bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recent advances and long‐standing problems in detecting oxidative damage and reactive oxygen species in skeletal muscle
Authors: Jackson Malcolm J. 
Published: March 2016

AbstractAn 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.
image
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.
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

SUMMARY

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

ABSTRACT

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.