A Knowledge-based System for Intelligent Support in Pharmacogenomics Evidence Assessment: Ontology-driven Evidence Representation, Retrieval, Classification and Interpretation

Thesis (Ph.D.)--University of Washington, 2016-06

Alternative harvest strategies to alleviate predation bottlenecks: a bioeconomic modeling approach to inform adaptive management

Thesis (Ph.D.)--University of Washington, 2016-06

A survey based analysis of IT adoption and 3PLs' performance

Purpose: In today's competitive scenario, effective supply chain management is increasingly dependent on third-party logistics (3PL) companies' capabilities and performance. The dissemination of information technology (IT) has contributed to change the supply chain role of 3PL companies and IT is considered an important element influencing the performance of modern logistics companies. Therefore, the purpose of this paper is to explore the relationship between IT and 3PLs' performance, assuming that logistics capabilities play a mediating role in this relationship. Design/methodology/approach: Empirical evidence based on a questionnaire survey conducted on a sample of logistics service companies operating in the Italian market was used to test a conceptual resource-based view (RBV) framework linking IT adoption, logistics capabilities and firm performance. Factor analysis and ordinary least square (OLS) regression analysis have been used to test hypotheses. The focus of the paper is multidisciplinary in nature; management of information systems, strategy, logistics and supply chain management approaches have been combined in the analysis. Findings: The results indicate strong relationships among data gathering technologies, transactional capabilities and firm performance, in terms of both efficiency and effectiveness. Moreover, a positive correlation between enterprise information technologies and 3PL financial performance has been found. Originality/value: The paper successfully uses the concept of logistics capabilities as mediating factor between IT adoption and firm performance. Objective measures have been proposed for IT adoption and logistics capabilities. Direct and indirect relationships among variables have been successfully tested. © Emerald Group Publishing Limited.

Management of allergic conjunctivitis and dry eye

Ocular allergy is a common eye condition encountered in clinical practice. However, little is known how seasonal allergic conjunctivitis (SAC), the most common subtype, is managed in clinical practice. Further, dry eye, another common eye condition, may be misdiagnosed as SAC and vice-versa as they share similar signs and symptoms. In addition, despite the frequent recommendation of non-pharmacological treatments for SAC, evidenceto support their use has not been identified in the scientific literature. The aim of this thesis was therefore to determine the actual diagnosis and management of SAC and dry eye in clinical practice and investigate the efficacy of non-pharmacological treatments for these conditions. The diagnostic and management strategies for SAC and dry eye employed by pharmacy staff are found to be inconsistent with current guidelines and scientific evidence based upon a mystery shopper design. Cluster analysis of tear film metrics in normal and dry eye patients identified several clinically relevant groups of patients that may allow for targeted treatment recommendations. Using a novel environmental chamber model of SAC, the use of artificial tears and cold compresses, either alone or combined is an effective treatment modality for acute and symptomatic SAC, on a par with topical anti-allergic medication, and has been demonstrated for the first time. In addition, eyelid warming therapy with a simple, readily available, seed filled device is an effective method of treating meibomian gland dysfunction (MGD) related evaporative dry eye, perhaps the most common dry eye subtype. A greater focus on ophthalmology must be implemented as part of the formal education and training of pharmacy staff, while greater professional communication between community pharmacists, optometrists and the population they serve is required. Artificial tears and cold compresses may be considered as front line agents for acute SAC by pharmacy staff and optometrists, to whom pharmacological treatment options are limited.

Introduction of soft budget constraint as an analyzing tool into public management. The case of the Hungarian public administration reform

Public management reforms are usually underpinned by arguments that they will make the public administration system more effective and efficient. In practice, however, it is very hard to determine whether a given reform will improve the efficiency and effectiveness of the public administration system in the long run. Here, I shall examine how the concept of the soft budget constraint (SBC) introduced by János Kornai (Kornai 1979, 1986; Kornai, Maskin & Roland 2003) can be applied to this problem. In the following, I shall describe the Hungarian public administration reforms implemented by the Orbán government from 2010 onward and analyze its reforms, focusing on which measures harden and which ones soften the budget constraint of the actors of the Hungarian public administration system. In the literature of economics, there is some evidence-based knowledge on how to harden/soften the budget constraint, which improves/reduces the effectiveness and hence the efficiency of the given system. By using the concept of SBC, I also hope to shed some light on the rationale behind the Hungarian government’s introduction of such a contradictory reform package. Previously, the concept of SBC was utilized narrowly in public management studies, mostly in the field of fiscal federalism. My goal is to apply the concept to a broader area of public management studies. My conclusion is that the concept of SBC can significantly contribute to public management studies by deepening our knowledge on the reasons behind the success and failure of public administration reforms.

An epistemic event -based correlation scheme for pervasive network management

Computer networks produce tremendous amounts of event-based data that can be collected and managed to support an increasing number of new classes of pervasive applications. Examples of such applications are network monitoring and crisis management. Although the problem of distributed event-based management has been addressed in the non-pervasive settings such as the Internet, the domain of pervasive networks has its own characteristics that make these results non-applicable. Many of these applications are based on time-series data that possess the form of time-ordered series of events. Such applications also embody the need to handle large volumes of unexpected events, often modified on-the-fly, containing conflicting information, and dealing with rapidly changing contexts while producing results with low-latency. Correlating events across contextual dimensions holds the key to expanding the capabilities and improving the performance of these applications. This dissertation addresses this critical challenge. It establishes an effective scheme for complex-event semantic correlation. The scheme examines epistemic uncertainty in computer networks by fusing event synchronization concepts with belief theory. Because of the distributed nature of the event detection, time-delays are considered. Events are no longer instantaneous, but duration is associated with them. Existing algorithms for synchronizing time are split into two classes, one of which is asserted to provide a faster means for converging time and hence better suited for pervasive network management. Besides the temporal dimension, the scheme considers imprecision and uncertainty when an event is detected. A belief value is therefore associated with the semantics and the detection of composite events. This belief value is generated by a consensus among participating entities in a computer network. The scheme taps into in-network processing capabilities of pervasive computer networks and can withstand missing or conflicting information gathered from multiple participating entities. Thus, this dissertation advances knowledge in the field of network management by facilitating the full utilization of characteristics offered by pervasive, distributed and wireless technologies in contemporary and future computer networks.

Statistical dialog management for health interventions

Research endeavors on spoken dialogue systems in the 1990s and 2000s have led to the deployment of commercial spoken dialogue systems (SDS) in microdomains such as customer service automation, reservation/booking and question answering systems. Recent research in SDS has been focused on the development of applications in different domains (e.g. virtual counseling, personal coaches, social companions) which requires more sophistication than the previous generation of commercial SDS. The focus of this research project is the delivery of behavior change interventions based on the brief intervention counseling style via spoken dialogue systems. ^ Brief interventions (BI) are evidence-based, short, well structured, one-on-one counseling sessions. Many challenges are involved in delivering BIs to people in need, such as finding the time to administer them in busy doctors' offices, obtaining the extra training that helps staff become comfortable providing these interventions, and managing the cost of delivering the interventions. Fortunately, recent developments in spoken dialogue systems make the development of systems that can deliver brief interventions possible. ^ The overall objective of this research is to develop a data-driven, adaptable dialogue system for brief interventions for problematic drinking behavior, based on reinforcement learning methods. The implications of this research project includes, but are not limited to, assessing the feasibility of delivering structured brief health interventions with a data-driven spoken dialogue system. Furthermore, while the experimental system focuses on harmful alcohol drinking as a target behavior in this project, the produced knowledge and experience may also lead to implementation of similarly structured health interventions and assessments other than the alcohol domain (e.g. obesity, drug use, lack of exercise), using statistical machine learning approaches. ^ In addition to designing a dialog system, the semantic and emotional meanings of user utterances have high impact on interaction. To perform domain specific reasoning and recognize concepts in user utterances, a named-entity recognizer and an ontology are designed and evaluated. To understand affective information conveyed through text, lexicons and sentiment analysis module are developed and tested.^

Text-messaging as a Tool for Medication Adherence and Behavior Change in Disease Management among Patients with Coronary Heart Disease

Background: Evidence-based medication and lifestyle modification are important for secondary prevention of cardiovascular disease but are underutilized. Mobile health strategies could address this gap but existing evidence is mixed. Therefore, we piloted a pre-post study to assess the impact of patient-directed text messages as a means of improving medication adherence and modifying major health risk behaviors among coronary heart disease (CHD) patients in Hainan, China.

Methods: 92 CVD patients were surveyed between June and August 2015 (before the intervention) and then between October and December 2015 (after 12 week intervention) about (a) medication use (b) smoking status,(c) fruit and vegetable consumption, and (d) physical activity uptake. Acceptability of text-messaging intervention was assessed at follow-up. Descriptive statistics, along with paired comparisons between the pre and post outcomes were conducted using both parametric (t-test) and non-parametric (Wilcoxon signed rank test) methods.

Results: The number of respondents at follow-up was 82 (89% retention rate). Significant improvements were observed for medication adherence (P<0.001) and for the number of cigarettes smoked per day (P=.022). However there was no change in the number of smokers who quitted smoking at follow-up. There were insignificant changes for physical activity (P=0.91) and fruit and vegetable consumption.

Statistical Dialog Management for Health Interventions

Research endeavors on spoken dialogue systems in the 1990s and 2000s have led to the deployment of commercial spoken dialogue systems (SDS) in microdomains such as customer service automation, reservation/booking and question answering systems. Recent research in SDS has been focused on the development of applications in different domains (e.g. virtual counseling, personal coaches, social companions) which requires more sophistication than the previous generation of commercial SDS. The focus of this research project is the delivery of behavior change interventions based on the brief intervention counseling style via spoken dialogue systems. Brief interventions (BI) are evidence-based, short, well structured, one-on-one counseling sessions. Many challenges are involved in delivering BIs to people in need, such as finding the time to administer them in busy doctors' offices, obtaining the extra training that helps staff become comfortable providing these interventions, and managing the cost of delivering the interventions. Fortunately, recent developments in spoken dialogue systems make the development of systems that can deliver brief interventions possible. The overall objective of this research is to develop a data-driven, adaptable dialogue system for brief interventions for problematic drinking behavior, based on reinforcement learning methods. The implications of this research project includes, but are not limited to, assessing the feasibility of delivering structured brief health interventions with a data-driven spoken dialogue system. Furthermore, while the experimental system focuses on harmful alcohol drinking as a target behavior in this project, the produced knowledge and experience may also lead to implementation of similarly structured health interventions and assessments other than the alcohol domain (e.g. obesity, drug use, lack of exercise), using statistical machine learning approaches. In addition to designing a dialog system, the semantic and emotional meanings of user utterances have high impact on interaction. To perform domain specific reasoning and recognize concepts in user utterances, a named-entity recognizer and an ontology are designed and evaluated. To understand affective information conveyed through text, lexicons and sentiment analysis module are developed and tested.

An Epistemic Event-based Correlation Scheme for Pervasive Network Management

Computer networks produce tremendous amounts of event-based data that can be collected and managed to support an increasing number of new classes of pervasive applications. Examples of such applications are network monitoring and crisis management. Although the problem of distributed event-based management has been addressed in the non-pervasive settings such as the Internet, the domain of pervasive networks has its own characteristics that make these results non-applicable. Many of these applications are based on time-series data that possess the form of time-ordered series of events. Such applications also embody the need to handle large volumes of unexpected events, often modified on-the-fly, containing conflicting information, and dealing with rapidly changing contexts while producing results with low-latency. Correlating events across contextual dimensions holds the key to expanding the capabilities and improving the performance of these applications. This dissertation addresses this critical challenge. It establishes an effective scheme for complex-event semantic correlation. The scheme examines epistemic uncertainty in computer networks by fusing event synchronization concepts with belief theory. Because of the distributed nature of the event detection, time-delays are considered. Events are no longer instantaneous, but duration is associated with them. Existing algorithms for synchronizing time are split into two classes, one of which is asserted to provide a faster means for converging time and hence better suited for pervasive network management. Besides the temporal dimension, the scheme considers imprecision and uncertainty when an event is detected. A belief value is therefore associated with the semantics and the detection of composite events. This belief value is generated by a consensus among participating entities in a computer network. The scheme taps into in-network processing capabilities of pervasive computer networks and can withstand missing or conflicting information gathered from multiple participating entities. Thus, this dissertation advances knowledge in the field of network management by facilitating the full utilization of characteristics offered by pervasive, distributed and wireless technologies in contemporary and future computer networks.

Functional management of ankle sprains: what volume and intensity of walking is undertaken in the first week

BACKGROUND:
Acute ankle sprains are usually managed functionally, with advice to undertake progressive weight-bearing and walking. Mechanical loading is an important modular of tissue repair; therefore, the clinical effectiveness of walking after ankle sprain may be dose dependent. The intensity, magnitude and duration of load associated with current functional treatments for ankle sprain are unclear.
AIM:
To describe physical activity (PA) in the first week after ankle sprain and to compare results with a healthy control group.
METHODS:
Participants (16-65 years) with an acute ankle sprain were randomised into two groups (standard or exercise). Both groups were advised to apply ice and compression, and walk within the limits of pain. The exercise group undertook additional therapeutic exercises. PA was measured using an activPAL accelerometer, worn for 7 days after injury. Comparisons were made with a non-injured control group.
RESULTS:
The standard group were significantly less active (1.2 ± 0.4 h activity/day; 5621 ± 2294 steps/day) than the exercise (1.7 ± 0 .7 h/day, p=0.04; 7886 ± 3075 steps/day, p=0.03) and non-injured control groups (1.7 ± 0.4 h/day, p=0.02; 8844 ± 2185 steps/day, p=0.002). Also, compared with the non-injured control group, the standard and exercise groups spent less time in moderate (38.3 ± 12.7 min/day vs 14.5 ± 11.4 min/day, p=0.001 and 22.5 ± 15.9 min/day, p=0.003) and high-intensity activity (4.1 ± 6.9 min/day vs 0.1 ± 0.1 min/day, p=0.001 and 0.62 ± 1.0 min/day p=0.005).
CONCLUSION:
PA patterns are reduced in the first week after ankle sprain, which is partly ameliorated with addition of therapeutic exercises. This study represents the first step towards developing evidence-based walking prescription after acute ankle sprain.

EULAR Recommendations for Women's Health and the Management of Family Planning, Assisted Reproduction, Pregnancy and Menopause in Patients with Systemic Lupus Erythematosus and/or Antiphospholipid Syndrome

OBJECTIVES: Develop recommendations for women's health issues and family planning in systemic lupus erythematosus (SLE) and/or antiphospholipid syndrome (APS). METHODS: Systematic review of evidence followed by modified Delphi method to compile questions, elicit expert opinions and reach consensus. RESULTS: Family planning should be discussed as early as possible after diagnosis. Most women can have successful pregnancies and measures can be taken to reduce the risks of adverse maternal or fetal outcomes. Risk stratification includes disease activity, autoantibody profile, previous vascular and pregnancy morbidity, hypertension and the use of drugs (emphasis on benefits from hydroxychloroquine and antiplatelets/anticoagulants). Hormonal contraception and menopause replacement therapy can be used in patients with stable/inactive disease and low risk of thrombosis. Fertility preservation with gonadotropin-releasing hormone analogues should be considered prior to the use of alkylating agents. Assisted reproduction techniques can be safely used in patients with stable/inactive disease; patients with positive antiphospholipid antibodies/APS should receive anticoagulation and/or low-dose aspirin. Assessment of disease activity, renal function and serological markers is important for diagnosing disease flares and monitoring for obstetrical adverse outcomes. Fetal monitoring includes Doppler ultrasonography and fetal biometry, particularly in the third trimester, to screen for placental insufficiency and small for gestational age fetuses. Screening for gynaecological malignancies is similar to the general population, with increased vigilance for cervical premalignant lesions if exposed to immunosuppressive drugs. Human papillomavirus immunisation can be used in women with stable/inactive disease. CONCLUSIONS: Recommendations for women's health issues in SLE and/or APS were developed using an evidence-based approach followed by expert consensus.

Best practice principles for management of children with developmental coordination disorder (DCD) : results of a scoping review

Background. Developmental coordination disorder (DCD) is a prevalent health condition that is frequently unrecognized despite the substantial evidence that has accumulated regarding how it affects children’s health, education and skills.Most literature focuses on measurement of impairment and description of intervention approaches for individual children; little is known about the principles that should guide best practice and service delivery for children with DCD as a population. The purpose of this study was to identify these principles. Methods. A scoping review was used to ‘map’ the information available to inform intervention and service delivery. Scholarly and grey literature written in English was identified in six databases, using a combination of keywords (e.g. guidelines, management, models and DCD); a ‘snow-balling’ technique was also used in Canada and the UK to access clinical protocols used in publicly funded health care systems. Over 500 documents were screened: 31 met inclusion criteria as they outlined practice principles for children with DCD as a population. Data regarding best practices were independently extracted by two reviewers and then compared with achieve consistency and consensus. Results. Two over-arching themes emerged, with five principles: (1) Organizing services to efficiently meet the comprehensive needs of children (e.g. Increasing awareness of DCD and coordination; Implementing clearly defined pathways; Using a graduated/staged approach); (2) Working collaboratively to offer evidence-based services (e.g. Integration of child and family views; Evidence-based interventions fostering function, participation and prevention). Conclusion Numerous documents support each of the principles, reflecting agreement across studies about recommended organization of services.While these principles may apply to many populations of children with disabilities, this review highlights how essential these principles are in DCD. Researchers, managers, clinicians, community partners and families are encouraged to work together in designing, implementing and evaluating interventions that reflect these principles.

Diagnosis, Treatment, And Follow-up Of Medullary Thyroid Carcinoma: Recommendations By The Thyroid Department Of The Brazilian Society Of Endocrinology And Metabolism.

Medullary thyroid carcinoma (MTC) originates in the thyroid parafollicular cells and represents 3-4% of the malignant neoplasms that affect this gland. Approximately 25% of these cases are hereditary due to activating mutations in the REarranged during Transfection (RET) proto-oncogene. The course of MTC is indolent, and survival rates depend on the tumor stage at diagnosis. The present article describes clinical evidence-based guidelines for the diagnosis, treatment, and follow-up of MTC. The aim of the consensus described herein, which was elaborated by Brazilian experts and sponsored by the Thyroid Department of the Brazilian Society of Endocrinology and Metabolism, was to discuss the diagnosis, treatment, and follow-up of individuals with MTC in accordance with the latest evidence reported in the literature. After clinical questions were elaborated, the available literature was initially surveyed for evidence in the MedLine-PubMed database, followed by the Embase and Scientific Electronic Library Online/Latin American and Caribbean Health Science Literature (SciELO/Lilacs) databases. The strength of evidence was assessed according to the Oxford classification of evidence levels, which is based on study design, and the best evidence available for each question was selected. Eleven questions corresponded to MTC diagnosis, 8 corresponded to its surgical treatment, and 13 corresponded to follow-up, for a total of 32 recommendations. The present article discusses the clinical and molecular diagnosis, initial surgical treatment, and postoperative management of MTC, as well as the therapeutic options for metastatic disease. MTC should be suspected in individuals who present with thyroid nodules and family histories of MTC, associations with pheochromocytoma and hyperparathyroidism, and/or typical phenotypic characteristics such as ganglioneuromatosis and Marfanoid habitus. Fine-needle nodule aspiration, serum calcitonin measurements, and anatomical-pathological examinations are useful for diagnostic confirmation. Surgery represents the only curative therapeutic strategy. The therapeutic options for metastatic disease remain limited and are restricted to disease control. Judicious postoperative assessments that focus on the identification of residual or recurrent disease are of paramount importance when defining the follow-up and later therapeutic management strategies.

Weight of evidence

Evidence-based Medicine (EBM) has become a major source of medical knowledge. It handles complexities of virtually every method or technique used in research. The knowledge on how the EBM researcher retrieves information, judges for relevance and analyzes derived data is invaluable for the skillful reader of medical scientific reports.