Comparison of i-gel® and LMA® Supreme™ for Facilitating Fiberoptic Endotracheal Intubation: A Prospective Randomized Trial.

Supraglottic airway (SGA) is an alternative to endotracheal intubation, however endotracheal intubation is often essential. One method to convert from an SGA to an endotracheal tube (ETT) is utilizing the SGA as a conduit for fiberoptic-guided advancement of an Aintree catheter (airway exchange catheter), and exchange of the SGA for an ETT. In this prospective randomized study, we compared two SGA devices in facilitating this exchange. Subjects were randomized to receive either the i-gel® or LMA® Supreme™ SGA. The SGA was placed and an Aintree intubation catheter was inserted through the SGA over a fiberoptic bronchoscope. Next, the SGA was removed, leaving the Aintree within the trachea, and an ETT was placed over the Aintree catheter and advanced into the trachea. The i-gel group exhibited shorter time to successful intubation (median, 191 vs. 434 seconds; P = .002). The i-gel group also had fewer study subjects requiring more than one attempt for successful Aintree placement (33% vs. 75%, P = .02). The i-gel group showed superior laryngeal view score (LVS) (6 vs. 4; P = .003). The i-gel SGA achieved a faster time to successful intubation, higher rate of first attempt Aintree placement, and superior LVS.

Welcome to the big leaves: Best practices for improving genome annotation in non-model plant genomes.

Premise: Robust standards to evaluate quality and completeness are lacking in eukaryotic structural genome annotation, as genome annotation software is developed using model organisms and typically lacks benchmarking to comprehensively evaluate the quality and accuracy of the final predictions. The annotation of plant genomes is particularly challenging due to their large sizes, abundant transposable elements, and variable ploidies. This study investigates the impact of genome quality, complexity, sequence read input, and method on protein-coding gene predictions. Methods: The impact of repeat masking, long-read and short-read inputs, and de novo and genome-guided protein evidence was examined in the context of the popular BRAKER and MAKER workflows for five plant genomes. The annotations were benchmarked for structural traits and sequence similarity. Results: Benchmarks that reflect gene structures, reciprocal similarity search alignments, and mono-exonic/multi-exonic gene counts provide a more complete view of annotation accuracy. Transcripts derived from RNA-read alignments alone are not sufficient for genome annotation. Gene prediction workflows that combine evidence-based and ab initio approaches are recommended, and a combination of short and long reads can improve genome annotation. Adding protein evidence from de novo assemblies, genome-guided transcriptome assemblies, or full-length proteins from OrthoDB generates more putative false positives as implemented in the current workflows. Post-processing with functional and structural filters is highly recommended. Discussion: While the annotation of non-model plant genomes remains complex, this study provides recommendations for inputs and methodological approaches. We discuss a set of best practices to generate an optimal plant genome annotation and present a more robust set of metrics to evaluate the resulting predictions.

Structural mechanism of mitochondrial membrane remodelling by human OPA1.

Distinct morphologies of the mitochondrial network support divergent metabolic and regulatory processes that determine cell function and fate1-3. The mechanochemical GTPase optic atrophy 1 (OPA1) influences the architecture of cristae and catalyses the fusion of the mitochondrial inner membrane4,5. Despite its fundamental importance, the molecular mechanisms by which OPA1 modulates mitochondrial morphology are unclear. Here, using a combination of cellular and structural analyses, we illuminate the molecular mechanisms that are key to OPA1-dependent membrane remodelling and fusion. Human OPA1 embeds itself into cardiolipin-containing membranes through a lipid-binding paddle domain. A conserved loop within the paddle domain inserts deeply into the bilayer, further stabilizing the interactions with cardiolipin-enriched membranes. OPA1 dimerization through the paddle domain promotes the helical assembly of a flexible OPA1 lattice on the membrane, which drives mitochondrial fusion in cells. Moreover, the membrane-bending OPA1 oligomer undergoes conformational changes that pull the membrane-inserting loop out of the outer leaflet and contribute to the mechanics of membrane remodelling. Our findings provide a structural framework for understanding how human OPA1 shapes mitochondrial morphology and show us how human disease mutations compromise OPA1 functions.

The structure of the human LACTB filament reveals the mechanisms of assembly and membrane binding.

Mitochondria are complex organelles that play a central role in metabolism. Dynamic membrane-associated processes regulate mitochondrial morphology and bioenergetics in response to cellular demand. In tumor cells, metabolic reprogramming requires active mitochondrial metabolism for providing key metabolites and building blocks for tumor growth and rapid proliferation. To counter this, the mitochondrial serine beta-lactamase-like protein (LACTB) alters mitochondrial lipid metabolism and potently inhibits the proliferation of a variety of tumor cells. Mammalian LACTB is localized in the mitochondrial intermembrane space (IMS), where it assembles into filaments to regulate the efficiency of essential metabolic processes. However, the structural basis of LACTB polymerization and regulation remains incompletely understood. Here, we describe how human LACTB self-assembles into micron-scale filaments that increase their catalytic activity. The electron cryo-microscopy (cryoEM) structure defines the mechanism of assembly and reveals how highly ordered filament bundles stabilize the active state of the enzyme. We identify and characterize residues that are located at the filament-forming interface and further show that mutations that disrupt filamentation reduce enzyme activity. Furthermore, our results provide evidence that LACTB filaments can bind lipid membranes. These data reveal the detailed molecular organization and polymerization-based regulation of human LACTB and provide new insights into the mechanism of mitochondrial membrane organization that modulates lipid metabolism.

Computational Modeling of Virally-encoded Ion Channel Structure.

Viroporins are ion channels encoded within a virus's genome, that facilitate a range of devastating infectious diseases such as COVID-19, HIV, and rotavirus. The non-structural protein 4 (NSP4) from rotavirus includes a viroporin domain that disrupts cellular Ca2+ homeostasis, initiating viral replication, and leading to life-threatening vomiting and diarrhea. Though the structure of soluble segments of NSP4 has been determined, membrane-associated regions, including the viroporin domain, remain elusive when utilizing well-established available experimental methods such as x-ray crystallography. However, two recently published protein folding algorithms, AlphaFold2 and trRosetta, demonstrated a high degree of accuracy, when determining the structure of membrane proteins from their primary amino acid sequences, though their training datasets are known to exclude proteins from viral systems. We tested the ability of these non-viral algorithms to predict functional molecular structures of the full-length NSP4 from SA11 rotavirus. We also compared the accuracy of these structures to predictions of other experimental structures of eukaryotic proteins from the Protein Data Banks (PDB), and show that the algorithms predict models more similar to corresponding experimental data than what we saw for the viroporin structure. Our data suggest that while AlphaFold2 and trRosetta each produced distinct NSP4 models, constructs based on either model showed viroporin activity when expressed in E. coli, consistent with that seen from other historical NSP4 sequences.

Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model.

Genome sequencing projects routinely generate haploid consensus sequences from diploid genomes, which are effectively chimeric sequences with the phase at heterozygous sites resolved at random. The impact of phasing errors on phylogenomic analyses under the multispecies coalescent (MSC) model is largely unknown. Here, we conduct a computer simulation to evaluate the performance of four phase-resolution strategies (the true phase resolution, the diploid analytical integration algorithm which averages over all phase resolutions, computational phase resolution using the program PHASE, and random resolution) on estimation of the species tree and evolutionary parameters in analysis of multilocus genomic data under the MSC model. We found that species tree estimation is robust to phasing errors when species divergences were much older than average coalescent times but may be affected by phasing errors when the species tree is shallow. Estimation of parameters under the MSC model with and without introgression is affected by phasing errors. In particular, random phase resolution causes serious overestimation of population sizes for modern species and biased estimation of cross-species introgression probability. In general, the impact of phasing errors is greater when the mutation rate is higher, the data include more samples per species, and the species tree is shallower with recent divergences. Use of phased sequences inferred by the PHASE program produced small biases in parameter estimates. We analyze two real data sets, one of East Asian brown frogs and another of Rocky Mountains chipmunks, to demonstrate that heterozygote phase-resolution strategies have similar impacts on practical data analyses. We suggest that genome sequencing projects should produce unphased diploid genotype sequences if fully phased data are too challenging to generate, and avoid haploid consensus sequences, which have heterozygous sites phased at random. In case the analytical integration algorithm is computationally unfeasible, computational phasing prior to population genomic analyses is an acceptable alternative. [BPP; introgression; multispecies coalescent; phase; species tree.].

Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome.

PREMISE: An informatics approach was used for the construction of an Axiom genotyping array from heterogeneous, high-throughput sequence data to assess the complex genome of loblolly pine (Pinus taeda). METHODS: High-throughput sequence data, sourced from exome capture and whole genome reduced-representation approaches from 2698 trees across five sequence populations, were analyzed with the improved genome assembly and annotation for the loblolly pine. A variant detection, filtering, and probe design pipeline was developed to detect true variants across and within populations. From 8.27 million variants, a total of 642,275 were evaluated and 423,695 of those were screened across a range-wide population. RESULTS: The final informatics and screening approach delivered an Axiom array representing 46,439 high-confidence variants to the forest tree breeding and genetics community. Based on the annotated reference genome, 34% were located in or directly upstream or downstream of genic regions. DISCUSSION: The Pita50K array represents a genome-wide resource developed from sequence data for an economically important conifer, loblolly pine. It uniquely integrates independent projects that assessed trees sampled across the native range. The challenges associated with the large and repetitive genome are addressed in the development of this resource.

Evaluating Subsurface Parameterization to Simulate Hyporheic Exchange: The Steinlach River Test Site.

Hyporheic exchange is the interaction of river water and groundwater, and is difficult to predict. One of the largest contributions to predictive uncertainty for hyporheic exchange has been attributed to the representation of heterogeneous subsurface properties. Our study evaluates the trade-offs between intrinsic (irreducible) and epistemic (reducible) model errors when choosing between homogeneous and highly complex subsurface parameter structures. We modeled the Steinlach River Test Site in Southwest Germany using a fully coupled surface water-groundwater model to simulate hyporheic exchange and to assess the predictive errors and uncertainties of transit time distributions. A highly parameterized model was built, treated as a "virtual reality" and used as a reference. We found that if the parameter structure is too simple, it will be limited by intrinsic model errors. By increasing subsurface complexity through the addition of zones or heterogeneity, we can begin to exchange intrinsic for epistemic errors. Thus, the appropriate level of detail to represent the subsurface depends on the acceptable range of intrinsic structural errors for the given modeling objectives and the available site data. We found that a zonated model is capable of reproducing the transit time distributions of a more detailed model, but only if the geological structures are known. An interpolated heterogeneous parameter field (cf. pilot points) showed the best trade-offs between the two errors, indicating fitness for practical applications. Parameter fields generated by multiple-point geostatistics (MPS) produce transit time distributions with the largest uncertainties, however, these are reducible by additional hydrogeological data, particularly flux measurements.

An Open, Object-Based Framework for Generating Anisotropy in Sedimentary Subsurface Models.

The spatial distribution of hydraulic properties in the subsurface controls groundwater flow and solute transport. However, many approaches to modeling these distributions do not produce geologically realistic results and/or do not model the anisotropy of hydraulic conductivity caused by bedding structures in sedimentary deposits. We have developed a flexible object-based package for simulating hydraulic properties in the subsurface-the Hydrogeological Virtual Realities (HyVR) simulation package. This implements a hierarchical modeling framework that takes into account geological rules about stratigraphic bounding surfaces and the geometry of specific sedimentary structures to generate realistic aquifer models, including full hydraulic-conductivity tensors. The HyVR simulation package can create outputs suitable for standard groundwater modeling tools (e.g., MODFLOW), is written in Python, an open-source programming language, and is openly available at an online repository. This paper presents an overview of the underlying modeling principles and computational methods, as well as an example simulation based on the Macrodispersion Experiment site in Columbus, Mississippi. Our simulation package can currently simulate porous media that mimic geological conceptual models in fluvial depositional environments, and that include fine-scale heterogeneity in distributed hydraulic parameter fields. The simulation results allow qualitative geological conceptual models to be converted into digital subsurface models that can be used in quantitative numerical flow-and-transport simulations, with the aim of improving our understanding of the influence of geological realism on groundwater flow and solute transport.

Feasibility of left atrial appendage device closure following chronically failed surgical ligation.

BACKGROUND: Incomplete surgical left atrial appendage occlusion (S-LAAO) with a narrow neck has been shown to predict an increased rate of embolic stroke. Patients with a previously attempted S-LAAO were systematically excluded from all clinical trials of LAA closure devices. OBJECTIVE: The purpose of this study was to evaluate the feasibility of Watchman LAA device closure for patients referred with chronically incomplete S-LAAO. METHODS: A prospective single-arm feasibility cohort evaluated only subjects undergoing Watchman LAA closure following incomplete S-LAAO. Patients referred and implanted were followed in the Vanderbilt LAA Registry. Preprocedure computed tomographic angiography and transesophageal echocardiography (TEE) were performed to evaluate suitability for closure, with 45-day follow-up TEE postimplant. RESULTS: All attempted LAA closures after incomplete S-LAAO were successful (n = 6). Mean age was 76.3 ± 7 years. Mean CHADS2Vasc score was 3.8 ± 0.8, and HAS-BLED score was 3.5 ± 0.5. At 45-day follow up, all subjects had complete device seal with no thrombus on device and had transitioned to clopidogrel plus aspirin. Three subjects had narrow ostial necks with a maximum diameter ≤9 mm. In all cases, the 4.7-mm Watchman access sheath was able to cross the ostial stricture. Mean occluder size implanted was 28 ± 4 mm. Mean LAA dimension by TEE in the 45° and 135° views for depth was 31 mm and ostial diameter was 11 × 16 mm, below the minimum Watchman indication for use of 17 mm. No major intraoperative complications occurred. CONCLUSION: Watchman LAA closure seems to be feasible in patients with chronically incomplete S-LAAO, including subjects with a narrow neck ≤9 mm in width.

Sensitivity of Simulated Hyporheic Exchange to River Bathymetry: The Steinlach River Test Site.

This study determines the aspects of river bathymetry that have the greatest influence on the predictive biases when simulating hyporheic exchange. To investigate this, we build a highly parameterized HydroGeoSphere model of the Steinlach River Test Site in southwest Germany as a reference. This model is then modified with simpler bathymetries, evaluating the changes to hyporheic exchange fluxes and transit time distributions. Results indicate that simulating hyporheic exchange with a high-resolution detailed bathymetry using a three-dimensional fully coupled model leads to nested multiscale hyporheic exchange systems. A poorly resolved bathymetry will underestimate the small-scale hyporheic exchange, biasing the simulated hyporheic exchange towards larger scales, thus leading to overestimates of hyporheic exchange residence times. This can lead to gross biases in the estimation of a catchment's capacity to attenuate pollutants when extrapolated to account for all meanders along an entire river within a watershed. The detailed river slope alone is not enough to accurately simulate the locations and magnitudes of losing and gaining river reaches. Thus, local bedforms in terms of bathymetric highs and lows within the river are required. Bathymetry surveying campaigns can be more effective by prioritizing bathymetry measurements along the thalweg and gegenweg of a meandering channel. We define the gegenweg as the line that connects the shallowest points in successive cross-sections along a river opposite to the thalweg under average flow conditions. Incorporating local bedforms will likely capture the nested nature of hyporheic exchange, leading to more physically meaningful simulations of hyporheic exchange fluxes and transit times.

The Left Atrial Appendage, Including LAA Occlusion Devices Line Watchman, Amulet, and Lariat.

Atrial fibrillation is a very common arrhythmia whose prevalence is expected to increase significantly as the population ages. The associated stroke risk is a major cause of morbidity and mortality. Stroke prevention by anticoagulation carries its own risks, leading to the search for alternative strategies. Multiple techniques have been developed to exclude the left atrial appendage (the main source of thromboembolism in atrial fibrillation) from the circulation. Such techniques offer the hope of stroke prevention without the risks of anticoagulation. This article describes the percutaneous approaches being currently performed in the United States. Particular emphasis is placed on the use of transesophageal echocardiography to guide these procedures.

Bulk metal concentrations versus total suspended solids in rivers: Time-invariant & catchment-specific relationships.

Suspended particles in rivers can act as carriers of potentially bioavailable metal species and are thus an emerging area of interest in river system monitoring. The delineation of bulk metals concentrations in river water into dissolved and particulate components is also important for risk assessment. Linear relationships between bulk metal concentrations in water (CW,tot) and total suspended solids (TSS) in water can be used to easily evaluate dissolved (CW, intercept) and particle-bound metal fluxes (CSUS, slope) in streams (CW,tot = CW + CSUS TSS). In this study, we apply this principle to catchments in Iran (Haraz) and Germany (Ammer, Goldersbach, and Steinlach) that show differences in geology, geochemistry, land use and hydrological characteristics. For each catchment, particle-bound and dissolved concentrations for a suite of metals in water were calculated based on linear regressions of total suspended solids and total metal concentrations. Results were replicable across sampling campaigns in different years and seasons (between 2013 and 2016) and could be reproduced in a laboratory sedimentation experiment. CSUS values generally showed little variability in different catchments and agree well with soil background values for some metals (e.g. lead and nickel) while other metals (e.g. copper) indicate anthropogenic influences. CW was elevated in the Haraz (Iran) catchment, indicating higher bioavailability and potential human and ecological health concerns (where higher values of CSUS/CW are considered as a risk indicator).

Incorrect Diagnosis of Type A Aortic Dissection Attributed to Motion Artifact During Computed Tomographic Angiography: A Case Report.

Early diagnosis of aortic dissection is important to reduce mortality, with surgical management representing standard treatment. Current methods of diagnosing type A aortic dissection include computed tomography angiography (CTA), magnetic resonance imaging, catheter-based arteriography, and transesophageal echocardiography. While each method has merits, there exists potential for false-positive findings. We present a case of a patient who was diagnosed with type A aortic dissection by CTA, but was found to not have an aortic dissection by transesophageal echocardiography under general anesthesia, preventing an unnecessary sternotomy. The echocardiographic findings suggested CTA artifact.

Complete Neurologic Recovery From Extreme Hypoglycemia Secondary to Cardiogenic Liver Failure: A Case Report.

Cardiogenic shock from acute severe mitral valve regurgitation can cause acute liver failure due to hypoperfusion. Impaired liver glycogenesis can then lead to profound hypoglycemia. The time frame for restoring normoglycemia without neurologic sequelae is not clearly established in humans. Thus, the clinical decision to provide further resuscitation in the setting of extreme hypoglycemia mainly depends on the patient's overall clinical condition, provider opinion, and/or institutional practice. Here, we report a case where the patient made complete neurologic recovery from extreme hypoglycemia (<5 mg/dL by central laboratory testing) secondary to acute cardiogenic shock and liver failure.

The Risk of Oxygen during Cardiac Surgery (ROCS) trial: study protocol for a randomized clinical trial.

BACKGROUND: Anesthesiologists administer excess supplemental oxygen (hyper-oxygenation) to patients during surgery to avoid hypoxia. Hyper-oxygenation, however, may increase the generation of reactive oxygen species and cause oxidative damage. In cardiac surgery, increased oxidative damage has been associated with postoperative kidney and brain injury. We hypothesize that maintenance of normoxia during cardiac surgery (physiologic oxygenation) decreases kidney injury and oxidative damage compared to hyper-oxygenation. METHODS/DESIGN: The Risk of Oxygen during Cardiac Surgery (ROCS) trial will randomly assign 200 cardiac surgery patients to receive physiologic oxygenation, defined as the lowest fraction of inspired oxygen (FIO2) necessary to maintain an arterial hemoglobin saturation of 95 to 97%, or hyper-oxygenation (FIO2 = 1.0) during surgery. The primary clinical endpoint is serum creatinine change from baseline to postoperative day 2, and the primary mechanism endpoint is change in plasma concentrations of F2-isoprostanes and isofurans. Secondary endpoints include superoxide production, clinical delirium, myocardial injury, and length of stay. An endothelial function substudy will examine the effects of oxygen treatment and oxidative stress on endothelial function, measured using flow mediated dilation, peripheral arterial tonometry, and wire tension myography of epicardial fat arterioles. DISCUSSION: The ROCS trial will test the hypothesis that intraoperative physiologic oxygenation decreases oxidative damage and organ injury compared to hyper-oxygenation in patients undergoing cardiac surgery. TRIAL REGISTRATION: ClinicalTrials.gov, ID: NCT02361944 . Registered on the 30th of January 2015.

Hyperlactemia Predicts Surgical Mortality in Patients Presenting With Acute Stanford Type-A Aortic Dissection.

OBJECTIVE: Inspired by the limited facility of the Penn classification, the authors aimed to determine a rapid and optimal preoperative assessment tool to predict surgical mortality after acute Stanford type-A aortic dissection (AAAD) repair. DESIGN: Patients who underwent an attempted surgical repair of AAAD were determined using a de-identified single institution database. The charts of 144 patients were reviewed retrospectively for preoperative demographics and surrogates for disease severity and malperfusion. Bivariate analysis was used to determine significant (p≤0.05) predictors of in-hospital and 1-year mortality, the primary endpoints. Receiver operating characteristic curve generation was used to define optimal cut-off values for continuous predictors. SETTING: Single center, level 1 trauma, university teaching hospital. PARTICIPANTS: The study included 144 cardiac surgical patients with acute type-A aortic dissection presenting for surgical correction. INTERVENTIONS: Surgical repair of aortic dissection with preoperative laboratory samples drawn before patient transfer to the operating room or immediately after arterial catheter placement intraoperatively. MEASUREMENTS AND MAIN RESULTS: The study cohort comprised 144 patients. In-hospital mortality was 9%, and the 1-year mortality rate was 17%. Variables that demonstrated a correlation with in-hospital mortality included an elevated serum lactic acid level (odds ratio [OR] 1.5 [1.3-1.9], p<0.001), a depressed ejection fraction (OR 0.91 [0.86-0.96], p = .001), effusion (OR 4.8 [1.02-22.5], p = 0.04), neurologic change (OR 5.3 [1.6-17.4], p = 0.006), severe aortic regurgitation (OR 8.2 [2.0-33.9], p = 0.006), and cardiopulmonary resuscitation (OR 6.8 [1.7-26.9], p = 0.01). Only an increased serum lactic acid level demonstrated a trend with 1-year mortality using univariate Cox regression (hazard ratio 1.1 [1.0-1.1], p = 0.006). Receiver operating characteristic analysis revealed optimal cut-off lactic acid levels of 6.0 mmol/L and 6.9 mmol/L for in-hospital and 1-year mortality, respectively. CONCLUSION: Lactic acidosis, ostensibly as a surrogate for systemic malperfusion, represents a novel, accurate, and easily obtainable preoperative predictor of short-term mortality after attempted AAAD repair. These data may improve identification of patients who would not benefit from surgery.