نتائج البحث - "Francis J, Doyle"

101

Optimal online selection of type 1 diabetes-glucose metabolism models

المؤلفون: Francis J. Doyle, Berno J. E. Misgeld, Philipp G. Tenbrock, Steffen Leonhardt, Eyal Dassau

المصدر: Control Engineering Practice. 71:108-119

مصطلحات موضوعية: 0209 industrial biotechnology, Mathematical optimization, Computer science, Applied Mathematics, Insulin delivery, 030209 endocrinology & metabolism, 02 engineering and technology, Kalman filter, Filter bank, Computer Science Applications, Set (abstract data type), 03 medical and health sciences, Identification (information), Nonlinear system, 020901 industrial engineering & automation, 0302 clinical medicine, Control and Systems Engineering, Electrical and Electronic Engineering, Selection (genetic algorithm)

الوصف: We address an optimal experimental design (OED) procedure for the online selection of type-1-diabetes (T1D) mellitus glucose metabolistic models. A fully observable reduced-order nonlinear dynamic model is presented and subsequently parameterised for Gottingen Minipigs and patients, that were both subject to an automatic insulin delivery. A bank of continuous–discrete unscented Kalman filters (CDUKF) is designed and parameterised for Gottingen Minipigs and patients. Based on this filter bank of CDUKF, a novel online OED design procedure is developed, that is used to identify the correct parameter set out of several available sets for measured blood glucose concentrations. The procedure utilises forward model simulations to calculate optimal system inputs. This leads to the identification of the correct parameter set under arbitrary conditions. Results are presented for both subgroups.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_________::cb9100dc48cfbca24c6a60330e81db06Test
https://doi.org/10.1016Test/j.conengprac.2017.10.007

102

Toward Multi-Input Control: A Dual-Feedback Loop Model of the Mammalian Circadian Clock

المؤلفون: Francis J. Doyle, Lindsey S. Brown

المصدر: IFAC-PapersOnLine. 51:24-27

مصطلحات موضوعية: 0301 basic medicine, Physics, Mathematical model, Differential equation, Circadian clock, Complex system, Feedback loop, 03 medical and health sciences, 030104 developmental biology, Amplitude, Control and Systems Engineering, Negative feedback, Biological system, Molecular clock

الوصف: Many mathematical models have been used to describe the mammalian circadian clock, ranging from phase-only models to complex systems of differential equations. Here, we develop a 14 state model of the molecular clock, which provides sufficient detail to consider multi-input control. Assuming mass action and Michaelis-Menten kinetics, we derive a model of the transcription-translation feedback loops in the mammalian clock. Using a genetic algorithm, we fit the parameters of the model to capture the appropriate peak to trough ratios, relative abundances, and phase differences of the model species. We show that this in silico model captures much of the behavior that is observed in vitro under knockout conditions of different molecular species, validating our model. Thus, this model gives a simple but valid model of both feedback loops in the mammalian clock, providing the opportunity for enhanced control of both the phase and amplitude of the clock through multi-input control in a combination of small molecules which act on the species in both the positive and negative feedback loops.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_________::ea008e4938b39581534cb72865f94a65Test
https://doi.org/10.1016Test/j.ifacol.2018.09.022

103

Review of automated insulin delivery systems for individuals with type 1 diabetes: tailored solutions for subpopulations

المؤلفون: Kelilah L. Wolkowicz, Eleonora Maria Aiello, Sunil Deshpande, Basak Ozaslan, Francis J. Doyle, Jordan E. Pinsker, Eyal Dassau

المصدر: Curr Opin Biomed Eng

مصطلحات موضوعية: Hypoglycemia unawareness, medicine.medical_specialty, Type 1 diabetes, biology, business.industry, Athletes, Biomedical Engineering, Insulin delivery, Medicine (miscellaneous), Bioengineering, biology.organism_classification, medicine.disease, Article, Biomaterials, medicine, Intensive care medicine, business, Clinical evaluation, Glycemic

الوصف: Automated insulin delivery (AID) systems have proven safe and effective in improving glycemic outcomes in individuals with type 1 diabetes (T1D). Clinical evaluation of this technology has progressed to large randomized, controlled outpatient studies and recent commercial approval of AID systems for children and adults. However, several challenges remain in improving these systems for different subpopulations (e.g., young children, athletes, pregnant women, seniors and those with hypoglycemia unawareness). In this review, we highlight the requirements and challenges in AID design for selected subpopulations, and discuss current advances from recent clinical studies.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cbbb7b605132ff3ca36bf3b6013d2000Test
https://doi.org/10.1016Test/j.cobme.2021.100312

104

International Consensus on Use of Continuous Glucose Monitoring

المساهمون: Children's Hospital 'Auf der Bult', Barbara Davis Center for Childhood Diabetes (BDC), University of Colorado Anschutz [Aurora], Dipartimento di Biologia Evoluzionistica 'Leo Pardi', Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), CIC Montpellier, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-CHU Saint-Eloi-Institut National de la Santé et de la Recherche Médicale (INSERM), Danne, Thoma, Nimri, Revital, Battelino, Tadej, Bergenstal, Richard M., Close, Kelly L., Devries, J. Han, Garg, Satish, Heinemann, Lutz, Hirsch, Irl, Amiel, Stephanie A., Beck, Roy, Bosi, Emanuele, Buckingham, Bruce, Cobelli, Claudio, Dassau, Eyal, Doyle, Francis J., Heller, Simon, Hovorka, Roman, Jia, Weiping, Jones, Tim, Kordonouri, Olga, Kovatchev, Bori, Kowalski, Aaron, Laffel, Lori, Maahs, David, Murphy, Helen R., Nørgaard, Kirsten, Parkin, Christopher G., Renard, Eric, Saboo, Banshi, Scharf, Mauro, Tamborlane, William V., Weinzimer, Stuart A., Phillip, Moshe, Endocrinology, AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, Danne, Thomas [0000-0003-0773-6961], Battelino, Tadej [0000-0002-0273-4732], DeVries, J Hans [0000-0001-9196-9906], Beck, Roy [0000-0002-5194-8446], Cobelli, Claudio [0000-0002-0169-6682], Dassau, Eyal [0000-0001-5333-6892], Doyle, Francis J [0000-0002-3293-9114], Heller, Simon [0000-0002-2425-9565], Jones, Tim [0000-0002-7989-1998], Kowalski, Aaron [0000-0002-0979-5343], Laffel, Lori [0000-0002-9675-3001], Parkin, Christopher G [0000-0001-6838-5355], Apollo - University of Cambridge Repository

المصدر: Diabetes Care
Diabetes Care, American Diabetes Association, 2017, 40 (12), pp.1631--1640. ⟨10.2337/dc17-1600⟩
Danne, T, Nimri, R, Battelino, T, Bergenstal, R M, Close, K L, DeVries, J H, Garg, S, Heinemann, L, Hirsch, I, Amiel, S A, Beck, R, Bosi, E, Buckingham, B, Cobelli, C, Dassau, E, Doyle, F J, Heller, S, Hovorka, R, Jia, W, Jones, T, Kordonouri, O, Kovatchev, B, Kowalski, A, Laffel, L, Maahs, D, Murphy, H R, Nørgaard, K, Parkin, C G, Renard, E, Saboo, B, Scharf, M, Tamborlane, W V, Weinzimer, S A & Phillip, M 2017, ' International consensus on use of continuous glucose monitoring ', Diabetes Care, vol. 40, no. 12, pp. 1631-1640 . https://doi.org/10.2337/dc17-1600Test
Diabetes care, 40(12), 1631-1640. American Diabetes Association Inc.

مصطلحات موضوعية: Blood Glucose, Glycated Hemoglobin A, endocrine system diseases, [SDV]Life Sciences [q-bio], Endocrinology, Diabetes and Metabolism, Continuous Glucose Monitoring and Risk of Hypoglycemia, chemistry.chemical_compound, 0302 clinical medicine, Insulin, 030212 general & internal medicine, Clinical Trials as Topic, Continuous glucose monitoring, Reference Standards, Research Personnel, 3. Good health, Postprandial, International Agencie, Human, medicine.medical_specialty, Consensus, MEDLINE, Consensu, 030209 endocrinology & metabolism, Hypoglycemia, 03 medical and health sciences, Physicians, Blood Glucose Self-Monitoring, Diabetes mellitus, Internal Medicine, medicine, Humans, Hypoglycemic Agents, Intensive care medicine, Reference standards, Glycemic, Glycated Hemoglobin, Advanced and Specialized Nursing, Hypoglycemic Agent, business.industry, International Agencies, nutritional and metabolic diseases, medicine.disease, Diabetes Mellitus, Type 1, Diabetes Mellitus, Type 2, chemistry, Physician, Hyperglycemia, Reference Standard, Glycated hemoglobin, business

الوصف: Measurement of glycated hemoglobin (HbA1c) has been the traditional method for assessing glycemic control. However, it does not reflect intra- and interday glycemic excursions that may lead to acute events (such as hypoglycemia) or postprandial hyperglycemia, which have been linked to both microvascular and macrovascular complications. Continuous glucose monitoring (CGM), either from real-time use (rtCGM) or intermittently viewed (iCGM), addresses many of the limitations inherent in HbA1c testing and self-monitoring of blood glucose. Although both provide themeans to move beyond the HbA1c measurement as the sole marker of glycemic control, standardized metrics for analyzing CGM data are lacking. Moreover, clear criteria for matching people with diabetes to themost appropriate glucose monitoring methodologies, as well as standardized advice about howbest to use the new information they provide, have yet to be established. In February 2017, the Advanced Technologies & Treatments for Diabetes (ATTD) Congress convened an international panel of physicians, researchers, and individuals with diabetes who are expert in CGM technologies to address these issues. This article summarizes the ATTD consensus recommendations and represents the current understanding of how CGM results can affect outcomes.

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4146a144f5adba6730465d71bc1fe487Test
https://doi.org/10.2337/dc17-1600Test

105

A kernel module for pulse-coupled time synchronization of sensor networks

المؤلفون: Yongqiang Wang, Francis J. Doyle, Socrates Deligeorges, Krishna Mosalakanti, Felipe Núñez

المصدر: Computer Networks. 127:161-172

الوصف: The biologically-inspired synchronization paradigm of pulse-coupled oscillators has received increased attention in the communications and sensor network communities as an appealing alternative to traditional packet-based synchronization strategies. Its inherent scalability, simplicity, and decentralized nature make pulse-coupled synchronization an attractive choice for time synchronization in wireless ad-hoc networks. However, in most current implementations, the pulse-coupled synchronization algorithm is coded in the application layer, which makes its performance susceptible to CPU processing load variations. Implementation of the pulse-coupled synchronization strategy in the physical layer is also reported, which however, is subject to difficulties in migration between different platforms. In this paper, we present the design, implementation, and evaluation of the pulse-coupled synchronization strategy as a Linux kernel module. Our goal is to leverage the high portability and prioritized CPU access of kernel modules to 1) reduce the influence of disturbances from application layer programs on the synchronization performance; and 2) simultaneously make the synchronization strategy easily installable in Linux-based sensor networks. Both lab experiments and field tests were conducted to confirm the effectiveness of the results.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_________::aef5749fa8a0a18d632806ca56c1c641Test
https://doi.org/10.1016Test/j.comnet.2017.08.009

106

Ontogeny of Circadian Rhythms and Synchrony in the Suprachiasmatic Nucleus

المؤلفون: Linda R. Petzold, Francis J. Doyle, Vania Carmona-Alcocer, Erik D. Herzog, John H. Abel, Carrie L. Simms, Tao C. Sun

المصدر: The Journal of neuroscience : the official journal of the Society for Neuroscience, vol 38, iss 6
Carmona-Alcocer, V; Abel, JH; Sun, TC; Petzold, LR; III, DFJ; Simms, CL; et al.(2018). Ontogeny of Circadian Rhythms and Synchrony in the Suprachiasmatic Nucleus. JOURNAL OF NEUROSCIENCE, 38(6), 1326-1334. doi: 10.1523/JNEUROSCI.2006-17.2017. UC Santa Barbara: Retrieved from: http://www.escholarship.org/uc/item/2f27r9ghTest

مصطلحات موضوعية: Male, 0301 basic medicine, Aging, endocrine system, animal structures, Endogeny, Biology, Inbred C57BL, Type II, Medical and Health Sciences, GABA Antagonists, Mice, 03 medical and health sciences, 0302 clinical medicine, Pregnancy, Receptors, clock genes, Animals, Circadian rhythm, Research Articles, Neurons, Neurology & Neurosurgery, Suprachiasmatic nucleus, General Neuroscience, Psychology and Cognitive Sciences, Neurosciences, Period Circadian Proteins, Bacterial circadian rhythms, Circadian Rhythm, Mice, Inbred C57BL, VIP, PER2, CLOCK, 030104 developmental biology, ontogeny, nervous system, Light effects on circadian rhythm, Hypothalamus, Receptors, Vasoactive Intestinal Peptide, Type II, Suprachiasmatic Nucleus, Female, sense organs, Sleep Research, Neuroscience, hormones, hormone substitutes, and hormone antagonists, 030217 neurology & neurosurgery, Vasoactive Intestinal Peptide

الوصف: In mammals, the suprachiasmatic nucleus (SCN) of the hypothalamus coordinates daily rhythms including sleep–wake, hormone release, and gene expression. The cells of the SCN must synchronize to each other to drive these circadian rhythms in the rest of the body. The ontogeny of circadian cycling and intercellular coupling in the SCN remains poorly understood. Recentin vitrostudies have recorded circadian rhythms from the whole embryonic SCN. Here, we tracked the onset and precision of rhythms in PERIOD2 (PER2), a clock protein, within the SCN isolated from embryonic and postnatal mice of undetermined sex. We found that a few SCN cells developed circadian periodicity in PER2 by 14.5 d after mating (E14.5) with no evidence for daily cycling on E13.5. On E15.5, the fraction of competent oscillators increased dramatically corresponding with stabilization of their circadian periods. The cells of the SCN harvested at E15.5 expressed sustained, synchronous daily rhythms. By postnatal day 2 (P2), SCN oscillators displayed the daily, dorsal-ventral phase wave in clock gene expression typical of the adult SCN. Strikingly, vasoactive intestinal polypeptide (VIP), a neuropeptide critical for synchrony in the adult SCN, and its receptor, VPAC2R, reached detectable levels after birth and after the onset of circadian synchrony. Antagonists of GABA or VIP signaling or action potentials did not disrupt circadian synchrony in the E15.5 SCN. We conclude that endogenous daily rhythms in the fetal SCN begin with few noisy oscillators on E14.5, followed by widespread oscillations that rapidly synchronize on E15.5 by an unknown mechanism.SIGNIFICANCE STATEMENTWe recorded the onset of PER2 circadian oscillations during embryonic development in the mouse SCN. When isolated at E13.5, the anlagen of the SCN expresses high, arrhythmic PER2. In contrast, a few cells show noisy circadian rhythms in the isolated E14.5 SCN and most show reliable, self-sustained, synchronized rhythms in the E15.5 SCN. Strikingly, this synchrony at E15.5 appears before expression of VIP or its receptor and persists in the presence of blockers of VIP, GABA or neuronal firing. Finally, the dorsal-ventral phase wave of PER2 typical of the adult SCN appears ∼P2, indicating that multiple signals may mediate circadian synchrony during the ontogeny of the SCN.

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2ace321cf219bd79deb6ce966f0346f5Test
https://doi.org/10.1523/jneurosci.2006-17.2017Test

107

A Personalized Week-to-Week Updating Algorithm to Improve Continuous Glucose Monitoring Performance

المؤلفون: Mei Mei Church, Stamatina Zavitsanou, Eyal Dassau, Jordan E. Pinsker, Joon Bok Lee, Francis J. Doyle

المصدر: Journal of Diabetes Science and Technology. 11:1070-1079

مصطلحات موضوعية: Adult, Blood Glucose, Male, medicine.medical_specialty, Time Factors, Endocrinology, Diabetes and Metabolism, Transducers, 0206 medical engineering, Real-time computing, Biomedical Engineering, 030209 endocrinology & metabolism, Bioengineering, 02 engineering and technology, Special Section: Artificial Pancreas: Models, Signals, and Control, 03 medical and health sciences, 0302 clinical medicine, Predictive Value of Tests, Blood Glucose Self-Monitoring, Internal Medicine, medicine, Humans, Hypoglycemic Agents, Glucose sensors, Least-Squares Analysis, Type 1 diabetes, business.industry, Continuous glucose monitoring, Reproducibility of Results, Signal Processing, Computer-Assisted, Equipment Design, Middle Aged, medicine.disease, 020601 biomedical engineering, Diabetes Mellitus, Type 1, Calibration, Emergency medicine, Linear Models, Female, business, Algorithms, Biomarkers

الوصف: Background: Continuous glucose monitoring (CGM) systems are increasingly becoming essential components in type 1 diabetes mellitus (T1DM) management. Current CGM technology requires frequent calibration to ensure accurate sensor performance. The accuracy of these systems is of great importance since medical decisions are made based on monitored glucose values and trends. Methods: In this work, we introduce a calibration strategy that is augmented with a weekly updating feature. During the life cycle of the sensor, the calibration mechanism periodically estimates the parameters of a calibration model to fit self-monitoring blood glucose (SMBG) measurements. At the end of each week of use, an optimization problem that minimizes the sum of squared residuals between past reference and predicted blood glucose values is solved remotely to identify personalized calibration parameters. The newly identified parameters are used to initialize the calibration mechanism of the following week. Results: The proposed method was evaluated using two sets of clinical data both consisting of 6 weeks of Dexcom G4 Platinum CGM data on 10 adults with T1DM (over 10 000 hours of CGM use), with seven SMBG data points per day measured by each subject in an unsupervised outpatient setting. Updating the calibration parameters using the history of calibration data indicated a positive trend of improving CGM performance. Conclusions: Although not statistically significant, the updating framework showed a relative improvement of CGM accuracy compared to the non-updating, static calibration method. The use of information collected for longer periods is expected to improve the performance of the sensor over time.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2d724e93b934c999b33f0849b55248dfTest
https://doi.org/10.1177/1932296817734367Test

108

Twelve-Week 24/7 Ambulatory Artificial Pancreas With Weekly Adaptation of Insulin Delivery Settings: Effect on Hemoglobin A1c and Hypoglycemia

المصدر: Diabetes Care. 40:1719-1726

الوصف: OBJECTIVE Artificial pancreas (AP) systems are best positioned for optimal treatment of type 1 diabetes (T1D) and are currently being tested in outpatient clinical trials. Our consortium developed and tested a novel adaptive AP in an outpatient, single-arm, uncontrolled multicenter clinical trial lasting 12 weeks. RESEARCH DESIGN AND METHODS Thirty adults with T1D completed a continuous glucose monitor (CGM)-augmented 1-week sensor-augmented pump (SAP) period. After the AP was started, basal insulin delivery settings used by the AP for initialization were adapted weekly, and carbohydrate ratios were adapted every 4 weeks by an algorithm running on a cloud-based server, with automatic data upload from devices. Adaptations were reviewed by expert study clinicians and patients. The primary end point was change in hemoglobin A1c (HbA1c). Outcomes are reported adhering to consensus recommendations on reporting of AP trials. RESULTS Twenty-nine patients completed the trial. HbA1c, 7.0 ± 0.8% at the start of AP use, improved to 6.7 ± 0.6% after 12 weeks (−0.3, 95% CI −0.5 to −0.2, P < 0.001). Compared with the SAP run-in, CGM time spent in the hypoglycemic range improved during the day from 5.0 to 1.9% (−3.1, 95% CI −4.1 to −2.1, P < 0.001) and overnight from 4.1 to 1.1% (−3.1, 95% CI −4.2 to −1.9, P < 0.001). Whereas carbohydrate ratios were adapted to a larger extent initially with minimal changes thereafter, basal insulin was adapted throughout. Approximately 10% of adaptation recommendations were manually overridden. There were no protocol-related serious adverse events. CONCLUSIONS Use of our novel adaptive AP yielded significant reductions in HbA1c and hypoglycemia.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::67b3d9cf252d5f86ad1e074bb4dcb9d9Test
https://doi.org/10.2337/dc17-1188Test

109

Guidelines for Genome-Scale Analysis of Biological Rhythms

المؤلفون: Achim Kramer, Karl Kornacker, Justin Blau, Susan S. Golden, Samuel S. C. Rund, Michael H. Hastings, Han Wang, Joanna C. Chiu, Pierre Baldi, Andrew J. Millar, David Gatfield, Tanya L. Leise, Christy Hoffmann, María Teresa Camacho Olmedo, Scott Sherrill-Mix, Derk-Jan Dijk, Debra J. Skene, Jason P. DeBruyne, Hanspeter Herzel, Charles J. Weitz, Gad Asher, Jiajia Li, Katja A. Lamia, Francis J. Doyle, John B. Hogenesch, Tomasz Zielinski, Stacey L. Harmer, Xiaodong Li, Jacob J. Hughey, Christian I. Hong, Zheng Chen, Michael Rosbash, Jennifer J. Loros, Maria S. Robles, Jennifer M. Hurley, Jerome S. Menet, Scott A. Lewis, Karyn A. Esser, Juergen Cox, M. Fernanda Ceriani, Ying-Hui Fu, Joseph S. Takahashi, Ying Xu, Hiroki R. Ueda, Giles E. Duffield, Garret A. FitzGerald, Michael E. Hughes, Deborah Bell-Pedersen, Carl Hirschie Johnson, Marc D. Ruben, Felix Naef, Paul de Goede, Amita Sehgal, Horacio O. de la Iglesia, Akhilesh B. Reddy, Alaaddin Bulak Arpat, Todd C. Mockler, Emi Nagoshi, Dmitri A. Nusinow, Luciano DiTacchio, Gang Wu, Lauren J. Francey, John Harer, Steve A. Kay, Charissa de Bekker, Aziz Sancar, Ron C. Anafi, Katherine C. Abruzzi, Seung Hee Yoo, Kai-Florian Storch, Nobuya Koike, Daniel B. Forger, Erik D. Herzog, Andrew C. Liu, Louis J. Ptáček, Carla B. Green, Michael W. Young, Michael N. Nitabach, Eric E. Zhang, Jay C. Dunlap, Alexander M. Crowell, Tami A. Martino, Frédéric Gachon, Ravi Allada, Pål O. Westermark, Till Roenneberg, Martha Merrow, Herman Wijnen, Kristin Eckel-Mahan, Steve Brown, Jeff Haspel, Paolo Sassone-Corsi, David A. Rand

المساهمون: ANS - Cellular & Molecular Mechanisms, Other departments, AGEM - Amsterdam Gastroenterology Endocrinology Metabolism

المصدر: Journal of Biological Rhythms, vol. 32, no. 5, pp. 380-393
CONICET Digital (CONICET)
Consejo Nacional de Investigaciones Científicas y Técnicas
instacron:CONICET
Journal of biological rhythms, 32(5), 380-393. SAGE Publications Inc.
Journal of Biological Rhythms
Hughes, M E, Abruzzi, K C, Allada, R, Anafi, R, Arpat, A B, Asher, G, Baldi, P, de Bekker, C, Bell-Pedersen, D, Blau, J, Brown, S, Ceriani, M F, Chen, Z, Chiu, J C, Cox, J, Crowell, A M, DeBruyne, J P, Dijk, D-J, DiTacchio, L, Doyle, F J, Duffield, G E, Dunlap, J C, Eckel-Mahan, K, Esser, K A, FitzGerald, G A, Forger, D B, Francey, L J, Fu, Y-H, Gachon, F, Gatfield, D, de Goede, P, Golden, S S, Green, C, Harer, J, Harmer, S, Haspel, J, Hastings, M H, Herzel, H, Herzog, E D, Hoffmann, C, Hong, C, Hughey, J J, Hurley, J M, de la Iglesia, H O, Johnson, C, Kay, S A, Koike, N, Kornacker, K, Kramer, A, Lamia, K, Leise, T, Lewis, S A, Li, J, Li, X, Liu, A C, Loros, J J, Martino, T A, Menet, J S, Merrow, M, Millar, A J, Mockler, T, Naef, F, Nagoshi, E, Nitabach, M N, Olmedo, M, Nusinow, D A, Ptáček, L J, Rand, D, Reddy, A B, Robles, M S, Roenneberg, T, Rosbash, M, Ruben, M D, Rund, S S C, Sancar, A, Sassone-Corsi, P, Sehgal, A, Sherrill-Mix, S, Skene, D J, Storch, K-F, Takahashi, J S, Ueda, H R, Wang, H, Weitz, C, Westermark, P O, Wijnen, H, Xu, Y, Wu, G, Yoo, S-H, Young, M, Zhang, E E, Zielinski, T & Hogenesch, J B 2017, ' Guidelines for Genome-Scale Analysis of Biological Rhythms ', Journal of biological rhythms, vol. 32, no. 5, 748730417728663, pp. 380-393 . https://doi.org/10.1177/0748730417728663Test
Hughes, ME; Abruzzi, KC; Allada, R; Anafi, R; Arpat, AB; Asher, G; et al.(2017). Guidelines for Genome-Scale Analysis of Biological Rhythms. Journal of Biological Rhythms, 32(5), 380-393. doi: 10.1177/0748730417728663. UC Irvine: Retrieved from: http://www.escholarship.org/uc/item/2dq117tjTest
Journal of biological rhythms, 32(5): 380-393

مصطلحات موضوعية: Proteomics, 0301 basic medicine, JBR Perspectives on Data Analysis, ChIP-seq, RNA-seq, biostatistics, circadian rhythms, computational biology, diurnal rhythms, functional genomics, guidelines, metabolomics, proteomics, systems biology, Physiology, Statistics as Topic, Big data, GUIDELINES, Genome, purl.org/becyt/ford/1 [https], DIURNAL RHYTHMS, RNA-SEQ, Systems Biology, CHIP-SEQ, Genomics, Circadian Rhythm, 3. Good health, SYSTEMS BIOLOGY, Benchmark (computing), PROTEOMICS, CIENCIAS NATURALES Y EXACTAS, COMPUTATIONAL BIOLOGY, Otras Ciencias Biológicas, Systems biology, Computational biology, Biology, METABOLOMICS, Ciencias Biológicas, QH301, 03 medical and health sciences, Physiology (medical), Humans, FUNCTIONAL GENOMICS, purl.org/becyt/ford/1.6 [https], Set (psychology), business.industry, Mechanism (biology), Computational Biology, BIOSTATISTICS, Data science, 030104 developmental biology, Genome Biology, CIRCADIAN RHYTHMS, business, Software

الوصف: Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding “big data” that are conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical considerations to generate reproducible, statistically sound, and broadly useful genome-scale data. Rather than suggest a set of rigid rules, we aim to codify principles by which investigators, reviewers, and readers of the primary literature can evaluate the suitability of different experimental designs for measuring different aspects of biological rhythms. We introduce CircaInSilico, a web-based application for generating synthetic genome biology data to benchmark statistical methods for studying biological rhythms. Finally, we discuss several unmet analytical needs, including applications to clinical medicine, and suggest productive avenues to address them. Fil: Hughes, Michael E.. Washington University School Of Medicine In St. Louis; Estados Unidos Fil: Abruzzi, Katherine C.. Brandeis University; Estados Unidos Fil: Allada, Ravi. Northwestern University; Estados Unidos Fil: Anafi, Ron. University of Pennsylvania; Estados Unidos Fil: Arpat, Alaaddin Bulak. Universite de Lausanne; Suiza Fil: Asher, Gad. Weizmann Institute Of Science Israel; Israel Fil: Baldi, Pierre. University of California at Irvine; Estados Unidos Fil: de Bekker, Charissa. University Of Central Florida; Estados Unidos Fil: Bell Pedersen, Deborah. Texas A&M University; Estados Unidos Fil: Blau, Justin. University of New York; Estados Unidos Fil: Brown, Steve. Universitat Zurich; Suiza Fil: Ceriani, Maria Fernanda. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Chen, Zheng. University Of Texas Health Science Center At Houston; Estados Unidos Fil: Chiu, Joanna C.. University of California at Davis; Estados Unidos Fil: Cox, Juergen. Max Planck Institute Of Biochemistry; Alemania Fil: Crowell, Alexander M.. Geisel School Of Medicine At Dartmouth; Estados Unidos Fil: DeBruyne, Jason P.. Morehouse School Of Medicine; Estados Unidos Fil: Dijk, Derk-Jan. University Of Surrey; Reino Unido Fil: DiTacchio, Luciano. University Of Kansas Medical Center; Estados Unidos Fil: Doyle, Francis J.. Harvard University; Estados Unidos Fil: Duffield, Giles E.. University of Notre Dame; Estados Unidos Fil: Dunlap, Jay C.. Geisel School Of Medicine At Dartmouth; Estados Unidos Fil: Eckel Mahan, Kristin. University Of Texas Medical School At Houston; Estados Unidos Fil: Esser, Karyn A.. University Of Florida College Of Medicine; Estados Unidos Fil: FitzGerald, Garret A.. University of Pennsylvania; Estados Unidos Fil: Forger, Daniel B.. University Of Michigan; Estados Unidos Fil: Francey, Lauren J.. Cincinnati Children's Hospital Medical Center; Estados Unidos Fil: Fu, Ying Hui. University of California; Estados Unidos Fil: Gachon, Frédéric. Nestlé Institute Of Health Sciences; Suiza Fil: Gatfield, David. Universite de Lausanne; Suiza Fil: de Goede, Paul. University Of Amsterdam; Países Bajos Fil: Golden, Susan S.. University of California at San Diego; Estados Unidos Fil: Green, Carla. University of Texas; Estados Unidos Fil: Harer, John. University of Duke; Estados Unidos Fil: Harmer, Stacey. University of California at Davis; Estados Unidos Fil: Haspel, Jeff. 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وصف الملف: application/pdf; text

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::98132f5b6879e2975b22c568261f17f7Test
https://doi.org/10.1177/0748730417728663Test

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دورية أكاديمية

Vulnerabilities in the tau network and the role of ultrasensitive points in tau pathophysiology.

المؤلفون: Theresa M Yuraszeck, Pierre Neveu, Maria Rodriguez-Fernandez, Anne Robinson, Kenneth S Kosik, Francis J Doyle

المصدر: PLoS Computational Biology, Vol 6, Iss 11, p e1000997 (2010)

مصطلحات موضوعية: Biology (General), QH301-705.5

الوصف: The multifactorial nature of disease motivates the use of systems-level analyses to understand their pathology. We used a systems biology approach to study tau aggregation, one of the hallmark features of Alzheimer's disease. A mathematical model was constructed to capture the current state of knowledge concerning tau's behavior and interactions in cells. The model was implemented in silico in the form of ordinary differential equations. The identifiability of the model was assessed and parameters were estimated to generate two cellular states: a population of solutions that corresponds to normal tau homeostasis and a population of solutions that displays aggregation-prone behavior. The model of normal tau homeostasis was robust to perturbations, and disturbances in multiple processes were required to achieve an aggregation-prone state. The aggregation-prone state was ultrasensitive to perturbations in diverse subsets of networks. Tau aggregation requires that multiple cellular parameters are set coordinately to a set of values that drive pathological assembly of tau. This model provides a foundation on which to build and increase our understanding of the series of events that lead to tau aggregation and may ultimately be used to identify critical intervention points that can direct the cell away from tau aggregation to aid in the treatment of tau-mediated (or related) aggregation diseases including Alzheimer's.

وصف الملف: electronic resource

العلاقة: http://europepmc.org/articles/PMC2978700?pdf=renderTest; https://doaj.org/toc/1553-734XTest; https://doaj.org/toc/1553-7358Test

الوصول الحر: https://doaj.org/article/99a8da51ecab4091a0cf5aec9f6e3ee9Test

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