Neuronal MAPT expression is mediated by long-range interactions with cis-regulatory elements.

Tauopathies are a group of neurodegenerative diseases defined by abnormal aggregates of tau, a microtubule-associated protein encoded by MAPT. MAPT expression is near absent in neural progenitor cells (NPCs) and increases during differentiation. This temporally dynamic expression pattern suggests that MAPT expression could be controlled by transcription factors and cis-regulatory elements specific to differentiated cell types. Given the relevance of MAPT expression to neurodegeneration pathogenesis, identification of such elements is relevant to understanding disease risk and pathogenesis. Here, we performed chromatin conformation assays (HiC & Capture-C), single-nucleus multiomics (RNA-seq+ATAC-seq), bulk ATAC-seq, and ChIP-seq for H3K27ac and CTCF in NPCs and differentiated neurons to nominate candidate cis-regulatory elements (cCREs). We assayed these cCREs using luciferase assays and CRISPR interference (CRISPRi) experiments to measure their effects on MAPT expression. Finally, we integrated cCRE annotations into an analysis of genetic variation in neurodegeneration-affected individuals and control subjects. We identified both proximal and distal regulatory elements for MAPT and confirmed the regulatory function for several regions, including three regions centromeric to MAPT beyond the H1/H2 haplotype inversion breakpoint. We also found that rare and predicted damaging genetic variation in nominated CREs was nominally depleted in dementia-affected individuals relative to control subjects, consistent with the hypothesis that variants that disrupt MAPT enhancer activity, and thereby reduced MAPT expression, may be protective against neurodegenerative disease. Overall, this study provides compelling evidence for pursuing detailed knowledge of CREs for genes of interest to permit better understanding of disease risk.

Probabilistic association of differentially expressed genes with cis-regulatory elements.

Differential gene expression in response to perturbations is mediated at least in part by changes in binding of transcription factors (TFs) and other proteins at specific genomic regions. Association of these cis-regulatory elements (CREs) with their target genes is a challenging task that is essential to address many biological and mechanistic questions. Many current approaches rely on chromatin conformation capture techniques or single-cell correlational methods to establish CRE-to-gene associations. These methods can be effective but have limitations, including resolution, gaps in detectable association distances, and cost. As an alternative, we have developed DegCre, a nonparametric method that evaluates correlations between measurements of perturbation-induced differential gene expression and differential regulatory signal at CREs to score possible CRE-to-gene associations. It has several unique features, including the ability to use any type of CRE activity measurement, yield probabilistic scores for CRE-to-gene pairs, and assess CRE-to-gene pairings across a wide range of sequence distances. We apply DegCre to six data sets, each using different perturbations and containing a variety of regulatory signal measurements, including chromatin openness, histone modifications, and TF occupancy. To test their efficacy, we compare DegCre associations to Hi-C loop calls and CRISPR-validated CRE-to-gene associations, establishing good performance by DegCre that is comparable or superior to competing methods. DegCre is a novel approach to the association of CREs to genes from a perturbation-differential perspective, with strengths that are complementary to existing approaches and allow for new insights into gene regulation.

Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands.

Massively parallel reporter assays (MPRAs) are useful tools to characterize regulatory elements in human genomes. An aspect of MPRAs that is not typically the focus of analysis is their intrinsic ability to differentiate activity levels for a given sequence element when placed in both of its possible orientations relative to the reporter construct. Here, we describe pervasive strand asymmetry of MPRA signals in data sets from multiple reporter configurations in both published and newly reported data. These effects are reproducible across different cell types and in different treatments within a cell type and are observed both within and outside of annotated regulatory elements. From elements in gene bodies, MPRA strand asymmetry favors the sense strand, suggesting that function related to endogenous transcription is driving the phenomenon. Similarly, we find that within Alu mobile element insertions, strand asymmetry favors the transcribed strand of the ancestral retrotransposon. The effect is consistent across the multiplicity of Alu elements in human genomes and is more pronounced in less diverged Alu elements. We find sequence features driving MPRA strand asymmetry and show its prediction from sequence alone. We see some evidence for RNA stabilization and transcriptional activation mechanisms and hypothesize that the effect is driven by natural selection favoring efficient transcription. Our results indicate that strand asymmetry is a pervasive and reproducible feature in MPRA data. More importantly, the fact that MPRA asymmetry favors naturally transcribed strands suggests that it stems from preserved biological functions that have a substantial, global impact on gene and genome evolution.

Buprenorphine for acute pain in older adults: a systematic review with meta-analysis.

BACKGROUND: Buprenorphine, a partial opioid agonist, has emerging evidence as an alternative to full agonist opioids for treatment of acute pain. This systematic review aimed to evaluate the safety and efficacy of buprenorphine for acute pain in older adults. METHODS: PubMed Medline, Embase, Cochrane Central Register of Controlled Trials, CINHAL, Web of Science database, and Google Scholar were searched. We included articles that reported buprenorphine as an intervention to treat acute pain among patients 60 years or older. Primary outcome was difference in pain scores for patients treated with buprenorphine compared to other analgesia. Secondary outcomes included adverse events, opioid consumption, and patient satisfaction. Meta-analysis was conducted on difference in pain scores and differences in nausea and vomiting. RESULTS: Twenty-two studies were included (n = 2610). Buprenorphine was administered as nerve blocks in six studies, transdermal in eight, intravenous or intramuscular in five, sublingual in two studies, and both intravenous and sublingual in one study. 10 out of 20 (50%) studies found improved pain control in buprenorphine groups. Meta-analysis found no significant difference in pain scores between buprenorphine and control analgesia at 24 hours (Cohen's d = -0.29 [95% CI -0.85 to 0.27]) and 7 days (Cohen's d = -0.89 [95% CI -2.66-0.88]). Six studies (54.5%) found reduced opioid consumption in patients receiving buprenorphine. There was no difference in adverse effects in most studies. CONCLUSIONS: This review did not find buprenorphine to be superior to alternative analgesia; however the mixed results provide scientific rationale for future studies testing buprenorphine in older populations.

Is the Compassion of Anesthesiologists Associated With Postoperative Pain and Patient Experience? A Prospective Cohort Study.

BACKGROUND: Patient perception of physician compassion may be associated with improved health outcomes, yet it is unclear whether it is associated with postoperative pain reduction or improved patient experience metrics in same-day surgery patients. We hypothesized that higher anesthesiologist compassion during the preanesthesia interview, rated by patients, is associated with lower postoperative pain via the anxiety pathway in same-day surgery patients. We also performed exploratory correlation analysis to assess whether compassion was associated with less opioid consumption and improved patient experience in same-day surgery patients. METHODS: We conducted a single-center, prospective, observational cohort study in American Society of Anesthesiologists (ASA) physical status I to III patients scheduled to undergo same-day surgery with anesthesia. Compassion was scored using a validated 5-item tool. State anxiety (SA) and trait anxiety (TA) were measured using the State-Trait Anxiety Inventory. Pain scores were obtained using a 0 to 10 Likert scale. Daily opioid use was recorded. Patient experience was assessed using the Consumer Assessment of Healthcare Providers and Systems Outpatient and Ambulatory Surgery Survey (OAS CAHPS) and the Surgical Care CAHPS. Mediation analysis was used to assess the association between compassion and pain scores via the anxiety pathway. Spearman correlation was performed to test for association between the compassion score and the secondary outcomes. RESULTS: A total of 147 subjects completed the study with a median age of 50 years and 81% female. Fifty percent underwent breast surgery, 35% abdominal surgery, and the rest underwent gynecological and urological surgeries. The median (Q1-Q3) postoperative pain scores on postoperative days 0 and 3 days later were 4 (1.5-6) and 3 (1-5), respectively.Mediation analysis results showed a same-day anxiety-mediated effect (95% confidence interval [CI]) of compassion on pain of -0.08 (-0.13 to -0.02), attributing to 9% of the total effect. On postoperative day 0, an increase in compassion was associated with a significant average drop in pain of between 0.02 and 0.13. In addition, higher compassion was correlated with better patient experience metrics (ρ= -0.53 [95% CI, -0.64 to -0.39]). CONCLUSIONS: The study results suggest that an anxiety-mediated pathway exists through which compassionate care may help improve the patient's perception of postoperative pain on the day of surgery (before discharge from the hospital). Higher compassion was also associated with better patient experience metrics.

Partial pressure of carbon dioxide/pH interaction and its association with mortality among patients mechanically ventilated in the emergency department.

OBJECTIVES: There is currently conflicting data as to the effects of hypercapnia on clinical outcomes among mechanically ventilated patients in the emergency department (ED). These conflicting results may be explained by the degree of acidosis. We sought to test the hypothesis that hypercapnia is associated with increased in-hospital mortality and decreased ventilator-free days at lower pH, but associated with decreased in-hospital mortality and increased ventilator-free days at higher pH, among patients requiring mechanical ventilation in the emergency department (ED). METHODS: Secondary analysis of patient level data from prior clinical trials and cohort studies that enrolled adult patients who required mechanical ventilation in the ED. Patients who had a documented blood gas while on mechanical ventilation in the ED were included in these analyses. The primary outcome was in-hospital mortality, and secondary outcome was ventilator-free days. Mixed-effects logistic, linear, and survival-time regression models were used to test if pH modified the association between partial pressure of carbon dioxide (pCO2) and outcome measures. RESULTS: Of the 2348 subjects included, the median [interquartile range (IQR)] pCO2 was 43 (35-54) and pH was 7.31 (7.22-7.39). Overall, in-hospital mortality was 27%. We found pH modified the association between pCO2 and outcomes, with higher pCO2 associated with increased probability of in-hospital mortality when pH is below 7.00, and decreased probability of in-hospital mortality when pH is above 7.10. These results remained consistent across multiple sensitivity and subgroup analyses. A similar relationship was found with ventilator-free days. CONCLUSIONS: Higher pCO2 is associated with decreased mortality and greater ventilator-free days when pH is >7.10; however, it is associated with increased mortality and fewer ventilator-free days when the pH is below 7.00. Targeting pCO2 based on pH in the ED may be a potential intervention target for future clinical trials to improve clinical outcomes.

The Practice Change and Clinical Impact of Lung-Protective Ventilation Initiated in the Emergency Department: A Secondary Analysis of Individual Patient-Level Data From Prior Clinical Trials and Cohort Studies.

OBJECTIVES: Mechanically ventilated emergency department (ED) patients experience high morbidity and mortality. In a prior trial at our center, ED-based lung-protective ventilation was associated with improved care delivery and outcomes. Whether this strategy has persisted in the years after the trial remains unclear. The objective was to assess practice change and clinical outcomes associated with ED lung-protective ventilation. DESIGN: Secondary analysis of individual patient-level data from prior clinical trials and cohort studies. SETTING: ED and ICUs of a single academic center. PATIENTS: Mechanically ventilated adults. INTERVENTIONS: A lung-protective ventilator protocol used as the default approach in the ED. MEASUREMENTS AND MAIN RESULTS: The primary ventilator-related outcome was tidal volume, and the primary clinical outcome was hospital mortality. Secondary outcomes included ventilator-, hospital-, and ICU-free days. Multivariable logistic regression, propensity score (PS)-adjustment, and multiple a priori subgroup analyses were used to evaluate outcome as a function of the intervention. A total of 1,796 patients in the preintervention period and 1,403 patients in the intervention period were included. In the intervention period, tidal volume was reduced from 8.2 mL/kg predicted body weight (PBW) (7.3-9.1) to 6.5 mL/kg PBW (6.1-7.1), and low tidal volume ventilation increased from 46.8% to 96.2% ( p < 0.01). The intervention period was associated with lower mortality (35.9% vs 19.1%), remaining significant after multivariable logistic regression analysis (adjusted odds ratio [aOR], 0.43; 95% CI, 0.35-0.53; p < 0.01). Similar results were seen after PS adjustment and in subgroups. The intervention group had more ventilator- (18.8 [10.1] vs 14.1 [11.9]; p < 0.01), hospital- (12.2 [9.6] vs 9.4 [9.5]; p < 0.01), and ICU-free days (16.6 [10.1] vs 13.1 [11.1]; p < 0.01). CONCLUSIONS: ED lung-protective ventilation has persisted in the years since implementation and was associated with improved outcomes. These data suggest the use of ED-based lung-protective ventilation as a means to improve outcome.

Arterial to end-tidal carbon dioxide gap and its characterization in mechanically ventilated adults in the emergency department.

PURPOSE: To evaluate early measurement of the arterial to end-tidal carbon dioxide (PaCO2-PetCO2) gap, a surrogate for physiologic dead space, and its association with clinical outcomes in intubated adults in the emergency department (ED). MATERIALS AND METHODS: Observational cohort study of invasively mechanically ventilated adults in an academic medical center (years 2009 to 2016). The association of the PaCO2-PetCO2 gap was evaluated with respect to clinical outcomes; the primary outcome was in-hospital mortality. RESULTS: 519 patients were included. 325 (63%) patients had an elevated (>5 mmHg) PaCO2-PetCO2. Patients with an elevated PaCO2-PetCO2 were significantly older, had higher APACHE II scores, more frequently had chronic obstructive pulmonary disease (COPD), had lower arterial oxygen to fraction of inspired oxygen (P:F) ratios, and were more likely to be intubated for exacerbation of COPD or sepsis. There was no difference in mortality for patients with an elevated PaCO2-PetCO2 (25% vs 26%) in unadjusted analysis (p = 0.829) or adjusted analysis (aOR = 0.81 [95% CI: 0.53-1.26]), as compared to a non-elevated PaCO2-PetCO2. CONCLUSIONS: An elevated PaCO2-PetCO2 gap is common in the post-intubation period in the ED, but not significantly associated with clinical outcomes.

Asymmetric effects of sudden changes in timbre on auditory stream segregation.

Two experiments explored the effects of abrupt transitions in timbral properties [amplitude modulation (AM), pure tones vs narrow-band noises, and attack/decay envelope] on streaming. Listeners reported continuously the number of streams heard during 18-s-long alternating low- and high-frequency (LHL-) sequences (frequency separation: 2-6 semitones) that underwent a coherent transition at 6 s or remained unchanged. In experiment 1, triplets comprised unmodulated pure tones or 100%-depth AM was created using narrowly spaced tone pairs (dyads: 30- or 50-Hz modulation). In experiment 2, triplets comprised narrow-band noises, dyads, or pure tones with quasi-trapezoidal envelopes (10/80/10 ms), fast attacks and slow decays (10/90 ms), or vice versa (90/10 ms). Abrupt transitions led to direction-dependent changes in stream segregation. Transitions from modulated to unmodulated (or slower-modulated) tones, from noise bands to pure tones, or from slow- to fast-attack tones typically caused substantial loss of segregation (resetting), whereas transitions in the opposite direction mostly caused less or no resetting. Furthermore, for the smallest frequency separation, transitions in the latter direction usually led to increased segregation (overshoot). Overall, the results are reminiscent of the perceptual asymmetries found in auditory search for targets with or without a salient additional feature (or greater activation of that feature).

Dynamics of microRNA expression during mouse prenatal development.

MicroRNAs (miRNAs) play a critical role as posttranscriptional regulators of gene expression. The ENCODE Project profiled the expression of miRNAs in an extensive set of organs during a time-course of mouse embryonic development and captured the expression dynamics of 785 miRNAs. We found distinct organ-specific and developmental stage-specific miRNA expression clusters, with an overall pattern of increasing organ-specific expression as embryonic development proceeds. Comparative analysis of conserved miRNAs in mouse and human revealed stronger clustering of expression patterns by organ type rather than by species. An analysis of messenger RNA expression clusters compared with miRNA expression clusters identifies the potential role of specific miRNA expression clusters in suppressing the expression of mRNAs specific to other developmental programs in the organ in which these miRNAs are expressed during embryonic development. Our results provide the most comprehensive time-course of miRNA expression as part of an integrated ENCODE reference data set for mouse embryonic development.

Low Tidal Volume Ventilation for Emergency Department Patients: A Systematic Review and Meta-Analysis on Practice Patterns and Clinical Impact.

OBJECTIVES: Data suggest that low tidal volume ventilation (LTVV) initiated in the emergency department (ED) has a positive impact on outcome. This systematic review and meta-analysis quantify the impact of ED-based LTVV on outcomes and ventilator settings in the ED and ICU. DATA SOURCES: We systematically reviewed MEDLINE, EMBASE, Scopus, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, references, conferences, and ClinicalTrials.gov. STUDY SELECTION: Randomized and nonrandomized studies of mechanically ventilated ED adults were eligible. DATA EXTRACTION: Two reviewers independently screened abstracts. The primary outcome was mortality. Secondary outcomes included ventilation duration, lengths of stay, and occurrence rate of acute respiratory distress syndrome (ARDS). We assessed impact of ED LTVV interventions on ED and ICU tidal volumes. DATA SYNTHESIS: The search identified 1,023 studies. Eleven studies (n = 12,912) provided outcome data and were meta-analyzed; 10 additional studies (n = 1,863) provided descriptive ED tidal volume data. Overall quality of evidence was low. Random effect meta-analytic models revealed that ED LTVV was associated with lower mortality (26.5%) versus non-LTVV (31.1%) (odds ratio, 0.80 [0.72-0.88]). ED LTVV was associated with shorter ICU (mean difference, -1.0; 95% CI, -1.7 to -0.3) and hospital (mean difference, -1.2; 95% CI, -2.3 to -0.1) lengths of stay, more ventilator-free days (mean difference, 1.4; 95% CI, 0.4-2.4), and lower occurrence rate (4.5% vs 8.3%) of ARDS (odds ratio, 0.57 [0.44-0.75]). ED LTVV interventions were associated with reductions in ED (-1.5-mL/kg predicted body weight [PBW] [-1.9 to -1.0]; p < 0.001) and ICU (-1.0-mL/kg PBW [-1.8 to -0.2]; p = 0.01) tidal volume. CONCLUSIONS: The use of LTVV in the ED is associated with improved clinical outcomes and increased use of lung protection, recognizing low quality of evidence in this domain. Interventions aimed at implementing and sustaining LTVV in the ED should be explored.

Awareness With Paralysis Among Critically Ill Emergency Department Patients: A Prospective Cohort Study.

OBJECTIVES: In mechanically ventilated patients, awareness with paralysis (AWP) can have devastating consequences, including post-traumatic stress disorder (PTSD), depression, and thoughts of suicide. Single-center data from the emergency department (ED) demonstrate an event rate for AWP factors higher than that reported from the operating room. However, there remains a lack of data on AWP among critically ill, mechanically ventilated patients. The objective was to assess the proportion of ED patients experiencing AWP and investigate modifiable variables associated with its occurrence. DESIGN: An a priori planned secondary analysis of a multicenter, prospective, before-and-after clinical trial. SETTING: The ED of three academic medical centers. PATIENTS: Mechanically ventilated adult patients that received neuromuscular blockers. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: All data related to sedation and analgesia were collected. AWP was the primary outcome, assessed with the modified Brice questionnaire, and was independently adjudicated by three expert reviewers. Perceived threat, in the causal pathway for PTSD, was the secondary outcome. A total of 388 patients were studied. The proportion of patients experiencing AWP was 3.4% ( n = 13), the majority of whom received rocuronium ( n = 12/13; 92.3%). Among patients who received rocuronium, 5.5% ( n = 12/230) experienced AWP, compared with 0.6% ( n = 1/158) among patients who did not receive rocuronium in the ED (odds ratio, 8.64; 95% CI, 1.11-67.15). Patients experiencing AWP had a higher mean ( sd ) threat perception scale score, compared with patients without AWP (15.6 [5.8] vs 7.7 [6.0]; p < 0.01). CONCLUSIONS: AWP was present in a concerning proportion of mechanically ventilated ED patients, was associated with rocuronium exposure in the ED, and led to increased levels of perceived threat, placing patients at greater risk for PTSD. Studies that aim to further quantify AWP in this vulnerable population and eliminate its occurrence are urgently needed.

The Feasibility of Implementing Targeted SEDation in Mechanically Ventilated Emergency Department Patients: The ED-SED Pilot Trial.

OBJECTIVES: Deep sedation in the emergency department (ED) is common, increases deep sedation in the ICU, and is negatively associated with outcome. Limiting ED deep sedation may, therefore, be a high-yield intervention to improve outcome. However, the feasibility of conducting an adequately powered ED-based clinical sedation trial is unknown. Our objectives were to assess trial feasibility in terms of: 1) recruitment, 2) protocol implementation and practice change, and 3) safety. Patient-centered clinical outcomes were assessed to better plan for a future large-scale clinical trial. DESIGN: Pragmatic, multicenter ( n = 3), prospective before-after pilot and feasibility trial. SETTING: The ED and ICUs at three medical centers. PATIENTS: Consecutive, adult mechanically ventilation ED patients. INTERVENTIONS: An educational initiative aimed at reliable ED sedation depth documentation and reducing the proportion of deeply sedated patients (primary outcome). MEASUREMENTS AND MAIN RESULTS: Sedation-related data in the ED and the first 48 ICU hours were recorded. Deep sedation was defined as a Richmond Agitation-Sedation Scale of -3 to -5 or a Sedation-Agitation Scale of 1-3. One thousand three hundred fifty-six patients were screened; 415 comprised the final population. Lighter ED sedation was achieved in the intervention group, and the proportion of deeply sedated patients was reduced from 60.2% to 38.8% ( p < 0.01). There were no concerning trends in adverse events (i.e., inadvertent extubation, device removal, and awareness with paralysis). Mortality was 10.0% in the intervention group and 20.4% in the preintervention group ( p < 0.01). Compared with preintervention, the intervention group experienced more ventilator-free days [22.0 (9.0) vs 19.9 (10.6)] and ICU-free days [20.8 (8.7) vs 18.1 (10.4)], p < 0.05 for both. CONCLUSIONS: This pilot trial confirmed the feasibility of targeting the ED in order to improve sedation practices and reduce deep sedation. These findings justify an appropriately powered clinical trial regarding ED-based sedation to improve clinical outcomes.

Validation of a 5-Item Tool to Measure Patient Assessment of Clinician Compassion in Hospitals.

BACKGROUND: We previously validated a 5-item compassion measure to assess patient experience of clinician compassion in the outpatient setting. However, currently, there is no validated and feasible method for health care systems to measure patient experience of clinician compassion in the inpatient setting across multiple hospitals. OBJECTIVE: To test if the 5-item compassion measure can validly and distinctly measure patient assessment of physician and nurse compassion in the inpatient setting. DESIGN: Cross-sectional study between July 1 and July 31, 2020, in a US health care network of 91 community hospitals across 16 states consisting of approximately 15,000 beds. PATIENTS: Adult patients who had an inpatient hospital stay and completed the Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) survey. MEASUREMENTS: We adapted the original 5-item compassion measure to be specific for physicians, as well as for nurses. We disseminated both measures with the HCAHPS survey and used confirmatory factor analysis for validity testing. We tested reliability using Cronbach's alpha, as well as convergent validity with patient assessment of physician and nursing communication and overall hospital rating questions from HCAHPS. RESULTS: We analyzed 4756 patient responses. Confirmatory factor analysis found good fit for two distinct constructs (i.e., physician and nurse compassion). Both measures demonstrated good internal consistency (alpha > 0.90) and good convergent validity but reflected a construct (compassionate care) distinct from what is currently captured in HCAHPS. CONCLUSION: We validated two 5-item tools that can distinctly measure patient experience of physician and nurse compassion for use in the inpatient hospital setting in conjunction with HCAHPS.

Meta-analysis of salt marsh vegetation impacts and recovery: a synthesis following the Deepwater Horizon oil spill.

Marine oil spills continue to be a global issue, heightened by spill events such as the 2010 Deepwater Horizon spill in the Gulf of Mexico, the largest marine oil spill in US waters and among the largest worldwide, affecting over 1,000 km of sensitive wetland shorelines, primarily salt marshes supporting numerous ecosystem functions. To synthesize the effects of the oil spill on foundational vegetation species in the salt marsh ecosystem, Spartina alterniflora and Juncus roemerianus, we performed a meta-analysis using data from 10 studies and 255 sampling sites over seven years post-spill. We examined the hypotheses that the oil spill reduced plant cover, stem density, vegetation height, aboveground biomass, and belowground biomass, and tracked the degree of effects temporally to estimate recovery time frames. All plant metrics indicated impacts from oiling, with 20-100% maximum reductions depending on oiling level and marsh zone. Peak reductions of ~70-90% in total plant cover, total aboveground biomass, and belowground biomass were observed for heavily oiled sites at the marsh edge. Both Spartina and Juncus were impacted, with Juncus affected to a greater degree. Most plant metrics had recovery time frames of three years or longer, including multiple metrics with incomplete recovery over the duration of our data, at least seven years post-spill. Belowground biomass was particularly concerning, because it declined over time in contrast with recovery trends in most aboveground metrics, serving as a strong indicator of ongoing impact, limited recovery, and impaired resilience. We conclude that the Deepwater Horizon spill had multiyear impacts on salt marsh vegetation, with full recovery likely to exceed 10 years, particularly in heavily oiled marshes, where erosion may preclude full recovery. Vegetation impacts and delayed recovery is likely to have exerted substantial influences on ecosystem processes and associated species, especially along heavily oiled shorelines. Our synthesis affords a greater understanding of ecosystem impacts and recovery following the Deepwater Horizon oil spill, and informs environmental impact analysis, contingency planning, emergency response, damage assessment, and restoration efforts related to oil spills.

A dual-center cohort study on the association between early deep sedation and clinical outcomes in mechanically ventilated patients during the COVID-19 pandemic: The COVID-SED study.

BACKGROUND: Mechanically ventilated patients have experienced greater periods of prolonged deep sedation during the coronavirus disease (COVID-19) pandemic. Multiple studies from the pre-COVID era demonstrate that early deep sedation is associated with worse outcome. Despite this, there is a lack of data on sedation depth and its impact on outcome for mechanically ventilated patients during the COVID-19 pandemic. We sought to characterize the emergency department (ED) and intensive care unit (ICU) sedation practices during the COVID-19 pandemic, and to determine if early deep sedation was associated with worse clinical outcomes. STUDY DESIGN AND METHODS: Dual-center, retrospective cohort study conducted over 6 months (March-August, 2020), involving consecutive, mechanically ventilated adults. All sedation-related data during the first 48 h were collected. Deep sedation was defined as Richmond Agitation-Sedation Scale of - 3 to - 5 or Riker Sedation-Agitation Scale of 1-3. To examine impact of early sedation depth on hospital mortality (primary outcome), we used a multivariable logistic regression model. Secondary outcomes included ventilator-, ICU-, and hospital-free days. RESULTS: 391 patients were studied, and 283 (72.4%) experienced early deep sedation. Deeply sedated patients received higher cumulative doses of fentanyl, propofol, midazolam, and ketamine when compared to light sedation. Deep sedation patients experienced fewer ventilator-, ICU-, and hospital-free days, and greater mortality (30.4% versus 11.1%) when compared to light sedation (p < 0.01 for all). After adjusting for confounders, early deep sedation remained significantly associated with higher mortality (adjusted OR 3.44; 95% CI 1.65-7.17; p < 0.01). These results were stable in the subgroup of patients with COVID-19. CONCLUSIONS: The management of sedation for mechanically ventilated patients in the ICU has changed during the COVID pandemic. Early deep sedation is common and independently associated with worse clinical outcomes. A protocol-driven approach to sedation, targeting light sedation as early as possible, should continue to remain the default approach.

Effects of stimulus naturalness and contralateral interferers on lexical bias in consonant identification.

Lexical bias is the tendency to perceive an ambiguous speech sound as a phoneme completing a word; more ambiguity typically causes greater reliance on lexical knowledge. A speech sound ambiguous between /g/ and /k/ is more likely to be perceived as /g/ before /ɪft/ and as /k/ before /ɪs/. The magnitude of this difference-the Ganong shift-increases when high cognitive load limits available processing resources. The effects of stimulus naturalness and informational masking on Ganong shifts and reaction times were explored. Tokens between /gɪ/ and /kɪ/ were generated using morphing software, from which two continua were created ("giss"-"kiss" and "gift"-"kift"). In experiment 1, Ganong shifts were considerably larger for sine- than noise-vocoded versions of these continua, presumably because the spectral sparsity and unnatural timbre of the former increased cognitive load. In experiment 2, noise-vocoded stimuli were presented alone or accompanied by contralateral interferers with constant within-band amplitude envelope, or within-band envelope variation that was the same or different across bands. The latter, with its implied spectro-temporal variation, was predicted to cause the greatest cognitive load. Reaction-time measures matched this prediction; Ganong shifts showed some evidence of greater lexical bias for frequency-varying interferers, but were influenced by context effects and diminished over time.

Seasonal impoundment management reduces nitrogen cycling but not resilience to surface fire in a tidal wetland.

Hydrology and salinity regimes of many impounded wetlands are manipulated to provide seasonal habitats for migratory waterfowl, with little-known consequences for ecosystem structure and function. Managed hydrology can alter ecosystems by directly changing soil properties and processes and by influencing plant community dynamics. Additionally, management history may influence ecosystem response to disturbance, including fires. To better understand how wetland management regime influences ecosystem response to disturbance, we quantified elevation, soil nitrogen concentrations and process rates, and plant community structure and diversity in a natural experiment following the 2018 Branscombe Fire. We measured paired burned-unburned patches in both tidally-influenced and managed, seasonally-impounded wetlands in Suisun Marsh, California, USA. Unburned ecosystem structure and nutrient cycling differed by wetland management history; unburned impounded wetlands were ∼1 m lower in elevation and plant community composition was dominated by succulents whereas the unburned tidal wetland was dominated by graminoids. Unburned impounded wetland soil nitrogen cycling (potential nitrification and denitrification) rates were <28% of those measured in unburned tidal wetland soils and soil extractable nitrate, ammonium, and dissolved inorganic phosphorus concentrations were also substantially lower in unburned impounded than unburned tidal wetlands. Despite these differences in pre-disturbance (i.e., unburned) conditions, all soil processes recovered to baseline levels within 6 months after surface fire, and we found no evidence of plant community change 1 year after fire in either wetland management type. Overall, water management history exerted stronger control on ecosystem processes and structure than surface fire disturbance. Low extractable soil nitrate and potential denitrification rates may indicate limitation of soil nitrogen removal in impounded wetlands, with implications for downstream environmental quality and eutrophication across managed landscapes.

Identification of a potent regulatory T cell epitope in factor V that modulates CD4+ and CD8+ memory T cell responses.

Identification of T cell epitopes that are recognized by Tregs may elucidate the relative contributions of thymic Tregs and induced Tregs to control of autoimmune diseases and allergy. One such T regulatory cell epitope or 'Tregitope', derived from blood Factor V, is described here. Tregs responding to Tregitope FV621 are potent suppressors of CD4+ T effector responses to Tetanus Toxoid in an in vitro bystander suppression assay, strongly inhibit proliferation of effector CD8+ T cells, down-modulate CD86 and HLA DR on antigen-presenting cells, and enhance expression of granzyme B in Tregs. Tregitope FV621 also suppresses anti-OVA immune responses in vivo. The immunomodulatory effect of Tregitope FV621 is enhanced when conjugated to albumin, suggesting that the short half-life of Tregitope peptides can be prolonged. The in silico tools used to prospectively identify the FV Tregitope described here, when combined with in vitro /in vivo validating assays, may facilitate future Tregitope discoveries.

Awareness With Paralysis in Mechanically Ventilated Patients in the Emergency Department and ICU: A Systematic Review and Meta-Analysis.

OBJECTIVE: Awareness with paralysis is a devastating complication for mechanically ventilated patients and can carry long-term psychologic sequelae. Hundreds of thousands of patients require mechanical ventilation in the emergency department and ICU annually, yet awareness has only been rigorously examined in the operating room (incidence ~0.1%). This report collates the global literature regarding the incidence of awareness with paralysis outside of the operating room. DATA SOURCES: We searched OvidMedline, Embase, Scopus, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, ClinicalTrials.gov, conference proceedings, and reference lists. STUDY SELECTION: Randomized or nonrandomized studies (except single case studies) reporting on awareness with paralysis in the emergency department or ICU were eligible. DATA EXTRACTION: Two independent reviewers screened abstracts for eligibility. DATA SYNTHESIS: The search identified 4,454 potentially eligible studies. Seven studies (n = 941 patients) were included for analysis. A random effects meta-analysis of proportions along with multiple subgroup analyses was performed. Significant between-study heterogeneity in reporting of awareness with paralysis was noted, and the quality of the evidence was low. Analyses stratified by: 1) good-quality studies and 2) use of the modified Brice questionnaire to detect awareness revealed estimates of 3.4% (95% CI, 0-10.2%) and 1.9% (95% CI, 1.0-3.0%), respectively. CONCLUSIONS: The incidence of awareness with paralysis in mechanically ventilated patients in the emergency department and ICU, as evaluated in a small number of qualifying studies from this comprehensive systematic review, appears much higher than that reported from the operating room. Given the clinical and statistical heterogeneity, caution is warranted in the interpretation of these findings. Further high-quality studies are needed to both define the true incidence and to target the prevention of awareness with paralysis in this vulnerable patient cohort.