bluuebunny/crossref_metadata_2025 huggingface dataset:
HLA‐A*02:513, a novel HLA‐A*02 allele
Authors: Pei Y. F. , Huang H. N. , Li H. C. , Shen W. D.
Published: March 2016

HLA‐A*02:513 shows one nucleotide difference with A*02:07:01 (125G > A).
Quality of red cells after combination of prion reduction and treatment with the intercept system for pathogen inactivation
Authors: Wiltshire M. , Meli A. , Schott MA , Erickson A. , Mufti N. , Thomas S. , Cardigan R.
Published: March 2016

SUMMARY

Background and objectives

The pathogen inactivation (PI) INTERCEPT Blood System for Red Blood Cells utilises amustaline (S‐303) to inactivate a broad range of pathogens in red cell concentrates (RCC). The aim of this study was to investigate the effect on red cell quality of INTERCEPT treatment with and without prion reduction.

Methods/materials

Five pools of five RCC each were prepared. These were split and treated as follows: (i) stored at 2–6 °C for 18 h, (ii) stored at 18–24 °C for 18 h, (iii) PI‐treated, (iv) PI‐treated then prion reduced and (v) prion reduced then PI‐treated. Prior to storage, PI‐treated RCC underwent an exchange step to remove S‐303 and other breakdown products. Components were tested throughout 35 days of storage for in vitro parameters of red cell quality.

Results

All RCC met specification for volume and haemoglobin content. Haemolysis, microvesicle formation, supernatant potassium and deformability were lower and ATP levels higher in PI‐treated units when compared with control units. The effect of prion reduction in addition to PI treatment was minimal in all parameters tested except haemolysis, which was increased in units prion‐reduced after being PI‐treated.

Conclusion

The PI‐treatment process did not increase red cell haemolysis or decrease ATP levels over storage. The lower haemolysis and supernatant potassium levels in treated RCC compared with control RCC were attributed to the exchange step. The effects of combining PI treatment and prion reduction were not more than additive when prion reduction precedes PI treatment.
Extending the biosynthetic repertoires of cyanobacteria and chloroplasts
Authors: Nielsen Agnieszka Zygadlo , Mellor Silas Busck , Vavitsas Konstantinos , Wlodarczyk Artur Jacek , Gnanasekaran Thiyagarajan , Perestrello Ramos H de Jesus Maria , King Brian Christopher , Bakowski Kamil , Jensen Poul Erik
Published: March 2016

Chloroplasts in plants and algae and photosynthetic microorganisms such as cyanobacteria are emerging hosts for sustainable production of valuable biochemicals, using only inorganic nutrients, water, CO2 and light as inputs. In the past decade, many bioengineering efforts have focused on metabolic engineering and synthetic biology in the chloroplast or in cyanobacteria for the production of fuels, chemicals and complex, high‐value bioactive molecules. Biosynthesis of all these compounds can be performed in photosynthetic organelles/organisms by heterologous expression of the appropriate pathways, but this requires optimization of carbon flux and reducing power, and a thorough understanding of regulatory pathways. Secretion or storage of the compounds produced can be exploited for the isolation or confinement of the desired compounds. In this review, we explore the use of chloroplasts and cyanobacteria as biosynthetic compartments and hosts, and we estimate the levels of production to be expected from photosynthetic hosts in light of the fraction of electrons and carbon that can potentially be diverted from photosynthesis. The supply of reducing power, in the form of electrons derived from the photosynthetic light reactions, appears to be non‐limiting, but redirection of the fixed carbon via precursor molecules presents a challenge. We also discuss the available synthetic biology tools and the need to expand the molecular toolbox to facilitate cellular reprogramming for increased production yields in both cyanobacteria and chloroplasts.
Nannizziopsis guarroi infection in 2 Inland Bearded Dragons (Pogona vitticeps): clinical, cytologic, histologic, and ultrastructural aspects
Authors: Le Donne Viviana , Crossland Nicholas , Brandão João , Sokolova Yuliya , Fowlkes Natalie , Nevarez Javier G. , Langohr Ingeborg M. , Gaunt Stephen D.
Published: March 2016

Chrysosporium‐related infections have been increasingly reported in reptiles over the last 2 decades. In this report, we describe clinical, cytologic, histopathologic, and ultrastructural aspects of Chrysosporium‐related infection in 2 Inland Bearded Dragons (Pogona vitticeps). Case 1 was presented for an enlarging raised lesion over the left eye and multiple additional masses over the dorsum. Case 2 was submitted to necropsy by the referring veterinarian for suspected yellow fungus disease. Impression smears of the nodules in case 1 revealed granulomatous to pyogranulomatous inflammation and many septate, variably long, 4–10 μm wide, often undulated hyphae, and very rare conidia. Postmortem impression smears of the superficial lesions of case 2 contained large numbers of solitary conidia and arthroconidia and low numbers of hyphae with similar morphology to case 1. Histopathology of the 2 cases revealed severe, multifocal, chronic, ulcerative, nodular pyogranulomatous dermatitis, with myriad intralesional septate hyphae, and arthroconidia. Fungal culture and molecular sequencing in both cases indicated infection with Nannizziopsis guarroi.
A WHO reference reagent to standardize haemagglutination testing for anti‐A and anti‐B in serum and plasma: international collaborative study to evaluate a candidate preparation
Authors: Thorpe S. J. , Fox B. , Sharp G. , White J. , Milkins C.
Published: March 2016

Background and Objectives

The aim of the study was to evaluate a lyophilized serum preparation, 14/300, for its suitability to serve as a World Health Organization (WHO) Reference Reagent to standardize and control haemagglutination titrations for anti‐A and anti‐B in serum and plasma, in an international collaborative study.

Materials and Methods

Serum preparation 14/300 and two plasma‐based reserve preparations, 14/304 (high titre anti‐A) and 14/208 (high titre anti‐B), were titrated by 24 laboratories in 13 countries using direct (DRT) and indirect (IAT) haemagglutination techniques.

Results

There was eightfold to 64‐fold variation in reported titres per preparation and method across laboratories, that is, titres extended over 4–7 dilutions, although intralaboratory variability was generally good, with over 90% of replicate titres within a twofold range. There was a reduction in interlaboratory variability when titres of the reserve preparations were adjusted relative to those of the candidate Reference Reagent.

Conclusion

The establishment of 14/300 as a WHO Reference Reagent for high titre anti‐A and anti‐B in serum, with nominal anti‐A and anti‐B titres of 128 for DRT, and nominal anti‐A and anti‐B titres of 256 for IAT, will facilitate global standardization of haemagglutination titrations for anti‐A and anti‐B in patient samples and blood components.
Effect of the Proximal Abducting Ulnar Osteotomy on Intra‐Articular Pressure Distribution and Contact Mechanics of Congruent and Incongruent Canine Elbows Ex Vivo
Authors: McConkey Marina J. , Valenzano Dominick M. , Wei Alexander , Li Ting , Thompson Margret S. , Mohammed Hussni O. , van der Meulen Marjolein C. H. , Krotscheck Ursula
Published: March 2016

Objective

To determine the effects of the Proximal Abducting Ulnar Osteotomy (PAUL) on contact pressures of congruent and incongruent (short radius) canine elbows.

Study Design

Ex vivo biomechanical study.

Sample Population

Unpaired normal cadaveric canine forelimbs (n=16).

Methods

A servohydraulic testing frame and thin‐film sensors were utilized to measure intra‐articular contact area (CA), mean contact pressure (mCP), and peak contact pressure (pCP) for medial and lateral elbow compartments. Percent contribution of the medial compartment relative to the whole (%Med) was also examined. Baseline data were collected in 9 congruent elbows and 7 incongruent elbows where the radius was shortened. Both sets of elbows were tested following ulnar osteotomy and sequential placement of 2 and 3 mm PAUL plates and paw repositioning (to account for any medial to lateral shift of transarticular forces). Paired t‐tests compared sequential procedural steps. P<.05 was significant.

Results

For congruent elbows, the 2 mm PAUL plate decreased CA in both compartments compared to baseline; lateral pCP increased with subsequent paw repositioning. Induction of radio‐ulnar incongruity decreased CA and increased mCP medially, decreased pCP laterally, and increased %MedCA and %MedmCP compared to baseline. Both PAUL plates decreased mCP and pCP medially, with no effect laterally. Paw repositioning had no effect.

Conclusion

The PAUL procedure had no effect on medial compartment pressure in the congruent elbow. It may ameliorate increased medial compartment pressure in the incongruent elbow. This change does not result from a medial to lateral compartmental shift and deserves further investigation.
Efficacy of Two Radiologic‐Assisted Prophylactic Gastropexy Techniques
Authors: Balsa Ingrid M. , Culp William T. N. , Johnson Eric G. , Glaiberman Craig B. , Grimes Millie , Mayhew Philipp D. , Palm Carrie A.
Published: March 2016

Objective

To describe the technique and clinical outcome of prophylactic percutaneous radiologic‐assisted gastropexy (PRG) and radiologic‐assisted incisional gastropexy (RIG) in client‐owned dogs.

Study Design

Prospective, nonrandomized clinical trial.

Animals

Fourteen client‐owned, large, and giant breed dogs.

Methods

Four dogs underwent PRG with fluoroscopic guidance to place 2 T‐fasteners into the pyloric antrum and secure it to the right body wall. Ten dogs underwent RIG, which was a modification of PRG. For RIG, the T‐fasteners were first used to approximate the pyloric antrum and body wall, then a full thickness incision through the body wall was made and the pyloric antrum was sutured to the internal abdominal wall. The duration and complications of each procedure were recorded. The gastropexy was assessed by abdominal ultrasound at day 1, week 2, and week 8 postoperative and by barium gastrogram at week 8 postoperative.

Results

No dogs undergoing PRG had a gastropexy present at week 2. All dogs undergoing RIG had ultrasonographic evidence of gastropexy at day 1, week 2, and week 8 postoperative. Gastrograms in 9/9 dogs were consistent with an intact gastropexy, appropriate gastric positioning and appropriate gastric emptying began. No major complications were noted.

Conclusion

The PRG was unsatisfactory and did not result in a permanent gastropexy. The RIG was safe and created a gastropexy that remained intact at 8 weeks postoperative. The RIG should be considered as a minimally invasive option for prophylactic gastropexy in dogs of at‐risk breeds.
Bilateral Superior Labial Mucosal Transposition Flaps to Correct Stenosis of the Nares Following Bilateral Rostral Maxillectomy Combined with Nasal Planum Resection in a Dog
Authors: Séguin Bernard , Steinke Julia R.
Published: March 2016

Objective

To describe a technique using labial mucosal flaps to correct stenosis of the nares subsequent to bilateral rostral maxillectomy and nasal planum resection.

Study Design

Case report

Animals

Client‐owned dog.

Methods

A 10‐year‐old, neutered male Golden Retriever developed repeated stenosis of the nares, at first after bilateral rostral maxillectomy and nasal planum resection, and again after revision surgery. Bilateral, superior labial mucosal transposition flaps were created and interpolated between the nasal mucosa and skin after debridement of scar tissue.

Results

The stenosis did not recur after mucosal flap transposition and the dog returned to normal quality of life (last follow‐up 25 months postoperative).

Conclusion

Single‐stage, superior labial mucosal transposition flaps can be used to correct nares stenosis subsequent to previous surgery.
Atorvastatin improves renal organic anion transporter 3 and renal function in gentamicin‐induced nephrotoxicity in rats
Authors: Jaikumkao Krit , Pongchaidecha Anchalee , Chattipakorn Nipon , Chatsudthipong Varanuj , Promsan Sasivimon , Arjinajarn Phatchawan , Lungkaphin Anusorn
Published: March 2016

New Findings

What is the central question of this study?

This study was designed to determine the renoprotective effects of atorvastatin treatment in an experimental model of gentamicin‐induced nephrotoxicity through modulating the Nrf2 pathway by decreasing the oxidative stress.

What is the main finding and its importance?

Atorvastatin exerts a nephroprotective effect by attenuating oxidative stress, protecting renal function and renal organic anion transporter 3 function from the effects of gentamicin. Atorvastatin might protect the tissues via its antioxidant property and by modulating the antioxidant enzymes through the Nrf2 signalling pathway, which may be the underlying mechanisms of these protective effects.

Recent evidence demonstrates that statins, 3‐hydroxy‐3‐methylglutaryl coenzyme A reductase inhibitors, exert not only lipid‐lowering effects but also antioxidant, anti‐inflammatory and anti‐apoptotic effects. Nephrotoxicity, a serious side‐effect of gentamicin, is related to an increase in reactive oxygen species in the kidney. This study was designed to determine the renoprotective effects of atorvastatin treatment in an experimental model of gentamicin‐induced nephrotoxicity. Male Sprague–Dawley rats were used. Nephrotocixity was induced by i.p. injection of gentamicin, 100 mg kg−1 day−1, for 15 days. Atorvastatin, 10 mg kg−1 day−1, was administered by gavage 30 min before gentamicin injection (pretreatment) for 15 days or only on days 10–15 (post‐treatment). Renal function and renal organic anion transporter 3 (Oat3) function and expression were examined. Gentamicin‐treated rats demonstrated impaired renal function by attenuation of creatinine clearance and increased oxidative stress. Gentamicin treatment also decreased renal Oat3 function and expression as shown by decreased [3H]estrone sulfate uptake into renal cortical slices and decreased expression. The protein expressions of protein kinase C, Nrf2, NAD(P)H:quinone oxidoreductase 1, haeme oxygenase 1 and glutamate–cysteine ligase were markedly increased in gentamicin‐treated rats, indicating the increase in oxidative stress. Administration of atorvastatin improved renal function and alleviated oxidative stress, and atorvastatin pretreatment had a greater ability to decrease oxidative stress than atorvastatin post‐treatment. These effects helped to preserve renal function and Oat3 function and expression. These results indicate that atorvastatin has a renoprotective effect against gentamicin‐induced nephrotoxicity by decreasing overoxidation in the kidney, and might be used in conjunction with gentamicin to protect against renal damage.
Recent advances and long‐standing problems in detecting oxidative damage and reactive oxygen species in skeletal muscle
Authors: Jackson Malcolm J.
Published: March 2016

An increasingly sophisticated array of approaches are now available for the study of the activities of reactive oxygen species and oxidative modifications in skeletal muscle, but the most up‐to‐date techniques are not readily available to many researchers in this field due to their requirement for sophisticated mass spectrometry, imaging or other high cost technologies. Most papers published therefore rely on a number of established approaches although the choice of approach is also clearly dependent upon the experimental model and access to skeletal muscle that is available to the investigator, how much detail is required and the overall question to be addressed. Numerous reports have described the problems associated with some of the popular approaches that are widely followed, including measurement of thiobarbituric acid substances and the sole use of fluorescence‐based probes such as dichlorodihydrofluorescein. This brief review reports the areas in which methods are improving to allow valid assessments to made in this area and indicates some of the more recent developments that provide alternative ways to assess the activity of individual species and endpoints in the various experimental models that may be examined.

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Pool Boiling Heat Transfer Enhancement of Water Using Brazed Copper Microporous Coatings
Authors: Jun Seongchul , Wi Hyoseong , Gurung Ajay , Amaya Miguel , You Seung M.
Published: March 2016

A novel, high-temperature, thermally conductive, microporous coating (HTCMC) is developed by brazing copper particles onto a copper surface. This coating is more durable than many previous microporous coatings and also effectively creates re-entrant cavities by varying brazing conditions. A parametric study of coating thicknesses of 49–283 μm with an average particle size of ∼25 μm was conducted using the HTCMC coating to understand nucleate boiling heat transfer (NBHT) enhancement on porous surfaces. It was found that there are three porous coating regimes according to their thicknesses. The first regime is “microporous” in which both NBHT and critical heat flux (CHF) enhancements gradually grow as the coating thickness increases. The second regime is “microporous-to-porous transition” where NBHT is further enhanced at lower heat fluxes but decreases at higher heat fluxes for increasing thickness. CHF in this regime continues to increase as the coating thickness increases. The last regime is named “porous,” and both NBHT and CHF decrease as the coating thickness increases beyond that of the other two regimes. The maximum NBHT coefficient observed was ∼350,000 W/m2K at 96 μm thickness (microporous regime) and the maximum CHF observed was ∼2.1 MW/m2 at ∼225 μm thickness (porous regime).
Coupled Thermal Radiation and Mixed Convection Step Flow of Nongray Gas
Authors: Atashafrooz M. , Gandjalikhan Nassab S. A. , Lari K.
Published: March 2016

The main goal of this paper is to analyze the thermal and hydrodynamic behaviors of laminar mixed convection flow of a nongray radiating gas over an inclined step in an inclined duct. The fluid is considered an air mixture with 10% CO2 and 20% H2O mole fractions, which is treated as homogeneous, absorbing, emitting, and nonscattering medium. The full-spectrum k-distribution (FSK) method is used to handle the nongray part of the problem, while the radiative transfer equation (RTE) is solved using the discrete ordinate method (DOM). In addition, the results are obtained for different medium assumptions such as pure mixed convection and gray medium to compare with the nongray calculations as a real case. The results show that in many cases, neglecting the radiation part in computations and also use of gray simulations are not acceptable and lead to considerable errors, especially at high values of the Grashof number in mixed convection flow.
Coupled Heat Transfers in a Refinery Furnace in View of Fouling Prediction
Authors: Pedot T. , Cuenot B. , Riber E. , Poinsot T.
Published: March 2016

In industrial refinery furnaces, the efficiency of thermal transfer to heat crude oil before distillation is often altered by coke deposition inside the fuel pipes. This leads to increased production and maintenance costs, and requires better understanding and control. Crude oil fouling is a chemical reaction that is, at first order, thermally controlled. In such large furnaces, the predominant heat transfer process is thermal radiation by the hot combustion products, which directly heats the pipes. As radiation fluxes depend on temperature differences, the pipe surface temperature also plays an important role and needs to be predicted with sufficient accuracy. This pipe surface temperature results from the energy balance between thermal radiation, convective heat transfer, and conduction in the solid material of the pipe, meaning that the thermal behavior of the whole system is a coupled radiation–convection–conduction problem. In this work, this coupled problem is solved in a cylindrical furnace, in which the crude oil flowing in vertical pipes is heated. The thermal radiation of combustion gases is modeled using the discrete ordinate method (DOM) with accurate spectral models and is coupled to heat conduction in the pipe to predict its wall temperature. The flame is described with a complex chemistry combustion model. An energy balance confirms that heat transfers are effectively dominated by thermal radiation. Good agreement with available measurements of the radiative heat flux on a real furnace shows that the proposed approach predicts the correct heat transfers to the pipe. This allows an accurate prediction of the temperature field on the pipe surface, which is a key parameter for liquid fouling inside the pipe. This shows that the thermal problem in furnaces can be handled with relatively simple models with good accuracy.
Waterborne chitosan–epoxysilane hybrid pretreatments for corrosion protection of zinc
Authors: Fernández-Solis Christian , Erbe Andreas
Published: March 2016

Biopolymer-based systems are extensively studied as green alternatives for traditional polymer coatings, e.g., in corrosion protection. Chitosan–epoxysilane hybrid films are presented in this work as a chitosan-based protective system, which could, e.g., be applied in a pretreatment step. For the preparation of the chitosan–epoxysilane hybrid systems, a sol–gel procedure was applied. The function of the silane is to ensure adhesion to the substrate. On zinc substrates, homogeneous thin films with thickness of 50–70 nm were obtained after thermal curing. The hybrid-coated zinc substrates were characterized by infrared spectroscopy, ellipsometry, and x-ray photoelectron spectroscopy. As model corrosion experiments, linear polarization resistance was measured, and cathodic delamination of the weak polymer coating poly(vinylbutyral) (PVB) was studied using scanning Kelvin probe. Overall, chitosan–epoxysilane hybrid pretreated samples showed lower delamination rates than unmodified chitosan coatings and pure PVB. Electrochemical impedance spectroscopy confirmed a reduced ion permeability and water uptake by chitosan–epoxysilane films compared to that of a nonmodified chitosan coating. Even though the coatings are hydrophobic and contain water, they slow down cathodic delamination by limiting ion transport.
Accelerated fast iterative shrinkage thresholding algorithms for sparsity‐regularized cone‐beam CT image reconstruction
Authors: Xu Qiaofeng , Yang Deshan , Tan Jun , Sawatzky Alex , Anastasio Mark A.
Published: March 2016

Purpose:

The development of iterative image reconstruction algorithms for cone‐beam computed tomography (CBCT) remains an active and important research area. Even with hardware acceleration, the overwhelming majority of the available 3D iterative algorithms that implement nonsmooth regularizers remain computationally burdensome and have not been translated for routine use in time‐sensitive applications such as image‐guided radiation therapy (IGRT). In this work, two variants of the fast iterative shrinkage thresholding algorithm (FISTA) are proposed and investigated for accelerated iterative image reconstruction in CBCT.

Methods:

Algorithm acceleration was achieved by replacing the original gradient‐descent step in the FISTAs by a subproblem that is solved by use of the ordered subset simultaneous algebraic reconstruction technique (OS‐SART). Due to the preconditioning matrix adopted in the OS‐SART method, two new weighted proximal problems were introduced and corresponding fast gradient projection‐type algorithms were developed for solving them. We also provided efficient numerical implementations of the proposed algorithms that exploit the massive data parallelism of multiple graphics processing units.

Results:

The improved rates of convergence of the proposed algorithms were quantified in computer‐simulation studies and by use of clinical projection data corresponding to an IGRT study. The accelerated FISTAs were shown to possess dramatically improved convergence properties as compared to the standard FISTAs. For example, the number of iterations to achieve a specified reconstruction error could be reduced by an order of magnitude. Volumetric images reconstructed from clinical data were produced in under 4 min.

Conclusions:

The FISTA achieves a quadratic convergence rate and can therefore potentially reduce the number of iterations required to produce an image of a specified image quality as compared to first‐order methods. We have proposed and investigated accelerated FISTAs for use with two nonsmooth penalty functions that will lead to further reductions in image reconstruction times while preserving image quality. Moreover, with the help of a mixed sparsity‐regularization, better preservation of soft‐tissue structures can be potentially obtained. The algorithms were systematically evaluated by use of computer‐simulated and clinical data sets.
Influence of amplitude‐related perfusion parameters in the parotid glands by non‐fat‐saturated dynamic contrast‐enhanced magnetic resonance imaging
Authors: Chiu Su‐Chin , Cheng Cheng‐Chieh , Chang Hing‐Chiu , Chung Hsiao‐Wen , Chiu Hui‐Chu , Liu Yi‐Jui , Hsu Hsian‐He , Juan Chun‐Jung
Published: March 2016

Purpose:

To verify whether quantification of parotid perfusion is affected by fat signals on non‐fat‐saturated (NFS) dynamic contrast‐enhanced magnetic resonance imaging (DCE‐MRI) and whether the influence of fat is reduced with fat saturation (FS).

Methods:

This study consisted of three parts. First, a retrospective study analyzed DCE‐MRI data previously acquired on different patients using NFS (n = 18) or FS (n = 18) scans. Second, a phantom study simulated the signal enhancements in the presence of gadolinium contrast agent at six concentrations and three fat contents. Finally, a prospective study recruited nine healthy volunteers to investigate the influence of fat suppression on perfusion quantification on the same subjects. Parotid perfusion parameters were derived from NFS and FS DCE‐MRI data using both pharmacokinetic model analysis and semiquantitative parametric analysis. T tests and linear regression analysis were used for statistical analysis with correction for multiple comparisons.

Results:

NFS scans showed lower amplitude‐related parameters, including parameter A, peak enhancement (PE), and slope than FS scans in the patients (all with P < 0.0167). The relative signal enhancement in the phantoms was proportional to the dose of contrast agent and was lower in NFS scans than in FS scans. The volunteer study showed lower parameter A (6.75 ± 2.38 a.u.), PE (42.12% ± 14.87%), and slope (1.43% ± 0.54% s−1) in NFS scans as compared to 17.63 ± 8.56 a.u., 104.22% ± 25.15%, and 9.68% ± 1.67% s−1, respectively, in FS scans (all with P < 0.005). These amplitude‐related parameters were negatively associated with the fat content in NFS scans only (all with P < 0.05).

Conclusions:

On NFS DCE‐MRI, quantification of parotid perfusion is adversely affected by the presence of fat signals for all amplitude‐related parameters. The influence could be reduced on FS scans.
Volume of interest CBCT and tube current modulation for image guidance using dynamic kV collimation
Authors: Parsons David , Robar James L.
Published: March 2016

Purpose:

The focus of this work is the development of a novel blade collimation system enabling volume of interest (VOI) CBCT with tube current modulation using the kV image guidance source on a linear accelerator. Advantages of the system are assessed, particularly with regard to reduction and localization of dose and improvement of image quality.

Methods:

A four blade dynamic kV collimator was developed to track a VOI during a CBCT acquisition. The current prototype is capable of tracking an arbitrary volume defined by the treatment planner for subsequent CBCT guidance. During gantry rotation, the collimator tracks the VOI with adjustment of position and dimension. CBCT image quality was investigated as a function of collimator dimension, while maintaining the same dose to the VOI, for a 22.2 cm diameter cylindrical water phantom with a 9 mm diameter bone insert centered on isocenter. Dose distributions were modeled using a dynamic BEAMnrc library and DOSXYZnrc. The resulting VOI dose distributions were compared to full‐field CBCT distributions to quantify dose reduction and localization to the target volume. A novel method of optimizing x‐ray tube current during CBCT acquisition was developed and assessed with regard to contrast‐to‐noise ratio (CNR) and imaging dose.

Results:

Measurements show that the VOI CBCT method using the dynamic blade system yields an increase in contrast‐to‐noise ratio by a factor of approximately 2.2. Depending upon the anatomical site, dose was reduced to 15%–80% of the full‐field CBCT value along the central axis plane and down to less than 1% out of plane. The use of tube current modulation allowed for specification of a desired SNR within projection data. For approximately the same dose to the VOI, CNR was further increased by a factor of 1.2 for modulated VOI CBCT, giving a combined improvement of 2.6 compared to full‐field CBCT.

Conclusions:

The present dynamic blade system provides significant improvements in CNR for the same imaging dose and localization of imaging dose to a predefined volume of interest. The approach is compatible with tube current modulation, allowing optimization of the imaging protocol.
Radiation dose and cancer risk to out‐of‐field and partially in‐field organs from radiotherapy for symptomatic vertebral hemangiomas
Authors: Mazonakis Michalis , Tzedakis Antonis , Lyraraki Efrossyni , Damilakis John
Published: March 2016

Purpose:

Vertebral hemangiomas (VHs) are the most common benign tumors of the spine that may cause bone resorption. Megavoltage irradiation is usually the treatment of choice for the management of symptomatic VHs. The current study was conducted to estimate the risk for carcinogenesis from radiotherapy of this benign disease on the basis of the calculated radiation doses to healthy organs.

Methods:

The Monte Carlo N‐particle transport code was employed to simulate the irradiation with 6 MV x‐rays of a VH presented in the cervical, upper thoracic, lower thoracic, and lumbar spine. The average radiation dose (Dav) received by each critical organ located outside the primarily irradiated area was calculated. Three‐dimensional treatment plans were also generated for the VHs occurring at the four different sites of the spinal cord based on patients’ computed tomography data. The organ equivalent dose (OED) to each radiosensitive structure, which was partly encompassed by the applied treatment fields, was calculated with the aid of differential dose–volume histograms. The Dav and the OED values were combined with a linear‐no‐threshold model and a nonlinear mechanistic model, respectively, to estimate the organ‐, age‐, and gender‐specific lifetime attributable risks (LARs) for cancer development. The estimated risks were compared with the respective nominal lifetime intrinsic risks (LIRs) for the unexposed population.

Results:

For a standard target dose of 34 Gy, the OED varied from 0.39–5.15 Gy by the organ of interest and the irradiation site. The Dav range for the out‐of‐field organs was 4.9 × 10−4 to 0.56 Gy. The LAR for the appearance of malignancies in the partially in‐field organs after radiotherapy of male and female patients was (0.08%–1.8%) and (0.09%–1.9%), respectively. These risk values were 1.5–15.5 times lower when compared to the respective LIRs. The lifetime probability for out‐of‐field cancer induction in irradiated males and females was (2.5 × 10−4 to 7.7 × 10−2)% and (1.4 × 10−4 to 2.6 × 10−1)%, respectively. The above risks were one to four orders of magnitude lower than the LIRs.

Conclusions:

The probability for the development of out‐of‐field malignancies due to radiotherapy for VHs is trivial with respect to the nominal risk for unexposed population. The respective cancer risks to partially in‐field organs are smaller than the nominal probabilities but they should not be considered as inconsiderable. These risks may be taken into account during the follow‐up of patients treated for a symptomatic VH.
Urinary bladder segmentation in CT urography using deep‐learning convolutional neural network and level sets
Authors: Cha Kenny H. , Hadjiiski Lubomir , Samala Ravi K. , Chan Heang‐Ping , Caoili Elaine M. , Cohan Richard H.
Published: March 2016

Purpose:

The authors are developing a computerized system for bladder segmentation in CT urography (CTU) as a critical component for computer‐aided detection of bladder cancer.

Methods:

A deep‐learning convolutional neural network (DL‐CNN) was trained to distinguish between the inside and the outside of the bladder using 160 000 regions of interest (ROI) from CTU images. The trained DL‐CNN was used to estimate the likelihood of an ROI being inside the bladder for ROIs centered at each voxel in a CTU case, resulting in a likelihood map. Thresholding and hole‐filling were applied to the map to generate the initial contour for the bladder, which was then refined by 3D and 2D level sets. The segmentation performance was evaluated using 173 cases: 81 cases in the training set (42 lesions, 21 wall thickenings, and 18 normal bladders) and 92 cases in the test set (43 lesions, 36 wall thickenings, and 13 normal bladders). The computerized segmentation accuracy using the DL likelihood map was compared to that using a likelihood map generated by Haar features and a random forest classifier, and that using our previous conjoint level set analysis and segmentation system (CLASS) without using a likelihood map. All methods were evaluated relative to the 3D hand‐segmented reference contours.

Results:

With DL‐CNN‐based likelihood map and level sets, the average volume intersection ratio, average percent volume error, average absolute volume error, average minimum distance, and the Jaccard index for the test set were 81.9% ± 12.1%, 10.2% ± 16.2%, 14.0% ± 13.0%, 3.6 ± 2.0 mm, and 76.2% ± 11.8%, respectively. With the Haar‐feature‐based likelihood map and level sets, the corresponding values were 74.3% ± 12.7%, 13.0% ± 22.3%, 20.5% ± 15.7%, 5.7 ± 2.6 mm, and 66.7% ± 12.6%, respectively. With our previous CLASS with local contour refinement (LCR) method, the corresponding values were 78.0% ± 14.7%, 16.5% ± 16.8%, 18.2% ± 15.0%, 3.8 ± 2.3 mm, and 73.9% ± 13.5%, respectively.

Conclusions:

The authors demonstrated that the DL‐CNN can overcome the strong boundary between two regions that have large difference in gray levels and provides a seamless mask to guide level set segmentation, which has been a problem for many gradient‐based segmentation methods. Compared to our previous CLASS with LCR method, which required two user inputs to initialize the segmentation, DL‐CNN with level sets achieved better segmentation performance while using a single user input. Compared to the Haar‐feature‐based likelihood map, the DL‐CNN‐based likelihood map could guide the level sets to achieve better segmentation. The results demonstrate the feasibility of our new approach of using DL‐CNN in combination with level sets for segmentation of the bladder.
An 8‐channel RF coil array for carotid artery MR imaging in humans at 3 T
Authors: Hu Xiaoqing , Zhang Lei , Zhang Xiaoliang , Zhu Huabin , Chen Xiao , Zhang Yongqin , Chung Yiu‐Cho , Liu Xin , Zheng Hairong , Li Ye
Published: March 2016

Purpose:

Carotid artery diseases due to plaque buildup at the carotid bifurcation are a leading cause of stroke. Accurate plaque quantification and characterization of plaque composition and morphology by magnetic resonance imaging (MRI) is essential to identifying high‐risk patients. Difficulties in detecting plaque, which is physically small, and the unique physiological structure of the carotid artery make use of a radio frequency (RF) coil array with high resolution, large longitudinal coverage, and deep penetration ideal for clinical examinations. The goal of this project was to design and fabricate a sensitive RF coil array with sufficient imaging coverage and signal‐to‐noise ratio (SNR) for carotid artery imaging at 3 T.

Methods:

Based on clinical requirements and the anatomical structure of the human carotid artery, an 8‐channel carotid coil array was designed and fabricated for 3 T MRI of the carotid artery in humans. The performance of the proposed 8‐channel carotid coil array was validated through bench tests and MR imaging experiments on a 3 T whole body MRI scanner. Its performance was also compared experimentally to the performance of a commercial 4‐channel phased array carotid coil designed by Machnet BV (Machnet BV coil, Roden, Netherlands).

Results:

The 8‐channel carotid coil array performed significantly better in imaging the carotid artery than the commercial 4‐channel Machnet BV coil in terms of the SNR, coverage, and penetration depth. In parallel imaging, the proposed 8‐channel carotid coil array demonstrated a much lower maximum value and average value of the geometry factor in the region of interest. Carotid artery images acquired in vivo using the proposed 8‐channel carotid artery coil and the commercial 4‐channel Machnet BV coil were also compared, demonstrating the former's potential for clinical diagnosis.

Conclusions:

Based on the analyses of phantom and in vivo imaging studies, the proposed 8‐channel carotid coil array has the potential for use in clinical diagnosis, performing better in terms of SNR, imaging coverage, and penetration depth than the commercial 4‐channel carotid artery coil array at 3 T. In future studies, the proposed 8‐channel carotid coil array can also serve as an important part of a large‐scale multichannel coil array for imaging the whole carotid artery system, including the extracranial and intracranial arteries.
High-Intensity Events in International Women’s Team Handball Matches
Authors: Luteberget Live S. , Spencer Matt
Published: March 2016

Purpose:

International women’s team handball is a physically demanding sport and is intermittent in nature. The aim of the study was to profile high-intensity events (HIEs) in international women’s team handball matches with regard to playing positions.

Methods:

Twenty female national-team handball players were equipped with inertial movement units (OptimEye S5, Catapult Sports, Australia) in 9 official international matches. Players were categorized in 4 different playing positions: backs, wings, pivots, and goalkeepers (GKs). PlayerLoad™, accelerations (Acc), changes of direction (CoD), decelerations (Dec), and the sum of the latter 3, HIEs, were extracted from raw-data files using the manufacturer’s software. All Acc, Dec, CoD, and HIEs >2.5 m/s were included. Data were log-transformed and differences were standardized for interpretation of magnitudes and reported with effect-size statistics.

Results:

Mean numbers of events were 0.7 ± 0.4 Acc/min, 2.3 ± 0.9 Dec/min, and 1.0 ± 0.4 CoD/min. Substantial differences between playing positions, ranging from small to very large, were found in the 3 parameters. Backs showed a most likely greater frequency for HIE/min (5.0 ± 1.1 HIE/min) than all other playing positions. Differences between playing positions were also apparent in PlayerLoad/min.

Conclusion:

HIEs in international women’s team handball are position specific, and the overall intensity depends on the positional role within a team. Specific HIE and intensity profiles from match play provide useful information for a better understanding of the overall game demands and for each playing position.
Restoring oxidant signaling suppresses proarthritogenic T cell effector functions in rheumatoid arthritis
Authors: Yang Zhen , Shen Yi , Oishi Hisashi , Matteson Eric L. , Tian Lu , Goronzy Jörg J. , Weyand Cornelia M.
Published: March 2016

ROS deficiency promotes proinflammatory T cells in rheumatoid arthritis.
Funding unfunded NIH research applications
Authors: Dueñas Martin A. , Bisceglio Isabelle , Pannucci James
Published: March 2016

A new public-private partnership with the NIH hopes to address the surplus of high-quality biomedical research applications that merit funding.
Limited diversity sparks inflammation at the mucosal border
Authors: Moore Daniel J.
Published: March 2016

Immunodeficiency in Omenn syndrome promotes microbiota-driven inflammation that can be controlled by antibiotics.
Intestinal Carriage of Carbapenemase-Producing Organisms: Current Status of Surveillance Methods
Authors: Viau Roberto , Frank Karen M. , Jacobs Michael R. , Wilson Brigid , Kaye Keith , Donskey Curtis J. , Perez Federico , Endimiani Andrea , Bonomo Robert A.
Published: March 2016

Carbapenemases have become a significant mechanism for broad-spectrum β-lactam resistance in
Enterobacteriaceae
and other Gram-negative bacteria such as
Pseudomonas
and
Acinetobacter
spp. Intestinal carriage of carbapenemase-producing organisms (CPOs) is an important source of transmission. Isolation of carriers is one strategy that can be used to limit the spread of these bacteria. In this review, we critically examine the clinical performance, advantages, and disadvantages of methods available for the detection of intestinal carriage of CPOs. Culture-based methods (Centers for Disease Control and Prevention [CDC] protocols, chromogenic media, specialized agars, and double-disk synergy tests) for detecting carriage of CPOs are convenient due to their ready availability and low cost, but their limited sensitivity and long turnaround time may not always be optimal for infection control practices. Contemporary nucleic acid amplification techniques (NAATs) such as real-time PCR, hybridization assays, loop-mediated isothermal amplification (LAMP), or a combined culture and NAAT approach may provide fast results and/or added sensitivity and specificity compared with culture-based methods. Infection control practitioners and clinical microbiologists should be aware of the strengths and limitations of available methods to determine the most suitable approach for their medical facility to fit their infection control needs.
Changes in the Eye Microbiota Associated with Contact Lens Wearing
Authors: Shin Hakdong , Price Kenneth , Albert Luong , Dodick Jack , Park Lisa , Dominguez-Bello Maria Gloria
Published: March 2016

Wearing contact lenses has been identified as a risk factor for the development of eye conditions such as giant papillary conjunctivitis and keratitis. We hypothesized that wearing contact lenses is associated with changes in the ocular microbiota. We compared the bacterial communities of the conjunctiva and skin under the eye from 58 subjects and analyzed samples from 20 subjects (9 lens wearers and 11 non-lens wearers) taken at 3 time points using a 16S rRNA gene-based sequencing technique (V4 region; Illumina MiSeq). We found that using anesthetic eye drops before sampling decreases the detected ocular microbiota diversity. Compared to those from non-lens wearers, dry conjunctival swabs from lens wearers had more variable and skin-like bacterial community structures (UniFrac;
P
 value = <0.001), with higher abundances of
Methylobacterium
,
Lactobacillus
,
Acinetobacter
, and
Pseudomonas
and lower abundances of
Haemophilus
,
Streptococcus
,
Staphylococcus
, and
Corynebacterium
(linear discriminant analysis [LDA] score = >3.0). The results indicate that wearing contact lenses alters the microbial structure of the ocular conjunctiva, making it more similar to that of the skin microbiota. Further research is needed to determine whether the microbiome structure provides less protection from ocular infections.

IMPORTANCE
As in other body sites (i.e., the gut, skin, and mouth), the eye has a normal community of bacteria which are expected to confer resistance that provides protection from invaders. However, the eye microbiome has been largely neglected and is relevant to eye health and understanding eye diseases and to discovery of its functions. This report of a baseline study shows differences in the eye microbiome of contact lens wearers in relation to those of non-lens wearers and has the potential to help future studies explore novel insights into a possible role of the microbiome in the increased risk for eye infections in contact lens wearers.
Role of Multicellular Aggregates in Biofilm Formation
Authors: Kragh Kasper N. , Hutchison Jaime B. , Melaugh Gavin , Rodesney Chris , Roberts Aled E. L. , Irie Yasuhiko , Jensen Peter Ø. , Diggle Stephen P. , Allen Rosalind J. , Gordon Vernita , Bjarnsholt Thomas
Published: March 2016

In traditional models of
in vitro
biofilm development, individual bacterial cells seed a surface, multiply, and mature into multicellular, three-dimensional structures. Much research has been devoted to elucidating the mechanisms governing the initial attachment of single cells to surfaces. However, in natural environments and during infection, bacterial cells tend to clump as multicellular aggregates, and biofilms can also slough off aggregates as a part of the dispersal process. This makes it likely that biofilms are often seeded by aggregates and single cells, yet how these aggregates impact biofilm initiation and development is not known. Here we use a combination of experimental and computational approaches to determine the relative fitness of single cells and preformed aggregates during early development of
Pseudomonas aeruginosa
biofilms. We find that the relative fitness of aggregates depends markedly on the density of surrounding single cells, i.e., the level of competition for growth resources. When competition between aggregates and single cells is low, an aggregate has a growth disadvantage because the aggregate interior has poor access to growth resources. However, if competition is high, aggregates exhibit higher fitness, because extending vertically above the surface gives cells at the top of aggregates better access to growth resources. Other advantages of seeding by aggregates, such as earlier switching to a biofilm-like phenotype and enhanced resilience toward antibiotics and immune response, may add to this ecological benefit. Our findings suggest that current models of biofilm formation should be reconsidered to incorporate the role of aggregates in biofilm initiation.

IMPORTANCE
During the past decades, there has been a consensus around the model of development of a biofilm, involving attachment of single planktonic bacterial cells to a surface and the subsequent development of a mature biofilm. This study presents results that call for a modification of this rigorous model. We show how free floating biofilm aggregates can have a profound local effect on biofilm development when attaching to a surface. Our findings show that an aggregate landing on a surface will eventually outcompete the biofilm population arising from single cells attached around the aggregate and dominate the local biofilm development. These results point to a regime where preformed biofilm aggregates may have a fitness advantage over planktonic cells when it comes to accessing nutrients. Our findings add to the increasingly prominent comprehension that biofilm lifestyle is the default for bacteria and that planktonic single cells may be only a transition state at the most.