Phylogenetic inference of inter-population transmission rates for infectious diseases.

Estimating transmission rates is a challenging yet essential aspect of comprehending and controlling the spread of infectious diseases. Various methods exist for estimating transmission rates, each with distinct assumptions, data needs, and constraints. This study introduces a novel phylogenetic approach called transRate, which integrates genetic information with traditional epidemiological approaches to estimate inter-population transmission rates. The phylogenetic method is statistically consistent as the sample size (i.e. the number of pathogen genomes) approaches infinity under the multi-population susceptible-infected-recovered model. Simulation analyses indicate that transRate can accurately estimate the transmission rate with a sample size of 200 ~ 400 pathogen genomes. Using transRate, we analyzed 40,028 high-quality sequences of SARS-CoV-2 in human hosts during the early pandemic. Our analysis uncovered significant transmission between populations even before widespread travel restrictions were implemented. The development of transRate provides valuable insights for scientists and public health officials to enhance their understanding of the pandemic's progression and aiding in preparedness for future viral outbreaks. As public databases for genomic sequences continue to expand, transRate is increasingly vital for tracking and mitigating the spread of infectious diseases.

External validity in distributed data networks.

PURPOSE: While much has been written about how distributed networks address internal validity, external validity is rarely discussed. We aimed to define key terms related to external validity, discuss how they relate to distributed networks, and identify how three networks (the US Food and Drug Administration's Sentinel System, the Canadian Network for Observational Drug Effect Studies [CNODES], and the National Patient Centered Clinical Research Network [PCORnet]) deal with external validity. METHODS: We define external validity, target populations, target validity, generalizability, and transportability and describe how each relates to distributed networks. We then describe Sentinel, CNODES, and PCORnet and how each approaches these concepts, including a sample case study. RESULTS: Each network approaches external validity differently. As its target population is US citizens and it includes only US data, Sentinel primarily worries about lack of external validity by not including some segments of the population. The fact that CNODES includes Canadian, United States, and United Kingdom data forces them to seriously consider whether the United States and United Kingdom data will be transportable to Canadian citizens when they meta-analyze database-specific estimates. PCORnet, with its focus on study-specific cohorts and pragmatic trials, conducts more case-by-case explorations of external validity for each new analytic data set it generates. CONCLUSIONS: There is no one-size-fits-all approach to external validity within distributed networks. With these networks and comparisons between their findings becoming a key part of pharmacoepidemiology, there is a need to adapt tools for improving external validity to the distributed network setting.

RTExtract: time-series NMR spectra quantification based on 3D surface ridge tracking.

MOTIVATION: Time-series nuclear magnetic resonance (NMR) has advanced our knowledge about metabolic dynamics. Before analyzing compounds through modeling or statistical methods, chemical features need to be tracked and quantified. However, because of peak overlap and peak shifting, the available protocols are time consuming at best or even impossible for some regions in NMR spectra. RESULTS: We introduce Ridge Tracking-based Extract (RTExtract), a computer vision-based algorithm, to quantify time-series NMR spectra. The NMR spectra of multiple time points were formulated as a 3D surface. Candidate points were first filtered using local curvature and optima, then connected into ridges by a greedy algorithm. Interactive steps were implemented to refine results. Among 173 simulated ridges, 115 can be tracked (RMSD < 0.001). For reproducing previous results, RTExtract took less than 2 h instead of ∼48 h, and two instead of seven parameters need tuning. Multiple regions with overlapping and changing chemical shifts are accurately tracked. AVAILABILITY AND IMPLEMENTATION: Source code is freely available within Metabolomics toolbox GitHub repository (https://github.com/artedison/Edison_Lab_Shared_Metabolomics_UGA/tree/master/metabolomics_toolbox/code/ridge_tracking) and is implemented in MATLAB and R. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

An Interrupted Time-series Evaluation of the Association Between State Laws Mandating Prescriber Use of Prescription Drug Monitoring Programs and Discontinuation of Chronic Opioid Therapy in US Veterans.

BACKGROUND: Most states have recently passed laws requiring prescribers to use prescription drug monitoring programs (PDMPs) before prescribing opioid medications. The impact of these mandates on discontinuing chronic opioid therapy among Veterans managed in the Veterans Health Administration (VA) is unknown. We assess the association between the earliest of these laws and discontinuation of chronic opioid therapy in Veterans receiving VA health care. METHODS: We conducted a comparative interrupted time-series study in the 5 states mandating PDMP use before August 2013 (Ohio, West Virginia, Kentucky, New Mexico, and Tennessee), adjusting for trends in the 17 neighboring control states without such mandates. We modeled 25 months of prescribing for each state centered on the month the mandate became effective. We included Veterans prescribed long-term outpatient opioid therapy (305 of the preceding 365 d). Our outcomes were discontinuation of chronic opioid therapy (primary outcome) and the average daily quantity of opioids per Veteran over the following 6 months (secondary outcome). RESULTS: We included 250 monthly cohorts with 225,665 unique Veterans and 3.4 million Veteran-months. Baseline discontinuation rates before the PDMP mandates were 0.4%-2.7% per month. Kentucky saw a discontinuation increase of 1 absolute percentage point following its PDMP mandate which decreased over time. The other 4 states had no significant association between their mandates and change in opioid discontinuation. There was no evidence of decreasing opioid quantities following PDMP mandates. CONCLUSION: We did not find consistent evidence that state laws mandating provider PDMP use were associated with the discontinuation of chronic opioid therapy within the VA for the time period studied.

Effect of Electronic Health Record-Based Coaching on Weight Maintenance: A Randomized Trial.

Background: Weight regain after intentional loss is common. Most evidence-based weight management programs focus on short-term loss rather than long-term maintenance. Objective: To evaluate the benefit of coaching in an electronic health record (EHR)-based weight maintenance intervention. Design: Randomized controlled trial. (ClinicalTrials.gov: NCT01946191). Setting: Practices affiliated with an academic medical center. Participants: Adult outpatients with body mass index (BMI) of 25 kg/m2 or higher, intentional weight loss of at least 5% in the previous 2 years, and no bariatric procedures in the previous 5 years. Intervention: Participants were randomly assigned to EHR tools (tracking group) versus EHR tools plus coaching (coaching group). The EHR tools included weight, diet, and physical activity tracking flow sheets; standardized surveys; and reminders. The coaching group received 24 months of personalized coaching through the EHR patient portal, with 24 scheduled contacts. Measurements: The primary outcome was weight change at 24 months. Secondary outcomes included 5% weight loss maintenance and changes in BMI, waist circumference, number of steps per day, health-related quality of life, physical function, blood pressure, and satisfaction. Results: Among 194 randomly assigned participants (mean age, 53.4 years [SD, 12.2]; 143 [74%] women; 171 [88%] white), 157 (81%) completed the trial. Mean baseline weight and BMI were 85.8 kg (SD, 19.1) and 30.4 kg/m2 (SD, 5.9). At 24 months, mean weight regain (± SE) was 2.1 ± 0.62 kg and 4.9 ± 0.63 kg in the coaching and tracking groups, respectively. The between-group difference in weight change at 24 months was significant (-2.86 kg [95% CI, -4.60 to -1.11 kg]) in the linear mixed model. At 24 months, 65% of participants in the coaching group and 50% in the tracking group maintained weight loss of at least 5%. Limitation: Single-site trial, which limits generalizability. Conclusion: Among adults with intentional weight loss of at least 5%, use of EHR tools plus coaching resulted in less weight regain than EHR tools alone. Primary Funding Source: Agency for Healthcare Research and Quality and National Institutes of Health.

Visualization of angiogenesis and vasculogenesis in a late tissue radiation injury of the chest wall treated with adjuvant hyperbaric oxygen therapy using fluorescence angiography.

Adjuvant radiation therapy for breast cancer treatment often involves high doses of radiation, making patients more susceptible to late radiation tissue injury (LRTI), severe complications of which involve necrosis and ulceration. Treatment of such wounds is challenging. One modality that can be utilized is hyperbaric oxygen (HBO2) therapy. However, an optimal dose and the objective evidence of its benefit in use as an adjunctive treatment modality is limited. Presented here is a case of a non-surgical candidate in which serial indocyanine green fluorescence angiography (ICGFA) was utilized to determine if it could detect changes in tissue perfusion over the course of treatment. Serial ICGFA allowed for visualization of the current phase of wound healing, angiogenesis and vasculogenesis. Future large studies should be employed to better determine the utility of serial ICGFA to improve HBO2 utilization in patients who are undergoing HBO2 as part of their course of treatment for LRTI.

What is Phase in Cellular Clocks?

Four inter-related measures of phase are described to study the phase synchronization of cellular oscillators, and computation of these measures is described and illustrated on single cell fluorescence data from the model filamentous fungus, Neurospora crassa. One of these four measures is the phase shift ϕ in a sinusoid of the form x(t) = A(cos(ωt + ϕ), where t is time. The other measures arise by creating a replica of the periodic process x(t) called the Hilbert transform x̃(t), which is 90 degrees out of phase with the original process x(t). The second phase measure is the phase angle FH(t) between the replica x̃(t) and x(t), taking values between -π and π. At extreme values the Hilbert Phase is discontinuous, and a continuous form FC(t) of the Hilbert Phase is used, measuring time on the nonnegative real axis (t). The continuous Hilbert Phase FC(t) is used to define the phase MC(t1,t0) for an experiment beginning at time t0 and ending at time t1. In that phase differences at time t0 are often of ancillary interest, the Hilbert Phase FC(t0) is subtracted from FC(t1). This difference is divided by 2π to obtain the phase MC(t1,t0) in cycles. Both the Hilbert Phase FC(t) and the phase MC(t1,t0) are functions of time and useful in studying when oscillators phase-synchronize in time in signal processing and circadian rhythms in particular. The phase of cellular clocks is fundamentally different from circadian clocks at the macroscopic scale because there is an hourly cycle superimposed on the circadian cycle.

Charcot Foot: Clinical Clues, Diagnostic Strategies, and Treatment Principles.

Acute Charcot neuroarthropathy of the foot and ankle is often difficult to diagnose because of limited findings in the patient history, physical examination, imaging, and laboratory studies. Delay in treatment results in the development of rigid foot and ankle deformities, increasing the risk of ulceration, infection, and major lower extremity amputation. Acute Charcot neuroarthropathy should be suspected in any patient 40 years or older with obesity and peripheral neuropathy who presents with an acutely swollen foot following minimal or no recalled trauma and who reports minimal to no pain, particularly if radiography and laboratory markers of infection are normal. Magnetic resonance imaging or computed tomography should be performed in these cases. If changes consistent with acute Charcot neuroarthropathy are observed, prompt immobilization and/or referral to a foot and ankle subspecialist is needed to minimize sequelae. Immobilization should continue until lower extremity edema and warmth resolve, and serial radiography shows evidence of osseous consolidation. Intranasal calcitonin salmon may have a role as adjunctive therapy. Although controversial, surgery may be indicated if there is severe dislocation or instability, concern for skin breakdown, or failure of conservative treatment to obtain a stable, plantigrade foot.

The EXPLORE Trial: A Feasibility Study Using Fluorescence Angiography to Evaluate Perfusion in the Oxygen-Rich Environment.

INTRODUCTION: Hyperbaric oxygen therapy (HBOT) is defined as breathing 100% oxygen at a pressure ≥1.4 atmospheres absolute (ATA). Adjunct HBOT is one modality used for treatment of certain complex wounds. The resulting increase in oxygen delivery to wounded tissue has been associated with reduced edema, reduced inflammation, improved infection control, increased collagen deposition, and increased angiogenesis. However, there remains a relative paucity of evidence supporting the use of HBOT in the treatment of certain acute and chronic, non-healing wounds. This feasibility study was undertaken to evaluate the ability of fluorescence angiography to provide real-time visualization and objective assessment of changes in local tissue perfusion over a standard course of HBOT. MATERIALS AND METHODS: This single-center, prospective, feasibility study included a total of 34 subjects with wounds of various etiologies deemed eligible for treatment with adjunct HBOT. Fluorescence angiography was performed pre- and post-HBOT sessions 1, 5, 10, 15, and 20. The imaging sequences were analyzed to determine the effects of HBOT on local tissue perfusion to the wounds. RESULTS: A total of 22 subjects received a minimum of 10 HBO sessions with associated pre- and post-fluorescence angiography performed and analyzed. Fluorescence angiography was able to provide both real-time visualization and objective assessment of changes in tissue perfusion over the course of adjunct HBOT. CONCLUSION: The results of this feasibility study suggest that serial fluorescence angiography can detect short- and long-term changes in wound area tissue perfusion associated with HBOT. These findings may assist in the selection and monitoring of patients undergoing HBOT.

Secondary structural entropy in RNA switch (Riboswitch) identification.

BACKGROUND: RNA regulatory elements play a significant role in gene regulation. Riboswitches, a widespread group of regulatory RNAs, are vital components of many bacterial genomes. These regulatory elements generally function by forming a ligand-induced alternative fold that controls access to ribosome binding sites or other regulatory sites in RNA. Riboswitch-mediated mechanisms are ubiquitous across bacterial genomes. A typical class of riboswitch has its own unique structural and biological complexity, making de novo riboswitch identification a formidable task. Traditionally, riboswitches have been identified through comparative genomics based on sequence and structural homology. The limitations of structural-homology-based approaches, coupled with the assumption that there is a great diversity of undiscovered riboswitches, suggests the need for alternative methods for riboswitch identification, possibly based on features intrinsic to their structure. As of yet, no such reliable method has been proposed. RESULTS: We used structural entropy of riboswitch sequences as a measure of their secondary structural dynamics. Entropy values of a diverse set of riboswitches were compared to that of their mutants, their dinucleotide shuffles, and their reverse complement sequences under different stochastic context-free grammar folding models. Significance of our results was evaluated by comparison to other approaches, such as the base-pairing entropy and energy landscapes dynamics. Classifiers based on structural entropy optimized via sequence and structural features were devised as riboswitch identifiers and tested on Bacillus subtilis, Escherichia coli, and Synechococcus elongatus as an exploration of structural entropy based approaches. The unusually long untranslated region of the cotH in Bacillus subtilis, as well as upstream regions of certain genes, such as the sucC genes were associated with significant structural entropy values in genome-wide examinations. CONCLUSIONS: Various tests show that there is in fact a relationship between higher structural entropy and the potential for the RNA sequence to have alternative structures, within the limitations of our methodology. This relationship, though modest, is consistent across various tests. Understanding the behavior of structural entropy as a fairly new feature for RNA conformational dynamics, however, may require extensive exploratory investigation both across RNA sequences and folding models.

APOE ϵ4, rated life experiences, and affect among centenarians.

OBJECTIVES: The purpose of this study was to assess the relationship between apolipoprotein E (APOE), life events and engagement, and subjective well-being (as measured by positive and negative affect) among centenarians. Based on the life stress paradigm, we predicted that higher levels of stress would allow APOE to influence positive and negative affect. METHOD: 196 centenarians and near-centenarians (98 years and older) of the Georgia Centenarian Study participated in this research. The APOE, positive and negative affect, the number of recent (last 2 years) and lifelong (more than 20 years prior to testing) events, as well as a number of life engagement tasks were assessed. RESULTS: Results suggested that centenarians carrying the APOE ϵ4 allele rated lower in positive affect, the number of lifelong events, and in engaged lifestyle, when compared to centenarians without the APOE ϵ4 allele (t = 3.43, p < .01; t = 3.19, p < .01; and t = 2.33, p < .05, respectively). Blockwise multiple regressions indicated that the APOE ϵ4 predicted positive but not negative affect after controlling for demographics. Gene-environment interactions were obtained for the APOE ϵ4 and lifelong events, suggesting that carriers of the APOE ϵ4 allele had higher scores of negative affect after having experienced more events, whereas noncarriers had reduced negative affect levels after having experienced more events. CONCLUSION: APOE ϵ4 is directly related to positive affect and is related to negative affect in interaction with life events.

The clock in growing hyphae and their synchronization in Neurospora crassa.

Utilizing a microfluidic chip with serpentine channels, we inoculated the chip with an agar plug with Neurospora crassa mycelium and successfully captured individual hyphae in channels. For the first time, we report the presence of an autonomous clock in hyphae. Fluorescence of a mCherry reporter gene driven by a clock-controlled gene-2 promoter (ccg-2p) was measured simultaneously along hyphae every half an hour for at least 6 days. We entrained single hyphae to light over a wide range of day lengths, including 6,12, 24, and 36 h days. Hyphae tracked in individual serpentine channels were highly synchronized (K = 0.60-0.78). Furthermore, hyphae also displayed temperature compensation properties, where the oscillation period was stable over a physiological range of temperatures from 24 °C to 30 °C (Q10 = 1.00-1.10). A Clock Tube Model developed could mimic hyphal growth observed in the serpentine chip and provides a mechanism for the stable banding patterns seen in race tubes at the macroscopic scale and synchronization through molecules riding the growth wave in the device.

Computer vision models enable mixed linear modeling to predict arbuscular mycorrhizal fungal colonization using fungal morphology.

The presence of Arbuscular Mycorrhizal Fungi (AMF) in vascular land plant roots is one of the most ancient of symbioses supporting nitrogen and phosphorus exchange for photosynthetically derived carbon. Here we provide a multi-scale modeling approach to predict AMF colonization of a worldwide crop from a Recombinant Inbred Line (RIL) population derived from Sorghum bicolor and S. propinquum. The high-throughput phenotyping methods of fungal structures here rely on a Mask Region-based Convolutional Neural Network (Mask R-CNN) in computer vision for pixel-wise fungal structure segmentations and mixed linear models to explore the relations of AMF colonization, root niche, and fungal structure allocation. Models proposed capture over 95% of the variation in AMF colonization as a function of root niche and relative abundance of fungal structures in each plant. Arbuscule allocation is a significant predictor of AMF colonization among sibling plants. Arbuscules and extraradical hyphae implicated in nutrient exchange predict highest AMF colonization in the top root section. Our work demonstrates that deep learning can be used by the community for the high-throughput phenotyping of AMF in plant roots. Mixed linear modeling provides a framework for testing hypotheses about AMF colonization phenotypes as a function of root niche and fungal structure allocations.

Pediatric Gastrointestinal Outcomes During the Post-Acute Phase of COVID-19: Findings from RECOVER Initiative from 29 Hospitals in the US.

Importance: The profile of gastrointestinal (GI) outcomes that may affect children in post-acute and chronic phases of COVID-19 remains unclear. Objective: To investigate the risks of GI symptoms and disorders during the post-acute phase (28 days to 179 days after SARS-CoV-2 infection) and the chronic phase (180 days to 729 days after SARS-CoV-2 infection) in the pediatric population. Design: We used a retrospective cohort design from March 2020 to Sept 2023. Setting: twenty-nine healthcare institutions. Participants: A total of 413,455 patients aged not above 18 with SARS-CoV-2 infection and 1,163,478 patients without SARS-CoV-2 infection. Exposures: Documented SARS-CoV-2 infection, including positive polymerase chain reaction (PCR), serology, or antigen tests for SARS-CoV-2, or diagnoses of COVID-19 and COVID-related conditions. Main Outcomes and Measures: Prespecified GI symptoms and disorders during two intervals: post-acute phase and chronic phase following the documented SARS-CoV-2 infection. The adjusted risk ratio (aRR) was determined using a stratified Poisson regression model, with strata computed based on the propensity score. Results: Our cohort comprised 1,576,933 patients, with females representing 48.0% of the sample. The analysis revealed that children with SARS-CoV-2 infection had an increased risk of developing at least one GI symptom or disorder in both the post-acute (8.64% vs. 6.85%; aRR 1.25, 95% CI 1.24-1.27) and chronic phases (12.60% vs. 9.47%; aRR 1.28, 95% CI 1.26-1.30) compared to uninfected peers. Specifically, the risk of abdominal pain was higher in COVID-19 positive patients during the post-acute phase (2.54% vs. 2.06%; aRR 1.14, 95% CI 1.11-1.17) and chronic phase (4.57% vs. 3.40%; aRR 1.24, 95% CI 1.22-1.27). Conclusions and Relevance: In the post-acute phase or chronic phase of COVID-19, the risk of GI symptoms and disorders was increased for COVID-positive patients in the pediatric population. Key Points: Question: Does COVID-19 increase the risk of gastrointestinal (GI) symptoms and diseases during the post-acute phase in children and adolescents?Findings: Newly diagnosed GI symptoms and disorders such as diarrhea, constipation, and vomiting are seen more commonly in children and adolescents with SARS-CoV-2 infection.Meaning: Clinicians need to be mindful that after SARS-CoV-2 infection in children, lingering GI symptoms without a unifying diagnosis may be more common than among uninfected children.

Post-acute and Chronic Kidney Function Outcomes of COVID-19 in Children and Adolescents: An EHR Cohort Study from the RECOVER Initiative.

We investigated the risks of post-acute and chronic adverse kidney outcomes of SARS-CoV-2 infection in the pediatric population via a retrospective cohort study using data from the RECOVER program. We included 1,864,637 children and adolescents under 21 from 19 children's hospitals and health institutions in the US with at least six months of follow-up time between March 2020 and May 2023. We divided the patients into three strata: patients with pre-existing chronic kidney disease (CKD), patients with acute kidney injury (AKI) during the acute phase (within 28 days) of SARS-CoV-2 infection, and patients without pre-existing CKD or AKI. We defined a set of adverse kidney outcomes for each stratum and examined the outcomes within the post-acute and chronic phases after SARS-CoV-2 infection. In each stratum, compared with the non-infected group, patients with COVID-19 had a higher risk of adverse kidney outcomes. For patients without pre-existing CKD, there were increased risks of CKD stage 2+ (HR 1.20; 95% CI: 1.13-1.28) and CKD stage 3+ (HR 1.35; 95% CI: 1.15-1.59) during the post-acute phase (28 days to 365 days) after SARS-CoV-2 infection. Within the post-acute phase of SARS-CoV-2 infection, children and adolescents with pre-existing CKD and those who experienced AKI were at increased risk of progression to a composite outcome defined by at least 50% decline in estimated glomerular filtration rate (eGFR), eGFR <15 mL/min/1.73m2, End Stage Kidney Disease diagnosis, dialysis, or transplant.

Long COVID incidence in adults and children between 2020 and 2023: a real-world data study from the RECOVER Initiative.

Estimates of post-acute sequelae of SARS-CoV-2 infection (PASC) incidence, also known as Long COVID, have varied across studies and changed over time. We estimated PASC incidence among adult and pediatric populations in three nationwide research networks of electronic health records (EHR) participating in the RECOVER Initiative using different classification algorithms (computable phenotypes). Overall, 7% of children and 8.5%-26.4% of adults developed PASC, depending on computable phenotype used. Excess incidence among SARS-CoV-2 patients was 4% in children and ranged from 4-7% among adults, representing a lower-bound incidence estimation based on two control groups - contemporary COVID-19 negative and historical patients (2019). Temporal patterns were consistent across networks, with peaks associated with introduction of new viral variants. Our findings indicate that preventing and mitigating Long COVID remains a public health priority. Examining temporal patterns and risk factors of PASC incidence informs our understanding of etiology and can improve prevention and management.

Tropical sharks feasting on and swimming through microplastics: First evidence from Malaysia.

Plastic can be degraded into microplastic (<5 mm) and has been polluting worldwide marine environment and negatively impact human health. Microplastics in marine organisms are still understudied in Malaysia, let alone from a subclass Elasmobranchii. Five tropical shark species (Carcharhinus dussumieri, Carcharhinus sorrah, Chiloscyllium hasseltii, Chiloscyllium punctatum, and Scoliodon laticaudus) were examined for the presence of microplastics. 74 sharks were sampled from the local wet market and 100 % of samples contained microplastics. A total of 2211 plastic particles were found in gastrointestinal tracts (GIT) and gills, where 29.88 ± 2.34 particles per shark (mean ± SEM). Black (40.07 %) and fiber (84.44 %) microplastics were the most dominant. Extracted microplastic sizes ranged from 0.007 mm to 4.992 mm. This study suggests that microplastic uptake is gender-related for some shark species. A subsample of microplastics (10 %) was used for polymer type identification, where polyester was recorded the highest (43.95 %).

Species-specific responses of marine bacteria to environmental perturbation.

Environmental perturbations shape the structure and function of microbial communities. Oil spills are a major perturbation and resolving spills often requires active measures like dispersant application that can exacerbate the initial disturbance. Species-specific responses of microorganisms to oil and dispersant exposure during such perturbations remain largely unknown. We merged metatranscriptomic libraries with pangenomes to generate Core-Accessory Metatranscriptomes (CA-Metatranscriptomes) for two microbial hydrocarbon degraders that played important roles in the aftermath of the Deepwater Horizon oil spill. The Colwellia CA-Metatranscriptome illustrated pronounced dispersant-driven acceleration of core (~41%) and accessory gene (~59%) transcription, suggesting an opportunistic strategy. Marinobacter responded to oil exposure by expressing mainly accessory genes (~93%), suggesting an effective hydrocarbon-degrading lifestyle. The CA-Metatranscriptome approach offers a robust way to identify the underlying mechanisms of key microbial functions and highlights differences of specialist-vs-opportunistic responses to environmental disturbance.

The ACTIV-6 Stakeholder Advisory Committee: a model for virtual engagement in decentralized clinical trials.

Introduction: Engaging patients, caregivers, and other stakeholders to help guide the research process is a cornerstone of patient-centered research. Lived expertise may help ensure the relevance of research questions, promote practices that are satisfactory to research participants, improve transparency, and assist with disseminating findings. Methods: Traditionally engagement has been conducted face-to-face in the local communities in which research operates. Decentralized platform trials pose new challenges for the practice of engagement. We used a remote model for stakeholder engagement, relying on Zoom meetings and blog communications. Results: Here we describe the approach used for research partnership with patients, caregivers, and clinicians in the planning and oversight of the ACTIV-6 trial and the impact of this work. We also present suggestions for future remote engagement. Conclusions: The ACTIV-6 experience may inform proposed strategies for future engagement in decentralized trials.

The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic.

A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic (prior to April 1, 2020). Using coalescent theory, the shallow (short branches relative to the hosts) consensus species tree provides evidence of recent gene flow events between bat and pangolin beta coronaviruses predating the zoonotic transfer to humans. The consensus species tree was also used to reconstruct the ancestral sequence of human SARS-CoV-2, which was 2 nucleotides different from the Wuhan sequence. The time to most recent common ancestor was estimated to be Dec 8, 2019 with a bat origin. Some human, bat, and pangolin coronavirus lineages found in China are phylogenetically distinct, a rare example of a class II phylogeography pattern (Avise et al. in Ann Rev Eco Syst 18:489-422, 1987). The consensus species tree is a product of evolutionary factors, providing evidence of repeated zoonotic transfers between bat and pangolin as a reservoir for future zoonotic transfers to humans.