SIM) of PML proved even more effective. Our results suggest that in contrast to PML NB-associated antiviral defense, PML-II may help transactivate viral gene expression and therefore play a novel role in activating Ad transcription during the early viral life cycle.
Visualizing a Complete Siphoviridae Member by Single-Particle Electron Microscopy: the Structure of Lactococcal Phage TP901-1
Authors: Bebeacua Cecilia , Lai Livia , Vegge Christina Skovgaard , Brøndsted Lone , van Heel Marin , Veesler David , Cambillau Christian
Published: November 2012

Tailed phages are genome delivery machines exhibiting unequaled efficiency acquired over more than 3 billion years of evolution. Siphophages from the P335 and 936 families infect the Gram-positive bacterium
Lactococcus lactis
using receptor-binding proteins anchored to the host adsorption apparatus (baseplate). Crystallographic and electron microscopy (EM) studies have shed light on the distinct adsorption strategies used by phages of these two families, suggesting that they might also rely on different infection mechanisms. Here, we report electron microscopy reconstructions of the whole phage TP901-1 (P335 species) and propose a composite EM model of this gigantic molecular machine. Our results suggest conservation of structural proteins among tailed phages and add to the growing body of evidence pointing to a common evolutionary origin for these virions. Finally, we propose that host adsorption apparatus architectures have evolved in correlation with the nature of the receptors used during infection.
Requirement of the N-Terminal Activation Domain of Herpes Simplex Virus ICP4 for Viral Gene Expression
Authors: Wagner Lauren M. , Bayer Avraham , DeLuca Neal A.
Published: November 2012

ICP4 is the major activator of herpes simplex virus (HSV) transcription. Previous studies have defined several regions of ICP4 that are important for viral gene expression, including a DNA binding domain and transactivation domains that are contained in the C-terminal and N-terminal 520 and 274 amino acids, respectively. Here we show that the N-terminal 210 amino acids of ICP4 are required for interactions with components of TFIID and mediator and, as a consequence, are necessary for the activation of viral genes. A mutant of ICP4 deleted for amino acids 30 to 210, d3-10, was unable to complement an ICP4 null virus at the level of viral replication. This was the result of a severe deficiency in viral gene and protein expression. The absence of viral gene expression coincided with a defect in the recruitment of RNA polymerase II to a representative early promoter (thymidine kinase [TK]). Affinity purification experiments demonstrated that d3-10 ICP4 was not found in complexes with components of TFIID and mediator, suggesting that the defect in RNA polymerase II (Pol II) recruitment was the result of ablated interactions between d3-10 and TFIID and mediator. Complementation assays suggested that the N-terminal and C-terminal regions of ICP4 cooperate to mediate gene expression. The complementation was the result of the formation of more functional heterodimers, which restored the ability of the d3-10-containing molecules to interact with TFIID. Together, these studies suggest that the N terminus contains a true activation domain, mediating interactions with TFIID, mediator, and perhaps other transcription factors, and that the C terminus of the molecule contains activities that augment the functions of the activation domain.
Seasonal change in bone, muscle and fat in professional rugby league players and its relationship to injury: a cohort study
Authors: Georgeson Erin C , Weeks Benjamin K , McLellan Chris , Beck Belinda R
Published: November 2012

Objectives

To examine the anthropometric characteristics of an Australian National Rugby League team and identify the relationship to type and incidence of injuries sustained during a professional season. It was hypothesised that body composition would not change discernibly across a season and that injury would be negatively related to preseason bone and muscle mass.

Design

A repeated measure, prospective, observational, cohort study.

Setting

Griffith University, Gold Coast, Australia.

Participants

37 professional male Australian National Rugby League players, 24.3 (3.8) years of age were recruited for preseason 1 testing, of whom 25 were retested preseason 2.

Primary and secondary outcome measures

Primary outcome measures included biometrics; body composition (bone, muscle and fat mass; dual-energy x-ray absorptiometry; XR800, Norland Medical Systems, Inc); bone geometry and strength (peripheral quantitative CT; XCT 3000, Stratec); calcaneal broadband ultrasound attenuation (BUA; QUS-2, Quidel); diet and physical activity history. Secondary outcome measures included player injuries across a single playing season.

Results

Lean mass decreased progressively throughout the season (pre=81.45(7.76) kg; post=79.89(6.72) kg; p≤0.05), while whole body (WB) bone mineral density (BMD) increased until mid-season (pre=1.235(0.087) g/cm2; mid=1.296(0.093) g/cm2; p≤0.001) then decreased thereafter (post=1.256(0.100); p≤0.001). Start-of-season WB BMD, fat and lean mass, weight and tibial mass measured at the 38% site predicted bone injury incidence, but no other relationship was observed between body composition and injury.

Conclusions

Significant anthropometric changes were observed in players across a professional rugby league season, including an overall loss of muscle and an initial increase, followed by a decrease in bone mass. Strong relationships between anthropometry and incidence of injury were not observed. Long-term tracking of large rugby league cohorts is indicated to obtain more injury data in order to examine anthropometric relationships with greater statistical power.
Deciding when to stop: towards evidence-based deprescribing of drugs in older populations
Authors: Scott Ian A , Gray Leonard C , Martin Jennifer H , Pillans Peter I , Mitchell Charles A
Published: November 2012

Minimising the harm from inappropriate prescribing in older populations is a major urgent concern for modern healthcare systems. In everyday encounters between prescribers and patients, opportunities should be taken to identify patients at high risk of harm from polypharmacy and reappraise their need for specific drugs. Attempts to reconcile life expectancy, comorbidity burden, care goals and patient preferences with the benefits and harms of medications should be made in every patient at significant risk. Drugs identified by this process of reconciliation as conferring little or no benefit and/or excessive risk of harm should be candidates for discontinuation. Evidence supporting a structured approach to drug discontinuation (or deprescribing) is emerging, and while many barriers to deprescribing exist in routine practice, various enabling strategies can help overcome them.
Clinical application of UF-1000i in combination with AX-4280 for the screening test ability of urinary formed elements
Authors: Zhao Feng , Jin Yi , Chen Xiaoyan , Xie Xinyou
Published: November 2012

Aims

To evaluate the screening test ability of UF-1000i combination with AX-4280 for major pathological urinary formed elements and to establish screening rules suitable for our laboratory.

Methods

A total of 2220 cases of urine samples were collected from out-patients and inpatients. The sample tests were finished within 4 h after collection. The results were verified and corroborated with microscopic tests.

Results

In ‘both-negative’ group, the negative predictive values for red blood cell, white blood cell and cast were 99.12%, 99.56% and 100%, respectively, and the false negative rates were 0.87%, 0.44% and 0%, respectively. In ‘both-positive’ group, the positive predictive values for red blood cell, white blood cell and cast were 69.18%, 74.41% and 33.33%, respectively, and the false positive rates were 30.82%, 25.59% and 66.67%, respectively. In ‘U positive/A negative’ group, the positive predictive values for red blood cell, white blood cell and cast were 32.47%, 23.67% and 8.57%, respectively, and the false positive rates were 67.53%, 76.36% and 91.43%, respectively. In ‘U negative/A positive’ group, the positive predictive values for red blood cell, white blood cell and cast were 8.18%, 19.50% and 4.67%, respectively, and the false positive rates were 91.82%, 50.50% and 95.24%, respectively.

Conclusions

When the results of the red blood cell, white blood cell and cast tested by UF-1000i were all negative, and the results of the red blood cell, white blood cell and protein tested by AX-4280 were negative, an automatic report stating ‘normal microscopic appearance’ was generated, and then the microscopic test rate was reduced by 37.6%. However, if any automated parameter measurement was out of the reference range, corroboration by manual microscopy was advisable.
HIV testing for acute medical admissions: evaluation of a pilot study in Leicester, England
Authors: Palfreeman Adrian , Nyatsanza Farai , Farn Helen , McKinnon Graham , Schober Paul , McNally Paul
Published: November 2012

Objectives

The 2008 UK National Guidelines for HIV testing recommended HIV testing should be offered to all general medical admissions aged 16–60 years in high prevalence areas, and that this should be evaluated to ensure this was effective in diagnosing previously undiagnosed HIV.

Methods

HIV testing was introduced as a routine test for all patients admitted to the acute medical admissions unit, comparisons were made between the testing rates before, during and after this intervention.

Results

The pilot was initiated in August 2009. Prior to the pilot the unit was carrying out 15 tests per month. However, when the pilot was introduced 82 tests were being carried out per month with a total of 10 new diagnoses since the start of the pilot. The proportion of patients tested versus those eligible for testing remained low varying between 6% and 22% month by month. 10 patients we found to be HIV positive with a prevalence of approximately 1%, 10 fold higher than the cut off for cost effectiveness used in the guidelines.

Conclusions

Overall the pilot showed that HIV testing could be delivered without the use of extra resources and is acceptable to patients.