11 research outputs found

    PGen: large-scale genomic variations analysis workflow and browser in SoyKB

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    Telehealth Acceptance Among Appalachian Respondents During COVID 19: a Secondary Data Analysis

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    Purpose: The purpose of this study is to examine the relationship between telehealth use, telehealth satisfaction, and chronic medical conditions among residents living in Appalachian and non-Appalachian communities. Sample: A COVID-19 public health survey was distributed via social media and healthcare clinics in the tri-state region of central Appalachia. Survey responses were limited to adults aged ≥18 years who consented to participate in the survey that self-identified as an individual with one or more chronic medical conditions (n=195). Method: Simple descriptive statistics including frequencies, percentages, means, and standard deviations (SDs) were calculated for variables of interest both overall and by subgroups of interest. Chi-squared tests were used to compare categorical outcomes between groups of interest, while two-sample t-tests were used for continuous outcomes. Significance for all tests was determined using an α level of 0.05. Findings: There is no statistically significant relationship between respondents with regard to using telehealth services, satisfaction rates related to telehealth use, or reasons for electing not to use telehealth services during the COVID-19 pandemic. However, there was a trending statistical relationship between county status and the use of telehealth services in Appalachia with those counties doing economically better being more likely to use telehealth services as compared to those fairing less well (p=0.053). Findings also suggest that people living in urban areas of Appalachia were more likely to be satisfied using telehealth services than those living in non-urban areas of Appalachia (p=0.01). Conclusions: Research is still limited as to how the expansion of broadband capabilities during the COVID-19 pandemic has benefited those residing in Appalachia in terms of managing chronic health conditions. Future research should focus on expanding participation among Appalachian respondents looking for specific differences related to location within Appalachia, age, gender, ethnicity, and socioeconomic status

    Exploring the potential of big data on the health care delivery value chain (CDVC): a preliminary literature and research agenda

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    Big data analytics (BDA) is emerging as a game changer in healthcare. While the practitioner literature has been speculating on the high potential of BDA in transforming the healthcare sector, few rigorous empirical studies have been conducted by scholars to assess the real potential of BDA. Drawing on the health care delivery value chain (CDVC) and an extensive literature review, this exploratory study aims to discuss current peer-reviewed articles dealing with BDA across the CDVC and discuss future research directions

    PGen: large-scale genomic variations analysis workflow and browser in SoyKB

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    Background: With the advances in next-generation sequencing (NGS) technology and significant reductions in sequencing costs, it is now possible to sequence large collections of germplasm in crops for detecting genome-scale genetic variations and to apply the knowledge towards improvements in traits. To efficiently facilitate large-scale NGS resequencing data analysis of genomic variations, we have developed " PGen", an integrated and optimized workflow using the Extreme Science and Engineering Discovery Environment (XSEDE) high-performance computing (HPC) virtual system, iPlant cloud data storage resources and Pegasus workflow management system (Pegasus-WMS). The workflow allows users to identify single nucleotide polymorphisms (SNPs) and insertion-deletions (indels), perform SNP annotations and conduct copy number variation analyses on multiple resequencing datasets in a user-friendly and seamless way. Results: We have developed both a Linux version in GitHub (https:// github. com/ pegasus-isi/ PGen-GenomicVariationsWorkflow) and a web-based implementation of the PGen workflow integrated within the Soybean Knowledge Base (SoyKB), (http:// soykb. org/ Pegasus/ index. php). Using PGen, we identified 10,218,140 single-nucleotide polymorphisms (SNPs) and 1,398,982 indels from analysis of 106 soybean lines sequenced at 15X coverage. 297,245 non-synonymous SNPs and 3330 copy number variation (CNV) regions were identified from this analysis. SNPs identified using PGen from additional soybean resequencing projects adding to 500+ soybean germplasm lines in total have been integrated. These SNPs are being utilized for trait improvement using genotype to phenotype prediction approaches developed in-house. In order to browse and access NGS data easily, we have also developed an NGS resequencing data browser (http:// soykb. org/ NGS_ Resequence/ NGS_ index. php) within SoyKB to provide easy access to SNP and downstream analysis results for soybean researchers. Conclusion: PGen workflow has been optimized for the most efficient analysis of soybean data using thorough testing and validation. This research serves as an example of best practices for development of genomics data analysis workflows by integrating remote HPC resources and efficient data management with ease of use for biological users. PGen workflow can also be easily customized for analysis of data in other species.Missouri Soybean Merchandising Council [368]; United Soybean Board [1320-532-5615]This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

    Driving Big Data – Integration and Synchronization of Data Sources for Artificial Intelligence Applications with the Example of Truck Driver Work Stress and Strain Analysis

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    This paper contributes to the issue of big data analysis and data quality with the specific field of time synchronization. As a highly relevant use case, big data analysis of work stress and strain factors for driving professions is outlined. Drivers experience work stress and strain due to trends like traffic congestion, time pressure or worsening work conditions. Although a large professional group with 2.5 million (US) and 3.5 million (EU) truck drivers, scientific analysis of work stress and strain factors is scarce. Driver shortage is growing into a large-scale economic and societal challenge, especially for small businesses. Empirical investigations require big data approaches with sources like physiological and truck, traffic, weather, planning or accident data. For such challenges, accurate data is required, especially regarding time synchronization. Awareness among researchers and practitioners is key and first solution approaches are provided, connecting to many further Machine Learning and big data applications

    Patients Using an Online Forum for Reporting Progress When Engaging With a Six-Week Exercise Program for Knee Conditioning: Feasibility Study

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    Background: The use of electronic health (eHealth) and Web-based resources for patients with knee pain is expanding. Padlet is an online noticeboard that can facilitate patient interaction by posting virtual “sticky notes.” Objective: The primary aim of this study was to determine feasibility of patients in a 6-week knee exercise program using Padlet as an online forum for self-reporting on outcome progression. Methods: Undergraduate manual therapy students were recruited as part of a 6-week study into knee conditioning. Participants were encouraged to post maximum effort readings from quadriceps and gluteal home exercises captured from standard bathroom scales on a bespoke Padlet. Experience and progression reporting were encouraged. Posted data were analyzed for association between engagement, entry frequency, and participant characteristics. Individual data facilitated single-subject, multiple-baseline analysis using statistical process control. Experiential narrative was analyzed thematically. Results: Nineteen participants were recruited (47%, 9/19 female); ages ranged from 19 to 53 years. Twelve individuals (63%) opted to engage with the forum (range 4-40 entries), with five (42%) reporting across all 6 weeks. Gender did not influence reporting (odds ratio [OR] 0.76, 95% CI 0.06-6.93). No significant difference manifested between body mass index and engagement P=.46); age and entry frequency did not correlate (R2=.054, 95% CI –0.42 to 0.51, P=.83). Statistically significant conditioning profiles arose in single participants. Themes of pain, mitigation, and response were inducted from the experiences posted. Conclusions: Patients will engage with an online forum for reporting progress when undertaking exercise programs. In contrast to related literature, no significant association was found with reporting and gender, age, or body mass index. Individual posted data allowed multiple-baseline analysis and experiential induction from participants. Conditioning responses were evident on visual inspection. The importance of individualized visual data to patients and the role of forums in monitoring patients’ progress in symptomatic knee pain populations need further consideration

    Personalized functional health and fall risk prediction using electronic health records and in-home sensor data

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    Research has shown the importance of Electronic Health Records (EHR) and in-home sensor data for continuous health tracking and health risk predictions. With the increased computational capabilities and advances in machine learning techniques, we have new opportunities to use multi-modal health big data to develop accurate health tracking models. This dissertation describes the development, evaluation, and testing of systems for predicting functional health and fall risks in community-dwelling older adults using health data and machine learning techniques. In an initial study, we focused on organizing and de-identifying EHR data for analysis using HIPAA regulations. The dataset contained nine years of structured and unstructured EHR data obtained from TigerPlace, a senior living facility at Columbia, MO. The de-identification of this data was done using custom automated algorithms. The de-identified EHR data was used in several studies described in this dissertation. We then developed personalized functional health tracking models using geriatric assessments in the EHR data. Studies show that higher levels of functional health in older adults lead to a higher quality of life and improves the ability to age-in-place. Even though several geriatric assessments capture several aspects of functional health, there is limited research in longitudinally tracking the personalized functional health of older adults using a combination of these assessments. In this study, data from 150 older adult residents were used to develop a composite functional health prediction model using Activities of Daily Living (ADL), Instrumental Activities of Daily Living (IADL), Mini-Mental State Examination (MMSE), Geriatric Depression Scale (GDS), and Short Form 12 (SF12). Tracking functional health objectively could help clinicians to make decisions for interventions in case of functional health deterioration. We next constructed models for fall risk prediction in older adults using geriatric assessments, demographic data, and GAITRite assessment data. A 6-month fall risk prediction model was developed with data from 93 older adult residents. Explainable AI techniques were used to provide explanations to the model predictions, such as which specific features increased the risk of fall in a particular model prediction. Such explanations to model predictions provide valuable insights for targeted interventions. In another study, we developed deep neural network models to predict fall risk from de-identified nursing notes data from 162 older adult residents from TigerPlace. Clinical nursing notes have been shown to contain valuable information related to fall risk factors. This analysis provides the groundwork for future experiments to predict fall risk in older adults using clinical notes. In addition to using EHR data to predict functional health and fall risk in older adults, two studies were conducted to predict fall and functional health from in-home sensor data. Models for in-home fall prediction using depth sensor imagery have been successfully used at TigerPlace. However, the model is prone to false fall alarms in several scenarios, such as pillows thrown on the floor and pets jumping from couches. A secondary fall analysis was performed by analyzing fall alert videos to further identify and remove false alarms. In the final study, we used in-home sensor data streaming from depth sensors and bed sensors to predict functional health and absolute geriatric assessment values. These prediction models can be used to predict the functional health of residents in absence of sparse and infrequent geriatric assessments. This can also provide continuous tracking of functional health in older adults using the streaming in-home sensor data
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