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Madsen K, Cornish A, Soper P, McKaigney C, Jijon H, Yachimec C, Doyle J, Jewell L, De Simone C. Probiotic bacteria enhance murine and human intestinal epithelial barrier function. Gastroenterology 2001; 121:580-91. [PMID: 11522742 DOI: 10.1053/gast.2001.27224] [Citation(s) in RCA: 736] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS The probiotic compound, VSL#3, is efficacious as maintenance therapy in pouchitis and ulcerative colitis. The aim of this study was to determine the efficacy of VSL#3 as a primary therapy in the treatment of colitis in the interleukin (IL)-10 gene-deficient mouse. Mechanisms of action of VSL#3 were investigated in T(84) monolayers. METHODS IL-10 gene-deficient and control mice received 2.8 x 10(8) colony-forming units per day of VSL#3 for 4 weeks. Colons were removed and analyzed for cytokine production, epithelial barrier function, and inflammation. VSL#3 or conditioned media was applied directly to T(84) monolayers. RESULTS Treatment of IL-10 gene-deficient mice with VSL#3 resulted in normalization of colonic physiologic function and barrier integrity in conjunction with a reduction in mucosal secretion of tumor necrosis factor alpha and interferon gamma and an improvement in histologic disease. In vitro studies showed that epithelial barrier function and resistance to Salmonella invasion could be enhanced by exposure to a proteinaceous soluble factor secreted by the bacteria found in the VSL#3 compound. CONCLUSIONS Oral administration of VSL#3 was effective as primary therapy in IL-10 gene-deficient mice, and had a direct effect on epithelial barrier function.
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Abstract
Robustness, the ability to maintain performance in the face of perturbations and uncertainty, is a long-recognized key property of living systems. Owing to intimate links to cellular complexity, however, its molecular and cellular basis has only recently begun to be understood. Theoretical approaches to complex engineered systems can provide guidelines for investigating cellular robustness because biology and engineering employ a common set of basic mechanisms in different combinations. Robustness may be a key to understanding cellular complexity, elucidating design principles, and fostering closer interactions between experimentation and theory.
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Yi TM, Huang Y, Simon MI, Doyle J. Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc Natl Acad Sci U S A 2000; 97:4649-53. [PMID: 10781070 PMCID: PMC18287 DOI: 10.1073/pnas.97.9.4649] [Citation(s) in RCA: 566] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2000] [Indexed: 11/18/2022] Open
Abstract
Integral feedback control is a basic engineering strategy for ensuring that the output of a system robustly tracks its desired value independent of noise or variations in system parameters. In biological systems, it is common for the response to an extracellular stimulus to return to its prestimulus value even in the continued presence of the signal-a process termed adaptation or desensitization. Barkai, Alon, Surette, and Leibler have provided both theoretical and experimental evidence that the precision of adaptation in bacterial chemotaxis is robust to dramatic changes in the levels and kinetic rate constants of the constituent proteins in this signaling network [Alon, U., Surette, M. G., Barkai, N. & Leibler, S. (1998) Nature (London) 397, 168-171]. Here we propose that the robustness of perfect adaptation is the result of this system possessing the property of integral feedback control. Using techniques from control and dynamical systems theory, we demonstrate that integral control is structurally inherent in the Barkai-Leibler model and identify and characterize the key assumptions of the model. Most importantly, we argue that integral control in some form is necessary for a robust implementation of perfect adaptation. More generally, integral control may underlie the robustness of many homeostatic mechanisms.
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Mills RP, Budenz DL, Lee PP, Noecker RJ, Walt JG, Siegartel LR, Evans SJ, Doyle JJ. Categorizing the stage of glaucoma from pre-diagnosis to end-stage disease. Am J Ophthalmol 2006; 141:24-30. [PMID: 16386972 DOI: 10.1016/j.ajo.2005.07.044] [Citation(s) in RCA: 370] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Revised: 07/15/2005] [Accepted: 07/16/2005] [Indexed: 11/25/2022]
Abstract
PURPOSE To provide a reliable, comprehensive staging system to assess glaucoma stage in the absence of an universally accepted glaucoma staging system (GSS) on the basis of visual field results. DESIGN Literature review and GSS adaptation. METHODS After a review of published GSSs was conducted, the Bascom Palmer (Hodapp-Anderson-Parrish) GSS was selected as an appropriate platform for a retrospective GSS on the basis of visual fields. The system was modified by a panel of glaucoma specialists, and additional modifications were made after pilot testing to cover the full range of disease progression, from preglaucoma diagnosis to complete blindness; the ordered stages reflect the typical progression of glaucoma. RESULTS The GSS is comprised of six ordered stages and is on the basis of the Humphrey visual field. The completed GSS was validated by reviewing patient charts from 12 US glaucoma centers. CONCLUSIONS The GSS allows accurate staging of 100% of glaucoma on the basis of visual fields and other data, enabling evaluation of disease progression and resource utilization at various glaucoma stages. Additionally, treatment costs may be assigned to determine cost-effectiveness of treatment. Research utilizing the GSS has found that cost of care increases with increasing disease severity. The GSS may be used as the basis for creating treatment guidelines, which have the potential to delay glaucoma progression and lower treatment costs.
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Chaudhari P, Lacey J, Doyle J, Galligan E, Lien SC, Callegari A, Hougham G, Lang ND, Andry PS, John R, Yang KH, Lu M, Cai C, Speidell J, Purushothaman S, Ritsko J, Samant M, Stöhr J, Nakagawa Y, Katoh Y, Saitoh Y, Sakai K, Satoh H, Odahara S, Nakano H, Nakagaki J, Shiota Y. Atomic-beam alignment of inorganic materials for liquid-crystal displays. Nature 2001; 411:56-9. [PMID: 11333974 DOI: 10.1038/35075021] [Citation(s) in RCA: 351] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The technique used to align liquid crystals-rubbing the surface of a substrate on which a liquid crystal is subsequently deposited-has been perfected by the multibillion-dollar liquid-crystal display industry. However, it is widely recognized that a non-contact alignment technique would be highly desirable for future generations of large, high-resolution liquid-crystal displays. A number of alternative alignment techniques have been reported, but none of these have so far been implemented in large-scale manufacturing. Here, we report a non-contact alignment process, which uses low-energy ion beams impinging at a glancing angle on amorphous inorganic films, such as diamond-like carbon. Using this approach, we have produced both laptop and desktop displays in pilot-line manufacturing, and found that displays of higher quality and reliability could be made at a lower cost than the rubbing technique. The mechanism of alignment is explained by adopting a random network model of atomic arrangement in the inorganic films. Order is induced by exposure to an ion beam because unfavourably oriented rings of atoms are selectively destroyed. The planes of the remaining rings are predominantly parallel to the direction of the ion beam.
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Behrens A, Doyle JJ, Stern L, Chuck RS, McDonnell PJ, Azar DT, Dua HS, Hom M, Karpecki PM, Laibson PR, Lemp MA, Meisler DM, Del Castillo JM, O'Brien TP, Pflugfelder SC, Rolando M, Schein OD, Seitz B, Tseng SC, van Setten G, Wilson SE, Yiu SC. Dysfunctional Tear Syndrome. Cornea 2006; 25:900-7. [PMID: 17102664 DOI: 10.1097/01.ico.0000214802.40313.fa] [Citation(s) in RCA: 348] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE To develop current treatment recommendations for dry eye disease from consensus of expert advice. METHODS Of 25 preselected international specialists on dry eye, 17 agreed to participate in a modified, 2-round Delphi panel approach. Based on available literature and standards of care, a survey was presented to each panelist. A two-thirds majority was used for consensus building from responses obtained. Treatment algorithms were created. Treatment recommendations for different types and severity levels of dry eye disease were the main outcome. RESULTS A new term for dry eye disease was proposed: dysfunctional tear syndrome (DTS). Treatment recommendations were based primarily on patient symptoms and signs. Available diagnostic tests were considered of secondary importance in guiding therapy. Development of algorithms was based on the presence or absence of lid margin disease and disturbances of tear distribution and clearance. Disease severity was considered the most important factor for treatment decision-making and was categorized into 4 levels. Severity was assessed on the basis of tear substitute requirements, symptoms of ocular discomfort, and visual disturbance. Clinical signs present in lids, tear film, conjunctiva, and cornea were also used for categorization of severity. Consensus was reached on treatment algorithms for DTS with and without concurrent lid disease. CONCLUSION Panelist opinion relied on symptoms and signs (not tests) for selection of treatment strategies. Therapy is chosen to match disease severity and presence versus absence of lid margin disease or tear distribution and clearance disturbances.
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Suomi JD, Greene JC, Vermillion JR, Doyle J, Chang JJ, Leatherwood EC. The effect of controlled oral hygiene procedures on the progression of periddontal disease in adults: results after third and final year. J Periodontol 1971; 42:152-60. [PMID: 4396693 DOI: 10.1902/jop.1971.42.3.152] [Citation(s) in RCA: 305] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Doyle JJ, Neugut AI, Jacobson JS, Grann VR, Hershman DL. Chemotherapy and Cardiotoxicity in Older Breast Cancer Patients: A Population-Based Study. J Clin Oncol 2005; 23:8597-605. [PMID: 16314622 DOI: 10.1200/jco.2005.02.5841] [Citation(s) in RCA: 266] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purpose Adjuvant chemotherapy, especially with anthracyclines, is known to cause acute and chronic cardiotoxicity in breast cancer patients. We studied the cardiac effects of chemotherapy in a population-based sample of breast cancer patients aged ≥ 65 years with long-term follow-up. Patients and Methods In the Surveillance, Epidemiology, and End Results (SEER)-Medicare database, we analyzed treatments and outcomes among women ≥ 65 years of age who were diagnosed with stage I to III breast cancer from January 1, 1992 to December 31, 1999. Propensity scores were used to control for baseline heart disease (HD) and other known predictors of chemotherapy, and Cox proportional hazards models were used to estimate the risk of cardiomyopathy (CM), congestive heart failure (CHF), and HD after chemotherapy. Results Of 31,748 women with stage I to III breast cancer, 5,575 (18%) received chemotherapy. Chemotherapy was associated with younger age, fewer comorbidities, hormone receptor negativity, multiple primary tumors, and advanced disease. Patients who received chemotherapy were less likely than other patients to have pre-existing HD (45% v 55%, respectively; P < .001). The hazard ratios for CM, CHF, and HD for patients treated with doxorubicin (DOX) compared with patients who received no chemotherapy were 2.48 (95% CI, 2.10 to 2.93), 1.38 (95% CI, 1.25 to 1.52), and 1.35 (95% CI, 1.26 to 1.44), respectively. The relative risk of cardiotoxicity among patients who received DOX compared with untreated patients remained elevated 5 years after diagnosis. Conclusion When baseline HD was taken into account, chemotherapy, especially with anthracyclines, was associated with a substantially increased risk of CM. As the number of long-term survivors grows, identifying and minimizing the late effects of treatment will become increasingly important.
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Abstract
Highly organized, universal structures underlying biological and technological networks mediate effective trade-offs among efficiency, robustness and evolvability, with predictable fragilities that can be used to understand disease pathogenesis. The aims of this article are to describe the features of one common organizational architecture in biology, the bow tie. Large-scale organizational frameworks such as the bow tie are necessary starting points for higher-resolution modeling of complex biologic processes
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Nicosia MA, Hind JA, Roecker EB, Carnes M, Doyle J, Dengel GA, Robbins J. Age effects on the temporal evolution of isometric and swallowing pressure. J Gerontol A Biol Sci Med Sci 2000; 55:M634-40. [PMID: 11078092 DOI: 10.1093/gerona/55.11.m634] [Citation(s) in RCA: 263] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The tongue plays a key role in bolus propulsion through the oropharyngeal chamber. In this study, possible age effects on the magnitude and timing of lingual pressure generation were analyzed. METHODS Oral pressure was measured during isometric and swallowing tasks for 10 elderly (mean age = 81 years) and 10 young (mean age = 51 years) subjects. Three trials each of the isometric task and swallows of three different boluses (3 ml semisolid, 3 ml liquid, and 10 ml liquid) were performed by each subject. The timing and magnitude of isometric and swallowing pressure generation along with the pattern of the swallowing pressure waveform were analyzed. RESULTS Whereas maximum lingual isometric pressures decreased with age (p < .001). no significant age difference was found for swallowing pressure. Time taken to reach peak pressure also was reduced with age in both the isometric task and swallows of liquid boluses (p < .05), while no significant age effect was found for semisolid swallows. Finally, only elderly subjects showed a pattern of liquid swallowing pressure generation in which multiple lingual gestures were required to reach peak pressure (termed "pressure building"), a pattern demonstrated by both young and elderly groups for semisolids. CONCLUSIONS Decreased lingual strength with age combined with unchanging swallowing pressure leads to a decreased "pressure reserve," perhaps leaving older individuals more at risk for dysphagia resulting from insults directly or indirectly to the swallowing system. Additionally, swallowing is generally "slowed" with age, apparently due to both central and peripheral factors, and this change may have an impact on bolus flow outcomes.
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Schiffman RM, Walt JG, Jacobsen G, Doyle JJ, Lebovics G, Sumner W. Utility assessment among patients with dry eye disease. Ophthalmology 2003; 110:1412-9. [PMID: 12867401 DOI: 10.1016/s0161-6420(03)00462-7] [Citation(s) in RCA: 250] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
PURPOSE To determine utilities (patient preferences) for dry eye disease. DESIGN Survey study. PARTICIPANTS Fifty-six patients with mild, moderate, or severe dry eye treated by ophthalmologists in the Eye Care Services department of Henry Ford Health Care System. TESTING Patients completed interactive software utility assessment questionnaires by the time trade-off (TTO) method. Utility scores were scaled such that a score of 1.0 = perfect health and 0 = death. Dry eye severity was independently classified using clinical parameters and physician/patient assessments. Global health status, visual functioning, and ocular symptoms were assessed by the Short Form-36 Health Survey, 25-Item National Eye Institute Visual Function Questionnaire (NEI VFQ-25), and Ocular Surface Disease Index survey instruments. MAIN OUTCOME MEASURES Utility scores for a range of dry eye severity states. These utilities were compared with utilities reported for other disease states. Correlations with the general and vision-related health status measures were conducted. RESULTS Fifty-six patients completed the utility assessments with acceptable reliability. Mean utilities for moderate (0.78) and severe dry eye (0.72) by TTO were similar to historical reports for moderate (0.75) and more severe (class III/IV) angina (0.71), respectively. Utility scores correlated with the NEI VFQ-25 composite score (rho = 0.32; P = 0.037) and with components of other health measures. CONCLUSIONS Utilities for the more severe forms of dry eye are in the range of conditions like class III/IV angina (0.71) that are widely recognized as lowering health utilities. Our results underscore how significantly dry eye impacts patients compared with other medical conditions.
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Arrieta MC, Madsen K, Doyle J, Meddings J. Reducing small intestinal permeability attenuates colitis in the IL10 gene-deficient mouse. Gut 2008; 58:41-8. [PMID: 18829978 PMCID: PMC2597688 DOI: 10.1136/gut.2008.150888] [Citation(s) in RCA: 235] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Defects in the small intestinal epithelial barrier have been associated with inflammatory bowel disease but their role in the causation of disease is still a matter of debate. In some models of disease increased permeability appears to be a very early event. The interleukin 10 (IL10) gene-deficient mouse spontaneously develops colitis after 12 weeks of age. These mice have been shown to have increased small intestinal permeability that appears early in life. Furthermore, the development of colitis is dependent upon luminal agents, as animals do not develop disease if raised under germ-free conditions. AIMS To determine if the elevated small bowel permeability can be prevented, and if by doing so colonic disease is prevented or attenuated. METHODS IL10 gene-deficient (IL10(-)/(-)) mice) were treated with AT-1001 (a zonulin peptide inhibitor), a small peptide previously demonstrated to reduce small intestinal permeability. Small intestinal permeability was measured, in vivo, weekly from 4 to 17 weeks of age. Colonic disease was assessed at 8 weeks in Ussing chambers, and at 17 weeks of age inflammatory cytokines and myeloperoxidase were measured in the colon. Colonic permeability and histology were also endpoints. RESULTS Treated animals showed a marked reduction in small intestinal permeability. Average area under the lactulose/mannitol time curve: 5.36 (SE 0.08) in controls vs 3.97 (SE 0.07) in the high-dose AT-1001 group, p<0.05. At 8 weeks of age there was a significant reduction of colonic mucosal permeability and increased electrical resistance. By 17 weeks of age, secretion of tumour necrosis factor alpha (TNFalpha) from a colonic explant was significantly lower in the treated group (25.33 (SE 4.30) pg/mg vs 106.93 (SE 17.51) pg/ml in controls, p<0.01). All other markers also demonstrated a clear reduction of colitis in the treated animals. Additional experiments were performed which demonstrated that AT-1001 was functionally active only in the small intestine. CONCLUSIONS This work suggests that increased intestinal permeability may be an important aetiological event in the development of colitis in IL10(-)/(-) mice.
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research-article |
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Abstract
Highly optimized tolerance (HOT) was recently introduced as a conceptual framework to study fundamental aspects of complexity. HOT is motivated primarily by systems from biology and engineering and emphasizes, (i) highly structured, nongeneric, self-dissimilar internal configurations, and (ii) robust yet fragile external behavior. HOT claims these are the most important features of complexity and not accidents of evolution or artifices of engineering design but are inevitably intertwined and mutually reinforcing. In the spirit of this collection, our paper contrasts HOT with alternative perspectives on complexity, drawing on real-world examples and also model systems, particularly those from self-organized criticality.
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Richardson PG, Riches ML, Kernan NA, Brochstein JA, Mineishi S, Termuhlen AM, Arai S, Grupp SA, Guinan EC, Martin PL, Steinbach G, Krishnan A, Nemecek ER, Giralt S, Rodriguez T, Duerst R, Doyle J, Antin JH, Smith A, Lehmann L, Champlin R, Gillio A, Bajwa R, D'Agostino RB, Massaro J, Warren D, Miloslavsky M, Hume RL, Iacobelli M, Nejadnik B, Hannah AL, Soiffer RJ. Phase 3 trial of defibrotide for the treatment of severe veno-occlusive disease and multi-organ failure. Blood 2016; 127:1656-65. [PMID: 26825712 PMCID: PMC4817309 DOI: 10.1182/blood-2015-10-676924] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/22/2016] [Indexed: 11/20/2022] Open
Abstract
Hepatic veno-occlusive disease (VOD), also called sinusoidal obstruction syndrome (SOS), is a potentially life-threatening complication of hematopoietic stem cell transplantation (HSCT). Untreated hepatic VOD/SOS with multi-organ failure (MOF) is associated with >80% mortality. Defibrotide has shown promising efficacy treating hepatic VOD/SOS with MOF in phase 2 studies. This phase 3 study investigated safety and efficacy of defibrotide in patients with established hepatic VOD/SOS and advanced MOF. Patients (n = 102) given defibrotide 25 mg/kg per day were compared with 32 historical controls identified out of 6867 medical charts of HSCT patients by blinded independent reviewers. Baseline characteristics between groups were well balanced. The primary endpoint was survival at day +100 post-HSCT; observed rates equaled 38.2% in the defibrotide group and 25% in the controls (23% estimated difference; 95.1% confidence interval [CI], 5.2-40.8;P= .0109, using a propensity-adjusted analysis). Observed day +100 complete response (CR) rates equaled 25.5% for defibrotide and 12.5% for controls (19% difference using similar methodology; 95.1% CI, 3.5-34.6;P= .0160). Defibrotide was generally well tolerated with manageable toxicity. Related adverse events (AEs) included hemorrhage or hypotension; incidence of common hemorrhagic AEs (including pulmonary alveolar [11.8% and 15.6%] and gastrointestinal bleeding [7.8% and 9.4%]) was similar between the defibrotide and control groups, respectively. Defibrotide was associated with significant improvement in day +100 survival and CR rate. The historical-control methodology offers a novel, meaningful approach for phase 3 evaluation of orphan diseases associated with high mortality. This trial was registered at www.clinicaltrials.gov as #.
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Clinical Trial, Phase III |
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Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J, Kitano H. Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2004; 7:355-72. [PMID: 14683609 DOI: 10.1089/153623103322637670] [Citation(s) in RCA: 196] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Researchers in quantitative systems biology make use of a large number of different software packages for modelling, analysis, visualization, and general data manipulation. In this paper, we describe the Systems Biology Workbench (SBW), a software framework that allows heterogeneous application components--written in diverse programming languages and running on different platforms--to communicate and use each others' capabilities via a fast binary encoded-message system. Our goal was to create a simple, high performance, opensource software infrastructure which is easy to implement and understand. SBW enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol. The interfaces to the system are encapsulated in client-side libraries that we provide for different programming languages. We describe in this paper the SBW architecture, a selection of current modules, including Jarnac, JDesigner, and SBWMeta-tool, and the close integration of SBW into BioSPICE, which enables both frameworks to share tools and compliment and strengthen each others capabilities.
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Research Support, U.S. Gov't, Non-P.H.S. |
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Massey GV, Zipursky A, Chang MN, Doyle JJ, Nasim S, Taub JW, Ravindranath Y, Dahl G, Weinstein HJ. A prospective study of the natural history of transient leukemia (TL) in neonates with Down syndrome (DS): Children's Oncology Group (COG) study POG-9481. Blood 2006; 107:4606-13. [PMID: 16469874 DOI: 10.1182/blood-2005-06-2448] [Citation(s) in RCA: 186] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A unique transient leukemia (TL) has been described in newborns with Down syndrome (DS; or trisomy 21 mosaics). This leukemia has a high incidence of spontaneous remission; however, early death and subsequent development of acute megakaryoblastic leukemia (AMKL) have been reported. We prospectively evaluated 48 infants with DS and TL to determine the natural history and biologic characteristics of this disease, identify the clinical characteristics associated with early death or subsequent leukemia, and assess the incidence of subsequent leukemia. Blast cells associated with TL in DS infants exhibited FAB M(7) morphology and phenotype. Most infants (74%) had trisomy 21 (or mosaicism) as the only cytogenetic abnormality in the blast cells. Most children were able to spontaneously clear peripheral blasts (89%), normalize blood counts (74%), and maintain a complete remission (64%). Early death occurred in 17% of infants and was significantly correlated with higher white blood cell count at diagnosis (P < .001), increased bilirubin and liver enzymes (P < .005), and a failure to normalize the blood count (P = .001). Recurrence of leukemia occurred in 19% of infants at a mean of 20 months. Development of leukemia was significantly correlated with karyotypic abnormalities in addition to trisomy 21 (P = .037). Ongoing collaborative clinical studies are needed to determine the optimal role of chemotherapy for infants at risk for increased mortality or disease recurrence and to further the knowledge of the unique biologic features of this TL.
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MESH Headings
- Bilirubin/blood
- Blast Crisis/blood
- Blast Crisis/mortality
- Blast Crisis/pathology
- Chromosomes, Human, Pair 21
- Down Syndrome/blood
- Down Syndrome/complications
- Down Syndrome/mortality
- Down Syndrome/pathology
- Enzymes/blood
- Female
- Follow-Up Studies
- Humans
- Infant
- Infant, Newborn
- Leukemia, Megakaryoblastic, Acute/blood
- Leukemia, Megakaryoblastic, Acute/complications
- Leukemia, Megakaryoblastic, Acute/mortality
- Leukemia, Megakaryoblastic, Acute/pathology
- Leukocyte Count
- Male
- Mosaicism
- Prospective Studies
- Recurrence
- Trisomy
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Multicenter Study |
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Morohashi M, Winn AE, Borisuk MT, Bolouri H, Doyle J, Kitano H. Robustness as a measure of plausibility in models of biochemical networks. J Theor Biol 2002; 216:19-30. [PMID: 12076125 DOI: 10.1006/jtbi.2002.2537] [Citation(s) in RCA: 178] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Theory, experiment, and observation suggest that biochemical networks which are conserved across species are robust to variations in concentrations and kinetic parameters. Here, we exploit this expectation to propose an approach to model building and selection. We represent a model as a mapping from parameter space to behavior space, and utilize bifurcation analysis to study the robustness of each region of steady-state behavior to parameter variations. The hypothesis that potential errors in models will result in parameter sensitivities is tested by analysis of two models of the biochemical oscillator underlying the Xenopus cell cycle. Our analysis successfully identifies known weaknesses in the older model and suggests areas for further investigation in the more recent, more plausible model. It also correctly highlights why the more recent model is more plausible.
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Abstract
The incidence of leukemia is higher in children with Down syndrome (DS) than in normals. In approximately 50% of cases the type of leukemia is acute megakaryoblastic leukemia (AMKL) and it occurs during the first 4 years of life. The leukemic cell also has features of erythroid progenitors and therefore appears to be a precursor cell with biphenotypic properties. In addition, newborns with DS frequently develop transient leukemia (TL), which is characterized by the presence of megakaryoblasts in the blood which disappear during the first 1-3 months of life. The incidence of this disorder is unknown although preliminary studies suggest that megakaryoblasts may be found frequently in the blood of DS newborns. TL does not occur in normal newborn infants. Although TL disappears spontaneously, many of these children will develop AMKL at 1-4 years of age. Recent surveys suggest that 20-30% of newborns with TL will develop AMKL. Preliminary evidence suggests that TL is a clonal proliferation, can be fatal, and may occur in a specific subgroup of DS children. The observations in this report are drawn from our own experience, reports in the literature, and data accumulated in the Canadian Down Syndrome Leukemia Registry.
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Review |
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Manos PS, Doyle JJ, Nixon KC. Phylogeny, biogeography, and processes of molecular differentiation in Quercus subgenus Quercus (Fagaceae). Mol Phylogenet Evol 1999; 12:333-49. [PMID: 10413627 DOI: 10.1006/mpev.1999.0614] [Citation(s) in RCA: 164] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Quercus is one of the most abundant and economically important genera of woody plants in the Northern Hemisphere. To infer phylogenetic relationships within Quercus subgenus Quercus, chloroplast DNA (cpDNA) restriction sites and nucleotide sequences of the internal transcribed spacers (ITS) and the 5.8S coding region of the nuclear ribosomal DNA repeat were obtained for 44 individuals, including 25 species, intraspecific samples, and three outgroups. Separate parsimony analyses of each data set showed that individual gene trees were congruent and often complementary in supporting clades that generally corresponded to previously recognized taxonomic groups. Only one instance of strongly supported gene tree incongruence was detected and this anomalous pattern was explained best by ancient introgression of cpDNA across sectional boundaries. Simultaneous parsimony analysis of the pruned data sets supported the recognition of the strictly Eurasian section Cerris and resolved a novel hypothesis for the major infrageneric groups (Cerris- (Lobatae- (Protobalanus + Quercus sensu stricto))). The biogeographic hypothesis that all major oak lineages evolved locally at middle latitudes within the general distribution of their fossil ancestors was fully supported. This set of relationships also suggested a New World origin for the widespread white oaks of the Northern Hemisphere (section Quercus s. s.). For both data sets, inter- and intraspecific sampling within section Protobalanus showed little correspondence to morphological species. Greater cladistic structure among the samples was obtained by cpDNA restriction sites and two well-delimited plastomes types comprising a total of 15 distinct haplotypes were resolved. Haplotypes of 2 of the peripheral species in this species complex occupy terminal portions of one of the plastome clades, suggesting a more recent origin relative to those of more widespread species. The phylogeography of the two divergent plastome types suggested a north-south pattern, consistent with a Late Tertiary disjunction in the ancestral distribution of section Protobalanus.
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Maoz BM, Herland A, Henry OYF, Leineweber WD, Yadid M, Doyle J, Mannix R, Kujala VJ, FitzGerald EA, Parker KK, Ingber DE. Organs-on-Chips with combined multi-electrode array and transepithelial electrical resistance measurement capabilities. LAB ON A CHIP 2017; 17:2294-2302. [PMID: 28608907 DOI: 10.1039/c7lc00412e] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Here we demonstrate that microfluidic cell culture devices, known as Organs-on-a-Chips can be fabricated with multifunctional, real-time, sensing capabilities by integrating both multi-electrode arrays (MEAs) and electrodes for transepithelial electrical resistance (TEER) measurements into the chips during their fabrication. To prove proof-of-concept, simultaneous measurements of cellular electrical activity and tissue barrier function were carried out in a dual channel, endothelialized, heart-on-a-chip device containing human cardiomyocytes and a channel-separating porous membrane covered with a primary human endothelial cell monolayer. These studies confirmed that the TEER-MEA chip can be used to simultaneously detect dynamic alterations of vascular permeability and cardiac function in the same chip when challenged with the inflammatory stimulus tumor necrosis factor alpha (TNF-α) or the cardiac targeting drug isoproterenol. Thus, this Organ Chip with integrated sensing capability may prove useful for real-time assessment of biological functions, as well as response to therapeutics.
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Jarrett RB, Kraft D, Doyle J, Foster BM, Eaves GG, Silver PC. Preventing recurrent depression using cognitive therapy with and without a continuation phase: a randomized clinical trial. ARCHIVES OF GENERAL PSYCHIATRY 2001; 58:381-8. [PMID: 11296099 PMCID: PMC1307495 DOI: 10.1001/archpsyc.58.4.381] [Citation(s) in RCA: 161] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
BACKGROUND Cognitive therapy (CT) may reduce depressive relapse and recurrence when patients learn and use the associated skills. Reported relapse and recurrence rates after CT discontinuation vary widely. The factors that determine when CT is preventive remain unidentified. We developed continuation-phase CT (C-CT) to teach responders skills to prevent relapse. This is the first randomized trial comparing CT with and without a continuation phase in responders to CT who were vulnerable, given their history of recurrent unipolar depression. METHODS Patients aged 18 to 65 years (n = 156) with recurrent DSM-IV major depressive disorder (MDD) entered 20 sessions of acute-phase CT (A-CT). Unmedicated responders (ie, no MDD and 17-item Hamilton Rating Scale for Depression score < or =9; n = 84) were randomized to either 8 months (10 sessions) of C-CT or control (evaluation without CT). Follow-up lasted an additional 16 months. A clinician blind to assignment evaluated relapse and recurrence (ie, DSM-IV MDD). RESULTS Over an 8-month period, C-CT significantly reduced relapse estimates more than control (10% vs 31%). Over 24 months, including the CT-free follow-up, age of onset and quality of remission during the late phase of A-CT each interacted with condition assignment to influence durability of effects. In patients with early-onset MDD, C-CT significantly reduced relapse and recurrence estimates (16% vs 67% in control). When patients had unstable remission during late A-CT, C-CT significantly reduced relapse and recurrence estimates to 37% (vs 62% in control). CONCLUSIONS Findings suggest that 8 months of C-CT significantly reduces relapse and recurrence in the highest-risk patients with recurrent MDD. Risk factors influenced the necessity for C-CT.
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Traverso CE, Walt JG, Kelly SP, Hommer AH, Bron AM, Denis P, Nordmann JP, Renard JP, Bayer A, Grehn F, Pfeiffer N, Cedrone C, Gandolfi S, Orzalesi N, Nucci C, Rossetti L, Azuara-Blanco A, Bagnis A, Hitchings R, Salmon JF, Bricola G, Buchholz PM, Kotak SV, Katz LM, Siegartel LR, Doyle JJ. Direct costs of glaucoma and severity of the disease: a multinational long term study of resource utilisation in Europe. Br J Ophthalmol 2005; 89:1245-9. [PMID: 16170109 PMCID: PMC1772870 DOI: 10.1136/bjo.2005.067355] [Citation(s) in RCA: 155] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Resource utilisation and direct costs associated with glaucoma progression in Europe are unknown. As population progressively ages, the economic impact of the disease will increase. METHODS From a total of 1655 consecutive cases, the records of 194 patients were selected and stratified by disease severity. Record selection was based on diagnoses of primary open angle glaucoma, glaucoma suspect, ocular hypertension, or normal tension glaucoma; 5 years minimum follow up were required. Glaucoma severity was assessed using a six stage glaucoma staging system based on static threshold visual field parameters. Resource utilisation data were abstracted from the charts and unit costs were applied to estimate direct costs to the payer. Resource utilisation and estimated direct cost of treatment, per person year, were calculated. RESULTS A statistically significant increasing linear trend (p = 0.018) in direct cost as disease severity worsened was demonstrated. The direct cost of treatment increased by an estimated 86 for each incremental step ranging from 455 euro per person year for stage 0 to 969 euro per person year for stage 4 disease. Medication costs ranged from 42% to 56% of total direct cost for all stages of disease. CONCLUSIONS These results demonstrate for the first time in Europe that resource utilisation and direct medical costs of glaucoma management increase with worsening disease severity. Based on these findings, managing glaucoma and effectively delaying disease progression would be expected to significantly reduce the economic burden of this disease. These data are relevant to general practitioners and healthcare administrators who have a direct influence on the distribution of resources.
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Lee PP, Walt JG, Doyle JJ, Kotak SV, Evans SJ, Budenz DL, Chen PP, Coleman AL, Feldman RM, Jampel HD, Katz LJ, Mills RP, Myers JS, Noecker RJ, Piltz-Seymour JR, Ritch RR, Schacknow PN, Serle JB, Trick GL. A Multicenter, Retrospective Pilot Study of Resource Use and Costs Associated With Severity of Disease in Glaucoma. ACTA ACUST UNITED AC 2006; 124:12-9. [PMID: 16401779 DOI: 10.1001/archopht.124.1.12] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
OBJECTIVE To examine resource consumption and the direct costs of treating glaucoma at different disease severity levels. DESIGN Observational, retrospective cohort study based on medical record review. PARTICIPANTS One hundred fifty-one records of patients with primary open-angle or normal-tension glaucoma, glaucoma suspect, or ocular hypertension (age > or =18 years) were randomly selected from 12 sites in the United States and stratified according to severity based on International Classification of Diseases, Ninth Revision, Clinical Modification codes. Patients had to have been followed up for a minimum of 5 years. Patients with concomitant ocular disease likely to affect glaucoma treatment-related resource consumption were excluded. METHODS Glaucoma severity was assessed and assigned using a 6-stage glaucoma staging system, modified from the Bascom Palmer (Hodapp-Anderson-Parrish) system. Clinical and resource use data were collected from the medical record review. Resource consumption for low-vision care and vision rehabilitation was estimated for patients with end-stage disease based on specialist surveys. For each stage of disease, publicly available economic data were then applied to assign resource valuation and estimate patient-level direct costs from the payer perspective. MAIN OUTCOME MEASURES Average annual resource use and estimated total annual direct cost of treatment were calculated at the patient level and stratified by stage of disease. Direct costs by specific resource types, including ophthalmology visits, glaucoma surgeries, medications, visual field examinations, and other glaucoma services, were also assessed. RESULTS Direct ophthalmology-related resource use, including ophthalmology visits, glaucoma surgeries, and medication use, increased as disease severity worsened. Average direct cost of treatment ranged from $623 per patient per year for glaucoma suspects or patients with early-stage disease to $2511 per patient per year for patients with end-stage disease. Medication costs composed the largest proportion of total direct cost for all stages of disease (range, 24%-61%). CONCLUSIONS The study results suggest that resource use and direct cost of glaucoma management increase with worsening disease severity. Based on these findings, a glaucoma treatment that delays the progression of disease could have the potential to significantly reduce the health economic burden of this chronic disease over many years.
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Klaassen RJ, Goodman TR, Pham B, Doyle JJ. "Low-risk" prediction rule for pediatric oncology patients presenting with fever and neutropenia. J Clin Oncol 2000; 18:1012-9. [PMID: 10694551 DOI: 10.1200/jco.2000.18.5.1012] [Citation(s) in RCA: 153] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
PURPOSE To prospectively derive and validate a clinical prediction rule to allow a more tailored approach to the management of pediatric oncology outpatients presenting with fever and neutropenia. PATIENTS AND METHODS The clinical prediction rule was derived over a 1-year period and then validated over the following 8 months in a new set of fever and neutropenia episodes. Patients were excluded if they presented with comorbidity or an abnormal chest x-ray (CXR). RESULTS Significant bacterial infection (SBI; defined as any blood or urine culture positive for bacteria, interstitial or lobar consolidation on CXR, or unexpected death from infection) was documented in 43 of the 227 episodes. Multivariate analysis found four significant factors: bone marrow disease, general appearance unwell on initial examination, monocyte count less than 0.1 x 10(9)/L, and peak oral or oral equivalent temperature greater than 39 degrees C. Only the monocyte count contributed to determining a low-risk group, excluding SBI with 84% sensitivity (95% confidence interval [CI], 61% to 100%), 42% specificity (95% CI, 38% to 46%), and a negative predictive value of 92% (95% CI, 76% to 100%). If the monocyte count was >/= 0.1 x 10(9)/L at the time of presentation (low risk), the incidences of SBI and bacteremia were 8% and 5%, respectively, versus 25% and 17% in the high-risk group. When validated in a new population of 136 episodes of fever and neutropenia, the incidences of SBI and bacteremia in the low-risk group were 12% and 5%, respectively, and 25% and 19% in the high-risk group. CONCLUSION Pediatric oncology outpatients with fever and neutropenia who present with an initial monocyte count of >/= 0.1 x 10(9)/L and do not have comorbidity or an abnormal CXR at the time of presentation are at lower risk for SBI and can be considered for less aggressive initial therapy.
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