Genomes and Genes
Summary: Principles, models, and laws that apply to complex interrelationships and interdependencies of sets of linked components which form a functioning whole, a system. Any system may be composed of components which are systems in their own right (sub-systems), such as several organs within an individual organism.
- Hramov A, Koronovskii A. An approach to chaotic synchronization. Chaos. 2004;14:603-10 pubmed..quot; The quantitative measure of chaotic oscillator synchronous behavior has been proposed. This approach has been applied for the coupled Rössler systems and two coupled Chua's circuits. ..
- Milo R, Itzkovitz S, Kashtan N, Levitt R, Shen Orr S, Ayzenshtat I, et al. Superfamilies of evolved and designed networks. Science. 2004;303:1538-42 pubmed..Additional superfamilies include power grids, protein-structure networks and geometric networks, World Wide Web links and social networks, and word-adjacency networks from different languages. ..
- Csete M, Doyle J. Reverse engineering of biological complexity. Science. 2002;295:1664-9 pubmed..This review describes insights from engineering theory and practice that can shed some light on biological complexity. ..
- Sauro H, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J, et al. Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. OMICS. 2003;7:355-72 pubmed
- Buchman T. The community of the self. Nature. 2002;420:246-51 pubmed..Today's physicians are already testing to 'see if the network is right'; tomorrow's physicians may well use therapies to 'make the network right'. ..
- Ingalls B, Sauro H. Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories. J Theor Biol. 2003;222:23-36 pubmed..The results are compared to previous treatments. The analysis is accompanied by a discussion of the computation of the sensitivity coefficients and an application to a model of phototransduction. ..
- McManus M, Long M, Cooper A, Litvak E. Queuing theory accurately models the need for critical care resources. Anesthesiology. 2004;100:1271-6 pubmed..Although the nature of arrivals for intensive care deserves further study, when demand is random, queuing theory provides an accurate means of determining the appropriate supply of beds. ..
- Wolkenhauer O. Systems biology: the reincarnation of systems theory applied in biology?. Brief Bioinform. 2001;2:258-70 pubmed..research institutes and research groups concerned with systems biology have appeared in recent years and systems theory, the study of organisation and behaviour per se, is indeed a natural conceptual framework for such a task...
- Bell I, Baldwin C, Schwartz G. Translating a nonlinear systems theory model for homeopathy into empirical tests. Altern Ther Health Med. 2002;8:58-66 pubmedVarious investigators have proposed that nonlinear systems theory, notably chaos and complexity theory, provides a heuristically useful modelfor conceptualizing the way in which complementary and alternative medicine therapies, which ..
- McDaniel R, Lanham H, Anderson R. Implications of complex adaptive systems theory for the design of research on health care organizations. Health Care Manage Rev. 2009;34:191-9 pubmed publisher..Practitioners can use the strategies proposed in this article to stimulate discussion with researchers seeking to conduct research in their HCO. ..
- Braithwaite J, Runciman W, Merry A. Towards safer, better healthcare: harnessing the natural properties of complex sociotechnical systems. Qual Saf Health Care. 2009;18:37-41 pubmed publisher..Being invited, empowered and nurtured rather than directed, micro-managed and controlled through a hierarchy is preferable. ..
- Guzman J, Yassi A, Baril R, Loisel P. Decreasing occupational injury and disability: the convergence of systems theory, knowledge transfer and action research. Work. 2008;30:229-39 pubmed..In trying to achieve coordinated action occupational health practitioners can learn valuable lessons from systems theory, knowledge transfer and action research...
- Anaf S, Drummond C, Sheppard L. Combining case study research and systems theory as a heuristic model. Qual Health Res. 2007;17:1309-15 pubmedThe combined use of case study and systems theory is not often seen in the literature...
- Ehrenberg M, Elf J, Aurell E, Sandberg R, Tegner J. Systems biology is taking off. Genome Res. 2003;13:2377-80 pubmed
- Clarke D, Betterton M, Liu X. Systems theory of Smad signalling. Syst Biol (Stevenage). 2006;153:412-24 pubmed..We therefore conclude that an imbalance in the rates of R-Smad phosphorylation and dephosphorylation is likely an important mechanism of Smad nuclear accumulation during TGFbeta signalling. ..
- Verhoef M, Vanderheyden L, Fønnebø V. A whole systems research approach to cancer care: why do we need it and how do we get started?. Integr Cancer Ther. 2006;5:287-92 pubmed..Only when modern healthseeking systems of treatment behaviors are thoroughly understood should fine-tuning of hypothesis-testing research methods be continued. ..
- Sterman J. Learning from evidence in a complex world. Am J Public Health. 2006;96:505-14 pubmed..Here I show how systems thinking and simulation modeling can help expand the boundaries of our mental models, enhance our ability to generate and learn from evidence, and catalyze effective change in public health and beyond. ..
- Shiraishi F, Hatoh Y, Irie T. An efficient method for calculation of dynamic logarithmic gains in biochemical systems theory. J Theor Biol. 2005;234:79-85 pubmedBiochemical systems theory (BST) characterizes a given biochemical system based on the logarithmic gains, rate-constant sensitivities and kinetic-order sensitivities defined at a steady state...
- Khushf G. Systems theory and the ethics of human enhancement: a framework for NBIC convergence. Ann N Y Acad Sci. 2004;1013:124-49 pubmed..I close by extending Engel's model so that it addresses all areas of enhancement envisioned as a part of NBIC convergence, and then identify areas where future research is still needed. ..
- Tamborrino M, Ditlevsen S, Lansky P. Parameter inference from hitting times for perturbed Brownian motion. Lifetime Data Anal. 2015;21:331-52 pubmed publisher..e. a Brownian motion, but with different parameters. Also covariates and handling of censored observations are incorporated into the statistical model, and the method is illustrated on lung cancer data. ..
- Cappella E, Kim H, Neal J, Jackson D. Classroom peer relationships and behavioral engagement in elementary school: the role of social network equity. Am J Community Psychol. 2013;52:367-79 pubmed publisher..Findings illuminate the need to consider classroom peer contexts in future research and intervention focused on the behavioral engagement of students in urban elementary schools. ..
- Hughes R. Improving patient safety within the context of everyday chaos and complexity. Creat Nurs. 2013;19:42-4 pubmed..Effectively improving patient safety requires embracing the complex health care environment, care processes, and patients. ..
- Bassett D, Porter M, Wymbs N, Grafton S, Carlson J, Mucha P. Robust detection of dynamic community structure in networks. Chaos. 2013;23:013142 pubmed publisher..To illustrate our results, we employ ensembles of time-dependent networks extracted from both nonlinear oscillators and empirical neuroscience data. ..
- Stovin V, Guymer I, Chappell M, Hattersley J. The use of deconvolution techniques to identify the fundamental mixing characteristics of urban drainage structures. Water Sci Technol. 2010;61:2075-81 pubmed publisher..This paper shows how a deconvolution approach derived from systems theory may be applied to identify the CRTDs associated with urban drainage structures.
- Curtis J. Improving osteoporosis care through multimodal interventions: insights from the University of Alabama at Birmingham Center for Education and Research on Therapeutics. Osteoporos Int. 2011;22 Suppl 3:445-50 pubmed publisher..This article describes evidence implementation as applied to osteoporosis care, drawing from several published or ongoing studies to illustrate challenges and potential solutions in improving the quality of osteoporosis care. ..
- Wolpaw J. Brain-computer interface research comes of age: traditional assumptions meet emerging realities. J Mot Behav. 2010;42:351-3 pubmed publisher..Thus, the central task of BCI research is to determine which brain signals users can best control, to maximize that control, and to translate it accurately and reliably into actions that accomplish the users' intentions. ..
- Katerndahl D, Wood R, Jaen C. A method for estimating relative complexity of ambulatory care. Ann Fam Med. 2010;8:341-7 pubmed publisher..21 +/- 0.0027 SE). This method estimates complexity based on the amount of care provided weighted by its diversity and variability. Such estimates could have broad use for interphysician comparisons as well as longitudinal applications. ..
- ..Much of this research appears as a natural extension of the cross-disciplinary field of systems theory. This is the 14th in a series of articles applying complex systems science to the traditional management ..
- Borland R, Young D, Coghill K, Zhang J. The tobacco use management system: analyzing tobacco control from a systems perspective. Am J Public Health. 2010;100:1229-36 pubmed publisher..We argue that this goal would be more readily achieved if the regulatory subsystem had dynamic power to regulate tobacco products and the tobacco industry as well as a responsive process for resourcing tobacco use control activities. ..
- Young D, Borland R, Coghill K. An actor-network theory analysis of policy innovation for smoke-free places: understanding change in complex systems. Am J Public Health. 2010;100:1208-17 pubmed publisher..Through our analysis, we identified approaches to help overcome some systemic barriers to the solution of the tobacco problem and comment on other complex transnational problems. ..
- Eberl G. A new vision of immunity: homeostasis of the superorganism. Mucosal Immunol. 2010;3:450-60 pubmed publisher..Together, we compose a superorganism that is capable of optimal living. In that context, the immune system is not a killer, but rather a force that shapes homeostasis within the superorganism. ..
- Jemmott J, Jemmott L, Fong G. Efficacy of a theory-based abstinence-only intervention over 24 months: a randomized controlled trial with young adolescents. Arch Pediatr Adolesc Med. 2010;164:152-9 pubmed publisher..No other differences between interventions and controls were significant. Theory-based abstinence-only interventions may have an important role in preventing adolescent sexual involvement. clinicaltrials.gov Identifier: NCT00640653. ..
- Wilson J, Ryan B, Schock A, Ferreira P, Smith S, Pitsopoulos J. Understanding safety and production risks in rail engineering planning and protection. Ergonomics. 2009;52:774-90 pubmed publisher..The paper addresses the relevant issues and does so in an under-published domain - rail systems engineering work. ..
- ..The decade-old discovery of scale-free networks was one of those events that had helped catalyze the emergence of network science, a new research field with its distinct set of challenges and accomplishments. ..
- Wiler J, Bolandifar E, Griffey R, Poirier R, Olsen T. An emergency department patient flow model based on queueing theory principles. Acad Emerg Med. 2013;20:939-46 pubmed publisher..More studies are needed to validate this model across other institutions. ..
- Bickel P, Chen A. A nonparametric view of network models and Newman-Girvan and other modularities. Proc Natl Acad Sci U S A. 2009;106:21068-73 pubmed publisher..Our analysis is asymptotic but we show by simulation and application to real examples that the theory is a reasonable guide to practice. ..
- Ramson K, Dudjak L, August Brady M, Stoltzfus J, Thomas P. Implementing an acuity-adaptable care model in a rural hospital setting. J Nurs Adm. 2013;43:455-60 pubmed publisher..This study also found a decrease in WHPPD, with a corresponding salary expense reduction reported. Acuity-adaptable units may be a viable strategy for rural facilities. ..
- Zhang C, Zhang H. Analysis of aerobic granular sludge formation based on grey system theory. J Environ Sci (China). 2013;25:710-6 pubmed..SVI transformation and rapid set-up demanded different optimal H/D ratio scopes (10-20 and 16-20). Meanwhile, different functions could be obtained through adjusting certain factors' scope. ..
- Reynolds J. Hospital charitable lotteries: taking a gamble on systems thinking. J Eval Clin Pract. 2013;19:1090-4 pubmed publisher..Findings from this article can inform the development of action strategies, including policy development at multiple levels. ..
- Martínez Romero M, Vázquez Naya J, Pereira J, Pereira M, Pazos A, Baños G. The iOSC3 system: using ontologies and SWRL rules for intelligent supervision and care of patients with acute cardiac disorders. Comput Math Methods Med. 2013;2013:650671 pubmed publisher..iOSC3 has been developed in collaboration with experts from the Cardiac Intensive Care Unit (CICU) of the Meixoeiro Hospital, one of the most significant hospitals in the northwest region of Spain. ..
- Sturmberg J, Martin C. Leadership and transitions: maintaining the science in complexity and complex systems. J Eval Clin Pract. 2012;18:186-9 pubmed publisher..The authors writing in the Forum on Complexity in Medicine and Healthcare since its inception are leaders in an intellectual transition to complex systems thinking in medicine and health. ..
- Barrett B. Dynamical systems and Jung, with a note on language. Am Psychol. 2011;66:157-8 pubmed publisher..Bui-Wrzosinska (see record 2010-08987-003). Vallacher et al presented an intriguing description of dynamical systems theory as applied to the understanding of intractable conflicts ranging from the intrapsychic to the international...
- Ronsse R, Sternad D. Bouncing between model and data: stability, passivity, and optimality in hybrid dynamics. J Mot Behav. 2010;42:389-99 pubmed publisher..The authors proceed to present a new model that accounts not only for fine-grained behavior but also reconciles passive and active control approaches with new predictions that will be put to test in the next set of experiments. ..
- Yu T. An exploratory data analysis method to reveal modular latent structures in high-throughput data. BMC Bioinformatics. 2010;11:440 pubmed publisher..In addition, the method also performed very well on data generated from sparse global latent factor models. The R code is available at http://userwww.service.emory.edu/~tyu8/MLSA/. ..
- Weberg D. Complexity leadership: a healthcare imperative. Nurs Forum. 2012;47:268-77 pubmed publisher..Compared to transactional and transformational leadership concepts, complexity leadership practices hold promise to improve cost and quality in health care. ..
- Ghorashi S, Enns J, Klein R, Di Lollo V. Spatial selection and target identification are separable processes in visual search. J Vis. 2010;10:7.1-12 pubmed publisher..We interpret the separability of spatial selection and identification as reflecting the independent operation of dorsal and ventral visual pathways, respectively, at least at the early stages of processing. ..
- Friedman R. Real change in the real world: an achievable goal. Adm Policy Ment Health. 2010;37:154-9 pubmed publisher..Such an approach would have implications for framing of the issue, for the strategies that are taken to try to achieve change, and for research/evaluation methods for studying complex, dynamic, nonlinear systems. ..
- Fleming C, Cummings N. Accuracy of perturbative master equations. Phys Rev E Stat Nonlin Soft Matter Phys. 2011;83:031117 pubmed..This result has a wide-ranging impact on the validity of coupling (or friction) sensitive results derived from second-order convolutionless, Nakajima-Zwanzig, Redfield, and Born-Markov master equations. ..
- Glisson C, Schoenwald S, HEMMELGARN A, Green P, Dukes D, Armstrong K, et al. Randomized trial of MST and ARC in a two-level evidence-based treatment implementation strategy. J Consult Clin Psychol. 2010;78:537-50 pubmed publisher..More research is needed to understand how such strategies can be used effectively in a variety of organizational contexts and with other types of evidence-based treatments. ..
- Whiteoak J, Mohamed S. Employee engagement, boredom and frontline construction workers feeling safe in their workplace. Accid Anal Prev. 2016;93:291-298 pubmed publisher..The paper explains that relatively small improvements in worker perceptions of safety can bring about significant improvements in employee engagement and productivity. ..