1,345 results on '"Brown, Matthew P."'
Search Results
102. Upcycling Compact Discs for Flexible and Stretchable Bioelectronic Applications
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Brown, Matthew S., Somma, Louis, Mendoza, Melissa, Noh, Yeonsik, Mahler, Gretchen J., and Koh, Ahyeon
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- 2022
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103. Diminished carbon and nitrate assimilation drive changes in diatom elemental stoichiometry independent of silicification in an iron-limited assemblage
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Maniscalco, Michael A., Brzezinski, Mark A., Lampe, Robert H., Cohen, Natalie R., McNair, Heather M., Ellis, Kelsey A., Brown, Matthew, Till, Claire P., Twining, Benjamin S., Bruland, Kenneth W., Marchetti, Adrian, and Thamatrakoln, Kimberlee
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- 2022
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104. Evolving etiologies and rates of revision total knee arthroplasty: a 10-year institutional report
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Brown, Matthew L., Javidan, Pooya, Early, Sam, and Bugbee, William
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- 2022
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105. The changes in structural and functional properties of the heart due to a programme of intra-dialytic cycling
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Graham-Brown, Matthew P. M.
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612.1 ,Medical and Health Sciences not elsewhere classified ,Exercise ,Cycling ,Dialysis ,Haemodialysis ,CKD ,Renal ,Cardiac MRI - Published
- 2018
106. Deep Reinforcement Learning for Dexterous Manipulation with Concept Networks
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Gudimella, Aditya, Story, Ross, Shaker, Matineh, Kong, Ruofan, Brown, Matthew, Shnayder, Victor, and Campos, Marcos
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Computer Science - Artificial Intelligence ,Computer Science - Robotics - Abstract
Deep reinforcement learning yields great results for a large array of problems, but models are generally retrained anew for each new problem to be solved. Prior learning and knowledge are difficult to incorporate when training new models, requiring increasingly longer training as problems become more complex. This is especially problematic for problems with sparse rewards. We provide a solution to these problems by introducing Concept Network Reinforcement Learning (CNRL), a framework which allows us to decompose problems using a multi-level hierarchy. Concepts in a concept network are reusable, and flexible enough to encapsulate feature extractors, skills, or other concept networks. With this hierarchical learning approach, deep reinforcement learning can be used to solve complex tasks in a modular way, through problem decomposition. We demonstrate the strength of CNRL by training a model to grasp a rectangular prism and precisely stack it on top of a cube using a gripper on a Kinova JACO arm, simulated in MuJoCo. Our experiments show that our use of hierarchy results in a 45x reduction in environment interactions compared to the state-of-the-art on this task.
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- 2017
107. Efficient generalized Golub-Kahan based methods for dynamic inverse problems
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Chung, Julianne, Saibaba, Arvind K., Brown, Matthew, and Westman, Erik
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Mathematics - Numerical Analysis - Abstract
We consider efficient methods for computing solutions to and estimating uncertainties in dynamic inverse problems, where the parameters of interest may change during the measurement procedure. Compared to static inverse problems, incorporating prior information in both space and time in a Bayesian framework can become computationally intensive, in part, due to the large number of unknown parameters. In these problems, explicit computation of the square root and/or inverse of the prior covariance matrix is not possible. In this work, we develop efficient, iterative, matrix-free methods based on the generalized Golub-Kahan bidiagonalization that allow automatic regularization parameter and variance estimation. We demonstrate that these methods can be more flexible than standard methods and develop efficient implementations that can exploit structure in the prior, as well as possible structure in the forward model. Numerical examples from photoacoustic tomography, deblurring, and passive seismic tomography demonstrate the range of applicability and effectiveness of the described approaches. Specifically, in passive seismic tomography, we demonstrate our approach on both synthetic and real data. To demonstrate the scalability of our algorithm, we solve a dynamic inverse problem with approximately $43,000$ measurements and $7.8$ million unknowns in under $40$ seconds on a standard desktop., Comment: 27 pages, 12 figures
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- 2017
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108. Unsupervised Learning of Depth and Ego-Motion from Video
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Zhou, Tinghui, Brown, Matthew, Snavely, Noah, and Lowe, David G.
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Computer Science - Computer Vision and Pattern Recognition - Abstract
We present an unsupervised learning framework for the task of monocular depth and camera motion estimation from unstructured video sequences. We achieve this by simultaneously training depth and camera pose estimation networks using the task of view synthesis as the supervisory signal. The networks are thus coupled via the view synthesis objective during training, but can be applied independently at test time. Empirical evaluation on the KITTI dataset demonstrates the effectiveness of our approach: 1) monocular depth performing comparably with supervised methods that use either ground-truth pose or depth for training, and 2) pose estimation performing favorably with established SLAM systems under comparable input settings., Comment: Accepted to CVPR 2017. Project webpage: https://people.eecs.berkeley.edu/~tinghuiz/projects/SfMLearner/
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- 2017
109. Pose2Instance: Harnessing Keypoints for Person Instance Segmentation
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Tripathi, Subarna, Collins, Maxwell, Brown, Matthew, and Belongie, Serge
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Human keypoints are a well-studied representation of people.We explore how to use keypoint models to improve instance-level person segmentation. The main idea is to harness the notion of a distance transform of oracle provided keypoints or estimated keypoint heatmaps as a prior for person instance segmentation task within a deep neural network. For training and evaluation, we consider all those images from COCO where both instance segmentation and human keypoints annotations are available. We first show how oracle keypoints can boost the performance of existing human segmentation model during inference without any training. Next, we propose a framework to directly learn a deep instance segmentation model conditioned on human pose. Experimental results show that at various Intersection Over Union (IOU) thresholds, in a constrained environment with oracle keypoints, the instance segmentation accuracy achieves 10% to 12% relative improvements over a strong baseline of oracle bounding boxes. In a more realistic environment, without the oracle keypoints, the proposed deep person instance segmentation model conditioned on human pose achieves 3.8% to 10.5% relative improvements comparing with its strongest baseline of a deep network trained only for segmentation.
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- 2017
110. Non-destructive on-machine inspection of machining-induced deformed layers.
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Brown, Matthew, Crawforth, Pete, and Curtis, David
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SUSTAINABILITY ,WORKPIECES ,SURFACE topography ,MATERIAL plasticity ,X-ray diffraction ,COOLANTS - Abstract
Complete inspection of workpiece surface integrity invariably involves a form of destructive testing to enable the assessment of microstructural defects such as machining-induced white layers and near-surface plastic deformation. The incumbent offline and destructive microscopy inspection process is incompatible with both a digital and sustainable manufacturing vision of zero waste, as such, a non-destructive technique which utilises a novel X-ray diffraction surface integrity inspection method (XRD-SIIM) has been developed. This approach has been designed to complement traditional machinability-type assessments of tool life and machined surface topography, establishing a new process flow for validation. In this paper, for the first time, non-destructive on-machine validation of workpiece microstructural surface integrity is demonstrated, via a comparative investigation into the effect of insert grade, cutting speed and coolant delivery method on the depth of the imparted plastic deformation depth. It is shown that XRD-SIIM allows repeatable, non-destructive determination of deformed layers within a typical machining centre enclosure, with comparable findings to the incumbent cross-sectional microscopy approach. The generation of surface integrity digital fingerprints of a machining operation facilitates rapid comparison between testing variables, with a transition to an objective quantifiable assessment rather than one which open to subjectivity. In turn, XRD-SIIM expedites the development and benchmarking of new operations, tooling, materials, or coolant. [ABSTRACT FROM AUTHOR]
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- 2024
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111. Skeletal Muscle Texture Assessment Using Ultrasonography: Comparison with Magnetic Resonance Imaging in Chronic Kidney Disease.
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Wilkinson, Thomas J., Baker, Luke A., Watson, Emma L., Nikopoulou, Katerina, Karatzaferi, Christina, Graham-Brown, Matthew PM., Smith, Alice C., and Sakkas, Giorgos K.
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Skeletal muscle dysfunction is common in chronic kidney disease (CKD). Of interest is the concept of "muscle quality," of which measures include ultrasound-derived echo intensity (EI). Alternative parameters of muscle texture, for example, gray level of co-occurrence matrix (GCLM), are available and may circumvent limitations in EI. The validity of EI is limited in humans, particularly in chronic diseases. This study aimed to investigate the associations between ultrasound-derived parameters of muscle texture with MRI. Images of the thigh were acquired using a 3 Tesla MRI scanner. Quantification of muscle (contractile), fat (non-contractile), and miscellaneous (connective tissue, fascia) components were estimated. Anatomical rectus femoris cross-sectional area was measured using B-mode 2D ultrasonography. To assess muscle texture, first (i.e., EI)- and second (i.e., GLCM)-order statistical analyses were performed. Fourteen participants with CKD were included (age: 58.0 ± 11.9 years, 50% male, eGFR: 27.0 ± 7.4 ml/min/1.73m
2 , 55% Stage 4). Higher EI was associated with lower muscle % (quadriceps: β = −.568, p =.034; hamstrings: β = −.644, p =.010). Higher EI was associated with a higher fat % in the hamstrings (β = −.626, p =.017). A higher angular second moment from GLCM analysis was associated with greater muscle % (β =.570, p =.033) and lower fat % (β = −.534, p =.049). A higher inverse difference moment was associated with greater muscle % (β =.610, p =.021 and lower fat % (β = −.599, p =.024). This is the first study to investigate the associations between ultrasound-derived parameters of muscle texture with MRI. Our preliminary findings suggest ultrasound-derived texture analysis provides a novel indicator of reduced skeletal muscle % and thus increased intramuscular fat. [ABSTRACT FROM AUTHOR]- Published
- 2024
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112. Improving self‐management behaviour through a digital lifestyle intervention: An internal pilot study.
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Lightfoot, Courtney J., Wilkinson, Thomas J., Vadaszy, Noemi, Graham‐Brown, Matthew P. M., Davies, Melanie J., Yates, Thomas, and Smith, Alice C.
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TREATMENT of chronic kidney failure ,PATIENT education ,SELF-management (Psychology) ,BEHAVIOR modification ,HUMAN services programs ,RESEARCH funding ,MEDICAL care ,EDUCATIONAL outcomes ,DIGITAL health ,STATISTICAL sampling ,PILOT projects ,BLIND experiment ,INTERVIEWING ,EVALUATION of human services programs ,INTERNET ,RANDOMIZED controlled trials ,CHRONIC kidney failure ,CONTROL groups ,PRE-tests & post-tests ,LONGITUDINAL method ,THEMATIC analysis ,HEALTH behavior ,RESEARCH ,RESEARCH methodology ,COMPARATIVE studies ,PATIENT satisfaction ,PATIENT participation ,BEHAVIOR therapy - Abstract
Background: Self‐management is a key component of successful chronic kidney disease (CKD) management. Here, we present the findings from the internal pilot of a multicentre randomised controlled trial (RCT) aimed to test the effect of a digital self‐management programme ('My Kidneys & Me' (MK&M)). Methods: Participants (aged ≥18 years and CKD stages 3‐4) were recruited from hospital kidney services across England. Study processes were completed virtually. Participants were randomised 2:1 to either intervention (MK&M) or control group. The first 60 participants recruited were included in a 10‐week internal pilot which assessed study feasibility and acceptability against pre‐specified progression criteria: 1) eligibility and recruitment, acceptability of 2) randomisation and 3) outcomes, 4) MK&M activation, and 5) retention and attrition rates. Semi‐structured interviews further explored views on trial participation. Results: Of the 60 participants recruited, 41 were randomised to MK&M and 19 to control. All participants completed baseline measures and 62% (n=37) completed post‐intervention outcome measures. All progression criteria met the minimum thresholds to proceed. Nine participants were interviewed. The themes identified were satisfaction with study recruitment processes (openness to participate, reading and agreeing to "terms and conditions"), acceptability of study design (remote study participation, acceptability of randomisation, completion of online assessment(s)), and methods to improve recruitment and retention (personalised approach, follow‐up communication). Conclusion: This internal pilot demonstrated the feasibility and acceptability of a virtually run RCT. Progression criteria thresholds to proceed to the definitive RCT were met. Areas for improvement were identified and protocol amendments were made to improve trial delivery. [ABSTRACT FROM AUTHOR]
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- 2024
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113. Incorporating Noncovalent Interactions in Transfer Learning Gaussian Process Regression Models for Molecular Simulations.
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Brown, Matthew L., Isamura, Bienfait K., Skelton, Jonathan M., and Popelier, Paul L. A.
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- 2024
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114. Design and Synthesis of Clinical Candidate PF-06852231 (CVL-231): A Brain Penetrant, Selective, Positive Allosteric Modulator of the M4 Muscarinic Acetylcholine Receptor.
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Butler, Christopher R., Popiolek, Michael, McAllister, Laura A., LaChapelle, Erik A., Kramer, Melissa, Beck, Elizabeth M., Mente, Scot, Brodney, Michael A., Brown, Matthew, Gilbert, Adam, Helal, Chris, Ogilvie, Kevin, Starr, Jeremy, Uccello, Daniel, Grimwood, Sarah, Edgerton, Jeremy, Garst-Orozco, Jonathan, Kozak, Rouba, Lotarski, Susan, and Rossi, Amie
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- 2024
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115. Non-destructive X-ray diffraction surface integrity inspection of an aeroengine component.
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Brown, Matthew, Lieder, Mattis, Crawforth, Pete, and Curtis, David
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Industry standard assessment of machined surface integrity typically requires a form of destructive testing to capture microstructural features such as white layers or distorted layers. The X-ray diffraction surface integrity inspection method (XRD-SIIM) offers a non-destructive alternative for the detection and sizing of fatigue-limiting microstructural features, without the sacrifice or alteration of a component which is required for cross-sectional microscopy. In this study XRD-SIIM was used to measure the surface integrity across a nickel-based superalloy gas turbine disc segment. XRD-SIIM microstructural feature detection and sizing models were trained and validated from a set of surfaces generated in a turning trial with a newly developed calibration procedure allowing these models to be adjusted for different instrument setups to facilitate measurement of the turbine disc segment. The non-destructive test was then able to show comparable inspection results to industry standard microscopy of microstructural features when inspecting the representative component, with over 90% of the outside surface of the component accessible by the diffractometer, and the internal surfaces accessible with appropriate hardware. Surface curvature only became a limiting factor for inspection of geometrical features with a small radius of curvature such as seal fins and the corner radii on fir tree sections. [ABSTRACT FROM AUTHOR]
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- 2024
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116. Impact of physical activity on surrogate markers of cardiovascular disease in the haemodialysis population.
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Hull, Katherine L, Abell, Lucy, Adenwalla, Sherna F, Billany, Roseanne E, Burns, Stephanie, Burton, James O, Churchward, Darren, Graham-Brown, Matthew P M, Gray, Laura J, Highton, Patrick, Lightfoot, Courtney J, Said, Rahma, Smith, Alice C, Young, Hannah M L, and March, Daniel S
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CARDIAC magnetic resonance imaging ,MULTI-degree of freedom ,METABOLIC equivalent ,VENTRICULAR ejection fraction ,PHYSICAL activity - Abstract
Background The haemodialysis (HD) population is sedentary, with substantial cardiovascular disease risk. In the general population, small increases in daily step count associate with significant reductions in cardiovascular mortality. This study explores the relationship between daily step count and surrogate markers of cardiovascular disease, including left ventricular ejection fraction (LVEF) and native T1 (a marker of diffuse myocardial fibrosis), within the HD population. Methods This was a post hoc analysis of the association between daily step count and metabolic equivalent of task (MET) and prognostically important cardiac magnetic resonance imaging parameters from the CYCLE-HD study (ISRCTN11299707). Unadjusted linear regression and multiple linear regression adjusted for age, body mass index, dialysis vintage, haemoglobin, hypertension and ultrafiltration volume were performed. Significant relationships were explored with natural cubic spline models with four degrees of freedom (five knots). Results A total of 107 participants were included [age 56.3 ± 14.1 years, 79 (73.8%) males]. The median daily step count was 2558 (interquartile range 1054–4352). There were significant associations between steps and LVEF (β = 0.292; P = .009) and steps and native T1 (β = −0.245; P = .035). Further modelling demonstrated most of the increase in LVEF occurred at up to 2000 steps/day and there was an inverse dose–response relationship between steps and native T1, with the most pronounced reduction in native T1 between ≈2500 and 6000 steps/day. Conclusions The results suggest an association between daily step count and parameters of cardiovascular health in the HD population. These findings support the recommendations for encouraging physical activity but are not the justification. Further research should evaluate whether a simple physical activity intervention improves cardiovascular outcomes in individuals receiving maintenance HD. [ABSTRACT FROM AUTHOR]
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- 2024
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117. Tumour draining lymph node-generated CD8 T cells play a role in controlling lung metastases after a primary tumour is removed but not when adjuvant immunotherapy is used
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Fear, Vanessa S., Forbes, Catherine A., Neeve, Samuel A., Fisher, Scott A., Chee, Jonathan, Waithman, Jason, Ma, Shao Kang, Lake, Richard, Nowak, Anna K., Creaney, Jenette, Brown, Matthew D., Saunders, Christobel, and Robinson, Bruce W. S.
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- 2021
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118. Mapping Social Values of the Sigatoka River Estuary, Nadroga-Navosa Province, Viti Levu, Fiji
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Pearce, Tristan D., Manuel, Lui, Leon, Javier, Currenti, Renee, Brown, Matthew, Ikurisaru, Ilaitia, Doran, Brendan, Scanlon, Halena, and Ford, James
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- 2021
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119. Building a high-resolution T2-weighted MR-based probabilistic model of tumor occurrence in the prostate
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Nagarajan, Mahesh B, Raman, Steven S, Lo, Pechin, Lin, Wei-Chan, Khoshnoodi, Pooria, Sayre, James W, Ramakrishna, Bharath, Ahuja, Preeti, Huang, Jiaoti, Margolis, Daniel JA, Lu, David SK, Reiter, Robert E, Goldin, Jonathan G, Brown, Matthew S, and Enzmann, Dieter R
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Biomedical and Clinical Sciences ,Clinical Sciences ,Oncology and Carcinogenesis ,Aging ,Prostate Cancer ,Urologic Diseases ,Biomedical Imaging ,Clinical Research ,Cancer ,Adult ,Aged ,Algorithms ,Biopsy ,Humans ,Image Interpretation ,Computer-Assisted ,Magnetic Resonance Imaging ,Male ,Middle Aged ,Neoplasm Grading ,Probability ,Prostatectomy ,Prostatic Neoplasms ,Retrospective Studies ,Prostate cancer ,Multi-parametric ,MRI ,Tumor occurrence probability map ,Prostate registration ,Multi-parametric MRI - Abstract
PurposeWe present a method for generating a T2 MR-based probabilistic model of tumor occurrence in the prostate to guide the selection of anatomical sites for targeted biopsies and serve as a diagnostic tool to aid radiological evaluation of prostate cancer.Materials and methodsIn our study, the prostate and any radiological findings within were segmented retrospectively on 3D T2-weighted MR images of 266 subjects who underwent radical prostatectomy. Subsequent histopathological analysis determined both the ground truth and the Gleason grade of the tumors. A randomly chosen subset of 19 subjects was used to generate a multi-subject-derived prostate template. Subsequently, a cascading registration algorithm involving both affine and non-rigid B-spline transforms was used to register the prostate of every subject to the template. Corresponding transformation of radiological findings yielded a population-based probabilistic model of tumor occurrence. The quality of our probabilistic model building approach was statistically evaluated by measuring the proportion of correct placements of tumors in the prostate template, i.e., the number of tumors that maintained their anatomical location within the prostate after their transformation into the prostate template space.ResultsProbabilistic model built with tumors deemed clinically significant demonstrated a heterogeneous distribution of tumors, with higher likelihood of tumor occurrence at the mid-gland anterior transition zone and the base-to-mid-gland posterior peripheral zones. Of 250 MR lesions analyzed, 248 maintained their original anatomical location with respect to the prostate zones after transformation to the prostate.ConclusionWe present a robust method for generating a probabilistic model of tumor occurrence in the prostate that could aid clinical decision making, such as selection of anatomical sites for MR-guided prostate biopsies.
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- 2018
120. Genomic Dissection of Bipolar Disorder and Schizophrenia, Including 28 Subphenotypes
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Consortium, Bipolar Disorder and Schizophrenia Working Group of the Psychiatric Genomics, Ruderfer, Douglas M, Ripke, Stephan, McQuillin, Andrew, Boocock, James, Stahl, Eli A, Pavlides, Jennifer M Whitehead, Mullins, Niamh, Charney, Alexander W, Ori, Anil PS, Loohuis, Loes M Olde, Domenici, Enrico, Di Florio, Arianna, Papiol, Sergi, Kalman, Janos L, Trubetskoy, Vassily, Adolfsson, Rolf, Agartz, Ingrid, Agerbo, Esben, Akil, Huda, Albani, Diego, Albus, Margot, Alda, Martin, Alexander, Madeline, Alliey-Rodriguez, Ney, Als, Thomas D, Amin, Farooq, Anjorin, Adebayo, Arranz, Maria J, Awasthi, Swapnil, Bacanu, Silviu A, Badner, Judith A, Baekvad-Hansen, Marie, Bakker, Steven, Band, Gavin, Barchas, Jack D, Barroso, Ines, Bass, Nicholas, Bauer, Michael, Baune, Bernhard T, Begemann, Martin, Bellenguez, Celine, Belliveau, Richard A, Bellivier, Frank, Bender, Stephan, Bene, Judit, Bergen, Sarah E, Berrettini, Wade H, Bevilacqua, Elizabeth, Biernacka, Joanna M, Bigdeli, Tim B, Black, Donald W, Blackburn, Hannah, Blackwell, Jenefer M, Blackwood, Douglas HR, Pedersen, Carsten Bocker, Boehnke, Michael, Boks, Marco, Borglum, Anders D, Bramon, Elvira, Breen, Gerome, Brown, Matthew A, Bruggeman, Richard, Buccola, Nancy G, Buckner, Randy L, Budde, Monika, Bulik-Sullivan, Brendan, Bumpstead, Suzannah J, Bunney, William, Burmeister, Margit, Buxbaum, Joseph D, Bybjerg-Grauholm, Jonas, Byerley, William, Cahn, Wiepke, Cai, Guiqing, Cairns, Murray J, Campion, Dominique, Cantor, Rita M, Carr, Vaughan J, Carrera, Noa, Casas, Juan P, Casas, Miquel, Catts, Stanley V, Cervantes, Pablo, Chambert, Kimberley D, Chan, Raymond CK, Chen, Eric YH, Chen, Ronald YL, Cheng, Wei, Cheung, Eric FC, Chong, Siow Ann, Clarke, Toni-Kim, Cloninger, C Robert, Cohen, David, Cohen, Nadine, Coleman, Jonathan RI, Collier, David A, Cormican, Paul, Coryell, William, and Craddock, Nicholas
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Human Genome ,Neurosciences ,Serious Mental Illness ,Bipolar Disorder ,Biotechnology ,Schizophrenia ,Brain Disorders ,Genetics ,Mental Health ,Mental health ,Good Health and Well Being ,Case-Control Studies ,Genetic Loci ,Genome-Wide Association Study ,Humans ,Multifactorial Inheritance ,Odds Ratio ,Phenotype ,Risk ,White People ,Bipolar Disorder and Schizophrenia Working Group of the Psychiatric Genomics Consortium. Electronic address: douglas.ruderfer@vanderbilt.edu ,Bipolar Disorder and Schizophrenia Working Group of the Psychiatric Genomics Consortium ,bipolar disorder ,polygenic risk ,psychosis ,schizophrenia ,subphenotypes ,Biological Sciences ,Medical and Health Sciences ,Developmental Biology - Abstract
Schizophrenia and bipolar disorder are two distinct diagnoses that share symptomology. Understanding the genetic factors contributing to the shared and disorder-specific symptoms will be crucial for improving diagnosis and treatment. In genetic data consisting of 53,555 cases (20,129 bipolar disorder [BD], 33,426 schizophrenia [SCZ]) and 54,065 controls, we identified 114 genome-wide significant loci implicating synaptic and neuronal pathways shared between disorders. Comparing SCZ to BD (23,585 SCZ, 15,270 BD) identified four genomic regions including one with disorder-independent causal variants and potassium ion response genes as contributing to differences in biology between the disorders. Polygenic risk score (PRS) analyses identified several significant correlations within case-only phenotypes including SCZ PRS with psychotic features and age of onset in BD. For the first time, we discover specific loci that distinguish between BD and SCZ and identify polygenic components underlying multiple symptom dimensions. These results point to the utility of genetics to inform symptomology and potential treatment.
- Published
- 2018
121. Proteasomal degradation of the histone acetyl transferase p300 contributes to beta-cell injury in a diabetes environment.
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Ruiz, Lucie, Gurlo, Tatyana, Ravier, Magalie A, Wojtusciszyn, Anne, Mathieu, Julia, Brown, Matthew R, Broca, Christophe, Bertrand, Gyslaine, Butler, Peter C, Matveyenko, Aleksey V, Dalle, Stéphane, and Costes, Safia
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Animals ,Mice ,Inbred C57BL ,Humans ,Diabetes Mellitus ,Melatonin ,Proteasome Endopeptidase Complex ,Glucose ,Receptors ,Melatonin ,Histones ,RNA ,Messenger ,Inflammation Mediators ,Cytokines ,Signal Transduction ,Apoptosis ,Acetylation ,Male ,Insulin-Secreting Cells ,E1A-Associated p300 Protein ,Proteolysis ,Diabetes ,Genetics ,2.1 Biological and endogenous factors ,Metabolic and Endocrine ,Mice ,Inbred C57BL ,Receptors ,RNA ,Messenger ,Oncology and Carcinogenesis ,Biochemistry and Cell Biology - Abstract
In type 2 diabetes, amyloid oligomers, chronic hyperglycemia, lipotoxicity, and pro-inflammatory cytokines are detrimental to beta-cells, causing apoptosis and impaired insulin secretion. The histone acetyl transferase p300, involved in remodeling of chromatin structure by epigenetic mechanisms, is a key ubiquitous activator of the transcriptional machinery. In this study, we report that loss of p300 acetyl transferase activity and expression leads to beta-cell apoptosis, and most importantly, that stress situations known to be associated with diabetes alter p300 levels and functional integrity. We found that proteasomal degradation is the mechanism subserving p300 loss in beta-cells exposed to hyperglycemia or pro-inflammatory cytokines. We also report that melatonin, a hormone produced in the pineal gland and known to play key roles in beta-cell health, preserves p300 levels altered by these toxic conditions. Collectively, these data imply an important role for p300 in the pathophysiology of diabetes.
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- 2018
122. Opioid Analgesic Use in Patients with Ankylosing Spondylitis: An Analysis of the Prospective Study of Outcomes in an Ankylosing Spondylitis Cohort
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Dau, Jonathan D, Lee, MinJae, Ward, Michael M, Gensler, Lianne S, Brown, Matthew A, Learch, Thomas J, Diekman, Laura A, Tahanan, Amirali, Rahbar, Mohammad H, Weisman, Michael H, and Reveille, John D
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Pharmacology and Pharmaceutical Sciences ,Biomedical and Clinical Sciences ,Clinical Sciences ,Depression ,Pain Research ,Clinical Research ,Mental Health ,Chronic Pain ,Musculoskeletal ,Adult ,Aged ,Analgesics ,Opioid ,Blood Sedimentation ,C-Reactive Protein ,Chi-Square Distribution ,Disability Evaluation ,Female ,Follow-Up Studies ,Humans ,Logistic Models ,Longitudinal Studies ,Male ,Middle Aged ,Multivariate Analysis ,Prospective Studies ,Risk Factors ,Self Report ,Severity of Illness Index ,Spondylitis ,Ankylosing ,Statistics ,Nonparametric ,Treatment Outcome ,PAIN ,COHORT STUDIES ,OPIOID ,ANKYLOSING SPONDYLITIS ,Immunology ,Public Health and Health Services ,Arthritis & Rheumatology ,Clinical sciences - Abstract
OBJECTIVE:Opioid analgesics may be prescribed to ankylosing spondylitis (AS) patients with pain that is unresponsive to antirheumatic treatment. Our study assessed factors associated with opioid usage in AS. METHODS:A prospective cohort of 706 patients with AS meeting modified New York criteria followed at least 2 years underwent comprehensive clinical evaluation of disease activity and functional impairment. These were assessed by the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) and Bath Ankylosing Spondylitis Functional Index (BASFI). Radiographic severity was assessed by the Bath Ankylosing Spondylitis Radiology Index and modified Stokes Ankylosing Spondylitis Scoring System. Medications taken concurrently with opioids, as well as C-reactive protein (CRP) levels and erythrocyte sedimentation rate (ESR), were determined at each study visit, performed every 6 months. Analyses were carried out at baseline, and longitudinal multivariable models were developed to identify factors independently associated with chronic and intermittent opioid usage over time. RESULTS:Factors significantly associated with opioid usage, especially chronic opioid use, included longer disease duration, smoking, lack of exercise, higher disease activity (BASDAI) and functional impairment (BASFI), depression, radiographic severity, and cardiovascular disease. Patients taking opioids were more likely to be using anxiolytic, hypnotic, antidepressant, and muscle relaxant medications. Multivariable analysis underscored the association with smoking, older age, antitumor necrosis factor agent use, and psychoactive drugs, as well as with subjective but not objective determinants of disease activity. CONCLUSION:Opioid usage was more likely to be associated with subjective measures (depression, BASDAI, BASFI) than objective measures (CRP, ESR), suggesting that pain in AS may derive from sources other than spinal inflammation alone.
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- 2018
123. Quantitative bone scan lesion area as an early surrogate outcome measure indicative of overall survival in metastatic prostate cancer
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Brown, Matthew S, Kim, Grace Hyun J, Chu, Gregory H, Ramakrishna, Bharath, Allen-Auerbach, Martin, Fischer, Cheryce P, Levine, Benjamin, Gupta, Pawan K, Schiepers, Christiaan W, and Goldin, Jonathan G
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Biomedical and Clinical Sciences ,Clinical Sciences ,Oncology and Carcinogenesis ,Aging ,Clinical Research ,Prostate Cancer ,Urologic Diseases ,Cancer ,Clinical Trials and Supportive Activities ,4.1 Discovery and preclinical testing of markers and technologies ,Evaluation of treatments and therapeutic interventions ,Detection ,screening and diagnosis ,6.1 Pharmaceuticals ,prostate cancer ,bone scan ,computer-aided diagnosis ,Clinical sciences ,Biomedical engineering - Abstract
A clinical validation of the bone scan lesion area (BSLA) as a quantitative imaging biomarker was performed in metastatic castration-resistant prostate cancer (mCRPC). BSLA was computed from whole-body bone scintigraphy at baseline and week 12 posttreatment in a cohort of 198 mCRPC subjects (127 treated and 71 placebo) from a clinical trial involving a different drug from the initial biomarker development. BSLA computation involved automated image normalization, lesion segmentation, and summation of the total area of segmented lesions on bone scan AP and PA views as a measure of tumor burden. As a predictive biomarker, treated subjects with baseline BSLA [Formula: see text] had longer survival than those with higher BSLA ([Formula: see text] and [Formula: see text]). As a surrogate outcome biomarker, subjects were categorized as progressive disease (PD) if the BSLA increased by a prespecified 30% or more from baseline to week 12 and non-PD otherwise. Overall survival rates between PD and non-PD groups were statistically different ([Formula: see text] and [Formula: see text]). Subjects without PD at week 12 had longer survival than subjects with PD: median 398 days versus 280 days. BSLA has now been demonstrated to be an early surrogate outcome for overall survival in different prostate cancer drug treatments.
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- 2018
124. Comparative genomic analysis of the 'pseudofungus' Hyphochytrium catenoides.
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Leonard, Guy, Labarre, Aurélie, Milner, David S, Monier, Adam, Soanes, Darren, Wideman, Jeremy G, Maguire, Finlay, Stevens, Sam, Sain, Divya, Grau-Bové, Xavier, Sebé-Pedrós, Arnau, Stajich, Jason E, Paszkiewicz, Konrad, Brown, Matthew W, Hall, Neil, Wickstead, Bill, and Richards, Thomas A
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Animals ,Rhinosporidium ,Phylogeny ,Genome ,Molecular Sequence Annotation ,Whole Genome Sequencing ,large DNA virus ,oomycete parasitic traits ,polarized filamentous growth ,secondary plastid endosymbiosis ,Biotechnology ,Infectious Diseases ,Human Genome ,Genetics ,Biochemistry and Cell Biology ,Microbiology ,Immunology - Abstract
Eukaryotic microbes have three primary mechanisms for obtaining nutrients and energy: phagotrophy, photosynthesis and osmotrophy. Traits associated with the latter two functions arose independently multiple times in the eukaryotes. The Fungi successfully coupled osmotrophy with filamentous growth, and similar traits are also manifested in the Pseudofungi (oomycetes and hyphochytriomycetes). Both the Fungi and the Pseudofungi encompass a diversity of plant and animal parasites. Genome-sequencing efforts have focused on host-associated microbes (mutualistic symbionts or parasites), providing limited comparisons with free-living relatives. Here we report the first draft genome sequence of a hyphochytriomycete 'pseudofungus'; Hyphochytrium catenoides Using phylogenomic approaches, we identify genes of recent viral ancestry, with related viral derived genes also present on the genomes of oomycetes, suggesting a complex history of viral coevolution and integration across the Pseudofungi. H. catenoides has a complex life cycle involving diverse filamentous structures and a flagellated zoospore with a single anterior tinselate flagellum. We use genome comparisons, drug sensitivity analysis and high-throughput culture arrays to investigate the ancestry of oomycete/pseudofungal characteristics, demonstrating that many of the genetic features associated with parasitic traits evolved specifically within the oomycete radiation. Comparative genomics also identified differences in the repertoire of genes associated with filamentous growth between the Fungi and the Pseudofungi, including differences in vesicle trafficking systems, cell-wall synthesis pathways and motor protein repertoire, demonstrating that unique cellular systems underpinned the convergent evolution of filamentous osmotrophic growth in these two eukaryotic groups.
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- 2018
125. Ethnicity and disease severity in ankylosing spondylitis a cross-sectional analysis of three ethnic groups
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Jamalyaria, Farokh, Ward, Michael M, Assassi, Shervin, Learch, Thomas J, Lee, MinJae, Gensler, Lianne S, Brown, Matthew A, Diekman, Laura, Tahanan, Amirali, Rahbar, Mohammad H, Weisman, Michael H, and Reveille, John D
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Biomedical and Clinical Sciences ,Clinical Sciences ,Autoimmune Disease ,Arthritis ,Adult ,Black or African American ,Black People ,Blood Sedimentation ,Cross-Sectional Studies ,Disease Progression ,Female ,HLA-B27 Antigen ,Hispanic or Latino ,Humans ,Longitudinal Studies ,Male ,Middle Aged ,Prospective Studies ,Reproducibility of Results ,Severity of Illness Index ,Spine ,Spondylitis ,Ankylosing ,White People ,Young Adult ,Ankylosing spondylitis ,Blacks ,Disease severity ,HLA-B27 ,Latinos ,Arthritis & Rheumatology ,Clinical sciences ,Immunology ,Allied health and rehabilitation science - Abstract
The purpose of this study is to compare disease severity in ankylosing spondylitis (AS) in three ethnic groups. We assessed 925 AS patients (57 Blacks, 805 Whites, 63 Latinos) enrolled in the longitudinal Prospective Study of Outcomes in AS (PSOAS) for functional impairment, disease activity, and radiographic severity. Comparisons of clinical characteristics and HLA-B27 frequency for each group were performed, in two multivariable regression models, we compared the baseline Bath Ankylosing Spondylitis Radiographic Index (BASRI) and modified Stokes Ankylosing Spondylitis Spine Score (mSASSS) by ethnicity, adjusting for covariates. Blacks had greater functional impairment (Bath Ankylosing Spondylitis Functional Index) (median 62.5 vs. 27.8 in Whites and 38.1 in Latinos; p
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- 2017
126. Ablation of manifest septal accessory pathways: a single-center experience
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Brown, Matthew T., Kiani, Soroosh, Black, George B., Lu, Marvin L. R., Lloyd, Michael, Leon, Angel R., Shah, Anand, Westerman, Stacy, Merchant, Faisal M., and El-Chami, Mikhael
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- 2021
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127. Ankylosing spondylitis: an autoimmune or autoinflammatory disease?
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Mauro, Daniele, Thomas, Ranjeny, Guggino, Giuliana, Lories, Rik, Brown, Matthew A., and Ciccia, Francesco
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- 2021
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128. Nonrigid Optical Flow Ground Truth for Real-World Scenes with Time-Varying Shading Effects
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Li, Wenbin, Cosker, Darren, Lv, Zhihan, and Brown, Matthew
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Computer Science - Computer Vision and Pattern Recognition - Abstract
In this paper we present a dense ground truth dataset of nonrigidly deforming real-world scenes. Our dataset contains both long and short video sequences, and enables the quantitatively evaluation for RGB based tracking and registration methods. To construct ground truth for the RGB sequences, we simultaneously capture Near-Infrared (NIR) image sequences where dense markers - visible only in NIR - represent ground truth positions. This allows for comparison with automatically tracked RGB positions and the formation of error metrics. Most previous datasets containing nonrigidly deforming sequences are based on synthetic data. Our capture protocol enables us to acquire real-world deforming objects with realistic photometric effects - such as blur and illumination change - as well as occlusion and complex deformations. A public evaluation website is constructed to allow for ranking of RGB image based optical flow and other dense tracking algorithms, with various statistical measures. Furthermore, we present an RGB-NIR multispectral optical flow model allowing for energy optimization by adoptively combining featured information from both the RGB and the complementary NIR channels. In our experiments we evaluate eight existing RGB based optical flow methods on our new dataset. We also evaluate our hybrid optical flow algorithm by comparing to two existing multispectral approaches, as well as varying our input channels across RGB, NIR and RGB-NIR., Comment: preprint of our paper accepted by RA-L'16
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- 2016
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129. Drift Robust Non-rigid Optical Flow Enhancement for Long Sequences
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Li, Wenbin, Cosker, Darren, and Brown, Matthew
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Computer Science - Computer Vision and Pattern Recognition - Abstract
It is hard to densely track a nonrigid object in long term, which is a fundamental research issue in the computer vision community. This task often relies on estimating pairwise correspondences between images over time where the error is accumulated and leads to a drift issue. In this paper, we introduce a novel optimization framework with an Anchor Patch constraint. It is supposed to significantly reduce overall errors given long sequences containing non-rigidly deformable objects. Our framework can be applied to any dense tracking algorithm, e.g. optical flow. We demonstrate the success of our approach by showing significant error reduction on 6 popular optical flow algorithms applied to a range of real-world nonrigid benchmarks. We also provide quantitative analysis of our approach given synthetic occlusions and image noise., Comment: Preprint version of our paper accepted by Journal of Intelligent and Fuzzy Systems
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- 2016
130. Decision Forests, Convolutional Networks and the Models in-Between
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Ioannou, Yani, Robertson, Duncan, Zikic, Darko, Kontschieder, Peter, Shotton, Jamie, Brown, Matthew, and Criminisi, Antonio
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence - Abstract
This paper investigates the connections between two state of the art classifiers: decision forests (DFs, including decision jungles) and convolutional neural networks (CNNs). Decision forests are computationally efficient thanks to their conditional computation property (computation is confined to only a small region of the tree, the nodes along a single branch). CNNs achieve state of the art accuracy, thanks to their representation learning capabilities. We present a systematic analysis of how to fuse conditional computation with representation learning and achieve a continuum of hybrid models with different ratios of accuracy vs. efficiency. We call this new family of hybrid models conditional networks. Conditional networks can be thought of as: i) decision trees augmented with data transformation operators, or ii) CNNs, with block-diagonal sparse weight matrices, and explicit data routing functions. Experimental validation is performed on the common task of image classification on both the CIFAR and Imagenet datasets. Compared to state of the art CNNs, our hybrid models yield the same accuracy with a fraction of the compute cost and much smaller number of parameters., Comment: Microsoft Research Technical Report
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- 2016
131. The nuclear receptor REV-ERBα is implicated in the alteration of β-cell autophagy and survival under diabetogenic conditions
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Brown, Matthew R., Laouteouet, Damien, Delobel, Morgane, Villard, Orianne, Broca, Christophe, Bertrand, Gyslaine, Wojtusciszyn, Anne, Dalle, Stéphane, Ravier, Magalie A., Matveyenko, Aleksey V., and Costes, Safia
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- 2022
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132. The effect of radiation dose reduction on computer‐aided detection (CAD) performance in a low‐dose lung cancer screening population
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Young, Stefano, Lo, Pechin, Kim, Grace, Brown, Matthew, Hoffman, John, Hsu, William, Wahi‐Anwar, Wasil, Flores, Carlos, Lee, Grace, Noo, Frederic, Goldin, Jonathan, and McNitt‐Gray, Michael
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Medical and Biological Physics ,Physical Sciences ,Cancer ,Clinical Research ,Prevention ,Health Services ,Biomedical Imaging ,Lung ,Lung Cancer ,Algorithms ,Diagnosis ,Computer-Assisted ,Humans ,Lung Neoplasms ,Mass Screening ,Radiation Dosage ,Tomography ,X-Ray Computed ,Other Physical Sciences ,Biomedical Engineering ,Oncology and Carcinogenesis ,Nuclear Medicine & Medical Imaging ,Biomedical engineering ,Medical and biological physics - Abstract
PurposeLung cancer screening with low-dose CT has recently been approved for reimbursement, heralding the arrival of such screening services worldwide. Computer-aided detection (CAD) tools offer the potential to assist radiologists in detecting nodules in these screening exams. In lung screening, as in all CT exams, there is interest in further reducing radiation dose. However, the effects of continued dose reduction on CAD performance are not fully understood. In this work, we investigated the effect of reducing radiation dose on CAD lung nodule detection performance in a screening population.MethodsThe raw projection data files were collected from 481 patients who underwent low-dose screening CT exams at our institution as part of the National Lung Screening Trial (NLST). All scans were performed on a multidetector scanner (Sensation 64, Siemens Healthcare, Forchheim Germany) according to the NLST protocol, which called for a fixed tube current scan of 25 effective mAs for standard-sized patients and 40 effective mAs for larger patients. The raw projection data were input to a reduced-dose simulation software to create simulated reduced-dose scans corresponding to 50% and 25% of the original protocols. All raw data files were reconstructed at the scanner with 1 mm slice thickness and B50 kernel. The lungs were segmented semi-automatically, and all images and segmentations were input to an in-house CAD algorithm trained on higher dose scans (75-300 mAs). CAD findings were compared to a reference standard generated by an experienced reader. Nodule- and patient-level sensitivities were calculated along with false positives per scan, all of which were evaluated in terms of the relative change with respect to dose. Nodules were subdivided based on size and solidity into categories analogous to the LungRADS assessment categories, and sub-analyses were performed.ResultsFrom the 481 patients in this study, 82 had at least one nodule (prevalence of 17%) and 399 did not (83%). A total of 118 nodules were identified. Twenty-seven nodules (23%) corresponded to LungRADS category 4 based on size and composition, while 18 (15%) corresponded to LungRADS category 3 and 73 (61%) corresponded to LungRADS category 2. For solid nodules ≥8 mm, patient-level median sensitivities were 100% at all three dose levels, and mean sensitivities were 72%, 63%, and 63% at original, 50%, and 25% dose, respectively. Overall mean patient-level sensitivities for nodules ranging from 3 to 45 mm were 38%, 37%, and 38% at original, 50%, and 25% dose due to the prevalence of smaller nodules and nonsolid nodules in our reference standard. The mean false-positive rates were 3, 5, and 13 per case.ConclusionsCAD sensitivity decreased very slightly for larger nodules as dose was reduced, indicating that reducing the dose to 50% of original levels may be investigated further for use in CT screening. However, the effect of dose was small relative to the effect of the nodule size and solidity characteristics. The number of false positives per scan increased substantially at 25% dose, illustrating the importance of tuning CAD algorithms to very challenging, high-noise screening exams.
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- 2017
133. Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration
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Arno, Gavin, Carss, Keren J, Hull, Sarah, Zihni, Ceniz, Robson, Anthony G, Fiorentino, Alessia, Hardcastle, Alison J, Holder, Graham E, Cheetham, Michael E, Plagnol, Vincent, Moore, Anthony, Raymond, F Lucy, Matter, Karl, Balda, Maria S, Webster, Andrew R, Black, Graeme, Hall, Georgina, Ingram, Stuart, Gillespie, Rachel, Manson, Forbes, Sergouniotis, Panagiotis, Inglehearn, Chris, Toomes, Carmel, Ali, Manir, McKibbin, Martin, Poulter, James, Khan, Kamron, Lord, Emma, Nemeth, Andrea, Downes, Susan, Halford, Stephanie, Yu, Jing, Lise, Stefano, Ponitkos, Nikos, Michaelides, Michel, Webster, Andrew, van Heyningen, Veronica, Aitman, Timothy, Alachkar, Hana, Ali, Sonia, Allen, Louise, Allsup, David, Ambegaonkar, Gautum, Anderson, Julie, Antrobus, Richard, Armstrong, Ruth, Arumugakani, Gururaj, Ashford, Sofie, Astle, William, Attwood, Antony, Austin, Steve, Bacchelli, Chiara, Bakchoul, Tamam, Bariana, Tadbir K, Baxendale, Helen, Bennett, David, Bethune, Claire, Bibi, Shahnaz, Bitner-Glindzicz, Maria, Bleda, Marta, Boggard, Harm, Bolton-Maggs, Paula, Booth, Claire, Bradley, John R, Brady, Angie, Brown, Matthew, Browning, Michael, Bryson, Christine, Burns, Siobhan, Calleja, Paul, Canham, Natalie, Carmichael, Jenny, Carss, Keren, Caulfield, Mark, Chalmers, Elizabeth, Chandra, Anita, Chinnery, Patrick, Chitre, Manali, Church, Colin, Clement, Emma, Clements-Brod, Naomi, Clowes, Virginia, Coghlan, Gerry, Collins, Peter, Cooper, Nichola, Creaser-Myers, Amanda, DaCosta, Rosa, Daugherty, Louise, Davies, Sophie, Davis, John, De Vries, Minka, Deegan, Patrick, Deevi, Sri VV, and Deshpande, Charu
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Biological Sciences ,Bioinformatics and Computational Biology ,Biomedical and Clinical Sciences ,Genetics ,Ophthalmology and Optometry ,Human Genome ,Rare Diseases ,Neurosciences ,Eye Disease and Disorders of Vision ,Aetiology ,2.1 Biological and endogenous factors ,Eye ,Adult ,Alleles ,Amino Acid Sequence ,Cell Polarity ,Epithelial Cells ,Exome ,Eye Proteins ,Female ,Genetic Variation ,Genome-Wide Association Study ,Genotype ,Humans ,Male ,Membrane Proteins ,Middle Aged ,Mutation ,Missense ,Nerve Tissue Proteins ,Pedigree ,Phenotype ,Retina ,Retinal Degeneration ,Retinal Dystrophies ,Rho Guanine Nucleotide Exchange Factors ,rhoA GTP-Binding Protein ,UK Inherited Retinal Disease Consortium ,NIHR Bioresource - Rare Diseases Consortium ,ARHGEF18 ,apicobasal polarity ,inherited retinal dystrophy ,p114RhoGEF ,retinal degeneration ,retinitis pigmentosa ,Medical and Health Sciences ,Genetics & Heredity ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
Mutations in more than 250 genes are implicated in inherited retinal dystrophy; the encoded proteins are involved in a broad spectrum of pathways. The presence of unsolved families after highly parallel sequencing strategies suggests that further genes remain to be identified. Whole-exome and -genome sequencing studies employed here in large cohorts of affected individuals revealed biallelic mutations in ARHGEF18 in three such individuals. ARHGEF18 encodes ARHGEF18, a guanine nucleotide exchange factor that activates RHOA, a small GTPase protein that is a key component of tight junctions and adherens junctions. This biological pathway is known to be important for retinal development and function, as mutation of CRB1, encoding another component, causes retinal dystrophy. The retinal structure in individuals with ARHGEF18 mutations resembled that seen in subjects with CRB1 mutations. Five mutations were found on six alleles in the three individuals: c.808A>G (p.Thr270Ala), c.1617+5G>A (p.Asp540Glyfs∗63), c.1996C>T (p.Arg666∗), c.2632G>T (p.Glu878∗), and c.2738_2761del (p.Arg913_Glu920del). Functional tests suggest that each disease genotype might retain some ARHGEF18 activity, such that the phenotype described here is not the consequence of nullizygosity. In particular, the p.Thr270Ala missense variant affects a highly conserved residue in the DBL homology domain, which is required for the interaction and activation of RHOA. Previously, knock-out of Arhgef18 in the medaka fish has been shown to cause larval lethality which is preceded by retinal defects that resemble those seen in zebrafish Crumbs complex knock-outs. The findings described here emphasize the peculiar sensitivity of the retina to perturbations of this pathway, which is highlighted as a target for potential therapeutic strategies.
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- 2017
134. Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease
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Carss, Keren J, Arno, Gavin, Erwood, Marie, Stephens, Jonathan, Sanchis-Juan, Alba, Hull, Sarah, Megy, Karyn, Grozeva, Detelina, Dewhurst, Eleanor, Malka, Samantha, Plagnol, Vincent, Penkett, Christopher, Stirrups, Kathleen, Rizzo, Roberta, Wright, Genevieve, Josifova, Dragana, Bitner-Glindzicz, Maria, Scott, Richard H, Clement, Emma, Allen, Louise, Armstrong, Ruth, Brady, Angela F, Carmichael, Jenny, Chitre, Manali, Henderson, Robert HH, Hurst, Jane, MacLaren, Robert E, Murphy, Elaine, Paterson, Joan, Rosser, Elisabeth, Thompson, Dorothy A, Wakeling, Emma, Ouwehand, Willem H, Michaelides, Michel, Moore, Anthony T, Consortium, NIHR-BioResource Rare Diseases, Aitman, Timothy, Alachkar, Hana, Ali, Sonia, Allsup, David, Ambegaonkar, Gautum, Anderson, Julie, Antrobus, Richard, Arumugakani, Gururaj, Ashford, Sofie, Astle, William, Attwood, Antony, Austin, Steve, Bacchelli, Chiara, Bakchoul, Tamam, Bariana, Tadbir K, Baxendale, Helen, Bennett, David, Bethune, Claire, Bibi, Shahnaz, Bleda, Marta, Boggard, Harm, Bolton-Maggs, Paula, Booth, Claire, Bradley, John R, Brady, Angie, Brown, Matthew, Browning, Michael, Bryson, Christine, Burns, Siobhan, Calleja, Paul, Canham, Natalie, Carss, Keren, Caulfield, Mark, Chalmers, Elizabeth, Chandra, Anita, Chinnery, Patrick, Church, Colin, Clements-Brod, Naomi, Clowes, Virginia, Coghlan, Gerry, Collins, Peter, Cooper, Nichola, Creaser-Myers, Amanda, DaCosta, Rosa, Daugherty, Louise, Davies, Sophie, Davis, John, De Vries, Minka, Deegan, Patrick, Deevi, Sri VV, Deshpande, Charu, Devlin, Lisa, Doffinger, Rainer, Dormand, Natalie, Drewe, Elizabeth, and Edgar, David
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Genetics ,Neurosciences ,Eye Disease and Disorders of Vision ,Human Genome ,Clinical Research ,2.1 Biological and endogenous factors ,Aetiology ,Eye ,Good Health and Well Being ,Adaptor Proteins ,Signal Transducing ,Alleles ,Base Sequence ,Choroideremia ,DNA Mutational Analysis ,Ethnicity ,Exome ,Female ,Genes ,Recessive ,Genetic Variation ,Genome ,Human ,Humans ,Introns ,Male ,Mutation ,Rare Diseases ,Retinal Diseases ,NIHR-BioResource Rare Diseases Consortium ,copy-number variants ,rare sequence variant ,retinal dystrophy ,whole-genome sequence ,Biological Sciences ,Medical and Health Sciences ,Genetics & Heredity - Abstract
Inherited retinal disease is a common cause of visual impairment and represents a highly heterogeneous group of conditions. Here, we present findings from a cohort of 722 individuals with inherited retinal disease, who have had whole-genome sequencing (n = 605), whole-exome sequencing (n = 72), or both (n = 45) performed, as part of the NIHR-BioResource Rare Diseases research study. We identified pathogenic variants (single-nucleotide variants, indels, or structural variants) for 404/722 (56%) individuals. Whole-genome sequencing gives unprecedented power to detect three categories of pathogenic variants in particular: structural variants, variants in GC-rich regions, which have significantly improved coverage compared to whole-exome sequencing, and variants in non-coding regulatory regions. In addition to previously reported pathogenic regulatory variants, we have identified a previously unreported pathogenic intronic variant in CHM in two males with choroideremia. We have also identified 19 genes not previously known to be associated with inherited retinal disease, which harbor biallelic predicted protein-truncating variants in unsolved cases. Whole-genome sequencing is an increasingly important comprehensive method with which to investigate the genetic causes of inherited retinal disease.
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- 2017
135. Demonstrating table-top interferometric imaging using a path-entangled single photon towards quantum telescopy
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Kammerer, Jens, Sallum, Stephanie, Sanchez-Bermudez, Joel, Brown, Matthew, Allgaier, Markus, Thiel, Valerian, Monnier, John, Raymer, Michael, and Smith, Brian
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- 2024
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136. Analysis of PM2.5, black carbon, and trace metals measurements from the Kansas City Transportation and Local-Scale Air Quality Study (KC-TRAQS)
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Duvall, Rachelle M., Kimbrough, Evelyn S., Krabbe, Stephen, Deshmukh, Parikshit, Baldauf, Richard W., Brouwer, Lydia H., McArthur, Timothy, Croghan, Carry, Varga, Joshua, Brown, Matthew, and Davis, Michael
- Abstract
ABSTRACTCommunities near transportation sources can be impacted by higher concentrations of particulate matter (PM) and other air pollutants. Few studies have reported on air quality in complex urban environments with multiple transportation sources. To better understand these environments, the Kansas City Transportation and Local-Scale Air Quality Study (KC-TRAQS) was conducted in three neighborhoods in Southeast Kansas City, Kansas. This area has several emissions sources including transportation (railyards, vehicles, diesel trucks), light industry, commercial facilities, and residential areas. Stationary samples were collected for 1-year (October 24, 2017, to October 31, 2018) at six sites using traditional sampling methods and lower-cost air sensor packages. This work examines PM less than 2.5 μm in diameter (PM2.5), black carbon (BC), and trace metals data collected during KC-TRAQS. PM2.5filter samples showed the highest 24-h mean concentrations (9.34 μg/m3) at the sites located within 20–50 m of the railyard. Mean 24-h PM2.5concentrations, ranging from 7.96 to 9.34 μg/m3, at all sites were lower than that of the nearby regulatory site (9.83 μg/m3). Daily maximum PM2.5concentrations were higher at the KC-TRAQS sites (ranging from 25.31 to 43.76 μg/m3) compared to the regulatory site (20.50 μg/m3), suggesting short-duration impacts of localized emissions sources. Across the KC-TRAQS sites, 24-h averaged PM2.5concentrations from the sensor package (P-POD) ranged from 3.24 to 5.69 µg/m3showing that, out-of-the-box, the PM sensor underestimated the reference concentrations. KC-TRAQS was supplemented by elemental and organic carbon (EC/OC) and trace metal analysis of filter samples. The EC/OC data suggested the presence of secondary organic aerosol formation, with the highest mean concentrations observed at the site within 20 m of the railyard. Trace metals data showed daily, monthly, and seasonal variations for iron, copper, zinc, chromium, and nickel, with elevated concentrations occurring during the summer at most of the sites.Implications: This work reports on findings from a year-long air quality study in Southeast Kansas City, Kansas to understand micro-scale air quality in neighborhoods impacted by multiple emissions sources such as transportation sources (including a large railyard operation), light industry, commercial facilities, and residential areas. While dozens of studies have reported on air quality near roadways, this work will provide more information on PM2.5, black carbon, and trace metals concentrations near other transportation sources in particular railyards. This work can also inform additional field studies near railyards.
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- 2024
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137. Design and Synthesis of Clinical Candidate PF-06852231 (CVL-231): A Brain Penetrant, Selective, Positive Allosteric Modulator of the M4Muscarinic Acetylcholine Receptor
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Butler, Christopher R., Popiolek, Michael, McAllister, Laura A., LaChapelle, Erik A., Kramer, Melissa, Beck, Elizabeth M., Mente, Scot, Brodney, Michael A., Brown, Matthew, Gilbert, Adam, Helal, Chris, Ogilvie, Kevin, Starr, Jeremy, Uccello, Daniel, Grimwood, Sarah, Edgerton, Jeremy, Garst-Orozco, Jonathan, Kozak, Rouba, Lotarski, Susan, Rossi, Amie, Smith, Deborah, O’Connor, Rebecca, Lazzaro, John, Steppan, Claire, and Steyn, Stefanus J.
- Abstract
Selective activation of the M4muscarinic acetylcholine receptor subtype offers a novel strategy for the treatment of psychosis in multiple neurological disorders. Although the development of traditional muscarinic activators has been stymied due to pan-receptor activation, muscarinic receptor subtype selectivity can be achieved through the utilization of a subtype of a unique allosteric site. A major challenge in capitalizing on this allosteric site to date has been achieving a balance of suitable potency and brain penetration. Herein, we describe the design of a brain penetrant series of M4selective positive allosteric modulators (PAMs), ultimately culminating in the identification of 21 (PF-06852231, now CVL-231/emraclidine), which is under active clinical development as a novel mechanism and approach for the treatment of schizophrenia.
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- 2024
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138. Ancient Plasmodiumgenomes shed light on the history of human malaria
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Michel, Megan, Skourtanioti, Eirini, Pierini, Federica, Guevara, Evelyn K., Mötsch, Angela, Kocher, Arthur, Barquera, Rodrigo, Bianco, Raffaela A., Carlhoff, Selina, Coppola Bove, Lorenza, Freilich, Suzanne, Giffin, Karen, Hermes, Taylor, Hiß, Alina, Knolle, Florian, Nelson, Elizabeth A., Neumann, Gunnar U., Papac, Luka, Penske, Sandra, Rohrlach, Adam B., Salem, Nada, Semerau, Lena, Villalba-Mouco, Vanessa, Abadie, Isabelle, Aldenderfer, Mark, Beckett, Jessica F., Brown, Matthew, Campus, Franco G. R., Chenghwa, Tsang, Cruz Berrocal, María, Damašek, Ladislav, Duffett Carlson, Kellie Sara, Durand, Raphaël, Ernée, Michal, Fântăneanu, Cristinel, Frenzel, Hannah, García Atiénzar, Gabriel, Guillén, Sonia, Hsieh, Ellen, Karwowski, Maciej, Kelvin, David, Kelvin, Nikki, Khokhlov, Alexander, Kinaston, Rebecca L., Korolev, Arkadii, Krettek, Kim-Louise, Küßner, Mario, Lai, Luca, Look, Cory, Majander, Kerttu, Mandl, Kirsten, Mazzarello, Vittorio, McCormick, Michael, de Miguel Ibáñez, Patxuka, Murphy, Reg, Németh, Rita E., Nordqvist, Kerkko, Novotny, Friederike, Obenaus, Martin, Olmo-Enciso, Lauro, Onkamo, Päivi, Orschiedt, Jörg, Patrushev, Valerii, Peltola, Sanni, Romero, Alejandro, Rubino, Salvatore, Sajantila, Antti, Salazar-García, Domingo C., Serrano, Elena, Shaydullaev, Shapulat, Sias, Emanuela, Šlaus, Mario, Stančo, Ladislav, Swanston, Treena, Teschler-Nicola, Maria, Valentin, Frederique, Van de Vijver, Katrien, Varney, Tamara L., Vigil-Escalera Guirado, Alfonso, Waters, Christopher K., Weiss-Krejci, Estella, Winter, Eduard, Lamnidis, Thiseas C., Prüfer, Kay, Nägele, Kathrin, Spyrou, Maria, Schiffels, Stephan, Stockhammer, Philipp W., Haak, Wolfgang, Posth, Cosimo, Warinner, Christina, Bos, Kirsten I., Herbig, Alexander, and Krause, Johannes
- Abstract
Malaria-causing protozoa of the genus Plasmodiumhave exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach of these species1. Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe1,2. To address these questions, we generated high-coverage ancient mitochondrial and nuclear genome-wide data from P. falciparum, P. vivaxand P. malariaefrom 16 countries spanning around 5,500 years of human history. We identified P. vivaxand P. falciparumacross geographically disparate regions of Eurasia from as early as the fourth and first millennia bce, respectively; for P. vivax, this evidence pre-dates textual references by several millennia3. Genomic analysis supports distinct disease histories for P. falciparumand P. vivaxin the Americas: similarities between now-eliminated European and peri-contact South American strains indicate that European colonizers were the source of American P. vivax, whereas the trans-Atlantic slave trade probably introduced P. falciparuminto the Americas. Our data underscore the role of cross-cultural contacts in the dissemination of malaria, laying the biomolecular foundation for future palaeo-epidemiological research into the impact of Plasmodiumparasites on human history. Finally, our unexpected discovery of P. falciparumin the high-altitude Himalayas provides a rare case study in which individual mobility can be inferred from infection status, adding to our knowledge of cross-cultural connectivity in the region nearly three millennia ago.
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- 2024
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139. Acute locomotor, heart rate and neuromuscular responses to added wearable resistance during soccer-specific training
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Brown, Matthew, Lacome, Mathieu, Leduc, Cedric, Hader, Karim, Guilhem, Gael, and Buchheit, Martin
- Abstract
ABSTRACTPurpose: Investigate acute locomotor, internal (heart rate (HR) and ratings of perceived exertion (RPE)) and neuromuscular responses to using wearable resistance loading for soccer-specific training. Methods: Twenty-six footballers from a French 5th division team completed a 9-week parallel-group training intervention (intervention group: n = 14, control: n = 12). The intervention group trained with wearable resistance (200-g on each posterior, distal-calf) for full-training sessions on Day + 2, D + 4 and unloaded on D + 5. Between-group differences in locomotor (GPS) and internal load were analyzed for full-training sessions and game simulation drills. Neuromuscular status was evaluated using pre- and post-training box-to-box runs. Data were analyzed using linear mixed-modelling, effect size ±90% confidence limits (ES ± 90%CL) and magnitude-based decisions. Results: Full-training sessions: Relative to the control, the wearable resistance group showed greater total distance (ES [lower, upper limits]: 0.25 [0.06, 0.44]), sprint distance (0.27 [0.08, 0.46]) and mechanical work (0.32 [0.13, 0.51]). Small game simulation (<190 m2/player): wearable resistance group showed small decreases in mechanical work (0.45 [0.14, 0.76]) and moderately lower average HR (0.68 [0.02, 1.34]). Large game simulation (>190 m2/player): no meaningful between-group differences were observed for all variables. Training induced small to moderate neuromuscular fatigue increases during post-training compared to pre-training box-to-box runs for both groups (Wearable resistance: 0.46 [0.31, 0.61], Control: 0.73 [0.53, 0.93]). Conclusion: For full training, wearable resistance induced higher locomotor responses, without affecting internal responses. Locomotor and internal outputs varied in response to game simulation size. Football-specific training with wearable resistance did not impact neuromuscular status differently than unloaded training.
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- 2024
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140. Prevalence Rates and Correlates of Likely Post-Traumatic Stress Disorder in Residents of Fort McMurray 6 Months After a Wildfire
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Agyapong, Vincent I. O., Juhas, Michal, Omege, Joy, Denga, Edward, Nwaka, Bernard, Akinjise, Idowu, Corbett, Sandra E., Brown, Matthew, Chue, Pierre, Li, Xin-Min, and Greenshaw, Andrew
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- 2021
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141. The cardiovascular determinants of physical function in patients with end-stage kidney disease on haemodialysis
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Adenwalla, Sherna F., Billany, Roseanne E., March, Daniel S., Gulsin, Gaurav S., Young, Hannah M. L., Highton, Patrick, Churchward, Darren C., Young, Robin, Careless, Alysha, Tomlinson, Clare L., McCann, Gerry P., Burton, James O., and Graham-Brown, Matthew P. M.
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- 2021
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142. The strength of a pair of point vortices in an incompressible inviscid fluid in 3d can blow up in finite time
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Brown, Matthew Radley
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Physics - Fluid Dynamics ,76B47 - Abstract
The evolution of a pair of point vortices in whole space, subject to the inviscid Euler equations for incompressible fluid flow, is solved exactly for rotationally symmetric initial conditions. This exact solution shows that the vortex strength for a pair of point vortices can either remain stable or blow up in finite time, depending on the initial data., Comment: 2 pages
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- 2015
143. Snapshots and ensembles of BTK and cIAP1 protein degrader ternary complexes
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Schiemer, James, Horst, Reto, Meng, Yilin, Montgomery, Justin I., Xu, Yingrong, Feng, Xidong, Borzilleri, Kris, Uccello, Daniel P., Leverett, Carolyn, Brown, Stephen, Che, Ye, Brown, Matthew F., Hayward, Matthew M., Gilbert, Adam M., Noe, Mark C., and Calabrese, Matthew F.
- Published
- 2021
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144. Transferability of Buckingham Parameters for Short-Range Repulsion between Topological Atoms.
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Chung, Jaiming J. K., Brown, Matthew L., and Popelier, Paul L. A.
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- 2024
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145. Socio-demographic and comorbid risk factors for poor prognosis in patients hospitalized with community-acquired bacterial pneumonia in southeastern US.
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Idigo, Adeniyi J., Wells, J. Michael, Brown, Matthew L., Wiener, Howard W., Griffin, Russell L., Cutter, Gary, Shrestha, Sadeep, and Lee, Rachael A.
- Abstract
• Certain comorbidities and socio-demographic characteristics increase the risk of a patient's hospitalization for community-acquired pneumonia (CAP). • How a patient's factors affect bacterial CAP prognosis during and after hospitalization is important in disease management. • Heart failure, stroke, diabetes, obesity, and COPD were associated with poor disease prognosis as measured by medical intensive care unit admission, higher length of hospital stay, in-hospital mortality, or readmission within one year with recurrent bacterial CAP. • Socio-demographic characteristics including age, sex, race, and admission source, were also associated with poor disease prognosis. How socio-demographic characteristics and comorbidities affect bacterial community-acquired pneumonia (CAP) prognosis during/after hospitalization is important in disease management. To identify predictors of medical intensive care unit (MICU) admission, length of hospital stay (LOS), in-hospital mortality, and bacterial CAP readmission in patients hospitalized with bacterial CAP. ICD-9/10 codes were used to query electronic medical records to identify a cohort of patients hospitalized for bacterial CAP at a tertiary hospital in Southeastern US between 01/01/2013–12/31/2019. Adjusted accelerated failure time and modified Poisson regression models were used to examine predictors of MICU admission, LOS, in-hospital mortality, and 1-year readmission. There were 1956 adults hospitalized with bacterial CAP. Median (interquartile range) LOS was 11 days (6–23), and there were 26 % (513) MICU admission, 14 % (266) in-hospital mortality, and 6 % (117) 1-year readmission with recurrent CAP. MICU admission was associated with heart failure (RR 1.38; 95 % CI 1.17–1.62) and obesity (RR 1.26; 95 % CI 1.04–1.52). Longer LOS was associated with heart failure (adjusted time ratio[TR] 1.27;95 %CI 1.12–1.43), stroke (TR 1.90;95 %CI 1.54,2.35), type 2 diabetes (TR 1.20;95 %CI 1.07–1.36), obesity (TR 1.50;95 %CI 1.31–1.72), Black race (TR 1.17;95 %CI 1.04–1.31), and males (TR 1.24;95 %CI 1.10–1.39). In-hospital mortality was associated with stroke (RR 1.45;95 %CI 1.03–2.04) and age ≥65 years (RR 1.34;95 %CI 1.06–1.68). 1-year readmission was associated with COPD (RR 1.55;95 %CI 1.05–2.27) and underweight BMI (RR 1.74;95 %CI 1.04–2.90). Comorbidities and socio-demographic characteristics have varying impacts on bacterial CAP in-hospital prognosis and readmission. More studies are warranted to confirm these findings to develop comprehensive care plans and inform public health interventions. [ABSTRACT FROM AUTHOR]
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- 2024
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146. Sports in South America : A History
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BROWN, MATTHEW and BROWN, MATTHEW
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- 2023
147. Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci
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Ellinghaus, David, Jostins, Luke, Spain, Sarah L, Cortes, Adrian, Bethune, Jörn, Han, Buhm, Park, Yu Rang, Raychaudhuri, Soumya, Pouget, Jennie G, Hübenthal, Matthias, Folseraas, Trine, Wang, Yunpeng, Esko, Tonu, Metspalu, Andres, Westra, Harm-Jan, Franke, Lude, Pers, Tune H, Weersma, Rinse K, Collij, Valerie, D'Amato, Mauro, Halfvarson, Jonas, Jensen, Anders Boeck, Lieb, Wolfgang, Degenhardt, Franziska, Forstner, Andreas J, Hofmann, Andrea, Schreiber, Stefan, Mrowietz, Ulrich, Juran, Brian D, Lazaridis, Konstantinos N, Brunak, Søren, Dale, Anders M, Trembath, Richard C, Weidinger, Stephan, Weichenthal, Michael, Ellinghaus, Eva, Elder, James T, Barker, Jonathan NWN, Andreassen, Ole A, McGovern, Dermot P, Karlsen, Tom H, Barrett, Jeffrey C, Parkes, Miles, Brown, Matthew A, and Franke, Andre
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Biological Sciences ,Genetics ,Prevention ,2.1 Biological and endogenous factors ,Aetiology ,Inflammatory and immune system ,Bayes Theorem ,Cholangitis ,Sclerosing ,Chronic Disease ,Colitis ,Ulcerative ,Comorbidity ,Crohn Disease ,Genetic Heterogeneity ,Genetic Pleiotropy ,Genetic Variation ,Genome-Wide Association Study ,Genotype ,Humans ,Inflammation ,Psoriasis ,Quantitative Trait Loci ,Spondylitis ,Ankylosing ,International IBD Genetics Consortium ,International Genetics of Ankylosing Spondylitis Consortium ,International PSC Study Group ,Genetic Analysis of Psoriasis Consortium ,Psoriasis Association Genetics Extension ,Medical and Health Sciences ,Developmental Biology ,Agricultural biotechnology ,Bioinformatics and computational biology - Abstract
We simultaneously investigated the genetic landscape of ankylosing spondylitis, Crohn's disease, psoriasis, primary sclerosing cholangitis and ulcerative colitis to investigate pleiotropy and the relationship between these clinically related diseases. Using high-density genotype data from more than 86,000 individuals of European ancestry, we identified 244 independent multidisease signals, including 27 new genome-wide significant susceptibility loci and 3 unreported shared risk loci. Complex pleiotropy was supported when contrasting multidisease signals with expression data sets from human, rat and mouse together with epigenetic and expressed enhancer profiles. The comorbidities among the five immune diseases were best explained by biological pleiotropy rather than heterogeneity (a subgroup of cases genetically identical to those with another disease, possibly owing to diagnostic misclassification, molecular subtypes or excessive comorbidity). In particular, the strong comorbidity between primary sclerosing cholangitis and inflammatory bowel disease is likely the result of a unique disease, which is genetically distinct from classical inflammatory bowel disease phenotypes.
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- 2016
148. Determination of Surface Potential and Electrical Double-Layer Structure at the Aqueous Electrolyte-Nanoparticle Interface
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Brown, Matthew A, Abbas, Zareen, Kleibert, Armin, Green, Richard G, Goel, Alok, May, Sylvio, and Squires, Todd M
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Quantum Physics - Published
- 2016
149. Robustness-Driven Feature Selection in Classification of Fibrotic Interstitial Lung Disease Patterns in Computed Tomography Using 3D Texture Features
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Chong, Daniel Y, Kim, Hyun J, Lo, Pechin, Young, Stefano, McNitt-Gray, Michael F, Abtin, Fereidoun, Goldin, Jonathan G, and Brown, Matthew S
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Information and Computing Sciences ,Clinical Research ,Lung ,Biomedical Imaging ,Bioengineering ,Respiratory ,Humans ,Image Processing ,Computer-Assisted ,Lung Diseases ,Interstitial ,Machine Learning ,Pattern Recognition ,Automated ,Pulmonary Fibrosis ,Tomography ,X-Ray Computed ,High-resolution computed tomography ,machine learning ,pattern recognition and classification ,fibrotic interstitial lung disease ,Engineering ,Nuclear Medicine & Medical Imaging ,Information and computing sciences - Abstract
Lack of classifier robustness is a barrier to widespread adoption of computer-aided diagnosis systems for computed tomography (CT). We propose a novel Robustness-Driven Feature Selection (RDFS) algorithm that preferentially selects features robust to variations in CT technical factors. We evaluated RDFS in CT classification of fibrotic interstitial lung disease using 3D texture features. CTs were collected for 99 adult subjects separated into three datasets: training, multi-reconstruction, testing. Two thoracic radiologists provided cubic volumes of interest corresponding to six classes: pulmonary fibrosis, ground-glass opacity, honeycombing, normal lung parenchyma, airway, vessel. The multi-reconstruction dataset consisted of CT raw sinogram data reconstructed by systematically varying slice thickness, reconstruction kernel, and tube current (using a synthetic reduced-tube-current algorithm). Two support vector machine classifiers were created, one using RDFS ("with-RDFS") and one not ("without-RDFS"). Classifier robustness was compared on the multi-reconstruction dataset, using Cohen's kappa to assess classification agreement against a reference reconstruction. Classifier performance was compared on the testing dataset using the extended g-mean (EGM) measure. With-RDFS exhibited superior robustness (kappa 0.899-0.989) compared to without-RDFS (kappa 0.827-0.968). Both classifiers demonstrated similar performance on the testing dataset (EGM 0.778 for with-RDFS; 0.785 for without-RDFS), indicating that RDFS does not compromise classifier performance when discarding nonrobust features. RDFS is highly effective at improving classifier robustness against slice thickness, reconstruction kernel, and tube current without sacrificing performance, a result that has implications for multicenter clinical trials that rely on accurate and reproducible quantitative analysis of CT images collected under varied conditions across multiple sites, scanners, and timepoints.
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- 2016
150. Quantum Dynamics, Minkowski-Hilbert space, and A Quantum Stochastic Duhamel Principle
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Brown, Matthew F.
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Mathematical Physics ,Computer Science - Information Theory ,Mathematics - Dynamical Systems ,Quantum Physics ,81S22 - Abstract
In this paper we shall re-visit the well-known Schr\"odinger and Lindblad dynamics of quantum mechanics. However, these equations may be realized as the consequence of a more general, underlying dynamical process. In both cases we shall see that the evolution of a quantum state $P_\psi=\varrho(0)$ has the not so well-known pseudo-quadratic form $\partial_t\varrho(t)=\mathbf{V}^\star\varrho(t)\mathbf{V}$ where $\mathbf{V}$ is a vector operator in a complex Minkowski space and the pseudo-adjoint $\mathbf{V}^\star$ is induced by the Minkowski metric $\boldsymbol{\eta}$. The interesting thing about this formalism is that its derivation has very deep roots in a new understanding of the differential calculus of time. This Minkowski-Hilbert representation of quantum dynamics is called the \emph{Belavkin Formalism}; a beautiful, but not well understood theory of mathematical physics that understands that both deterministic and stochastic dynamics may be `unraveled' in a second-quantized Minkowski space. Working in such a space provided the author with the means to construct a QS (quantum stochastic) Duhamel principle and known applications to a Schr\"odinger dynamics perturbed by a continual measurement process are considered. What is not known, but presented here, is the role of the Lorentz transform in quantum measurement, and the appearance of Riemannian geometry in quantum measurement is also discussed.
- Published
- 2014
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