cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.60773/e4v6-7k61
title: NIEHS Diagnostic-Prognostic RNAseq

description: Infectious disease outbreaks like Coronavirus Disease 2019 (COVID-19) can overwhelm healthcare systems when screening tools are lacking or scarce. In the face of an ongoing COVID-19 pandemic and with single-plex qPCR fluorometry inadequate for high throughput clinical diagnostics, the demand for testing exceeds the capacity, leading to limited availability, long queue times, backlogs in COVID-19 diagnoses, and delayed access to specialized treatment for COVID-19 patients. The goal of this RADx funded project was to develop an easily scalable and massively paralleled multiplexed screening method by next generation sequencing (NGS) with sample-specific barcoded indexes to allow pooling of up to 9200 samples. The approach enabled detection of SARS-COV-2 viral gRNA content (load) and expression profiles; detection of host's transcriptional response to infection simultaneously (expression profile). Transcriptional profiles were analyzed in the context of clinical data (electronic medical records of symptoms, treatments and outcomes) in order to identify and select features (biomarkers) that were predictive of clinical outcome using machine learning methods. These selected biomarkers were then validated in an independent clinical sample. Comparative testing of alternative sample collection (NP swab, saliva, oral swab) and handling protocols is ongoing with the goal of matching new protocols with existing SOPs for PCR-based testing in CLIA-certified facilities. In addition to increasing testing throughput, this precision medicine approach may have provided a very early look at who may be asymptomatic but infectious, or who is about to get very sick. Methods developed during this project may be adaptable to viruses or other pathogens in future pandemics. The initial aim of this project was to demonstrate proof of principle that the methodology can capture both virus and host RNA sequence using commercially available anonymous NP, OP and saliva samples.
DOI: 10.60773/w35s-2a90
title: Broad-Spectrum Detection of VOC and Non-VOC Biomarkers from Patient Exhalant Using a Biomimetic Multiplexed eNose Biosensor for COVID-19 Diagnosis

description: This project developed a biomimetic olfaction-and gustation-based sensors for detecting volatile organic compound (VOC) biomarkers against SARS-CoV-2. The project used computational design to deduce sets of odorant binding peptide (OBP) sequences that selectively bind to exhaled VOCs associated with SARS-CoV-2 from libraries of olfactory proteins. Chimeric peptides including these OBP sequence and a aromatic carbon-binding group were then synthesized, validated for vapor phase VOC binding, and then bound on to separate low-cost graphene and carbon nanotube sensor field effect transistors in multiplexed arrays developed in this project. The exhalant or simulated exhalant response data from these multiplexed OBP-functionalized sensor arrays were used to train an AI-driven diagnosis system to create a rapid, easily scalable test for SARS-CoV-2 based on direct exhaled breath.
DOI: 10.60773/xb7r-qw92
title: Longitudinal at Home Smell Testing to Detect Infection by SARS-CoV-2

description: Self-report of sudden loss of smell or taste substantially increases the odds of being infected with SARS-CoV-2. However, self-report of smell function is an unreliable predictor of smell loss. The study created a self-administered easy to use "at home" 5-minute objective smell test to uncover alterations in smell function unbeknownst to many individuals and confer increased risk of infection by SARS- CoV-2. The new smell test consists of a physical smell card containing peel and sniff odor labels and a web- based application. Each participant accessed the web-based app on their own smartphone, tablet, or computer. The study developed a native app to conduct longitudinal COVID Smell Test (Aim 1), collect data on asymptomatic health care workers, symptomatic patients, and undergraduates (Aim 2) and develop algorithms for the longitudinal smell test for personalized thresholds, differentiate smell loss from COVID relative to influenza (Aim 3). The Longitudinal COVID Smell Test was accessible, affordable, and readily scalable. Effective screening with the COVID smell test better informed students and employees if they should not report to school or work and seek an evaluation by a healthcare professional.
DOI: 10.60773/38sx-dw45
title: Evidence-based Interventions - Individual, Community, and Structural Factors That Predict Lower Rates of COVID-19 Screening Testing in Underserved and Vulnerable Populations

description: The purpose of this proposal was to identify individual, community (population) and structural factors associated with lower rates of COVID-19 testing in Northern New England (NNE), with a focus on underserved and vulnerable populations. This study included several COVID-19 medically and/or socially vulnerable populations: communities with high levels of social vulnerability; community-dwelling older adults; individuals with medical comorbidities known to increase risk of severe COVID-19 and, particularly, rural and remote communities. Analytically, the study qualitatively estimated individual, population and structural factors associated with higher or lower probability of having been tested for COVID-19 by combining comprehensive all-payer claims data across two states with state-level COVID-19 testing data and the CDC vulnerable community index. This study also assessed the geospatial distribution of disparities in COVID-19 testing in NNE using geographic information system methods to examine factors like testing center density and distance on testing rates. The study exploited differences in structure between Vermont and Maine to identify system level factors, including provider accessibility, testing availability and provider payment rules. The key outcomes were COVID-19 testing, hospitalizations and excess mortality among underserved and vulnerable populations in NNE. This study augmented the quantitative analysis with focus groups to identify additional barriers to testing. This study conducted multiple focus groups with individuals from vulnerable populations to identify barriers to COVID-19 testing. Once the individual, community (population) and structural factors that create barriers to COVID-19 testing and excess mortality were identified, potential interventions were tested in two different ways, First, the study developed and deployed a Discrete Choice Experiment (DCE) both in vulnerable communities in NNE and in a nationally representative sample of rural adults to test optimal strategies to increase testing using hypothetical scenarios. Second, the study tested the effect of targeted communication using a rural communication network using optimal communication strategies to facilitate increased testing and test if the communications change individual behavior and reduce health disparities. This study was conducted in partnership with the Department of Health in both Vermont and Maine and numerous community partners. This mixed methods project combined data from qualitative and quantitative analyses to identify barriers to COVID-19 testing with a focus on individuals and communities with high social vulnerability. Approaches to reduce testing disparities using experimental and interventional data were then tested.
DOI: 10.60773/yn52-cp83
title: Exosome-Based Non-Traditional Technologies Towards Multi-Parametric and Integrated Approaches for SARS-CoV-2

description: The urgent need to curb the spread of SARS-CoV-2 demands availability of diagnostics that are more rapid, accurate, sensitive and affordable than qPCR and antibody tests. Current qPCR tests are specific and sensitive, but lengthy turnaround times limit interventions against disease spread. Antibody testing is faster, but false- positive/negative rates are high. Here, this study proposed to repurpose extracellular vesicle (EV) separation and characterization technologies into a fully automated SARS-CoV-2 testing platform that is low-cost, accurate, sensitive, rapid (within 3 h), and practical. The device was optimized to analyze blood, saliva, and nasopharyngeal (NP) swabs collected at home, without risking transmission to healthcare workers. The sample is processed with an automated device developed with Sognef, and data are transferred to the Sognef servers for analysis through an app that can be downloaded to any smart device. This technology is similar to Abbott's recently launched BinaxNOW COVID-19 Ag Card, but has the advantage of multiparametric detection of viral RNA (vRNA), including Spike (S) and Nucleocapsid (N) protein-coding regions, plus a panel of host EV microRNAs (exomiRs) that reveals infection even when viral loads are below detectable limits. This approach decreased false-positives/negatives, the major limitation of antigen/antibody tests. Examine relationships of miRNA panels with characteristics such as: symptomatic vs asymptomatic, qPCR-determined viral load, biological sex, age (including pediatric populations), and comorbidities. The study optimized a COVID-19 device that uses simple bind-elute microfluidics for sample separation followed by electrical, probe-based detection of i) all validated exomiRs from Aim 1 and ii) three conserved vRNAs. It is envisioned that the device will be used first for either finger-pricked blood or saliva, followed, if positive, by an optional confirmatory second test of NP swab viral transport medium (VTM) that could be done with the same device. The device was tested in multiple centers worldwide in two phases: Phase 1 – every center will perform a double-blinded validation using their biorepository specimen, and Phase 2 – in a β-testing phase, the study provided a large number of devices to healthcare providers for regular testing of workers.
DOI: 10.60773/veb6-px50
title: Engaging Church Health Ministries to Decrease SARS-CoV-2 Vaccine Hesitancy in Underserved Populations in Baton Rouge

description: In the US, COVID-19 unveiled a disproportionate health burden in low income and underserved segments of society. In Louisiana, some of the greatest health and economic consequences are evident in Black communities. Furthermore, despite the widespread availability of SARS-CoV-2 vaccines, approximately 30% of the US population reports that they will not get vaccinated, and Black citizens and those with lower socio-economic status are more likely to have vaccine hesitancy. Thus, there is an urgent need to address vaccine hesitancy within the context of the COVID-19 pandemic and the current testing environment. The Louisiana Clinical and Translational Science (LA CaTS) Center provides the essential infrastructure and key foundational support for biomedical research in the region and is uniquely positioned to lead a community-engaged research project to determine solutions to decrease vaccine hesitancy and improve testing rates in the most underserved populations. Faith-based organizations (churches, mosques, temples, etc.) are trusted sources of information, especially among Black communities, and may represent an opportunity to convey accurate, unbiased health information regarding COVID-19 vaccinations and testing to the community. Many Black churches have well-developed health ministries that integrate faith and health for their members and the communities they serve. This study used a mixed-methods study design to determine the effectiveness of training church health ministers to educate their congregations about the safety and efficacy of COVID-19 vaccines for decreasing vaccine hesitancy and improving testing knowledge in underserved Black communities. The study randomized 98 participants from five churches to an intervention group that received counseling from their health ministers on the benefits of getting vaccinated and tested, or to a delayed intervention control group. The effects of the intervention on the primary outcome, vaccine hesitancy measured by a questionnaire, were administered to both groups after three weeks. Following the three-week control period, the delayed intervention control group also received the intervention and again administered the questionnaire. The study then conducted focus groups among a sub-sample of participants to obtain more granular information on sources of vaccine hesitancy and for their vaccine-related decisions. The achievement of the study's goals significantly increased the understanding of vaccine hesitancy within Black urban communities in Louisiana. The results informed the development of targeted interventions to increase vaccine coverage in the large, underserved populations across the American South.
DOI: 10.60773/ewt6-jf83
title: Conducting Correctional COVID Research and Implementing Novel, Ethically Sound, Sustainable Surveillance Systems (CRAINES)

description: Throughout the COVID-19 pandemic in the U.S., persons in jails have borne a share of disease 3-fold or greater than that seen in the general population. While many cases have been imported from surrounding communities, crowding in these congregate settings has led to rapid in-house transmission, especially since testing in jails has been sparse. Vaccine hesitancy among staff and those detained mean the population is ill prepared for new waves of infection, perhaps from virus variants. Better surveillance could warn systems earlier, and allow jails to stem the tide of a new outbreak. At least half, if not more, of infected persons shed coronavirus in their stool. Monitoring wastewater is a promising practice that only a few jails have adopted. The overarching goal was to introduce or refine Wastewater Based Surveillance (WBS) as an evidence-based strategy for SARS-CoV-2 surveillance in the jails of Atlanta, Chicago, suburban Boston and Washington DC. It was adapted to the needs of jail settings and evaluated the implementation with the Consolidated Framework for Implementation Research. Implementation teams were formed of both correctional staff and formerly incarcerated individuals. Project aims: (1) To assess the barriers to and facilitators of implementing WBS for SARS-CoV-2 detection in 4 jail demonstration sites. Guided by CFIR, an informational webinar was held followed by focus groups. Four were with leaders at each of the jails; these discussed the site-specific context in which WBS was introduced or refined. A fifth, cross-site focus group of jail workers, and a sixth, cross-site group of persons with lived jail experience, reflected on characteristics of WBS approaches and implementation strategies in jail settings. (2) To measure implementation outcomes associated with WBS and use these outcomes to inform key stakeholders, using a knowledge to action framework. The study examined uptake, acceptability, appropriateness and feasibility of WBS as a sensitive early warning system and a way of quantifying SARS-CoV-2 levels to monitor trends in COVID-19 prevalence. Feasibility, the suitability of how WBS data are acted upon, was of utmost importance. The study used the Knowledge to Action process model, leveraging implementation outcomes to further engage stakeholders and characterize the adaptions needed to successfully implement WBS in jails. (3, Pilot) To study the process and the perceived effectiveness of incorporating diverse stakeholders, including the formerly incarcerated, on the WBS implementation team. The study used the Research Engagement Survey Tool (REST), to survey early in the implementation process and eight months later, individuals on the implementation team who have lived experience in jail; all other consenting implementation team members were surveyed once early in the implementation process. Successfully completing the aims determined factors that promote WBS implementation to improve disease.
DOI: 10.60773/0va3-6933
title: Test Us At Home

description: Objective: To evaluate performance of Ag-RDT for detection of SARS-CoV-2 in relation to onset of infection for symptomatic and asymptomatic participants. Design, Setting, and Participants: Prospective cohort study conducted from October 2021 to February 2022 among participants > 2 years-old from across the US who enrolled using a smartphone app. During each testing encounter, participants self-collected one nasal swab and performed Ag-RDT at home; at-least fifteen minutes later, a second nasal swab was self-collected and shipped for SARS-CoV-2 RT-PCR at a central lab. Both nasal swabs were collected 7 times at 48-hour intervals (over approximately 14 days) followed by an extra nasal swab collection with home Ag-RDT test 48-hours after their last PCR sample. Each participant was assigned to one of the three emergency use authorized (EUA) Ag-RDT tests used in this study. This analysis was limited to participants who were asymptomatic and tested negative by antigen and molecular tests on their first day of study participation.
DOI: 10.60773/6hh3-jr12
title: Self-Testing for Our Protection from COVID-19 (STOP COVID-19) Study

description: The study sought to understand how and why people perform SARS-CoV-2 testing and report their results to the public health department. Participants participated in this study for three months and received home-delivery of rapid antigen and PCR-collection kits if they report to be at-risk for SARS-CoV-2 infection i.e. recently became symptomatic or were exposed to someone who tested positive. This study also collected wearable device data from participants to understand if signals from wearable devices can help detect onset of SARS-CoV-2 infection.
DOI: 10.60773/k8wj-0k62
title: Test Us At Home Daily

description: Symptomatic or close-contact participants were enrolled and asked to perform daily tests for 10 days. Each participant performed a rapid antigen test (Quidel or Abbott) followed by home-based sample collection and subsequent highly sensitive RT-qPCR assay (Roche, LOD = 1,800 NDU/mL) performed in a CLIA-certified lab.
DOI: 10.60773/18dv-6j23
title: You & Me: Test and Treat

description: This project evaluated a systematic and scalable community-engaged test and treat protocol that provided rapid access to COVID-19 at-home tests for self-administration, next steps/guidance and education, and information on local resources to facilitate treatment in underserved populations. The protocol was designed and implemented in two communities, Pitt County, NC, and Merced County, CA, in collaboration with key community partners over a 15-month period. As part of this test and treat protocol, a community engagement toolkit as a resource was evaluated to implement community-based test distribution and test and treat responses in underserved populations. The central hypothesis was that the toolkit will enable rapid design and implementation of a community driven, scientifically robust, and impactful COVID-19 test and public health intervention.
DOI: 10.60773/66qd-hj95
title: Supported Employment to Create a Community Culture of Rapid Testing Among People Who Inject Drugs: PeerConnect2Test

description: This Phase III project built on the successes of the Phase I and Phase II projects but used a novel approach to adapt to the changing pandemic context; facilitation of rapid testing by people who inject drugs (PWID) via a supported employment program that trains PWID as peer health workers (PHW). PWID are vulnerable to contracting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and to the effects of the disease caused by SARS-CoV-2, coronavirus disease 2019 (COVID-19) due to structural disadvantage, health vulnerabilities, and stigmatization that prevents adequate access to medical care. While the project has previously processed more than 6,000 self-collected polymerase chain reaction (PCR) tests for PWID across the state of Oregon, the ever-changing nature of the pandemic, including new variants and the availability of SARS-CoV-2 vaccines, called for additional strategies that can increase access to and uptake of testing among PWID. Rapid tests may offer an advantage over PCR tests for PWID experiencing structural vulnerabilities such as houselessness and lack of access to technology so that they can receive results in real-time and be quickly connected to needed resources. Accessibility of rapid testing for PWID has been previously limited by workforce shortages and the inability to reach PWID who need testing. This study proposed a novel community-engaged strategy to improve the accessibility of rapid tests through a supported employment program for PWID, Peer Connect2Test (PeerC2T), to become PHW to distribute SARS-CoV-2 rapid test kits to other PWID. It was expected that PeerC2T would improve knowledge, self-efficacy, and health behaviors among PHW (Aim 1). The RE-AIM framework was used in Aims 2 and 3 to evaluate whether PeerC2T improves SARS-CoV-2 testing uptake among other PWID (RE; Aim 2) and identify intervention considerations (AIM; Aim 3). The overall goal of this project was to build on the partnership with HIVA to develop a transformative community-driven intervention to promote widespread access to rapid testing among PWID. Collaboration will continue with the RADx-UP Coordination and Data Collection Center. Findings will clarify the implications of supported employment programs for PWID for SARS-CoV-2 testing uptake among PWID and other public health efforts to improve health outcomes among PWID. Thus, findings from this study may have broad public health implications for leveraging supported employment programs for PWID to prevent the transmission of other infectious diseases.
DOI: 10.60773/jrhz-2h83
title: RADx Tech COVID-19 Viral Dynamics/COVID Detect

description: The COVID Detect/COVID-19 viral dynamics study was planned and performed to assess SARS-CoV-2 viral dynamics in early infection, accuracy/persistence of SARS-CoV-2 antigen/PCR testing, clinical aspects of mild COVID-19, and potential SARS-CoV-2 transmission dynamics or risk factors. This study included a cohort of adult students and employees of University of Illinois Urbana-Champaign (UIUC) and Northwestern University who tested positive for SARS-CoV-2 as part of campus surveillance programs (isolation participants) or close contacts (particularly roommates) of individuals testing positive for SARS-CoV-2 (quarantine participants). Isolation participants were enrolled within 24 hours of positive testing and quarantine participants were enrolled within 5 days of last known exposure. All participants were required to have negative campus surveillance testing within 7 days of enrollment. Isolation participants completed daily surveys and collected observed nasal swabs and saliva (UIUC only) for 14 days. Quarantine participants completed daily surveys and collected samples for 7 days if SARS-CoV-2 RT-PCR remained negative; if converted positive by SARS-CoV-2 PCR, they collected daily samples for full 14 days. Each day of sample collection were analyzed as follows: nasal swab for SARS-CoV-2 POC Quidel antigen, nasal swab into VTM for SARS-CoV-2 Roche RT-PCR, saliva for SARS-CoV-2 PCR (UIUC only), and nasal swab into VTM for storage and subsequent whole genome virus sequencing and viral culture assay.