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1.  Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research 
BMC Genomics  2008;9(Suppl 2):I1.
Supported by National Science Foundation (NSF), International Society of Intelligent Biological Medicine (ISIBM), International Journal of Computational Biology and Drug Design and International Journal of Functional Informatics and Personalized Medicine, IEEE 7th Bioinformatics and Bioengineering attracted more than 600 papers and 500 researchers and medical doctors. It was the only synergistic inter/multidisciplinary IEEE conference with 24 Keynote Lectures, 7 Tutorials, 5 Cutting-Edge Research Workshops and 32 Scientific Sessions including 11 Special Research Interest Sessions that were designed dynamically at Harvard in response to the current research trends and advances. The committee was very grateful for the IEEE Plenary Keynote Lectures given by: Dr. A. Keith Dunker (Indiana), Dr. Jun Liu (Harvard), Dr. Brian Athey (Michigan), Dr. Mark Borodovsky (Georgia Tech and President of ISIBM), Dr. Hamid Arabnia (Georgia and Vice-President of ISIBM), Dr. Ruzena Bajcsy (Berkeley and Member of United States National Academy of Engineering and Member of United States Institute of Medicine of the National Academies), Dr. Mary Yang (United States National Institutes of Health and Oak Ridge, DOE), Dr. Chih-Ming Ho (UCLA and Member of United States National Academy of Engineering and Academician of Academia Sinica), Dr. Andy Baxevanis (United States National Institutes of Health), Dr. Arif Ghafoor (Purdue), Dr. John Quackenbush (Harvard), Dr. Eric Jakobsson (UIUC), Dr. Vladimir Uversky (Indiana), Dr. Laura Elnitski (United States National Institutes of Health) and other world-class scientific leaders. The Harvard meeting was a large academic event 100% full-sponsored by IEEE financially and academically. After a rigorous peer-review process, the committee selected 27 high-quality research papers from 600 submissions. The committee is grateful for contributions from keynote speakers Dr. Russ Altman (IEEE BIBM conference keynote lecturer on combining simulation and machine learning to recognize function in 4D), Dr. Mary Qu Yang (IEEE BIBM workshop keynote lecturer on new initiatives of detecting microscopic disease using machine learning and molecular biology, http://ieeexplore.ieee.org/servlet/opac?punumber=4425386) and Dr. Jack Y. Yang (IEEE BIBM workshop keynote lecturer on data mining and knowledge discovery in translational medicine) from the first IEEE Computer Society BioInformatics and BioMedicine (IEEE BIBM) international conference and workshops, November 2-4, 2007, Silicon Valley, California, USA.
doi:10.1186/1471-2164-9-S2-I1
PMCID: PMC3226104  PMID: 18831773
2.  New IEEE standard enables data collection for medical applications. 
The IEEE has gone to ballot on a "Standard for Medical Device Communications", IEEE P1073. The lower layer, hardware portions of the standard are expected to be approved by the IEEE Standards Board at their December 11-13, 1994 meeting. Other portions of the standard are in the initial stages of the IEEE ballot process. The intent of the standard is to allow hospitals and other users to interface medical electronic devices to host computer systems in a standard, interchangeable manner. The standard is optimized for acute care environments such as ICU's, operating rooms, and emergency rooms. [1] IEEE General Committee and Subcommittee work has been on-going since 1984. Significant amounts of work have been done to discover and meet the needs of the patient care setting. Surveys performed in 1989 identified the following four key user requirements for medical device communications: 1) Frequent reconfiguration of the network. 2) Allow "plug and play" operation by users. 3) Associate devices with a specific bed and patient. 4) Support a wide range of hospital computer system topologies. Additionally, the most critical difference in the acute care setting is patient safety, which has an overall effect on the standard. The standard that went to ballot meets these requirements. The standard is based on existing ISO standards. P1073 is compliant with the OSI seven layer model. P1073 specifies the entire communication stack, from object-oriented software to hospital unique connectors. The standard will be able to be put forward as a true international standard, much in the way that the IEEE 802.x family of standards (like Ethernet) were presented as draft ISO standards.(ABSTRACT TRUNCATED AT 250 WORDS)
PMCID: PMC2247755  PMID: 7949984
3.  Prototypes for Content-Based Image Retrieval in Clinical Practice 
Content-based image retrieval (CBIR) has been proposed as key technology for computer-aided diagnostics (CAD). This paper reviews the state of the art and future challenges in CBIR for CAD applied to clinical practice.
We define applicability to clinical practice by having recently demonstrated the CBIR system on one of the CAD demonstration workshops held at international conferences, such as SPIE Medical Imaging, CARS, SIIM, RSNA, and IEEE ISBI. From 2009 to 2011, the programs of CADdemo@CARS and the CAD Demonstration Workshop at SPIE Medical Imaging were sought for the key word “retrieval” in the title. The systems identified were analyzed and compared according to the hierarchy of gaps for CBIR systems.
In total, 70 software demonstrations were analyzed. 5 systems were identified meeting the criterions. The fields of application are (i) bone age assessment, (ii) bone fractures, (iii) interstitial lung diseases, and (iv) mammography. Bridging the particular gaps of semantics, feature extraction, feature structure, and evaluation have been addressed most frequently.
In specific application domains, CBIR technology is available for clinical practice. While system development has mainly focused on bridging content and feature gaps, performance and usability have become increasingly important. The evaluation must be based on a larger set of reference data, and workflow integration must be achieved before CBIR-CAD is really established in clinical practice.
doi:10.2174/1874431101105010058
PMCID: PMC3149811  PMID: 21892374
Content-based image retrieval; medical image retrieval; diagnosis aid; prototypes.
4.  The unfoldomics decade: an update on intrinsically disordered proteins 
BMC Genomics  2008;9(Suppl 2):S1.
Background
Our first predictor of protein disorder was published just over a decade ago in the Proceedings of the IEEE International Conference on Neural Networks (Romero P, Obradovic Z, Kissinger C, Villafranca JE, Dunker AK (1997) Identifying disordered regions in proteins from amino acid sequence. Proceedings of the IEEE International Conference on Neural Networks, 1: 90–95). By now more than twenty other laboratory groups have joined the efforts to improve the prediction of protein disorder. While the various prediction methodologies used for protein intrinsic disorder resemble those methodologies used for secondary structure prediction, the two types of structures are entirely different. For example, the two structural classes have very different dynamic properties, with the irregular secondary structure class being much less mobile than the disorder class. The prediction of secondary structure has been useful. On the other hand, the prediction of intrinsic disorder has been revolutionary, leading to major modifications of the more than 100 year-old views relating protein structure and function. Experimentalists have been providing evidence over many decades that some proteins lack fixed structure or are disordered (or unfolded) under physiological conditions. In addition, experimentalists are also showing that, for many proteins, their functions depend on the unstructured rather than structured state; such results are in marked contrast to the greater than hundred year old views such as the lock and key hypothesis. Despite extensive data on many important examples, including disease-associated proteins, the importance of disorder for protein function has been largely ignored. Indeed, to our knowledge, current biochemistry books don't present even one acknowledged example of a disorder-dependent function, even though some reports of disorder-dependent functions are more than 50 years old. The results from genome-wide predictions of intrinsic disorder and the results from other bioinformatics studies of intrinsic disorder are demanding attention for these proteins.
Results
Disorder prediction has been important for showing that the relatively few experimentally characterized examples are members of a very large collection of related disordered proteins that are wide-spread over all three domains of life. Many significant biological functions are now known to depend directly on, or are importantly associated with, the unfolded or partially folded state. Here our goal is to review the key discoveries and to weave these discoveries together to support novel approaches for understanding sequence-function relationships.
Conclusion
Intrinsically disordered protein is common across the three domains of life, but especially common among the eukaryotic proteomes. Signaling sequences and sites of posttranslational modifications are frequently, or very likely most often, located within regions of intrinsic disorder. Disorder-to-order transitions are coupled with the adoption of different structures with different partners. Also, the flexibility of intrinsic disorder helps different disordered regions to bind to a common binding site on a common partner. Such capacity for binding diversity plays important roles in both protein-protein interaction networks and likely also in gene regulation networks. Such disorder-based signaling is further modulated in multicellular eukaryotes by alternative splicing, for which such splicing events map to regions of disorder much more often than to regions of structure. Associating alternative splicing with disorder rather than structure alleviates theoretical and experimentally observed problems associated with the folding of different length, isomeric amino acid sequences. The combination of disorder and alternative splicing is proposed to provide a mechanism for easily "trying out" different signaling pathways, thereby providing the mechanism for generating signaling diversity and enabling the evolution of cell differentiation and multicellularity. Finally, several recent small molecules of interest as potential drugs have been shown to act by blocking protein-protein interactions based on intrinsic disorder of one of the partners. Study of these examples has led to a new approach for drug discovery, and bioinformatics analysis of the human proteome suggests that various disease-associated proteins are very rich in such disorder-based drug discovery targets.
doi:10.1186/1471-2164-9-S2-S1
PMCID: PMC2559873  PMID: 18831774
5.  Electronic Symptom Reporting Between Patient and Provider for Improved Health Care Service Quality: A Systematic Review of Randomized Controlled Trials. Part 2: Methodological Quality and Effects 
Background
We conducted in two parts a systematic review of randomized controlled trials (RCTs) on electronic symptom reporting between patients and providers to improve health care service quality. Part 1 reviewed the typology of patient groups, health service innovations, and research targets. Four innovation categories were identified: consultation support, monitoring with clinician support, self-management with clinician support, and therapy.
Objective
To assess the methodological quality of the RCTs, and summarize effects and benefits from the methodologically best studies.
Methods
We searched Medline, EMBASE, PsycINFO, Cochrane Central Register of Controlled Trials, and IEEE Xplore for original studies presented in English-language articles between 1990 and November 2011. Risk of bias and feasibility were judged according to the Cochrane recommendation, and theoretical evidence and preclinical testing were evaluated according to the Framework for Design and Evaluation of Complex Interventions to Improve Health. Three authors assessed the risk of bias and two authors extracted the effect data independently. Disagreement regarding bias assessment, extraction, and interpretation of results were resolved by consensus discussions.
Results
Of 642 records identified, we included 32 articles representing 29 studies. No articles fulfilled all quality requirements. All interventions were feasible to implement in a real-life setting, and theoretical evidence was provided for almost all studies. However, preclinical testing was reported in only a third of the articles. We judged three-quarters of the articles to have low risk for random sequence allocation and approximately half of the articles to have low risk for the following biases: allocation concealment, incomplete outcome data, and selective reporting. Slightly more than one fifth of the articles were judged as low risk for blinding of outcome assessment. Only 1 article had low risk of bias for blinding of participants and personnel. We excluded 12 articles showing high risk or unclear risk for both selective reporting and blinding of outcome assessment from the effect assessment. The authors’ hypothesis was confirmed for 13 (65%) of the 20 remaining articles. Articles on self-management support were of higher quality, allowing us to assess effects in a larger proportion of studies. All except one self-management interventions were equally effective to or better than the control option. The self-management articles document substantial benefits for patients, and partly also for health professionals and the health care system.
Conclusion
Electronic symptom reporting between patients and providers is an exciting area of development for health services. However, the research generally is of low quality. The field would benefit from increased focus on methods for conducting and reporting RCTs. It appears particularly important to improve blinding of outcome assessment and to precisely define primary outcomes to avoid selective reporting. Supporting self-management seems to be especially promising, but consultation support also shows encouraging results.
doi:10.2196/jmir.2216
PMCID: PMC3510713  PMID: 23032363
Electronic symptom reporting; physician-patient relationship; patient participation; shared decision making; review; consultation; monitoring; self-management; bias
6.  Development and implementation of a mini-Clinical Evaluation Exercise (mini-CEX) program to assess the clinical competencies of internal medicine residents: from faculty development to curriculum evaluation 
BMC Medical Education  2013;13:31.
Background
The mini-CEX is a valid and reliable method to assess the clinical competencies of trainees. Its data could be useful for educators to redesign curriculum as a process of quality improvement. The aim of this study was to evaluate a mini-CEX assessment program in our internal medicine residency training. We investigated the impact of mini-CEX workshops as a faculty development program on the acquisition of cognitive knowledge and the difference of practice behaviors among faculty members used the mini-CEX to assess residents’ performance at work.
Methods
We designed an observational, two-phase study. In the faculty development program, we started a mini-CEX workshop for trainers in 2010, and the short-term outcome of the program was evaluated by comparing the pretest and posttest results to demonstrate the improvement in cognitive knowledge on mini-CEX. From September 2010 to August 2011, we implemented a monthly mini-CEX assessment program in our internal medicine residency training. The data of these mini-CEX assessment forms were collected and analyzed.
Results
In the group of 49 mini-CEX workshop attendees, there was a statistically significant improvement in cognitive knowledge by comparing the pretest and posttest results (67.35 ± 15.25 versus 81.22 ± 10.34, p < 0.001). Among the 863 clinical encounters of mini-CEX, which involved 97 residents and 139 evaluators, 229 (26.5%), 326 (37.8%), and 308 (35.7%) evaluations were completed by the first-year, second-year, and third- year residents separately. We found a statistically significant interaction between level of training and score in dimensions of mini-CEX. The scores in all dimensions measured were better for senior residents. Participation in mini-CEX workshops as a faculty development program strengthened the adherence of trainers to the principles of mini-CEX as a formative assessment in regard to provision of feedback. However, a deficiency in engaging residents’ reflection was found.
Conclusions
Faculty development is a prerequisite to train evaluators in order to implement a successful mini-CEX assessment program. We demonstrated the effectiveness of our mini-CEX workshops in terms of knowledge acquisition and enhancement of giving feedback when the faculty members used the tool. Further programs on providing effective feedback should be conducted to increase the impact of the mini-CEX as a formative assessment.
doi:10.1186/1472-6920-13-31
PMCID: PMC3599226  PMID: 23442216
Mini-CEX; Mini clinical evaluation exercise; Faculty development
7.  Art-making in a family medicine clerkship: how does it affect medical student empathy? 
BMC Medical Education  2014;14(1):247.
Background
To provide patient-centred holistic care, doctors must possess good interpersonal and empathic skills. Medical schools traditionally adopt a skills-based approach to such training but creative engagement with the arts has also been effective. A novel arts-based approach may help medical students develop empathic understanding of patients and thus contribute to medical students’ transformative process into compassionate doctors. This study aimed to evaluate the impact of an arts-making workshop on medical student empathy.
Methods
This was a mixed-method quantitative-qualitative study. In the 2011–12 academic year, all 161 third year medical students at the University of Hong Kong were randomly allocated into either an arts-making workshop or a problem-solving workshop during the Family Medicine clerkship according to a centrally-set timetable. Students in the arts-making workshop wrote a poem, created artwork and completed a reflective essay while students in the conventional workshop problem-solved clinical cases and wrote a case commentary. All students who agreed to participate in the study completed a measure of empathy for medical students, the Jefferson Scale of Empathy (JSE) (student version), at the start and end of the clerkship. Quantitative data analysis: Paired t-test and repeated measures ANOVA was used to compare the change within and between groups respectively. Qualitative data analysis: Two researchers independently chose representational narratives based on criteria adapted from art therapy. The final 20 works were agreed upon by consensus and thematically analysed using a grounded theory approach.
Results
The level of empathy declined in both groups over time, but with no statistically significant differences between groups. For JSE items relating to emotional influence on medical decision making, participants in the arts-making workshop changed more than those in the problem-solving workshop. From the qualitative data, students perceived benefits in arts-making, and gained understanding in relation to self, patients, pain and suffering, and the role of the doctor.
Conclusions
Though quantitative findings showed little difference in empathy between groups, arts-making workshop participants gained empathic understanding in four different thematic areas. This workshop also seemed to promote greater self-awareness which may help medical students recognize the potential for emotions to sway judgment. Future art workshops should focus on emotional awareness and regulation.
doi:10.1186/s12909-014-0247-4
PMCID: PMC4256925  PMID: 25431323
Medical humanities; Empathy; Art; Reflective writing; Family Medicine; Medical student
8.  A self-evaluation tool for integrated care services: the Development Model for Integrated Care applied in practice 
Purpose
The purpose of the workshop is to show the applications of the Development Model for Integrated Care (DMIC) in practice. This relatively new and validated model, can be used by integrated care practices to evaluate their integrated care, to assess their phase of development and reveal improvement areas. In the workshop the results of the use of the model in three types of integrated care settings in the Netherlands will be presented. Participants are offered practical instruments based on the validated DMIC to use in their own setting and will be introduced to the webbased tool.
Context
To integrate care from multiple providers into a coherent and streamlined client-focused service, a large number of activities and agreements have to be implemented like streamlining information flows and adequate transfers of clients. In the large range of possible activities it is often not clear what essential activities are and where to start or continue. Also, knowledge about how to further develop integrated care services is needed. The Development Model for Integrated Care (DMIC), based on PhD research of Mirella Minkman, describes nine clusters containing in total 89 elements that contribute to the integration of care. The clusters are named: ‘client-centeredness’, ‘delivery system’, ‘performance management’, ‘quality of care’, ‘result-focused learning’, ‘interprofessional teamwork’, ‘roles and tasks’, ‘commitment’, and ‘transparant entrepreneurship’ [1–3]. In 2011 a new digital webbased self-evolution tool which contains the 89 elements grouped in nine clusters was developed. The DMIC also describes four phases of development [4]. The model is empirically validated in practice by assessing the relevance and implementation of the elements and development phases in 84 integrated care services in The Netherlands: in stroke, acute myocardial infarct (AMI), and dementia services. The validation studies are recently published [5, 6]. In 2011 also other integrated care services started using the model [7]. Vilans developed a digital web-based self-evaluation tool for integrated care services based on the DMIC. A palliative care network, four diabetes services, a youth care service and a network for autism used the self-evaluation tool to evaluate the development of their integrated care service. Because of its generic character, the model and tool are believed to be also interesting internationally.
Data sources
In the workshop we will present the results of three studies in integrated diabetes, youth and palliative care. The three projects consist of multiple steps, see below. Workshop participants could also work with the DMIC following these steps.
One: Preparation of the digital self-evolution tool for integrated care services
Although they are very different, the three integrated care services all wanted to gain insight in their development and improvement opportunities. We tailored the digital self-evaluation tool for each specific integrated care services, but for all the basis was the DMIC. Personal accounts for the digital DMIC self-evalution survey were sent to multiple partners working in each integrated care service (4–16 partners).
Two: Use of the online self-evaluation tool each partner of the local integrated care setting evaluated the integrated care by filling in the web-based questionnaire. The tool consists of three parts (A-C) named: general information about the integrated care practice (A); the clusters and elements of the DMIC (B); and the four phases of development (C). The respondents rated the relevance and presence of each element in their integrated care practice. Respondents were asked to estimate in which phase of development their thought their service was.
Three: Analysing the results
Advisers from Vilans, the Centre of excellence for long-term care in the Netherlands, analysed the self-evolution results in cooperation with the integrated care coordinators. The results show the total amount of implemented integrated care elements per cluster in spider graphs and the development phase as calculated by the DMIC model. Suggestions for further development of the integrated care services were analysed and reported.
Four: Discussing the implications for further development
In a workshop with the local integrated care partners the results of the self-evaluation were presented and discussed. We noticed remarkable results and highlight elements for further development. In addition, we gave advice for further development appropriate to the development phase of the integrated care service. Furthermore, the professionals prioritized the elements and decided which elements to start working on. This resulted in a (quality improvement) plan for the further development of the integrated care service.
Five: Reporting results
In a report all the results of the survey (including consensus scores) and the workshops came together. The integrated care coordinators stated that the reports really helped them to assess their improvement strategy. Also, there was insight in the development phase of their service which gave tools for further development.
Case description
The three cases presented are a palliative network, an integrated diabetes services and an integrated care network for youth in the Netherlands. The palliative care network wanted to reflect on their current development, to build a guiding framework for further development of the network. About sixteen professionals within the network worked with the digital self-evaluation tool and the DMIC: home care organisations, welfare organizations, hospice centres, health care organisations, community organizations.
For diabetes care, a Dutch health care insurance company wished to gain insight in the development of the contracted integrated care services to stimulate further development of the services. Professionals of three diabetes integrated care services were invited to fill in the digital self-evaluation tool. Of each integrated care service professionals like a general practitioner, a diabetes nurse, a medical specialist, a dietician and a podiatrist were invited. In youth care, a local health organisation wondered whether the DMIC could be helpful to visualize the results of youth integrated care services at process- and organisational level. The goal of the project was to define indicators at a process- and organisational level for youth care services based on the DMIC. In the future, these indicators might be used to evaluate youth care integrated care services and improve the quality of youth care within the Netherlands.
Conclusions and discussion
It is important for the quality of integrated care services that the involved coordinators, managers and professionals are aware of the development process of the integrated care service and that they focus on elements which can further develop and improve their integrated care. However, we noticed that integrated care services in the Netherlands experience difficulties in developing their integrated care service. It is often not clear what essential activities are to work on and how to further develop the integrated care service. A guiding framework for the development of integrated care was missing. The DMIC model has been developed for that reason and offers a useful tool for assessment, self-evaluation or improvement of integrated care services in practice. The model has been validated for AMI, dementia and stroke services. The latest new studies in diabetes, palliative care and youth care gave further insight in the generic character of the DMIC. Based on these studies it can be assumed that the DMIC can be used for multiple types of integrated care services. The model is assumed to be interesting for an international audience. Improving integrated care is a complex topic in a large number of countries; the DMIC is also based on the international literature. Dutch integrated care coordinators stated that the DMIC helped them to assess their integrated care development in practice and supported them in obtaining ideas for expanding and improving their integrated care activities.
The web-based self-evaluation tool focuses on a process- and organisational level of integrated care. Also, the self assessed development phase can be compared to the development phase as calculated by the DMIC tool. The cases showed this is fruitful input for discussions. When using the tool, the results can also be used in quality policy reports and improvement plans. The web-based tool is being tested at this moment in practice, but in San Marino we can present the latest webversion and demonstrate with a short video how to use the tool and model. During practical exercises in the workshop the participants will experience how the application of the DMIC can work for them in practice or in research. For integrated care researchers and policy makers, the DMIC questionnaire and tool is a promising method for further research and policy plans in integrated care.
PMCID: PMC3617779
development model for integrated care; development of integrated care services; implementation and improvement of integrated care; self evaluation
9.  Changing Job Satisfaction, Absenteeism, and Healthcare Claims Costs In a Hospital Culture 
Global Advances in Health and Medicine  2014;3(Suppl 1):BPA01.
Introduction:
Fairfield Medical Center is a 222-bed community hospital located in Lancaster, Ohio. Organizational leadership chose to invest in the Transforming Stress Workshop, a 6-hour workshop with a 2-hour follow-up workshop, in order to improve the well-being of its staff and physicians.
Special thought and consideration were given to being able to sustain any benefits and/or improvements long-term. As a result, strategies were developed to integrate the program into our culture.
Methods:
Four staff members from a variety of disciplines were selected and sent to HeartMath Train-the-Trainer to gain proficiency in HeartMath methodology and tools, expanding their duties to deliver the classes. Biweekly workshops were offered from August 2007 through December 2010, educating a total of 975 employees, or 48% of the staff.
Other tactics providing a sustainable program included senior leadership support and championing, management team training, positive employee comments published internally, use of tools in committee and department meetings, incorporation into orientation and on-boarding processes, part of major initiative roll-outs, element in clinical ladder, expansion to include Transforming Team Workshops, sharing of Participant and Organizational Quality Assessment-Revised data, a lead HeartMath instructor who provides consulting to other organizations, provision of classes to local educators, and open workshops for employee family members.
Results:
Three metrics were selected to measure the success of the program: employee satisfaction, absenteeism rates, and healthcare claims cost. Statistically significant cultural and financial return on investment were demonstrated. Employees who received HeartMath training experienced a 2:1 savings on healthcare claims as compared to employees who had not received training. Employee Opinion Survey results demonstrated that employees who had HeartMath training had higher overall satisfaction scores than those who had not received training (Table and Figure) HeartMath participants demonstrated a lower overall absenteeism rate (P = 0), resulting in a $94,794 savings over a 3-year period. Cultural and financial returns on investment were demonstrated using these indicators.
Healthcare Claims Costs
Abbreviations: PMPM, per member per month; PMPY, per member per year.
HeartMath claims expense excludes five outlier claims in excess of $20 000 for conditions that could not have been avoided using HeartMath.
Non-HeartMath participants’ total claims expenses excludes six outlier cases with payments > $125 000.
Employee opinion survey: Impact of HeartMath Training, over all scores.
Conclusion:
Investing in HeartMath training and ongoing practice has proven to be a wise decision and continues to be valuable when initiating new concepts in a stressful, changing environment. Sustainability is key to long-term success and true cultural change. Continued employee training of the HeartMath tools and the continued use of the tools enriches the program planning and implementation of new initiatives at Fairfield Medical Center.
doi:10.7453/gahmj.2014.BPA01
PMCID: PMC3923278
Job satisfaction; absenteeism; healthcare claims costs; stress; HeartMath; return on investment (ROI); biofeedback
10.  IEEE P1157 Medical Data Interchange (MEDIX) Committee Overview and Status Report 
Working under the auspices of the Institute of Electrical and Electronic Engineers Engineering in Medicine and Biology Society (IEEE EMBS), the IEEE P1157 Medical Data Interchange (MEDIX) Committee has been chartered with developing international standards for communication of medical information between heterogeneous healthcare information systems. The IEEE P1157 Standards are based upon, and will conform to, the International Standards Organization (ISO) Reference Model for Open Systems Interconnection (OSI)[1].
The IEEE P1157 Committee has adopted a phased approach and is working towards balloting the initial standards, which apply to communications between a patient care system (PCS) and selected ancillaries in the medical center setting.
A parallel, longer range effort, focused on developing a reference model for electronic exchange of the medical record structure, content, and related medical knowledge, is in progress.
PMCID: PMC2245469
11.  Sparse representation and Bayesian detection of genome copy number alterations from microarray data 
Bioinformatics  2008;24(3):309-318.
Motivation: Genomic instability in cancer leads to abnormal genome copy number alterations (CNA) that are associated with the development and behavior of tumors. Advances in microarray technology have allowed for greater resolution in detection of DNA copy number changes (amplifications or deletions) across the genome. However, the increase in number of measured signals and accompanying noise from the array probes present a challenge in accurate and fast identification of breakpoints that define CNA. This article proposes a novel detection technique that exploits the use of piece wise constant (PWC) vectors to represent genome copy number and sparse Bayesian learning (SBL) to detect CNA breakpoints.
Methods: First, a compact linear algebra representation for the genome copy number is developed from normalized probe intensities. Second, SBL is applied and optimized to infer locations where copy number changes occur. Third, a backward elimination (BE) procedure is used to rank the inferred breakpoints; and a cut-off point can be efficiently adjusted in this procedure to control for the false discovery rate (FDR).
Results: The performance of our algorithm is evaluated using simulated and real genome datasets and compared to other existing techniques. Our approach achieves the highest accuracy and lowest FDR while improving computational speed by several orders of magnitude. The proposed algorithm has been developed into a free standing software application (GADA, Genome Alteration Detection Algorithm).
Availability: http://biron.usc.edu/~piquereg/GADA
Contact: jpei@chop.swmed.edu and rpique@ieee.org
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btm601
PMCID: PMC2704547  PMID: 18203770
12.  Evaluation of current algorithms for segmentation of scar tissue from late Gadolinium enhancement cardiovascular magnetic resonance of the left atrium: an open-access grand challenge 
Background
Late Gadolinium enhancement (LGE) cardiovascular magnetic resonance (CMR) imaging can be used to visualise regions of fibrosis and scarring in the left atrium (LA) myocardium. This can be important for treatment stratification of patients with atrial fibrillation (AF) and for assessment of treatment after radio frequency catheter ablation (RFCA). In this paper we present a standardised evaluation benchmarking framework for algorithms segmenting fibrosis and scar from LGE CMR images. The algorithms reported are the response to an open challenge that was put to the medical imaging community through an ISBI (IEEE International Symposium on Biomedical Imaging) workshop.
Methods
The image database consisted of 60 multicenter, multivendor LGE CMR image datasets from patients with AF, with 30 images taken before and 30 after RFCA for the treatment of AF. A reference standard for scar and fibrosis was established by merging manual segmentations from three observers. Furthermore, scar was also quantified using 2, 3 and 4 standard deviations (SD) and full-width-at-half-maximum (FWHM) methods. Seven institutions responded to the challenge: Imperial College (IC), Mevis Fraunhofer (MV), Sunnybrook Health Sciences (SY), Harvard/Boston University (HB), Yale School of Medicine (YL), King’s College London (KCL) and Utah CARMA (UTA, UTB). There were 8 different algorithms evaluated in this study.
Results
Some algorithms were able to perform significantly better than SD and FWHM methods in both pre- and post-ablation imaging. Segmentation in pre-ablation images was challenging and good correlation with the reference standard was found in post-ablation images. Overlap scores (out of 100) with the reference standard were as follows: Pre: IC = 37, MV = 22, SY = 17, YL = 48, KCL = 30, UTA = 42, UTB = 45; Post: IC = 76, MV = 85, SY = 73, HB = 76, YL = 84, KCL = 78, UTA = 78, UTB = 72.
Conclusions
The study concludes that currently no algorithm is deemed clearly better than others. There is scope for further algorithmic developments in LA fibrosis and scar quantification from LGE CMR images. Benchmarking of future scar segmentation algorithms is thus important. The proposed benchmarking framework is made available as open-source and new participants can evaluate their algorithms via a web-based interface.
doi:10.1186/1532-429X-15-105
PMCID: PMC3878126  PMID: 24359544
Late gadolinium enhancement; Cardiovascular magnetic resonance; Atrial fibrillation; Segmentation; Algorithm benchmarking
13.  Promoting synergistic research and education in genomics and bioinformatics 
BMC Genomics  2008;9(Suppl 1):I1.
Bioinformatics and Genomics are closely related disciplines that hold great promises for the advancement of research and development in complex biomedical systems, as well as public health, drug design, comparative genomics, personalized medicine and so on. Research and development in these two important areas are impacting the science and technology.
High throughput sequencing and molecular imaging technologies marked the beginning of a new era for modern translational medicine and personalized healthcare. The impact of having the human sequence and personalized digital images in hand has also created tremendous demands of developing powerful supercomputing, statistical learning and artificial intelligence approaches to handle the massive bioinformatics and personalized healthcare data, which will obviously have a profound effect on how biomedical research will be conducted toward the improvement of human health and prolonging of human life in the future. The International Society of Intelligent Biological Medicine (http://www.isibm.org) and its official journals, the International Journal of Functional Informatics and Personalized Medicine (http://www.inderscience.com/ijfipm) and the International Journal of Computational Biology and Drug Design (http://www.inderscience.com/ijcbdd) in collaboration with International Conference on Bioinformatics and Computational Biology (Biocomp), touch tomorrow's bioinformatics and personalized medicine throughout today's efforts in promoting the research, education and awareness of the upcoming integrated inter/multidisciplinary field. The 2007 international conference on Bioinformatics and Computational Biology (BIOCOMP07) was held in Las Vegas, the United States of American on June 25-28, 2007. The conference attracted over 400 papers, covering broad research areas in the genomics, biomedicine and bioinformatics. The Biocomp 2007 provides a common platform for the cross fertilization of ideas, and to help shape knowledge and scientific achievements by bridging these two very important disciplines into an interactive and attractive forum. Keeping this objective in mind, Biocomp 2007 aims to promote interdisciplinary and multidisciplinary education and research. 25 high quality peer-reviewed papers were selected from 400+ submissions for this supplementary issue of BMC Genomics. Those papers contributed to a wide-range of important research fields including gene expression data analysis and applications, high-throughput genome mapping, sequence analysis, gene regulation, protein structure prediction, disease prediction by machine learning techniques, systems biology, database and biological software development. We always encourage participants submitting proposals for genomics sessions, special interest research sessions, workshops and tutorials to Professor Hamid R. Arabnia (hra@cs.uga.edu) in order to ensure that Biocomp continuously plays the leadership role in promoting inter/multidisciplinary research and education in the fields. Biocomp received top conference ranking with a high score of 0.95/1.00. Biocomp is academically co-sponsored by the International Society of Intelligent Biological Medicine and the Research Laboratories and Centers of Harvard University – Massachusetts Institute of Technology, Indiana University - Purdue University, Georgia Tech – Emory University, UIUC, UCLA, Columbia University, University of Texas at Austin and University of Iowa etc. Biocomp - Worldcomp brings leading scientists together across the nation and all over the world and aims to promote synergistic components such as keynote lectures, special interest sessions, workshops and tutorials in response to the advances of cutting-edge research.
doi:10.1186/1471-2164-9-S1-I1
PMCID: PMC3226105  PMID: 18366597
14.  The implementation of a participatory manuscript development process with Native American tribal awardees as part of the CDC Communities Putting Prevention to Work initiative: Challenges and opportunities 
Preventive medicine  2014;67(0 1):S51-S57.
Objective
In 2009, the Centers for Disease Control and Prevention funded 50 communities, including three tribal awardees, to implement environmental approaches to address obesity and smoking through the Communities Putting Prevention to Work initiative. The tribes were among the selected awardees offered training support for analyzing, writing, and publishing their findings. This article describes the process of translating the workshops, guided by a participatory framework, for implementation with the tribes.
Methods
Nine participants from three tribes attended the workshops in Decatur, Georgia, in August and October of 2012: 1) a one-day pre-conference workshop focused on integrating both Indigenous and academic evaluation methods; 2) a 4 day data analysis workshop; and 3) a 5 day scientific writing workshop. Participants were provided with technical assistance following the workshops.
Results
Participants viewed the workshops positively and have continued to develop their manuscripts. To date one tribal awardee has submitted their manuscript for publication.
Conclusion
The participatory manuscript development process described here is the first of its kind outlining a pathway for tribal community health practitioners to translate and publish their work. Further development of this process could increase the number of community-developed manuscripts, thereby advancing the field of translational intervention science and leading to improved health equity.
doi:10.1016/j.ypmed.2014.01.027
PMCID: PMC4125542  PMID: 24513172
American Indian; Native American; Community-based participatory research; Participatory publication; Participatory evaluation
15.  Mortality in Iraq Associated with the 2003–2011 War and Occupation: Findings from a National Cluster Sample Survey by the University Collaborative Iraq Mortality Study 
PLoS Medicine  2013;10(10):e1001533.
Based on a survey of 2,000 randomly selected households throughout Iraq, Amy Hagopian and colleagues estimate that close to half a million excess deaths are attributable to the recent Iraq war and occupation.
Please see later in the article for the Editors' Summary
Background
Previous estimates of mortality in Iraq attributable to the 2003 invasion have been heterogeneous and controversial, and none were produced after 2006. The purpose of this research was to estimate direct and indirect deaths attributable to the war in Iraq between 2003 and 2011.
Methods and Findings
We conducted a survey of 2,000 randomly selected households throughout Iraq, using a two-stage cluster sampling method to ensure the sample of households was nationally representative. We asked every household head about births and deaths since 2001, and all household adults about mortality among their siblings. We used secondary data sources to correct for out-migration. From March 1, 2003, to June 30, 2011, the crude death rate in Iraq was 4.55 per 1,000 person-years (95% uncertainty interval 3.74–5.27), more than 0.5 times higher than the death rate during the 26-mo period preceding the war, resulting in approximately 405,000 (95% uncertainty interval 48,000–751,000) excess deaths attributable to the conflict. Among adults, the risk of death rose 0.7 times higher for women and 2.9 times higher for men between the pre-war period (January 1, 2001, to February 28, 2003) and the peak of the war (2005–2006). We estimate that more than 60% of excess deaths were directly attributable to violence, with the rest associated with the collapse of infrastructure and other indirect, but war-related, causes. We used secondary sources to estimate rates of death among emigrants. Those estimates suggest we missed at least 55,000 deaths that would have been reported by households had the households remained behind in Iraq, but which instead had migrated away. Only 24 households refused to participate in the study. An additional five households were not interviewed because of hostile or threatening behavior, for a 98.55% response rate. The reliance on outdated census data and the long recall period required of participants are limitations of our study.
Conclusions
Beyond expected rates, most mortality increases in Iraq can be attributed to direct violence, but about a third are attributable to indirect causes (such as from failures of health, sanitation, transportation, communication, and other systems). Approximately a half million deaths in Iraq could be attributable to the war.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
War is a major public health problem. Its health effects include violent deaths among soldiers and civilians as well as indirect increases in mortality and morbidity caused by conflict. Unlike those of other causes of death and disability, however, the consequences of war on population health are rarely studied scientifically. In conflict situations, deaths and diseases are not reliably measured and recorded, and estimating the proportion caused, directly or indirectly, by a war or conflict is challenging. Population-based mortality survey methods—asking representative survivors about deaths they know about—were developed by public health researchers to estimate death rates. By comparing death rate estimates for periods before and during a conflict, researchers can derive the number of excess deaths that are attributable to the conflict.
Why Was This Study Done?
A number of earlier studies have estimated the death toll in Iraq since the beginning of the war in March 2003. The previous studies covered different periods from 2003 to 2006 and derived different rates of overall deaths and excess deaths attributable to the war and conflict. All of them have been controversial, and their methodologies have been criticized. For this study, based on a population-based mortality survey, the researchers modified and improved their methodology in response to critiques of earlier surveys. The study covers the period from the beginning of the war in March 2003 until June 2011, including a period of high violence from 2006 to 2008. It provides population-based estimates for excess deaths in the years after 2006 and covers most of the period of the war and subsequent occupation.
What Did the Researchers Do and Find?
Interviewers trained by the researchers conducted the survey between May 2011 and July 2011 and collected data from 2,000 randomly selected households in 100 geographical clusters, distributed across Iraq's 18 governorates. The interviewers asked the head of each household about deaths among household members from 2001 to the time of the interview, including a pre-war period from January 2001 to March 2003 and the period of the war and occupation. They also asked all adults in the household about deaths among their siblings during the same period. From the first set of data, the researchers calculated the crude death rates (i.e., the number of deaths during a year per 1,000 individuals) before and during the war. They found the wartime crude death rate in Iraq to be 4.55 per 1,000, more than 50% higher than the death rate of 2.89 during the two-year period preceding the war. By multiplying those rates by the annual Iraq population, the authors estimate the total excess Iraqi deaths attributable to the war through mid-2011 to be about 405,000. The researchers also estimated that an additional 56,000 deaths were not counted due to migration. Including this number, their final estimate is that approximately half a million people died in Iraq as a result of the war and subsequent occupation from March 2003 to June 2011.
The risk of death at the peak of the conflict in 2006 almost tripled for men and rose by 70% for women. Respondents attributed 20% of household deaths to war-related violence. Violent deaths were attributed primarily to coalition forces (35%) and militia (32%). The majority (63%) of violent deaths were from gunshots. Twelve percent were attributed to car bombs. Based on the responses from adults in the surveyed households who reported on the alive-or-dead status of their siblings, the researchers estimated the total number of deaths among adults aged 15–60 years, from March 2003 to June 2011, to be approximately 376,000; 184,000 of these deaths were attributed to the conflict, and of those, the authors estimate that 132,000 were caused directly by war-related violence.
What Do These Findings Mean?
These findings provide the most up-to-date estimates of the death toll of the Iraq war and subsequent conflict. However, given the difficult circumstances, the estimates are associated with substantial uncertainties. The researchers extrapolated from a small representative sample of households to estimate Iraq's national death toll. In addition, respondents were asked to recall events that occurred up to ten years prior, which can lead to inaccuracies. The researchers also had to rely on outdated census data (the last complete population census in Iraq dates back to 1987) for their overall population figures. Thus, to accompany their estimate of 460,000 excess deaths from March 2003 to mid-2011, the authors used statistical methods to determine the likely range of the true estimate. Based on the statistical methods, the researchers are 95% confident that the true number of excess deaths lies between 48,000 and 751,000—a large range. More than two years past the end of the period covered in this study, the conflict in Iraq is far from over and continues to cost lives at alarming rates. As discussed in an accompanying Perspective by Salman Rawaf, violence and lawlessness continue to the present day. In addition, post-war Iraq has limited capacity to re-establish and maintain its battered public health and safety infrastructure.
Additional Information
Please access these websites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001533
This study is further discussed in a PLOS Medicine Perspective by Salman Rawaf.
The Geneva Declaration on Armed Violence and Development website provides information on the global burden of armed violence.
The International Committee of the Red Cross provides information about war and international humanitarian law (in several languages).
Medact, a global health charity, has information on health and conflict.
Columbia University has a program on forced migration and health.
Johns Hopkins University runs the Center for Refugee and Disaster Response.
University of Washington's Health Alliance International website also has information about war and conflict.
doi:10.1371/journal.pmed.1001533
PMCID: PMC3797136  PMID: 24143140
16.  Role of Environmental Chemicals in Diabetes and Obesity: A National Toxicology Program Workshop Review 
Environmental Health Perspectives  2012;120(6):779-789.
Background: There has been increasing interest in the concept that exposures to environmental chemicals may be contributing factors to the epidemics of diabetes and obesity. On 11–13 January 2011, the National Institute of Environmental Health Sciences (NIEHS) Division of the National Toxicology Program (NTP) organized a workshop to evaluate the current state of the science on these topics of increasing public health concern.
Objective: The main objective of the workshop was to develop recommendations for a research agenda after completing a critical analysis of the literature for humans and experimental animals exposed to certain environmental chemicals. The environmental exposures considered at the workshop were arsenic, persistent organic pollutants, maternal smoking/nicotine, organotins, phthalates, bisphenol A, and pesticides. High-throughput screening data from Toxicology in the 21st Century (Tox21) were also considered as a way to evaluate potential cellular pathways and generate -hypotheses for testing which and how certain chemicals might perturb biological processes related to diabetes and obesity.
Conclusions: Overall, the review of the existing literature identified linkages between several of the environmental exposures and type 2 diabetes. There was also support for the “developmental obesogen” hypothesis, which suggests that chemical exposures may increase the risk of obesity by altering the differentiation of adipocytes or the development of neural circuits that regulate feeding behavior. The effects may be most apparent when the developmental exposure is combined with consumption of a high-calorie, high-carbohydrate, or high-fat diet later in life. Research on environmental chemical exposures and type 1 diabetes was very limited. This lack of research was considered a critical data gap. In this workshop review, we outline the major themes that emerged from the workshop and discuss activities that NIEHS/NTP is undertaking to address research recommendations. This review also serves as an introduction to an upcoming series of articles that review the literature regarding specific exposures and outcomes in more detail.
doi:10.1289/ehp.1104597
PMCID: PMC3385443  PMID: 22296744
animal; diabetes; environment; epidemiology; glucose; insulin; in vitro; metabolic syndrome; obesity; pollution
17.  Electronic Symptom Reporting Between Patient and Provider for Improved Health Care Service Quality: A Systematic Review of Randomized Controlled Trials. Part 1: State of the Art 
Background
Over the last two decades, the number of studies on electronic symptom reporting has increased greatly. However, the field is very heterogeneous: the choices of patient groups, health service innovations, and research targets seem to involve a broad range of foci. To move the field forward, it is necessary to build on work that has been done and direct further research to the areas holding most promise. Therefore, we conducted a comprehensive review of randomized controlled trials (RCTs) focusing on electronic communication between patient and provider to improve health care service quality, presented in two parts. Part 2 investigates the methodological quality and effects of the RCTs, and demonstrates some promising benefits of electronic symptom reporting.
Objective
To give a comprehensive overview of the most mature part of this emerging field regarding (1) patient groups, (2) health service innovations, and (3) research targets relevant to electronic symptom reporting.
Methods
We searched Medline, EMBASE, PsycINFO, Cochrane Central Register of Controlled Trials, and IEEE Xplore for original studies presented in English-language articles published from 1990 to November 2011. Inclusion criteria were RCTs of interventions where patients or parents reported health information electronically to the health care system for health care purposes and were given feedback.
Results
Of 642 records identified, we included 32 articles representing 29 studies. The included articles were published from 2002, with 24 published during the last 5 years. The following five patient groups were represented: respiratory and lung diseases (12 studies), cancer (6), psychiatry (6), cardiovascular (3), and diabetes (1). In addition to these, 1 study had a mix of three groups. All included studies, except 1, focused on long-term conditions. We identified four categories of health service innovations: consultation support (7 studies), monitoring with clinician support (12), self-management with clinician support (9), and therapy (1). Most of the research (21/29, 72%) was conducted within four combinations: consultation support innovation in the cancer group (5/29, 17%), monitoring innovation in the respiratory and lung diseases group (8/29, 28%), and self-management innovations in psychiatry (4/29, 14%) and in the respiratory and lung diseases group (4/29, 14%). Research targets in the consultation support studies focused on increased patient centeredness, while monitoring and self-management mainly aimed at documenting health benefits. All except 1 study aiming for reduced health care costs were in the monitoring group.
Conclusion
RCT-based research on electronic symptom reporting has developed enormously since 2002. Research including additional patient groups or new combinations of patient groups with the four identified health service innovations can be expected in the near future. We suggest that developing a generic model (not diagnosis specific) for electronic patient symptom reporting for long-term conditions may benefit the field.
doi:10.2196/jmir.2214
PMCID: PMC3510721  PMID: 23032300
Electronic symptom reporting; physician-patient relationship; patient participation; shared decision making; review; consultation; monitoring; self-management
18.  Effect of Rater Training on Reliability and Accuracy of Mini-CEX Scores: A Randomized, Controlled Trial 
Background
Mini-CEX scores assess resident competence. Rater training might improve mini-CEX score interrater reliability, but evidence is lacking.
Objective
Evaluate a rater training workshop using interrater reliability and accuracy.
Design
Randomized trial (immediate versus delayed workshop) and single-group pre/post study (randomized groups combined).
Setting
Academic medical center.
Participants
Fifty-two internal medicine clinic preceptors (31 randomized and 21 additional workshop attendees).
Intervention
The workshop included rater error training, performance dimension training, behavioral observation training, and frame of reference training using lecture, video, and facilitated discussion. Delayed group received no intervention until after posttest.
Measurements
Mini-CEX ratings at baseline (just before workshop for workshop group), and four weeks later using videotaped resident–patient encounters; mini-CEX ratings of live resident–patient encounters one year preceding and one year following the workshop; rater confidence using mini-CEX.
Results
Among 31 randomized participants, interrater reliabilities in the delayed group (baseline intraclass correlation coefficient [ICC] 0.43, follow-up 0.53) and workshop group (baseline 0.40, follow-up 0.43) were not significantly different ( = 0.19). Mean ratings were similar at baseline (delayed 4.9 [95% confidence interval 4.6–5.2], workshop 4.8 [4.5–5.1]) and follow-up (delayed 5.4 [5.0–5.7], workshop 5.3 [5.0–5.6];  = 0.88 for interaction). For the entire cohort, rater confidence (1 = not confident, 6 = very confident) improved from mean (SD) 3.8 (1.4) to 4.4 (1.0),  = 0.018. Interrater reliability for ratings of live encounters (entire cohort) was higher after the workshop (ICC 0.34) than before (ICC 0.18) but the standard error of measurement was similar for both periods.
Conclusions
Rater training did not improve interrater reliability or accuracy of mini-CEX scores.
Clinical trials registration
clinicaltrials.gov identifier NCT00667940
Electronic supplementary material
The online version of this article (doi:10.1007/s11606-008-0842-3) contains supplementary material, which is available to authorized users.
doi:10.1007/s11606-008-0842-3
PMCID: PMC2607488  PMID: 19002533
medical education; faculty development; rater training; clinical competence; assessment; randomized trial
19.  User-centered design and the development of patient decision aids: protocol for a systematic review 
Systematic Reviews  2015;4(1):11.
Background
Providing patient-centered care requires that patients partner in their personal health-care decisions to the full extent desired. Patient decision aids facilitate processes of shared decision-making between patients and their clinicians by presenting relevant scientific information in balanced, understandable ways, helping clarify patients’ goals, and guiding decision-making processes. Although international standards stipulate that patients and clinicians should be involved in decision aid development, little is known about how such involvement currently occurs, let alone best practices. This systematic review consisting of three interlinked subreviews seeks to describe current practices of user involvement in the development of patient decision aids, compare these to practices of user-centered design, and identify promising strategies.
Methods/design
A research team that includes patient and clinician representatives, decision aid developers, and systematic review method experts will guide this review according to the Cochrane Handbook and PRISMA reporting guidelines. A medical librarian will hand search key references and use a peer-reviewed search strategy to search MEDLINE, EMBASE, PubMed, Web of Science, the Cochrane Library, the ACM library, IEEE Xplore, and Google Scholar. We will identify articles across all languages and years describing the development or evaluation of a patient decision aid, or the application of user-centered design or human-centered design to tools intended for patient use. Two independent reviewers will assess article eligibility and extract data into a matrix using a structured pilot-tested form based on a conceptual framework of user-centered design. We will synthesize evidence to describe how research teams have included users in their development process and compare these practices to user-centered design methods. If data permit, we will develop a measure of the user-centeredness of development processes and identify practices that are likely to be optimal.
Discussion
This systematic review will provide evidence of current practices to inform approaches for involving patients and other stakeholders in the development of patient decision aids. We anticipate that the results will help move towards the establishment of best practices for the development of patient-centered tools and, in turn, help improve the experiences of people who face difficult health decisions.
Systematic review registration
PROSPERO CRD42014013241
Electronic supplementary material
The online version of this article (doi:10.1186/2046-4053-4-11) contains supplementary material, which is available to authorized users.
doi:10.1186/2046-4053-4-11
PMCID: PMC4328638  PMID: 25623074
Patient decision aids; Decision support; Shared decision-making; Patient education; Counseling; User-centered design; Human-centered design; Patient partnership; Stakeholder engagement; Implementation; Knowledge translation; Patient-centered care
20.  Modelling biological systems from molecules to dynamical networks 
BMC Systems Biology  2012;6(Suppl 1):S1.
A report of the 5th IEEE International Conference on Systems Biology (IEEE ISB2011), 2-4 September 2011, Zhuhai, China.
doi:10.1186/1752-0509-6-S1-S1
PMCID: PMC3403002  PMID: 23046669
21.  More discussions for granger causality and new causality measures 
Cognitive Neurodynamics  2011;6(1):33-42.
Granger causality (GC) has been widely applied in economics and neuroscience to reveal causality influence of time series. In our previous paper (Hu et al., in IEEE Trans on Neural Netw, 22(6), pp. 829–844, 2011), we proposed new causalities in time and frequency domains and particularly focused on new causality in frequency domain by pointing out the shortcomings/limitations of GC or Granger-alike causality metrics and the advantages of new causality. In this paper we continue our previous discussions and focus on new causality and GC or Granger-alike causality metrics in time domain. Although one strong motivation was introduced in our previous paper (Hu et al., in IEEE Trans on Neural Netw, 22(6), pp. 829–844, 2011) we here present additional motivation for the proposed new causality metric and restate the previous motivation for completeness. We point out one property of conditional GC in time domain and the shortcomings/limitations of conditional GC which cannot reveal the real strength of the directional causality among three time series. We also show the shortcomings/limitations of directed causality (DC) or normalize DC for multivariate time series and demonstrate it cannot reveal real causality at all. By calculating GC and new causality values for an example we demonstrate the influence of one of the time series on the other is linearly increased as the coupling strength is linearly increased. This fact further supports reasonability of new causality metric. We point out that larger instantaneous correlation does not necessarily mean larger true causality (e.g., GC and new causality), or vice versa. Finally we conduct analysis of statistical test for significance and asymptotic distribution property of new causality metric by illustrative examples.
doi:10.1007/s11571-011-9175-8
PMCID: PMC3253161  PMID: 23372618
Granger causality; New causality; Linear regression model; Prediction
22.  Effect of Facilitation of Local Maternal-and-Newborn Stakeholder Groups on Neonatal Mortality: Cluster-Randomized Controlled Trial 
PLoS Medicine  2013;10(5):e1001445.
Lars Åke Persson and colleagues conduct a cluster randomised control in northern Vietnam to analyze the effect of the activity of local community-based maternal-and-newborn stakeholder groups on neonatal mortality.
Please see later in the article for the Editors' Summary
Background
Facilitation of local women's groups may reportedly reduce neonatal mortality. It is not known whether facilitation of groups composed of local health care staff and politicians can improve perinatal outcomes. We hypothesised that facilitation of local stakeholder groups would reduce neonatal mortality (primary outcome) and improve maternal, delivery, and newborn care indicators (secondary outcomes) in Quang Ninh province, Vietnam.
Methods and Findings
In a cluster-randomized design 44 communes were allocated to intervention and 46 to control. Laywomen facilitated monthly meetings during 3 years in groups composed of health care staff and key persons in the communes. A problem-solving approach was employed. Births and neonatal deaths were monitored, and interviews were performed in households of neonatal deaths and of randomly selected surviving infants. A latent period before effect is expected in this type of intervention, but this timeframe was not pre-specified. Neonatal mortality rate (NMR) from July 2008 to June 2011 was 16.5/1,000 (195 deaths per 11,818 live births) in the intervention communes and 18.4/1,000 (194 per 10,559 live births) in control communes (adjusted odds ratio [OR] 0.96 [95% CI 0.73–1.25]). There was a significant downward time trend of NMR in intervention communes (p = 0.003) but not in control communes (p = 0.184). No significant difference in NMR was observed during the first two years (July 2008 to June 2010) while the third year (July 2010 to June 2011) had significantly lower NMR in intervention arm: adjusted OR 0.51 (95% CI 0.30–0.89). Women in intervention communes more frequently attended antenatal care (adjusted OR 2.27 [95% CI 1.07–4.8]).
Conclusions
A randomized facilitation intervention with local stakeholder groups composed of primary care staff and local politicians working for three years with a perinatal problem-solving approach resulted in increased attendance to antenatal care and reduced neonatal mortality after a latent period.
Trial registration
Current Controlled Trials ISRCTN44599712
Please see later in the article for the Editors' Summary
Editors' Summary
Background
Over the past few years, there has been enormous international effort to meet the target set by Millennium Development Goal 4 to reduce the under-five child mortality rate by two-thirds and to reduce the number of maternal deaths by three-quarters, respectively, from the 1990 level by 2015. There has been some encouraging progress and according to the latest figures from the World Health Organization, in 2011, just under 7 million children aged under 5 years died, a fall of almost 3 million from a decade ago. However, currently, 41% of all deaths among children under the age of 5 years occur around birth and the first 28 days of life (perinatal and neonatal mortality). Simple interventions can substantially reduce neonatal deaths and there have been several international, national, and local efforts to implement effective care packages to help reduce the number of neonatal deaths.
Why Was This Study Done?
In order for these interventions to be most effective, it is important that the local community becomes involved. Community mobilization, especially through local women's groups, can empower women to prioritize specific interventions to help improve their own health and that of their baby. An alternative strategy might be to mobilize people who already have responsibility to promote health and welfare in society, such as primary care staff, village health workers, and elected political representatives. However, it is unclear if the activities of such stakeholder groups result in improved neonatal survival. So in this study from northern Vietnam, the researchers analyzed the effect of the activity of local maternal-and-newborn stakeholder groups on neonatal mortality.
What Did the Researchers Do and Find?
Between 2008 and 2011, the researchers conducted a cluster-randomized controlled trial in 90 communes within the Quang Ninh province of northeast of Vietnam: 44 communes were allocated to intervention and 46 to the control. The local women's union facilitated recruitment to the intervention, local stakeholder groups (Maternal and Newborn Health Groups), which comprised primary care staff, village health workers, women's union representatives, and the person with responsibility for health in the commune. The groups' role was to identify and prioritize local perinatal health problems and implement actions to help overcome these problems.
Over the three-year period, the Maternal and Newborn Health Groups in the 44 intervention communes had 1,508 meetings. Every year 15–27 unique problems were identified and addressed 94–151 times. The problem-solving processes resulted in an annual number of 19–27 unique actions that were applied 297–649 times per year. The top priority problems and actions identified by these groups dealt with antenatal care attendance, post-natal visits, nutrition and rest during pregnancy, home deliveries, and breast feeding. Neonatal mortality in the intervention group did not change over the first two years but showed a significant improvement in the third year. The three leading causes of death were prematurity/low birth-weight (36%), intrapartum-related neonatal deaths (30%), and infections (15%). Stillbirth rates were 7.4 per 1,000 births in the intervention arm and 9.0 per 1,000 births in the control arm. There was one maternal death in the intervention communes and four in the control communes and there was a significant improvement in antenatal care attendance in the intervention arm. However, there were no significant differences between the intervention and control groups of other outcomes, including tetanus immunization, delivery preparedness, institutional delivery, temperature control at delivery, early initiation of breastfeeding, or home visit of a midwife during the first week after delivery.
What Do These Findings Mean?
These findings suggest that local stakeholder groups comprised of primary care staff and local politicians using a problem-solving approach may help to reduce the neonatal mortality rate after three years of implementation (although the time period for an expected reduction in neonatal mortality was not specified before the trial started) and may also increase the rate of antenatal care attendance. However, the intervention had no effect on other important outcomes such as the rate of institutional delivery and breast feeding. This study used a novel approach of community-based activity that was implemented into the public sector system at low cost. A further reduction in neonatal deaths around delivery might be achieved by neonatal resuscitation training and home visits to the mother and her baby.
Additional Information
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001445.
The World Health Organization provides comprehensive statistics on neonatal mortality
The Healthy Newborn Network has information on community interventions to help reduce neonatal mortality from around the world
doi:10.1371/journal.pmed.1001445
PMCID: PMC3653802  PMID: 23690755
23.  Framing the evidence for health smart homes and home-based consumer health technologies as a public health intervention for independent aging: a systematic review 
Introduction
There is a critical need for public health interventions to support the independence of older adults as the world’s population ages. Health smart homes (HSH) and home-based consumer health (HCH) technologies may play a role in these interventions.
Methods
We conducted a systematic review of HSH and HCH literature from indexed repositories for health care and technology disciplines (e.g., MEDLINE, CINAHL, and IEEE Xplore) and classified included studies according to an evidence-based public health (EBPH) typology.
Results
One thousand, six hundred and thirty nine candidate articles were identified. Thirty-one studies from the years 1998–2011 were included. Twenty-one included studies were classified as emerging, 10 as promising and 3 as effective (first tier).
Conclusion
The majority of included studies were published in the period beginning in the year 2005. All 3 effective (first tier) studies and 9 of 10 of promising studies were published during this period. Almost all studies included an activity sensing component and most of these used passive infrared motion sensors. The three effective (first tier) studies all used a multicomponent technology approach that included activity sensing, reminders and other technologies tailored to individual preferences. Future research should explore the use of technology for self-management of health by older adults, social support and self-reported health measures incorporated into personal health records, electronic medical records, and community health registries.
doi:10.1016/j.ijmedinf.2013.03.007
PMCID: PMC3740158  PMID: 23639263
Health Smart Homes; Evidence-Based Public Health; Aging in Place; Independent Aging; STARE-HI
24.  “Nonparametric Local Smoothing” is not image registration 
BMC Research Notes  2012;5:610.
Background
Image registration is one of the most important and universally useful computational tasks in biomedical image analysis. A recent article by Xing & Qiu (IEEE Transactions on Pattern Analysis and Machine Intelligence, 33(10):2081–2092, 2011) is based on an inappropriately narrow conceptualization of the image registration problem as the task of making two images look alike, which disregards whether the established spatial correspondence is plausible. The authors propose a new algorithm, Nonparametric Local Smoothing (NLS) for image registration, but use image similarities alone as a measure of registration performance, although these measures do not relate reliably to the realism of the correspondence map.
Results
Using data obtained from its authors, we show experimentally that the method proposed by Xing & Qiu is not an effective registration algorithm. While it optimizes image similarity, it does not compute accurate, interpretable transformations. Even judged by image similarity alone, the proposed method is consistently outperformed by a simple pixel permutation algorithm, which is known by design not to compute valid registrations.
Conclusions
This study has demonstrated that the NLS algorithm proposed recently for image registration, and published in one of the most respected journals in computer science, is not, in fact, an effective registration method at all. Our results also emphasize the general need to apply registration evaluation criteria that are sensitive to whether correspondences are accurate and mappings between images are physically interpretable. These goals cannot be achieved by simply reporting image similarities.
doi:10.1186/1756-0500-5-610
PMCID: PMC3740790  PMID: 23116330
Image registration; Correspondence; Accuracy
25.  Toward an International Initiative for Traumatic Brain Injury Research 
Journal of Neurotrauma  2013;30(14):1211-1222.
Abstract
The European Commission (EC) and the National Institutes of Health (NIH) jointly sponsored a workshop on October 18–20, 2011 in Brussels to discuss the feasibility and benefits of an international collaboration in the field of traumatic brain injury (TBI) research. The workshop brought together scientists, clinicians, patients, and industry representatives from around the globe as well as funding agencies from the EU, Spain, the United States, and Canada. Sessions tackled both the possible goals and governance of a future initiative and the scientific questions that would most benefit from an integrated international effort: how to optimize data collection and sharing; injury classification; outcome measures; clinical study design; and statistical analysis. There was a clear consensus that increased dialogue and coordination of research at an international level would be beneficial for advancing TBI research, treatment, and care. To this end, the EC, the NIH, and the Canadian Institutes of Health Research expressed interest in developing a framework for an international initiative for TBI Research (InTBIR). The workshop participants recommended that InTBIR initially focus on collecting, standardizing, and sharing clinical TBI data for comparative effectiveness research, which will ultimately result in better management and treatments for TBI.
doi:10.1089/neu.2013.2896
PMCID: PMC3713440  PMID: 23731282
geriatric brain injury; head trauma; human studies; pediatric brain injury

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