bluuebunny/crossref_metadata_2025_split huggingface dataset:
SU‐F‐BRF‐01: A GPU Framework for Developing Interactive High‐Resolution Patient‐Specific Biomechanical Models
Authors: Neylon J , Qi S , Sheng K , Kupelian P , Santhanam A 
Published: July 2014

Purpose:To develop a GPU‐based framework that can generate highresolution and patient‐specific biomechanical models from a given simulation CT and contoured structures, optimized to run at interactive speeds, for addressing adaptive radiotherapy objectives.Method:A Massspring‐damping (MSD) model was generated from a given simulation CT. The model's mass elements were generated for every voxel of anatomy, and positioned in a deformation space in the GPU memory. MSD connections were established between neighboring mass elements in a dense distribution. Contoured internal structures allowed control over elastic material properties of different tissues. Once the model was initialized in GPU memory, skeletal anatomy was actuated using rigid‐body transformations, while soft tissues were governed by elastic corrective forces and constraints, which included tensile forces, shear forces, and spring damping forces. The model was validated by applying a known load to a soft tissue block and comparing the observed deformation to ground truth calculations from established elastic mechanics.Results:Our analyses showed that both local and global load experiments yielded results with a correlation coefficient R2 > 0.98 compared to ground truth. Models were generated for several anatomical regions. Head and neck models accurately simulated posture changes by rotating the skeletal anatomy in three dimensions. Pelvic models were developed for realistic deformations for changes in bladder volume. Thoracic models demonstrated breast deformation due to gravity when changing treatment position from supine to prone. The GPU framework performed at greater than 30 iterations per second for over 1 million mass elements with up to 26 MSD connections each.Conclusions:Realistic simulations of site‐specific, complex posture and physiological changes were simulated at interactive speeds using patient data. Incorporating such a model with live patient tracking would facilitate real time assessment of variations of the actual anatomy and delivered dose for adaptive intervention and re‐planning.
SU‐F‐BRF‐02: Automated Lung Segmentation Method Using Atlas‐Based Sparse Shape Composition with a Shape Constrained Deformable Model
Authors: Zhou J , yan z , zhang s , Zhang B , Lasio G , Prado K , D' Souza W 
Published: July 2014

Purpose:To develop an automated lung segmentation method, which combines the atlas‐based sparse shape composition with a shape constrained deformable model in thoracic CT for patients with compromised lung volumes.Methods:Ten thoracic computed tomography scans for patients with large lung tumors were collected and reference lung ROIs in each scan was manually segmented to assess the performance of the method. We propose an automated and robust framework for lung tissue segmentation by using single statistical atlas registration to initialize a robust deformable model in order to perform fine segmentation that includes compromised lung tissue. First, a statistical image atlas with sparse shape composition is constructed and employed to obtain an approximate estimation of lung volume. Next, a robust deformable model with shape prior is initialized from this estimation. Energy terms from ROI edge potential and interior ROI region based potential as well as the initial ROI are combined in this model for accurate and robust segmentation.Results:The proposed segmentation method is applied to segment right lung on three CT scans. The quantitative results of our segmentation method achieved mean dice score of (0.92–0.95), mean accuracy of (0.97,0.98), and mean relative error of (0.10,0.16) with 95% CI. The quantitative results of previously published RASM segmentation method achieved mean dice score of (0.74,0.96), mean accuracy of (0.66,0.98), and mean relative error of (0.04, 0.38) with 95% CI. The qualitative and quantitative comparisons show that our proposed method can achieve better segmentation accuracy with less variance compared with a robust active shape model method.Conclusion:The atlas‐based segmentation approach achieved relatively high accuracy with less variance compared to RASM in the sample dataset and the proposed method will be useful in image analysis applications for lung nodule or lung cancer diagnosis and radiotherapy assessment in thoracic computed tomography.
SU‐F‐BRF‐03: Quality Assurance of Deformable Image Registration in Radiotherapy
Authors: Watkins W.T. , Bzdusek K. , Siebers J.V. 
Published: July 2014

Purpose:To introduce methods to analyze Deformable Image Registration (DIR) and identify regions of potential DIR errors.Methods:DIR Deformable Vector Fields (DVFs) quantifying patient anatomic changes were evaluated using the Jacobian determinant and the magnitude of DVF curl as functions of tissue density and tissue type. These quantities represent local relative deformation and rotation, respectively. Large values in dense tissues can potentially identify non‐physical DVF errors. For multiple DVFs per patient, histograms and visualization of DVF differences were also considered. To demonstrate the capabilities of methods, we computed multiple DVFs for each of five Head and Neck (H' N) patients (P1–P5) via a Fast‐symmetric Demons (FSD) algorithm and via a Diffeomorphic Demons (DFD) algorithm, and show the potential to identify DVF errors.Results:Quantitative comparisons of the FSD and DFD registrations revealed <0.3 cm DVF differences in >99% of all voxels for P1, >96% for P2, and >90% of voxels for P3. While the FSD and DFD registrations were very similar for these patients, the Jacobian determinant was >50% in 9–15% of soft tissue and in 3–17% of bony tissue in each of these cases. The volumes of large soft tissue deformation were consistent for all five patients using the FSD algorithm (mean 15%±4% volume), whereas DFD reduced regions of large deformation by 10% volume (785 cm3) for P4 and by 14% volume (1775 cm3) for P5. The DFD registrations resulted in fewer regions of large DVF‐curl; 50% rotations in FSD registrations averaged 209±136 cm3 in soft tissue and 10±11 cm3 in bony tissue, but using DFD these values were reduced to 42±53 cm3 and 1.1±1.5 cm3, respectively.Conclusion:Analysis of Jacobian determinant and curl as functions of tissue density can identify regions of potential DVF errors by identifying non‐physical deformations and rotations.Collaboration with Phillips Healthcare, as indicated in authorship.
SU‐F‐BRF‐04: Evaluation of Five Commercially‐Available Algorithms for Deformable Image Registration
Authors: Shah A , Pukala J , Johnson P , Staton R , Meeks S 
Published: July 2014

Purpose:Deformable image registration (DIR) is increasingly being used in various clinical applications. Although there are several DIR packages all making successful attempts at modeling complex anatomical changes using even more complex mathematical approximations, they are all subject to various uncertainties. Many studies have attempted to quantify the spatial uncertainty with DIR. This is the first study to compare the uncertainty for interfraction DIR for 5 different commercially‐available algorithms. The aim of this study was to benchmark the performance of the most commonlyused DIR algorithms offered through these 5 software packages: Eclipse, MIM, Pinnacle, RaySearch, and Velocity.Methods:A set of 10 virtual H' N phantoms [Pukala et al. MedPhys. 40(11) 2013] with known deformations were used to determine the spatial errors that might be seen when performing DIR. The “ground‐truth” deformation vector field (DVF) was compared to the DVF output of the 5 commercially‐available algorithms in order to evaluate spatial errors for six regions of interest (ROIs): brainstem, cord, mandible, left parotid, right parotid, and the external body contour.Results:We found that each software package had varying uncertainties with the various ROIs, but were generally all comparable to one another – with mean spatial errors for each algorithm below 3.5 mm for each ROI (averaged across all phantoms). We also found that no single algorithm was the clear winner over the other 4 algorithms. However, at times, we found huge maximum errors in our results (e.g. phantom #9 maximum errors: right parotid = 22.9 mm, external contour = 30.5mm) with the varying DIR algorithms.Conclusion:Although our evaluation was limited to H' N patients, we show that our methods are a single‐assessment analysis tool that could be used by any physicist, within any type of facility, to compare their DIR software before initiating widespread use within their daily radiotherapy practice.
SU‐F‐BRF‐05: Influence of Rigid Registration On the Deformable Registration Quality in the Context of Atlas Contouring
Authors: von Lavante E , Galerneau C , Gooding M 
Published: July 2014

Purpose:Deformable registration requires a rigid registration as an initialization. Normally, a global rigid is assumed acceptable. However, for many use‐cases, such as atlas contouring, there is no obvious “best” global rigid. Thus, we have investigated how a rigid registration affects the deformable registration in the context of atlas contouring and if a “global best” rigid registration can be found.Methods:All possible combinations of source and target images from a database of 7 expertly delineated head and neck images (26 organs) were evaluated. For each source‐target‐pair, the image centroids were aligned, and subsequently rigid registrations were simulated by sweeping the target over an isotropic grid (−100mm to +100mm with respect to centroid alignment, in 10mm steps). Deformable registration was performed following each initialization using commercial software (RTx, Mirada Medical, Oxford, UK). Contours were transformed from source to target. DICE coefficients between the transformed and original contours were calculated on the target. Successful registration was taken to be where DICE was within 80% of the maximum achievable. The capture range was determined by fitting a least‐squares ellipsoid to the space of initialisations resulting in success. The mean of the ellipsoid centers determined the “best” global rigid registration, and the distance of each ellipsoid center to this was computed.Results:The extent of the capture range averaged over all organs and cases was x=64.3mm, y=51.4mm, z=32.3mm. The standard deviation of the ellipsoid centers from the “best” rigid was x=37.8mm, y=56.6mm, z=38.6mm. This per‐organ deviation from the global rigid is in the same order of magnitude than the capture range of the deformable algorithm.Conclusion:Finding the “best” rigid registration is an ill‐posed problem, as the optimum rigid registration will differ between target organs. Thus, having an algorithm with a large capture range is essential to a good deformable registration.All authors were employed by Mirada Medical Ltd., Oxford, Oxfordshire, United Kingdom.
SU‐E‐QI‐04: Curve Fitting of Time‐Density Data From CT Circulation Timing Scans for Estimation of Cardiac Output
Authors: Ogden K , Scalzetti E , Rajebi H 
Published: July 2014

Purpose:To develop a robust algorithm for fitting gamma variate functions to time‐density data acquired during a circulation time scan in preparation for a CT pulmonary angiogram (CTPA).Methods:Timedensity information in the main pulmonary artery (MPA), ascending aorta (AA), and descending aorta (DA) was retrospectively collected for 10 patients undergoing CTPA. Measurements prior to the arrival of contrast were used to estimate the baseline (blood) density value. The estimated contrast arrival delay time was varied over a range of values and the maximum correlation coefficient was used to estimate the delay time. In a second approach, an additional step was performed by shifting the data in time relative to the best‐fit gamma variate and calculating a mean‐squared difference (MSD). The minimum MSD was used to find a new estimate of the delay time, after which a new gamma variate fit was performed. This process was iterated five times. The final gamma variate fit was used to estimate the cardiac output (CO).Results:The mean CO for all patients and all vessels was 6.8 l/min for both methods. To compare the robustness of the two methods, coefficient of variation (CV) of CO for the three vessels was computed for each patient. For method 1, the average CV was 0.054, for method 2 it was 0.023. Using method 2, the CV decreased for all but one patient, for whom it increased from 0.01 to 0.02. On average the CV was reduced by 57% using method 2.Conclusion:Cardiac output may be estimated by using the time‐dilution data collected during a circulation timing scan acquired at CTPA. Care must be taken in fitting a model to the data to ensure robust results. The method described has proven to reduce the variability in CO values estimated for different vessels in a single scan.
SU‐F‐BRD‐16: Under Dose Regions Recalculated by Monte Carlo Cannot Predict the Local Failure for NSCLC Patients Treated with SBRT
Authors: Liu H , Cherian S , Stephans K , Videtic G , Qi P , Xia P , Zhuang T 
Published: July 2014

Purpose:To investigate whether Monte Carlo (MC) recalculated dose distributions can predict the geometric location of the recurrence for nonsmall cell lung cancer (NSCLC) patients treated with stereotactic body radiotherapy (SBRT).Methods:Thirty NSCLC patients with local recurrence were retrospectively selected for this study. The recurred gross target volumes (rGTV) were delineated on the follow‐up CT/PET images and then rigidly transferred via imaging fusion to the original planning CTs. Failure pattern was defined according to the overlap between the rGTV and planning GTV (pGTV) as: (a) in‐field failure (≥80%), (b) marginal failure (20%–80%), and (c) out‐of‐field failure (≤20%). All clinical plans were calculated initially with pencil beam (PB) with or without heterogeneity correction dependent of protocols. These plans were recalculated with MC with heterogeneity correction. Because of non‐uniform dose distributions in the rGTVs, the rGTVs were further divided into four regions: inside the pGTV (GTVin), inside the PTV (PTVin), outside the pGTV (GTVout), and outside the PTV (PTVout). The mean doses to these regions were reported and analyzed separately.Results:Among 30 patients, 10 patients had infield recurrences, 15 marginal and 5 out‐of‐field failures. With MC calculations, D95 and D99 of the PTV were reduced by (10.6 ± 7.4)% and (11.7 ± 7.9)%. The average MC calculated mean doses of GTVin, GTVout, PTVin and PTVout were 48.2 ± 5.3 Gy, 48.2 ± 5.5 Gy, 46.3 ± 6.2 Gy and 46.6 ± 5.6 Gy, respectively. No significant dose differences between GTVin and GTVout (p=0.65), PTVin and PTVout (p=0.19) were observed, using the paired students t‐test.Conclusion:Although the PB calculations underestimated the tumor target doses, the geometric location of the recurrence did not correlate with the mean doses of subsections of the recurrent GTV. Under dose regions recalculated by MC cannot predict the local failure for NSCLC patients treated with SBRT.
Lactobacillus rhamnosus GG Inhibits the Toxic Effects of Staphylococcus aureus on Epidermal Keratinocytes
Authors: Mohammedsaeed Walaa , McBain Andrew J. , Cruickshank Sheena M. , O'Neill Catherine A. 
Published: July 2014

ABSTRACT

Few studies have evaluated the potential benefits of the topical application of probiotic bacteria or material derived from them. We have investigated whether a probiotic bacterium,
Lactobacillus rhamnosus
GG, can inhibit
Staphylococcus aureus
infection of human primary keratinocytes in culture. When primary human keratinocytes were exposed to
S. aureus
, only 25% of the keratinocytes remained viable following 24 h of incubation. However, in the presence of 10
8
CFU/ml of live
L. rhamnosus
GG, the viability of the infected keratinocytes increased to 57% (
P
= 0.01).
L. rhamnosus
GG lysates and spent culture fluid also provided significant protection to keratinocytes, with 65% (
P
= 0.006) and 57% (
P
= 0.01) of cells, respectively, being viable following 24 h of incubation. Keratinocyte survival was significantly enhanced regardless of whether the probiotic was applied in the viable form or as cell lysates 2 h before or simultaneously with (
P
= 0.005) or 12 h after (
P
= 0.01)
S. aureus
infection. However, spent culture fluid was protective only if added before or simultaneously with
S. aureus
. With respect to mechanism, both
L. rhamnosus
GG lysate and spent culture fluid apparently inhibited adherence of
S. aureus
to keratinocytes by competitive exclusion, but only viable bacteria or the lysate could displace
S. aureus
(
P
= 0.04 and 0.01, respectively). Furthermore, growth of
S. aureus
was inhibited by either live bacteria or lysate but not spent culture fluid. Together, these data suggest at least two separate activities involved in the protective effects of
L. rhamnosus
GG against
S. aureus
, growth inhibition and reduction of bacterial adhesion.
Metatranscriptomic Analysis of Arctic Peat Soil Microbiota
Authors: Tveit Alexander T. , Urich Tim , Svenning Mette M. 
Published: July 2014

ABSTRACT

Recent advances in meta-omics and particularly metatranscriptomic approaches have enabled detailed studies of the structure and function of microbial communities in many ecosystems. Molecular analyses of peat soils, ecosystems important to the global carbon balance, are still challenging due to the presence of coextracted substances that inhibit enzymes used in downstream applications. We sampled layers at different depths from two high-Arctic peat soils in Svalbard for metatranscriptome preparation. Here we show that enzyme inhibition in the preparation of metatranscriptomic libraries can be circumvented by linear amplification of diluted template RNA. A comparative analysis of mRNA-enriched and nonenriched metatranscriptomes showed that mRNA enrichment resulted in a 2-fold increase in the relative abundance of mRNA but biased the relative distribution of mRNA. The relative abundance of transcripts for cellulose degradation decreased with depth, while the transcripts for hemicellulose debranching increased, indicating that the polysaccharide composition of the peat was different in the deeper and older layers. Taxonomic annotation revealed that
Actinobacteria
and
Bacteroidetes
were the dominating polysaccharide decomposers. The relative abundances of 16S rRNA and mRNA transcripts of methanogenic
Archaea
increased substantially with depth. Acetoclastic methanogenesis was the dominating pathway, followed by methanogenesis from formate. The relative abundances of 16S rRNA and mRNA assigned to the methanotrophic
Methylococcaceae
, primarily
Methylobacter
, increased with depth. In conclusion, linear amplification of total RNA and deep sequencing constituted the preferred method for metatranscriptomic preparation to enable high-resolution functional and taxonomic analyses of the active microbiota in Arctic peat soil.
SmoXYB1C1Z of Mycobacterium sp. Strain NBB4: a Soluble Methane Monooxygenase (sMMO)-Like Enzyme, Active on C
2
to C
4
Alkanes and Alkenes
Authors: Martin Kiri E. , Ozsvar Jazmin , Coleman Nicholas V. 
Published: July 2014

ABSTRACT

Monooxygenase (MO) enzymes initiate the aerobic oxidation of alkanes and alkenes in bacteria. A cluster of MO genes (
smoXYB1C1Z
) of thus-far-unknown function was found previously in the genomes of two
Mycobacterium
strains (NBB3 and NBB4) which grow on hydrocarbons. The predicted Smo enzymes have only moderate amino acid identity (30 to 60%) to their closest homologs, the soluble methane and butane MOs (sMMO and sBMO), and the
smo
gene cluster has a different organization from those of sMMO and sBMO. The
smoXYB1C1Z
genes of NBB4 were cloned into pMycoFos to make pSmo, which was transformed into
Mycobacterium smegmatis
mc
2
-155. Cells of mc
2
-155(pSmo) metabolized C
2
to C
4
alkanes, alkenes, and chlorinated hydrocarbons. The activities of mc
2
-155(pSmo) cells were 0.94, 0.57, 0.12, and 0.04 nmol/min/mg of protein with ethene, ethane, propane, and butane as substrates, respectively. The mc
2
-155(pSmo) cells made epoxides from ethene, propene, and 1-butene, confirming that Smo was an oxygenase. Epoxides were not produced from larger alkenes (1-octene and styrene). Vinyl chloride and 1,2-dichloroethane were biodegraded by cells expressing Smo, with production of inorganic chloride. This study shows that Smo is a functional oxygenase which is active against small hydrocarbons.
M. smegmatis
mc
2
-155(pSmo) provides a new model for studying sMMO-like monooxygenases.
Biosynthesis of Novel Pyoverdines by Domain Substitution in a Nonribosomal Peptide Synthetase of Pseudomonas aeruginosa
Authors: Calcott Mark J. , Owen Jeremy G. , Lamont Iain L. , Ackerley David F. 
Published: July 2014

ABSTRACT

Pyoverdine is a fluorescent nonribosomal peptide siderophore made by fluorescent pseudomonads. The
Pseudomonas aeruginosa
nonribosomal peptide synthetase (NRPS) PvdD contains two modules that each incorporate an
l
-threonine residue at the C-terminal end of pyoverdine. In an attempt to generate modified pyoverdine peptides, we substituted alternative-substrate-specifying adenylation (A) and peptide bond-catalyzing condensation (C) domains into the second module of PvdD. When just the A domain was substituted, the resulting strains produced only wild-type pyoverdine—at high levels if the introduced A domain specified threonine or at trace levels otherwise. The high levels of pyoverdine synthesis observed whenever the introduced A domain specified threonine indicated that these nonnative A domains were able to communicate effectively with the PvdD C domain. Moreover, the unexpected observation that non-threonine-specifying A domains nevertheless incorporated threonine into pyoverdine suggests that the native PvdD C domain exhibited stronger selectivity than these A domains for the incorporated amino acid substrate (i.e., misactivation of a threonine residue by the introduced A domains was more frequent than misincorporation of a nonthreonine residue by the PvdD C domain). In contrast, substitution of both the C and A domains of PvdD generated high yields of rationally modified pyoverdines in two instances, these pyoverdines having either a lysine or a serine residue in place of the terminal threonine. However, C-A domain substitution more commonly yielded a truncated peptide product, likely due to stalling of synthesis on a nonfunctional recombinant NRPS template.