Medical correlates of first-term attrition in US Navy personnel

INTRODUCTION

First-term attrition (FTA), or failure of a military service member to complete their initial service contract, is a major financial burden and source of lost manpower in the US Navy. The objective of the present study was to examine medical correlates of FTA using healthcare and disability rating data.

METHODS

In this retrospective cohort study, all US Navy-enlisted personnel between the years 2003 and 2018 with FTA (n=58 777) and regular discharge (n=203 084) were identified for analysis from accession dates in the Career History Archival Medical and Personnel System. Medical diagnoses from outpatient and inpatient records were abstracted from the Military Health System Data Repository. For a subgroup of the study population discharged with a disability rating (n=12 880), diagnoses were identified from the Integrated Disability Evaluation System. The FTA and regular discharge groups were compared using relative risks (RRs) and 95% CIs, and per cent differences for the disability subgroup analysis.

RESULTS

Compared with regular discharges, those with FTA were more likely to have outpatient and inpatient diagnoses for mental health disorders. Personality disorder yielded the strongest association with FTA in both outpatient (RR=10.45, 95% CI 9.79 to 11.16) and inpatient settings (RR=18.97, 95% CI 14.16 to 25.42). Other disorders associated with FTA included schizophrenia, substance-related disorders, poisoning by psychotropic agents and adjustment disorders. In the disability analysis, the FTA group relative to regular discharges had the largest per cent differences for 'arthritis, degenerative (hypertrophic or osteoarthritis)' (10.8% vs 2.5%) and 'tibia and fibula, impairment' (3.0% vs 0.4%).

CONCLUSIONS

This study provides evidence that FTA is associated with both mental and physical health conditions. Mental and physical factors related to FTA require further examination, particularly whether pre-enlistment screening or early career intervention could lead to mitigation strategies. Future research should extend this analysis to other services and population subgroups.

Phonological impairments in Hindi aphasics: Error analyses and cross-linguistic comparisons

We assessed phonological and apraxic impairments in Hindi persons with aphasia (PwA) and compared them to Italian PwA reported in previous studies. Overall, we found strong similarities. Phonological errors were present across production tasks (repetition, reading and naming), most errors were non-lexical and, among those, a majority involved individual phonemes. There were significant effects of length, but not frequency. Hindi PwA, like the Italian PwA, showed strong effects of syllabic structure, with most errors occurring on consonants and weak syllabic positions, preserving syllable structure and simplifying phonemes or syllabic templates. These similarities were modulated by some language-specific patterns. Vowel insertions were more common in Hindi, possibly due to the presence of a central vowel, and segmental simplifications concentrated on marked aspiration and retroflection features. We hope our study will encourage further research in Hindi and other Indian languages. This will improve clinical diagnosis and our understanding of cross-linguistic differences.

The inseparability of context and clinical reasoning

Early descriptions of clinical reasoning have described a dual process model that relies on analytical or nonanalytical approaches to develop a working diagnosis. In this classic research, clinical reasoning is portrayed as an individual-driven cognitive process based on gathering information from the patient encounter, forming mental representations that rely on previous experience and engaging developed patterns to drive working diagnoses and management plans. Indeed, approaches to patient safety, as well as teaching and assessing clinical reasoning focus on the individual clinician, often ignoring the complexity of the system surrounding the diagnostic process. More recent theories and evidence portray clinical reasoning as a dynamic collection of processes that takes place among and between persons across clinical settings. Yet, clinical reasoning, taken as both an individual and a system process, is insufficiently supported by theories of cognition based on individual clinicals and lacks the specificity needed to describe the phenomenology of clinical reasoning. In this review, we reinforce that the modern healthcare ecosystem - with its people, processes and technology - is the context in which health care encounters and clinical reasoning take place.

Exploring Competency-Based Medical Education Through the Lens of the UME-GME Transition: A Qualitative Study

PURPOSE

Competency-based medical education (CBME) represents a shift to a paradigm with shared definitions, explicit outcomes, and assessments of competence. The groundwork has been laid to ensure all learners achieve the desired outcomes along the medical education continuum using the principles of CBME. However, this continuum spans the major transition from undergraduate medical education (UME) to graduate medical education (GME) that is also evolving. This study explores the experiences of medical educators working to use CBME assessments in the context of the UME-GME transition and their perspectives on the existing challenges.

METHOD

This study used a constructivist-oriented qualitative methodology. In-depth, semistructured interviews of UME and GME leaders in CBME were performed between February 2019 and January 2020 via Zoom. When possible, each interviewee was interviewed by 2 team members, one with UME and one with GME experience, which allowed follow-up questions to be pursued that reflected the perspectives of both UME and GME educators more fully. A multistep iterative process of thematic analysis was used to analyze the transcripts and identify patterns across interviews.

RESULTS

The 9 interviewees represented a broad swath of UME and GME leadership positions, though most had an internal medicine training background. Analysis identified 4 overarching themes: mistrust (a trust chasm exists between UME and GME); misaligned goals (the residency selection process is antithetical to CBME); inadequate communication (communication regarding competence is infrequent, often unidirectional, and lacks a shared language); and inflexible timeframes (current training timeframes do not account for individual learners' competency trajectories).

CONCLUSIONS

Despite the mutual desire and commitment to move to CBME across the continuum, mistrust, misaligned goals, inadequate communication, and inflexible timeframes confound such efforts of individual schools and programs. If current efforts to improve the UME-GME transition address the themes identified, educators may be more successful implementing CBME along the continuum.

Characterization of antibiotic overuse for common infectious disease states at hospital discharge

Objective

To evaluate rates of and outcomes associated with antibiotic overuse at hospital discharge for patients with common infectious diseases states.

Design

Single-center, respective cohort study.

Setting

A large, academic medical center in the Midwest United States.

Patients

Adult patients who received antibiotics for community-acquired pneumonia (CAP), uncomplicated cystitis, or mild, non-purulent cellulitis. Patients were excluded if they did not receive antibiotic(s) upon hospital discharge, were pregnant, severely immunocompromised, had concomitant infections, died during hospitalization, or were transferred to another hospital or to an intensive care unit.

Methods

Data were abstracted from the electronic medical record of ambulatory antibiotic orders for included patients based on inpatient encounters from August 1, 2021 through July 31, 2022.

Results

Of the 182 patients included in the study, antibiotic overuse was common for all three infectious disease states: CAP (n = 87/125, 69.6%), uncomplicated cystitis (n = 21/28, 75.0%), mild, non-purulent cellulitis (n = 28/29, 96.6%). The prevailing reason for overuse was excessive antibiotic duration (n = 127/182, 69.8%; mean antibiotic duration 5.39 vs. 8.32 days, p = 0.001). Antibiotic overuse was associated with approximately one additional day in the hospital (2.48 vs. 3.32 days, p = 0.001), and an increase in emergency department visits within 30 days after discharge (1 vs. 31, p = 0.001) compared to patients without antibiotic overuse at discharge.

Conclusion

Antibiotic overuse was prevalent upon hospital discharge for these three common infectious disease states. Transitions of care should be prioritized as an area for antimicrobial stewardship intervention.

Scalable Strategies to Increase Efficiency and Augment Public Health Activities During Epidemic Peaks

OBJECTIVE

Scalable strategies to reduce the time burden and increase contact tracing efficiency are crucial during early waves and peaks of infectious transmission.

DESIGN

We enrolled a cohort of SARS-CoV-2-positive seed cases into a peer recruitment study testing social network methodology and a novel electronic platform to increase contact tracing efficiency.

SETTING

Index cases were recruited from an academic medical center and requested to recruit their local social contacts for enrollment and SARS-CoV-2 testing.

PARTICIPANTS

A total of 509 adult participants enrolled over 19 months (384 seed cases and 125 social peers).

INTERVENTION

Participants completed a survey and were then eligible to recruit their social contacts with unique "coupons" for enrollment. Peer participants were eligible for SARS-CoV-2 and respiratory pathogen screening.

MAIN OUTCOME MEASURES

The main outcome measures were the percentage of tests administered through the study that identified new SARS-CoV-2 cases, the feasibility of deploying the platform and the peer recruitment strategy, the perceived acceptability of the platform and the peer recruitment strategy, and the scalability of both during pandemic peaks.

RESULTS

After development and deployment, few human resources were needed to maintain the platform and enroll participants, regardless of peaks. Platform acceptability was high. Percent positivity tracked with other testing programs in the area.

CONCLUSIONS

An electronic platform may be a suitable tool to augment public health contact tracing activities by allowing participants to select an online platform for contact tracing rather than sitting for an interview.

Mitigating Racial And Ethnic Bias And Advancing Health Equity In Clinical Algorithms: A Scoping Review

In August 2022 the Department of Health and Human Services (HHS) issued a notice of proposed rulemaking prohibiting covered entities, which include health care providers and health plans, from discriminating against individuals when using clinical algorithms in decision making. However, HHS did not provide specific guidelines on how covered entities should prevent discrimination. We conducted a scoping review of literature published during the period 2011-22 to identify health care applications, frameworks, reviews and perspectives, and assessment tools that identify and mitigate bias in clinical algorithms, with a specific focus on racial and ethnic bias. Our scoping review encompassed 109 articles comprising 45 empirical health care applications that included tools tested in health care settings, 16 frameworks, and 48 reviews and perspectives. We identified a wide range of technical, operational, and systemwide bias mitigation strategies for clinical algorithms, but there was no consensus in the literature on a single best practice that covered entities could employ to meet the HHS requirements. Future research should identify optimal bias mitigation methods for various scenarios, depending on factors such as patient population, clinical setting, algorithm design, and types of bias to be addressed.

Machine learning functional impairment classification with electronic health record data

BACKGROUND

Poor functional status is a key marker of morbidity, yet is not routinely captured in clinical encounters. We developed and evaluated the accuracy of a machine learning algorithm that leveraged electronic health record (EHR) data to provide a scalable process for identification of functional impairment.

METHODS

We identified a cohort of patients with an electronically captured screening measure of functional status (Older Americans Resources and Services ADL/IADL) between 2018 and 2020 (N = 6484). Patients were classified using unsupervised learning K means and t-distributed Stochastic Neighbor Embedding into normal function (NF), mild to moderate functional impairment (MFI), and severe functional impairment (SFI) states. Using 11 EHR clinical variable domains (832 variable input features), we trained an Extreme Gradient Boosting supervised machine learning algorithm to distinguish functional status states, and measured prediction accuracies. Data were randomly split into training (80%) and test (20%) sets. The SHapley Additive Explanations (SHAP) feature importance analysis was used to list the EHR features in rank order of their contribution to the outcome.

RESULTS

Median age was 75.3 years, 62% female, 60% White. Patients were classified as 53% NF (n = 3453), 30% MFI (n = 1947), and 17% SFI (n = 1084). Summary of model performance for identifying functional status state (NF, MFI, SFI) was AUROC (area under the receiving operating characteristic curve) 0.92, 0.89, and 0.87, respectively. Age, falls, hospitalization, home health use, labs (e.g., albumin), comorbidities (e.g., dementia, heart failure, chronic kidney disease, chronic pain), and social determinants of health (e.g., alcohol use) were highly ranked features in predicting functional status states.

CONCLUSION

A machine learning algorithm run on EHR clinical data has potential utility for differentiating functional status in the clinical setting. Through further validation and refinement, such algorithms can complement traditional screening methods and result in a population-based strategy for identifying patients with poor functional status who need additional health resources.

How does work environment relate to diagnostic quality? A prospective, mixed methods study in primary care

OBJECTIVES

The quest to measure and improve diagnosis has proven challenging; new approaches are needed to better understand and measure key elements of the diagnostic process in clinical encounters. The aim of this study was to develop a tool assessing key elements of the diagnostic assessment process and apply it to a series of diagnostic encounters examining clinical notes and encounters' recorded transcripts. Additionally, we aimed to correlate and contextualise these findings with measures of encounter time and physician burnout.

DESIGN

We audio-recorded encounters, reviewed their transcripts and associated them with their clinical notes and findings were correlated with concurrent Mini Z Worklife measures and physician burnout.

SETTING

Three primary urgent-care settings.

PARTICIPANTS

We conducted in-depth evaluations of 28 clinical encounters delivered by seven physicians.

RESULTS

Comparing encounter transcripts with clinical notes, in 24 of 28 (86%) there was high note/transcript concordance for the diagnostic elements on our tool. Reliably included elements were red flags (92% of notes/encounters), aetiologies (88%), likelihood/uncertainties (71%) and follow-up contingencies (71%), whereas psychosocial/contextual information (35%) and mentioning common pitfalls (7%) were often missing. In 22% of encounters, follow-up contingencies were in the note, but absent from the recorded encounter. There was a trend for higher burnout scores being associated with physicians less likely to address key diagnosis items, such as psychosocial history/context.

CONCLUSIONS

A new tool shows promise as a means of assessing key elements of diagnostic quality in clinical encounters. Work conditions and physician reactions appear to correlate with diagnostic behaviours. Future research should continue to assess relationships between time pressure and diagnostic quality.

Development and psychometric testing of the Diagnostic Competency During Simulation-based (DCDS) learning tool

BACKGROUND

Despite diagnostic errors impacting an estimated 12 million people yearly in the United States, educational strategies that foster diagnostic performance among nurse practitioner (NP) students remain elusive. One possible solution is to focus explicitly on competencies fundamental for diagnostic excellence. Currently, no educational tools were found that comprehensively address individual diagnostic reasoning competencies during simulated-based learning experiences.

PURPOSE

Our research team developed and explored psychometric properties of the "Diagnostic Competency During Simulation-based (DCDS) Learning Tool."

METHOD

Items and domains were developed based on existing frameworks. Content validity was determined by a convenience sample of eight experts. Inter-rater reliability was determined by four faculty rating eight simulation scenarios.

RESULTS

Final individual competency domain scale content validity index (CVI) scores ranged between 0.9175 and 1.0; total scale CVI score was 0.98. The intra-class correlation coefficient (ICC) for the tool was 0.548 (p < 0.0001, 95 % confidence interval CI [0.482-0.612]).

CONCLUSIONS

Results suggest that the DCDS Learning Tool is relevant to diagnostic reasoning competencies and may be implemented with moderate reliability across varied simulation scenarios and performance levels. The DCDS tool expands the landscape of diagnostic reasoning assessment by providing NP educators with granular, actionable, competency-specific assessment measures to foster improvement.

Predictive Value of Early Autism Detection Models Based on Electronic Health Record Data Collected Before Age 1 Year

IMPORTANCE

Autism detection early in childhood is critical to ensure that autistic children and their families have access to early behavioral support. Early correlates of autism documented in electronic health records (EHRs) during routine care could allow passive, predictive model-based monitoring to improve the accuracy of early detection.

OBJECTIVE

To quantify the predictive value of early autism detection models based on EHR data collected before age 1 year.

DESIGN, SETTING, AND PARTICIPANTS

This retrospective diagnostic study used EHR data from children seen within the Duke University Health System before age 30 days between January 2006 and December 2020. These data were used to train and evaluate L2-regularized Cox proportional hazards models predicting later autism diagnosis based on data collected from birth up to the time of prediction (ages 30-360 days). Statistical analyses were performed between August 1, 2020, and April 1, 2022.

MAIN OUTCOMES AND MEASURES

Prediction performance was quantified in terms of sensitivity, specificity, and positive predictive value (PPV) at clinically relevant model operating thresholds.

RESULTS

Data from 45 080 children, including 924 (1.5%) meeting autism criteria, were included in this study. Model-based autism detection at age 30 days achieved 45.5% sensitivity and 23.0% PPV at 90.0% specificity. Detection by age 360 days achieved 59.8% sensitivity and 17.6% PPV at 81.5% specificity and 38.8% sensitivity and 31.0% PPV at 94.3% specificity.

CONCLUSIONS AND RELEVANCE

In this diagnostic study of an autism screening test, EHR-based autism detection achieved clinically meaningful accuracy by age 30 days, improving by age 1 year. This automated approach could be integrated with caregiver surveys to improve the accuracy of early autism screening.

Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes

INTRODUCTION

Sorghum (Sorghum bicolor (L.) Moench) is an agriculturally and economically important staple crop that has immense potential as a bioenergy feedstock due to its relatively high productivity on marginal lands. To capitalize on and further improve sorghum as a potential source of sustainable biofuel, it is essential to understand the genomic mechanisms underlying complex traits related to yield, composition, and environmental adaptations.

METHODS

Expanding on a recently developed mapping population, we generated de novo genome assemblies for 10 parental genotypes from this population and identified a comprehensive set of over 24 thousand large structural variants (SVs) and over 10.5 million single nucleotide polymorphisms (SNPs).

RESULTS

We show that SVs and nonsynonymous SNPs are enriched in different gene categories, emphasizing the need for long read sequencing in crop species to identify novel variation. Furthermore, we highlight SVs and SNPs occurring in genes and pathways with known associations to critical bioenergy-related phenotypes and characterize the landscape of genetic differences between sweet and cellulosic genotypes.

DISCUSSION

These resources can be integrated into both ongoing and future mapping and trait discovery for sorghum and its myriad uses including food, feed, bioenergy, and increasingly as a carbon dioxide removal mechanism.

The impact of metabolic control on cognition, neurophysiology, and well-being in PKU: A systematic review and meta-analysis of the within-participant literature

Phenylketonuria (PKU) is a metabolic disease where Phenylalanine (Phe) rises much above normal levels. Cross-sectional and correlational studies provide valuable information on the importance of maintaining low blood-Phe to achieve good outcomes, but they may be confounded, at least partially, by differences in participant demographics. Moreover, the effect of Phe at older ages is difficult to ascertain because of strong associations between Phe levels across ages. Within-participant studies avoid confounding issues. We have reviewed these studies. We followed PRISMA guidelines to search the literature for studies reporting the impact of Phe changes within participants. Phe was either increased or decreased through diet relaxation/resumption or through pharmacological interventions. Forty-six separate articles reported, singly or in combination, results on cognition (N = 37), well-being (N = 22) and neurophysiological health (N = 14). For all studies, we established, in a binary way, whether a benefit of lower Phe was or was not demonstrated and compared numbers showing benefit versus a null or negative outcome. We then analyzed whether critical parameters (e.g., length of the study/condition for the change, size of Phe change achieved) influenced presence or absence of benefit. For a subset of studies that reported quantitative cognitive outcomes, we carried out a meta-analysis to estimate the size of change in cognitive performance associated with a change in Phe and its significance. There were significantly more studies with benefits than no benefits, both for cognitive and well-being outcomes, and a trend in this direction for neurophysiological outcomes. The meta-analysis showed a highly significant effect size both overall (0.55) and when studies with adults/adolescents were considered separately (0.57). There was some indication that benefits were easier to demonstrate when differences in Phe were larger and achieved across a longer period, but these effects were not always consistent. These results reinforce results from the literature by demonstrating the importance of lower Phe in children as well as in adolescents and adults, even when confounding factors in group composition are eliminated. The field would benefit from further studies where Phe levels are contrasted within-participants to ascertain how much Phe needs to be changed and for how long to see a difference and which measures demonstrate a difference (e.g., which cognitive tasks).

Meta-analyses of cognitive functions in early-treated adults with phenylketonuria

Our study estimated size of impairment for different cognitive functions in early-treated adults with PKU (AwPKU) by combining literature results in a meta-analytic way. We analysed a large set of functions (N = 19), each probed by different measures (average = 12). Data were extracted from 26 PKU groups and matched controls, with 757 AwPKU contributing 220 measures. Effect sizes (ESs) were computed using Glass' ∆ where differences in performance between clinical/PKU and control groups are standardized using the mean and standard deviation of the control groups. Significance was assessed using measures nested within independent PKU groups as a random factor. The weighted Glass' ∆ was - 0.44 for all functions taken together, and - 0.60 for IQ, both highly significant. Separate, significant impairments were found for most functions, but with great variability (ESs from -1.02 to -0.18). The most severe impairments were in reasoning, visual-spatial attention speed, sustained attention, visuo-motor control, and flexibility. Effect sizes were larger with speed than accuracy measures, and with visuo-spatial than verbal stimuli. Results show a specific PKU profile that needs consideration when monitoring the disease.

Improving hospital sepsis care using PAs and NPs on a rapid response team

ABSTRACT

Sepsis carries a high mortality in the United States. Hospitals across the country are working to find new ways to recognize, treat, and streamline care for patients with sepsis. At an academic medical center in the Midwest, a quality improvement project was developed using a sepsis rapid response team with physician associates/assistants (PAs) and NPs. This improved hospital adherence to sepsis evaluation and order set use from 48% to 86%. The added evaluation of the patient by a PA or NP, along with ensuring adherence to the sepsis order set, made an effective first step to improve care of patients with sepsis in this hospital.

Role of a ZF-HD Transcription Factor in miR157-Mediated Feed-Forward Regulatory Module That Determines Plant Architecture in Arabidopsis

In plants, vegetative and reproductive development are associated with agronomically important traits that contribute to grain yield and biomass. Zinc finger homeodomain (ZF-HD) transcription factors (TFs) constitute a relatively small gene family that has been studied in several model plants, including Arabidopsis thaliana L. and Oryza sativa L. The ZF-HD family members play important roles in plant growth and development, but their contribution to the regulation of plant architecture remains largely unknown due to their functional redundancy. To understand the gene regulatory network controlled by ZF-HD TFs, we analyzed multiple loss-of-function mutants of ZF-HD TFs in Arabidopsis that exhibited morphological abnormalities in branching and flowering architecture. We found that ZF-HD TFs, especially HB34, negatively regulate the expression of miR157 and positively regulate SQUAMOSA PROMOTER BINDING-LIKE 10 (SPL10), a target of miR157. Genome-wide chromatin immunoprecipitation sequencing (ChIP-Seq) analysis revealed that miR157D and SPL10 are direct targets of HB34, creating a feed-forward loop that constitutes a robust miRNA regulatory module. Network motif analysis contains overrepresented coherent type IV feedforward motifs in the amiR zf-HD and hbq mutant background. This finding indicates that miRNA-mediated ZF-HD feedforward modules modify branching and inflorescence architecture in Arabidopsis. Taken together, these findings reveal a guiding role of ZF-HD TFs in the regulatory network module and demonstrate its role in plant architecture in Arabidopsis.

Metabolic engineering of oleaginous yeast Rhodotorula toruloides for overproduction of triacetic acid lactone

The plant‐sourced polyketide triacetic acid lactone (TAL) has been recognized as a promising platform chemical for the biorefinery industry. However, its practical application was rather limited due to low natural abundance and inefficient cell factories for biosynthesis. Here, we report the metabolic engineering of oleaginous yeast Rhodotorula toruloides for TAL overproduction. We first introduced a 2‐pyrone synthase gene from Gerbera hybrida (GhPS) into R. toruloides and investigated the effects of different carbon sources on TAL production. We then systematically employed a variety of metabolic engineering strategies to increase the flux of acetyl‐CoA by enhancing its biosynthetic pathways and disrupting its competing pathways. We found that overexpression of ATP‐citrate lyase (ACL1) improved TAL production by 45% compared to the GhPS overexpressing strain, and additional overexpression of acetyl‐CoA carboxylase (ACC1) further increased TAL production by 29%. Finally, we characterized the resulting strain I12‐ACL1‐ACC1 using fed‐batch bioreactor fermentation in glucose or oilcane juice medium with acetate supplementation and achieved a titer of 28 or 23 g/L TAL, respectively. This study demonstrates that R. toruloides is a promising host for the production of TAL and other acetyl‐CoA‐derived polyketides from low‐cost carbon sources.

Effects of delay, length, and frequency on onset RTs and word durations: Articulatory planning uses flexible units but cannot be prepared

There is debate regarding whether most articulatory planning occurs offline (rather than online) and whether the products of off-line processing are stored in a separate articulatory buffer until a large enough chunk is ready for production. This hypothesis predicts that delayed naming conditions should reduce not only onset RTs but also word durations because articulatory plans will be buffered and kept ready. We have tested this hypothesis with young control speakers, an aphasic speaker , and an age and education-matched speaker, using repetition, reading and picture-naming tasks. Contrary to the off-line hypothesis, delayed conditions strongly reduced onset RTs, but had no benefit for word durations. In fact, we found small effects in the opposite direction. Moreover, frequency and imageability affected word durations even in delayed conditions, consistent with articulatory processing continuing on-line. The same pattern of results was found in CS and in control participants, strengthening confidence in our results. There is debate regarding whether most articulatory planning occurs offline (rather than online) and whether the results of off-line processing are stored in a separate articulatory buffer until a large enough chunk is ready for production. This hypothesis predicts that delayed naming conditions should reduce not only onset RTs but also word durations because articulatory plans will be buffered and kept ready. We have tested young control speakers, an aphasic speaker, and an age and education matched speaker, using repetition, reading and picture naming tasks. Contrary to the off-line hypothesis, delayed conditions strongly reduced onset RTs, but had no benefit for word durations. In fact, we found small effects in the opposite direction. Moreover, frequency and imageability affected word durations even in delayed conditions, consistent with articulatory processing continuing on-line. The same pattern of results was found in CS and in control participants, strengthening confidence in our results.

Comparison of Outcomes and Process of Care for Patients Treated at Hospitals Dedicated for COVID-19 Care vs Other Hospitals

IMPORTANCE

Early in the SARS-CoV-2 pandemic, the M Health Fairview Hospital System established dedicated hospitals for establishing cohorts and caring for patients with COVID-19, yet the association between treatment at COVID-19-dedicated hospitals and mortality and complications is not known.

OBJECTIVE

To analyze the mortality rate and complications associated with treatment at the COVID-19-dedicated hospitals.

DESIGN, SETTING, AND PARTICIPANTS

This retrospective cohort study evaluated data prospectively collected from March 1, 2020, through June 30, 2021, from 11 hospitals in Minnesota, including 2 hospitals created solely to care for patients with COVID-19. Data obtained included demographic characteristics, treatments, and outcomes of interest for all patients with a confirmed COVID-19 infection admitted to this hospital system during the study period.

EXPOSURES

Patients were grouped based on whether they received treatment from 1 of the 2 COVID-19-dedicated hospitals compared with the remainder of the hospitals within the hospital system.

MAIN OUTCOMES AND MEASURES

Multivariate analyses, including risk-adjusted logistic regression and propensity score matching, were performed to evaluate the primary outcome of in-hospital mortality and secondary outcomes, including complications and use of COVID-specific therapeutics.

RESULTS

There were 5504 patients with COVID-19 admitted during the study period (median age, 62.5 [IQR, 45.0-75.6] years; 2854 women [51.9%]). Of these, 2077 patients (37.7%) (median age, 63.4 [IQR, 50.7-76.1] years; 1080 men [52.0%]) were treated at 1 of the 2 COVID-19-dedicated hospitals compared with 3427 (62.3%; median age, 62.0 [40.0-75.1] years; 1857 women (54.2%) treated at other hospitals. The mortality rate was 11.6% (n = 241) at the dedicated hospitals compared with 8.0% (n = 274) at the other hospitals (P < .001). However, risk-adjusted in-hospital mortality was significantly lower for patients in the COVID-19-dedicated hospitals in both the unmatched group (n = 2077; odds ratio [OR], 0.75; 95% CI, 0.59-0.95) and the propensity score-matched group (n = 1317; OR, 0.78; 95% CI, 0.58-0.99). The rate of overall complications in the propensity score-matched group was significantly lower (OR, 0.81; 95% CI, 0.66-0.99) and the use of COVID-19-specific therapeutics including deep vein thrombosis prophylaxis (83.9% vs 56.9%; P < .001), high-dose corticosteroids (56.1% vs 22.2%; P < .001), remdesivir (61.5% vs 44.5%; P < .001), and tocilizumab (7.9% vs 2.0; P < .001) was significantly higher.

CONCLUSIONS AND RELEVANCE

In this cohort study, COVID-19-dedicated hospitals had multiple benefits, including providing high-volume repetitive treatment and isolating patients with the infection. This experience suggests improved in-hospital mortality for patients treated at dedicated hospitals owing to improved processes of care and supports the use of establishing cohorts for future pandemics.

SorghumBase: a web-based portal for sorghum genetic information and community advancement

SorghumBase provides a community portal that integrates genetic, genomic, and breeding resources for sorghum germplasm improvement. Public research and development in agriculture rely on proper data and resource sharing within stakeholder communities. For plant breeders, agronomists, molecular biologists, geneticists, and bioinformaticians, centralizing desirable data into a user-friendly hub for crop systems is essential for successful collaborations and breakthroughs in germplasm development. Here, we present the SorghumBase web portal ( https://www.sorghumbase.org ), a resource for the sorghum research community. SorghumBase hosts a wide range of sorghum genomic information in a modular framework, built with open-source software, to provide a sustainable platform. This initial release of SorghumBase includes: (1) five sorghum reference genome assemblies in a pan-genome browser; (2) genetic variant information for natural diversity panels and ethyl methanesulfonate (EMS)-induced mutant populations; (3) search interface and integrated views of various data types; (4) links supporting interconnectivity with other repositories including genebank, QTL, and gene expression databases; and (5) a content management system to support access to community news and training materials. SorghumBase offers sorghum investigators improved data collation and access that will facilitate the growth of a robust research community to support genomics-assisted breeding.

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl.org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. Here, we present our largest increase in plant, metazoan and fungal genomes since the project's inception creating one of the world's most comprehensive genomic resources and describe our efforts to reduce genome redundancy in our Bacteria portal. We detail our new efforts in gene annotation, our emerging support for pangenome analysis, our efforts to accelerate data dissemination through the Ensembl Rapid Release resource and our new AlphaFold visualization. Finally, we present details of our future plans including updates on our integration with Ensembl, and how we plan to improve our support for the microbial research community. Software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license). Data updates are synchronised with Ensembl's release cycle.

Microbial synthesis of wax esters

Microbial synthesis of wax esters (WE) from low-cost renewable and sustainable feedstocks is a promising path to achieve cost-effectiveness in biomanufacturing. WE are industrially high-value molecules, which are widely used for applications in chemical, pharmaceutical, and food industries. Since the natural WE resources are limited, the WE production mostly rely on chemical synthesis from rather expensive starting materials, and therefore solution are sought from development of efficient microbial cell factories. Here we report to engineer the yeast Yarrowia lipolytica and bacterium Escherichia coli to produce WE at the highest level up to date. First, the key genes encoding fatty acyl-CoA reductases and wax ester synthase from different sources were investigated, and the expression system for two different Y. lipolytica hosts were compared and optimized for enhanced WE production and the strain stability. To improve the metabolic pathway efficiency, different carbon sources including glucose, free fatty acid, soybean oil, and waste cooking oil (WCO) were compared, and the corresponding pathway engineering strategies were optimized. It was found that using a lipid substrate such as WCO to replace glucose led to a 60-fold increase in WE production. The engineered yeast was able to produce 7.6 g/L WE with a yield of 0.31 (g/g) from WCO within 120 h and the produced WE contributed to 57% of the yeast DCW. After that, E. coli BL21(DE3), with a faster growth rate than the yeast, was engineered to significantly improve the WE production rate. Optimization of the expression system and the substrate feeding strategies led to production of 3.7-4.0 g/L WE within 40 h in a 1-L bioreactor. The predominant intracellular WE produced by both Y. lipolytica and E. coli in the presence of hydrophobic substrates as sole carbon sources were C₃₆, C₃₄ and C₃₂, in an order of decreasing abundance and with a large proportion being unsaturated. This work paved the way for the biomanufacturing of WE at a large scale.

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.

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.

Dynamin impacts homology-directed repair and breast cancer response to chemotherapy

After the initial responsiveness of triple-negative breast cancers (TNBCs) to chemotherapy, they often recur as chemotherapy-resistant tumors, and this has been associated with upregulated homology-directed repair (HDR). Thus, inhibitors of HDR could be a useful adjunct to chemotherapy treatment of these cancers. We performed a high-throughput chemical screen for inhibitors of HDR from which we obtained a number of hits that disrupted microtubule dynamics. We postulated that high levels of the target molecules of our screen in tumors would correlate with poor chemotherapy response. We found that inhibition or knockdown of dynamin 2 (DNM2), known for its role in endocytic cell trafficking and microtubule dynamics, impaired HDR and improved response to chemotherapy of cells and of tumors in mice. In a retrospective analysis, levels of DNM2 at the time of treatment strongly predicted chemotherapy outcome for estrogen receptor-negative and especially for TNBC patients. We propose that DNM2-associated DNA repair enzyme trafficking is important for HDR efficiency and is a powerful predictor of sensitivity to breast cancer chemotherapy and an important target for therapy.