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Mathis SM, Webber AE, León TM, Murray EL, Sun M, White LA, Brooks LC, Green A, Hu AJ, McDonald DJ, Rosenfeld R, Shemetov D, Tibshirani RJ, Kandula S, Pei S, Shaman J, Yaari R, Yamana TK, Agarwal P, Balusu S, Gururajan G, Kamarthi H, Prakash BA, Raman R, Rodríguez A, Zhao Z, Meiyappan A, Omar S, Baccam P, Gurung HL, Stage SA, Suchoski BT, Ajelli M, Kummer AG, Litvinova M, Ventura PC, Wadsworth S, Niemi J, Carcelen E, Hill AL, Jung SM, Lemaitre JC, Lessler J, Loo SL, McKee CD, Sato K, Smith C, Truelove S, McAndrew T, Ye W, Bosse N, Hlavacek WS, Lin YT, Mallela A, Chen Y, Lamm SM, Lee J, Posner RG, Perofsky AC, Viboud C, Clemente L, Lu F, Meyer AG, Santillana M, Chinazzi M, Davis JT, Mu K, Piontti APY, Vespignani A, Xiong X, Ben-Nun M, Riley P, Turtle J, Hulme-Lowe C, Jessa S, Nagraj VP, Turner SD, Williams D, Basu A, Drake JM, Fox SJ, Gibson GC, Suez E, Thommes EW, Cojocaru MG, Cramer EY, Gerding A, Stark A, Ray EL, Reich NG, Shandross L, Wattanachit N, Wang Y, Zorn MW, Al Aawar M, Srivastava A, Meyers LA, Adiga A, Hurt B, Kaur G, Lewis BL, Marathe M, Venkatramanan S, Butler P, Farabow A, Muralidhar N, Ramakrishnan N, Reed C, Biggerstaff M, Borchering RK. Evaluation of FluSight influenza forecasting in the 2021-22 and 2022-23 seasons with a new target laboratory-confirmed influenza hospitalizations. medRxiv 2023:2023.12.08.23299726. [PMID: 38168429 PMCID: PMC10760285 DOI: 10.1101/2023.12.08.23299726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Accurate forecasts can enable more effective public health responses during seasonal influenza epidemics. Forecasting teams were asked to provide national and jurisdiction-specific probabilistic predictions of weekly confirmed influenza hospital admissions for one through four weeks ahead for the 2021-22 and 2022-23 influenza seasons. Across both seasons, 26 teams submitted forecasts, with the submitting teams varying between seasons. Forecast skill was evaluated using the Weighted Interval Score (WIS), relative WIS, and coverage. Six out of 23 models outperformed the baseline model across forecast weeks and locations in 2021-22 and 12 out of 18 models in 2022-23. Averaging across all forecast targets, the FluSight ensemble was the 2nd most accurate model measured by WIS in 2021-22 and the 5th most accurate in the 2022-23 season. Forecast skill and 95% coverage for the FluSight ensemble and most component models degraded over longer forecast horizons and during periods of rapid change. Current influenza forecasting efforts help inform situational awareness, but research is needed to address limitations, including decreased performance during periods of changing epidemic dynamics.
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Affiliation(s)
- Sarabeth M Mathis
- Centers for Disease Control and Prevention, Atlanta, Georgia, 30329, USA
| | - Alexander E Webber
- Centers for Disease Control and Prevention, Atlanta, Georgia, 30329, USA
| | - Tomás M León
- California Department of Public Health, Richmond, CA, 95899
| | - Erin L Murray
- California Department of Public Health, Richmond, CA, 95899
| | - Monica Sun
- California Department of Public Health, Richmond, CA, 95899
| | - Lauren A White
- California Department of Public Health, Richmond, CA, 95899
| | - Logan C Brooks
- Carnegie Mellon University, Pittsburgh, PA, 15213
- University of California, Berkeley, Berkeley, CA 94720
| | - Alden Green
- Carnegie Mellon University, Pittsburgh, PA, 15213
| | - Addison J Hu
- Carnegie Mellon University, Pittsburgh, PA, 15213
| | | | | | | | - Ryan J Tibshirani
- Carnegie Mellon University, Pittsburgh, PA, 15213
- University of California, Berkeley, Berkeley, CA 94720
| | | | - Sen Pei
- Columbia University, New York, NY, 10032
| | - Jeffrey Shaman
- Columbia University, New York, NY, 10032
- Columbia University School of Climate, New York, NY 10025
| | - Rami Yaari
- Columbia University, New York, NY, 10032
| | | | | | | | | | | | | | - Rishi Raman
- Georgia Institute of Technology, Atlanta, GA, 30318
| | | | - Zhiyuan Zhao
- Georgia Institute of Technology, Atlanta, GA, 30318
| | | | - Shalina Omar
- Guidehouse Advisory and Consulting Services, McClean VA, 22102
| | | | | | | | | | - Marco Ajelli
- Indiana University School of Public Health, Bloomington, IN, 47405
| | | | - Maria Litvinova
- Indiana University School of Public Health, Bloomington, IN, 47405
| | - Paulo C Ventura
- Indiana University School of Public Health, Bloomington, IN, 47405
| | | | | | | | | | - Sung-Mok Jung
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Justin Lessler
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sara L Loo
- Johns Hopkins University, Baltimore, MD, 21205
| | | | - Koji Sato
- Johns Hopkins University, Baltimore, MD, 21205
| | | | | | | | | | - Nikos Bosse
- London School of Health and Tropical Medicine, London, UK, WC1E 7HT
| | | | - Yen Ting Lin
- Los Alamos National Laboratory, Los Alamos, NM, 87545
| | | | - Ye Chen
- Northern Arizona University, Flagstaff, AZ, 86011
| | | | - Jaechoul Lee
- Northern Arizona University, Flagstaff, AZ, 86011
| | | | - Amanda C Perofsky
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892
| | | | - Fred Lu
- Northeastern University, Boston, MA, 02115
| | | | | | | | | | - Kunpeng Mu
- Northeastern University, Boston, MA, 02115
| | | | | | | | | | - Pete Riley
- Predictive Science Inc, San Diego, CA 92121
| | | | | | | | - V P Nagraj
- Signature Science, LLC, Charlottesville, VA, 22911
| | | | | | | | | | | | | | - Ehsan Suez
- University of Georgia, Athens, GA, 30609
| | - Edward W Thommes
- University of Guelph, Guelph, ON N1G 2W1, Canada
- Sanofi, Toronto, ON, M2R 3T4
| | | | | | - Aaron Gerding
- University of Massachusetts Amherst, Amherst, MA, 01003
| | - Ariane Stark
- University of Massachusetts Amherst, Amherst, MA, 01003
| | - Evan L Ray
- University of Massachusetts Amherst, Amherst, MA, 01003
| | | | - Li Shandross
- University of Massachusetts Amherst, Amherst, MA, 01003
| | | | - Yijin Wang
- University of Massachusetts Amherst, Amherst, MA, 01003
| | - Martha W Zorn
- University of Massachusetts Amherst, Amherst, MA, 01003
| | - Majd Al Aawar
- University of Southern California, Los Angeles, CA, 90089
| | | | | | | | | | | | | | | | | | | | | | | | | | - Carrie Reed
- Centers for Disease Control and Prevention, Atlanta, Georgia, 30329, USA
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Thorve S, Wilson ML, Lewis BL, Swarup S, Vullikanti AKS, Marathe MV. EpiViewer: an epidemiological application for exploring time series data. BMC Bioinformatics 2018; 19:449. [PMID: 30466409 PMCID: PMC6251172 DOI: 10.1186/s12859-018-2439-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 05/31/2018] [Accepted: 10/15/2018] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Visualization plays an important role in epidemic time series analysis and forecasting. Viewing time series data plotted on a graph can help researchers identify anomalies and unexpected trends that could be overlooked if the data were reviewed in tabular form; these details can influence a researcher's recommended course of action or choice of simulation models. However, there are challenges in reviewing data sets from multiple data sources - data can be aggregated in different ways (e.g., incidence vs. cumulative), measure different criteria (e.g., infection counts, hospitalizations, and deaths), or represent different geographical scales (e.g., nation, HHS Regions, or states), which can make a direct comparison between time series difficult. In the face of an emerging epidemic, the ability to visualize time series from various sources and organizations and to reconcile these datasets based on different criteria could be key in developing accurate forecasts and identifying effective interventions. Many tools have been developed for visualizing temporal data; however, none yet supports all the functionality needed for easy collaborative visualization and analysis of epidemic data. RESULTS In this paper, we present EpiViewer, a time series exploration dashboard where users can upload epidemiological time series data from a variety of sources and compare, organize, and track how data evolves as an epidemic progresses. EpiViewer provides an easy-to-use web interface for visualizing temporal datasets either as line charts or bar charts. The application provides enhanced features for visual analysis, such as hierarchical categorization, zooming, and filtering, to enable detailed inspection and comparison of multiple time series on a single canvas. Finally, EpiViewer provides several built-in statistical Epi-features to help users interpret the epidemiological curves. CONCLUSION EpiViewer is a single page web application that provides a framework for exploring, comparing, and organizing temporal datasets. It offers a variety of features for convenient filtering and analysis of epicurves based on meta-attribute tagging. EpiViewer also provides a platform for sharing data between groups for better comparison and analysis. Our user study demonstrated that EpiViewer is easy to use and fills a particular niche in the toolspace for visualization and exploration of epidemiological data.
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Affiliation(s)
- Swapna Thorve
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA
- Network Dynamics and Simulation Science Laboratory, Biocomplexity Institute of Virginia Tech, Blacksburg, Virginia, USA
| | - Mandy L. Wilson
- Biocomplexity Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Bryan L. Lewis
- Biocomplexity Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Samarth Swarup
- Biocomplexity Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Anil Kumar S. Vullikanti
- Department of Computer Science, University of Virginia, Charlottesville, Virginia, USA
- Biocomplexity Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Madhav V. Marathe
- Department of Computer Science, University of Virginia, Charlottesville, Virginia, USA
- Biocomplexity Institute, University of Virginia, Charlottesville, Virginia, USA
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Alexander KA, Sanderson CE, Marathe M, Lewis BL, Rivers CM, Shaman J, Drake JM, Lofgren E, Dato VM, Eisenberg MC, Eubank S. What factors might have led to the emergence of Ebola in West Africa? PLoS Negl Trop Dis 2015; 9:e0003652. [PMID: 26042592 PMCID: PMC4456362 DOI: 10.1371/journal.pntd.0003652] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
An Ebola outbreak of unprecedented scope emerged in West Africa in December 2013 and presently continues unabated in the countries of Guinea, Sierra Leone, and Liberia. Ebola is not new to Africa, and outbreaks have been confirmed as far back as 1976. The current West African Ebola outbreak is the largest ever recorded and differs dramatically from prior outbreaks in its duration, number of people affected, and geographic extent. The emergence of this deadly disease in West Africa invites many questions, foremost among these: why now, and why in West Africa? Here, we review the sociological, ecological, and environmental drivers that might have influenced the emergence of Ebola in this region of Africa and its spread throughout the region. Containment of the West African Ebola outbreak is the most pressing, immediate need. A comprehensive assessment of the drivers of Ebola emergence and sustained human-to-human transmission is also needed in order to prepare other countries for importation or emergence of this disease. Such assessment includes identification of country-level protocols and interagency policies for outbreak detection and rapid response, increased understanding of cultural and traditional risk factors within and between nations, delivery of culturally embedded public health education, and regional coordination and collaboration, particularly with governments and health ministries throughout Africa. Public health education is also urgently needed in countries outside of Africa in order to ensure that risk is properly understood and public concerns do not escalate unnecessarily. To prevent future outbreaks, coordinated, multiscale, early warning systems should be developed that make full use of these integrated assessments, partner with local communities in high-risk areas, and provide clearly defined response recommendations specific to the needs of each community.
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Affiliation(s)
- Kathleen A. Alexander
- Department of Fisheries and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Claire E. Sanderson
- Department of Fisheries and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Madav Marathe
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America
- Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Bryan L. Lewis
- Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Caitlin M. Rivers
- Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Jeffrey Shaman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - John M. Drake
- Odum School of Ecology, University of Georgia, Athens, Georgia, United States of America
| | - Eric Lofgren
- Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Virginia M. Dato
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Marisa C. Eisenberg
- Departments of Epidemiology and Mathematics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Stephen Eubank
- Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America
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Abstract
BACKGROUND An Ebola outbreak of unparalleled size is currently affecting several countries in West Africa, and international efforts to control the outbreak are underway. However, the efficacy of these interventions, and their likely impact on an Ebola epidemic of this size, is unknown. Forecasting and simulation of these interventions may inform public health efforts. METHODS We use existing data from Liberia and Sierra Leone to parameterize a mathematical model of Ebola and use this model to forecast the progression of the epidemic, as well as the efficacy of several interventions, including increased contact tracing, improved infection control practices, the use of a hypothetical pharmaceutical intervention to improve survival in hospitalized patients. FINDINGS Model forecasts until Dec. 31, 2014 show an increasingly severe epidemic with no sign of having reached a peak. Modeling results suggest that increased contact tracing, improved infection control, or a combination of the two can have a substantial impact on the number of Ebola cases, but these interventions are not sufficient to halt the progress of the epidemic. The hypothetical pharmaceutical intervention, while impacting mortality, had a smaller effect on the forecasted trajectory of the epidemic. INTERPRETATION Near-term, practical interventions to address the ongoing Ebola epidemic may have a beneficial impact on public health, but they will not result in the immediate halting, or even obvious slowing of the epidemic. A long-term commitment of resources and support will be necessary to address the outbreak.
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Affiliation(s)
- Caitlin M Rivers
- Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
| | - Eric T Lofgren
- Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
| | - Madhav Marathe
- Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
| | - Stephen Eubank
- Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
| | - Bryan L Lewis
- Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
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Abstract
Background: An Ebola outbreak of unparalleled size is currently affecting several countries in West Africa, and international efforts to control the outbreak are underway. However, the efficacy of these interventions, and their likely impact on an Ebola epidemic of this size, is unknown. Forecasting and simulation of these interventions may inform public health efforts.
Methods: We use existing data from Liberia and Sierra Leone to parameterize a mathematical model of Ebola and use this model to forecast the progression of the epidemic, as well as the efficacy of several interventions, including increased contact tracing, improved infection control practices, the use of a hypothetical pharmaceutical intervention to improve survival in hospitalized patients.
Findings: Model forecasts until Dec. 31, 2014 show an increasingly severe epidemic with no sign of having reached a peak. Modeling results suggest that increased contact tracing, improved infection control, or a combination of the two can have a substantial impact on the number of Ebola cases, but these interventions are not sufficient to halt the progress of the epidemic. The hypothetical pharmaceutical intervention, while impacting mortality, had a smaller effect on the forecasted trajectory of the epidemic.
Interpretation: Near-term, practical interventions to address the ongoing Ebola epidemic may have a beneficial impact on public health, but they will not result in the immediate halting, or even obvious slowing of the epidemic. A long-term commitment of resources and support will be necessary to address the outbreak.
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Affiliation(s)
- Caitlin M Rivers
- Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
| | - Eric T Lofgren
- Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
| | - Madhav Marathe
- Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
| | - Stephen Eubank
- Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
| | - Bryan L Lewis
- Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
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Abstract
Wildlife species are identified as an important source of emerging zoonotic disease. Accordingly, public health programs have attempted to expand in scope to include a greater focus on wildlife and its role in zoonotic disease outbreaks. Zoonotic disease transmission dynamics involving wildlife are complex and nonlinear, presenting a number of challenges. First, empirical characterization of wildlife host species and pathogen systems are often lacking, and insight into one system may have little application to another involving the same host species and pathogen. Pathogen transmission characterization is difficult due to the changing nature of population size and density associated with wildlife hosts. Infectious disease itself may influence wildlife population demographics through compensatory responses that may evolve, such as decreased age to reproduction. Furthermore, wildlife reservoir dynamics can be complex, involving various host species and populations that may vary in their contribution to pathogen transmission and persistence over space and time. Mathematical models can provide an important tool to engage these complex systems, and there is an urgent need for increased computational focus on the coupled dynamics that underlie pathogen spillover at the human-wildlife interface. Often, however, scientists conducting empirical studies on emerging zoonotic disease do not have the necessary skill base to choose, develop, and apply models to evaluate these complex systems. How do modeling frameworks differ and what considerations are important when applying modeling tools to the study of zoonotic disease? Using zoonotic disease examples, we provide an overview of several common approaches and general considerations important in the modeling of wildlife-associated zoonoses.
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Affiliation(s)
- Kathleen A Alexander
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University , Blacksburg, VA 24061, USA.
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Bayly PV, Lewis BL, Ranz EC, Okamoto RJ, Pless RB, Dutcher SK. Propulsive forces on the flagellum during locomotion of Chlamydomonas reinhardtii. Biophys J 2011; 100:2716-25. [PMID: 21641317 DOI: 10.1016/j.bpj.2011.05.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 05/02/2011] [Accepted: 05/04/2011] [Indexed: 12/23/2022] Open
Abstract
The distributed propulsive forces exerted on the flagellum of the swimming alga Chlamydomonas reinhardtii by surrounding fluid were estimated from experimental image data. Images of uniflagellate mutant Chlamydomonas cells were obtained at 350 frames/s with 125-nm spatial resolution, and the motion of the cell body and the flagellum were analyzed in the context of low-Reynolds-number fluid mechanics. Wild-type uniflagellate cells, as well as uniflagellate cells lacking inner dynein arms (ida3) or outer dynein arms (oda2) were studied. Ida3 cells exhibit stunted flagellar waveforms, whereas oda2 cells beat with lower frequency. Image registration and sorting algorithms provided high-resolution estimates of the motion of the cell body, as well as detailed kinematics of the flagellum. The swimming cell was modeled as an ellipsoid in Stokes flow, propelled by viscous forces on the flagellum. The normal and tangential components of force on the flagellum (f(N) and f(T)) were related by resistive coefficients (C(N) and C(T)) to the corresponding components of velocity (V(N) and V(T)).The values of these coefficients were estimated by satisfying equilibrium requirements for force and torque on the cell. The estimated values of the resistive coefficients are consistent among all three genotypes and similar to theoretical predictions.
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Affiliation(s)
- P V Bayly
- Department of Mechanical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA.
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Bayly PV, Lewis BL, Kemp PS, Pless RB, Dutcher SK. Efficient spatiotemporal analysis of the flagellar waveform of Chlamydomonas reinhardtii. Cytoskeleton (Hoboken) 2010; 67:56-69. [PMID: 20169530 PMCID: PMC4109274 DOI: 10.1002/cm.20424] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2009] [Accepted: 10/23/2009] [Indexed: 01/04/2023]
Abstract
The 9 + 2 axoneme is a microtubule-based machine that powers the oscillatory beating of cilia and flagella. Its highly regulated movement is essential for the normal function of many organs; ciliopathies cause congenital defects, chronic respiratory tract infections and infertility. We present an efficient method to obtain a quantitative description of flagellar motion, with high spatial and temporal resolution, from high speed video recording of bright field images. This highly automated technique provides the shape, shear angle, curvature, and bend propagation speeds along the length of the flagellum, with approximately 200 temporal samples per beat. We compared the waveforms of uniflagellated wild-type and ida3 mutant cells, which lack the I1 inner dynein complex. Video images were captured at 350 fps. Rigid-body motion was eliminated by fast Fourier transform (FFT)-based registration, and the Cartesian (x-y) coordinates of points on the flagellum were identified. These x-y "point clouds" were embedded in two data dimensions using Isomap, a nonlinear dimension reduction method, and sorted by phase in the flagellar cycle. A smooth surface was fitted to the sorted point clouds, which provides high-resolution estimates of shear angle and curvature. Wild-type and ida3 cells exhibit large differences in shear amplitude, but similar maximum and minimum curvature values. In ida3 cells, the reverse bend begins earlier and travels more slowly relative to the principal bend, than in wild-type cells. The regulation of flagellar movement must involve I1 dynein in a manner consistent with these results.
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Affiliation(s)
- P V Bayly
- Department of Mechanical, Aerospace, and Structural Engineering, Washington University, St. Louis, Missouri 63130, USA.
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Hall LW, Anderson RD, Lewis BL, Arnold WR. The influence of salinity and dissolved organic carbon on the toxicity of copper to the estuarine copepod, Eurytemora affinis. Arch Environ Contam Toxicol 2008; 54:44-56. [PMID: 17721798 DOI: 10.1007/s00244-007-9010-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Accepted: 05/31/2007] [Indexed: 05/16/2023]
Abstract
The objectives of this study were to determine the influence of salinity (2.5, 5, 15, and 25 ppt) at dissolved organic carbon (DOC) concentrations of 1.3-3.3 mg/L and DOC concentrations of 2, 4, 6, and 8 mg/L at a fixed salinity of 10 ppt on the acute toxicity (96-h LC50s) of copper to the sensitive estuarine copepod, Eurytemora affinis. For both salinity and DOC experiments, various other chemical constituents such as DOC, Ca2+, Cl(-), Mg2+, Na+, K+, SO4 (2-) , hardness, alkalinity, salinity, pH, temperature, and dissolved oxygen were measured at selected copper concentrations at test initiation and test termination. Dissolved copper, copper speciation, and organic copper complexation were measured at various test conditions during the salinity and DOC experiments. Ninety-six-hour dissolved copper LC50 values for the four salinities ranged from 58 microg/L (25 ppt) to 104 microg/L (5 ppt) with intermediate values of 71 microg/L (2.5 ppt) and 68 microg/L (15 ppt). The 58, 68, and 71 microg/L LC50 values were not significantly different. Copper LC50 values at 5 ppt were higher than at both 15 and 25 ppt. The isosmotic salinity of E. affinis is approximately 5-10 ppt, which was a likely factor for why the LC50 value increased for copper at 5 ppt. The dissolved copper 96-h LC50s for E. affinis increased from 76 to 166 microg/L as DOC increased from 2 to 8 mg/L. This result is not surprising and is consistent with reported values for other saltwater species.
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Affiliation(s)
- L W Hall
- Wye Research and Education Center, University of Maryland, PO Box 169, Queenstown, MD 21658, USA.
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Luck J, Peabody JW, Lewis BL. An automated scoring algorithm for computerized clinical vignettes: Evaluating physician performance against explicit quality criteria. Int J Med Inform 2006; 75:701-7. [PMID: 16324882 DOI: 10.1016/j.ijmedinf.2005.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2005] [Revised: 08/08/2005] [Accepted: 10/16/2005] [Indexed: 11/18/2022]
Abstract
OBJECTIVE To evaluate the accuracy of an automated algorithm for scoring physicians' responses to open-ended clinical vignettes against explicit, evidence-based quality criteria. METHODS One hundred sixteen physicians completed a total of 915 computerized clinical vignettes at 4 sites. Each vignette simulated an outpatient primary care visit for one of 8 different clinical cases. The automated algorithm scored disease-specific quality criterion as done or not done by recognizing the presence or absence of predefined patterns in the physician's text response to the vignette. Scores generated by the automated algorithm for each criterion were compared to scores generated by trained human abstractors. Vignette responses were divided into development and test sets. Percentage agreement between automated and manual scores was computed separately for the development and test sets. Sensitivity and specificity were calculated. Costs of automated and manual scoring were compared. RESULTS Accuracy of the algorithm exceeds 90% for both the development and test sets, and is high for care items that were deemed either necessary or unnecessary, across diverse clinical cases, and for all domains of the outpatient clinical encounter. The sensitivity of the automated scoring algorithm is 89.0%, and specificity is 93.5%. Automated scoring is approximately 84% less expensive than manual scoring. CONCLUSION Automated scoring of computerized vignettes appears feasible and accurate. Computerized vignettes incorporating accurate automated scoring offer the promise of a highly standardized but relatively inexpensive measurement tool for a wide range of quality assessments within and across health systems.
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Affiliation(s)
- J Luck
- Veterans Affairs Greater Los Angeles Health Care System, USA.
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Abstract
BACKGROUND An important concept in epidemiology is attributable risk, defined as the difference in risk between an exposed and an unexposed group. For example, in an intervention trial, the attributable risk is the difference in risk between a group that receives an intervention and another that does not. A fundamental assumption in estimating the attributable risk associated with the intervention is that disease outcomes are independent. When estimating population risks associated with treatment regimens designed to affect exposure to infectious pathogens, however, there may be bias due to the fact that infectious pathogens can be transmitted from host to host causing a potential statistical dependency in disease status among participants. METHODS To estimate this bias, we used a mathematical model of community- and household-level disease transmission to explicitly incorporate the dependency among participants. We illustrate the method using a plausible model of infectious diarrheal disease. RESULTS Analysis of the model suggests that this bias in attributable risk estimates is a function of transmission from person to person, either directly or indirectly via the environment. CONCLUSIONS By incorporating these dependencies among individuals in a transmission model, we show how the bias of attributable risk estimates could be quantified to adjust effect estimates reported from intervention trials.
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Affiliation(s)
- Joseph N S Eisenberg
- School of Public Health, University of California, Berkeley, CA 94720-7360, USA.
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Lewis BL, O'Donnell P. Ventral tegmental area afferents to the prefrontal cortex maintain membrane potential 'up' states in pyramidal neurons via D(1) dopamine receptors. Cereb Cortex 2000; 10:1168-75. [PMID: 11073866 DOI: 10.1093/cercor/10.12.1168] [Citation(s) in RCA: 214] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The electrophysiological nature of dopamine actions has been controversial for years, with data supporting both inhibitory and excitatory actions. In this study, we tested whether stimulation of the ventral tegmental area (VTA), the source of the dopamine innervation of the prefrontal cortex, would exert different responses depending on the membrane potential states that pyramidal neurons exhibit when recorded in vivo, and whether VTA stimulation would have a role in controlling transitions between these states. Prefrontal cortical neurons have a very negative resting membrane potential (down state) interrupted by plateau depolarizations (up state). Although the up state had been shown to be dependent on hippocampal afferents in nucleus accumbens neurons, our results indicate that neither hippocampal nor thalamic inputs are sufficient to drive up events in prefrontal cortical neurons. Electrical VTA stimulation resulted in a variety of actions, in many cases depending on the neuron membrane potential state. Trains of stimuli resembling burst firing evoked a long-lasting transition to the up state, an effect blocked by a D(1) antagonist and mimicked by chemical VTA stimulation. These results indicate that projections from the VTA to the prefrontal cortex may be involved in controlling membrane potential states that define assemblies of activable pyramidal neurons in this region.
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Affiliation(s)
- B L Lewis
- Center for Neuropharmacology and Neuroscience, Albany Medical College, Albany, NY 12208, USA
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Affiliation(s)
- Y M Peters
- Department of Pharmacology & Neuroscience, Albany Medical College, New York 12208, USA
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14
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Abstract
Pennartz et al. have proposed that functions of the nucleus accumbens (NA) are subserved by the activity of ensembles of neurons rather than by an overall neuronal activation. Indeed, the NA is a site of convergence for a large number of inputs from limbic structures that may modulate the flow of prefrontal cortical information and contribute to defining such ensembles, as exemplified in the ability of hippocampal input to gate cortical throughput in the nucleus accumbens. NA neurons exhibit a bistable membrane potential, characterized by a very negative resting membrane potential (down state), periodically interrupted by plateau depolarizations (up state), during which the cells may fire in response to cortical inputs. A dynamic ensemble can be the result of a distributed set of neurons in their up state, determined by the moment-to-moment changes in the spatial distribution of hippocampal inputs responsible for transitions to the up state. Ensembles may change as an adaptation to the contextual information provided by the hippocampal input. Furthermore, for dynamic ensembles to be functionally relevant, the model calls for near synchronous transitions to the up state in a group of neurons. This can be accomplished by the cell-to-cell transfer of information via gap junctions, a mechanism that can allow for a transfer of slow electrical signals, including "up" events between coupled cells. Furthermore, gap junction permeability is tightly modulated by a number of factors, including levels of dopamine and nitric oxide, and cortical inputs, allowing for fine-tuning of this synchronization of up events. The continuous selection of such dynamic ensembles in the NA may be disputed in schizophrenia, resulting in an inappropriate level of activity of thalamocortical systems.
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Affiliation(s)
- P O'Donnell
- Department of Pharmacology, Albany Medical College, NY 12208, USA. patricio.o'
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Brittain D, Concannon PW, Flanders JA, Flahive WJ, Lewis BL, Meyers-Wallen V, Moise NS. Use of surgical intrauterine insemination to manage infertility in a colony of research German shepherd dogs. Lab Anim Sci 1995; 45:404-7. [PMID: 7474880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A colony of German shepherd dogs with inherited ventricular arrhythmias and sudden death had infertility that was resolved by intrauterine insemination. Mating of German shepherd males to related German shepherd females (40 cycles) by vaginal artificial insemination resulted in a low pregnancy rate of 35% and a small median litter size of 3.5. When these same German shepherd males were bred to female beagles by vaginal artificial insemination, the pregnancy rate of 100% (P = 0.02) and median litter size of 7.0 were significantly (P = 0.04) greater. Therefore, inadequate fertility existed when the German shepherds were mated. Because matings between these dogs were necessary, surgical intrauterine insemination of fresh semen was instituted in eight German shepherd females over nine cycles. In bypassing the cervix with this method, German shepherd fecundity increased significantly, with a pregnancy rate of 100% (P = 0.002) and median litter size of 8.0 (P = 0.001). Surgical intrauterine insemination may be an important method for management of canine infertility in the research environment.
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Affiliation(s)
- D Brittain
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853-6401, USA
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Abstract
NADP(H) measurements by enzymatic amplification are described in which the interface step between cycling (glucose-6-phosphate and glutamic dehydrogenases) and indicator (6-phosphogluconic dehydrogenase) enzymes has been reconfigured, permitting the entire operation to run as a continuous assay on a centrifugal fast analyzer. This is accomplished by using the sequential load feature of the analyzer and incorporating either sodium dodecyl sulfate (SDS) or SDS and hydrogen peroxide as kill reagents to replace the thermal step (destruction of cycle enzymes by boiling). The ability of SDS to render a cycle inoperative during the run time of the indicator enzyme depends on the inherent resistivity and absolute amount of its enzyme proteins to this surfactant. Criteria used to judge the efficacy of a potential kill reagent are based on the sample blank time-response curve and the cycle product recovery by the indicator enzyme. Various other enzyme cycling systems which can be fitted to the centrifugal fast analyzer are highlighted.
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Affiliation(s)
- B L Lewis
- Department of Chemistry, Seton Hall University, South Orange, New Jersey 07079
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Abstract
The occurrence of multihospital systems, two or more hospitals owned, leased, or managed by a separate organization, represents a note-worthy change in the way health care is organized today. The impact of this for small rural hospitals, however, has only been studied indirectly or anecdotally. This investigation, using data from national surveys, systematically documents and analyzes this trend and discusses its potential impact. By 1983 almost one quarter of all small rural hospitals were affiliated with multihospital systems. This growth occurred primarily over the last few years, and was accompanied by a rapid surge in the involvement of for-profit systems. This contrasts sharply with traditional rural hospital care which had been provided primarily by nonprofit or religious institutions. There also were differences in the form of affiliation the hospitals had with their parent organizations, with the most recent movement toward management contracts. Differential changes also occurred in the patterns of affiliation by geographic region.
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Lewis BL, Alexander J. A taxonomic analysis of multihospital systems. Health Serv Res 1986; 21:29-56. [PMID: 3710802 PMCID: PMC1068933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Research to date on multihospital systems has proved largely uninformative, in part because similarities and differences among these organizations have not been addressed systematically. Through numeric classification, this article identifies populations of multihospital systems that share similar organizational attributes. Drawing on McKelvey's classification theory, 16 organizational characteristics of 160 multihospital systems are analyzed using a series of taxonomic techniques, including cluster analysis, multiple discriminant analysis, and analysis of coefficients of variation. Fifteen distinct subgroups of systems are identified and described, and their implications for organization research discussed.
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Meador-Woodruff JH, Yoshino JE, Bigbee JW, Lewis BL, Devries GH. Differential proliferative responses of cultured Schwann cells to axolemma and myelin-enriched fractions. II. Morphological studies. J Neurocytol 1985; 14:619-35. [PMID: 3934342 DOI: 10.1007/bf01200801] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Axolemma-enriched and myelin-enriched fractions were prepared from bovine CNS white matter and conjugated to fluorescein isothiocyanate (FITC). Both unlabelled and FITC-labelled axolemma and myelin were mitogenic for cultured rat Schwann cells. Treatment of Schwann cells with the FITC-labelled mitogens for up to 24 h resulted in two distinct morphological appearances. FITC-myelin-treated cells were filled with numerous round, fluorescent-labelled intracellular vesicles, while FITC-axolemma-treated cells appeared to be coated with a patchy, ill-defined fluorescence, primarily concentrated around the cell body but extending onto the cell processes. These observations were corroborated under phase microscopy. Electron microscopy revealed multiple, membrane-bound, membrane-containing phagosomes within myelin-treated cells and to a far lesser extent in axolemma-treated cells. The effect on the expression of the myelin-mediated and axolemma-mediated mitogenic signal when Schwann cells were treated with the lysosomal inhibitors, ammonium chloride and chloroquine, was evaluated. The mitogenicity of myelin was reduced 70-80% by these agents whereas the mitogenicity of axolemma was not significantly altered under these conditions. These results suggest that axolemma and myelin stimulate the proliferation of cultured Schwann cells by different mechanisms. Myelin requires endocytosis and lysosomal processing for expression of its mitogenic signal; in contrast, the mitogenicity of axolemma may be transduced at the Schwann cell surface.
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Abstract
Inconsistency and lack of utility in multihospital systems research is often attributable to misspecification of the unit of analysis and lack of generalizability of research findings. The typical, system-level focus takes an "organizations are all alike" approach that masks potentially important variation among constituent hospitals in systems. This article develops and validates a multivariate, empirical typology of hospitals affiliated with multihospital systems. The objective of the typology is to identify prevalent types of system hospitals that share similar organizational and operational characteristics. Three hundred and sixty-six hospitals affiliated with secular, not-for-profit multihospital systems were subjected to cluster analysis within and across affiliation categories (owned, leased, and contract managed). Findings indicate that the population of hospitals in not-for-profit systems is organizationally heterogeneous but that distinct groupings of hospitals, based largely on size and affiliation status, occur within this population. Homogeneous groupings of hospitals were tested for differences in governance and performance characteristics. Although these clusters differ only slightly in their governance characteristics, they do manifest several differences in performance characteristics. Implications and applications of these findings are discussed.
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Yoshino JE, Dinneen MP, Lewis BL, Meador-Woodruff JH, Devries GH. Differential proliferative responses of cultured Schwann cells to axolemma- and myelin-enriched fractions. I. Biochemical studies. J Biophys Biochem Cytol 1984; 99:2309-13. [PMID: 6501427 PMCID: PMC2113533 DOI: 10.1083/jcb.99.6.2309] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Cultured rat Schwann cells were treated for 72 h with axolemma- and myelin-enriched fractions prepared from rat brainstem. [3H]Thymidine was added to the cultures 48 h before the termination of the experiment. Although, both fractions produced a dose-dependent uptake of label into Schwann cells, the shape of the dose response curves and rates at which [3H]thymidine was incorporated were different. The axolemma-enriched fraction produced a sigmoid dose response curve with a Hill coefficient of 2.05. The dose response curve for myelin rose sharply and saturated at a level that was approximately 50% of the maximal response observed with axolemma. Schwann cells that had been treated with axolemma exhibited little change in the rate of [3H]thymidine incorporation from 36-72 h after the addition of the membranes. In contrast, Schwann cells accumulated label three times faster during the 48-72-h period following the addition of myelin to the cultures when compared with the rate during the preceding 12-h interval. Furthermore, the mitogenic activity of the myelin-enriched fraction was decreased by the addition of ammonium chloride, a lysosomal inhibitor, whereas the activity of the axolemmal fraction was not impaired.
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Alexander JA, Lewis BL. Hospital contract management: a descriptive profile. Health Serv Res 1984; 19:461-77. [PMID: 6490376 PMCID: PMC1068827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Despite the dramatic growth in hospital contract management in the last decade, research only recently has begun to provide insights into the structure, operation, and effectiveness of these arrangements. Two descriptive questions regarding hospital contract management are addressed in an effort to increase correspondence between theoretical and evaluative research in this area: (1) how do contract-managed hospitals differ from traditionally managed hospitals? and (2) how do contract-managed hospitals differ from each other? Principal discriminating variables in the analyses are hospital size, control, urban-rural location, region, management organization control, and management organization size. Results of the analysis on a sample of 406 contract-managed hospitals and 401 unaffiliated hospitals reveal important differences between contract-managed and traditionally managed hospitals as well as among contract management organizations. These findings are discussed in terms of their implications for future research and performance evaluations on contract management arrangements.
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Meador-Woodruff JH, Lewis BL, DeVries GH. Cyclic AMP and calcium as potential mediators of stimulation of cultured Schwann cell proliferation by axolemma-enriched and myelin-enriched membrane fractions. Biochem Biophys Res Commun 1984; 122:373-80. [PMID: 6331451 DOI: 10.1016/0006-291x(84)90485-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The roles of cyclic AMP and calcium in the transduction of the mitogenic effects of central nervous system axolemma and myelin-enriched fractions on cultured Schwann cells were examined. Cyclic AMP levels were not elevated in axolemma or myelin-stimulated Schwann cells, but were increased when stimulated with cholera toxin, an adenyl cyclase activator. The mitogenicity of axolemma and myelin was markedly reduced by 2.5 mM citrate, a calcium chelator, and 10 uM trifluoroperazine, an inhibitor of calmodulin. Treatment of Schwann cells with several tumor-promoting phorbol esters caused significant enhancement of the mitogenicity of the axolemma and myelin preparations. These data suggest that the mitogenic effects of axolemma and myelin are not mediated by cyclic AMP, but may be mediated by calcium ions.
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Abstract
Axolemma-enriched fractions isolated from rat CNS stimulated cultured Schwann cells to divide without changing their morphology. Fluorescent activated cell sorter analysis of the axolemma-stimulated cells demonstrated an approximate 3-fold increase in the number of Schwann cells in the S-phase of the cell cycle. This increase correlated well with increases in the number of [3H]thymidine-labeled nuclei observed by light level radioautography. The membrane-bound mitogen was relatively heat-stable, but trypsin-sensitive, and was inactivated both by lipid extraction and sonication. Liver plasma membranes did not increase the mitotic index over that of untreated cells, indicating the axolemma-induced mitosis was not a general response to exogenous membranes. Increasing serum concentrations in the presence of a constant level of axolemma did not change the mitotic index, suggesting that the axolemma did not cause mitosis by removal of an inhibitory factor in serum. Potential mitogens such as gangliosides, myelin basic protein, heparin, an axolemmal lipid extract, and cGMP had no effect on the cultured Schwann cells. The characteristics of the axolemma-related mitogenic factor are discussed relative to other known mitogens for cultured Schwann cells.
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Abstract
Family functioning was examined as a mediating variable affecting adjustment in children with cystic fibrosis. Three groups of children (cystic fibrosis, asthma, and healthy control subjects) were initially compared on two dimensions of adjustment: self-concept and frequency of behavior problems. The families of these children were compared according to functional level of "cohesion" and "adaptability" (assessed by an as yet unvalidated family functioning measure). No significant difference was found between the groups in family functioning or children's self-concept. The two groups of chronically ill children did have significantly higher frequencies of behavior problems than had the healthy children. When there was statistical control for effects related to family functioning, however, this difference was not significant. Family functioning was found to be a better predictor of child adjustment than was the presence of illness. These results are consistent with recent research suggesting that children with cystic fibrosis adjust in basically healthy ways and that any deficits result more from mediating factors. In this study family functioning was found to be an important mediating factor in this process.
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Lewis BL. Junctional activity recurring over an incompletely removed balloon cell nevus. Arch Dermatol 1971; 104:513-4. [PMID: 5120177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Lewis BL. Clinical appearance of a balloon cell nevus. Arch Dermatol 1969; 100:312-3. [PMID: 5822375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Lewis BL. Metal sensitivity and duodenal ulcer. JAMA 1967; 201:1052. [PMID: 6072488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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