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Sparacino L, Antonacci Y, Barà C, Švec D, Javorka M, Faes L. A method to assess linear self-predictability of physiologic processes in the frequency domain: application to beat-to-beat variability of arterial compliance. Front Netw Physiol 2024; 4:1346424. [PMID: 38638612 PMCID: PMC11024367 DOI: 10.3389/fnetp.2024.1346424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/19/2024] [Indexed: 04/20/2024]
Abstract
The concept of self-predictability plays a key role for the analysis of the self-driven dynamics of physiological processes displaying richness of oscillatory rhythms. While time domain measures of self-predictability, as well as time-varying and local extensions, have already been proposed and largely applied in different contexts, they still lack a clear spectral description, which would be significantly useful for the interpretation of the frequency-specific content of the investigated processes. Herein, we propose a novel approach to characterize the linear self-predictability (LSP) of Gaussian processes in the frequency domain. The LSP spectral functions are related to the peaks of the power spectral density (PSD) of the investigated process, which is represented as the sum of different oscillatory components with specific frequency through the method of spectral decomposition. Remarkably, each of the LSP profiles is linked to a specific oscillation of the process, and it returns frequency-specific measures when integrated along spectral bands of physiological interest, as well as a time domain self-predictability measure with a clear meaning in the field of information theory, corresponding to the well-known information storage, when integrated along the whole frequency axis. The proposed measure is first illustrated in a theoretical simulation, showing that it clearly reflects the degree and frequency-specific location of predictability patterns of the analyzed process in both time and frequency domains. Then, it is applied to beat-to-beat time series of arterial compliance obtained in young healthy subjects. The results evidence that the spectral decomposition strategy applied to both the PSD and the spectral LSP of compliance identifies physiological responses to postural stress of low and high frequency oscillations of the process which cannot be traced in the time domain only, highlighting the importance of computing frequency-specific measures of self-predictability in any oscillatory physiologic process.
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Affiliation(s)
- Laura Sparacino
- Department of Engineering, University of Palermo, Palermo, Italy
| | - Yuri Antonacci
- Department of Engineering, University of Palermo, Palermo, Italy
| | - Chiara Barà
- Department of Engineering, University of Palermo, Palermo, Italy
| | - Dávid Švec
- Department of Physiology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Michal Javorka
- Department of Physiology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Luca Faes
- Department of Engineering, University of Palermo, Palermo, Italy
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2
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Vegué M, Thibeault V, Desrosiers P, Allard A. Dimension reduction of dynamics on modular and heterogeneous directed networks. PNAS Nexus 2023; 2:pgad150. [PMID: 37215634 PMCID: PMC10198746 DOI: 10.1093/pnasnexus/pgad150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/17/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023]
Abstract
Dimension reduction is a common strategy to study nonlinear dynamical systems composed by a large number of variables. The goal is to find a smaller version of the system whose time evolution is easier to predict while preserving some of the key dynamical features of the original system. Finding such a reduced representation for complex systems is, however, a difficult task. We address this problem for dynamics on weighted directed networks, with special emphasis on modular and heterogeneous networks. We propose a two-step dimension-reduction method that takes into account the properties of the adjacency matrix. First, units are partitioned into groups of similar connectivity profiles. Each group is associated to an observable that is a weighted average of the nodes' activities within the group. Second, we derive a set of equations that must be fulfilled for these observables to properly represent the original system's behavior, together with a method for approximately solving them. The result is a reduced adjacency matrix and an approximate system of ODEs for the observables' evolution. We show that the reduced system can be used to predict some characteristic features of the complete dynamics for different types of connectivity structures, both synthetic and derived from real data, including neuronal, ecological, and social networks. Our formalism opens a way to a systematic comparison of the effect of various structural properties on the overall network dynamics. It can thus help to identify the main structural driving forces guiding the evolution of dynamical processes on networks.
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Affiliation(s)
- Marina Vegué
- Département de physique, de génie physique et d'optique, Université Laval, 2325 rue de l'Université, G1V 0A6 Québec, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, 2325 rue de l'Université, G1V 0A6 Québec, Canada
| | - Vincent Thibeault
- Département de physique, de génie physique et d'optique, Université Laval, 2325 rue de l'Université, G1V 0A6 Québec, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, 2325 rue de l'Université, G1V 0A6 Québec, Canada
| | - Patrick Desrosiers
- Département de physique, de génie physique et d'optique, Université Laval, 2325 rue de l'Université, G1V 0A6 Québec, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, 2325 rue de l'Université, G1V 0A6 Québec, Canada
- CERVO Brain Research Center, 2301 avenue d'Estimauville, G1E 1T2 Québec, Canada
| | - Antoine Allard
- Département de physique, de génie physique et d'optique, Université Laval, 2325 rue de l'Université, G1V 0A6 Québec, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, 2325 rue de l'Université, G1V 0A6 Québec, Canada
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3
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Khalili F, Gamage PT, Taebi A, Johnson ME, Roberts RB, Mitchel J. Spectral Decomposition and Sound Source Localization of Highly Disturbed Flow through a Severe Arterial Stenosis. Bioengineering (Basel) 2021; 8:bioengineering8030034. [PMID: 33806695 PMCID: PMC8000318 DOI: 10.3390/bioengineering8030034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 02/07/2021] [Accepted: 02/22/2021] [Indexed: 01/01/2023] Open
Abstract
For the early detection of atherosclerosis, it is imperative to explore the capabilities of new, effective noninvasive diagnosis techniques to significantly reduce the associated treatment costs and mortality rates. In this study, a multifaceted comprehensive approach involving advanced computational fluid dynamics combined with signal processing techniques was exploited to investigate the highly turbulent fluctuating flow through arterial stenosis. The focus was on localizing high-energy mechano-acoustic source potential to transmit to the epidermal surface. The flow analysis results showed the existence of turbulent pressure fluctuations inside the stenosis and in the post-stenotic region. After analyzing the turbulent kinetic energy and pressure fluctuations on the flow centerline and the vessel wall, the point of maximum excitation in the flow was observed around two diameters downstream of the stenosis within the fluctuating zone. It was also found that the concentration of pressure fluctuation closer to the wall was higher inside the stenosis compared to the post-stenotic region. Additionally, the visualization of the most energetic proper orthogonal decomposition (POD) mode and spectral decomposition of the flow indicated that the break frequencies ranged from 80 to 220 Hz and were correlated to the eddies generated within these regions.
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Affiliation(s)
- Fardin Khalili
- Department of Mechanical Engineering, Embry-Riddle Aeronautical University, 1 Aerospace Boulevard, Daytona Beach, FL 32114, USA
- Correspondence:
| | - Peshala T. Gamage
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, 2930 Science Cir., Melbourne, FL 32901, USA;
| | - Amirtahà Taebi
- Department of Biomedical Engineering, University of California Davis, One Shields Avenue, Davis, CA 95616, USA;
| | - Mark E. Johnson
- Telecraft Engineering Inc., 1254 Mount Carmel Church Lane, Canton, GA 30114, USA; (M.E.J.); (R.B.R.)
| | - Randal B. Roberts
- Telecraft Engineering Inc., 1254 Mount Carmel Church Lane, Canton, GA 30114, USA; (M.E.J.); (R.B.R.)
| | - John Mitchel
- Infrasonix Inc., 1665 Lakes Parkway, Suite 102, Lawrenceville, GA 30043, USA;
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Chen K, Massie C, Berger AJ. Soft-tissue spectral subtraction improves transcutaneous Raman estimates of murine bone strength in vivo. J Biophotonics 2020; 13:e202000256. [PMID: 32749067 PMCID: PMC8320303 DOI: 10.1002/jbio.202000256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/26/2020] [Accepted: 07/30/2020] [Indexed: 06/11/2023]
Abstract
Transcutaneous determination of a bone's Raman spectrum is challenging because the type I collagen in the overlying soft tissue is spectroscopically identical to that in bone. In a previous transcutaneous study of murine tibiae, we developed a library-based model called SOLD to unmix spatially offset Raman measurements into three spectra: a bone estimate, a soft tissue estimate, and a residual. Here, we demonstrate the value of combining the bone estimate and the residual to produce a "top layer subtracted" (tls) spectrum. We report superior prediction of two standard bone metrics (volumetric bone mineralization density and maximum torque) using partial least squares regression models based upon tls spectra rather than SOLD bone estimates, implying that the spectral residuals contain useful information. Simulations reinforce experimental in vivo findings. This chemometric approach, which we denote as SOLD/TLS, could have broad applicability in situations where comprehensive spectral libraries are difficult to acquire.
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Affiliation(s)
- Keren Chen
- The Institute of Optics, University of Rochester, New York, USA
- Contributed equally to this work and should be considered joint first authors
| | - Christine Massie
- Department of Biomedical Engineering, University of Rochester, New York, USA
- Contributed equally to this work and should be considered joint first authors
| | - Andrew J. Berger
- The Institute of Optics, University of Rochester, New York, USA
- Department of Biomedical Engineering, University of Rochester, New York, USA
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Labussière M, Laconte J, Pomerleau F. Geometry Preserving Sampling Method Based on Spectral Decomposition for Large-Scale Environments. Front Robot AI 2020; 7:572054. [PMID: 33501332 PMCID: PMC7806074 DOI: 10.3389/frobt.2020.572054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/21/2020] [Indexed: 11/18/2022] Open
Abstract
In the context of 3D mapping, larger and larger point clouds are acquired with lidar sensors. Although pleasing to the eye, dense maps are not necessarily tailored for practical applications. For instance, in a surface inspection scenario, keeping geometric information such as the edges of objects is essential to detect cracks, whereas very dense areas of very little information such as the ground could hinder the main goal of the application. Several strategies exist to address this problem by reducing the number of points. However, they tend to underperform with non-uniform density, large sensor noise, spurious measurements, and large-scale point clouds, which is the case in mobile robotics. This paper presents a novel sampling algorithm based on spectral decomposition analysis to derive local density measures for each geometric primitive. The proposed method, called Spectral Decomposition Filter (SpDF), identifies and preserves geometric information along the topology of point clouds and is able to scale to large environments with a non-uniform density. Finally, qualitative and quantitative experiments verify the feasibility of our method and present a large-scale evaluation of SpDF with other seven point cloud sampling algorithms, in the context of the 3D registration problem using the Iterative Closest Point (ICP) algorithm on real-world datasets. Results show that a compression ratio up to 97 % can be achieved when accepting a registration error within the range accuracy of the sensor, here for large scale environments of less than 2 cm.
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Affiliation(s)
- Mathieu Labussière
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut Pascal, Clermont-Ferrand, France
- Northern Robotics Laboratory, Université Laval, Québec City, QC, Canada
| | - Johann Laconte
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut Pascal, Clermont-Ferrand, France
- Northern Robotics Laboratory, Université Laval, Québec City, QC, Canada
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Shinotsuka H, Nagata K, Yoshikawa H, Mototake YI, Shouno H, Okada M. Development of spectral decomposition based on Bayesian information criterion with estimation of confidence interval. Sci Technol Adv Mater 2020; 21:402-419. [PMID: 32939165 PMCID: PMC7476551 DOI: 10.1080/14686996.2020.1773210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
We develop an automatic peak fitting algorithm using the Bayesian information criterion (BIC) fitting method with confidence-interval estimation in spectral decomposition. First, spectral decomposition is carried out by adopting the Bayesian exchange Monte Carlo method for various artificial spectral data, and the confidence interval of fitting parameters is evaluated. From the results, an approximated model formula that expresses the confidence interval of parameters and the relationship between the peak-to-peak distance and the signal-to-noise ratio is derived. Next, for real spectral data, we compare the confidence interval of each peak parameter obtained using the Bayesian exchange Monte Carlo method with the confidence interval obtained from the BIC-fitting with the model selection function and the proposed approximated formula. We thus confirm that the parameter confidence intervals obtained using the two methods agree well. It is therefore possible to not only simply estimate the appropriate number of peaks by BIC-fitting but also obtain the confidence interval of fitting parameters.
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Affiliation(s)
- Hiroshi Shinotsuka
- Research and Services Division of Materials Data and Integrated System, National Institute for Materials Science, Tsukuba, Japan
| | - Kenji Nagata
- Research and Services Division of Materials Data and Integrated System, National Institute for Materials Science, Tsukuba, Japan
| | - Hideki Yoshikawa
- Research and Services Division of Materials Data and Integrated System, National Institute for Materials Science, Tsukuba, Japan
| | - Yoh-Ichi Mototake
- Research Center for Statistical Machine Learning, The Institute of Statistical Mathematics, Tachikawa, Japan
| | - Hayaru Shouno
- Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Japan
| | - Masato Okada
- Research and Services Division of Materials Data and Integrated System, National Institute for Materials Science, Tsukuba, Japan
- Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Japan
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7
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Liu X, Li JB, Pan JS. Feature Point Matching Based on Distinct Wavelength Phase Congruency and Log-Gabor Filters in Infrared and Visible Images. Sensors (Basel) 2019; 19:s19194244. [PMID: 31569596 PMCID: PMC6806253 DOI: 10.3390/s19194244] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/20/2019] [Accepted: 09/24/2019] [Indexed: 11/17/2022]
Abstract
Infrared and visible image matching methods have been rising in popularity with the emergence of more kinds of sensors, which provide more applications in visual navigation, precision guidance, image fusion, and medical image analysis. In such applications, image matching is utilized for location, fusion, image analysis, and so on. In this paper, an infrared and visible image matching approach, based on distinct wavelength phase congruency (DWPC) and log-Gabor filters, is proposed. Furthermore, this method is modified for non-linear image matching with different physical wavelengths. Phase congruency (PC) theory is utilized to obtain PC images with intrinsic and affluent image features for images containing complex intensity changes or noise. Then, the maximum and minimum moments of the PC images are computed to obtain the corners in the matched images. In order to obtain the descriptors, log-Gabor filters are utilized and overlapping subregions are extracted in a neighborhood of certain pixels. In order to improve the accuracy of the algorithm, the moments of PCs in the original image and a Gaussian smoothed image are combined to detect the corners. Meanwhile, it is improper that the two matched images have the same PC wavelengths, due to the images having different physical wavelengths. Thus, in the experiment, the wavelength of the PC is changed for different physical wavelengths. For realistic application, BiDimRegression method is proposed to compute the similarity between two points set in infrared and visible images. The proposed approach is evaluated on four data sets with 237 pairs of visible and infrared images, and its performance is compared with state-of-the-art approaches: the edge-oriented histogram descriptor (EHD), phase congruency edge-oriented histogram descriptor (PCEHD), and log-Gabor histogram descriptor (LGHD) algorithms. The experimental results indicate that the accuracy rate of the proposed approach is 50% higher than the traditional approaches in infrared and visible images.
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Affiliation(s)
- Xiaomin Liu
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150001, China.
- Information and Electronic Technology Institute, Jiamusi University, Jiamusi 154002, China.
| | - Jun-Bao Li
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150001, China.
| | - Jeng-Shyang Pan
- College of Computer Science and Engineering, Shandong University of Science and Technology, Qingdao 266510, China.
- Fujian Provincial Key Laboratory of Big Data Minning and Applications, Fujian University of Technology, Fuzhou 350118, China.
- College of Informatics, Chaoyang University of Science and Technology, Taichung 413, Taiwan.
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Pereira-Ferrero VH, Lewis TG, Ferrero LGP, Duarte LT. Complex Networks Models and Spectral Decomposition in the Analysis of Swimming Athletes' Performance at Olympic Games. Front Physiol 2019; 10:1134. [PMID: 31551810 PMCID: PMC6733958 DOI: 10.3389/fphys.2019.01134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/16/2019] [Indexed: 01/08/2023] Open
Abstract
This study aims to present complex network models which analyze professional swimmers of 50-m freestyle Olympic competitions, comparing characteristics and variables that are considered performance determinants. This comparative research includes Olympic medalists’ versus non-medalists’ behavior. Using data from 40 athletes with a mean age, weight and height of 26 ± 2.9 years, 87 ± 5.59 kg, 193 ± 3.85 cm, respectively, at the Olympics of 2000, 2004, 2008, 2012, and 2016 (16-year interval), we built two types of complex networks (graphs) for each edition, using mathematical correlations, metrics and the spectral decomposition analysis. It is possible to show that complex metrics behave differently between medalists and non-medalists. The spectral radius (SR) proved to be an important form of evaluation since in all 5 editions it was higher among medalists (SR results: 3.75, 3.5, 3.39, 2.91, and 3.66) compared to non-medalists (2.18, 2.51, 2.23, 2.07, and 2.04), with significantly differences between. This study introduces a remarkable tool in the evaluation of the performance of groups of swimming athletes by complex networks, and is relevant to athletes, coaches, and even amateurs, regarding how individual variables relate to competition results and are reflected in the SR for the best performance. In addition, this is a general method and may, in the future, be developed in the analysis of other competitive sports.
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Affiliation(s)
| | - Theodore Gyle Lewis
- Center for Homeland Defense and Security, Naval Postgraduate School, Monterey, CA, United States
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9
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ElGamacy M, Riss M, Zhu H, Truffault V, Coles M. Mapping Local Conformational Landscapes of Proteins in Solution. Structure 2019; 27:853-865.e5. [PMID: 30930065 DOI: 10.1016/j.str.2019.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 10/05/2018] [Accepted: 03/07/2019] [Indexed: 01/19/2023]
Abstract
The ability of proteins to adopt multiple conformational states is essential to their function, and elucidating the details of such diversity under physiological conditions has been a major challenge. Here we present a generalized method for mapping protein population landscapes by NMR spectroscopy. Experimental NOESY spectra are directly compared with a set of expectation spectra back-calculated across an arbitrary conformational space. Signal decomposition of the experimental spectrum then directly yields the relative populations of local conformational microstates. In this way, averaged descriptions of conformation can be eliminated. As the method quantitatively compares experimental and expectation spectra, it inherently delivers an R factor expressing how well structural models explain the input data. We demonstrate that our method extracts sufficient information from a single 3D NOESY experiment to perform initial model building, refinement, and validation, thus offering a complete de novo structure determination protocol.
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Affiliation(s)
- Mohammad ElGamacy
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Michael Riss
- Department of Informatics, Technical University of Munich, Boltzmannstrasse 3, 85748 Garching, Germany
| | - Hongbo Zhu
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Vincent Truffault
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Murray Coles
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany.
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10
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Ren X, Li S, Shen C, Yu Z. Linear and nonlinear variable selection in competing risks data. Stat Med 2018; 37:2134-2147. [PMID: 29579776 DOI: 10.1002/sim.7637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 01/12/2018] [Accepted: 01/24/2018] [Indexed: 11/12/2022]
Abstract
Subdistribution hazard model for competing risks data has been applied extensively in clinical researches. Variable selection methods of linear effects for competing risks data have been studied in the past decade. There is no existing work on selection of potential nonlinear effects for subdistribution hazard model. We propose a two-stage procedure to select the linear and nonlinear covariate(s) simultaneously and estimate the selected covariate effect(s). We use spectral decomposition approach to distinguish the linear and nonlinear parts of each covariate and adaptive LASSO to select each of the 2 components. Extensive numerical studies are conducted to demonstrate that the proposed procedure can achieve good selection accuracy in the first stage and small estimation biases in the second stage. The proposed method is applied to analyze a cardiovascular disease data set with competing death causes.
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Affiliation(s)
- Xiaowei Ren
- IUSM-Department of Biostatistics, Indiana University, Indianapolis, IN, USA
| | - Shanshan Li
- IUSM-Department of Biostatistics, Indiana University, Indianapolis, IN, USA
| | - Changyu Shen
- Beth Israel Deaconess Medical Center, Smith Center, Havard University, Boston, MA, USA
| | - Zhangsheng Yu
- Department of Bioinformatics and Biostatistics, SJTU - Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China
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11
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Lau JYC, Geraghty BJ, Chen AP, Cunningham CH. Improved tolerance to off-resonance in spectral-spatial EPI of hyperpolarized [1- 13 C]pyruvate and metabolites. Magn Reson Med 2018; 80:925-934. [PMID: 29380423 DOI: 10.1002/mrm.27086] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/28/2017] [Accepted: 12/24/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Justin Y C Lau
- Physical Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin J Geraghty
- Physical Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | | | - Charles H Cunningham
- Physical Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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12
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Goryawala MZ, Sheriff S, Stoyanova R, Maudsley AA. Spectral decomposition for resolving partial volume effects in MRSI. Magn Reson Med 2017; 79:2886-2895. [PMID: 29130515 DOI: 10.1002/mrm.26991] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/28/2017] [Accepted: 10/11/2017] [Indexed: 01/09/2023]
Abstract
PURPOSE Estimation of brain metabolite concentrations by MR spectroscopic imaging (MRSI) is complicated by partial volume contributions from different tissues. This study evaluates a method for increasing tissue specificity that incorporates prior knowledge of tissue distributions. METHODS A spectral decomposition (sDec) technique was evaluated for separation of spectra from white matter (WM) and gray matter (GM), and for measurements in small brain regions using whole-brain MRSI. Simulation and in vivo studies compare results of metabolite quantifications obtained with the sDec technique to those obtained by spectral fitting of individual voxels using mean values and linear regression against tissue fractions and spectral fitting of regionally integrated spectra. RESULTS Simulation studies showed that, for GM and the putamen, the sDec method offers < 2% and 3.5% error, respectively, in metabolite estimates. These errors are considerably reduced in comparison to methods that do not account for partial volume effects or use regressions against tissue fractions. In an analysis of data from 197 studies, significant differences in mean metabolite values and changes with age were found. Spectral decomposition resulted in significantly better linewidth, signal-to-noise ratio, and spectral fitting quality as compared to individual spectral analysis. Moreover, significant partial volume effects were seen on correlations of neurometabolite estimates with age. CONCLUSION The sDec analysis approach is of considerable value in studies of pathologies that may preferentially affect WM or GM, as well as smaller brain regions significantly affected by partial volume effects. Magn Reson Med 79:2886-2895, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
| | - Sulaiman Sheriff
- Department of Radiology, University of Miami, Miami, Florida, USA
| | - Radka Stoyanova
- Department of Radiation Oncology, University of Miami, Miami, Florida, USA
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Abstract
This Correspondence article is a comment which directly relates to the paper "A study of problems encountered in Granger causality analysis from a neuroscience perspective" ( Stokes and Purdon, 2017). We agree that interpretation issues of Granger causality (GC) in neuroscience exist, partially due to the historically unfortunate use of the name "causality", as described in previous literature. On the other hand, we think that Stokes and Purdon use a formulation of GC which is outdated (albeit still used) and do not fully account for the potential of the different frequency-domain versions of GC; in doing so, their paper dismisses GC measures based on a suboptimal use of them. Furthermore, since data from simulated systems are used, the pitfalls that are found with the used formulation are intended to be general, and not limited to neuroscience. It would be a pity if this paper, even if written in good faith, became a wildcard against all possible applications of GC, regardless of the large body of work recently published which aims to address faults in methodology and interpretation. In order to provide a balanced view, we replicate the simulations of Stokes and Purdon, using an updated GC implementation and exploiting the combination of spectral and causal information, showing that in this way the pitfalls are mitigated or directly solved.
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Affiliation(s)
- Luca Faes
- BIOtech, Department of Industrial Engineering, University of Trento, Trento, Italy
| | - Sebastiano Stramaglia
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy.,Dipartimento di Fisica, Università degli Studi Aldo Moro, Bari, Italy
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Mazeres S, Fereidouni F, Joly E. Using spectral decomposition of the signals from laurdan-derived probes to evaluate the physical state of membranes in live cells. F1000Res 2017; 6:763. [PMID: 28663788 PMCID: PMC5473435 DOI: 10.12688/f1000research.11577.2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/28/2017] [Indexed: 01/22/2023] Open
Abstract
Background: We wanted to investigate the physical state of biological membranes in live cells under the most physiological conditions possible. Methods: For this we have been using laurdan, C-laurdan or M-laurdan to label a variety of cells, and a biphoton microscope equipped with both a thermostatic chamber and a spectral analyser. We also used a flow cytometer to quantify the 450/530 nm ratio of fluorescence emissions by whole cells. Results: We find that using all the information provided by spectral analysis to perform spectral decomposition dramatically improves the imaging resolution compared to using just two channels, as commonly used to calculate generalized polarisation (GP). Coupled to a new plugin called Fraction Mapper, developed to represent the fraction of light intensity in the first component in a stack of two images, we obtain very clear pictures of both the intra-cellular distribution of the probes, and the polarity of the cellular environments where the lipid probes are localised. Our results lead us to conclude that, in live cells kept at 37°C, laurdan, and M-laurdan to a lesser extent, have a strong tendency to accumulate in the very apolar environment of intra-cytoplasmic lipid droplets, but label the plasma membrane (PM) of mammalian cells ineffectively. On the other hand, C-laurdan labels the PM very quickly and effectively, and does not detectably accumulate in lipid droplets. Conclusions: From using these probes on a variety of mammalian cell lines, as well as on cells from
Drosophila and
Dictyostelium discoideum, we conclude that, apart from the lipid droplets, which are very apolar, probes in intracellular membranes reveal a relatively polar and hydrated environment, suggesting a very marked dominance of liquid disordered states. PMs, on the other hand, are much more apolar, suggesting a strong dominance of liquid ordered state, which fits with their high sterol contents.
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Affiliation(s)
- Serge Mazeres
- Membrane and DNA Dynamics Team, Institut de Pharmacologie et de Biologie Structurale, CNRS, Université de Toulouse, Toulouse, F-31077, France
| | - Farzad Fereidouni
- Department of Pathology and Laboratory Medicine, University of California Davis Medical Center, CA 95817, CA, 4400, USA
| | - Etienne Joly
- Membrane and DNA Dynamics Team, Institut de Pharmacologie et de Biologie Structurale, CNRS, Université de Toulouse, Toulouse, F-31077, France
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15
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Mazeres S, Fereidouni F, Joly E. Using spectral decomposition of the signals from laurdan-derived probes to evaluate the physical state of membranes in live cells. F1000Res 2017; 6:763. [PMID: 28663788 DOI: 10.12688/f1000research.11577.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/26/2017] [Indexed: 12/13/2022] Open
Abstract
Background: We wanted to investigate the physical state of biological membranes in live cells under the most physiological conditions possible. Methods: For this we have been using laurdan, C-laurdan or M-laurdan to label a variety of cells, and a biphoton microscope equipped with both a thermostatic chamber and a spectral analyser. We also used a flow cytometer to quantify the 450/530 nm ratio of fluorescence emissions by whole cells. Results: We find that using all the information provided by spectral analysis to perform spectral decomposition dramatically improves the imaging resolution compared to using just two channels, as commonly used to calculate generalized polarisation (GP). Coupled to a new plugin called Fraction Mapper, developed to represent the fraction of light intensity in the first component in a stack of two images, we obtain very clear pictures of both the intra-cellular distribution of the probes, and the polarity of the cellular environments where the lipid probes are localised. Our results lead us to conclude that, in live cells kept at 37°C, laurdan, and M-laurdan to a lesser extent, have a strong tendency to accumulate in the very apolar environment of intra-cytoplasmic lipid droplets, but label the plasma membrane (PM) of mammalian cells ineffectively. On the other hand, C-laurdan labels the PM very quickly and effectively, and does not detectably accumulate in lipid droplets. Conclusions: From using these probes on a variety of mammalian cell lines, as well as on cells from Drosophila and Dictyostelium discoideum, we conclude that, apart from the lipid droplets, which are very apolar, probes in intracellular membranes reveal a relatively polar and hydrated environment, suggesting a very marked dominance of liquid disordered states. PMs, on the other hand, are much more apolar, suggesting a strong dominance of liquid ordered state, which fits with their high sterol contents.
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Affiliation(s)
- Serge Mazeres
- Membrane and DNA Dynamics Team, Institut de Pharmacologie et de Biologie Structurale, CNRS, Université de Toulouse, Toulouse, F-31077, France
| | - Farzad Fereidouni
- Department of Pathology and Laboratory Medicine, University of California Davis Medical Center, CA 95817, CA, 4400, USA
| | - Etienne Joly
- Membrane and DNA Dynamics Team, Institut de Pharmacologie et de Biologie Structurale, CNRS, Université de Toulouse, Toulouse, F-31077, France
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16
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Cervera M, Tesei C. An Energy-Equivalent d⁺/d - Damage Model with Enhanced Microcrack Closure-Reopening Capabilities for Cohesive-Frictional Materials. Materials (Basel) 2017; 10:ma10040433. [PMID: 28772793 PMCID: PMC5507001 DOI: 10.3390/ma10040433] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 04/12/2017] [Accepted: 04/18/2017] [Indexed: 11/16/2022]
Abstract
In this paper, an energy-equivalent orthotropic d+/d− damage model for cohesive-frictional materials is formulated. Two essential mechanical features are addressed, the damage-induced anisotropy and the microcrack closure-reopening (MCR) effects, in order to provide an enhancement of the original d+/d− model proposed by Faria et al. 1998, while keeping its high algorithmic efficiency unaltered. First, in order to ensure the symmetry and positive definiteness of the secant operator, the new formulation is developed in an energy-equivalence framework. This proves thermodynamic consistency and allows one to describe a fundamental feature of the orthotropic damage models, i.e., the reduction of the Poisson’s ratio throughout the damage process. Secondly, a “multidirectional” damage procedure is presented to extend the MCR capabilities of the original model. The fundamental aspects of this approach, devised for generic cyclic conditions, lie in maintaining only two scalar damage variables in the constitutive law, while preserving memory of the degradation directionality. The enhanced unilateral capabilities are explored with reference to the problem of a panel subjected to in-plane cyclic shear, with or without vertical pre-compression; depending on the ratio between shear and pre-compression, an absent, a partial or a complete stiffness recovery is simulated with the new multidirectional procedure.
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Affiliation(s)
- Miguel Cervera
- International Center for Numerical Methods in Engineering (CIMNE), Universidad Politécnica de Cataluña, Campus Norte UPC, 08034 Barcelona, Spain.
| | - Claudia Tesei
- Department of Structural, Building and Geotechnical Engineering (DISEG), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
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17
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Astitha M, Luo H, Rao ST, Hogrefe C, Mathur R, Kumar N. Dynamic Evaluation of Two Decades of WRF-CMAQ Ozone Simulations over the Contiguous United States. Atmos Environ (1994) 2017; 164:102-116. [PMID: 30078987 PMCID: PMC6071429 DOI: 10.1016/j.atmosenv.2017.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Dynamic evaluation of the fully coupled Weather Research and Forecasting (WRF)- Community Multi-scale Air Quality (CMAQ) model ozone simulations over the contiguous United States (CONUS) using two decades of simulations covering the period from 1990 to 2010 is conducted to assess how well the changes in observed ozone air quality are simulated by the model. The changes induced by variations in meteorology and/or emissions are also evaluated during the same timeframe using spectral decomposition of observed and modeled ozone time series with the aim of identifying the underlying forcing mechanisms that control ozone exceedances and making informed recommendations for the optimal use of regional-scale air quality models. The evaluation is focused on the warm season's (i.e., May-September) daily maximum 8-hr (DM8HR) ozone concentrations, the 4th highest (4th) and average of top 10 DM8HR ozone values (top10), as well as the spectrally-decomposed components of the DM8HR ozone time series using the Kolmogorov-Zurbenko (KZ) filter. Results of the dynamic evaluation are presented for six regions in the U.S., consistent with the National Oceanic and Atmospheric Administration (NOAA) climatic regions. During the earlier 11-yr period (1990-2000), the simulated and observed trends are not statistically significant. During the more recent 2000-2010 period, all trends are statistically significant and WRF-CMAQ captures the observed trend in most regions. Given large number of sites for the 2000-2010 period, the model captures the observed trends in the Southwest (SW) and MW but has significantly different trend from that seen in observations for the other regions. Observational analysis reveals that it is the long-term forcing that dictates how high the ozone exceedances will be; there is a strong linear relationship between the long-term forcing and the 4th highest or the average of the top10 ozone concentrations in both observations and model output. This finding indicates that improving the model's ability to reproduce the long-term component will also enable better simulation of ozone extreme values that are of interest to regulatory agencies.
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Affiliation(s)
- Marina Astitha
- Department of Civil and Environmental Engineering, University of Connecticut, Storrs, CT, USA
| | - Huiying Luo
- Department of Civil and Environmental Engineering, University of Connecticut, Storrs, CT, USA
| | - S. Trivikrama Rao
- Department of Civil and Environmental Engineering, University of Connecticut, Storrs, CT, USA
- North Carolina State University, Raleigh, NC, USA
| | - Christian Hogrefe
- U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Rohit Mathur
- U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
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18
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Onton JA, Kang DY, Coleman TP. Visualization of Whole-Night Sleep EEG From 2-Channel Mobile Recording Device Reveals Distinct Deep Sleep Stages with Differential Electrodermal Activity. Front Hum Neurosci 2016; 10:605. [PMID: 27965558 PMCID: PMC5126123 DOI: 10.3389/fnhum.2016.00605] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 11/14/2016] [Indexed: 11/17/2022] Open
Abstract
Brain activity during sleep is a powerful marker of overall health, but sleep lab testing is prohibitively expensive and only indicated for major sleep disorders. This report demonstrates that mobile 2-channel in-home electroencephalogram (EEG) recording devices provided sufficient information to detect and visualize sleep EEG. Displaying whole-night sleep EEG in a spectral display allowed for quick assessment of general sleep stability, cycle lengths, stage lengths, dominant frequencies and other indices of sleep quality. By visualizing spectral data down to 0.1 Hz, a differentiation emerged between slow-wave sleep with dominant frequency between 0.1–1 Hz or 1–3 Hz, but rarely both. Thus, we present here the new designations, Hi and Lo Deep sleep, according to the frequency range with dominant power. Simultaneously recorded electrodermal activity (EDA) was primarily associated with Lo Deep and very rarely with Hi Deep or any other stage. Therefore, Hi and Lo Deep sleep appear to be physiologically distinct states that may serve unique functions during sleep. We developed an algorithm to classify five stages (Awake, Light, Hi Deep, Lo Deep and rapid eye movement (REM)) using a Hidden Markov Model (HMM), model fitting with the expectation-maximization (EM) algorithm, and estimation of the most likely sleep state sequence by the Viterbi algorithm. The resulting automatically generated sleep hypnogram can help clinicians interpret the spectral display and help researchers computationally quantify sleep stages across participants. In conclusion, this study demonstrates the feasibility of in-home sleep EEG collection, a rapid and informative sleep report format, and novel deep sleep designations accounting for spectral and physiological differences.
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Affiliation(s)
- Julie A Onton
- Institute for Neural Computation, University of California, San DiegoLa Jolla, CA, USA; Naval Health Research CenterSan Diego, CA, USA
| | - Dae Y Kang
- Department of Bioengineering, University of California, San Diego La Jolla, CA, USA
| | - Todd P Coleman
- Department of Bioengineering, University of California, San Diego La Jolla, CA, USA
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19
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Park C, Kang MG. Color Restoration of RGBN Multispectral Filter Array Sensor Images Based on Spectral Decomposition. Sensors (Basel) 2016; 16:E719. [PMID: 27213381 DOI: 10.3390/s16050719] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 05/12/2016] [Accepted: 05/13/2016] [Indexed: 11/17/2022]
Abstract
A multispectral filter array (MSFA) image sensor with red, green, blue and near-infrared (NIR) filters is useful for various imaging applications with the advantages that it obtains color information and NIR information simultaneously. Because the MSFA image sensor needs to acquire invisible band information, it is necessary to remove the IR cut-offfilter (IRCF). However, without the IRCF, the color of the image is desaturated by the interference of the additional NIR component of each RGB color channel. To overcome color degradation, a signal processing approach is required to restore natural color by removing the unwanted NIR contribution to the RGB color channels while the additional NIR information remains in the N channel. Thus, in this paper, we propose a color restoration method for an imaging system based on the MSFA image sensor with RGBN filters. To remove the unnecessary NIR component in each RGB color channel, spectral estimation and spectral decomposition are performed based on the spectral characteristics of the MSFA sensor. The proposed color restoration method estimates the spectral intensity in NIR band and recovers hue and color saturation by decomposing the visible band component and the NIR band component in each RGB color channel. The experimental results show that the proposed method effectively restores natural color and minimizes angular errors.
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20
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Arakawa A, Taniguchi M, Hayashi T, Mikawa S. Variational bayesian method of estimating variance components. Anim Sci J 2016; 87:863-72. [PMID: 26877207 DOI: 10.1111/asj.12514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/02/2015] [Accepted: 06/18/2015] [Indexed: 11/30/2022]
Abstract
We developed a Bayesian analysis approach by using a variational inference method, a so-called variational Bayesian method, to determine the posterior distributions of variance components. This variational Bayesian method and an alternative Bayesian method using Gibbs sampling were compared in estimating genetic and residual variance components from both simulated data and publically available real pig data. In the simulated data set, we observed strong bias toward overestimation of genetic variance for the variational Bayesian method in the case of low heritability and low population size, and less bias was detected with larger population sizes in both methods examined. The differences in the estimates of variance components between the variational Bayesian and the Gibbs sampling were not found in the real pig data. However, the posterior distributions of the variance components obtained with the variational Bayesian method had shorter tails than those obtained with the Gibbs sampling. Consequently, the posterior standard deviations of the genetic and residual variances of the variational Bayesian method were lower than those of the method using Gibbs sampling. The computing time required was much shorter with the variational Bayesian method than with the method using Gibbs sampling.
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Affiliation(s)
- Aisaku Arakawa
- Animal Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Masaaki Taniguchi
- Animal Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Takeshi Hayashi
- Agroinformatics Division, National Agriculture and Food Research Organization, Agricultural Research Center, Tsukuba, Ibaraki, Japan
| | - Satoshi Mikawa
- Animal Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
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21
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Ba D, Babadi B, Purdon PL, Brown EN. Robust spectrotemporal decomposition by iteratively reweighted least squares. Proc Natl Acad Sci U S A 2014; 111:E5336-45. [PMID: 25468968 DOI: 10.1073/pnas.1320637111] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Classical nonparametric spectral analysis uses sliding windows to capture the dynamic nature of most real-world time series. This universally accepted approach fails to exploit the temporal continuity in the data and is not well-suited for signals with highly structured time-frequency representations. For a time series whose time-varying mean is the superposition of a small number of oscillatory components, we formulate nonparametric batch spectral analysis as a Bayesian estimation problem. We introduce prior distributions on the time-frequency plane that yield maximum a posteriori (MAP) spectral estimates that are continuous in time yet sparse in frequency. Our spectral decomposition procedure, termed spectrotemporal pursuit, can be efficiently computed using an iteratively reweighted least-squares algorithm and scales well with typical data lengths. We show that spectrotemporal pursuit works by applying to the time series a set of data-derived filters. Using a link between Gaussian mixture models, l1 minimization, and the expectation-maximization algorithm, we prove that spectrotemporal pursuit converges to the global MAP estimate. We illustrate our technique on simulated and real human EEG data as well as on human neural spiking activity recorded during loss of consciousness induced by the anesthetic propofol. For the EEG data, our technique yields significantly denoised spectral estimates that have significantly higher time and frequency resolution than multitaper spectral estimates. For the neural spiking data, we obtain a new spectral representation of neuronal firing rates. Spectrotemporal pursuit offers a robust spectral decomposition framework that is a principled alternative to existing methods for decomposing time series into a small number of smooth oscillatory components.
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22
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Abstract
Advances in video and time series analysis have greatly enhanced our ability to study the bodily synchronization that occurs in natural interactions. Past research has demonstrated that the behavioral synchronization involved in social interactions is similar to dynamical synchronization found generically in nature. The present study investigated how the bodily synchronization in a joke telling task is spread across different nested temporal scales. Pairs of participants enacted knock–knock jokes and times series of their bodily activity were recorded. Coherence and relative phase analyses were used to evaluate the synchronization of bodily rhythms for the whole trial as well as at the subsidiary time scales of the whole joke, the setup of the punch line, the two-person exchange and the utterance. The analyses revealed greater than chance entrainment of the joke teller’s and joke responder’s movements at all time scales and that the relative phasing of the teller’s movements led those of the responder at the longer time scales. Moreover, this entrainment was greater when visual information about the partner’s movements was present but was decreased particularly at the shorter time scales when explicit gesturing in telling the joke was performed. In short, the results demonstrate that a complex interpersonal bodily “dance” occurs during structured conversation interactions and that this “dance” is constructed from a set of rhythms associated with the nested behavioral structure of the interaction.
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Affiliation(s)
- R C Schmidt
- Department of Psychology, College of the Holy Cross Worcester, MA, USA
| | - Lin Nie
- Center for the Ecological Study of Perception and Action, University of Connecticut Storrs, CT, USA
| | - Alison Franco
- Department of Psychology, College of the Holy Cross Worcester, MA, USA
| | - Michael J Richardson
- Center for Cognition, Action and Perception, Department of Psychology, University of Cincinnati Cincinnati, OH, USA
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23
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Oh JJ, Byun SS, Lee SE, Hong SK, Jeong CW, Kim D, Kim HJ, Myung SC. Genetic variations in VDR associated with prostate cancer risk and progression in a Korean population. Gene 2014. [PMID: 24120391 DOI: 10.1016/j.gene.2013.09.119.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Low levels of vitamin D are implicated as a potential risk factor for prostate cancer, and the vitamin D receptor (VDR) gene may be important in the onset and progression of prostate cancer. In this study, sequence variants in the VDR gene were investigated in a Korean study cohort to determine whether they are associated with prostate cancer risk. We evaluated the association between 47 single nucleotide polymorphisms (SNPs) in the VDR gene and prostate cancer risk as well as clinical characteristics (prostate-specific antigen level, clinical stage, pathological stage and Gleason score) in Korean men (272 prostate cancer patients and 173 benign prostatic hyperplasia patient who underwent a prostate biopsy, which was negative for malignancy) using unconditional logistic regression. The statistical analysis suggested that two VDR sequence variants (rs2408876 and rs2239182) had a significant association with prostate cancer risk (odds ratio [OR]. 1.41; p=0.03; OR, 0.73; p=0.05, respectively). Logistic analyses of the VDR polymorphisms with several prostate cancer related factors showed that several SNPs were significant; nine SNPs to PSA level, three to clinical stage, two to pathological stage, and three SNPs to the Gleason score. The results suggest that some VDR gene polymorphisms in Korean men might not only be associated with prostate cancer risk but also significantly related to prostate cancer-related risk factors such as PSA level, tumor stage, and Gleason score. However, current limitation for small cohort with not-healthy control group might have false positive effects; therefore it should be overcome via further large-scale validating studies.
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Affiliation(s)
- Jong Jin Oh
- Department of Urology, CHA Bundang Medical Center, CHA University, Seongnam, South Korea; CHA Cancer Research Center, CHA University, Seoul, South Korea
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24
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Oh JJ, Byun SS, Lee SE, Hong SK, Jeong CW, Kim D, Kim HJ, Myung SC. Genetic variations in VDR associated with prostate cancer risk and progression in a Korean population. Gene 2013; 533:86-93. [PMID: 24120391 DOI: 10.1016/j.gene.2013.09.119] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 09/27/2013] [Accepted: 09/28/2013] [Indexed: 11/15/2022]
Abstract
Low levels of vitamin D are implicated as a potential risk factor for prostate cancer, and the vitamin D receptor (VDR) gene may be important in the onset and progression of prostate cancer. In this study, sequence variants in the VDR gene were investigated in a Korean study cohort to determine whether they are associated with prostate cancer risk. We evaluated the association between 47 single nucleotide polymorphisms (SNPs) in the VDR gene and prostate cancer risk as well as clinical characteristics (prostate-specific antigen level, clinical stage, pathological stage and Gleason score) in Korean men (272 prostate cancer patients and 173 benign prostatic hyperplasia patient who underwent a prostate biopsy, which was negative for malignancy) using unconditional logistic regression. The statistical analysis suggested that two VDR sequence variants (rs2408876 and rs2239182) had a significant association with prostate cancer risk (odds ratio [OR]. 1.41; p=0.03; OR, 0.73; p=0.05, respectively). Logistic analyses of the VDR polymorphisms with several prostate cancer related factors showed that several SNPs were significant; nine SNPs to PSA level, three to clinical stage, two to pathological stage, and three SNPs to the Gleason score. The results suggest that some VDR gene polymorphisms in Korean men might not only be associated with prostate cancer risk but also significantly related to prostate cancer-related risk factors such as PSA level, tumor stage, and Gleason score. However, current limitation for small cohort with not-healthy control group might have false positive effects; therefore it should be overcome via further large-scale validating studies.
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Affiliation(s)
- Jong Jin Oh
- Department of Urology, CHA Bundang Medical Center, CHA University, Seongnam, South Korea; CHA Cancer Research Center, CHA University, Seoul, South Korea
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25
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Berner D. How much can the orientation of G's eigenvectors tell us about genetic constraints? Ecol Evol 2012; 2:1834-42. [PMID: 22957186 PMCID: PMC3433988 DOI: 10.1002/ece3.306] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 05/24/2012] [Accepted: 05/25/2012] [Indexed: 12/04/2022] Open
Abstract
A key goal in evolutionary quantitative genetics is to understand how evolutionary trajectories are constrained by pleiotropic coupling among multiple traits. Because studying pleiotropic constraints directly at the molecular genetic level remains very difficult, several analytical approaches attempt to draw conclusions about constraints by relating the orientation of the eigenvectors of the traits' (co)variance matrix to vectors of multivariate selection. On the basis of explicit models of genetic architecture, I here argue that the value of such approaches is greatly overestimated. The reason is that eigenvector orientation can be highly unstable and lack a biologically meaningful relationship with the underlying traits' genetic architecture. Genetic constraints are more profitably explored through experimental approaches avoiding the mathematical abstraction inherent in eigenanalysis.
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Affiliation(s)
- Daniel Berner
- Zoological Institute, University of Basel Vesalgasse 1, CH-4051, Basel, Switzerland
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