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1.  Caregiver- and Patient-Directed Interventions for Dementia 
Executive Summary
In early August 2007, the Medical Advisory Secretariat began work on the Aging in the Community project, an evidence-based review of the literature surrounding healthy aging in the community. The Health System Strategy Division at the Ministry of Health and Long-Term Care subsequently asked the secretariat to provide an evidentiary platform for the ministry’s newly released Aging at Home Strategy.
After a broad literature review and consultation with experts, the secretariat identified 4 key areas that strongly predict an elderly person’s transition from independent community living to a long-term care home. Evidence-based analyses have been prepared for each of these 4 areas: falls and fall-related injuries, urinary incontinence, dementia, and social isolation. For the first area, falls and fall-related injuries, an economic model is described in a separate report.
Please visit the Medical Advisory Secretariat Web site,, to review these titles within the Aging in the Community series.
Aging in the Community: Summary of Evidence-Based Analyses
Prevention of Falls and Fall-Related Injuries in Community-Dwelling Seniors: An Evidence-Based Analysis
Behavioural Interventions for Urinary Incontinence in Community-Dwelling Seniors: An Evidence-Based Analysis
Caregiver- and Patient-Directed Interventions for Dementia: An Evidence-Based Analysis
Social Isolation in Community-Dwelling Seniors: An Evidence-Based Analysis
The Falls/Fractures Economic Model in Ontario Residents Aged 65 Years and Over (FEMOR)
This report features the evidence-based analysis on caregiver- and patient-directed interventions for dementia and is broken down into 4 sections:
Caregiver-Directed Interventions for Dementia
Patient-Directed Interventions for Dementia
Economic Analysis of Caregiver- and Patient-Directed Interventions for Dementia
Caregiver-Directed Interventions for Dementia
To identify interventions that may be effective in supporting the well-being of unpaid caregivers of seniors with dementia living in the community.
Clinical Need: Target Population and Condition
Dementia is a progressive and largely irreversible syndrome that is characterized by a loss of cognitive function severe enough to impact social or occupational functioning. The components of cognitive function affected include memory and learning, attention, concentration and orientation, problem-solving, calculation, language, and geographic orientation. Dementia was identified as one of the key predictors in a senior’s transition from independent community living to admission to a long-term care (LTC) home, in that approximately 90% of individuals diagnosed with dementia will be institutionalized before death. In addition, cognitive decline linked to dementia is one of the most commonly cited reasons for institutionalization.
Prevalence estimates of dementia in the Ontario population have largely been extrapolated from the Canadian Study of Health and Aging conducted in 1991. Based on these estimates, it is projected that there will be approximately 165,000 dementia cases in Ontario in the year 2008, and by 2010 the number of cases will increase by nearly 17% over 2005 levels. By 2020 the number of cases is expected to increase by nearly 55%, due to a rise in the number of people in the age categories with the highest prevalence (85+). With the increase in the aging population, dementia will continue to have a significant economic impact on the Canadian health care system. In 1991, the total costs associated with dementia in Canada were $3.9 billion (Cdn) with $2.18 billion coming from LTC.
Caregivers play a crucial role in the management of individuals with dementia because of the high level of dependency and morbidity associated with the condition. It has been documented that a greater demand is faced by dementia caregivers compared with caregivers of persons with other chronic diseases. The increased burden of caregiving contributes to a host of chronic health problems seen among many informal caregivers of persons with dementia. Much of this burden results from managing the behavioural and psychological symptoms of dementia (BPSD), which have been established as a predictor of institutionalization for elderly patients with dementia.
It is recognized that for some patients with dementia, an LTC facility can provide the most appropriate care; however, many patients move into LTC unnecessarily. For individuals with dementia to remain in the community longer, caregivers require many types of formal and informal support services to alleviate the stress of caregiving. These include both respite care and psychosocial interventions. Psychosocial interventions encompass a broad range of interventions such as psychoeducational interventions, counseling, supportive therapy, and behavioural interventions.
Assuming that 50% of persons with dementia live in the community, a conservative estimate of the number of informal caregivers in Ontario is 82,500. Accounting for the fact that 29% of people with dementia live alone, this leaves a remaining estimate of 58,575 Ontarians providing care for a person with dementia with whom they reside.
Description of Interventions
The 2 main categories of caregiver-directed interventions examined in this review are respite care and psychosocial interventions. Respite care is defined as a break or relief for the caregiver. In most cases, respite is provided in the home, through day programs, or at institutions (usually 30 days or less). Depending on a caregiver’s needs, respite services will vary in delivery and duration. Respite care is carried out by a variety of individuals, including paid staff, volunteers, family, or friends.
Psychosocial interventions encompass a broad range of interventions and have been classified in various ways in the literature. This review will examine educational, behavioural, dementia-specific, supportive, and coping interventions. The analysis focuses on behavioural interventions, that is, those designed to help the caregiver manage BPSD. As described earlier, BPSD are one of the most challenging aspects of caring for a senior with dementia, causing an increase in caregiver burden. The analysis also examines multicomponent interventions, which include at least 2 of the above-mentioned interventions.
Methods of Evidence-Based Analysis
A comprehensive search strategy was used to identify systematic reviews and randomized controlled trials (RCTs) that examined the effectiveness of interventions for caregivers of dementia patients.
Section 2.1
Are respite care services effective in supporting the well-being of unpaid caregivers of seniors with dementia in the community?
Do respite care services impact on rates of institutionalization of these seniors?
Section 2.2
Which psychosocial interventions are effective in supporting the well-being of unpaid caregivers of seniors with dementia in the community?
Which interventions reduce the risk for institutionalization of seniors with dementia?
Outcomes of Interest
any quantitative measure of caregiver psychological health, including caregiver burden, depression, quality of life, well-being, strain, mastery (taking control of one’s situation), reactivity to behaviour problems, etc.;
rate of institutionalization; and
Assessment of Quality of Evidence
The quality of the evidence was assessed as High, Moderate, Low, or Very low according to the GRADE methodology and GRADE Working Group. As per GRADE the following definitions apply:
Summary of Findings
Conclusions in Table 1 are drawn from Sections 2.1 and 2.2 of the report.
Summary of Conclusions on Caregiver-Directed Interventions
There is limited evidence from RCTs that respite care is effective in improving outcomes for those caring for seniors with dementia.
There is considerable qualitative evidence of the perceived benefits of respite care.
Respite care is known as one of the key formal support services for alleviating caregiver burden in those caring for dementia patients.
Respite care services need to be tailored to individual caregiver needs as there are vast differences among caregivers and patients with dementia (severity, type of dementia, amount of informal/formal support available, housing situation, etc.)
There is moderate- to high-quality evidence that individual behavioural interventions (≥ 6 sessions), directed towards the caregiver (or combined with the patient) are effective in improving psychological health in dementia caregivers.
There is moderate- to high-quality evidence that multicomponent interventions improve caregiver psychosocial health and may affect rates of institutionalization of dementia patients.
RCT indicates randomized controlled trial.
Patient-Directed Interventions for Dementia
The section on patient-directed interventions for dementia is broken down into 4 subsections with the following questions:
3.1 Physical Exercise for Seniors with Dementia – Secondary Prevention
What is the effectiveness of physical exercise for the improvement or maintenance of basic activities of daily living (ADLs), such as eating, bathing, toileting, and functional ability, in seniors with mild to moderate dementia?
3.2 Nonpharmacologic and Nonexercise Interventions to Improve Cognitive Functioning in Seniors With Dementia – Secondary Prevention
What is the effectiveness of nonpharmacologic interventions to improve cognitive functioning in seniors with mild to moderate dementia?
3.3 Physical Exercise for Delaying the Onset of Dementia – Primary Prevention
Can exercise decrease the risk of subsequent cognitive decline/dementia?
3.4 Cognitive Interventions for Delaying the Onset of Dementia – Primary Prevention
Does cognitive training decrease the risk of cognitive impairment, deterioration in the performance of basic ADLs or instrumental activities of daily living (IADLs),1 or incidence of dementia in seniors with good cognitive and physical functioning?
Clinical Need: Target Population and Condition
Secondary Prevention2
Physical deterioration is linked to dementia. This is thought to be due to reduced muscle mass leading to decreased activity levels and muscle atrophy, increasing the potential for unsafe mobility while performing basic ADLs such as eating, bathing, toileting, and functional ability.
Improved physical conditioning for seniors with dementia may extend their independent mobility and maintain performance of ADL.
Nonpharmacologic and Nonexercise Interventions
Cognitive impairments, including memory problems, are a defining feature of dementia. These impairments can lead to anxiety, depression, and withdrawal from activities. The impact of these cognitive problems on daily activities increases pressure on caregivers.
Cognitive interventions aim to improve these impairments in people with mild to moderate dementia.
Primary Prevention3
Various vascular risk factors have been found to contribute to the development of dementia (e.g., hypertension, hypercholesterolemia, diabetes, overweight).
Physical exercise is important in promoting overall and vascular health. However, it is unclear whether physical exercise can decrease the risk of cognitive decline/dementia.
Nonpharmacologic and Nonexercise Interventions
Having more years of education (i.e., a higher cognitive reserve) is associated with a lower prevalence of dementia in crossectional population-based studies and a lower incidence of dementia in cohorts followed longitudinally. However, it is unclear whether cognitive training can increase cognitive reserve or decrease the risk of cognitive impairment, prevent or delay deterioration in the performance of ADLs or IADLs or reduce the incidence of dementia.
Description of Interventions
Physical exercise and nonpharmacologic/nonexercise interventions (e.g., cognitive training) for the primary and secondary prevention of dementia are assessed in this review.
Evidence-Based Analysis Methods
A comprehensive search strategy was used to identify systematic reviews and RCTs that examined the effectiveness, safety and cost effectiveness of exercise and cognitive interventions for the primary and secondary prevention of dementia.
Section 3.1: What is the effectiveness of physical exercise for the improvement or maintenance of ADLs in seniors with mild to moderate dementia?
Section 3.2: What is the effectiveness of nonpharmacologic/nonexercise interventions to improve cognitive functioning in seniors with mild to moderate dementia?
Section 3.3: Can exercise decrease the risk of subsequent cognitive decline/dementia?
Section 3.4: Does cognitive training decrease the risk of cognitive impairment, prevent or delay deterioration in the performance of ADLs or IADLs, or reduce the incidence of dementia in seniors with good cognitive and physical functioning?
Assessment of Quality of Evidence
The quality of the evidence was assessed as High, Moderate, Low, or Very low according to the GRADE methodology. As per GRADE the following definitions apply:
Summary of Findings
Table 2 summarizes the conclusions from Sections 3.1 through 3.4.
Summary of Conclusions on Patient-Directed Interventions*
Previous systematic review indicated that “cognitive training” is not effective in patients with dementia.
A recent RCT suggests that CST (up to 7 weeks) is effective for improving cognitive function and quality of life in patients with dementia.
Regular leisure time physical activity in midlife is associated with a reduced risk of dementia in later life (mean follow-up 21 years).
Regular physical activity in seniors is associated with a reduced risk of cognitive decline (mean follow-up 2 years).
Regular physical activity in seniors is associated with a reduced risk of dementia (mean follow-up 6–7 years).
Evidence that cognitive training for specific functions (memory, reasoning, and speed of processing) produces improvements in these specific domains.
Limited inconclusive evidence that cognitive training can offset deterioration in the performance of self-reported IADL scores and performance assessments.
1° indicates primary; 2°, secondary; CST, cognitive stimulation therapy; IADL, instrumental activities of daily living; RCT, randomized controlled trial.
Benefit/Risk Analysis
As per the GRADE Working Group, the overall recommendations consider 4 main factors:
the trade-offs, taking into account the estimated size of the effect for the main outcome, the confidence limits around those estimates, and the relative value placed on the outcome;
the quality of the evidence;
translation of the evidence into practice in a specific setting, taking into consideration important factors that could be expected to modify the size of the expected effects such as proximity to a hospital or availability of necessary expertise; and
uncertainty about the baseline risk for the population of interest.
The GRADE Working Group also recommends that incremental costs of health care alternatives should be considered explicitly alongside the expected health benefits and harms. Recommendations rely on judgments about the value of the incremental health benefits in relation to the incremental costs. The last column in Table 3 reflects the overall trade-off between benefits and harms (adverse events) and incorporates any risk/uncertainty (cost-effectiveness).
Overall Summary Statement of the Benefit and Risk for Patient-Directed Interventions*
Economic Analysis
Budget Impact Analysis of Effective Interventions for Dementia
Caregiver-directed behavioural techniques and patient-directed exercise programs were found to be effective when assessing mild to moderate dementia outcomes in seniors living in the community. Therefore, an annual budget impact was calculated based on eligible seniors in the community with mild and moderate dementia and their respective caregivers who were willing to participate in interventional home sessions. Table 4 describes the annual budget impact for these interventions.
Annual Budget Impact (2008 Canadian Dollars)
Assumed 7% prevalence of dementia aged 65+ in Ontario.
Assumed 8 weekly sessions plus 4 monthly phone calls.
Assumed 12 weekly sessions plus biweekly sessions thereafter (total of 20).
Assumed 2 sessions per week for first 5 weeks. Assumed 90% of seniors in the community with dementia have mild to moderate disease. Assumed 4.5% of seniors 65+ are in long-term care, and the remainder are in the community. Assumed a rate of participation of 60% for both patients and caregivers and of 41% for patient-directed exercise. Assumed 100% compliance since intervention administered at the home. Cost for trained staff from Ministry of Health and Long-Term Care data source. Assumed cost of personal support worker to be equivalent to in-home support. Cost for recreation therapist from Alberta government Website.
Note: This budget impact analysis was calculated for the first year after introducing the interventions from the Ministry of Health and Long-Term Care perspective using prevalence data only. Prevalence estimates are for seniors in the community with mild to moderate dementia and their respective caregivers who are willing to participate in an interventional session administered at the home setting. Incidence and mortality rates were not factored in. Current expenditures in the province are unknown and therefore were not included in the analysis. Numbers may change based on population trends, rate of intervention uptake, trends in current programs in place in the province, and assumptions on costs. The number of patients was based on patients likely to access these interventions in Ontario based on assumptions stated below from the literature. An expert panel confirmed resource consumption.
PMCID: PMC3377513  PMID: 23074509
2.  AHEC library services: from circuit rider to virtual librarian 
The North Carolina Area Health Education Centers Library and Information Services (NC AHEC LIS) Network provides library outreach services to rural health care providers in all nine AHEC regions of North Carolina. Over the last twenty-five years, the AHEC and university-based librarians have collaborated to create a model program for support of community-based clinical education and information access for rural health care providers. Through several collaborative projects, they have supported Internet access for rural health clinics. The NC AHEC Digital Library—under development by NC AHEC, University of North Carolina at Chapel Hill, Duke University, East Carolina University, and Wake Forest University—will further extend access to electronic biomedical information and resources to health professionals in a statewide digital library.
PMCID: PMC35258  PMID: 11055304
3.  The NIF DISCO Framework: Facilitating Automated Integration of Neuroscience Content on the Web 
Neuroinformatics  2010;8(2):10.1007/s12021-010-9068-8.
This paper describes the capabilities of DISCO, an extensible approach that supports integrative Web-based information dissemination. DISCO is a component of the Neuroscience Information Framework (NIF), an NIH Neuroscience Blueprint initiative that facilitates integrated access to diverse neuroscience resources via the Internet. DISCO facilitates the automated maintenance of several distinct capabilities using a collection of files 1) that are maintained locally by the developers of participating neuroscience resources and 2) that are “harvested” on a regular basis by a central DISCO server. This approach allows central NIF capabilities to be updated as each resource’s content changes over time. DISCO currently supports the following capabilities: 1) resource descriptions, 2) “LinkOut” to a resource’s data items from NCBI Entrez resources such as PubMed, 3) Web-based interoperation with a resource, 4) sharing a resource’s lexicon and ontology, 5) sharing a resource’s database schema, and 6) participation by the resource in neuroscience-related RSS news dissemination. The developers of a resource are free to choose which DISCO capabilities their resource will participate in. Although DISCO is used by NIF to facilitate neuroscience data integration, its capabilities have general applicability to other areas of research.
PMCID: PMC3819210  PMID: 20387131
Data integration; database federation; database interoperation; neuroinformatics
4.  OReFiL: an online resource finder for life sciences 
BMC Bioinformatics  2007;8:287.
Many online resources for the life sciences have been developed and introduced in peer-reviewed papers recently, ranging from databases and web applications to data-analysis software. Some have been introduced in special journal issues or websites with a search function, but others remain scattered throughout the Internet and in the published literature. The searchable resources on these sites are collected and maintained manually and are therefore of higher quality than automatically updated sites, but also require more time and effort.
We developed an online resource search system called OReFiL to address these issues. We developed a crawler to gather all of the web pages whose URLs appear in MEDLINE abstracts and full-text papers on the BioMed Central open-access journals. The URLs were extracted using regular expressions and rules based on our heuristic knowledge. We then indexed the online resources to facilitate their retrieval and comparison by researchers. Because every online resource has at least one PubMed ID, we can easily acquire its summary with Medical Subject Headings (MeSH) terms and confirm its credibility through reference to the corresponding PubMed entry. In addition, because OReFiL automatically extracts URLs and updates the index, minimal time and effort is needed to maintain the system.
We developed OReFiL, a search system for online life science resources, which is freely available. The system's distinctive features include the ability to return up-to-date query-relevant online resources introduced in peer-reviewed papers; the ability to search using free words, MeSH terms, or author names; easy verification of each hit following links to the corresponding PubMed entry or to papers citing the URL through the search systems of BioMed Central, Scirus, HighWire Press, or Google Scholar; and quick confirmation of the existence of an online resource web page.
PMCID: PMC1976328  PMID: 17683589
5.  Functional Status Assessment of COPD Based on Ability to Perform Daily Living Activities: A Systematic Review of Paper and Pencil Instruments 
Global Journal of Health Science  2015;8(3):210-223.
Activity of daily living (ADL) is an important predictor of mortality in patients with chronic obstructive pulmonary disease (COPD). Increasing ADL is important in patients with COPD and assessment of ADL is one of the best ways to evaluate the status of COPD patients.
The objective of this systematic review was to provide an overview of the psychometric properties of paper and pencil instruments measuring ADL in patients with COPD.
Data Sources:
English papers published from 1980 to 2014 regarding ADL in patients with COPD were searched in Web of Science, MEDLINE, Google Scholar, Cochrane, PubMed, ProQuest, and CINAHL databases using the following keywords: “COPD”, “ADL”, “activities of daily living”, “daily activities”, “instrument”, “questionnaire”, “paper-and-pencil instruments”, and “measure”. Following the Internet search, manual search was also done to find article references.
Study Selection:
A total of 186 articles were found. Of those, 31 met the inclusion criteria. Full texts of articles meeting the inclusion criteria were studied. Consensus-based standards for the selection of health measurement instruments”(COSMIN) were used to assess the quality of the studies.
Data Extraction:
Data extraction form based on research aims developed by researchers and psychometric experts, with 17 questions was used.
In these articles, 14 pen and paper instruments were identified for examining ADL in patients with COPD; of which, 4 dealt directly with ADL while 9 assessed other criteria i.e. dyspnea as ADL indicator. The majority of instruments only dealt with two main dimensions of ADL: Basic Activities of Daily Living (BADL) and Instrumental Activities of Daily Living (IADL), and did not consider Advanced Activities of Daily Living (AADL), which is influenced by cultural and motivational factors.
Despite several ADL instruments identified, complete psychometric processes have only been done in a few of them. Selection of the appropriate instrument should focus on the aim of the study and the target construct.
PMCID: PMC4803967  PMID: 26493419
activity of daily living; instrument; paper and pencil instruments; chronic obstructive pulmonary disease; systematic review
6.  Capturing patients’ needs in casemix: a systematic literature review on the value of adding functioning information in reimbursement systems 
Contemporary casemix systems for health services need to ensure that payment rates adequately account for actual resource consumption based on patients’ needs for services. It has been argued that functioning information, as one important determinant of health service provision and resource use, should be taken into account when developing casemix systems. However, there has to date been little systematic collation of the evidence on the extent to which the addition of functioning information into existing casemix systems adds value to those systems with regard to the predictive power and resource variation explained by the groupings of these systems. Thus, the objective of this research was to examine the value of adding functioning information into casemix systems with respect to the prediction of resource use as measured by costs and length of stay.
A systematic literature review was performed. Peer-reviewed studies, published before May 2014 were retrieved from CINAHL, EconLit, Embase, JSTOR, PubMed and Sociological Abstracts using keywords related to functioning (‘Functioning’, ‘Functional status’, ‘Function*, ‘ICF’, ‘International Classification of Functioning, Disability and Health’, ‘Activities of Daily Living’ or ‘ADL’) and casemix systems (‘Casemix’, ‘case mix’, ‘Diagnosis Related Groups’, ‘Function Related Groups’, ‘Resource Utilization Groups’ or ‘AN-SNAP’). In addition, a hand search of reference lists of included articles was conducted. Information about study aims, design, country, setting, methods, outcome variables, study results, and information regarding the authors’ discussion of results, study limitations and implications was extracted.
Ten included studies provided evidence demonstrating that adding functioning information into casemix systems improves predictive ability and fosters homogeneity in casemix groups with regard to costs and length of stay. Collection and integration of functioning information varied across studies. Results suggest that, in particular, DRG casemix systems can be improved in predicting resource use and capturing outcomes for frail elderly or severely functioning-impaired patients.
Further exploration of the value of adding functioning information into casemix systems is one promising approach to improve casemix systems ability to adequately capture the differences in patient’s needs for services and to better predict resource use.
Electronic supplementary material
The online version of this article (doi:10.1186/s12913-016-1277-x) contains supplementary material, which is available to authorized users.
PMCID: PMC4741002  PMID: 26847062
Functioning information; DRG; Casemix; Systematic review; Resource utilization
7.  Developing an efficient scheduling template of a chemotherapy treatment unit 
The Australasian Medical Journal  2011;4(10):575-588.
This study was undertaken to improve the performance of a Chemotherapy Treatment Unit by increasing the throughput and reducing the average patient’s waiting time. In order to achieve this objective, a scheduling template has been built. The scheduling template is a simple tool that can be used to schedule patients' arrival to the clinic. A simulation model of this system was built and several scenarios, that target match the arrival pattern of the patients and resources availability, were designed and evaluated. After performing detailed analysis, one scenario provide the best system’s performance. A scheduling template has been developed based on this scenario. After implementing the new scheduling template, 22.5% more patients can be served.
CancerCare Manitoba is a provincially mandated cancer care agency. It is dedicated to provide quality care to those who have been diagnosed and are living with cancer. MacCharles Chemotherapy unit is specially built to provide chemotherapy treatment to the cancer patients of Winnipeg. In order to maintain an excellent service, it tries to ensure that patients get their treatment in a timely manner. It is challenging to maintain that goal because of the lack of a proper roster, the workload distribution and inefficient resource allotment. In order to maintain the satisfaction of the patients and the healthcare providers, by serving the maximum number of patients in a timely manner, it is necessary to develop an efficient scheduling template that matches the required demand with the availability of resources. This goal can be reached using simulation modelling. Simulation has proven to be an excellent modelling tool. It can be defined as building computer models that represent real world or hypothetical systems, and hence experimenting with these models to study system behaviour under different scenarios.1, 2
A study was undertaken at the Children's Hospital of Eastern Ontario to identify the issues behind the long waiting time of a emergency room.3 A 20-­‐day field observation revealed that the availability of the staff physician and interaction affects the patient wait time. Jyväskylä et al.4 used simulation to test different process scenarios, allocate resources and perform activity-­‐based cost analysis in the Emergency Department (ED) at the Central Hospital. The simulation also supported the study of a new operational method, named "triage-team" method without interrupting the main system. The proposed triage team method categorises the entire patient according to the urgency to see the doctor and allows the patient to complete the necessary test before being seen by the doctor for the first time. The simulation study showed that it will decrease the throughput time of the patient and reduce the utilisation of the specialist and enable the ordering all the tests the patient needs right after arrival, thus quickening the referral to treatment.
Santibáñez et al.5 developed a discrete event simulation model of British Columbia Cancer Agency"s ambulatory care unit which was used to study the impact of scenarios considering different operational factors (delay in starting clinic), appointment schedule (appointment order, appointment adjustment, add-­‐ons to the schedule) and resource allocation. It was found that the best outcomes were obtained when not one but multiple changes were implemented simultaneously. Sepúlveda et al.6 studied the M. D. Anderson Cancer Centre Orlando, which is a cancer treatment facility and built a simulation model to analyse and improve flow process and increase capacity in the main facility. Different scenarios were considered like, transferring laboratory and pharmacy areas, adding an extra blood draw room and applying different scheduling techniques of patients. The study shows that by increasing the number of short-­‐term (four hours or less) patients in the morning could increase chair utilisation.
Discrete event simulation also helps improve a service where staff are ignorant about the behaviour of the system as a whole; which can also be described as a real professional system. Niranjon et al.7 used simulation successfully where they had to face such constraints and lack of accessible data. Carlos et al. 8 used Total quality management and simulation – animation to improve the quality of the emergency room. Simulation was used to cover the key point of the emergency room and animation was used to indicate the areas of opportunity required. This study revealed that a long waiting time, overload personnel and increasing withdrawal rate of patients are caused by the lack of capacity in the emergency room.
Baesler et al.9 developed a methodology for a cancer treatment facility to find stochastically a global optimum point for the control variables. A simulation model generated the output using a goal programming framework for all the objectives involved in the analysis. Later a genetic algorithm was responsible for performing the search for an improved solution. The control variables that were considered in this research are number of treatment chairs, number of drawing blood nurses, laboratory personnel, and pharmacy personnel. Guo et al. 10 presented a simulation framework considering demand for appointment, patient flow logic, distribution of resources, scheduling rules followed by the scheduler. The objective of the study was to develop a scheduling rule which will ensure that 95% of all the appointment requests should be seen within one week after the request is made to increase the level of patient satisfaction and balance the schedule of each doctor to maintain a fine harmony between "busy clinic" and "quiet clinic".
Huschka et al.11 studied a healthcare system which was about to change their facility layout. In this case a simulation model study helped them to design a new healthcare practice by evaluating the change in layout before implementation. Historical data like the arrival rate of the patients, number of patients visited each day, patient flow logic, was used to build the current system model. Later, different scenarios were designed which measured the changes in the current layout and performance.
Wijewickrama et al.12 developed a simulation model to evaluate appointment schedule (AS) for second time consultations and patient appointment sequence (PSEQ) in a multi-­‐facility system. Five different appointment rule (ARULE) were considered: i) Baily; ii) 3Baily; iii) Individual (Ind); iv) two patients at a time (2AtaTime); v) Variable Interval and (V-­‐I) rule. PSEQ is based on type of patients: Appointment patients (APs) and new patients (NPs). The different PSEQ that were studied in this study were: i) first-­‐ come first-­‐serve; ii) appointment patient at the beginning of the clinic (APBEG); iii) new patient at the beginning of the clinic (NPBEG); iv) assigning appointed and new patients in an alternating manner (ALTER); v) assigning a new patient after every five-­‐appointment patients. Also patient no show (0% and 5%) and patient punctuality (PUNCT) (on-­‐time and 10 minutes early) were also considered. The study found that ALTER-­‐Ind. and ALTER5-­‐Ind. performed best on 0% NOSHOW, on-­‐time PUNCT and 5% NOSHOW, on-­‐time PUNCT situation to reduce WT and IT per patient. As NOSHOW created slack time for waiting patients, their WT tends to reduce while IT increases due to unexpected cancellation. Earliness increases congestion whichin turn increases waiting time.
Ramis et al.13 conducted a study of a Medical Imaging Center (MIC) to build a simulation model which was used to improve the patient journey through an imaging centre by reducing the wait time and making better use of the resources. The simulation model also used a Graphic User Interface (GUI) to provide the parameters of the centre, such as arrival rates, distances, processing times, resources and schedule. The simulation was used to measure the waiting time of the patients in different case scenarios. The study found that assigning a common function to the resource personnel could improve the waiting time of the patients.
The objective of this study is to develop an efficient scheduling template that maximises the number of served patients and minimises the average patient's waiting time at the given resources availability. To accomplish this objective, we will build a simulation model which mimics the working conditions of the clinic. Then we will suggest different scenarios of matching the arrival pattern of the patients with the availability of the resources. Full experiments will be performed to evaluate these scenarios. Hence, a simple and practical scheduling template will be built based on the indentified best scenario. The developed simulation model is described in section 2, which consists of a description of the treatment room, and a description of the types of patients and treatment durations. In section 3, different improvement scenarios are described and their analysis is presented in section 4. Section 5 illustrates a scheduling template based on one of the improvement scenarios. Finally, the conclusion and future direction of our work is exhibited in section 6.
Simulation Model
A simulation model represents the actual system and assists in visualising and evaluating the performance of the system under different scenarios without interrupting the actual system. Building a proper simulation model of a system consists of the following steps.
Observing the system to understand the flow of the entities, key players, availability of resources and overall generic framework.
Collecting the data on the number and type of entities, time consumed by the entities at each step of their journey, and availability of resources.
After building the simulation model it is necessary to confirm that the model is valid. This can be done by confirming that each entity flows as it is supposed to and the statistical data generated by the simulation model is similar to the collected data.
Figure 1 shows the patient flow process in the treatment room. On the patient's first appointment, the oncologist comes up with the treatment plan. The treatment time varies according to the patient’s condition, which may be 1 hour to 10 hours. Based on the type of the treatment, the physician or the clinical clerk books an available treatment chair for that time period.
On the day of the appointment, the patient will wait until the booked chair is free. When the chair is free a nurse from that station comes to the patient, verifies the name and date of birth and takes the patient to a treatment chair. Afterwards, the nurse flushes the chemotherapy drug line to the patient's body which takes about five minutes and sets up the treatment. Then the nurse leaves to serve another patient. Chemotherapy treatment lengths vary from less than an hour to 10 hour infusions. At the end of the treatment, the nurse returns, removes the line and notifies the patient about the next appointment date and time which also takes about five minutes. Most of the patients visit the clinic to take care of their PICC line (a peripherally inserted central catheter). A PICC is a line that is used to inject the patient with the chemical. This PICC line should be regularly cleaned, flushed to maintain patency and the insertion site checked for signs of infection. It takes approximately 10–15 minutes to take care of a PICC line by a nurse.
Cancer Care Manitoba provided access to the electronic scheduling system, also known as "ARIA" which is comprehensive information and image management system that aggregates patient data into a fully-­‐electronic medical chart, provided by VARIAN Medical System. This system was used to find out how many patients are booked in every clinic day. It also reveals which chair is used for how many hours. It was necessary to search a patient's history to find out how long the patient spends on which chair. Collecting the snapshot of each patient gives the complete picture of a one day clinic schedule.
The treatment room consists of the following two main limited resources:
Treatment Chairs: Chairs that are used to seat the patients during the treatment.
Nurses: Nurses are required to inject the treatment line into the patient and remove it at the end of the treatment. They also take care of the patients when they feel uncomfortable.
Mc Charles Chemotherapy unit consists of 11 nurses, and 5 stations with the following description:
Station 1: Station 1 has six chairs (numbered 1 to 6) and two nurses. The two nurses work from 8:00 to 16:00.
Station 2: Station 2 has six chairs (7 to 12) and three nurses. Two nurses work from 8:00 to 16:00 and one nurse works from 12:00 to 20:00.
Station 3: Station 4 has six chairs (13 to 18) and two nurses. The two nurses work from 8:00 to 16:00.
Station 4: Station 4 has six chairs (19 to 24) and three nurses. One nurse works from 8:00 to 16:00. Another nurse works from 10:00 to 18:00.
Solarium Station: Solarium Station has six chairs (Solarium Stretcher 1, Solarium Stretcher 2, Isolation, Isolation emergency, Fire Place 1, Fire Place 2). There is only one nurse assigned to this station that works from 12:00 to 20:00. The nurses from other stations can help when need arises.
There is one more nurse known as the "float nurse" who works from 11:00 to 19:00. This nurse can work at any station. Table 1 summarises the working hours of chairs and nurses. All treatment stations start at 8:00 and continue until the assigned nurse for that station completes her shift.
Currently, the clinic uses a scheduling template to assign the patients' appointments. But due to high demand of patient appointment it is not followed any more. We believe that this template can be improved based on the availability of nurses and chairs. Clinic workload was collected from 21 days of field observation. The current scheduling template has 10 types of appointment time slot: 15-­‐minute, 1-­‐hour, 1.5-­‐hour, 2-­‐hour, 3-­‐hour, 4-­‐hour, 5-­‐hour, 6-­‐hour, 8-­‐hour and 10-­‐hour and it is designed to serve 95 patients. But when the scheduling template was compared with the 21 days observations, it was found that the clinic is serving more patients than it is designed for. Therefore, the providers do not usually follow the scheduling template. Indeed they very often break the time slots to accommodate slots that do not exist in the template. Hence, we find that some of the stations are very busy (mostly station 2) and others are underused. If the scheduling template can be improved, it will be possible to bring more patients to the clinic and reduce their waiting time without adding more resources.
In order to build or develop a simulation model of the existing system, it is necessary to collect the following data:
Types of treatment durations.
Numbers of patients in each treatment type.
Arrival pattern of the patients.
Steps that the patients have to go through in their treatment journey and required time of each step.
Using the observations of 2,155 patients over 21 days of historical data, the types of treatment durations and the number of patients in each type were estimated. This data also assisted in determining the arrival rate and the frequency distribution of the patients. The patients were categorised into six types. The percentage of these types and their associated service times distributions are determined too.
ARENA Rockwell Simulation Software (v13) was used to build the simulation model. Entities of the model were tracked to verify that the patients move as intended. The model was run for 30 replications and statistical data was collected to validate the model. The total number of patients that go though the model was compared with the actual number of served patients during the 21 days of observations.
Improvement Scenarios
After verifying and validating the simulation model, different scenarios were designed and analysed to identify the best scenario that can handle more patients and reduces the average patient's waiting time. Based on the clinic observation and discussion with the healthcare providers, the following constraints have been stated:
The stations are filled up with treatment chairs. Therefore, it is literally impossible to fit any more chairs in the clinic. Moreover, the stakeholders are not interested in adding extra chairs.
The stakeholders and the caregivers are not interested in changing the layout of the treatment room.
Given these constraints the options that can be considered to design alternative scenarios are:
Changing the arrival pattern of the patients: that will fit over the nurses' availability.
Changing the nurses' schedule.
Adding one full time nurse at different starting times of the day.
Figure 2 compares the available number of nurses and the number of patients' arrival during different hours of a day. It can be noticed that there is a rapid growth in the arrival of patients (from 13 to 17) between 8:00 to 10:00 even though the clinic has the equal number of nurses during this time period. At 12:00 there is a sudden drop of patient arrival even though there are more available nurses. It is clear that there is an imbalance in the number of available nurses and the number of patient arrivals over different hours of the day. Consequently, balancing the demand (arrival rate of patients) and resources (available number of nurses) will reduce the patients' waiting time and increases the number of served patients. The alternative scenarios that satisfy the above three constraints are listed in Table 2. These scenarios respect the following rules:
Long treatments (between 4hr to 11hr) have to be scheduled early in the morning to avoid working overtime.
Patients of type 1 (15 minutes to 1hr treatment) are the most common. They can be fitted in at any time of the day because they take short treatment time. Hence, it is recommended to bring these patients in at the middle of the day when there are more nurses.
Nurses get tired at the end of the clinic day. Therefore, fewer patients should be scheduled at the late hours of the day.
In Scenario 1, the arrival pattern of the patient was changed so that it can fit with the nurse schedule. This arrival pattern is shown Table 3. Figure 3 shows the new patients' arrival pattern compared with the current arrival pattern. Similar patterns can be developed for the remaining scenarios too.
Analysis of Results
ARENA Rockwell Simulation software (v13) was used to develop the simulation model. There is no warm-­‐up period because the model simulates day-­‐to-­‐day scenarios. The patients of any day are supposed to be served in the same day. The model was run for 30 days (replications) and statistical data was collected to evaluate each scenario. Tables 4 and 5 show the detailed comparison of the system performance between the current scenario and Scenario 1. The results are quite interesting. The average throughput rate of the system has increased from 103 to 125 patients per day. The maximum throughput rate can reach 135 patients. Although the average waiting time has increased, the utilisation of the treatment station has increased by 15.6%. Similar analysis has been performed for the rest of the other scenarios. Due to the space limitation the detailed results are not given. However, Table 6 exhibits a summary of the results and comparison between the different scenarios. Scenario 1 was able to significantly increase the throughput of the system (by 21%) while it still results in an acceptable low average waiting time (13.4 minutes). In addition, it is worth noting that adding a nurse (Scenarios 3, 4, and 5) does not significantly reduce the average wait time or increase the system's throughput. The reason behind this is that when all the chairs are busy, the nurses have to wait until some patients finish the treatment. As a consequence, the other patients have to wait for the commencement of their treatment too. Therefore, hiring a nurse, without adding more chairs, will not reduce the waiting time or increase the throughput of the system. In this case, the only way to increase the throughput of the system is by adjusting the arrival pattern of patients over the nurses' schedule.
Developing a Scheduling Template based on Scenario 1
Scenario 1 provides the best performance. However a scheduling template is necessary for the care provider to book the patients. Therefore, a brief description is provided below on how scheduling the template is developed based on this scenario.
Table 3 gives the number of patients that arrive hourly, following Scenario 1. The distribution of each type of patient is shown in Table 7. This distribution is based on the percentage of each type of patient from the collected data. For example, in between 8:00-­‐9:00, 12 patients will come where 54.85% are of Type 1, 34.55% are of Type 2, 15.163% are of Type 3, 4.32% are of Type 4, 2.58% are of Type 5 and the rest are of Type 6. It is worth noting that, we assume that the patients of each type arrive as a group at the beginning of the hourly time slot. For example, all of the six patients of Type 1 from 8:00 to 9:00 time slot arrive at 8:00.
The numbers of patients from each type is distributed in such a way that it respects all the constraints described in Section 1.3. Most of the patients of the clinic are from type 1, 2 and 3 and they take less amount of treatment time compared with the patients of other types. Therefore, they are distributed all over the day. Patients of type 4, 5 and 6 take a longer treatment time. Hence, they are scheduled at the beginning of the day to avoid overtime. Because patients of type 4, 5 and 6 come at the beginning of the day, most of type 1 and 2 patients come at mid-­‐day (12:00 to 16:00). Another reason to make the treatment room more crowded in between 12:00 to 16:00 is because the clinic has the maximum number of nurses during this time period. Nurses become tired at the end of the clinic which is a reason not to schedule any patient after 19:00.
Based on the patient arrival schedule and nurse availability a scheduling template is built and shown in Figure 4. In order to build the template, if a nurse is available and there are patients waiting for service, a priority list of these patients will be developed. They are prioritised in a descending order based on their estimated slack time and secondarily based on the shortest service time. The secondary rule is used to break the tie if two patients have the same slack. The slack time is calculated using the following equation:
Slack time = Due time - (Arrival time + Treatment time)
Due time is the clinic closing time. To explain how the process works, assume at hour 8:00 (in between 8:00 to 8:15) two patients in station 1 (one 8-­‐hour and one 15-­‐ minute patient), two patients in station 2 (two 12-­‐hour patients), two patients in station 3 (one 2-­‐hour and one 15-­‐ minute patient) and one patient in station 4 (one 3-­‐hour patient) in total seven patients are scheduled. According to Figure 2, there are seven nurses who are available at 8:00 and it takes 15 minutes to set-­‐up a patient. Therefore, it is not possible to schedule more than seven patients in between 8:00 to 8:15 and the current scheduling is also serving seven patients by this time. The rest of the template can be justified similarly.
PMCID: PMC3562880  PMID: 23386870
8.  Effect of Resistance Exercises on Function in Older Adults with Osteoporosis or Osteopenia: A Systematic Review 
Physiotherapy Canada  2012;64(4):386-394.
Purpose: To examine the effect of resistance exercises on self-reported physical function and activities of daily living (ADL) in older adults with osteoporosis or osteopenia. Methods: A search of available literature was conducted using PubMed, CINAHL, SPORTDiscus, PEDro, ProQuest Nursing and Allied Health Source, and Cochrane Controlled Trials Register. Studies were included if they involved (1) randomized controlled trials; (2) participants with osteoporosis or osteopenia; (3) resistance exercise as an intervention; and (4) self-report of physical function or ADL. Articles were independently reviewed for quality by two authors using the Physiotherapy Evidence Database (PEDro) scale. Cohen's d effect size was calculated by dividing standardized mean differences by the standard deviation to determine treatment effect in terms of physical function or ADL. Results: Five full-text articles were selected for inclusion. PEDro scores ranged from 5 to 7 (out of 10). Effect size mean differences as a result of resistance intervention ranged from 0.08 to 1.74, suggesting “trivial” to “large” effects on self-reported physical function and ADL. Conclusion: Results suggest that interventions using resistance training have a beneficial impact on the domains of physical function and ADL in participants with osteoporosis or osteopenia. More high-quality studies are needed to lend further validity to this supposition.
PMCID: PMC3484910  PMID: 23997394
activities of daily living; exercise; osteopenia; osteoporosis; resistance training; activités de la vie quotidienne; exercice; fonction; ostéoporose; ostéopénie; entraînement avec résistance; entraînement en force
9.  Impairment in the activities of daily living in older adults with and without osteoporosis, osteoarthritis and chronic back pain: a secondary analysis of population-based health survey data 
Independence in performing activities of daily living (ADLs) is a central aspect of functioning. Older adults frequently experience impairments and limitations in functioning in various life areas. The aim of this survey was to explore the limitations in the ADLs in older adults in a population-based survey in Austria.
A population-based cross-sectional study in 3097 subjects aged ≥65 years who were included in the Austrian health interview survey was performed. Descriptive statistics were used to calculate frequencies of problems in the ADLs. A principal component analysis was applied to analyze the main dimensions of 19 ADL items. Binary logistic regression models were used with the ADL dimensions as the dependent variables and osteoarthritis, chronic back pain, osteoporosis, sex, education level, anxiety or depression, age and pain intensity as independent variables.
People with musculoskeletal conditions were significantly more often affected by ADL problems than people without these diseases. The ADL domain which caused problems in the highest proportion of people was “doing heavy housework” (43.9 %). It was followed by the ADL domains “bending or kneeling down” (39.3 %), “climbing stairs up and down without walking aids” (23.1 %), and “walking 500 m without walking aids” (22.8 %). The principal components analysis revealed four dimensions of ADLs: (1) intense “heavy burden” ADLs, (2) basic instrumental ADLs, (3) basic ADLs and (3) hand-focused ADLs. The proportion of subjects who had problems with the respective dimensions was 58.2, 29.2, 23.0, and 9.2 %. Anxiety/depression (greatest effect), followed by the chronic musculoskeletal disease itself, female sex, higher age and pain intensity were significant predictors of ADL problems.
This population-based survey indicates that older people have considerable ADL problems. More attention should be paid to the high impact of pain intensity, anxiety and depression on ADLs.
PMCID: PMC4810518  PMID: 27020532
Activities of daily living; Population-based study; Occupational therapy
10.  Incidence of ADL Disability in Older Persons, Physical Activities as a Protective Factor and the Need for Informal and Formal Care – Results from the SNAC-N Project 
PLoS ONE  2015;10(9):e0138901.
The aim of the study was to examine 1) the incidence of disability in Activities of Daily Living (ADL), in persons 78 years and older 2) explore whether being physical active earlier is a significant predictor of being disability free at follow-up and 3) describe the amount of informal and formal care in relation to ADL-disability.
Data were used from a longitudinal community-based study in Nordanstig (SNAC-N), a part of the Swedish National Study on Aging and Care (SNAC). To study objectives 1) and 2) all ADL-independent participants at baseline (N = 307) were included; for objective 3) all participants 78 years and older were included (N = 316). Data were collected at baseline and at 3- and 6-year follow-ups. ADL-disability was defined as a need for assistance in one or more activities. Informal and formal care were measured using the Resource utilization in Dementia (RUD)-instrument.
The incidence rates for men were similar in the age groups 78-81and 84 years and older, 42.3 vs. 42.5/1000 person-years. For women the incidence rate for ADL-disability increased significantly from the age group 78–81 to the age group 84 years and older, 20.8 vs.118.3/1000 person-years. In the age group 78–81 years, being physically active earlier (aOR 6.2) and during the past 12 month (aOR 2.9) were both significant preventive factors for ADL-disability. Both informal and formal care increased with ADL-disability and the amount of informal care was greater than formal care. The incidence rate for ADL-disability increases with age for women and being physically active is a protective factor for ADL-disability.
The incidence rate for ADL-disability increases with age for women, and being physical active is a protective factor for ADL-disability.
PMCID: PMC4583409  PMID: 26407207
11.  Predicting ADL disability in community-dwelling elderly people using physical frailty indicators: a systematic review 
BMC Geriatrics  2011;11:33.
Disability in Activities of Daily Living (ADL) is an adverse outcome of frailty that places a burden on frail elderly people, care providers and the care system. Knowing which physical frailty indicators predict ADL disability is useful in identifying elderly people who might benefit from an intervention that prevents disability or increases functioning in daily life. The objective of this study was to systematically review the literature on the predictive value of physical frailty indicators on ADL disability in community-dwelling elderly people.
A systematic search was performed in 3 databases (PubMed, CINAHL, EMBASE) from January 1975 until April 2010. Prospective, longitudinal studies that assessed the predictive value of individual physical frailty indicators on ADL disability in community-dwelling elderly people aged 65 years and older were eligible for inclusion. Articles were reviewed by two independent reviewers who also assessed the quality of the included studies.
After initial screening of 3081 titles, 360 abstracts were scrutinized, leaving 64 full text articles for final review. Eventually, 28 studies were included in the review. The methodological quality of these studies was rated by both reviewers on a scale from 0 to 27. All included studies were of high quality with a mean quality score of 22.5 (SD 1.6). Findings indicated that individual physical frailty indicators, such as weight loss, gait speed, grip strength, physical activity, balance, and lower extremity function are predictors of future ADL disability in community-dwelling elderly people.
This review shows that physical frailty indicators can predict ADL disability in community-dwelling elderly people. Slow gait speed and low physical activity/exercise seem to be the most powerful predictors followed by weight loss, lower extremity function, balance, muscle strength, and other indicators. These findings should be interpreted with caution because the data of the different studies could not be pooled due to large variations in operationalization of the indicators and ADL disability across the included studies. Nevertheless, our study suggests that monitoring physical frailty indicators in community-dwelling elderly people might be useful to identify elderly people who could benefit from disability prevention programs.
PMCID: PMC3142492  PMID: 21722355
12.  Functional assessment and performance evaluation for assistive robotic manipulators: Literature review 
The user interface development of assistive robotic manipulators can be traced back to the 1960s. Studies include kinematic designs, cost-efficiency, user experience involvements, and performance evaluation. This paper is to review studies conducted with clinical trials using activities of daily living (ADLs) tasks to evaluate performance categorized using the International Classification of Functioning, Disability, and Health (ICF) frameworks, in order to give the scope of current research and provide suggestions for future studies.
We conducted a literature search of assistive robotic manipulators from 1970 to 2012 in PubMed, Google Scholar, and University of Pittsburgh Library System – PITTCat.
Twenty relevant studies were identified.
Studies were separated into two broad categories: user task preferences and user-interface performance measurements of commercialized and developing assistive robotic manipulators. The outcome measures and ICF codes associated with the performance evaluations are reported. Suggestions for the future studies include (1) standardized ADL tasks for the quantitative and qualitative evaluation of task efficiency and performance to build comparable measures between research groups, (2) studies relevant to the tasks from user priority lists and ICF codes, and (3) appropriate clinical functional assessment tests with consideration of constraints in assistive robotic manipulator user interfaces. In addition, these outcome measures will help physicians and therapists build standardized tools while prescribing and assessing assistive robotic manipulators.
PMCID: PMC3758524  PMID: 23820143
Spinal cord injuries; Paralysis; Robotics; Wheelchairs; Task performance; Assistive technology; Assistive robotic manipulators; User interfaces; Functional assessment; Outcome measures; Disability; Rehabilitation; Physical; Vocational; Activities of daily living; Muscular dystrophy; Spinal cord injury; Spinal muscular atrophy; Multiple sclerosis; Amyotrophic lateral sclerosis; Cerebral palsy; Rheumatoid arthritis; Postpolio syndrome; Locked-in syndrome
13.  Estimated Quality-Adjusted Life-Year Associated with the Degree of Activities of Daily Living in Patients with Alzheimer's Disease 
The quality-adjusted life-year (QALY) and health state utility values (HSUVs) are major quality of life scales that are used for the analyses of health economics of diseases such as Alzheimer's disease (AD). In Japan, the most common dementia disease is AD with cerebrovascular diseases (CVD), followed by ‘pure’ AD. There is a need to reconsider QALY and HSUVs in the context of activities of daily living (ADL) levels in AD and AD with CVD.
Studies on QALY and HSUVs based on ADL levels in AD were identified using a PubMed search. HSUVs were estimated in AD patients with ADL levels A (independent walking and eating), B (some problems with walking but sitting without assistance), and C (confined to bed). These three ADL levels correspond approximately to the stages of Mobility on the EQ-5D.
There has been no previous report on HSUVs related to the level of physical activity of patients with AD. From the previous reports and EQ-5D, we estimated that the HSUVs of pure AD and AD with CVD for ADL levels A, B, and C were 0.61 and 0.58, 0.53 and 0.28, and 0.19 and 0.05, respectively.
Effects of ADL should be considered during the decision making process in health policy for dementia care in Japan.
PMCID: PMC3919497  PMID: 24516416
Quality-adjusted life-year; Activities of daily living; Alzheimer's disease

14.  Availability of renal literature in six bibliographic databases 
Clinical Kidney Journal  2012;5(6):610-617.
When searching for renal literature, nephrologists must choose between several different bibliographic databases. We compared the availability of renal clinical studies in six major bibliographic databases.
We gathered 151 renal systematic reviews, which collectively contained 2195 unique citations referencing primary studies in the form of journal articles, meeting articles or meeting abstracts published between 1963 and 2008. We searched for each citation in three subscription-free bibliographic databases (PubMed, Google Scholar and Scirus) and three subscription-based databases (EMBASE, Ovid-MEDLINE and ISI Web of Knowledge). For the subscription-free databases, we determined which full-text journal articles were available free of charge via links to the article source.
The proportion of journal articles contained within each of the six databases ranged from 96 to 97%; results were similar for meeting articles. Availability of meeting abstracts was poor, ranging from 0 to 37% (P < 0.01) with ISI Web of Knowledge containing the largest proportion [37%, 95% confidence interval (95% CI) 32–43%]. Among the subscription-free databases, free access to full-text articles was highest in Google Scholar (38% free, 95% CI 36–41%), and was only marginally higher (39%) when all subscription-free databases were searched. After 2000, free access to full-text articles increased to 49%.
Over 99% of renal clinical journal articles are available in at least one major bibliographic database. Subscription-free databases provide free full-text access to almost half of the articles published after the year 2000, which may be of particular interest to clinicians in settings with limited access to subscription-based resources.
PMCID: PMC3506156  PMID: 23185693
bibliographic databases; content coverage; evidence-based medicine; information storage and retrieval; literature searching; renal informatics
15.  Recognition of activities of daily living in healthy subjects using two ad-hoc classifiers 
Activities of daily living (ADL) are important for quality of life. They are indicators of cognitive health status and their assessment is a measure of independence in everyday living. ADL are difficult to reliably assess using questionnaires due to self-reporting biases. Various sensor-based (wearable, in-home, intrusive) systems have been proposed to successfully recognize and quantify ADL without relying on self-reporting. New classifiers required to classify sensor data are on the rise. We propose two ad-hoc classifiers that are based only on non-intrusive sensor data.
A wireless sensor system with ten sensor boxes was installed in the home of ten healthy subjects to collect ambient data over a duration of 20 consecutive days. A handheld protocol device and a paper logbook were also provided to the subjects. Eight ADL were selected for recognition. We developed two ad-hoc ADL classifiers, namely the rule based forward chaining inference engine (RBI) classifier and the circadian activity rhythm (CAR) classifier. The RBI classifier finds facts in data and matches them against the rules. The CAR classifier works within a framework to automatically rate routine activities to detect regular repeating patterns of behavior. For comparison, two state-of-the-art [Naïves Bayes (NB), Random Forest (RF)] classifiers have also been used. All classifiers were validated with the collected data sets for classification and recognition of the eight specific ADL.
Out of a total of 1,373 ADL, the RBI classifier correctly determined 1,264, while missing 109 and the CAR determined 1,305 while missing 68 ADL. The RBI and CAR classifier recognized activities with an average sensitivity of 91.27 and 94.36%, respectively, outperforming both RF and NB.
The performance of the classifiers varied significantly and shows that the classifier plays an important role in ADL recognition. Both RBI and CAR classifier performed better than existing state-of-the-art (NB, RF) on all ADL. Of the two ad-hoc classifiers, the CAR classifier was more accurate and is likely to be better suited than the RBI for distinguishing and recognizing complex ADL.
Electronic supplementary material
The online version of this article (doi:10.1186/s12938-015-0050-4) contains supplementary material, which is available to authorized users.
PMCID: PMC4457983  PMID: 26048452
Naïve Bayes; Random Forest; Activities of daily living; ADL recognition; Wireless sensor; Forward chaining inference engine; Circadian activity rhythm; Rule based inference; Classifiers
16.  Why Do Women Not Use Antenatal Services in Low- and Middle-Income Countries? A Meta-Synthesis of Qualitative Studies 
PLoS Medicine  2013;10(1):e1001373.
In a synthesis of 21 qualitative studies representing the views of more than 1,230 women from 15 countries, Kenneth Finlayson and Soo Downe examine the reasons why many women in low- and middle-income countries do not receive adequate antenatal care.
Almost 50% of women in low- and middle-income countries (LMICs) don't receive adequate antenatal care. Women's views can offer important insights into this problem. Qualitative studies exploring inadequate use of antenatal services have been undertaken in a range of countries, but the findings are not easily transferable. We aimed to inform the development of future antenatal care programmes through a synthesis of findings in all relevant qualitative studies.
Methods and Findings
Using a predetermined search strategy, we identified robust qualitative studies reporting on the views and experiences of women in LMICs who received inadequate antenatal care. We used meta-ethnographic techniques to generate themes and a line-of-argument synthesis. We derived policy-relevant hypotheses from the findings. We included 21 papers representing the views of more than 1,230 women from 15 countries. Three key themes were identified: “pregnancy as socially risky and physiologically healthy”, “resource use and survival in conditions of extreme poverty”, and “not getting it right the first time”. The line-of-argument synthesis describes a dissonance between programme design and cultural contexts that may restrict access and discourage return visits. We hypothesize that centralised, risk-focused antenatal care programmes may be at odds with the resources, beliefs, and experiences of pregnant women who underuse antenatal services.
Our findings suggest that there may be a misalignment between current antenatal care provision and the social and cultural context of some women in LMICs. Antenatal care provision that is theoretically and contextually at odds with local contextual beliefs and experiences is likely to be underused, especially when attendance generates increased personal risks of lost family resources or physical danger during travel, when the promised care is not delivered because of resource constraints, and when women experience covert or overt abuse in care settings.
Please see later in the article for the Editors' Summary
Editors' Summary
Although maternal deaths worldwide have almost halved since 1990, according to the latest figures, every day roughly 800 women and adolescent girls still die from the complications of pregnancy or childbirth: in 2010, 287,000 women died during or following pregnancy and childbirth, with almost all of these deaths (99%) occurring in low-resource settings. Most maternal deaths are avoidable, as the interventions to prevent or manage the most common complications (severe bleeding, infections, high blood pressure during pregnancy, and unsafe abortion) are well known. Furthermore, many of these complications can be prevented, detected, or treated during antenatal care visits with trained health workers.
Why Was This Study Done?
The World Health Organization (WHO) recommends a minimum of four antenatal visits per pregnancy, but according to WHO figures, between 2005 and 2010 only 53% of pregnant women worldwide attended the recommended four antenatal visits; in low-income countries, this figure was a disappointing 36%. Unfortunately, despite huge international efforts to promote and provide antenatal care, there has been little improvement in these statistics over the past decade. It is therefore important to investigate the reasons for poor antenatal attendance and to seek the views of users of antenatal care. In this study, the researchers combined studies from low- and middle-income countries (LMICs) that included women's views on antenatal care in a meta-synthesis of qualitative studies (qualitative research uses techniques, such as structured interviews, to gather an in-depth understanding of human behaviour, and a meta-synthesis combines and interprets information across studies, contexts, and populations).
What Did the Researchers Do and Find?
The researchers searched several medical, sociological, and psychological databases to find appropriate qualitative studies published between January 1980 and February 2012 that explored the antenatal care experiences, attitudes, and beliefs of women from LMICs who had chosen to access antenatal care late (after 12 weeks' gestation), infrequently (less than four times), or not at all. The researchers included 21 studies (out of the 2,997 initially identified) in their synthesis, representing the views of 1,239 women from 15 countries (Bangladesh, Benin, Cambodia, Gambia, India, Indonesia, Kenya, Lebanon, Mexico, Mozambique, Nepal, Pakistan, South Africa, Tanzania, and Uganda) who were either interviewed directly or gave their opinion as part of a focus group.
The researchers identified three main themes. The first theme reflects women's views that pregnancy is a healthy state and so saw little reason to visit health professionals when they perceived no risk to their well-being—the researchers called this theme, “pregnancy as socially contingent and physiologically healthy.” The second theme relates to women's limited financial resources, so that even when antenatal care was offered free of charge, the cost of transport to get there, the loss of earnings associated with the visit, and the possibility of having to pay for medicines meant that women were unable to attend—the researchers called this theme “resource use and survival in conditions of extreme poverty.” The third theme the researchers identified related to women's views that the antenatal services were inadequate and that the benefits of attending did not outweigh any potential harms. For example, pregnant women who initially recognized the benefits of antenatal care were often disappointed by the lack of resources they found when they got there and, consequently, decided not to return. The researchers called this theme “not getting it right the first time.”
What Do These Findings Mean?
These findings suggest that there may be a misalignment between the principles that underpin the provision of antenatal care and the beliefs and socio-economic contexts of pregnant women in LMICs, meaning that even high-quality antenatal care may not be used by some pregnant women unless their views and concerns are addressed. The themes identified in this meta-synthesis could provide the basis for a new approach to the design and delivery of antenatal care that takes local beliefs and values and resource availability into account. Such programs might help ensure that antenatal care meets pregnant women's expectations and treats them appropriately so that they want to regularly attend antenatal care.
Additional Information
Please access these websites via the online version of this summary at
Wikipedia describes antenatal care (note that Wikipedia is a free online encyclopedia that anyone can edit)
The World Health Organization has a wealth of information relating to pregnancy, including antenatal care
The UK National Institute for Health and Clinical Excellence has evidence-based guidelines on antenatal care
The White Ribbon Alliance for Safe Motherhood has a series of web pages and links relating to respectful maternity care in LMICs
International Federation of Gynecology and Obstetrics is an international organization with connections to various maternity initiatives in LMICs
International Confederation of Midwives has details of the Millennium Development Goals relating to maternity care
PMCID: PMC3551970  PMID: 23349622
17.  LabeledIn: Cataloging Labeled Indications for Human Drugs 
Drug-disease treatment relationships, i.e., which drug(s) are indicated to treat which disease(s), are among the most frequently sought information in PubMed®. Such information is useful for feeding the Google Knowledge Graph, designing computational methods to predict novel drug indications, and validating clinical information in EMRs. Given the importance and utility of this information, there have been several efforts to create repositories of drugs and their indications. However, existing resources are incomplete. Furthermore, they neither label indications in a structured way nor differentiate them by drug-specific properties such as dosage form, and thus do not support computer processing or semantic interoperability. More recently, several studies have proposed automatic methods to extract structured indications from drug descriptions; however, their performance is limited by natural language challenges in disease named entity recognition and indication selection.
In response, we report LabeledIn: a human-reviewed, machine-readable and source-linked catalog of labeled indications for human drugs. More specifically, we describe our semi-automatic approach to derive LabeledIn from drug descriptions through human annotations with aids from automatic methods. As the data source, we use the drug labels (or package inserts) submitted to the FDA by drug manufacturers and made available in DailyMed. Our machine-assisted human annotation workflow comprises: (i) a grouping method to remove redundancy and identify representative drug labels to be used for human annotation, (ii) an automatic method to recognize and normalize mentions of diseases in drug labels as candidate indications, and (iii) a two-round annotation workflow for human experts to judge the pre-computed candidates and deliver the final gold standard.
In this study, we focused on 250 highly accessed drugs in PubMed Health, a newly developed public web resource for consumers and clinicians on prevention and treatment of diseases. These 250 drugs corresponded to more than 8,000 drug labels (500 unique) in DailyMed in which 2,950 candidate indications were pre-tagged by an automatic tool. After being reviewed independently by two experts, 1,618 indications were selected, and additional 97 (missed by computer) were manually added, with an inter-annotator agreement of 88.35% as measured by the Kappa coefficient. Our final annotation results in LabeledIn consist of 7,805 drug-disease treatment relationships where drugs are represented as a triplet of ingredient, dose form, and strength.
A systematic comparison of LabeledIn with an existing computer-derived resource revealed significant discrepancies, confirming the need to involve humans in the creation of such a resource. In addition, LabeledIn is unique in that it contains detailed textual context of the selected indications in drug labels, making it suitable for the development of advanced computational methods for the automatic extraction of indications from free text. Finally, motivated by the studies on drug nomenclature and medication errors in EMRs, we adopted a fine-grained drug representation scheme, which enables the automatic identification of drugs with indications specific to certain dose forms or strengths. Future work includes expanding our coverage to more drugs and integration with other resources.
PMCID: PMC4260997  PMID: 25220766
Corpus Annotation; Drug Labels; Drug Indications; Natural Language Processing
18.  Drug information resources used by nurse practitioners and collaborating physicians at the point of care in Nova Scotia, Canada: a survey and review of the literature 
BMC Nursing  2006;5:5.
Keeping current with drug therapy information is challenging for health care practitioners. Technologies are often implemented to facilitate access to current and credible drug information sources. In the Canadian province of Nova Scotia, legislation was passed in 2002 to allow nurse practitioners (NPs) to practice collaboratively with physician partners. The purpose of this study was to determine the current utilization patterns of information technologies by these groups of practitioners.
Nurse practitioners and their collaborating physician partners in Nova Scotia were sent a survey in February 2005 to determine the frequency of use, usefulness, accessibility, credibility, and current/timeliness of personal digital assistant (PDA), computer, and print drug information resources. Two surveys were developed (one for PDA users and one for computer users) and revised based on a literature search, stakeholder consultation, and pilot-testing results. A second distribution to nonresponders occurred two weeks following the first. Data were entered and analysed with SPSS.
Twenty-seven (14 NPs and 13 physicians) of 36 (75%) recipients responded. 22% (6) returned personal digital assistant (PDA) surveys. Respondents reported print, health professionals, and online/electronic resources as the most to least preferred means to access drug information, respectively. 37% and 35% of respondents reported using "both print and electronic but print more than electronic" and "print only", respectively, to search monograph-related drug information queries whereas 4% reported using "PDA only". Analysis of respondent ratings for all resources in the categories print, health professionals and other, and online/electronic resources, indicated that the Compendium of Pharmaceuticals and Specialties and pharmacists ranked highly for frequency of use, usefulness, accessibility, credibility, and current/timeliness by both groups of practitioners. Respondents' preferences and resource ratings were consistent with self-reported methods for conducting drug information queries. Few differences existed between NP and physician rankings of resources.
The use of computers and PDAs remains limited, which is also consistent with preferred and frequent use of print resources. Education for these practitioners regarding available electronic drug information resources may facilitate future computer and PDA use. Further research is needed to determine methods to increase computer and PDA use and whether these technologies affect prescribing and patient outcomes.
PMCID: PMC1590010  PMID: 16822323
19.  The impact of multimorbidity on adult physical and mental health in low- and middle-income countries: what does the study on global ageing and adult health (SAGE) reveal? 
BMC Medicine  2015;13:178.
Chronic diseases contribute a large share of disease burden in low- and middle-income countries (LMICs). Chronic diseases have a tendency to occur simultaneously and where there are two or more such conditions, this is termed as ‘multimorbidity’. Multimorbidity is associated with adverse health outcomes, but limited research has been undertaken in LMICs. Therefore, this study examines the prevalence and correlates of multimorbidity as well as the associations between multimorbidity and self-rated health, activities of daily living (ADLs), quality of life, and depression across six LMICs.
Data was obtained from the WHO’s Study on global AGEing and adult health (SAGE) Wave-1 (2007/10). This was a cross-sectional population based survey performed in LMICs, namely China, Ghana, India, Mexico, Russia, and South Africa, including 42,236 adults aged 18 years and older. Multimorbidity was measured as the simultaneous presence of two or more of eight chronic conditions including angina pectoris, arthritis, asthma, chronic lung disease, diabetes mellitus, hypertension, stroke, and vision impairment. Associations with four health outcomes were examined, namely ADL limitation, self-rated health, depression, and a quality of life index. Random-intercept multilevel regression models were used on pooled data from the six countries.
The prevalence of morbidity and multimorbidity was 54.2 % and 21.9 %, respectively, in the pooled sample of six countries. Russia had the highest prevalence of multimorbidity (34.7 %) whereas China had the lowest (20.3 %). The likelihood of multimorbidity was higher in older age groups and was lower in those with higher socioeconomic status. In the pooled sample, the prevalence of 1+ ADL limitation was 14 %, depression 5.7 %, self-rated poor health 11.6 %, and mean quality of life score was 54.4. Substantial cross-country variations were seen in the four health outcome measures. The prevalence of 1+ ADL limitation, poor self-rated health, and depression increased whereas quality of life declined markedly with an increase in number of diseases.
Findings highlight the challenge of multimorbidity in LMICs, particularly among the lower socioeconomic groups, and the pressing need for reorientation of health care resources considering the distribution of multimorbidity and its adverse effect on health outcomes.
Electronic supplementary material
The online version of this article (doi:10.1186/s12916-015-0402-8) contains supplementary material, which is available to authorized users.
PMCID: PMC4524360  PMID: 26239481
Activities of daily living; Low- and middle-income countries; Mental health; Multimorbidity; Non-communicable diseases; Quality of life
20.  A Survey of Bioinformatics Database and Software Usage through Mining the Literature 
PLoS ONE  2016;11(6):e0157989.
Computer-based resources are central to much, if not most, biological and medical research. However, while there is an ever expanding choice of bioinformatics resources to use, described within the biomedical literature, little work to date has provided an evaluation of the full range of availability or levels of usage of database and software resources. Here we use text mining to process the PubMed Central full-text corpus, identifying mentions of databases or software within the scientific literature. We provide an audit of the resources contained within the biomedical literature, and a comparison of their relative usage, both over time and between the sub-disciplines of bioinformatics, biology and medicine. We find that trends in resource usage differs between these domains. The bioinformatics literature emphasises novel resource development, while database and software usage within biology and medicine is more stable and conservative. Many resources are only mentioned in the bioinformatics literature, with a relatively small number making it out into general biology, and fewer still into the medical literature. In addition, many resources are seeing a steady decline in their usage (e.g., BLAST, SWISS-PROT), though some are instead seeing rapid growth (e.g., the GO, R). We find a striking imbalance in resource usage with the top 5% of resource names (133 names) accounting for 47% of total usage, and over 70% of resources extracted being only mentioned once each. While these results highlight the dynamic and creative nature of bioinformatics research they raise questions about software reuse, choice and the sharing of bioinformatics practice. Is it acceptable that so many resources are apparently never reused? Finally, our work is a step towards automated extraction of scientific method from text. We make the dataset generated by our study available under the CC0 license here:
PMCID: PMC4917176  PMID: 27331905
21.  A Statewide Approach to Health Care Personnel Maldistribution—The California Area Health Education Center System 
Western Journal of Medicine  1984;140(5):798-802.
An Area Health Education Center (AHEC) system has been established in California to address the maldistribution of physicians and other health care professionals. The AHEC program uses educational incentives to recruit and retain health care personnel in underserved areas by linking the academic resources of university health science centers with local educational and clinical facilities. The medical schools, working in partnership with urban or rural AHECs throughout the state, are implementing educational programs to attract trainees and licensed professionals to work in underserved communities. The California AHEC project entered its fifth year in October of 1983 with the participation of all eight medical schools and the Charles Drew Postgraduate School of Medicine, 35 other health professions schools, 17 independent AHECs and more than 400 clinical training sites. Educational programs are reaching more than 22,000 students and practicing health professionals throughout California. We review the current status of the California AHEC system and use the AHEC programs at Loma Linda University to illustrate the effect this intervention is having.
PMCID: PMC1011113  PMID: 6730500
22.  Human genome meeting 2016 
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Human Genomics  2016;10(Suppl 1):12.
Table of contents
O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder
A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson
O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents
R. Polimanti, J. Gelernter
O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort
X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group
O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus
A. Kapoor, D. Lee, A. Chakravarti
O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells
C. Maercker, F. Graf, M. Boutros
O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies
G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis
O7 Role of microRNA in LCL to IPSC reprogramming
S. Kumar, J. Curran, J. Blangero
O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease
S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti
O9 Metabolomic profiling for the diagnosis of neurometabolic disorders
T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea
O10 A novel causal methylation network approach to Alzheimer’s disease
Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett
O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway
A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni
O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types
B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest
O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types
C. A. Semple
O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer
E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project
O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer
F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu
O16 Modeling genetic interactions associated with molecular subtypes of breast cancer
B. Ji, A. Tyler, G. Ananda, G. Carter
O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors
H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski
O18 Predictive biomarkers to metastatic pancreatic cancer treatment
J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman
O19 DDIT4 gene expression as a prognostic marker in several malignant tumors
L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto
O20 Spatial organization of the genome and genomic alterations in human cancers
K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group
O21 Landscape of targeted therapies in solid tumors
S. Patterson, C. Statz, S. Mockus
O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma
S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis
O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis
S. Likhitrattanapisal
O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study
S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen
O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array
T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada
O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation
A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics
O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4
C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung
O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13
K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone
O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data
N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh
O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review
S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs
O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio
S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle
O32 Legal interoperability: a sine qua non for international data sharing
A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group
O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target
H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci
O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs
J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio
O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes
R. Ghosh, S. Plon
O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing
S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs
O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma
T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman
O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver
E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker
O40 A general statistic framework for genome-based disease risk prediction
M. Xiong, L. Ma, N. Lin, C. Amos
O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies
N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong
O42 Big data and NGS data analysis: the cloud to the rescue
O. Dobretsberger, M. Egger, F. Leimgruber
O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing
S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance
O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data
V. A. A. Antonio, N. Ono, Clark Kendrick C. Go
O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data
Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar
O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans
C. Zeng, J. Shao
O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations
H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula
O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing
Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng
O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes?
I. Campbell, M.-A. Young, P. James, Lifepool
O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS
C. Schumacher, S. Sandhu, T. Harkins, V. Makarov
O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform
H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs
O55 Rapid capture methods for clinical sequencing
J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs
O56 A diploid personal human genome model for better genomes from diverse sequence data
K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs
O57 Development of PacBio long range capture for detection of pathogenic structural variants
Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs
O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans
R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers
O59 Assessing RNA structure disruption induced by single-nucleotide variation
J. Lin, Y. Zhang, Z. Ouyang
P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number
A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt
P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility
E. S. Chen
P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients
H. Bahrami, A. Khoshzaban, S. Heidari Keshal
P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population
K. K. R. Alharbi
P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding
M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova
P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population
M. Matar
P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization
N. Mili, R. Molinari, Y. Ma, S. Guerrier
P9 Vulnerability of genetic variants to the risk of autism among Saudi children
N. Elhawary, M. Tayeb, N. Bogari, N. Qotb
P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction
S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion
P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3rd7 mice
Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina
P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients
B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel
P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments
A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey
P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome
D. Graur
P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients
J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak
P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns
B. S. Soibam
P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer
D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder
P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes
J. J. Gruber, N. Jaeger, M. Snyder
P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors
K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson
P23 RNA sequencing identifies gene mutations for neuroblastoma
K. Zhang
P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines
M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales
P25 Targeted Methylation Sequencing of Prostate Cancer
N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder
P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico
S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía
P28 Genetic modifiers of Alström syndrome
J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina
P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos
E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group
P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D
K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess
P34 Molecular regulation of chondrogenic human induced pluripotent stem cells
M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah
P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting
M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid
P36 Accessing genomic evidence for clinical variants at NCBI
S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko
P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA
C. Xiao, E. Yaschenko, S. Sherry
P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling
C. Rangel-Escareño, H. Rueda-Zarate
P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr
S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang
P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data
S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs
P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells
T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium
P43 Rapid and scalable typing of structural variants for disease cohorts
W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs
P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population
A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim
P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations
J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras
P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits
L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups
P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study
S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu
P49 Common variants in casr gene are associated with serum calcium levels in koreans
S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung
P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions
Y. Zhou, S. Xu
P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies
X. Wang, V. Philip, G. Carter
P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment
A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol
P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling
A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar
P54 Direct enrichment for the rapid preparation of targeted NGS libraries
C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel
P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System
R. Nitsche, L. Prieto-Lafuente
P57 ClinVar: a multi-source archive for variant interpretation
M. Landrum, J. Lee, W. Rubinstein, D. Maglott
P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome
Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad
P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation
A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler
P61 Compound heterozygous mutation in the LDLR gene in Saudi patients suffering severe hypercholesterolemia
F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar
PMCID: PMC4896275  PMID: 27294413
23.  MedReach: building an Area Health Education Center medical information outreach system for Northwest Ohio*† 
In collaboration with regional partners in northwest Ohio, the Area Health Education Center (AHEC) program at the Medical College of Ohio (MCO) at Toledo is reaching out to underserved areas, helping to provide educational opportunities to health care professionals in these communities. This paper describes the development of MedReach, a medical information outreach system that connects regional AHEC sites to MCO via the Internet. MedReach provides physicians and other health care professionals access and support to search computerized textbooks and databases for current information on medical diagnoses, treatments, and research. A unique aspect of the MedReach project is that users are able to receive personal help with information retrieval by calling or emailing MCO's outreach librarian. Periodically, the AHEC program and the Mulford Library at MCO also sponsor an educational program, titled “Medical Applications of Computers,” for regional practitioners. Current feedback on both the medical information outreach system and the educational program has been positive.
PMCID: PMC116405  PMID: 12113517
24. Web Services, a free and integrated toolkit for computational modelling software 
Briefings in Bioinformatics  2009;11(3):270-277.
Exchanging and sharing scientific results are essential for researchers in the field of computational modelling. defines agreed-upon standards for model curation. A fundamental one, MIRIAM (Minimum Information Requested in the Annotation of Models), standardises the annotation and curation process of quantitative models in biology. To support this standard, MIRIAM Resources maintains a set of standard data types for annotating models, and provides services for manipulating these annotations. Furthermore, creates controlled vocabularies, such as SBO (Systems Biology Ontology) which strictly indexes, defines and links terms used in Systems Biology. Finally, BioModels Database provides a free, centralised, publicly accessible database for storing, searching and retrieving curated and annotated computational models. Each resource provides a web interface to submit, search, retrieve and display its data. In addition, the team provides a set of Web Services which allows the community to programmatically access the resources. A user is then able to perform remote queries, such as retrieving a model and resolving all its MIRIAM Annotations, as well as getting the details about the associated SBO terms. These web services use established standards. Communications rely on SOAP (Simple Object Access Protocol) messages and the available queries are described in a WSDL (Web Services Description Language) file. Several libraries are provided in order to simplify the development of client software. Web Services make one step further for the researchers to simulate and understand the entirety of a biological system, by allowing them to retrieve biological models in their own tool, combine queries in workflows and efficiently analyse models.
PMCID: PMC2913671  PMID: 19939940; Systems Biology; modelling; Web Services; annotation; ontology
25.  Access to electronic health knowledge in five countries in Africa: a descriptive study 
Access to medical literature in developing countries is helped by open access publishing and initiatives to allow free access to subscription only journals. The effectiveness of these initiatives in Africa has not been assessed. This study describes awareness, reported use and factors influencing use of on-line medical literature via free access initiatives.
Descriptive study in four teaching hospitals in Cameroon, Nigeria, Tanzania and Uganda plus one externally funded research institution in The Gambia. Survey with postgraduate doctors and research scientists to determine Internet access patterns, reported awareness of on-line medical information and free access initiatives; semi structured interviews with a sub-sample of survey participants to explore factors influencing use.
In the four African teaching hospitals, 70% of the 305 postgraduate doctors reported textbooks as their main source of information; 66% had used the Internet for health information in the last week. In two hospitals, Internet cafés were the main Internet access point. For researchers at the externally-funded research institution, electronic resources were their main source, and almost all had used the Internet in the last week. Across all 333 respondents, 90% had heard of PubMed, 78% of BMJ on line, 49% the Cochrane Library, 47% HINARI, and 19% BioMedCentral. HINARI use correlates with accessing the Internet on computers located in institutions. Qualitative data suggested there are difficulties logging into HINARI and that sometimes it is librarians that limit access to passwords.
Text books remain an important resource for postgraduate doctors in training. Internet use is common, but awareness of free-access initiatives is limited. HINARI and other initiatives could be more effective with strong institutional endorsement and management to promote and ensure access.
PMCID: PMC1885254  PMID: 17509132

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