1,171 research outputs found

    Accuracy Validation of an Automated Method for Prostate Segmentation in Magnetic Resonance Imaging

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    Three dimensional (3D) manual segmentation of the prostate on magnetic resonance imaging (MRI) is a laborious and time-consuming task that is subject to inter-observer variability. In this study, we developed a fully automatic segmentation algorithm for T2-weighted endorectal prostate MRI and evaluated its accuracy within different regions of interest using a set of complementary error metrics. Our dataset contained 42 T2-weighted endorectal MRI from prostate cancer patients. The prostate was manually segmented by one observer on all of the images and by two other observers on a subset of 10 images. The algorithm first coarsely localizes the prostate in the image using a template matching technique. Then, it defines the prostate surface using learned shape and appearance information from a set of training images. To evaluate the algorithm, we assessed the error metric values in the context of measured inter-observer variability and compared performance to that of our previously published semi-automatic approach. The automatic algorithm needed an average execution time of ∌60 s to segment the prostate in 3D. When compared to a single-observer reference standard, the automatic algorithm has an average mean absolute distance of 2.8 mm, Dice similarity coefficient of 82%, recall of 82%, precision of 84%, and volume difference of 0.5 cm in the mid-gland. Concordant with other studies, accuracy was highest in the mid-gland and lower in the apex and base. Loss of accuracy with respect to the semi-automatic algorithm was less than the measured inter-observer variability in manual segmentation for the same task.

    Utilization of a novel digital measurement tool for quantitative assessment of upper extremity motor dexterity: a controlled pilot study.

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    BackgroundThe current methods of assessing motor function rely primarily on the clinician's judgment of the patient's physical examination and the patient's self-administered surveys. Recently, computerized handgrip tools have been designed as an objective method to quantify upper-extremity motor function. This pilot study explores the use of the MediSens handgrip as a potential clinical tool for objectively assessing the motor function of the hand.MethodsEleven patients with cervical spondylotic myelopathy (CSM) were followed for three months. Eighteen age-matched healthy participants were followed for two months. The neuromotor function and the patient-perceived motor function of these patients were assessed with the MediSens device and the Oswestry Disability Index respectively. The MediSens device utilized a target tracking test to investigate the neuromotor capacity of the participants. The mean absolute error (MAE) between the target curve and the curve tracing achieved by the participants was used as the assessment metric. The patients' adjusted MediSens MAE scores were then compared to the controls. The CSM patients were further classified as either "functional" or "nonfunctional" in order to validate the system's responsiveness. Finally, the correlation between the MediSens MAE score and the ODI score was investigated.ResultsThe control participants had lower MediSens MAE scores of 8.09%±1.60%, while the cervical spinal disorder patients had greater MediSens MAE scores of 11.24%±6.29%. Following surgery, the functional CSM patients had an average MediSens MAE score of 7.13%±1.60%, while the nonfunctional CSM patients had an average score of 12.41%±6.32%. The MediSens MAE and the ODI scores showed a statistically significant correlation (r=-0.341, p<1.14×10⁻⁔). A Bland-Altman plot was then used to validate the agreement between the two scores. Furthermore, the percentage improvement of the the two scores after receiving the surgical intervention showed a significant correlation (r=-0.723, p<0.04).ConclusionsThe MediSens handgrip device is capable of identifying patients with impaired motor function of the hand. The MediSens handgrip scores correlate with the ODI scores and may serve as an objective alternative for assessing motor function of the hand

    A global database of lake surface temperatures collected by in situ and satellite methods from 1985–2009

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    Global environmental change has influenced lake surface temperatures, a key driver of ecosystem structure and function. Recent studies have suggested significant warming of water temperatures in individual lakes across many different regions around the world. However, the spatial and temporal coherence associated with the magnitude of these trends remains unclear. Thus, a global data set of water temperature is required to understand and synthesize global, long-term trends in surface water temperatures of inland bodies of water. We assembled a database of summer lake surface temperatures for 291 lakes collected in situ and/or by satellites for the period 1985–2009. In addition, corresponding climatic drivers (air temperatures, solar radiation, and cloud cover) and geomorphometric characteristics (latitude, longitude, elevation, lake surface area, maximum depth, mean depth, and volume) that influence lake surface temperatures were compiled for each lake. This unique dataset offers an invaluable baseline perspective on global-scale lake thermal conditions as environmental change continues

    Postediting prostate magnetic resonance imaging segmentation consistency and operator time using manual and computer-assisted segmentation: Multiobserver study

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    Prostate segmentation on T2w MRI is important for several diagnostic and therapeutic procedures for prostate cancer. Manual segmentation is time-consuming, labor-intensive, and subject to high interobserver variability. This study investigated the suitability of computer-assisted segmentation algorithms for clinical translation, based on measurements of interoperator variability and measurements of the editing time required to yield clinically acceptable segmentations. A multioperator pilot study was performed under three pre-and postediting conditions: manual, semiautomatic, and automatic segmentation. We recorded the required editing time for each segmentation and measured the editing magnitude based on five different spatial metrics. We recorded average editing times of 213, 328, and 393 s for manual, semiautomatic, and automatic segmentation respectively, while an average fully manual segmentation time of 564 s was recorded. The reduced measured postediting interoperator variability of semiautomatic and automatic segmentations compared to the manual approach indicates the potential of computer-assisted segmentation for generating a clinically acceptable segmentation faster with higher consistency. The lack of strong correlation between editing time and the values of typically used error metrics (ρ\u3c0.5) implies that the necessary postsegmentation editing time needs to be measured directly in order to evaluate an algorithm\u27s suitability for clinical translation

    Rapid and highly variable warming of lake surface waters around the globe

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    In this first worldwide synthesis of in situ and satellite‐derived lake data, we find that lake summer surface water temperatures rose rapidly (global mean = 0.34°C decade−1) between 1985 and 2009. Our analyses show that surface water warming rates are dependent on combinations of climate and local characteristics, rather than just lake location, leading to the counterintuitive result that regional consistency in lake warming is the exception, rather than the rule. The most rapidly warming lakes are widely geographically distributed, and their warming is associated with interactions among different climatic factors—from seasonally ice‐covered lakes in areas where temperature and solar radiation are increasing while cloud cover is diminishing (0.72°C decade−1) to ice‐free lakes experiencing increases in air temperature and solar radiation (0.53°C decade−1). The pervasive and rapid warming observed here signals the urgent need to incorporate climate impacts into vulnerability assessments and adaptation efforts for lakes

    Modeling Landowner Interactions and Development Patterns at the Urban Fringe

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    Population growth and unrestricted development policies are driving low-density urbanization and fragmentation of peri-urban landscapes across North America. While private individuals own most undeveloped land, little is known about how their decision-making processes shape landscape-scale patterns of urbanization over time. We introduce a hybrid agent-based modeling (ABM) – cellular automata (CA) modeling approach, developed for analyzing dynamic feedbacks between landowners’ decisions to sell their land for development, and resulting patterns of landscape fragmentation. Our modeling approach builds on existing conceptual frameworks in land systems modeling by integrating an ABM into an established grid-based land-change model – FUTURES. The decision-making process within the ABM involves landowner agents whose decision to sell their land to developers is a function of heterogeneous preferences and peer-influences (i.e., spatial neighborhood relationships). Simulating landowners’ decision to sell allows an operational link between the ABM and the CA module. To test our hybrid ABM-CA approach, we used empirical data for a rapidly growing region in North Carolina for parameterization. We conducted a sensitivity analysis focusing on the two most relevant parameters—spatial actor distribution and peer-influence intensity—and evaluated the dynamic behavior of the model simulations. The simulation results indicate different peer-influence intensities lead to variable landscape fragmentation patterns, suggesting patterns of spatial interaction among landowners indirectly affect landscape-scale patterns of urbanization and the fragmentation of undeveloped forest and farmland

    Utilization of a novel digital measurement tool for quantitative assessment of upper extremity motor dexterity: a controlled pilot study

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    BACKGROUND: The current methods of assessing motor function rely primarily on the clinician’s judgment of the patient’s physical examination and the patient’s self-administered surveys. Recently, computerized handgrip tools have been designed as an objective method to quantify upper-extremity motor function. This pilot study explores the use of the MediSens handgrip as a potential clinical tool for objectively assessing the motor function of the hand. METHODS: Eleven patients with cervical spondylotic myelopathy (CSM) were followed for three months. Eighteen age-matched healthy participants were followed for two months. The neuromotor function and the patient-perceived motor function of these patients were assessed with the MediSens device and the Oswestry Disability Index respectively. The MediSens device utilized a target tracking test to investigate the neuromotor capacity of the participants. The mean absolute error (MAE) between the target curve and the curve tracing achieved by the participants was used as the assessment metric. The patients’ adjusted MediSens MAE scores were then compared to the controls. The CSM patients were further classified as either “functional” or “nonfunctional” in order to validate the system’s responsiveness. Finally, the correlation between the MediSens MAE score and the ODI score was investigated. RESULTS: The control participants had lower MediSens MAE scores of 8.09%±1.60%, while the cervical spinal disorder patients had greater MediSens MAE scores of 11.24%±6.29%. Following surgery, the functional CSM patients had an average MediSens MAE score of 7.13%±1.60%, while the nonfunctional CSM patients had an average score of 12.41%±6.32%. The MediSens MAE and the ODI scores showed a statistically significant correlation (r=-0.341, p<1.14×10(-5)). A Bland-Altman plot was then used to validate the agreement between the two scores. Furthermore, the percentage improvement of the the two scores after receiving the surgical intervention showed a significant correlation (r=-0.723, p<0.04). CONCLUSIONS: The MediSens handgrip device is capable of identifying patients with impaired motor function of the hand. The MediSens handgrip scores correlate with the ODI scores and may serve as an objective alternative for assessing motor function of the hand. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1743-0003-11-121) contains supplementary material, which is available to authorized users

    A Systematic Review of How Multiple Stressors from an Extreme Event Drove Ecosystem-Wide Loss of Resilience in an Iconic Seagrass Community

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    A central question in contemporary ecology is how climate change will alter ecosystem structure and function across scales of space and time. Climate change has been shown to alter ecological patterns from individuals to ecosystems, often with negative implications for ecosystem functions and services. Furthermore, as climate change fuels more frequent and severe extreme climate events (ECEs) like marine heatwaves (MHWs), such acute events become increasingly important drivers of rapid ecosystem change. However, our understanding of ECE impacts is hampered by limited collection of broad scale in situ data where such events occur. In 2011, a MHW known as the Ningaloo Niño bathed the west coast of Australia in waters up to 4°C warmer than normal summer temperatures for almost 2 months over 1000s of kilometres of coastline. We revisit published and unpublished data on the effects of the Ningaloo Niño in the seagrass ecosystem of Shark Bay, Western Australia (24.6 – 26.6o S), at the transition zone between temperate and tropical seagrasses. Therein we focus on resilience, including resistance to and recovery from disturbance across local, regional and ecosystem-wide spatial scales and over the past 8 yearsThermal effects on temperate seagrass health were severe and exacerbated by simultaneous reduced light conditions associated with sediment inputs from record floods in the south-eastern embayment and from increased detrital loads and sediment destabilisation. Initial extensive defoliation of Amphibolis antarctica, the dominant seagrass, was followed by rhizome death that occurred in 60-80% of the bay’s meadows, equating to decline of over 1000 km2 of meadows. This loss, driven by direct abiotic forcing, has persisted, while indirect biotic effects (e.g. dominant seagrass loss) have allowed colonisation of some areas by small fast-growing tropical species (e.g. Halodule uninervis). Those biotic effects also impacted multiple consumer populations including turtles and dugongs, with implications for species dynamics, food web structure, and ecosystem recovery. We show multiple stressors can combine to evoke extreme ecological responses by pushing ecosystems beyond their tolerance. Finally, both direct abiotic and indirect biotic effects need to be explicitly considered when attempting to understand and predict how ECEs will alter marine ecosystem dynamics

    LSST Science Book, Version 2.0

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    A survey that can cover the sky in optical bands over wide fields to faint magnitudes with a fast cadence will enable many of the exciting science opportunities of the next decade. The Large Synoptic Survey Telescope (LSST) will have an effective aperture of 6.7 meters and an imaging camera with field of view of 9.6 deg^2, and will be devoted to a ten-year imaging survey over 20,000 deg^2 south of +15 deg. Each pointing will be imaged 2000 times with fifteen second exposures in six broad bands from 0.35 to 1.1 microns, to a total point-source depth of r~27.5. The LSST Science Book describes the basic parameters of the LSST hardware, software, and observing plans. The book discusses educational and outreach opportunities, then goes on to describe a broad range of science that LSST will revolutionize: mapping the inner and outer Solar System, stellar populations in the Milky Way and nearby galaxies, the structure of the Milky Way disk and halo and other objects in the Local Volume, transient and variable objects both at low and high redshift, and the properties of normal and active galaxies at low and high redshift. It then turns to far-field cosmological topics, exploring properties of supernovae to z~1, strong and weak lensing, the large-scale distribution of galaxies and baryon oscillations, and how these different probes may be combined to constrain cosmological models and the physics of dark energy.Comment: 596 pages. Also available at full resolution at http://www.lsst.org/lsst/sciboo
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