scholarly journals gene.iobio: an interactive web tool for versatile, clinically-driven variant interrogation and prioritization

2021 ◽  
Author(s):  
Tonya DiSera ◽  
Matt Velinder ◽  
Alistair Ward ◽  
Yi Qiao ◽  
Stephanie Georges ◽  
...  
Keyword(s):  
Web Application ◽  
Clinical Care ◽  
Single Gene ◽  
Genomic Data ◽  
Standard Of Care ◽  
Clinical Settings ◽  
Care Providers ◽  
Genomic Analyses ◽  
Clinical Diagnoses ◽  
Analysis Environment

Abstract With increasing utilization of comprehensive genomic data to guide clinical care, anticipated to become the standard of care in many clinical settings, the practice of diagnostic medicine is undergoing a notable shift. However, the move from single-gene or panel-based genetic testing to exome and genome sequencing has not been matched by the development of tools to enable diagnosticians to interpret increasingly complex or uncertain genomic findings. Here, we present gene.iobio, a real-time, intuitive and interactive web application for clinically-driven variant interrogation and prioritization. We show gene.iobio is a novel and effective approach that significantly improves upon and reimagines existing methods. In a radical departure from existing methods that present variants and genomic data in text and table formats, gene.iobio provides an interactive, intuitive and visually-driven analysis environment. We demonstrate that adoption of gene.iobio in clinical and research settings empowers clinical care providers to interact directly with patient genomic data both for establishing clinical diagnoses and informing patient care, using sophisticated genomic analyses that previously were only accessible via complex command line tools.

scholarly journals Gene.iobio: an interactive web tool for versatile, clinically-driven variant interrogation and prioritization

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tonya Di Sera ◽  
Matt Velinder ◽  
Alistair Ward ◽  
Yi Qiao ◽  
Stephanie Georges ◽  
...  
Keyword(s):  
Web Application ◽  
Clinical Care ◽  
Single Gene ◽  
Genomic Data ◽  
Standard Of Care ◽  
Clinical Settings ◽  
Care Providers ◽  
Genomic Analyses ◽  
Clinical Diagnoses ◽  
Analysis Environment

AbstractWith increasing utilization of comprehensive genomic data to guide clinical care, anticipated to become the standard of care in many clinical settings, the practice of diagnostic medicine is undergoing a notable shift. However, the move from single-gene or panel-based genetic testing to exome and genome sequencing has not been matched by the development of tools to enable diagnosticians to interpret increasingly complex or uncertain genomic findings. Here, we present gene.iobio, a real-time, intuitive and interactive web application for clinically-driven variant interrogation and prioritization. We show gene.iobio is a novel and effective approach that significantly improves upon and reimagines existing methods. In a radical departure from existing methods that present variants and genomic data in text and table formats, gene.iobio provides an interactive, intuitive and visually-driven analysis environment. We demonstrate that adoption of gene.iobio in clinical and research settings empowers clinical care providers to interact directly with patient genomic data both for establishing clinical diagnoses and informing patient care, using sophisticated genomic analyses that previously were only accessible via complex command line tools.

scholarly journals gene.iobio: an interactive web tool for versatile, clinically-driven variant interrogation and prioritization

2020 ◽  
Author(s):  
Tonya Di Sera ◽  
Matt Velinder ◽  
Alistair Ward ◽  
Yi Qiao ◽  
Stephanie Georges ◽  
...  
Keyword(s):  
Web Application ◽  
Clinical Care ◽  
Single Gene ◽  
Genetic Counselor ◽  
Genomic Data ◽  
Standard Of Care ◽  
Clinical Settings ◽  
Care Providers ◽  
New Paradigm ◽  
Clinical Diagnoses

AbstractWith increasing utilization of comprehensive genomic data to guide clinical care, anticipated to become the standard of care in many clinical settings, the practice of diagnostic medicine is undergoing a notable shift. However, the move from single-gene or panel-based genetic testing to exome and genome sequencing has not been matched by the development of tools to enable diagnosticians to interpret increasingly complex genomic findings. A new paradigm has emerged, where genome-based tests are often evaluated by a large multi-disciplinary collaborative team, typically including a diagnostic pathologist, a bioinformatician, a genetic counselor, and often a subspeciality clinician. This team-based approach calls for new computational tools to allow every member of the clinical care provider team, at varying levels of genetic knowledge and diagnostic expertise, to quickly and easily analyze and interpret complex genomic data. Here, we present gene.iobio, a real-time, intuitive and interactive web application for clinically-driven variant interrogation and prioritization. We show gene.iobio is a novel and effective approach that significantly improves upon and reimagines existing methods. In a radical departure from existing methods that present variants and genomic data in text and table formats, gene.iobio provides an interactive, intuitive and visually-driven analysis environment. We demonstrate that adoption of gene.iobio in clinical and research settings empowers clinical care providers to interact directly with patient genomic data both for establishing clinical diagnoses and informing patient care, using sophisticated genomic analyses that previously were only accessible via complex command line tools.

A Novel Computer-Based Virtual Counselor-Delivered Alcohol Reduction Intervention: Acceptability, Adaptability and Feasibility among Adults with HIV or TB in Indian Clinical Settings (Preprint)

2021 ◽  
Author(s):  
Nishi Suryavanshi ◽  
Gauri Dhumal ◽  
Samyra Cox ◽  
Shashikala Sangle ◽  
Andrea DeLuca ◽  
...  
Keyword(s):  
Alcohol Use ◽  
Health Care Providers ◽  
Clinical Care ◽  
Clinical Settings ◽  
Care Hospital ◽  
Care Providers ◽  
Unhealthy Alcohol Use ◽  
Unhealthy Alcohol ◽  
Computer Based ◽  
Alcohol Reduction

BACKGROUND Unhealthy alcohol use is associated with increased morbidity and mortality among persons with HIV and/or TB. Computer-Based interventions (CBI) can reduce unhealthy alcohol use, are scalable, and may improve outcomes among patients with HIV or TB. OBJECTIVE We assessed the acceptability, adaptability, and feasibility of a novel CBI for alcohol reduction in HIV and TB clinical settings in Pune, India. METHODS We conducted 10 in-depth interviews (IDIs) with persons with alcohol use disorder (AUD); [TB (n=6), HIV (n=2), HIV-TB co-infected (n=1) selected using convenience sampling method, No HIV or TB disease (n=1)], one focus group (FG) with members of alcoholics anonymous (AA) (n=12, and two FGs with health care providers (HCPs) of a tertiary care hospital (n=22). All participants reviewed and provided feedback on a CBI for AUD delivered by a 3-D virtual counselor. Qualitative data were analyzed using structured framework analysis. RESULTS Majority (n=9) of IDI respondents were male with median age 42 (IQR; 38-45) years. AA FG participants were all male (n=12) and HCPs FG participants were predominantly female (n=15). Feedback was organized into 3 domains: 1) Virtual counselor acceptability; 2) Intervention adaptability; and 3) feasibility of CBI intervention in clinic settings. Overall IDI participants found the virtual counselor to be acceptable and felt comfortable honestly answering alcohol-related questions. All FG participants preferred a human virtual counselor to an animal virtual counselor so as to potentially increase CBI engagement. Additionally, interaction with a live human counselor would further enhance the program’s effectiveness by providing more flexible interaction. HCP FGs noted the importance of adding information on the effects of alcohol on HIV and TB outcomes because patients were not viewed as appreciating these linkages. For local adaptation, more information on types of alcoholic drinks, additional drinking triggers, motivators and activities to substitute for drinking alcohol were suggested by all FG participants. Intervention duration (~20 minutes) and pace were deemed appropriate. HCPs reported that CBI provides systematic, standardized counseling. All FG and IDI reported that CBI could be implemented in Indian clinical settings with assistance from HIV or TB program staff. CONCLUSIONS With cultural tailoring to patients with HIV and TB in Indian clinical care settings, a virtual counselor-delivered alcohol intervention is acceptable, appears feasible to implement, particularly if coupled with person-delivered counseling.

scholarly journals Experiences of Health Care Providers Using a Mobile Medical Photography Application

2020 ◽  
Vol 11 (01) ◽  
pp. 122-129 ◽  
Author(s):  
Kirk D. Wyatt ◽  
Brian N. Willaert ◽  
Christine M. Lohse ◽  
Peter J. Pallagi ◽  
James A. Yiannias ◽  
...  
Keyword(s):  
Health Care ◽  
Clinical Practice ◽  
Health Care Providers ◽  
Point Of Care ◽  
Clinical Care ◽  
Mail Survey ◽  
Standard Of Care ◽  
Clinical Documentation ◽  
Care Providers ◽  
Medical Photography

Abstract Objective To understand the ways in which providers use a mobile photography application integrated with the electronic health record (EHR) to facilitate clinical care, and the process outcomes that result from the application's use. Methods An e-mail survey was sent on November 13, 2017, to 1,463 health care providers at Mayo Clinic who had used an internally developed, EHR-integrated medical photography application. Results The survey was completed by 712 (49%) providers. Providers reported using the application on approximately 1 in 7 days spent in clinical practice. Median provider satisfaction with the use of the application (0–100 scale; higher numbers indicate favorable response) was 94 (interquartile range [IQR]: 74–100). Although the use for store-and-forward telemedicine was reported (22% often or frequently used the application to send photographs to a specialist for advice), the most common use was for clinical documentation (65% often or frequently used the application to supplement text-based notes with photographs, and 71% often or frequently used the application to take photographs for reference by a colleague who may see the patient in the future). Of the health care providers, 36% indicated that the application's use often or frequently expedited treatment. Discussion Health care providers reported using a mobile point-of-care medical photography application regularly in clinical practice and were generally satisfied with the application. Conclusion Point-of-care medical photography using a secure mobile, EHR-integrated application has potential to become a new standard of care for clinical documentation and may facilitate continuity across the continuum of care with multiple providers who see a patient.

scholarly journals From Genetics to Genomics: Facing the Liability Implications in Clinical Care

2020 ◽  
Vol 48 (1) ◽  
pp. 11-43 ◽  
Author(s):  
Gary Marchant ◽  
Mark Barnes ◽  
James P. Evans ◽  
Bonnie LeRoy ◽  
Susan M. Wolf ◽  
...  
Keyword(s):  
Health Care ◽  
Health Care Providers ◽  
Clinical Care ◽  
Single Gene ◽  
Disease Diagnosis ◽  
Care Providers ◽  
Health Care Transition ◽  
Gene Testing ◽  
Gene Panels ◽  
Liability Risks

Health care is transitioning from genetics to genomics, in which single-gene testing for diagnosis is being replaced by multi-gene panels, genome-wide sequencing, and other multi-genic tests for disease diagnosis, prediction, prognosis, and treatment. This health care transition is spurring a new set of increased or novel liability risks for health care providers and test laboratories. This article describes this transition in both medical care and liability, and addresses 11 areas of potential increased or novel liability risk, offering recommendations to both health care and legal actors to address and manage those liability risks.

Communication and psychological safety in veterans health administration work environments

2014 ◽  
Vol 28 (6) ◽  
pp. 754-776 ◽  
Author(s):  
Nancy J. Yanchus ◽  
Ryan Derickson ◽  
Scott C. Moore ◽  
Daniele Bologna ◽  
Katerine Osatuke
Keyword(s):  
Health Care Providers ◽  
Care Delivery ◽  
Clinical Care ◽  
Psychological Safety ◽  
Veterans Health Administration ◽  
Employee Perceptions ◽  
Veterans Health ◽  
Health Administration ◽  
Care Providers ◽  
Content Type

Purpose – The purpose of this paper is to explore employee perceptions of communication in psychologically safe and unsafe clinical care environments. Design/methodology/approach – Clinical providers at the USA Veterans Health Administration were interviewed as part of planning organizational interventions. They discussed strengths, weaknesses, and desired changes in their workplaces. A subset of respondents also discussed workplace psychological safety (i.e. employee perceptions of being able to speak up or report errors without retaliation or ostracism – Edmondson, 1999). Two trained coders analysed the interview data using a grounded theory-based method. They excerpted passages that discussed job-related communication and summarized specific themes. Subsequent analyses compared frequencies of themes across workgroups defined as having psychologically safe vs unsafe climate based upon an independently administered employee survey. Findings – Perceptions of work-related communication differed across clinical provider groups with high vs low psychological safety. The differences in frequencies of communication-related themes across the compared groups matched the expected pattern of problem-laden communication characterizing psychologically unsafe workplaces. Originality/value – Previous research implied the existence of a connection between communication and psychological safety whereas this study offers substantive evidence of it. The paper summarized the differences in perceptions of communication in high vs low psychological safety environments drawing from qualitative data that reflected clinical providers’ direct experience on the job. The paper also illustrated the conclusions with multiple specific examples. The findings are informative to health care providers seeking to improve communication within care delivery teams.

scholarly journals Onset of Multiple Chronic Conditions and Depressive Symptoms: A Life Events Perspective

2017 ◽  
Vol 1 (2) ◽  
Author(s):  
Maureen Wilson-Genderson ◽  
Allison R Heid ◽  
Rachel Pruchno
Keyword(s):  
Heart Disease ◽  
Depressive Symptoms ◽  
Pulmonary Disease ◽  
Chronic Conditions ◽  
Clinical Care ◽  
Psychological Impact ◽  
Multiple Chronic Conditions ◽  
Care Providers ◽  
The Subject ◽  
Independent Effects

Abstract Background While the association between depressive symptoms and chronic illness has been the subject of many studies, little is known about whether depressive symptoms differ as a function of the illnesses people have as they transition to living with multiple chronic conditions. Methods Self-reports of five diagnosed chronic conditions (arthritis, diabetes, heart disease, hypertension, and pulmonary disease) and depressive symptoms were provided by 3,396 people participating in three waves of the ORANJ BOWLSM research panel. Longitudinal multilevel modeling was used to examine the effects that transitioning to having a diagnosis of multiple chronic conditions has on depressive symptoms. Results Between 2006 and 2014, controlling for age, gender, income, race, and a lifetime diagnosis of depression, people who transitioned to having a diagnosis of multiple chronic conditions had significantly higher levels of depressive symptoms than people who did not make this transition. The diagnosis of arthritis, diabetes, heart disease, and pulmonary disease, but not hypertension had independent effects, increasing depressive symptoms. Conclusions Having a diagnosis of multiple chronic conditions leads to increases in depressive symptoms, but not all illnesses have the same effect. Findings highlight the need for clinicians to be aware of mental health risks in patients diagnosed with multiple chronic conditions, particularly those with a diagnosis of arthritis, diabetes, heart disease, and pulmonary disease. Clinical care providers should take account of these findings, encouraging psychosocial supports for older adults who develop multiple chronic conditions to minimize the negative psychological impact of illness diagnosis.

scholarly journals Nurses' performance on hospital discharge: patients' point of view

2007 ◽  
Vol 20 (3) ◽  
pp. 345-350 ◽  
Author(s):  
Daniele Alcalá Pompeo ◽  
Maria Helena Pinto ◽  
Claudia Bernardi Cesarino ◽  
Renilda Rosa Dias Ferreira de Araújo ◽  
Nadia Antonia Aparecida Poletti
Keyword(s):  
Health Care ◽  
Hospital Discharge ◽  
Health Care Providers ◽  
Clinical Care ◽  
Educational Process ◽  
Discharge Process ◽  
Care Providers ◽  
Discharge Instructions ◽  
Effective Discharge ◽  
Number Of Patients

OBJECTIVE: To know the hospital discharge process in place and the nurses' performance in preparing patients for discharge. METHODS: A descriptive study using semi-structured interviews was used to collect data from 43 patients of medical-surgical units of a major teaching hospital in the state of São Paulo, Brazil. RESULTS: The majority of patients (83.72%) received tailored discharge instructions. However, a great number of patients (72.08%) reported discharge instructions were not given by nurses. Almost a half of patients (48.84%) reported that discharge instructions were given by their physicians. CONCLUSION: The findings of this study provide insights to improve the educational process of new nurses and their preparation to provide effective discharge instructions. There is also a need to design and implement a hospital discharge process that promotes the participation of interdisciplinary health care providers who are involved in patient clinical care. This discharge process might be an effective way to change health care providers' attitude toward discharge instructions.

scholarly journals XML Data and Knowledge-Encoding Structure for a Web-Based and Mobile Antenatal Clinical Decision Support System: Development Study

10.2196/17512 ◽  
2020 ◽  
Vol 4 (10) ◽  
pp. e17512
Author(s):  
Ever Augusto Torres Silva ◽  
Sebastian Uribe ◽  
Jack Smith ◽  
Ivan Felipe Luna Gomez ◽  
Jose Fernando Florez-Arango
Keyword(s):  
Decision Support ◽  
Antenatal Care ◽  
Clinical Decision Support ◽  
Web Application ◽  
Clinical Care ◽  
Clinical Decision Support Systems ◽  
Clinical Decision ◽  
Structure Design ◽  
Mobile App ◽  
Clinical Workflow

Background Displeasure with the functionality of clinical decision support systems (CDSSs) is considered the primary challenge in CDSS development. A major difficulty in CDSS design is matching the functionality to the desired and actual clinical workflow. Computer-interpretable guidelines (CIGs) are used to formalize medical knowledge in clinical practice guidelines (CPGs) in a computable language. However, existing CIG frameworks require a specific interpreter for each CIG language, hindering the ease of implementation and interoperability. Objective This paper aims to describe a different approach to the representation of clinical knowledge and data. We intended to change the clinician’s perception of a CDSS with sufficient expressivity of the representation while maintaining a small communication and software footprint for both a web application and a mobile app. This approach was originally intended to create a readable and minimal syntax for a web CDSS and future mobile app for antenatal care guidelines with improved human-computer interaction and enhanced usability by aligning the system behavior with clinical workflow. Methods We designed and implemented an architecture design for our CDSS, which uses the model-view-controller (MVC) architecture and a knowledge engine in the MVC architecture based on XML. The knowledge engine design also integrated the requirement of matching clinical care workflow that was desired in the CDSS. For this component of the design task, we used a work ontology analysis of the CPGs for antenatal care in our particular target clinical settings. Results In comparison to other common CIGs used for CDSSs, our XML approach can be used to take advantage of the flexible format of XML to facilitate the electronic sharing of structured data. More importantly, we can take advantage of its flexibility to standardize CIG structure design in a low-level specification language that is ubiquitous, universal, computationally efficient, integrable with web technologies, and human readable. Conclusions Our knowledge representation framework incorporates fundamental elements of other CIGs used in CDSSs in medicine and proved adequate to encode a number of antenatal health care CPGs and their associated clinical workflows. The framework appears general enough to be used with other CPGs in medicine. XML proved to be a language expressive enough to describe planning problems in a computable form and restrictive and expressive enough to implement in a clinical system. It can also be effective for mobile apps, where intermittent communication requires a small footprint and an autonomous app. This approach can be used to incorporate overlapping capabilities of more specialized CIGs in medicine.

scholarly journals Availability of Safe Second-Trimester Abortion Services in Health Facilities in Accra, Ghana

2021 ◽  
Author(s):  
Fred Yao Gbagbo ◽  
Renee Aku Sitsofe Morhe ◽  
Emmanuel Komla Senanu Morhe
Keyword(s):  
Service Providers ◽  
Social Stigma ◽  
Clinical Care ◽  
Internal Validity ◽  
Health Facilities ◽  
Accurate Information ◽  
Second Trimester ◽  
Care Providers ◽  
Trimester Abortion ◽  
Second Trimester Abortion

Abstract Background Despite a liberal abortion law, access to safe second trimester abortion services in Ghana are challenging for many women. This study sought to examine providers, methods employed, cost, and other determinants of availability of second-trimester abortion services in health facilities in Accra, Ghana in 2019 to inform policy and program decisions. Methods A two-stage mixed quantitative and qualitative study designs were employed in the conduct of this study. The first stage was a short interaction of the mystery client with a clinical care provider to identify health facilities that provide second trimester induced abortion, the cost, and referral practices, where the facility did not have the service. The second stage was in-depth interviews of second-trimester abortion care providers and non-providers in various health facilities. For internal validity, it also explored the procedure cost, referral, and other practices at the health facilities included in the study, independent of what was captured in the mystery client survey. Results Second-trimester abortion services in Accra, Ghana are widely unavailable even in most facilities that provided abortion services. Referral policies and practices indicated by the service providers at various facility levels were inadequate. Criminalization of the procedure, social stigma, and fear of complications are the main factors that adversely influence the availability of second-trimester abortion in health facilities in Accra. Conclusions Albeit increasing demand for second-trimester abortion in health facilities in Accra, services are not readily available due to the ambiguity of the law, its interpretation, and limited flow of accurate information on providers. Policies and programs that limit access to Second-trimester abortions in Ghana are amendable to ensure safe services.

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