Evaluation of an Intrahospital Telemedicine Program for Patients Admitted With COVID-19: Mixed Methods Study

BACKGROUND

The increasing incidence of COVID-19 infection has challenged health care systems to increase capacity while conserving personal protective equipment (PPE) supplies and minimizing nosocomial spread. Telemedicine shows promise to address these challenges but lacks comprehensive evaluation in the inpatient environment.

OBJECTIVE

The aim of this study is to evaluate an intrahospital telemedicine program (virtual care), along with its impact on exposure risk and communication.

METHODS

We conducted a natural experiment of virtual care on patients admitted for COVID-19. The primary exposure variable was documented use of virtual care. Patient characteristics, PPE use rates, and their association with virtual care use were assessed. In parallel, we conducted surveys with patients and clinicians to capture satisfaction with virtual care along the domains of communication, medical treatment, and exposure risk.

RESULTS

Of 137 total patients in our primary analysis, 43 patients used virtual care. In total, there were 82 inpatient days of use and 401 inpatient days without use. Hospital utilization and illness severity were similar in patients who opted in versus opted out. Virtual care was associated with a significant reduction in PPE use and physical exam rate. Surveys of 41 patients and clinicians showed high rates of recommendation for further use, and subjective improvements in communication. However, providers and patients expressed limitations in usability, medical assessment, and empathetic communication.

CONCLUSIONS

In this pilot natural experiment, only a subset of patients used inpatient virtual care. When used, virtual care was associated with reductions in PPE use, reductions in exposure risk, and patient and provider satisfaction.

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research

Gramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide. The resource is committed to open access and reproducible science based on the FAIR data principles. Since the last NAR update, we made nine releases; doubled the genome portal's content; expanded curated genes, pathways and expression sets; and implemented the Domain Informational Vocabulary Extraction (DIVE) algorithm for extracting gene function information from publications. The current release, #63 (October 2020), hosts 93 reference genomes-over 3.9 million genes in 122 947 families with orthologous and paralogous classifications. Plant Reactome portrays pathway networks using a combination of manual biocuration in rice (320 reference pathways) and orthology-based projections to 106 species. The Reactome platform facilitates comparison between reference and projected pathways, gene expression analyses and overlays of gene-gene interactions. Gramene integrates ontology-based protein structure-function annotation; information on genetic, epigenetic, expression, and phenotypic diversity; and gene functional annotations extracted from plant-focused journals using DIVE. We train plant researchers in biocuration of genes and pathways; host curated maize gene structures as tracks in the maize genome browser; and integrate curated rice genes and pathways in the Plant Reactome.

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research

Gramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide. The resource is committed to open access and reproducible science based on the FAIR data principles. Since the last NAR update, we made nine releases; doubled the genome portal's content; expanded curated genes, pathways and expression sets; and implemented the Domain Informational Vocabulary Extraction (DIVE) algorithm for extracting gene function information from publications. The current release, #63 (October 2020), hosts 93 reference genomes-over 3.9 million genes in 122 947 families with orthologous and paralogous classifications. Plant Reactome portrays pathway networks using a combination of manual biocuration in rice (320 reference pathways) and orthology-based projections to 106 species. The Reactome platform facilitates comparison between reference and projected pathways, gene expression analyses and overlays of gene-gene interactions. Gramene integrates ontology-based protein structure-function annotation; information on genetic, epigenetic, expression, and phenotypic diversity; and gene functional annotations extracted from plant-focused journals using DIVE. We train plant researchers in biocuration of genes and pathways; host curated maize gene structures as tracks in the maize genome browser; and integrate curated rice genes and pathways in the Plant Reactome.

Health system utilization before age 1 among children later diagnosed with autism or ADHD

Children with autism spectrum disorder (ASD) or attention deficit hyperactivity disorder (ADHD) have 2-3 times increased healthcare utilization and annual costs once diagnosed, but little is known about their utilization patterns early in life. Quantifying their early health system utilization could uncover condition-specific health trajectories to facilitate earlier detection and intervention. Patients born 10/1/2006-10/1/2016 with ≥ 2 well-child visits within the Duke University Health System before age 1 were grouped as ASD, ADHD, ASD + ADHD, or No Diagnosis using retrospective billing codes. An additional comparison group was defined by later upper respiratory infection diagnosis. Adjusted odds ratios (AOR) for hospital admissions, procedures, emergency department (ED) visits, and outpatient clinic encounters before age 1 were compared between groups via logistic regression models. Length of hospital encounters were compared between groups via Mann-Whitney U test. In total, 29,929 patients met study criteria (ASD N = 343; ADHD N = 1175; ASD + ADHD N = 140). ASD was associated with increased procedures (AOR = 1.5, p < 0.001), including intubation and ventilation (AOR = 2.4, p < 0.001); and outpatient specialty care, including physical therapy (AOR = 3.5, p < 0.001) and ophthalmology (AOR = 3.1, p < 0.001). ADHD was associated with increased procedures (AOR = 1.41, p < 0.001), including blood transfusion (AOR = 4.7, p < 0.001); hospital admission (AOR = 1.60, p < 0.001); and ED visits (AOR = 1.58, p < 0.001). Median length of stay was increased after birth in ASD (+ 6.5 h, p < 0.001) and ADHD (+ 3.8 h, p < 0.001), and after non-birth admission in ADHD (+ 1.1 d, p < 0.001) and ASD + ADHD (+ 2.4 d, p = 0.003). Each condition was associated with increased health system utilization and distinctive patterns of utilization before age 1. Recognizing these patterns may contribute to earlier detection and intervention.

Visualization of proximal coronary arteries on high-pitch electrocardiogram-triggered computed tomography in pediatric congenital heart disease: effects of heart rate and body surface area

BACKGROUND

As CT technology has advanced, techniques for pediatric cardiac CT in congenital heart disease have evolved from retrospective electrocardiography (ECG)-gating with relatively high radiation doses to lower-dose prospective ECG-gating and even single-beat gated scans. Despite these advances, coronary artery imaging in children remains challenging because of their small vessel size and high heart rates, often necessitating retrospective gating.

OBJECTIVE

Evaluate coronary artery visualization in pediatric patients (<20 years) who underwent low-dose high-pitch ECG-triggered scans and stratify the probability of coronary artery visualization based upon heart rate and body surface area (BSA).

MATERIALS AND METHODS

Two hundred eleven high-pitch ECG-triggered studies from April 2014 to November 2017 were reviewed by two pediatric cardiac imagers in this retrospective study. Patient age, gender, BSA, average heart rate, heart rate variability and use of general anesthesia were recorded as well as dose-length product (DLP) and volumetric CT dose index (CTDI_vol). We assessed the coronary artery score using a 5-point scale, with score of ≥3 considered of diagnostic quality. We performed multivariate statistical analysis including logistic regression to analyze effects of heart rate and BSA.

RESULTS

Patient age range was 1 day to 19 years (median age 3 years). Heart rate range was 49-188 beats per minute (bpm; median 122 bpm) and BSA range was 0.15-2.07 m² (median 0.53 m²). The origin and proximal coronary arteries were confidently seen (score ≥3) in 61% of studies in this cohort. Coronary artery visualization scores further increased with increased BSA (P<0.002) and with decreased heart rate (P<0.001). At heart rates <100 bpm or in patients with BSA>0.58, adequate coronary artery visualization was present 72% of the time.

CONCLUSION

While in many patients the coronary artery origins are visualized using high-pitch ECG-triggered technique, the importance of coronary artery visualization needs to be weighed with the radiation dose penalty in individual patients to achieve optimal imaging.

Ensembl Genomes 2020-enabling non-vertebrate genomic research

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life.

Plant Reactome: a knowledgebase and resource for comparative pathway analysis

Plant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project. It uses Oryza sativa (rice) as a reference species for manual curation of pathways and extends pathway knowledge to another 82 plant species via gene-orthology projection using the Reactome data model and framework. It currently hosts 298 reference pathways, including metabolic and transport pathways, transcriptional networks, hormone signaling pathways, and plant developmental processes. In addition to browsing plant pathways, users can upload and analyze their omics data, such as the gene-expression data, and overlay curated or experimental gene-gene interaction data to extend pathway knowledge. The curation team actively engages researchers and students on gene and pathway curation by offering workshops and online tutorials. The Plant Reactome supports, implements and collaborates with the wider community to make data and tools related to genes, genomes, and pathways Findable, Accessible, Interoperable and Re-usable (FAIR).

Competencies for improving diagnosis: an interprofessional framework for education and training in health care

Background Given an unacceptably high incidence of diagnostic errors, we sought to identify the key competencies that should be considered for inclusion in health professions education programs to improve the quality and safety of diagnosis in clinical practice. Methods An interprofessional group reviewed existing competency expectations for multiple health professions, and conducted a search that explored quality, safety, and competency in diagnosis. An iterative series of group discussions and concept prioritization was used to derive a final set of competencies. Results Twelve competencies were identified: Six of these are individual competencies: The first four (#1-#4) focus on acquiring the key information needed for diagnosis and formulating an appropriate, prioritized differential diagnosis; individual competency #5 is taking advantage of second opinions, decision support, and checklists; and #6 is using reflection and critical thinking to improve diagnostic performance. Three competencies focus on teamwork: Involving the patient and family (#1) and all relevant health professionals (#2) in the diagnostic process; and (#3) ensuring safe transitions of care and handoffs, and "closing the loop" on test result communication. The final three competencies emphasize system-related aspects of care: (#1) Understanding how human-factor elements influence the diagnostic process; (#2) developing a supportive culture; and (#3) reporting and disclosing diagnostic errors that are recognized, and learning from both successful diagnosis and from diagnostic errors. Conclusions These newly defined competencies are relevant to all health professions education programs and should be incorporated into educational programs.

Variant phasing and haplotypic expression from long-read sequencing in maize

Haplotype phasing maize genetic variants is important for genome interpretation, population genetic analysis and functional analysis of allelic activity. We performed an isoform-level phasing study using two maize inbred lines and their reciprocal crosses, based on single-molecule, full-length cDNA sequencing. To phase and analyze transcripts between hybrids and parents, we developed IsoPhase. Using this tool, we validated the majority of SNPs called against matching short-read data from embryo, endosperm and root tissues, and identified allele-specific, gene-level and isoform-level differential expression between the inbred parental lines and hybrid offspring. After phasing 6907 genes in the reciprocal hybrids, we annotated the SNPs and identified large-effect genes. In addition, we identified parent-of-origin isoforms, distinct novel isoforms in maize parent and hybrid lines, and imprinted genes from different tissues. Finally, we characterized variation in cis- and trans-regulatory effects. Our study provides measures of haplotypic expression that could increase accuracy in studies of allelic expression.

Impact on 30-d readmissions for cirrhotic patients with ascites after an educational intervention: A pilot study

BACKGROUND

A low proportion of patients admitted to hospital with cirrhosis receive quality care with timely paracentesis an important target for improvement. We hypothesized that a medical educational intervention, delivered to medical residents caring for patients with cirrhosis, would improve quality of care.

AIM

To determine if an educational intervention can improve quality of care in cirrhotic patients admitted to hospital with ascites.

METHODS

We performed a pilot prospective cohort study with time-based randomization over six months at a large teaching hospital. Residents rotating on hospital medicine teams received an educational intervention while residents rotating on hospital medicine teams on alternate months comprised the control group. The primary outcome was provision of quality care- defined as adherence to all quality-based indicators derived from evidence-based practice guidelines- in admissions for patients with cirrhosis and ascites. Patient clinical outcomes- including length of hospital stay (LOS); 30-d readmission; in-hospital mortality and overall mortality- and resident educational outcomes were also evaluated.

RESULTS

Eighty-five admissions (60 unique patients) met inclusion criteria over the study period-46 admissions in the intervention group and 39 admissions in the control group. Thirty-seven admissions were female patients, and 44 admissions were for alcoholic liver disease. Mean model for end-stage liver disease (MELD)-Na score at admission was 25.8. Forty-seven (55.3%) admissions received quality care. There was no difference in the provision of quality care (56.41% vs 54.35%, P = 0.9) between the two groups. 30-d readmission was lower in the intervention group (35% vs 52.78%, P = 0.1) and after correction for age, gender and MELD-Na score [RR = 0.62 (0.39, 1.00), P = 0.05]. No significant differences were seen for LOS, complications, in-hospital mortality or overall mortality between the two groups. Resident medical knowledge and self-efficacy with paracentesis improved after the educational intervention.

CONCLUSION

Medical education has the potential to improve clinical outcomes in patients admitted to hospital with cirrhosis and ascites.

Paying for Palliative Care in Medicare: Evidence From the Four Seasons/Duke CMMI Demonstration

CONTEXT

Palliative care improves patient and family outcomes and may reduce the cost of care, but this service is underutilized among Medicare beneficiaries.

OBJECTIVES

To describe enrollment patterns and outcomes associated with the Center for Medicare and Medicaid Innovation expansion of a multisetting community palliative care program in North and South Carolina.

METHODS

This observational study characterizes the Center for Medicare and Medicaid Innovation cohort's care and cost trajectories after enrollment. Program participants were age-eligible Medicare fee-for-service beneficiaries living in Western North Carolina and South Carolina who enrolled in a palliative care program from September 1, 2014, to August 31, 2017. End-of-life costs were compared between enrolled and nonenrolled decedents. Program administrative data and 100% Medicare claims data were used.

RESULTS

A total of 5243 Medicare beneficiaries enrolled in the program from community (19%), facility (21%), small hospital (27%), or large hospital (33%) settings. Changes in Medicare expenditures in the 30 days after enrollment varied by setting. Adjusted odds of hospice use were 60% higher (OR = 1.60; CI = 1.47, 1.75) for enrolled decedents relative to nonenrolled decedents. Participants discharged to hospice vs. participants not had 17% (OR = 0.83 CI = 0.72, 0.94) lower costs. Among enrolled decedents those enrolled for at least 30 days vs. <30 days had 42% (OR = 0.58, CI = 0.49, 0.69) lower costs in the last 30 days of life.

CONCLUSIONS

Expansion of community palliative care programs into multiple enrollment settings is feasible. It may improve hospice utilization among enrollees. Heterogeneous program participation by program setting pose challenges to a standardizing reimbursement policy.

Use of Hospital Referral Regions in Evaluating End-of-Life Care

Background: Hospital referral regions (HRRs) are often used to characterize inpatient referral patterns, but it is unknown how well these geographic regions are aligned with variation in Medicare-financed hospice care, which is largely provided at home. Objective: Our objective was to characterize the variability in hospice use rates among elderly Medicare decedents by HRR and county. Methods: Using 2014 Master Beneficiary File for decedents 65 and older from North and South Carolina, we applied Bayesian mixed models to quantify variation in hospice use rates explained by HRR fixed effects, county random effects, and residual error among Medicare decedents. Results: We found HRRs and county indicators are significant predictors of hospice use in NC and SC; however, the relative variation within HRRs and associated residual variation is substantial. On average, HRR fixed effects explained more variation in hospice use rates than county indicators with a standard deviation (SD) of 10.0 versus 5.1 percentage points. The SD of the residual error is 5.7 percentage points. On average, variation within HRRs is about half the variation between regions (52%). Conclusions: The magnitude of unexplained residual variation in hospice use for NC and SC suggests that novel, end-of-life-specific service areas should be developed and tested to better capture geographic differences and inform research, health systems, and policy.

Gramene 2018: unifying comparative genomics and pathway resources for plant research

Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous and paralogous gene classification, whole-genome alignments, and synteny. Additional gene annotations include ontology-based protein structure and function; genetic, epigenetic, and phenotypic diversity; and pathway associations. Gramene's Plant Reactome provides a knowledgebase of cellular-level plant pathway networks. Specifically, it uses curated rice reference pathways to derive pathway projections for an additional 66 species based on gene orthology, and facilitates display of gene expression, gene-gene interactions, and user-defined omics data in the context of these pathways. As a community portal, Gramene integrates best-of-class software and infrastructure components including the Ensembl genome browser, Reactome pathway browser, and Expression Atlas widgets, and undergoes periodic data and software upgrades. Via powerful, intuitive search interfaces, users can easily query across various portals and interactively analyze search results by clicking on diverse features such as genomic context, highly augmented gene trees, gene expression anatomograms, associated pathways, and external informatics resources. All data in Gramene are accessible through both visual and programmatic interfaces.

Pharmacy Education Needs to Address Diagnostic Safety

The American Association of Colleges of Pharmacy, the Accreditation Council for Pharmacy Education, and the Center for the Advancement of Pharmacy Education frame patient safety from the perspective of medication management, which is also the current focus of pharmacy education and training. With the growing appreciation that diagnostic errors represent an urgent and actionable patient safety concern, the National Academy of Medicine has recommended diagnostic safety training for all health care professions. The Society to Improve Diagnosis in Medicine has worked with an interprofessional consensus group to identify a set of 12 key competencies necessary to achieve diagnostic quality and safety that focuses on individual, team-based, and system-related competencies. Much of this already exists in pharmacy education, but pharmacy training programs need to give graduates more guidance on how they contribute to the diagnostic process and the prevention and detection of diagnostic errors. We describe the current state of progress in this regard, and what steps are needed by training programs to provide content and assessment so that graduates achieve the requisite competencies. Governing and advisory bodies need to expand the expectations around patient safety to include diagnostic safety.

Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing

Advances in transcriptomics have provided an exceptional opportunity to study functional implications of the genetic variability. Technologies such as RNA-Seq have emerged as state-of-the-art techniques for transcriptome analysis that take advantage of high-throughput next-generation sequencing. However, similar to their predecessors, these approaches continue to impose major challenges on full-length transcript structure identification, primarily due to inherent limitations of read length. With the development of single-molecule sequencing (SMS) from PacBio, a growing number of studies on the transcriptome of different organisms have been reported. SMS has emerged as advantageous for comprehensive genome annotation including identification of novel genes/isoforms, long non-coding RNAs and fusion transcripts. This approach can be used across a broad spectrum of species to better interpret the coding information of the genome, and facilitate the biological function study. We provide an overview of SMS platform and its diverse applications in various biological studies, and our perspective on the challenges associated with the transcriptome studies.

A retrospective cohort study comparing dairy calf treatment decisions by farm personnel with veterinary observations of clinical signs

Antimicrobials are frequently administered to calves with diarrhea, despite evidence suggesting questionable efficacy. Even if efficacious, providing the appropriate therapy to an animal requires accurate disease detection. The objective of this study was to use previously collected data and compare clinical scoring by a veterinarian to treatment decisions by on-farm personnel. Data describing daily clinical scores and farm treatments were previously collected from 4 farms for calves from birth to age 28 d. In this data set, a total of 460 calves were enrolled. Daily observations and clinical assessments were made on each farm by the same veterinarian, for a total of 12,101 calf observation days. Farm personnel made all treatment decisions based on their own observations, and these treatments were recorded by study personnel. Overall, the cumulative incidence of a calf exhibiting at least one abnormal clinical sign over the 28-d observation period was 0.93, with cumulative incidences of 0.85 and 0.33 for diarrhea and dehydration, respectively. The cumulative incidence of any treatment (including antibiotics and electrolytes) was 0.85, although the majority of treatments used an antimicrobial. The farm-specific probabilities that a calf with clinical signs of dehydration or diarrhea, respectively, received fluid or electrolyte therapy ranged from 0.08 to 0.27 and 0.03 to 0.12. These probabilities were greater for the day a clinical sign was first observed. The farm-specific probabilities that a calf with clinical signs of diarrhea received an antimicrobial was 0.23 to 0.65, and the probability that a calf exhibiting clinical signs of respiratory disease received an antimicrobial was 0.33 to 0.76. The first observation of diarrhea had similar probabilities to those for all observations of diarrhea. There was greater probability of treatment for calves with their first observed abnormal respiratory signs. Probabilities that treatment with antimicrobials, or fluids or electrolytes, was associated with an abnormal clinical sign were low-that is, calves received treatments in the absence of any abnormal clinical signs. This study illustrates incongruity between treatment decisions by calf treaters (the designated personnel on each farm responsible for calf health assessment and treatment decisions) and those of an observer using a clinical scoring system to identify calves with abnormal clinical signs. These findings indicate opportunities and the need for dairy farmers and advisors to evaluate calf treatment protocols, reasons for treatment, and training programs for calf health and disease detection, as well as to develop monitoring programs for treatment protocol compliance and health outcomes following therapy.

Markers of cognitive function in individuals with metabolic disease: Morquio syndrome and tyrosinemia type III

We characterized cognitive function in two metabolic diseases. MPS-IVa (mucopolysaccharidosis IVa, Morquio) and tyrosinemia type III individuals were assessed using tasks of attention, language and oculomotor function. MPS-IVa individuals were slower in visual search, but the display size effects were normal, and slowing was not due to long reaction times (ruling out slow item processing or distraction). Maintaining gaze in an oculomotor task was difficult. Results implicated sustained attention and task initiation or response processing. Shifting attention, accumulating evidence and selecting targets were unaffected. Visual search was also slowed in tyrosinemia type III, and patterns in visual search and fixation tasks pointed to sustained attention impairments, although there were differences from MPS-IVa. Language was impaired in tyrosinemia type III but not MPS-IVa. Metabolic diseases produced selective cognitive effects. Our results, incorporating new methods for developmental data and model selection, illustrate how cognitive data can contribute to understanding function in biochemical brain systems.

Microglia are effector cells of CD47-SIRPα antiphagocytic axis disruption against glioblastoma

Glioblastoma multiforme (GBM) is a highly aggressive malignant brain tumor with fatal outcome. Tumor-associated macrophages and microglia (TAMs) have been found to be major tumor-promoting immune cells in the tumor microenvironment. Hence, modulation and reeducation of tumor-associated macrophages and microglia in GBM is considered a promising antitumor strategy. Resident microglia and invading macrophages have been shown to have distinct origin and function. Whereas yolk sac-derived microglia reside in the brain, blood-derived monocytes invade the central nervous system only under pathological conditions like tumor formation. We recently showed that disruption of the SIRPα-CD47 signaling axis is efficacious against various brain tumors including GBM primarily by inducing tumor phagocytosis. However, most effects are attributed to macrophages recruited from the periphery but the role of the brain resident microglia is unknown. Here, we sought to utilize a model to distinguish resident microglia and peripheral macrophages within the GBM-TAM pool, using orthotopically xenografted, immunodeficient, and syngeneic mouse models with genetically color-coded macrophages (Ccr2RFP) and microglia (Cx3cr1GFP). We show that even in the absence of phagocytizing macrophages (Ccr2RFP/RFP), microglia are effector cells of tumor cell phagocytosis in response to anti-CD47 blockade. Additionally, macrophages and microglia show distinct morphological and transcriptional changes. Importantly, the transcriptional profile of microglia shows less of an inflammatory response which makes them a promising target for clinical applications.