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Sample records for optimal clinical pathway

  1. Optimizing a magnetic resonance care pathway: A strategy for radiography managers

    International Nuclear Information System (INIS)

    Castillo, J.; Caruana, C.J.; Morgan, P.S.; Westbrook, C.

    2015-01-01

    Purpose: This study reports the optimization of a local MR care pathway. A search of the literature did not result in any studies regarding the optimization of MRI care pathways through a formal research process. Discussions with international MR radiographers indicated that such development is often carried out using informal methods that are highly dependent on local conditions, that are rarely reported in the public domain and the validities of which are therefore not open to scrutiny; in addition, care pathways need to be specific to local healthcare needs and culture. In this study, the authors propose a formal documented methodology for developing a local MRI care pathway based on the well-established nominal group technique. Methods and materials: A nominal group technique was conducted amongst a multi-professional panel. Results: 14 participants accepted the invitation to participate: an executive from the principal public general hospital, a manager from the national Ministry for Health, a service development manager from the allied healthcare professional sector, 2 senior physiotherapists, 3 nursing officers, 3 MRI radiographers, 2 medical physicists, 1 radiologist. Ten optimization related issues were identified and ranked in order of decreasing importance. Highest ranking scores were assigned to patient safety, education of referrers and use of quality criteria. The NGT method also brought forward novel themes in particular the need for a radiographer's technical report and the need for referrers to indicate pain levels of patients. Conclusion: The design of an MR care pathway was successfully optimized using a collaborative multi-stakeholder approach. - Highlights: • We optimized an MRI clinical pathway using a nominal group technique. • The NGT brought forward novel themes such as the introduction of radiographer technical report. • The MRI clinical pathway will help management to establish knowledge, skills and competences.

  2. Modelling and performance analysis of clinical pathways using the stochastic process algebra PEPA.

    Science.gov (United States)

    Yang, Xian; Han, Rui; Guo, Yike; Bradley, Jeremy; Cox, Benita; Dickinson, Robert; Kitney, Richard

    2012-01-01

    Hospitals nowadays have to serve numerous patients with limited medical staff and equipment while maintaining healthcare quality. Clinical pathway informatics is regarded as an efficient way to solve a series of hospital challenges. To date, conventional research lacks a mathematical model to describe clinical pathways. Existing vague descriptions cannot fully capture the complexities accurately in clinical pathways and hinders the effective management and further optimization of clinical pathways. Given this motivation, this paper presents a clinical pathway management platform, the Imperial Clinical Pathway Analyzer (ICPA). By extending the stochastic model performance evaluation process algebra (PEPA), ICPA introduces a clinical-pathway-specific model: clinical pathway PEPA (CPP). ICPA can simulate stochastic behaviours of a clinical pathway by extracting information from public clinical databases and other related documents using CPP. Thus, the performance of this clinical pathway, including its throughput, resource utilisation and passage time can be quantitatively analysed. A typical clinical pathway on stroke extracted from a UK hospital is used to illustrate the effectiveness of ICPA. Three application scenarios are tested using ICPA: 1) redundant resources are identified and removed, thus the number of patients being served is maintained with less cost; 2) the patient passage time is estimated, providing the likelihood that patients can leave hospital within a specific period; 3) the maximum number of input patients are found, helping hospitals to decide whether they can serve more patients with the existing resource allocation. ICPA is an effective platform for clinical pathway management: 1) ICPA can describe a variety of components (state, activity, resource and constraints) in a clinical pathway, thus facilitating the proper understanding of complexities involved in it; 2) ICPA supports the performance analysis of clinical pathway, thereby assisting

  3. Pathway Design, Engineering, and Optimization.

    Science.gov (United States)

    Garcia-Ruiz, Eva; HamediRad, Mohammad; Zhao, Huimin

    The microbial metabolic versatility found in nature has inspired scientists to create microorganisms capable of producing value-added compounds. Many endeavors have been made to transfer and/or combine pathways, existing or even engineered enzymes with new function to tractable microorganisms to generate new metabolic routes for drug, biofuel, and specialty chemical production. However, the success of these pathways can be impeded by different complications from an inherent failure of the pathway to cell perturbations. Pursuing ways to overcome these shortcomings, a wide variety of strategies have been developed. This chapter will review the computational algorithms and experimental tools used to design efficient metabolic routes, and construct and optimize biochemical pathways to produce chemicals of high interest.

  4. An Automated Pipeline for Engineering Many-Enzyme Pathways: Computational Sequence Design, Pathway Expression-Flux Mapping, and Scalable Pathway Optimization.

    Science.gov (United States)

    Halper, Sean M; Cetnar, Daniel P; Salis, Howard M

    2018-01-01

    Engineering many-enzyme metabolic pathways suffers from the design curse of dimensionality. There are an astronomical number of synonymous DNA sequence choices, though relatively few will express an evolutionary robust, maximally productive pathway without metabolic bottlenecks. To solve this challenge, we have developed an integrated, automated computational-experimental pipeline that identifies a pathway's optimal DNA sequence without high-throughput screening or many cycles of design-build-test. The first step applies our Operon Calculator algorithm to design a host-specific evolutionary robust bacterial operon sequence with maximally tunable enzyme expression levels. The second step applies our RBS Library Calculator algorithm to systematically vary enzyme expression levels with the smallest-sized library. After characterizing a small number of constructed pathway variants, measurements are supplied to our Pathway Map Calculator algorithm, which then parameterizes a kinetic metabolic model that ultimately predicts the pathway's optimal enzyme expression levels and DNA sequences. Altogether, our algorithms provide the ability to efficiently map the pathway's sequence-expression-activity space and predict DNA sequences with desired metabolic fluxes. Here, we provide a step-by-step guide to applying the Pathway Optimization Pipeline on a desired multi-enzyme pathway in a bacterial host.

  5. An optimization model for metabolic pathways.

    Science.gov (United States)

    Planes, F J; Beasley, J E

    2009-10-15

    Different mathematical methods have emerged in the post-genomic era to determine metabolic pathways. These methods can be divided into stoichiometric methods and path finding methods. In this paper we detail a novel optimization model, based upon integer linear programming, to determine metabolic pathways. Our model links reaction stoichiometry with path finding in a single approach. We test the ability of our model to determine 40 annotated Escherichia coli metabolic pathways. We show that our model is able to determine 36 of these 40 pathways in a computationally effective manner.

  6. Wound care clinical pathway: a conceptual model.

    Science.gov (United States)

    Barr, J E; Cuzzell, J

    1996-08-01

    A clinical pathway is a written sequence of clinical processes or events that guides a patient with a defined problem toward an expected outcome. Clinical pathways are tools to assist with the cost-effective management of clinical outcomes related to specific problems or disease processes. The primary obstacles to developing clinical pathways for wound care are the chronic natures of some wounds and the many variables that can delay healing. The pathway introduced in this article was modeled upon the three phases of tissue repair: inflammatory, proliferative, and maturation. This physiology-based model allows clinicians to identify and monitor outcomes based on observable and measurable clinical parameters. The pathway design, which also includes educational and behavioral outcomes, allows the clinician to individualize the expected timeframe for outcome achievement based on individual patient criteria and expert judgement. Integral to the pathway are the "4P's" which help standardize the clinical processes by wound type: Protocols, Policies, Procedures, and Patient education tools. Four categories into which variances are categorized based on the cause of the deviation from the norm are patient, process/system, practitioner, and planning/discharge. Additional research is warranted to support the value of this clinical pathway in the clinical arena.

  7. Experimental application of Business Process Management technology to manage clinical pathways: a pediatric kidney transplantation follow up case.

    Science.gov (United States)

    Andellini, Martina; Fernandez Riesgo, Sandra; Morolli, Federica; Ritrovato, Matteo; Cosoli, Piero; Petruzzellis, Silverio; Rosso, Nicola

    2017-11-03

    To test the application of Business Process Management technology to manage clinical pathways, using a pediatric kidney transplantation as case study, and to identify the benefits obtained from using this technology. Using a Business Process Management platform, we implemented a specific application to manage the clinical pathway of pediatric patients, and monitored the activities of the coordinator in charge of the case management during a 6-month period (from June 2015 to November 2015) using two methodologies: the traditional procedure and the one under study. The application helped physicians and nurses to optimize the amount of time and resources devoted to management purposes. In particular, time reduction was close to 60%. In addition, the reduction of data duplication, the integrated event management and the efficient data collection improved the quality of the service. The use of Business Process Management technology, usually related to well-defined processes with high management costs, is an established procedure in multiple environments; its use in healthcare, however, is innovative. The use of already accepted clinical pathways is known to improve outcomes. The combination of these two techniques, well established in their respective areas of application, could represent a revolution in clinical pathway management. The study has demonstrated that the use of this technology in a clinical environment, using a proper architecture and identifying a well-defined process, leads to real benefits in terms of resources optimization and quality improvement.

  8. Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort.

    Science.gov (United States)

    Jeschek, Markus; Gerngross, Daniel; Panke, Sven

    2016-03-31

    Rational flux design in metabolic engineering approaches remains difficult since important pathway information is frequently not available. Therefore empirical methods are applied that randomly change absolute and relative pathway enzyme levels and subsequently screen for variants with improved performance. However, screening is often limited on the analytical side, generating a strong incentive to construct small but smart libraries. Here we introduce RedLibs (Reduced Libraries), an algorithm that allows for the rational design of smart combinatorial libraries for pathway optimization thereby minimizing the use of experimental resources. We demonstrate the utility of RedLibs for the design of ribosome-binding site libraries by in silico and in vivo screening with fluorescent proteins and perform a simple two-step optimization of the product selectivity in the branched multistep pathway for violacein biosynthesis, indicating a general applicability for the algorithm and the proposed heuristics. We expect that RedLibs will substantially simplify the refactoring of synthetic metabolic pathways.

  9. Current therapeutic interventions in the glycation pathway: evidence from clinical studies.

    Science.gov (United States)

    Engelen, L; Stehouwer, C D A; Schalkwijk, C G

    2013-08-01

    The increased formation of advanced glycation endproducts (AGEs) constitutes a potential mechanism of hyperglycaemia-induced micro- and macrovascular disease in diabetes. In vitro and animal experiments have shown that various interventions can inhibit formation and/or actions of AGEs, in particular the specific AGE inhibitor aminoguanidine and the AGEs crosslink breaker alagebrium, and the B vitamins pyridoxamine and thiamine, and the latter's synthetic derivative, benfotiamine. The potential clinical value of these interventions, however, remains to be established. The present review provides, from the clinical point of view, an overview of current evidence on interventions in the glycation pathway relating to (i) the clinical benefits of specific AGE inhibitors and AGE breakers and (ii) the potential AGE-inhibiting effects of therapies developed for purposes unrelated to the glycation pathway. We found that safety and/or efficacy in clinical studies with the specific AGE inhibitor, aminoguanidine and the AGE breaker, alagebrium, appeared to be a concern. The clinical evidence on the potential AGE-inhibiting effects of B vitamins is still limited. Finally, current evidence for AGE inhibition by therapies developed for purposes unrelated to glycation is limited due to a large heterogeneity in study designs and/or measurement techniques, which have often been sub-optimal. We conclude that, clinical evidence on interventions to inhibit formation and/or action of AGEs is currently weak and unconvincing. © 2012 Blackwell Publishing Ltd.

  10. Improving outcomes following penetrating colon wounds: application of a clinical pathway.

    Science.gov (United States)

    Miller, Preston R; Fabian, Timothy C; Croce, Martin A; Magnotti, Louis J; Elizabeth Pritchard, F; Minard, Gayle; Stewart, Ronald M

    2002-06-01

    During World War II, failure to treat penetrating colon injuries with diversion could result in court martial. Based on this wartime experience, colostomy for civilian colon wounds became the standard of care for the next 4 decades. Previous work from our institution demonstrated that primary repair was the optimal management for nondestructive colon wounds. Optimal management of destructive wounds requiring resection remains controversial. To address this issue, we performed a study that demonstrated risk factors (pre or intraoperative transfusion requirement of more than 6 units of packed red blood cells, significant comorbid diseases) that were associated with a suture line failure rate of 14%, and of whom 33% died. Based on these outcomes, a clinical pathway for management of destructive colon wounds was developed. The results of the implementation of this pathway are the focus of this report. Patients with penetrating colon injury were identified from the registry of a level I trauma center over a 5-year period. Records were reviewed for demographics, injury characteristics, and outcome. Patients with nondestructive injuries underwent primary repair. Patients with destructive wounds but no comorbidities or large transfusion requirement underwent resection and anastomosis, while patients with destructive wounds and significant medical illness or transfusion requirements of more than 6 units/blood received end colostomy. The current patients (CP) were compared to the previous study (PS) to determine the impact of the clinical pathway. Outcomes examined included colon related mortality and morbidity (suture line leak and abscess). Over a 5.5-year period, 231 patients had penetrating colon wounds. 209 survived more 24 hours and comprise the study population. Primary repair was performed on 153 (73%) patients, and 56 patients had destructive injuries (27%). Of these, 40 (71%) had resection and anastomosis and 16 (29%) had diversion. More destructive injuries were

  11. Clinical pathways for primary care: current use, interest and perceived usability.

    Science.gov (United States)

    Waters, Richard C; Toy, Jennifer M; Drechsler, Adam

    2018-02-26

    Translating clinical evidence to daily practice remains a challenge and may improve with clinical pathways. We assessed interest in and usability of clinical pathways by primary care professionals. An online survey was created. Interest in pathways for patient care and learning was assessed at start and finish. Participants completed baseline questions then pathway-associated question sets related to management of 2 chronic diseases. Perceived pathway usability was assessed using the system usability scale. Accuracy and confidence of answers was compared for baseline and pathway-assisted questions. Of 115 participants, 17.4% had used clinical pathways, the lowest of decision support tool types surveyed. Accuracy and confidence in answers significantly improved for all pathways. Interest in using pathways daily or weekly was above 75% for the respondents. There is low utilization of, but high interest in, clinical pathways by primary care clinicians. Pathways improve accuracy and confidence in answering written clinical questions.

  12. Modelling and Decision Support of Clinical Pathways

    Science.gov (United States)

    Gabriel, Roland; Lux, Thomas

    The German health care market is under a rapid rate of change, forcing especially hospitals to provide high-quality services at low costs. Appropriate measures for more effective and efficient service provision are process orientation and decision support by information technology of clinical pathway of a patient. The essential requirements are adequate modelling of clinical pathways as well as usage of adequate systems, which are capable of assisting the complete path of a patient within a hospital, and preferably also outside of it, in a digital way. To fulfil these specifications the authors present a suitable concept, which meets the challenges of well-structured clinical pathways as well as rather poorly structured diagnostic and therapeutic decisions, by interplay of process-oriented and knowledge-based hospital information systems.

  13. Clinical pathway for video-assisted thoracic surgery: the Hong Kong story.

    Science.gov (United States)

    Sihoe, Alan D L

    2016-02-01

    A clinical pathway provides a scheduled, objective protocol for the multi-disciplinary, evidence-based management of patients with a specific condition or undergoing a specific procedure. In implementing a clinical pathway for the care of patients receiving video-assisted thoracic surgery (VATS) in Hong Kong, many insights were gained into what makes a clinical pathway work: meticulous preparation and team-building are keys to success; the pathway must be constantly reviewed and revisions made in response to evolving clinical need; and data collection is a key element to allow auditing and clinical research. If these can be achieved, a clinical pathway delivers not only measurable improvements in patient outcomes, but also fundamentally complements clinical advances such as VATS. This article narrates the story of how the clinical pathway for VATS in Hong Kong was created and evolved, highlighting how the above lessons were learned.

  14. DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals

    DEFF Research Database (Denmark)

    Chen, Xiulai; Gao, Cong; Guo, Liang

    2018-01-01

    , and pathway optimization at the systems level, offers a conceptual and technological framework to exploit potential pathways, modify existing pathways and create new pathways for the optimal production of desired chemicals. Here, we summarize recent progress of DCEO biotechnology and examples of its......Chemical synthesis is a well established route for producing many chemicals on a large scale, but some drawbacks still exist in this process, such as unstable intermediates, multistep reactions, complex process control, etc. Biobased production provides an attractive alternative to these challenges......, but how to make cells into efficient factories is challenging. As a key enabling technology to develop efficient cell factories, design-construction-evaluation-optimization (DCEO) biotechnology, which incorporates the concepts and techniques of pathway design, pathway construction, pathway evaluation...

  15. Clinical Implications of Hedgehog Pathway Signaling in Prostate Cancer

    Directory of Open Access Journals (Sweden)

    Daniel L. Suzman

    2015-09-01

    Full Text Available Activity in the Hedgehog pathway, which regulates GLI-mediated transcription, is important in organogenesis and stem cell regulation in self-renewing organs, but is pathologically elevated in many human malignancies. Mutations leading to constitutive activation of the pathway have been implicated in medulloblastoma and basal cell carcinoma, and inhibition of the pathway has demonstrated clinical responses leading to the approval of the Smoothened inhibitor, vismodegib, for the treatment of advanced basal cell carcinoma. Aberrant Hedgehog pathway signaling has also been noted in prostate cancer with evidence suggesting that it may render prostate epithelial cells tumorigenic, drive the epithelial-to-mesenchymal transition, and contribute towards the development of castration-resistance through autocrine and paracrine signaling within the tumor microenvironment and cross-talk with the androgen pathway. In addition, there are emerging clinical data suggesting that inhibition of the Hedgehog pathway may be effective in the treatment of recurrent and metastatic prostate cancer. Here we will review these data and highlight areas of active clinical research as they relate to Hedgehog pathway inhibition in prostate cancer.

  16. Can a management pathway for chronic cough in children improve clinical outcomes: protocol for a multicentre evaluation

    Directory of Open Access Journals (Sweden)

    Masters IB

    2010-11-01

    Full Text Available Abstract Background Chronic cough is common and is associated with significant economic and human costs. While cough can be a problematic symptom without serious consequences, it could also reflect a serious underlying illness. Evidence shows that the management of chronic cough in children needs to be improved. Our study tests the hypothesis that the management of chronic cough in children with an evidence-based management pathway is feasible and reliable, and improves clinical outcomes. Methods/Design We are conducting a multicentre randomised controlled trial based in respiratory clinics in 5 major Australian cities. Children (n = 250 fulfilling inclusion criteria (new patients with chronic cough are randomised (allocation concealed to the standardised clinical management pathway (specialist starts clinical pathway within 2 weeks or usual care (existing care until review by specialist at 6 weeks. Cough diary, cough-specific quality of life (QOL and generic QOL are collected at baseline and at 6, 10, 14, 26, and 52 weeks. Children are followed-up for 6 months after diagnosis and cough resolution (with at least monthly contact from study nurses. A random sample from each site will be independently examined to determine adherence to the pathway. Primary outcomes are group differences in QOL and proportion of children that are cough free at week 6. Discussion The clinical management pathway is based on data from Cochrane Reviews combined with collective clinical experience (250 doctor years. This study will provide additional evidence on the optimal management of chronic cough in children. Trial registration ACTRN12607000526471

  17. Marketing research: Pathway to optimal market oriented products ...

    African Journals Online (AJOL)

    This paper examines the role of marketing research as pathway to developing optimal market oriented products. The objectives of this paper among others are to (i) Establish whether the use of marketing research has effect on new product adoption process by consumers (ii) Find out if there is any relationship between the ...

  18. Clinical pathways for inborn errors of metabolism: warranted and feasible

    Directory of Open Access Journals (Sweden)

    Demirdas Serwet

    2013-02-01

    Full Text Available Abstract Inborn errors of metabolism (IEMs are known for their low prevalence and multidisciplinary care mostly founded on expert opinion. Clinical pathways are multidisciplinary tools to organise care which provide a clear route to the best care and improve communication. In 2010 the Dutch Society for Children and Adults with an Inborn Error of Metabolism (VKS initiated development of clinical pathways for inborn errors of metabolism. In this letter to the editor we describe why it is warranted to develop clinical pathways for IEMs and shortly discuss the process of development for these pathways in the Netherlands.

  19. A proposed clinical research support career pathway for noninvestigators.

    Science.gov (United States)

    Smith, Sheree; Gullick, Janice; Ballard, Jacqueline; Perry, Lin

    2018-03-08

    To discuss the international experience of clinical research support for noninvestigator roles and to propose a new pathway for Australia, to promote a sustainable research support workforce capable of delivering high-quality clinical research. Noninvestigator research support roles are currently characterized by an ad hoc approach to training, with limited role delineation and perceived professional isolation with implications for study completion rates and participant safety. A focused approach to developing and implementing research support pathways has improved patient recruitment, study completion, job satisfaction, and research governance. The Queensland and New South Wales state-based Nurses' Awards, the Australian Qualifications Framework, and a University Professional (Research) Staff Award. Research nurses in the clinical environment improve study coordination, adherence to study protocol, patient safety, and clinical care. A career pathway that guides education and outlines position descriptions and skill sets would enhance development of the research support workforce. This pathway could contribute to changing the patient outcomes through coordination and study completion of high-quality research. A wide consultative approach is required to determine a cost-effective and feasible approach to implementation and evaluation of the proposed pathway. © 2018 John Wiley & Sons Australia, Ltd.

  20. What is a clinical pathway? Refinement of an operational definition to identify clinical pathway studies for a Cochrane systematic review

    OpenAIRE

    Lawal, Adegboyega K.; Rotter, Thomas; Kinsman, Leigh; Machotta, Andreas; Ronellenfitsch, Ulrich; Scott, Shannon D.; Goodridge, Donna; Plishka, Christopher; Groot, Gary

    2016-01-01

    textabstractClinical pathways (CPWs) are a common component in the quest to improve the quality of health. CPWs are used to reduce variation, improve quality of care, and maximize the outcomes for specific groups of patients. An ongoing challenge is the operationalization of a definition of CPW in healthcare. This may be attributable to both the differences in definition and a lack of conceptualization in the field of clinical pathways. This correspondence article describes a process of refin...

  1. Optimal time points sampling in pathway modelling.

    Science.gov (United States)

    Hu, Shiyan

    2004-01-01

    Modelling cellular dynamics based on experimental data is at the heart of system biology. Considerable progress has been made to dynamic pathway modelling as well as the related parameter estimation. However, few of them gives consideration for the issue of optimal sampling time selection for parameter estimation. Time course experiments in molecular biology rarely produce large and accurate data sets and the experiments involved are usually time consuming and expensive. Therefore, to approximate parameters for models with only few available sampling data is of significant practical value. For signal transduction, the sampling intervals are usually not evenly distributed and are based on heuristics. In the paper, we investigate an approach to guide the process of selecting time points in an optimal way to minimize the variance of parameter estimates. In the method, we first formulate the problem to a nonlinear constrained optimization problem by maximum likelihood estimation. We then modify and apply a quantum-inspired evolutionary algorithm, which combines the advantages of both quantum computing and evolutionary computing, to solve the optimization problem. The new algorithm does not suffer from the morass of selecting good initial values and being stuck into local optimum as usually accompanied with the conventional numerical optimization techniques. The simulation results indicate the soundness of the new method.

  2. Critical success factors in implementing clinical pathways/case management.

    Science.gov (United States)

    Choo, J

    2001-07-01

    With the advent of casemix reimbursement implementation, rapid technological changes, an ageing population and changing consumer behaviour, the Singapore health care industry is faced with the impetus to provide a cost-effective and efficient care delivery system. One ubiquitous tool used is the establishment of a clinical pathway/case management programme within the hospital. As the concept of clinical pathway for patient care is a relatively new concept in Singapore, several critical factors must be considered to ensure successful implementation of clinical pathway/case management programme. One key success factor lies in continued clinician support and acceptance. Other factors include top management leadership and support and a dedicated team of case managers, nurses and paramedical professionals.

  3. Effects of clinical pathways in the joint replacement: a meta-analysis

    Directory of Open Access Journals (Sweden)

    Faggiano F

    2009-07-01

    Full Text Available Abstract Background A meta-analysis was performed to evaluate the use of clinical pathways for hip and knee joint replacements when compared with standard medical care. The impact of clinical pathways was evaluated assessing the major outcomes of in-hospital hip and knee joint replacement processes: postoperative complications, number of patients discharged at home, length of in-hospital stay and direct costs. Methods Medline, Cinahl, Embase and the Cochrane Central Register of Controlled Trials were searched. The search was performed from 1975 to 2007. Each study was assessed independently by two reviewers. The assessment of methodological quality of the included studies was based on the Jadad methodological approach and on the New Castle Ottawa Scale. Data analysis abided by the guidelines set out by The Cochrane Collaboration regarding statistical methods. Meta-analyses were performed using RevMan software, version 4.2. Results Twenty-two studies met the study inclusion criteria and were included in the meta-analysis for a total sample of 6,316 patients. The aggregate overall results showed significantly fewer patients suffering postoperative complications in the clinical pathways group when compared with the standard care group. A shorter length of stay in the clinical pathway group was also observed and lower costs during hospital stay were associated with the use of the clinical pathways. No significant differences were found in the rates of discharge to home. Conclusion The results of this meta-analysis show that clinical pathways can significantly improve the quality of care even if it is not possible to conclude that the implementation of clinical pathways is a cost-effective process, because none of the included studies analysed the cost of the development and implementation of the pathways. Based on the results we assume that pathways have impact on the organisation of care if the care process is structured in a standardised way

  4. Incorporating Topic Assignment Constraint and Topic Correlation Limitation into Clinical Goal Discovering for Clinical Pathway Mining

    Directory of Open Access Journals (Sweden)

    Xiao Xu

    2017-01-01

    Full Text Available Clinical pathways are widely used around the world for providing quality medical treatment and controlling healthcare cost. However, the expert-designed clinical pathways can hardly deal with the variances among hospitals and patients. It calls for more dynamic and adaptive process, which is derived from various clinical data. Topic-based clinical pathway mining is an effective approach to discover a concise process model. Through this approach, the latent topics found by latent Dirichlet allocation (LDA represent the clinical goals. And process mining methods are used to extract the temporal relations between these topics. However, the topic quality is usually not desirable due to the low performance of the LDA in clinical data. In this paper, we incorporate topic assignment constraint and topic correlation limitation into the LDA to enhance the ability of discovering high-quality topics. Two real-world datasets are used to evaluate the proposed method. The results show that the topics discovered by our method are with higher coherence, informativeness, and coverage than the original LDA. These quality topics are suitable to represent the clinical goals. Also, we illustrate that our method is effective in generating a comprehensive topic-based clinical pathway model.

  5. Evaluating the effect of clinical care pathways on quality of cancer care: analysis of breast, colon and rectal cancer pathways.

    Science.gov (United States)

    Bao, Han; Yang, Fengjuan; Su, Shaofei; Wang, Xinyu; Zhang, Meiqi; Xiao, Yaming; Jiang, Hao; Wang, Jiaying; Liu, Meina

    2016-05-01

    Substantial gaps exist between clinical practice and evidence-based cancer care, potentially leading to adverse clinical outcomes and decreased quality of life for cancer patients. This study aimed to evaluate the usefulness of clinical pathways as a tool for improving quality of cancer care, using breast, colon, and rectal cancer pathways as demonstrations. Newly diagnosed patients with invasive breast, colon, and rectal cancer were enrolled as pre-pathway groups, while patients with the same diagnoses treated according to clinical pathways were recruited for post-pathway groups. Compliance with preoperative core biopsy or fine-needle aspiration, utilization of sentinel lymph node biopsy, and proportion of patients whose tumor hormone receptor status was stated in pathology report were significantly increased after implementation of clinical pathway for breast cancer. For colon cancer, compliance with two care processes was significantly improved: surgical resection with anastomosis and resection of at least 12 lymph nodes. Regarding rectal cancer, there was a significant increase in compliance with preoperative evaluation of depth of tumor invasion, total mesorectal excision treatment of middle- or low-position rectal cancer, and proportion of patients who had undergone rectal cancer surgery whose pathology report included margin status. Moreover, total length of hospital stay was decreased remarkably for all three cancer types, and postoperative complications remained unchanged following implementation of the clinical pathways. Clinical pathways can improve compliance with standard care by implementing evidence-based quality indicators in daily practice, which could serve as a useful tool for narrowing the gap between clinical practice and evidence-based care.

  6. Design of an optimization algorithm for clinical use

    International Nuclear Information System (INIS)

    Gustafsson, Anders

    1995-01-01

    Radiation therapy optimization has received much attention in the past few years. In combination with biological objective functions, the different optimization schemes has shown a potential to considerably increase the treatment outcome. With improved radiobiological models and increased computer capacity, radiation therapy optimization has now reached a stage where implementation in a clinical treatment planning system is realistic. A radiation therapy optimization method has been investigated with respect to its feasibility as a tool in a clinical 3D treatment planning system. The optimization algorithm is a constrained iterative gradient method. Photon dose calculation is performed using the clinically validated pencil-beam based algorithm of the clinical treatment planning system. Dose calculation within the optimization scheme is very time consuming and measures are required to decrease the calculation time. Different methods for more effective dose calculation within the optimization scheme have been investigated. The optimization results for adaptive sampling of calculation points, and secondary effect approximations in the dose calculation algorithm are compared with the optimization result for accurate dose calculation in all voxels of interest

  7. A career path in clinical pathways.

    Science.gov (United States)

    Bower, K A

    1998-03-01

    Much like the development of a clinical path, the creation of a career path requires knowledge of patterns of behavior, needs for standardized education and skill development, along with variance analysis and individualized care. This nationally known nursing entrepreneur tells the story of her involvement in the development of case management and clinical pathways and how she turned that into a successful business that has changed how patient care is managed nationally and internationally.

  8. Advancing the educational and career pathway for clinical trials nurses.

    Science.gov (United States)

    Scott, Kathleen; White, Kathryn; Roydhouse, Jessica K

    2013-04-01

    Clinical trials nurses play a pivotal role in the conduct of clinical research, but the educational and career pathway for these nurses remains unclear. This article reports findings from a survey of nurses working in cancer clinical trials research in Australia. Most participants held postgraduate qualifications (42 of 61); however, clinical trials education was primarily attained through short professional development courses. Interest in pursuing trial-specific postgraduate education was high, but barriers were identified, including cost, time, and unclear benefit for career advancement. Job titles varied substantially, which is indicative of an unclear employment pathway. These findings suggest that initiatives to improve the educational and career pathway for clinical trials nurses are needed and should include the following: formal educational preparation, greater consistency in employment status, and clearer career progression. These strategies should be underpinned by broad professional recognition of the clinical trials nurse as a specialized nursing role. Copyright 2013, SLACK Incorporated.

  9. Dispositional optimism and sleep quality: a test of mediating pathways.

    Science.gov (United States)

    Uchino, Bert N; Cribbet, Matthew; de Grey, Robert G Kent; Cronan, Sierra; Trettevik, Ryan; Smith, Timothy W

    2017-04-01

    Dispositional optimism has been related to beneficial influences on physical health outcomes. However, its links to global sleep quality and the psychological mediators responsible for such associations are less studied. This study thus examined if trait optimism predicted global sleep quality, and if measures of subjective well-being were statistical mediators of such links. A community sample of 175 participants (93 men, 82 women) completed measures of trait optimism, depression, and life satisfaction. Global sleep quality was assessed using the Pittsburgh Sleep Quality Index. Results indicated that trait optimism was a strong predictor of better PSQI global sleep quality. Moreover, this association was mediated by depression and life satisfaction in both single and multiple mediator models. These results highlight the importance of optimism for the restorative process of sleep, as well as the utility of multiple mediator models in testing distinct psychological pathways.

  10. [Review of the initiation and development of the conception of clinical pathway].

    Science.gov (United States)

    Wang, Zhen-E; Shangguan, Qing-Miao; Wu, Ping

    2010-11-01

    Dupont, an American company, used the concept of "pathway" in industry to improve the quality of their products in 1957. In the 1970s, under the pressure of a rise in medical costs, some people realized the concept of the "key pathway" could be used in medicine too. In 1985, the Boston New England Medical Center Hospital (NEMC) succeeded in using the concept of the clinical pathway in medical practice, and afterwards the concept gradually found worldwide application. In 1996, the Fourth Military Medical University in China reported the application of clinical pathway in America. The West China Hospital began to try out the clinical pathway in 1998 and the concept gradually found application in China.

  11. CSF Proteomics Identifies Specific and Shared Pathways for Multiple Sclerosis Clinical Subtypes.

    Directory of Open Access Journals (Sweden)

    Timucin Avsar

    Full Text Available Multiple sclerosis (MS is an immune-mediated, neuro-inflammatory, demyelinating and neurodegenerative disease of the central nervous system (CNS with a heterogeneous clinical presentation and course. There is a remarkable phenotypic heterogeneity in MS, and the molecular mechanisms underlying it remain unknown. We aimed to investigate further the etiopathogenesis related molecular pathways in subclinical types of MS using proteomic and bioinformatics approaches in cerebrospinal fluids of patients with clinically isolated syndrome, relapsing remitting MS and progressive MS (n=179. Comparison of disease groups with controls revealed a total of 151 proteins that are differentially expressed in clinically different MS subtypes. KEGG analysis using PANOGA tool revealed the disease related pathways including aldosterone-regulated sodium reabsorption (p=8.02x10-5 which is important in the immune cell migration, renin-angiotensin (p=6.88x10-5 system that induces Th17 dependent immunity, notch signaling (p=1.83x10-10 pathway indicating the activated remyelination and vitamin digestion and absorption pathways (p=1.73x10-5. An emerging theme from our studies is that whilst all MS clinical forms share common biological pathways, there are also clinical subtypes specific and pathophysiology related pathways which may have further therapeutic implications.

  12. Optimization and planning of operating theatre activities: an original definition of pathways and process modeling.

    Science.gov (United States)

    Barbagallo, Simone; Corradi, Luca; de Ville de Goyet, Jean; Iannucci, Marina; Porro, Ivan; Rosso, Nicola; Tanfani, Elena; Testi, Angela

    2015-05-17

    The Operating Room (OR) is a key resource of all major hospitals, but it also accounts for up 40% of resource costs. Improving cost effectiveness, while maintaining a quality of care, is a universal objective. These goals imply an optimization of planning and a scheduling of the activities involved. This is highly challenging due to the inherent variable and unpredictable nature of surgery. A Business Process Modeling Notation (BPMN 2.0) was used for the representation of the "OR Process" (being defined as the sequence of all of the elementary steps between "patient ready for surgery" to "patient operated upon") as a general pathway ("path"). The path was then both further standardized as much as possible and, at the same time, keeping all of the key-elements that would allow one to address or define the other steps of planning, and the inherent and wide variability in terms of patient specificity. The path was used to schedule OR activity, room-by-room, and day-by-day, feeding the process from a "waiting list database" and using a mathematical optimization model with the objective of ending up in an optimized planning. The OR process was defined with special attention paid to flows, timing and resource involvement. Standardization involved a dynamics operation and defined an expected operating time for each operation. The optimization model has been implemented and tested on real clinical data. The comparison of the results reported with the real data, shows that by using the optimization model, allows for the scheduling of about 30% more patients than in actual practice, as well as to better exploit the OR efficiency, increasing the average operating room utilization rate up to 20%. The optimization of OR activity planning is essential in order to manage the hospital's waiting list. Optimal planning is facilitated by defining the operation as a standard pathway where all variables are taken into account. By allowing a precise scheduling, it feeds the process of

  13. Shared care and implementation of a pediatric clinical pathway

    DEFF Research Database (Denmark)

    Langfrits, Mette Sørensen; Thomsen, RW; Rubak, Jens Mørck

    with uncontrolled asthma should be followed at the pediatrics department. Study 2) An increased overall proportion of children with well-controlled asthma. Study 3) Favorable changes in the use of asthma medication. Study 4) Self-reported higher quality of life among children with asthma Material and methods...... specialist out-patient clinic at the pediatrics department at Viborg hospital or at one of 100 GPs in the Viborg area. At baseline the involved health care professionals participated in an introduction to the clinical pathway and treatment guide. Furthermore the clinical pathway and treatment guide...... Midten. We sincerely thank Lars G. Hansen (Head of Department of Pediatrics, Viborg Hospital) for his help and participation....

  14. Construction and Optimization of a Heterologous Pathway for Protocatechuate Catabolism in Escherichia coli Enables Bioconversion of Model Aromatic Compounds.

    Science.gov (United States)

    Clarkson, Sonya M; Giannone, Richard J; Kridelbaugh, Donna M; Elkins, James G; Guss, Adam M; Michener, Joshua K

    2017-09-15

    The production of biofuels from lignocellulose yields a substantial lignin by-product stream that currently has few applications. Biological conversion of lignin-derived compounds into chemicals and fuels has the potential to improve the economics of lignocellulose-derived biofuels, but few microbes are able both to catabolize lignin-derived aromatic compounds and to generate valuable products. While Escherichia coli has been engineered to produce a variety of fuels and chemicals, it is incapable of catabolizing most aromatic compounds. Therefore, we engineered E. coli to catabolize protocatechuate, a common intermediate in lignin degradation, as the sole source of carbon and energy via heterologous expression of a nine-gene pathway from Pseudomonas putida KT2440. We next used experimental evolution to select for mutations that increased growth with protocatechuate more than 2-fold. Increasing the strength of a single ribosome binding site in the heterologous pathway was sufficient to recapitulate the increased growth. After optimization of the core pathway, we extended the pathway to enable catabolism of a second model compound, 4-hydroxybenzoate. These engineered strains will be useful platforms to discover, characterize, and optimize pathways for conversions of lignin-derived aromatics. IMPORTANCE Lignin is a challenging substrate for microbial catabolism due to its polymeric and heterogeneous chemical structure. Therefore, engineering microbes for improved catabolism of lignin-derived aromatic compounds will require the assembly of an entire network of catabolic reactions, including pathways from genetically intractable strains. Constructing defined pathways for aromatic compound degradation in a model host would allow rapid identification, characterization, and optimization of novel pathways. We constructed and optimized one such pathway in E. coli to enable catabolism of a model aromatic compound, protocatechuate, and then extended the pathway to a related

  15. Optimal processing pathway selection for microalgae-based biorefinery under uncertainty

    DEFF Research Database (Denmark)

    Rizwan, Muhammad; Zaman, Muhammad; Lee, Jay H.

    2015-01-01

    We propose a systematic framework for the selection of optimal processing pathways for a microalgaebased biorefinery under techno-economic uncertainty. The proposed framework promotes robust decision making by taking into account the uncertainties that arise due to inconsistencies among...... and shortage in the available technical information. A stochastic mixed integer nonlinear programming (sMINLP) problem is formulated for determining the optimal biorefinery configurations based on a superstructure model where parameter uncertainties are modeled and included as sampled scenarios. The solution...... the accounting of uncertainty are compared with respect to different objectives. (C) 2015 Elsevier Ltd. All rights reserved....

  16. Optimal structural inference of signaling pathways from unordered and overlapping gene sets.

    Science.gov (United States)

    Acharya, Lipi R; Judeh, Thair; Wang, Guangdi; Zhu, Dongxiao

    2012-02-15

    A plethora of bioinformatics analysis has led to the discovery of numerous gene sets, which can be interpreted as discrete measurements emitted from latent signaling pathways. Their potential to infer signaling pathway structures, however, has not been sufficiently exploited. Existing methods accommodating discrete data do not explicitly consider signal cascading mechanisms that characterize a signaling pathway. Novel computational methods are thus needed to fully utilize gene sets and broaden the scope from focusing only on pairwise interactions to the more general cascading events in the inference of signaling pathway structures. We propose a gene set based simulated annealing (SA) algorithm for the reconstruction of signaling pathway structures. A signaling pathway structure is a directed graph containing up to a few hundred nodes and many overlapping signal cascades, where each cascade represents a chain of molecular interactions from the cell surface to the nucleus. Gene sets in our context refer to discrete sets of genes participating in signal cascades, the basic building blocks of a signaling pathway, with no prior information about gene orderings in the cascades. From a compendium of gene sets related to a pathway, SA aims to search for signal cascades that characterize the optimal signaling pathway structure. In the search process, the extent of overlap among signal cascades is used to measure the optimality of a structure. Throughout, we treat gene sets as random samples from a first-order Markov chain model. We evaluated the performance of SA in three case studies. In the first study conducted on 83 KEGG pathways, SA demonstrated a significantly better performance than Bayesian network methods. Since both SA and Bayesian network methods accommodate discrete data, use a 'search and score' network learning strategy and output a directed network, they can be compared in terms of performance and computational time. In the second study, we compared SA and

  17. Enhanced recovery pathways optimize health outcomes and resource utilization: A meta-analysis of randomized controlled trials in colorectal surgery

    DEFF Research Database (Denmark)

    Adamina, Michel; Kehlet, Henrik; Tomlinson, George A

    2011-01-01

    in costs that threatens the stability of health care systems. Enhanced recovery pathways (ERP) have been proposed as a means to reduce morbidity and improve effectiveness of care. We have reviewed the evidence supporting the implementation of ERP in clinical practice. Methods Medline, Embase...... of health care processes. Thus, while accelerating recovery and safely reducing hospital stay, ERPs optimize utilization of health care resources. ERPs can and should be routinely used in care after colorectal and other major gastrointestinal procedures....

  18. Environmental and energy system analysis of bio-methane production pathways : A comparison between feedstocks and process optimizations

    NARCIS (Netherlands)

    Pierie, F.; van Someren, C. E. J.; Benders, R. M. J.; Bekkering, J.; van Gemert, W. J. Th; Moll, H. C.

    2015-01-01

    The energy efficiency and sustainability of an anaerobic green gas production pathway was evaluated, taking into account five biomass feedstocks, optimization of the green gas production pathway, replacement of current waste management pathways by mitigation, and transport of the feedstocks.

  19. Environmental and energy system analysis of bio-methane production pathways : a comparison between feedstocks and process optimizations

    NARCIS (Netherlands)

    Pierie, Frank; van Someren, Christian; Benders, René M.J.; Bekkering, Jan; van Gemert, Wim; Moll, Henri C.

    2015-01-01

    The energy efficiency and sustainability of an anaerobic green gas production pathway was evaluated, taking into account five biomass feedstocks, optimization of the green gas production pathway, replacement of current waste management pathways by mitigation, and transport of the feedstocks.

  20. Study of the optimal reaction conditions for assay of the mouse alternative complement pathway

    NARCIS (Netherlands)

    Dijk, H. van; Rademaker, P.M.; Klerx, J.P.A.M.; Willers, J.M.M.

    1985-01-01

    The optimal reaction conditions for hemolytic assay of alternative complement pathway activity in mouse serum were investigated. A microtiter system was used, in which a number of 7.5×106 rabbit erythrocytes per test well appeared to be optimal. Rabbit erythrocytes were superior as target cells over

  1. Clinical Presentation and Outcome of Patients With Optic Pathway Glioma.

    Science.gov (United States)

    Robert-Boire, Viviane; Rosca, Lorena; Samson, Yvan; Ospina, Luis H; Perreault, Sébastien

    2017-10-01

    Optic pathway gliomas (OPGs) occur sporadically or in patients with neurofibromatosis type 1 (NF1). The purpose of this study was to evaluate the clinical presentation at diagnosis and at progression of patients with OPGs. We conducted a chart review of patients with OPGs diagnosed in a single center over a period of 15 years. Demographic data including age, sex, NF1 status, clinical presentation, and outcome were collected. Of the 40 patients who were identified, 23 had sporadic tumors (57.5%) and 17 had NF1-related tumors (42.5%). Among the children with NF1, there was a significant overrepresentation of girls (82.3%) (P = 0.02), while among the children without NF1, there were slightly more boys (56.5%) than girls (43.5%). The presence of nystagmus was strongly associated with sporadic optic pathway gliomas. Poor visual outcome was related to tumor affecting both optic pathways, hydrocephalus at diagnosis, and optic nerve atrophy. Of the 40 patients, five died of OPG complications (12.5%) and all had sporadic tumors. Our cohort is one of the largest with OPGs and a detailed description of the clinical presentation both at diagnosis and at progression. We observed a significant difference between sporadic and NF1 optic pathway gliomas in terms of demographics, clinical presentation, and outcome. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Development of a renal transplant clinical pathway: one hospital's journey.

    Science.gov (United States)

    Darrikhuma, I M

    1999-05-01

    Mounting pressures to resolve multiple challenges related to quality, cost, and access in a resource-driven, customer-focused health care environment have compelled clinicians to develop innovative strategies to provide cost-effective, state-of-the-art care. Targeted patient groups include those associated with high cost, high volume, or high resource use. Patients undergoing renal transplantation fall into one or more of these categories. Recently, the management of patients with end-stage renal disease (ESRD) has come under national focus, as evidenced by the fact that Health Care Financing Administration (HCFA) has commissioned an ESRD managed care demonstration project. The purpose of this article is to describe how one case management tool--the clinical pathway--can be used to decrease costs and improve outcomes associated with renal transplantation. This discussion will include a review of the origins and components of clinical pathways and a description of how one institution developed, implemented, evaluated, and refined a renal transplantation clinical pathway.

  3. CLINICAL PATHWAYS IN 17 EUROPEAN UNION COUNTRIES: A SURVEY OF EXPERT OPINIONS

    Directory of Open Access Journals (Sweden)

    Don Hindle

    2004-11-01

    Full Text Available Background. The main focus of the survey is on the extent to which clinical pathways are being used, and whether it might provide a basis for improved service planning and consequently strategic asset planning in health care.Methods. In the first stage, our aim was to make contact with one agency in each country (the primary agency below that would be able to provide contacts within that country with a mix of experts from each of the following types of agencies: Health sector government regulator, Health care purchasing (insurance agencies, Senior clinical managers in hospitals, Senior clinical managers in non-hospital care provider agencies (eg, home care, or primary medical care, Health professional societies (preferably medical and nursing, Accreditation or audit agencies, Consumer associations and Public or private agencies concerned with health facilities development. Definitions of these agencies and other terms were attached to the questionnaire itself. We would then ask the primary agency to choose the experts that were most likely to be aware of clinical pathway use. The persons thus contacted would then be asked to complete the questionnaire and send it back to the researchers. The aim was not to attempt to establish a random sample, but rather to target well-informed people.Results. 51 completed questionnaires were provided by largely self-selected experts from 17 EU countries. Respondents reported that pathways are important and becoming increasingly widely used (although the rate of progress is highly variable, the main constraints to their use are a cultural aversion among doctors and little encouragement from external parties, and there is growing recognition that multi-setting pathways have the greatest potential value.Conclusions. More needs to be done to achieve a common understanding of the ideas of pathways, strategic asset planning, and the interrelationships. Systems problems need systems solutions. In the case of clinical

  4. Cost unit accounting based on a clinical pathway: a practical tool for DRG implementation.

    Science.gov (United States)

    Feyrer, R; Rösch, J; Weyand, M; Kunzmann, U

    2005-10-01

    Setting up a reliable cost unit accounting system in a hospital is a fundamental necessity for economic survival, given the current general conditions in the healthcare system. Definition of a suitable cost unit is a crucial factor for success. We present here the development and use of a clinical pathway as a cost unit as an alternative to the DRG. Elective coronary artery bypass grafting was selected as an example. Development of the clinical pathway was conducted according to a modular concept that mirrored all the treatment processes across various levels and modules. Using service records and analyses the process algorithms of the clinical pathway were developed and visualized with CorelTM iGrafix Process 2003. A detailed process cost record constituted the basis of the pathway costing, in which financial evaluation of the treatment processes was performed. The result of this study was a structured clinical pathway for coronary artery bypass grafting together with a cost calculation in the form of cost unit accounting. The use of a clinical pathway as a cost unit offers considerable advantages compared to the DRG or clinical case. The variance in the diagnoses and procedures within a pathway is minimal, so the consumption of resources is homogeneous. This leads to a considerable improvement in the value of cost unit accounting as a strategic control instrument in hospitals.

  5. Optimal processing pathway for the production of biodiesel from microalgal biomass: A superstructure based approach

    DEFF Research Database (Denmark)

    Rizwan, Muhammad; Lee, Jay H.; Gani, Rafiqul

    2013-01-01

    In this study, we propose a mixed integer nonlinear programming (MINLP) model for superstructure based optimization of biodiesel production from microalgal biomass. The proposed superstructure includes a number of major processing steps for the production of biodiesel from microalgal biomass......, such as the harvesting of microalgal biomass, pretreatments including drying and cell disruption of harvested biomass, lipid extraction, transesterification, and post-transesterfication purification. The proposed model is used to find the optimal processing pathway among the large number of potential pathways that exist...... for the production of biodiesel from microalgae. The proposed methodology is tested by implementing on a specific case with different choices of objective functions. The MINLP model is implemented and solved in GAMS using a database built in Excel. The results from the optimization are analyzed...

  6. Construction and Optimization of a Heterologous Pathway for Protocatechuate Catabolism in Escherichia coli Enables Bioconversion of Model Aromatic Compounds

    Energy Technology Data Exchange (ETDEWEB)

    Clarkson, Sonya M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Giannone, Richard J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Chemical Sciences Division; Kridelbaugh, Donna M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Elkins, James G. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Guss, Adam M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Michener, Joshua K. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division, BioEnergy Science Center; Vieille, Claire [Michigan State Univ., East Lansing, MI (United States)

    2017-07-21

    The production of biofuels from lignocellulose yields a substantial lignin by-product stream that currently has few applications. Biological conversion of lignin-derived compounds into chemicals and fuels has the potential to improve the economics of lignocellulose-derived biofuels, but few microbes are able both to catabolize lignin-derived aromatic compounds and to generate valuable products. WhileEscherichia colihas been engineered to produce a variety of fuels and chemicals, it is incapable of catabolizing most aromatic compounds. Therefore, we engineeredE. colito catabolize protocatechuate, a common intermediate in lignin degradation, as the sole source of carbon and energy via heterologous expression of a nine-gene pathway fromPseudomonas putidaKT2440. Then, we used experimental evolution to select for mutations that increased growth with protocatechuate more than 2-fold. Increasing the strength of a single ribosome binding site in the heterologous pathway was sufficient to recapitulate the increased growth. After optimization of the core pathway, we extended the pathway to enable catabolism of a second model compound, 4-hydroxybenzoate. These engineered strains will be useful platforms to discover, characterize, and optimize pathways for conversions of lignin-derived aromatics.

    IMPORTANCELignin is a challenging substrate for microbial catabolism due to its polymeric and heterogeneous chemical structure. Therefore, engineering microbes for improved catabolism of lignin-derived aromatic compounds will require the assembly of an entire network of catabolic reactions, including pathways from genetically intractable strains. By constructing defined pathways for aromatic compound degradation in a model host would allow rapid

  7. Ontology modeling for generation of clinical pathways

    Directory of Open Access Journals (Sweden)

    Jasmine Tehrani

    2012-12-01

    Full Text Available Purpose: Increasing costs of health care, fuelled by demand for high quality, cost-effective healthcare has drove hospitals to streamline their patient care delivery systems. One such systematic approach is the adaptation of Clinical Pathways (CP as a tool to increase the quality of healthcare delivery. However, most organizations still rely on are paper-based pathway guidelines or specifications, which have limitations in process management and as a result can influence patient safety outcomes. In this paper, we present a method for generating clinical pathways based on organizational semiotics by capturing knowledge from syntactic, semantic and pragmatic to social level. Design/methodology/approach: The proposed modeling approach to generation of CPs adopts organizational semiotics and enables the generation of semantically rich representation of CP knowledge. Semantic Analysis Method (SAM is applied to explicitly represent the semantics of the concepts, their relationships and patterns of behavior in terms of an ontology chart. Norm Analysis Method (NAM is adopted to identify and formally specify patterns of behavior and rules that govern the actions identified on the ontology chart. Information collected during semantic and norm analysis is integrated to guide the generation of CPs using best practice represented in BPMN thus enabling the automation of CP. Findings: This research confirms the necessity of taking into consideration social aspects in designing information systems and automating CP. The complexity of healthcare processes can be best tackled by analyzing stakeholders, which we treat as social agents, their goals and patterns of action within the agent network. Originality/value: The current modeling methods describe CPs from a structural aspect comprising activities, properties and interrelationships. However, these methods lack a mechanism to describe possible patterns of human behavior and the conditions under which the

  8. Clinical Pathways and the Patient Perspective in the Pursuit of Value-Based Oncology Care.

    Science.gov (United States)

    Ersek, Jennifer L; Nadler, Eric; Freeman-Daily, Janet; Mazharuddin, Samir; Kim, Edward S

    2017-01-01

    The art of practicing oncology has evolved substantially in the past 5 years. As more and more diagnostic tests, biomarker-directed therapies, and immunotherapies make their way to the oncology marketplace, oncologists will find it increasingly difficult to keep up with the many therapeutic options. Additionally, the cost of cancer care seems to be increasing. Clinical pathways are a systematic way to organize and display detailed, evidence-based treatment options and assist the practitioner with best practice. When selecting which treatment regimens to include on a clinical pathway, considerations must include the efficacy and safety, as well as costs, of the therapy. Pathway treatment regimens must be continually assessed and modified to ensure that the most up-to-date, high-quality options are incorporated. Value-based models, such as the ASCO Value Framework, can assist providers in presenting economic evaluations of clinical pathway treatment options to patients, thus allowing the patient to decide the overall value of each treatment regimen. Although oncologists and pathway developers can decide which treatment regimens to include on a clinical pathway based on the efficacy of the treatment, assessment of the value of that treatment regimen ultimately lies with the patient. Patient definitions of value will be an important component to enhancing current value-based oncology care models and incorporating new, high-quality, value-based therapeutics into oncology clinical pathways.

  9. A cluster randomized trial to assess the impact of clinical pathways for patients with stroke: rationale and design of the Clinical Pathways for Effective and Appropriate Care Study [NCT00673491

    Directory of Open Access Journals (Sweden)

    Barbieri Antonella

    2008-11-01

    Full Text Available Abstract Background Patients with stroke should have access to a continuum of care from organized stroke units in the acute phase, to appropriate rehabilitation and secondary prevention measures. Moreover to improve the outcomes for acute stroke patients from an organizational perspective, the use of multidisciplinary teams and the delivery of continuous stroke education both to the professionals and to the public, and the implementation of evidence-based stroke care are recommended. Clinical pathways are complex interventions that can be used for this purpose. However in stroke care the use of clinical pathways remains questionable because little prospective controlled data has demonstrated their effectiveness. The purpose of this study is to determine whether clinical pathways could improve the quality of the care provided to the patients affected by stroke in hospital and through the continuum of the care. Methods Two-arm, cluster-randomized trial with hospitals and rehabilitation long-term care facilities as randomization units. 14 units will be randomized either to arm 1 (clinical pathway or to arm 2 (no intervention, usual care. The sample will include 238 in each group, this gives a power of 80%, at 5% significance level. The primary outcome measure is 30-days mortality. The impact of the clinical pathways along the continuum of care will also be analyzed by comparing the length of hospital stay, the hospital re-admissions rates, the institutionalization rates after hospital discharge, the patients' dependency levels, and complication rates. The quality of the care provided to the patients will be assessed by monitoring the use of diagnostic and therapeutic procedures during hospital stay and rehabilitation, and by the use of key quality indicators at discharge. The implementation of organized care will be also evaluated. Conclusion The management of patients affected by stroke involves the expertise of several professionals, which can

  10. What is a clinical pathway? Refinement of an operational definition to identify clinical pathway studies for a Cochrane systematic review

    NARCIS (Netherlands)

    A.K. Lawal (Adegboyega K.); T. Rotter (Thomas); L. Kinsman (Leigh); A. Machotta (Andreas); U. Ronellenfitsch (Ulrich); S.D. Scott (Shannon D.); D. Goodridge (Donna); C. Plishka (Christopher); G. Groot (Gary)

    2016-01-01

    textabstractClinical pathways (CPWs) are a common component in the quest to improve the quality of health. CPWs are used to reduce variation, improve quality of care, and maximize the outcomes for specific groups of patients. An ongoing challenge is the operationalization of a definition of CPW in

  11. Identification of mutated driver pathways in cancer using a multi-objective optimization model.

    Science.gov (United States)

    Zheng, Chun-Hou; Yang, Wu; Chong, Yan-Wen; Xia, Jun-Feng

    2016-05-01

    New-generation high-throughput technologies, including next-generation sequencing technology, have been extensively applied to solve biological problems. As a result, large cancer genomics projects such as the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium are producing large amount of rich and diverse data in multiple cancer types. The identification of mutated driver genes and driver pathways from these data is a significant challenge. Genome aberrations in cancer cells can be divided into two types: random 'passenger mutation' and functional 'driver mutation'. In this paper, we introduced a Multi-objective Optimization model based on a Genetic Algorithm (MOGA) to solve the maximum weight submatrix problem, which can be employed to identify driver genes and driver pathways promoting cancer proliferation. The maximum weight submatrix problem defined to find mutated driver pathways is based on two specific properties, i.e., high coverage and high exclusivity. The multi-objective optimization model can adjust the trade-off between high coverage and high exclusivity. We proposed an integrative model by combining gene expression data and mutation data to improve the performance of the MOGA algorithm in a biological context. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. A cluster randomised trial to assess the impact of clinical pathways on AMI management in rural Australian emergency departments

    Directory of Open Access Journals (Sweden)

    Snow Pamela C

    2009-05-01

    Full Text Available Abstract Background People living in rural Australia are more likely to die in hospital following an acute myocardial infarction than those living in major cities. While several factors, including time taken to access hospital care, contribute to this risk, it is also partially attributable to the lower uptake of evidence-based guidelines for the administration of thrombolytic drugs in rural emergency departments where up to one-third of eligible patients do not receive this life-saving intervention. Clinical pathways have the potential to link evidence to practice by integrating guidelines into local systems, but their impact has been hampered by variable implementation strategies and sub-optimal research designs. The purpose of this study is to determine the impact of a five-step clinical pathways implementation process on the timely and efficient administration of thrombolytic drugs for acute myocardial infarctions managed in rural Australian emergency departments. Methods/Design The design is a two-arm, cluster-randomised trial with rural hospital emergency departments that treat and do not routinely transfer acute myocardial infarction patients. Six rural hospitals in the state of Victoria will participate, with three in the intervention group and three in the control group. Intervention hospitals will participate in a five-step clinical pathway implementation process: engagement of clinicians, pathway development according to local resources and systems, reminders, education, and audit and feedback. Hospitals in the control group will each receive a hard copy of Australian national guidelines for chest pain and acute myocardial infarction management. Each group will include 90 cases to give a power of 80% at 5% significance level for the two primary outcome measures: proportion of those eligible for thrombolysis receiving the drug and time to delivery of thrombolytic drug. Discussion Improved compliance with thrombolytic guidelines via

  13. Research fellowship programs as a pathway for training independent clinical pharmacy scientists.

    Science.gov (United States)

    Mueller, Eric W; Bishop, Jeffrey R; Kanaan, Abir O; Kiser, Tyree H; Phan, Hanna; Yang, Katherine Y

    2015-03-01

    The American College of Clinical Pharmacy (ACCP) Research Affairs Committee published a commentary in 2013 on training clinical pharmacy scientists in the context of changes in economic, professional, political, and research environments. The commentary centered on the opportunities for pharmacists in clinical/translational research including strategies for ACCP, colleges of pharmacy, and the profession to increase the number and impact of clinical pharmacy scientists. A postdoctoral fellowship is cited as a current training pathway, capable of producing independent and productive pharmacy researchers. However, a decline in the number of programs, decreased funding availability, and variability in fellowship program activities and research focus have brought into question the relevance of this research training pathway to meet demand and opportunities. In response to these points, this commentary examines the state of research fellowship training including the current ACCP research fellowship review process, the need for standardization of research fellowship programs, and strategies to strengthen and promote research fellowships as relevant researcher training pathways. © 2015 Pharmacotherapy Publications, Inc.

  14. Collaboration pathway(s) using new tools for optimizing `operational' climate monitoring from space

    Science.gov (United States)

    Helmuth, Douglas B.; Selva, Daniel; Dwyer, Morgan M.

    2015-09-01

    Consistently collecting the earth's climate signatures remains a priority for world governments and international scientific organizations. Architecting a long term solution requires transforming scientific missions into an optimized robust `operational' constellation that addresses the collective needs of policy makers, scientific communities and global academic users for trusted data. The application of new tools offers pathways for global architecture collaboration. Recent rule-based expert system (RBES) optimization modeling of the intended NPOESS architecture becomes a surrogate for global operational climate monitoring architecture(s). These rulebased systems tools provide valuable insight for global climate architectures, by comparison/evaluation of alternatives and the sheer range of trade space explored. Optimization of climate monitoring architecture(s) for a partial list of ECV (essential climate variables) is explored and described in detail with dialogue on appropriate rule-based valuations. These optimization tool(s) suggest global collaboration advantages and elicit responses from the audience and climate science community. This paper will focus on recent research exploring joint requirement implications of the high profile NPOESS architecture and extends the research and tools to optimization for a climate centric case study. This reflects work from SPIE RS Conferences 2013 and 2014, abridged for simplification30, 32. First, the heavily securitized NPOESS architecture; inspired the recent research question - was Complexity (as a cost/risk factor) overlooked when considering the benefits of aggregating different missions into a single platform. Now years later a complete reversal; should agencies considering Disaggregation as the answer. We'll discuss what some academic research suggests. Second, using the GCOS requirements of earth climate observations via ECV (essential climate variables) many collected from space-based sensors; and accepting their

  15. Modular optimization of heterologous pathways for de novo synthesis of (2S-naringenin in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Junjun Wu

    Full Text Available Due to increasing concerns about food safety and environmental issues, bio-based production of flavonoids from safe, inexpensive, and renewable substrates is increasingly attracting attention. Here, the complete biosynthetic pathway, consisting of 3-deoxy-D-arabinoheptulosonate 7-phosphate synthase (DAHPS, chorismate mutase/prephenate dehydrogenase (CM/PDH, tyrosine ammonia lyase (TAL, 4-coumarate:CoA ligase (4CL, chalcone synthase (CHS, chalcone isomerase (CHI, malonate synthetase, and malonate carrier protein, was constructed using pre-made modules to overproduce (2S-naringenin from D-glucose. Modular pathway engineering strategies were applied to the production of the flavonoid precursor (2S-naringenin from L-tyrosine to investigate the metabolic space for efficient conversion. Modular expression was combinatorially tuned by modifying plasmid gene copy numbers and promoter strengths to identify an optimally balanced pathway. Furthermore, a new modular pathway from D-glucose to L-tyrosine was assembled and re-optimized with the identified optimal modules to enable de novo synthesis of (2S-naringenin. Once this metabolic balance was achieved, the optimum strain was capable of producing 100.64 mg/L (2S-naringenin directly from D-glucose, which is the highest production titer from D-glucose in Escherichia coli. The fermentation system described here paves the way for the development of an economical process for microbial production of flavonoids.

  16. Cost-effectiveness analysis of a postoperative clinical care pathway in head and neck surgery with microvascular reconstruction.

    Science.gov (United States)

    Dautremont, Jonathan F; Rudmik, Luke R; Yeung, Justin; Asante, Tiffany; Nakoneshny, Steve C; Hoy, Monica; Lui, Amanda; Chandarana, Shamir P; Matthews, Thomas W; Schrag, Christiaan; Dort, Joseph C

    2013-12-19

    The objective of this study is to evaluate the cost-effectiveness of a postoperative clinical care pathway for patients undergoing major head and neck oncologic surgery with microvascular reconstruction. This is a comparative trial of a prospective treatment group managed on a postoperative clinical care pathway and a historical group managed prior to pathway implementation. Effectiveness outcomes evaluated were total hospital days, return to OR, readmission to ICU and rate of pulmonary complications. Costing perspective was from the government payer. 118 patients were included in the study. All outcomes demonstrated that the postoperative pathway group was both more effective and less costly, and is therefore a dominant clinical intervention. The overall mean pre- and post-pathway costs are $22,733 and $16,564 per patient, respectively. The incremental cost reduction associated with the postoperative pathway was $6,169 per patient. Implementing the postoperative clinical care pathway in patients undergoing head and neck oncologic surgery with reconstruction resulted in improved clinical outcomes and reduced costs.

  17. Quantum optimal control pathways of ozone isomerization dynamics subject to competing dissociation: A two-state one-dimensional model

    International Nuclear Information System (INIS)

    Kurosaki, Yuzuru; Ho, Tak-San; Rabitz, Herschel

    2014-01-01

    We construct a two-state one-dimensional reaction-path model for ozone open → cyclic isomerization dynamics. The model is based on the intrinsic reaction coordinate connecting the cyclic and open isomers with the O 2 + O asymptote on the ground-state 1 A ′ potential energy surface obtained with the high-level ab initio method. Using this two-state model time-dependent wave packet optimal control simulations are carried out. Two possible pathways are identified along with their respective band-limited optimal control fields; for pathway 1 the wave packet initially associated with the open isomer is first pumped into a shallow well on the excited electronic state potential curve and then driven back to the ground electronic state to form the cyclic isomer, whereas for pathway 2 the corresponding wave packet is excited directly to the primary well of the excited state potential curve. The simulations reveal that the optimal field for pathway 1 produces a final yield of nearly 100% with substantially smaller intensity than that obtained in a previous study [Y. Kurosaki, M. Artamonov, T.-S. Ho, and H. Rabitz, J. Chem. Phys. 131, 044306 (2009)] using a single-state one-dimensional model. Pathway 2, due to its strong coupling to the dissociation channel, is less effective than pathway 1. The simulations also show that nonlinear field effects due to molecular polarizability and hyperpolarizability are small for pathway 1 but could become significant for pathway 2 because much higher field intensity is involved in the latter. The results suggest that a practical control may be feasible with the aid of a few lowly excited electronic states for ozone isomerization

  18. Alternative oxidase pathway optimizes photosynthesis during osmotic and temperature stress by regulating cellular ROS, malate valve and antioxidative systems

    Directory of Open Access Journals (Sweden)

    DINAKAR eCHALLABATHULA

    2016-02-01

    Full Text Available The present study reveals the importance of alternative oxidase (AOX pathway in optimizing photosynthesis under osmotic and temperature stress conditions in the mesophyll protoplasts of Pisum sativum. The responses of photosynthesis and respiration were monitored at saturating light intensity of 1000 µmoles m-2 s-1 at 25 oC under a range of sorbitol concentrations from 0.4 M to 1.0M to induce hyper-osmotic stress and by varying the temperature of the thermo-jacketed pre-incubation chamber from 25 oC to 10 oC to impose sub-optimal temperature stress. Compared to controls (0.4 M sorbitol and 25 OC, the mesophyll protoplasts showed remarkable decrease in NaHCO3-dependent O2 evolution (indicator of photosynthetic carbon assimilation, under both hyper-osmotic (1.0 M sorbitol and sub-optimal temperature stress conditions (10 OC, while the decrease in rates of respiratory O2 uptake were marginal. The capacity of AOX pathway increased significantly in parallel to increase in intracellular pyruvate and reactive oxygen species (ROS levels under both hyper-osmotic stress and sub-optimal temperature stress under the background of saturating light. The ratio of redox couple (Malate/OAA related to malate valve increased in contrast to the ratio of redox couple (GSH/GSSG related to antioxidative system during hyper-osmotic stress. Nevertheless, the ratio of GSH/GSSG decreased in the presence of sub-optimal temperature, while the ratio of Malate/OAA showed no visible changes. Also, the redox ratios of pyridine nucleotides increased under hyper-osmotic (NADH/NAD and sub-optimal temperature (NADPH/NADP stresses, respectively. However, upon restriction of AOX pathway by using salicylhydroxamic acid (SHAM, the observed changes in NaHCO3 dependent O2 evolution, cellular ROS, redox ratios of Malate/OAA, NAD(PH/NAD(P and GSH/GSSG were further aggravated under stress conditions with concomitant modulations in NADP-MDH and antioxidant enzymes. Taken together, the

  19. A gene expression signature of RAS pathway dependence predicts response to PI3K and RAS pathway inhibitors and expands the population of RAS pathway activated tumors.

    Science.gov (United States)

    Loboda, Andrey; Nebozhyn, Michael; Klinghoffer, Rich; Frazier, Jason; Chastain, Michael; Arthur, William; Roberts, Brian; Zhang, Theresa; Chenard, Melissa; Haines, Brian; Andersen, Jannik; Nagashima, Kumiko; Paweletz, Cloud; Lynch, Bethany; Feldman, Igor; Dai, Hongyue; Huang, Pearl; Watters, James

    2010-06-30

    Hyperactivation of the Ras signaling pathway is a driver of many cancers, and RAS pathway activation can predict response to targeted therapies. Therefore, optimal methods for measuring Ras pathway activation are critical. The main focus of our work was to develop a gene expression signature that is predictive of RAS pathway dependence. We used the coherent expression of RAS pathway-related genes across multiple datasets to derive a RAS pathway gene expression signature and generate RAS pathway activation scores in pre-clinical cancer models and human tumors. We then related this signature to KRAS mutation status and drug response data in pre-clinical and clinical datasets. The RAS signature score is predictive of KRAS mutation status in lung tumors and cell lines with high (> 90%) sensitivity but relatively low (50%) specificity due to samples that have apparent RAS pathway activation in the absence of a KRAS mutation. In lung and breast cancer cell line panels, the RAS pathway signature score correlates with pMEK and pERK expression, and predicts resistance to AKT inhibition and sensitivity to MEK inhibition within both KRAS mutant and KRAS wild-type groups. The RAS pathway signature is upregulated in breast cancer cell lines that have acquired resistance to AKT inhibition, and is downregulated by inhibition of MEK. In lung cancer cell lines knockdown of KRAS using siRNA demonstrates that the RAS pathway signature is a better measure of dependence on RAS compared to KRAS mutation status. In human tumors, the RAS pathway signature is elevated in ER negative breast tumors and lung adenocarcinomas, and predicts resistance to cetuximab in metastatic colorectal cancer. These data demonstrate that the RAS pathway signature is superior to KRAS mutation status for the prediction of dependence on RAS signaling, can predict response to PI3K and RAS pathway inhibitors, and is likely to have the most clinical utility in lung and breast tumors.

  20. A gene expression signature of RAS pathway dependence predicts response to PI3K and RAS pathway inhibitors and expands the population of RAS pathway activated tumors

    Directory of Open Access Journals (Sweden)

    Paweletz Cloud

    2010-06-01

    Full Text Available Abstract Background Hyperactivation of the Ras signaling pathway is a driver of many cancers, and RAS pathway activation can predict response to targeted therapies. Therefore, optimal methods for measuring Ras pathway activation are critical. The main focus of our work was to develop a gene expression signature that is predictive of RAS pathway dependence. Methods We used the coherent expression of RAS pathway-related genes across multiple datasets to derive a RAS pathway gene expression signature and generate RAS pathway activation scores in pre-clinical cancer models and human tumors. We then related this signature to KRAS mutation status and drug response data in pre-clinical and clinical datasets. Results The RAS signature score is predictive of KRAS mutation status in lung tumors and cell lines with high (> 90% sensitivity but relatively low (50% specificity due to samples that have apparent RAS pathway activation in the absence of a KRAS mutation. In lung and breast cancer cell line panels, the RAS pathway signature score correlates with pMEK and pERK expression, and predicts resistance to AKT inhibition and sensitivity to MEK inhibition within both KRAS mutant and KRAS wild-type groups. The RAS pathway signature is upregulated in breast cancer cell lines that have acquired resistance to AKT inhibition, and is downregulated by inhibition of MEK. In lung cancer cell lines knockdown of KRAS using siRNA demonstrates that the RAS pathway signature is a better measure of dependence on RAS compared to KRAS mutation status. In human tumors, the RAS pathway signature is elevated in ER negative breast tumors and lung adenocarcinomas, and predicts resistance to cetuximab in metastatic colorectal cancer. Conclusions These data demonstrate that the RAS pathway signature is superior to KRAS mutation status for the prediction of dependence on RAS signaling, can predict response to PI3K and RAS pathway inhibitors, and is likely to have the most clinical

  1. Disease-specific clinical pathways - are they feasible in primary care? A mixed-methods study.

    Science.gov (United States)

    Grimsmo, Anders; Løhre, Audhild; Røsstad, Tove; Gjerde, Ingunn; Heiberg, Ina; Steinsbekk, Aslak

    2018-04-12

    To explore the feasibility of disease-specific clinical pathways when used in primary care. A mixed-method sequential exploratory design was used. First, merging and exploring quality interview data across two cases of collaboration between the specialist care and primary care on the introduction of clinical pathways for four selected chronic diseases. Secondly, using quantitative data covering a population of 214,700 to validate and test hypothesis derived from the qualitative findings. Primary care and specialist care collaborating to manage care coordination. Primary-care representatives expressed that their patients often have complex health and social needs that clinical pathways guidelines seldom consider. The representatives experienced that COPD, heart failure, stroke and hip fracture, frequently seen in hospitals, appear in low numbers in primary care. The quantitative study confirmed the extensive complexity among home healthcare nursing patients and demonstrated that, for each of the four selected diagnoses, a homecare nurse on average is responsible for preparing reception of the patient at home after discharge from hospital, less often than every other year. The feasibility of disease-specific pathways in primary care is limited, both from a clinical and organisational perspective, for patients with complex needs. The low prevalence in primary care of patients with important chronic conditions, needing coordinated care after hospital discharge, constricts transferring tasks from specialist care. Generic clinical pathways are likely to be more feasible and efficient for patients in this setting. Key points Clinical pathways in hospitals apply to single-disease guidelines, while more than 90% of the patients discharged to community health care for follow-up have multimorbidity. Primary care has to manage the health care of the patient holistically, with all his or her complex needs. Patients most frequently admitted to hospitals, i.e. patients with COPD

  2. Optimizer convergence and local minima errors and their clinical importance

    International Nuclear Information System (INIS)

    Jeraj, Robert; Wu, Chuan; Mackie, Thomas R

    2003-01-01

    Two of the errors common in the inverse treatment planning optimization have been investigated. The first error is the optimizer convergence error, which appears because of non-perfect convergence to the global or local solution, usually caused by a non-zero stopping criterion. The second error is the local minima error, which occurs when the objective function is not convex and/or the feasible solution space is not convex. The magnitude of the errors, their relative importance in comparison to other errors as well as their clinical significance in terms of tumour control probability (TCP) and normal tissue complication probability (NTCP) were investigated. Two inherently different optimizers, a stochastic simulated annealing and deterministic gradient method were compared on a clinical example. It was found that for typical optimization the optimizer convergence errors are rather small, especially compared to other convergence errors, e.g., convergence errors due to inaccuracy of the current dose calculation algorithms. This indicates that stopping criteria could often be relaxed leading into optimization speed-ups. The local minima errors were also found to be relatively small and typically in the range of the dose calculation convergence errors. Even for the cases where significantly higher objective function scores were obtained the local minima errors were not significantly higher. Clinical evaluation of the optimizer convergence error showed good correlation between the convergence of the clinical TCP or NTCP measures and convergence of the physical dose distribution. On the other hand, the local minima errors resulted in significantly different TCP or NTCP values (up to a factor of 2) indicating clinical importance of the local minima produced by physical optimization

  3. Best strategies to implement clinical pathways in an emergency department setting: study protocol for a cluster randomized controlled trial.

    Science.gov (United States)

    Jabbour, Mona; Curran, Janet; Scott, Shannon D; Guttman, Astrid; Rotter, Thomas; Ducharme, Francine M; Lougheed, M Diane; McNaughton-Filion, M Louise; Newton, Amanda; Shafir, Mark; Paprica, Alison; Klassen, Terry; Taljaard, Monica; Grimshaw, Jeremy; Johnson, David W

    2013-05-22

    The clinical pathway is a tool that operationalizes best evidence recommendations and clinical practice guidelines in an accessible format for 'point of care' management by multidisciplinary health teams in hospital settings. While high-quality, expert-developed clinical pathways have many potential benefits, their impact has been limited by variable implementation strategies and suboptimal research designs. Best strategies for implementing pathways into hospital settings remain unknown. This study will seek to develop and comprehensively evaluate best strategies for effective local implementation of externally developed expert clinical pathways. We will develop a theory-based and knowledge user-informed intervention strategy to implement two pediatric clinical pathways: asthma and gastroenteritis. Using a balanced incomplete block design, we will randomize 16 community emergency departments to receive the intervention for one clinical pathway and serve as control for the alternate clinical pathway, thus conducting two cluster randomized controlled trials to evaluate this implementation intervention. A minimization procedure will be used to randomize sites. Intervention sites will receive a tailored strategy to support full clinical pathway implementation. We will evaluate implementation strategy effectiveness through measurement of relevant process and clinical outcomes. The primary process outcome will be the presence of an appropriately completed clinical pathway on the chart for relevant patients. Primary clinical outcomes for each clinical pathway include the following: Asthma--the proportion of asthmatic patients treated appropriately with corticosteroids in the emergency department and at discharge; and Gastroenteritis--the proportion of relevant patients appropriately treated with oral rehydration therapy. Data sources include chart audits, administrative databases, environmental scans, and qualitative interviews. We will also conduct an overall process

  4. PROPOSAL OF A CLINICAL CARE PATHWAY FOR THE MANAGEMENT OF ACUTE UPPER GASTROINTESTINAL BLEEDING.

    Science.gov (United States)

    Franco, Matheus Cavalcante; Nakao, Frank Shigueo; Rodrigues, Rodrigo; Maluf-Filho, Fauze; Paulo, Gustavo Andrade de; Libera, Ermelindo Della

    2015-12-01

    Upper gastrointestinal bleeding implies significant clinical and economic repercussions. The correct establishment of the latest therapies for the upper gastrointestinal bleeding is associated with reduced in-hospital mortality. The use of clinical pathways for the upper gastrointestinal bleeding is associated with shorter hospital stay and lower hospital costs. The primary objective is the development of a clinical care pathway for the management of patients with upper gastrointestinal bleeding, to be used in tertiary hospital. It was conducted an extensive literature review on the management of upper gastrointestinal bleeding, contained in the primary and secondary information sources. The result is a clinical care pathway for the upper gastrointestinal bleeding in patients with evidence of recent bleeding, diagnosed by melena or hematemesis in the last 12 hours, who are admitted in the emergency rooms and intensive care units of tertiary hospitals. In this compact and understandable pathway, it is well demonstrated the management since the admission, with definition of the inclusion and exclusion criteria, passing through the initial clinical treatment, posterior guidance for endoscopic therapy, and referral to rescue therapies in cases of persistent or rebleeding. It was also included the care that must be taken before hospital discharge for all patients who recover from an episode of bleeding. The introduction of a clinical care pathway for patients with upper gastrointestinal bleeding may contribute to standardization of medical practices, decrease in waiting time for medications and services, length of hospital stay and costs.

  5. The role of clinical pathway on the outcomes of ischemic stroke patients at Bethesda Hospital Yogyakarta

    Directory of Open Access Journals (Sweden)

    Francisca Diana Alexandra, Iwan Dwiprahasto, Rizaldy Pinzon

    2014-04-01

    Full Text Available Stroke becomes world health problem all over the world because it is the causal factor of high mortality and disability. Good and well-organized process of healthcare service will improve the outcome of the patients with stroke. Clinical pathway may be used as clear standard to help reduce unnecessary variations of medical treatment and measure. The study aimed at finding out the correlation between the use of clinical pathway and the outcome of the patients with ischemic stroke in Bethesda Hospital Yogyakarta. It was an observational and analytic study with cohort restorative study design. The author compared the outcomes of acute ischemic stroke between the group with clinical pathway and the group without the clinical pathway. Data was collected using consecutive sampling from the electronic registry and medical record data of the patients from January 1st, 2011 to December 31st, 2011. It was conducted to 124 patients with ischemic stroke assigned to two groups (the first groups of 62 patients with clinical pathway and the second groups of 62 patients without clinical pathway. The basic characteristics of the two groups were the same. The results of the analysis showed that there was a significant decrease in the incidence of complication and a significant increase in the use of antiplatelete drugs, antidiabetic drugs and statin as secondary preventive measure of the recurrent stroke. There was not any significant difference in the duration of the hospitalized healthcare, the financing and the mortality between the two observation groups. The study indicated that the use of the clinical pathway in the stroke treatment improved the outcome of the patients with stroke. It was necessary to conduct further study to evaluate the effectiveness of the clinical pathway in improving the outcome of the patients with bigger number of the subjects and the longer period of time.

  6. [Analysis of Applying Chinese Medical Clinical Pathway for Treating Attention-deficit Hyperactivity Disorder].

    Science.gov (United States)

    Guo, Yu-qing; Han, Xin-min; Zhu, Xian-kang; Zhou, Zheng; Ma, Bing-xiang; Zhang, Bao-qing; Li, Yan-ning; Feng, Yu-lin; Xue, Zheng; Wang, Yong-hong; Li, Yi-min; Jiang, Zhi-mei; Xu, Jin-xing; Yue, Wei-zhen; Xiang, Xi-xiong

    2015-12-01

    To evaluate the application effect of Chinese medical clinical pathway for treating attention-deficit hyperactivity disorder (ADHD), and to provide evidence for further improving clinical pathways. Totally 270 ADHD children patients were recruited and treated at pediatrics clinics of 9 cooperative hospitals from December 2011 to December 2012. The treatment course for all was 3 months. Scores of attention deficit and hyperactivity rating scale, scores of behavior, Conners index of hyperactivity (CIH), and Chinese medical syndrome scores were compared between before and after treatment. The efficacy difference in various sexes, ages, and disease courses were evaluated by judging standards for Chinese medical syndrome and ADHD. Fifteen children patients who entered clinical pathway dropped out, and the rest 255 completed this trial. Compared with before treatment, total scores of attention deficit and hyperactivity rating scale, scores of attention deficit and hyperactivity rating scale, CIH, and Chinese medical syndrome scores obviously decreased (all P < 0.01). The total effective rate in disease efficacy was 87.8% (224/255 cases), and the total effective rate in Chinese medical syndrome curative effect was 87.5% (223/255 cases). The clinical curative effect was not influenced by age, gender, or course of disease when statistically analyzed from judging standards for Chinese medical syndrome or for disease efficacy. Intervention by Chinese medical clinical pathway could improve ADHD patients' symptoms, and its efficacy was not influenced by sex, age, or course of disease.

  7. Experimenting clinical pathways in general practice: a focus group investigation with Italian general practitioners

    Directory of Open Access Journals (Sweden)

    Lucia Zannini

    2012-07-01

    Full Text Available Background. Clinical governance is considered crucial in primary care. Since 2005, clinical pathways have been experimentally implemented at the Local Health Authority of Monza Brianza (ASLMB, Italy, to develop general practitioners’ (GPs care of patients affected by some chronic diseases. The experimentation was aimed at introducing clinical governance in primary care, increasing GPs’ involvement in the care of their patients, and improving both patients’ and professionals’ satisfaction. In the period 2005-2006, 12% of the 763 employed GPs in the ASLMB were involved in the experiment, while this percentage increased to 15-20% in 2007-2008. Design and Methods. Twenty-four GPs were purposively sampled, randomly divided into two groups and asked to participate in focus groups (FGs held in 2008, aimed at evaluating their perception of the experiment. The FGs were audio-recorded, dialogues were typed out and undergone to a thematic analysis, according to the Interpretative Phenomenological Approach. Results. Four major themes emerged: i clinical pathways can result in GPs working in a more efficient and effective fashion; ii they can assure higher levels of both patient and professional satisfaction, since they sustain a caring approach and strengthen the GPs’ role; iii nevertheless, clinical pathways increase the bureaucratic workload and problems can arise in relationships among GPs and the LHA; iv the implementation of clinical pathways can be improved, especially by reducing bureaucracy and by assuring their continuity. Conclusions. Managerial aspects should be considered with care in order to experimentally introduce clinical pathways in general practice, and continuity of the experimentation should be guaranteed to improve GPs’ adherence and commitment.

  8. Clinical Pathways: A Catalyst for the Adoption of Hypofractionation for Early-Stage Breast Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Chapman, Bhavana V.; Rajagopalan, Malolan S.; Heron, Dwight E.; Flickinger, John C.; Beriwal, Sushil, E-mail: beriwals@upmc.edu

    2015-11-15

    Purpose: Hypofractionated whole-breast irradiation (HF-WBI) remains underutilized in the United States despite support by multiple clinical trials. We evaluated the success of iterative modifications of our breast cancer clinical pathway on the adoption of HF-WBI in a large, integrated radiation oncology network. Methods and Materials: The breast clinical pathway was modified in January 2011 (Amendment 1) to recommend HF-WBI as the first option for women ≥70 of age with stages 0 to IIA, while maintaining conventional fractionation (CF) as a pathway-concordant secondary option. In January 2013 (Amendment 2), the pathway's HF-WBI recommendation was extended to women ≥50 years of age. In January 2014 (Amendment 3), the pathway mandated HF-WBI as the only pathway-concordant option in women ≥50 years of age, and all pathway-discordant plans were subject to peer review and justification. Women ≥50 years of age with ductal carcinoma in situ or invasive breast cancer who underwent breast conserving surgery and adjuvant WBI were included in this analysis. Results: We identified 5112 patients from 2009 to 2014 who met inclusion criteria. From 2009 to 2012, the overall HF-WBI use rate was 8.3%. Following Amendments 2 and 3 (2013 and 2014, respectively), HF-WBI use significantly increased to 21.8% (17.3% in the community, 39.7% at academic sites) and 76.7% (75.5% in the community, 81.4% at academic sites), respectively (P<.001). Compared to 2009 to 2012, the relative risk of using HF-WBI was 7.9 (95% confidence interval: 7.1-8.6, P<.001) and 10.7 (95% CI: 10.3-11.0, P<.001), respectively, after Amendments 2 and 3, respectively. Age ≥70 and treatment at an academic site increased the likelihood of receiving HF-WBI in 2009 to 2012 and following Amendment 2 (P<.001). Conclusions: This study demonstrates the transformative effect of a clinical pathway on patterns of care for breast radiation therapy. Although our initial HF-WBI use rate was low (8%-22%) and

  9. Clinical Pathways: A Catalyst for the Adoption of Hypofractionation for Early-Stage Breast Cancer

    International Nuclear Information System (INIS)

    Chapman, Bhavana V.; Rajagopalan, Malolan S.; Heron, Dwight E.; Flickinger, John C.; Beriwal, Sushil

    2015-01-01

    Purpose: Hypofractionated whole-breast irradiation (HF-WBI) remains underutilized in the United States despite support by multiple clinical trials. We evaluated the success of iterative modifications of our breast cancer clinical pathway on the adoption of HF-WBI in a large, integrated radiation oncology network. Methods and Materials: The breast clinical pathway was modified in January 2011 (Amendment 1) to recommend HF-WBI as the first option for women ≥70 of age with stages 0 to IIA, while maintaining conventional fractionation (CF) as a pathway-concordant secondary option. In January 2013 (Amendment 2), the pathway's HF-WBI recommendation was extended to women ≥50 years of age. In January 2014 (Amendment 3), the pathway mandated HF-WBI as the only pathway-concordant option in women ≥50 years of age, and all pathway-discordant plans were subject to peer review and justification. Women ≥50 years of age with ductal carcinoma in situ or invasive breast cancer who underwent breast conserving surgery and adjuvant WBI were included in this analysis. Results: We identified 5112 patients from 2009 to 2014 who met inclusion criteria. From 2009 to 2012, the overall HF-WBI use rate was 8.3%. Following Amendments 2 and 3 (2013 and 2014, respectively), HF-WBI use significantly increased to 21.8% (17.3% in the community, 39.7% at academic sites) and 76.7% (75.5% in the community, 81.4% at academic sites), respectively (P<.001). Compared to 2009 to 2012, the relative risk of using HF-WBI was 7.9 (95% confidence interval: 7.1-8.6, P<.001) and 10.7 (95% CI: 10.3-11.0, P<.001), respectively, after Amendments 2 and 3, respectively. Age ≥70 and treatment at an academic site increased the likelihood of receiving HF-WBI in 2009 to 2012 and following Amendment 2 (P<.001). Conclusions: This study demonstrates the transformative effect of a clinical pathway on patterns of care for breast radiation therapy. Although our initial HF-WBI use rate was low (8%-22%) and

  10. PROPOSAL OF A CLINICAL CARE PATHWAY FOR THE MANAGEMENT OF ACUTE UPPER GASTROINTESTINAL BLEEDING

    Directory of Open Access Journals (Sweden)

    Matheus Cavalcante FRANCO

    2015-12-01

    Full Text Available Background - Upper gastrointestinal bleeding implies significant clinical and economic repercussions. The correct establishment of the latest therapies for the upper gastrointestinal bleeding is associated with reduced in-hospital mortality. The use of clinical pathways for the upper gastrointestinal bleeding is associated with shorter hospital stay and lower hospital costs. Objective - The primary objective is the development of a clinical care pathway for the management of patients with upper gastrointestinal bleeding, to be used in tertiary hospital. Methods - It was conducted an extensive literature review on the management of upper gastrointestinal bleeding, contained in the primary and secondary information sources. Results - The result is a clinical care pathway for the upper gastrointestinal bleeding in patients with evidence of recent bleeding, diagnosed by melena or hematemesis in the last 12 hours, who are admitted in the emergency rooms and intensive care units of tertiary hospitals. In this compact and understandable pathway, it is well demonstrated the management since the admission, with definition of the inclusion and exclusion criteria, passing through the initial clinical treatment, posterior guidance for endoscopic therapy, and referral to rescue therapies in cases of persistent or rebleeding. It was also included the care that must be taken before hospital discharge for all patients who recover from an episode of bleeding. Conclusion - The introduction of a clinical care pathway for patients with upper gastrointestinal bleeding may contribute to standardization of medical practices, decrease in waiting time for medications and services, length of hospital stay and costs.

  11. Experimenting Clinical Pathways in General Practice: a Focus Group Investigation with Italian General Practitioners

    Science.gov (United States)

    Zannini, Lucia; Cattaneo, Cesarina; Peduzzi, Paolo; Lopiccoli, Silvia; Auxilia, Francesco

    2012-01-01

    Background Clinical governance is considered crucial in primary care. Since 2005, clinical pathways have been experimentally implemented at the Local Health Authority of Monza Brianza (ASLMB), Italy, to develop general practitioners’ (GPs) care of patients affected by some chronic diseases. The experimentation was aimed at introducing clinical governance in primary care, increasing GPs’ involvement in the care of their patients, and improving both patients’ and professionals’ satisfaction. In the period 2005-2006, 12% of the 763 employed GPs in the ASLMB were involved in the experiment, while this percentage increased to 15-20% in 2007-2008. Design and Methods Twenty-four GPs were purposively sampled, randomly divided into two groups and asked to participate in focus groups (FGs) held in 2008, aimed at evaluating their perception of the experiment. The FGs were audio-recorded, dialogues were typed out and undergone to a thematic analysis, according to the Interpretative Phenomenological Approach. Results Four major themes emerged: i) clinical pathways can result in GPs working in a more efficient and effective fashion; ii) they can assure higher levels of both patient and professional satisfaction, since they sustain a caring approach and strengthen the GPs’ role; iii) nevertheless, clinical pathways increase the bureaucratic workload and problems can arise in relationships among GPs and the LHA; iv) the implementation of clinical pathways can be improved, especially by reducing bureaucracy and by assuring their continuity. Conclusions Managerial aspects should be considered with care in order to experimentally introduce clinical pathways in general practice, and continuity of the experimentation should be guaranteed to improve GPs’ adherence and commitment. Acknowledgments the Authors thank Dr. AP. Cantù and Dr D. Cereda who participated in the two focus groups as observers. PMID:25181354

  12. Feasibility of a Clinical Pathway with Early Oral Intake and Discharge for Laparoscopic Gastrectomy.

    Science.gov (United States)

    Nakagawa, M; Tomii, C; Inokuchi, M; Otsuki, S; Kojima, K

    2017-12-01

    Although some studies have reported the safety of early oral intake after gastrectomy, it still remains controversial. This study focused on the feasibility of a clinical pathway with early oral intake and discharge setting for exclusively laparoscopic distal gastrectomy. A clinical pathway was applied to 403 patients until December 2014. In the protocol, patients are allowed to take a sip of water and a soft diet on the first and second days after the operation, respectively, and the discharge day is set as the fifth to seventh day after the operation. Clinicopathological variables were prospectively collected, and risk factors for discharge variances were analyzed. The completion rate of the clinical pathway was 76.9%. There were five re-admissions (1.2%). The overall morbidity rate was 18% ( n = 72), and major complications (Clavien-Dindo IIIa or greater) occurred in 13 patients (3%). Complications were the causes for discharge variances in 68 cases (73%), while the attending surgeons' judgment was the cause in 25 cases (27%). On multivariate analysis, age (odds ratio = 2.23, 95% confidence interval = 1.38-3.60, p = 0.001) and operative time (odds ratio = 2.38, 95% confidence interval = 1.45-3.98, p = 0.001) were independent risk factors for discharge variances. A high completion rate of a clinical pathway with early oral intake and discharge setting for laparoscopic distal gastrectomy was achievable with an acceptably low re-admission rate. Laparoscopic distal gastrectomy is recommended as a first step for a clinical pathway with an early oral intake and discharge protocol.

  13. What is a clinical pathway? Refinement of an operational definition to identify clinical pathway studies for a Cochrane systematic review.

    Science.gov (United States)

    Lawal, Adegboyega K; Rotter, Thomas; Kinsman, Leigh; Machotta, Andreas; Ronellenfitsch, Ulrich; Scott, Shannon D; Goodridge, Donna; Plishka, Christopher; Groot, Gary

    2016-02-23

    Clinical pathways (CPWs) are a common component in the quest to improve the quality of health. CPWs are used to reduce variation, improve quality of care, and maximize the outcomes for specific groups of patients. An ongoing challenge is the operationalization of a definition of CPW in healthcare. This may be attributable to both the differences in definition and a lack of conceptualization in the field of clinical pathways. This correspondence article describes a process of refinement of an operational definition for CPW research and proposes an operational definition for the future syntheses of CPWs literature. Following the approach proposed by Kinsman et al. (BMC Medicine 8(1):31, 2010) and Wieland et al. (Alternative Therapies in Health and Medicine 17(2):50, 2011), we used a four-stage process to generate a five criteria checklist for the definition of CPWs. We refined the operational definition, through consensus, merging two of the checklist's criteria, leading to a more inclusive criterion for accommodating CPW studies conducted in various healthcare settings. The following four criteria for CPW operational definition, derived from the refinement process described above, are (1) the intervention was a structured multidisciplinary plan of care; (2) the intervention was used to translate guidelines or evidence into local structures; (3) the intervention detailed the steps in a course of treatment or care in a plan, pathway, algorithm, guideline, protocol or other 'inventory of actions' (i.e. the intervention had time-frames or criteria-based progression); and (4) the intervention aimed to standardize care for a specific population. An intervention meeting all four criteria was considered to be a CPW. The development of operational definitions for complex interventions is a useful approach to appraise and synthesize evidence for policy development and quality improvement.

  14. Preserving breastfeeding for the rehospitalized infant: a clinical pathway.

    Science.gov (United States)

    Spatz, Diane L; Goldschmidt, Karen A

    2006-01-01

    The benefits of feeding newborns with human milk are well established. Unfortunately some hospital practices do not support successful breastfeeding; practices such as early hospital discharge after birth, lack of appropriate follow-up primary care providers, and lack of access to breastfeeding support services can contribute to breastfeeding failure, as well as morbidity and mortality in the infant. Infants experiencing breastfeeding difficulties are sometimes admitted to the hospital with diagnoses such as hyperbilirubinemia/jaundice, dehydration/hypernatremia, rule out sepsis, and weight loss/failure to thrive. This article describes a clinical pathway developed with the express purpose of maintaining and enhancing lactation in mother-infant dyads experiencing breastfeeding difficulties. The goal of the pathway is to maintain lactation and breastfeeding while returning the infant to a state of health. A key focus of the pathway is milk transfer, a concept that is missing from much of the research on lactation difficulties. The pathway considers breastfeeding from both a maternal and an infant perspective, with a goal of preserving breastfeeding. It uses technology to support the breastfeeding process and could be useful for all practitioners working with mother-infant dyads experiencing breastfeeding difficulties.

  15. Implementation of a clinical pathway may improve alcohol treatment outcome

    DEFF Research Database (Denmark)

    Nielsen, Anette Søgaard; Nielsen, Bent

    2015-01-01

    This article describes the design, implementation, and evaluation of a clinical pathway system in a two-cohort quasi-experimental study before and after implementation, controlling for confounders. The main outcome measures were retention in care and sensible alcohol use (defined as abstinent...

  16. Rising utilization of inpatient pediatric asthma pathways.

    Science.gov (United States)

    Kaiser, Sunitha V; Rodean, Jonathan; Bekmezian, Arpi; Hall, Matt; Shah, Samir S; Mahant, Sanjay; Parikh, Kavita; Morse, Rustin; Puls, Henry; Cabana, Michael D

    2018-02-01

    Clinical pathways are detailed care plans that operationalize evidence-based guidelines into an accessible format for health providers. Their goal is to link evidence to practice to optimize patient outcomes and delivery efficiency. It is unknown to what extent inpatient pediatric asthma pathways are being utilized nationally. (1) Describe inpatient pediatric asthma pathway design and implementation across a large hospital network. (2) Compare characteristics of hospitals with and without pathways. We conducted a descriptive, cross-sectional, survey study of hospitals in the Pediatric Research in Inpatient Settings Network (75% children's hospitals, 25% community hospitals). Our survey determined if each hospital used a pathway and pathway characteristics (e.g. pathway elements, implementation methods). Hospitals with and without pathways were compared using Chi-square tests (categorical variables) and Student's t-tests (continuous variables). Surveys were distributed to 3-5 potential participants from each hospital and 302 (74%) participants responded, representing 86% (106/123) of surveyed hospitals. From 2005-2015, the proportion of hospitals utilizing inpatient asthma pathways increased from 27% to 86%. We found variation in pathway elements, implementation strategies, electronic medical record integration, and compliance monitoring across hospitals. Hospitals with pathways had larger inpatient pediatric programs [mean 12.1 versus 6.1 full-time equivalents, p = 0.04] and were more commonly free-standing children's hospitals (52% versus 23%, p = 0.05). From 2005-2015, there was a dramatic rise in implementation of inpatient pediatric asthma pathways. We found variation in many aspects of pathway design and implementation. Future studies should determine optimal implementation strategies to better support hospital-level efforts in improving pediatric asthma care and outcomes.

  17. Clinical pathway across tertiary and community care after an interventional cardiology procedure.

    Science.gov (United States)

    Doran, K; Sampson, B; Staus, R; Ahern, C; Schiro, D

    1997-01-01

    Many patients who receive medical interventional cardiology procedures at a tertiary hospital live outside the metropolitan area and may experience fragmentation in care, less emotional support by family members, inaccurate and delayed communication, and lack of educational follow-up on discharge from the hospital. A clinical pathway titled "Heart Health Care Patterns" was developed to link acute phase, recovery phase, rehabilitation phase, and enhancement/maintenance phase. The 12-month clinical pathway combines Gordon's Functional Health Patterns and the Omaha System developed by the Omaha Visiting Nurse Association. The rating scale for outcomes assesses the patient at different phases to provide objective data and information throughout the year.

  18. Neuro-ophthalmological conditions: Study of the clinical care pathway.

    Science.gov (United States)

    Layat, I; Challe, G; LeHoang, P; Bodaghi, B; Touitou, V

    2017-06-01

    Neuro-ophthalmologic conditions require specialized multidisciplinary management, both medical and surgical, for patients affected by visual loss due to nervous system disease. The primary goal of this study is to define the specificity of neuro-ophthalmology within the realm of visual health. The secondary goal is to review clinical care pathways by studying the organization of management, in terms of accessibility to care and personalization of the care pathway. A field study was carried out from February to June 2015, within the ophthalmology service of the Pitié-Salpêtrière University Medical Center in Paris. A 30-minute interview with the patient before or after his or her neuro-ophthalmology consultation was performed, to describe the clinical care pathway. The medical records of interviewed patients were also analyzed. Seventeen care pathways (10 women and 7 men) were reviewed. The mean age at appearance of visual involvement was 44.5 years (±8.4 years). If we exclude 3 patients over 66 years and retired, 35.71% were active, 35.71% were disabled, and 28.57% were on sick leave. Ten patients (58.82%) met the criteria for admission to long-term care. The first step had been carried out by local private practitioners. The first physician seen was the general medicine physician (59%), then the private ophthalmologist on an emergency basis (17%). On average, patients went through 8 steps during their care pathway (from 6 to 10 steps) and 14 medical departments were involved. The study showed collaboration with the other services of the University Hospital Department of Vision and Disabilities (notably with the Fondation Rothschild, the Quinze-Vingts National Ophthalmology Hospital, and the Fondation Sainte-Marie). In addition to rehabilitation services, health care professionals participating in the outpatient care of the patients included an orthoptist (11.7%), a psychologist (11.7%), and an optician specializing in low vision for visual aids. Finally

  19. Next-generation mTOR inhibitors in clinical oncology: how pathway complexity informs therapeutic strategy.

    LENUS (Irish Health Repository)

    Wander, Seth A

    2011-04-01

    Mammalian target of rapamycin (mTOR) is a PI3K-related kinase that regulates cell growth, proliferation, and survival via mTOR complex 1 (mTORC1) and mTORC2. The mTOR pathway is often aberrantly activated in cancers. While hypoxia, nutrient deprivation, and DNA damage restrain mTORC1 activity, multiple genetic events constitutively activate mTOR in cancers. Here we provide a brief overview of the signaling pathways up- and downstream of mTORC1 and -2, and discuss the insights into therapeutic anticancer targets - both those that have been tried in the clinic with limited success and those currently under clinical development - that knowledge of these pathways gives us.

  20. Environmental and energy system analysis of bio-methane production pathways: A comparison between feedstocks and process optimizations

    International Nuclear Information System (INIS)

    Pierie, F.; Someren, C.E.J. van; Benders, R.M.J.; Bekkering, J.; Gemert, W.J.Th. van; Moll, H.C.

    2015-01-01

    Highlights: • Using local waste feedstock and optimization improves environmental sustainability. • Optimization favors waste feedstocks. • Transport distances should not exceed 150 km. • The produced energy should be used for powering the green gas process first. • The AD process should be used primarily for local waste treatment. - Abstract: The energy efficiency and sustainability of an anaerobic green gas production pathway was evaluated, taking into account five biomass feedstocks, optimization of the green gas production pathway, replacement of current waste management pathways by mitigation, and transport of the feedstocks. Sustainability is expressed by three main factors: efficiency in (Process) Energy Returned On Invested (P)EROI, carbon footprint in Global Warming Potential GWP(100), and environmental impact in EcoPoints. The green gas production pathway operates on a mass fraction of 50% feedstock with 50% manure. The sustainability of the analyzed feedstocks differs substantially, favoring biomass waste flows over, the specially cultivated energy crop, maize. The use of optimization, in the shape of internal energy production, green gas powered trucks, and mitigation can significantly improve the sustainability for all feedstocks, but favors waste materials. Results indicate a possible improvement from an average (P)EROI for all feedstocks of 2.3 up to an average of 7.0 GJ/GJ. The carbon footprint can potentially be reduced from an average of 40 down to 18 kgCO_2eq/GJ. The environmental impact can potentially be reduced from an average of 5.6 down to 1.8 Pt/GJ. Internal energy production proved to be the most effective optimization. However, the use of optimization aforementioned will result in les green gas injected into the gas grid as it is partially consumed internally. Overall, the feedstock straw was the most energy efficient, where the feedstock harvest remains proved to be the most environmentally sustainable. Furthermore, transport

  1. Evaluating glymphatic pathway function utilizing clinically relevant intrathecal infusion of CSF tracer.

    Science.gov (United States)

    Yang, Lijun; Kress, Benjamin T; Weber, Harris J; Thiyagarajan, Meenakshisundaram; Wang, Baozhi; Deane, Rashid; Benveniste, Helene; Iliff, Jeffrey J; Nedergaard, Maiken

    2013-05-01

    Neurodegenerative diseases such as Alzheimer's are associated with the aggregation of endogenous peptides and proteins that contribute to neuronal dysfunction and loss. The glymphatic system, a brain-wide perivascular pathway along which cerebrospinal fluid (CSF) and interstitial fluid (ISF) rapidly exchange, has recently been identified as a key contributor to the clearance of interstitial solutes from the brain, including amyloid β. These findings suggest that measuring changes in glymphatic pathway function may be an important prognostic for evaluating neurodegenerative disease susceptibility or progression. However, no clinically acceptable approach to evaluate glymphatic pathway function in humans has yet been developed. Time-sequenced ex vivo fluorescence imaging of coronal rat and mouse brain slices was performed at 30-180 min following intrathecal infusion of CSF tracer (Texas Red- dextran-3, MW 3 kD; FITC- dextran-500, MW 500 kD) into the cisterna magna or lumbar spine. Tracer influx into different brain regions (cortex, white matter, subcortical structures, and hippocampus) in rat was quantified to map the movement of CSF tracer following infusion along both routes, and to determine whether glymphatic pathway function could be evaluated after lumbar intrathecal infusion. Following lumbar intrathecal infusions, small molecular weight TR-d3 entered the brain along perivascular pathways and exchanged broadly with the brain ISF, consistent with the initial characterization of the glymphatic pathway in mice. Large molecular weight FITC-d500 remained confined to the perivascular spaces. Lumbar intrathecal infusions exhibited a reduced and delayed peak parenchymal fluorescence intensity compared to intracisternal infusions. Lumbar intrathecal contrast delivery is a clinically useful approach that could be used in conjunction with dynamic contrast enhanced MRI nuclear imaging to assess glymphatic pathway function in humans.

  2. A cluster randomized controlled trial of a clinical pathway for hospital treatment of heart failure: study design and population

    Directory of Open Access Journals (Sweden)

    Gardini Andrea

    2007-11-01

    Full Text Available Abstract Background The hospital treatment of heart failure frequently does not follow published guidelines, potentially contributing to the high morbidity, mortality and economic cost of this disorder. Consequently the development of clinical pathways has the potential to reduce the current variability in care, enhance guideline adherence, and improve outcomes for patients. Despite enthusiasm and diffusion, the widespread acceptance of clinical pathways remain questionable because very little prospective controlled data demonstrated their effectiveness. The Experimental Prospective Study on the Effectiveness and Efficiency of the Implementation of Clinical Pathways was designed in order to conduct a rigorous evaluation of clinical pathways in hospital treatment of acute heart failure. The primary objective of the trial was to evaluate the effectiveness of the implementation of clinical pathways for hospital treatment of heart failure in Italian hospitals. Methods/design Two-arm, cluster-randomized trial. 14 community hospitals were randomized either to arm 1 (clinical pathway: appropriate use of practice guidelines and supplies of drugs and ancillary services, new organization and procedures, patient education, etc. or to arm 2 (no intervention, usual care. 424 patients sample (212 in each group, 80% of power at the 5% significance level (two-sided. The primary outcome measure is in-hospital mortality. We will also analyze the impact of the clinical pathways comparing the length and the appropriateness of the stay, the rate of unscheduled readmissions, the customers' satisfaction and the costs treating the patients with the pathways and with the current practice along all the observation period. The quality of the care will be assessed by monitoring the use of diagnostic and therapeutic procedures during hospital stay and by measuring key quality indicators at discharge. Discussion This paper examines the design of the evaluation of a complex

  3. Pros and Cons of Clinical Pathway Software Management: A Qualitative Study.

    Science.gov (United States)

    Aarnoutse, M F; Brinkkemper, S; de Mul, M; Askari, M

    2018-01-01

    In this study we aimed to assess the perceived effectiveness of clinical pathway management software for healthcare professionals. A case study on the clinical pathway management software program Check-It was performed in three departments at an academic medical center. Four months after the implementation of the software, interviews were held with healthcare professionals who work with the system. The interview questions were posed in a semi-structured interview format and the participant were asked about the perceived positive or negative effects of Check-It, and whether they thought the software is effective for them. The interviews were recorded and transcribed based on grounded theory, using different coding techniques. Our results showed fewer overlooked tasks, pre-filled orders and letters, better overview, and increased protocol insight as positive aspects of using the software. Being not flexible enough was experienced as a negative aspect.

  4. Cost-effectiveness analysis of a postoperative clinical care pathway in head and neck surgery with microvascular reconstruction

    OpenAIRE

    Dautremont, Jonathan F; Rudmik, Luke R; Yeung, Justin; Asante, Tiffany; Nakoneshny, Steve C; Hoy, Monica; Lui, Amanda; Chandarana, Shamir P; Matthews, Thomas W; Schrag, Christiaan; Dort, Joseph C

    2013-01-01

    Background The objective of this study is to evaluate the cost-effectiveness of a postoperative clinical care pathway for patients undergoing major head and neck oncologic surgery with microvascular reconstruction. Methods This is a comparative trial of a prospective treatment group managed on a postoperative clinical care pathway and a historical group managed prior to pathway implementation. Effectiveness outcomes evaluated were total hospital days, return to OR, readmission to ICU and rate...

  5. An Interactive Platform to Visualize Data-Driven Clinical Pathways for the Management of Multiple Chronic Conditions.

    Science.gov (United States)

    Zhang, Yiye; Padman, Rema

    2017-01-01

    Patients with multiple chronic conditions (MCC) pose an increasingly complex health management challenge worldwide, particularly due to the significant gap in our understanding of how to provide coordinated care. Drawing on our prior research on learning data-driven clinical pathways from actual practice data, this paper describes a prototype, interactive platform for visualizing the pathways of MCC to support shared decision making. Created using Python web framework, JavaScript library and our clinical pathway learning algorithm, the visualization platform allows clinicians and patients to learn the dominant patterns of co-progression of multiple clinical events from their own data, and interactively explore and interpret the pathways. We demonstrate functionalities of the platform using a cluster of 36 patients, identified from a dataset of 1,084 patients, who are diagnosed with at least chronic kidney disease, hypertension, and diabetes. Future evaluation studies will explore the use of this platform to better understand and manage MCC.

  6. How Effective Are Clinical Pathways With and Without Online Peer-Review? An Analysis of Bone Metastases Pathway in a Large, Integrated National Cancer Institute-Designated Comprehensive Cancer Center Network

    Energy Technology Data Exchange (ETDEWEB)

    Beriwal, Sushil, E-mail: beriwals@upmc.edu [Department of Radiation Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, PA (United States); Rajagopalan, Malolan S.; Flickinger, John C.; Rakfal, Susan M. [Department of Radiation Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, PA (United States); Rodgers, Edwin [Via Oncology, Pittsburgh, PA (United States); Heron, Dwight E. [Department of Radiation Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, PA (United States)

    2012-07-15

    Purpose: Clinical pathways are an important tool used to manage the quality in health care by standardizing processes. This study evaluated the impact of the implementation of a peer-reviewed clinical pathway in a large, integrated National Cancer Institute-Designated Comprehensive Cancer Center Network. Methods: In 2003, we implemented a clinical pathway for the management of bone metastases with palliative radiation therapy. In 2009, we required the entry of management decisions into an online tool that records pathway choices. The pathway specified 1 or 5 fractions for symptomatic bone metastases with the option of 10-14 fractions for certain clinical situations. The data were obtained from 13 integrated sites (3 central academic, 10 community locations) from 2003 through 2010. Results: In this study, 7905 sites were treated with 64% of courses delivered in community practice and 36% in academic locations. Academic practices were more likely than community practices to treat with 1-5 fractions (63% vs. 23%; p < 0.0001). The number of delivered fractions decreased gradually from 2003 to 2010 for both academic and community practices (p < 0.0001); however, greater numbers of fractions were selected more often in community practices (p < 0.0001). Using multivariate logistic regression, we found that a significantly greater selection of 1-5 fractions developed after implementation online pathway monitoring (2009) with an odds ratio of 1.2 (confidence interval, 1.1-1.4) for community and 1.3 (confidence interval, 1.1-1.6) for academic practices. The mean number of fractions also decreased after online peer review from 6.3 to 6.0 for academic (p = 0.07) and 9.4 to 9.0 for community practices (p < 0.0001). Conclusion: This is one of the first studies to examine the efficacy of a clinical pathway for radiation oncology in an integrated cancer network. Clinical pathway implementation appears to be effective in changing patterns of care, particularly with online clinical

  7. How Effective Are Clinical Pathways With and Without Online Peer-Review? An Analysis of Bone Metastases Pathway in a Large, Integrated National Cancer Institute–Designated Comprehensive Cancer Center Network

    International Nuclear Information System (INIS)

    Beriwal, Sushil; Rajagopalan, Malolan S.; Flickinger, John C.; Rakfal, Susan M.; Rodgers, Edwin; Heron, Dwight E.

    2012-01-01

    Purpose: Clinical pathways are an important tool used to manage the quality in health care by standardizing processes. This study evaluated the impact of the implementation of a peer-reviewed clinical pathway in a large, integrated National Cancer Institute–Designated Comprehensive Cancer Center Network. Methods: In 2003, we implemented a clinical pathway for the management of bone metastases with palliative radiation therapy. In 2009, we required the entry of management decisions into an online tool that records pathway choices. The pathway specified 1 or 5 fractions for symptomatic bone metastases with the option of 10–14 fractions for certain clinical situations. The data were obtained from 13 integrated sites (3 central academic, 10 community locations) from 2003 through 2010. Results: In this study, 7905 sites were treated with 64% of courses delivered in community practice and 36% in academic locations. Academic practices were more likely than community practices to treat with 1–5 fractions (63% vs. 23%; p < 0.0001). The number of delivered fractions decreased gradually from 2003 to 2010 for both academic and community practices (p < 0.0001); however, greater numbers of fractions were selected more often in community practices (p < 0.0001). Using multivariate logistic regression, we found that a significantly greater selection of 1–5 fractions developed after implementation online pathway monitoring (2009) with an odds ratio of 1.2 (confidence interval, 1.1–1.4) for community and 1.3 (confidence interval, 1.1–1.6) for academic practices. The mean number of fractions also decreased after online peer review from 6.3 to 6.0 for academic (p = 0.07) and 9.4 to 9.0 for community practices (p < 0.0001). Conclusion: This is one of the first studies to examine the efficacy of a clinical pathway for radiation oncology in an integrated cancer network. Clinical pathway implementation appears to be effective in changing patterns of care, particularly with

  8. Optimism and recovery after acute coronary syndrome: a clinical cohort study.

    Science.gov (United States)

    Ronaldson, Amy; Molloy, Gerard J; Wikman, Anna; Poole, Lydia; Kaski, Juan-Carlos; Steptoe, Andrew

    2015-04-01

    Optimism is associated with reduced cardiovascular mortality, but its impact on recovery after acute coronary syndrome (ACS) is poorly understood. We hypothesized that greater optimism would lead to more effective physical and emotional adaptation after ACS and would buffer the impact of persistent depressive symptoms on clinical outcomes. This prospective observational clinical study took place in an urban general hospital and involved 369 patients admitted with a documented ACS. Optimism was assessed with a standardized questionnaire. The main outcomes were physical health status, depressive symptoms, smoking, physical activity, and fruit and vegetable consumption measured 12 months after ACS, and composite major adverse cardiac events (cardiovascular death, readmission with reinfarction or unstable angina, and coronary artery bypass graft surgery) assessed over an average of 45.7 months. We found that optimism predicted better physical health status 12 months after ACS independently of baseline physical health, age, sex, ethnicity, social deprivation, and clinical risk factors (B = 0.65, 95% confidence interval [CI] = 0.10-1.20). Greater optimism also predicted reduced risk of depressive symptoms (odds ratio = 0.82, 95% CI = 0.74-0.90), more smoking cessation, and more fruit and vegetable consumption at 12 months. Persistent depressive symptoms 12 months after ACS predicted major adverse cardiac events over subsequent years (odds ratio = 2.56, 95% CI = 1.16-5.67), but only among individuals low in optimism (optimism × depression interaction; p = .014). Optimism predicts better physical and emotional health after ACS. Measuring optimism may help identify individuals at risk. Pessimistic outlooks can be modified, potentially leading to improved recovery after major cardiac events.

  9. Optimizing value utilizing Toyota Kata methodology in a multidisciplinary clinic.

    Science.gov (United States)

    Merguerian, Paul A; Grady, Richard; Waldhausen, John; Libby, Arlene; Murphy, Whitney; Melzer, Lilah; Avansino, Jeffrey

    2015-08-01

    Value in healthcare is measured in terms of patient outcomes achieved per dollar expended. Outcomes and cost must be measured at the patient level to optimize value. Multidisciplinary clinics have been shown to be effective in providing coordinated and comprehensive care with improved outcomes, yet tend to have higher cost than typical clinics. We sought to lower individual patient cost and optimize value in a pediatric multidisciplinary reconstructive pelvic medicine (RPM) clinic. The RPM clinic is a multidisciplinary clinic that takes care of patients with anomalies of the pelvic organs. The specialties involved include Urology, General Surgery, Gynecology, and Gastroenterology/Motility. From May 2012 to November 2014 we performed time-driven activity-based costing (TDABC) analysis by measuring provider time for each step in the patient flow. Using observed time and the estimated hourly cost of each of the providers we calculated the final cost at the individual patient level, targeting clinic preparation. We utilized Toyota Kata methodology to enhance operational efficiency in an effort to optimize value. Variables measured included cost, time to perform a task, number of patients seen in clinic, percent value-added time (VAT) to patients (face to face time) and family experience scores (FES). At the beginning of the study period, clinic costs were $619 per patient. We reduced conference time from 6 min/patient to 1 min per patient, physician preparation time from 8 min to 6 min and increased Medical Assistant (MA) preparation time from 9.5 min to 20 min, achieving a cost reduction of 41% to $366 per patient. Continued improvements further reduced the MA preparation time to 14 min and the MD preparation time to 5 min with a further cost reduction to $194 (69%) (Figure). During this study period, we increased the number of appointments per clinic. We demonstrated sustained improvement in FES with regards to the families overall experience with their providers

  10. [Clinical pathway for hip fracture patients].

    Science.gov (United States)

    Sáez López, Pilar; Sánchez Hernández, Natalia; Paniagua Tejo, Sonsoles; Valverde García, José Antonio; Montero Díaz, Margarita; Alonso García, Noelia; Freites Esteve, Alfonso

    2015-01-01

    Hip fracture in the elderly often occurs in patients with high co-morbidity. Effective management requires a comprehensive and multidisciplinary approach. To evaluate the effect of a quality improvement intervention in the detection and treatment of complications in elderly patients admitted for hip fracture. A comparative study was conducted between two groups of patients admitted for hip fracture prior to 2010, and after a quality improvement intervention in 2013. The intervention consisted of implementing improved multidisciplinary measures in accordance with recent scientific evidence. The degree of compliance of the implemented measures was quantified. Patients admitted due to hip fracture in 2010 (216 patients) and 2013 (196 patients) were similar in age, sex, Barthel Index, and a reduced Charlson Index, although there were more comorbidities in 2013. After implementation of the protocols, the detection of delirium, malnutrition, anemia, and electrolyte disturbances increased. A larger number of patients in 2013 were precribed intravenous iron (24% more) and osteoporosis treatment (61.3% more). The average stay was reduced by 45.3% and surgical delay by 29.4%, achieving better functional efficiency. The implementation of a clinical pathway in geriatric patients with hip fracture is useful to detect and treat complications at an early stage, and to reduce pre-operative and overall stay, all without a negative clinical or functional impact. Copyright © 2014 SEGG. Published by Elsevier Espana. All rights reserved.

  11. Methylphenidate dose optimization for ADHD treatment: review of safety, efficacy, and clinical necessity

    Directory of Open Access Journals (Sweden)

    Huss M

    2017-07-01

    Full Text Available Michael Huss,1 Praveen Duhan,2 Preetam Gandhi,3 Chien-Wei Chen,4 Carsten Spannhuth,3 Vinod Kumar5 1Child and Adolescent Psychiatry, University Medicine, Mainz, Germany; 2Global Medical Affairs, Novartis Healthcare Pvt. Ltd., Hyderabad, India; 3Development Franchise, Established Medicine Neuroscience, Novartis Pharma AG, Basel, Switzerland; 4Biostatistics Cardio-Metabolic & Established Medicine, Novartis Pharmaceuticals Corporation, East Hanover, NJ, USA; 5Established Medicines, Novartis Pharmaceuticals Corporation, East Hanover, NJ, USA Abstract: Attention-deficit/hyperactivity disorder (ADHD is a chronic psychiatric disorder characterized by hyperactivity and/or inattention and is often associated with a substantial impact on psychosocial functioning. Methylphenidate (MPH, a central nervous system stimulant, is commonly used for pharmacological treatment of adults and children with ADHD. Current practice guidelines recommend optimizing MPH dosage to individual patient needs; however, the clinical benefits of individual dose optimization compared with fixed-dose regimens remain unclear. Here we review the available literature on MPH dose optimization from clinical trials and real-world experience on ADHD management. In addition, we report safety and efficacy data from the largest MPH modified-release long-acting Phase III clinical trial conducted to examine benefits of dose optimization in adults with ADHD. Overall, MPH is an effective ADHD treatment with a good safety profile; data suggest that dose optimization may enhance the safety and efficacy of treatment. Further research is required to establish the extent to which short-term clinical benefits of MPH dose optimization translate into improved long-term outcomes for patients with ADHD. Keywords: methylphenidate, dose optimization, attention-deficit/hyperactivity disorder, ADHD

  12. Implementation of an acute venous thromboembolism clinical pathway reduces healthcare utilization and mitigates health disparities.

    Science.gov (United States)

    Misky, Gregory J; Carlson, Todd; Thompson, Elaina; Trujillo, Toby; Nordenholz, Kristen

    2014-07-01

    Acute venous thromboembolism (VTE) is prevalent, expensive, and deadly. Published data at our institution identified significant VTE care variation based on payer source. We developed a VTE clinical pathway to standardize care, decrease hospital utilization, provide education, and mitigate disparities. Target population for our interdisciplinary pathway was acute medical VTE patients. The intervention included order sets, system-wide education, follow-up phone calls, and coordinated posthospital care. Study data (n = 241) were compared to historical data (n = 234), evaluating outcomes of hospital admission, length of stay (LOS), and reutilization, stratified by payer source. A total of 241 patients entered the VTE clinical care pathway: 107 with deep venous thrombosis (44.4%) and 134 with a pulmonary embolism (55.6%). Within the pathway, uninsured VTE patients were admitted at a lower rate than insured patients (65.9 vs 79.1%; P = 0.032). LOS decreased from 4.4 to 3.1 days (P historical patients (9.4%, P = 0.254). Individual cost of care decreased from $7610 to $5295 (P cost, particularly among uninsured patients. Results of this novel study demonstrate a model for improving transitional care coordination with local community health clinics and delivering care to vulnerable populations. Other disease populations may benefit from the development of a similar model. © 2014 Society of Hospital Medicine.

  13. New methods for clinical pathways-Business Process Modeling Notation (BPMN) and Tangible Business Process Modeling (t.BPM).

    Science.gov (United States)

    Scheuerlein, Hubert; Rauchfuss, Falk; Dittmar, Yves; Molle, Rüdiger; Lehmann, Torsten; Pienkos, Nicole; Settmacher, Utz

    2012-06-01

    Clinical pathways (CP) are nowadays used in numerous institutions, but their real impact is still a matter of debate. The optimal design of a clinical pathway remains unclear and is mainly determined by the expectations of the individual institution. The purpose of the here described pilot project was the development of two CP (colon and rectum carcinoma) according to Business Process Modeling Notation (BPMN) and Tangible Business Process Modeling (t.BPM). BPMN is an established standard for business process modelling in industry and economy. It is, in the broadest sense, a computer programme which enables the description and a relatively easy graphical imaging of complex processes. t.BPM is a modular construction system of the BPMN symbols which enables the creation of an outline or raw model, e.g. by placing the symbols on a spread-out paper sheet. The thus created outline can then be transferred to the computer and further modified as required. CP for the treatment of colon and rectal cancer have been developed with support of an external IT coach. The pathway was developed in an interdisciplinary and interprofessional manner (55 man-days over 15 working days). During this time, necessary interviews with medical, nursing and administrative staffs were conducted as well. Both pathways were developed parallel. Subsequent analysis was focussed on feasibility, expenditure, clarity and suitability for daily clinical practice. The familiarization with BPMN was relatively quick and intuitive. The use of t.BPM enabled the pragmatic, effective and results-directed creation of outlines for the CP. The development of both CP was finished from the diagnostic evaluation to the adjuvant/neoadjuvant therapy and rehabilitation phase. The integration of checklists, guidelines and important medical or other documents is easily accomplished. A direct integration into the hospital computer system is currently not possible for technical reasons. BPMN and t.BPM are sufficiently

  14. Cost-Optimal Pathways to 75% Fuel Reduction in Remote Alaskan Villages: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Simpkins, Travis; Cutler, Dylan; Hirsch, Brian; Olis, Dan; Anderson, Kate

    2015-10-28

    There are thousands of isolated, diesel-powered microgrids that deliver energy to remote communities around the world at very high energy costs. The Remote Communities Renewable Energy program aims to help these communities reduce their fuel consumption and lower their energy costs through the use of high penetration renewable energy. As part of this program, the REopt modeling platform for energy system integration and optimization was used to analyze cost-optimal pathways toward achieving a combined 75% reduction in diesel fuel and fuel oil consumption in a select Alaskan village. In addition to the existing diesel generator and fuel oil heating technologies, the model was able to select from among wind, battery storage, and dispatchable electric heaters to meet the electrical and thermal loads. The model results indicate that while 75% fuel reduction appears to be technically feasible it may not be economically viable at this time. When the fuel reduction target was relaxed, the results indicate that by installing high-penetration renewable energy, the community could lower their energy costs by 21% while still reducing their fuel consumption by 54%.

  15. Optimization of contrast-enhanced spectral mammography depending on clinical indication.

    Science.gov (United States)

    Dromain, Clarisse; Canale, Sandra; Saab-Puong, Sylvie; Carton, Ann-Katherine; Muller, Serge; Fallenberg, Eva Maria

    2014-10-01

    The objective is to optimize low-energy (LE) and high-energy (HE) exposure parameters of contrast-enhanced spectral mammography (CESM) examinations in four different clinical applications for which different levels of average glandular dose (AGD) and ratios between LE and total doses are required. The optimization was performed on a Senographe DS with a SenoBright® upgrade. Simulations were performed to find the optima by maximizing the contrast-to-noise ratio (CNR) on the recombined CESM image using different targeted doses and LE image quality. The linearity between iodine concentration and CNR as well as the minimal detectable iodine concentration was assessed. The image quality of the LE image was assessed on the CDMAM contrast-detail phantom. Experiments confirmed the optima found on simulation. The CNR was higher for each clinical indication than for SenoBright®, including the screening indication for which the total AGD was 22% lower. Minimal iodine concentrations detectable in the case of a 3-mm-diameter round tumor were 12.5% lower than those obtained for the same dose in the clinical routine. LE image quality satisfied EUREF acceptable limits for threshold contrast. This newly optimized set of acquisition parameters allows increased contrast detectability compared to parameters currently used without a significant loss in LE image quality.

  16. Clinical trial optimization: Monte Carlo simulation Markov model for planning clinical trials recruitment.

    Science.gov (United States)

    Abbas, Ismail; Rovira, Joan; Casanovas, Josep

    2007-05-01

    The patient recruitment process of clinical trials is an essential element which needs to be designed properly. In this paper we describe different simulation models under continuous and discrete time assumptions for the design of recruitment in clinical trials. The results of hypothetical examples of clinical trial recruitments are presented. The recruitment time is calculated and the number of recruited patients is quantified for a given time and probability of recruitment. The expected delay and the effective recruitment durations are estimated using both continuous and discrete time modeling. The proposed type of Monte Carlo simulation Markov models will enable optimization of the recruitment process and the estimation and the calibration of its parameters to aid the proposed clinical trials. A continuous time simulation may minimize the duration of the recruitment and, consequently, the total duration of the trial.

  17. Clinical and prognostic value of the C-Met/HGF signaling pathway in cervical cancer.

    Science.gov (United States)

    Boromand, Nadia; Hasanzadeh, Malihe; ShahidSales, Soodabeh; Farazestanian, Marjaneh; Gharib, Masoumeh; Fiuji, Hamid; Behboodi, Negin; Ghobadi, Niloofar; Hassanian, Seyed Mahdi; Ferns, Gordon A; Avan, Amir

    2018-06-01

    Aberrant activation of the HGF/c-Met signalling pathway is reported to be associated with cell proliferation, progression, and metastasis features of several tumor types, including cervical cancer, suggesting that it may be of potential value as a novel therapeutic target. Furthermore, HPV-positive patients had a higher serum level of HGF or c-Met protein, compared with HPV-negative patients. c-Met or HGF overexpression in lesions of cervical cancer is reported to be related to a poorer prognosis, and hence this may be of value as a prognostic and predictive biomarker. Several approaches have been developed for targeting HGF and/or c-Met. One of these is crizotinib (a dual c-Met/ALK inhibitor). This has been approved by FDA for the treatment of lung-cancer. Further investigations are required to evaluate and optimize the use of c-Met inhibitors in cervical cancer or parallel targeting signalling pathway associated/activated via MET/HGF pathway. The main aim of current review was to give an overview of the potential of the c-Met/HGF pathway as a prognostic, or predictive biomarker in cervical cancer. © 2017 Wiley Periodicals, Inc.

  18. Pharmacists as Interprofessional Collaborators and Leaders through Clinical Pathways

    Directory of Open Access Journals (Sweden)

    Sherine Ismail

    2018-03-01

    Full Text Available Pharmacists possess pivotal competencies and expertise in developing clinical pathways (CPs. We present a tertiary care facility experience of pharmacists vis-a-vis interprofessional collaboration for designing and implementing CPs. We participated in the development of CPs as leading members of a collaborative team of healthcare professionals. We reviewed literature, aligning it with hospital formulary and institutional standards, and participated in weekly team meetings for six months. Several tools and services were adapted to guide prescribing and standardization of care through time-bound order sets. Fifteen CPs leading to admissions in medical wards were developed and integrated into Computerized Prescriber Order Entry (CPOE sets. Tools and services included (1 reporting of creatinine clearance to guide optimum dosing; (2 advisory flags for dosing and infusion rates; (3 piloting of medication reconciliation and counseling services before discharge were initiated; (4 Arabic drug leaflets were designed to educate patients; and (5 five CPs were included in pragmatic randomized control trials with a clinical pharmacist as co-investigator. Clinical pharmacists conducted continuous orientation to various healthcare professionals throughout the process. CPs provide unique opportunities for establishing and evaluating patient-centered pharmaceutical services and allow clinical pharmacists to demonstrate interprofessional leadership in collaboration with multidisciplinary teams.

  19. Process mining routinely collected electronic health records to define real-life clinical pathways during chemotherapy.

    Science.gov (United States)

    Baker, Karl; Dunwoodie, Elaine; Jones, Richard G; Newsham, Alex; Johnson, Owen; Price, Christopher P; Wolstenholme, Jane; Leal, Jose; McGinley, Patrick; Twelves, Chris; Hall, Geoff

    2017-07-01

    There is growing interest in the use of routinely collected electronic health records to enhance service delivery and facilitate clinical research. It should be possible to detect and measure patterns of care and use the data to monitor improvements but there are methodological and data quality challenges. Driven by the desire to model the impact of a patient self-test blood count monitoring service in patients on chemotherapy, we aimed to (i) establish reproducible methods of process-mining electronic health records, (ii) use the outputs derived to define and quantify patient pathways during chemotherapy, and (iii) to gather robust data which is structured to be able to inform a cost-effectiveness decision model of home monitoring of neutropenic status during chemotherapy. Electronic Health Records at a UK oncology centre were included if they had (i) a diagnosis of metastatic breast cancer and received adjuvant epirubicin and cyclosphosphamide chemotherapy or (ii) colorectal cancer and received palliative oxaliplatin and infusional 5-fluorouracil chemotherapy, and (iii) were first diagnosed with cancer between January 2004 and February 2013. Software and a Markov model were developed, producing a schematic of patient pathways during chemotherapy. Significant variance from the assumed care pathway was evident from the data. Of the 535 patients with breast cancer and 420 with colorectal cancer there were 474 and 329 pathway variants respectively. Only 27 (5%) and 26 (6%) completed the planned six cycles of chemotherapy without having unplanned hospital contact. Over the six cycles, 169 (31.6%) patients with breast cancer and 190 (45.2%) patients with colorectal cancer were admitted to hospital. The pathways of patients on chemotherapy are complex. An iterative approach to addressing semantic and data quality issues enabled the effective use of routinely collected patient records to produce accurate models of the real-life experiences of chemotherapy patients and

  20. A novel model to combine clinical and pathway-based transcriptomic information for the prognosis prediction of breast cancer.

    Directory of Open Access Journals (Sweden)

    Sijia Huang

    2014-09-01

    Full Text Available Breast cancer is the most common malignancy in women worldwide. With the increasing awareness of heterogeneity in breast cancers, better prediction of breast cancer prognosis is much needed for more personalized treatment and disease management. Towards this goal, we have developed a novel computational model for breast cancer prognosis by combining the Pathway Deregulation Score (PDS based pathifier algorithm, Cox regression and L1-LASSO penalization method. We trained the model on a set of 236 patients with gene expression data and clinical information, and validated the performance on three diversified testing data sets of 606 patients. To evaluate the performance of the model, we conducted survival analysis of the dichotomized groups, and compared the areas under the curve based on the binary classification. The resulting prognosis genomic model is composed of fifteen pathways (e.g., P53 pathway that had previously reported cancer relevance, and it successfully differentiated relapse in the training set (log rank p-value = 6.25e-12 and three testing data sets (log rank p-value < 0.0005. Moreover, the pathway-based genomic models consistently performed better than gene-based models on all four data sets. We also find strong evidence that combining genomic information with clinical information improved the p-values of prognosis prediction by at least three orders of magnitude in comparison to using either genomic or clinical information alone. In summary, we propose a novel prognosis model that harnesses the pathway-based dysregulation as well as valuable clinical information. The selected pathways in our prognosis model are promising targets for therapeutic intervention.

  1. GDC-0449-a potent inhibitor of the hedgehog pathway.

    Science.gov (United States)

    Robarge, Kirk D; Brunton, Shirley A; Castanedo, Georgette M; Cui, Yong; Dina, Michael S; Goldsmith, Richard; Gould, Stephen E; Guichert, Oivin; Gunzner, Janet L; Halladay, Jason; Jia, Wei; Khojasteh, Cyrus; Koehler, Michael F T; Kotkow, Karen; La, Hank; Lalonde, Rebecca L; Lau, Kevin; Lee, Leslie; Marshall, Derek; Marsters, James C; Murray, Lesley J; Qian, Changgeng; Rubin, Lee L; Salphati, Laurent; Stanley, Mark S; Stibbard, John H A; Sutherlin, Daniel P; Ubhayaker, Savita; Wang, Shumei; Wong, Susan; Xie, Minli

    2009-10-01

    SAR for a wide variety of heterocyclic replacements for a benzimidazole led to the discovery of functionalized 2-pyridyl amides as novel inhibitors of the hedgehog pathway. The 2-pyridyl amides were optimized for potency, PK, and drug-like properties by modifications to the amide portion of the molecule resulting in 31 (GDC-0449). Amide 31 produced complete tumor regression at doses as low as 12.5mg/kg BID in a medulloblastoma allograft mouse model that is wholly dependent on the Hh pathway for growth and is currently in human clinical trials, where it is initially being evaluated for the treatment of BCC.

  2. A peer review process as part of the implementation of clinical pathways in radiation oncology: Does it improve compliance?

    Science.gov (United States)

    Gebhardt, Brian J; Heron, Dwight E; Beriwal, Sushil

    Clinical pathways are patient management plans that standardize evidence-based practices to ensure high-quality and cost-effective medical care. Implementation of a pathway is a collaborative process in our network, requiring the active involvement of physicians. This approach promotes acceptance of pathway recommendations, although a peer review process is necessary to ensure compliance and to capture and approve off-pathway selections. We investigated the peer review process and factors associated with time to completion of peer review. Our cancer center implemented radiation oncology pathways for every disease site throughout a large, integrated network. Recommendations are written based upon national guidelines, published literature, and institutional experience with evidence evaluated hierarchically in order of efficacy, toxicity, and then cost. Physicians enter decisions into an online, menu-driven decision support tool that integrates with medical records. Data were collected from the support tool and included the rate of on- and off-pathway selections, peer review decisions performed by disease site directors, and time to complete peer review. A total of 6965 treatment decisions were entered in 2015, and 605 (8.7%) were made off-pathway and were subject to peer review. The median time to peer review decision was 2 days (interquartile range, 0.2-6.8). Factors associated with time to peer review decision >48 hours on univariate analysis include disease site (P peer review (P 48 hours. Clinical pathways are an integral tool for standardizing evidence-based care throughout our large, integrated network, with 91.3% of all treatment decisions being made as per pathway. The peer review process was feasible, with peer review of treatment decisions encourages compliance with clinical pathway recommendations. Copyright © 2017 American Society for Radiation Oncology. Published by Elsevier Inc. All rights reserved.

  3. A new course in the clinical pathways for metabolic syndrome

    International Nuclear Information System (INIS)

    Kageyama, Shoko; Wada, Yumi; Nakamura, Rie

    2006-01-01

    Metabolic syndrome is consisted with multiple risk factors such as diabetes, dyslipidemia, and hypertension based on visceral fat accumulation, for the development of arteriosclerosis. We present, here, a clinical pathway for education of patients with metabolic syndrome. The program contains an adequate explanation of the high risk for arteriosclerosis to the patients, the measurement of visceral fat content by computed tomography, and several clinical examinations for the evaluation of arteriosclerotic lesions. We have presented this program on the ward of diabetes center in our hospital for patients diagnosed as having metabolic syndrome. Because the focus of education is to clarify understanding of the harmful effects of visceral fat and the benefits of its reduction, it might be a valuable tool to motivate and empower the patient and improve the patient's lifestyle. (author)

  4. A new course in the clinical pathways for metabolic syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Kageyama, Shoko; Wada, Yumi; Nakamura, Rie [Sumitomo Hospital, Osaka, Osaka (Japan)

    2006-07-15

    Metabolic syndrome is consisted with multiple risk factors such as diabetes, dyslipidemia, and hypertension based on visceral fat accumulation, for the development of arteriosclerosis. We present, here, a clinical pathway for education of patients with metabolic syndrome. The program contains an adequate explanation of the high risk for arteriosclerosis to the patients, the measurement of visceral fat content by computed tomography, and several clinical examinations for the evaluation of arteriosclerotic lesions. We have presented this program on the ward of diabetes center in our hospital for patients diagnosed as having metabolic syndrome. Because the focus of education is to clarify understanding of the harmful effects of visceral fat and the benefits of its reduction, it might be a valuable tool to motivate and empower the patient and improve the patient's lifestyle. (author)

  5. Intensity-modulated radiation therapy (IMRT) for locally advanced paranasal sinus tumors: incorporating clinical decisions in the optimization process

    International Nuclear Information System (INIS)

    Tsien, Christina; Eisbruch, Avraham; McShan, Daniel; Kessler, Marc; Marsh, Robin C.; Fraass, Benedick

    2003-01-01

    Purpose: Intensity-modulated radiotherapy (IMRT) plans require decisions about priorities and tradeoffs among competing goals. This study evaluates the incorporation of various clinical decisions into the optimization system, using locally advanced paranasal sinus tumors as a model. Methods and Materials: Thirteen patients with locally advanced paranasal sinus tumors were retrospectively replanned using inverse planning. Two clinical decisions were assumed: (1) Spare both optic pathways (OP), or (2) Spare only the contralateral OP. In each case, adequate tumor coverage (treated to 70 Gy in 35 fractions) was required. Two beamlet IMRT plans were thus developed for each patient using a class solution cost function. By altering one key variable at a time, different levels of risk of OP toxicity and planning target volume (PTV) compromise were compared in a systematic manner. The resulting clinical tradeoffs were analyzed using dosimetric criteria, tumor control probability (TCP), equivalent uniform dose (EUD), and normal tissue complication probability. Results: Plan comparisons representing the two clinical decisions (sparing both OP and sparing only the contralateral OP), with respect to minimum dose, TCP, V 95 , and EUD, demonstrated small, yet statistically significant, differences. However, when individual cases were analyzed further, significant PTV underdosage (>5%) was present in most cases for plans sparing both OP. In 6/13 cases (46%), PTV underdosage was between 5% and 15%, and in 3 cases (23%) was greater than 15%. By comparison, adequate PTV coverage was present in 8/13 cases (62%) for plans sparing only the contralateral OP. Mean target EUD comparisons between the two plans (including 9 cases where a clinical tradeoff between PTV coverage and OP sparing was required) were similar: 68.6 Gy and 69.1 Gy, respectively (p=0.02). Mean TCP values for those 9 cases were 56.5 vs. 61.7, respectively (p=0.006). Conclusions: In IMRT plans for paranasal sinus tumors

  6. Optimization of chest radiography. Experimental and clinical studies using rare earths screen

    Energy Technology Data Exchange (ETDEWEB)

    Bergonzini, R; Robecchi, D; Amato, M; Gallini, R; Giugni, V

    1986-01-01

    The optimization of chest radiography is a still unresolved problem, as it must answer to various clinical requirements. Even if sometimes the choice is not difficult, it becomes hard when the best film-screen combination is needed. In order to assess the optimization image quality and exposition, different experimental and clinical conditions have been investigated referring to the various combination of screen, film and tension. The Trimax system has been chosen for our investigations, performed in two different phases: the former on an anthropomorphous chest phantom, the latter on 25 patients affected by lung interstitial diseases, mainly nodular. The results are discussed.

  7. Implementation and Evaluation of a Clinical Pathway for Pancreaticoduodenectomy Procedures: a Prospective Cohort Study

    NARCIS (Netherlands)

    Kolk, M. van der; Boogaard, M.H.W.A. van den; Becking-Verhaar, F.; Custers, H.; Hoeven, H. van der; Pickkers, P.; Laarhoven, K. van

    2017-01-01

    INTRODUCTION: Medical and nursing protocols in perioperative care for pancreaticoduodenectomy are mainly mono-disciplinary, limiting their integration and transparency in a continuous health care system. The aims of this study were to evaluate adherence to a multidisciplinary clinical pathway for

  8. Use of a clinical pathway to improve the acute management of vaso-occlusive crisis pain in pediatric sickle cell disease.

    Science.gov (United States)

    Ender, Katherine L; Krajewski, Jennifer A; Babineau, John; Tresgallo, Mary; Schechter, William; Saroyan, John M; Kharbanda, Anupam

    2014-04-01

    The most common, debilitating morbidity of sickle cell disease (SCD) is vaso-occlusive crisis (VOC) pain. Although guidelines exist for its management, they are generally not well-followed, and research in other pediatric diseases has shown that clinical pathways improve care. The purpose of our study was to determine whether a clinical pathway improves the acute management of sickle cell vaso-occlusive crisis (VOC) pain in the pediatric emergency department (PED). Pain management practices were prospectively investigated before and after the initiation of a clinical pathway in the PED of an urban, tertiary care center with 50,000 ED visits per year and approximately 200 active sickle cell patients. The pathway included instructions for triage, monitoring, medication administration, and timing of assessments and interventions. Data were eligible from 35 pre-pathway and 33 post-pathway visits. Primary outcome was time interval to administration of first analgesic medication. Statistical analysis was by Student's t-test, using natural-log-transformed data for outcomes with skewed distribution curves. Time interval to first analgesic improved from 74 to 42 minutes (P = 0.012) and to first opioid from 94 to 46 minutes (P = 0.013). The percentage of patients who received ketorolac increased from 57% to 82% (P = 0.03). Decrease in time interval to subsequent pain score assessment was not statistically significant (110 to 72 minutes (P = 0.07)), and change in pain score was not different (P = 0.25). The use of a clinical pathway for sickle cell VOC in the PED can improve important aspects of pain management and merits further investigation and implementation. © 2013 Wiley Periodicals, Inc.

  9. Optimizing clinical drug product performance

    DEFF Research Database (Denmark)

    Dickinson, Paul A.; Kesisoglou, Filippos; Flanagan, Talia

    2016-01-01

    The aim of Biopharmaceutics Risk Assessment Roadmap (BioRAM) and the BioRAM Scoring Grid is to facilitate optimization of clinical performance of drug products. BioRAM strategy relies on therapy-driven drug delivery and follows an integrated systems approach for formulating and addressing critical...... questions and decision-making (J Pharm Sci. 2014,103(11): 3777-97). In BioRAM, risk is defined as not achieving the intended in vivo drug product performance, and success is assessed by time to decision-making and action. Emphasis on time to decision-making and time to action highlights the value of well....... Application of the BioRAM Scoring Grid is illustrated using published literature. Organizational considerations for implementing BioRAM strategy, including the interactions, function, and skillsets of the BioRAM group members, are also reviewed. As a creative and innovative systems approach, we believe...

  10. Effect of a redesigned fracture management pathway and 'virtual' fracture clinic on ED performance.

    Science.gov (United States)

    Vardy, J; Jenkins, P J; Clark, K; Chekroud, M; Begbie, K; Anthony, I; Rymaszewski, L A; Ireland, A J

    2014-06-13

    Collaboration between the orthopaedic and emergency medicine (ED) services has resulted in standardised treatment pathways, leaflet supported discharge and a virtual fracture clinic review. Patients with minor, stable fractures are discharged with no further follow-up arranged. We aimed to examine the time taken to assess and treat these patients in the ED along with the rate of unplanned reattendance. A retrospective study was undertaken that covered 1 year before the change and 1 year after. Prospectively collected administrative data from the electronic patient record system were analysed and compared before and after the change. An ED and orthopaedic unit, serving a population of 300 000, in a publicly funded health system. 2840 patients treated with referral to a traditional fracture clinic and 3374 patients managed according to the newly redesigned protocol. Time for assessment and treatment of patients with orthopaedic injuries not requiring immediate operative management, and 7-day unplanned reattendance. Where plaster backslabs were replaced with removable splints, the consultation time was reduced. There was no change in treatment time for other injuries treated by the new discharge protocol. There was no increase in unplanned ED attendance, related to the injury, within 7 days (p=0.149). There was a decrease in patients reattending the ED due to a missed fracture clinic appointment. This process did not require any new time resources from the ED staff. This process brought significant benefits to the ED as treatment pathways were agreed. The pathway reduced unnecessary reattendance of patients at face-to-face fracture clinics for a review of stable, self-limiting injuries. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  11. An improved hybrid of particle swarm optimization and the gravitational search algorithm to produce a kinetic parameter estimation of aspartate biochemical pathways.

    Science.gov (United States)

    Ismail, Ahmad Muhaimin; Mohamad, Mohd Saberi; Abdul Majid, Hairudin; Abas, Khairul Hamimah; Deris, Safaai; Zaki, Nazar; Mohd Hashim, Siti Zaiton; Ibrahim, Zuwairie; Remli, Muhammad Akmal

    2017-12-01

    Mathematical modelling is fundamental to understand the dynamic behavior and regulation of the biochemical metabolisms and pathways that are found in biological systems. Pathways are used to describe complex processes that involve many parameters. It is important to have an accurate and complete set of parameters that describe the characteristics of a given model. However, measuring these parameters is typically difficult and even impossible in some cases. Furthermore, the experimental data are often incomplete and also suffer from experimental noise. These shortcomings make it challenging to identify the best-fit parameters that can represent the actual biological processes involved in biological systems. Computational approaches are required to estimate these parameters. The estimation is converted into multimodal optimization problems that require a global optimization algorithm that can avoid local solutions. These local solutions can lead to a bad fit when calibrating with a model. Although the model itself can potentially match a set of experimental data, a high-performance estimation algorithm is required to improve the quality of the solutions. This paper describes an improved hybrid of particle swarm optimization and the gravitational search algorithm (IPSOGSA) to improve the efficiency of a global optimum (the best set of kinetic parameter values) search. The findings suggest that the proposed algorithm is capable of narrowing down the search space by exploiting the feasible solution areas. Hence, the proposed algorithm is able to achieve a near-optimal set of parameters at a fast convergence speed. The proposed algorithm was tested and evaluated based on two aspartate pathways that were obtained from the BioModels Database. The results show that the proposed algorithm outperformed other standard optimization algorithms in terms of accuracy and near-optimal kinetic parameter estimation. Nevertheless, the proposed algorithm is only expected to work well in

  12. Transforming clinical practice guidelines and clinical pathways into fast-and-frugal decision trees to improve clinical care strategies.

    Science.gov (United States)

    Djulbegovic, Benjamin; Hozo, Iztok; Dale, William

    2018-02-27

    Contemporary delivery of health care is inappropriate in many ways, largely due to suboptimal Q5 decision-making. A typical approach to improve practitioners' decision-making is to develop evidence-based clinical practice guidelines (CPG) by guidelines panels, who are instructed to use their judgments to derive practice recommendations. However, mechanisms for the formulation of guideline judgments remains a "black-box" operation-a process with defined inputs and outputs but without sufficient knowledge of its internal workings. Increased explicitness and transparency in the process can be achieved by implementing CPG as clinical pathways (CPs) (also known as clinical algorithms or flow-charts). However, clinical recommendations thus derived are typically ad hoc and developed by experts in a theory-free environment. As any recommendation can be right (true positive or negative), or wrong (false positive or negative), the lack of theoretical structure precludes the quantitative assessment of the management strategies recommended by CPGs/CPs. To realize the full potential of CPGs/CPs, they need to be placed on more solid theoretical grounds. We believe this potential can be best realized by converting CPGs/CPs within the heuristic theory of decision-making, often implemented as fast-and-frugal (FFT) decision trees. This is possible because FFT heuristic strategy of decision-making can be linked to signal detection theory, evidence accumulation theory, and a threshold model of decision-making, which, in turn, allows quantitative analysis of the accuracy of clinical management strategies. Fast-and-frugal provides a simple and transparent, yet solid and robust, methodological framework connecting decision science to clinical care, a sorely needed missing link between CPGs/CPs and patient outcomes. We therefore advocate that all guidelines panels express their recommendations as CPs, which in turn should be converted into FFTs to guide clinical care. © 2018 John Wiley

  13. Development and implementation of a clinical pathway approach to simulation-based training for foregut surgery.

    Science.gov (United States)

    Miyasaka, Kiyoyuki W; Buchholz, Joseph; LaMarra, Denise; Karakousis, Giorgos C; Aggarwal, Rajesh

    2015-01-01

    Contemporary demands on resident education call for integration of simulation. We designed and implemented a simulation-based curriculum for Post Graduate Year 1 surgery residents to teach technical and nontechnical skills within a clinical pathway approach for a foregut surgery patient, from outpatient visit through surgery and postoperative follow-up. The 3-day curriculum for groups of 6 residents comprises a combination of standardized patient encounters, didactic sessions, and hands-on training. The curriculum is underpinned by a summative simulation "pathway" repeated on days 1 and 3. The "pathway" is a series of simulated preoperative, intraoperative, and postoperative encounters in following up a single patient through a disease process. The resident sees a standardized patient in the clinic presenting with distal gastric cancer and then enters an operating room to perform a gastrojejunostomy on a porcine tissue model. Finally, the resident engages in a simulated postoperative visit. All encounters are rated by faculty members and the residents themselves, using standardized assessment forms endorsed by the American Board of Surgery. A total of 18 first-year residents underwent this curriculum. Faculty ratings of overall operative performance significantly improved following the 3-day module. Ratings of preoperative and postoperative performance were not significantly changed in 3 days. Resident self-ratings significantly improved for all encounters assessed, as did reported confidence in meeting the defined learning objectives. Conventional surgical simulation training focuses on technical skills in isolation. Our novel "pathway" curriculum targets an important gap in training methodologies by placing both technical and nontechnical skills in their clinical context as part of managing a surgical patient. Results indicate consistent improvements in assessments of performance as well as confidence and support its continued usage to educate surgery residents

  14. Intensity modulated radiotherapy for sinonasal malignancies with a focus on optic pathway preservation

    Directory of Open Access Journals (Sweden)

    Chi Alexander

    2013-01-01

    Full Text Available Abstract Purpose To assess if intensity-modulated radiotherapy (IMRT can possibly lead to improved local control and lower incidence of vision impairment/blindness in comparison to non-IMRT techniques when treating sinonasal malignancies; what is the most optimal dose constraints for the optic pathway; and the impact of different IMRT strategies on optic pathway sparing in this setting. Methods and materials A literature search in the PubMed databases was conducted in July, 2012. Results Clinical studies on IMRT and 2D/3D (2 dimensional/3 dimensional RT for sinonasal malignancies suggest improved local control and lower incidence of severe vision impairment with IMRT in comparison to non-IMRT techniques. As observed in the non-IMRT studies, blindness due to disease progression may occur despite a lack of severe toxicity possibly due to the difficulty of controlling locally very advanced disease with a dose ≤ 70 Gy. Concurrent chemotherapy’s influence on the the risk of severe optic toxicity after radiotherapy is unclear. A maximum dose of ≤ 54 Gy with conventional fractionation to the optic pathway may decrease the risk of blindness. Increased magnitude of intensity modulation through increasing the number of segments, beams, and using a combination of coplanar and non-coplanar arrangements may help increase dose conformality and optic pathway sparing when IMRT is used. Conclusion IMRT optimized with appropriate strategies may be the treatment of choice for the most optimal local control and optic pathway sparing when treating sinonasal malignancy.

  15. Protein design for pathway engineering.

    Science.gov (United States)

    Eriksen, Dawn T; Lian, Jiazhang; Zhao, Huimin

    2014-02-01

    Design and construction of biochemical pathways has increased the complexity of biosynthetically-produced compounds when compared to single enzyme biocatalysis. However, the coordination of multiple enzymes can introduce a complicated set of obstacles to overcome in order to achieve a high titer and yield of the desired compound. Metabolic engineering has made great strides in developing tools to optimize the flux through a target pathway, but the inherent characteristics of a particular enzyme within the pathway can still limit the productivity. Thus, judicious protein design is critical for metabolic and pathway engineering. This review will describe various strategies and examples of applying protein design to pathway engineering to optimize the flux through the pathway. The proteins can be engineered for altered substrate specificity/selectivity, increased catalytic activity, reduced mass transfer limitations through specific protein localization, and reduced substrate/product inhibition. Protein engineering can also be expanded to design biosensors to enable high through-put screening and to customize cell signaling networks. These strategies have successfully engineered pathways for significantly increased productivity of the desired product or in the production of novel compounds. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. Impact of care pathways for in-hospital management of COPD exacerbation: a systematic review.

    Science.gov (United States)

    Lodewijckx, C; Sermeus, W; Panella, M; Deneckere, S; Leigheb, F; Decramer, M; Vanhaecht, K

    2011-11-01

    In-hospital management of COPD exacerbation is suboptimal, and outcomes are poor. Care pathways are a possible strategy for optimizing care processes and outcomes. The aim of the literature review was to explore characteristics of existing care pathways for in-hospital management of COPD exacerbations and to address their impact on performance of care processes, clinical outcomes, and team functioning. A literature search was conducted for articles published between 1990 and 2010 in the electronic databases of Medline, CINAHL, EMBASE, and Cochrane Library. Main inclusion criteria were (I) patients hospitalized for a COPD exacerbation; (II) implementation and evaluation of a care pathway; (III) report of original research, including experimental and quasi experimental designs, variance analysis, and interviews of professionals and patients about their perception on pathway effectiveness. Four studies with a quasi experimental design were included. Three studies used a pre-post test design; the fourth study was a non randomized controlled trial comparing an experimental group where patients were treated according to a care pathway with a control group where usual care was provided. The four studied care pathways were multidisciplinary structured care plans, outlining time-specific clinical interventions and responsibilities by discipline. Statistic analyses were rarely performed, and the trials used very divergent indicators to evaluate the impact of the care pathways. The studies described positive effects on blood sampling, daily weight measurement, arterial blood gas measurement, referral to rehabilitation, feelings of anxiety, length of stay, readmission, and in-hospital mortality. Research on COPD care pathways is very limited. The studies described few positive effects of the care pathways on diagnostic processes and on clinical outcomes. Though due to limited statistical analysis and weak design of the studies, the internal validity of results is limited

  17. The Fanconi Anemia BRCA Pathway as a Predictor of Benefit from Bevacizumab in a Large Phase 3 Clinical Trial in Ovarian Cancer

    Science.gov (United States)

    2014-12-01

    1 AWARD NUMBER: W81XWH-13-1-0421 TITLE: The Fanconi Anemia BRCA Pathway as a Predictor of Benefit from Bevacizumab in a Large Phase III Clinical...DATES COVERED 30Sep2013 - 29Sep2015 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER W81XWH-13-1-0421 The Fanconi Anemia BRCA Pathway as a Predictor of...another upfront clinical trial GOG262. We found that germline or somatic mutations in the BRCA- Fanconi anemia pathway was significantly associated with

  18. Understanding implementation processes of clinical pathways and clinical practice guidelines in pediatric contexts: a study protocol

    Directory of Open Access Journals (Sweden)

    Scott Shannon D

    2011-12-01

    Full Text Available Abstract Background Canada is among the most prosperous nations in the world, yet the health and wellness outcomes of Canadian children are surprisingly poor. There is some evidence to suggest that these poor health outcomes are partly due to clinical practice variation, which can stem from failure to apply the best available research evidence in clinical practice, otherwise known as knowledge translation (KT. Surprisingly, clinical practice variation, even for common acute paediatric conditions, is pervasive. Clinical practice variation results in unnecessary medical treatments, increased suffering, and increased healthcare costs. This study focuses on improving health outcomes for common paediatric acute health concerns by evaluating strategies that improve KT and reduce clinical practice variation. Design/Methods Using a multiple case study design, qualitative and quantitative data will be collected from four emergency departments in western Canada. Data sources will include: pre- and post-implementation focus group data from multidisciplinary healthcare professionals; individual interviews with the local champions, KT intervention providers, and unit/site leaders/managers; Alberta Context Tool (ACT survey data; and aggregated patient outcome data. Qualitative and quantitative data will be systematically triangulated, and matrices will be built to do cross-case comparison. Explanations will be built about the success or lack of success of the clinical practice guidelines (CPG and clinical pathways (CPs uptake based upon the cross-case comparisons. Significance This study will generate new knowledge about the potential causal mechanisms and factors which shape implementation. Future studies will track the impact of the CPG/CPs implementation on children's health outcome, and healthcare costs.

  19. A Swarm Optimization approach for clinical knowledge mining.

    Science.gov (United States)

    Christopher, J Jabez; Nehemiah, H Khanna; Kannan, A

    2015-10-01

    Rule-based classification is a typical data mining task that is being used in several medical diagnosis and decision support systems. The rules stored in the rule base have an impact on classification efficiency. Rule sets that are extracted with data mining tools and techniques are optimized using heuristic or meta-heuristic approaches in order to improve the quality of the rule base. In this work, a meta-heuristic approach called Wind-driven Swarm Optimization (WSO) is used. The uniqueness of this work lies in the biological inspiration that underlies the algorithm. WSO uses Jval, a new metric, to evaluate the efficiency of a rule-based classifier. Rules are extracted from decision trees. WSO is used to obtain different permutations and combinations of rules whereby the optimal ruleset that satisfies the requirement of the developer is used for predicting the test data. The performance of various extensions of decision trees, namely, RIPPER, PART, FURIA and Decision Tables are analyzed. The efficiency of WSO is also compared with the traditional Particle Swarm Optimization. Experiments were carried out with six benchmark medical datasets. The traditional C4.5 algorithm yields 62.89% accuracy with 43 rules for liver disorders dataset where as WSO yields 64.60% with 19 rules. For Heart disease dataset, C4.5 is 68.64% accurate with 98 rules where as WSO is 77.8% accurate with 34 rules. The normalized standard deviation for accuracy of PSO and WSO are 0.5921 and 0.5846 respectively. WSO provides accurate and concise rulesets. PSO yields results similar to that of WSO but the novelty of WSO lies in its biological motivation and it is customization for rule base optimization. The trade-off between the prediction accuracy and the size of the rule base is optimized during the design and development of rule-based clinical decision support system. The efficiency of a decision support system relies on the content of the rule base and classification accuracy. Copyright

  20. Learning pathways during clinical placement of physiotherapy students: a Malaysian experience of using learning contracts and reflective diaries

    Directory of Open Access Journals (Sweden)

    Ayiesah Ramli

    2013-07-01

    Full Text Available Purpose: Learning contracts and reflective diaries are educational tools that have been recently introduced to physiotherapy students from Malaysia during clinical education. It is unclear how students perceive the experience of using a learning contract and reflective diary. This study explores the learning pathways of the students after using a learning contract and a reflective diary for the first time in their clinical placement. Methods: A total of 26 final-year physiotherapy students completed a learning contract and a reflective diary during clinical placements. Two researchers explored the data qualitatively by the thematic content analysis method using NVivo. Results: A total of four and six main learning themes were identified from the data of the students through a learning contract and reflective diary. Conclusion: These learning themes reflected the views of the students about what they have considered to be important learning pathways during their clinical placements. They give valuable insights into the experiences and opinions of students during their clinical education process, which should be useful for enhancing teaching and learning methods in physiotherapy education.

  1. Optimizing the patient transport function at Mayo Clinic.

    Science.gov (United States)

    Kuchera, Dustin; Rohleder, Thomas R

    2011-01-01

    In this article, we report on the implementation of a computerized scheduling tool to optimize staffing for patient transport at the Mayo Clinic. The tool was developed and implemented in Microsoft Excel and Visual Basic for Applications and includes an easy-to-use interface. The tool allows transport management to consider the trade-offs between patient waiting time and staffing levels. While improved staffing efficiency was a desire of the project, it was important that patient service quality was also maintained. The results show that staffing could be reduced while maintaining historical patient service levels.

  2. The usefulness of lean six sigma to the development of a clinical pathway for hip fractures.

    Science.gov (United States)

    Niemeijer, Gerard C; Flikweert, Elvira; Trip, Albert; Does, Ronald J M M; Ahaus, Kees T B; Boot, Anja F; Wendt, Klaus W

    2013-10-01

    The objective of this study was to show the usefulness of lean six sigma (LSS) for the development of a multidisciplinary clinical pathway. A single centre, both retrospective and prospective, non-randomized controlled study design was used to identify the variables of a prolonged length of stay (LOS) for hip fractures in the elderly and to measure the effect of the process improvements--with the aim of improving efficiency of care and reducing the LOS. The project identified several variables influencing LOS, and interventions were designed to improve the process of care. Significant results were achieved by reducing both the average LOS by 4.2 days (-31%) and the average duration of surgery by 57 minutes (-36%). The average LOS of patients discharged to a nursing home reduced by 4.4 days. The findings of this study show a successful application of LSS methodology within the development of a clinical pathway. Further research is needed to explore the effect of the use of LSS methodology at clinical outcome and quality of life. © 2012 John Wiley & Sons Ltd.

  3. Pump-shaped dump optimal control reveals the nuclear reaction pathway of isomerization of a photoexcited cyanine dye.

    Science.gov (United States)

    Dietzek, Benjamin; Brüggemann, Ben; Pascher, Torbjörn; Yartsev, Arkady

    2007-10-31

    Using optimal control as a spectroscopic tool we decipher the details of the molecular dynamics of the essential multidimensional excited-state photoisomerization - a fundamental chemical reaction of key importance in biology. Two distinct nuclear motions are identified in addition to the overall bond-twisting motion: Initially, the reaction is dominated by motion perpendicular to the torsion coordinate. At later times, a second optically active vibration drives the system along the reaction path to the bottom of the excited-state potential. The time scales of the wavepacket motion on a different part of the excited-state potential are detailed by pump-shaped dump optimal control. This technique offers new means to control a chemical reaction far from the Franck-Condon point of absorption and to map details of excited-state reaction pathways revealing unique insights into the underlying reaction mechanism.

  4. Associations between purine metabolites and clinical symptoms in schizophrenia.

    Directory of Open Access Journals (Sweden)

    Jeffrey K Yao

    Full Text Available The antioxidant defense system, which is known to be dysregulated in schizophrenia, is closely linked to the dynamics of purine pathway. Thus, alterations in the homeostatic balance in the purine pathway may be involved in the pathophysiology of schizophrenia.Breakdown products in purine pathway were measured using high-pressure liquid chromatography coupled with a coulometric multi-electrode array system for 25 first-episode neuroleptic-naïve patients with schizophrenia at baseline and at 4-weeks following initiation of treatment with antipsychotic medication. Associations between these metabolites and clinical and neurological symptoms were examined at both time points. The ratio of uric acid and guanine measured at baseline predicted clinical improvement following four weeks of treatment with antipsychotic medication. Baseline levels of purine metabolites also predicted clinical and neurological symtpoms recorded at baseline; level of guanosine was associated with degree of clinical thought disturbance, and the ratio of xanthosine to guanosine at baseline predicted degree of impairment in the repetition and sequencing of actions.Findings suggest an association between optimal levels of purine byproducts and dynamics in clinical symptoms and adjustment, as well as in the integrity of sensory and motor processing. Taken together, alterations in purine catabolism may have clinical relevance in schizophrenia pathology.

  5. Tumour angiogenesis pathways: related clinical issues and implications for nuclear medicine imaging

    International Nuclear Information System (INIS)

    Wiele, Christophe van de; De Winter, Olivier; Dierckx, Rudi Andre; Oltenfreiter, Ruth; Slegers, Guido; Signore, Alberto

    2002-01-01

    Tumour angiogenesis is essential for growth, invasion and metastasis. Retrospective studies suggest that it is an independent prognostic factor that merits prospective validation. Furthermore, as tumour blood vessels show many differences from normal vessels and are not genetically unstable, they form a key area for therapy development. However, as anti-angiogenic therapy is primarily cytostatic and not cytotoxic, novel tailor-made specific end-points for treatment monitoring are required. In this regard, suitable molecular parameters for imaging tumour angiogenesis by means of nuclear medicine are being explored. Here we review current knowledge on the multiple pathways controlling tumour angiogenesis and try to assess which are the most clinically relevant for nuclear medicine imaging. Parameters that may influence the imaging potential of radiopharmaceuticals for angiogenesis imaging such as molecular weight and structure, their targeted location within the tumour and their usefulness in terms of specificity and constancy of the targeted molecular pathway are discussed. (orig.)

  6. Clinical trials in hospitalized heart failure patients: targeting interventions to optimal phenotypic subpopulations.

    Science.gov (United States)

    Vaduganathan, Muthiah; Butler, Javed; Roessig, Lothar; Fonarow, Gregg C; Greene, Stephen J; Metra, Marco; Cotter, Gadi; Kupfer, Stuart; Zalewski, Andrew; Sato, Naoki; Filippatos, Gerasimos; Gheorghiade, Mihai

    2015-07-01

    With one possible exception, the last decade of clinical trials in hospitalized heart failure (HHF) patients has failed to demonstrate improvement in long-term clinical outcomes. This trend necessitates a need to evaluate optimal drug development strategies and standards of trial conduct. It has become increasingly important to recognize the heterogeneity among HHF patients and the differential characterization of novel drug candidates. Targeting these agents to specific subpopulations may afford optimal net response related to the particular mode of action of the drug. Analyses of previous trials demonstrate profound differences in the baseline characteristics of patients enrolled across global regions and participating sites. Such differences may influence risks for events and interpretation of results. Therefore, the actual execution of trials and the epidemiology of HHF populations at the investigative sites must be taken into consideration. Collaboration among participating sites including the provision of registry data tailored to the planned development program will optimize trial conduct. Observational data prior to study initiation may enable sites to feedback and engage in protocol development to allow for feasible and valid clinical trial conduct. This site-centered, epidemiology-based network environment may facilitate studies in specific patient populations and promote optimal data collection and clear interpretation of drug safety and efficacy. This review summarizes the roundtable discussion held by a multidisciplinary team of representatives from academia, National Institutes of Health, industry, regulatory agencies, payers, and contract and academic research organizations to answer the question: Who should be targeted for novel therapies in HHF?

  7. Confinement Sensing and Signal Optimization via Piezo1/PKA and Myosin II Pathways

    Directory of Open Access Journals (Sweden)

    Wei-Chien Hung

    2016-05-01

    Full Text Available Summary: Cells adopt distinct signaling pathways to optimize cell locomotion in different physical microenvironments. However, the underlying mechanism that enables cells to sense and respond to physical confinement is unknown. Using microfabricated devices and substrate-printing methods along with FRET-based biosensors, we report that, as cells transition from unconfined to confined spaces, intracellular Ca2+ level is increased, leading to phosphodiesterase 1 (PDE1-dependent suppression of PKA activity. This Ca2+ elevation requires Piezo1, a stretch-activated cation channel. Moreover, differential regulation of PKA and cell stiffness in unconfined versus confined cells is abrogated by dual, but not individual, inhibition of Piezo1 and myosin II, indicating that these proteins can independently mediate confinement sensing. Signals activated by Piezo1 and myosin II in response to confinement both feed into a signaling circuit that optimizes cell motility. This study provides a mechanism by which confinement-induced signaling enables cells to sense and adapt to different physical microenvironments. : Hung et al. demonstrate that a Piezo1-dependent intracellular calcium increase negatively regulates protein kinase A (PKA as cells transit from unconfined to confined spaces. The Piezo1/PKA and myosin II signaling modules constitute two confinement-sensing mechanisms. This study provides a paradigm by which signaling enables cells to sense and adapt to different microenvironments.

  8. MiYA, an efficient machine-learning workflow in conjunction with the YeastFab assembly strategy for combinatorial optimization of heterologous metabolic pathways in Saccharomyces cerevisiae.

    Science.gov (United States)

    Zhou, Yikang; Li, Gang; Dong, Junkai; Xing, Xin-Hui; Dai, Junbiao; Zhang, Chong

    2018-05-01

    Facing boosting ability to construct combinatorial metabolic pathways, how to search the metabolic sweet spot has become the rate-limiting step. We here reported an efficient Machine-learning workflow in conjunction with YeastFab Assembly strategy (MiYA) for combinatorial optimizing the large biosynthetic genotypic space of heterologous metabolic pathways in Saccharomyces cerevisiae. Using β-carotene biosynthetic pathway as example, we first demonstrated that MiYA has the power to search only a small fraction (2-5%) of combinatorial space to precisely tune the expression level of each gene with a machine-learning algorithm of an artificial neural network (ANN) ensemble to avoid over-fitting problem when dealing with a small number of training samples. We then applied MiYA to improve the biosynthesis of violacein. Feed with initial data from a colorimetric plate-based, pre-screened pool of 24 strains producing violacein, MiYA successfully predicted, and verified experimentally, the existence of a strain that showed a 2.42-fold titer improvement in violacein production among 3125 possible designs. Furthermore, MiYA was able to largely avoid the branch pathway of violacein biosynthesis that makes deoxyviolacein, and produces very pure violacein. Together, MiYA combines the advantages of standardized building blocks and machine learning to accelerate the Design-Build-Test-Learn (DBTL) cycle for combinatorial optimization of metabolic pathways, which could significantly accelerate the development of microbial cell factories. Copyright © 2018 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  9. Clinical evidence on the magnitude of change in growth pathway activity in relation to Tamoxifen resistance is required.

    Science.gov (United States)

    Mansouri, Sepideh; Farahmand, Leila; Teymourzadeh, Azin; Majidzadeh-A, Keivan

    2017-08-08

    Despite prolonged disease-free survival and overall survival rates in estrogen receptor (ER)-positive patients undergoing adjuvant treatment, Tamoxifen therapy tends to fail due to eventual acquisition of resistance. Although numerous studies have emphasized the role of receptor tyrosine kinases (RTKs) in the development of Tamoxifen resistance, inadequate clinical evidence is available regarding the alteration of biomarker expression during acquired resistance, thus undermining the validity of the findings. Results of two meta-analyses investigating the effect of HER2 status on the prognosis of Tamoxifen-receiving patients have demonstrated that despite HER2-negative patients having longer disease-free survival; there is no difference in overhaul survival between the two groups. Furthermore, due to the intricate molecular interactions among estrogen receptors including ERα36, ERα66, and also RTKs, it is not surprising that RTK suppression does not restore Tamoxifen sensitivity. In considering such a complex network, we speculate that by the time HER2/EGFR is suppressed via targeted therapies, activation of ERα66 and ERα36 initiate molecular signaling pathways downstream of RTKs, thereby enhancing cell proliferation even in the presence of both Tamoxifen and RTK inhibitors. Although clinical findings regarding the molecular pathways downstream of RTKs have been thoroughly discussed in this review, further clinical studies are required in determining a consistency between preclinical and clinical findings. Discovering the best targets in preventing tumor progression requires thorough comprehension of estrogen-dependent and estrogen-independent pathways during Tamoxifen resistance development. Indeed, exploring additional clinically-proven targets would allow for better characterized treatments being available for breast cancer patients. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  10. Optimized Clinical Use of RNALater and FFPE Samples for Quantitative Proteomics

    DEFF Research Database (Denmark)

    Bennike, Tue Bjerg; Kastaniegaard, Kenneth; Padurariu, Simona

    2015-01-01

    Introduction and Objectives The availability of patient samples is essential for clinical proteomic research. Biobanks worldwide store mainly samples stabilized in RNAlater as well as formalin-fixed and paraffin embedded (FFPE) biopsies. Biobank material is a potential source for clinical...... we compare to FFPE and frozen samples being the control. Methods From the sigmoideum of two healthy participants’ twenty-four biopsies were extracted using endoscopy. The biopsies was stabilized either by being directly frozen, RNAlater, FFPE or incubated for 30 min at room temperature prior to FFPE...... information. Conclusion We have demonstrated that quantitative proteome analysis and pathway mapping of samples stabilized in RNAlater as well as by FFPE is feasible with minimal impact on the quality of protein quantification and post-translational modifications....

  11. Targeting the Wnt/beta-catenin pathway in cancer: Update on effectors and inhibitors.

    Science.gov (United States)

    Krishnamurthy, Nithya; Kurzrock, Razelle

    2018-01-01

    The Wnt/beta-catenin pathway is a family of proteins that is implicated in many vital cellular functions such as stem cell regeneration and organogenesis. Several intra-cellular signal transduction pathways are induced by Wnt, notably the Wnt/beta-catenin dependent pathway or canonical pathway and the non-canonical or beta-catenin-independent pathway; the latter includes the Wnt/Ca2+ and Planar Cell Polarity pathway (PCP). Wnt activation occurs at the intestinal crypt floor, and is critical to optimal maintenance of stem cells. Colorectal cancers show evidence of Wnt signaling pathway activation and this is associated with loss of function of the tumor regulator APC. Wnt activation has been observed in breast, lung, and hematopoietic malignancies and contributes to tumor recurrence. The Wnt pathway cross talks with the Notch and Sonic Hedgehog pathways, which has implications for therapeutic interventions in cancers. There are significant challenges in targeting the Wnt pathway, including finding agents that are efficacious without damaging the system of normal somatic stem cell function in cellular repair and tissue homeostasis. Here, we comprehensively review the Wnt pathway and its interactions with the Notch and Sonic Hedgehog pathways. We present the state of the field in effectors and inhibitors of Wnt signaling, including updates on clinical trials in various cancers with inhibitors of Wnt, Notch, and Sonic Hedgehog. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. [Development of a clinical pathway for the attention of patients with amyotrophic lateral sclerosis in a regional network. ALS Assistance Network-Comunidad de Madrid].

    Science.gov (United States)

    Rodríguez de Rivera, F J; Grande, M; García-Caballero, J; Muñoz-Blanco, J; Mora, J; Esteban, J; Guerrero, A; Matias-Guiu, J; de Andrés-Colsa, R; Buey, C; Díez-Tejedor, E

    2007-01-01

    Amyotrophic lateral sclerosis (ALS) requires complex multidisciplinary attention. Clinical pathways are assistance plans for certain diseases with a predictable course. These plans are established in isolated centers, not in multicenter regions. The aim is to develop a clinical pathway capable of organizing and homogenizing assistance given in ALS Assistance Network-Comunidad de Madrid which is made up of five hospitals, from the beginning until the end of the disease. In successive meetings, neurologists of these hospitals and members of the Madrid Health Service evaluated published therapeutic guidelines and other documents used in ALS assistance. A clinical pathway was developed adapting this information to social-health care conditions in the Comunidad de Madrid following the FOCUS-PDCA model. A clinical pathway was created consisting of a scientist-technical framework which arranges the attention in relationship to the diagnosis and treatment, according to the degree of disease progression and a chronogram. This is accompanied by several patient information documents on the disease and the tests that are required, and a patient assistance evaluation form. The standards are established to reach and to promote 354 constant improvement in patient care. Clinical pathway for the ALS assistance in a regional network organizes the attention and cares that the patients must receive from the beginning to the end of the disease. This arrangement and homogenization of the attention improves the quality of patient care, diminishes variability and rationalizes the use of the health care resources.

  13. KeyPathwayMinerWeb

    DEFF Research Database (Denmark)

    List, Markus; Alcaraz, Nicolas; Dissing-Hansen, Martin

    2016-01-01

    , for instance), KeyPathwayMiner extracts connected sub-networks containing a high number of active or differentially regulated genes (proteins, metabolites) in the molecular profiles. The web interface at (http://keypathwayminer.compbio.sdu.dk) implements all core functionalities of the KeyPathwayMiner tool set......We present KeyPathwayMinerWeb, the first online platform for de novo pathway enrichment analysis directly in the browser. Given a biological interaction network (e.g. protein-protein interactions) and a series of molecular profiles derived from one or multiple OMICS studies (gene expression...... such as data integration, input of background knowledge, batch runs for parameter optimization and visualization of extracted pathways. In addition to an intuitive web interface, we also implemented a RESTful API that now enables other online developers to integrate network enrichment as a web service...

  14. Association between frequent cardiac resynchronization therapy optimization and long-term clinical response: a post hoc analysis of the Clinical Evaluation on Advanced Resynchronization (CLEAR) pilot study

    Science.gov (United States)

    Delnoy, Peter Paul; Ritter, Philippe; Naegele, Herbert; Orazi, Serafino; Szwed, Hanna; Zupan, Igor; Goscinska-Bis, Kinga; Anselme, Frederic; Martino, Maria; Padeletti, Luigi

    2013-01-01

    Aims The long-term clinical value of the optimization of atrioventricular (AVD) and interventricular (VVD) delays in cardiac resynchronization therapy (CRT) remains controversial. We studied retrospectively the association between the frequency of AVD and VVD optimization and 1-year clinical outcomes in the 199 CRT patients who completed the Clinical Evaluation on Advanced Resynchronization study. Methods and results From the 199 patients assigned to CRT-pacemaker (CRT-P) (New York Heart Association, NYHA, class III/IV, left ventricular ejection fraction failure-related hospitalization, NYHA functional class, and Quality of Life score, at 1 year. Systematic CRT optimization was associated with a higher percentage of improved patients based on the composite endpoint (85% in Group 1 vs. 61% in Group 2, P < 0.001), with fewer deaths (3% in Group 1 vs. 14% in Group 2, P = 0.014) and fewer hospitalizations (8% in Group 1 vs. 23% in Group 2, P = 0.007), at 1 year. Conclusion These results further suggest that AVD and VVD frequent optimization (at implant, at 3 and 6 months) is associated with improved long-term clinical response in CRT-P patients. PMID:23493410

  15. Cerebrospinal and interstitial fluid transport via the glymphatic pathway modeled by optimal mass transport.

    Science.gov (United States)

    Ratner, Vadim; Gao, Yi; Lee, Hedok; Elkin, Rena; Nedergaard, Maiken; Benveniste, Helene; Tannenbaum, Allen

    2017-05-15

    The glymphatic pathway is a system which facilitates continuous cerebrospinal fluid (CSF) and interstitial fluid (ISF) exchange and plays a key role in removing waste products from the rodent brain. Dysfunction of the glymphatic pathway may be implicated in the pathophysiology of Alzheimer's disease. Intriguingly, the glymphatic system is most active during deep wave sleep general anesthesia. By using paramagnetic tracers administered into CSF of rodents, we previously showed the utility of MRI in characterizing a macroscopic whole brain view of glymphatic transport but we have yet to define and visualize the specific flow patterns. Here we have applied an alternative mathematical analysis approach to a dynamic time series of MRI images acquired every 4min over ∼3h in anesthetized rats, following administration of a small molecular weight paramagnetic tracer into the CSF reservoir of the cisterna magna. We use Optimal Mass Transport (OMT) to model the glymphatic flow vector field, and then analyze the flow to find the network of CSF-ISF flow channels. We use 3D visualization computational tools to visualize the OMT defined network of CSF-ISF flow channels in relation to anatomical and vascular key landmarks from the live rodent brain. The resulting OMT model of the glymphatic transport network agrees largely with the current understanding of the glymphatic transport patterns defined by dynamic contrast-enhanced MRI revealing key CSF transport pathways along the ventral surface of the brain with a trajectory towards the pineal gland, cerebellum, hypothalamus and olfactory bulb. In addition, the OMT analysis also revealed some interesting previously unnoticed behaviors regarding CSF transport involving parenchymal streamlines moving from ventral reservoirs towards the surface of the brain, olfactory bulb and large central veins. Copyright © 2017. Published by Elsevier Inc.

  16. [Imaging center - optimization of the imaging process].

    Science.gov (United States)

    Busch, H-P

    2013-04-01

    Hospitals around the world are under increasing pressure to optimize the economic efficiency of treatment processes. Imaging is responsible for a great part of the success but also of the costs of treatment. In routine work an excessive supply of imaging methods leads to an "as well as" strategy up to the limit of the capacity without critical reflection. Exams that have no predictable influence on the clinical outcome are an unjustified burden for the patient. They are useless and threaten the financial situation and existence of the hospital. In recent years the focus of process optimization was exclusively on the quality and efficiency of performed single examinations. In the future critical discussion of the effectiveness of single exams in relation to the clinical outcome will be more important. Unnecessary exams can be avoided, only if in addition to the optimization of single exams (efficiency) there is an optimization strategy for the total imaging process (efficiency and effectiveness). This requires a new definition of processes (Imaging Pathway), new structures for organization (Imaging Center) and a new kind of thinking on the part of the medical staff. Motivation has to be changed from gratification of performed exams to gratification of process quality (medical quality, service quality, economics), including the avoidance of additional (unnecessary) exams. © Georg Thieme Verlag KG Stuttgart · New York.

  17. Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways.

    Science.gov (United States)

    Mitsos, Alexander; Melas, Ioannis N; Morris, Melody K; Saez-Rodriguez, Julio; Lauffenburger, Douglas A; Alexopoulos, Leonidas G

    2012-01-01

    Modeling of signal transduction pathways plays a major role in understanding cells' function and predicting cellular response. Mathematical formalisms based on a logic formalism are relatively simple but can describe how signals propagate from one protein to the next and have led to the construction of models that simulate the cells response to environmental or other perturbations. Constrained fuzzy logic was recently introduced to train models to cell specific data to result in quantitative pathway models of the specific cellular behavior. There are two major issues in this pathway optimization: i) excessive CPU time requirements and ii) loosely constrained optimization problem due to lack of data with respect to large signaling pathways. Herein, we address both issues: the former by reformulating the pathway optimization as a regular nonlinear optimization problem; and the latter by enhanced algorithms to pre/post-process the signaling network to remove parts that cannot be identified given the experimental conditions. As a case study, we tackle the construction of cell type specific pathways in normal and transformed hepatocytes using medium and large-scale functional phosphoproteomic datasets. The proposed Non Linear Programming (NLP) formulation allows for fast optimization of signaling topologies by combining the versatile nature of logic modeling with state of the art optimization algorithms.

  18. Non Linear Programming (NLP formulation for quantitative modeling of protein signal transduction pathways.

    Directory of Open Access Journals (Sweden)

    Alexander Mitsos

    Full Text Available Modeling of signal transduction pathways plays a major role in understanding cells' function and predicting cellular response. Mathematical formalisms based on a logic formalism are relatively simple but can describe how signals propagate from one protein to the next and have led to the construction of models that simulate the cells response to environmental or other perturbations. Constrained fuzzy logic was recently introduced to train models to cell specific data to result in quantitative pathway models of the specific cellular behavior. There are two major issues in this pathway optimization: i excessive CPU time requirements and ii loosely constrained optimization problem due to lack of data with respect to large signaling pathways. Herein, we address both issues: the former by reformulating the pathway optimization as a regular nonlinear optimization problem; and the latter by enhanced algorithms to pre/post-process the signaling network to remove parts that cannot be identified given the experimental conditions. As a case study, we tackle the construction of cell type specific pathways in normal and transformed hepatocytes using medium and large-scale functional phosphoproteomic datasets. The proposed Non Linear Programming (NLP formulation allows for fast optimization of signaling topologies by combining the versatile nature of logic modeling with state of the art optimization algorithms.

  19. p-Nitrophenol degradation by electro-Fenton process: Pathway, kinetic model and optimization using central composite design.

    Science.gov (United States)

    Meijide, J; Rosales, E; Pazos, M; Sanromán, M A

    2017-10-01

    The chemical process scale-up, from lab studies to industrial production, is challenging and requires deep knowledge of the kinetic model and the reactions that take place in the system. This knowledge is also useful in order to be employed for the reactor design and the determination of the optimal operational conditions. In this study, a model substituted phenol such as p-nitrophenol was degraded by electro-Fenton process and the reaction products yielded along the treatment were recorded. The kinetic model was developed using Matlab software and was based on main reactions that occurred until total mineralization which allowed predicting the degradation pathway under this advanced oxidation process. The predicted concentration profiles of p-nitrophenol, their intermediates and by-products in electro-Fenton process were validated with experimental assays and the results were consistent. Finally, based on the developed kinetic model the degradation process was optimized using central composite design taking as key parameters the ferrous ion concentration and current density. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Experiences of women with a diagnosis of breast cancer: a clinical pathway approach.

    Science.gov (United States)

    Lindop, E; Cannon, S

    2001-06-01

    The study presented in this paper formed the first part of a large survey of breast cancer patients in one health authority in England, UK looking at individual needs expressed by women with a diagnosis of breast cancer. The paper provides an account of the experiences of 12 women with a diagnosis of breast cancer. The women represent a wide age range and different stages of illness. The transcribed accounts of the women were analysed by means of Qualitative Solutions and Research, Non-Numerical Unstructured Data Indexing Searching and Theorising (QSR*NUDIST). The study examined the individual experiences of women with a diagnosis of breast cancer and its aftermath as they passed through different stages related to it. The women's experiences are presented within the conceptual framework of the clinical pathway and their accounts represent their journey along the pathway. Various significant points in this journey are portrayed representing the women's reactions to diagnosis, treatment, femininity and body image, support, family and friends, information and after care.

  1. Modulation of Metabolic Detoxification Pathways Using Foods and Food-Derived Components: A Scientific Review with Clinical Application

    Directory of Open Access Journals (Sweden)

    Romilly E. Hodges

    2015-01-01

    Full Text Available Research into human biotransformation and elimination systems continues to evolve. Various clinical and in vivo studies have been undertaken to evaluate the effects of foods and food-derived components on the activity of detoxification pathways, including phase I cytochrome P450 enzymes, phase II conjugation enzymes, Nrf2 signaling, and metallothionein. This review summarizes the research in this area to date, highlighting the potential for foods and nutrients to support and/or modulate detoxification functions. Clinical applications to alter detoxification pathway activity and improve patient outcomes are considered, drawing on the growing understanding of the relationship between detoxification functions and different disease states, genetic polymorphisms, and drug-nutrient interactions. Some caution is recommended, however, due to the limitations of current research as well as indications that many nutrients exert biphasic, dose-dependent effects and that genetic polymorphisms may alter outcomes. A whole-foods approach may, therefore, be prudent.

  2. Linear Energy Transfer-Guided Optimization in Intensity Modulated Proton Therapy: Feasibility Study and Clinical Potential

    Energy Technology Data Exchange (ETDEWEB)

    Giantsoudi, Drosoula, E-mail: dgiantsoudi@partners.org [Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts (United States); Grassberger, Clemens; Craft, David; Niemierko, Andrzej; Trofimov, Alexei; Paganetti, Harald [Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts (United States)

    2013-09-01

    Purpose: To investigate the feasibility and potential clinical benefit of linear energy transfer (LET) guided plan optimization in intensity modulated proton therapy (IMPT). Methods and Materials: A multicriteria optimization (MCO) module was used to generate a series of Pareto-optimal IMPT base plans (BPs), corresponding to defined objectives, for 5 patients with head-and-neck cancer and 2 with pancreatic cancer. A Monte Carlo platform was used to calculate dose and LET distributions for each BP. A custom-designed MCO navigation module allowed the user to interpolate between BPs to produce deliverable Pareto-optimal solutions. Differences among the BPs were evaluated for each patient, based on dose–volume and LET–volume histograms and 3-dimensional distributions. An LET-based relative biological effectiveness (RBE) model was used to evaluate the potential clinical benefit when navigating the space of Pareto-optimal BPs. Results: The mean LET values for the target varied up to 30% among the BPs for the head-and-neck patients and up to 14% for the pancreatic cancer patients. Variations were more prominent in organs at risk (OARs), where mean LET values differed by a factor of up to 2 among the BPs for the same patient. An inverse relation between dose and LET distributions for the OARs was typically observed. Accounting for LET-dependent variable RBE values, a potential improvement on RBE-weighted dose of up to 40%, averaged over several structures under study, was noticed during MCO navigation. Conclusions: We present a novel strategy for optimizing proton therapy to maximize dose-averaged LET in tumor targets while simultaneously minimizing dose-averaged LET in normal tissue structures. MCO BPs show substantial LET variations, leading to potentially significant differences in RBE-weighted doses. Pareto-surface navigation, using both dose and LET distributions for guidance, provides the means for evaluating a large variety of deliverable plans and aids in

  3. Linear Energy Transfer-Guided Optimization in Intensity Modulated Proton Therapy: Feasibility Study and Clinical Potential

    International Nuclear Information System (INIS)

    Giantsoudi, Drosoula; Grassberger, Clemens; Craft, David; Niemierko, Andrzej; Trofimov, Alexei; Paganetti, Harald

    2013-01-01

    Purpose: To investigate the feasibility and potential clinical benefit of linear energy transfer (LET) guided plan optimization in intensity modulated proton therapy (IMPT). Methods and Materials: A multicriteria optimization (MCO) module was used to generate a series of Pareto-optimal IMPT base plans (BPs), corresponding to defined objectives, for 5 patients with head-and-neck cancer and 2 with pancreatic cancer. A Monte Carlo platform was used to calculate dose and LET distributions for each BP. A custom-designed MCO navigation module allowed the user to interpolate between BPs to produce deliverable Pareto-optimal solutions. Differences among the BPs were evaluated for each patient, based on dose–volume and LET–volume histograms and 3-dimensional distributions. An LET-based relative biological effectiveness (RBE) model was used to evaluate the potential clinical benefit when navigating the space of Pareto-optimal BPs. Results: The mean LET values for the target varied up to 30% among the BPs for the head-and-neck patients and up to 14% for the pancreatic cancer patients. Variations were more prominent in organs at risk (OARs), where mean LET values differed by a factor of up to 2 among the BPs for the same patient. An inverse relation between dose and LET distributions for the OARs was typically observed. Accounting for LET-dependent variable RBE values, a potential improvement on RBE-weighted dose of up to 40%, averaged over several structures under study, was noticed during MCO navigation. Conclusions: We present a novel strategy for optimizing proton therapy to maximize dose-averaged LET in tumor targets while simultaneously minimizing dose-averaged LET in normal tissue structures. MCO BPs show substantial LET variations, leading to potentially significant differences in RBE-weighted doses. Pareto-surface navigation, using both dose and LET distributions for guidance, provides the means for evaluating a large variety of deliverable plans and aids in

  4. Joint recovery programme versus usual care - An economic evaluation of a clinical pathway for joint replacement surgery

    NARCIS (Netherlands)

    Brunenberg, DE; van Steyn, MJ; Sluimer, JC; Bekebrede, LL; Bulstra, SK; Joore, MA

    2005-01-01

    Objective: The objective of the present study was to determine the incremental cost-effectiveness of a clinical pathway for patients undergoing joint replacement, the Joint Recovery Programme (JRP), as compared with usual care. The existing care process was revised to contain costs and shorten

  5. Geometrically based optimization for extracranial radiosurgery

    International Nuclear Information System (INIS)

    Liu Ruiguo; Wagner, Thomas H; Buatti, John M; Modrick, Joseph; Dill, John; Meeks, Sanford L

    2004-01-01

    For static beam conformal intracranial radiosurgery, geometry of the beam arrangement dominates overall dose distribution. Maximizing beam separation in three dimensions decreases beam overlap, thus maximizing dose conformality and gradient outside of the target volume. Webb proposed arrangements of isotropically convergent beams that could be used as the starting point for a radiotherapy optimization process. We have developed an extracranial radiosurgery optimization method by extending Webb's isotropic beam arrangements to deliverable beam arrangements. This method uses an arrangement of N maximally separated converging vectors within the space available for beam delivery. Each bouquet of isotropic beam vectors is generated by a random sampling process that iteratively maximizes beam separation. Next, beam arrangement is optimized for critical structure avoidance while maintaining minimal overlap between beam entrance and exit pathways. This geometrically optimized beam set can then be used as a template for either conformal beam or intensity modulated extracranial radiosurgery. Preliminary results suggest that using this technique with conformal beam planning provides high plan conformality, a steep dose gradient outside of the tumour volume and acceptable critical structure avoidance in the majority of clinical cases

  6. Clinical Performance of an Ultrahigh Resolution Chromosomal Microarray Optimized for Neurodevelopmental Disorders.

    Science.gov (United States)

    Ho, Karen S; Twede, Hope; Vanzo, Rena; Harward, Erin; Hensel, Charles H; Martin, Megan M; Page, Stephanie; Peiffer, Andreas; Mowery-Rushton, Patricia; Serrano, Moises; Wassman, E Robert

    2016-01-01

    Copy number variants (CNVs) as detected by chromosomal microarray analysis (CMA) significantly contribute to the etiology of neurodevelopmental disorders, such as developmental delay (DD), intellectual disability (ID), and autism spectrum disorder (ASD). This study summarizes the results of 3.5 years of CMA testing by a CLIA-certified clinical testing laboratory 5487 patients with neurodevelopmental conditions were clinically evaluated for rare copy number variants using a 2.8-million probe custom CMA optimized for the detection of CNVs associated with neurodevelopmental disorders. We report an overall detection rate of 29.4% in our neurodevelopmental cohort, which rises to nearly 33% when cases with DD/ID and/or MCA only are considered. The detection rate for the ASD cohort is also significant, at 25%. Additionally, we find that detection rate and pathogenic yield of CMA vary significantly depending on the primary indications for testing, the age of the individuals tested, and the specialty of the ordering doctor. We also report a significant difference between the detection rate on the ultrahigh resolution optimized array in comparison to the array from which it originated. This increase in detection can significantly contribute to the efficient and effective medical management of neurodevelopmental conditions in the clinic.

  7. Divergent pathways to influence: Cognition and behavior differentially mediate the effects of optimism on physical and mental quality of life in Chinese university students.

    Science.gov (United States)

    Ramsay, Jonathan E; Yang, Fang; Pang, Joyce S; Lai, Ching-Man; Ho, Roger Cm; Mak, Kwok-Kei

    2015-07-01

    Previous research has indicated that both cognitive and behavioral variables mediate the positive effect of optimism on quality of life; yet few attempts have been made to accommodate these constructs into a single explanatory framework. Adopting Fredrickson's broaden-and-build perspective, we examined the relationships between optimism, self-rated health, resilience, exercise, and quality of life in 365 Chinese university students using path analysis. For physical quality of life, a two-stage model, in which the effects of optimism were sequentially mediated by cognitive and behavioral variables, provided the best fit. A one-stage model, with full mediation by cognitive variables, provided the best fit for mental quality of life. This suggests that optimism influences physical and mental quality of life via different pathways. © The Author(s) 2013.

  8. Optimizing oncology therapeutics through quantitative translational and clinical pharmacology: challenges and opportunities.

    Science.gov (United States)

    Venkatakrishnan, K; Friberg, L E; Ouellet, D; Mettetal, J T; Stein, A; Trocóniz, I F; Bruno, R; Mehrotra, N; Gobburu, J; Mould, D R

    2015-01-01

    Despite advances in biomedical research that have deepened our understanding of cancer hallmarks, resulting in the discovery and development of targeted therapies, the success rates of oncology drug development remain low. Opportunities remain for objective dose selection informed by exposure-response understanding to optimize the benefit-risk balance of novel therapies for cancer patients. This review article discusses the principles and applications of modeling and simulation approaches across the lifecycle of development of oncology therapeutics. Illustrative examples are used to convey the value gained from integration of quantitative clinical pharmacology strategies from the preclinical-translational phase through confirmatory clinical evaluation of efficacy and safety. © 2014 American Society for Clinical Pharmacology and Therapeutics.

  9. [Results following the implementation of a clinical pathway in the process of care to elderly patients with osteoporotic hip fracture in a second level hospital].

    Science.gov (United States)

    Sánchez-Hernández, N; Sáez-López, P; Paniagua-Tejo, S; Valverde-García, J A

    2016-01-01

    To evaluate the efficiency of a clinical pathway in the management of elderly patients with fragility hip fracture in a second level hospital in terms of length of stay time to surgery, morbidity, hospital mortality, and improved functional outcome. A comparative and prospective study was carried out between two groups of patients with hip fracture aged 75 and older prior to 2010 (n=216), and after a quality improvement intervention in 2013 (n=196). A clinical pathway based on recent scientific evidence was implemented. The degree of compliance with the implemented measures was quantified. The characteristics of the patients in both groups were similar in age, gender, functional status (Barthel Index) and comorbidity (Charlson Index). Median length of stay was reduced by more than 45% in 2013 (16.61 vs. 9.08 days, p=.000). Also, time to surgery decreased 29.4% in the multidisciplinary intervention group (6.23 vs. 4.4 days, p=.000). Patients assigned to the clinical pathway group showed higher medical complications rate (delirium, malnutrition, anaemia and electrolyte disorders), but a lower hospital mortality (5.10 vs. 2.87%, p>.005). The incidence of surgical wound infection (p=.031) and functional efficiency (p=.001) also improved in 2013. An increased number of patients started treatment for osteoporosis (14.80 vs. 76.09%, p=.001) after implementing the clinical pathway. The implementation of a clinical pathway in the care process of elderly patients with hip fracture reduced length of stay and time to surgery, without a negative impact on associated clinical and functional outcomes. Copyright © 2015 SECOT. Published by Elsevier Espana. All rights reserved.

  10. [Clinical pathway for management of patients with acute asthma attack].

    Science.gov (United States)

    Azuma, Naoto; Katada, Yoshinori; Kobayashi, Masaaki; Kojima, Makiko; Nakajima, Yumi; Shibano, Miyo; Tomita, Hitomi; Yamanaka, Takao; Harada, Yoshinori; Ishii, Taeko; Saeki, Yukihiko

    2008-11-01

    There have been few reports of clinical pathway (CP) for treatment of asthma attack, because patients with asthma always admit emergently and the severity varies. We introduced CP so that standard asthma treatment can be widely used, and investigated its clinical usefulness. We designed a new CP for treating asthma attack according to the guideline (Japanese guideline (JGL) and Global Initiative for Asthma (GINA)). 136 patients who admitted to our hospital due to asthma attack from January 1999 to November 2006, were enrolled our study. Excluding cases complicated with pneumonia, COPD or cardiac failure, we evaluated 46 cases treated with the CP comparing with 19 cases treated without the CP. The clinical evaluations include systemic and inhaled steroid use, FEV1.0%, history of asthma, and the duration of asthma attack. Furthermore, we investigated difference between cases with and without prolonged admission. While the rates of systemic and inhaled steroid use in cases without the CP were 57.9% and 52.6% respectively, those in cases with the CP were approximately 100%. Employing the CP, FEV 1.0% at discharge time was elevated from 71.7% to 76.3% and the duration of hospitalization was shortened from 14.2 days to 11.5 days. Mean age of the cases with prolonged admission was higher than the rest. The asthma CP is an effective way for the standard treatment according to the guideline to be used widely even by doctors who are not familiar with asthma treatment. It improves the efficacy of in-hospital treatment.

  11. Inverse optimization of objective function weights for treatment planning using clinical dose-volume histograms

    Science.gov (United States)

    Babier, Aaron; Boutilier, Justin J.; Sharpe, Michael B.; McNiven, Andrea L.; Chan, Timothy C. Y.

    2018-05-01

    We developed and evaluated a novel inverse optimization (IO) model to estimate objective function weights from clinical dose-volume histograms (DVHs). These weights were used to solve a treatment planning problem to generate ‘inverse plans’ that had similar DVHs to the original clinical DVHs. Our methodology was applied to 217 clinical head and neck cancer treatment plans that were previously delivered at Princess Margaret Cancer Centre in Canada. Inverse plan DVHs were compared to the clinical DVHs using objective function values, dose-volume differences, and frequency of clinical planning criteria satisfaction. Median differences between the clinical and inverse DVHs were within 1.1 Gy. For most structures, the difference in clinical planning criteria satisfaction between the clinical and inverse plans was at most 1.4%. For structures where the two plans differed by more than 1.4% in planning criteria satisfaction, the difference in average criterion violation was less than 0.5 Gy. Overall, the inverse plans were very similar to the clinical plans. Compared with a previous inverse optimization method from the literature, our new inverse plans typically satisfied the same or more clinical criteria, and had consistently lower fluence heterogeneity. Overall, this paper demonstrates that DVHs, which are essentially summary statistics, provide sufficient information to estimate objective function weights that result in high quality treatment plans. However, as with any summary statistic that compresses three-dimensional dose information, care must be taken to avoid generating plans with undesirable features such as hotspots; our computational results suggest that such undesirable spatial features were uncommon. Our IO-based approach can be integrated into the current clinical planning paradigm to better initialize the planning process and improve planning efficiency. It could also be embedded in a knowledge-based planning or adaptive radiation therapy framework to

  12. Optimizing perioperative decision making: improved information for clinical workflow planning.

    Science.gov (United States)

    Doebbeling, Bradley N; Burton, Matthew M; Wiebke, Eric A; Miller, Spencer; Baxter, Laurence; Miller, Donald; Alvarez, Jorge; Pekny, Joseph

    2012-01-01

    Perioperative care is complex and involves multiple interconnected subsystems. Delayed starts, prolonged cases and overtime are common. Surgical procedures account for 40-70% of hospital revenues and 30-40% of total costs. Most planning and scheduling in healthcare is done without modern planning tools, which have potential for improving access by assisting in operations planning support. We identified key planning scenarios of interest to perioperative leaders, in order to examine the feasibility of applying combinatorial optimization software solving some of those planning issues in the operative setting. Perioperative leaders desire a broad range of tools for planning and assessing alternate solutions. Our modeled solutions generated feasible solutions that varied as expected, based on resource and policy assumptions and found better utilization of scarce resources. Combinatorial optimization modeling can effectively evaluate alternatives to support key decisions for planning clinical workflow and improving care efficiency and satisfaction.

  13. Is Generalized Maternal Optimism or Pessimism During Pregnancy Associated with Unplanned Cesarean Section Deliveries in China?

    Directory of Open Access Journals (Sweden)

    Cheryl A. Moyer

    2010-01-01

    Full Text Available This research examines whether maternal optimism/pessimism is associated with unplanned Cesarean section deliveries in China. If so, does the association remain after controlling for clinical factors associated with C-sections? A sample of 227 mostly primiparous women in the third trimester of pregnancy was surveyed in a large tertiary care hospital in Beijing, China. Post-delivery data were collected from medical records. In bivariate analysis, both optimism and pessimism were related to unplanned c-section. However, when optimism and pessimism were entered into a regression model together, optimism was no longer statistically significant. Pessimism remained significant, even when adjusting for clinical factors such as previous abortion, previous miscarriage, pregnancy complications, infant gestational age, infant birthweight, labor duration, birth complications, and self-rated difficulty of the pregnancy. This research suggests that maternal mindset during pregnancy has a role in mode of delivery. However, more research is needed to elucidate potential causal pathways and test potential interventions.

  14. Care pathways for organ donation after brain death: guidance from available literature?

    Science.gov (United States)

    Hoste, Pieter; Vanhaecht, Kris; Ferdinande, Patrick; Rogiers, Xavier; Eeckloo, Kristof; Blot, Stijn; Hoste, Eric; Vogelaers, Dirk; Vandewoude, Koenraad

    2016-10-01

    A discussion of the literature concerning the impact of care pathways in the complex and by definition multidisciplinary process of organ donation following brain death. Enhancing the quality and safety of organs for transplantation has become a central concern for governmental and professional organizations. At the local hospital level, a donor coordinator can use a range of interventions to improve the donation and procurement process. Care pathways have been proven to represent an effective intervention in several settings for optimizing processes and outcomes. A discussion paper. A systematic review of the Medline, CINAHL, EMBASE and The Cochrane Library databases was conducted for articles published until June 2015, using the keywords donation after brain death and care pathways. Each paper was reviewed to investigate the effects of existing care pathways for donation after brain death. An additional search for unpublished information was conducted. Although literature supports care pathways as an effective intervention in several settings, few studies have explored its use and effectiveness for complex care processes such as donation after brain death. Nurses should be aware of their role in the donation process. Care pathways have the potential to support them, but their effectiveness has been insufficiently explored. Further research should focus on the development and standardization of the clinical content of a care pathway for donation after brain death and the identification of quality indicators. These should be used in a prospective effectiveness assessment of the proposed pathway. © 2016 John Wiley & Sons Ltd.

  15. The Effect of Anxiety, Depression, and Optimism on Postoperative Satisfaction and Clinical Outcomes in Lumbar Spinal Stenosis and Degenerative Spondylolisthesis Patients: Cohort Study.

    Science.gov (United States)

    Lee, Jaewon; Kim, Hong-Sik; Shim, Kyu-Dong; Park, Ye-Soo

    2017-06-01

    The aim of this study is to evaluate the effect of depression, anxiety, and optimism on postoperative satisfaction and clinical outcomes in patients who underwent less than two-level posterior instrumented fusions for lumbar spinal stenosis and degenerative spondylolisthesis. Preoperative psychological status of subjects, such as depression, anxiety, and optimism, was evaluated using the Hospital Anxiety and Depression Scale (HADS) and the Revised Life Orientation Test (LOT-R). Clinical evaluation was determined by measuring changes in a visual analogue scale (VAS) and the Oswestry Disability Index (ODI) before and after surgery. Postoperative satisfaction of subjects assessed using the North American Spine Society lumbar spine questionnaire was comparatively analyzed against the preoperative psychological status. The correlation between patient's preoperative psychological status (depression, anxiety, and optimism) and clinical outcomes (VAS and ODI) was evaluated. VAS and ODI scores significantly decreased after surgery ( p optimism) was not related to the degree of improvement in clinical outcomes (VAS and ODI) after surgery. However, postoperative satisfaction was moderately correlated with optimism. Anxiety and optimism were more correlated with patient satisfaction than clinical outcomes. Accordingly, the surgeon can predict postoperative satisfaction of patients based on careful evaluation of psychological status before surgery.

  16. Combining clinical variables to optimize prediction of antidepressant treatment outcomes.

    Science.gov (United States)

    Iniesta, Raquel; Malki, Karim; Maier, Wolfgang; Rietschel, Marcella; Mors, Ole; Hauser, Joanna; Henigsberg, Neven; Dernovsek, Mojca Zvezdana; Souery, Daniel; Stahl, Daniel; Dobson, Richard; Aitchison, Katherine J; Farmer, Anne; Lewis, Cathryn M; McGuffin, Peter; Uher, Rudolf

    2016-07-01

    The outcome of treatment with antidepressants varies markedly across people with the same diagnosis. A clinically significant prediction of outcomes could spare the frustration of trial and error approach and improve the outcomes of major depressive disorder through individualized treatment selection. It is likely that a combination of multiple predictors is needed to achieve such prediction. We used elastic net regularized regression to optimize prediction of symptom improvement and remission during treatment with escitalopram or nortriptyline and to identify contributing predictors from a range of demographic and clinical variables in 793 adults with major depressive disorder. A combination of demographic and clinical variables, with strong contributions from symptoms of depressed mood, reduced interest, decreased activity, indecisiveness, pessimism and anxiety significantly predicted treatment outcomes, explaining 5-10% of variance in symptom improvement with escitalopram. Similar combinations of variables predicted remission with area under the curve 0.72, explaining approximately 15% of variance (pseudo R(2)) in who achieves remission, with strong contributions from body mass index, appetite, interest-activity symptom dimension and anxious-somatizing depression subtype. Escitalopram-specific outcome prediction was more accurate than generic outcome prediction, and reached effect sizes that were near or above a previously established benchmark for clinical significance. Outcome prediction on the nortriptyline arm did not significantly differ from chance. These results suggest that easily obtained demographic and clinical variables can predict therapeutic response to escitalopram with clinically meaningful accuracy, suggesting a potential for individualized prescription of this antidepressant drug. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  17. Calcium Signaling Pathway Is Associated with the Long-Term Clinical Response to Selective Serotonin Reuptake Inhibitors (SSRI and SSRI with Antipsychotics in Patients with Obsessive-Compulsive Disorder.

    Directory of Open Access Journals (Sweden)

    Hidehiro Umehara

    Full Text Available Selective serotonin reuptake inhibitors (SSRI are established first-line pharmacological treatments for obsessive-compulsive disorder (OCD, while antipsychotics are used as an augmentation strategy for SSRI in OCD patients who have either no response or a partial response to SSRI treatment. The goal of the present study was to identify genetic variants and pathways that are associated with the long-term clinical response of OCD patients to SSRI or SSRI with antipsychotics.We first performed a genome-wide association study of 96 OCD patients to examine genetic variants contributing to the response to SSRI or SSRI with antipsychotics. Subsequently, we conducted pathway-based analyses by using Improved Gene Set Enrichment Analysis for Genome-wide Association Study (i-GSEA4GWAS to examine the combined effects of genetic variants on the clinical response in OCD.While we failed to detect specific genetic variants associated with clinical responses to SSRI or to SSRI with an atypical antipsychotic at genome-wide levels of significance, we identified 8 enriched pathways for the SSRI treatment response and 5 enriched pathways for the treatment response to SSRI with an antipsychotic medication. Notably, the calcium signaling pathway was identified in both treatment responses.Our results provide novel insight into the molecular mechanisms underlying the variability in clinical response to SSRI and SSRI with antipsychotics in OCD patients.

  18. How Does Optimism Suppress Immunity? Evaluation of Three Affective Pathways

    OpenAIRE

    Segerstrom, Suzanne C.

    2006-01-01

    Studies have linked optimism to poorer immunity during difficult stressors. In the present report, when first-year law students (N = 46) relocated to attend law school, reducing conflict among curricular and extracurricular goals, optimism predicted larger delayed type hypersensitivity responses, indicating more robust in vivo cellular immunity. However, when students did not relocate, increasing goal conflict, optimism predicted smaller responses. Although this effect has been attributed to ...

  19. Pan-cancer analysis of TCGA data reveals notable signaling pathways

    International Nuclear Information System (INIS)

    Neapolitan, Richard; Horvath, Curt M.; Jiang, Xia

    2015-01-01

    A signal transduction pathway (STP) is a network of intercellular information flow initiated when extracellular signaling molecules bind to cell-surface receptors. Many aberrant STPs have been associated with various cancers. To develop optimal treatments for cancer patients, it is important to discover which STPs are implicated in a cancer or cancer-subtype. The Cancer Genome Atlas (TCGA) makes available gene expression level data on cases and controls in ten different types of cancer including breast cancer, colon adenocarcinoma, glioblastoma, kidney renal papillary cell carcinoma, low grade glioma, lung adenocarcinoma, lung squamous cell carcinoma, ovarian carcinoma, rectum adenocarcinoma, and uterine corpus endometriod carcinoma. Signaling Pathway Impact Analysis (SPIA) is a software package that analyzes gene expression data to identify whether a pathway is relevant in a given condition. We present the results of a study that uses SPIA to investigate all 157 signaling pathways in the KEGG PATHWAY database. We analyzed each of the ten cancer types mentioned above separately, and we perform a pan-cancer analysis by grouping the data for all the cancer types. In each analysis several pathways were found to be markedly more significant than all the other pathways. We call them notable. Research has already established a connection between many of these pathways and the corresponding cancer type. However, some of our discovered pathways appear to be new findings. Altogether there were 37 notable findings in the separate analyses, 26 of them occurred in 7 pathways. These 7 pathways included the 4 notable pathways discovered in the pan-cancer analysis. So, our results suggest that these 7 pathways account for much of the mechanisms of cancer. Furthermore, by looking at the overlap among pathways, we identified possible regions on the pathways where the aberrant activity is occurring. We obtained 37 notable findings concerning 18 pathways. Some of them appear to be

  20. Independent prescriber physiotherapist led balance clinic: the Southport and Ormskirk pathway.

    Science.gov (United States)

    Burrows, L; Lesser, T H; Kasbekar, A V; Roland, N; Billing, M

    2017-05-01

    To report the introduction and impact of non-medical prescribing, initiated to improve patient pathways for those presenting with dizziness and balance disorders. The Southport and Ormskirk physiotherapy-led vestibular clinic sees and treats all patients with dizziness and balance disorders referred to the ENT department. Letters are triaged by an audiologist, who also performs an otological examination and hearing test; this is followed by an assessment with the independent prescriber physiotherapist. An ENT consultant is nearby if joint consultation is needed. Diagnoses, treatments and patient satisfaction were studied, with an analysis of the impact of medication management (stopping or starting medicines) on patients and service. In 12 months, 413 new patients with dizziness and balance disorders had appointments. The most common diagnoses were benign paroxysmal positional vertigo and vestibular migraine. Eighty-four per cent of patients required self-management strategies, 50 per cent exercise therapy, 48 per cent medication management and 24 per cent a particle repositioning manoeuvre. Patient satisfaction was high (99 per cent). Having an independent prescriber physiotherapist leading the balance clinic has reduced the number of hospital visits and onward referrals. Nearly half of all patients required medication management as part of their dizziness or balance treatment.

  1. Review of SPECT collimator selection, optimization, and fabrication for clinical and preclinical imaging

    Energy Technology Data Exchange (ETDEWEB)

    Van Audenhaege, Karen, E-mail: karen.vanaudenhaege@ugent.be; Van Holen, Roel; Vandenberghe, Stefaan; Vanhove, Christian [Department of Electronics and Information Systems, MEDISIP-IBiTech, Ghent University–iMinds Medical IT, De Pintelaan 185 block B/5, Ghent B-9000 (Belgium); Metzler, Scott D. [Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (United States); Moore, Stephen C. [Division of Nuclear Medicine, Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, 75 Francis Street, Boston, Massachusetts 02115 (United States)

    2015-08-15

    In single photon emission computed tomography, the choice of the collimator has a major impact on the sensitivity and resolution of the system. Traditional parallel-hole and fan-beam collimators used in clinical practice, for example, have a relatively poor sensitivity and subcentimeter spatial resolution, while in small-animal imaging, pinhole collimators are used to obtain submillimeter resolution and multiple pinholes are often combined to increase sensitivity. This paper reviews methods for production, sensitivity maximization, and task-based optimization of collimation for both clinical and preclinical imaging applications. New opportunities for improved collimation are now arising primarily because of (i) new collimator-production techniques and (ii) detectors with improved intrinsic spatial resolution that have recently become available. These new technologies are expected to impact the design of collimators in the future. The authors also discuss concepts like septal penetration, high-resolution applications, multiplexing, sampling completeness, and adaptive systems, and the authors conclude with an example of an optimization study for a parallel-hole, fan-beam, cone-beam, and multiple-pinhole collimator for different applications.

  2. Natural selection and optimality

    International Nuclear Information System (INIS)

    Torres, J.L.

    1989-01-01

    It is assumed that Darwin's principle translates into optimal regimes of operation along metabolical pathways in an ecological system. Fitness is then defined in terms of the distance of a given individual's thermodynamic parameters from their optimal values. The method is illustrated testing maximum power as a criterion of merit satisfied in ATP synthesis. (author). 26 refs, 2 figs

  3. Clinical translation of photobiomodulation therapy using evidences from precision molecular pathway analyses (Conference Presentation)

    Science.gov (United States)

    Arany, Praveen

    2017-02-01

    Can `light' be a Drug? To satisfy this definition as a pharmaceutical agent, light must be absorbed and change bodily function. Much evidence from our understanding of our visual cycle and Vitamin D metabolism have all noted this phenomenon. Advances in optophotonic technologies along with a better understanding of light-tissue interactions, especially in in vivo optical imaging and optogenetics, are spearheading the popularity of biophotonics in biology and medicine. The use of lasers and light devices at high doses in dermatology, ophthalmology, oncology and dentistry are now considered mainstream for certain clinical applications such as surgery, skin rejuvenation, ocular and soft tissue recontouring, anti-tumor and anti-microbial photodynamic therapy. In contrast, therapeutic use of low dose biophotonics devices is called Low Level Light / Laser Therapy (LLLT), now termed Photobiomodulation (PBM) Therapy. This therapy is defined as a non-thermal use of non-ionizing forms of electromagnetic radiation to alleviate pain, inflammation, modulating the immune responses and promoting wound healing and tissue regeneration. Surprisingly, despite vast volumes of scientific literature from both clinical and laboratory studies noting the phenomenological evidences for this innovative therapy, limited mechanistic insights have prevented the development of rigorous, reproducible clinical protocols. This presentation will outline our current efforts at ongoing efforts in our group to assess molecular pathways and precisely define clinical treatment variables to enable clinical translation with PBM therapies.

  4. SU-G-BRC-01: A Data-Driven Pre-Optimization Method for Prediction of Achievability of Clinical Objectives in IMRT

    Energy Technology Data Exchange (ETDEWEB)

    Ranganathan, V; Kumar, P [Philips India Limited, Bangalore, Karnataka (India); Bzdusek, K [Philips, Fitchburg, WI (United States); Das, J Maria [Sanjay Gandhi PG Inst Med Scienes, Lucknow (India)

    2016-06-15

    Purpose: We propose a novel data-driven method to predict the achievability of clinical objectives upfront before invoking the IMRT optimization. Methods: A new metric called “Geometric Complexity (GC)” is used to estimate the achievability of clinical objectives. Here, GC is the measure of the number of “unmodulated” beamlets or rays that intersect the Region-of-interest (ROI) and the target volume. We first compute the geometric complexity ratio (GCratio) between the GC of a ROI (say, parotid) in a reference plan and the GC of the same ROI in a given plan. The GCratio of a ROI indicates the relative geometric complexity of the ROI as compared to the same ROI in the reference plan. Hence GCratio can be used to predict if a defined clinical objective associated with the ROI can be met by the optimizer for a given case. Basically a higher GCratio indicates a lesser likelihood for the optimizer to achieve the clinical objective defined for a given ROI. Similarly, a lower GCratio indicates a higher likelihood for the optimizer to achieve the clinical objective defined for the given ROI. We have evaluated the proposed method on four Head and Neck cases using Pinnacle3 (version 9.10.0) Treatment Planning System (TPS). Results: Out of the total of 28 clinical objectives from four head and neck cases included in the study, 25 were in agreement with the prediction, which implies an agreement of about 85% between predicted and obtained results. The Pearson correlation test shows a positive correlation between predicted and obtained results (Correlation = 0.82, r2 = 0.64, p < 0.005). Conclusion: The study demonstrates the feasibility of the proposed method in head and neck cases for predicting the achievability of clinical objectives with reasonable accuracy.

  5. Optimization and scale up of microfluidic nanolipomer production method for preclinical and potential clinical trials.

    Science.gov (United States)

    Gdowski, Andrew; Johnson, Kaitlyn; Shah, Sunil; Gryczynski, Ignacy; Vishwanatha, Jamboor; Ranjan, Amalendu

    2018-02-12

    The process of optimization and fabrication of nanoparticle synthesis for preclinical studies can be challenging and time consuming. Traditional small scale laboratory synthesis techniques suffer from batch to batch variability. Additionally, the parameters used in the original formulation must be re-optimized due to differences in fabrication techniques for clinical production. Several low flow microfluidic synthesis processes have been reported in recent years for developing nanoparticles that are a hybrid between polymeric nanoparticles and liposomes. However, use of high flow microfluidic synthetic techniques has not been described for this type of nanoparticle system, which we will term as nanolipomer. In this manuscript, we describe the successful optimization and functional assessment of nanolipomers fabricated using a microfluidic synthesis method under high flow parameters. The optimal total flow rate for synthesis of these nanolipomers was found to be 12 ml/min and flow rate ratio 1:1 (organic phase: aqueous phase). The PLGA polymer concentration of 10 mg/ml and a DSPE-PEG lipid concentration of 10% w/v provided optimal size, PDI and stability. Drug loading and encapsulation of a representative hydrophobic small molecule drug, curcumin, was optimized and found that high encapsulation efficiency of 58.8% and drug loading of 4.4% was achieved at 7.5% w/w initial concentration of curcumin/PLGA polymer. The final size and polydispersity index of the optimized nanolipomer was 102.11 nm and 0.126, respectively. Functional assessment of uptake of the nanolipomers in C4-2B prostate cancer cells showed uptake at 1 h and increased uptake at 24 h. The nanolipomer was more effective in the cell viability assay compared to free drug. Finally, assessment of in vivo retention in mice of these nanolipomers revealed retention for up to 2 h and were completely cleared at 24 h. In this study, we have demonstrated that a nanolipomer formulation can be successfully

  6. Optimizing the Use of Aripiprazole Augmentation in the Treatment of Major Depressive Disorder: From Clinical Trials to Clinical Practice

    Science.gov (United States)

    Han, Changsu; Wang, Sheng-Min; Lee, Soo-Jung; Jun, Tae-Youn

    2015-01-01

    Major depressive disorder (MDD) is a recurrent, chronic, and devastating disorder leading to serious impairment in functional capacity as well as increasing public health care costs. In the previous decade, switching therapy and dose adjustment of ongoing antidepressants was the most frequently chosen subsequent treatment option for MDD. However, such recommendations were not based on firmly proven efficacy data from well-designed, placebo-controlled, randomized clinical trials (RCTs) but on practical grounds and clinical reasoning. Aripiprazole augmentation has been dramatically increasing in clinical practice owing to its unique action mechanisms as well as proven efficacy and safety from adequately powered and well-controlled RCTs. Despite the increased use of aripiprazole in depression, limited clinical information and knowledge interfere with proper and efficient use of aripiprazole augmentation for MDD. The objective of the present review was to enhance clinicians' current understanding of aripiprazole augmentation and how to optimize the use of this therapy in the treatment of MDD. PMID:26306301

  7. A pathway to optimize the properties of magnetocaloric Mn_2_-_xFe_xP_1_-_yGe_y for magnetic refrigeration

    International Nuclear Information System (INIS)

    Liu, D.M.; Zhang, Z.L.; Zhou, S.L.; Huang, Q.Z.; Deng, X.J.; Yue, M.; Liu, C.X.; Zhang, J.X.; Lynn, J.W.

    2016-01-01

    Magnetocaloric materials can be useful in magnetic refrigeration applications, but to be practical the magneto-refrigerant needs to have a very large magnetocaloric effect (MCE) near room temperature for modest applied fields (<2 T) with small hysteresis and magnetostriction, and should have a complete magnetic transition, and environmentally friendly. One system that may fulfill these requirements is Mn_2_-_xFe_xP_1_-_yGe_y, where a combined first-order structural and magnetic transition occurs between the high temperature paramagnetic and low temperature ferromagnetic phase. We have used neutron diffraction, differential scanning calorimetry, and magnetization measurements to study the effects of Mn and Ge location in the structure on the ordered magnetic moment, MCE, and hysteresis for a series of compositions of the system near optimal doping. The diffraction results indicate that the Mn ions located on the 3f site enhance the desirable properties, while those located on the 3 g sites are detrimental. The phase fraction that transforms, hysteresis of the transition, and entropy change can be affected greatly by both the compositional homogeneity and the particle size, and an annealing procedure has been developed that substantially improves the performance of all three properties of the material. We also establish a correlation between applied magnetic field to complete the transition and the temperature range of coexistence of the PM and FM phase. On the basis of these results we have identified a pathway to understand the nature and to optimize the MCE properties of this system for magnetic refrigeration applications. - Highlights: • Compositional homogeneity and particle size affect the MCE properties. • Mn ions located on the 3f site enhance the desirable MCE properties. • A pathway to understand the nature and to optimize the MCE properties was identified.

  8. DTI fiber tractography of cerebro-cerebellar pathways and clinical evaluation of ataxia in childhood posterior fossa tumor survivors.

    Science.gov (United States)

    Oh, Myung Eun; Driever, Pablo Hernáiz; Khajuria, Rajiv K; Rueckriegel, Stefan Mark; Koustenis, Elisabeth; Bruhn, Harald; Thomale, Ulrich-Wilhelm

    2017-01-01

    Pediatric posterior fossa (PF) tumor survivors experience long-term motor deficits. Specific cerebrocerebellar connections may be involved in incidence and severity of motor dysfunction. We examined the relationship between long-term ataxia as well as fine motor function and alteration of differential cerebellar efferent and afferent pathways using diffusion tensor imaging (DTI) and tractography. DTI-based tractography was performed in 19 patients (10 pilocytic astrocytoma (PA) and 9 medulloblastoma patients (MB)) and 20 healthy peers. Efferent Cerebello-Thalamo-Cerebral (CTC) and afferent Cerebro-Ponto-Cerebellar (CPC) tracts were reconstructed and analyzed concerning fractional anisotropy (FA) and volumetric measurements. Clinical outcome was assessed with the International Cooperative Ataxia Rating Scale (ICARS). Kinematic parameters of fine motor function (speed, automation, variability, and pressure) were obtained by employing a digitizing graphic tablet. ICARS scores were significantly higher in MB patients than in PA patients. Poorer ICARS scores and impaired fine motor function correlated significantly with volume loss of CTC pathway in MB patients, but not in PA patients. Patients with pediatric post-operative cerebellar mutism syndrome showed higher loss of CTC pathway volume and were more atactic. CPC pathway volume was significantly reduced in PA patients, but not in MB patients. Neither relationship was observed between the CPC pathway and ICARS or fine motor function. There was no group difference of FA values between the patients and healthy peers. Reduced CTC pathway volumes in our cohorts were associated with severity of long-term ataxia and impaired fine motor function in survivors of MBs. We suggest that the CTC pathway seems to play a role in extent of ataxia and fine motor dysfunction after childhood cerebellar tumor treatment. DTI may be a useful tool to identify relevant structures of the CTC pathway and possibly avoid surgically induced long

  9. Optimizing megakaryocyte polyploidization by targeting multiple pathways of cytokinesis.

    Science.gov (United States)

    Avanzi, Mauro P; Chen, Amanda; He, Wu; Mitchell, W Beau

    2012-11-01

    Large-scale in vitro production of platelets (PLTs) from cord blood stem cells is one goal of stem cell research. One step toward this goal will be to produce polyploid megakaryocytes capable of releasing high numbers of PLTs. Megakaryocyte polyploidization requires distinct cytoskeletal and cellular mechanisms, including actin polymerization, myosin activation, microtubule formation, and increased DNA production. In this study we variably combined inhibition of these principal mechanisms of cytokinesis with the goal of driving polyploidization in megakaryocytes. Megakaryocytes were derived from umbilical cord blood and cultured with reagents that inhibit distinct mechanisms of cytokinesis: Rho-Rock inhibitor (RRI), Src inhibitor (SI), nicotinamide (NIC), aurora B inhibitor (ABI), and myosin light chain kinase inhibitor (MLCKI). Combinations of reagents were used to determine their interactions and to maximize megakaryocyte ploidy. Treatment with RRI, NIC, SI, and ABI, but not with MLCKI, increased the final ploidy and RRI was the most effective single reagent. RRI and MLCKI, both inhibitors of MLC activation, resulted in opposite ploidy outcomes. Combinations of reagents also increased ploidy and the use of NIC, SI, and ABI was as effective as RRI alone. Addition of MLCKI to NIC, SI, and ABI reached the highest level of polyploidization. Megakaryocyte polyploidization results from modulation of a combination of distinct cytokinesis pathways. Reagents targeting distinct cytoskeletal pathways produced additive effects in final megakaryocyte ploidy. The RRI, however, showed no additive effect but produced a high final ploidy due to overlapping inhibition of multiple cytokinesis pathways. © 2012 American Association of Blood Banks.

  10. Economic modelling of diagnostic and treatment pathways in National Institute for Health and Care Excellence clinical guidelines: the Modelling Algorithm Pathways in Guidelines (MAPGuide) project.

    Science.gov (United States)

    Lord, J; Willis, S; Eatock, J; Tappenden, P; Trapero-Bertran, M; Miners, A; Crossan, C; Westby, M; Anagnostou, A; Taylor, S; Mavranezouli, I; Wonderling, D; Alderson, P; Ruiz, F

    2013-12-01

    National Institute for Health and Care Excellence (NICE) clinical guidelines (CGs) make recommendations across large, complex care pathways for broad groups of patients. They rely on cost-effectiveness evidence from the literature and from new analyses for selected high-priority topics. An alternative approach would be to build a model of the full care pathway and to use this as a platform to evaluate the cost-effectiveness of multiple topics across the guideline recommendations. In this project we aimed to test the feasibility of building full guideline models for NICE guidelines and to assess if, and how, such models can be used as a basis for cost-effectiveness analysis (CEA). A 'best evidence' approach was used to inform the model parameters. Data were drawn from the guideline documentation, advice from clinical experts and rapid literature reviews on selected topics. Where possible we relied on good-quality, recent UK systematic reviews and meta-analyses. Two published NICE guidelines were used as case studies: prostate cancer and atrial fibrillation (AF). Discrete event simulation (DES) was used to model the recommended care pathways and to estimate consequent costs and outcomes. For each guideline, researchers not involved in model development collated a shortlist of topics suggested for updating. The modelling teams then attempted to evaluate options related to these topics. Cost-effectiveness results were compared with opinions about the importance of the topics elicited in a survey of stakeholders. The modelling teams developed simulations of the guideline pathways and disease processes. Development took longer and required more analytical time than anticipated. Estimates of cost-effectiveness were produced for six of the nine prostate cancer topics considered, and for five of eight AF topics. The other topics were not evaluated owing to lack of data or time constraints. The modelled results suggested 'economic priorities' for an update that differed from

  11. Clinical Trials

    Medline Plus

    Full Text Available ... questions and clinical trials. Optimizing our Clinical Trials Enterprise NHLBI has a strong tradition of supporting clinical ... multi-pronged approach to Optimize our Clinical Trials Enterprise that will make our clinical trials enterprise even ...

  12. Role of care pathways in interprofessional teamwork.

    Science.gov (United States)

    Scaria, Minimol Kulakkottu

    2016-08-24

    Cohesive interprofessional teamwork is essential to successful healthcare services. Interprofessional teamwork is the means by which different healthcare professionals - with diverse knowledge, skills and talents - collaborate to achieve a common goal. Several interventions are available to improve teamwork in the healthcare setting. This article explores the role of care pathways in improving interprofessional teamwork. Care pathways enhance teamwork by promoting coordination, collaboration, communication and decision making to achieve optimal healthcare outcomes. They result in improved staff knowledge, communication, documentation and interprofessional relations. Care pathways also contribute to patient-centred care and increase patient satisfaction.

  13. Clinical Pathway and Monthly Feedback Improve Adherence to Antibiotic Guideline Recommendations for Community-Acquired Pneumonia.

    Directory of Open Access Journals (Sweden)

    Maher Almatar

    Full Text Available Compliance with community-acquired pneumonia (CAP guidelines remains poor despite a substantial body of evidence indicating that guideline-concordant care improves patient outcomes. The aim of this study was to compare the relative effectiveness of a general educational and a targeted emergency department intervention on improving physicians' concordance with CAP guidelines.Two distinct interventions were implemented over specific time periods. The first intervention was educational, focusing on the development of local CAP guidelines and their dissemination through hospital-wide educational programmes. The second intervention was a targeted one for the emergency department, where a clinical pathway for the initial management of CAP patients was introduced, followed by monthly feedback to the emergency department (ED physicians about concordance rates with the guidelines. Data on the concordance rate to CAP guidelines was collected from a retrospective chart review.A total of 398 eligible patient records were reviewed to measure concordance to CAP guidelines over the study period. Concordance rates during the baseline and educational intervention periods were similar (28.1% vs. 31.2%; p > 0.05. Significantly more patients were treated in accordance with the CAP guidelines after the ED focused intervention when compared to the baseline (61.5% vs. 28.1%; p < 0.05 or educational period (61.5% vs. 31.2%; p < 0.05.A targeted intervention with a CAP clinical pathway and monthly feedback was a successful strategy to increase adherence to empirical antibiotic recommendations in CAP guidelines.

  14. The exploration of contrasting pathways in Triple Negative Breast Cancer (TNBC).

    Science.gov (United States)

    Narrandes, Shavira; Huang, Shujun; Murphy, Leigh; Xu, Wayne

    2018-01-04

    Triple Negative Breast Cancers (TNBCs) lack the appropriate targets for currently used breast cancer therapies, conferring an aggressive phenotype, more frequent relapse and poorer survival rates. The biological heterogeneity of TNBC complicates the clinical treatment further. We have explored and compared the biological pathways in TNBC and other subtypes of breast cancers, using an in silico approach and the hypothesis that two opposing effects (Yin and Yang) pathways in cancer cells determine the fate of cancer cells. Identifying breast subgroup specific components of these opposing pathways may aid in selecting potential therapeutic targets as well as further classifying the heterogeneous TNBC subtype. Gene expression and patient clinical data from The Cancer Genome Atlas (TCGA) and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) were used for this study. Gene Set Enrichment Analysis (GSEA) was used to identify the more active pathways in cancer (Yin) than in normal and the more active pathways in normal (Yang) than in cancer. The clustering analysis was performed to compare pathways of TNBC with other types of breast cancers. The association of pathway classified TNBC sub-groups to clinical outcomes was tested using Cox regression model. Among 4729 curated canonical pathways in GSEA database, 133 Yin pathways (FDR pathways (p-value pathway while PPARα is the top Yang pathway in TNBC. The TNBC and other types of breast cancers showed different pathways enrichment significance profiles. Using top Yin and Yang pathways as classifier, the TNBC can be further subtyped into six sub-groups each having different clinical outcomes. We first reported that the FOMX1 pathway is the most upregulated and the PPARα pathway is the most downregulated pathway in TNBC. These two pathways could be simultaneously targeted in further studies. Also the pathway classifier we performed in this study provided insight into the TNBC heterogeneity.

  15. Determination of the optimal sample size for a clinical trial accounting for the population size.

    Science.gov (United States)

    Stallard, Nigel; Miller, Frank; Day, Simon; Hee, Siew Wan; Madan, Jason; Zohar, Sarah; Posch, Martin

    2017-07-01

    The problem of choosing a sample size for a clinical trial is a very common one. In some settings, such as rare diseases or other small populations, the large sample sizes usually associated with the standard frequentist approach may be infeasible, suggesting that the sample size chosen should reflect the size of the population under consideration. Incorporation of the population size is possible in a decision-theoretic approach either explicitly by assuming that the population size is fixed and known, or implicitly through geometric discounting of the gain from future patients reflecting the expected population size. This paper develops such approaches. Building on previous work, an asymptotic expression is derived for the sample size for single and two-arm clinical trials in the general case of a clinical trial with a primary endpoint with a distribution of one parameter exponential family form that optimizes a utility function that quantifies the cost and gain per patient as a continuous function of this parameter. It is shown that as the size of the population, N, or expected size, N∗ in the case of geometric discounting, becomes large, the optimal trial size is O(N1/2) or O(N∗1/2). The sample size obtained from the asymptotic expression is also compared with the exact optimal sample size in examples with responses with Bernoulli and Poisson distributions, showing that the asymptotic approximations can also be reasonable in relatively small sample sizes. © 2016 The Author. Biometrical Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Clinical implementation of stereotaxic brain implant optimization

    International Nuclear Information System (INIS)

    Rosenow, U.F.; Wojcicka, J.B.

    1991-01-01

    This optimization method for stereotaxic brain implants is based on seed/strand configurations of the basic type developed for the National Cancer Institute (NCI) atlas of regular brain implants. Irregular target volume shapes are determined from delineation in a stack of contrast enhanced computed tomography scans. The neurosurgeon may then select up to ten directions, or entry points, of surgical approach of which the program finds the optimal one under the criterion of smallest target volume diameter. Target volume cross sections are then reconstructed in 5-mm-spaced planes perpendicular to the implantation direction defined by the entry point and the target volume center. This information is used to define a closed line in an implant cross section along which peripheral seed strands are positioned and which has now an irregular shape. Optimization points are defined opposite peripheral seeds on the target volume surface to which the treatment dose rate is prescribed. Three different optimization algorithms are available: linear least-squares programming, quadratic programming with constraints, and a simplex method. The optimization routine is implemented into a commercial treatment planning system. It generates coordinate and source strength information of the optimized seed configurations for further dose rate distribution calculation with the treatment planning system, and also the coordinate settings for the stereotaxic Brown-Roberts-Wells (BRW) implantation device

  17. A Multidisciplinary Clinical Pathway Decreases Rib Fracture-Associated Infectious Morbidity and Mortality in High-Risk Trauma Patients

    Science.gov (United States)

    2006-01-01

    RT respiratory therapy ; PT physical therapy ; OT occupational therapy ; GCS Glasgow Coma Scale. 808 S.R. Todd et al. / The American Journal of...Morbidity form rib fractures increases after age 45. J Am Coll Surg 2003;196:549–55. [14] Pierson DJ, Kacmarek R. Foundations of Respiratory Care. New...Papers presented A multidisciplinary clinical pathway decreases rib fracture –associated infectious morbidity and mortality in high-risk trauma

  18. Ethnic identity and mental health in American Indian youth: examining mediation pathways through self-esteem, and future optimism.

    Science.gov (United States)

    Smokowski, Paul R; Evans, Caroline B R; Cotter, Katie L; Webber, Kristina C

    2014-03-01

    Mental health functioning in American Indian youth is an understudied topic. Given the increased rates of depression and anxiety in this population, further research is needed. Using multiple group structural equation modeling, the current study illuminates the effect of ethnic identity on anxiety symptoms, depressive symptoms, and externalizing behavior in a group of Lumbee adolescents and a group of Caucasian, African American, and Latino/Hispanic adolescents. This study examined two possible pathways (i.e., future optimism and self-esteem) through which ethnic identity is associated with adolescent mental health. The sample (N = 4,714) is 28.53% American Indian (Lumbee) and 51.38% female. The study findings indicate that self-esteem significantly mediated the relationships between ethnic identity and anxiety symptoms, depressive symptoms, and externalizing behavior for all racial/ethnic groups (i.e., the total sample). Future optimism significantly mediated the relationship between ethnic identity and externalizing behavior for all racial/ethnic groups and was a significant mediator between ethnic identity and depressive symptoms for American Indian youth only. Fostering ethnic identity in all youth serves to enhance mental health functioning, but is especially important for American Indian youth due to the collective nature of their culture.

  19. Optimism on quality of life in Portuguese chronic patients: moderator/mediator?

    Science.gov (United States)

    Vilhena, Estela; Pais-Ribeiro, José; Silva, Isabel; Pedro, Luísa; Meneses, Rute F; Cardoso, Helena; Silva, António Martins da; Mendonça, Denisa

    2014-07-01

    optimism is an important variable that has consistently been shown to affect adjustment to quality of life in chronic diseases. This study aims to clarify if dispositional optimism exerts a moderating or a mediating influence on the personality traits-quality of life association, in Portuguese chronic patients. multiple regression models were used to test the moderation and mediation effects of dispositional optimism in quality of life. A sample of 729 patients was recruited in Portugal's main hospitals and completed self-reported questionnaires assessing socio-demographic and clinical variables, personality, dispositional optimism, quality of life (QoL) and subjective well-being (SWB). the results of the regression models showed that dispositional optimism did not moderate the relationships between personality traits and quality of life. After controlling for gender, age, education level and severity of disease perception, the effects of personality traits on QoL and in SWB were mediated by dispositional optimism (partially and completely), except for the links between neuroticism/openness to experience and physical health. dispositional optimism is more likely to play a mediating, rather than a moderating role in personality traits-quality of life pathway in Portuguese chronic patients, suggesting that "the expectation that good things will happen" contributes to a better quality of life and subjective well-being.

  20. A putative biomarker signature for clinically effective AKT inhibition: correlation of in vitro, in vivo and clinical data identifies the importance of modulation of the mTORC1 pathway.

    Science.gov (United States)

    Cheraghchi-Bashi, Azadeh; Parker, Christine A; Curry, Ed; Salazar, Jean-Frederic; Gungor, Hatice; Saleem, Azeem; Cunnea, Paula; Rama, Nona; Salinas, Cristian; Mills, Gordon B; Morris, Shannon R; Kumar, Rakesh; Gabra, Hani; Stronach, Euan A

    2015-12-08

    Our identification of dysregulation of the AKT pathway in ovarian cancer as a platinum resistance specific event led to a comprehensive analysis of in vitro, in vivo and clinical behaviour of the AKT inhibitor GSK2141795. Proteomic biomarker signatures correlating with effects of GSK2141795 were developed using in vitro and in vivo models, well characterised for related molecular, phenotypic and imaging endpoints. Signatures were validated in temporally paired biopsies from patients treated with GSK2141795 in a clinical study. GSK2141795 caused growth-arrest as single agent in vitro, enhanced cisplatin-induced apoptosis in vitro and reduced tumour volume in combination with platinum in vivo. GSK2141795 treatment in vitro and in vivo resulted in ~50-90% decrease in phospho-PRAS40 and 20-80% decrease in fluoro-deoxyglucose (FDG) uptake. Proteomic analysis of GSK2141795 in vitro and in vivo identified a signature of pathway inhibition including changes in AKT and p38 phosphorylation and total Bim, IGF1R, AR and YB1 levels. In patient biopsies, prior to treatment with GSK2141795 in a phase 1 clinical trial, this signature was predictive of post-treatment changes in the response marker CA125. Development of this signature represents an opportunity to demonstrate the clinical importance of AKT inhibition for re-sensitisation of platinum resistant ovarian cancer to platinum.

  1. Clinical dosimetry in molecular radiotherapy: protocol optimization and clinical implementation

    International Nuclear Information System (INIS)

    Ferrer, Ludovic

    2011-01-01

    Molecular radiotherapy (mrt) consists in destructing tumour targets by radiolabelled vectors. This nuclear medicine specialty is being considered with increasing interest for example via the success achieved in the treatment of non-Hodgkin lymphomas by radioimmunotherapy. One of the keys of mrt optimization relies on the personalising of absorbed doses delivered to the patient: This is required to ascertain that irradiation is focused on tumour cells while keeping surrounding healthy tissue irradiation at an acceptable - non-toxic - level. Radiation dose evaluation in mrt requires in one hand, the spatial and temporal localization of injected radioactive sources by scintigraphic imaging, and on a second hand, the knowledge of the emitted radiation propagating media, given by CT imaging. Global accuracy relies on the accuracy of each of the steps that contribute to clinical dosimetry. There is no reference, standardized dosimetric protocol to date. Due to heterogeneous implementations, evaluation of the accuracy of the absorbed dose is a difficult task. In this thesis, we developed and evaluated different dosimetric approaches that allow us to find a relationship between the absorbed dose to the bone marrow and haematological toxicity. Besides, we built a scientific project, called DosiTest, which aims at evaluating the impact of the various step that contribute to the realization of a dosimetric study, by means of a virtual multicentric comparison based on Monte-Carlo modelling. (author) [fr

  2. Renewable energy from Cyanobacteria: energy production optimization by metabolic pathway engineering.

    Science.gov (United States)

    Quintana, Naira; Van der Kooy, Frank; Van de Rhee, Miranda D; Voshol, Gerben P; Verpoorte, Robert

    2011-08-01

    The need to develop and improve sustainable energy resources is of eminent importance due to the finite nature of our fossil fuels. This review paper deals with a third generation renewable energy resource which does not compete with our food resources, cyanobacteria. We discuss the current state of the art in developing different types of bioenergy (ethanol, biodiesel, hydrogen, etc.) from cyanobacteria. The major important biochemical pathways in cyanobacteria are highlighted, and the possibility to influence these pathways to improve the production of specific types of energy forms the major part of this review.

  3. Modeling Ignition of a Heptane Isomer: Improved Thermodynamics, Reaction Pathways, Kinetic, and Rate Rule Optimizations for 2-Methylhexane

    KAUST Repository

    Mohamed, Samah; Cai, Liming; Khaled, Fathi; Banyon, Colin; Wang, Zhandong; Rachidi, Mariam El; Pitsch, Heinz; Curran, Henry J.; Farooq, Aamir; Sarathy, Mani

    2016-01-01

    Accurate chemical kinetic combustion models of lightly branched alkanes (e.g., 2-methylalkanes) are important to investigate the combustion behavior of real fuels. Improving the fidelity of existing kinetic models is a necessity, as new experiments and advanced theories show inaccuracies in certain portions of the models. This study focuses on updating thermodynamic data and the kinetic reaction mechanism for a gasoline surrogate component, 2-methylhexane, based on recently published thermodynamic group values and rate rules derived from quantum calculations and experiments. Alternative pathways for the isomerization of peroxy-alkylhydroperoxide (OOQOOH) radicals are also investigated. The effects of these updates are compared against new high-pressure shock tube and rapid compression machine ignition delay measurements. It is shown that rate constant modifications are required to improve agreement between kinetic modeling simulations and experimental data. We further demonstrate the ability to optimize the kinetic model using both manual and automated techniques for rate parameter tunings to improve agreement with the measured ignition delay time data. Finally, additional low temperature chain branching reaction pathways are shown to improve the model’s performance. The present approach to model development provides better performance across extended operating conditions while also strengthening the fundamental basis of the model.

  4. Modeling Ignition of a Heptane Isomer: Improved Thermodynamics, Reaction Pathways, Kinetic, and Rate Rule Optimizations for 2-Methylhexane

    KAUST Repository

    Mohamed, Samah

    2016-03-21

    Accurate chemical kinetic combustion models of lightly branched alkanes (e.g., 2-methylalkanes) are important to investigate the combustion behavior of real fuels. Improving the fidelity of existing kinetic models is a necessity, as new experiments and advanced theories show inaccuracies in certain portions of the models. This study focuses on updating thermodynamic data and the kinetic reaction mechanism for a gasoline surrogate component, 2-methylhexane, based on recently published thermodynamic group values and rate rules derived from quantum calculations and experiments. Alternative pathways for the isomerization of peroxy-alkylhydroperoxide (OOQOOH) radicals are also investigated. The effects of these updates are compared against new high-pressure shock tube and rapid compression machine ignition delay measurements. It is shown that rate constant modifications are required to improve agreement between kinetic modeling simulations and experimental data. We further demonstrate the ability to optimize the kinetic model using both manual and automated techniques for rate parameter tunings to improve agreement with the measured ignition delay time data. Finally, additional low temperature chain branching reaction pathways are shown to improve the model’s performance. The present approach to model development provides better performance across extended operating conditions while also strengthening the fundamental basis of the model.

  5. Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data.

    Science.gov (United States)

    Melas, Ioannis N; Mitsos, Alexander; Messinis, Dimitris E; Weiss, Thomas S; Rodriguez, Julio-Saez; Alexopoulos, Leonidas G

    2012-04-01

    Construction of large and cell-specific signaling pathways is essential to understand information processing under normal and pathological conditions. On this front, gene-based approaches offer the advantage of large pathway exploration whereas phosphoproteomic approaches offer a more reliable view of pathway activities but are applicable to small pathway sizes. In this paper, we demonstrate an experimentally adaptive approach to construct large signaling pathways from phosphoproteomic data within a 3-day time frame. Our approach--taking advantage of the fast turnaround time of the xMAP technology--is carried out in four steps: (i) screen optimal pathway inducers, (ii) select the responsive ones, (iii) combine them in a combinatorial fashion to construct a phosphoproteomic dataset, and (iv) optimize a reduced generic pathway via an Integer Linear Programming formulation. As a case study, we uncover novel players and their corresponding pathways in primary human hepatocytes by interrogating the signal transduction downstream of 81 receptors of interest and constructing a detailed model for the responsive part of the network comprising 177 species (of which 14 are measured) and 365 interactions.

  6. A service oriented approach for guidelines-based clinical decision support using BPMN.

    Science.gov (United States)

    Rodriguez-Loya, Salvador; Aziz, Ayesha; Chatwin, Chris

    2014-01-01

    Evidence-based medical practice requires that clinical guidelines need to be documented in such a way that they represent a clinical workflow in its most accessible form. In order to optimize clinical processes to improve clinical outcomes, we propose a Service Oriented Architecture (SOA) based approach for implementing clinical guidelines that can be accessed from an Electronic Health Record (EHR) application with a Web Services enabled communication mechanism with the Enterprise Service Bus. We have used Business Process Modelling Notation (BPMN) for modelling and presenting the clinical pathway in the form of a workflow. The aim of this study is to produce spontaneous alerts in the healthcare workflow in the diagnosis of Chronic Obstructive Pulmonary Disease (COPD). The use of BPMN as a tool to automate clinical guidelines has not been previously employed for providing Clinical Decision Support (CDS).

  7. Program Design Analysis using BEopt Building Energy Optimization Software: Defining a Technology Pathway Leading to New Homes with Zero Peak Cooling Demand; Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, R.; Christensen, C.; Horowitz, S.

    2006-08-01

    An optimization method based on the evaluation of a broad range of different combinations of specific energy efficiency and renewable-energy options is used to determine the least-cost pathway to the development of new homes with zero peak cooling demand. The optimization approach conducts a sequential search of a large number of possible option combinations and uses the most cost-effective alternatives to generate a least-cost curve to achieve home-performance levels ranging from a Title 24-compliant home to a home that uses zero net source energy on an annual basis. By evaluating peak cooling load reductions on the least-cost curve, it is then possible to determine the most cost-effective combination of energy efficiency and renewable-energy options that both maximize annual energy savings and minimize peak-cooling demand.

  8. Engineering the spatial organization of metabolic pathways

    DEFF Research Database (Denmark)

    Albertsen, Line; Maury, Jerome; Bach, Lars Stougaard

    One of the goals of metabolic engineering is to optimize the production of valuable metabolites in cell factories. In this context, modulating the gene expression and activity of enzymes are tools that have been extensively used. Another approach that is gaining interest is the engineering...... of the spatial organization of biosynthetic pathways. Several natural systems for ensuring optimal spatial arrangement of biosynthetic enzymes exist. Sequentially acting enzymes can for example be positioned in close proximity by attachment to cellular structures, up-concentration in membrane enclosed organelles...... or assembly into large complexes. The vision is that by positioning sequentially acting enzymes in close proximity, the cell can accelerate reaction rates and thereby prevent loss of intermediates through diffusion, degradation or competing pathways. The production of valuable metabolites in cell factories...

  9. Optimal Methods to Screen Men and Women for Intimate Partner Violence: Results from an Internal Medicine Residency Continuity Clinic

    Science.gov (United States)

    Kapur, Nitin A.; Windish, Donna M.

    2011-01-01

    Contradictory data exist regarding optimal methods and instruments for intimate partner violence (IPV) screening in primary care settings. The purpose of this study was to determine the optimal method and screening instrument for IPV among men and women in a primary-care resident clinic. We conducted a cross-sectional study at an urban, academic,…

  10. Use of plan quality degradation to evaluate tradeoffs in delivery efficiency and clinical plan metrics arising from IMRT optimizer and sequencer compromises

    Science.gov (United States)

    Wilkie, Joel R.; Matuszak, Martha M.; Feng, Mary; Moran, Jean M.; Fraass, Benedick A.

    2013-01-01

    Purpose: Plan degradation resulting from compromises made to enhance delivery efficiency is an important consideration for intensity modulated radiation therapy (IMRT) treatment plans. IMRT optimization and/or multileaf collimator (MLC) sequencing schemes can be modified to generate more efficient treatment delivery, but the effect those modifications have on plan quality is often difficult to quantify. In this work, the authors present a method for quantitative assessment of overall plan quality degradation due to tradeoffs between delivery efficiency and treatment plan quality, illustrated using comparisons between plans developed allowing different numbers of intensity levels in IMRT optimization and/or MLC sequencing for static segmental MLC IMRT plans. Methods: A plan quality degradation method to evaluate delivery efficiency and plan quality tradeoffs was developed and used to assess planning for 14 prostate and 12 head and neck patients treated with static IMRT. Plan quality was evaluated using a physician's predetermined “quality degradation” factors for relevant clinical plan metrics associated with the plan optimization strategy. Delivery efficiency and plan quality were assessed for a range of optimization and sequencing limitations. The “optimal” (baseline) plan for each case was derived using a clinical cost function with an unlimited number of intensity levels. These plans were sequenced with a clinical MLC leaf sequencer which uses >100 segments, assuring delivered intensities to be within 1% of the optimized intensity pattern. Each patient's optimal plan was also sequenced limiting the number of intensity levels (20, 10, and 5), and then separately optimized with these same numbers of intensity levels. Delivery time was measured for all plans, and direct evaluation of the tradeoffs between delivery time and plan degradation was performed. Results: When considering tradeoffs, the optimal number of intensity levels depends on the treatment

  11. A Model of an Integrated Immune System Pathway in Homo sapiens and Its Interaction with Superantigen Producing Expression Regulatory Pathway in Staphylococcus aureus: Comparing Behavior of Pathogen Perturbed and Unperturbed Pathway

    Science.gov (United States)

    Tomar, Namrata; De, Rajat K.

    2013-01-01

    Response of an immune system to a pathogen attack depends on the balance between the host immune defense and the virulence of the pathogen. Investigation of molecular interactions between the proteins of a host and a pathogen helps in identifying the pathogenic proteins. It is necessary to understand the dynamics of a normally behaved host system to evaluate the capacity of its immune system upon pathogen attack. In this study, we have compared the behavior of an unperturbed and pathogen perturbed host system. Moreover, we have developed a formalism under Flux Balance Analysis (FBA) for the optimization of conflicting objective functions. We have constructed an integrated pathway system, which includes Staphylococcal Superantigen (SAg) expression regulatory pathway and TCR signaling pathway of Homo sapiens. We have implemented the method on this pathway system and observed the behavior of host signaling molecules upon pathogen attack. The entire study has been divided into six different cases, based on the perturbed/unperturbed conditions. In other words, we have investigated unperturbed and pathogen perturbed human TCR signaling pathway, with different combinations of optimization of concentrations of regulatory and signaling molecules. One of these cases has aimed at finding out whether minimization of the toxin production in a pathogen leads to the change in the concentration levels of the proteins coded by TCR signaling pathway genes in the infected host. Based on the computed results, we have hypothesized that the balance between TCR signaling inhibitory and stimulatory molecules can keep TCR signaling system into resting/stimulating state, depending upon the perturbation. The proposed integrated host-pathogen interaction pathway model has accurately reflected the experimental evidences, which we have used for validation purpose. The significance of this kind of investigation lies in revealing the susceptible interaction points that can take back the

  12. SU-E-T-175: Clinical Evaluations of Monte Carlo-Based Inverse Treatment Plan Optimization for Intensity Modulated Radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Chi, Y; Li, Y; Tian, Z; Gu, X; Jiang, S; Jia, X [UT Southwestern Medical Center, Dallas, TX (United States)

    2015-06-15

    Purpose: Pencil-beam or superposition-convolution type dose calculation algorithms are routinely used in inverse plan optimization for intensity modulated radiation therapy (IMRT). However, due to their limited accuracy in some challenging cases, e.g. lung, the resulting dose may lose its optimality after being recomputed using an accurate algorithm, e.g. Monte Carlo (MC). It is the objective of this study to evaluate the feasibility and advantages of a new method to include MC in the treatment planning process. Methods: We developed a scheme to iteratively perform MC-based beamlet dose calculations and plan optimization. In the MC stage, a GPU-based dose engine was used and the particle number sampled from a beamlet was proportional to its optimized fluence from the previous step. We tested this scheme in four lung cancer IMRT cases. For each case, the original plan dose, plan dose re-computed by MC, and dose optimized by our scheme were obtained. Clinically relevant dosimetric quantities in these three plans were compared. Results: Although the original plan achieved a satisfactory PDV dose coverage, after re-computing doses using MC method, it was found that the PTV D95% were reduced by 4.60%–6.67%. After re-optimizing these cases with our scheme, the PTV coverage was improved to the same level as in the original plan, while the critical OAR coverages were maintained to clinically acceptable levels. Regarding the computation time, it took on average 144 sec per case using only one GPU card, including both MC-based beamlet dose calculation and treatment plan optimization. Conclusion: The achieved dosimetric gains and high computational efficiency indicate the feasibility and advantages of the proposed MC-based IMRT optimization method. Comprehensive validations in more patient cases are in progress.

  13. Creating and parameterizing patient-specific deep brain stimulation pathway-activation models using the hyperdirect pathway as an example.

    Science.gov (United States)

    Gunalan, Kabilar; Chaturvedi, Ashutosh; Howell, Bryan; Duchin, Yuval; Lempka, Scott F; Patriat, Remi; Sapiro, Guillermo; Harel, Noam; McIntyre, Cameron C

    2017-01-01

    Deep brain stimulation (DBS) is an established clinical therapy and computational models have played an important role in advancing the technology. Patient-specific DBS models are now common tools in both academic and industrial research, as well as clinical software systems. However, the exact methodology for creating patient-specific DBS models can vary substantially and important technical details are often missing from published reports. Provide a detailed description of the assembly workflow and parameterization of a patient-specific DBS pathway-activation model (PAM) and predict the response of the hyperdirect pathway to clinical stimulation. Integration of multiple software tools (e.g. COMSOL, MATLAB, FSL, NEURON, Python) enables the creation and visualization of a DBS PAM. An example DBS PAM was developed using 7T magnetic resonance imaging data from a single unilaterally implanted patient with Parkinson's disease (PD). This detailed description implements our best computational practices and most elaborate parameterization steps, as defined from over a decade of technical evolution. Pathway recruitment curves and strength-duration relationships highlight the non-linear response of axons to changes in the DBS parameter settings. Parameterization of patient-specific DBS models can be highly detailed and constrained, thereby providing confidence in the simulation predictions, but at the expense of time demanding technical implementation steps. DBS PAMs represent new tools for investigating possible correlations between brain pathway activation patterns and clinical symptom modulation.

  14. Creating and parameterizing patient-specific deep brain stimulation pathway-activation models using the hyperdirect pathway as an example.

    Directory of Open Access Journals (Sweden)

    Kabilar Gunalan

    Full Text Available Deep brain stimulation (DBS is an established clinical therapy and computational models have played an important role in advancing the technology. Patient-specific DBS models are now common tools in both academic and industrial research, as well as clinical software systems. However, the exact methodology for creating patient-specific DBS models can vary substantially and important technical details are often missing from published reports.Provide a detailed description of the assembly workflow and parameterization of a patient-specific DBS pathway-activation model (PAM and predict the response of the hyperdirect pathway to clinical stimulation.Integration of multiple software tools (e.g. COMSOL, MATLAB, FSL, NEURON, Python enables the creation and visualization of a DBS PAM. An example DBS PAM was developed using 7T magnetic resonance imaging data from a single unilaterally implanted patient with Parkinson's disease (PD. This detailed description implements our best computational practices and most elaborate parameterization steps, as defined from over a decade of technical evolution.Pathway recruitment curves and strength-duration relationships highlight the non-linear response of axons to changes in the DBS parameter settings.Parameterization of patient-specific DBS models can be highly detailed and constrained, thereby providing confidence in the simulation predictions, but at the expense of time demanding technical implementation steps. DBS PAMs represent new tools for investigating possible correlations between brain pathway activation patterns and clinical symptom modulation.

  15. Energy pathway analysis - a hydrogen fuel cycle framework for system studies

    International Nuclear Information System (INIS)

    Badin, J.S.; Tagore, S.

    1997-01-01

    An analytical framework has been developed that can be used to estimate a range of life-cycle costs and impacts that result from the incremental production, storage, transport, and use of different fuels or energy carriers, such as hydrogen, electricity, natural gas, and gasoline. This information is used in a comparative analysis of energy pathways. The pathways provide the U.S. Department of Energy (DOE) with an indication of near-, mid-, and long-term technologies that have the greatest potential for advancement and can meet the cost goals. The methodology and conceptual issues are discussed. Also presented are results for selected pathways from the E3 (Energy, Economics, Emissions) Pathway Analysis Model. This model will be expanded to consider networks of pathways and to be compatible with a linear programming optimization processor. Scenarios and sets of constraints (energy demands, sources, emissions) will be defined so the effects on energy transformation activities included in the solution and on the total optimized system cost can be investigated. This evaluation will be used as a guide to eliminate technically feasible pathways if they are not cost effective or do not meet the threshold requirements for the market acceptance. (Author)

  16. The TGF-β/Smad4 Signaling Pathway in Pancreatic Carcinogenesis and Its Clinical Significance

    Directory of Open Access Journals (Sweden)

    Sunjida Ahmed

    2017-01-01

    Full Text Available Pancreatic ductal adenocarcinoma (PDAC is one of the most fatal human cancers due to its complicated genomic instability. PDAC frequently presents at an advanced stage with extensive metastasis, which portends a poor prognosis. The known risk factors associated with PDAC include advanced age, smoking, long-standing chronic pancreatitis, obesity, and diabetes. Its association with genomic and somatic mutations is the most important factor for its aggressiveness. The most common gene mutations associated with PDAC include KRas2, p16, TP53, and Smad4. Among these, Smad4 mutation is relatively specific and its inactivation is found in more than 50% of invasive pancreatic adenocarcinomas. Smad4 is a member of the Smad family of signal transducers and acts as a central mediator of transforming growth factor beta (TGF-β signaling pathways. The TGF-β signaling pathway promotes many physiological processes, including cell growth, differentiation, proliferation, fibrosis, and scar formation. It also plays a major role in the development of tumors through induction of angiogenesis and immune suppression. In this review, we will discuss the molecular mechanism of TGF-β/Smad4 signaling in the pathogenesis of pancreatic adenocarcinoma and its clinical implication, particularly potential as a prognostic factor and a therapeutic target.

  17. [Treatment pathways in the care of patients with schizophrenia and depression].

    Science.gov (United States)

    Salize, H J; Voß, E; Werner, A; Falkai, P; Hauth, I

    2015-11-01

    In mental healthcare the concept of pathways addresses diverse issues and problem areas, such as heterogeneous health service offers, the regional variability of treatment concepts and clear-cut guidelines on how and where to obtain treatment for a particular mental disorder. The ambiguous aspects of the concept require international and national definitions and consensus which must also cover quality criteria. This article gives an overview of currently available evidence for the analysis of clinical pathways and pathways to care in international mental healthcare, covering studies on schizophrenia and depression from 2010 to 2014. The ambiguity of the concept impedes the overview and does not provide unequivocal results. The development, implementation and analyses of guidelines or clear-cut clinical and pathways to care must consider individual, clinical and care system aspects as well as the interplay of these factors. Results suggest that system aspects tend to dominate over clinical factors of schizophrenia and depression. As a consequence, the definition, implementation and evaluation of clinical pathways or pathways to mental healthcare is first and foremost a responsibility of the respective national mental healthcare system and must be understood on that level, before findings are summarized internationally and models of best practice are debated.

  18. Measurement of glomerular filtration rate by impulse synthesis: Clinical validation and optimization

    International Nuclear Information System (INIS)

    Palagi, B.; Verga, P.; Broggi, A.; Picozzi, R.; Villa, F.; Guzzini, F.; Cozzi, C.; Tomasi, A.

    1988-01-01

    Impulse synthesis is a technique which relies upon the logic of continuous infusion but extracts the clearance value from single-injection data by shifting and adding them until an asymptotic value is attained. This study has been aimed at validating and optimizing clinically the measurement of glomerular filtration rate by impulse synthesis. A single intravenous injection of 51 Cr-EDTA has been made in 32 patients and plasma activity monitored over the next 6 h. Glomerular filtration rate computed by a single-exponential fit method (GFR-SEF) has been shown to be significantly (p [de

  19. Diffusion-weighted and dynamic contrast-enhanced imaging as markers of clinical behavior in children with optic pathway glioma

    International Nuclear Information System (INIS)

    Jost, Sarah C.; Ackerman, Joseph W.; Garbow, Joel R.; Manwaring, Linda P.; Gutmann, David H.; McKinstry, Robert C.

    2008-01-01

    Optic pathway gliomas (OPGs) are common pediatric brain tumors that pose significant clinical challenges with regard to predicting which tumors are likely to become symptomatic and require treatment. These tumors can arise sporadically or in the context of the inherited cancer predisposition syndrome neurofibromatosis type 1 (NF1). Few studies have suggested biological or imaging markers that predict the clinical course of this disease. In this cross-sectional study, we hypothesized that the clinical behavior of OPGs in children can be differentiated by diffusion-weighted (DW) and dynamic contrast-enhanced (DCE) MRI. A total of 27 children with OPG were studied using DW and DCE MRI protocols. Diffusivity and permeability were calculated and correlated with the clinical behavior the OPG. Mean diffusivity values of 1.39 μm 2 /ms and mean permeability values of 2.10 ml/min per 100 cm 3 of tissue were measured. Clinically aggressive OPGs had significantly higher mean permeability values (P = 0.05) than clinically stable tumors. In addition, there was a strong correlation between clinical aggressiveness and the absence of NF1 (P < 0.01). These results suggest that DCE MRI might be a useful biomarker for clinically aggressive OPG, which should be confirmed in larger prospective longitudinal studies. (orig.)

  20. Risk stratification in non-ST elevation acute coronary syndromes: Risk scores, biomarkers and clinical judgment

    Directory of Open Access Journals (Sweden)

    David Corcoran

    2015-09-01

    Clinical guidelines recommend an early invasive strategy in higher risk NSTE-ACS. The Global Registry of Acute Coronary Events (GRACE risk score is a validated risk stratification tool which has incremental prognostic value for risk stratification compared with clinical assessment or troponin testing alone. In emergency medicine, there has been a limited adoption of the GRACE score in some countries (e.g. United Kingdom, in part related to a delay in obtaining timely blood biochemistry results. Age makes an exponential contribution to the GRACE score, and on an individual patient basis, the risk of younger patients with a flow-limiting culprit coronary artery lesion may be underestimated. The future incorporation of novel cardiac biomarkers into this diagnostic pathway may allow for earlier treatment stratification. The cost-effectiveness of the new diagnostic pathways based on high-sensitivity troponin and copeptin must also be established. Finally, diagnostic tests and risk scores may optimize patient care but they cannot replace patient-focused good clinical judgment.

  1. [Targeting high-risk drugs to optimize clinical pharmacists' intervention].

    Science.gov (United States)

    Mouterde, Anne-Laure; Bourdelin, Magali; Maison, Ophélie; Coursier, Sandra; Bontemps, Hervé

    2016-12-01

    By the Order of 6 April 2011, the pharmacist must validate all the prescriptions containing "high-risk drugs" or those of "patients at risk". To optimize this clinical pharmacy activity, we identified high-risk drugs. A list of high-risk drugs has been established using literature, pharmacists' interventions (PI) performed in our hospital and a survey sent to hospital pharmacists. In a prospective study (analysis of 100 prescriptions for each high-risk drug selected), we have identified the most relevant to target. We obtained a statistically significant PI rate (P<0.05) for digoxin, oral anticoagulants direct, oral methotrexate and colchicine. This method of targeted pharmaceutical validation based on high-risk drugs is relevant to detect patients with high risk of medicine-related illness. Copyright © 2016 Société française de pharmacologie et de thérapeutique. Published by Elsevier Masson SAS. All rights reserved.

  2. Optimism on quality of life in Portuguese chronic patients: moderator/mediator?

    Directory of Open Access Journals (Sweden)

    Estela Vilhena

    2014-07-01

    Full Text Available Objective: optimism is an important variable that has consistently been shown to affect adjustment to quality of life in chronic diseases. This study aims to clarify if dispositional optimism exerts a moderating or a mediating influence on the personality traits-quality of life association, in Portuguese chronic patients. Methods: multiple regression models were used to test the moderation and mediation effects of dispositional optimism in quality of life. A sample of 729 patients was recruited in Portugal's main hospitals and completed self-reported questionnaires assessing socio-demographic and clinical variables, personality, dispositional optimism, quality of life (QoL and subjective well-being (SWB. Results: the results of the regression models showed that dispositional optimism did not moderate the relationships between personality traits and quality of life. After controlling for gender, age, education level and severity of disease perception, the effects of personality traits on QoL and in SWB were mediated by dispositional optimism (partially and completely, except for the links between neuroticism/openness to experience and physical health. Conclusion: dispositional optimism is more likely to play a mediating, rather than a moderating role in personality traits-quality of life pathway in Portuguese chronic patients, suggesting that "the expectation that good things will happen" contributes to a better quality of life and subjective well-being.

  3. NICE-Accredited Commissioning Guidance for Weight Assessment and Management Clinics: a Model for a Specialist Multidisciplinary Team Approach for People with Severe Obesity.

    Science.gov (United States)

    Welbourn, Richard; Dixon, John; Barth, Julian H; Finer, Nicholas; Hughes, Carly A; le Roux, Carel W; Wass, John

    2016-03-01

    Despite increasing prevalence of obesity, no country has successfully implemented comprehensive pathways to provide advice to all the severely obese patients that seek treatment. We aimed to formulate pathways for referral into and out of weight assessment and management clinics (WAMCs) that include internal medicine/primary care physicians as part of a multidisciplinary team that could provide specialist advice and interventions, including referral for bariatric surgery. Using a National Institute of Health and Care Excellence (NICE)-accredited process, a Guidance Development Group conducted a literature search identifying existing WAMCs. As very few examples of effective structures and clinical pathways existed, the current evidence base for optimal assessment and management of bariatric surgery patients was used to reach a consensus. The model we describe could be adopted internationally by health services to manage severely obese patients.

  4. TRWG developmental pathway for biospecimen-based assessment modalities

    Energy Technology Data Exchange (ETDEWEB)

    Translational Research Working Group; Srivastava, Sudhir; Gray, Joe W.; Reid, Brian J.; Grad, Oren; Greenwood, Addison; Hawk, Ernest T.

    2008-09-03

    The Translational Research Working Group (TRWG) was created as a national initiative to evaluate the current status of NCI's investment in translational research and envision its future. The TRWG conceptualized translational research as a set of six developmental processes or pathways focused on various clinical goals. One of those pathways describes the development of biospecimen-based assays that utilize biomarkers for the detection, diagnosis, prognosis, and assessment of response to cancer treatment. The biospecimen-based assessment modality (BM) pathway was conceived not as comprehensive description of the corresponding real-world processes, but rather as a tool designed to facilitate movement of a candidate assay through the translational process to the point where it can be handed off for definitive clinical testing. This paper introduces the pathway in the context of prior work and discusses key challenges associated with the biomarker development process in light of the pathway.

  5. A combined hands-on teaching programme and clinical pathway focused on pleural ultrasound and procedure supervision transforms pleural procedure outcomes.

    Science.gov (United States)

    Edwards, Timothy; Cook, Alistair; Salamonsen, Matthew; Bashirzadeh, Farzad; Fielding, David

    2017-11-01

    Management of pleural effusions is a common diagnostic and management problem. We reviewed the outcomes from pleural procedures after the instigation of pleural effusion management guidelines, focusing on pleural ultrasound and a hands-on teaching programme followed by procedure supervision that enabled many operators to perform such procedures. This is a retrospective analysis of all procedures performed for pleural effusions on medical patients. Outcomes were assessed prior to the instigation of pleural effusion management guidelines (pleural pathway) and hands-on teaching (January 2010 to June 2011) and following these interventions (January 2012 to June 2013). A total of 171 procedures involving 129 patients (pre-pathway group) and 146 procedures involving 115 patients (post-pathway group) was analysed. The rate of complications prior to the pleural pathway was 22.2% (38 of 171 procedures). Following the pathway, the rate of complications declined to 7.5% (11 of 146 procedures, P < 0.003). The use of pleural ultrasound increased dramatically (72.5 vs 90.2%). The number of patients who underwent repeated procedures (defined as ≥3) reduced dramatically (21 vs 7, P < 0.01). This improvement occurred using many supervised operators who completed the hands-on teaching programme (n = 32) and followed the pleural pathway (127 of 146 procedures). The instigation of a clinical pathway focused on the use of bedside pleural ultrasound, and teaching of drainage techniques with procedure supervision vastly improved patient outcomes. This not only allowed better quality of care for patients, it also provided the acquisition of new skills to medical staff, not limiting these skills to specialised staff. © 2017 Royal Australasian College of Physicians.

  6. Reiterative Recombination for the in vivo assembly of libraries of multigene pathways

    OpenAIRE

    Wingler, Laura M.; Cornish, Virginia W.

    2011-01-01

    The increasing sophistication of synthetic biology is creating a demand for robust, broadly accessible methodology for constructing multigene pathways inside of the cell. Due to the difficulty of rationally designing pathways that function as desired in vivo, there is a further need to assemble libraries of pathways in parallel, in order to facilitate the combinatorial optimization of performance. While some in vitro DNA assembly methods can theoretically make libraries of pathways, these tec...

  7. Optimal medication dosing from suboptimal clinical examples: a deep reinforcement learning approach.

    Science.gov (United States)

    Nemati, Shamim; Ghassemi, Mohammad M; Clifford, Gari D

    2016-08-01

    Misdosing medications with sensitive therapeutic windows, such as heparin, can place patients at unnecessary risk, increase length of hospital stay, and lead to wasted hospital resources. In this work, we present a clinician-in-the-loop sequential decision making framework, which provides an individualized dosing policy adapted to each patient's evolving clinical phenotype. We employed retrospective data from the publicly available MIMIC II intensive care unit database, and developed a deep reinforcement learning algorithm that learns an optimal heparin dosing policy from sample dosing trails and their associated outcomes in large electronic medical records. Using separate training and testing datasets, our model was observed to be effective in proposing heparin doses that resulted in better expected outcomes than the clinical guidelines. Our results demonstrate that a sequential modeling approach, learned from retrospective data, could potentially be used at the bedside to derive individualized patient dosing policies.

  8. Optimizing clinical performance and geometrical robustness of a new electrode device for intracranial tumor electroporation

    DEFF Research Database (Denmark)

    Mahmood, Faisal; Gehl, Julie

    2011-01-01

    and genes to intracranial tumors in humans, and demonstrate a method to optimize the design (i.e. geometry) of the electrode device prototype to improve both clinical performance and geometrical tolerance (robustness). We have employed a semiempirical objective function based on constraints similar to those...... sensitive to random geometrical deviations. The method is readily applicable to other electrode configurations....

  9. Developing a clinical pathway for the identification and management of anxiety and depression in adult cancer patients: an online Delphi consensus process.

    Science.gov (United States)

    Shaw, Joanne M; Price, Melanie A; Clayton, Josephine M; Grimison, Peter; Shaw, Tim; Rankin, Nicole; Butow, Phyllis N

    2016-01-01

    People with cancer and their families experience high levels of psychological morbidity. However, many cancer services do not routinely screen patients for anxiety and depression, and there are no standardized clinical referral pathways. This study aimed to establish consensus on elements of a draft clinical pathway tailored to the Australian context. A two-round Delphi study was conducted to gain consensus among Australian oncology and psycho-oncology clinicians about the validity of 39 items that form the basis of a clinical pathway that includes screening, assessment, referral and stepped care management of anxiety and depression in the context of cancer. The expert panel comprised 87 multidisciplinary clinician members of the Australian Psycho-oncology Co-operative Research Group (PoCoG). Respondents rated their level of agreement with each statement on a 5-point Likert scale. Consensus was defined as >80% of respondents scoring within 2 points on the Likert scale. Consensus was reached for 21 of 39 items, and a further 15 items approached consensus except for specific contextual factors, after two Delphi rounds. Formal screening for anxiety and depression, a stepped care model of management and recommendations for inclusion of length of treatment and time to review were endorsed. Consensus was not reached on items related to roles and responsibilities, particularly those not applicable across cancer settings. This study identified a core set of evidence- and consensus-based principles considered essential to a stepped care model of care incorporating identification, referral and management of anxiety and depression in adult cancer patients.

  10. Gaussian processes with optimal kernel construction for neuro-degenerative clinical onset prediction

    Science.gov (United States)

    Canas, Liane S.; Yvernault, Benjamin; Cash, David M.; Molteni, Erika; Veale, Tom; Benzinger, Tammie; Ourselin, Sébastien; Mead, Simon; Modat, Marc

    2018-02-01

    Gaussian Processes (GP) are a powerful tool to capture the complex time-variations of a dataset. In the context of medical imaging analysis, they allow a robust modelling even in case of highly uncertain or incomplete datasets. Predictions from GP are dependent of the covariance kernel function selected to explain the data variance. To overcome this limitation, we propose a framework to identify the optimal covariance kernel function to model the data.The optimal kernel is defined as a composition of base kernel functions used to identify correlation patterns between data points. Our approach includes a modified version of the Compositional Kernel Learning (CKL) algorithm, in which we score the kernel families using a new energy function that depends both the Bayesian Information Criterion (BIC) and the explained variance score. We applied the proposed framework to model the progression of neurodegenerative diseases over time, in particular the progression of autosomal dominantly-inherited Alzheimer's disease, and use it to predict the time to clinical onset of subjects carrying genetic mutation.

  11. Sources of Hematopoietic Stem and Progenitor Cells and Methods to Optimize Yields for Clinical Cell Therapy.

    Science.gov (United States)

    Panch, Sandhya R; Szymanski, James; Savani, Bipin N; Stroncek, David F

    2017-08-01

    Bone marrow (BM) aspirates, mobilized peripheral blood, and umbilical cord blood (UCB) have developed as graft sources for hematopoietic stem and progenitor cells (HSPCs) for stem cell transplantation and other cellular therapeutics. Individualized techniques are necessary to enhance graft HSPC yields and cell quality from each graft source. BM aspirates yield adequate CD34 + cells but can result in relative delays in engraftment. Granulocyte colony-stimulating factor (G-CSF)-primed BM HSPCs may facilitate faster engraftment while minimizing graft-versus-host disease in certain patient subsets. The levels of circulating HSPCs are enhanced using mobilizing agents, such as G-CSF and/or plerixafor, which act via the stromal cell-derived factor 1/C-X-C chemokine receptor type 4 axis. Alternate niche pathway mediators, including very late antigen-4/vascular cell adhesion molecule-1, heparan sulfate proteoglycans, parathyroid hormone, and coagulation cascade intermediates, may offer promising alternatives for graft enhancement. UCB grafts have been expanded ex vivo with cytokines, notch-ligand, or mesenchymal stromal cells, and most studies demonstrated greater quantities of CD34 + cells ex vivo and improved short-term engraftment. No significant changes were observed in long-term repopulating potential or in patient survival. Early phase clinical trials using nicotinamide and StemReginin1 may offer improved short- and long-term repopulating ability. Breakthroughs in genome editing and stem cell reprogramming technologies may hasten the generation of pooled, third-party HSPC grafts. This review elucidates past, present, and potential future approaches to HSPC graft optimization. Published by Elsevier Inc.

  12. A Method to Evaluate Critical Factors for Successful Implementation of Clinical Pathways.

    Science.gov (United States)

    Dong, W; Huang, Z

    2015-01-01

    Clinical pathways (CPs) have been viewed as a multidisciplinary tool to improve the quality and efficiency of evidence-based care. Despite widespread enthusiasm for CPs, research has shown that many CP initiatives are unsuccessful. To this end, this study provides a methodology to evaluate critical success factors (CSFs) that can aid healthcare organizations to achieve successful CP implementation. This study presents a new approach to evaluate CP implementation CSFs, with the aims being: (1) to identify CSFs for implementation of CPs through a comprehensive literature review and interviews with collaborative experts; (2) to use a filed study data with a robust fuzzy DEMATEL (the decision making trial and evaluation laboratory) approach to visualize the structure of complicated causal relationships between CSFs and obtain the influence level of these factors. The filed study data is provided by ten clinical experts of a Chinese hospital. 23 identified CSF factors which are initially identified through a review of the literature and interviews with collaborative experts. Then, a number of direct and indirect relationships are derived from the data such that different perceptions can be integrated into a compromised cause and effect model of CP implementation. The results indicate that the proposed approach can systematically evaluate CSFs and realize the importance of each factor such that the most common causes of failure of CP implementation could be eliminated or avoided. Therefore, the tool proposed would help healthcare organizations to manage CP implementation in a more effective and proactive way.

  13. Magnetic resonance imaging of the visual pathway - anatomical and technical considerations

    International Nuclear Information System (INIS)

    Sosnowski, P.; Paprzycki, W.

    1993-01-01

    Magnetic resonance tomography creates possibility of imaging the whole visual pathway and is superior to CT. Plenitude of MR techniques can sometimes be the reason of unnecessary prolongation of the examination. This study tries to evaluate usefulness of different MR techniques and planes for optimal imaging of consecutive sections of visual pathway. (author)

  14. Case Example of Dose Optimization Using Data From Bortezomib Dose-Finding Clinical Trials.

    Science.gov (United States)

    Lee, Shing M; Backenroth, Daniel; Cheung, Ying Kuen Ken; Hershman, Dawn L; Vulih, Diana; Anderson, Barry; Ivy, Percy; Minasian, Lori

    2016-04-20

    The current dose-finding methodology for estimating the maximum tolerated dose of investigational anticancer agents is based on the cytotoxic chemotherapy paradigm. Molecularly targeted agents (MTAs) have different toxicity profiles, which may lead to more long-lasting mild or moderate toxicities as well as to late-onset and cumulative toxicities. Several approved MTAs have been poorly tolerated during long-term administration, leading to postmarketing dose optimization studies to re-evaluate the optimal treatment dose. Using data from completed bortezomib dose-finding trials, we explore its toxicity profile, optimize its dose, and examine the appropriateness of current designs for identifying an optimal dose. We classified the toxicities captured from 481 patients in 14 bortezomib dose-finding studies conducted through the National Cancer Institute Cancer Therapy Evaluation Program, computed the incidence of late-onset toxicities, and compared the incidence of dose-limiting toxicities (DLTs) among groups of patients receiving different doses of bortezomib. A total of 13,008 toxicities were captured: 46% of patients' first DLTs and 88% of dose reductions or discontinuations of treatment because of toxicity were observed after the first cycle. Moreover, for the approved dose of 1.3 mg/m(2), the estimated cumulative incidence of DLT was > 50%, and the estimated cumulative incidence of dose reduction or treatment discontinuation because of toxicity was nearly 40%. When considering the entire course of treatment, the approved bortezomib dose exceeds the conventional ceiling DLT rate of 20% to 33%. Retrospective analysis of trial data provides an opportunity for dose optimization of MTAs. Future dose-finding studies of MTAs should take into account late-onset toxicities to ensure that a tolerable dose is identified for future efficacy and comparative trials. © 2016 by American Society of Clinical Oncology.

  15. Dendritic cells for active immunotherapy: optimizing design and manufacture in order to develop commercially and clinically viable products.

    Science.gov (United States)

    Nicolette, C A; Healey, D; Tcherepanova, I; Whelton, P; Monesmith, T; Coombs, L; Finke, L H; Whiteside, T; Miesowicz, F

    2007-09-27

    Dendritic cell (DC) active immunotherapy is potentially efficacious in a broad array of malignant disease settings. However, challenges remain in optimizing DC-based therapy for maximum clinical efficacy within manufacturing processes that permit quality control and scale-up of consistent products. In this review we discuss the critical issues that must be addressed in order to optimize DC-based product design and manufacture, and highlight the DC based platforms currently addressing these issues. Variables in DC-based product design include the type of antigenic payload used, DC maturation steps and activation processes, and functional assays. Issues to consider in development include: (a) minimizing the invasiveness of patient biological material collection; (b) minimizing handling and manipulations of tissue at the clinical site; (c) centralized product manufacturing and standardized processing and capacity for commercial-scale production; (d) rapid product release turnaround time; (e) the ability to manufacture sufficient product from limited starting material; and (f) standardized release criteria for DC phenotype and function. Improvements in the design and manufacture of DC products have resulted in a handful of promising leads currently in clinical development.

  16. The experience of seeking, gaining and maintaining employment after traumatic spinal cord injury and the vocational pathways involved.

    Science.gov (United States)

    Hilton, Gillean; Unsworth, Carolyn A; Stuckey, Ruth; Murphy, Gregory C

    2018-01-01

    Vocational potential in people with spinal cord injury (SCI) are unrealised with rates of employment substantially lower than in the labour force participation of the general population and the pre-injury employment rates. To understand the experience and pathway of people achieving employment outcome after traumatic spinal cord injury by; classifying participants into employment outcome groups of stable, unstable and without employment; identifying pre and post-injury pathways for participants in each group and, exploring the experiences of people of seeking, gaining and maintaining employment. Thirty-one participants were interviewed. Mixed methods approach including interpretive phenomenological analysis and vocational pathway mapping of quantitative data. The most common pathway identified was from study and work pre-injury to stable employment post-injury. Four super-ordinate themes were identified from the interpretive phenomenological analysis; expectations of work, system impacts, worker identity and social supports. Implications for clinical practice include fostering cultural change, strategies for system navigation, promotion of worker identity and optimal use of social supports. The findings increase insight and understanding of the complex experience of employment after spinal cord injury. There is opportunity to guide experimental research, policy development and education concerning the complexity of the return to work experience and factors that influence pathways.

  17. The “CROMa” Project: A Care Pathway for Clinical Management of Patients with Bisphosphonate Exposure

    Directory of Open Access Journals (Sweden)

    Mauro Capocci

    2014-01-01

    Full Text Available Aim. To describe 7 years of activity of “CROMa” (Coordination of Research on Osteonecrosis of the Jaws project of “Sapienza” University of Rome. Materials and Methods. A preventive and therapeutic care pathway was created for patients with bisphosphonates (BPs exposure. Demographic, social, behavioural, pharmacological, and clinical variables were registered in a dedicated database. Results. In the project, 502 patients, 403 females and 99 males, were observed. Bone pathologies were 79% osteometabolic diseases (OMD and 21% metastatic cancer (CA. Females were 90% in OMD group and 41% in CA. BP administration was 54% oral, 31% IV, and 11% IM; 89% of BPs were amino-BP and 11% non-amino-BP. Consistently with bone pathology (OMD/CA, alendronate appears to be prevalent for OMD (40% relative, while zoledronate was indicated in 92% of CA patients. Out of 502 cases collected, 28 BRONJ were detected: 17 of them were related to IV BP treatment. Preventive oral assessment was required for 50% of CA patients and by 4% of OMD patients. Conclusions. The proposed care pathway protocols for BP exposed patients appeared to be useful to meet treatment and preventive needs, in both oncological and osteometabolic diseases patients. Patients’ and physicians’ prevention awareness can be the starting point of a multilevel prevention system.

  18. Synthesis of Optimal Processing Pathway for Microalgae-based Biorefinery under Uncertainty

    DEFF Research Database (Denmark)

    Rizwan, Muhammad; Lee, Jay H.; Gani, Rafiqul

    2015-01-01

    decision making, we propose a systematic framework for the synthesis and optimal design of microalgae-based processing network under uncertainty. By incorporating major uncertainties into the biorefinery superstructure model we developed previously, a stochastic mixed integer nonlinear programming (s......The research in the field of microalgae-based biofuels and chemicals is in early phase of the development, and therefore a wide range of uncertainties exist due to inconsistencies among and shortage of technical information. In order to handle and address these uncertainties to ensure robust......MINLP) problem is formulated for determining the optimal biorefinery structure under given parameter uncertainties modelled as sampled scenarios. The solution to the sMINLP problem determines the optimal decisions with respect to processing technologies, material flows, and product portfolio in the presence...

  19. The Importance of Clinical Phenotype in Understanding and Preventing Spontaneous Preterm Birth.

    Science.gov (United States)

    Esplin, M Sean

    2016-02-01

    Spontaneous preterm birth (SPTB) is a well-known cause of maternal and neonatal morbidity. The search for the underlying pathways, documentation of the genetic causes, and identification of markers of spontaneous PTB have been marginally successful due to the fact that it is highly complex, with numerous processes that lead to a final common pathway. There is a great need for a comprehensive, consistent, and uniform classification system, which will be useful in identifying mechanisms, assigning prognosis, aiding in clinical management, and can identify areas of interest for intervention and future study. Effective classification systems must overcome obstacles including the lack of widely accepted definitions and uncertainty about inclusion of classifying features (e.g., presentation at delivery and multiple gestations) and levels of detail of these features. The optimal classification system should be based on the clinical phenotype, including characteristics of the mother, fetus, placenta, and the presentation for delivery. We present a proposed phenotyping system for spontaneous PTB. Future classification systems must establish a universally accepted set of definitions and a standardized clinical workup for all PTBs including the minimum clinical data to be collected and the laboratory and pathologic evaluation that should be completed. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  20. Automatic selection of optimal cardiac-phase in coronary CT angiography. Its clinical usefulness for patients with atrial fibrillation

    International Nuclear Information System (INIS)

    Matsumoto, Ryota; Narita, Hiroshi; Anno, Hirofumi; Ida, Yoshihiro; Sanda, Yoshihiro; Katada, Kazuhiro; Motoyama, Sadako; Sarai, Masayoshi; Tsuyuki, Masaharu

    2008-01-01

    The optimal cardiac phases for coronary CT angiography (CTA) are end-systole and mid-diastole, in which cardiac movement is slow. In conventional methods, these cardiac phases are determined by visual selection. We have compared the images in the optimal cardiac phases that were selected by the conventional method and cardiac-phase search software (Phase Navi), and examined the clinical usefulness of Phase Navi in patients with atrial fibrillation. The subjects were 38 patients (regular rhythm: 20, atrial fibrillation: 18). The continuity scores of patients with regular rhythm (Phase Navi, conventional methods) were 2.4±0.3-2.5±0.3 in end-systole and 2.4±0.5-2.4±0.4 in mid-diastole. The scores of patients with atrial fibrillation (Phase Navi, conventional methods) were 2.3±0.4-2.3±0.4 in end-systole, and 2.2±0.5-2.1±0.6 in mid-diastole. Because the continuity scores of the optimal images from Phase Navi were similar to those from the conventional method, Phase Navi had clinical usefulness in patients with atrial fibrillation. (author)

  1. [Retrospective Analysis of the Afatinib Clinical Pathway during the 28-Day Introductory Period-The Japanese Style of Collaborative Drug Therapy Management(J-CDTM)].

    Science.gov (United States)

    Iwata, Kaori; Ryota, Noriko; Hikita, Ami; Sando, Masumi; Suzuki, Hidekazu; Tamiya, Motohiro; Azuma, Yuichiro; Tani, Eriko; Hamaguchi, Masanari; Tanaka, Ayako; Shiroyama, Takayuki; Morishita, Naoko; Okamoto, Norio; Futagami, Sumiko; Hirashima, Tomonori

    2015-08-01

    Afatinib is a newly approved second-generation epidermal growth factor receptor-tyrosine kinase inhibito r(EGFR-TKI). Afatinib has been shown to prolongthe overall survival of patients with non-small cell lungcancer (NSCLC) with EGFR mutations compared with the standard chemotherapy. However, Grade 3 or 4 toxicities, includingdiarrhea, rash, paronychia, and stomatitis, have been observed more frequently in patients treated with afatinib than in those treated with first-generation EGFR-TKIs. Accordingly, our institution developed an afatinib clinical pathway (the afatinib pathway), which was designed by certified nurses, medical physicians, and certified pharmacists, with the goal of reducing the severity of diarrhea and rash that occur most frequently duringthe 28-day introductory period of afatinib treatment. Between May and October 2014, afatinib was administered accordingto the afatinib pathway to 14 patients with NSCLC and EGFR mutations. Of these patients, only one (7.1%) experienced Grade 3 diarrhea. No other patient experienced Grade 3 or 4 toxicity. The afatinib pathway was effective in reducingthe severities of the diarrhea and rash duringthe 28-day introductory period of the afatinib treatment. Our implementation of the afatinib pathway could be considered the Japanese style of collaborative drugtherapy management (J-CDTM).

  2. DESHARKY: automatic design of metabolic pathways for optimal cell growth.

    Science.gov (United States)

    Rodrigo, Guillermo; Carrera, Javier; Prather, Kristala Jones; Jaramillo, Alfonso

    2008-11-01

    The biological solution for synthesis or remediation of organic compounds using living organisms, particularly bacteria and yeast, has been promoted because of the cost reduction with respect to the non-living chemical approach. In that way, computational frameworks can profit from the previous knowledge stored in large databases of compounds, enzymes and reactions. In addition, the cell behavior can be studied by modeling the cellular context. We have implemented a Monte Carlo algorithm (DESHARKY) that finds a metabolic pathway from a target compound by exploring a database of enzymatic reactions. DESHARKY outputs a biochemical route to the host metabolism together with its impact in the cellular context by using mathematical models of the cell resources and metabolism. Furthermore, we provide the sequence of amino acids for the enzymes involved in the route closest phylogenetically to the considered organism. We provide examples of designed metabolic pathways with their genetic load characterizations. Here, we have used Escherichia coli as host organism. In addition, our bioinformatic tool can be applied for biodegradation or biosynthesis and its performance scales with the database size. Software, a tutorial and examples are freely available and open source at http://soft.synth-bio.org/desharky.html

  3. NCC-AUC: an AUC optimization method to identify multi-biomarker panel for cancer prognosis from genomic and clinical data.

    Science.gov (United States)

    Zou, Meng; Liu, Zhaoqi; Zhang, Xiang-Sun; Wang, Yong

    2015-10-15

    In prognosis and survival studies, an important goal is to identify multi-biomarker panels with predictive power using molecular characteristics or clinical observations. Such analysis is often challenged by censored, small-sample-size, but high-dimensional genomic profiles or clinical data. Therefore, sophisticated models and algorithms are in pressing need. In this study, we propose a novel Area Under Curve (AUC) optimization method for multi-biomarker panel identification named Nearest Centroid Classifier for AUC optimization (NCC-AUC). Our method is motived by the connection between AUC score for classification accuracy evaluation and Harrell's concordance index in survival analysis. This connection allows us to convert the survival time regression problem to a binary classification problem. Then an optimization model is formulated to directly maximize AUC and meanwhile minimize the number of selected features to construct a predictor in the nearest centroid classifier framework. NCC-AUC shows its great performance by validating both in genomic data of breast cancer and clinical data of stage IB Non-Small-Cell Lung Cancer (NSCLC). For the genomic data, NCC-AUC outperforms Support Vector Machine (SVM) and Support Vector Machine-based Recursive Feature Elimination (SVM-RFE) in classification accuracy. It tends to select a multi-biomarker panel with low average redundancy and enriched biological meanings. Also NCC-AUC is more significant in separation of low and high risk cohorts than widely used Cox model (Cox proportional-hazards regression model) and L1-Cox model (L1 penalized in Cox model). These performance gains of NCC-AUC are quite robust across 5 subtypes of breast cancer. Further in an independent clinical data, NCC-AUC outperforms SVM and SVM-RFE in predictive accuracy and is consistently better than Cox model and L1-Cox model in grouping patients into high and low risk categories. In summary, NCC-AUC provides a rigorous optimization framework to

  4. Reiterative Recombination for the in vivo assembly of libraries of multigene pathways.

    Science.gov (United States)

    Wingler, Laura M; Cornish, Virginia W

    2011-09-13

    The increasing sophistication of synthetic biology is creating a demand for robust, broadly accessible methodology for constructing multigene pathways inside of the cell. Due to the difficulty of rationally designing pathways that function as desired in vivo, there is a further need to assemble libraries of pathways in parallel, in order to facilitate the combinatorial optimization of performance. While some in vitro DNA assembly methods can theoretically make libraries of pathways, these techniques are resource intensive and inherently require additional techniques to move the DNA back into cells. All previously reported in vivo assembly techniques have been low yielding, generating only tens to hundreds of constructs at a time. Here, we develop "Reiterative Recombination," a robust method for building multigene pathways directly in the yeast chromosome. Due to its use of endonuclease-induced homologous recombination in conjunction with recyclable markers, Reiterative Recombination provides a highly efficient, technically simple strategy for sequentially assembling an indefinite number of DNA constructs at a defined locus. In this work, we describe the design and construction of the first Reiterative Recombination system in Saccharomyces cerevisiae, and we show that it can be used to assemble multigene constructs. We further demonstrate that Reiterative Recombination can construct large mock libraries of at least 10(4) biosynthetic pathways. We anticipate that our system's simplicity and high efficiency will make it a broadly accessible technology for pathway construction and render it a valuable tool for optimizing pathways in vivo.

  5. Modular pathway rewiring of Saccharomyces cerevisiae enables high-level production of L-ornithine

    DEFF Research Database (Denmark)

    Qin, Jiufu; Zhou, Yongjin J.; Krivoruchko, Anastasia

    2015-01-01

    intermediates can serve as platform cell factories for production of such products. Here we implement a modular pathway rewiring (MPR) strategy and demonstrate its use for pathway optimization resulting in high-level production of L-ornithine, an intermediate of L-arginine biosynthesis and a precursor...

  6. Gene Expression Meta-Analysis identifies Cytokine Pathways and 5q Aberrations involved in Metastasis of ERBB2 Amplified and Basal Breast Cancer

    DEFF Research Database (Denmark)

    Thomassen, Mads; Tan, Qihua; Burton, Mark

    2013-01-01

    Background: Breast tumors have been described by molecular subtypes characterized by pervasively different gene expression profiles. The subtypes are associated with different clinical parameters and origin of precursor cells. However, the biological pathways and chromosomal aberrations that differ...... the subgroups impact metastasis. Results: We have scrutinized publicly available gene expression datasets and identified molecular subtypes in 1,394 breast tumors with outcome data. By analysis of chromosomal regions and pathways using “Gene set enrichment analysis” followed by a meta-analysis, we identified...... between the subgroups are less well characterized. The molecular subtypes are associated with different risk of metastatic recurrence of the disease. Nevertheless, the performance of these overall patterns to predict outcome is far from optimal, suggesting that biological mechanisms that extend beyond...

  7. Computer-assisted engineering of the synthetic pathway for biodegradation of a toxic persistent pollutant.

    Science.gov (United States)

    Kurumbang, Nagendra Prasad; Dvorak, Pavel; Bendl, Jaroslav; Brezovsky, Jan; Prokop, Zbynek; Damborsky, Jiri

    2014-03-21

    Anthropogenic halogenated compounds were unknown to nature until the industrial revolution, and microorganisms have not had sufficient time to evolve enzymes for their degradation. The lack of efficient enzymes and natural pathways can be addressed through a combination of protein and metabolic engineering. We have assembled a synthetic route for conversion of the highly toxic and recalcitrant 1,2,3-trichloropropane to glycerol in Escherichia coli, and used it for a systematic study of pathway bottlenecks. Optimal ratios of enzymes for the maximal production of glycerol, and minimal toxicity of metabolites were predicted using a mathematical model. The strains containing the expected optimal ratios of enzymes were constructed and characterized for their viability and degradation efficiency. Excellent agreement between predicted and experimental data was observed. The validated model was used to quantitatively describe the kinetic limitations of currently available enzyme variants and predict improvements required for further pathway optimization. This highlights the potential of forward engineering of microorganisms for the degradation of toxic anthropogenic compounds.

  8. Bioprospecting and evolving alternative xylose and arabinose pathway enzymes for use in Saccharomyces cerevisiae.

    Science.gov (United States)

    Lee, Sun-Mi; Jellison, Taylor; Alper, Hal S

    2016-03-01

    Bioprospecting is an effective way to find novel enzymes from strains with desirable phenotypes. Such bioprospecting has enabled organisms such as Saccharomyces cerevisiae to utilize nonnative pentose sugars. Yet, the efficiency of this pentose catabolism (especially for the case of arabinose) remains suboptimal. Thus, further pathway optimization or identification of novel, optimal pathways is needed. Previously, we identified a novel set of xylan catabolic pathway enzymes from a superior pentose-utilizing strain of Ustilago bevomyces. These enzymes were used to successfully engineer a xylan-utilizing S. cerevisiae through a blended approach of bioprospecting and evolutionary engineering. Here, we expanded this approach to xylose and arabinose catabolic pathway engineering and demonstrated that bioprospected xylose and arabinose catabolic pathways from U. bevomyces offer alternative choices for enabling efficient pentose catabolism in S. cerevisiae. By introducing a novel set of xylose catabolic genes from U. bevomyces, growth rates were improved up to 85 % over a set of traditional Scheffersomyces stipitis pathway genes. In addition, we suggested an alternative arabinose catabolic pathway which, after directed evolution and pathway engineering, enabled S. cerevisiae to grow on arabinose as a sole carbon source in minimal medium with growth rates upwards of 0.05 h(-1). This pathway represents the most efficient growth of yeast on pure arabinose minimal medium. These pathways provide great starting points for further strain development and demonstrate the utility of bioprospecting from U. bevomyces.

  9. Aberrant Signaling Pathways in Glioma

    International Nuclear Information System (INIS)

    Nakada, Mitsutoshi; Kita, Daisuke; Watanabe, Takuya; Hayashi, Yutaka; Teng, Lei; Pyko, Ilya V.; Hamada, Jun-Ichiro

    2011-01-01

    Glioblastoma multiforme (GBM), a WHO grade IV malignant glioma, is the most common and lethal primary brain tumor in adults; few treatments are available. Median survival rates range from 12–15 months. The biological characteristics of this tumor are exemplified by prominent proliferation, active invasiveness, and rich angiogenesis. This is mainly due to highly deregulated signaling pathways in the tumor. Studies of these signaling pathways have greatly increased our understanding of the biology and clinical behavior of GBM. An integrated view of signal transduction will provide a more useful approach in designing novel therapies for this devastating disease. In this review, we summarize the current understanding of GBM signaling pathways with a focus on potential molecular targets for anti-signaling molecular therapies

  10. Pathway of care among patients with Dhat syndrome attending a psychosexual clinic in tertiary care center in North India

    Directory of Open Access Journals (Sweden)

    Sandeep Grover

    2016-01-01

    Full Text Available Aim: The aim of this study was to understand the pathway to care among patients with Dhat syndrome and to study the factors leading to delay in seeking professional psychiatric help. Materials and Methods: Forty-seven patients diagnosed with Dhat syndrome as per the International Classification of Diseases-10 criteria were assessed for sociodemographic and clinical details and information regarding previous treatment taken to determine the pathways to care at their first contact with the outpatient psychosexual clinic. Results: Majority of the patients were single (70.2%, received formal education for at least more than 10 years (66.0%, were employed (59.6%, followers of Hinduism (68.1 and from middle socio-economic class (59.6%, nuclear family setup (53.2%, and rural locality (63.8%. Comorbidity in the form of any psychiatric illness or sexual dysfunction was present on 61.7% of the patients. The mean age at onset of symptoms of Dhat syndrome was 20.38 years (standard deviation [SD] - 6.91. The mean duration of symptoms of Dhat before the patients presented to our psychosexual clinic was 6.78 years (SD - 6.94 while the mean number of agencies/help contacted before was 2.85 (SD - 1.40; range: 1–5. The favorite choice for the first contact was indigenous practitioners, followed by asking for help from friends or relatives, allopathic doctors, and traditional faith healers or pharmacists. The preference to visit indigenous practitioners gradually declined at each stage. Ayurvedic doctors remained the most preferred among all indigenous practitioners. The absence of any comorbid sexual dysfunction in patients with Dhat syndrome predicted an earlier visit to our center as compared to the patients with any comorbid sexual dysfunction. Conclusions: Majority of the patients with Dhat syndrome present very late to specialized psychosexual clinics. There is a need for improving the sexual knowledge and attitude at the community level which will

  11. Pathway-based identification of biomarkers for targeted therapeutics: personalized oncology with PI3K pathway inhibitors.

    Science.gov (United States)

    Andersen, Jannik N; Sathyanarayanan, Sriram; Di Bacco, Alessandra; Chi, An; Zhang, Theresa; Chen, Albert H; Dolinski, Brian; Kraus, Manfred; Roberts, Brian; Arthur, William; Klinghoffer, Rich A; Gargano, Diana; Li, Lixia; Feldman, Igor; Lynch, Bethany; Rush, John; Hendrickson, Ronald C; Blume-Jensen, Peter; Paweletz, Cloud P

    2010-08-04

    Although we have made great progress in understanding the complex genetic alterations that underlie human cancer, it has proven difficult to identify which molecularly targeted therapeutics will benefit which patients. Drug-specific modulation of oncogenic signaling pathways in specific patient subpopulations can predict responsiveness to targeted therapy. Here, we report a pathway-based phosphoprofiling approach to identify and quantify clinically relevant, drug-specific biomarkers for phosphatidylinositol 3-kinase (PI3K) pathway inhibitors that target AKT, phosphoinositide-dependent kinase 1 (PDK1), and PI3K-mammalian target of rapamycin (mTOR). We quantified 375 nonredundant PI3K pathway-relevant phosphopeptides, all containing AKT, PDK1, or mitogen-activated protein kinase substrate recognition motifs. Of these phosphopeptides, 71 were drug-regulated, 11 of them by all three inhibitors. Drug-modulated phosphoproteins were enriched for involvement in cytoskeletal reorganization (filamin, stathmin, dynamin, PAK4, and PTPN14), vesicle transport (LARP1, VPS13D, and SLC20A1), and protein translation (S6RP and PRAS40). We then generated phosphospecific antibodies against selected, drug-regulated phosphorylation sites that would be suitable as biomarker tools for PI3K pathway inhibitors. As proof of concept, we show clinical translation feasibility for an antibody against phospho-PRAS40(Thr246). Evaluation of binding of this antibody in human cancer cell lines, a PTEN (phosphatase and tensin homolog deleted from chromosome 10)-deficient mouse prostate tumor model, and triple-negative breast tumor tissues showed that phospho-PRAS40(Thr246) positively correlates with PI3K pathway activation and predicts AKT inhibitor sensitivity. In contrast to phosphorylation of AKT(Thr308), the phospho-PRAS40(Thr246) epitope is highly stable in tissue samples and thus is ideal for immunohistochemistry. In summary, our study illustrates a rational approach for discovery of drug

  12. The 5 Clinical Pillars of Value for Total Joint Arthroplasty in a Bundled Payment Paradigm.

    Science.gov (United States)

    Kim, Kelvin; Iorio, Richard

    2017-06-01

    Our large, urban, tertiary, university-based institution reflects on its 4-year experience with Bundled Payments for Care Improvement. We will describe the importance of 5 clinical pillars that have contributed to the early success of our bundled payment initiative. We are convinced that value-based care delivered through bundled payment initiatives is the best method to optimize patient outcomes while rewarding surgeons and hospitals for adapting to the evolving healthcare reforms. We summarize a number of experiences and lessons learned since the implementation of Bundled Payments for Care Improvement at our institution. Our experience has led to the development of more refined clinical pathways and coordination of care through evidence-based approaches. We have established that the success of the bundled payment program rests on the following 5 main clinical pillars: (1) optimizing patient selection and comorbidities; (2) optimizing care coordination, patient education, shared decision making, and patient expectations; (3) using a multimodal pain management protocol and minimizing narcotic use to facilitate rapid rehabilitation; (4) optimizing blood management, and standardizing venous thromboembolic disease prophylaxis treatment by risk standardizing patients and minimizing the use of aggressive anticoagulation; and (5) minimizing post-acute facility and resource utilization, and maximizing home resources for patient recovery. From our extensive experience with bundled payment models, we have established 5 clinical pillars of value for bundled payments. Our hope is that these principles will help ease the transition to value-based care for less-experienced healthcare systems. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. A cluster randomized trial to assess the effect of clinical pathways for patients with stroke: results of the clinical pathways for effective and appropriate care study

    Directory of Open Access Journals (Sweden)

    Panella Massimiliano

    2012-07-01

    Full Text Available Abstract Background Clinical pathways (CPs are used to improve the outcomes of acute stroke, but their use in stroke care is questionable, because the evidence on their effectiveness is still inconclusive. The objective of this study was to evaluate whether CPs improve the outcomes and the quality of care provided to patients after acute ischemic stroke. Methods This was a multicentre cluster-randomized trial, in which 14 hospitals were randomized to the CP arm or to the non intervention/usual care (UC arm. Healthcare workers in the CP arm received 3 days of training in quality improvement of CPs and in use of a standardized package including information on evidence-based key interventions and indicators. Healthcare workers in the usual-care arm followed their standard procedures. The teams in the CP arm developed their CPs over a 6-month period. The primary end point was mortality. Secondary end points were: use of diagnostic and therapeutic procedures, implementation of organized care, length of stay, re-admission and institutionalization rates after discharge, dependency levels, and complication rates. Results Compared with the patients in the UC arm, the patients in the CP arm had a significantly lower risk of mortality at 7 days (OR = 0.10; 95% CI 0.01 to 0.95 and significantly lower rates of adverse functional outcomes, expressed as the odds of not returning to pre-stroke functioning in their daily life (OR = 0.42; 95 CI 0.18 to 0.98. There was no significant effect on 30-day mortality. Compared with the UC arm, the hospital diagnostic and therapeutic procedures were performed more appropriately in the CP arm, and the evidence-based key interventions and organized care were more applied in the CP arm. Conclusions CPs can significantly improve the outcomes of patients with ischemic patients with stroke, indicating better application of evidence-based key interventions and of diagnostic and therapeutic procedures. This study tested a new

  14. Implementation of a guideline-based clinical pathway of care to improve health outcomes following whiplash injury (Whiplash ImPaCT: protocol of a randomised, controlled trial

    Directory of Open Access Journals (Sweden)

    Trudy Rebbeck

    2016-04-01

    Discussion: This research is significant as it will be the first study to address the heterogeneity of whiplash by implementing a clinical pathway of care that matches evidence-based interventions to projected risk of poor recovery. The results of this trial have the potential to change clinical practice for WAD, thereby maximising treatment effects, improving patient outcomes, reducing costs and maintaining the compulsory third party system.

  15. Signaling Pathways in Cardiac Myocyte Apoptosis

    Science.gov (United States)

    Xia, Peng; Liu, Yuening

    2016-01-01

    Cardiovascular diseases, the number 1 cause of death worldwide, are frequently associated with apoptotic death of cardiac myocytes. Since cardiomyocyte apoptosis is a highly regulated process, pharmacological intervention of apoptosis pathways may represent a promising therapeutic strategy for a number of cardiovascular diseases and disorders including myocardial infarction, ischemia/reperfusion injury, chemotherapy cardiotoxicity, and end-stage heart failure. Despite rapid growth of our knowledge in apoptosis signaling pathways, a clinically applicable treatment targeting this cellular process is currently unavailable. To help identify potential innovative directions for future research, it is necessary to have a full understanding of the apoptotic pathways currently known to be functional in cardiac myocytes. Here, we summarize recent progress in the regulation of cardiomyocyte apoptosis by multiple signaling molecules and pathways, with a focus on the involvement of these pathways in the pathogenesis of heart disease. In addition, we provide an update regarding bench to bedside translation of this knowledge and discuss unanswered questions that need further investigation. PMID:28101515

  16. Technological cost-reduction pathways for attenuator wave energy converters in the marine hydrokinetic environment.

    Energy Technology Data Exchange (ETDEWEB)

    Bull, Diana L; Ochs, Margaret Ellen

    2013-09-01

    This report considers and prioritizes the primary potential technical costreduction pathways for offshore wave activated body attenuators designed for ocean resources. This report focuses on technical research and development costreduction pathways related to the device technology rather than environmental monitoring or permitting opportunities. Three sources of information were used to understand current cost drivers and develop a prioritized list of potential costreduction pathways: a literature review of technical work related to attenuators, a reference device compiled from literature sources, and a webinar with each of three industry device developers. Data from these information sources were aggregated and prioritized with respect to the potential impact on the lifetime levelized cost of energy, the potential for progress, the potential for success, and the confidence in success. Results indicate the five most promising costreduction pathways include advanced controls, an optimized structural design, improved power conversion, planned maintenance scheduling, and an optimized device profile.

  17. Precision Oncology Medicine: The Clinical Relevance of Patient-Specific Biomarkers Used to Optimize Cancer Treatment.

    Science.gov (United States)

    Schmidt, Keith T; Chau, Cindy H; Price, Douglas K; Figg, William D

    2016-12-01

    Precision medicine in oncology is the result of an increasing awareness of patient-specific clinical features coupled with the development of genomic-based diagnostics and targeted therapeutics. Companion diagnostics designed for specific drug-target pairs were the first to widely utilize clinically applicable tumor biomarkers (eg, HER2, EGFR), directing treatment for patients whose tumors exhibit a mutation susceptible to an FDA-approved targeted therapy (eg, trastuzumab, erlotinib). Clinically relevant germline mutations in drug-metabolizing enzymes and transporters (eg, TPMT, DPYD) have been shown to impact drug response, providing a rationale for individualized dosing to optimize treatment. The use of multigene expression-based assays to analyze an array of prognostic biomarkers has been shown to help direct treatment decisions, especially in breast cancer (eg, Oncotype DX). More recently, the use of next-generation sequencing to detect many potential "actionable" cancer molecular alterations is further shifting the 1 gene-1 drug paradigm toward a more comprehensive, multigene approach. Currently, many clinical trials (eg, NCI-MATCH, NCI-MPACT) are assessing novel diagnostic tools with a combination of different targeted therapeutics while also examining tumor biomarkers that were previously unexplored in a variety of cancer histologies. Results from ongoing trials such as the NCI-MATCH will help determine the clinical utility and future development of the precision-medicine approach. © 2016, The American College of Clinical Pharmacology.

  18. Analysis of effectiveness, safety and optimization of tocilizumab in a cohort of patients with rheumatoid arthritis in clinical practice.

    Science.gov (United States)

    Mena-Vázquez, Natalia; Manrique-Arija, Sara; Rojas-Giménez, Marta; Ureña-Garnica, Inmaculada; Jiménez-Núñez, Francisco G; Fernández-Nebro, Antonio

    2017-07-01

    To evaluate the effectiveness and safety of tocilizumab (TCZ) in patients with rheumatoid arthritis (RA) in clinical practice, establishing the optimized regimen and switching from intravenous (IV) to subcutaneous (SC) therapy. Retrospective observational study. We included 53 RA patients treated with TCZ. The main outcome was TCZ effectiveness at week 24. Secondary outcome variables included effectiveness at week 52, therapeutic maintenance, physical function and safety. The effectiveness of optimization and the switch from IV to SC was evaluated at 3 and 6 months. The efficacy was measured with the Disease Activity Score. Paired t-tests or Wilcoxon were used to evaluate effectiveness and survival time using Kaplan-Meier. The proportion of patients who achieved remission or low disease activity at weeks 24 and 52 was 75.5% and 87.3%, respectively. The mean retention time (95% confidence interval [95% CI] was 81.7 months [76.6-86.7]). Twenty-one of 53 patients (39.6%) optimized the TCZ dose and 35 patients switched from IV TCZ to SC, with no changes in effectiveness. The adverse event rate was 13.6 events/100 patient-years. Tocilizumab appears to be effective and safe in RA in clinical practice. The optimized regimen appears to be effective in most patients in remission, even when they change from IV to SC. Copyright © 2017 Elsevier España, S.L.U. and Sociedad Española de Reumatología y Colegio Mexicano de Reumatología. All rights reserved.

  19. Cerebrospinal and Interstitial Fluid Transport via the Glymphatic Pathway Modeled by Optimal Mass Transport

    OpenAIRE

    Ratner, Vadim; Gao, Yi; Lee, Hedok; Elkin, Rena; Nedergaard, Maiken; Benveniste, Helene; Tannenbaum, Allen

    2017-01-01

    The glymphatic pathway is a system which facilitates continuous cerebrospinal fluid (CSF) and interstitial fluid (ISF) exchange and plays a key role in removing waste products from the rodent brain. Dysfunction of the glymphatic pathway may be implicated in the pathophysiology of Alzheimer's disease. Intriguingly, the glymphatic system is most active during deep wave sleep general anesthesia. By using paramagnetic tracers administered into CSF of rodents, we previously showed the utility of M...

  20. Advancing clinical development pathways for new CFTR modulators in cystic fibrosis.

    Science.gov (United States)

    Mayer-Hamblett, Nicole; Boyle, Michael; VanDevanter, Donald

    2016-05-01

    Cystic fibrosis (CF) is a life-shortening genetic disease affecting approximately 70,000 individuals worldwide. Until recently, drug development efforts have emphasised therapies treating downstream signs and symptoms resulting from the underlying CF biological defect: reduced function of the CF transmembrane conductance regulator (CFTR) protein. The current CF drug development landscape has expanded to include therapies that enhance CFTR function by either restoring wild-type CFTR protein expression or increasing (modulating) the function of mutant CFTR proteins in cells. To date, two systemic small-molecule CFTR modulators have been evaluated in pivotal clinical trials in individuals with CF and specific mutant CFTR genotypes that have led to regulatory review and/or approval. Advances in the discovery of CFTR modulators as a promising new class of therapies have been impressive, yet work remains to develop highly effective, disease-modifying modulators for individuals of all CF genotypes. The objectives of this review are to outline the challenges and opportunities in drug development created by systemic genotype-specific CFTR modulators, highlight the advantages of sweat chloride as an established biomarker of CFTR activity to streamline early-phase development and summarise options for later phase clinical trial designs that respond to the adoption of approved genotype-specific modulators into standard of care. An optimal development framework will be needed to move the most promising therapies efficiently through the drug development pipeline and ultimately deliver efficacious and safe therapies to all individuals with CF. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  1. Drug efficiency: a new concept to guide lead optimization programs towards the selection of better clinical candidates.

    Science.gov (United States)

    Braggio, Simone; Montanari, Dino; Rossi, Tino; Ratti, Emiliangelo

    2010-07-01

    As a result of their wide acceptance and conceptual simplicity, drug-like concepts are having a major influence on the drug discovery process, particularly in the selection of the 'optimal' absorption, distribution, metabolism, excretion and toxicity and physicochemical parameters space. While they have an undisputable value when assessing the potential of lead series or in evaluating inherent risk of a portfolio of drug candidates, they result much less useful in weighing up compounds for the selection of the best potential clinical candidate. We introduce the concept of drug efficiency as a new tool both to guide the drug discovery program teams during the lead optimization phase and to better assess the developability potential of a drug candidate.

  2. Symptoms of major depressive disorder subsequent to child maltreatment: Examining change across multiple levels of analysis to identify transdiagnostic risk pathways.

    Science.gov (United States)

    Shenk, Chad E; Griffin, Amanda M; O'Donnell, Kieran J

    2015-11-01

    Major depressive disorder (MDD) is a prevalent psychiatric condition in the child maltreatment population. However, not all children who have been maltreated will develop MDD or MDD symptoms, suggesting the presence of unique risk pathways that explain how certain children develop MDD symptoms when others do not. The current study tested several candidate risk pathways to MDD symptoms following child maltreatment: neuroendocrine, autonomic, affective, and emotion regulation. Female adolescents (N = 110; age range = 14-19) were recruited into a substantiated child maltreatment or comparison condition and completed a laboratory stressor, saliva samples, and measures of emotion regulation, negative affect, and MDD symptoms. MDD symptoms were reassessed 18 months later. Mediational modeling revealed that emotion regulation was the only significant indirect effect of the relationship between child maltreatment and subsequent MDD symptoms, demonstrating that children exposed to maltreatment had greater difficulties managing affective states that in turn led to more severe MDD symptoms. These results highlight the importance of emotion dysregulation as a central risk pathway to MDD following child maltreatment. Areas of future research and implications for optimizing prevention and clinical intervention through the direct targeting of transdiagnostic risk pathways are discussed.

  3. Symptoms of Major Depressive Disorder Subsequent to Child Maltreatment: Examining Change across Multiple Levels of Analysis to Identify Transdiagnostic Risk Pathways

    Science.gov (United States)

    Shenk, Chad E.; Griffin, Amanda M.; O’Donnell, Kieran J.

    2016-01-01

    Major depressive disorder (MDD) is a prevalent psychiatric condition in the child maltreatment population. However, not all children who have been maltreated will develop MDD or MDD symptoms, suggesting the presence of unique risk pathways that explain how certain children develop MDD symptoms when others do not. The current study tested several candidate risk pathways to MDD symptoms following child maltreatment: 1) neuroendocrine, 2) autonomic, 3) affective, and 4) emotion regulation. Female adolescents (N=110; Age range: 14–19) were recruited into a substantiated child maltreatment or comparison condition and completed a laboratory stressor, saliva samples, and measures of emotion regulation, negative affect, and MDD symptoms. MDD symptoms were reassessed eighteen months later. Mediational modeling revealed that emotion regulation was the only significant indirect effect of the relationship between child maltreatment and subsequent MDD symptoms, demonstrating that children exposed to maltreatment had greater difficulties managing affective states that in turn led to more severe MDD symptoms. These results highlight the importance of emotion dysregulation as a central risk pathway to MDD following child maltreatment. Areas of future research and implications for optimizing prevention and clinical intervention through the direct targeting of transdiagnostic risk pathways are discussed. PMID:26535940

  4. [Construction of high-yield strain by optimizing lycopene cyclase for β-carotene production].

    Science.gov (United States)

    Jin, Yingfu; Han, Li; Zhang, Shasha; Li, Shizhong; Liu, Weifeng; Tao, Yong

    2017-11-25

    To optimize key enzymes, such as to explore the gene resources and to modify the expression level, can maximize metabolic pathways of target products. β-carotene is a terpenoid compound with important application value. Lycopene cyclase (CrtY) is the key enzyme in β-carotene biosynthesis pathway, catalyzing flavin adenine dinucleotide (FAD)-dependent cyclization reaction and β-carotene synthesis from lycopene precursor. We optimized lycopene cyclase (CrtY) to improve the synthesis of β-carotene and determined the effect of CrtY expression on metabolic pathways. Frist, we developed a β-carotene synthesis module by coexpressing the lycopene β-cyclase gene crtY with crtEBI module in Escherichia coli. Then we simultaneously optimized the ribosome-binding site (RBS) intensity and the species of crtY using oligo-linker mediated DNA assembly method (OLMA). Five strains with high β-carotene production capacity were screened out from the OLMA library. The β-carotene yields of these strains were up to 15.79-18.90 mg/g DCW (Dry cell weight), 65% higher than that of the original strain at shake flask level. The optimal strain CP12 was further identified and evaluated for β-carotene production at 5 L fermentation level. After process optimization, the final β-carotene yield could reach to 1.9 g/L. The results of RBS strength and metabolic intermediate analysis indicated that an appropriate expression level of CrtY could be beneficial for the function of the β-carotene synthesis module. The results of this study provide important insight into the optimization of β-carotene synthesis pathway in metabolic engineering.

  5. Aligning Event Logs to Task-Time Matrix Clinical Pathways in BPMN for Variance Analysis.

    Science.gov (United States)

    Yan, Hui; Van Gorp, Pieter; Kaymak, Uzay; Lu, Xudong; Ji, Lei; Chiau, Choo Chiap; Korsten, Hendrikus H M; Duan, Huilong

    2018-03-01

    Clinical pathways (CPs) are popular healthcare management tools to standardize care and ensure quality. Analyzing CP compliance levels and variances is known to be useful for training and CP redesign purposes. Flexible semantics of the business process model and notation (BPMN) language has been shown to be useful for the modeling and analysis of complex protocols. However, in practical cases one may want to exploit that CPs often have the form of task-time matrices. This paper presents a new method parsing complex BPMN models and aligning traces to the models heuristically. A case study on variance analysis is undertaken, where a CP from the practice and two large sets of patients data from an electronic medical record (EMR) database are used. The results demonstrate that automated variance analysis between BPMN task-time models and real-life EMR data are feasible, whereas that was not the case for the existing analysis techniques. We also provide meaningful insights for further improvement.

  6. Standardising school nursing practice: developing and implementing a care pathways package.

    Science.gov (United States)

    Turney, Nicy; Clarke, Maggie; Stevenson, Emily

    2012-11-01

    The NHS has a longstanding relationship with care pathways for managing clinical processes and patient outcomes. Care pathways are an effective mechanism to improve the delivery of services in managing children's health. However, few individual NHS trusts have successfully developed and implemented local pathways. This paper describes the development and implementation of a comprehensive care pathways package for school nursing in a community health services trust in the East Midlands.

  7. The dual pathway model of overeating. Replication and extension with actual food consumption

    NARCIS (Netherlands)

    Ouwens, Machteld A; van Strien, T; Leeuwe, J.F.J.; van der Staak, C P F

    van Strien et al. [van Strien, T., Engels, R. C. M. E., van Leeuwe, J., Snoek, H. M. (2005). The Stice model of overeating: tests in clinical and non-clinical samples. Appetite, 45, 205-213] extended the negative affect pathway of Stice's dual pathway model of overeating Stice [Stice, E. (1994).

  8. MoCha: Molecular Characterization of Unknown Pathways.

    Science.gov (United States)

    Lobo, Daniel; Hammelman, Jennifer; Levin, Michael

    2016-04-01

    Automated methods for the reverse-engineering of complex regulatory networks are paving the way for the inference of mechanistic comprehensive models directly from experimental data. These novel methods can infer not only the relations and parameters of the known molecules defined in their input datasets, but also unknown components and pathways identified as necessary by the automated algorithms. Identifying the molecular nature of these unknown components is a crucial step for making testable predictions and experimentally validating the models, yet no specific and efficient tools exist to aid in this process. To this end, we present here MoCha (Molecular Characterization), a tool optimized for the search of unknown proteins and their pathways from a given set of known interacting proteins. MoCha uses the comprehensive dataset of protein-protein interactions provided by the STRING database, which currently includes more than a billion interactions from over 2,000 organisms. MoCha is highly optimized, performing typical searches within seconds. We demonstrate the use of MoCha with the characterization of unknown components from reverse-engineered models from the literature. MoCha is useful for working on network models by hand or as a downstream step of a model inference engine workflow and represents a valuable and efficient tool for the characterization of unknown pathways using known data from thousands of organisms. MoCha and its source code are freely available online under the GPLv3 license.

  9. Clinical review: Optimal dose of continuous renal replacement therapy in acute kidney injury.

    Science.gov (United States)

    Prowle, John R; Schneider, Antoine; Bellomo, Rinaldo

    2011-01-01

    Continuous renal replacement therapy (CRRT) is the preferred treatment for acute kidney injury in intensive care units (ICUs) throughout much of the world. Despite the widespread use of CRRT, controversy and center-specific practice variation in the clinical application of CRRT continue. In particular, whereas two single-center studies have suggested survival benefit from delivery of higher-intensity CRRT to patients with acute kidney injury in the ICU, other studies have been inconsistent in their results. Now, however, two large multi-center randomized controlled trials - the Veterans Affairs/National Institutes of Health Acute Renal Failure Trial Network (ATN) study and the Randomized Evaluation of Normal versus Augmented Level (RENAL) Replacement Therapy Study - have provided level 1 evidence that effluent flow rates above 25 mL/kg per hour do not improve outcomes in patients in the ICU. In this review, we discuss the concept of dose of CRRT, its relationship with clinical outcomes, and what target optimal dose of CRRT should be pursued in light of the high-quality evidence now available.

  10. YAP and the Hippo pathway in pediatric cancer.

    Science.gov (United States)

    Ahmed, Atif A; Mohamed, Abdalla D; Gener, Melissa; Li, Weijie; Taboada, Eugenio

    2017-01-01

    The Hippo pathway is an important signaling pathway that controls cell proliferation and apoptosis. It is evolutionarily conserved in mammals and is stimulated by cell-cell contact, inhibiting cell proliferation in response to increased cell density. During early embryonic development, the Hippo signaling pathway regulates organ development and size, and its functions result in the coordinated balance between proliferation, apoptosis, and differentiation. Its principal effectors, YAP and TAZ, regulate signaling by the embryonic stem cells and determine cell fate and histogenesis. Dysfunction of this pathway contributes to cancer development in adults and children. Emerging studies have shed light on the upregulation of Hippo pathway members in several pediatric cancers and may offer prognostic information on rhabdomyosarcoma, osteosarcoma, Wilms tumor, neuroblastoma, medulloblastoma, and other brain gliomas. We review the results of such published studies and highlight the potential clinical application of this pathway in pediatric oncologic and pathologic studies. These studies support targeting this pathway as a novel treatment strategy.

  11. Pathway Distiller - multisource biological pathway consolidation.

    Science.gov (United States)

    Doderer, Mark S; Anguiano, Zachry; Suresh, Uthra; Dashnamoorthy, Ravi; Bishop, Alexander J R; Chen, Yidong

    2012-01-01

    One method to understand and evaluate an experiment that produces a large set of genes, such as a gene expression microarray analysis, is to identify overrepresentation or enrichment for biological pathways. Because pathways are able to functionally describe the set of genes, much effort has been made to collect curated biological pathways into publicly accessible databases. When combining disparate databases, highly related or redundant pathways exist, making their consolidation into pathway concepts essential. This will facilitate unbiased, comprehensive yet streamlined analysis of experiments that result in large gene sets. After gene set enrichment finds representative pathways for large gene sets, pathways are consolidated into representative pathway concepts. Three complementary, but different methods of pathway consolidation are explored. Enrichment Consolidation combines the set of the pathways enriched for the signature gene list through iterative combining of enriched pathways with other pathways with similar signature gene sets; Weighted Consolidation utilizes a Protein-Protein Interaction network based gene-weighting approach that finds clusters of both enriched and non-enriched pathways limited to the experiments' resultant gene list; and finally the de novo Consolidation method uses several measurements of pathway similarity, that finds static pathway clusters independent of any given experiment. We demonstrate that the three consolidation methods provide unified yet different functional insights of a resultant gene set derived from a genome-wide profiling experiment. Results from the methods are presented, demonstrating their applications in biological studies and comparing with a pathway web-based framework that also combines several pathway databases. Additionally a web-based consolidation framework that encompasses all three methods discussed in this paper, Pathway Distiller (http://cbbiweb.uthscsa.edu/PathwayDistiller), is established to allow

  12. Design, synthesis and optimization of bis-amide derivatives as CSF1R inhibitors.

    Science.gov (United States)

    Ramachandran, Sreekanth A; Jadhavar, Pradeep S; Miglani, Sandeep K; Singh, Manvendra P; Kalane, Deepak P; Agarwal, Anil K; Sathe, Balaji D; Mukherjee, Kakoli; Gupta, Ashu; Haldar, Srijan; Raja, Mohd; Singh, Siddhartha; Pham, Son M; Chakravarty, Sarvajit; Quinn, Kevin; Belmar, Sebastian; Alfaro, Ivan E; Higgs, Christopher; Bernales, Sebastian; Herrera, Francisco J; Rai, Roopa

    2017-05-15

    Signaling via the receptor tyrosine kinase CSF1R is thought to play an important role in recruitment and differentiation of tumor-associated macrophages (TAMs). TAMs play pro-tumorigenic roles, including the suppression of anti-tumor immune response, promotion of angiogenesis and tumor cell metastasis. Because of the role of this signaling pathway in the tumor microenvironment, several small molecule CSF1R kinase inhibitors are undergoing clinical evaluation for cancer therapy, either as a single agent or in combination with other cancer therapies, including immune checkpoint inhibitors. Herein we describe our lead optimization effort that resulted in the identification of a potent, cellular active and orally bioavailable bis-amide CSF1R inhibitor. Docking and biochemical analysis allowed the removal of a metabolically labile and poorly permeable methyl piperazine group from an early lead compound. Optimization led to improved metabolic stability and Caco2 permeability, which in turn resulted in good oral bioavailability in mice. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. The dual pathway model of overeating. Replication and extension with actual food consumption

    NARCIS (Netherlands)

    Ouwens, M.A.; Strien, T. van; Leeuwe, J.F.J. van; Staak, C.P.F. van der

    2009-01-01

    van Strien et al. [van Strien, T., Engels, R. C. M. E., van Leeuwe, J., Snoek, H. M. (2005). The Stice model of overeating: tests in clinical and non-clinical samples. Appetite, 45, 205–213] extended the negative affect pathway of Stice's dual pathway model of overeating Stice [Stice, E. (1994).

  14. Transtemporal amygdalohippocampectomy: a novel minimally-invasive technique with optimal clinical results and low cost

    Directory of Open Access Journals (Sweden)

    Juan Antonio Castro Flores

    Full Text Available ABSTRACT Mesial temporal sclerosis creates a focal epileptic syndrome that usually requires surgical resection of mesial temporal structures. Objective: To describe a novel operative technique for treatment of temporal lobe epilepsy and its clinical results. Methods: Prospective case-series at a single institution, performed by a single surgeon, from 2006 to 2012. A total of 120 patients were submitted to minimally-invasive keyhole transtemporal amygdalohippocampectomy. Results: Of the patients, 55% were male, and 85% had a right-sided disease. The first 70 surgeries had a mean surgical time of 2.51 hours, and the last 50 surgeries had a mean surgical time of 1.62 hours. There was 3.3% morbidity, and 5% mild temporal muscle atrophy. There was no visual field impairment. On the Engel Outcome Scale at the two-year follow-up, 71% of the patients were Class I, 21% were Class II, and 6% were Class III. Conclusion: This novel technique is feasible and reproducible, with optimal clinical results.

  15. A strategy for evaluating pathway analysis methods.

    Science.gov (United States)

    Yu, Chenggang; Woo, Hyung Jun; Yu, Xueping; Oyama, Tatsuya; Wallqvist, Anders; Reifman, Jaques

    2017-10-13

    Researchers have previously developed a multitude of methods designed to identify biological pathways associated with specific clinical or experimental conditions of interest, with the aim of facilitating biological interpretation of high-throughput data. Before practically applying such pathway analysis (PA) methods, we must first evaluate their performance and reliability, using datasets where the pathways perturbed by the conditions of interest have been well characterized in advance. However, such 'ground truths' (or gold standards) are often unavailable. Furthermore, previous evaluation strategies that have focused on defining 'true answers' are unable to systematically and objectively assess PA methods under a wide range of conditions. In this work, we propose a novel strategy for evaluating PA methods independently of any gold standard, either established or assumed. The strategy involves the use of two mutually complementary metrics, recall and discrimination. Recall measures the consistency of the perturbed pathways identified by applying a particular analysis method to an original large dataset and those identified by the same method to a sub-dataset of the original dataset. In contrast, discrimination measures specificity-the degree to which the perturbed pathways identified by a particular method to a dataset from one experiment differ from those identifying by the same method to a dataset from a different experiment. We used these metrics and 24 datasets to evaluate six widely used PA methods. The results highlighted the common challenge in reliably identifying significant pathways from small datasets. Importantly, we confirmed the effectiveness of our proposed dual-metric strategy by showing that previous comparative studies corroborate the performance evaluations of the six methods obtained by our strategy. Unlike any previously proposed strategy for evaluating the performance of PA methods, our dual-metric strategy does not rely on any ground truth

  16. A mechanistic understanding of allosteric immune escape pathways in the HIV-1 envelope glycoprotein.

    Directory of Open Access Journals (Sweden)

    Anurag Sethi

    Full Text Available The HIV-1 envelope (Env spike, which consists of a compact, heterodimeric trimer of the glycoproteins gp120 and gp41, is the target of neutralizing antibodies. However, the high mutation rate of HIV-1 and plasticity of Env facilitates viral evasion from neutralizing antibodies through various mechanisms. Mutations that are distant from the antibody binding site can lead to escape, probably by changing the conformation or dynamics of Env; however, these changes are difficult to identify and define mechanistically. Here we describe a network analysis-based approach to identify potential allosteric immune evasion mechanisms using three known HIV-1 Env gp120 protein structures from two different clades, B and C. First, correlation and principal component analyses of molecular dynamics (MD simulations identified a high degree of long-distance coupled motions that exist between functionally distant regions within the intrinsic dynamics of the gp120 core, supporting the presence of long-distance communication in the protein. Then, by integrating MD simulations with network theory, we identified the optimal and suboptimal communication pathways and modules within the gp120 core. The results unveil both strain-dependent and -independent characteristics of the communication pathways in gp120. We show that within the context of three structurally homologous gp120 cores, the optimal pathway for communication is sequence sensitive, i.e. a suboptimal pathway in one strain becomes the optimal pathway in another strain. Yet the identification of conserved elements within these communication pathways, termed inter-modular hotspots, could present a new opportunity for immunogen design, as this could be an additional mechanism that HIV-1 uses to shield vulnerable antibody targets in Env that induce neutralizing antibody breadth.

  17. The Glymphatic Pathway.

    Science.gov (United States)

    Benveniste, Helene; Lee, Hedok; Volkow, Nora D

    2017-01-01

    The overall premise of this review is that cerebrospinal fluid (CSF) is transported within a dedicated peri-vascular network facilitating metabolic waste clearance from the central nervous system while we sleep. The anatomical profile of the network is complex and has been defined as a peri-arterial CSF influx pathway and peri-venous clearance routes, which are functionally coupled by interstitial bulk flow supported by astrocytic aquaporin 4 water channels. The role of the newly discovered system in the brain is equivalent to the lymphatic system present in other body organs and has been termed the "glymphatic pathway" or "(g)lymphatics" because of its dependence on glial cells. We will discuss and review the general anatomy and physiology of CSF from the perspective of the glymphatic pathway, a discovery which has greatly improved our understanding of key factors that control removal of metabolic waste products from the central nervous system in health and disease and identifies an additional purpose for sleep. A brief historical and factual description of CSF production and transport will precede the ensuing discussion of the glymphatic system along with a discussion of its clinical implications.

  18. Stepwise multi-criteria optimization for robotic radiosurgery

    International Nuclear Information System (INIS)

    Schlaefer, A.; Schweikard, A.

    2008-01-01

    Achieving good conformality and a steep dose gradient around the target volume remains a key aspect of radiosurgery. Clearly, this involves a trade-off between target coverage, conformality of the dose distribution, and sparing of critical structures. Yet, image guidance and robotic beam placement have extended highly conformal dose delivery to extracranial and moving targets. Therefore, the multi-criteria nature of the optimization problem becomes even more apparent, as multiple conflicting clinical goals need to be considered coordinate to obtain an optimal treatment plan. Typically, planning for robotic radiosurgery is based on constrained optimization, namely linear programming. An extension of that approach is presented, such that each of the clinical goals can be addressed separately and in any sequential order. For a set of common clinical goals the mapping to a mathematical objective and a corresponding constraint is defined. The trade-off among the clinical goals is explored by modifying the constraints and optimizing a simple objective, while retaining feasibility of the solution. Moreover, it becomes immediately obvious whether a desired goal can be achieved and where a trade-off is possible. No importance factors or predefined prioritizations of clinical goals are necessary. The presented framework forms the basis for interactive and automated planning procedures. It is demonstrated for a sample case that the linear programming formulation is suitable to search for a clinically optimal treatment, and that the optimization steps can be performed quickly to establish that a Pareto-efficient solution has been found. Furthermore, it is demonstrated how the stepwise approach is preferable compared to modifying importance factors

  19. The role of ethnicity in clinical psychopathology and care pathways of adults with intellectual disabilities.

    LENUS (Irish Health Repository)

    Tsakanikos, Elias

    2011-04-27

    The objective of this study was to explore whether people with intellectual disability from ethnic minority groups have higher rates of mental health problems and access different care pathways than their White counterparts. Clinical and socio-demographic data were collected for 806 consecutive new referrals to a specialist mental health service for people with intellectual disabilities in South London. Referrals were grouped according to their ethnic origin. The analyses showed that there was an over-representation of referrals from ethnic minority groups with diagnoses of schizophrenia spectrum disorder. In addition, Black participants were more likely to have an autistic spectrum disorder. Referrals of ethnic minority groups were considerably younger than White referrals, and less likely to be in supported residences. The results are discussed in the context of cultural and familial factors in particular ethnic groups that may play an important role in accessing and using mental health services.

  20. Optimization of isopropanol production by engineered cyanobacteria with a synthetic metabolic pathway.

    Science.gov (United States)

    Hirokawa, Yasutaka; Suzuki, Iwane; Hanai, Taizo

    2015-05-01

    Cyanobacterium is an attractive host for the production of various chemicals and alternative fuels using solar energy and carbon dioxide. In previous study, we succeeded to produce isopropanol using engineered Synechococcus elongatus PCC 7942 under dark and anaerobic conditions (0.43 mM, 26.5 mg/l). In the present study, we report the further optimization of this isopropanol producing condition. We then optimized growth conditions for production of isopropanol by the engineered cyanobacteria, including the use of cells in early stationary phase and buffering of the production medium to neutral pH. We observed that shifting of cultures from dark and anaerobic to light and aerobic conditions during the production phase dramatically increased isopropanol production by conversion to isopropanol from acetate, byproduct under dark and anaerobic condition. Under the optimized production conditions, the titer of isopropanol was elevated 6-fold, to 2.42 mM (146 mg/l). Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  1. A musculoskeletal foot model for clinical gait analysis.

    Science.gov (United States)

    Saraswat, Prabhav; Andersen, Michael S; Macwilliams, Bruce A

    2010-06-18

    Several full body musculoskeletal models have been developed for research applications and these models may potentially be developed into useful clinical tools to assess gait pathologies. Existing full-body musculoskeletal models treat the foot as a single segment and ignore the motions of the intrinsic joints of the foot. This assumption limits the use of such models in clinical cases with significant foot deformities. Therefore, a three-segment musculoskeletal model of the foot was developed to match the segmentation of a recently developed multi-segment kinematic foot model. All the muscles and ligaments of the foot spanning the modeled joints were included. Muscle pathways were adjusted with an optimization routine to minimize the difference between the muscle flexion-extension moment arms from the model and moment arms reported in literature. The model was driven by walking data from five normal pediatric subjects (aged 10.6+/-1.57 years) and muscle forces and activation levels required to produce joint motions were calculated using an inverse dynamic analysis approach. Due to the close proximity of markers on the foot, small marker placement error during motion data collection may lead to significant differences in musculoskeletal model outcomes. Therefore, an optimization routine was developed to enforce joint constraints, optimally scale each segment length and adjust marker positions. To evaluate the model outcomes, the muscle activation patterns during walking were compared with electromyography (EMG) activation patterns reported in the literature. Model-generated muscle activation patterns were observed to be similar to the EMG activation patterns. Published by Elsevier Ltd.

  2. Factors affecting optimal linear endovenous energy density for endovenous laser ablation in incompetent lower limb truncal veins - A review of the clinical evidence.

    Science.gov (United States)

    Cowpland, Christine A; Cleese, Amy L; Whiteley, Mark S

    2017-06-01

    Objectives The objective is to identify the factors that affect the optimal linear endovenous energy density (LEED) to ablate incompetent truncal veins. Methods We performed a literature review of clinical studies, which reported truncal vein ablation rates and LEED. A PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) flow diagram documents the search strategy. We analysed 13 clinical papers which fulfilled the criteria to be able to compare results of great saphenous vein occlusion as defined by venous duplex ultrasound, with the LEED used in the treatment. Results Evidence suggests that the optimal LEED for endovenous laser ablation of the great saphenous vein is >80 J/cm and water might have a lower optimal LEED. A LEED 80 J/cm and <95 J/cm based on current evidence for shorter wavelength lasers. There is evidence that longer wavelength lasers may be effective at LEEDs of <85 J/cm.

  3. Nutraceuticals for prostate cancer chemoprevention: from molecular mechanisms to clinical application.

    Science.gov (United States)

    Wang, Zhijun; Fan, Jeffery; Liu, Mandy; Yeung, Steven; Chang, Andy; Chow, Moses S S; Pon, Doreen; Huang, Ying

    2013-12-01

    Nutraceutical is a food, or part of a food, used for the prevention and/or treatment of diseases. A number of nutraceuticals serve as candidates for development of prostate cancer chemopreventive agents because of promising epidemiological, preclinical and pilot clinical findings. Their mechanisms of action may involve an ability to target multiple molecular pathways in carcinogenesis without eliciting toxic side effects. This review provides an overview of several nutraceuticals, including green tea polyphenol, omega-3 fatty acids, vitamin D, lycopene, genistein, quercetin, resveratrol and sulforaphane, for the clinical relevance to chemoprevention of prostate cancer. Their mechanisms of action on regulating key processes of carcinogenesis are also discussed. For each of these agents, a brief summary of completed or currently ongoing clinical trials related to the chemopreventive efficacy on prostate cancer is given. Even though a few clinical trials have been conducted, review of these results indicate that further studies are required to confirm the clinical efficacy and safety, and to provide a guidance on how to use nutraceuticals for optimal effect. Future cancer prevention clinical trials for the nutraceuticals should recruit men with an increased risk of prostate cancer.

  4. Determining the Optimal Protocol for Measuring an Albuminuria Class Transition in Clinical Trials in Diabetic Kidney Disease

    DEFF Research Database (Denmark)

    Kröpelin, Tobias F; de Zeeuw, Dick; Remuzzi, Giuseppe

    2016-01-01

    Albuminuria class transition (normo- to micro- to macroalbuminuria) is used as an intermediate end point to assess renoprotective drug efficacy. However, definitions of such class transition vary between trials. To determine the most optimal protocol, we evaluated the approaches used in four...... effect increased (decreased precision) with stricter end point definitions, resulting in a loss of statistical significance. In conclusion, the optimal albuminuria transition end point for use in drug intervention trials can be determined with a single urine collection for albuminuria assessment per...... clinical trials testing the effect of renin-angiotensin-aldosterone system intervention on albuminuria class transition in patients with diabetes: the BENEDICT, the DIRECT, the ALTITUDE, and the IRMA-2 Trial. The definition of albuminuria class transition used in each trial differed from the definitions...

  5. Developing a pathway for high-value, patient-centered total joint arthroplasty.

    Science.gov (United States)

    Van Citters, Aricca D; Fahlman, Cheryl; Goldmann, Donald A; Lieberman, Jay R; Koenig, Karl M; DiGioia, Anthony M; O'Donnell, Beth; Martin, John; Federico, Frank A; Bankowitz, Richard A; Nelson, Eugene C; Bozic, Kevin J

    2014-05-01

    Total joint arthroplasty (TJA) is one of the most widely performed elective procedures; however, there are wide variations in cost and quality among facilities where the procedure is performed. The purposes of this study were to (1) develop a generalizable clinical care pathway for primary TJA using inputs from clinical, academic, and patient stakeholders; and (2) identify system- and patient-level processes to provide safe, effective, efficient, and patient-centered care for patients undergoing TJA. We used a combination of quantitative and qualitative methods to design a care pathway that spans 14 months beginning with the presurgical office visit and concluding 12 months after discharge. We derived care suggestions from interviews with 16 hospitals selected based on readmission rates, cost, and quality (n = 10) and author opinion (n = 6). A 32-member multistakeholder panel refined the pathway during a 1-day workshop. Participants were selected based on leadership in orthopaedic (n = 4) and anesthesia (n = 1) specialty societies; involvement in organizations specializing in safety and high reliability care (n = 3), lean production/consumption of care (n = 3), and patient experience of care (n = 3); membership in an interdisciplinary care team of a hospital selected for interviewing (n = 8); recent receipt of a TJA (n = 1); and participation in the pathway development team (n = 9). The care pathway includes 40 suggested processes to improve care, 37 techniques to reduce waste, and 55 techniques to improve communication. Central themes include standardization and process improvement, interdisciplinary communication and collaboration, and patient/family engagement and education. Selected recommendations include standardizing care protocols and staff roles; aligning information flow with patient and process flow; identifying a role accountable for care delivery and communication; managing patient expectations; and stratifying patients into the most appropriate care

  6. Therapeutic Potential of Thymoquinone in Glioblastoma Treatment: Targeting Major Gliomagenesis Signaling Pathways

    Directory of Open Access Journals (Sweden)

    Fabliha Ahmed Chowdhury

    2018-01-01

    Full Text Available Glioblastoma multiforme (GBM is one of the most devastating brain tumors with median survival of one year and presents unique challenges to therapy because of its aggressive behavior. Current treatment strategy involves surgery, radiotherapy, immunotherapy, and adjuvant chemotherapy even though optimal management requires a multidisciplinary approach and knowledge of potential complications from both the disease and its treatment. Thymoquinone (TQ, the main bioactive component of Nigella sativa L., has exhibited anticancer effects in numerous preclinical studies. Due to its multitargeting nature, TQ interferes in a wide range of tumorigenic processes and counteract carcinogenesis, malignant growth, invasion, migration, and angiogenesis. TQ can specifically sensitize tumor cells towards conventional cancer treatments and minimize therapy-associated toxic effects in normal cells. Its potential to enter brain via nasal pathway due to volatile nature of TQ adds another advantage in overcoming blood-brain barrier. In this review, we summarized the potential role of TQ in different signaling pathways in GBM that have undergone treatment with standard therapeutic modalities or with TQ. Altogether, we suggest further comprehensive evaluation of TQ in preclinical and clinical level to delineate its implied utility as novel therapeutics to combat the challenges for the treatment of GBM.

  7. Implementation of a clinical pathway for emergency department out-patient management of deep vein thrombosis.

    LENUS (Irish Health Repository)

    Kidney, R

    2010-09-01

    There is good evidence demonstrating that outpatient management of deep venous thrombosis (DVT) is feasible and safe. However, few emergency departments in Ireland have implemented care pathways for outpatient management of DVT. The aim of this study was to examine the safety and efficacy of implementing an Emergency Department (ED)- care pathway for outpatient management of patients with DVT. A retrospective observational study of this care pathway introduced at our institution was performed. The primary outcome measure was the number of hospital admissions avoided by using the care pathway. Two hundred and eighty-four patients presenting to the ED with suspected lower limb DVT, were managed using the care pathway over a 6 month period. Forty-nine patients (17%) had a DVT diagnosed. Thirty-nine patients (81%) were suitable for outpatient DVT management. Ten patients (19%) were admitted to hospital. At 3 months there were no reported cases of the following complications: missed DVT, pulmonary embolism or death.

  8. Building Data-Driven Pathways From Routinely Collected Hospital Data: A Case Study on Prostate Cancer

    Science.gov (United States)

    Clark, Jeremy; Cooper, Colin S; Mills, Robert; Rayward-Smith, Victor J; de la Iglesia, Beatriz

    2015-01-01

    Background Routinely collected data in hospitals is complex, typically heterogeneous, and scattered across multiple Hospital Information Systems (HIS). This big data, created as a byproduct of health care activities, has the potential to provide a better understanding of diseases, unearth hidden patterns, and improve services and cost. The extent and uses of such data rely on its quality, which is not consistently checked, nor fully understood. Nevertheless, using routine data for the construction of data-driven clinical pathways, describing processes and trends, is a key topic receiving increasing attention in the literature. Traditional algorithms do not cope well with unstructured processes or data, and do not produce clinically meaningful visualizations. Supporting systems that provide additional information, context, and quality assurance inspection are needed. Objective The objective of the study is to explore how routine hospital data can be used to develop data-driven pathways that describe the journeys that patients take through care, and their potential uses in biomedical research; it proposes a framework for the construction, quality assessment, and visualization of patient pathways for clinical studies and decision support using a case study on prostate cancer. Methods Data pertaining to prostate cancer patients were extracted from a large UK hospital from eight different HIS, validated, and complemented with information from the local cancer registry. Data-driven pathways were built for each of the 1904 patients and an expert knowledge base, containing rules on the prostate cancer biomarker, was used to assess the completeness and utility of the pathways for a specific clinical study. Software components were built to provide meaningful visualizations for the constructed pathways. Results The proposed framework and pathway formalism enable the summarization, visualization, and querying of complex patient-centric clinical information, as well as the

  9. Optimizing participation of children with autism spectrum disorder experiencing sensory challenges: a clinical reasoning framework.

    Science.gov (United States)

    Ashburner, Jill K; Rodger, Sylvia A; Ziviani, Jenny M; Hinder, Elizabeth A

    2014-02-01

    Remedial sensory interventions currently lack supportive evidence and can be challenging to implement for families and clinicians. It may be timely to shift the focus to optimizing participation of children with autism spectrum disorders (ASD) through accommodation and self-regulation of their sensory differences. A framework to guide practitioners in selecting strategies is proposed based on clinical reasoning considerations, including (a) research evidence, (b) client- and family-centredness, (c) practice contexts, (d) occupation-centredness, and (e) risks. Information-sharing with families and coaching constitute the basis for intervention. Specific strategies are identified where sensory aversions or seeking behaviours, challenges with modulation of arousal, or sensory-related behaviours interfere with participation. Self-regulatory strategies are advocated. The application of universal design principles to shared environments is also recommended. The implications of this framework for future research, education, and practice are discussed. The clinical utility of the framework now needs to be tested.

  10. Disposition pathways and pharmacokinetics of herbal medicines in humans.

    Science.gov (United States)

    He, S-M; Li, C G; Liu, J-P; Chan, E; Duan, W; Zhou, S-F

    2010-01-01

    full understanding of their pharmacokinetic profiles. To optimize the use of herbal remedies, further clinical studies to explore their biological fate including the disposition pathways and kinetics in the human body are certainly needed.

  11. Optimizing supercritical carbon dioxide in the inactivation of bacteria in clinical solid waste by using response surface methodology

    International Nuclear Information System (INIS)

    Hossain, Md. Sohrab; Nik Ab Rahman, Nik Norulaini; Balakrishnan, Venugopal; Alkarkhi, Abbas F.M.; Ahmad Rajion, Zainul; Ab Kadir, Mohd Omar

    2015-01-01

    Highlights: • Supercritical carbon dioxide sterilization of clinical solid waste. • Inactivation of bacteria in clinical solid waste using supercritical carbon dioxide. • Reduction of the hazardous exposure of clinical solid waste. • Optimization of the supercritical carbon dioxide experimental conditions. - Abstract: Clinical solid waste (CSW) poses a challenge to health care facilities because of the presence of pathogenic microorganisms, leading to concerns in the effective sterilization of the CSW for safe handling and elimination of infectious disease transmission. In the present study, supercritical carbon dioxide (SC-CO 2 ) was applied to inactivate gram-positive Staphylococcus aureus, Enterococcus faecalis, Bacillus subtilis, and gram-negative Escherichia coli in CSW. The effects of SC-CO 2 sterilization parameters such as pressure, temperature, and time were investigated and optimized by response surface methodology (RSM). Results showed that the data were adequately fitted into the second-order polynomial model. The linear quadratic terms and interaction between pressure and temperature had significant effects on the inactivation of S. aureus, E. coli, E. faecalis, and B. subtilis in CSW. Optimum conditions for the complete inactivation of bacteria within the experimental range of the studied variables were 20 MPa, 60 °C, and 60 min. The SC-CO 2 -treated bacterial cells, observed under a scanning electron microscope, showed morphological changes, including cell breakage and dislodged cell walls, which could have caused the inactivation. This espouses the inference that SC-CO 2 exerts strong inactivating effects on the bacteria present in CSW, and has the potential to be used in CSW management for the safe handling and recycling-reuse of CSW materials

  12. Optimizing supercritical carbon dioxide in the inactivation of bacteria in clinical solid waste by using response surface methodology

    Energy Technology Data Exchange (ETDEWEB)

    Hossain, Md. Sohrab [Department of Environmental Technology, School of Industrial Technology, Universiti Sains Malaysia, 11800 Penang (Malaysia); Nik Ab Rahman, Nik Norulaini [School of Distance Education, Universiti Sains Malaysia, 11800 Penang (Malaysia); Balakrishnan, Venugopal [Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang (Malaysia); Alkarkhi, Abbas F.M. [Department of Environmental Technology, School of Industrial Technology, Universiti Sains Malaysia, 11800 Penang (Malaysia); Ahmad Rajion, Zainul [School of Dental Science, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan (Malaysia); Ab Kadir, Mohd Omar, E-mail: akmomar@usm.my [Department of Environmental Technology, School of Industrial Technology, Universiti Sains Malaysia, 11800 Penang (Malaysia)

    2015-04-15

    Highlights: • Supercritical carbon dioxide sterilization of clinical solid waste. • Inactivation of bacteria in clinical solid waste using supercritical carbon dioxide. • Reduction of the hazardous exposure of clinical solid waste. • Optimization of the supercritical carbon dioxide experimental conditions. - Abstract: Clinical solid waste (CSW) poses a challenge to health care facilities because of the presence of pathogenic microorganisms, leading to concerns in the effective sterilization of the CSW for safe handling and elimination of infectious disease transmission. In the present study, supercritical carbon dioxide (SC-CO{sub 2}) was applied to inactivate gram-positive Staphylococcus aureus, Enterococcus faecalis, Bacillus subtilis, and gram-negative Escherichia coli in CSW. The effects of SC-CO{sub 2} sterilization parameters such as pressure, temperature, and time were investigated and optimized by response surface methodology (RSM). Results showed that the data were adequately fitted into the second-order polynomial model. The linear quadratic terms and interaction between pressure and temperature had significant effects on the inactivation of S. aureus, E. coli, E. faecalis, and B. subtilis in CSW. Optimum conditions for the complete inactivation of bacteria within the experimental range of the studied variables were 20 MPa, 60 °C, and 60 min. The SC-CO{sub 2}-treated bacterial cells, observed under a scanning electron microscope, showed morphological changes, including cell breakage and dislodged cell walls, which could have caused the inactivation. This espouses the inference that SC-CO{sub 2} exerts strong inactivating effects on the bacteria present in CSW, and has the potential to be used in CSW management for the safe handling and recycling-reuse of CSW materials.

  13. Efficacy and efficiency of a lean cataract pathway: a comparative study.

    Science.gov (United States)

    van Vliet, Ellen Joan; Sermeus, Walter; van Gaalen, Claudia M; Sol, Johannes C A; Vissers, Jan M H

    2010-12-01

    The demand for cataract surgery is rising, calling for pathways that have good access and are cost-effective. Lean thinking is a management strategy, aimed at improving quality while reducing costs. Lean production processes are designed to identify gaps between expected and actual performance. To analyse the efficacy and efficiency of a lean cataract pathway. Lean care delivered to a prospective cohort (616 cataract patients) was compared (1) with traditional care delivered to a historical cohort (591 cataract patients) and (2) with expected lean care in the prospective cohort. To evaluate efficacy, the authors analysed how many patients received care that adhered to the lean pathway's specifications. To evaluate efficiency, the authors analysed how often patients visited the hospital and how many additional patients could access the pathway. In the lean pathway, patient visits decreased by 23%, and access to the cataract pathway increased with 42%. A 40% decrease in patient visits and a 76% increase in access could have been realised if healthcare staff would have adhered to the lean pathway's specifications. Lean pathways can realise large improvements, and still have a significant gap between expected and actual care delivery. The challenge for healthcare teams is not to improve care delivery by using lean pathways as opposed to using traditional pathways, but to strive for optimal performance by consistently adhering to the specifications of the lean pathway.

  14. The Stice model of overeating: Tests in clinical and non-clinical samples

    NARCIS (Netherlands)

    Strien, T. van; Engels, R.C.M.E.; Leeuwe, J.F.J. van; Snoek, H.M.

    2005-01-01

    The present study tested the dual pathway model of Stice [Stice, E (1994). A review of the evidence for a sociocultural model of bulimia nervosa and an exploration of the mechanisms of action. Clinical Psychology Review, 14, 633-661 and Stice, E. (2001). A prospective test of the dual-pathway model

  15. Electronic SSKIN pathway: reducing device-related pressure ulcers.

    Science.gov (United States)

    Campbell, Natalie

    2016-08-11

    This article describes how an interprofessional project in a London NHS Foundation Trust was undertaken to develop an intranet-based medical device-related pressure ulcer prevention and management pathway for clinical staff working across an adult critical care directorate, where life-threatening events require interventions using medical devices. The aim of this project was to improve working policies and processes to define key prevention strategies and provide clinicians with a clear, standardised approach to risk and skin assessment, equipment use, documentation and reporting clinical data using the Trust's CareVue (electronic medical records), Datix (incident reporting and risk-management tool) and eTRACE (online clinical protocol ordering) systems. The process included the development, trial and local implementation of the pathway using collaborative teamwork and the SSKIN care bundle tool. The experience of identifying issues, overcoming challenges, defining best practice and cascading SSKIN awareness training is shared.

  16. Optimizing therapeutic efficacy of chemopreventive agents: A critical review of delivery strategies in oral cancer chemoprevention clinical trials

    OpenAIRE

    Andrew S Holpuch; Kashappa-Goud H Desai; Steven P Schwendeman; Susan R Mallery

    2011-01-01

    Due to its characterized progression from recognized premalignant oral epithelial changes (i.e., oral epithelial dysplasia) to invasive cancer, oral squamous cell carcinoma represents an optimal disease for chemopreventive intervention prior to malignant transformation. The primary goal of oral cancer chemoprevention is to reverse, suppress, or inhibit the progression of premalignant lesions to cancer. Over the last several decades, numerous oral cancer chemoprevention clinical trials have as...

  17. Which factors are important for the successful development and implementation of clinical pathways? A qualitative study.

    Science.gov (United States)

    De Allegri, Manuela; Schwarzbach, Matthias; Loerbroks, Adrian; Ronellenfitsch, Ulrich

    2011-03-01

    Clinical pathways (CPs) are detailed longitudinal care plans delineating measures to be conducted during a patient's treatment. Although positive effects on resource consumption and quality of care have been shown, CPs are still underutilised in many clinical settings because their development and implementation are difficult. Evidence underpinning successful development and implementation is sparse. The authors conducted semistructured face-to-face interviews with key staff members involved in the design and implementation of CPs in a large surgery department. Interviewees were asked to provide opinions on various issues, which were previously identified as potentially important in CP development and implementation. The transcribed text was read and coded independently by two researchers. Respondents highlighted the importance of a multidisciplinary participatory approach for CP design and implementation. There was a strong initial fear of losing individual freedom of treatment, which subsided after people worked with CPs in clinical everyday life. It was appreciated that the project originated from people at different levels of the department's hierarchy. Likewise, it was felt that CP implementation granted more autonomy to lower-level staff. The structured qualitative approach of this study provides information on what issues are considered important by staff members for CP design and implementation. Whereas some concepts such as the importance of a multidisciplinary approach or continuous feedback of results are known from theories, others such as strengthening the authority especially of lower-level health professionals through CPs have not been described so far. Many of the findings point towards strong interactions between factors important for CP implementation and a department's organisational structure.

  18. Evaluating Dopamine Reward Pathway in ADHD; clinical implications

    Energy Technology Data Exchange (ETDEWEB)

    Volkow, N.D.; Wang, G.; Volkow, N.D.; Wang, G.-J.; Kollins, S.H., Wigal, t.L.; Newcorn, J.H.; Telang, F.; Fowler, J.S.; Zhu, W.; Logan, J.; Ma, Y.; Pradhan, K.; Wong, C.T.; Swanson, J.M.

    2009-09-09

    Attention-deficit/hyperactivity disorder (ADHD) - characterized by symptoms of inattention and hyperactivity-impulsivity - is the most prevalent childhood psychiatric disorder that frequently persists into adulthood, and there is increasing evidence of reward-motivation deficits in this disorder. To evaluate biological bases that might underlie a reward/motivation deficit by imaging key components of the brain dopamine reward pathway (mesoaccumbens). We used positron emission tomography to measure dopamine synaptic markers (transporters and D{sub 2}/D{sub 3} receptors) in 53 nonmedicated adults with ADHD and 44 healthy controls between 2001-2009 at Brookhaven National Laboratory. We measured specific binding of positron emission tomographic radioligands for dopamine transporters (DAT) using [{sup 11}C]cocaine and for D{sub 2}/D{sub 3} receptors using [{sup 11}C]raclopride, quantified as binding potential (distribution volume ratio -1). For both ligands, statistical parametric mapping showed that specific binding was lower in ADHD than in controls (threshold for significance set at P < .005) in regions of the dopamine reward pathway in the left side of the brain. Region-of-interest analyses corroborated these findings. The mean (95% confidence interval [CI] of mean difference) for DAT in the nucleus accumbens for controls was 0.71 vs 0.63 for those with ADHD (95% CI, 0.03-0.13, P = .004) and in the midbrain for controls was 0.16 vs 0.09 for those with ADHD (95% CI, 0.03-0.12; P {le} .001); for D{sub 2}/D{sub 3} receptors, the mean accumbens for controls was 2.85 vs 2.68 for those with ADHD (95% CI, 0.06-0.30, P = .004); and in the midbrain, it was for controls 0.28 vs 0.18 for those with ADHD (95% CI, 0.02-0.17, P = .01). The analysis also corroborated differences in the left caudate: the mean DAT for controls was 0.66 vs 0.53 for those with ADHD (95% CI, 0.04-0.22; P = .003) and the mean D{sub 2}/D{sub 3} for controls was 2.80 vs 2.47 for those with ADHD (95% CI, 0

  19. Controlled release of optimized electroporation enhances the transdermal efficiency of sinomenine hydrochloride for treating arthritis in vitro and in clinic

    Science.gov (United States)

    Feng, Shun; Zhu, Lijun; Huang, Zhisheng; Wang, Haojia; Li, Hong; Zhou, Hua; Lu, Linlin; Wang, Ying; Liu, Zhongqiu; Liu, Liang

    2017-01-01

    Sinomenine hydrochloride (SH) is an ideal drug for the treatment of rheumatoid arthritis and osteoarthritis. However, high plasma concentration of systemically administered SH can release histamine, which can cause rash and gastrointestinal side effects. Topical delivery can increase SH concentration in the synovial fluid without high plasma level, thus minimizing systemic side effects. However, passive diffusion of SH was found to be inefficient because of the presence of the stratum corneum layer. Therefore, an effective method is required to compensate for the low efficiency of SH passive diffusion. In this study, transdermal experiments in vitro and clinical tests were utilized to explore the optimized parameters for electroporation of topical delivery for SH. Fluorescence experiment and hematoxylin and eosin staining analysis were performed to reveal the mechanism by which electroporation promoted permeation. In vitro, optimized electroporation parameters were 3 KHz, exponential waveform, and intensity 10. Using these parameters, transdermal permeation of SH was increased by 1.9–10.1 fold in mice skin and by 1.6–47.1 fold in miniature pig skin compared with passive diffusion. After the electroporation stimulation, the intercellular intervals and epidermal cracks in the skin increased. In clinical tests, SH concentration in synovial fluid was 20.84 ng/mL after treatment with electroporation. Therefore, electroporation with optimized parameters could significantly enhance transdermal permeation of SH. The mechanism by which electroporation promoted permeation was that the electronic pulses made the skin structure looser. To summarize, electroporation may be an effective complementary method for transdermal permeation of SH. The controlled release of electroporation may be a promising clinical method for transdermal drug administration. PMID:28670109

  20. Curation and Computational Design of Bioenergy-Related Metabolic Pathways

    Energy Technology Data Exchange (ETDEWEB)

    Karp, Peter D. [SRI International, Menlo Park, CA (United States)

    2014-09-12

    . The pathways were to be generated using metabolic reactions from a reference database (DB). 5: Develop computational tools for ranking the pathways generated in objective (4) according to their optimality. The ranking criteria include stoichiometric yield, the number and cost of additional inputs and the cofactor compounds required by the pathway, pathway length, and pathway energetics. 6: Develop tools for visualizing generated pathways to facilitate the evaluation of a large space of generated pathways.

  1. Interaction of Adverse Disease Related Pathways in Hypertrophic Cardiomyopathy.

    Science.gov (United States)

    Rowin, Ethan J; Maron, Martin S; Chan, Raymond H; Hausvater, Anais; Wang, Wendy; Rastegar, Hassan; Maron, Barry J

    2017-12-15

    Hypertrophic cardiomyopathy (HC) has been characterized as a generally progressive genetic heart disease, creating an ominous perspective for patients and managing cardiologists. We explored the HC disease burden and interaction of adverse clinical pathways to clarify patient expectations over long time periods in the contemporary therapeutic era. We studied 1,000 consecutive HC patients (52 ± 17 years) at Tufts Medical Center, followed 9.3 ± 8 years from diagnosis, employing a novel disease pathway model: 46% experienced a benign course free of adverse pathways, but 42% of patients progressed along 1 major pathway, most commonly refractory heart failure to New York Heart Association class III or IV requiring surgical myectomy (or alcohol ablation) or heart transplant; repetitive or permanent atrial fibrillation; and least commonly arrhythmic sudden death events. Eleven percent experienced 2 of these therapeutic end points at different times in their clinical course, most frequently the combination of advanced heart failure and atrial fibrillation, whereas only 1% incurred all 3 pathways. Freedom of progression from 1 to 2 disease pathways, or from 2 to 3 was 80% and 93% at 5 years, respectively. Annual HC-related mortality did not differ according to the number of pathways: 1 (0.8%), 2 (0.8%), or 3 (2.4%) (p = 0.56), and 93% of patients were in New York Heart Association classes I or II at follow-up. In conclusion, it is uncommon for HC patients to experience multiple adverse (but treatable) disease pathways, underscoring the principle that HC is not a uniformly progressive disease. These observations provide a measure of clarity and/or reassurance to patients regarding the true long-term disease burden of HC. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Effects of introducing heterologous pathways on microbial metabolism with respect to metabolic optimality

    DEFF Research Database (Denmark)

    Kim, Hyun Uk; Kim, Byoungjin; Seung, Do Young

    2014-01-01

    reactions are more frequently introduced into various microbial hosts. The genome-scale metabolic simulations of Escherichia coli strains engineered to produce 1,4-butanediol, 1,3-propanediol, and amorphadiene suggest that microbial metabolism shows much different responses to the introduced heterologous...... reactions in a strain-specific manner than typical gene knockouts in terms of the energetic status (e.g., ATP and biomass generation) and chemical production capacity. The 1,4-butanediol and 1,3-propanediol producers showed greater metabolic optimality than the wild-type strains and gene knockout mutants...... for the energetic status, while the amorphadiene producer was metabolically less optimal. For the optimal chemical production capacity, additional gene knockouts were most effective for the strain producing 1,3-propanediol, but not for the one producing 1,4-butanediol. These observations suggest that strains having...

  3. The physics of an optimal basketball free throw

    OpenAIRE

    Barzykina, Irina

    2017-01-01

    A physical model is developed, which suggests a pathway to determining the optimal release conditions for a basketball free throw. Theoretical framework is supported by Monte Carlo simulations and a series of free throws performed and analysed at Southbank International School. The model defines a smile-shaped success region in angle-velocity space where a free throw will score. A formula for the minimum throwing angle is derived analytically. The optimal throwing conditions are determined nu...

  4. Digital mammography--DQE versus optimized image quality in clinical environment: an on site study

    Science.gov (United States)

    Oberhofer, Nadia; Fracchetti, Alessandro; Springeth, Margareth; Moroder, Ehrenfried

    2010-04-01

    The intrinsic quality of the detection system of 7 different digital mammography units (5 direct radiography DR; 2 computed radiography CR), expressed by DQE, has been compared with their image quality/dose performances in clinical use. DQE measurements followed IEC 62220-1-2 using a tungsten test object for MTF determination. For image quality assessment two different methods have been applied: 1) measurement of contrast to noise ratio (CNR) according to the European guidelines and 2) contrast-detail (CD) evaluation. The latter was carried out with the phantom CDMAM ver. 3.4 and the commercial software CDMAM Analyser ver. 1.1 (both Artinis) for automated image analysis. The overall image quality index IQFinv proposed by the software has been validated. Correspondence between the two methods has been shown figuring out a linear correlation between CNR and IQFinv. All systems were optimized with respect to image quality and average glandular dose (AGD) within the constraints of automatic exposure control (AEC). For each equipment, a good image quality level was defined by means of CD analysis, and the corresponding CNR value considered as target value. The goal was to achieve for different PMMA-phantom thicknesses constant image quality, that means the CNR target value, at minimum dose. All DR systems exhibited higher DQE and significantly better image quality compared to CR systems. Generally switching, where available, to a target/filter combination with an x-ray spectrum of higher mean energy permitted dose savings at equal image quality. However, several systems did not allow to modify the AEC in order to apply optimal radiographic technique in clinical use. The best ratio image quality/dose was achieved by a unit with a-Se detector and W anode only recently available on the market.

  5. COPD care delivery pathways in five European Union countries: mapping and health care professionals’ perceptions

    Directory of Open Access Journals (Sweden)

    Kayyali R

    2016-11-01

    Full Text Available Reem Kayyali,1 Bassel Odeh,1 Inéz Frerichs,2 Nikki Davies,3 Eleni Perantoni,4 Shona D’arcy,5 Anouk W Vaes,6 John Chang,3 Martijn A Spruit,6 Brenda Deering,7 Nada Philip,1 Roshan Siva,3 Evangelos Kaimakamis,8 Ioanna Chouvarda,8 Barbara Pierscionek,1 Norbert Weiler,2 Emiel FM Wouters,6 Andreas Raptopoulos,9 Shereen Nabhani-Gebara1 1Faculty of Science, Engineering and Computing, Kingston University, Kingston-Upon-Thames, UK; 2Department of Anaesthesiology and Intensive Care Medicine, University Medical Centre Schleswig-Holstein, Kiel, Germany; 3Chest Clinic and Research and Development, Croydon University Hospital, Croydon, UK; 4Pulmonary Clinic, AHEPA University Hospital, Thessaloniki, Greece; 5Department of Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland; 6Research and Education, CIRO – Centre of Expertise for Chronic Organ Failure, Horn, the Netherlands; 7COPD Outreach, Beaumont Hospital, Dublin, Ireland; 8Medical School, Aristotle University, Thessaloniki, 9Research and Development, Exodus Information Technology SA, Athens, Greece Background: COPD is among the leading causes of chronic morbidity and mortality in the European Union with an estimated annual economic burden of €25.1 billion. Various care pathways for COPD exist across Europe leading to different responses to similar problems. Determining these differences and the similarities may improve health and the functioning of health services.Objective: The aim of this study was to compare COPD patients’ care pathway in five European Union countries including England, Ireland, the Netherlands, Greece, and Germany and to explore health care professionals’ (HCPs perceptions about the current pathways.Methods: HCPs were interviewed in two stages using a qualitative, semistructured email interview and a face-to-face semistructured interview.Results: Lack of communication among different health care providers managing COPD and comorbidities was a common feature of the

  6. Pathways to youth homelessness.

    Science.gov (United States)

    Martijn, Claudine; Sharpe, Louise

    2006-01-01

    Research documents high levels of psychopathology among homeless youth. Most research, however, has not distinguished between disorders that are present prior to homelessness and those that develop following homelessness. Hence whether psychological disorders are the cause or consequence of homelessness has not been established. The aim of this study is to investigate causal pathways to homelessness amongst currently homeless youth in Australia. The study uses a quasi-qualitative methodology to generate hypotheses for larger-scale research. High rates of psychological disorders were confirmed in the sample 35 homeless youth aged 14-25. The rates of psychological disorders at the point of homelessness were greater than in normative samples, but the rates of clinical disorder increased further once homeless. Further in-depth analyses were conducted to identify the temporal sequence for each individual with a view to establishing a set of causal pathways to homelessness and trajectories following homelessness that characterised the people in the sample. Five pathways to homelessness and five trajectories following homelessness were identified that accounted for the entire sample. Each pathway constituted a series of interactions between different factors similar to that described by Craig and Hodson (1998. Psychological Medicine, 28, 1379-1388) as "complex subsidiary pathways". The major findings were that (1) trauma is a common experience amongst homeless youth prior to homelessness and figured in the causal pathways to homelessness for over half of the sample; (2) once homeless, for the majority of youth there is an increase in the number of psychological diagnoses including drug and alcohol diagnoses; and (3) crime did not precede homelessness for all but one youth; however, following homelessness, involvement in criminal activity was common and became a distinguishing factor amongst youth. The implications of these findings for future research and service

  7. Molecular pathways and therapeutic targets in lung cancer

    Science.gov (United States)

    Shtivelman, Emma; Hensing, Thomas; Simon, George R.; Dennis, Phillip A.; Otterson, Gregory A.; Bueno, Raphael; Salgia, Ravi

    2014-01-01

    Lung cancer is still the leading cause of cancer death worldwide. Both histologically and molecularly lung cancer is heterogeneous. This review summarizes the current knowledge of the pathways involved in the various types of lung cancer with an emphasis on the clinical implications of the increasing number of actionable molecular targets. It describes the major pathways and molecular alterations implicated in the development and progression of non-small cell lung cancer (adenocarcinoma and squamous cancer), and of small cell carcinoma, emphasizing the molecular alterations comprising the specific blueprints in each group. The approved and investigational targeted therapies as well as the immune therapies, and clinical trials exploring the variety of targeted approaches to treatment of lung cancer are the main focus of this review. PMID:24722523

  8. cGAS/STING Pathway in Cancer: Jekyll and Hyde Story of Cancer Immune Response.

    Science.gov (United States)

    Bose, Debojit

    2017-11-18

    The last two decades have witnessed enormous growth in the field of cancer immunity. Mechanistic insights of cancer immunoediting have not only enhanced our understanding but also paved the way to target and/or harness the innate immune system to combat cancer, called cancer immunotherapy. Cyclic GMP-AMP synthase (cGAS)/Stimulator of interferon genes(STING) pathway has recently emerged as nodal player in cancer immunity and is currently being explored as potential therapeutic target. Although therapeutic activation of this pathway has shown promising anti-tumor effects in vivo, evidence also indicates the role of this pathway in inflammation mediated carcinogenesis. This review highlights our current understanding of cGAS/STING pathway in cancer, its therapeutic targeting and potential alternate approaches to target this pathway. Optimal therapeutic targeting and artificial tunability of this pathway still demand in depth understanding of cGAS/STING pathway regulation and homeostasis.

  9. cGAS/STING Pathway in Cancer: Jekyll and Hyde Story of Cancer Immune Response

    Directory of Open Access Journals (Sweden)

    Debojit Bose

    2017-11-01

    Full Text Available The last two decades have witnessed enormous growth in the field of cancer immunity. Mechanistic insights of cancer immunoediting have not only enhanced our understanding but also paved the way to target and/or harness the innate immune system to combat cancer, called cancer immunotherapy. Cyclic GMP-AMP synthase (cGAS/Stimulator of interferon genes(STING pathway has recently emerged as nodal player in cancer immunity and is currently being explored as potential therapeutic target. Although therapeutic activation of this pathway has shown promising anti-tumor effects in vivo, evidence also indicates the role of this pathway in inflammation mediated carcinogenesis. This review highlights our current understanding of cGAS/STING pathway in cancer, its therapeutic targeting and potential alternate approaches to target this pathway. Optimal therapeutic targeting and artificial tunability of this pathway still demand in depth understanding of cGAS/STING pathway regulation and homeostasis.

  10. Fragile X mental retardation protein participates in non-coding RNA pathways.

    Science.gov (United States)

    Li, En-Hui; Zhao, Xin; Zhang, Ce; Liu, Wei

    2018-02-20

    Fragile X syndrome is one of the most common forms of inherited intellectual disability. It is caused by mutations of the Fragile X mental retardation 1(FMR1) gene, resulting in either the loss or abnormal expression of the Fragile X mental retardation protein (FMRP). Recent research showed that FMRP participates in non-coding RNA pathways and plays various important roles in physiology, thereby extending our knowledge of the pathogenesis of the Fragile X syndrome. Initial studies showed that the Drosophila FMRP participates in siRNA and miRNA pathways by interacting with Dicer, Ago1 and Ago2, involved in neural activity and the fate determination of the germline stem cells. Subsequent studies showed that the Drosophila FMRP participates in piRNA pathway by interacting with Aub, Ago1 and Piwi in the maintenance of normal chromatin structures and genomic stability. More recent studies showed that FMRP is associated with lncRNA pathway, suggesting a potential role for the involvement in the clinical manifestations. In this review, we summarize the novel findings and explore the relationship between FMRP and non-coding RNA pathways, particularly the piRNA pathway, thereby providing critical insights on the molecular pathogenesis of Fragile X syndrome, and potential translational applications in clinical management of the disease.

  11. The development of a comprehensive multidisciplinary care pathway for patients with a hip fracture: design and results of a clinical trial.

    Science.gov (United States)

    Flikweert, Elvira R; Izaks, Gerbrand J; Knobben, Bas A S; Stevens, Martin; Wendt, Klaus

    2014-05-30

    Hip fractures frequently occur in older persons and severely decrease life expectancy and independence. Several care pathways have been developed to lower the risk of negative outcomes but most pathways are limited to only one aspect of care. The aim of this study was therefore to develop a comprehensive care pathway for older persons with a hip fracture and to conduct a preliminary analysis of its effect. A comprehensive multidisciplinary care pathway for patients aged 60 years or older with a hip fracture was developed by a multidisciplinary team. The new care pathway was evaluated in a clinical trial with historical controls. The data of the intervention group were collected prospectively. The intervention group included all patients with a hip fracture who were admitted to University Medical Center Groningen between 1 July 2009 and 1 July 2011. The data of the control group were collected retrospectively. The control group comprised all patients with a hip fracture who were admitted between 1 January 2006 and 1 January 2008. The groups were compared with the independent sample t-test, the Mann-Whitney U-test or the Chi-squared test (Phi test). The effect of the intervention on fasting time and length of stay was adjusted by linear regression analysis for differences between the intervention and control group. The intervention group included 256 persons (women, 68%; mean age (SD), 78 (9) years) and the control group 145 persons (women, 72%; mean age (SD), 80 (10) years). Median preoperative fasting time and median length of hospital stay were significantly lower in the intervention group: 9 vs. 17 hours (p < 0.001), and 7 vs. 11 days (p < 0.001), respectively. A similar result was found after adjustment for age, gender, living condition and American Society of Anesthesiologists (ASA) classification. In-hospital mortality was also lower in the intervention group: 2% vs. 6% (p < 0.05). There were no statistically significant differences in other

  12. S.E. Mitchell Vascular Anomalies Flow Chart (SEMVAFC): A visual pathway combining clinical and imaging findings for classification of soft-tissue vascular anomalies

    International Nuclear Information System (INIS)

    Tekes, A.; Koshy, J.; Kalayci, T.O.; Puttgen, K.; Cohen, B.; Redett, R.; Mitchell, S.E.

    2014-01-01

    Classification of vascular anomalies (VAs) is challenging due to overlapping clinical symptoms, confusing terminology in the literature and unfamiliarity with this complex entity. It is important to recognize that VAs include two distinct entities, vascular tumours (VTs) and vascular malformations (VaMs). In this article, we describe SE Mitchell Vascular Anomalies Flow Chart (SEMVAFC), which arises from a multidisciplinary approach that incorporates clinical symptoms, physical examination and magnetic resonance imaging (MRI) findings to establish International Society for the Study of Vascular Anomalies (ISSVA)-based classification of the VAs. SEMVAFC provides a clear visual pathway for physicians to accurately diagnose Vas, which is important as treatment, management, and prognosis differ between VTs and VaMs

  13. Autoimmunity and autoinflammation: A systems view on signaling pathway dysregulation profiles.

    Directory of Open Access Journals (Sweden)

    Arsen Arakelyan

    Full Text Available Autoinflammatory and autoimmune disorders are characterized by aberrant changes in innate and adaptive immunity that may lead from an initial inflammatory state to an organ specific damage. These disorders possess heterogeneity in terms of affected organs and clinical phenotypes. However, despite the differences in etiology and phenotypic variations, they share genetic associations, treatment responses and clinical manifestations. The mechanisms involved in their initiation and development remain poorly understood, however the existence of some clear similarities between autoimmune and autoinflammatory disorders indicates variable degrees of interaction between immune-related mechanisms.Our study aims at contributing to a holistic, pathway-centered view on the inflammatory condition of autoimmune and autoinflammatory diseases. We have evaluated similarities and specificities of pathway activity changes in twelve autoimmune and autoinflammatory disorders by performing meta-analysis of publicly available gene expression datasets generated from peripheral blood mononuclear cells, using a bioinformatics pipeline that integrates Self Organizing Maps and Pathway Signal Flow algorithms along with KEGG pathway topologies.The results reveal that clinically divergent disease groups share common pathway perturbation profiles. We identified pathways, similarly perturbed in all the studied diseases, such as PI3K-Akt, Toll-like receptor, and NF-kappa B signaling, that serve as integrators of signals guiding immune cell polarization, migration, growth, survival and differentiation. Further, two clusters of diseases were identified based on specifically dysregulated pathways: one gathering mostly autoimmune and the other mainly autoinflammatory diseases. Cluster separation was driven not only by apparent involvement of pathways implicated in adaptive immunity in one case, and inflammation in the other, but also by processes not explicitly related to immune

  14. A Scholarly Pathway in Quality Improvement and Patient Safety.

    Science.gov (United States)

    Ferguson, Catherine C; Lamb, Geoffrey

    2015-10-01

    There are several challenges to teaching quality improvement (QI) and patient safety material to medical students, as successful programs should combine didactic and experiential teaching methods, integrate the material into the preclinical and clinical years, and tailor the material to the schools' existing curriculum. The authors describe the development, implementation, and assessment of the Quality Improvement and Patient Safety (QuIPS) Scholarly Pathway-a faculty-mentored, three-year experience for students interested in gaining exposure to QI and patient safety concepts at the Medical College of Wisconsin (MCW). The QuIPS pathway capitalized on the existing structure of scholarly pathways for MCW medical students, allowing QI and patient safety to be incorporated into the existing curriculum using didactic and experiential instruction and spanning preclinical and clinical education. Student reaction to the QuIPS pathway has been favorable. Preliminary data demonstrate that student knowledge as measured by the Quality Improvement Knowledge Assessment Tool significantly increased after the first year of implementation. A novel curriculum such as the QuIPS pathway provides an important opportunity to develop and test new assessment tools for curricula in systems-based practice and practice-based learning and improvement. The authors also hope that by bringing together local QI and patient safety experts and stakeholders during the curricular development process, they have laid the groundwork for the creation of a more pervasive curriculum that will reach all MCW students in the future. The model may be generalizable to other U.S. medical schools with scholarly pathways as well.

  15. Responses of Synechocystis sp. PCC 6803 to heterologous biosynthetic pathways

    DEFF Research Database (Denmark)

    Vavitsas, Konstantinos; Rue, Emil Østergaard; Stefánsdóttir, Lára Kristín

    2017-01-01

    BACKGROUND: There are an increasing number of studies regarding genetic manipulation of cyanobacteria to produce commercially interesting compounds. The majority of these works study the expression and optimization of a selected heterologous pathway, largely ignoring the wholeness and complexity...... different compounds, the cyanogenic glucoside dhurrin and the diterpenoid 13R-manoyl oxide in Synechocystis PCC 6803. We used genome-scale metabolic modelling to study fluxes in individual reactions and pathways, and we determined the concentrations of key metabolites, such as amino acids, carotenoids...

  16. Optimization of biotechnological systems through geometric programming

    Directory of Open Access Journals (Sweden)

    Torres Nestor V

    2007-09-01

    Full Text Available Abstract Background In the past, tasks of model based yield optimization in metabolic engineering were either approached with stoichiometric models or with structured nonlinear models such as S-systems or linear-logarithmic representations. These models stand out among most others, because they allow the optimization task to be converted into a linear program, for which efficient solution methods are widely available. For pathway models not in one of these formats, an Indirect Optimization Method (IOM was developed where the original model is sequentially represented as an S-system model, optimized in this format with linear programming methods, reinterpreted in the initial model form, and further optimized as necessary. Results A new method is proposed for this task. We show here that the model format of a Generalized Mass Action (GMA system may be optimized very efficiently with techniques of geometric programming. We briefly review the basics of GMA systems and of geometric programming, demonstrate how the latter may be applied to the former, and illustrate the combined method with a didactic problem and two examples based on models of real systems. The first is a relatively small yet representative model of the anaerobic fermentation pathway in S. cerevisiae, while the second describes the dynamics of the tryptophan operon in E. coli. Both models have previously been used for benchmarking purposes, thus facilitating comparisons with the proposed new method. In these comparisons, the geometric programming method was found to be equal or better than the earlier methods in terms of successful identification of optima and efficiency. Conclusion GMA systems are of importance, because they contain stoichiometric, mass action and S-systems as special cases, along with many other models. Furthermore, it was previously shown that algebraic equivalence transformations of variables are sufficient to convert virtually any types of dynamical models into

  17. PathwayAccess: CellDesigner plugins for pathway databases.

    Science.gov (United States)

    Van Hemert, John L; Dickerson, Julie A

    2010-09-15

    CellDesigner provides a user-friendly interface for graphical biochemical pathway description. Many pathway databases are not directly exportable to CellDesigner models. PathwayAccess is an extensible suite of CellDesigner plugins, which connect CellDesigner directly to pathway databases using respective Java application programming interfaces. The process is streamlined for creating new PathwayAccess plugins for specific pathway databases. Three PathwayAccess plugins, MetNetAccess, BioCycAccess and ReactomeAccess, directly connect CellDesigner to the pathway databases MetNetDB, BioCyc and Reactome. PathwayAccess plugins enable CellDesigner users to expose pathway data to analytical CellDesigner functions, curate their pathway databases and visually integrate pathway data from different databases using standard Systems Biology Markup Language and Systems Biology Graphical Notation. Implemented in Java, PathwayAccess plugins run with CellDesigner version 4.0.1 and were tested on Ubuntu Linux, Windows XP and 7, and MacOSX. Source code, binaries, documentation and video walkthroughs are freely available at http://vrac.iastate.edu/~jlv.

  18. Designing a Care Pathway Model - A Case Study of the Outpatient Total Hip Arthroplasty Care Pathway.

    Science.gov (United States)

    Oosterholt, Robin I; Simonse, Lianne Wl; Boess, Stella U; Vehmeijer, Stephan Bw

    2017-03-09

    Although the clinical attributes of total hip arthroplasty (THA) care pathways have been thoroughly researched, a detailed understanding of the equally important organisational attributes is still lacking. The aim of this article is to contribute with a model of the outpatient THA care pathway that depicts how the care team should be organised to enable patient discharge on the day of surgery. The outpatient THA care pathway enables patients to be discharged on the day of surgery, shortening the length of stay and intensifying the provision and organisation of care. We utilise visual care modelling to construct a visual design of the organisation of the care pathway. An embedded case study was conducted of the outpatient THA care pathway at a teaching hospital in the Netherlands. The data were collected using a visual care modelling toolkit in 16 semi-structured interviews. Problems and inefficiencies in the care pathway were identified and addressed in the iterative design process. The results are two visual models of the most critical phases of the outpatient THA care pathway: diagnosis & preparation (1) and mobilisation & discharge (4). The results show the care team composition, critical value exchanges, and sequence that enable patient discharge on the day of surgery. The design addressed existing problems and is an optimisation of the case hospital's pathway. The network of actors consists of the patient (1), radiologist (1), anaesthetist (1), nurse specialist (1), pharmacist (1), orthopaedic surgeon (1,4), physiotherapist (1,4), nurse (4), doctor (4) and patient application (1,4). The critical value exchanges include patient preparation (mental and practical), patient education, aligned care team, efficient sequence of value exchanges, early patient mobilisation, flexible availability of the physiotherapist, functional discharge criteria, joint decision making and availability of the care team.

  19. Mild-moderate TBI: clinical recommendations to optimize neurobehavioral functioning, learning, and adaptation.

    Science.gov (United States)

    Chen, Anthony J-W; Loya, Fred

    2014-11-01

    Traumatic brain injury (TBI) can result in functional deficits that persist long after acute injury. The authors present a case study of an individual who experienced some of the most common debilitating problems that characterize the chronic phase of mild-to-moderate TBI-difficulties with neurobehavioral functions that manifest via complaints of distractibility, poor memory, disorganization, poor frustration tolerance, and feeling easily overwhelmed. They present a rational strategy for management that addresses important domain-general targets likely to have far-ranging benefits. This integrated, longitudinal, and multifaceted approach first addresses approachable targets and provides an important foundation to enhance the success of other, more specific interventions requiring specialty intervention. The overall approach places an emphasis on accomplishing two major categories of clinical objectives: optimizing current functioning and enhancing learning and adaptation to support improvement of functioning in the long-term for individuals living with brain injury. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  20. Microbial chemical factories: recent advances in pathway engineering for synthesis of value added chemicals.

    Science.gov (United States)

    Dhamankar, Himanshu; Prather, Kristala L J

    2011-08-01

    The dwindling nature of petroleum and other fossil reserves has provided impetus towards microbial synthesis of fuels and value added chemicals from biomass-derived sugars as a renewable resource. Microbes have naturally evolved enzymes and pathways that can convert biomass into hundreds of unique chemical structures, a property that can be effectively exploited for their engineering into Microbial Chemical Factories (MCFs). De novo pathway engineering facilitates expansion of the repertoire of microbially synthesized compounds beyond natural products. In this review, we visit some recent successes in such novel pathway engineering and optimization, with particular emphasis on the selection and engineering of pathway enzymes and balancing of their accessory cofactors. Copyright © 2011 Elsevier Ltd. All rights reserved.

  1. Early drug development of inhibitors of the insulin-like growth factor-I receptor pathway: lessons from the first clinical trials.

    Science.gov (United States)

    Rodon, Jordi; DeSantos, Victoria; Ferry, Robert Jean; Kurzrock, Razelle

    2008-09-01

    The insulin-like growth factor-I receptor (IGF-IR) was first cloned in 1986. Since then, intense work has defined classic phosphorelays activated via the IGF-IR, which regulate cell proliferation, apoptosis, motility, and fate. The understanding of the roles of hormones in cancer and the growth hormone-IGF-IGF-binding protein axis specifically has yield to a second wave of development: the design of specific inhibitors that interrupt the signaling associated with this axis. The ability to manipulate these pathways holds not only significant therapeutic implications but also increase the chance of deeper insight about the role of the axis in carcinogenesis and metastasis. Nowadays, >25 molecules with the same goal are at different stages of development. Here, we review the clinical and preclinical experience with the two most-investigated strategies, tyrosine kinase inhibitors and monoclonal antibodies, and the advantages and disadvantages of each strategy, as well as other alternatives and possible drug combinations. We also review the biomarkers explored in the first clinical trials, the strategies that have been explored thus far, and the clinical trials that are going to explore their role in cancer treatment.

  2. Quality assurance for high dose rate brachytherapy treatment planning optimization: using a simple optimization to verify a complex optimization

    International Nuclear Information System (INIS)

    Deufel, Christopher L; Furutani, Keith M

    2014-01-01

    As dose optimization for high dose rate brachytherapy becomes more complex, it becomes increasingly important to have a means of verifying that optimization results are reasonable. A method is presented for using a simple optimization as quality assurance for the more complex optimization algorithms typically found in commercial brachytherapy treatment planning systems. Quality assurance tests may be performed during commissioning, at regular intervals, and/or on a patient specific basis. A simple optimization method is provided that optimizes conformal target coverage using an exact, variance-based, algebraic approach. Metrics such as dose volume histogram, conformality index, and total reference air kerma agree closely between simple and complex optimizations for breast, cervix, prostate, and planar applicators. The simple optimization is shown to be a sensitive measure for identifying failures in a commercial treatment planning system that are possibly due to operator error or weaknesses in planning system optimization algorithms. Results from the simple optimization are surprisingly similar to the results from a more complex, commercial optimization for several clinical applications. This suggests that there are only modest gains to be made from making brachytherapy optimization more complex. The improvements expected from sophisticated linear optimizations, such as PARETO methods, will largely be in making systems more user friendly and efficient, rather than in finding dramatically better source strength distributions. (paper)

  3. Accurate DNA assembly and genome engineering with optimized uracil excision cloning

    DEFF Research Database (Denmark)

    Cavaleiro, Mafalda; Kim, Se Hyeuk; Seppala, Susanna

    2015-01-01

    Simple and reliable DNA editing by uracil excision (a.k.a. USER cloning) has been described by several research groups, but the optimal design of cohesive DNA ends for multigene assembly remains elusive. Here, we use two model constructs based on expression of gfp and a four-gene pathway that pro......Simple and reliable DNA editing by uracil excision (a.k.a. USER cloning) has been described by several research groups, but the optimal design of cohesive DNA ends for multigene assembly remains elusive. Here, we use two model constructs based on expression of gfp and a four-gene pathway...... that produces β-carotene to optimize assembly junctions and the uracil excision protocol. By combining uracil excision cloning with a genomic integration technology, we demonstrate that up to six DNA fragments can be assembled in a one-tube reaction for direct genome integration with high accuracy, greatly...... facilitating the advanced engineering of robust cell factories....

  4. Targeting Cytosolic Nucleic Acid-Sensing Pathways for Cancer Immunotherapies.

    Science.gov (United States)

    Iurescia, Sandra; Fioretti, Daniela; Rinaldi, Monica

    2018-01-01

    The innate immune system provides the first line of defense against pathogen infection though also influences pathways involved in cancer immunosurveillance. The innate immune system relies on a limited set of germ line-encoded sensors termed pattern recognition receptors (PRRs), signaling proteins and immune response factors. Cytosolic receptors mediate recognition of danger damage-associated molecular patterns (DAMPs) signals. Once activated, these sensors trigger multiple signaling cascades, converging on the production of type I interferons and proinflammatory cytokines. Recent studies revealed that PRRs respond to nucleic acids (NA) released by dying, damaged, cancer cells, as danger DAMPs signals, and presence of signaling proteins across cancer types suggests that these signaling mechanisms may be involved in cancer biology. DAMPs play important roles in shaping adaptive immune responses through the activation of innate immune cells and immunological response to danger DAMPs signals is crucial for the host response to cancer and tumor rejection. Furthermore, PRRs mediate the response to NA in several vaccination strategies, including DNA immunization. As route of double-strand DNA intracellular entry, DNA immunization leads to expression of key components of cytosolic NA-sensing pathways. The involvement of NA-sensing mechanisms in the antitumor response makes these pathways attractive drug targets. Natural and synthetic agonists of NA-sensing pathways can trigger cell death in malignant cells, recruit immune cells, such as DCs, CD8 + T cells, and NK cells, into the tumor microenvironment and are being explored as promising adjuvants in cancer immunotherapies. In this minireview, we discuss how cGAS-STING and RIG-I-MAVS pathways have been targeted for cancer treatment in preclinical translational researches. In addition, we present a targeted selection of recent clinical trials employing agonists of cytosolic NA-sensing pathways showing how these pathways

  5. Anterior wrist and medial malleolus: the optimal sites for tissue selection in electric death through hand-to-foot circuit pathway.

    Science.gov (United States)

    Xu, Guangtao; Su, Ruibing; Lv, Junyao; Lai, Xiaoping; Li, Xianxian; Wu, Jiayan; Hu, Bo; Xu, Long; Shen, Ruilin; Gu, Jiang; Yu, Xiaojun

    2017-03-01

    Specific morphological changes may be absent in some cases of electrocution shocked by the voltage of 220 V or lower. In this study, we attempted to demonstrate that the anterior wrist and medial malleolus were the optimal sites with promising and significant changes in electric death through the hand-to-foot circuit pathway. We established an electric shock rat model and observed histopathologic changes in the anterior wrist and medial malleolus. The results showed that the current intensities in the left anterior wrist and right medial malleolus were remarkably higher than those in the other sites, and the nuclei long/short (L/S) axis ratios of the arterial endotheliocyte and the skeletal muscle cell in these two areas were significantly higher than those in other parts of the body. These findings suggested that the anterior wrist and/or medial malleolus soft tissues as the narrowest parts of the limbs could be used as promising and useful sites for the assessment of electrical shock death, especially in forensic pathologic evaluation.

  6. Optimal design of microalgae-based biorefinery: Economics, opportunities and challenges

    DEFF Research Database (Denmark)

    Rizwan, Muhammad; Lee, Jay H.; Gani, Rafiqul

    2015-01-01

    Microalgae have great potential as a feedstock for the production of a wide range of end-products under the broad concept of biorefinery. In an earlier work, we proposed a superstructure based optimization model to find the optimal processing pathway for the production of biodiesel from microalgal...... biomass, and identified several challenges with the focus being on utilizing lipids extracted microalgal biomass for economic and environmentally friendly production of useful energy products. In this paper, we expand the previous optimization framework by considering the processing of microalgae residue...

  7. Promoter library-based module combination (PLMC) technology for optimization of threonine biosynthesis in Corynebacterium glutamicum.

    Science.gov (United States)

    Wei, Liang; Xu, Ning; Wang, Yiran; Zhou, Wei; Han, Guoqiang; Ma, Yanhe; Liu, Jun

    2018-05-01

    Due to the lack of efficient control elements and tools, the fine-tuning of gene expression in the multi-gene metabolic pathways is still a great challenge for engineering microbial cell factories, especially for the important industrial microorganism Corynebacterium glutamicum. In this study, the promoter library-based module combination (PLMC) technology was developed to efficiently optimize the expression of genes in C. glutamicum. A random promoter library was designed to contain the putative - 10 (NNTANANT) and - 35 (NNGNCN) consensus motifs, and refined through a three-step screening procedure to achieve numerous genetic control elements with different strength levels, including fluorescence-activated cell sorting (FACS) screening, agar plate screening, and 96-well plate screening. Multiple conventional strategies were employed for further precise characterizations of the promoter library, such as real-time quantitative PCR, sodium dodecyl sulfate polyacrylamide gel electrophoresis, FACS analysis, and the lacZ reporter system. These results suggested that the established promoter elements effectively regulated gene expression and showed varying strengths over a wide range. Subsequently, a multi-module combination technology was created based on the efficient promoter elements for combination and optimization of modules in the multi-gene pathways. Using this technology, the threonine biosynthesis pathway was reconstructed and optimized by predictable tuning expression of five modules in C. glutamicum. The threonine titer of the optimized strain was significantly improved to 12.8 g/L, an approximate 6.1-fold higher than that of the control strain. Overall, the PLMC technology presented in this study provides a rapid and effective method for combination and optimization of multi-gene pathways in C. glutamicum.

  8. Simulation Modeling to Compare High-Throughput, Low-Iteration Optimization Strategies for Metabolic Engineering.

    Science.gov (United States)

    Heinsch, Stephen C; Das, Siba R; Smanski, Michael J

    2018-01-01

    Increasing the final titer of a multi-gene metabolic pathway can be viewed as a multivariate optimization problem. While numerous multivariate optimization algorithms exist, few are specifically designed to accommodate the constraints posed by genetic engineering workflows. We present a strategy for optimizing expression levels across an arbitrary number of genes that requires few design-build-test iterations. We compare the performance of several optimization algorithms on a series of simulated expression landscapes. We show that optimal experimental design parameters depend on the degree of landscape ruggedness. This work provides a theoretical framework for designing and executing numerical optimization on multi-gene systems.

  9. Pathway-based Analysis of the Hidden Genetic Heterogeneities in Cancers

    Directory of Open Access Journals (Sweden)

    Xiaolei Zhao

    2014-02-01

    Full Text Available Many cancers apparently showing similar phenotypes are actually distinct at the molecular level, leading to very different responses to the same treatment. It has been recently demonstrated that pathway-based approaches are robust and reliable for genetic analysis of cancers. Nevertheless, it remains unclear whether such function-based approaches are useful in deciphering molecular heterogeneities in cancers. Therefore, we aimed to test this possibility in the present study. First, we used a NCI60 dataset to validate the ability of pathways to correctly partition samples. Next, we applied the proposed method to identify the hidden subtypes in diffuse large B-cell lymphoma (DLBCL. Finally, the clinical significance of the identified subtypes was verified using survival analysis. For the NCI60 dataset, we achieved highly accurate partitions that best fit the clinical cancer phenotypes. Subsequently, for a DLBCL dataset, we identified three hidden subtypes that showed very different 10-year overall survival rates (90%, 46% and 20% and were highly significantly (P = 0.008 correlated with the clinical survival rate. This study demonstrated that the pathway-based approach is promising for unveiling genetic heterogeneities in complex human diseases.

  10. Glucose metabolism via the Entner-Doudoroff pathway in Campylobacter

    DEFF Research Database (Denmark)

    Vegge, Christina Skovgaard; van Rensburg, Melissa J. Jansen; Rasmussen, Janus Jagd

    2016-01-01

    for ED pathway genes in a wide range of Campylobacter isolates and in the C. jejuni/coli PubMLST database revealed that 1.7% of >6,000 genomes encoded a complete ED pathway, including both C. jejuni and C. coli from diverse clinical, environmental and animal sources. In rich media, glucose significantly...

  11. Optimal use of MRI in clinical trials, clinical care and clinical registries of patients with rheumatoid arthritis

    DEFF Research Database (Denmark)

    Østergaard, Mikkel; Møller-Bisgaard, Signe

    2014-01-01

    the benefits of including MRI in treat-to-target strategies. The benefits of incorporating MRI into clinical registries are not yet known, but may include improved knowledge about the real-life advantages of MRI, as well as opportunities to develop better clinical and laboratory composite measures to monitor......Magnetic resonance imaging (MRI) clearly is more sensitive than clinical examination and conventional radiography (x-ray) for detection of inflammation (synovitis, bone marrow oedema (osteitis) and tenosynovitis) and damage (bone erosion and cartilage loss/joint space narrowing) in patients...... with rheumatoid arthritis (RA). The question is when and how MRI should be used. The present article reviews our knowledge about, and provides suggestions for, the use of MRI in clinical trials, clinical care and clinical registries. In clinical trials, the OMERACT RA MRI scoring system (RAMRIS) is a thoroughly...

  12. Energy in the Netherlands. Optimized pathways to CO2 reduction in the Dutch context

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2011-09-15

    This document reports the findings of research undertaken by the Energy Forum NL (EFNL) which consists of companies active in different parts of the energy sector. The group strives for a more long-term, stable energy policy and investment climate in the Netherlands, one that will help realize overall climate ambitions. This report is part of the group's contribution to the energy debate in the Netherlands; it lays out a fact-based, objective analysis of the potential energy mix if one assumes a continued focus on carbon abatement. In this report, the Energy Forum NL provides pathways that show how the Netherlands can best contribute to the EU target of 80% CO2e emission reduction by 2050 compared to 1990. They particularly focus on the goal for the next 20 years: reducing CO2e emissions by 40% by 2030 compared to 1990. The Forum selected 40% as a midway target for 80% in 2050; this falls within the EU ambition of 40%-44% in 2030.1 The period beyond 2030, which is much more uncertain, is modeled in less detail. However, the Forum took care to not let the choice of any pathway during 2010-2030 lock a pathway after 2030 in or out. A 'least cost' approach, which works across sectors, is used to reduce emissions. In a 'least cost' approach, all emission reduction measures are ranked on costs and implemented progressively (starting from the cheapest) until the targeted abatement level is reached. In addition, a few developing technologies are implemented even if they are more expensive than alternatives. This choice prevents technology lock-in, ensures a more versatile, resilient energy system and provides a reasonable starting position for the period post-2030. The report assumes a pan-European approach for the power sector, which is the key sector in the Emissions Trading Scheme (ETS); in this case, Dutch abatement options 'compete' with those in other EU countries. For the other sectors it uses a national approach. Non-cost factors

  13. A study of optimization techniques in HDR brachytherapy for the prostate

    Science.gov (United States)

    Pokharel, Ghana Shyam

    . Based on our study, DVH based objective function performed better than traditional variance based objective function in creating a clinically acceptable plan when executed under identical conditions. Thirdly, we studied the multiobjective optimization strategy using both DVH and variance based objective functions. The optimization strategy was to create several Pareto optimal solutions by scanning the clinically relevant part of the Pareto front. This strategy was adopted to decouple optimization from decision such that user could select final solution from the pool of alternative solutions based on his/her clinical goals. The overall quality of treatment plan improved using this approach compared to traditional class solution approach. In fact, the final optimized plan selected using decision engine with DVH based objective was comparable to typical clinical plan created by an experienced physicist. Next, we studied the hybrid technique comprising both stochastic and deterministic algorithm to optimize both dwell positions and dwell times. The simulated annealing algorithm was used to find optimal catheter distribution and the DVH based algorithm was used to optimize 3D dose distribution for given catheter distribution. This unique treatment planning and optimization tool was capable of producing clinically acceptable highly reproducible treatment plans in clinically reasonable time. As this algorithm was able to create clinically acceptable plans within clinically reasonable time automatically, it is really appealing for real time procedures. Next, we studied the feasibility of multiobjective optimization using evolutionary algorithm for real time HDR brachytherapy for the prostate. The algorithm with properly tuned algorithm specific parameters was able to create clinically acceptable plans within clinically reasonable time. However, the algorithm was let to run just for limited number of generations not considered optimal, in general, for such algorithms. This was

  14. Development, Implementation and Compliance of Treatment Pathways in Radiation Medicine

    Directory of Open Access Journals (Sweden)

    Louis ePotters

    2013-05-01

    Full Text Available INTRODUCTION: While much emphasis on safety in the radiation oncology clinic is placed on process, there remains considerable opportunity to increase safety, enhance outcomes and avoid ad-hoc care by instituting detailed treatment pathways. The purpose of this study was to review the process of developing evidence and consensus-based, outcomes-oriented treatment pathways that standardize treatment and patient management in a large multicenter radiation oncology practice. Further, we reviewed our compliance in incorporating these directives into our day-to-day clinical practice. METHODS: Using the Institute of Medicine guideline for developing treatment pathways, 87 disease specific pathways were developed and incorporated into the electronic medical system in our multi-facility radiation oncology department. Compliance in incorporating treatment pathways was assessed by mining our EMR data from January 1, 2010 through February 2012 for patients with breast and prostate cancer. RESULTS: This retrospective analysis of data from electronic medical records found overall compliance to breast and prostate cancer treatment pathways to be 97% and 99%, respectively. The reason for non-compliance proved to be either a failure to complete the prescribed care based on grade II or III toxicity (n=1 breast, 3 prostate or patient elected discontinuance of care (n=1 prostate or the physician chose a higher dose for positive/close margins (n=3 breast. CONCLUSION: This study demonstrates that consensus and evidence-based treatment pathways can be developed and implemented in a multi-center department of radiation oncology. And that for prostate and breast cancer there was a high degree of compliance using these directives. The development and implementation of these pathways serve as a key component of our safety program, most notably in our effort to facilitate consistent decision-making and reducing variation between physicians.

  15. Exploring communication pathways to better health: Clinician communication of expectations for acupuncture effectiveness

    Science.gov (United States)

    Street, Richard L.; Cox, Vanessa; Kallen, Michael A.; Suarez-Almazor, Maria E.

    2012-01-01

    Objective This study tested a pathway whereby acupuncturists’ communication of optimism for treatment effectiveness would enhance patients’ satisfaction during treatment, which in turn would contribute to better pain and function outcomes for patients with osteoarthritis of the knee. Methods Secondary analysis from a 2 arm (real vs. sham acupuncture, high vs. neutral expectations) RCT. 311 patients with knee osteoarthritis received acupuncture over 10–12 sessions. Coders rated the degree to which acupuncturists communicated optimism for the treatment’s effectiveness. Satisfaction with acupuncture was assessed 4 weeks into treatment. Pain and function were assessed 6 weeks following treatment. Results Patients experiencing better outcomes were more satisfied with acupuncture during treatment, were younger, and had better baseline pain and function scores. Satisfaction during treatment was greater when patients interacted with more optimistic clinicians and had higher pretreatment expectations for acupuncture efficacy. Conclusion Acupuncturists’ communication of optimism about treatment effectiveness contributed to pain and function outcomes indirectly through its effect on satisfaction during treatment. Future research should model pathways through which clinician-patient communication affects mediating variables that in turn lead to improved health outcomes. Practical Implications While clinicians should not mislead patients, communicating hope and optimism for treatment effectiveness has therapeutic value for patients. PMID:22857778

  16. Impact of Targeted Preoperative Optimization on Clinical Outcome in Emergency Abdominal Surgeries: A Prospective Randomized Trial.

    Science.gov (United States)

    Sethi, Ashish; Debbarma, Miltan; Narang, Neeraj; Saxena, Anudeep; Mahobia, Mamta; Tomar, Gaurav Singh

    2018-01-01

    Perforation peritonitis continues to be one of the most common surgical emergencies that need a surgical intervention most of the times. Anesthesiologists are invariably involved in managing such cases efficiently in perioperative period. The assessment and evaluation of Acute Physiology and Chronic Health Evaluation II (APACHE II) score at presentation and 24 h after goal-directed optimization, administration of empirical broad-spectrum antibiotics, and definitive source control postoperatively. Outcome assessment in terms of duration of hospital stay and mortality in with or without optimization was also measured. It is a prospective, randomized, double-blind controlled study in hospital setting. One hundred and one patients aged ≥18 years, of the American Society of Anesthesiologists physical Status I and II (E) with clinical diagnosis of perforation peritonitis posted for surgery were enrolled. Enrolled patients were randomly divided into two groups. Group A is optimized by goal-directed optimization protocol in the preoperative holding room by anesthesiology residents whereas in Group S, managed by surgery residents in the surgical wards without any fixed algorithm. The assessment of APACHE II score was done as a first step on admission and 24 h postoperatively. Duration of hospital stay and mortality in both the groups were also measured and compared. Categorical data are presented as frequency counts (percent) and compared using the Chi-square or Fisher's exact test. The statistical significance for categorical variables was determined by Chi-square analysis. For continuous variables, a two-sample t -test was applied. The mean APACHE II score on admission in case and control groups was comparable. Significant lowering of serial scores in case group was observed as compared to control group ( P = 0.02). There was a significant lowering of mean duration of hospital stay seen in case group (9.8 ± 1.7 days) as compared to control group ( P = 0

  17. Time optimized path-choice in the termite hunting ant Megaponera analis.

    Science.gov (United States)

    Frank, Erik T; Hönle, Philipp O; Linsenmair, K Eduard

    2018-05-10

    Trail network systems among ants have received a lot of scientific attention due to their various applications in problem solving of networks. Recent studies have shown that ants select the fastest available path when facing different velocities on different substrates, rather than the shortest distance. The progress of decision-making by these ants is determined by pheromone-based maintenance of paths, which is a collective decision. However, path optimization through individual decision-making remains mostly unexplored. Here we present the first study of time-optimized path selection via individual decision-making by scout ants. Megaponera analis scouts search for termite foraging sites and lead highly organized raid columns to them. The path of the scout determines the path of the column. Through installation of artificial roads around M. analis nests we were able to influence the pathway choice of the raids. After road installation 59% of all recorded raids took place completely or partly on the road, instead of the direct, i.e. distance-optimized, path through grass from the nest to the termites. The raid velocity on the road was more than double the grass velocity, the detour thus saved 34.77±23.01% of the travel time compared to a hypothetical direct path. The pathway choice of the ants was similar to a mathematical model of least time allowing us to hypothesize the underlying mechanisms regulating the behavior. Our results highlight the importance of individual decision-making in the foraging behavior of ants and show a new procedure of pathway optimization. © 2018. Published by The Company of Biologists Ltd.

  18. Active PI3K pathway causes an invasive phenotype which can be reversed or promoted by blocking the pathway at divergent nodes.

    Directory of Open Access Journals (Sweden)

    Jeffrey J Wallin

    Full Text Available The PTEN/PI3K pathway is commonly mutated in cancer and therefore represents an attractive target for therapeutic intervention. To investigate the primary phenotypes mediated by increased pathway signaling in a clean, patient-relevant context, an activating PIK3CA mutation (H1047R was knocked-in to an endogenous allele of the MCF10A non-tumorigenic human breast epithelial cell line. Introduction of an endogenously mutated PIK3CA allele resulted in a marked epithelial-mesenchymal transition (EMT and invasive phenotype, compared to isogenic wild-type cells. The invasive phenotype was linked to enhanced PIP(3 production via a S6K-IRS positive feedback mechanism. Moreover, potent and selective inhibitors of PI3K were highly effective in reversing this phenotype, which is optimally revealed in 3-dimensional cell culture. In contrast, inhibition of Akt or mTOR exacerbated the invasive phenotype. Our results suggest that invasion is a core phenotype mediated by increased PTEN/PI3K pathway activity and that therapeutic agents targeting different nodes of the PI3K pathway may have dramatic differences in their ability to reverse or promote cancer metastasis.

  19. Ipsilateral motor pathways after stroke: implications for noninvasive brain stimulation

    Directory of Open Access Journals (Sweden)

    Lynley V Bradnam

    2013-05-01

    Full Text Available In humans the two cerebral hemispheres have essential roles in controlling the upper limb. The purpose of this article is to draw attention to the potential importance of ipsilateral descending pathways for functional recovery after stroke, and the use of noninvasive brain stimulation (NBS protocols of the contralesional primary motor cortex (M1. Conventionally NBS is used to suppress contralesional M1, and to attenuate transcallosal inhibition onto the ipsilesional M1. There has been little consideration of the fact that contralesional M1 suppression may also reduce excitability of ipsilateral descending pathways that may be important for paretic upper limb control for some patients. One such ipsilateral pathway is the cortico-reticulo-propriospinal pathway (CRPP. In this review we outline a neurophysiological model to explain how contralesional M1 may gain control of the paretic arm via the CRPP. We conclude that the relative importance of the CRPP for motor control in individual patients must be considered before using NBS to suppress contralesional M1. Neurophysiological, neuroimaging and clinical assessments can assist this decision making and facilitate the translation of NBS into the clinical setting.

  20. Pathway-Based Kernel Boosting for the Analysis of Genome-Wide Association Studies

    Science.gov (United States)

    Manitz, Juliane; Burger, Patricia; Amos, Christopher I.; Chang-Claude, Jenny; Wichmann, Heinz-Erich; Kneib, Thomas; Bickeböller, Heike

    2017-01-01

    The analysis of genome-wide association studies (GWAS) benefits from the investigation of biologically meaningful gene sets, such as gene-interaction networks (pathways). We propose an extension to a successful kernel-based pathway analysis approach by integrating kernel functions into a powerful algorithmic framework for variable selection, to enable investigation of multiple pathways simultaneously. We employ genetic similarity kernels from the logistic kernel machine test (LKMT) as base-learners in a boosting algorithm. A model to explain case-control status is created iteratively by selecting pathways that improve its prediction ability. We evaluated our method in simulation studies adopting 50 pathways for different sample sizes and genetic effect strengths. Additionally, we included an exemplary application of kernel boosting to a rheumatoid arthritis and a lung cancer dataset. Simulations indicate that kernel boosting outperforms the LKMT in certain genetic scenarios. Applications to GWAS data on rheumatoid arthritis and lung cancer resulted in sparse models which were based on pathways interpretable in a clinical sense. Kernel boosting is highly flexible in terms of considered variables and overcomes the problem of multiple testing. Additionally, it enables the prediction of clinical outcomes. Thus, kernel boosting constitutes a new, powerful tool in the analysis of GWAS data and towards the understanding of biological processes involved in disease susceptibility. PMID:28785300

  1. Pathway-Based Kernel Boosting for the Analysis of Genome-Wide Association Studies.

    Science.gov (United States)

    Friedrichs, Stefanie; Manitz, Juliane; Burger, Patricia; Amos, Christopher I; Risch, Angela; Chang-Claude, Jenny; Wichmann, Heinz-Erich; Kneib, Thomas; Bickeböller, Heike; Hofner, Benjamin

    2017-01-01

    The analysis of genome-wide association studies (GWAS) benefits from the investigation of biologically meaningful gene sets, such as gene-interaction networks (pathways). We propose an extension to a successful kernel-based pathway analysis approach by integrating kernel functions into a powerful algorithmic framework for variable selection, to enable investigation of multiple pathways simultaneously. We employ genetic similarity kernels from the logistic kernel machine test (LKMT) as base-learners in a boosting algorithm. A model to explain case-control status is created iteratively by selecting pathways that improve its prediction ability. We evaluated our method in simulation studies adopting 50 pathways for different sample sizes and genetic effect strengths. Additionally, we included an exemplary application of kernel boosting to a rheumatoid arthritis and a lung cancer dataset. Simulations indicate that kernel boosting outperforms the LKMT in certain genetic scenarios. Applications to GWAS data on rheumatoid arthritis and lung cancer resulted in sparse models which were based on pathways interpretable in a clinical sense. Kernel boosting is highly flexible in terms of considered variables and overcomes the problem of multiple testing. Additionally, it enables the prediction of clinical outcomes. Thus, kernel boosting constitutes a new, powerful tool in the analysis of GWAS data and towards the understanding of biological processes involved in disease susceptibility.

  2. Interior point algorithms: guaranteed optimality for fluence map optimization in IMRT

    Energy Technology Data Exchange (ETDEWEB)

    Aleman, Dionne M [Department of Mechanical and Industrial Engineering, University of Toronto, 5 King' s College Road, Toronto, ON M5S 3G8 (Canada); Glaser, Daniel [Division of Optimization and Systems Theory, Department of Mathematics, Royal Institute of Technology, Stockholm (Sweden); Romeijn, H Edwin [Department of Industrial and Operations Engineering, University of Michigan, Ann Arbor, MI 48109-2117 (United States); Dempsey, James F, E-mail: aleman@mie.utoronto.c, E-mail: romeijn@umich.ed, E-mail: jfdempsey@viewray.co [ViewRay, Inc. 2 Thermo Fisher Way, Village of Oakwood, OH 44146 (United States)

    2010-09-21

    One of the most widely studied problems of the intensity-modulated radiation therapy (IMRT) treatment planning problem is the fluence map optimization (FMO) problem, the problem of determining the amount of radiation intensity, or fluence, of each beamlet in each beam. For a given set of beams, the fluences of the beamlets can drastically affect the quality of the treatment plan, and thus it is critical to obtain good fluence maps for radiation delivery. Although several approaches have been shown to yield good solutions to the FMO problem, these solutions are not guaranteed to be optimal. This shortcoming can be attributed to either optimization model complexity or properties of the algorithms used to solve the optimization model. We present a convex FMO formulation and an interior point algorithm that yields an optimal treatment plan in seconds, making it a viable option for clinical applications.

  3. Interior point algorithms: guaranteed optimality for fluence map optimization in IMRT

    International Nuclear Information System (INIS)

    Aleman, Dionne M; Glaser, Daniel; Romeijn, H Edwin; Dempsey, James F

    2010-01-01

    One of the most widely studied problems of the intensity-modulated radiation therapy (IMRT) treatment planning problem is the fluence map optimization (FMO) problem, the problem of determining the amount of radiation intensity, or fluence, of each beamlet in each beam. For a given set of beams, the fluences of the beamlets can drastically affect the quality of the treatment plan, and thus it is critical to obtain good fluence maps for radiation delivery. Although several approaches have been shown to yield good solutions to the FMO problem, these solutions are not guaranteed to be optimal. This shortcoming can be attributed to either optimization model complexity or properties of the algorithms used to solve the optimization model. We present a convex FMO formulation and an interior point algorithm that yields an optimal treatment plan in seconds, making it a viable option for clinical applications.

  4. Reduced in-hospital mortality for heart failure with clinical pathways: the results of a cluster randomised controlled trial.

    Science.gov (United States)

    Panella, M; Marchisio, S; Demarchi, M L; Manzoli, L; Di Stanislao, F

    2009-10-01

    Hospital treatment of heart failure (HF) frequently does not follow published guidelines, potentially contributing to HF high morbidity, mortality and economic cost. The Experimental Prospective Study on the Effectiveness and Efficiency of the Implementation of Clinical Pathways was undertaken to determine how clinical pathways (CP) for hospital treatment of HF affected care variability, guidelines adherence, in-hospital mortality and outcomes at discharge. Methods/ Two-arm, cluster-randomised trial. Fourteen community hospitals were randomised either to the experimental arm (CP: appropriate therapeutic guidelines use, new organisation and procedures, patient education) or to the control arm (usual care). The main outcome was in-hospital mortality; secondary outcomes were length and appropriateness of the stay, rate of unscheduled readmissions, customer satisfaction, usage of diagnostic and therapeutic procedures during hospital stay and quality indicators at discharge. All outcomes were measured using validated instruments available in literature. In-hospital mortality was 5.6% in the experimental arm (n = 12); 15.4% in controls (n = 33, p = 0.001). In CP and usual care groups, the mean rates of unscheduled readmissions were 7.9% and 13.9%, respectively. Adjusting for age, smoking, New York Heart Association score, hypertension and source of referral, patients in the CP group, as compared to controls, had a significantly lower risk of in-hospital death (OR 0.18; 95% CI 0.07 to 0.46) and unscheduled readmissions (OR 0.42; 95% CI 0.20 to 0.87). No differences were found between CP and control with respect to the appropriateness of the stay, costs and patient's satisfaction. Except for electrocardiography, all recommended diagnostic procedures were used more in the CP group. Similarly, pharmaceuticals use was significantly greater in CP, with the exception of diuretics and anti-platelets agents. The introduction of a specifically tailored CP for the hospital

  5. LEAN SIX SIGMA TECHNIQUES TO IMPROVE OPHTHALMOLOGY CLINIC EFFICIENCY.

    Science.gov (United States)

    Ciulla, Thomas A; Tatikonda, Mohan V; ElMaraghi, Yehya A; Hussain, Rehan M; Hill, Amanda L; Clary, Julie M; Hattab, Eyas

    2017-07-18

    Ophthalmologists serve an increasing volume of a growing elderly population undergoing increasingly complex outpatient medical care, including extensive diagnostic testing and treatment. The resulting prolonged patient visit times ("patient flow times") limit quality, patient and employee satisfaction, and represent waste. Lean Six Sigma process improvement was used in a vitreoretinal practice to decrease patient flow time, demonstrating that this approach can yield significant improvement in health care. Process flow maps were created to determine the most common care pathways within clinic. Three months' visits from the electronic medical record system, which tracks patient task times at each process step in the office were collected. Care tasks and care pathways consuming the greatest time and variation were identified and modified. Follow-up analysis from 6 weeks' visits was conducted to assess improvement. Nearly all patients took one of five paths through the office. Patient flow was redesigned to reduce waiting room time by having staff members immediately start patients into one of those five paths; staffing was adjusted to address high demand tasks, and scheduling was optimized around derived predictors of patient flow times. Follow-up analysis revealed a statistically significant decline in mean patient flow time by 18% and inpatient flow time SD by 4.6%. Patient and employee satisfaction scores improved. Manufacturing industry techniques, such as Lean and Six Sigma, can be used to improve patient care, minimize waste, and enhance patient and staff satisfaction in outpatient clinics.

  6. Nursing Informatics Certification Worldwide: History, Pathway, Roles, and Motivation

    Science.gov (United States)

    Cummins, M. R.; Gundlapalli, A. V.; Murray, P.; Park, H.-A.; Lehmann, C. U.

    2016-01-01

    Summary Introduction Official recognition and certification for informatics professionals are essential aspects of workforce development. Objective: To describe the history, pathways, and nuances of certification in nursing informatics across the globe; compare and contrast those with board certification in clinical informatics for physicians. Methods (1) A review of the representative literature on informatics certification and related competencies for nurses and physicians, and relevant websites for nursing informatics associations and societies worldwide; (2) similarities and differences between certification processes for nurses and physicians, and (3) perspectives on roles for nursing informatics professionals in healthcare Results The literature search for ‘nursing informatics certification’ yielded few results in PubMed; Google Scholar yielded a large number of citations that extended to magazines and other non-peer reviewed sources. Worldwide, there are several nursing informatics associations, societies, and workgroups dedicated to nursing informatics associated with medical/health informatics societies. A formal certification program for nursing informatics appears to be available only in the United States. This certification was established in 1992, in concert with the formation and definition of nursing informatics as a specialty practice of nursing by the American Nurses Association. Although informatics is inherently interprofessional, certification pathways for nurses and physicians have developed separately, following long-standing professional structures, training, and pathways aligned with clinical licensure and direct patient care. There is substantial similarity with regard to the skills and competencies required for nurses and physicians to obtain informatics certification in their respective fields. Nurses may apply for and complete a certification examination if they have experience in the field, regardless of formal training. Increasing

  7. Recent updates of precision therapy for gastric cancer: Towards optimal tailored management.

    Science.gov (United States)

    Joo, Moon Kyung; Park, Jong-Jae; Chun, Hoon Jai

    2016-05-21

    Signaling pathways of gastric carcinogenesis and gastric cancer progression are being avidly studied to seek optimal treatment of gastric cancer. Among them, hepatocyte growth factor (HGF)/c-MET, phosphoinositide 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) and janus kinase 2/signal transducer and activator of transcription 3 (JAK2/STAT3) pathways have been widely investigated. Their aberrant expression or mutation has been significantly associated with advanced stage or poor prognosis of gastric cancer. Recently, aberrations of immune checkpoints including programmed cell death-1/programmed cell death ligand-1 (PD-1/PD-L1) have been suggested as an important step in the formation of a microenvironment favorable for gastric cancer. Accomplishments in basic research have led to the development of novel agents targeting these signaling pathways. However, phase III studies of selective anti-HGF/c-MET antibodies and mTOR inhibitor failed to show significant benefits in terms of overall survival and progression-free survival. Few agents directly targeting STAT3 have been developed. However, this target is still critical issue in terms of chemoresistance, and SH2-containing protein tyrosine phosphatase 1 might be a significant link to effectively inhibit STAT3 activity. Inhibition of PD-1/PD-L1 showed durable efficacy in phase I studies, and phase III evaluation is warranted. Therapeutic strategy to concurrently inhibit multiple tyrosine kinases is a reasonable option, however, lapatinib needs to be further evaluated to identify good responders. Regorafenib has shown promising effectiveness in prolonging progression-free survival in a phase II study. In this topic highlight, we review the biologic roles and outcomes of clinical studies targeting these signaling pathways.

  8. Designing a Care Pathway Model – A Case Study of the Outpatient Total Hip Arthroplasty Care Pathway

    Directory of Open Access Journals (Sweden)

    Robin I. Oosterholt

    2017-03-01

    Full Text Available Introduction: Although the clinical attributes of total hip arthroplasty (THA care pathways have been thoroughly researched, a detailed understanding of the equally important organisational attributes is still lacking. The aim of this article is to contribute with a model of the outpatient THA care pathway that depicts how the care team should be organised to enable patient discharge on the day of surgery. Theory: The outpatient THA care pathway enables patients to be discharged on the day of surgery, short- ening the length of stay and intensifying the provision and organisation of care. We utilise visual care modelling to construct a visual design of the organisation of the care pathway. Methods: An embedded case study was conducted of the outpatient THA care pathway at a teaching hospital in the Netherlands. The data were collected using a visual care modelling toolkit in 16 semi- structured interviews. Problems and inefficiencies in the care pathway were identified and addressed in the iterative design process. Results: The results are two visual models of the most critical phases of the outpatient THA care pathway: diagnosis & preparation (1 and mobilisation & discharge (4. The results show the care team composition, critical value exchanges, and sequence that enable patient discharge on the day of surgery. Conclusion: The design addressed existing problems and is an optimisation of the case hospital’s pathway. The network of actors consists of the patient (1, radiologist (1, anaesthetist (1, nurse specialist (1, pharmacist (1, orthopaedic surgeon (1,4, physiotherapist (1,4, nurse (4, doctor (4 and patient applica- tion (1,4. The critical value exchanges include patient preparation (mental and practical, patient education, aligned care team, efficient sequence of value exchanges, early patient mobilisation, flexible availability of the physiotherapist, functional discharge criteria, joint decision making and availability of the care team.

  9. Subtype and pathway specific responses to anticancer compounds in breast cancer.

    Science.gov (United States)

    Heiser, Laura M; Sadanandam, Anguraj; Kuo, Wen-Lin; Benz, Stephen C; Goldstein, Theodore C; Ng, Sam; Gibb, William J; Wang, Nicholas J; Ziyad, Safiyyah; Tong, Frances; Bayani, Nora; Hu, Zhi; Billig, Jessica I; Dueregger, Andrea; Lewis, Sophia; Jakkula, Lakshmi; Korkola, James E; Durinck, Steffen; Pepin, François; Guan, Yinghui; Purdom, Elizabeth; Neuvial, Pierre; Bengtsson, Henrik; Wood, Kenneth W; Smith, Peter G; Vassilev, Lyubomir T; Hennessy, Bryan T; Greshock, Joel; Bachman, Kurtis E; Hardwicke, Mary Ann; Park, John W; Marton, Laurence J; Wolf, Denise M; Collisson, Eric A; Neve, Richard M; Mills, Gordon B; Speed, Terence P; Feiler, Heidi S; Wooster, Richard F; Haussler, David; Stuart, Joshua M; Gray, Joe W; Spellman, Paul T

    2012-02-21

    Breast cancers are comprised of molecularly distinct subtypes that may respond differently to pathway-targeted therapies now under development. Collections of breast cancer cell lines mirror many of the molecular subtypes and pathways found in tumors, suggesting that treatment of cell lines with candidate therapeutic compounds can guide identification of associations between molecular subtypes, pathways, and drug response. In a test of 77 therapeutic compounds, nearly all drugs showed differential responses across these cell lines, and approximately one third showed subtype-, pathway-, and/or genomic aberration-specific responses. These observations suggest mechanisms of response and resistance and may inform efforts to develop molecular assays that predict clinical response.

  10. Metabolic pathway analysis and kinetic studies for production of nattokinase in Bacillus subtilis.

    Science.gov (United States)

    Unrean, Pornkamol; Nguyen, Nhung H A

    2013-01-01

    We have constructed a reaction network model of Bacillus subtilis. The model was analyzed using a pathway analysis tool called elementary mode analysis (EMA). The analysis tool was used to study the network capabilities and the possible effects of altered culturing conditions on the production of a fibrinolytic enzyme, nattokinase (NK) by B. subtilis. Based on all existing metabolic pathways, the maximum theoretical yield for NK synthesis in B. subtilis under different substrates and oxygen availability was predicted and the optimal culturing condition for NK production was identified. To confirm model predictions, experiments were conducted by testing these culture conditions for their influence on NK activity. The optimal culturing conditions were then applied to batch fermentation, resulting in high NK activity. The EMA approach was also applied for engineering B. subtilis metabolism towards the most efficient pathway for NK synthesis by identifying target genes for deletion and overexpression that enable the cell to produce NK at the maximum theoretical yield. The consistency between experiments and model predictions proves the feasibility of EMA being used to rationally design culture conditions and genetic manipulations for the efficient production of desired products.

  11. Biochemical systems identification by a random drift particle swarm optimization approach

    Science.gov (United States)

    2014-01-01

    Background Finding an efficient method to solve the parameter estimation problem (inverse problem) for nonlinear biochemical dynamical systems could help promote the functional understanding at the system level for signalling pathways. The problem is stated as a data-driven nonlinear regression problem, which is converted into a nonlinear programming problem with many nonlinear differential and algebraic constraints. Due to the typical ill conditioning and multimodality nature of the problem, it is in general difficult for gradient-based local optimization methods to obtain satisfactory solutions. To surmount this limitation, many stochastic optimization methods have been employed to find the global solution of the problem. Results This paper presents an effective search strategy for a particle swarm optimization (PSO) algorithm that enhances the ability of the algorithm for estimating the parameters of complex dynamic biochemical pathways. The proposed algorithm is a new variant of random drift particle swarm optimization (RDPSO), which is used to solve the above mentioned inverse problem and compared with other well known stochastic optimization methods. Two case studies on estimating the parameters of two nonlinear biochemical dynamic models have been taken as benchmarks, under both the noise-free and noisy simulation data scenarios. Conclusions The experimental results show that the novel variant of RDPSO algorithm is able to successfully solve the problem and obtain solutions of better quality than other global optimization methods used for finding the solution to the inverse problems in this study. PMID:25078435

  12. Clinical- and cost-effectiveness of the STAR care pathway compared to usual care for patients with chronic pain after total knee replacement: study protocol for a UK randomised controlled trial.

    Science.gov (United States)

    Wylde, Vikki; Bertram, Wendy; Beswick, Andrew D; Blom, Ashley W; Bruce, Julie; Burston, Amanda; Dennis, Jane; Garfield, Kirsty; Howells, Nicholas; Lane, Athene; McCabe, Candy; Moore, Andrew J; Noble, Sian; Peters, Tim J; Price, Andrew; Sanderson, Emily; Toms, Andrew D; Walsh, David A; White, Simon; Gooberman-Hill, Rachael

    2018-02-21

    Approximately 20% of patients experience chronic pain after total knee replacement. There is little evidence for effective interventions for the management of this pain, and current healthcare provision is patchy and inconsistent. Given the complexity of this condition, multimodal and individualised interventions matched to pain characteristics are needed. We have undertaken a comprehensive programme of work to develop a care pathway for patients with chronic pain after total knee replacement. This protocol describes the design of a randomised controlled trial to evaluate the clinical- and cost-effectiveness of a complex intervention care pathway compared with usual care. This is a pragmatic two-armed, open, multi-centred randomised controlled trial conducted within secondary care in the UK. Patients will be screened at 2 months after total knee replacement and 381 patients with chronic pain at 3 months postoperatively will be recruited. Recruitment processes will be optimised through qualitative research during a 6-month internal pilot phase. Patients are randomised using a 2:1 intervention:control allocation ratio. All participants receive usual care as provided by their hospital. The intervention comprises an assessment clinic appointment at 3 months postoperatively with an Extended Scope Practitioner and up to six telephone follow-up calls over 12 months. In the assessment clinic, a standardised protocol is followed to identify potential underlying causes for the chronic pain and enable appropriate onward referrals to existing services for targeted and individualised treatment. Outcomes are assessed by questionnaires at 6 and 12 months after randomisation. The co-primary outcomes are pain severity and pain interference assessed using the Brief Pain Inventory at 12 months after randomisation. Secondary outcomes relate to resource use, function, neuropathic pain, mental well-being, use of pain medications, satisfaction with pain relief, pain frequency, capability

  13. Prediction of novel synthetic pathways for the production of desired chemicals

    Directory of Open Access Journals (Sweden)

    Park Jin

    2010-03-01

    Full Text Available Abstract Background There have been several methods developed for the prediction of synthetic metabolic pathways leading to the production of desired chemicals. In these approaches, novel pathways were predicted based on chemical structure changes, enzymatic information, and/or reaction mechanisms, but the approaches generating a huge number of predicted results are difficult to be applied to real experiments. Also, some of these methods focus on specific pathways, and thus are limited to expansion to the whole metabolism. Results In the present study, we propose a system framework employing a retrosynthesis model with a prioritization scoring algorithm. This new strategy allows deducing the novel promising pathways for the synthesis of a desired chemical together with information on enzymes involved based on structural changes and reaction mechanisms present in the system database. The prioritization scoring algorithm employing Tanimoto coefficient and group contribution method allows examination of structurally qualified pathways to recognize which pathway is more appropriate. In addition, new concepts of binding site covalence, estimation of pathway distance and organism specificity were taken into account to identify the best synthetic pathway. Parameters of these factors can be evolutionarily optimized when a newly proven synthetic pathway is registered. As the proofs of concept, the novel synthetic pathways for the production of isobutanol, 3-hydroxypropionate, and butyryl-CoA were predicted. The prediction shows a high reliability, in which experimentally verified synthetic pathways were listed within the top 0.089% of the identified pathway candidates. Conclusions It is expected that the system framework developed in this study would be useful for the in silico design of novel metabolic pathways to be employed for the efficient production of chemicals, fuels and materials.

  14. SWITCH: a dynamic CRISPR tool for genome engineering and metabolic pathway control for cell factory construction in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Garcia Vanegas, Katherina; Lehka, Beata Joanna; Mortensen, Uffe Hasbro

    2017-01-01

    to the pathway control state where production was optimized by downregulating an essential gene TSC13, hence, reducing formation of a byproduct. Conclusions We have successfully integrated two CRISPR tools, one for genetic engineering and one for pathway control, into one system and successfully used it for cell...

  15. The role of AV and VV optimization for CRT

    Directory of Open Access Journals (Sweden)

    William W. Brabham, M.D.

    2013-06-01

    Full Text Available Cardiac resynchronization therapy is an effective therapy for patients with left ventricular systolic dysfunction and a ventricular conduction delay; however, approximately 30% of patients do not experience significant clinical improvement with this treatment. Modern devices allow individualized programming of the AV delay and VV offset, which offer the possibility of improving clinical response rates with optimized programming. AV and VV delay optimization techniques have included echocardiography, device-based algorithms, and several other novel noninvasive techniques. While an acute improvement in hemodynamic function has been clearly demonstrated with optimized device settings, long-term clinical benefit is limited. In the majority of cases, an empiric AV delay with simultaneous biventricular or left ventricular pacing is adequate. The value of optimization of these intervals in “non-responders” still requires further investigation.

  16. Developing optimal search strategies for detecting clinically sound prognostic studies in MEDLINE: an analytic survey

    Directory of Open Access Journals (Sweden)

    Haynes R Brian

    2004-06-01

    Full Text Available Abstract Background Clinical end users of MEDLINE have a difficult time retrieving articles that are both scientifically sound and directly relevant to clinical practice. Search filters have been developed to assist end users in increasing the success of their searches. Many filters have been developed for the literature on therapy and reviews but little has been done in the area of prognosis. The objective of this study is to determine how well various methodologic textwords, Medical Subject Headings, and their Boolean combinations retrieve methodologically sound literature on the prognosis of health disorders in MEDLINE. Methods An analytic survey was conducted, comparing hand searches of journals with retrievals from MEDLINE for candidate search terms and combinations. Six research assistants read all issues of 161 journals for the publishing year 2000. All articles were rated using purpose and quality indicators and categorized into clinically relevant original studies, review articles, general papers, or case reports. The original and review articles were then categorized as 'pass' or 'fail' for methodologic rigor in the areas of prognosis and other clinical topics. Candidate search strategies were developed for prognosis and run in MEDLINE – the retrievals being compared with the hand search data. The sensitivity, specificity, precision, and accuracy of the search strategies were calculated. Results 12% of studies classified as prognosis met basic criteria for scientific merit for testing clinical applications. Combinations of terms reached peak sensitivities of 90%. Compared with the best single term, multiple terms increased sensitivity for sound studies by 25.2% (absolute increase, and increased specificity, but by a much smaller amount (1.1% when sensitivity was maximized. Combining terms to optimize both sensitivity and specificity achieved sensitivities and specificities of approximately 83% for each. Conclusion Empirically derived

  17. Isotopic evidence for nitrous oxide production pathways in a partial nitritation-anammox reactor.

    Science.gov (United States)

    Harris, Eliza; Joss, Adriano; Emmenegger, Lukas; Kipf, Marco; Wolf, Benjamin; Mohn, Joachim; Wunderlin, Pascal

    2015-10-15

    Nitrous oxide (N2O) production pathways in a single stage, continuously fed partial nitritation-anammox reactor were investigated using online isotopic analysis of offgas N2O with quantum cascade laser absorption spectroscopy (QCLAS). N2O emissions increased when reactor operating conditions were not optimal, for example, high dissolved oxygen concentration. SP measurements indicated that the increase in N2O was due to enhanced nitrifier denitrification, generally related to nitrite build-up in the reactor. The results of this study confirm that process control via online N2O monitoring is an ideal method to detect imbalances in reactor operation and regulate aeration, to ensure optimal reactor conditions and minimise N2O emissions. Under normal operating conditions, the N2O isotopic site preference (SP) was much higher than expected - up to 40‰ - which could not be explained within the current understanding of N2O production pathways. Various targeted experiments were conducted to investigate the characteristics of N2O formation in the reactor. The high SP measurements during both normal operating and experimental conditions could potentially be explained by a number of hypotheses: i) unexpectedly strong heterotrophic N2O reduction, ii) unknown inorganic or anammox-associated N2O production pathway, iii) previous underestimation of SP fractionation during N2O production from NH2OH, or strong variations in SP from this pathway depending on reactor conditions. The second hypothesis - an unknown or incompletely characterised production pathway - was most consistent with results, however the other possibilities cannot be discounted. Further experiments are needed to distinguish between these hypotheses and fully resolve N2O production pathways in PN-anammox systems. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. CLINICAL AND PHARMACOLOGICAL APPROACHES TO OPTIMIZE THE DOSING REGIMEN OF ANTIBACTERIAL DRUGS IN PEDIATRICS

    Directory of Open Access Journals (Sweden)

    Natal’ya B. Lazareva

    2018-01-01

    Full Text Available The rational use of antibacterial drugs in children implies an adequate choice of the necessary medication, its dosing regimen, and the duration of treatment in order to achieve maximum efficacy and minimize toxic effects. The knowledge of pharmacokinetic and pharmacodynamic profiles of the antibacterial drug plays a crucial role for optimizing the dosing regimen. The strategy of individual choice of the dosing regimen, taking into account the principles of pharmacokinetics and pharmacodynamics, can be especially effective in patients with the expectedly changed parameters of pharmacokinetics and in infections caused by bacteria strains with low sensitivity to antibiotics. The review presents a contemporary view of pharmacokinetic and pharmacodynamic profiles of antibacterial drugs most commonly used in pediatrics and their relationship to the clinical efficacy of the administered therapy.

  19. Interactively exploring optimized treatment plans

    International Nuclear Information System (INIS)

    Rosen, Isaac; Liu, H. Helen; Childress, Nathan; Liao Zhongxing

    2005-01-01

    Purpose: A new paradigm for treatment planning is proposed that embodies the concept of interactively exploring the space of optimized plans. In this approach, treatment planning ignores the details of individual plans and instead presents the physician with clinical summaries of sets of solutions to well-defined clinical goals in which every solution has been optimized in advance by computer algorithms. Methods and materials: Before interactive planning, sets of optimized plans are created for a variety of treatment delivery options and critical structure dose-volume constraints. Then, the dose-volume parameters of the optimized plans are fit to linear functions. These linear functions are used to show in real time how the target dose-volume histogram (DVH) changes as the DVHs of the critical structures are changed interactively. A bitmap of the space of optimized plans is used to restrict the feasible solutions. The physician selects the critical structure dose-volume constraints that give the desired dose to the planning target volume (PTV) and then those constraints are used to create the corresponding optimized plan. Results: The method is demonstrated using prototype software, Treatment Plan Explorer (TPEx), and a clinical example of a patient with a tumor in the right lung. For this example, the delivery options included 4 open beams, 12 open beams, 4 wedged beams, and 12 wedged beams. Beam directions and relative weights were optimized for a range of critical structure dose-volume constraints for the lungs and esophagus. Cord dose was restricted to 45 Gy. Using the interactive interface, the physician explored how the tumor dose changed as critical structure dose-volume constraints were tightened or relaxed and selected the best compromise for each delivery option. The corresponding treatment plans were calculated and compared with the linear parameterization presented to the physician in TPEx. The linear fits were best for the maximum PTV dose and worst

  20. The Pathways fertility preservation decision aid website for women with cancer: development and field testing.

    Science.gov (United States)

    Woodard, Terri L; Hoffman, Aubri S; Covarrubias, Laura A; Holman, Deborah; Schover, Leslie; Bradford, Andrea; Hoffman, Derek B; Mathur, Aakrati; Thomas, Jerah; Volk, Robert J

    2018-02-01

    To improve survivors' awareness and knowledge of fertility preservation counseling and treatment options, this study engaged survivors and providers to design, develop, and field-test Pathways: a fertility preservation patient decision aid website for young women with cancer©. Using an adapted user-centered design process, our stakeholder advisory group and research team designed and optimized the Pathways patient decision aid website through four iterative cycles of review and revision with clinicians (n = 21) and survivors (n = 14). Field-testing (n = 20 survivors) assessed post-decision aid scores on the Fertility Preservation Knowledge Scale, feasibility of assessing women's decision-making values while using the website, and website usability/acceptability ratings. Iterative stakeholder engagement optimized the Pathways decision aid website to meet survivors' and providers' needs, including providing patient-friendly information and novel features such as interactive value clarification exercises, testimonials that model shared decision making, financial/referral resources, and a printable personal summary. Survivors scored an average of 8.2 out of 13 (SD 1.6) on the Fertility Preservation Knowledge Scale. They rated genetic screening and having a biological child as strong factors in their decision-making, and 71% indicated a preference for egg freezing. Most women (> 85%) rated Pathways favorably, and all women (100%) said they would recommend it to other women. The Pathways decision aid is a usable and acceptable tool to help women learn about fertility preservation. The Pathways decision aid may help women make well-informed values-based decisions and prevent future infertility-related distress.

  1. The PD1:PD-L1/2 Pathway from Discovery to Clinical Implementation.

    Science.gov (United States)

    Bardhan, Kankana; Anagnostou, Theodora; Boussiotis, Vassiliki A

    2016-01-01

    The immune system maintains a critically organized network to defend against foreign particles, while evading self-reactivity simultaneously. T lymphocytes function as effectors and play an important regulatory role to orchestrate the immune signals. Although central tolerance mechanism results in the removal of the most of the autoreactive T cells during thymic selection, a fraction of self-reactive lymphocytes escapes to the periphery and pose a threat to cause autoimmunity. The immune system evolved various mechanisms to constrain such autoreactive T cells and maintain peripheral tolerance, including T cell anergy, deletion, and suppression by regulatory T cells (T Regs ). These effects are regulated by a complex network of stimulatory and inhibitory receptors expressed on T cells and their ligands, which deliver cell-to-cell signals that dictate the outcome of T cell encountering with cognate antigens. Among the inhibitory immune mediators, the pathway consisting of the programed cell death 1 (PD-1) receptor (CD279) and its ligands PD-L1 (B7-H1, CD274) and PD-L2 (B7-DC, CD273) plays an important role in the induction and maintenance of peripheral tolerance and for the maintenance of the stability and the integrity of T cells. However, the PD-1:PD-L1/L2 pathway also mediates potent inhibitory signals to hinder the proliferation and function of T effector cells and have inimical effects on antiviral and antitumor immunity. Therapeutic targeting of this pathway has resulted in successful enhancement of T cell immunity against viral pathogens and tumors. Here, we will provide a brief overview on the properties of the components of the PD-1 pathway, the signaling events regulated by PD-1 engagement, and their consequences on the function of T effector cells.

  2. The PD1: PD-L1/2 pathway from discovery to clinical implementation

    Directory of Open Access Journals (Sweden)

    Kankana Bardhan

    2016-12-01

    Full Text Available The immune system has the difficult challenge of discerning and defending against a diversity of microbial pathogens, while simultaneously avoiding self-reactivity. T lymphocytes function as effectors and regulators of the immune system. While central tolerance mechanism results in deletion of the majority of self-reactive T lymphocytes during thymic selection, a fraction of self reactive lymphocytes escapes to the periphery and retains the potential to inflict destructive autoimmune pathology. The immune system evolved various mechanisms to restrain such auto-reactive T cells and maintain peripheral tolerance, including T cell anergy, deletion, and suppression by regulatory T cells (TRegs. These effects are regulated by a complex network of stimulatory and inhibitory receptors expressed on T cells and their ligands, which deliver cell-to-cell signals that dictate the outcome of T cell encountering with cognate antigens. Among the inhibitory immune mediators, the pathway consisting of the programmed cell death 1 (PD-1 receptor (CD279 and its ligands PD-L1 (B7-H1, CD274 and PD-L2 (B7-DC; CD273 plays a vital role in the induction and maintenance of peripheral tolerance and for the maintenance of T cell homeostasis. In contrast to its beneficial role in self-tolerance, the PD-1: PD-L1/L2 pathway mediates potent inhibitory signals that prevent the expansion and function of T effector cells and have detrimental effects on antiviral and antitumor immunity. Therapeutic targeting of this pathway has resulted in successful enhancement of T cell immunity against viral pathogens and tumors. Here, we will provide a brief overview on the properties of the components of the PD-1 pathway, the signaling events that are regulated by PD-1 triggering, and their consequences on the function of T effector cells.

  3. A Functional Neuroimaging Analysis of the Trail Making Test-B: Implications for Clinical Application

    Directory of Open Access Journals (Sweden)

    Mark D. Allen

    2011-01-01

    Full Text Available Recent progress has been made using fMRI as a clinical assessment tool, often employing analogues of traditional “paper and pencil” tests. The Trail Making Test (TMT, popular for years as a neuropsychological exam, has been largely ignored in the realm of neuroimaging, most likely because its physical format and administration does not lend itself to straightforward adaptation as an fMRI paradigm. Likewise, there is relatively more ambiguity about the neural systems associated with this test than many other tests of comparable clinical use. In this study, we describe an fMRI version of Trail Making Test-B (TMTB that maintains the core functionality of the TMT while optimizing its use for both research and clinical settings. Subjects (N = 32 were administered the Functional Trail Making Test-B (f-TMTB. Brain region activations elicited by the f-TMTB were consistent with expectations given by prior TMT neurophysiological studies, including significant activations in the ventral and dorsal visual pathways and the medial pre-supplementary motor area. The f-TMTB was further evaluated for concurrent validity with the traditional TMTB using an additional sample of control subjects (N = 100. Together, these results support the f-TMTB as a viable neuroimaging adaptation of the TMT that is optimized to evoke maximally robust fMRI activation with minimal time and equipment requirements.

  4. Durable efficacy of enfuvirtide over 48 weeks in heavily treatment-experienced HIV-1-infected patients in the T-20 versus optimized background regimen only 1 and 2 clinical trials

    NARCIS (Netherlands)

    Nelson, Mark; Arastéh, Keikawus; Clotet, Bonaventura; Cooper, David A.; Henry, Keith; Katlama, Christine; Lalezari, Jacob P.; Lazzarin, Adriano; Montaner, Julio S. G.; O'Hearn, Mary; Piliero, Peter J.; Reynes, Jacques; Trottier, Benoit; Walmsley, Sharon L.; Cohen, Calvin; Eron, Joseph J.; Kuritzkes, Daniel R.; Lange, Joep; Stellbrink, Hans-Jürgen; Delfraissy, Jean-François; Buss, Neil E.; Donatacci, Lucille; Wat, Cynthia; Smiley, Lynn; Wilkinson, Martin; Valentine, Adeline; Guimaraes, Denise; DeMasi, Ralph; Chung, Jain; Salgo, Miklos P.

    2005-01-01

    The T-20 Versus Optimized Background Regimen Only (TORO) 1 and TORO 2 clinical trials are open-label, controlled, parallel-group, phase 3 studies comparing enfuvirtide plus an optimized background (OB) of antiretrovirals (n = 661) with OB alone (n = 334) in treatment-experienced HIV-1-infected

  5. Pareto optimality in organelle energy metabolism analysis.

    Science.gov (United States)

    Angione, Claudio; Carapezza, Giovanni; Costanza, Jole; Lió, Pietro; Nicosia, Giuseppe

    2013-01-01

    In low and high eukaryotes, energy is collected or transformed in compartments, the organelles. The rich variety of size, characteristics, and density of the organelles makes it difficult to build a general picture. In this paper, we make use of the Pareto-front analysis to investigate the optimization of energy metabolism in mitochondria and chloroplasts. Using the Pareto optimality principle, we compare models of organelle metabolism on the basis of single- and multiobjective optimization, approximation techniques (the Bayesian Automatic Relevance Determination), robustness, and pathway sensitivity analysis. Finally, we report the first analysis of the metabolic model for the hydrogenosome of Trichomonas vaginalis, which is found in several protozoan parasites. Our analysis has shown the importance of the Pareto optimality for such comparison and for insights into the evolution of the metabolism from cytoplasmic to organelle bound, involving a model order reduction. We report that Pareto fronts represent an asymptotic analysis useful to describe the metabolism of an organism aimed at maximizing concurrently two or more metabolite concentrations.

  6. Metabolic engineering of E. coli top 10 for production of vanillin through FA catabolic pathway and bioprocess optimization using RSM.

    Science.gov (United States)

    Chakraborty, Debkumar; Gupta, Gaganjot; Kaur, Baljinder

    2016-12-01

    Metabolic engineering and construction of recombinant Escherichia coli strains carrying feruloyl-CoA synthetase and enoyl-CoA hydratase genes for the bioconversion of ferulic acid to vanillin offers an alternative way to produce vanillin. Isolation and designing of fcs and ech genes was carried out using computer assisted protocol and the designed vanillin biosynthetic gene cassette was cloned in pCCIBAC expression vector for introduction in E. coli top 10. Recombinant strain was implemented for the statistical optimization of process parameters influencing F A to vanillin biotransformation. CCD matrix constituted of process variables like FA concentration, time, temperature and biomass with intracellular, extracellular and total vanillin productions as responses. Production was scaled up and 68 mg/L of vanillin was recovered from 10 mg/L of FA using cell extracts from 1 mg biomass within 30 min. Kinetic activity of enzymes were characterized. From LCMS-ESI analysis a metabolic pathway of FA degradation and vanillin production was predicted. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. What is the optimal management of high risk, clinically localized prostate cancer?

    Science.gov (United States)

    Eastham, James A; Evans, Christopher P; Zietman, Anthony

    2010-01-01

    To summarize the presentations and debate regarding the optimal treatment of localized high-risk prostate cancer as presented at the 2009 Spring Meeting of the Society of Urologic Oncology. The debate was centered on presentations arguing for radical prostatectomy (RP) or radiotherapy as the optimal treatment for this condition. The meeting presentations are summarized by their respective presenters herein. Dr. James Eastham presents the varied definitions for "high-risk" prostate cancer as strongly influencing which patients end up in this cohort. Based upon this, between 3% and 38% of patients with high-risk features could be defined as "high-risk". Despite that, these men do not have a uniformly poor prognosis after RP, and attention to surgical principles as outlined improve outcomes. Disease-specific survival at 12 years is excellent and up to one-half of these men may not need adjuvant or salvage therapies, depending on their specific disease characteristics. Adjuvant or salvage radiotherapies improve outcomes and are part of a sequential approach to treating these patients. Dr. Anthony Zietman presented radiotherapy as the gold-standard based upon large, randomized clinical trials of intermediate- and high-risk prostate cancer patients. Compared with androgen deprivation alone, the addition of radiotherapy provided a 12% cancer-specific survival advantage and 10% overall survival advantage. Dose escalation seems to confer further improvements in cancer control without significant escalation of toxicities, with more data forthcoming. There are no randomized trials comparing RP to radiotherapy for any risk category. In high-risk prostate cancer patients, both approaches have potential benefits and cumulative toxicities that must be matched to disease characteristics and patient expectations in selecting a treatment course. Copyright (c) 2010 Elsevier Inc. All rights reserved.

  8. Evaluating Dopamine Reward Pathway in ADHD; clinical implications

    International Nuclear Information System (INIS)

    Volkow, N.D.; Wang, G.; Volkow, N.D.; Wang, G.-J.; Kollins, S.H.; Wigal, T.L.; Newcorn, J.H.; Telang, F.; Fowler, J.S.; Zhu, W.; Logan, J.; Ma, Y.; Pradhan, K.; Wong, C.T.; Swanson, J.M.

    2009-01-01

    Attention-deficit/hyperactivity disorder (ADHD) - characterized by symptoms of inattention and hyperactivity-impulsivity - is the most prevalent childhood psychiatric disorder that frequently persists into adulthood, and there is increasing evidence of reward-motivation deficits in this disorder. To evaluate biological bases that might underlie a reward/motivation deficit by imaging key components of the brain dopamine reward pathway (mesoaccumbens). We used positron emission tomography to measure dopamine synaptic markers (transporters and D 2 /D 3 receptors) in 53 nonmedicated adults with ADHD and 44 healthy controls between 2001-2009 at Brookhaven National Laboratory. We measured specific binding of positron emission tomographic radioligands for dopamine transporters (DAT) using [ 11 C]cocaine and for D 2 /D 3 receptors using [ 11 C]raclopride, quantified as binding potential (distribution volume ratio -1). For both ligands, statistical parametric mapping showed that specific binding was lower in ADHD than in controls (threshold for significance set at P 2 /D 3 receptors, the mean accumbens for controls was 2.85 vs 2.68 for those with ADHD (95% CI, 0.06-0.30, P = .004); and in the midbrain, it was for controls 0.28 vs 0.18 for those with ADHD (95% CI, 0.02-0.17, P = .01). The analysis also corroborated differences in the left caudate: the mean DAT for controls was 0.66 vs 0.53 for those with ADHD (95% CI, 0.04-0.22; P = .003) and the mean D 2 /D 3 for controls was 2.80 vs 2.47 for those with ADHD (95% CI, 0.10-0.56; P = .005) and differences in D 2 /D 3 in the hypothalamic region, with controls having a mean of 0.12 vs 0.05 for those with ADHD (95% CI, 0.02-0.12; P = .004). Ratings of attention correlated with D 2 /D 3 in the accumbens (r = 0.35; 95% CI, 0.15-0.52; P = .001), midbrain (r = 0.35; 95% CI, 0.14-0.52; P = .001), caudate (r = 0.32; 95% CI, 0.11-0.50; P = .003), and hypothalamic (r = 0.31; CI, 0.10-0.49; P = .003) regions and with DAT in the midbrain

  9. Improving mental health care transitions for children and youth: a protocol to implement and evaluate an emergency department clinical pathway.

    Science.gov (United States)

    Jabbour, Mona; Reid, S; Polihronis, C; Cloutier, P; Gardner, W; Kennedy, A; Gray, C; Zemek, R; Pajer, K; Barrowman, N; Cappelli, M

    2016-07-07

    While the emergency department (ED) is often a first point of entry for children and youth with mental health (MH) concerns, there is a limited capacity to respond to MH needs in this setting. Child MH systems are typically fragmented among multiple ministries, organizations, and providers. Communication among these groups is often poor, resulting in gaps, particularly in transitions of care, for this vulnerable population. The evidence-based Emergency Department Mental Health Clinical Pathway (EDMHCP) was created with two main goals: (1) to guide risk assessment and disposition decision-making for children and youth presenting to the ED with MH concerns and (2) to provide a streamlined transition to follow-up services with community MH agencies (CMHAs) and other providers. The purpose of this paper is to describe our study protocol to implement and evaluate the EDMHCP. This mixed methods health services research project will involve implementation and evaluation of the EDMHCP in four exemplar ED-CMHA dyads. The Theoretical Domains Framework will be used to develop a tailored intervention strategy to implement the EDMHCP. A multiple baseline study design and interrupted time-series analysis will be used to determine if the EDMHCP has improved health care utilization, medical management of the MH problems, and health sector coordination. The primary process outcome will be the proportion of patients with MH-specific recommendations documented in the health record. The primary service outcome will be the proportion of patients receiving the EDMHCP-recommended follow-up at 24-h or at 7 days. Data sources will include qualitative interviews, health record audits, administrative databases, and patient surveys. A concurrent process evaluation will be conducted to assess the degree of variability and fidelity in implementation across the sites. This paper presents a novel model for measuring the effects of the EDMHCP. Our development process will identify how the EDMHCP

  10. Multi-objective optimization of inverse planning for accurate radiotherapy

    International Nuclear Information System (INIS)

    Cao Ruifen; Pei Xi; Cheng Mengyun; Li Gui; Hu Liqin; Wu Yican; Jing Jia; Li Guoli

    2011-01-01

    The multi-objective optimization of inverse planning based on the Pareto solution set, according to the multi-objective character of inverse planning in accurate radiotherapy, was studied in this paper. Firstly, the clinical requirements of a treatment plan were transformed into a multi-objective optimization problem with multiple constraints. Then, the fast and elitist multi-objective Non-dominated Sorting Genetic Algorithm (NSGA-II) was introduced to optimize the problem. A clinical example was tested using this method. The results show that an obtained set of non-dominated solutions were uniformly distributed and the corresponding dose distribution of each solution not only approached the expected dose distribution, but also met the dose-volume constraints. It was indicated that the clinical requirements were better satisfied using the method and the planner could select the optimal treatment plan from the non-dominated solution set. (authors)

  11. Optimization of fractionated radiotherapy of tumors

    International Nuclear Information System (INIS)

    Ivanov, V.K.

    1984-01-01

    Underlying modern conceptions of clinical radiobiology and mathematic methods in system theory a model of radiation therapy for tumors is developed. To obtain optimal fractionating conditions the principle of gradual optimization is used. A optimal therapeutic method permits to minimize the survival of a tumor cell population with localized lesions of the intact tissue. An analytic research is carried out for the simplest variant of the model. By help of a SORT-program unit the conditions are ascertained for gradual optimization of radiotherapy. (author)

  12. Navigating the pathway to robotic competency in general thoracic surgery.

    Science.gov (United States)

    Seder, Christopher W; Cassivi, Stephen D; Wigle, Dennis A

    2013-01-01

    Although robotic technology has addressed many of the limitations of traditional videoscopic surgery, robotic surgery has not gained widespread acceptance in the general thoracic community. We report our initial robotic surgery experience and propose a structured, competency-based pathway for the development of robotic skills. Between December 2008 and February 2012, a total of 79 robot-assisted pulmonary, mediastinal, benign esophageal, or diaphragmatic procedures were performed. Data on patient characteristics and perioperative outcomes were retrospectively collected and analyzed. During the study period, one surgeon and three residents participated in a triphasic, competency-based pathway designed to teach robotic skills. The pathway consisted of individual preclinical learning followed by mentored preclinical exercises and progressive clinical responsibility. The robot-assisted procedures performed included lung resection (n = 38), mediastinal mass resection (n = 19), hiatal or paraesophageal hernia repair (n = 12), and Heller myotomy (n = 7), among others (n = 3). There were no perioperative mortalities, with a 20% complication rate and a 3% readmission rate. Conversion to a thoracoscopic or open approach was required in eight pulmonary resections to facilitate dissection (six) or to control hemorrhage (two). Fewer major perioperative complications were observed in the later half of the experience. All residents who participated in the thoracic surgery robotic pathway perform robot-assisted procedures as part of their clinical practice. Robot-assisted thoracic surgery can be safely learned when skill acquisition is guided by a structured, competency-based pathway.

  13. Genome wide expression analysis in HPV16 Cervical Cancer: identification of altered metabolic pathways

    Directory of Open Access Journals (Sweden)

    Salcedo Mauricio

    2007-09-01

    Full Text Available Abstract Background Cervical carcinoma (CC is a leading cause of death among women worldwide. Human papilloma virus (HPV is a major etiological factor in CC and HPV 16 is the more frequent viral type present. Our aim was to characterize metabolic pathways altered in HPV 16 tumor samples by means of transcriptome wide analysis and bioinformatics tools for visualizing expression data in the context of KEGG biological pathways. Results We found 2,067 genes significantly up or down-modulated (at least 2-fold in tumor clinical samples compared to normal tissues, representing ~3.7% of analyzed genes. Cervical carcinoma was associated with an important up-regulation of Wnt signaling pathway, which was validated by in situ hybridization in clinical samples. Other up-regulated pathways were those of calcium signaling and MAPK signaling, as well as cell cycle-related genes. There was down-regulation of focal adhesion, TGF-β signaling, among other metabolic pathways. Conclusion This analysis of HPV 16 tumors transcriptome could be useful for the identification of genes and molecular pathways involved in the pathogenesis of cervical carcinoma. Understanding the possible role of these proteins in the pathogenesis of CC deserves further studies.

  14. Chapter 3: Omics Advances of Biosynthetic Pathways of Isoprenoid Production in Microalgae

    Energy Technology Data Exchange (ETDEWEB)

    Paniagua-Michel, J.; Subramanian, Venkataramanan

    2017-01-01

    In this chapter, the current status of microalgal isoprenoids and the role of omics technologies, or otherwise specified, in bioproducts optimization and applications are reviewed. Emphasis is focused in the metabolic pathways of microalgae involved in the production of commercially important products, namely, hydrocarbons and biofuels, nutraceuticals, and pharmaceuticals.

  15. Can we safely target the WNT pathway?

    Science.gov (United States)

    Kahn, Michael

    2015-01-01

    WNT–β-catenin signalling is involved in a multitude of developmental processes and the maintenance of adult tissue homeostasis by regulating cell proliferation, differentiation, migration, genetic stability and apoptosis, as well as by maintaining adult stem cells in a pluripotent state. Not surprisingly, aberrant regulation of this pathway is therefore associated with a variety of diseases, including cancer, fibrosis and neurodegeneration. Despite this knowledge, therapeutic agents specifically targeting the WNT pathway have only recently entered clinical trials and none has yet been approved. This Review examines the problems and potential solutions to this vexing situation and attempts to bring them into perspective. PMID:24981364

  16. The evolution of the TOR pathway and its role in cancer.

    Science.gov (United States)

    Beauchamp, E M; Platanias, L C

    2013-08-22

    The target of rapamycin (TOR) pathway is highly conserved among eukaryotes and has evolved to couple nutrient sensing to cellular growth. TOR is found in two distinct signaling complexes in cells, TOR complex 1 (TORC1) and TOR complex 2 (TORC2). These complexes are differentially regulated and act as effectors for the generation of signals that drive diverse cellular processes such as growth, proliferation, protein synthesis, rearrangement of the cytoskeleton, autophagy, metabolism and survival. Mammalian TOR (mTOR) is very important for development in embryos, while in adult organisms it is linked to aging and lifespan effects. In humans, the mTOR pathway is implicated in the tumorigenesis of multiple cancer types and its deregulation is associated with familial cancer syndromes. Because of its high biological relevance, different therapeutic strategies have been developed to target this signaling cascade, resulting in the emergence of unique pharmacological inhibitors that are either already approved for use in clinical oncology or currently under preclinical or clinical development. Multimodal treatment strategies that simultaneously target multiple nodes of the pathway and/or negative feedback regulatory loops may ultimately provide the best therapeutic advantage in targeting this pathway for the treatment of malignancies.

  17. Simultaneous optimization of sequential IMRT plans

    International Nuclear Information System (INIS)

    Popple, Richard A.; Prellop, Perri B.; Spencer, Sharon A.; Santos, Jennifer F. de los; Duan, Jun; Fiveash, John B.; Brezovich, Ivan A.

    2005-01-01

    Radiotherapy often comprises two phases, in which irradiation of a volume at risk for microscopic disease is followed by a sequential dose escalation to a smaller volume either at a higher risk for microscopic disease or containing only gross disease. This technique is difficult to implement with intensity modulated radiotherapy, as the tolerance doses of critical structures must be respected over the sum of the two plans. Techniques that include an integrated boost have been proposed to address this problem. However, clinical experience with such techniques is limited, and many clinicians are uncomfortable prescribing nonconventional fractionation schemes. To solve this problem, we developed an optimization technique that simultaneously generates sequential initial and boost IMRT plans. We have developed an optimization tool that uses a commercial treatment planning system (TPS) and a high level programming language for technical computing. The tool uses the TPS to calculate the dose deposition coefficients (DDCs) for optimization. The DDCs were imported into external software and the treatment ports duplicated to create the boost plan. The initial, boost, and tolerance doses were specified and used to construct cost functions. The initial and boost plans were optimized simultaneously using a gradient search technique. Following optimization, the fluence maps were exported to the TPS for dose calculation. Seven patients treated using sequential techniques were selected from our clinical database. The initial and boost plans used to treat these patients were developed independently of each other by dividing the tolerance doses proportionally between the initial and boost plans and then iteratively optimizing the plans until a summation that met the treatment goals was obtained. We used the simultaneous optimization technique to generate plans that met the original planning goals. The coverage of the initial and boost target volumes in the simultaneously optimized

  18. Optimizing resource allocation and patient flow: process analysis and reorganization in three chemotherapy outpatient clinics.

    Science.gov (United States)

    Holmes, Morgan; Bodie, Kelly; Porter, Geoffrey; Sullivan, Victoria; Tarasuk, Joy; Trembley, Jodie; Trudeau, Maureen

    2010-01-01

    Optimizing human and physical resources is a major concern for cancer care decision-makers and practitioners. This issue is particularly acute in the context of ambulatory out patient chemotherapy clinics, especially when - as is the case almost everywhere in the industrialized world - the number of people requiring systemic therapy is increasing while budgets, staffing and physical space remain static. Recent initiatives at three hospital-based chemotherapy units - in Halifax, Toronto and Kingston - shed light on the value of process analysis and reorganization for using existing human and physical resources to their full potential, improving patient flow and enhancing patient satisfaction. The steps taken in these settings are broadly applicable to other healthcare settings and would likely result in similar benefits in those environments.

  19. Henoch schonlein purpura--a 5-year review and proposed pathway.

    Directory of Open Access Journals (Sweden)

    Louise Watson

    Full Text Available Henoch Schonlein Purpura (HSP is the commonest systemic vasculitis of childhood typically presenting with a palpable purpuric rash and frequently involving the renal system. We are the first group to clinically assess, critically analyse and subsequently revise a nurse led monitoring pathway for this condition.A cohort of 102 children presenting with HSP to a secondary/tertiary level UK paediatric hospital over a five year period, were monitored using a nurse led care pathway. Using this cohort, the incidence (6.21 cases per 100,000 children per year and natural disease course of HSP nephritis (46% initial renal inflammation; 9% subsequent renal referral; 1% renal biopsy and immunosuppression was determined. Older patients were at higher risk of requiring a renal referral (renal referral 12.3 (8.4-13.5 years vs. normal outcome 6.0 (3.7-8.5 years; p<0.01. A normal urinalysis on day 7 had a 97% (confidence interval 90 to 99% negative predictive value in predicting a normal renal outcome.Using this data and existing literature base, The Alder Hey Henoch Schonlein Purpura Pathway was developed, a revised pathway for the screening of poor renal outcome in HSP. This is based on a six-month monitoring period for all patients presenting with HSP, which importantly prioritises patients according to the urine findings on day 7 and thus intensively monitors those at higher risk of developing nephritis. The pathway could be easily adapted for use in different settings and resources.The introduction of a standardised pathway for the monitoring of HSP will facilitate the implementation of disease registries to further our understanding of the condition and permit future clinical trials.

  20. Cost comparison of orthopaedic fracture pathways using discrete event simulation in a Glasgow hospital

    Science.gov (United States)

    Jenkins, Paul J; McDonald, David A; Van Der Meer, Robert; Morton, Alec; Nugent, Margaret; Rymaszewski, Lech A

    2017-01-01

    Objective Healthcare faces the continual challenge of improving outcome while aiming to reduce cost. The aim of this study was to determine the micro cost differences of the Glasgow non-operative trauma virtual pathway in comparison to a traditional pathway. Design Discrete event simulation was used to model and analyse cost and resource utilisation with an activity-based costing approach. Data for a full comparison before the process change was unavailable so we used a modelling approach, comparing a virtual fracture clinic (VFC) with a simulated traditional fracture clinic (TFC). Setting The orthopaedic unit VFC pathway pioneered at Glasgow Royal Infirmary has attracted significant attention and interest and is the focus of this cost study. Outcome measures Our study focused exclusively on patients with non-operative trauma attending emergency department or the minor injuries unit and the subsequent step in the patient pathway. Retrospective studies of patient outcomes as a result of the protocol introductions for specific injuries are presented in association with activity costs from the models. Results Patients are satisfied with the new pathway, the information provided and the outcome of their injuries (Evidence Level IV). There was a 65% reduction in the number of first outpatient face-to-face (f2f) attendances in orthopaedics. In the VFC pathway, the resources required per day were significantly lower for all staff groups (p≤0.001). The overall cost per patient of the VFC pathway was £22.84 (95% CI 21.74 to 23.92) per patient compared with £36.81 (95% CI 35.65 to 37.97) for the TFC pathway. Conclusions Our results give a clearer picture of the cost comparison of the virtual pathway over a wholly traditional f2f clinic system. The use of simulation-based stochastic costings in healthcare economic analysis has been limited to date, but this study provides evidence for adoption of this method as a basis for its application in other healthcare settings

  1. Multiparameter optimization of mammography: an update

    Science.gov (United States)

    Jafroudi, Hamid; Muntz, E. P.; Jennings, Robert J.

    1994-05-01

    Previously in this forum we have reported the application of multiparameter optimization techniques to the design of a minimum dose mammography system. The approach used a reference system to define the physical imaging performance required and the dose to which the dose for the optimized system should be compared. During the course of implementing the resulting design in hardware suitable for laboratory testing, the state of the art in mammographic imaging changed, so that the original reference system, which did not have a grid, was no longer appropriate. A reference system with a grid was selected in response to this change, and at the same time the optimization procedure was modified, to make it more general and to facilitate study of the optimized design under a variety of conditions. We report the changes in the procedure, and the results obtained using the revised procedure and the up- to-date reference system. Our results, which are supported by laboratory measurements, indicate that the optimized design can image small objects as well as the reference system using only about 30% of the dose required by the reference system. Hardware meeting the specification produced by the optimization procedure and suitable for clinical use is currently under evaluation in the Diagnostic Radiology Department at the Clinical Center, NH.

  2. Conventional treatment planning optimization using simulated annealing

    International Nuclear Information System (INIS)

    Morrill, S.M.; Langer, M.; Lane, R.G.

    1995-01-01

    Purpose: Simulated annealing (SA) allows for the implementation of realistic biological and clinical cost functions into treatment plan optimization. However, a drawback to the clinical implementation of SA optimization is that large numbers of beams appear in the final solution, some with insignificant weights, preventing the delivery of these optimized plans using conventional (limited to a few coplanar beams) radiation therapy. A preliminary study suggested two promising algorithms for restricting the number of beam weights. The purpose of this investigation was to compare these two algorithms using our current SA algorithm with the aim of producing a algorithm to allow clinically useful radiation therapy treatment planning optimization. Method: Our current SA algorithm, Variable Stepsize Generalized Simulated Annealing (VSGSA) was modified with two algorithms to restrict the number of beam weights in the final solution. The first algorithm selected combinations of a fixed number of beams from the complete solution space at each iterative step of the optimization process. The second reduced the allowed number of beams by a factor of two at periodic steps during the optimization process until only the specified number of beams remained. Results of optimization of beam weights and angles using these algorithms were compared using a standard cadre of abdominal cases. The solution space was defined as a set of 36 custom-shaped open and wedged-filtered fields at 10 deg. increments with a target constant target volume margin of 1.2 cm. For each case a clinically-accepted cost function, minimum tumor dose was maximized subject to a set of normal tissue binary dose-volume constraints. For this study, the optimized plan was restricted to four (4) fields suitable for delivery with conventional therapy equipment. Results: The table gives the mean value of the minimum target dose obtained for each algorithm averaged over 5 different runs and the comparable manual treatment

  3. Clinically Applicable Inhibitors Impacting Genome Stability.

    Science.gov (United States)

    Prakash, Anu; Garcia-Moreno, Juan F; Brown, James A L; Bourke, Emer

    2018-05-13

    Advances in technology have facilitated the molecular profiling (genomic and transcriptomic) of tumours, and has led to improved stratification of patients and the individualisation of treatment regimes. To fully realize the potential of truly personalised treatment options, we need targeted therapies that precisely disrupt the compensatory pathways identified by profiling which allow tumours to survive or gain resistance to treatments. Here, we discuss recent advances in novel therapies that impact the genome (chromosomes and chromatin), pathways targeted and the stage of the pathways targeted. The current state of research will be discussed, with a focus on compounds that have advanced into trials (clinical and pre-clinical). We will discuss inhibitors of specific DNA damage responses and other genome stability pathways, including those in development, which are likely to synergistically combine with current therapeutic options. Tumour profiling data, combined with the knowledge of new treatments that affect the regulation of essential tumour signalling pathways, is revealing fundamental insights into cancer progression and resistance mechanisms. This is the forefront of the next evolution of advanced oncology medicine that will ultimately lead to improved survival and may, one day, result in many cancers becoming chronic conditions, rather than fatal diseases.

  4. Thrombolysis and clinical outcome in patients with stroke after implementation of the Tyrol Stroke Pathway: a retrospective observational study.

    Science.gov (United States)

    Willeit, Johann; Geley, Theresa; Schöch, Johannes; Rinner, Heinrich; Tür, Andreas; Kreuzer, Hans; Thiemann, Norbert; Knoflach, Michael; Toell, Thomas; Pechlaner, Raimund; Willeit, Karin; Klingler, Natalie; Praxmarer, Silvia; Baubin, Michael; Beck, Gertrud; Berek, Klaus; Dengg, Christian; Engelhardt, Klaus; Erlacher, Thomas; Fluckinger, Thomas; Grander, Wilhelm; Grossmann, Josef; Kathrein, Hermann; Kaiser, Norbert; Matosevic, Benjamin; Matzak, Heinrich; Mayr, Markus; Perfler, Robert; Poewe, Werner; Rauter, Alexandra; Schoenherr, Gudrun; Schoenherr, Hans-Robert; Schinnerl, Adolf; Spiss, Heinrich; Thurner, Theresa; Vergeiner, Gernot; Werner, Philipp; Wöll, Ewald; Willeit, Peter; Kiechl, Stefan

    2015-01-01

    Intravenous thrombolysis for ischaemic stroke remains underused worldwide. We aimed to assess whether our statewide comprehensive stroke management programme would improve thrombolysis use and clinical outcome in patients. In 2008-09, we designed the Tyrol Stroke Pathway, which provided information campaigns for the public and standardised the entire treatment pathway from stroke onset to outpatient rehabilitation. It was commenced in Tyrol, Austria, as a long-term routine-care programme and aimed to include all patients with stroke in the survey area. We focused on thrombolysis use and outcome in the first full 4 years of implementation (2010-13). We enrolled 4947 (99%) of 4992 patients with ischaemic stroke who were admitted to hospitals in Tyrol; 675 (14%) of the enrollees were treated with alteplase. Thrombolysis administration in Tyrol increased after programme implementation, from 160 of 1238 patients (12·9%, 95% CI 11·1-14·9) in 2010 to 213 of 1266 patients (16·8%, 14·8-19·0) in 2013 (ptrend 2010-13stroke programmes, thrombolysis administration remained stable or declined between 2010 and 2013 (mean reduction 14·4%, 95% CI 10·9-17·9). Although the 3-month mortality was not affected by our programme (137 [13%] of 1060 patients in 2010 vs 143 [13%] of 1069 patients in 2013), 3-month functional outcome significantly improved (modified Rankin Scale score 0-1 in 375 [40%] of 944 patients in 2010 vs 493 [53%] of 939 in 2013; score 0-2 in 531 [56%] patients in 2010 and 615 [65%] in 2013; ptrend 2010-13stroke management programme, thrombolysis administration increased and clinical outcome significantly improved, although mortality did not change. We hope that these results will guide health authorities and stroke physicians elsewhere when implementing similar programmes for patients with stroke. Reformpool of the Tyrolean Health Care Fund. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Apoptotic pathways of epothilone BMS 310705.

    Science.gov (United States)

    Uyar, Denise; Takigawa, Nagio; Mekhail, Tarek; Grabowski, Dale; Markman, Maurie; Lee, Francis; Canetta, Renzo; Peck, Ron; Bukowski, Ronald; Ganapathi, Ram

    2003-10-01

    BMS 310705 is a novel water-soluble analog of epothilone B currently in phase I clinical evaluation in the treatment of malignancies such as ovarian, renal, bladder, and lung carcinoma. Using an early passage cell culture model derived from the ascites of a patient clinically refractory to platinum/paclitaxel therapy, we evaluated the pathway of caspase-mediated apoptosis. Cells were treated for 1 h and subsequently evaluated for apoptosis, survival, and caspase activity. Apoptosis was determined by fluorescent microscopy. Caspase-3, -8, and -9 activities were determined by fluorometry using target tetrapeptide substrates. Mitochondrial release of cytochrome c was determined by immunoblot analysis. After treatment with BMS 310705, apoptosis was confirmed in >25% of cells at 24 h. Survival was significantly lower (P < 0.02) in cells treated with 0.05 micro M BMS 310705 vs paclitaxel. Analysis revealed an increase of caspase-9 and -3 activity; no caspase -8 activity was observed. Release of cytochrome c was detected at 12 h following treatment. SN-38 and topotecan failed to induce apoptosis. BMS 310705 induces significant apoptosis, decreases survival, and utilizes the mitochondrial-mediated pathway for apoptosis in this model.

  6. Targeting arachidonic acid pathway by natural products for cancer prevention and therapy.

    Science.gov (United States)

    Yarla, Nagendra Sastry; Bishayee, Anupam; Sethi, Gautam; Reddanna, Pallu; Kalle, Arunasree M; Dhananjaya, Bhadrapura Lakkappa; Dowluru, Kaladhar S V G K; Chintala, Ramakrishna; Duddukuri, Govinda Rao

    2016-10-01

    Arachidonic acid (AA) pathway, a metabolic process, plays a key role in carcinogenesis. Hence, AA pathway metabolic enzymes phospholipase A 2 s (PLA 2 s), cyclooxygenases (COXs) and lipoxygenases (LOXs) and their metabolic products, such as prostaglandins and leukotrienes, have been considered novel preventive and therapeutic targets in cancer. Bioactive natural products are a good source for development of novel cancer preventive and therapeutic drugs, which have been widely used in clinical practice due to their safety profiles. AA pathway inhibitory natural products have been developed as chemopreventive and therapeutic agents against several cancers. Curcumin, resveratrol, apigenin, anthocyans, berberine, ellagic acid, eugenol, fisetin, ursolic acid, [6]-gingerol, guggulsteone, lycopene and genistein are well known cancer chemopreventive agents which act by targeting multiple pathways, including COX-2. Nordihydroguaiaretic acid and baicalein can be chemopreventive molecules against various cancers by inhibiting LOXs. Several PLA 2 s inhibitory natural products have been identified with chemopreventive and therapeutic potentials against various cancers. In this review, we critically discuss the possible utility of natural products as preventive and therapeutic agents against various oncologic diseases, including prostate, pancreatic, lung, skin, gastric, oral, blood, head and neck, colorectal, liver, cervical and breast cancers, by targeting AA pathway. Further, the current status of clinical studies evaluating AA pathway inhibitory natural products in cancer is reviewed. In addition, various emerging issues, including bioavailability, toxicity and explorability of combination therapy, for the development of AA pathway inhibitory natural products as chemopreventive and therapeutic agents against human malignancy are also discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. The effectiveness of non-invasive brain stimulation in improving clinical signs of hyperkinetic movement disorders

    Directory of Open Access Journals (Sweden)

    Ignacio eObeso

    2016-01-01

    Full Text Available Repetitive transcranial magnetic stimulation (rTMS is a safe and non-invasive method for stimulating cortical neurons. In neurological realm, rTMS has prevalently been applied to understand pathophysiological mechanisms underlying movement disorders. However, this tool has also the potential to be translated into a clinically applicable therapeutic use. Several available studies supported this hypothesis, but differences in protocols, clinical enrollment and variability of rTMS effects across individuals complicate better understanding of efficient clinical protocols.The aim of this present review is to discuss to what extent the evidence provided by the therapeutic use of rTMS may be generalized. In particular, we attempted to define optimal cortical regions and stimulation protocols that have been demonstrated to maximize the effectiveness seen in the actual literature for the three most prevalent hyperkinetic movement disorders: Parkinson´s disease with levodopa-induced dyskinesias, essential tremor and dystonia. A total of 28 rTMS studies met our search criteria. Despite clinical and methodological differences, overall these studies demonstrated that therapeutic applications of rTMS to normalize pathologically decreased or increased levels of cortical activity have given moderate progress in patient´s quality of life. Moreover, the present literature suggests that altered pathophysiology in hyperkinetic movement disorders establishes motor, premotor or cerebellar structures as candidate regions to reset cortico-subcortical pathways back to normal. Although rTMS has the potential to become a powerful tool for ameliorating the clinical outcome of hyperkinetic neurological patients, until now there is not a clear consensus on optimal protocols for these motor disorders. Well-controlled multicenter randomized clinical trials with high numbers of patients are urgently required.

  8. Benfotiamine blocks three major pathways of hyperglycemic damage and prevents experimental diabetic retinopathy.

    Science.gov (United States)

    Hammes, Hans-Peter; Du, Xueliang; Edelstein, Diane; Taguchi, Tetsuya; Matsumura, Takeshi; Ju, Qida; Lin, Jihong; Bierhaus, Angelika; Nawroth, Peter; Hannak, Dieter; Neumaier, Michael; Bergfeld, Regine; Giardino, Ida; Brownlee, Michael

    2003-03-01

    Three of the major biochemical pathways implicated in the pathogenesis of hyperglycemia induced vascular damage (the hexosamine pathway, the advanced glycation end product (AGE) formation pathway and the diacylglycerol (DAG)-protein kinase C (PKC) pathway) are activated by increased availability of the glycolytic metabolites glyceraldehyde-3-phosphate and fructose-6-phosphate. We have discovered that the lipid-soluble thiamine derivative benfotiamine can inhibit these three pathways, as well as hyperglycemia-associated NF-kappaB activation, by activating the pentose phosphate pathway enzyme transketolase, which converts glyceraldehyde-3-phosphate and fructose-6-phosphate into pentose-5-phosphates and other sugars. In retinas of diabetic animals, benfotiamine treatment inhibited these three pathways and NF-kappaB activation by activating transketolase, and also prevented experimental diabetic retinopathy. The ability of benfotiamine to inhibit three major pathways simultaneously might be clinically useful in preventing the development and progression of diabetic complications.

  9. Clinical practice guidelines for the management of acute limb compartment syndrome following trauma.

    Science.gov (United States)

    Wall, Christopher J; Lynch, Joan; Harris, Ian A; Richardson, Martin D; Brand, Caroline; Lowe, Adrian J; Sugrue, Michael

    2010-03-01

    Acute compartment syndrome is a serious and not uncommon complication of limb trauma. The condition is a surgical emergency, and is associated with significant morbidity if not managed appropriately. There is variation in management of acute limb compartment syndrome in Australia. Clinical practice guidelines for the management of acute limb compartment syndrome following trauma were developed in accordance with Australian National Health and Medical Research Council recommendations. The guidelines were based on critically appraised literature evidence and the consensus opinion of a multidisciplinary team involved in trauma management who met in a nominal panel process. Recommendations were developed for key decision nodes in the patient care pathway, including methods of diagnosis in alert and unconscious patients, appropriate assessment of compartment pressure, timing and technique of fasciotomy, fasciotomy wound management, and prevention of compartment syndrome in patients with limb injuries. The recommendations were largely consensus based in the absence of well-designed clinical trial evidence. Clinical practice guidelines for the management of acute limb compartment syndrome following trauma have been developed that will support consistency in management and optimize patient health outcomes.

  10. Survival-related profile, pathways, and transcription factors in ovarian cancer.

    Directory of Open Access Journals (Sweden)

    Anne P G Crijns

    2009-02-01

    Full Text Available BACKGROUND: Ovarian cancer has a poor prognosis due to advanced stage at presentation and either intrinsic or acquired resistance to classic cytotoxic drugs such as platinum and taxoids. Recent large clinical trials with different combinations and sequences of classic cytotoxic drugs indicate that further significant improvement in prognosis by this type of drugs is not to be expected. Currently a large number of drugs, targeting dysregulated molecular pathways in cancer cells have been developed and are introduced in the clinic. A major challenge is to identify those patients who will benefit from drugs targeting these specific dysregulated pathways.The aims of our study were (1 to develop a gene expression profile associated with overall survival in advanced stage serous ovarian cancer, (2 to assess the association of pathways and transcription factors with overall survival, and (3 to validate our identified profile and pathways/transcription factors in an independent set of ovarian cancers. METHODS AND FINDINGS: According to a randomized design, profiling of 157 advanced stage serous ovarian cancers was performed in duplicate using approximately 35,000 70-mer oligonucleotide microarrays. A continuous predictor of overall survival was built taking into account well-known issues in microarray analysis, such as multiple testing and overfitting. A functional class scoring analysis was utilized to assess pathways/transcription factors for their association with overall survival. The prognostic value of genes that constitute our overall survival profile was validated on a fully independent, publicly available dataset of 118 well-defined primary serous ovarian cancers. Furthermore, functional class scoring analysis was also performed on this independent dataset to assess the similarities with results from our own dataset. An 86-gene overall survival profile discriminated between patients with unfavorable and favorable prognosis (median survival, 19

  11. A study of the LCA based biofuel supply chain multi-objective optimization model with multi-conversion paths in China

    International Nuclear Information System (INIS)

    Liu, Zhexuan; Qiu, Tong; Chen, Bingzhen

    2014-01-01

    Highlights: • A LCA based biofuel supply chain model considering 3E criteria was proposed. • The model was used to design a supply chain considering three conversion pathways. • An experimental biofuel supply chain for China was designed. • A Pareto-optimal solution surface of this multi-objective problem was obtained. • The designed supply chain was rather robust to price variation. - Abstract: In this paper we present a life cycle assessment (LCA) based biofuel supply chain model with multi-conversion pathways. This model was formulated as a mixed integer linear programming (MILP) problem which took economic, energy, and environmental criteria (3E) into consideration. The economic objective was measured by the total annual profit. The energy objective was measured by using the average fossil energy input per megajoule (MJ) of biofuel. The environmental objective was measured by greenhouse gas (GHG) emissions per MJ of biofuel. After carefully consideration of the current situation in China, we chose to examine three conversion pathways: bio-ethanol (BE), bio-methanol (BM) and bio-diesel (BD). LCA was integrated to a multi-objective supply chain model by dividing each pathway into several individual parts and analyzing each part. The multi-objective MILP problem was solved using a ε-constraint method by defining the total annual profit as the optimization objective and assigning the average fossil energy input per MJ biofuel and GHG emissions per MJ biofuel as constraints. This model was then used to design an experimental biofuel supply chain for China. A surface of the Pareto optimal solutions was obtained by linear interpolation of the non-inferior solutions. The optimal results included the choice of optimal conversion pathway, biomass type, biomass locations, facility locations, and network topology structure in the biofuel supply chain. Distributed and centralized systems were also factored into our experimental system design. In addition, the

  12. Clinical Evaluation of Direct Aperture Optimization When Applied to Head-And-Neck IMRT

    International Nuclear Information System (INIS)

    Jones, Stephen; Williams, Matthew

    2008-01-01

    Direct Machine Parameter Optimization (DMPO) is a leaf segmentation program released as an optional item of the Pinnacle planning system (Philips Radiation Oncology Systems, Milpitas, CA); it is based on the principles of direct aperture optimization where the size, shape, and weight of individual segments are optimized to produce an intensity modulated radiation treatment (IMRT) plan. In this study, we compare DMPO to the traditional method of IMRT planning, in which intensity maps are optimized prior to conversion into deliverable multileaf collimator (MLC) apertures, and we determine if there was any dosimetric improvement, treatment efficiency gain, or planning advantage provided by the use of DMPO. Eleven head-and-neck patients treated with IMRT had treatment plans generated using each optimization method. For each patient, the same planning parameters were used for each optimization method. All calculations were performed using Pinnacle version 7.6c software and treatments were delivered using a step-and-shoot IMRT method on a Varian 2100EX linear accelerator equipped with a 120-leaf Millennium MLC (Varian Medical Systems, Palo Alto, CA). Each plan was assessed based on the calculation time, a conformity index, the composite objective value used in the optimization, the number of segments, monitor units (MUs), and treatment time. The results showed DMPO to be superior to the traditional optimization method in all areas. Considerable advantages were observed in the dosimetric quality of DMPO plans, which also required 32% less time to calculate, 42% fewer MUs, and 35% fewer segments than the conventional optimization method. These reductions translated directly into a 29% decrease in treatment times. While considerable gains were observed in planning and treatment efficiency, they were specific to our institution, and the impact of direct aperture optimization on plan quality and workflow will be dependent on the planning parameters, planning system, and

  13. Benchmarking pathway interaction network for colorectal cancer to identify dysregulated pathways

    Directory of Open Access Journals (Sweden)

    Q. Wang

    Full Text Available Different pathways act synergistically to participate in many biological processes. Thus, the purpose of our study was to extract dysregulated pathways to investigate the pathogenesis of colorectal cancer (CRC based on the functional dependency among pathways. Protein-protein interaction (PPI information and pathway data were retrieved from STRING and Reactome databases, respectively. After genes were aligned to the pathways, each pathway activity was calculated using the principal component analysis (PCA method, and the seed pathway was discovered. Subsequently, we constructed the pathway interaction network (PIN, where each node represented a biological pathway based on gene expression profile, PPI data, as well as pathways. Dysregulated pathways were then selected from the PIN according to classification performance and seed pathway. A PIN including 11,960 interactions was constructed to identify dysregulated pathways. Interestingly, the interaction of mRNA splicing and mRNA splicing-major pathway had the highest score of 719.8167. Maximum change of the activity score between CRC and normal samples appeared in the pathway of DNA replication, which was selected as the seed pathway. Starting with this seed pathway, a pathway set containing 30 dysregulated pathways was obtained with an area under the curve score of 0.8598. The pathway of mRNA splicing, mRNA splicing-major pathway, and RNA polymerase I had the maximum genes of 107. Moreover, we found that these 30 pathways had crosstalks with each other. The results suggest that these dysregulated pathways might be used as biomarkers to diagnose CRC.

  14. Optimum swimming pathways of fish spawning migrations in rivers

    Science.gov (United States)

    McElroy, Brandon; DeLonay, Aaron; Jacobson, Robert

    2012-01-01

    Fishes that swim upstream in rivers to spawn must navigate complex fluvial velocity fields to arrive at their ultimate locations. One hypothesis with substantial implications is that fish traverse pathways that minimize their energy expenditure during migration. Here we present the methodological and theoretical developments necessary to test this and similar hypotheses. First, a cost function is derived for upstream migration that relates work done by a fish to swimming drag. The energetic cost scales with the cube of a fish's relative velocity integrated along its path. By normalizing to the energy requirements of holding a position in the slowest waters at the path's origin, a cost function is derived that depends only on the physical environment and not on specifics of individual fish. Then, as an example, we demonstrate the analysis of a migration pathway of a telemetrically tracked pallid sturgeon (Scaphirhynchus albus) in the Missouri River (USA). The actual pathway cost is lower than 105 random paths through the surveyed reach and is consistent with the optimization hypothesis. The implication—subject to more extensive validation—is that reproductive success in managed rivers could be increased through manipulation of reservoir releases or channel morphology to increase abundance of lower-cost migration pathways.

  15. Expression and clinical significance of the HIF-1a/ET-2 signaling pathway during the development and treatment of polycystic ovary syndrome.

    Science.gov (United States)

    Wang, Fan; Zhang, Zhenghong; Wang, Zhaokai; Xiao, Kaizhuan; Wang, Qing; Su, Jingqian; Wang, Zhengchao

    2015-04-01

    Polycystic ovary syndrome (PCOS) is a major health problem in reproductive-aged women worldwide, but the precise pathogenesis of PCOS remains unclear. Our previous study revealed that hypoxia-inducible factor (HIF)-1a mediated endothelin (ET)-2 signaling plays an important role in ovulation in rats. Therefore, the present study used a PCOS rat model to test the hypotheses that HIF-1a signaling is expressed and inhibited in ovaries during PCOS formation and that the HIF-1a/ET-2 signaling pathway is a target of dimethyldiguanide (DMBG) in the clinical treatment of PCOS. First, the development of a PCOS model and the effect of DMBG treatment were examined through ovarian histology and serum hormone levels, which were consistent with previous reports. Second, HIF-1a and ET-2 expression were detected by immunohistochemistry and western blot. The results showed decreased HIF-1a/ET-2 expression in the ovaries of PCOS rats, whereas DMBG treatment reversed the protein decreases and improved the PCOS symptoms. Third, to understand the molecular mechanism, HIF-1a/ET-2 mRNA expression was also examined. Interestingly, HIF-1a mRNA increased in the ovaries of PCOS rats, while ET-2 mRNA decreased, indicating that HIF-1a protein degradation may be involved in POCS development and treatment. Finally, HIF prolyl hydroxylase (PHD) activity was examined to further clarify the contribution of HIF-1a signaling to the development and treatment of PCOS. The results suggested that the inhibition of HIF-1a/ET-2 signaling may be caused by increased PHD activity in PCOS. DMBG-treated PCOS may further activate HIF-1a signaling at least partly through inhibiting PHD activity. Taken together, these results indicate that HIF-1a signaling is inhibited in a PCOS rat model through increasing PHD activity. DMBG treatment improved PCOS by rescuing this pathway, suggesting that HIF-1a signaling plays an important role in the development and treatment of PCOS. This HIF-1a-mediated ET-2 signaling pathway

  16. A simple biosynthetic pathway for large product generation from small substrate amounts

    Science.gov (United States)

    Djordjevic, Marko; Djordjevic, Magdalena

    2012-10-01

    A recently emerging discipline of synthetic biology has the aim of constructing new biosynthetic pathways with useful biological functions. A major application of these pathways is generating a large amount of the desired product. However, toxicity due to the possible presence of toxic precursors is one of the main problems for such production. We consider here the problem of generating a large amount of product from a potentially toxic substrate. To address this, we propose a simple biosynthetic pathway, which can be induced in order to produce a large number of the product molecules, by keeping the substrate amount at low levels. Surprisingly, we show that the large product generation crucially depends on fast non-specific degradation of the substrate molecules. We derive an optimal induction strategy, which allows as much as three orders of magnitude increase in the product amount through biologically realistic parameter values. We point to a recently discovered bacterial immune system (CRISPR/Cas in E. coli) as a putative example of the pathway analysed here. We also argue that the scheme proposed here can be used not only as a stand-alone pathway, but also as a strategy to produce a large amount of the desired molecules with small perturbations of endogenous biosynthetic pathways.

  17. A simple biosynthetic pathway for large product generation from small substrate amounts

    Energy Technology Data Exchange (ETDEWEB)

    Djordjevic, Marko [Institute of Physiology and Biochemistry, Faculty of Biology, University of Belgrade (Serbia); Djordjevic, Magdalena [Institute of Physics Belgrade, University of Belgrade (Serbia)

    2012-10-01

    A recently emerging discipline of synthetic biology has the aim of constructing new biosynthetic pathways with useful biological functions. A major application of these pathways is generating a large amount of the desired product. However, toxicity due to the possible presence of toxic precursors is one of the main problems for such production. We consider here the problem of generating a large amount of product from a potentially toxic substrate. To address this, we propose a simple biosynthetic pathway, which can be induced in order to produce a large number of the product molecules, by keeping the substrate amount at low levels. Surprisingly, we show that the large product generation crucially depends on fast non-specific degradation of the substrate molecules. We derive an optimal induction strategy, which allows as much as three orders of magnitude increase in the product amount through biologically realistic parameter values. We point to a recently discovered bacterial immune system (CRISPR/Cas in E. coli) as a putative example of the pathway analysed here. We also argue that the scheme proposed here can be used not only as a stand-alone pathway, but also as a strategy to produce a large amount of the desired molecules with small perturbations of endogenous biosynthetic pathways. (paper)

  18. A simple biosynthetic pathway for large product generation from small substrate amounts

    International Nuclear Information System (INIS)

    Djordjevic, Marko; Djordjevic, Magdalena

    2012-01-01

    A recently emerging discipline of synthetic biology has the aim of constructing new biosynthetic pathways with useful biological functions. A major application of these pathways is generating a large amount of the desired product. However, toxicity due to the possible presence of toxic precursors is one of the main problems for such production. We consider here the problem of generating a large amount of product from a potentially toxic substrate. To address this, we propose a simple biosynthetic pathway, which can be induced in order to produce a large number of the product molecules, by keeping the substrate amount at low levels. Surprisingly, we show that the large product generation crucially depends on fast non-specific degradation of the substrate molecules. We derive an optimal induction strategy, which allows as much as three orders of magnitude increase in the product amount through biologically realistic parameter values. We point to a recently discovered bacterial immune system (CRISPR/Cas in E. coli) as a putative example of the pathway analysed here. We also argue that the scheme proposed here can be used not only as a stand-alone pathway, but also as a strategy to produce a large amount of the desired molecules with small perturbations of endogenous biosynthetic pathways. (paper)

  19. Clinical neuropsychology in South Korea.

    Science.gov (United States)

    Kim, Myung-Sun; Chey, Jeanyung

    2016-11-01

    Clinical neuropsychology in South Korea, albeit its relatively short history, has advanced dramatically. We review a brief history and current status of clinical neuropsychology in South Korea. The history, the educational pathway, the training pathway, the certification process, and careers in clinical neuropsychology in South Korea are reviewed. We have reviewed the neuropsychological services, including assessment and treatment, research on neurological and psychiatric populations, and neuropsychology education and the requirements related to education, training, and board examinations of those providing neuropsychological services in South Korea. We also describe how the Korean Society for Neuropsychology Research, the first and only meeting for neuropsychologists in the country established in 1999, has played a major role in how clinical neuropsychology is practiced and developed as a professional field in South Korea. Clinical neuropsychology in South Korea has achieved major progress over just a quarter of a century, and its future is promising in light of the increasing demand for neuropsychological services and advances in neuroscience in the country. Challenges that the community of clinical neuropsychologists are currently facing in South Korea, including formalizing neuropsychological curriculum and training programs and developing advanced credentialing procedures, are discussed.

  20. Pathway cross-talk network analysis identifies critical pathways in neonatal sepsis.

    Science.gov (United States)

    Meng, Yu-Xiu; Liu, Quan-Hong; Chen, Deng-Hong; Meng, Ying

    2017-06-01

    Despite advances in neonatal care, sepsis remains a major cause of morbidity and mortality in neonates worldwide. Pathway cross-talk analysis might contribute to the inference of the driving forces in bacterial sepsis and facilitate a better understanding of underlying pathogenesis of neonatal sepsis. This study aimed to explore the critical pathways associated with the progression of neonatal sepsis by the pathway cross-talk analysis. By integrating neonatal transcriptome data with known pathway data and protein-protein interaction data, we systematically uncovered the disease pathway cross-talks and constructed a disease pathway cross-talk network for neonatal sepsis. Then, attract method was employed to explore the dysregulated pathways associated with neonatal sepsis. To determine the critical pathways in neonatal sepsis, rank product (RP) algorithm, centrality analysis and impact factor (IF) were introduced sequentially, which synthetically considered the differential expression of genes and pathways, pathways cross-talks and pathway parameters in the network. The dysregulated pathways with the highest IF values as well as RPpathways in neonatal sepsis. By integrating three kinds of data, only 6919 common genes were included to perform the pathway cross-talk analysis. By statistic analysis, a total of 1249 significant pathway cross-talks were selected to construct the pathway cross-talk network. Moreover, 47 dys-regulated pathways were identified via attract method, 20 pathways were identified under RPpathways with the highest IF were also screened from the pathway cross-talk network. Among them, we selected 8 common pathways, i.e. critical pathways. In this study, we systematically tracked 8 critical pathways involved in neonatal sepsis by integrating attract method and pathway cross-talk network. These pathways might be responsible for the host response in infection, and of great value for advancing diagnosis and therapy of neonatal sepsis. Copyright © 2017

  1. Pathway for inpatients with depressive episode in Flemish psychiatric hospitals: a qualitative study

    Directory of Open Access Journals (Sweden)

    Simoens Steven R

    2009-10-01

    Full Text Available Abstract Background Within the context of a biopsychosocial model of the treatment of depressive episodes, a multidisciplinary approach is needed. Clinical pathways have been developed and implemented in hospitals to support multidisciplinary teamwork. The aim of this study is to explore current practice for the treatment of depressive episodes in Flemish psychiatric hospitals. Current practice in different hospitals is studied to get an idea of the similarities (outlined as a pathway and the differences in the treatment of depressive episodes. Methods A convenience sample of 11 Flemish psychiatric hospitals participated in this qualitative study. Semi-structured interviews were conducted with different types of health care professionals (n = 43. The websites of the hospitals were searched for information on their approach to treating depressive episodes. Results A flow chart was made including the identified stages of the pathway: pre-admission, admission (observation and treatment, discharge and follow-up care. The characteristics of each stage are described. Although the stages are identified in all hospitals, differences between hospitals on various levels of the pathway exist. Hospitals emphasized the individual approach of each patient. The results point to a biopsychosocial approach to treating depressive episodes. Conclusion This study outlined current practice as a pathway for Flemish inpatients with depressive episodes. Within the context of surveillance of quality and quantity of care, this study may encourage hospitals to consider developing clinical pathways.

  2. Patient engagement in healthcare: pathways for effective medical decision making

    Directory of Open Access Journals (Sweden)

    Serena Barello

    2015-04-01

    Full Text Available Making patients protagonists of decisions about their care is a primacy in the 21st century medical ethics. Precisely, to favor shared treatment decisions potentially enables patients’ autonomy and self-determination, and protects patients’ rights to make decisions about their own future care. To fully accomplish this goal, medicine should take into account the complexity of the healthcare decision making processes: patients may experience dilemmas when having to take decisions that not only concern their patient role/identity but also involve the psychosocial impact of treatments on their overall life quality. A deeper understanding of the patients’ expected role in the decision making process across their illness journey may favor the optimal implementation of this practice into the day-to-day medical agenda. In this paper, authors discuss the value of assuming the Patient Health Engagement Model to sustain successful pathways for effective medical decision making throughout the patient’s illness course. This model and its relational implication for the clinical encounter might be the base for an innovative “patient-doctor relational agenda” able to sustain an “engagement-sensitive” medical decision making.

  3. Putting Research Findings into Clinical Practice; Feasibility of integrated evidence-based care pathways in otorhinolaryngology head and neck surgery at Sultan Qaboos University Hospital, Oman

    Directory of Open Access Journals (Sweden)

    Deepa Bhargava

    2012-05-01

    Full Text Available Objectives: A perception exists that clinicians in Oman are reluctant to adopt evidence-based practice (EBP. This pilot study was undertaken to study the feasibility of using EBP pathways at the point of care in otorhinolaryngology head and neck surgery. The ultimate aim was to facilitate EBP with the probability of developing a new system for implementing research findings/translational research at the clinical point of care. Methods: A cross-sectional prospective questionnaire pilot survey of clinicians at Sultan Qaboos University Hospital (SQUH, Oman, a tertiary care medical centre, was undertaken. Respondents included 135 physicians and surgeons with between 3 months and 25 years of clinical experience and included personnel ranging from interns to senior consultants, in areas ranging from primary care to specialist care. Results: Of those polled, 90% (95% confidence interval (CI 85–95% either strongly agreed or agreed that evidence-based practice protocols (EBPP could help in decision making. A total of 87.4% of participants (95% CI 81.8–93% either strongly agreed or agreed that EBPPs can improve clinical outcomes; 91.8% of participants (95% CI 87.2–96.4% would use and apply EBPP in day-to-day care if they were available at the point of care and embedded in the hospital information system. Conclusions: The perception that clinicians at SQUH are reluctant to adopt EBP is incorrect. The introduction of EBP pathways is very feasible at the primary care level. Institutional support for embedding EBP in hospital information systems is needed as well as further outcome research to assess the improvement in quality of care.

  4. Towards Clinically Optimized MRI-guided Surgical Manipulator for Minimally Invasive Prostate Percutaneous Interventions: Constructive Design*

    Science.gov (United States)

    Eslami, Sohrab; Fischer, Gregory S.; Song, Sang-Eun; Tokuda, Junichi; Hata, Nobuhiko; Tempany, Clare M.; Iordachita, Iulian

    2013-01-01

    This paper undertakes the modular design and development of a minimally invasive surgical manipulator for MRI-guided transperineal prostate interventions. Severe constraints for the MRI-compatibility to hold the minimum artifact on the image quality and dimensions restraint of the bore scanner shadow the design procedure. Regarding the constructive design, the manipulator kinematics has been optimized and the effective analytical needle workspace is developed and followed by proposing the workflow for the manual needle insertion. A study of the finite element analysis is established and utilized to improve the mechanism weaknesses under some inevitable external forces to ensure the minimum structure deformation. The procedure for attaching a sterile plastic drape on the robot manipulator is discussed. The introduced robotic manipulator herein is aimed for the clinically prostate biopsy and brachytherapy applications. PMID:24683502

  5. Introducing care pathway commissioning to primary dental care: measuring performance.

    Science.gov (United States)

    Harris, R; Bridgman, C; Ahmad, M; Bowes, L; Haley, R; Saleem, S; Singh, R; Taylor, S

    2011-12-09

    Care pathways have been used in a variety of ways: firstly to support quality improvement through standardising clinical processes, but also for secondary purposes, by purchasers of healthcare, to monitor activity and health outcomes and to commission services. This paper focuses on reporting a secondary use of care pathways: to commission and monitor performance of primary dental care services. Findings of a project involving three dental practices implementing a system based on rating patients according to their risk of disease and need for care are outlined. Data from surgery-based clinical databases and interviews from commissioners and providers are reported. The use of both process and outcome key performance indicators in this context is discussed, as well as issues which arise such as attributability of outcome measures and strategic approaches to improving quality of care.

  6. Robust optimization methods for cardiac sparing in tangential breast IMRT

    Energy Technology Data Exchange (ETDEWEB)

    Mahmoudzadeh, Houra, E-mail: houra@mie.utoronto.ca [Mechanical and Industrial Engineering Department, University of Toronto, Toronto, Ontario M5S 3G8 (Canada); Lee, Jenny [Radiation Medicine Program, UHN Princess Margaret Cancer Centre, Toronto, Ontario M5G 2M9 (Canada); Chan, Timothy C. Y. [Mechanical and Industrial Engineering Department, University of Toronto, Toronto, Ontario M5S 3G8, Canada and Techna Institute for the Advancement of Technology for Health, Toronto, Ontario M5G 1P5 (Canada); Purdie, Thomas G. [Radiation Medicine Program, UHN Princess Margaret Cancer Centre, Toronto, Ontario M5G 2M9 (Canada); Department of Radiation Oncology, University of Toronto, Toronto, Ontario M5S 3S2 (Canada); Techna Institute for the Advancement of Technology for Health, Toronto, Ontario M5G 1P5 (Canada)

    2015-05-15

    Purpose: In left-sided tangential breast intensity modulated radiation therapy (IMRT), the heart may enter the radiation field and receive excessive radiation while the patient is breathing. The patient’s breathing pattern is often irregular and unpredictable. We verify the clinical applicability of a heart-sparing robust optimization approach for breast IMRT. We compare robust optimized plans with clinical plans at free-breathing and clinical plans at deep inspiration breath-hold (DIBH) using active breathing control (ABC). Methods: Eight patients were included in the study with each patient simulated using 4D-CT. The 4D-CT image acquisition generated ten breathing phase datasets. An average scan was constructed using all the phase datasets. Two of the eight patients were also imaged at breath-hold using ABC. The 4D-CT datasets were used to calculate the accumulated dose for robust optimized and clinical plans based on deformable registration. We generated a set of simulated breathing probability mass functions, which represent the fraction of time patients spend in different breathing phases. The robust optimization method was applied to each patient using a set of dose-influence matrices extracted from the 4D-CT data and a model of the breathing motion uncertainty. The goal of the optimization models was to minimize the dose to the heart while ensuring dose constraints on the target were achieved under breathing motion uncertainty. Results: Robust optimized plans were improved or equivalent to the clinical plans in terms of heart sparing for all patients studied. The robust method reduced the accumulated heart dose (D10cc) by up to 801 cGy compared to the clinical method while also improving the coverage of the accumulated whole breast target volume. On average, the robust method reduced the heart dose (D10cc) by 364 cGy and improved the optBreast dose (D99%) by 477 cGy. In addition, the robust method had smaller deviations from the planned dose to the

  7. Hedgehog signaling pathway in neuroblastoma differentiation.

    Science.gov (United States)

    Souzaki, Ryota; Tajiri, Tatsuro; Souzaki, Masae; Kinoshita, Yoshiaki; Tanaka, Sakura; Kohashi, Kenichi; Oda, Yoshinao; Katano, Mitsuo; Taguchi, Tomoaki

    2010-12-01

    The hedgehog (Hh) signaling pathway is activated in some adult cancers. On the other hand, the Hh signaling pathway plays an important role in the development of the neural crest in embryos. The aim of this study is to show the activation of Hh signaling pathway in neuroblastoma (NB), a pediatric malignancy arising from neural crest cells, and to reveal the meaning of the Hh signaling pathway in NB development. This study analyzed the expression of Sonic hedgehog (Shh), GLI1, and Patched 1 (Ptch1), transactivators of Hh signaling pathway, by immunohistochemistry in 82 NB and 10 ganglioneuroblastoma cases. All 92 cases were evaluated for the status of MYCN amplification. Of the 92 cases, 67 (73%) were positive for Shh, 62 cases (67%) were positive for GLI1, and 73 cases (79%) were positive for Ptch1. Only 2 (10%) of the 20 cases with MYCN amplification were positive for Shh and GLI1, and 4 cases (20%) were positive for Ptch1 (MYCN amplification vs no MYCN amplification, P ≦ .01). The percentage of GLI1-positive cells in the cases with INSS stage 1 without MYCN amplification was significantly higher than that with INSS stage 4. Of 72 cases without MYCN amplification, 60 were GLI1-positive. Twelve cases were GLI1-negative, and the prognosis of the GLI1-positive cases was significantly better than that of the GLI1-negative cases (P = .015). Most of NBs without MYCN amplification were positive for Shh, GLI1, and Ptch1. In the cases without MYCN amplification, the high expression of GLI1 was significantly associated with early clinical stage and a good prognosis of the patients. In contrast to adult cancers, the activation of the Hh signaling pathway in NB may be associated with the differentiation of the NB. Copyright © 2010 Elsevier Inc. All rights reserved.

  8. Improved prognostic classification of breast cancer defined by antagonistic activation patterns of immune response pathway modules

    International Nuclear Information System (INIS)

    Teschendorff, Andrew E; Gomez, Sergio; Arenas, Alex; El-Ashry, Dorraya; Schmidt, Marcus; Gehrmann, Mathias; Caldas, Carlos

    2010-01-01

    Elucidating the activation pattern of molecular pathways across a given tumour type is a key challenge necessary for understanding the heterogeneity in clinical response and for developing novel more effective therapies. Gene expression signatures of molecular pathway activation derived from perturbation experiments in model systems as well as structural models of molecular interactions ('model signatures') constitute an important resource for estimating corresponding activation levels in tumours. However, relatively few strategies for estimating pathway activity from such model signatures exist and only few studies have used activation patterns of pathways to refine molecular classifications of cancer. Here we propose a novel network-based method for estimating pathway activation in tumours from model signatures. We find that although the pathway networks inferred from cancer expression data are highly consistent with the prior information contained in the model signatures, that they also exhibit a highly modular structure and that estimation of pathway activity is dependent on this modular structure. We apply our methodology to a panel of 438 estrogen receptor negative (ER-) and 785 estrogen receptor positive (ER+) breast cancers to infer activation patterns of important cancer related molecular pathways. We show that in ER negative basal and HER2+ breast cancer, gene expression modules reflecting T-cell helper-1 (Th1) and T-cell helper-2 (Th2) mediated immune responses play antagonistic roles as major risk factors for distant metastasis. Using Boolean interaction Cox-regression models to identify non-linear pathway combinations associated with clinical outcome, we show that simultaneous high activation of Th1 and low activation of a TGF-beta pathway module defines a subtype of particularly good prognosis and that this classification provides a better prognostic model than those based on the individual pathways. In ER+ breast cancer, we find that

  9. User Interface Requirements for Web-Based Integrated Care Pathways: Evidence from the Evaluation of an Online Care Pathway Investigation Tool.

    Science.gov (United States)

    Balatsoukas, Panos; Williams, Richard; Davies, Colin; Ainsworth, John; Buchan, Iain

    2015-11-01

    Integrated care pathways (ICPs) define a chronological sequence of steps, most commonly diagnostic or treatment, to be followed in providing care for patients. Care pathways help to ensure quality standards are met and to reduce variation in practice. Although research on the computerisation of ICP progresses, there is still little knowledge on what are the requirements for designing user-friendly and usable electronic care pathways, or how users (normally health care professionals) interact with interfaces that support design, analysis and visualisation of ICPs. The purpose of the study reported in this paper was to address this gap by evaluating the usability of a novel web-based tool called COCPIT (Collaborative Online Care Pathway Investigation Tool). COCPIT supports the design, analysis and visualisation of ICPs at the population level. In order to address the aim of this study, an evaluation methodology was designed based on heuristic evaluations and a mixed method usability test. The results showed that modular visualisation and direct manipulation of information related to the design and analysis of ICPs is useful for engaging and stimulating users. However, designers should pay attention to issues related to the visibility of the system status and the match between the system and the real world, especially in relation to the display of statistical information about care pathways and the editing of clinical information within a care pathway. The paper concludes with recommendations for interface design.

  10. Clinical indicators associated with successful tracheostomy cuff deflation.

    Science.gov (United States)

    Pryor, Lee N; Ward, Elizabeth C; Cornwell, Petrea L; O'Connor, Stephanie N; Chapman, Marianne J

    2016-08-01

    Tracheostomy cuff deflation is a necessary stage of the decannulation pathway, yet the optimal clinical indicators to guide successful cuff deflation are unknown. The study aims were to identify (1) the proportion of patients tolerating continuous cuff deflation at first attempt; (2) the clinical observations associated with cuff deflation success or failure, including volume of above cuff secretions and (3) the predictive capacity of these observations within a heterogeneous cohort. A retrospective review of 113 acutely tracheostomised patients with a subglottic suction tube in situ was conducted. Ninety-five percent of patients (n=107) achieved continuous cuff deflation on the first attempt. The clinical observations recorded as present in the 24h preceding cuff deflation included: (1) medical stability, (2) respiratory stability, (3) fraction of inspired oxygen ≤0.4, (4) tracheal suction ≤1-2 hourly, (5) sputum thin and easy to suction, (6) sputum clear or white, (7) ≥moderate cough strength, (8) above cuff secretions ≤1ml per hour and (9) alertness≥eyes open to voice. Using the presence of all 9 indicators as predictors of successful cuff deflation tolerance, specificity and positive predictive value were 100%, although sensitivity was only 77% and negative predictive value 19%. Refinement to a set of 3 clinically driven criteria (medical and respiratory stability, above cuff secretions ≤1ml/h) provided high specificity (100%), sensitivity (95%), positive predictive value (100%) and an improved negative predictive value (55%). Key criteria can help guide clinical decision-making on patient readiness for cuff deflation. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

  11. Treatment and Outcome in 65 Children with Optic Pathway Gliomas.

    Science.gov (United States)

    El Beltagy, Mohamed A; Reda, Mohamed; Enayet, Abdelrhman; Zaghloul, Mohamed Saad; Awad, Madeha; Zekri, Wael; Taha, Hala; El-Khateeb, Nada

    2016-05-01

    Optic pathway gliomas (OPGs) are rare neoplasms in children with an unpredictable clinical course. There is significant controversy regarding the optimal management and outcome of these patients. Charts of all patients with OPG diagnosed and treated at Children's Cancer Hospital Egypt between July 2007 and July 2014 were retrospectively reviewed. We evaluated the roles of surgical, ophthalmologic, endocrinologic, neurologic, and treatment aspects of care. Sixty-five patients were included in this study, with a mean age of 5.3 years. OPGs were chiasmatic (n = 25), optic nerve (n = 18), hypothalamic (n = 7), and chiasmatic/hypothalamic (n = 7). Extensive involvement of the optic pathway was seen in an additional 8 patients. Twenty cases had neurofibromatosis type 1. Four cases underwent surgical debulking, and 28 were biopsied (16 open, 11 stereotactic, and 1 endoscopic). Nine of the 18 optic nerve tumors were managed by total excision. Twenty-four patients did not undergo any surgical intervention. Forty-five patients received chemotherapy. Histopathology revealed pilocytic (n = 20), pilomyxoid (n = 15), fibrillary astrocytoma (n = 4), and grade I papillary-glioneuronal tumor (n = 1). Nonrepresentative sample (n = 1). The 4-year overall survival rate was 86.3% with mean follow-up period of 32.2 months. The initial role of surgery in newly developed OPG is biopsy for tissue diagnosis and relief of the hydrocephalus, if present, followed by chemotherapy. Chemotherapy decreases or stabilizes the tumor size in most cases, leading to preservation of both visual and endocrinal functions. The most significant prognostic factor confirmed in this study was the age of the patient. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Evaluating the fundamental qualities of a nuclear medicine radiographer for the provision of an optimal clinical service

    International Nuclear Information System (INIS)

    Griffiths, Marc; King, Simon; Stewart, Rob; Dawson, Gary

    2010-01-01

    The developing nature of nuclear medicine practice highlights the need for an evaluation of the fundamental qualities of a Radiographer working within this discipline. Existing guidelines appear to be in place for clinical technologists working within nuclear medicine. However, limited guidance has been provided for Radiographers practicing within this discipline. This article aims to discuss the fundamental qualities that are considered essential for optimal service delivery, following consultation with various stakeholders. Areas such as technical expertise and knowledge, appropriate use of imaging equipment and current models of safe working practice will be discussed. Patient care and ethical considerations will also be evaluated, along with some core recommendations for future advanced practice.

  13. Discrepancies between selected Pareto optimal plans and final deliverable plans in radiotherapy multi-criteria optimization.

    Science.gov (United States)

    Kyroudi, Archonteia; Petersson, Kristoffer; Ghandour, Sarah; Pachoud, Marc; Matzinger, Oscar; Ozsahin, Mahmut; Bourhis, Jean; Bochud, François; Moeckli, Raphaël

    2016-08-01

    Multi-criteria optimization provides decision makers with a range of clinical choices through Pareto plans that can be explored during real time navigation and then converted into deliverable plans. Our study shows that dosimetric differences can arise between the two steps, which could compromise the clinical choices made during navigation. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  14. High-throughput enzyme screening platform for the IPP-bypass mevalonate pathway for isopentenol production

    DEFF Research Database (Denmark)

    Kang, Aram; Meadows, Corey W.; Canu, Nicolas

    2017-01-01

    Isopentenol (or isoprenol, 3-methyl-3-buten-1-ol) is a drop-in biofuel and a precursor for commodity chemicals such as isoprene. Biological production of isopentenol via the mevalonate pathway has been optimized extensively in Escherichia coli, yielding 70% of its theoretical maximum. However, high...... ATP requirements and isopentenyl diphosphate (IPP) toxicity pose immediate challenges for engineering bacterial strains to overproduce commodities utilizing IPP as an intermediate. To overcome these limitations, we developed an “IPP-bypass� isopentenol pathway using the promiscuous activity...

  15. Clinical treatment planning optimization by Powell's method for gamma unit treatment system

    International Nuclear Information System (INIS)

    Yan Yulong; Shu Huazhong; Bao Xudong; Luo Limin; Bai Yi

    1997-01-01

    Purpose: This article presents a new optimization method for stereotactic radiosurgery treatment planning for gamma unit treatment system. Methods and Materials: The gamma unit has been utilized in stereotactic radiosurgery for about 30 years, but the usual procedure for a physician-physicist team to design a treatment plan is a trial-and-error approach. Isodose curves are viewed on two-dimensional computed tomography (CT) or magnetic resonance (MR) image planes, which is not only time consuming but also seldom achieves the optimal treatment plan, especially when the isocenter weights are regarded. We developed a treatment-planning system on a computer workstation in which Powell's optimization method is realized. The optimization process starts with the initial parameters (the number of iso centers as well as corresponding 3D iso centers' coordinates, collimator sizes, and weight factors) roughly determined by the physician-physicist team. The objective function can be changed to consider protection of sensitive tissues. Results: We use the plan parameters given by a well-trained physician-physicist team, or ones that the author give roughly as the initial parameters for the optimization procedure. Dosimetric results of optimization show a better high dose-volume conformation to the target volume compared to the doctor's plan. Conclusion: This method converges quickly and is not sensitive to the initial parameters. It achieves an excellent conformation of the estimated isodose curves with the contours of the target volume. If the initial parameters are varied, there will be a little difference in parameters' configuration, but the dosimetric results proved almost to be the same

  16. A hypothesis on improving foreign accents by optimizing variability in vocal learning brain circuits.

    Science.gov (United States)

    Simmonds, Anna J

    2015-01-01

    Rapid vocal motor learning is observed when acquiring a language in early childhood, or learning to speak another language later in life. Accurate pronunciation is one of the hardest things for late learners to master and they are almost always left with a non-native accent. Here, I propose a novel hypothesis that this accent could be improved by optimizing variability in vocal learning brain circuits during learning. Much of the neurobiology of human vocal motor learning has been inferred from studies on songbirds. Jarvis (2004) proposed the hypothesis that as in songbirds there are two pathways in humans: one for learning speech (the striatal vocal learning pathway), and one for production of previously learnt speech (the motor pathway). Learning new motor sequences necessary for accurate non-native pronunciation is challenging and I argue that in late learners of a foreign language the vocal learning pathway becomes inactive prematurely. The motor pathway is engaged once again and learners maintain their original native motor patterns for producing speech, resulting in speaking with a foreign accent. Further, I argue that variability in neural activity within vocal motor circuitry generates vocal variability that supports accurate non-native pronunciation. Recent theoretical and experimental work on motor learning suggests that variability in the motor movement is necessary for the development of expertise. I propose that there is little trial-by-trial variability when using the motor pathway. When using the vocal learning pathway variability gradually increases, reflecting an exploratory phase in which learners try out different ways of pronouncing words, before decreasing and stabilizing once the "best" performance has been identified. The hypothesis proposed here could be tested using behavioral interventions that optimize variability and engage the vocal learning pathway for longer, with the prediction that this would allow learners to develop new motor

  17. Development and implementation of a decision pathway for general practitioners for the management or referral of suspected allergy

    Directory of Open Access Journals (Sweden)

    Ray B. Jones

    2014-07-01

    Full Text Available Many patients with suspected allergy are referred to specialist care inappropriately. We aimed to develop and implement an online decision pathway to aid General Practitioners’ (GPs management decisions in suspected allergy. Our study involved 1487 GPs, 3 referral management centres, 5 GP system suppliers, 4 primary care trusts, and 1 specialist allergy clinic. The pathway was implemented by 3/5 GP system suppliers, published to Map of Medicine and on a specialist clinic website. In the first year, the pathway ranked in the top 10/160 local care maps accessed via Map of Medicine and was viewed 900 times. Only 96 GPs registered to use the clinic website. Only 110 (7% GPs responded to the feedback request, of which 13/110 (12% had used the pathway; nearly all thought it useful. It was used by referral management centres as explanation of rejected referrals. Alternative approaches to embed its use are required.

  18. Rewiring the Glucose Transportation and Central Metabolic Pathways for Overproduction of N-Acetylglucosamine in Bacillus subtilis.

    Science.gov (United States)

    Gu, Yang; Deng, Jieying; Liu, Yanfeng; Li, Jianghua; Shin, Hyun-Dong; Du, Guocheng; Chen, Jian; Liu, Long

    2017-10-01

    N-acetylglucosamine (GlcNAc) is an important amino sugar extensively used in the healthcare field. In a previous study, the recombinant Bacillus subtilis strain BSGN6-P xylA -glmS-pP43NMK-GNA1 (BN0-GNA1) had been constructed for microbial production of GlcNAc by pathway design and modular optimization. Here, the production of GlcNAc is further improved by rewiring both the glucose transportation and central metabolic pathways. First, the phosphotransferase system (PTS) is blocked by deletion of three genes, yyzE (encoding the PTS system transporter subunit IIA YyzE), ypqE (encoding the PTS system transporter subunit IIA YpqE), and ptsG (encoding the PTS system glucose-specific EIICBA component), resulting in 47.6% increase in the GlcNAc titer (from 6.5 ± 0.25 to 9.6 ± 0.16 g L -1 ) in shake flasks. Then, reinforcement of the expression of the glcP and glcK genes and optimization of glucose facilitator proteins are performed to promote glucose import and phosphorylation. Next, the competitive pathways for GlcNAc synthesis, namely glycolysis, peptidoglycan synthesis pathway, pentose phosphate pathway, and tricarboxylic acid cycle, are repressed by initiation codon-optimization strategies, and the GlcNAc titer in shake flasks is improved from 10.8 ± 0.25 to 13.2 ± 0.31 g L -1 . Finally, the GlcNAc titer is further increased to 42.1 ± 1.1 g L -1 in a 3-L fed-batch bioreactor, which is 1.72-fold that of the original strain, BN0-GNA1. This study shows considerably enhanced GlcNAc production, and the metabolic engineering strategy described here will be useful for engineering other prokaryotic microorganisms for the production of GlcNAc and related molecules. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Optimizing clinical trial supply requirements: simulation of computer-controlled supply chain management.

    Science.gov (United States)

    Peterson, Magnus; Byrom, Bill; Dowlman, Nikki; McEntegart, Damian

    2004-01-01

    Computer-controlled systems are commonly used in clinical trials to control dispensing and manage site inventories of trial supplies. Typically such systems are used with an interactive telephone or web system that provide an interface with the study site. Realizing the maximum savings in medication associated with this approach has, in the past, been problematic as it has been difficult to fully estimate medication requirements due to the complexities of these algorithms and the inherent variation in the clinical trial recruitment process. We describe the traditional and automated methods of supplying sites. We detail a simulation approach that models the automated system. We design a number of simulation experiments using this model to investigate the supply strategy properties that influence medication overage and other strategy performance metrics. The computer-controlled medication system gave superior performance to the traditional method. In one example, a 75% overage of wasted medication in the traditional system was associated with higher supply failure than an automated system strategy with an overage of 47%. In a further example, we demonstrate that the impact of using a country stratified as opposed to site stratified scheme affects the number of deliveries and probability of supply failures more than the amount of drug wasted with respective increases of 20, 2300 and 4%. Medication savings with automated systems are particularly significant in repeat dispensing designs. We show that the number of packs required can fall by as much as 50% if one uses a predictive medication algorithm. We conclude that a computer-controlled supply chain enables medication savings to be realized and that it is possible to quantify the distribution of these savings using a simulation model. The simulation model can be used to optimize the prestudy medication supply strategy and for midstudy monitoring using real-time data contained in the study database.

  20. Optimal pharmacological therapy in ST-elevation myocardial infarction-a review : A review of antithrombotic therapies in STEMI.

    Science.gov (United States)

    Hermanides, R S; Kilic, S; van 't Hof, A W J

    2018-04-23

    Antithrombotic therapy is an essential component in the optimisation of clinical outcomes in patients with ST-elevation myocardial infarction (STEMI) undergoing primary percutaneous coronary intervention. There are currently several intravenous anticoagulant drugs available for primary percutaneous coronary intervention. Dual antiplatelet therapy comprising aspirin and P2Y12 inhibitor represents the cornerstone treatment for STEMI. However, these effective treatment strategies may be associated with bleeding complications. Compared with clopidogrel, prasugrel and ticagrelor are more potent and predictable, which translates into better clinical outcomes. Therefore, these agents are the first-line treatment in primary percutaneous coronary intervention. However, patients can still experience adverse ischaemic events, which might be in part attributed to alternative pathways triggering thrombosis. In this review, we provide a critical and updated review of currently available antithrombotic therapies used in patients with STEMI undergoing primary PCI. Finding a balance that minimises both thrombotic and bleeding risk is difficult, but crucial. Further randomised trials for this optimal balance are needed.

  1. Role of clinical questionnaires in optimizing everyday care of chronic obstructive pulmonary disease

    Science.gov (United States)

    Jones, Paul W; Price, David; van der Molen, Thys

    2011-01-01

    Chronic obstructive pulmonary disease (COPD) is a leading cause of disability in all its stages, and death in patients with moderate or severe obstruction. At present, COPD is suboptimally managed; current health is often not measured properly and hardly taken into account in management plans, and the future risk for patients with regard to health status and quality of life is not being evaluated. This review addresses the effect of COPD on the lives of patients and examines ways in which existing assessment tools meet physicians’ needs for a standardized, simple method to measure consistently the full impact of COPD on patients in routine clinical practice. Current assessment of COPD severity tends to focus on airflow limitation, but this does not capture the full impact of the disease and is not well correlated with patient perception of symptoms and health-related quality of life. Qualitative studies have demonstrated that patients usually consider COPD impact in terms of frequency and severity of symptoms, and physical and emotional wellbeing. However, patients often have difficulty expressing their disease burden and physicians generally have insufficient time to collect this information. Therefore, it is important that methods are implemented to help generate a more complete understanding of the impact of COPD. This can be achieved most efficiently using a quick, reliable, and standardized measure of disease impact, such as a short questionnaire that can be applied in daily clinical practice. Questionnaires are precision instruments that contribute sensitive and specific information, and can potentially help physicians provide optimal care for patients with COPD. Two short, easy-to-use, specific measures, ie, the COPD Assessment Test and the Clinical COPD Questionnaire, enable physicians to assess patients’ health status accurately and improve disease management. Such questionnaires provide important measurements that can assist primary care physicians to

  2. Optimization of 3D-VIBE for MR mammography. Phantom study and clinical application

    International Nuclear Information System (INIS)

    Nishikawa, Kazuyuki; Tozaki, Mitsuhiro; Takimoto, Teruo; Nagano, Shinya; Kishi, Takayuki; Shibata, Kimmochi; Fukuda, Kunihiko

    2003-01-01

    Our study objective was to select moderate parameters for dynamic high-spatial-resolution MR mammography with three-dimensional volumetric interpolated breath-hold examination (3D-VIBE) sequence. In phantom experiments, signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were measured with various flip angles as a function of gadolinium (Gd) concentration. CNR showed a constant increase as the concentration of Gd increased. CNR increased rapidly with flip angles of 25 deg and 30 deg. A comparison of flip angles of 25 deg and 30 deg for SNR showed that 25 deg was superior. In clinical studies, the flip angle was selected to optimize breast parenchyma-to-fat CNR. CNR with various flip angles was lowest with a 25 deg flip angle. We found that tumor-to-breast parenchyma contrast was highest with 25 deg flip angle due to the suppression of signal of the breast parenchyma. In conclusion, a moderate parameter for dynamic high-spatial-resolution MR mammography with 3D-VIBE sequence is a 25 deg flip angle. (author)

  3. Cost comparison of orthopaedic fracture pathways using discrete event simulation in a Glasgow hospital.

    Science.gov (United States)

    Anderson, Gillian H; Jenkins, Paul J; McDonald, David A; Van Der Meer, Robert; Morton, Alec; Nugent, Margaret; Rymaszewski, Lech A

    2017-09-07

    Healthcare faces the continual challenge of improving outcome while aiming to reduce cost. The aim of this study was to determine the micro cost differences of the Glasgow non-operative trauma virtual pathway in comparison to a traditional pathway. Discrete event simulation was used to model and analyse cost and resource utilisation with an activity-based costing approach. Data for a full comparison before the process change was unavailable so we used a modelling approach, comparing a virtual fracture clinic (VFC) with a simulated traditional fracture clinic (TFC). The orthopaedic unit VFC pathway pioneered at Glasgow Royal Infirmary has attracted significant attention and interest and is the focus of this cost study. Our study focused exclusively on patients with non-operative trauma attending emergency department or the minor injuries unit and the subsequent step in the patient pathway. Retrospective studies of patient outcomes as a result of the protocol introductions for specific injuries are presented in association with activity costs from the models. Patients are satisfied with the new pathway, the information provided and the outcome of their injuries (Evidence Level IV). There was a 65% reduction in the number of first outpatient face-to-face (f2f) attendances in orthopaedics. In the VFC pathway, the resources required per day were significantly lower for all staff groups (p≤0.001). The overall cost per patient of the VFC pathway was £22.84 (95% CI 21.74 to 23.92) per patient compared with £36.81 (95% CI 35.65 to 37.97) for the TFC pathway. Our results give a clearer picture of the cost comparison of the virtual pathway over a wholly traditional f2f clinic system. The use of simulation-based stochastic costings in healthcare economic analysis has been limited to date, but this study provides evidence for adoption of this method as a basis for its application in other healthcare settings. © Article author(s) (or their employer(s) unless otherwise

  4. Optimization guidance to post-accident intervention: a specific case

    International Nuclear Information System (INIS)

    Garcia-Ramirez, J.E.; Reyes-Sanchez, M.A.

    1996-01-01

    ICRP recommends the application of the system of protection to intervention situations, i.e. those in which exposure pathways are already present; e.g the public exposure following an accident. This implies that intervention must be justified and optimized, being the optimization the process of deciding the nature of protective action in order to obtain the maximum net benefit. This paper provides an example of one optimization model to guide a decision making process in a specific case of post-accident intervention. The involved scenario postulates the contamination of big quantities of reinforcing steel bars used in construction industry, and a lot of them present in the structure of several dwellings. Inhabitants of these dwellings must be protected and the proposed action is to demolish those homes exceeding some intervention criterion. The objective of this study is to reach such intervention level trough an optimization process economically focused. (author)

  5. Investigating multiple dysregulated pathways in rheumatoid arthritis based on pathway interaction network.

    Science.gov (United States)

    Song, Xian-Dong; Song, Xian-Xu; Liu, Gui-Bo; Ren, Chun-Hui; Sun, Yuan-Bo; Liu, Ke-Xin; Liu, Bo; Liang, Shuang; Zhu, Zhu

    2018-03-01

    The traditional methods of identifying biomarkers in rheumatoid arthritis (RA) have focussed on the differentially expressed pathways or individual pathways, which however, neglect the interactions between pathways. To better understand the pathogenesis of RA, we aimed to identify dysregulated pathway sets using a pathway interaction network (PIN), which considered interactions among pathways. Firstly, RA-related gene expression profile data, protein-protein interactions (PPI) data and pathway data were taken up from the corresponding databases. Secondly, principal component analysis method was used to calculate the pathway activity of each of the pathway, and then a seed pathway was identified using data gleaned from the pathway activity. A PIN was then constructed based on the gene expression profile, pathway data, and PPI information. Finally, the dysregulated pathways were extracted from the PIN based on the seed pathway using the method of support vector machines and an area under the curve (AUC) index. The PIN comprised of a total of 854 pathways and 1064 pathway interactions. The greatest change in the activity score between RA and control samples was observed in the pathway of epigenetic regulation of gene expression, which was extracted and regarded as the seed pathway. Starting with this seed pathway, one maximum pathway set containing 10 dysregulated pathways was extracted from the PIN, having an AUC of 0.8249, and the result indicated that this pathway set could distinguish RA from the controls. These 10 dysregulated pathways might be potential biomarkers for RA diagnosis and treatment in the future.

  6. Economic comparison of common treatment protocols and J5 vaccination for clinical mastitis in dairy herds using optimized culling decisions.

    Science.gov (United States)

    Kessels, J A; Cha, E; Johnson, S K; Welcome, F L; Kristensen, A R; Gröhn, Y T

    2016-05-01

    This study used an existing dynamic optimization model to compare costs of common treatment protocols and J5 vaccination for clinical mastitis in US dairy herds. Clinical mastitis is an infection of the mammary gland causing major economic losses in dairy herds due to reduced milk production, reduced conception, and increased risk of mortality and culling for infected cows. Treatment protocols were developed to reflect common practices in dairy herds. These included targeted therapy following pathogen identification, and therapy without pathogen identification using a broad-spectrum antimicrobial or treating with the cheapest treatment option. The cost-benefit of J5 vaccination was also estimated. Effects of treatment were accounted for as changes in treatment costs, milk loss due to mastitis, milk discarded due to treatment, and mortality. Following ineffective treatments, secondary decisions included extending the current treatment, alternative treatment, discontinuing treatment, and pathogen identification followed by recommended treatment. Average net returns for treatment protocols and vaccination were generated using an existing dynamic programming model. This model incorporates cow and pathogen characteristics to optimize management decisions to treat, inseminate, or cull cows. Of the treatment protocols where 100% of cows received recommended treatment, pathogen-specific identification followed by recommended therapy yielded the highest average net returns per cow per year. Out of all treatment scenarios, the highest net returns were achieved with selecting the cheapest treatment option and discontinuing treatment, or alternate treatment with a similar spectrum therapy; however, this may not account for the full consequences of giving nonrecommended therapies to cows with clinical mastitis. Vaccination increased average net returns in all scenarios. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  7. A method of segment weight optimization for intensity modulated radiation therapy

    International Nuclear Information System (INIS)

    Pei Xi; Cao Ruifen; Jing Jia; Cheng Mengyun; Zheng Huaqing; Li Jia; Huang Shanqing; Li Gui; Song Gang; Wang Weihua; Wu Yican; FDS Team

    2011-01-01

    The error caused by leaf sequencing often leads to planning of Intensity-Modulated Radiation Therapy (IMRT) arrange system couldn't meet clinical demand. The optimization approach in this paper can reduce this error and improve efficiency of plan-making effectively. Conjugate Gradient algorithm was used to optimize segment weight and readjust segment shape, which could minimize the error anterior-posterior leaf sequencing eventually. Frequent clinical cases were tasted by precise radiotherapy system, and then compared Dose-Volume histogram between target area and organ at risk as well as isodose line in computed tomography (CT) film, we found that the effect was improved significantly after optimizing segment weight. Segment weight optimizing approach based on Conjugate Gradient method can make treatment planning meet clinical request more efficiently, so that has extensive application perspective. (authors)

  8. Construction of a controllable β-carotene biosynthetic pathway by decentralized assembly strategy in Saccharomyces cerevisiae.

    Science.gov (United States)

    Xie, Wenping; Liu, Min; Lv, Xiaomei; Lu, Wenqiang; Gu, Jiali; Yu, Hongwei

    2014-01-01

    Saccharomyces cerevisiae is an important platform organism for the synthesis of a great number of natural products. However, the assembly of controllable and genetically stable heterogeneous biosynthetic pathways in S. cerevisiae still remains a significant challenge. Here, we present a strategy for reconstructing controllable multi-gene pathways by employing the GAL regulatory system. A set of marker recyclable integrative plasmids (pMRI) was designed for decentralized assembly of pathways. As proof-of-principle, a controllable β-carotene biosynthesis pathway (∼16 kb) was reconstructed and optimized by repeatedly using GAL10-GAL1 bidirectional promoters with high efficiency (80-100%). By controling the switch time of the pathway, production of 11 mg/g DCW of total carotenoids (72.57 mg/L) and 7.41 mg/g DCW of β-carotene was achieved in shake-flask culture. In addition, the engineered yeast strain exhibited high genetic stability after 20 generations of subculture. The results demonstrated a controllable and genetically stable biosynthetic pathway capable of increasing the yield of target products. Furthermore, the strategy presented in this study could be extended to construct other pathways in S. cerevisisae. © 2013 Wiley Periodicals, Inc.

  9. Pathways to Carbon-Negative Liquid Biofuels

    Science.gov (United States)

    Woolf, D.; Lehmann, J.

    2017-12-01

    Many climate change mitigation scenarios assume that atmospheric carbon dioxide removal will be delivered at scale using bioenergy power generation with carbon capture and storage (BECCS). However, other pathways to negative emission technologies (NETs) in the energy sector are possible, but have received relatively little attention. Given that the costs, benefits and life-cycle emissions of technologies vary widely, more comprehensive analyses of the policy options for NETs are critical. This study provides a comparative assessment of the potential pathways to carbon-negative liquid biofuels. It is often assumed that that decarbonisation of the transport sector will include use of liquid biofuels, particularly for applications that are difficult to electrify such as aviation and maritime transport. However, given that biomass and land on which to grow it sustainably are limiting factors in the scaling up of both biofuels and NETs, these two strategies compete for shared factors of production. One way to circumvent this competition is carbon-negative biofuels. Because capture of exhaust CO2 in the transport sector is impractical, this will likely require carbon capture during biofuel production. Potential pathways include, for example, capture of CO2 from fermentation, or sequestration of biochar from biomass pyrolysis in soils, in combination with thermochemical or bio-catalytic conversion of syngas to alcohols or alkanes. Here we show that optimal pathway selection depends on specific resource constraints. As land availability becomes increasingly limiting if bioenergy is scaled up—particularly in consideration that abandoned degraded land is widely considered to be an important resource that does not compete with food fiber or habitat—then systems which enhance land productivity by increasing soil fertility using soil carbon sequestration become increasingly preferable compared to bioenergy systems that deplete or degrade the land resource on which they

  10. An evaluation of the implementation of maternal obesity pathways of care: a mixed methods study with data integration.

    Directory of Open Access Journals (Sweden)

    Nicola Heslehurst

    Full Text Available Maternal obesity has multiple associated risks and requires substantial intervention. This research evaluated the implementation of maternal obesity care pathways from multiple stakeholder perspectives.A simultaneous mixed methods model with data integration was used. Three component studies were given equal priority. 1: Semi-structured qualitative interviews explored obese pregnant women's experiences of being on the pathways. 2: A quantitative and qualitative postal survey explored healthcare professionals' experiences of delivering the pathways. 3: A case note audit quantitatively assessed pathway compliance. Data were integrated using following a thread and convergence coding matrix methods to search for agreement and disagreement between studies.Study 1: Four themes were identified: women's overall (positive and negative views of the pathways; knowledge and understanding of the pathways; views on clinical and weight management advice and support; and views on the information leaflet. Key results included positive views of receiving additional clinical care, negative experiences of risk communication, and weight management support was considered a priority. Study 2: Healthcare professionals felt the pathways were worthwhile, facilitated good practice, and increased confidence. Training was consistently identified as being required. Healthcare professionals predominantly focussed on women's response to sensitive obesity communication. Study 3: There was good compliance with antenatal clinical interventions. However, there was poor compliance with public health and postnatal interventions. There were some strong areas of agreement between component studies which can inform future development of the pathways. However, disagreement between studies included a lack of shared priorities between healthcare professionals and women, different perspectives on communication issues, and different perspectives on women's prioritisation of weight

  11. An Evaluation of the Implementation of Maternal Obesity Pathways of Care: A Mixed Methods Study with Data Integration

    Science.gov (United States)

    Heslehurst, Nicola; Dinsdale, Sarah; Sedgewick, Gillian; Simpson, Helen; Sen, Seema; Summerbell, Carolyn Dawn; Rankin, Judith

    2015-01-01

    Objectives Maternal obesity has multiple associated risks and requires substantial intervention. This research evaluated the implementation of maternal obesity care pathways from multiple stakeholder perspectives. Study Design A simultaneous mixed methods model with data integration was used. Three component studies were given equal priority. 1: Semi-structured qualitative interviews explored obese pregnant women’s experiences of being on the pathways. 2: A quantitative and qualitative postal survey explored healthcare professionals’ experiences of delivering the pathways. 3: A case note audit quantitatively assessed pathway compliance. Data were integrated using following a thread and convergence coding matrix methods to search for agreement and disagreement between studies. Results Study 1: Four themes were identified: women’s overall (positive and negative) views of the pathways; knowledge and understanding of the pathways; views on clinical and weight management advice and support; and views on the information leaflet. Key results included positive views of receiving additional clinical care, negative experiences of risk communication, and weight management support was considered a priority. Study 2: Healthcare professionals felt the pathways were worthwhile, facilitated good practice, and increased confidence. Training was consistently identified as being required. Healthcare professionals predominantly focussed on women’s response to sensitive obesity communication. Study 3: There was good compliance with antenatal clinical interventions. However, there was poor compliance with public health and postnatal interventions. There were some strong areas of agreement between component studies which can inform future development of the pathways. However, disagreement between studies included a lack of shared priorities between healthcare professionals and women, different perspectives on communication issues, and different perspectives on women

  12. Coverage-based constraints for IMRT optimization

    Science.gov (United States)

    Mescher, H.; Ulrich, S.; Bangert, M.

    2017-09-01

    Radiation therapy treatment planning requires an incorporation of uncertainties in order to guarantee an adequate irradiation of the tumor volumes. In current clinical practice, uncertainties are accounted for implicitly with an expansion of the target volume according to generic margin recipes. Alternatively, it is possible to account for uncertainties by explicit minimization of objectives that describe worst-case treatment scenarios, the expectation value of the treatment or the coverage probability of the target volumes during treatment planning. In this note we show that approaches relying on objectives to induce a specific coverage of the clinical target volumes are inevitably sensitive to variation of the relative weighting of the objectives. To address this issue, we introduce coverage-based constraints for intensity-modulated radiation therapy (IMRT) treatment planning. Our implementation follows the concept of coverage-optimized planning that considers explicit error scenarios to calculate and optimize patient-specific probabilities q(\\hat{d}, \\hat{v}) of covering a specific target volume fraction \\hat{v} with a certain dose \\hat{d} . Using a constraint-based reformulation of coverage-based objectives we eliminate the trade-off between coverage and competing objectives during treatment planning. In-depth convergence tests including 324 treatment plan optimizations demonstrate the reliability of coverage-based constraints for varying levels of probability, dose and volume. General clinical applicability of coverage-based constraints is demonstrated for two cases. A sensitivity analysis regarding penalty variations within this planing study based on IMRT treatment planning using (1) coverage-based constraints, (2) coverage-based objectives, (3) probabilistic optimization, (4) robust optimization and (5) conventional margins illustrates the potential benefit of coverage-based constraints that do not require tedious adjustment of target volume objectives.

  13. Design principles and operating principles: the yin and yang of optimal functioning.

    Science.gov (United States)

    Voit, Eberhard O

    2003-03-01

    Metabolic engineering has as a goal the improvement of yield of desired products from microorganisms and cell lines. This goal has traditionally been approached with experimental biotechnological methods, but it is becoming increasingly popular to precede the experimental phase by a mathematical modeling step that allows objective pre-screening of possible improvement strategies. The models are either linear and represent the stoichiometry and flux distribution in pathways or they are non-linear and account for the full kinetic behavior of the pathway, which is often significantly effected by regulatory signals. Linear flux analysis is simpler and requires less input information than a full kinetic analysis, and the question arises whether the consideration of non-linearities is really necessary for devising optimal strategies for yield improvements. The article analyzes this question with a generic, representative pathway. It shows that flux split ratios, which are the key criterion for linear flux analysis, are essentially sufficient for unregulated, but not for regulated branch points. The interrelationships between regulatory design on one hand and optimal patterns of operation on the other suggest the investigation of operating principles that complement design principles, like a user's manual complements the hardwiring of electronic equipment.

  14. International Study to Predict Optimized Treatment for Depression (iSPOT-D, a randomized clinical trial: rationale and protocol

    Directory of Open Access Journals (Sweden)

    Cooper Nicholas J

    2011-01-01

    Full Text Available Abstract Background Clinically useful treatment moderators of Major Depressive Disorder (MDD have not yet been identified, though some baseline predictors of treatment outcome have been proposed. The aim of iSPOT-D is to identify pretreatment measures that predict or moderate MDD treatment response or remission to escitalopram, sertraline or venlafaxine; and develop a model that incorporates multiple predictors and moderators. Methods/Design The International Study to Predict Optimized Treatment - in Depression (iSPOT-D is a multi-centre, international, randomized, prospective, open-label trial. It is enrolling 2016 MDD outpatients (ages 18-65 from primary or specialty care practices (672 per treatment arm; 672 age-, sex- and education-matched healthy controls. Study-eligible patients are antidepressant medication (ADM naïve or willing to undergo a one-week wash-out of any non-protocol ADM, and cannot have had an inadequate response to protocol ADM. Baseline assessments include symptoms; distress; daily function; cognitive performance; electroencephalogram and event-related potentials; heart rate and genetic measures. A subset of these baseline assessments are repeated after eight weeks of treatment. Outcomes include the 17-item Hamilton Rating Scale for Depression (primary and self-reported depressive symptoms, social functioning, quality of life, emotional regulation, and side-effect burden (secondary. Participants may then enter a naturalistic telephone follow-up at weeks 12, 16, 24 and 52. The first half of the sample will be used to identify potential predictors and moderators, and the second half to replicate and confirm. Discussion First enrolment was in December 2008, and is ongoing. iSPOT-D evaluates clinical and biological predictors of treatment response in the largest known sample of MDD collected worldwide. Trial registration International Study to Predict Optimised Treatment - in Depression (iSPOT-D ClinicalTrials.gov Identifier

  15. Optimizing clopidogrel dose response: a new clinical algorithm comprising CYP2C19 pharmacogenetics and drug interactions

    Directory of Open Access Journals (Sweden)

    Saab YB

    2015-09-01

    Full Text Available Yolande B Saab,1 Rony Zeenny,2 Wijdan H Ramadan2 1School of Pharmacy, Pharmaceutical Sciences Department, 2School of Pharmacy, Pharmacy Practice Department, Lebanese American University, Byblos, Lebanon Purpose: Response to clopidogrel varies widely with nonresponse rates ranging from 4% to 30%. A reduced function of the gene variant of the CYP2C19 has been associated with lower drug metabolite levels, and hence diminished platelet inhibition. Drugs that alter CYP2C19 activity may also mimic genetic variants. The aim of the study is to investigate the cumulative effect of CYP2C19 gene polymorphisms and drug interactions that affects clopidogrel dosing, and apply it into a new clinical-pharmacogenetic algorithm that can be used by clinicians in optimizing clopidogrel-based treatment. Method: Clopidogrel dose optimization was analyzed based on two main parameters that affect clopidogrel metabolite area under the curve: different CYP2C19 genotypes and concomitant drug intake. Clopidogrel adjusted dose was computed based on area under the curve ratios for different CYP2C19 genotypes when a drug interacting with CYP2C19 is added to clopidogrel treatment. A clinical-pharmacogenetic algorithm was developed based on whether clopidogrel shows 1 expected effect as per indication, 2 little or no effect, or 3 clinical features that patients experience and fit with clopidogrel adverse drug reactions. Results: The study results show that all patients under clopidogrel treatment, whose genotypes are different from *1*1, and concomitantly taking other drugs metabolized by CYP2C19 require clopidogrel dose adjustment. To get a therapeutic effect and avoid adverse drug reactions, therapeutic dose of 75 mg clopidogrel, for example, should be lowered to 6 mg or increased to 215 mg in patients with different genotypes. Conclusion: The implementation of clopidogrel new algorithm has the potential to maximize the benefit of clopidogrel pharmacological therapy

  16. Efficiency and CO[sub 2] emission analysis of pathways by which methane can provide transportation services

    Energy Technology Data Exchange (ETDEWEB)

    Crane, P; Scott, D S [Victoria Univ., BC (Canada). Inst. for Integrated Energy Systems Victoria Univ., BC (Canada). Dept. of Mechanical Engineering

    1992-07-01

    Methane is expected to have an increasingly important role as an energy source in the future. As a result, methane will become a major energy source for the transportation sector. Future energy systems will also be selected for efficiency and environmental gentility. Six candidate pathways by which the energy for service transportation can be provided, using methane as the sole energy source, are proposed and are compared with the use of gasoline from petroleum. These pathways involve methanol, methane and hydrogen used in spark ignition engines and solid polymer fuel cells. The energy conversion processes in each pathway are analysed based on the second law of thermodynamics. Two performance criteria are used: total exergy input to the pathway and total carbon dioxide produced along the pathway. All results are normalized to a unit of transportation service, in this case 1 km of city driving. A surprising result is that the methanol spark ignition engine pathway is the least efficient and produces the greatest amount of carbon dioxide, of the pathways examined. Hydrogen and fuel cell pathways are found to be optimal using the criteria of this paper. (author)

  17. Clinically Applicable Monte Carlo–based Biological Dose Optimization for the Treatment of Head and Neck Cancers With Spot-Scanning Proton Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Wan Chan Tseung, Hok Seum, E-mail: wanchantseung.hok@mayo.edu; Ma, Jiasen; Kreofsky, Cole R.; Ma, Daniel J.; Beltran, Chris

    2016-08-01

    Purpose: Our aim is to demonstrate the feasibility of fast Monte Carlo (MC)–based inverse biological planning for the treatment of head and neck tumors in spot-scanning proton therapy. Methods and Materials: Recently, a fast and accurate graphics processor unit (GPU)–based MC simulation of proton transport was developed and used as the dose-calculation engine in a GPU-accelerated intensity modulated proton therapy (IMPT) optimizer. Besides dose, the MC can simultaneously score the dose-averaged linear energy transfer (LET{sub d}), which makes biological dose (BD) optimization possible. To convert from LET{sub d} to BD, a simple linear relation was assumed. By use of this novel optimizer, inverse biological planning was applied to 4 patients, including 2 small and 1 large thyroid tumor targets, as well as 1 glioma case. To create these plans, constraints were placed to maintain the physical dose (PD) within 1.25 times the prescription while maximizing target BD. For comparison, conventional intensity modulated radiation therapy (IMRT) and IMPT plans were also created using Eclipse (Varian Medical Systems) in each case. The same critical-structure PD constraints were used for the IMRT, IMPT, and biologically optimized plans. The BD distributions for the IMPT plans were obtained through MC recalculations. Results: Compared with standard IMPT, the biologically optimal plans for patients with small tumor targets displayed a BD escalation that was around twice the PD increase. Dose sparing to critical structures was improved compared with both IMRT and IMPT. No significant BD increase could be achieved for the large thyroid tumor case and when the presence of critical structures mitigated the contribution of additional fields. The calculation of the biologically optimized plans can be completed in a clinically viable time (<30 minutes) on a small 24-GPU system. Conclusions: By exploiting GPU acceleration, MC-based, biologically optimized plans were created for

  18. Pseudomonas Exotoxin A: optimized by evolution for effective killing

    Directory of Open Access Journals (Sweden)

    Marta eMichalska

    2015-09-01

    Full Text Available Pseudomonas Exotoxin A (PE is the most toxic virulence factor of the pathogenic bacterium Pseudomonas aeruginosa. This review describes current knowledge about the intoxication pathways of PE. Moreover, PE represents a remarkable example for pathoadaptive evolution, how bacterial molecules have been structurally and functionally optimized under evolutionary pressure to effectively impair and kill their host cells.

  19. When does treatment plan optimization require inverse planning?

    International Nuclear Information System (INIS)

    Sherouse, George W.

    1995-01-01

    Increasing maturity of image-based computer-aided design of three-dimensional conformal radiotherapy has recently sparked a great deal of work in the area of treatment plan optimization. Optimization of a conformal photon beam treatment plan is that exercise through which a set of intensity-modulated static beams or arcs is specified such that, when the plan is executed, 1) a region of homogeneous dose is produced in the patient with a shape which geometrically conforms (within a specified tolerance) to the three-dimensional shape of a designated target volume and 2) acceptably low incidental dose is delivered to non-target tissues. Interest in conformal radiotherapy arise from a fundamental assumption that there is significant value to be gained from aggressive customization of the treatment for each individual patient In our efforts to design optimal treatments, however, it is important to remember that, given the biological and economic realities of clinical radiotherapy, mathematical optimization of dose distribution metrics with respect to some minimal constraint set is not a necessary or even sufficient condition for design of a clinically optimal treatment. There is wide variation in the complexity of the clinical situations encountered in practice and there are a number of non-physical criteria to be considered in planning. There is also a complementary variety of computational and engineering means for achieving optimization. To date, the scientific dialogue regarding these techniques has concentrated on development of solutions to worst-case scenarios, largely in the absence of consideration of appropriate matching of solution complexity to problem complexity. It is the aim of this presentation to propose a provisional stratification of treatment planning problems, stratified by relative complexity, and to identify a corresponding stratification of necessary treatment planning techniques. It is asserted that the subset of clinical radiotherapy cases for

  20. Activation of DNA damage repair pathways by murine polyomavirus

    Energy Technology Data Exchange (ETDEWEB)

    Heiser, Katie; Nicholas, Catherine; Garcea, Robert L., E-mail: Robert.Garcea@Colorado.edu

    2016-10-15

    Nuclear replication of DNA viruses activates DNA damage repair (DDR) pathways, which are thought to detect and inhibit viral replication. However, many DNA viruses also depend on these pathways in order to optimally replicate their genomes. We investigated the relationship between murine polyomavirus (MuPyV) and components of DDR signaling pathways including CHK1, CHK2, H2AX, ATR, and DNAPK. We found that recruitment and retention of DDR proteins at viral replication centers was independent of H2AX, as well as the viral small and middle T-antigens. Additionally, infectious virus production required ATR kinase activity, but was independent of CHK1, CHK2, or DNAPK signaling. ATR inhibition did not reduce the total amount of viral DNA accumulated, but affected the amount of virus produced, indicating a defect in virus assembly. These results suggest that MuPyV may utilize a subset of DDR proteins or non-canonical DDR signaling pathways in order to efficiently replicate and assemble. -- Highlights: •Murine polyomavirus activates and recruits DNA damage repair (DDR) proteins to replication centers. •Large T-antigen mediates recruitment of DDR proteins to viral replication centers. •Inhibition or knockout of CHK1, CHK2, DNA-PK or H2AX do not affect viral titers. •Inhibition of ATR activity reduces viral titers, but not viral DNA accumulation.

  1. Biomarkers in the clinical development of asthma therapies.

    Science.gov (United States)

    Staton, Tracy L; Choy, David F; Arron, Joseph R

    2016-01-01

    Here we review how biomarkers have been used in the design, execution and interpretation of recent clinical studies of therapeutic candidates targeting cytokine-mediated inflammatory pathways in asthma. This review focuses on type 2 inflammation, as there are multiple therapeutics and/or clinical studies that can be compared within that specific pathway. Comparative analyses of data from these clinical studies illustrate the utility of biomarkers to quantify pharmacodynamic effects, clarify mechanism of action and stratify patients, which may facilitate the interpretation of outcomes in the development of molecularly targeted therapies. These case examples provide a basis for biomarker considerations in the design of future studies in the asthma setting.

  2. [Clinical research of using optimal compliance to determine positive end-expiratory pressure].

    Science.gov (United States)

    Xu, Lei; Feng, Quan-sheng; Lian, Fu; Shao, Xin-hua; Li, Zhi-bo; Wang, Zhi-yong; Li, Jun

    2012-07-01

    To observe the availability and security of optimal compliance strategy to titrate the optimal positive end-expiratory pressure (PEEP), compared with quasi-static pressure-volume curve (P-V curve) traced by low-flow method. Fourteen patients received mechanical ventilation with acute respiratory distress syndrome (ARDS) admitted in intensive care unit (ICU) of Tianjin Third Central Hospital from November 2009 to December 2010 were divided into two groups(n = 7). The quasi-static P-V curve method and the optimal compliance titration were used to set the optimal PEEP respectively, repeated 3 times in a row. The optimal PEEP and the consistency of repeated experiments were compared between groups. The hemodynamic parameters, oxygenation index (OI), lung compliance (C), cytokines and pulmonary surfactant-associated protein D (SP-D) concentration in plasma before and 2, 4, and 6 hours after the experiment were observed in each group. (1) There were no significant differences in gender, age and severity of disease between two groups. (2)The optimal PEEP [cm H(2)O, 1 cm H(2)O=0.098 kPa] had no significant difference between quasi-static P-V curve method group and the optimal compliance titration group (11.53 ± 2.07 vs. 10.57 ± 0.87, P>0.05). The consistency of repeated experiments in quasi-static P-V curve method group was poor, the slope of the quasi-static P-V curve in repeated experiments showed downward tendency. The optimal PEEP was increasing in each measure. There was significant difference between the first and the third time (10.00 ± 1.58 vs. 12.80 ± 1.92, P vs. 93.71 ± 5.38, temperature: 38.05 ± 0.73 vs. 36.99 ± 1.02, IL-6: 144.84 ± 23.89 vs. 94.73 ± 5.91, TNF-α: 151.46 ± 46.00 vs. 89.86 ± 13.13, SP-D: 33.65 ± 8.66 vs. 16.63 ± 5.61, MAP: 85.47 ± 9.24 vs. 102.43 ± 8.38, CCI: 3.00 ± 0.48 vs. 3.81 ± 0.81, OI: 62.00 ± 21.45 vs. 103.40 ± 37.27, C: 32.10 ± 2.92 vs. 49.57 ± 7.18, all P safety and usability.

  3. Density Functional Theory Study of Competitive Reaction Pathways of Ti+ with Fluorinated Acetone in the Gas Phase

    International Nuclear Information System (INIS)

    Hong, Kiryong; Kim, Tae Kyu

    2012-01-01

    We investigate the doublet and quartet potential energy surfaces associated with the gas-phase reaction between Ti + and CF 3 COCH 3 for two plausible reaction pathways, TiF 2 + and TiO + formation pathways by using the density functional theory (DFT) method. The molecular structures of intermediates and transition states involved in these reaction pathways are optimized at the DFT level by using the PBE0 functional. All transition states are identified by using the intrinsic reaction coordinate (IRC) method, and the resulting reaction coordinates describe how Ti + activates CF 3 COCH 3 and produces TiF 2 + and TiO + as products. On the basis of presented results, we propose the most favorable reaction pathway in the reaction between Ti + and CF 3 COCH 3

  4. Production of Odd-Carbon Dicarboxylic Acids in Escherichia coli Using an Engineered Biotin-Fatty Acid Biosynthetic Pathway.

    Science.gov (United States)

    Haushalter, Robert W; Phelan, Ryan M; Hoh, Kristina M; Su, Cindy; Wang, George; Baidoo, Edward E K; Keasling, Jay D

    2017-04-05

    Dicarboxylic acids are commodity chemicals used in the production of plastics, polyesters, nylons, fragrances, and medications. Bio-based routes to dicarboxylic acids are gaining attention due to environmental concerns about petroleum-based production of these compounds. Some industrial applications require dicarboxylic acids with specific carbon chain lengths, including odd-carbon species. Biosynthetic pathways involving cytochrome P450-catalyzed oxidation of fatty acids in yeast and bacteria have been reported, but these systems produce almost exclusively even-carbon species. Here we report a novel pathway to odd-carbon dicarboxylic acids directly from glucose in Escherichia coli by employing an engineered pathway combining enzymes from biotin and fatty acid synthesis. Optimization of the pathway will lead to industrial strains for the production of valuable odd-carbon diacids.

  5. Whole-heart 3D late gadolinium-enhanced MR imaging. Investigation of optimal scan parameters and clinical usefulness

    International Nuclear Information System (INIS)

    Yorimitsu, Misako; Yokoyama, Kenichi; Nitatori, Toshiaki; Yoshino, Hideaki; Isono, Sachiko; Kuhara, Shigehide

    2012-01-01

    Whole-heart 3-dimensional (3D) late-gadolinium-enhanced magnetic resonance (MR) imaging (WH-LGE) uses respiratory gating combined with acquisition of 3D data for the entire heart in a single scan, which permits reconstruction of any plane with high resolution. We investigated the optimal scan parameters and compared WH-LGE with the conventional scanning method. We employed inversion recovery 3D fast field echo using a 1.5-tesla system and scan parameters: repetition time (TR), 6.6 ms; echo time (TE), 2.5 ms; number of segments, 2; parallel imaging factor, 1.8; matrix size, 128 x 256; field of view (FOV), 320 x 320 mm; and acquisition slice thickness, 3 mm (reconstruction slice thickness, 1.5 mm). Five healthy volunteers underwent scanning during free breathing with real-time motion correction, from which we determined optimal scan parameters. We then used those parameters to scan 25 patients with myocardial infarction to compare scan time and image quality between the WH-LGE and conventional 3D breath-holding methods (slice thickness, 10 mm; matrix size, 128 x 256). Results in volunteers showed optimal scan parameters of 12deg flip angle, fat suppression turned off in combination, and interleaved ordering. In clinical cases, scan times did not differ significantly. Sharpness of the margins of normal myocardium at the apex of the heart and contrast between enhanced and nonenhanced myocardium improved significantly with WH-LGE. WH-LGE yields high resolution images during free breathing and is considered useful for accurately estimating the area and transmural extent of myocardial infarction. (author)

  6. A Longitudinal Empirical Investigation of the Pathways Model of Problem Gambling.

    Science.gov (United States)

    Allami, Youssef; Vitaro, Frank; Brendgen, Mara; Carbonneau, René; Lacourse, Éric; Tremblay, Richard E

    2017-12-01

    The pathways model of problem gambling suggests the existence of three developmental pathways to problem gambling, each differentiated by a set of predisposing biopsychosocial characteristics: behaviorally conditioned (BC), emotionally vulnerable (EV), and biologically vulnerable (BV) gamblers. This study examined the empirical validity of the Pathways Model among adolescents followed up to early adulthood. A prospective-longitudinal design was used, thus overcoming limitations of past studies that used concurrent or retrospective designs. Two samples were used: (1) a population sample of French-speaking adolescents (N = 1033) living in low socio-economic status (SES) neighborhoods from the Greater Region of Montreal (Quebec, Canada), and (2) a population sample of adolescents (N = 3017), representative of French-speaking students in Quebec. Only participants with at-risk or problem gambling by mid-adolescence or early adulthood were included in the main analysis (n = 180). Latent Profile Analyses were conducted to identify the optimal number of profiles, in accordance with participants' scores on a set of variables prescribed by the Pathways Model and measured during early adolescence: depression, anxiety, impulsivity, hyperactivity, antisocial/aggressive behavior, and drug problems. A four-profile model fit the data best. Three profiles differed from each other in ways consistent with the Pathways Model (i.e., BC, EV, and BV gamblers). A fourth profile emerged, resembling a combination of EV and BV gamblers. Four profiles of at-risk and problem gamblers were identified. Three of these profiles closely resemble those suggested by the Pathways Model.

  7. Regulation of mat responses by a differentiation MAPK pathway in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Sheelarani Karunanithi

    Full Text Available Fungal species exhibit diverse behaviors when presented with extracellular challenges. Pathogenic fungi can undergo cell differentiation and biofilm formation in response to fluctuating nutrient levels, and these responses are required for virulence. In the model fungal eukaryote Saccharomyces cerevisiae, nutrient limitation induces filamentous growth and biofilm/mat formation. Both responses require the same signal transduction (MAPK pathway and the same cell adhesion molecule (Flo11 but have been studied under different conditions. We found that filamentous growth and mat formation are aspects of a related response that is regulated by the MAPK pathway. Cells in yeast-form mats differentiated into pseudohyphae in response to nutrient limitation. The MAPK pathway regulated mat expansion (in the plane of the XY-axis and substrate invasion (downward in the plane of the Z-axis, which optimized the mat's response to extracellular nutrient levels. The MAPK pathway also regulated an upward growth pattern (in the plane of the Z-axis in response to nutrient limitation and changes in surface rigidity. Upward growth allowed for another level of mat responsiveness and resembled a type of colonial chemorepulsion. Together our results show that signaling pathways play critical roles in regulating social behaviors in which fungal cells participate. Signaling pathways may regulate similar processes in pathogens, whose highly nuanced responses are required for virulence.

  8. Pivotal role of the muscle-contraction pathway in cryptorchidism and evidence for genomic connections with cardiomyopathy pathways in RASopathies

    KAUST Repository

    Cannistraci, Carlo

    2013-02-14

    Background: Cryptorchidism is the most frequent congenital disorder in male children; however the genetic causes of cryptorchidism remain poorly investigated. Comparative integratomics combined with systems biology approach was employed to elucidate genetic factors and molecular pathways underlying testis descent. Methods. Literature mining was performed to collect genomic loci associated with cryptorchidism in seven mammalian species. Information regarding the collected candidate genes was stored in MySQL relational database. Genomic view of the loci was presented using Flash GViewer web tool (http://gmod.org/wiki/Flashgviewer/). DAVID Bioinformatics Resources 6.7 was used for pathway enrichment analysis. Cytoscape plug-in PiNGO 1.11 was employed for protein-network-based prediction of novel candidate genes. Relevant protein-protein interactions were confirmed and visualized using the STRING database (version 9.0). Results. The developed cryptorchidism gene atlas includes 217 candidate loci (genes, regions involved in chromosomal mutations, and copy number variations) identified at the genomic, transcriptomic, and proteomic level. Human orthologs of the collected candidate loci were presented using a genomic map viewer. The cryptorchidism gene atlas is freely available online: http://www.integratomics-time.com/cryptorchidism/. Pathway analysis suggested the presence of twelve enriched pathways associated with the list of 179 literature-derived candidate genes. Additionally, a list of 43 network-predicted novel candidate genes was significantly associated with four enriched pathways. Joint pathway analysis of the collected and predicted candidate genes revealed the pivotal importance of the muscle-contraction pathway in cryptorchidism and evidence for genomic associations with cardiomyopathy pathways in RASopathies. Conclusions: The developed gene atlas represents an important resource for the scientific community researching genetics of cryptorchidism. The

  9. Referral pathways for patients with TIA avoiding hospital admission: a scoping review.

    Science.gov (United States)

    Evans, Bridie Angela; Ali, Khalid; Bulger, Jenna; Ford, Gary A; Jones, Matthew; Moore, Chris; Porter, Alison; Pryce, Alan David; Quinn, Tom; Seagrove, Anne C; Snooks, Helen; Whitman, Shirley; Rees, Nigel

    2017-02-14

    To identify the features and effects of a pathway for emergency assessment and referral of patients with suspected transient ischaemic attack (TIA) in order to avoid admission to hospital. Scoping review. PubMed, CINAHL Web of Science, Scopus. Reports of primary research on referral of patients with suspected TIA directly to specialist outpatient services. We screened studies for eligibility and extracted data from relevant studies. Data were analysed to describe setting, assessment and referral processes, treatment, implementation and outcomes. 8 international studies were identified, mostly cohort designs. 4 pathways were used by family doctors and 3 pathways by emergency department physicians. No pathways used by paramedics were found. Referrals were made to specialist clinic either directly or via a 24-hour helpline. Practitioners identified TIA symptoms and risk of further events using a checklist including the ABCD2 tool or clinical assessment. Antiplatelet medication was often given, usually aspirin unless contraindicated. Some patients underwent tests before referral and discharge. 5 studies reported reduced incident of stroke at 90 days, from 6-10% predicted rate to 1.3-2.1% actual rate. Between 44% and 83% of suspected TIA cases in these studies were referred through the pathways. Research literature has focused on assessment and referral by family doctors and ED physicians to reduce hospitalisation of patients with TIA. No pathways for paramedical use were reported. We will use results of this scoping review to inform development of a paramedical referral pathway to be tested in a feasibility trial. ISRCTN85516498. Stage: pre-results. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  10. A novel dysregulated pathway-identification analysis based on global influence of within-pathway effects and crosstalk between pathways

    Science.gov (United States)

    Han, Junwei; Li, Chunquan; Yang, Haixiu; Xu, Yanjun; Zhang, Chunlong; Ma, Jiquan; Shi, Xinrui; Liu, Wei; Shang, Desi; Yao, Qianlan; Zhang, Yunpeng; Su, Fei; Feng, Li; Li, Xia

    2015-01-01

    Identifying dysregulated pathways from high-throughput experimental data in order to infer underlying biological insights is an important task. Current pathway-identification methods focus on single pathways in isolation; however, consideration of crosstalk between pathways could improve our understanding of alterations in biological states. We propose a novel method of pathway analysis based on global influence (PAGI) to identify dysregulated pathways, by considering both within-pathway effects and crosstalk between pathways. We constructed a global gene–gene network based on the relationships among genes extracted from a pathway database. We then evaluated the extent of differential expression for each gene, and mapped them to the global network. The random walk with restart algorithm was used to calculate the extent of genes affected by global influence. Finally, we used cumulative distribution functions to determine the significance values of the dysregulated pathways. We applied the PAGI method to five cancer microarray datasets, and compared our results with gene set enrichment analysis and five other methods. Based on these analyses, we demonstrated that PAGI can effectively identify dysregulated pathways associated with cancer, with strong reproducibility and robustness. We implemented PAGI using the freely available R-based and Web-based tools (http://bioinfo.hrbmu.edu.cn/PAGI). PMID:25551156

  11. Thermodynamic analysis of computed pathways integrated into the metabolic networks of E. coli and Synechocystis reveals contrasting expansion potential.

    Science.gov (United States)

    Asplund-Samuelsson, Johannes; Janasch, Markus; Hudson, Elton P

    2018-01-01

    Introducing biosynthetic pathways into an organism is both reliant on and challenged by endogenous biochemistry. Here we compared the expansion potential of the metabolic network in the photoautotroph Synechocystis with that of the heterotroph E. coli using the novel workflow POPPY (Prospecting Optimal Pathways with PYthon). First, E. coli and Synechocystis metabolomic and fluxomic data were combined with metabolic models to identify thermodynamic constraints on metabolite concentrations (NET analysis). Then, thousands of automatically constructed pathways were placed within each network and subjected to a network-embedded variant of the max-min driving force analysis (NEM). We found that the networks had different capabilities for imparting thermodynamic driving forces toward certain compounds. Key metabolites were constrained differently in Synechocystis due to opposing flux directions in glycolysis and carbon fixation, the forked tri-carboxylic acid cycle, and photorespiration. Furthermore, the lysine biosynthesis pathway in Synechocystis was identified as thermodynamically constrained, impacting both endogenous and heterologous reactions through low 2-oxoglutarate levels. Our study also identified important yet poorly covered areas in existing metabolomics data and provides a reference for future thermodynamics-based engineering in Synechocystis and beyond. The POPPY methodology represents a step in making optimal pathway-host matches, which is likely to become important as the practical range of host organisms is diversified. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  12. Epigenetic pathways in macrophages emerge as novel targets in atherosclerosis

    NARCIS (Netherlands)

    Neele, Annette E.; van den Bossche, Jan; Hoeksema, Marten A.; de Winther, Menno P. J.

    2015-01-01

    Atherosclerosis is a lipid-driven chronic inflammatory disorder. Monocytes and macrophages are key immune cells in the development of disease and clinical outcome. It is becoming increasingly clear that epigenetic pathways govern many aspects of monocyte and macrophage differentiation and

  13. Costimulatory Pathways: Physiology and Potential Therapeutic Manipulation in Systemic Lupus Erythematosus

    Directory of Open Access Journals (Sweden)

    Nien Yee Kow

    2013-01-01

    Full Text Available System lupus erythematosus (SLE is an immune-complex-mediated autoimmune condition with protean immunological and clinical manifestation. While SLE has classically been advocated as a B-cell or T-cell disease, it is unlikely that a particular cell type is more pathologically predominant than the others. Indeed, SLE is characterized by an orchestrated interplay amongst different types of immunopathologically important cells participating in both innate and adaptive immunity including the dendritic cells, macrophages, neutrophils and lymphocytes, as well as traditional nonimmune cells such as endothelial, epithelial, and renal tubular cells. Amongst the antigen-presenting cells and lymphocytes, and between lymphocytes, the costimulatory pathways which involve mutual exchange of information and signalling play an essential role in initiating, perpetuating, and, eventually, attenuating the proinflammatory immune response. In this review, advances in the knowledge of established costimulatory pathways such as CD28/CTLA-4-CD80/86, ICOS-B7RP1, CD70-CD27, OX40-OX40L, and CD137-CD137L as well as their potential roles involved in the pathophysiology of SLE will be discussed. Attempts to target these costimulatory pathways therapeutically will pave more potential treatment avenues for patients with SLE. Preliminary laboratory and clinical evidence of the potential therapeutic value of manipulating these costimulatory pathways in SLE will also be discussed in this review.

  14. Evaluating glymphatic pathway function utilizing clinically relevant intrathecal infusion of CSF tracer

    OpenAIRE

    Yang, Lijun; Kress, Benjamin T; Weber, Harris J; Thiyagarajan, Meenakshisundaram; Wang, Baozhi; Deane, Rashid; Benveniste, Helene; Iliff, Jeffrey J; Nedergaard, Maiken

    2013-01-01

    Background Neurodegenerative diseases such as Alzheimer?s are associated with the aggregation of endogenous peptides and proteins that contribute to neuronal dysfunction and loss. The glymphatic system, a brain-wide perivascular pathway along which cerebrospinal fluid (CSF) and interstitial fluid (ISF) rapidly exchange, has recently been identified as a key contributor to the clearance of interstitial solutes from the brain, including amyloid ?. These findings suggest that measuring changes i...

  15. The putative roles of the ubiquitin/proteasome pathway in resistance to anticancer therapy.

    Science.gov (United States)

    Smith, Laura; Lind, Michael J; Drew, Philip J; Cawkwell, Lynn

    2007-11-01

    The ubiquitin/proteasome (UP) pathway plays a significant role in many important biological functions and alterations in this pathway have been shown to contribute to the pathology of many human diseases, including cancer. Proteasome inhibit