scholarly journals Disclosure of personal identifying information in studies of neighborhood contexts and patient outcomes. (Preprint)

2021 ◽  
Author(s):  
Andrew Graham Rundle ◽  
Michael David Miller Bader ◽  
Stephen John Mooney
Keyword(s):  
Patient Outcomes ◽  
Neighborhood Effects ◽  
Clinical Epidemiology ◽  
Health Care Research ◽  
R Package ◽  
Third Party ◽  
Patient Privacy ◽  
Address Data ◽  
Subsequent Publication ◽  
Personal Identifying Information

UNSTRUCTURED Clinical epidemiology and patient-oriented health care research that incorporates neighborhood-level data is becoming increasingly common. A key step in conducting this research is converting patient address data to longitude and latitude data, a process known as geocoding. Several commonly used approaches to geocoding (e.g. the tidygeocoder R package) send patient addresses over the internet to online third party geocoding services. Here we describe how these approaches to geocoding disclose patient’s Personal Identifying Information (PII) and then how subsequent publication of the research findings discloses these same patient’s Protected Heath Information (PHI). We describe how these disclosures can occur and strategies to maintain patient privacy while studying neighborhood effects on patient outcomes.

scholarly journals Portal Design for the Open Data Initiative: A Preliminary Study

Proceedings ◽  
2018 ◽  
Vol 2 (19) ◽  
pp. 1244
Author(s):  
Netzahualcoyotl Hernandez ◽  
Ian McChesney ◽  
Joe Rafferty ◽  
Chris Nugent ◽  
Jonathan Synnott ◽  
...  
Keyword(s):  
User Interface ◽  
Data Model ◽  
Open Data ◽  
Health Care Research ◽  
Research Community ◽  
Third Party ◽  
Technical Review ◽  
Pervasive Health ◽  
Preliminary Study ◽  
Variable Quality

The Open Data Initiative (ODI) has been previously proposed to facilitate the sharing of annotated datasets within the pervasive health care research community. This paper outlines the requirements for the ODI portal based on the ontological data model of the ODI and its typical usage scenarios. In the context of an action research framework, the paper outlines the ODI platform, the design of a prototype user interface for the purposes of initial evaluation and its technical review by third-party researchers (n = 3). The main findings from the technical review were found to be the need for a more flexible user interface to reflect the different experimental configurations in the research community, provision for describing dataset usage, and dissemination conditions. The technical review also identified the value of permitting datasets with variable quality, as noisy datasets are useful in the testing of activity recognition algorithms. Revisions to the ODI ontology and platform are proposed based on the findings from this study.

scholarly journals Neighbor QTL: an interval mapping method for quantitative trait loci underlying plant neighborhood effects

2020 ◽  
Author(s):  
Yasuhiro Sato ◽  
Kazuya Takeda ◽  
Atsushi J. Nagano
Keyword(s):  
Qtl Mapping ◽  
Neighborhood Effects ◽  
Quantitative Trait ◽  
Recombinant Inbred Lines ◽  
Insect Herbivory ◽  
R Package ◽  
Interval Mapping ◽  
Mapping Method ◽  
Neighbor Effects ◽  
Genotype Probabilities

AbstractPhenotypes of sessile organisms, such as plants, rely not only on their own genotype but also on the genotypes of neighboring individuals. Previously, we incorporated such neighbor effects into a single-marker regression using the Ising model of ferromagnetism. However, little is known about how to incorporate neighbor effects in quantitative trait locus (QTL) mapping. In this study, we propose a new method for interval QTL mapping of neighbor effects, named “Neighbor QTL”. The algorithm of neighbor QTL involves the following: (i) obtaining conditional self-genotype probabilities with recombination fraction between flanking markers, (ii) calculating neighbor genotypic identity using the self-genotype probabilities, and (iii) estimating additive and dominance deviation for neighbor effects. Our simulation using F2 and backcross lines showed that the power to detect neighbor effects increased as the effective range became smaller. The neighbor QTL was applied to insect herbivory on Col × Kas recombinant inbred lines of Arabidopsis thaliana. Consistent with previous evidence, the pilot experiment detected a self QTL effect on the herbivory at GLABRA1 locus. We also observed a weak QTL on chromosome 4 regarding neighbor effects on the herbivory. The neighbor QTL method is available as an R package (https://cran.r-project.org/package=rNeighborQTL), providing a novel tool to investigate neighbor effects in QTL studies.

scholarly journals Identification, annotation and visualisation of extreme changes in splicing from RNA-seq experiments with SwitchSeq

2014 ◽  
Author(s):  
Mar Gonzàlez-Porta ◽  
Alvis Brazma
Keyword(s):  
Enrichment Analysis ◽  
R Package ◽  
Third Party ◽  
Pathway Enrichment Analysis ◽  
Rna Seq ◽  
Differential Splicing ◽  
Protein Coding ◽  
Downstream Analysis ◽  
Intuitive Manner ◽  
Abundant Transcript

In the past years, RNA sequencing has become the method of choice for the study of transcriptome composition. When working with this type of data, several tools exist to quantify differences in splicing across conditions and to address the significance of those changes. However, the number of genes predicted to undergo differential splicing is often high, and further interpretation of the results becomes a challenging task. Here we present SwitchSeq, a novel set of tools designed to help the users in the interpretation of differential splicing events that affect protein coding genes. More specifically, we provide a framework to identify switch events, i.e., cases where, for a given gene, the identity of the most abundant transcript changes across conditions. The identified events are then annotated by incorporating information from several public databases and third-party tools, and are further visualised in an intuitive manner with the independent R package tviz. All the results are displayed in a self-contained HTML document, and are also stored in txt and json format to facilitate the integration with any further downstream analysis tools. Such analysis approach can be used complementarily to Gene Ontology and pathway enrichment analysis, and can also serve as an aid in the validation of predicted changes in mRNA and protein abundance. The latest version of SwitchSeq, including installation instructions and use cases, can be found at https://github.com/mgonzalezporta/SwitchSeq. Additionally, the plot capabilities are provided as an independent R package at https://github.com/mgonzalezporta/tviz.

scholarly journals Direct Access Compared With Referred Physical Therapy Episodes of Care: A Systematic Review

2014 ◽  
Vol 94 (1) ◽  
pp. 14-30 ◽  
Author(s):  
Heidi A. Ojha ◽  
Rachel S. Snyder ◽  
Todd E. Davenport
Keyword(s):  
Systematic Review ◽  
Health Care ◽  
Physical Therapy ◽  
Patient Outcomes ◽  
Health Care Costs ◽  
Third Party ◽  
Direct Access ◽  
Physician Referral ◽  
Episodes Of Care ◽  
Care Costs

Background Evidence suggests that physical therapy through direct access may help decrease costs and improve patient outcomes compared with physical therapy by physician referral. Purpose The purpose of this study was to conduct a systematic review of the literature on patients with musculoskeletal injuries and compare health care costs and patient outcomes in episodes of physical therapy by direct access compared with referred physical therapy. Data Sources Ovid MEDLINE, CINAHL (EBSCO), Web of Science, and PEDro were searched using terms related to physical therapy and direct access. Included articles were hand searched for additional references. Study Selection Included studies compared data from physical therapy by direct access with physical therapy by physician referral, studying cost, outcomes, or harm. The studies were appraised using the Centre for Evidence-Based Medicine (CEBM) levels of evidence criteria and assigned a methodological score. Data Extraction Of the 1,501 articles that were screened, 8 articles at levels 3 to 4 on the CEBM scale were included. There were statistically significant and clinically meaningful findings across studies that satisfaction and outcomes were superior, and numbers of physical therapy visits, imaging ordered, medications prescribed, and additional non–physical therapy appointments were less in cohorts receiving physical therapy by direct access compared with referred episodes of care. There was no evidence for harm. Data Synthesis There is evidence across level 3 and 4 studies (grade B to C CEBM level of recommendation) that physical therapy by direct access compared with referred episodes of care is associated with improved patient outcomes and decreased costs. Limitations Primary limitations were lack of group randomization, potential for selection bias, and limited generalizability. Conclusions Physical therapy by way of direct access may contain health care costs and promote high-quality health care. Third-party payers should consider paying for physical therapy by direct access to decrease health care costs and incentivize optimal patient outcomes.

The Earth Observation Time Series Analysis Toolbox (EOTSA) - An R package with WPS, Web-Client and Spark integration

2020 ◽  
Author(s):  
Ulrich Leopold ◽  
Benedikt Gräler ◽  
Henning Bredel ◽  
J. Arturo Torres-Matallana ◽  
Philippe Pinheiro ◽  
...  
Keyword(s):  
Time Series ◽  
Time Series Analysis ◽  
European Space Agency ◽  
R Package ◽  
Observation Time ◽  
Third Party ◽  
Space Applications ◽  
Web Mapping ◽  
Series Analysis ◽  
External Data

<p>We present an implementation of a time series analysis toolbox for remote sensing imagery in R which has been largely funded by the European Space Agency within the PROBA-V MEP Third Party Services project. The toolbox is developed according to the needs of the time series analysis community. The data is provided by the PROBA-V mission exploitation platform (MEP) at VITO. The toolbox largely builds on existing specialized R packages and functions for raster and time series analysis combining these in a common framework.</p><p>In order to ease access and usage of the toolbox, it has been deployed in the MEP Spark Cluster to bring the algorithm to the data. All functions are also wrapped in a Web Processing Service (WPS) using 52°North’s WPS4R extension for interoperability across web platforms. The WPS can be orchestrated in the Automatic Service Builder (ASB) developed by Space Applications. Hence, the space-time analytics developed in R can be integrated into a larger workflow potentially integrating external data and services. The WPS provides a Webclient including a preview of the results in a map window for usage within the MEP. Results are offered for download or through Web Mapping and Web Coverage Services (WMS, WCS) provided through a Geoserver instance.</p><p>Through its interoperability features the EOTSA toolbox provides a contribution towards collaborative science.</p>

scholarly journals WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

2019 ◽  
Vol 47 (W1) ◽  
pp. W199-W205 ◽  
Author(s):  
Yuxing Liao ◽  
Jing Wang ◽  
Eric J Jaehnig ◽  
Zhiao Shi ◽  
Bing Zhang
Keyword(s):  
User Interfaces ◽  
Large Scale ◽  
Data Interpretation ◽  
R Package ◽  
Third Party ◽  
Gene Set Analysis ◽  
Functional Categories ◽  
User Friendliness ◽  
The Core ◽  
Gene Sets

Abstract WebGestalt is a popular tool for the interpretation of gene lists derived from large scale -omics studies. In the 2019 update, WebGestalt supports 12 organisms, 342 gene identifiers and 155 175 functional categories, as well as user-uploaded functional databases. To address the growing and unique need for phosphoproteomics data interpretation, we have implemented phosphosite set analysis to identify important kinases from phosphoproteomics data. We have completely redesigned result visualizations and user interfaces to improve user-friendliness and to provide multiple types of interactive and publication-ready figures. To facilitate comprehension of the enrichment results, we have implemented two methods to reduce redundancy between enriched gene sets. We introduced a web API for other applications to get data programmatically from the WebGestalt server or pass data to WebGestalt for analysis. We also wrapped the core computation into an R package called WebGestaltR for users to perform analysis locally or in third party workflows. WebGestalt can be freely accessed at http://www.webgestalt.org.

scholarly journals Making Trade-Offs for Safe, Effective, and Secure Patient Care

2016 ◽  
Vol 11 (2) ◽  
pp. 213-215 ◽  
Author(s):  
Dan Lyon
Keyword(s):  
Patient Outcomes ◽  
Medical Devices ◽  
Development Process ◽  
Patient Privacy ◽  
Care Model ◽  
Time To Market ◽  
On Demand ◽  
Secure Care ◽  
Trade Offs ◽  
Health Care Model

As the health care model evolves to deliver on demand care, patients are becoming more responsible and interested in their data. The security of the medical devices and connected systems becomes increasingly more important because it plays a significant role in achieving better patient outcomes. Diabetes patients are at the forefront of this evolution and yet on the receiving end of diabetic equipment manufacturers delivering systems that support secure care. In order to deliver the best patient outcomes, complex trade-offs are required, including (1) usability, (2) cost, (3) time to market, (4) device life cycle, and (5) patient privacy. These trade-offs for security cannot be made without a comprehensive informed development process.

Consensus Guidelines for Coordinated Outpatient Oral Anticoagulation Therapy Management

1997 ◽  
Vol 31 (5) ◽  
pp. 604-615 ◽  
Author(s):  
Jack E Ansell ◽  
Marissa L Buttaro ◽  
Orsula Voltis Thomas ◽  
Calvin H Knowlton ◽  
Keyword(s):  
Patient Care ◽  
Patient Outcomes ◽  
Current Practice ◽  
Systems Of Care ◽  
Anticoagulation Therapy ◽  
Anticoagulation Clinic ◽  
Third Party ◽  
Patient Specific ◽  
Anticoagulation Management ◽  
The Impact

OBJECTIVE: TO provide primary and referring healthcare practitioners with guidelines for the provision of safe and effective anticoagulation management in any venue to standardize and improve quality of care and to permit negotiation for reimbursement from third-party payers. DATA EXTRACTION AND SYNTHESIS: Data on the current practice of anticoagulation providers and outcomes related to anticoagulation clinic care were obtained through the literature, interviews with anticoagulation providers, and a focus group meeting of anticoagulation clinic stakeholders. This information collation process revealed that an anticoagulation service consists of three separate areas for which guidelines should be developed. Based on the consensus opinions of the committee members, the literature review, and the current practice of anticoagulation services providers, a draft guideline was developed and reviewed by an independent multidisciplinary panel of anticoagulation services providers whose comments were incorporated into the final guideline. CONCLUSIONS: Systematic outpatient anticoagulation services are systems of care designed to coordinate and optimize the delivery of anticoagulation therapy by (1) evaluating patient-specific risks and benefits to determine the appropriateness of therapy; (2) facilitating the management of anticoagulation dosages and prescription pick up or delivery; (3) providing ongoing education of the patient and other caregivers about warfarin and the importance of self-care behavior leading to optimal outcomes; (4) providing continuous systematic monitoring of patients, international normalized ratio results, diet, concomitant drug therapy, and disease states; and (5) communicating with other healthcare practitioners involved in the care of the patient. To create a reproducible framework for the provision of these services, guidelines for structure, process, and outcomes of coordinated outpatient anticoagulation management services were developed. Guidelines for organization and management include (1) qualifications for personnel, (2) supervision, (3) care management and coordination, (4) communication and documentation, and (5) laboratory monitoring. Guidelines for the process of patient care include (6) patient selection and assessment, (7) initiation of therapy, (8) maintenance and management of therapy, (9) patient education, and (10) management and triage of therapy-related and unrelated problems. Guidelines for the evaluation of patient outcomes include (11) organizational components and (12) patient outcomes. The impact of these 12 guidelines on patient care and reimbursement procurement will depend on their implementation and the perceived value of their use.

scholarly journals Measuring doctor appointment availability in Northland general practice

2017 ◽  
Vol 9 (1) ◽  
pp. 56 ◽  
Author(s):  
Kyle Eggleton ◽  
Liane Penney ◽  
Jenni Moore
Keyword(s):  
General Practice ◽  
Patient Outcomes ◽  
Third Party ◽  
Reliable Measure ◽  
Primary Care Access ◽  
Care Access ◽  
Practice Characteristics ◽  
The Mean ◽  
Appointment Availability ◽  
Practice Patient

ABSTRACT INTRODUCTION Primary care access is associated with improved patient outcomes. Availability of appointments in general practice is one measure of access. Northland’s demographics and high ambulatory sensitive hospitalisation rates may indicate constrained appointment availability. Our study aims were to determine appointment availability and establish the feasibility of measuring appointment availability through an automated process. METHODS An automated electronic query was created, run through a third party software programme that interrogated Northland general practice patient management systems. The time to third next available appointment (TNAA) was calculated for each general practitioner (GP) and a mean calculated for each practice and across the region. A research assistant telephone request for an urgent GP appointment captured the time to the urgent appointment and type of urgent appointment used to fit patients in. Regression analysis was used to determine the relationships between deprivation, patients per GP, and the use of walk-in clinics. RESULTS The mean TNAA was 2.5 days. 12% of practices offered walk-in clinics. There was a significant relationship between TNAA and increasing number of walk-in clinics. CONCLUSION The TNAA of 2.5 days indicates the possibility that routine appointments are constrained in Northland. However, TNAA may not give a reliable measure of urgent appointment availability and the measure needs to be interpreted by taking into account practice characteristics. Walk-in clinics, although increasing the availability of urgent appointments, may lead to more pressure on routine appointments. Using an electronic query is a feasible way to measure routine GP appointment availability.

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