bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental and Numerical Investigation of the Aerodynamic Noise Radiated From a Centrifugal Blower
Authors: Chen Jiandong , Sun Beibei , Zhang Jianrun , Xue Fei , Liu Xin
Published: September 2015

Centrifugal blowers are widely used as garden machines, however, the aerodynamic noise generated by these machines cause serious problems. Although many researches focus on the generation mechanism and prediction method of centrifugal fan noise, most of these researches analysis the simplified centrifugal fan models and ignore the diffraction and scattering effect. In this paper, both experimental and numerical methods are carried out to analysis and measure the aerodynamic noise of the centrifugal blower. In order to calculate the flow field, a CFD (Computational Fluid Dynamics) numerical model is established, and the LES (Large Eddy Simulation) model is used to solve the three-dimensional unsteady flow, while the FW-H (Ffows Williams-Hawkings) model is used to calculate the acoustic source. To consider the diffraction and scattering effect, a BEM method is used to predict the sound radiated from the blower. A parallel experiment is carried out to measure the aerodynamic noise in a semi-anechoic room, and the numerical result shows a good agreement with the experiment result. The effect of outlet and inlet ducts on the sound radiation of the centrifugal blower is also investigated in this paper.
Understanding Tire Acoustics Through Computational Fluid Dynamics (CFD) of Grooves With Deforming Walls
Authors: Gautam Prashanta , Chandy Abhilash J.
Published: September 2015

Reducing tire noise has been a topic of increased focus in the recent years in industrial countries in order to decrease road traffic noise. Computational fluid dynamics (CFD) simulations conducted using ANSYS FLUENT are presented here to provide a better understanding of the small-scale noise generation mechanisms due to air-pumping at the tire-road interface. The CFD model employs a large eddy simulation (LES) turbulence modeling approach, where the filtered compressible Navier-Stokes equations are solved for simple groove geometries with a moving bottom wall that represents the deformation due to the tire movement along the road surface. A horizontally moving wall is used to represent the motion of the tire groove in and out of the contact patch while the deformation of the groove is prescribed. Temporal and spatially accurate pressure fluctuations are utilized to determine sound pressure levels and dominant frequencies. In addition to an understanding of noise generation mechanisms in such grooves, the CFD model developed here can potentially provide a series of control parameters that can help optimize the tire performance in terms of tire acoustics.
Experimental Analysis of Vibration and Radiated Sound Power Reduction Using an Array of Acoustic Black Holes
Authors: Feurtado Philip A. , Conlon Stephen C.
Published: September 2015

The Acoustic Black Hole (ABH) has been developed in recent years as an effective, passive, and lightweight method for attenuating bending wave vibrations in beams and plates. The acoustic black hole effect utilizes a local change in the plate or beam thickness to reduce the bending wave speed and increase the transverse vibration amplitude. Attaching a viscoelastic damping layer to the ABH results in effective energy dissipation and vibration reduction. Surface averaged mobility and radiated sound power measurements were performed on an aluminum plate containing an array of 20 two-dimensional ABHs with damping layers and compared to a similar uniform plate. Detailed laser vibrometer scans of an ABH cell were also performed to analyze the vibratory characteristics of the individual ABHs and compared with mode shapes calculated using Finite Elements. The diameter of the damping layer was reduced in successive steps to experimentally demonstrate the effect of damping layer distribution on the ABH performance. The experimental analysis demonstrated the importance of low order ABH modes in reducing the vibration and radiated sound power of plates with embedded ABHs. The results will be useful for designing the low frequency performance of future ABH systems and describing ABH performance in terms of design parameters.
Structural-Acoustic Responses of a Coupled Panel Cavity System Using a Deterministic-Statistical Approach
Authors: Jiao Renqiang , Zhang Jianrun , Xue Fei , Liao Xin , Liu Xin
Published: September 2015

The coupled panel cavity system composed of an acoustic space and a wall surface is a reasonable representation of many engineering applications. A good understanding of the structural-acoustic interaction between the structural vibration and sound pressure response inside the cavity is of critical importance to, for instance, the control of sound fields in car compartments, airplane and ship cabins, etc. Motivated by above, an investigation on the structural-acoustic responses of a coupled panel cavity system is presented. A rectangular acoustic cavity bounded by a flexible panel with elastically restrained edges is examined. In this paper, for the so called “mid-frequency” problem, a hybrid deterministic and statistic approach is employed to overcome the defects in application of pure deterministic or statistical methods. Then the vibration and interior sound pressure response analysis for the panel-cavity system are conducted using this method under external normal concentrated force acting at the flexible plate. Finally, comparisons between the numerical and test results are presented and the relevant frequency ranges for which the hybrid deterministic and statistical approaches work in are discussed for the given structure.
Two- and Three-Dimensional Model for Sound Attenuation by Objects on Propagation
Authors: Li W. , Zheng Z. C. , Zhang J. , Ke G.
Published: September 2015

It is well known that the performance of open field acoustic sensors is affected by complex sound propagation phenomena occurring in outdoor settings, such as ground effects, noise from atmospheric turbulence, refraction by wind and temperature gradients, diffraction over buildings and hills, and acoustic sensors on moving platforms. In addition, the behavior of sound propagation changes at the interface of different media. We have developed a time-domain simulation that enables the numerical simulation of all the mentioned factors. This capability provides information on the effect of sound waves once they reach a sensor or a target. We are implementing this algorithm for 3D, long-distance propagations. The challenge is three-fold: a) efficient parallelization; b) moving frame capability in 3D for long-distance propagation simulation; c) accurately implementing the perfectly match layer (PML) methods to represent the free boundaries.

In this paper, we have selected cylinders as the objects for sound wave to propagate through. Both 2D and 3D simulations were conducted. The results are compared with available measurement data in the literature. The phenomena are discussed in the context of 2D and 3D propagation behaviors.
Atomic layer deposition of molybdenum oxide from (NtBu)2(NMe2)2Mo and O2 plasma
Authors: Vos Martijn F. J. , Macco Bart , Thissen Nick F. W. , Bol Ageeth A. , Kessels W. M. M. (Erwin)
Published: September 2015

Molybdenum oxide (MoOx) films have been deposited by atomic layer deposition using bis(tert-butylimido)-bis(dimethylamido)molybdenum and oxygen plasma, within a temperature range of 50–350 °C. Amorphous film growth was observed between 50 and 200 °C at a growth per cycle (GPC) around 0.80 Å. For deposition temperatures of 250 °C and higher, a transition to polycrystalline growth was observed, accompanied by an increase in GPC up to 1.88 Å. For all deposition temperatures the O/Mo ratio was found to be just below three, indicating the films were slightly substoichiometric with respect to MoO3 and contained oxygen vacancies. The high purity of the films was demonstrated in the absence of detectable C and N contamination in Rutherford backscattering measurements, and a H content varying between 3 and 11 at. % measured with elastic recoil detection. In addition to the chemical composition, the optical properties are reported as well.
Fabrication of a planar light source utilizing monoalkali antimonide photocathodes as emitters
Authors: Jeong Hyo-Soo , Keller Kris , Culkin Brad
Published: September 2015

This paper presents a new concept for a planar light source utilizing Cs3Sb photocathodes as flat electron emitters. The design concept of the devices with a diode structure was that the photocathodes were to be operated in a reflective mode. Commercially available P-22 phosphors were used as a light source of desirable wavelengths. Light emission from the devices was induced by photoemitted electrons, accelerated by an anode electric field that was shielded from the photoemitter surface. The luminescent characteristics of the devices were investigated by measuring the optical parameters as functions of applied anode voltages. The results showed the possibility to produce a more directable and easily controllable stream of light. These make the devices suitable for a variety of planar lighting applications.
Thermal safety of ultrasound‐enhanced ocular drug delivery: A modeling study
Authors: Nabili Marjan , Geist Craig , Zderic Vesna
Published: September 2015

Purpose:

Delivery of sufficient amounts of therapeutic drugs into the eye for treatment of various ocular diseases is often a challenging task. Ultrasound was shown to be effective in enhancing ocular drug delivery in the authors’ previous in vitro and in vivo studies.

Methods:

The study reported here was designed to investigate the safety of ultrasound application and its potential thermal effects in the eye using PZFlex modeling software. The safety limit in this study was set as a temperature increase of no more than 1.5 °C based on regulatory recommendations and previous experimental safety studies. Acoustic and thermal specifications of different human eye tissues were obtained from the published literature. The tissues of particular interest in this modeling safety study were cornea, lens, and the location of optic nerve in the posterior eye. Ultrasound application was modeled at frequencies of 400 kHz–1 MHz, intensities of 0.3–1 W/cm2, and exposure duration of 5 min, which were the parameters used in the authors’ previous drug delivery experiments. The baseline eye temperature was 37 °C.

Results:

The authors’ results showed that the maximal tissue temperatures after 5 min of ultrasound application were 38, 39, 39.5, and 40 °C in the cornea, 39.5, 40, 42, and 43 °C in the center of the lens, and 37.5, 38.5, and 39 °C in the back of the eye (at the optic nerve location) at frequencies of 400, 600, 800 kHz, and 1 MHz, respectively.

Conclusions:

The ocular temperatures reached at higher frequencies were considered unsafe based on current recommendations. At a frequency of 400 kHz and intensity of 0.8 W/cm2 (parameters shown in the authors’ previous in vivo studies to be optimal for ocular drug delivery), the temperature increase was small enough to be considered safe inside different ocular tissues. However, the impact of orbital bone and tissue perfusion should be included in future modeling efforts to determine the safety of this method in the whole orbit especially regarding potential adverse optic nerve heating at the location of the bone.
SPEQTACLE: An automated generalized fuzzy C‐means algorithm for tumor delineation in PET
Authors: Lapuyade‐Lahorgue Jérôme , Visvikis Dimitris , Pradier Olivier , Cheze Le Rest Catherine , Hatt Mathieu
Published: September 2015

Purpose:

Accurate tumor delineation in positron emission tomography (PET) images is crucial in oncology. Although recent methods achieved good results, there is still room for improvement regarding tumors with complex shapes, low signal‐to‐noise ratio, and high levels of uptake heterogeneity.

Methods:

The authors developed and evaluated an original clustering‐based method called spatial positron emission quantification of tumor—Automatic Lp‐norm estimation (SPEQTACLE), based on the fuzzy C‐means (FCM) algorithm with a generalization exploiting a Hilbertian norm to more accurately account for the fuzzy and non‐Gaussian distributions of PET images. An automatic and reproducible estimation scheme of the norm on an image‐by‐image basis was developed. Robustness was assessed by studying the consistency of results obtained on multiple acquisitions of the NEMA phantom on three different scanners with varying acquisition parameters. Accuracy was evaluated using classification errors (CEs) on simulated and clinical images. SPEQTACLE was compared to another FCM implementation, fuzzy local information C‐means (FLICM) and fuzzy locally adaptive Bayesian (FLAB).

Results:

SPEQTACLE demonstrated a level of robustness similar to FLAB (variability of 14% ± 9% vs 14% ± 7%, p = 0.15) and higher than FLICM (45% ± 18%, p < 0.0001), and improved accuracy with lower CE (14% ± 11%) over both FLICM (29% ± 29%) and FLAB (22% ± 20%) on simulated images. Improvement was significant for the more challenging cases with CE of 17% ± 11% for SPEQTACLE vs 28% ± 22% for FLAB (p = 0.009) and 40% ± 35% for FLICM (p < 0.0001). For the clinical cases, SPEQTACLE outperformed FLAB and FLICM (15% ± 6% vs 37% ± 14% and 30% ± 17%, p < 0.004).

Conclusions:

SPEQTACLE benefitted from the fully automatic estimation of the norm on a case‐by‐case basis. This promising approach will be extended to multimodal images and multiclass estimation in future developments.
Automatic detection of large pulmonary solid nodules in thoracic CT images
Authors: Setio Arnaud A. A. , Jacobs Colin , Gelderblom Jaap , van Ginneken Bram
Published: September 2015

Purpose:

Current computer‐aided detection (CAD) systems for pulmonary nodules in computed tomography (CT) scans have a good performance for relatively small nodules, but often fail to detect the much rarer larger nodules, which are more likely to be cancerous. We present a novel CAD system specifically designed to detect solid nodules larger than 10 mm.

Methods:

The proposed detection pipeline is initiated by a three‐dimensional lung segmentation algorithm optimized to include large nodules attached to the pleural wall via morphological processing. An additional preprocessing is used to mask out structures outside the pleural space to ensure that pleural and parenchymal nodules have a similar appearance. Next, nodule candidates are obtained via a multistage process of thresholding and morphological operations, to detect both larger and smaller candidates. After segmenting each candidate, a set of 24 features based on intensity, shape, blobness, and spatial context are computed. A radial basis support vector machine (SVM) classifier was used to classify nodule candidates, and performance was evaluated using ten‐fold cross‐validation on the full publicly available lung image database consortium database.

Results:

The proposed CAD system reaches a sensitivity of 98.3% (234/238) and 94.1% (224/238) large nodules at an average of 4.0 and 1.0 false positives/scan, respectively.

Conclusions:

The authors conclude that the proposed dedicated CAD system for large pulmonary nodules can identify the vast majority of highly suspicious lesions in thoracic CT scans with a small number of false positives.
Determinants of the reliability of ultrasound tomography sound speed estimates as a surrogate for volumetric breast density
Authors: Khodr Zeina G. , Sak Mark A. , Pfeiffer Ruth M. , Duric Nebojsa , Littrup Peter , Bey‐Knight Lisa , Ali Haythem , Vallieres Patricia , Sherman Mark E. , Gierach Gretchen L.
Published: September 2015

Purpose:

High breast density, as measured by mammography, is associated with increased breast cancer risk, but standard methods of assessment have limitations including 2D representation of breast tissue, distortion due to breast compression, and use of ionizing radiation. Ultrasound tomography (UST) is a novel imaging method that averts these limitations and uses sound speed measures rather than x‐ray imaging to estimate breast density. The authors evaluated the reproducibility of measures of speed of sound and changes in this parameter using UST.

Methods:

One experienced and five newly trained raters measured sound speed in serial UST scans for 22 women (two scans per person) to assess inter‐rater reliability. Intrarater reliability was assessed for four raters. A random effects model was used to calculate the percent variation in sound speed and change in sound speed attributable to subject, scan, rater, and repeat reads. The authors estimated the intraclass correlation coefficients (ICCs) for these measures based on data from the authors’ experienced rater.

Results:

Median (range) time between baseline and follow‐up UST scans was five (1–13) months. Contributions of factors to sound speed variance were differences between subjects (86.0%), baseline versus follow‐up scans (7.5%), inter‐rater evaluations (1.1%), and intrarater reproducibility (∼0%). When evaluating change in sound speed between scans, 2.7% and ∼0% of variation were attributed to inter‐ and intrarater variation, respectively. For the experienced rater's repeat reads, agreement for sound speed was excellent (ICC = 93.4%) and for change in sound speed substantial (ICC = 70.4%), indicating very good reproducibility of these measures.

Conclusions:

UST provided highly reproducible sound speed measurements, which reflect breast density, suggesting that UST has utility in sensitively assessing change in density.
Sustained Improvements in Dynamic Balance and Landing Mechanics After a 6-Week Neuromuscular Training Program in College Women’s Basketball Players
Authors: Pfile Kate R. , Gribble Phillip A. , Buskirk Gretchen E. , Meserth Sara M. , Pietrosimone Brian G.
Published: September 2015

Context:

Epidemiological data demonstrate the need for lower-extremity injury-prevention training. Neuromuscularcontrol (NMC) programs are immediately effective at minimizing lower-extremity injury risk and improving sport-related performance measures. Research investigating lasting effects after an injury-prevention program is limited.

Objective:

To determine whether dynamic balance, landing mechanics, and hamstring and quadriceps strength could be improved after a 6-wk NMC intervention and maintained for a season.

Design:

Prospective case series.

Setting:

Controlled laboratory.

Participants:

11 Division I women’s basketball players (age 19.40 ± 1.35 y, height 178.05 ± 7.52 cm, mass 72.86 ± 10.70 kg).

Interventions:

Subjects underwent testing 3 times, completing the Star Excursion Balance Test (SEBT), Landing Error Scoring System (LESS), and isometric strength testing for the hamstrings and quadriceps muscles. Pretest and posttest 1 occurred immediately before and after the intervention, respectively, and posttest 2 at the end of the competitive season, 9 mo after posttest 1. Subjects participated in eighteen 30-min plyometric and NMC-training sessions over a 6-wk period.

Main Outcome Measures:

The normalized SEBT composite score, normalized peak isometric hamstrings:quadriceps (H:Q) ratio, and the LESS total score.

Results:

The mean composite reach significantly improved over time (F2,10 = 6.96, P = .005) where both posttest scores were significantly higher than pretest (70.41% ± 4.08%) (posttest 1 73.48% ± 4.19%, t10 = –3.11, P = .011) and posttest 2 (74.2% ± 4.77%, t10 = –3.78, P = .004). LESS scores significantly improved over time (F2,10 = 6.29, P = .009). The pretest LESS score (7.30 ± 3.40) was higher than posttest 1 (4.9 ± 1.20, t10 = 2.71, P = .024) and posttest 2 (5.44 ± 1.83, t10 = 2.58, P = .030). There were no statistically significant differences (P > .05) over time for the H:Q ratio when averaging both legs (F2,10 = 0.83, P = .45).

Conclusions:

A 6-wk NMC program improved landing mechanics and dynamic balance over a 9-mo period in women’s basketball players. NMC adaptations can be retained without an in-season maintenance program.
Dengue virus NS1 triggers endothelial permeability and vascular leak that is prevented by NS1 vaccination
Authors: Beatty P. Robert , Puerta-Guardo Henry , Killingbeck Sarah S. , Glasner Dustin R. , Hopkins Kaycie , Harris Eva
Published: September 2015

Dengue virus NS1 triggers endothelial permeability and vascular leak, and vaccination with NS1 induces a protective antibody response.
Factors Impacting Unbound Vancomycin Concentrations in Different Patient Populations
Authors: Oyaert Matthijs , Spriet Isabel , Allegaert Karel , Smits Anne , Vanstraelen Kim , Peersman Nele , Wauters Joost , Verhaegen Jan , Vermeersch Pieter , Pauwels Steven
Published: September 2015

The unbound drug hypothesis states that only unbound drug concentrations are active and available for clearance, and highly variable results regarding unbound vancomycin fractions have been reported in the literature. We have determined the unbound vancomycin fractions in four different patient groups by a liquid chromatography tandem mass spectrometry (LC-MS/MS) method and identified factors that modulate vancomycin binding. We have further developed and validated a prediction model to estimate unbound vancomycin concentrations. Vancomycin (unbound and total) concentrations were measured in 90 patients in four different hospital wards (hematology [
n
= 33 samples], intensive care unit [ICU] [
n
= 51], orthopedics [
n
= 44], and pediatrics [age range, 6 months to 14 years;
n
= 18]) by a validated LC-MS/MS method. Multiple linear mixed model analysis was performed to identify patient variables that were predictive of unbound vancomycin fractions and concentrations. The variables included in the model were patient age, ward, number of coadministered drugs with high protein binding, kidney function (estimated glomerular filtration rate [determined by Chronic Kidney Disease Epidemiology Collaboration formula]), alpha-1-acid glycoprotein, albumin, total bilirubin, IgA, IgM, urea, and total vancomycin concentrations. In the pediatric cohort, the median unbound vancomycin fraction was 81.3% (range, 61.9 to 95.9%), which was significantly higher (
P
< 0.01) than the unbound fraction found in the three adult patient cohorts (hematology, 60.6% [48.7 to 90.6%]; ICU, 61.7% [47.0 to 87.6%]; orthopedics, 56.4% [45.9 to 78.0%]). The strongest significant predictor of the unbound vancomycin concentration was the total drug concentration, completed by albumin in the pediatric cohort and albumin and IgA in the adult cohorts. Validation of our model was performed with data from 13 adult patients. A mean difference of 0.3 mg/liter (95% confidence interval [CI], −1.3 to 0.7 mg/liter;
R
2
= 0.99 [95% CI, 0.95 to 0.99]) between measured and calculated unbound vancomycin concentrations demonstrated that the predictive performance of our model was favorable. Unbound vancomycin fractions vary significantly between pediatric and adult patients. We developed a formula to estimate the unbound fraction derived from total vancomycin, albumin, and IgA concentrations in adult patients.
Population Pharmacokinetics of Piperacillin in the Early Phase of Septic Shock: Does Standard Dosing Result in Therapeutic Plasma Concentrations?
Authors: Öbrink-Hansen Kristina , Juul Rasmus Vestergaard , Storgaard Merete , Thomsen Marianne Kragh , Hardlei Tore Forsingdal , Brock Birgitte , Kreilgaard Mads , Gjedsted Jakob
Published: September 2015

Antibiotic dosing in septic shock patients poses a challenge for clinicians due to the pharmacokinetic (PK) variability seen in this patient population. Piperacillin-tazobactam is often used for empirical treatment, and initial appropriate dosing is crucial for reducing mortality. Accordingly, we determined the pharmacokinetic profile of piperacillin (4 g) every 8 h, during the third consecutive dosing interval, in 15 patients treated empirically for septic shock. We developed a population pharmacokinetic model to assess empirical dosing and to simulate alternative dosing regimens and modes of administration. Time above the MIC (
T
>MIC) predicted for each patient was evaluated against clinical breakpoint MIC for
Pseudomonas aeruginosa
(16 mg/liter). Pharmacokinetic-pharmacodynamic (PK/PD) targets evaluated were 50%
fT
>4×MIC and 100%
fT
>MIC. A population PK model was developed using NONMEM, and data were best described by a two-compartment model. Central and intercompartmental clearances were 3.6 liters/h (relative standard error [RSE], 15.7%) and 6.58 liters/h (RSE, 16.4%), respectively, and central and peripheral volumes were 7.3 liters (RSE, 11.8%) and 3.9 liters (RSE, 9.7%), respectively. Piperacillin plasma concentrations varied considerably between patients and were associated with levels of plasma creatinine. Patients with impaired renal function were more likely to achieve predefined PK/PD targets than were patients with preserved or augmented renal function. Simulations of alternative dosing regimens showed that frequent intermittent bolus dosing as well as dosing by extended and continuous infusion increases the probability of attaining therapeutic plasma concentrations. For septic shock patients with preserved or augmented renal function, dose increment or prolonged infusion of the drug needs to be considered. (This study has been registered at ClinicalTrials.gov under registration no. NCT02306928.)
The Makes Caterpillars Floppy (MCF)-Like Domain of Vibrio vulnificus Induces Mitochondrion-Mediated Apoptosis
Authors: Agarwal Shivangi , Zhu Yeuming , Gius David R. , Satchell Karla J. F.
Published: September 2015

The multifunctional-autoprocessing repeats-in-toxin (MARTX
Vv
) toxin of
Vibrio vulnificus
plays a significant role in the pathogenesis of this bacterium through delivery of up to five effector domains to the host cells. Previous studies have established that the MARTX
Vv
toxin is linked to
V. vulnificus
dependent induction of apoptosis, but the region of the large multifunction protein essential for this activity was not previously identified. Recently, we showed that the Makes Caterpillar Floppy-like MARTX effector domain (MCF
Vv
) is an autoproteolytic cysteine protease that induces rounding of various cell types. In this study, we demonstrate that cell rounding induced by MCF
Vv
is coupled to reduced metabolic rate and inhibition of cellular proliferation. Moreover, delivery of MCF
Vv
into host cells either as a fusion to the N-terminal fragment of anthrax toxin lethal factor or when naturally delivered as a
V. vulnificus
MARTX toxin led to loss of mitochondrial membrane potential, release of cytochrome
c
, activation of Bax and Bak, and processing of caspases and poly-(ADP-ribose) polymerase (PARP-γ). These studies specifically link the MCF
Vv
effector domain to induction of the intrinsic apoptosis pathway by
V. vulnificus
.
Beyond the Crystal Structure: Insight into the Function and Vaccine Potential of TbpA Expressed by Neisseria gonorrhoeae
Authors: Cash Devin R. , Noinaj Nicholas , Buchanan Susan K. , Cornelissen Cynthia Nau
Published: September 2015

Neisseria gonorrhoeae
, the causative agent of the sexually transmitted infection gonorrhea, is not preventable by vaccination and is rapidly developing resistance to antibiotics. However, the transferrin (Tf) receptor system, composed of TbpA and TbpB, is an ideal target for novel therapeutics and vaccine development. Using a three-dimensional structure of gonococcal TbpA, we investigated two hypotheses, i.e., that loop-derived antibodies can interrupt ligand-receptor interactions in the native bacterium and that the loop 3 helix is a critical functional domain. Preliminary loop-derived antibodies, as well as optimized second-generation antibodies, demonstrated similar modest ligand-blocking effects on the gonococcal surface but different effects in
Escherichia coli
. Mutagenesis of loop 3 helix residues was employed, generating 11 mutants. We separately analyzed the mutants' abilities to (i) bind Tf and (ii) internalize Tf-bound iron in the absence of the coreceptor TbpB. Single residue mutations resulted in up to 60% reductions in ligand binding and up to 85% reductions in iron utilization. All strains were capable of growing on Tf as the sole iron source. Interestingly, in the presence of TbpB, only a 30% reduction in Tf-iron utilization was observed, indicating that the coreceptor can compensate for TbpA impairment. Complete deletion of the loop 3 helix of TbpA eliminated the abilities to bind Tf, internalize iron, and grow with Tf as the sole iron source. Our studies demonstrate that while the loop 3 helix is a key functional domain, its function does not exclusively rely on any single residue.
Refined Live Attenuated Salmonella enterica Serovar Typhimurium and Enteritidis Vaccines Mediate Homologous and Heterologous Serogroup Protection in Mice
Authors: Tennant Sharon M. , Schmidlein Patrick , Simon Raphael , Pasetti Marcela F. , Galen James E. , Levine Myron M.
Published: September 2015

Invasive nontyphoidalSalmonella(NTS) infections constitute a major health problem among infants and toddlers in sub-Saharan Africa; these infections also occur in infants and the elderly in developed countries. We genetically engineered aSalmonella entericaserovar Typhimurium strain of multilocus sequence type 313, the predominant genotype circulating in sub-Saharan Africa. We evaluated the capacities ofS. Typhimurium andSalmonella entericaserovar Enteritidis ΔguaBAΔclpXlive oral vaccines to protect mice against a highly lethal challenge dose of the homologous serovar and determined protection against other group B and D serovars circulating in sub-Saharan Africa. The vaccinesS. Typhimurium CVD 1931 andS. Enteritidis CVD 1944 were immunogenic and protected BALB/c mice against 10,000 50% lethal doses (LD50) ofS. Typhimurium orS. Enteritidis, respectively.S. Typhimurium CVD 1931 protected mice against the group B serovarSalmonella entericaserovar Stanleyville (91% vaccine efficacy), andS. Enteritidis CVD 1944 protected mice against the group D serovarSalmonella entericaserovar Dublin (85% vaccine efficacy). High rates of survival were observed when mice were infected 12 weeks postimmunization, indicating that the vaccines elicited long-lived protective immunity. Whereas CVD 1931 did not protect againstS. Enteritidis R11, CVD 1944 did mediate protection againstS. Typhimurium D65 (81% efficacy). These findings suggest that a bivalent (S. Typhimurium andS. Enteritidis) vaccine would provide broad protection against the majority of invasive NTS infections in sub-Saharan Africa.
STAT1 Signaling within Macrophages Is Required for Antifungal Activity against Cryptococcus neoformans
Authors: Leopold Wager Chrissy M. , Hole Camaron R. , Wozniak Karen L. , Olszewski Michal A. , Mueller Mathias , Wormley Floyd L.
Published: September 2015

Cryptococcus neoformans, the predominant etiological agent of cryptococcosis, is an opportunistic fungal pathogen that primarily affects AIDS patients and patients undergoing immunosuppressive therapy. In immunocompromised individuals,C. neoformanscan lead to life-threatening meningoencephalitis. Studies using a virulent strain ofC. neoformansengineered to produce gamma interferon (IFN-γ), denoted H99γ, demonstrated that protection against pulmonaryC. neoformansinfection is associated with the generation of a T helper 1 (Th1)-type immune response and signal transducer and activator of transcription 1 (STAT1)-mediated classical (M1) macrophage activation. However, the critical mechanism by which M1 macrophages mediate their anti-C. neoformansactivity remains unknown. The current studies demonstrate that infection withC. neoformansstrain H99γ in mice with macrophage-specific STAT1 ablation resulted in severely increased inflammation of the pulmonary tissue, a dysregulated Th1/Th2-type immune response, increased fungal burden, deficient M1 macrophage activation, and loss of protection. STAT1-deficient macrophages produced significantly less nitric oxide (NO) than STAT1-sufficient macrophages, correlating with an inability to control intracellular cryptococcal proliferation, even in the presence of reactive oxygen species (ROS). Furthermore, macrophages from inducible nitric oxide synthase knockout mice, which had intact ROS production, were deficient in anticryptococcal activity. These data indicate that STAT1 activation within macrophages is required for M1 macrophage activation and anti-C. neoformansactivity via the production of NO.
Antimicrobial Peptide Conformation as a Structural Determinant of Omptin Protease Specificity
Authors: Brannon John R. , Thomassin Jenny-Lee , Gruenheid Samantha , Le Moual Hervé
Published: September 2015

Bacterial proteases contribute to virulence by cleaving host or bacterial proteins to promote survival and dissemination. Omptins are a family of proteases embedded in the outer membrane of Gram-negative bacteria that cleave various substrates, including host antimicrobial peptides, with a preference for cleaving at dibasic motifs. OmpT, the enterohemorrhagic
Escherichia coli
(EHEC) omptin, cleaves and inactivates the human cathelicidin LL-37. Similarly, the omptin CroP, found in the murine pathogen
Citrobacter rodentium
, which is used as a surrogate model to study human-restricted EHEC, cleaves the murine cathelicidin-related antimicrobial peptide (CRAMP). Here, we compared the abilities of OmpT and CroP to cleave LL-37 and CRAMP. EHEC OmpT degraded LL-37 and CRAMP at similar rates. In contrast,
C. rodentium
CroP cleaved CRAMP more rapidly than LL-37. The different cleavage rates of LL-37 and CRAMP were independent of the bacterial background and substrate sequence specificity, as OmpT and CroP have the same preference for cleaving at dibasic sites. Importantly, LL-37 was α-helical and CRAMP was unstructured under our experimental conditions. By altering the α-helicity of LL-37 and CRAMP, we found that decreasing LL-37 α-helicity increased its rate of cleavage by CroP. Conversely, increasing CRAMP α-helicity decreased its cleavage rate. This structural basis for CroP substrate specificity highlights differences between the closely related omptins of
C. rodentium
and
E. coli
. In agreement with previous studies, this difference in CroP and OmpT substrate specificity suggests that omptins evolved in response to the substrates present in their host microenvironments.

IMPORTANCE
Omptins are recognized as key virulence factors for various Gram-negative pathogens. Their localization to the outer membrane, their active site facing the extracellular environment, and their unique catalytic mechanism make them attractive targets for novel therapeutic strategies. Gaining insights into similarities and variations between the different omptin active sites and subsequent substrate specificities will be critical to develop inhibitors that can target multiple omptins. Here, we describe subtle differences between the substrate specificities of two closely related omptins, CroP and OmpT. This is the first reported example of substrate conformation acting as a structural determinant for omptin activity between OmpT-like proteases.
Finding Regulators Associated with the Expression of the Long Polar Fimbriae in Enteropathogenic Escherichia coli
Authors: Hu Jia , Ross Brittany N. , Cieza Roberto J. , Torres Alfredo G.
Published: September 2015

Enteropathogenic
Escherichia coli
(EPEC) is a human pathogen that requires initial adhesion to the intestine in order to cause disease. Multiple adhesion factors have been identified in
E. coli
strains, among them the long polar fimbriae (Lpf), a colonization factor associated with intestinal adhesion. The conditions of Lpf expression are well understood in enterohemorrhagic
E. coli
(EHEC); however, the expression of EPEC
lpf
has been found to be repressed under any
in vitro
condition tested. Therefore, we decided to identify those factors silencing expression of EPEC
lpf
. Because histone-like nucleoid structuring protein (H-NS) is a known repressor of EHEC
lpf
, we tested it and found that H-NS is a repressor of EPEC
lpf
. We also found that the adhesion of the EPEC Δ
hns
strain was significantly enhanced compared to the wild-type strain. Because
lpf
expression was modestly increased in the
hns
mutant, transposon mutagenesis was performed to find a strain displaying higher
lpf
expression than EPEC Δ
hns
. One Tn
5
insertion was identified within the
yhjX
gene, and further
in vitro
characterization revealed increased
lpf
expression and adhesion to Caco-2 cells compared with EPEC Δ
hns
. However, in a murine model of intestinal infection, the EPEC Δ
hns
and EPEC Δ
hns
Tn
5
mutants had only a slight change in colonization pattern compared to the wild-type strain. Our data showed that EPEC Lpf is transcribed, but its role in EPEC intestinal colonization requires further analysis.

IMPORTANCE
Data are presented demonstrating that the long polar fimbriae (
lpf
) operon in enteropathogenic
E. coli
(EPEC) is highly regulated; however, derepression occurs by mutagenizing two proteins associated with its control. The study demonstrates that the EPEC
lpf
operon can be expressed and, therefore, participates in the EPEC adherence phenotype.
Regulation of Bioluminescence in Photobacterium leiognathi Strain KNH6
Authors: Dunn Anne K. , Rader Bethany A. , Stabb Eric V. , Mandel Mark J.
Published: September 2015

Bacterial bioluminescence is taxonomically restricted to certain proteobacteria, many of which belong to the
Vibrionaceae
. In the most well-studied cases, pheromone signaling plays a key role in regulation of light production. However, previous reports have indicated that certain
Photobacterium
strains do not use this regulatory method for controlling luminescence. In this study, we combined genome sequencing with genetic approaches to characterize the regulation of luminescence in
Photobacterium leiognathi
strain KNH6, an extremely bright isolate. Using transposon mutagenesis and screening for decreased luminescence, we identified insertions in genes encoding components necessary for the luciferase reaction (
lux
,
lum
, and
rib
operons) as well as in nine other loci. These additional loci encode gene products predicted to be involved in the tricarboxylic acid (TCA) cycle, DNA and RNA metabolism, transcriptional regulation, and the synthesis of cytochrome
c
, peptidoglycan, and fatty acids. The mutagenesis screen did not identify any mutants with disruptions of predicted pheromone-related loci. Using targeted gene insertional disruptions, we demonstrate that under the growth conditions tested, luminescence levels do not appear to be controlled through canonical pheromone signaling systems in this strain.

IMPORTANCE
Despite the long-standing interest in luminous bacteria, outside a few model organisms, little is known about the regulation and function of luminescence. Light-producing marine bacteria are widely distributed and have diverse lifestyles, suggesting that the control and significance of luminescence may be similarly diverse. In this study, we apply genetic tools to the study of regulation of light production in the extremely bright isolate
Photobacterium leiognathi
KNH6. Our results suggest an unusual lack of canonical pheromone-mediated control of luminescence and contribute to a better understanding of alternative strategies for regulation of a key bacterial behavior. These experiments lay the groundwork for further study of the regulation and role of bioluminescence in
P. leiognathi
.
Interactions of the Metalloregulatory Protein SloR from Streptococcus mutans with Its Metal Ion Effectors and DNA Binding Site
Authors: Spatafora Grace , Corbett John , Cornacchione Louis , Daly William , Galan Diego , Wysota Michael , Tivnan Patrick , Collins Justin , Nye Dillon , Levitz Talya , Breyer Wendy A. , Glasfeld Arthur
Published: September 2015

Streptococcus mutans
is the causative agent of dental caries, a significant concern for human health, and therefore an attractive target for therapeutics development. Previous work in our laboratory has identified a homodimeric, manganese-dependent repressor protein, SloR, as an important regulator of cariogenesis and has used site-directed mutagenesis to map functions to specific regions of the protein. Here we extend those studies to better understand the structural interaction between SloR and its operator and its effector metal ions. The results of DNase I assays indicate that SloR protects a 42-bp region of DNA that overlaps the
sloABC
promoter on the
S. mutans
UA159 chromosome, while electrophoretic mobility shift and solution binding assays indicate that each of two SloR dimers binds to this region. Real-time semiquantitative reverse transcriptase PCR (real-time semi-qRT-PCR) experiments were used to determine the individual base pairs that contribute to SloR-DNA binding specificity. Solution studies indicate that Mn
2+
is better than Zn
2+
at specifically activating SloR to bind DNA, and yet the 2.8-Å resolved crystal structure of SloR bound to Zn
2+
provides insight into the means by which selective activation by Mn
2+
may be achieved and into how SloR may form specific interactions with its operator. Taken together, these experimental observations are significant because they can inform rational drug design aimed at alleviating and/or preventing
S. mutans
-induced caries formation.

IMPORTANCE
This report focuses on investigating the SloR protein as a regulator of essential metal ion transport and virulence gene expression in the oral pathogen
Streptococcus mutans
and on revealing the details of SloR binding to its metal ion effectors and binding to DNA that together facilitate this expression. We used molecular and biochemical approaches to characterize the interaction of SloR with Mn
2+
and with its SloR recognition element to gain a clearer picture of the regulatory networks that optimize SloR-mediated metal ion homeostasis and virulence gene expression in
S. mutans
. These experiments can have a significant impact on caries treatment and/or prevention by revealing the
S. mutans
SloR-DNA binding interface as an appropriate target for the development of novel therapeutic interventions.
Transcriptome Profiling of the Endophyte Burkholderia phytofirmans PsJN Indicates Sensing of the Plant Environment and Drought Stress
Authors: Sheibani-Tezerji Raheleh , Rattei Thomas , Sessitsch Angela , Trognitz Friederike , Mitter Birgit
Published: September 2015

It is widely accepted that bacterial endophytes actively colonize plants, interact with their host, and frequently show beneficial effects on plant growth and health. However, the mechanisms of plant-endophyte communication and bacterial adaption to the plant environment are still poorly understood. Here, whole-transcriptome sequencing of
B. phytofirmans
PsJN colonizing potato (
Solanum tuberosum
L.
) plants was used to analyze
in planta
gene activity and the response of strain PsJN to plant stress. The transcriptome of PsJN colonizing
in vitro
potato plants showed a broad array of functionalities encoded in the genome of strain PsJN. Transcripts upregulated in response to plant drought stress were mainly involved in transcriptional regulation, cellular homeostasis, and the detoxification of reactive oxygen species, indicating an oxidative stress response in PsJN. Genes with modulated expression included genes for extracytoplasmatic function (ECF) group IV sigma factors. These cell surface signaling elements allow bacteria to sense changing environmental conditions and to adjust their metabolism accordingly. TaqMan quantitative PCR (TaqMan-qPCR) was performed to identify ECF sigma factors in PsJN that were activated in response to plant stress. Six ECF sigma factor genes were expressed in PsJN colonizing potato plants. The expression of one ECF sigma factor was upregulated whereas that of another one was downregulated in a plant genotype-specific manner when the plants were stressed. Collectively, our study results indicate that endophytic
B. phytofirmans
PsJN cells are active inside plants. Moreover, the activity of strain PsJN is affected by plant drought stress; it senses plant stress signals and adjusts its gene expression accordingly.

IMPORTANCE
In recent years, plant growth-promoting endophytes have received steadily growing interest as an inexpensive alternative to resource-consuming agrochemicals in sustainable agriculture. Even though promising effects are recurrently observed under controlled conditions, these are rarely reproducible in the field or show undesirably strong variations. Obviously, a better understanding of endophyte activities in plants and the influence of plant physiology on these activities is needed to develop more-successful application strategies. So far, research has focused mainly on analyzing the plant response to bacterial inoculants. This prompted us to study the gene expression of the endophyte
Burkholderia phytofirmans
PsJN in potato plants. We found that endophytic PsJN cells express a wide array of genes and pathways, pointing to high metabolic activity inside plants. Moreover, the strain senses changes in the plant physiology due to plant stress and adjusts its gene expression pattern to cope with and adapt to the altered conditions.
Bradycardia in anorexia nervosa
Authors: Sall Hanish , Timperley Jonathan
Published: September 2015

We present a case of a 24-year-old woman initially referred for a permanent pacemaker for symptomatic sinus bradycardia. Further consultations revealed significant weight loss and subsequent psychiatric review confirmed a diagnosis of anorexia nervosa.
Experiences with, perceptions of and attitudes towards traditional Korean medicine (TKM) in patients with chronic fatigue: a qualitative, one-on-one, in-depth interview study
Authors: Son Haeng-Mi , Park Eun Young , Kim Duck Hee , Kim Eunjeong , Shin Mi-Suk , Kim Tae-Hun
Published: September 2015

Objectives

To explore perceptions and experiences of patients with chronic fatigue with traditional Korean medicine (TKM) and their motivation for choosing TKM.

Design

Qualitative, one-on-one, in-depth interview study.

Setting

Primary TKM hospitals in Seoul, Incheon and Daejeon, South Korea.

Results

15 patients with chronic fatigue were interviewed in this study. Patients with chronic fatigue experienced physical and psychological symptoms that resulted in severe difficulties associated with routine daily activities. The motivations for choosing TKM were primarily dissatisfaction with conventional medicine and previous positive experiences with TKM. While undergoing TKM treatment, patients found that TKM practitioners considered fatigue to be a treatable illness; also, patients felt comfortable with the doctor–patient relationship in TKM.

Conclusions

Healthcare providers need to be concerned about the symptoms of chronic fatigue to a degree that is in line with the patient's own perceptions. Korean patients with chronic fatigue choose TKM as an alternative to fulfil their long-term needs that were unmet by conventional medicine, and they are greatly positively influenced by TKM. TKM may present a possible therapy to alleviate symptoms of diseases that conventional medicine does not address and is an approach that has a considerable effect on Korean patients.