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Wang Y, Lv B, Yu T, Wang L, Wang Z. Design of High-Precision Driving Control System for Charge Management. Sensors (Basel) 2024; 24:2883. [PMID: 38732989 PMCID: PMC11086223 DOI: 10.3390/s24092883] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
Due to the interaction of accumulated charges on the surface of a test mass with the surrounding electric and magnetic fields, the performance of inertial sensors is affected, necessitating charge management for the test mass. Discharge technology based on Ultraviolet LEDs is internationally recognized as the optimal solution for charge management. Precision driving of Ultraviolet LEDs is considered a key technology in charge management. This paper presents the driving control system used for Ultraviolet LEDs, achieving precision pulse-width-modulation-type current output with controllable pulse width and amplitude. The system generates the pulse-width-controllable pulse voltage signal via analog pulse-width modulation, and subsequently regulates the amplitude of the PWM signal through range switching. To convert the voltage into the pulse-width-modulation-type driving current, the improved Howland current source is employed. The test results demonstrate that the driving control system can output controllable current in the range of 0.01 mA to 10 mA, with a minimum step of 0.01 mA. The accuracy of the current reaches 1%, the stability within 1 h is better than 1%, and the load regulation is better than 2%. The driving control system provides an important reference for the integration of charge management system and the precision drive control method for LEDs.
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Affiliation(s)
- Yang Wang
- College of Engineering and Technology, Jilin Agricultural University, Changchun 130118, China; (Y.W.)
| | - Boyan Lv
- College of Engineering and Technology, Jilin Agricultural University, Changchun 130118, China; (Y.W.)
| | - Tao Yu
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, China
| | - Longqi Wang
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, China
| | - Zhi Wang
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, China
- School of Fundamental Physics and Mathematical Sciences, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
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Tonchev IR, Chieng D, Hawson J, Segan L, Sugumar H, Voskoboinik A, Prabhu S, Ling LH, Lee G, Kalman JM, Kistler PM. P-Wave Morphology From Common Nonpulmonary Vein Trigger Sites Following Pulmonary Vein and Posterior Wall Isolation. JACC Clin Electrophysiol 2023:S2405-500X(23)00835-6. [PMID: 38180432 DOI: 10.1016/j.jacep.2023.11.007] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/12/2023] [Accepted: 11/15/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND Non-pulmonary vein (PV) triggers are increasingly targeted during atrial fibrillation (AF) ablation. P-wave morphology (PWM) can be useful because point mapping of AF triggers is challenging. The impact of prior ablation on PWM is yet to be determined. OBJECTIVES This study sought to report PWM before and after left atrial (LA) ablation and construct a P-wave algorithm of common non-PV trigger locations. METHODS This multicenter, prospective, observational study analyzed the paced PWM of 30 patients with persistent AF undergoing pulmonary vein isolation (PVI) and posterior wall isolation (PWI). Pace mapping was performed at the SVC, crista terminalis, inferior tricuspid annulus, coronary sinus ostium, left septum, left atrial appendage, Ligament of Marshall, and inferoposterior LA. The PWM was reported before PVI, then blinded comparisons were made post-PVI and post-PVI + PWI. A P-wave algorithm was constructed. RESULTS A total of 8,352 paced P waves were prospectively recorded. No significant changes in the PWM were seen post-PVI alone in 2,775 of 2,784 (99.7%) and post-PWI in 2,715 of 2,784 (97.5%). Changes in PWM were predominantly at the IPLA (53 P waves) with a positive P-wave in leads V2 to V6 before biphasic post-PWI, LA appendage (9 P waves), coronary sinus ostium (6 P waves), and ligament of Marshall (3 P waves). A PWM algorithm was created before PVI and accurately predicted the location in 93% post-PVI + PWI. CONCLUSIONS Minimal change was observed in PWM post-PV and PWI aside from the IPLA location. A P-wave algorithm created before and applied after PVI + PWI provided an accuracy of 93%. PWM provides a reliable tool to guide the localization of common non-PV trigger sites even after PV and PWI.
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Affiliation(s)
- Ivaylo R Tonchev
- Department of Cardiology, Royal Melbourne Hospital, Melbourne, Australia
| | - David Chieng
- Department of Cardiology, The Alfred Hospital, Melbourne, Australia; The Baker Heart and Diabetes Research Institute, Melbourne, Australia; University of Melbourne, Melbourne, Australia; Cabrini Medical Centre, Melbourne, Australia
| | - Joshua Hawson
- Department of Cardiology, Royal Melbourne Hospital, Melbourne, Australia
| | - Louise Segan
- Department of Cardiology, The Alfred Hospital, Melbourne, Australia
| | - Hariharan Sugumar
- Department of Cardiology, The Alfred Hospital, Melbourne, Australia; The Baker Heart and Diabetes Research Institute, Melbourne, Australia; University of Melbourne, Melbourne, Australia; Cabrini Medical Centre, Melbourne, Australia
| | - Alexandr Voskoboinik
- Department of Cardiology, The Alfred Hospital, Melbourne, Australia; The Baker Heart and Diabetes Research Institute, Melbourne, Australia; University of Melbourne, Melbourne, Australia; Cabrini Medical Centre, Melbourne, Australia
| | - Sandeep Prabhu
- Department of Cardiology, The Alfred Hospital, Melbourne, Australia; The Baker Heart and Diabetes Research Institute, Melbourne, Australia; University of Melbourne, Melbourne, Australia
| | - Liang Han Ling
- Department of Cardiology, The Alfred Hospital, Melbourne, Australia; The Baker Heart and Diabetes Research Institute, Melbourne, Australia; University of Melbourne, Melbourne, Australia
| | - Geoff Lee
- Department of Cardiology, Royal Melbourne Hospital, Melbourne, Australia; University of Melbourne, Melbourne, Australia
| | - Jonathan M Kalman
- Department of Cardiology, Royal Melbourne Hospital, Melbourne, Australia; University of Melbourne, Melbourne, Australia
| | - Peter M Kistler
- Department of Cardiology, The Alfred Hospital, Melbourne, Australia; The Baker Heart and Diabetes Research Institute, Melbourne, Australia; University of Melbourne, Melbourne, Australia; Cabrini Medical Centre, Melbourne, Australia; Monash University, Melbourne, Australia.
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Wang J, Li M, Jiang W, Huang Y, Lin R. A Design of FPGA-Based Neural Network PID Controller for Motion Control System. Sensors (Basel) 2022; 22:889. [PMID: 35161635 DOI: 10.3390/s22030889] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/17/2022]
Abstract
In the actual industrial production process, the method of adaptively tuning proportional–integral–derivative (PID) parameters online by neural network can adapt to different characteristics of different controlled objects better than the controller with PID. However, the commonly used microcontroller unit (MCU) cannot meet the application scenarios of real time and high reliability. Therefore, in this paper, a closed-loop motion control system based on BP neural network (BPNN) PID controller by using a Xilinx field programmable gate array (FPGA) solution is proposed. In the design of the controller, it is divided into several sub-modules according to the modular design idea. The forward propagation module is used to complete the forward propagation operation from the input layer to the output layer. The PID module implements the mapping of PID arithmetic to register transfer level (RTL) and is responsible for completing the output of control amount. The main state machine module generates enable signals that control the sequential execution of each sub-module. The error backpropagation and weight update module completes the update of the weights of each layer of the network. The peripheral modules of the control system are divided into two main parts. The speed measurement module completes the acquisition of the output pulse signal of the encoder and the measurement of the motor speed. The pulse width modulation (PWM) signal generation module generates PWM waves with different duty cycles to control the rotation speed of the motor. A co-simulation of Modelsim and Simulink is used to simulate and verify the system, and a test analysis is also performed on the development platform. The results show that the proposed system can realize the self-tuning of PID control parameters, and also has the characteristics of reliable performance, high real-time performance, and strong anti-interference. Compared with MCU, the convergence speed is far more than three orders of magnitude, which proves its superiority.
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Abstract
Multiple sequence alignment (MSA) is the basis for almost all sequence comparison and molecular phylogenetic inferences. Large-scale genomic analyses are typically associated with automated progressive MSA without subsequent manual adjustment, which itself is often error-prone because of the lack of a consistent and explicit criterion. Here, I outlined several commonly encountered alignment errors that cannot be avoided by progressive MSA for nucleotide, amino acid, and codon sequences. Methods that could be automated to fix such alignment errors were then presented. I emphasized the utility of position weight matrix as a new tool for MSA refinement and illustrated its usage by refining the MSA of nucleotide and amino acid sequences. The main advantages of the position weight matrix approach include (1) its use of information from all sequences, in contrast to other commonly used methods based on pairwise alignment scores and inconsistency measures, and (2) its speedy computation, making it suitable for a large number of long viral genomic sequences.
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Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, Marie-Curie Private, Ottawa, ON K1N 9A7, Canada; ; Tel.: +1-613-562-5718
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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Kistler PM, Chieng D, Tonchev IR, Sugumar H, Voskoboinik A, Schwartz LA, McLellan AJ, Prabhu S, Ling LH, Al-Kaisey A, Parameswaran R, Anderson RD, Lee G, Kalman JM. P-Wave Morphology in Focal Atrial Tachycardia: An Updated Algorithm to Predict Site of Origin. JACC Clin Electrophysiol 2021:S2405-500X(21)00444-8. [PMID: 34217661 DOI: 10.1016/j.jacep.2021.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/03/2021] [Accepted: 05/12/2021] [Indexed: 11/24/2022]
Abstract
OBJECTIVES This study sought to report P-wave morphology (PWM) from a series of paraseptal (PS) atrial tachycardia (AT), revise then prospectively evaluate a simplified PWM algorithm against a contemporary consecutive cohort with focal AT. BACKGROUND The 2006 PWM algorithm was useful in predicting the origin of focal AT. An updated algorithm was developed given advances in multipolar 3-dimensional mapping, potential limitations of PWM in separating PS sites, and a renewed interest in the P-wave in mapping non-pulmonary vein triggers. METHODS The PWM from a consecutive series of 67 patients with PS AT were analyzed. PS sites included were coronary sinus ostium, perinodal, left and right septum, septal tricuspid annulus, superior mitral annulus, and noncoronary cusp. Next the P-wave algorithm was revised and prospectively evaluated by 3 blinded assessors. RESULTS The P-wave for PS sites was neg/pos (n = 50), iso/pos (n = 10), or isoelectric (n = 4) in lead V1 (96%). The P-wave algorithm was modified and prospectively applied to 30 consecutive patients with focal AT who underwent successful ablation. Foci (n = 30) originated from the right atrium (33.3%), left atrium (30%), and PS (36.7%). Using the PW algorithm, the correct anatomic location was identified in 93%. Incorrect interpretation of the terminal positive P-wave component (n = 3) and initial negative P-wave deflection (n = 1) in lead V1 misidentified 4 paraseptal cases. CONCLUSIONS The revised PWM algorithm offers a simplified and accurate method of localizing the responsible site for focal AT. The P-wave remains an important first step in mapping atrial arrhythmias.
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Suvorova YM, Kamionskaya AM, Korotkov EV. Search for SINE repeats in the rice genome using correlation-based position weight matrices. BMC Bioinformatics 2021; 22:42. [PMID: 33530928 PMCID: PMC7852121 DOI: 10.1186/s12859-021-03977-0] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 01/21/2021] [Indexed: 11/21/2022] Open
Abstract
Background Transposable elements (TEs) constitute a significant part of eukaryotic genomes. Short interspersed nuclear elements (SINEs) are non-autonomous TEs, which are widely represented in mammalian genomes and also found in plants. After insertion in a new position in the genome, TEs quickly accumulate mutations, which complicate their identification and annotation by modern bioinformatics methods. In this study, we searched for highly divergent SINE copies in the genome of rice (Oryza sativa subsp. japonica) using the Highly Divergent Repeat Search Method (HDRSM). Results The HDRSM considers correlations of neighboring symbols to construct position weight matrix (PWM) for a SINE family, which is then used to perform a search for new copies. In order to evaluate the accuracy of the method and compare it with the RepeatMasker program, we generated a set of SINE copies containing nucleotide substitutions and indels and inserted them into an artificial chromosome for analysis. The HDRSM showed better results both in terms of the number of identified inserted repeats and the accuracy of determining their boundaries. A search for the copies of 39 SINE families in the rice genome produced 14,030 hits; among them, 5704 were not detected by RepeatMasker. Conclusions The HDRSM could find divergent SINE copies, correctly determine their boundaries, and offer a high level of statistical significance. We also found that RepeatMasker is able to find relatively short copies of the SINE families with a higher level of similarity, while HDRSM is able to find more diverged copies. To obtain a comprehensive profile of SINE distribution in the genome, combined application of the HDRSM and RepeatMasker is recommended.
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Affiliation(s)
- Yulia M Suvorova
- Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 1, Moscow, Russia.
| | - Anastasia M Kamionskaya
- Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 1, Moscow, Russia
| | - Eugene V Korotkov
- Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 1, Moscow, Russia
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Rosolem JB, Argentato MC, Bassan FR, Penze RS, Floridia C, Silva AA, Vasconcelos D, Ramos Junior MA. Demonstration of a Filterless, Multi-Point, and Temperature-Independent Fiber Bragg Grating Dynamical Demodulator Using Pulse-Width Modulation. Sensors (Basel) 2020; 20:E5825. [PMID: 33076267 DOI: 10.3390/s20205825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 11/17/2022]
Abstract
We demonstrated in this work a filterless, multi-point and temperature-independent FBG (fiber Bragg grating) dynamical demodulator using pulse-width-modulation (PWM). In this approach, the FBG interrogation system is composed of a tunable laser and a demodulator that is designed to detect the wavelength shift of the FBG sensor without any optical filter making it very suitable to be used in harsh environments. In this work, we applied the proposed method that uses the PWM technique for FBG sensors placed in high pressure and high-temperature environments. The proposed method was characterized in the laboratory using an FBG sensor modulated in a frequency of 6 Hz, with a 1 kHz sweeping frequency in the wavelength range from 1527 to 1534 nm. Also, the method was evaluated in a field test in an engine of a thermoelectric power plant.
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Ambrosini G, Vorontsov I, Penzar D, Groux R, Fornes O, Nikolaeva DD, Ballester B, Grau J, Grosse I, Makeev V, Kulakovskiy I, Bucher P. Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study. Genome Biol 2020; 21:114. [PMID: 32393327 PMCID: PMC7212583 DOI: 10.1186/s13059-020-01996-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 03/11/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Positional weight matrix (PWM) is a de facto standard model to describe transcription factor (TF) DNA binding specificities. PWMs inferred from in vivo or in vitro data are stored in many databases and used in a plethora of biological applications. This calls for comprehensive benchmarking of public PWM models with large experimental reference sets. RESULTS Here we report results from all-against-all benchmarking of PWM models for DNA binding sites of human TFs on a large compilation of in vitro (HT-SELEX, PBM) and in vivo (ChIP-seq) binding data. We observe that the best performing PWM for a given TF often belongs to another TF, usually from the same family. Occasionally, binding specificity is correlated with the structural class of the DNA binding domain, indicated by good cross-family performance measures. Benchmarking-based selection of family-representative motifs is more effective than motif clustering-based approaches. Overall, there is good agreement between in vitro and in vivo performance measures. However, for some in vivo experiments, the best performing PWM is assigned to an unrelated TF, indicating a binding mode involving protein-protein cooperativity. CONCLUSIONS In an all-against-all setting, we compute more than 18 million performance measure values for different PWM-experiment combinations and offer these results as a public resource to the research community. The benchmarking protocols are provided via a web interface and as docker images. The methods and results from this study may help others make better use of public TF specificity models, as well as public TF binding data sets.
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Affiliation(s)
- Giovanna Ambrosini
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), CH-1015, Lausanne, Switzerland
| | - Ilya Vorontsov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, Russia, 119991
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Pushchino, Russia, 142290
| | - Dmitry Penzar
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, Russia, 119991
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye gory 1-73, Moscow, Russia, 119234
- Moscow Institute of Physics and Technology (State University), Institutskiy per. 9, Dolgoprudny, Russia, 141700
| | - Romain Groux
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), CH-1015, Lausanne, Switzerland
| | - Oriol Fornes
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Daria D Nikolaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye gory 1-73, Moscow, Russia, 119234
| | | | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Ivo Grosse
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Vsevolod Makeev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, Russia, 119991
- Moscow Institute of Physics and Technology (State University), Institutskiy per. 9, Dolgoprudny, Russia, 141700
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, Russia, 119991
| | - Ivan Kulakovskiy
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, Russia, 119991
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Pushchino, Russia, 142290
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, Russia, 119991
| | - Philipp Bucher
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), CH-1015, Lausanne, Switzerland.
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Ma B, Li C, Wu Z, Huang Y, van der Zijp-Tan AC, Tan S, Li D, Fong A, Basetty C, Borchert GM, Benton R, Wu B, Huang J. Muscle fatigue detection and treatment system driven by internet of things. BMC Med Inform Decis Mak 2019; 19:275. [PMID: 31865898 PMCID: PMC6927109 DOI: 10.1186/s12911-019-0982-x] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Internet of things is fast becoming the norm in everyday life, and integrating the Internet into medical treatment, which is increasing day by day, is of high utility to both clinical doctors and patients. While there are a number of different health-related problems encountered in daily life, muscle fatigue is a common problem encountered by many. Methods To facilitate muscle fatigue detection, a pulse width modulation (PWM) and ESP8266-based fatigue detection and recovery system is introduced in this paper to help alleviate muscle fatigue. The ESP8266 is employed as the main controller and communicator, and PWM technology is employed to achieve adaptive muscle recovery. Muscle fatigue can be detected by surface electromyography signals and monitored in real-time via a wireless network. Results With the help of the proposed system, human muscle fatigue status can be monitored in real-time, and the recovery vibration motor status can be optimized according to muscle activity state. Discussion Environmental factors had little effect on the response time and accuracy of the system, and the response time was stable between 1 and 2 s. As indicated by the consistent change of digital value, muscle fatigue was clearly diminished using this system. Conclusions Experiments show that environmental factors have little effect on the response time and accuracy of the system. The response time is stably between 1 and 2 s, and, as indicated by the consistent change of digital value, our systems clearly diminishes muscle fatigue. Additionally, the experimental results show that the proposed system requires minimal power and is both sensitive and stable.
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Affiliation(s)
- Bin Ma
- Qilu University of Technology (Shandong Academy of Science), Jinan, Shandong, China
| | - Chunxiao Li
- Qilu University of Technology (Shandong Academy of Science), Jinan, Shandong, China
| | - Zhaolong Wu
- Qilu University of Technology (Shandong Academy of Science), Jinan, Shandong, China
| | - Yulong Huang
- College of Allied Health Professions, University of South Alabama, Mobile, AL, 36608, USA
| | | | - Shaobo Tan
- School of Computing, University of South Alabama, Mobile, AL, 36688, USA
| | - Dongqi Li
- School of Computing, University of South Alabama, Mobile, AL, 36688, USA
| | - Ada Fong
- School of Computing, University of South Alabama, Mobile, AL, 36688, USA
| | - Chandan Basetty
- College of Allied Health Professions, University of South Alabama, Mobile, AL, 36608, USA
| | - Glen M Borchert
- College of Medicine, University of South Alabama, Mobile, AL, 36688, USA
| | - Ryan Benton
- School of Computing, University of South Alabama, Mobile, AL, 36688, USA
| | - Bin Wu
- First Affiliated Hospital, Kunming Medical University, Kunming, Yunnan, China.
| | - Jingshan Huang
- Qilu University of Technology (Shandong Academy of Science), Jinan, Shandong, China. .,School of Computing, University of South Alabama, Mobile, AL, 36688, USA.
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Javed M, Sinha A, Shukla LI. Evaluation of mature miR398 family, expression analysis and the post-transcriptional regulation evidence in gamma-irradiated and nitrogen-stressed Medicago sativa seedlings. Int J Radiat Biol 2018; 95:585-596. [PMID: 30557071 DOI: 10.1080/09553002.2019.1558298] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
BACKGROUND The miR398 (microRNA398) posttranscriptionally regulates the superoxide dismutase (Cu/Zn-SOD). MATERIALS AND METHODS The miR398 level was quantitated in gamma-irradiated (20Gy and 200Gy) and nitrogen-stressed seedlings by stem-loop RT-PCR (Real Time-Polymerase chain reaction). The positional preference of nucleotide (nt) for miR398 families and new targets was done. The SOD enzyme was assayed in native PAGE (Polyacrylamide gel electrophoresis). RESULTS A relative increase in miR398-3p expression in the roots, and reduction in shoots for gamma-irradiated tissue and downregulation in miR398-5p in shoots is noted. The nitrogen stress shows upregulation of miR398-3p in roots and shoots, whereas the expression of miR398-5p is upregulated in roots and downregulated in shoots. Positional preference in miR398-3p for 1-14 nt is 90% conserved unlike miR398-5p where no nucleotide positional preference is seen. Targets obtained were functionally characterized. CONCLUSIONS The mature miR398-5p and miR398-3p levels estimated in gamma-irradiated (20 and 200Gy) and nitrogen-stressed Medicago sativa seedlings show differential levels in roots and shoots. Native PAGE of Cu/Zn-SOD suggests its negative correlation with miR398 in shoots of irradiated and nitrogen-stressed samples. The nucleotide preferences for the nucleotide for a given position and functional characterization of targets are reported herein.
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Affiliation(s)
- Mohammed Javed
- a Department of Biotechnology, School of Life Sciences , Pondicherry University , Kalapet , Puducherry , India
| | - Anshika Sinha
- a Department of Biotechnology, School of Life Sciences , Pondicherry University , Kalapet , Puducherry , India
| | - Lata Israni Shukla
- a Department of Biotechnology, School of Life Sciences , Pondicherry University , Kalapet , Puducherry , India
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Liu Q, Liu M, Wu W. Strong/Weak Feature Recognition of Promoters Based on Position Weight Matrix and Ensemble Set-Valued Models. J Comput Biol 2018; 25:1152-1160. [PMID: 29993261 DOI: 10.1089/cmb.2018.0067] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In this article, we propose a method to recognize the strong/weak property of the promoters based on the nucleotide sequence. To the best of our knowledge, it is the first time to predict the strong/weak property of the promoters. First, position weight matrix (PWM) is used to evaluate the contributions of the nucleotides to the promoter strength. Then, the set-valued model is used to describe the relation between the nucleotide sequence and the strength. Considering the small-sample and imbalance features of the promoter data, we propose an ensemble approach to predict the strong/weak property of the promoters. The proposed method is used to recognize 60 [Formula: see text] promoters of Escherichia coli. The results show the effectiveness of the proposed method. This article provides a simple way for a biologist to evaluate the strong/weak feature of promoters from the nucleotide sequence.
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Affiliation(s)
- Qie Liu
- Department of Automation, Tsinghua University , Beijing, China
| | - Min Liu
- Department of Automation, Tsinghua University , Beijing, China
| | - Wenfa Wu
- Department of Automation, Tsinghua University , Beijing, China
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Harrison C, Keleş S, Hudson R, Shin S, Dutra I. atSNPInfrastructure, a case study for searching billions of records while providing significant cost savings over cloud providers. IEEE Int Symp Parallel Distrib Process Workshops Phd Forum 2018; 2018:497-506. [PMID: 30349760 PMCID: PMC6195815 DOI: 10.1109/ipdpsw.2018.00086] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We explore the feasibility of a database storage engine housing up to 307 billion genetic Single Nucleotide Polymorphisms (SNP) for online access. We evaluate database storage engines and implement a solution utilizing factors such as dataset size, information gain, cost and hardware constraints. Our solution provides a full feature functional model for scalable storage and query-ability for researchers exploring the SNP's in the human genome. We address the scalability problem by building physical infrastructure and comparing final costs to a major cloud provider.
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Affiliation(s)
- Christopher Harrison
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, Wisconsin USA
- Departamento de Ciência de Computadores, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Sündüz Keleş
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, Wisconsin USA
| | - Rebecca Hudson
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, Wisconsin USA
| | - Sunyoung Shin
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, Wisconsin USA
| | - Inês Dutra
- Departamento de Ciência de Computadores, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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Meher PK, Sahu TK, Rao AR. Prediction of donor splice sites using random forest with a new sequence encoding approach. BioData Min 2016; 9:4. [PMID: 26807151 PMCID: PMC4724119 DOI: 10.1186/s13040-016-0086-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [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: 03/02/2015] [Accepted: 01/19/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Detection of splice sites plays a key role for predicting the gene structure and thus development of efficient analytical methods for splice site prediction is vital. This paper presents a novel sequence encoding approach based on the adjacent di-nucleotide dependencies in which the donor splice site motifs are encoded into numeric vectors. The encoded vectors are then used as input in Random Forest (RF), Support Vector Machines (SVM) and Artificial Neural Network (ANN), Bagging, Boosting, Logistic regression, kNN and Naïve Bayes classifiers for prediction of donor splice sites. RESULTS The performance of the proposed approach is evaluated on the donor splice site sequence data of Homo sapiens, collected from Homo Sapiens Splice Sites Dataset (HS3D). The results showed that RF outperformed all the considered classifiers. Besides, RF achieved higher prediction accuracy than the existing methods viz., MEM, MDD, WMM, MM1, NNSplice and SpliceView, while compared using an independent test dataset. CONCLUSION Based on the proposed approach, we have developed an online prediction server (MaLDoSS) to help the biological community in predicting the donor splice sites. The server is made freely available at http://cabgrid.res.in:8080/maldoss. Due to computational feasibility and high prediction accuracy, the proposed approach is believed to help in predicting the eukaryotic gene structure.
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Affiliation(s)
- Prabina Kumar Meher
- Division of Statistical Genetics, Indian Agricultural Statistics Research Institute, New Delhi, 110 012 India
| | - Tanmaya Kumar Sahu
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi, 110 012 India
| | - Atmakuri Ramakrishna Rao
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi, 110 012 India
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Abstract
Short, linear motifs (SLiMs) in proteins are functional microdomains consisting of contiguous residue segments along the protein sequence, typically not more than 10 consecutive amino acids in length with less than 5 defined positions. Many positions are 'degenerate' thus offering flexibility in terms of the amino acid types allowed at those positions. Their short length and degenerate nature confers evolutionary plasticity meaning that SLiMs often evolve convergently. Further, SLiMs have a propensity to occur within intrinsically unstructured protein segments and this confers versatile functionality to unstructured regions of the proteome. SLiMs mediate multiple types of protein interactions based on domain-peptide recognition and guide functions including posttranslational modifications, subcellular localization of proteins, and ligand binding. SLiMs thus behave as modular interaction units that confer versatility to protein function and SLiM-mediated interactions are increasingly being recognized as therapeutic targets. In this chapter we start with a brief description about the properties of SLiMs and their interactions and then move on to discuss algorithms and tools including several web-based methods that enable the discovery of novel SLiMs (de novo motif discovery) as well as the prediction of novel occurrences of known SLiMs. Both individual amino acid sequences as well as sets of protein sequences can be scanned using these methods to obtain statistically overrepresented sequence patterns. Lists of putatively functional SLiMs are then assembled based on parameters such as evolutionary sequence conservation, disorder scores, structural data, gene ontology terms and other contextual information that helps to assess the functional credibility or significance of these motifs. These bioinformatics methods should certainly guide experiments aimed at motif discovery.
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Affiliation(s)
- Pallab Bhowmick
- VIB Department of Structural Biology, Vrije Universiteit Brussel (VUB), Building E, Pleinlaan 2, 1050, Brussels, Belgium
| | - Mainak Guharoy
- VIB Department of Structural Biology, Vrije Universiteit Brussel (VUB), Building E, Pleinlaan 2, 1050, Brussels, Belgium.
| | - Peter Tompa
- VIB Department of Structural Biology, Vrije Universiteit Brussel (VUB), Building E, Pleinlaan 2, 1050, Brussels, Belgium. .,Institute of Enzymology, Research Center of Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.
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Najjari B, Barakati SM, Mohammadi A, Futohi MJ, Bostanian M. Position control of an electro-pneumatic system based on PWM technique and FLC. ISA Trans 2014; 53:647-657. [PMID: 24485509 DOI: 10.1016/j.isatra.2013.12.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 11/27/2013] [Accepted: 12/20/2013] [Indexed: 06/03/2023]
Abstract
In this paper, modeling and PWM based control of an electro-pneumatic system, including the four 2-2 valves and a double acting cylinder are studied. Dynamic nonlinear behavior of the system, containing fast switching solenoid valves and a pneumatic cylinder, as well as electrical, magnetic, mechanical, and fluid subsystems are modeled. A DC-DC power converter is employed to improve solenoid valve performance and suppress system delay. Among different position control methods, a proportional integrator derivative (PID) controller and fuzzy logic controller (FLC) are evaluated. An experimental setup, using an AVR microcontroller is implemented. Simulation and experimental results verify the effectiveness of the proposed control strategies.
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Affiliation(s)
- Behrouz Najjari
- Department of Mechanical Engineering, University of Sistan and Baluchestan, Zahedan, Sistan and Baluchestan, Iran
| | - S Masoud Barakati
- Faculty of Electrical and Computer Engineering, University of Sistan and Baluchestan Zahedan 98155-987, Sistan and Baluchestan, Iran.
| | - Ali Mohammadi
- Faculty of Electrical and Computer Engineering, University of Sistan and Baluchestan Zahedan 98155-987, Sistan and Baluchestan, Iran
| | - Muhammad J Futohi
- Department of Mechanical Engineering, University of Sistan and Baluchestan, Zahedan, Sistan and Baluchestan, Iran
| | - Muhammad Bostanian
- Department of Mechanical Engineering, University of Sistan and Baluchestan, Zahedan, Sistan and Baluchestan, Iran
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Genster N, Ma YJ, Munthe-Fog L, Garred P. The pattern recognition molecule ficolin-1 exhibits differential binding to lymphocyte subsets, providing a novel link between innate and adaptive immunity. Mol Immunol 2014; 57:181-90. [PMID: 24161415 DOI: 10.1016/j.molimm.2013.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 09/28/2013] [Indexed: 10/26/2022]
Abstract
Ficolin-1 is a soluble pattern recognition molecule synthesized by myeloid cells and capable of activating the lectin pathway of complement on the surface of pathogens. It is tethered to the membranes of monocytes and granulocytes; however, the biological significance of cell-associated ficolin-1 is unknown. Recognition of healthy host cells by a pattern recognition molecule constitutes a potential hazard to self cells and tissues, emphasizing the importance of further elucidating the reported self-recognition. In the current study we investigated the potential recognition of lymphocytes by ficolin-1 and demonstrated that CD56(dim) NK-cells and both CD4(+) and CD8(+) subsets of activated T-cells were recognized by ficolin-1. In contrast we did not detect binding of ficolin-1 to CD56(bright) NK-cells, NKT-cells, resting T-cells or B-cells. Furthermore, we showed that the protein-lymphocyte interaction occurred via the pathogen-recognition domain of ficolin-1 to sialic acid on the cell surface. Thus, the differential binding of ficolin-1 to lymphocyte subsets suggests ficolin-1 as a novel link between innate and adaptive immunity. Our results provide new insight about the recognition properties of ficolin-1 and point toward additional immune modulating functions of the molecule besides its role in pathogen recognition.
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Affiliation(s)
- Ninette Genster
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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Bragin EY, Shtratnikova VY, Dovbnya DV, Schelkunov MI, Pekov YA, Malakho SG, Egorova OV, Ivashina TV, Sokolov SL, Ashapkin VV, Donova MV. Comparative analysis of genes encoding key steroid core oxidation enzymes in fast-growing Mycobacterium spp. strains. J Steroid Biochem Mol Biol 2013; 138:41-53. [PMID: 23474435 DOI: 10.1016/j.jsbmb.2013.02.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/28/2013] [Accepted: 02/24/2013] [Indexed: 11/27/2022]
Abstract
A comparative genome analysis of Mycobacterium spp. VKM Ac-1815D, 1816D and 1817D strains used for efficient production of key steroid intermediates (androst-4-ene-3,17-dione, AD, androsta-1,4-diene-3,17-dione, ADD, 9α-hydroxy androst-4-ene-3,17-dione, 9-OH-AD) from phytosterol has been carried out by deep sequencing. The assembled contig sequences were analyzed for the presence putative genes of steroid catabolism pathways. Since 3-ketosteroid-9α-hydroxylases (KSH) and 3-ketosteroid-Δ(1)-dehydrogenase (Δ(1) KSTD) play key role in steroid core oxidation, special attention was paid to the genes encoding these enzymes. At least three genes of Δ(1) KSTD (kstD), five genes of KSH subunit A (kshA), and one gene of KSH subunit B of 3-ketosteroid-9α-hydroxylases (kshB) have been found in Mycobacterium sp. VKM Ac-1817D. Strains of Mycobacterium spp. VKM Ac-1815D and 1816D were found to possess at least one kstD, one kshB and two kshA genes. The assembled genome sequence of Mycobacterium sp. VKM Ac-1817D differs from those of 1815D and 1816D strains, whereas these last two are nearly identical, differing by 13 single nucleotide substitutions (SNPs). One of these SNPs is located in the coding region of a kstD gene and corresponds to an amino acid substitution Lys (135) in 1816D for Ser (135) in 1815D. The findings may be useful for targeted genetic engineering of the biocatalysts for biotechnological application.
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Key Words
- 2,3-dehydroxyphenyl dioxygenase
- 2-enoyl acyl-CoA hydratase
- 2-hydroxypenta-2,4-dienoate hydratase
- 3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione 4,5-dioxygenase
- 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione monooxygenase
- 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione monooxygenase subunit
- 3-ketosteroid-9α-hydroxylase
- 3-ketosteroid-Δ(1)-dehydrogenase
- 3β-hydroxysteroid-dehydrogenase
- 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
- 4-hydroxy-2-oxovalerate aldolase
- 9-OH-AD
- 9α-hydroxy androst-4-ene-3,17-dione
- AD
- ADD
- Androst-1,4-diene-3,17-dione
- Androst-4-ene-3,17-dione
- BWA
- Broadband-Wheeler Aligner
- CTAB
- ChoX
- ChoX(D,E)
- EchA19
- FAD
- FadA5
- FadD17
- FadD19
- FadE26
- FadE27
- FadE28
- Genome sequencing
- HSD
- HTH-type transcriptional repressor
- HsaA
- HsaAB
- HsaB
- HsaC
- HsaD
- HsaE
- HsaF
- HsaG
- Hsd4A
- Hsd4B
- KSH
- KshA
- KshB
- KstR
- KstR2
- Ltp2
- Ltp3
- Ltp4
- Mycobacterium
- ORFs
- PWM
- Phytosterol
- SNP
- Steroid bioconversion
- TesB
- YrbE4A
- YrbE4B
- acetaldehyde dehydrogenase
- acetyl-CoA acetyltransferase
- acyl-CoA dehydrogenase
- acyl-CoA synthetase
- acyl-CoA thioesterase II
- androst-4-ene-3,17-dione
- androsta-1,4-diene-3,17-dione
- base pair
- bp
- cetyl trimethyl ammonium bromide
- cholesterol oxidase
- enoyl-CoA hydratase
- flavin adenine dinucleotide
- hydroxysteroid dehydrogenase
- integral membrane protein
- lipid transfer protein 4 (keto acyl-CoA thiolase)
- lipid-transfer protein 2
- lipid-transfer protein 3 (acetyl-CoA acetyltransferase)
- open reading frames
- position weight matrix
- single nucleotide substitution
- subunit A of 3-ketosteroid-9α-hydroxylase
- subunit B of 3-ketosteroid-9α-hydroxylases
- Δ(1) KSTD
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Affiliation(s)
- E Yu Bragin
- Center of Innovations and Technologies "Biological Active Compounds and Their Applications", Russian Academy of Sciences, Moscow 119991, Russian Federation; G.K.Skryabin Institute of Biochemistry & Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation.
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Vanos JK, Cakmak S, Bristow C, Brion V, Tremblay N, Martin SL, Sheridan SS. Synoptic weather typing applied to air pollution mortality among the elderly in 10 Canadian cities. Environ Res 2013; 126:66-75. [PMID: 24012249 DOI: 10.1016/j.envres.2013.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 07/25/2013] [Accepted: 08/12/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND Synoptic circulation patterns (large-scale weather systems) affect ambient levels of air pollution, as well as the relationship between air pollution and human health. OBJECTIVE To investigate the air pollution-mortality relationship within weather types and seasons, and to determine which combination of atmospheric conditions may pose increased health threats in the elderly age categories. METHODS The relative risk of mortality (RR) due to air pollution was examined using Poisson generalized linear models (GLMs) within specific weather types. Analysis was completed by weather type and age group (all ages, ≤64, 65-74, 75-84, ≥85 years) in ten Canadian cities from 1981 to 1999. RESULTS There was significant modification of RR by weather type and age. When examining the entire population, weather type was shown to have the greatest modifying effect on the risk of dying due to ozone (O3). This effect was highest on average for the dry tropical (DT) weather type, with the all-age RR of mortality at a population weighted mean (PWM) found to be 1.055 (95% CI 1.026-1.085). All-weather type risk estimates increased with age due to exposure to carbon monoxide (CO), nitrogen dioxide (NO2), and sulphur dioxide (SO2). On average, RR increased by 2.6, 3.8 and 1.5% for the respective pollutants between the ≤64 and ≥85 age categories. Conversely, mean ozone estimates remained relatively consistent with age. Elevated levels of air pollution were found to be detrimental to the health of elderly individuals for all weather types. However, the entire population was negatively effected by air pollution on the hot dry (DT) and hot humid (MT) days. CONCLUSIONS We identified a significant modification of RR for mortality due to air pollution by age, which is enhanced under specific weather types. Efforts should be targeted at minimizing pollutant exposure to the elderly and/or all age groups with respect to weather type in question.
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Affiliation(s)
- Jennifer K Vanos
- Health Canada, Environmental Health Science and Research Bureau, Population Studies Division, 50 Colombine Driveway, Ottawa, ON, Canada K1A 0K9
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Bladowska J, Zimny A, Knysz B, Małyszczak K, Kołtowska A, Szewczyk P, Gąsiorowski J, Furdal M, Sąsiadek MJ. Evaluation of early cerebral metabolic, perfusion and microstructural changes in HCV-positive patients: a pilot study. J Hepatol 2013; 59:651-7. [PMID: 23680314 DOI: 10.1016/j.jhep.2013.05.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [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] [Received: 12/27/2012] [Revised: 04/09/2013] [Accepted: 05/06/2013] [Indexed: 12/30/2022]
Abstract
BACKGROUND & AIMS The aim of the study was to evaluate early metabolic perfusion, and microstructural cerebral changes in patients with the hepatitis C virus (HCV) infection and normal appearing brain on plain MR using advanced MR techniques, as well as to assess correlations of MR measurements with the liver histology activity index (HAI). METHODS Fifteen HCV-positive patients and 18 control subjects underwent single voxel MR spectroscopy (MRS), perfusion weighted imaging (PWI), and diffusion tensor imaging (DTI), using a 1.5T MR unit. MRS metabolite ratios (NAA/Cr, Cho/Cr, mI/Cr) were calculated. PWI values of relative cerebral blood volume (rCBV) were assessed from 8 areas including several cortical locations, basal ganglia, and fronto-parietal white matter. DTI fractional anisotropy (FA) and apparent diffusion coefficient (ADC) values were obtained from 14 white matter tracts. RESULTS Compared to controls, HCV-positive patients showed significantly (p < 0.05) lower NAA/Cr ratios within frontal and parietal white matters, lower rCBV values within frontal and temporo-parietal cortices, decreased FA values, as well as increased ADC values in several white matter tracts. We also found elevated rCBV values in basal ganglia regions. The increase in mI/Cr and Cho/Cr ratio was correlated with a higher HAI score. CONCLUSIONS The results of advanced MR techniques indicate neurotoxicity of HCV reflected by neuronal impairment within white matter, cortical hypoperfusion, and disintegrity within several white matter tracts. Hyperperfusion in basal ganglia may be an indicator of brain inflammation in HCV patients. Our findings may suggest a biologic link between HCV-related liver disease and cerebral dysfunction.
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Affiliation(s)
- Joanna Bladowska
- Department of General Radiology, Interventional Radiology and Neuroradiology, Chair of Radiology, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland.
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Abstract
The glial cells of the cerebellum, and particularly astrocytes and oligodendrocytes, are characterized by a remarkable phenotypic variety, in which highly peculiar morphological features are associated with specific functional features, unique among the glial cells of the entire CNS. Here, we provide a critical report about the present knowledge of the development of cerebellar glia, including lineage relationships between cerebellar neurons, astrocytes and oligodendrocytes, the origins and the genesis of the repertoire of glial types, and the processes underlying their acquisition of mature morphological and functional traits. In parallel, we describe and discuss some fundamental roles played by specific categories of glial cells during cerebellar development. In particular, we propose that Bergmann glia exerts a crucial scaffolding activity that, together with the organizing function of Purkinje cells, is necessary to achieve the normal pattern of foliation and layering of the cerebellar cortex. Moreover, we discuss some of the functional tasks of cerebellar astrocytes and oligodendrocytes that are distinctive of cerebellar glia throughout the CNS. Notably, we report about the regulation of synaptic signalling in the molecular and granular layer mediated by Bergmann glia and parenchymal astrocytes, and the functional interaction between oligodendrocyte precursor cells and neurons. On the whole, this review provides an extensive overview of the available literature and some novel insights about the origin and differentiation of the variety of cerebellar glial cells and their function in the developing and mature cerebellum.
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Affiliation(s)
- Annalisa Buffo
- Rita Levi-Montalcini Department of Neuroscience, University of Turin, Corso Raffaello, 30, 10125 Turin, Italy; Neuroscience Institute Cavalieri Ottolenghi, Neuroscience Institute of Turin, University of Turin, Regione Gonzole 10, 10043 Orbassano, Turin, Italy.
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