Data visualization for truth maintenance in clinical decision support systems

Background and objectives The goal is to inform proactive initiatives to expand the knowledge base of clinical decision support systems. Design and setting We describe an initiative in which research informationists and health services researchers employ visualization tools to map logic models for clinical decision support within an electronic health record. Materials and methods We mapped relationships using software for social network analysis: NodeXL and CMAP. We defined relationships by shared observations, such as two Arden rules within medical logic modules that consider the same clinical observation, or by the presence of common keywords that were used to label rules according to standardized vocabularies. Results We studied the Child Health Improvement through Computer Automation (CHICA) system, an electronic medical record that contains 170 unique variables representing discrete clinical observations. These variables were used in 300 medical logic modules (MLM's) that prompted health care providers to deliver preventive counseling or otherwise served as clinical decision support. Using data visualization tools, we generated maps that illustrate connections, or lack thereof, between clinical topics within CHICA's MLMs. Conclusions The development of such maps may allow multiple disciplines commonly interacting over EMR platforms, and various perspectives (clinicians, programmers, informationists) to work more effectively as teams to refine the EMR by programming logic routines to address co-morbidities or other instances where domains of medical knowledge should be connected

Using GPS-enabled cell phones to track the travel patterns of adolescents

<p>Abstract</p> <p>Background</p> <p>Few tools exist to directly measure the microsocial and physical environments of adolescents in circumstances where participatory observation is not practical or ethical. Yet measuring these environments is important as they are significantly associated with adolescent health-risk. For example, health-related behaviors such as cigarette smoking often occur in specific places where smoking may be relatively surreptitious.</p> <p>Results</p> <p>We assessed the feasibility of using GPS-enabled cell phones to track adolescent travel patterns and gather daily diary data. We enrolled 15 adolescent women from a clinic-based setting and asked them to carry the phones for 1 week. We found that these phones can accurately and reliably track participant locations, as well as record diary information on adolescent behaviors. Participants had variable paths extending beyond their immediate neighborhoods, and denied that GPS-tracking influenced their activity.</p> <p>Conclusion</p> <p>GPS-enabled cell phones offer a feasible and, in many ways, ideal modality of monitoring the location and travel patterns of adolescents. In addition, cell phones allow space- and time-specific interaction, probing, and intervention which significantly extends both research and health promotion beyond a clinical setting. Future studies can employ GPS-enabled cell phones to better understand adolescent environments, how they are associated with health-risk behaviors, and perhaps intervene to change health behavior.</p

A Field Approach to 3D Gene Expression Pattern Characterization

We present a vector field method for obtaining the spatial organization of 3D patterns of gene expression based on gradients and lines of force obtained by numerical integration. The convergence of these lines of force in local maxima are centers of gene expression, providing a natural and powerful framework to characterize the organization and dynamics of biological structures. We apply this novel methodology to analyze the expression pattern of the Enhanced Green Fluorescent Protein (EGFP) driven by the promoter of light chain myosin II during zebrafish heart formation.Comment: 9 pages, 2 figures, The following article has been submitted to Applied Physics Letters. If it is published, it will be found online at http://apl.aip.or

Real-World Evaluation of the Feasibility, Acceptability and Safety of a Remote, Self-Management Parkinson’s Disease Care Pathway: A Healthcare Improvement Initiative

Background: There is significant unmet need for effective and efficiently delivered care for people with Parkinson’s disease (PwP). We undertook a service improvement initiative to co-develop and implement a new care pathway, Home Based Care (HBC), based on supported self-management, remote monitoring and the ability to trigger a healthcare contact when needed. Objective: To evaluate feasibility, acceptability and safety of Home Based Care. Methods: We evaluated data from the first 100 patients on HBC for 6 months. Patient monitoring, performed at baseline and 6-monthly, comprised motor (MDS-UPDRS II and accelerometer), non-motor (NMSQ, PDSS-2, HADS) and quality of life (PDQ) measures. Care quality was audited against Parkinson’s UK national audit standards. Process measures captured feasibility. Acceptability was assessed using a mixed-methods approach comprising questionnaires and semi-structured interviews. Results: Between October 2019 and January 2021, 108 PwP were enrolled onto HBC, with data from 100 being available at 6 months. Over 90% of all questionnaires were returned, 97% were complete or had &lt; 3 missing items. Reporting and communications occurred within agreed timeframes. Compared with baseline, after 6m on HBC, PD symptoms were stable; more PwP felt listened to (90% vs. 79%) and able to seek help (79% vs. 68%). HBC met 93% of national audit criteria. Key themes from the interviews included autonomy and empowerment. Conclusions: We have demonstrated acceptability, feasibility and safety of our novel remotely delivered Parkinson’s care pathway. Ensuring scalability will widen its reach and realize its benefits for underserved communities, enabling formal comparisons with standard care and cost-effectiveness evaluation

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Search for the standard model Higgs boson in the H to ZZ to 2l 2nu channel in pp collisions at sqrt(s) = 7 TeV

A search for the standard model Higgs boson in the H to ZZ to 2l 2nu decay channel, where l = e or mu, in pp collisions at a center-of-mass energy of 7 TeV is presented. The data were collected at the LHC, with the CMS detector, and correspond to an integrated luminosity of 4.6 inverse femtobarns. No significant excess is observed above the background expectation, and upper limits are set on the Higgs boson production cross section. The presence of the standard model Higgs boson with a mass in the 270-440 GeV range is excluded at 95% confidence level.Comment: Submitted to JHE

Search for New Physics with Jets and Missing Transverse Momentum in pp collisions at sqrt(s) = 7 TeV

A search for new physics is presented based on an event signature of at least three jets accompanied by large missing transverse momentum, using a data sample corresponding to an integrated luminosity of 36 inverse picobarns collected in proton--proton collisions at sqrt(s)=7 TeV with the CMS detector at the LHC. No excess of events is observed above the expected standard model backgrounds, which are all estimated from the data. Exclusion limits are presented for the constrained minimal supersymmetric extension of the standard model. Cross section limits are also presented using simplified models with new particles decaying to an undetected particle and one or two jets

Combined search for the quarks of a sequential fourth generation

Results are presented from a search for a fourth generation of quarks produced singly or in pairs in a data set corresponding to an integrated luminosity of 5 inverse femtobarns recorded by the CMS experiment at the LHC in 2011. A novel strategy has been developed for a combined search for quarks of the up and down type in decay channels with at least one isolated muon or electron. Limits on the mass of the fourth-generation quarks and the relevant Cabibbo-Kobayashi-Maskawa matrix elements are derived in the context of a simple extension of the standard model with a sequential fourth generation of fermions. The existence of mass-degenerate fourth-generation quarks with masses below 685 GeV is excluded at 95% confidence level for minimal off-diagonal mixing between the third- and the fourth-generation quarks. With a mass difference of 25 GeV between the quark masses, the obtained limit on the masses of the fourth-generation quarks shifts by about +/- 20 GeV. These results significantly reduce the allowed parameter space for a fourth generation of fermions.Comment: Replaced with published version. Added journal reference and DO

Measurement of the t t-bar production cross section in the dilepton channel in pp collisions at sqrt(s) = 7 TeV

The t t-bar production cross section (sigma[t t-bar]) is measured in proton-proton collisions at sqrt(s) = 7 TeV in data collected by the CMS experiment, corresponding to an integrated luminosity of 2.3 inverse femtobarns. The measurement is performed in events with two leptons (electrons or muons) in the final state, at least two jets identified as jets originating from b quarks, and the presence of an imbalance in transverse momentum. The measured value of sigma[t t-bar] for a top-quark mass of 172.5 GeV is 161.9 +/- 2.5 (stat.) +5.1/-5.0 (syst.) +/- 3.6(lumi.) pb, consistent with the prediction of the standard model.Comment: Replaced with published version. Included journal reference and DO