bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computerized assessment of pulmonary fissure integrity using high resolution CT
Authors: Pu Jiantao , Fuhrman Carl , Durick Janet , Leader Joseph K. , Klym Amy , Sciurba Frank C. , Gur David 
Published: August 2010

Purpose:Knowledge of pulmonary interlobar fissure integrity is of interest in a number of clinical and investigational applications. The authors developed and tested a high resolution CT based automated computerized scheme for this purpose.Methods:The fissure integrity assessment scheme consists of the following steps: (1) Fissure detection, (2) individual fissure identification, (3) fissure type determination, (4) “complete” interlobe surface estimation, and (5) fissure integrity estimation. For evaluation purposes, 50 anonymized chest CT examinations were ascertained and the complete and “incomplete” regions of the fissures of interest were manually marked by two experienced radiologists. After applying the scheme to the same examinations, differences among fissure percent completeness estimates based on the radiologists’ manual markings and the automated computerized scheme were computed and compared.Results:Average differences in estimated fissure percent completeness (integrity) between the results of the computerized scheme and that based on each of the two radiologists’ markings were, , and for the right major fissures, the right minor fissures, and the left major fissures, respectively. The differences between results based on radiologists’ markings for the same fissures were , , and , respectively. The difference among the three matched measurement sets for each fissure were statistically significant (Friedman's test, ) but paired comparisons showed that much of the observed difference was related to inter‐reader differences rather than reader‐computerized scheme differences. Computerized estimates were correlated with each of the radiologist's estimates (Spearman, ).Conclusions:While variability between readers‐based estimates of fissure integrity was smaller than differences between the computerized scheme and each of the readers, the result reported here are quite encouraging in that the magnitude of these differences were in the same magnitude, demonstrating the feasibility of using a computerized scheme for this purpose.
Comparison between diffusion‐weighted imaging, ‐weighted, and postcontrast ‐weighted imaging after MR‐guided, high intensity, focused ultrasound treatment of uterine leiomyomata: Preliminary results
Authors: Jacobs Michael A. , Gultekin David H. , Kim Hyun S. 
Published: August 2010

Purpose: To investigate the comparison between diffusion‐weighted imaging (DWI),‐weighted imaging, and contrast ‐weighted imaging in uterine leiomyoma following treatment by magnetic resonance imaging‐guided, high intensity focused ultrasound surgery (MRg‐HIFUS).Methods: Twenty one patients with clinical symptoms of uterine leiomyoma (fibroids) were treated by MRg‐HIFUS using an integrated 1.5T MRI‐HIFUS system. MRI parameters consisted of DWI, , and ‐weighted fast spoiled gradient echo before and after contrast. The post‐MRg‐HIFUS treatment volume in the fibroid was assessed by and DWI. Trace apparent diffusion coefficient maps were constructed for quantitative analysis. The regions of the treated uterine tissue were defined by a semisupervised segmentation method called the “eigenimage filter,” using both and DWI. Signal‐to‐noise ratios were determined for the pretreatment images. Segmented regions were tested by a similarity index for congruence. Descriptive, regression, and Bland–Altman statistics were calculated.Results: All the patients exhibited heterogeneously increased DWI signal intensity localized in the treated fibroid regions and were colocalized with the defined area. The mean pretreatment signal intensity ratios were and . The congruence between the regions was significant, with a similarity of 84% and a difference of 8% between the regions. Regression analyses of the and DWI segmented treatment volumes were found to be significantly correlated with the linear equation, . There is good agreement between the regions defined by cT1WI and DWI in most of the cases as shown from the Bland–Altman plots.Conclusions: Diffusion‐weighted imaging exhibited excellent agreement, congruence, and correlation with the‐defined region of treatment in uterine fibroid. Therefore, DWI could be useful as an adjunct for assessing treatment of uterine fibroids by MRg‐HIFUS.
Lung dosimetry in a linac‐MRI radiotherapy unit with a longitudinal magnetic field
Authors: Kirkby C. , Murray B. , Rathee S. , Fallone B. G. 
Published: August 2010

Purpose: There is interest in developing linac‐MR systems for MRI‐guided radiation therapy. To date, the designs for such linac‐MR devices have been restricted to a transverse geometry where the static magnetic field is oriented perpendicular to the direction of the incident photon beam. This work extends possibilities in this field by proposing and examining by Monte Carlo simulations, a probable longitudinal configuration where the magnetic field is oriented in the same direction as the photon beam.Methods: The EGSnrc Monte Carlo (MC) radiation transport codes with algorithms implemented to account for the magnetic field deflection of charged particles were used to compare dose distributions for linac‐MR systems in transverse and longitudinal geometries. Specifically, the responses to a 6 MV pencil photon beam incident on water and lung slabs were investigated for 1.5 and 3.0 T magnetic fields. Further a five field lung plan was simulated in the longitudinal and transverse geometries across a range of magnetic field strengths from 0.2 through 3.0 T.Results: In a longitudinal geometry, the magnetic field is shown to restrict the radial spread of secondary electrons to a small degree in water, but significantly in low density tissues such as lung in contrast to the lateral shift in dose distribution seen in the transverse geometry. These effects extend to the patient case, where the longitudinal configuration demonstrated dose distributions more tightly confined to the primary photon fields, which increased dose to the planning target volume (PTV), bettered dose homogeneity within a heterogeneous (in density) PTV, and reduced the tissue interface effects associated with the transverse geometry.Conclusions: Dosimetry issues observed in a transverse linac‐MR geometry such as changes to the depth dose distribution and tissue interface effects were significantly reduced or eliminated in a longitudinal geometry on a representative lung plan. Further, an increase in dose to the PTV, resulting from the magnetic field confining electrons to the forward direction, shows potential for a reduction in dose to the surrounding tissues.
A wavelet‐based SPECT reconstruction algorithm for nonuniformly attenuated Radon transform
Authors: Wen Junhai , Kong Lingkai 
Published: August 2010

Purpose:Single photon emission computed tomography (SPECT) is a tomography technique that can greatly show information about the metabolic activity in the body and improve the clinical diagnosis. In SPECT, because of photoelectric absorption and Compton scattering, the emitted gamma photons are attenuated inside the body before arriving at the detector. The goal of quantitative SPECT reconstruction is to obtain an accurate image of the radioactivity distribution in the interested area of a human body, so the compensation for nonuniform attenuation and the treatment of Poisson noise are necessary in the quantitative SPECT reconstruction.Methods:The authors know that the wavelet transform has characteristics of multiresolution and localized nature, and these characteristics can be applied for denoising and localized reconstruction. Based on the explicit inversion formula for the attenuated Radon transform, the authors present a wavelet‐based SPECT reconstruction algorithm with compensation for nonuniform attenuation.Results:The wavelet‐based SPECT reconstruction algorithm offers the ability for denoising in the reconstruction processing. In simulation, 128 projections were simulated evenly spaced over 360° by a circular orbit, each with 128 bins. Simulation results show that the wavelet‐based denoising is effective in SPECT reconstruction.Conclusions:The authors present a wavelet‐based SPECT reconstruction algorithm with compensation for nonuniform attenuation. The reconstruction results from computer simulations show that the wavelet‐based SPECT reconstruction algorithm is accurate.
Clinical application and validation of an iterative forward projection matching algorithm for permanent brachytherapy seed localization from conebeam‐CT x‐ray projections
Authors: Pokhrel Damodar , Murphy Martin J. , Todor Dorin A. , Weiss Elisabeth , Williamson Jeffrey F. 
Published: August 2010

Purpose:To experimentally validate a new algorithm for reconstructing the 3D positions of implanted brachytherapy seeds from postoperatively acquired 2D conebeam‐CT (CBCT) projection images.Methods:The iterative forward projection matching (IFPM) algorithm finds the 3D seed geometry that minimizes the sum of the squared intensity differences between computed projections of an initial estimate of the seed configuration and radiographic projections of the implant. In‐house machined phantoms, containing arrays of 12 and 72 seeds, respectively, are used to validate this method. Also, four postimplant patients are scanned using an ACUITY digital simulator. Three to ten x‐ray images are selected from the CBCT projection set and processed to create binary seed‐only images. To quantify IFPM accuracy, the reconstructed seed positions are forward projected and overlaid on the measured seed images to find the nearest‐neighbor distance between measured and computed seed positions for each image pair. Also, the estimated 3D seed coordinates are compared to known seed positions in the phantom and clinically obtained VariSeed planning coordinates for the patient data.Results:For the phantom study, seed localization error is. For all four patient cases, the mean registration error is better than 1 mm while compared against the measured seed projections. IFPM converges in 20–28 iterations, with a computation time of about 1.9–2.8 min/iteration on a 1 GHz processor.Conclusions:The IFPM algorithm avoids the need to match corresponding seeds in each projection as required by standard back‐projection methods. The authors’ results demonstrate accuracy in reconstructing the 3D positions of brachytherapy seeds from the measured 2D projections. This algorithm also successfully localizes overlapping clustered and highly migrated seeds in the implant.
Optimizing principal component models for representing interfraction variation in lung cancer radiotherapy
Authors: Badawi Ahmed M. , Weiss Elisabeth , Sleeman William C. , Yan Chenyu , Hugo Geoffrey D. 
Published: August 2010

Purpose:To optimize modeling of interfractional anatomical variation during active breath‐hold radiotherapy in lung cancer using principal component analysis (PCA).Methods:In 12 patients analyzed, weekly CT sessions consisting of three repeat intrafraction scans were acquired with active breathing control at the end of normal inspiration. The gross tumor volume (GTV) and lungs were delineated and reviewed on the first week image by physicians and propagated to all other images using deformable image registration. PCA was used to model the target and lung variability during treatment. Four PCA models were generated for each specific patient: (1) Individual models for the GTV and each lung from one image per week (week to week, W2W); (2) a W2W composite model of all structures; (3) individual models using all images (weekly plus repeat intrafraction images, allscans); and (4) composite model with all images. Models were reconstructed retrospectively (using all available images acquired) and prospectively (using only data acquired up to a time point during treatment). Dominant modes representing at least 95% of the total variability were used to reconstruct the observed anatomy. Residual reconstruction error between the model‐reconstructed and observed anatomy was calculated to compare the accuracy of the models.Results:An average of 3.4 and 4.9 modes was required for the allscans models, for the GTV and composite models, respectively. The W2W model required one less mode in 40% of the patients. For the retrospective composite W2W model, the average reconstruction error was, which increased to when the allscans model was used. Individual and composite models did not have significantly different errors (, paired ‐test). The average reconstruction error for the prospective models of the GTV stabilized after four measurements at and for the composite model after five measurements at .Conclusions:Retrospective PCA models were capable of reconstructing original GTV and lung shapes and positions within several millimeters with three to four dominant modes, on average. Prospective models achieved similar accuracy after four to five measurements.
Detectability of perfusion defect in five‐dimensional gated‐dynamic cardiac SPECT images
Authors: Niu Xiaofeng , Yang Yongyi , King Michael A. , Wernick Miles N. 
Published: August 2010

Purpose:In previous work, the authors developed and demonstrated the concept of an image reconstruction procedure aimed to unify gated and dynamic nuclear cardiac imaging, which the authors have termedfive‐dimensional (5D) SPECT. Gated imaging permits the clinician to evaluate wall motion and, through the use of stress and rest scans, allows perfusion defects to be observed. Dynamic imaging depicts kinetics in the myocardium, which can be used to evaluate perfusion, but traditional dynamic images are motionless and do not depict wall motion. In this article, the authors investigate the degree to which perfusion defects can be detected from the dynamic information conveyed by 5D images, a problem that is particularly challenging in the absence of multiple fast camera rotations.Methods:The authors first demonstrate the usefulness of dynamic reconstructed images for perfusion detection by using linear discriminant analyses (Fisher linear discriminant analysis and principal component analysis) and a numerical channelized Hotelling observer. The authors then derive three types of discriminant metrics for characterizing the temporal kinetic information in reconstructed dynamic images for differentiating perfusion defects from normal cardiac perfusion, which are the Fisher linear discriminant map, temporal derivative map, and kinetic parametric images.Results:Results are based on the NURBS‐based cardiac‐torso phantom with simulation of Tc99m‐teboroxime as the imaging agent. The derived metric maps and quantitative contrast‐to‐noise ratio results demonstrate that the reconstructed dynamic images could yield higher detectability of the perfusion defect than conventional gated reconstruction while providing wall motion information simultaneously.Conclusions:The proposed metrics can be used to produce new types of visualizations, showing wall motion and perfusion information, that may potentially be useful for clinical evaluation. Since 5D imaging permits wall motion and kinetics to be observed simultaneously, it may ultimately obviate the need for separate stress and rest scans.
Prevalence, Mutation Patterns, and Effects on Protease Inhibitor Susceptibility of the L76V Mutation in HIV-1 Protease
Authors: Young Thomas P. , Parkin Neil T. , Stawiski Eric , Pilot-Matias Tami , Trinh Roger , Kempf Dale J. , Norton Michael 
Published: August 2010

ABSTRACTPatterns of HIV-1 protease inhibitor (PI) resistance-associated mutations (RAMs) and effects on PI susceptibility associated with the L76V mutation were studied in a large database. Of 20,501 sequences with ≥1 PI RAM, 3.2% contained L76V; L76V was alone in 0.04%. Common partner mutations included M46I, I54V, V82A, I84V, and L90M. L76V was associated with a 2- to 6-fold decrease in susceptibility to lopinavir, darunavir, amprenavir, and indinavir and a 7- to 8-fold increase in susceptibility to atazanavir and saquinavir.
Peptidoglycan Deacetylation in
Helicobacter pylori
Contributes to Bacterial Survival by Mitigating Host Immune Responses
Authors: Wang Ge , Maier Susan E. , Lo Leja F. , Maier George , Dosi Shruti , Maier Robert J. 
Published: August 2010

ABSTRACT

An oxidative stress-induced enzyme, peptidoglycan deacetylase (PgdA), in the human gastric pathogen
Helicobacter pylori
was previously identified and characterized. In this study, we constructed
H. pylori pgdA
mutants in two mouse-adapted strains, X47 and B128, to investigate the role of PgdA
in vivo
(to determine the mutants’ abilities to colonize mice and to induce an immune response).
H. pylori pgdA
mutant cells showed increased sensitivity to lysozyme compared to the sensitivities of the parent strains. We demonstrated that the expression of PgdA was significantly induced (3.5-fold) when
H. pylori
cells were in contact with macrophages, similar to the effect observed with oxidative stress as the environmental inducer. Using a mouse infection model, we first examined the mouse colonization ability of an
H. pylori pgdA
mutant in X47, a strain deficient in the major pathway (
cag
pathogenicity island [PAI] encoded) for delivery of peptidoglycan into host cells. No animal colonization difference between the wild type and the mutant was observed 3 weeks after inoculation. However, the
pgdA
mutant showed a significantly attenuated ability to colonize mouse stomachs (9-fold-lower bacterial load) at 9 weeks postinoculation. With the
cag
PAI-positive strain B128, a significant colonization difference between the wild type and the
pgdA
mutant was observed at 3 weeks postinoculation (1.32 × 10
4
versus 1.85 × 10
3
CFU/gram of stomach). To monitor the immune responses elicited by
H. pylori
in the mouse infection model, we determined the concentrations of cytokines present in mouse sera. In the mice infected with the
pgdA
mutant strain, we observed a highly significant increase in the level of MIP-2. In addition, significant increases in interleukin-10 and tumor necrosis factor alpha in the
pgdA
mutant-infected mice compared to the levels in the wild-type
H. pylori
-infected mice were also observed. These results indicated that
H. pylori
peptidoglycan deacetylation is an important mechanism for mitigating host immune detection; this likely contributes to pathogen persistence.
Automated monitoring of clusters of falls associated with severe winter weather using the BioSense system
Authors: Dey Achintya N , Hicks Peter , Benoit Stephen , Tokars Jerome I 
Published: August 2010

ObjectivesTo identify and characterise clusters of emergency department (ED) visits for fall injuries during the 2007–2008 winter season.MethodsHospital ED chief complaints and diagnoses from hospitals reporting to the Centers for Disease Control and Prevention BioSense system were analysed. The authors performed descriptive analyses, used time series charts on data aggregated by metropolitan statistical areas (MSAs), and used SaTScan to find spatial–temporal clusters of visits from falls.ResultsIn 2007–2008, 17 clusters of falls in 13 MSAs were found; the median number of excess ED visits for falls was 71 per day. SaTScan identified 11 clusters of falls, of which seven corresponded to MSA clusters found by time series and five included more than one state/district. Most clusters coincided with known periods of snowfall or freezing rain.ConclusionThe results show the role that a national automated system can play in tracking widespread injuries. Such a system could be harnessed to assist with prevention strategies.
Determinants of agricultural injury: a novel application of population health theory
Authors: Pickett William , Hagel Louise M , Day Andrew G , Day Lesley , Sun Xiaoqun , Brison Robert J , Marlenga Barbara L , King Matthew , Crowe Trever , Pahwa Punam , Koehncke Niels , Dosman James 
Published: August 2010

Objectives(1) To apply novel population health theory to the modelling of injury experiences in one particular research context. (2) To enhance understanding of the conditions and practices that lead to farm injury.DesignProspective, cohort study conducted over 2 years (2007–09).Setting50 rural municipalities in the Province of Saskatchewan, Canada.Subjects5038 participants from 2169 Saskatchewan farms, contributing 10 092 person-years of follow-up.Main measuresIndividual exposure: self-reported times involved in farm work. Contextual factors: scaled measures describe socioeconomic, physical, and cultural farm environments. Outcome: time to first self-reported farm injury.Results450 farm injuries were reported for 370 individuals on 338 farms over 2 years of follow-up. Times involved in farm work were strongly and consistently related to time to first injury event, with strong monotonic increases in risk observed between none, part-time, and full-time work hour categories. Relationships between farm work hours and time to first injury were not modified by the contextual factors. Respondents reporting high versus low levels of physical farm hazards at baseline experienced increased risks for farm injury on follow-up (HR 1.54; 95% CI 1.16 to 1.47).ConclusionsBased on study findings, firm conclusions cannot be drawn about the application of population health theory to the study of farm injury aetiology. Injury prevention efforts should continue to focus on: (1) sound occupational health and safety practices associated with long work hours; (2) physical risks and hazards on farms.
A real-time Java chip-multiprocessor
Authors: Pitter Christof , Schoeberl Martin 
Published: August 2010

Chip-multiprocessors are an emerging trend for embedded systems. In this article, we introduce a real-time Java multiprocessor called JopCMP. It is a symmetric shared-memory multiprocessor, and consists of up to eight Java Optimized Processor (JOP) cores, an arbitration control device, and a shared memory. All components are interconnected via a system on chip bus. The arbiter synchronizes the access of multiple CPUs to the shared main memory. In this article, three different arbitration policies are presented, evaluated, and compared with respect to their real-time and average-case performance: a fixed priority, a fair-based, and a time-sliced arbiter.
Tasks running on different CPUs of a chip-multiprocessor (CMP) influence each others' execution times when accessing a shared memory. Therefore, the system needs an arbiter that is able to limit the worst-case execution time of a task running on a CPU, even though tasks executing simultaneously on other CPUs access the main memory. Our research shows that timing analysis is in fact possible for homogeneous multiprocessor systems with a shared memory. The timing analysis of tasks, executing on the CMP using time-sliced memory arbitration, leads to viable worst-case execution time bounds.
The time-sliced arbiter divides the memory access time into equal time slots, one time slot for each CPU. This memory arbitration scheme allows for a calculation of upper bounds of Java application worst-case execution times, depending on the number of CPUs, the time slot size, and the memory access time. Examples of worst-case execution time calculation are presented, and the analyzed results of a real-world application task are compared to measured execution time results. Finally, we evaluate the tradeoffs when using a time-predictable solution compared to using average-case optimized chip-multiprocessors, applying three different benchmarks. These experiments are carried out by executing the programs on the CMP prototype.