Far-red and sensitive sensor for monitoring real time H2O2 dynamics with subcellular resolution and in multi-parametric imaging applications.

H2O2 is a key oxidant in mammalian biology and a pleiotropic signaling molecule at the physiological level, and its excessive accumulation in conjunction with decreased cellular reduction capacity is often found to be a common pathological marker. Here, we present a red fluorescent Genetically Encoded H2O2 Indicator (GEHI) allowing versatile optogenetic dissection of redox biology. Our new GEHI, oROS-HT, is a chemigenetic sensor utilizing a HaloTag and Janelia Fluor (JF) rhodamine dye as fluorescent reporters. We developed oROS-HT through a structure-guided approach aided by classic protein structures and recent protein structure prediction tools. Optimized with JF635, oROS-HT is a sensor with 635 nm excitation and 650 nm emission peaks, allowing it to retain its brightness while monitoring intracellular H2O2 dynamics. Furthermore, it enables multi-color imaging in combination with blue-green fluorescent sensors for orthogonal analytes and low auto-fluorescence interference in biological tissues. Other advantages of oROS-HT over alternative GEHIs are its fast kinetics, oxygen-independent maturation, low pH sensitivity, lack of photo-artifact, and lack of intracellular aggregation. Here, we demonstrated efficient subcellular targeting and how oROS-HT can map inter and intracellular H2O2 diffusion at subcellular resolution. Lastly, we used oROS-HT with other green fluorescence reporters to investigate the transient effect of the anti-inflammatory agent auranofin on cellular redox physiology and calcium levels via multi-parametric, dual-color imaging.

Machine learning-guided engineering of genetically encoded fluorescent calcium indicators.

Here we used machine learning to engineer genetically encoded fluorescent indicators, protein-based sensors critical for real-time monitoring of biological activity. We used machine learning to predict the outcomes of sensor mutagenesis by analyzing established libraries that link sensor sequences to functions. Using the GCaMP calcium indicator as a scaffold, we developed an ensemble of three regression models trained on experimentally derived GCaMP mutation libraries. The trained ensemble performed an in silico functional screen on 1,423 novel, uncharacterized GCaMP variants. As a result, we identified the ensemble-derived GCaMP (eGCaMP) variants, eGCaMP and eGCaMP+, which achieve both faster kinetics and larger ∆F/F0 responses upon stimulation than previously published fast variants. Furthermore, we identified a combinatorial mutation with extraordinary dynamic range, eGCaMP2+, which outperforms the tested sixth-, seventh- and eighth-generation GCaMPs. These findings demonstrate the value of machine learning as a tool to facilitate the efficient engineering of proteins for desired biophysical characteristics.

Far-red and sensitive sensor for monitoring real time H2O2 dynamics with subcellular resolution and in multi-parametric imaging applications.

H2O2 is a key oxidant in mammalian biology and a pleiotropic signaling molecule at the physiological level, and its excessive accumulation in conjunction with decreased cellular reduction capacity is often found to be a common pathological marker. Here, we present a red fluorescent Genetically Encoded H2O2 Indicator (GEHI) allowing versatile optogenetic dissection of redox biology. Our new GEHI, oROS-HT, is a chemigenetic sensor utilizing a HaloTag and Janelia Fluor (JF) rhodamine dye as fluorescent reporters. We developed oROS-HT through a structure-guided approach aided by classic protein structures and recent protein structure prediction tools. Optimized with JF635, oROS-HT is a sensor with 635 nm excitation and 650 nm emission peaks, allowing it to retain its brightness while monitoring intracellular H2O2 dynamics. Furthermore, it enables multi-color imaging in combination with blue-green fluorescent sensors for orthogonal analytes and low auto-fluorescence interference in biological tissues. Other advantages of oROS-HT over alternative GEHIs are its fast kinetics, oxygen-independent maturation, low pH sensitivity, lack of photo-artifact, and lack of intracellular aggregation. Here, we demonstrated efficient subcellular targeting and how oROS-HT can map inter and intracellular H2O2 diffusion at subcellular resolution. Lastly, we used oROS-HT with the green fluorescent calcium indicator Fluo-4 to investigate the transient effect of the anti-inflammatory agent auranofin on cellular redox physiology and calcium levels via multi-parametric, dual-color imaging.

In-Hospital Amantadine Does Not Improve Outcomes After Severe Traumatic Brain Injury: An 11-Year Propensity-Matched Retrospective Analysis.

BACKGROUND: Disruption of dopamine neurotransmission is associated with functional impairment after severe traumatic brain injury (sTBI). This has prompted the study of dopamine agonists, such as amantadine, to assist recovery of consciousness. Randomized trials have mostly addressed the posthospital setting, with inconsistent findings. Therefore, we evaluated the efficacy of early amantadine administration on recovery of consciousness after sTBI. METHODS: We searched the medical records of all patients with sTBI admitted to our hospital between 2010 and 2021 who survived 10 days postinjury. We identified all patients receiving amantadine and compared them with all patients not receiving amantadine and a propensity score-matched nonamantadine group. Primary outcome measures included discharge Glasgow Coma Scale, Glasgow Outcome Scale-Extended score, length of stay, mortality, recovery of command-following (CF), and days to CF. RESULTS: In our study population, 60 patients received amantadine and 344 did not. Compared with the propensity score-matched nonamantadine group, the amantadine group had no difference in mortality (86.67% vs. 88.33%, P = 0.783), rates of CF (73.33% vs. 76.67%, P = 0.673), or percentage of patients with severe (3-8) discharge Glasgow Coma Scale scores (11.11% vs. 12.28%, P = 0.434). In addition, the amantadine group was less likely to have a favorable recovery (discharge Glasgow Outcome Scale-Extended score 5-8) (14.53% vs. 16.67%, P < 0.001), had a longer length of stay (40.5 vs. 21.0 days, P < 0.001), and had a longer time to CF (11.5 vs. 6.0 days, P = 0.011). No difference in adverse events existed between groups. CONCLUSIONS: Our findings do not support the early administration of amantadine for sTBI. Larger inpatient randomized trials are necessary to further investigate amantadine treatment for sTBI.

Machine learning meets Monte Carlo methods for models of muscle's molecular machinery to classify mutations.

The timing and magnitude of force generation by a muscle depend on complex interactions in a compliant, contractile filament lattice. Perturbations in these interactions can result in cardiac muscle diseases. In this study, we address the fundamental challenge of connecting the temporal features of cardiac twitches to underlying rate constants and their perturbations associated with genetic cardiomyopathies. Current state-of-the-art metrics for characterizing the mechanical consequence of cardiac muscle disease do not utilize information embedded in the complete time course of twitch force. We pair dimension reduction techniques and machine learning methods to classify underlying perturbations that shape the timing of twitch force. To do this, we created a large twitch dataset using a spatially explicit Monte Carlo model of muscle contraction. Uniquely, we modified the rate constants of this model in line with mouse models of cardiac muscle disease and varied mutation penetrance. Ultimately, the results of this study show that machine learning models combined with biologically informed dimension reduction techniques can yield excellent classification accuracy of underlying muscle perturbations.

Low-molecular-weight heparin compared with unfractionated heparin in critically ill COVID-19 patients.

BACKGROUND: Thrombosis in COVID-19 worsens mortality. In our study, we sought to investigate how the dose and type of anticoagulation (AC) can influence patient outcomes. METHODS: This is a single-center retrospective analysis of critically ill intubated patients with COVID-19, comparing low-molecular-weight heparin (LMWH) and unfractionated heparin (UFH) at therapeutic and prophylactic doses. Of 218 patients, 135 received LMWH (70 prophylactic, 65 therapeutic) and 83 UFH (11 prophylactic, 72 therapeutic). The primary outcome was mortality. Secondary outcomes were thromboembolic complications confirmed on imaging and major bleeding complications. Cox proportional-hazards regression models were used to determine whether the type and dose of AC were independent predictors of survival. We performed Kaplan-Meier survival analysis to compare the cumulative survivals. RESULTS: Overall, therapeutic AC, with either LMWH (65% vs 79%, P = .09) or UFH (32% vs 46%, P = .73), conveyed no survival benefit over prophylactic AC. UFH was associated with a higher mortality rate than LMWH (66% vs 28%, P = .001), which was also evident in the multivariable analysis (LMWH vs UFH mortality, hazard ratio: 0.47, P = .001) and in the Kaplan-Meier survival analysis. Thrombotic and bleeding complications did not depend on the AC type (prophylactic LMWH vs UFH: thrombosis P = .49, bleeding P = .075; therapeutic LMWH vs UFH: thrombosis P = .5, bleeding P = .17). When comparing prophylactic with therapeutic AC, the rate of both thrombotic and bleeding complications was higher with the use of LMWH compared with UFH. In addition, transfusion requirements were significantly higher with both therapeutic LMWH and UFH. CONCLUSIONS: Among intubated critically ill COVID-19 intensive care unit patients, therapeutic AC, with either LMWH or UFH, conveyed no survival benefit over prophylactic AC. AC with LMWH was associated with higher cumulative survival compared with AC with UFH.

Acute Gastrointestinal Injury and Feeding Intolerance as Prognostic Factors in Critically Ill COVID-19 Patients.

BACKGROUND: Although acute gastrointestinal injury (AGI) and feeding intolerance (FI) are known independent determinants of worse outcomes and high mortality in intensive care unit (ICU) patients, the incidence of AGI and FI in critically ill COVID-19 patients and their prognostic importance have not been thoroughly studied. METHODS: We reviewed 218 intubated patients at Stony Brook University Hospital and stratified them into three groups based on AGI severity, according to data collected in the first 10 days of ICU course. We used chi-square test to compare categorical variables such as age and sex and two-sample t-test or Mann-Whitney U-tests for continuous variables, including important laboratory values. Cox proportional hazards regression models were utilized to determine whether AGI score was an independent predictor of survival, and multivariable analysis was performed to compare risk factors that were deemed significant in the univariable analysis. We performed Kaplan-Meier survival analysis based on the AGI score and the presence of FI. RESULTS: The overall incidence of AGI was 95% (45% AGI I/II, 50% AGI III/IV), and FI incidence was 63%. Patients with AGI III/IV were more likely to have prolonged mechanical ventilation (22 days vs 16 days, P-value <0.002) and higher mortality rate (58% vs 28%, P-value <0.001) compared to patients with AGI 0/I/II. This was confirmed with multivariable analysis which showed that AGI score III/IV was an independent predictor of higher mortality (AGI III/IV vs AGI 0/I/II hazard ratio (HR), 2.68; 95% confidence interval (CI), 1.69-4.25; P-value <0.0001). Kaplan-Meier survival analysis showed that both AGI III/IV and FI (P-value <0.001) were associated with worse outcomes. Patients with AGI III/IV had higher daily and mean D-dimer and CRP levels compared to AGI 0/I/II (P-value <0.0001). CONCLUSIONS: The prevalence of AGI and FI among critically ill COVID-19 patients was high. AGI grades III/IV were associated with higher risk for prolonged mechanical ventilation and mortality compared to AGI 0/I/II, while it also correlated with higher D-dimer and C-reactive protein (CRP) levels. FI was independently associated with higher mortality. The development of high-grade AGI and FI during the first days of ICU stay can serve as prognostic tools to predict outcomes in critically ill COVID-19 patients.

Aggressive Anticoagulation May Decrease Mortality in Obese Critically Ill COVID-19 Patients.

BACKGROUND: Obesity is a widely accepted risk factor for the development of severe COVID-19. We sought to determine the survival benefit of early initiation of aggressive anticoagulation in obese critically ill COVID-19 patients. METHODS: We retrospectively reviewed 237 intubated patients at a single academic accredited bariatric center and stratified them based on their BMI into 2 groups, obese (BMI > 30) and non-obese (BMI ≤ 30). We used chi-square tests to compare categorical variables such as age and sex, and two-sample t-tests or Mann Whitney U-tests for continuous variables, including important laboratory values. Cox proportional-hazards regression models were utilized to determine whether obesity was an independent predictor of survival and multivariable analysis was performed to compare risk factors that were deemed significant in the univariable analysis. Survival with respect to BMI and its association with level of anticoagulation in the obese cohort was evaluated using Kaplan-Meier models. RESULTS: The overall mortality in the obese and non-obese groups was similar at 47% and 44%, respectively (p = 0.65). Further analysis based on the level of AC showed that obese patients placed on early aggressive AC protocol had improved survival compared to obese patients who did not receive protocol based aggressive AC (ON-aggressive AC protocol 26% versus OFF-aggressive AC protocol 61%, p = 0.0004). CONCLUSIONS: The implementation of early aggressive anticoagulation may balance the negative effects of obesity on the overall mortality in critically ill COVID-19 patients.

D-Dimer-Driven Anticoagulation Reduces Mortality in Intubated COVID-19 Patients: A Cohort Study With a Propensity-Matched Analysis.

Objective: Examine the possible beneficial effects of early, D-dimer driven anticoagulation in preventing thrombotic complications and improving the overall outcomes of COVID-19 intubated patients. Methods: To address COVID-19 hypercoagulability, we developed a clinical protocol to escalate anticoagulation based on serum D-dimer levels. We retrospectively reviewed all our first 240 intubated patients with COVID-19. Of the 240, 195 were stratified into patients treated based on this protocol (ON-protocol, n = 91) and the control group, patients who received standard thromboprophylaxis (OFF-protocol, n = 104). All patients were admitted to the Stony Brook University Hospital intensive care units (ICUs) between February 7th, 2020 and May 17, 2020 and were otherwise treated in the same manner for all aspects of COVID-19 disease. Results: We found that the overall mortality was significantly lower ON-protocol compared to OFF-protocol (27.47 vs. 58.66%, P < 0.001). Average maximum D-dimer levels were significantly lower in the ON-protocol group (7,553 vs. 12,343 ng/mL), as was serum creatinine (2.2 vs. 2.8 mg/dL). Patients with poorly controlled D-dimer levels had higher rates of kidney dysfunction and mortality. Transfusion requirements and serious bleeding events were similar between groups. To address any possible between-group differences, we performed a propensity-matched analysis of 124 of the subjects (62 matched pairs, ON-protocol and OFF-protocol), which showed similar findings (31 vs. 57% overall mortality in the ON-protocol and OFF-protocol group, respectively). Conclusions: D-dimer-driven anticoagulation appears to be safe in patients with COVID-19 infection and is associated with improved survival. What This Paper Adds: It has been shown that hypercoagulability in patients with severe COVID-19 infection leads to thromboembolic complications and organ dysfunction. Anticoagulation has been variably administered to these patients, but it is unknown whether routine or escalated thromboprophylaxis provides a survival benefit. Our data shows that escalated D-dimer driven anticoagulation is associated with improved organ function and overall survival in intubated COVID-19 ICU patients at our institution. Importantly, we found that timely escalation of this anticoagulation is critical in preventing organ dysfunction and mortality in patients with severe COVID-19 infection.

In vivo X-ray diffraction and simultaneous EMG reveal the time course of myofilament lattice dilation and filament stretch.

Muscle function within an organism depends on the feedback between molecular and meter-scale processes. Although the motions of muscle's contractile machinery are well described in isolated preparations, only a handful of experiments have documented the kinematics of the lattice occurring when multi-scale interactions are fully intact. We used time-resolved X-ray diffraction to record the kinematics of the myofilament lattice within a normal operating context: the tethered flight of Manduca sexta As the primary flight muscles of M.sexta are synchronous, we used these results to reveal the timing of in vivo cross-bridge recruitment, which occurred 24 ms (s.d. 26) following activation. In addition, the thick filaments stretched an average of 0.75% (s.d. 0.32) and thin filaments stretched 1.11% (s.d. 0.65). In contrast to other in vivo preparations, lattice spacing changed an average of 2.72% (s.d. 1.47). Lattice dilation of this magnitude significantly affects shortening velocity and force generation, and filament stretching tunes force generation. While the kinematics were consistent within individual trials, there was extensive variation between trials. Using a mechanism-free machine learning model we searched for patterns within and across trials. Although lattice kinematics were predictable within trials, the model could not create predictions across trials. This indicates that the variability we see across trials may be explained by latent variables occurring in this naturally functioning system. The diverse kinematic combinations we documented mirror muscle's adaptability and may facilitate its robust function in unpredictable conditions.