Exploring the ability of the MD+FoldX method to predict SARS-CoV-2 antibody escape mutations using large-scale data.

Antibody escape mutations pose a significant challenge to the effectiveness of vaccines and antibody-based therapies. The ability to predict these escape mutations with computer simulations would allow us to detect threats early and develop effective countermeasures, but a lack of large-scale experimental data has hampered the validation of these calculations. In this study, we evaluate the ability of the MD+FoldX molecular modeling method to predict escape mutations by leveraging a large deep mutational scanning dataset, focusing on the SARS-CoV-2 receptor binding domain. Our results show a positive correlation between predicted and experimental data, indicating that mutations with reduced predicted binding affinity correlate moderately with higher experimental escape fractions. We also demonstrate that higher precision can be achieved using affinity cutoffs tailored to distinct SARS-CoV-2 antibodies from four different classes rather than a one-size-fits-all approach. Further, we suggest that the quartile values of optimized cutoffs reported for each class in this study can serve as a valuable guide for future work on escape mutation predictions. We find that 70% of the systems surpass the 50% precision mark, and demonstrate success in identifying mutations present in significant variants of concern and variants of interest. Despite promising results for some systems, our study highlights the challenges in comparing predicted and experimental values. It also emphasizes the need for new binding affinity methods with improved accuracy that are fast enough to estimate hundreds to thousands of antibody-antigen binding affinities.

Molecular Mechanisms Underlying the Spectral Shift in Zebrafish Cone Opsins.

Visual pigments are essential for converting light into electrical signals during vision. Composed of an opsin protein and a retinal-based chromophore, pigments in vertebrate rods (Rh1) and cones (Rh2) have different spectral sensitivities, with distinct peak absorption wavelengths determined by the shape and composition of the chromophore binding pocket. Despite advances in understanding Rh1 pigments such as bovine rhodopsin, the molecular basis of spectral shifts in Rh2 cone opsins has been less studied, particularly the E122Q mutation, which accounts for about half of the observed spectral shift in these pigments. In this study, we employed molecular modeling and quantum mechanical techniques to investigate the molecular mechanisms behind the spectral difference in blue-shifted Rh2-1 (absorption peak = 467 nm, 122Q) and green-shifted Rh2-4 (absorption peak = 505 nm, 122E) zebrafish cone opsins. We modeled the pigments 3D structures based on their sequences and conducted all-atom molecular dynamics simulations totaling 2 microseconds. Distance analysis of the trajectories identified three key sites: E113, E181, and E122. The E122Q mutation, previously known, validates our findings, while E181 and E113 are newly identified contributors. Structural analysis revealed key features with differing values that explain the divergent spectral sensitivities of Rh2-1 and Rh2-4: 1) chromophore atom fluctuations and C5-C6 torsion angle, 2) binding pocket volume, 3) hydration patterns, and 4) E113-chromophore interaction stability. Quantum mechanics further confirms the critical role of residue E181 in Rh2-1 and E122 in Rh2-4 for their spectral behavior. Our study provides new insights into the molecular determinants of spectral shifts in cone opsins, and we anticipate that it will serve as a starting point for a broader understanding of the functional diversity of visual pigments.

Leveraging neural networks to correct FoldX free energy estimates.

Proteins play a pivotal role in many biological processes, and changes in their amino acid sequences can lead to dysfunction and disease. These changes can affect protein folding or interaction with other biomolecules, such as preventing antibodies from inhibiting a viral infection or causing proteins to misfold. The ability to predict the effects of mutations in proteins is crucial. Although experimental techniques can accurately quantify the effect of mutations on protein folding free energies and protein-protein binding free energies, they are often time-consuming and costly. By contrast, computational techniques offer fast and cost-effective alternatives for estimating free energies, but they typically suffer from lower accuracy. Enhancing the accuracy of computational predictions is therefore of high importance, with the potential to greatly impact fields ranging from drug design to understanding disease mechanisms. One such widely used computational method, FoldX, is capable of rapidly predicting the relative folding stability (ΔΔG fold ) for a protein as well as the relative binding affinity (ΔΔG bind ) between proteins using a single protein structure as input. However, it can suffer from low accuracy, especially for antibody-antigen systems. In this work, we trained a neural network on FoldX output to enhance its prediction accuracy. We first performed FoldX calculations on the largest datasets available for mutations that affect binding (SKEMPIv2) and folding (ProTherm4) with experimentally measured ΔΔG. Features were then extracted from the FoldX output files including its prediction for ΔΔG. We then developed and optimized a neural network framework to predict the difference between FoldX's estimated ΔΔG and the experimental data, creating a model capable of producing a correction factor. Our approach showed significant improvements in Pearson correlation performance. For single mutations affecting folding, the correlation improved from a baseline of 0.3 to 0.66. In terms of binding, performance increased from 0.37 to 0.61 for single mutations and from 0.52 to 0.81 for double mutations. For epistasis, the correlation for binding affinity (both singles and doubles) improved from 0.19 to 0.59. Our results also indicated that models trained on double mutations enhanced accuracy when predicting higher-order mutations (such as triple or quadruple mutations), whereas models trained on singles did not. This suggests that interaction energy and epistasis effects present in the FoldX output are not fully utilized by FoldX itself. Once trained, these models add minimal computational time but provide a substantial increase in performance, especially for higher-order mutations and epistasis. This makes them a valuable addition to any free energy prediction pipeline using FoldX. Furthermore, we believe this technique can be further optimized and tested for predicting antibody escape, aiding in the efficient development of watch lists.

Hispanic individuals' cervical cancer screening disparities amidst the COVID-19 pandemic.

OBJECTIVE: To examine the impact of the COVID-19 pandemic on cervical cancer screening rates of Hispanic individuals compared to non-Hispanic White (NHW) individuals in the United States, whether a responsive surge in catch-up screenings occurred as society adapted to pandemic changes, and to investigate the sociodemographic characteristics between the study populations. METHODS: Using cross-sectional data from the All of Us Research Program, which incorporates electronic health record data and survey data from a demographically, geographically, and medically diverse participant group, we assessed the annual cervical cancer screening rates during 2019-2021 by race/ethnicity among eligible individuals ages 21-64. RESULTS: Among 116,052 unique individuals (78,829 NHW and 37,223 Hispanic), Hispanic individuals had lower annual cervical cancer screening rates than NHWI across the three years studied. They experienced a more significant decrease in screening from 2019 to 2020 (39.27 %) compared to NHWIs (21.15 %) and less of a rebound increase in the following year, 2021 (10.33 % vs 13.83 %). Hispanic individuals aged 50-64 experienced the sharpest decline in screening rates (-43.01 % from 2019 to 2020). Hispanic individuals also experienced greater adverse social conditions, including lack of insurance or employment, lower educational attainment, and lower household income. CONCLUSIONS: Hispanic individuals experienced a more significant decrease in cervical cancer screening rates with the onset of the COVID-19 pandemic compared with NHW individuals and did not experience a robust rebound in cervical cancer screening rates in 2021. As a result, the disparity in cervical cancer screening rates between NHW and Hispanic individuals considerably worsened with the COVID-19 pandemic.

Implementation and impact of a surgical dashboard on pediatric tonsillectomy outcomes: A quality improvement study.

Introduction: In pediatric tonsillectomy management, the consistent tracking of surgical outcomes and adherence to guidelines are vital. This study explores how a surgical dashboard can serve as a tool in research analysis, translating AAO-HNSF guidelines into measurable performance improvements. Methods: Using a prospective registry from three pediatric hospitals, a Tableau dashboard was constructed to graphically visualize key demographic and postoperative outcomes (including intensive care unit [ICU] utilization, 30-day emergency department (ED) visits, and postoperative bleed rates) in children undergoing tonsillectomy from 2020 to 2024. From the dashboard data, a retrospective cohort study analyzing 6767 tonsillectomies was conducted from January 2, 2020, to June 20, 2023. Patients were categorized into low-risk, OSA-only (by ICD-10 codes), and high-risk groups based on comorbidities. Logistic regression identified factors influencing ED revisits and unplanned nursing calls. Three quality initiatives were assessed: preoperative school absence notes, perioperative dexamethasone recording, and post-tonsillectomy parental education. Results: A total of 2122 (31%) were low-risk, 2648 (39%) were OSA-only, and 1997 (30%) high risk. Risk factors that increased the likelihood of ED visits were high-risk comorbidities (OR = 1.46; 95% CI = 1.24-1.74; p < 0.001) and older age (OR = 1.05; 95% CI = 1.03-1.08; p < 0.001). Risk factors that increased the likelihood of an unplanned nursing communication were high-risk comorbidities (OR = 1.53; 95% CI = 1.34-1.75; p < 0.001), older age (OR = 1.03, 95% CI = 1.01-1.04; p = 0.001), and Medicaid insurance (OR = 1.25; 95% CI = 1.09-1.43; p = 0.002). Postoperative bleed control was generally comparable between the groups, at 2.8% (low risk), 2.7% (OSA), 3.2 (high risk) (p = 0.651). Conclusion: The dashboard aided in data collection, data visualization, and data analysis of quality improvement initiatives, effectively translating guidelines into tangible measures to enhance care. Level of evidence: NA.

The effect of hydrostatic pressure on lipid membrane lateral structure.

High pressure is both an environmental challenge to which deep sea biology has to adapt, and a highly sensitive thermodynamic tool that can be used to trigger structural changes in biological molecules and assemblies. Lipid membranes are amongst the most pressure sensitive biological assemblies and pressure can have a large influence on their structure and properties. In this chapter, we will explore the use of high pressure small angle X-ray diffraction and high pressure microscopy to measure and quantify changes in the lateral structure of lipid membranes under both equilibrium high pressure conditions and in response to pressure jumps.

Exploring the ability of the MD+FoldX method to predict SARS-CoV-2 antibody escape mutations using large-scale data.

Antibody escape mutations pose a significant challenge to the effectiveness of vaccines and antibody-based therapies. The ability to predict these escape mutations with computer simulations would allow us to detect threats early and develop effective countermeasures, but a lack of large-scale experimental data has hampered the validation of these calculations. In this study, we evaluate the ability of the MD+FoldX molecular modeling method to predict escape mutations by leveraging a large deep mutational scanning dataset, focusing on the SARS-CoV-2 receptor binding domain. Our results show a positive correlation between predicted and experimental data, indicating that mutations with reduced predicted binding affinity correlate moderately with higher experimental escape fractions. We also demonstrate that better performance can be achieved using affinity cutoffs tailored to distinct antibody-antigen interactions rather than a one-size-fits-all approach. We find that 70% of the systems surpass the 50% precision mark, and demonstrate success in identifying mutations present in significant variants of concern and variants of interest. Despite promising results for some systems, our study highlights the challenges in comparing predicted and experimental values. It also emphasizes the need for new binding affinity methods with improved accuracy that are fast enough to estimate hundreds to thousands of antibody-antigen binding affinities.

Safety and Immunogenicity of an Accelerated Ebola Vaccination Schedule in People with and without Human Immunodeficiency Virus: A Randomized Clinical Trial.

The safety and immunogenicity of the two-dose Ebola vaccine regimen MVA-BN-Filo, Ad26.ZEBOV, 14 days apart, was evaluated in people without HIV (PWOH) and living with HIV (PLWH). In this observer-blind, placebo-controlled, phase 2 trial, healthy adults were randomized (4:1) to receive MVA-BN-Filo (dose 1) and Ad26.ZEBOV (dose 2), or two doses of saline/placebo, administered intramuscularly 14 days apart. The primary endpoints were safety (adverse events (AEs)) and immunogenicity (Ebola virus (EBOV) glycoprotein-specific binding antibody responses). Among 75 participants (n = 50 PWOH; n = 25 PLWH), 37% were female, the mean age was 44 years, and 56% were Black/African American. AEs were generally mild/moderate, with no vaccine-related serious AEs. At 21 days post-dose 2, EBOV glycoprotein-specific binding antibody responder rates were 100% among PWOH and 95% among PLWH; geometric mean antibody concentrations were 6286 EU/mL (n = 36) and 2005 EU/mL (n = 19), respectively. A total of 45 neutralizing and other functional antibody responses were frequently observed. Ebola-specific CD4+ and CD8+ T-cell responses were polyfunctional and durable to at least 12 months post-dose 2. The regimen was well tolerated and generated robust, durable immune responses in PWOH and PLWH. Findings support continued evaluation of accelerated vaccine schedules for rapid deployment in populations at immediate risk. Trial registration: NCT02598388 (submitted 14 November 2015).

Safety and Immunogenicity of Accelerated Heterologous Two-dose Ebola Vaccine Regimens in Adults With and Without HIV in Africa.

BACKGROUND: Shorter prophylactic vaccine schedules may offer more rapid protection against Ebola in resource-limited settings. METHODS: This randomized, observer-blind, placebo-controlled, phase 2 trial conducted in five sub-Saharan African countries included people without HIV (PWOH, n = 249) and people living with HIV (PLWH, n = 250). Adult participants received one of two accelerated Ebola vaccine regimens (MVA-BN-Filo, Ad26.ZEBOV administered 14 days apart [n = 79] or Ad26.ZEBOV, MVA-BN-Filo administered 28 days apart [n = 322]) or saline/placebo (n = 98). The primary endpoints were safety (adverse events [AEs]) and immunogenicity (Ebola virus [EBOV] glycoprotein-specific binding antibody responses). Binding antibody responders were defined as participants with a > 2.5-fold increase from baseline or the lower limit of quantification if negative at baseline. RESULTS: The mean age was 33.4 years, 52% of participants were female, and among PLWH, the median (interquartile range) CD4+ cell count was 560.0 (418.0-752.0) cells/µL. AEs were generally mild/moderate with no vaccine-related serious AEs or remarkable safety profile differences by HIV status. At 21 days post-dose 2, EBOV glycoprotein-specific binding antibody response rates in vaccine recipients were 99% for the 14-day regimen (geometric mean concentrations [GMCs]: 5168 enzyme-linked immunosorbent assay units (EU)/mL in PWOH; 2509 EU/mL in PLWH), and 98% for the 28-day regimen (GMCs: 6037 EU/mL in PWOH; 2939 EU/mL in PLWH). At 12 months post-dose 2, GMCs in PWOH and PLWH were 635 and 514 EU/mL, respectively, for the 14-day regimen and 331 and 360 EU/mL, respectively, for the 28-day regimen. CONCLUSIONS: Accelerated 14- and 28-day Ebola vaccine regimens were safe and immunogenic in PWOH and PLWH in Africa. TRIAL REGISTRATION: NCT02598388.

Altered microbial bile acid metabolism exacerbates T cell-driven inflammation during graft-versus-host disease.

Microbial transformation of bile acids affects intestinal immune homoeostasis but its impact on inflammatory pathologies remains largely unknown. Using a mouse model of graft-versus-host disease (GVHD), we found that T cell-driven inflammation decreased the abundance of microbiome-encoded bile salt hydrolase (BSH) genes and reduced the levels of unconjugated and microbe-derived bile acids. Several microbe-derived bile acids attenuated farnesoid X receptor (FXR) activation, suggesting that loss of these metabolites during inflammation may increase FXR activity and exacerbate the course of disease. Indeed, mortality increased with pharmacological activation of FXR and decreased with its genetic ablation in donor T cells during mouse GVHD. Furthermore, patients with GVHD after allogeneic hematopoietic cell transplantation showed similar loss of BSH and the associated reduction in unconjugated and microbe-derived bile acids. In addition, the FXR antagonist ursodeoxycholic acid reduced the proliferation of human T cells and was associated with a lower risk of GVHD-related mortality in patients. We propose that dysbiosis and loss of microbe-derived bile acids during inflammation may be an important mechanism to amplify T cell-mediated diseases.

Perioperative Delta Weight and Pediatric Obstructive Sleep Apnea Resolution after Adenotonsillectomy.

OBJECTIVE(S): The first-line treatment for pediatric obstructive sleep apnea (OSA) is adenotonsillectomy. Post-operative weight gain is a well-documented phenomenon. We hypothesized that higher peri-adenotonsillectomy delta weight correlates with lower rates of OSA resolution in pediatric patients. METHODS: This was a retrospective cohort study consisting of 250 patients from 2 to 17 years of age at a tertiary academic medical center between January 2021 and December 2022. Polysomnography results and body mass index (BMI) changes were collected through the electronic health record. Univariate and multivariate logistical regression analyses were performed, adjusting for confounding factors. RESULTS: Perioperative delta weight and pre-operative baseline AHI values were significant predictors of residual OSA. For every 1-kilogram gain in weight, the odds of residual OSA (AHI >5) increase by 6.0% (OR = 1.06, 95% CI = 1.02-1.10, p < 0.002), and the odds of residual severe OSA (AHI > 10) increase by 8% (OR = 1.08, 95% CI = 1.04-1.12, p < 0.001). Increased AHI, Black/African American race, and male sex were also factors associated with incomplete OSA resolution. CONCLUSIONS: Increased peri-adenotonsillectomy delta weight is associated with higher rates of residual OSA in children. Patients and families should be counseled about appropriate weight loss and control methods before adenotonsillectomy. LEVEL OF EVIDENCE: IV Laryngoscope, 134:4141-4147, 2024.

[Modified reverse puncture technique for esophagojejunostomy during totally laparoscopic total gastrectomy for gastric cancer].

Objective: To evaluate the value of implementing a modified reverse puncture procedure for esophagojejunostomy during totally laparoscopic total gastrectomy. Methods: This was a descriptive case series. Relevant clinical data, including the operative procedure, recovery, and pathological findings of 35 patients with gastric cancer who had undergone esophagojejunostomy with a modified reverse puncture technique during totally laparoscopic total gastrectomy in the Department of Gastrointestinal Surgery, Fujian Provincial Hospital, from June 2022 to January 2023, were prospectively collected and retrospectively analyzed. The age of all patients in the group was (64.9±8.0) years old, with 22 males (62.9%) and a body mass index of (23.2±2.4) kg/m2. The tumors were located in the upper and middle parts of the stomach in 24 cases (68.6%) and in the junction of the esophagus and stomach in 11 cases (31.4%). Important technical aspects of the modified reverse puncture procedure are as follows. (1) Site of the esophageal incision: a transverse incision is made across the right lateral wall of the esophagus at the expected site of esophageal disjunction. (2) Technique for inserting an anvil: after threading a silk thread through the tip of anvil, the end of the thread is knotted and fixed as the traction thread, after which an anvil is inserted into the esophagus through the esophageal incision, leaving the end of the traction line exposed. Next, a 60-mm linear cutter is placed through the right midclavicular trocar to straighten the opened esophagus vertically, after which the rod of the anvil is pulled out of a small incision that has been made in the esophagus by pulling the traction thread, thus completing anvil placement. (3) Jejunal binding: the jejunum on the central bar of the stapler is fastened with silk thread to the stump of the jejunum, and then tied to the output loop of the jejunum with a gauze strip. Results: All 35 surgeries were successful, with no mortality or conversion to laparotomy. The operation time, anvil insertion time, and digestive tract reconstruction time were (232.7±34.4), (8.5±1.4), and (40.5±4.8) minutes, respectively. The intraoperative blood loss was 100 (20-250) mL and the incision was (5.3±0.9) cm long. The upper surgical margin was negative in all patients and the mean distance between the upper and tumor margins was (3.5±1.2) cm. The mean number of lymph nodes dissected per patient was 33.9±7.1. The times to initial ambulation, initial passage of flatus , postoperative fluid intake, and length of postoperative hospital stay were (3.2±1.1), (3.7±1.5), (4.6±2.3), and (9.8±3.2) days, respectively. Postoperative complications occurred in five patients: one case of anastomotic leak, two of anastomotic stenosis, one of pulmonary infection, and one of incomplete intestinal obstruction, all of which were successfully managed conservatively. Conclusion: Esophagojejunostomy using a modified reverse puncture technique during totally laparoscopic total gastrectomy is safe and feasible for gastric cancer, requiring only a small incision and achieving higher upper esophageal resection margins and good postoperative recovery, and therefore warrants further implementation.

Surfactant-like Additives Assisted the Lateral Growth of Pentacene Films.

Lateral growth of thin films is crucial for organic electronic devices, such as field-effect transistors. Here, we report a strategy to improve the lateral growth of pentacene films using rubrene as a surfactant-like additive. Atomic force microscopy (AFM) images confirm the enhanced lateral growth with the presence of rubrene, resulting in smooth and enlarged molecule domains in the films in comparison to those without rubrene. Molecular dynamics simulations are conducted to explore the interlayer diffusion of pentacene molecules during the growth. With the rubrene molecules as surfactant-like additives, mean square displacement (MSD) analysis shows that the pentacene molecules have a descending diffusion coefficient of 2.0 × 10-5 cm2 s-1, which is greater than the ascending diffusion coefficient of 1.6 × 10-5 cm2 s-1. The more descending molecules lead to an enhanced lateral growth of pentacene films, which is in good agreement with the experiments. As a result, the pentacene films grown with rubrene exhibit a rapid increase in carrier mobility over thickness due to the well-connected domains resulting from enhanced lateral growth. This finding will provide a new strategy to modulate the morphology of organic films for high-performance devices.

A Review of Transition Metal Boride, Carbide, Pnictide, and Chalcogenide Water Oxidation Electrocatalysts.

Transition metal borides, carbides, pnictides, and chalcogenides (X-ides) have emerged as a class of materials for the oxygen evolution reaction (OER). Because of their high earth abundance, electrical conductivity, and OER performance, these electrocatalysts have the potential to enable the practical application of green energy conversion and storage. Under OER potentials, X-ide electrocatalysts demonstrate various degrees of oxidation resistance due to their differences in chemical composition, crystal structure, and morphology. Depending on their resistance to oxidation, these catalysts will fall into one of three post-OER electrocatalyst categories: fully oxidized oxide/(oxy)hydroxide material, partially oxidized core@shell structure, and unoxidized material. In the past ten years (from 2013 to 2022), over 890 peer-reviewed research papers have focused on X-ide OER electrocatalysts. Previous review papers have provided limited conclusions and have omitted the significance of "catalytically active sites/species/phases" in X-ide OER electrocatalysts. In this review, a comprehensive summary of (i) experimental parameters (e.g., substrates, electrocatalyst loading amounts, geometric overpotentials, Tafel slopes, etc.) and (ii) electrochemical stability tests and post-analyses in X-ide OER electrocatalyst publications from 2013 to 2022 is provided. Both mono and polyanion X-ides are discussed and classified with respect to their material transformation during the OER. Special analytical techniques employed to study X-ide reconstruction are also evaluated. Additionally, future challenges and questions yet to be answered are provided in each section. This review aims to provide researchers with a toolkit to approach X-ide OER electrocatalyst research and to showcase necessary avenues for future investigation.

Surface-Induced Hydrophobin Assemblies with Versatile Properties and Distinct Underlying Structures.

Hydrophobins are remarkable proteins due to their ability to self-assemble into amphipathic coatings that reverse surface wettability. Here, the versatility of the Class I hydrophobins EASΔ15 and DewY in diverse nanosuspension and coating applications is demonstrated. The hydrophobins are shown to coat or emulsify a range of substrates including oil, hydrophobic drugs, and nanodiamonds and alter their solution and surface behavior. Surprisingly, while the coatings confer new properties, only a subset is found to be resistant to hot detergent treatment, a feature previously thought to be characteristic of the functional amyloid form of Class I hydrophobins. These results demonstrate that substrate surface properties can influence the molecular structures and physiochemical properties of hydrophobin and possibly other functional amyloids. Functional amyloid assembly with different substrates and conditions may be analogous to the propagation of different polymorphs of disease-associated amyloid fibrils with distinct structures, stability, and clinical phenotypes. Given that amyloid formation is not required for Class I hydrophobins to serve diverse applications, our findings open up new opportunities for their use in applications requiring a range of chemical and physical properties. In hydrophobin nanotechnological applications where high stability of assemblies is required, simultaneous structural and functional characterization should be carried out. Finally, while results in this study pertain to synthetic substrates, they raise the possibility that at least some members of the pseudo-Class I and Class III hydrophobins, reported to form assemblies with noncanonical properties, may be Class I hydrophobins adopting alternative structures in response to environmental cues.

Fabrication of Isolated Iron Nanowires.

Nanoscale interconnects are an important component of molecular electronics. Here we use X-ray spectromicroscopy techniques as well as scanning probe methods to explore the self-assembled growth of insulated iron nanowires as a potential means of supplying an earth abundant solution. The intrinsic anisotropy of a TiO2(110) substrate directs the growth of micron length iron wires at elevated temperatures, with a strong metal-support interaction giving rise to ilmenite (FeTiO3) encapsulation. Iron nanoparticles that decorate the nanowires display magnetic properties that suggest other possible applications.

[Efficacy of off-pump minimally invasive via a single left intercostal space incision compared with median sternotomy multi-vesselcoronary artery bypass grafting].

Objective: To compare the efficacy of off-pump minimally invasive cardiac surgery (MICS) via a single left intercostal space incision with median sternotomy multi-vesselcoronary artery bypass grafting (CABG). Methods: Patients who were diagnosed with multi-artery coronary artery disease (CAD) in the Ward 10 of the Department of Cardiac Surgery, Beijing Anzhen Hospital Affiliated to Capital Medical University and underwent CABG from July 2019 to January 2022 were retrospectively collected. All the patients were divided into MICS group and conventional CABG group according to the surgical methods. The perioperative outcomes were compared between thetwo groups, including intraoperative blood loss, postoperative 24 h thoracic drainage volume, ventilation duration, length of stay (LOS) in intensive care unit (ICU) and total LOS in hospital. Intraoperative blood flow of graft vesselswas measured by transit-time flow measurement (TTFM) after vascular anastomosis, and mean flow (MF) and pulsatile index (PI) were compared between the two groups. Results: A total of 444 patients were in the final analysis, with 351 males and 93 females, and the mean age of (62.0±8.9) years. There were 179 patients in MICS group and 265 cases in conventional CABG group, respectively. There were no statistically significant differences in the preoperative profiles between the two groups (all P>0.05) except that younger age [(60.7±9.3) years vs (62.8±8.5) years, P=0.017] and lower proportion of female [10.1% (18/179) vs 28.3% (75/265), P<0.001] were detected in MICS group. Likewise, there was no significant difference in the number of graft vessels between MICS group (3.18±0.74) and conventional CABG group (3.28±0.86) (P=0.234). Compared with those in conventional CABG group, patients in MICS group showed longer operation duration [ (5.10±1.09) h vs (4.33±0.86) h], fewer intraoperative blood loss [500 (200, 700) ml vs 700 (600, 900) ml], fewer postoperative 24 h thoracic drainage volume [300 (200, 400) ml vs 400 (250, 500) ml], shorter postoperative ventilation duration [15.0 (12.0, 17.0) h vs 16.5 (12.5, 19.0) h, P<0.001], LOS in ICU [18.0 (15.0, 20.0) h vs 20.0 (16.0, 23.0) h, P<0.001] and total LOS in hospital [(12.6±2.7) d vs (14.5±3.9) d, P<0.001]. MI and PI of graft vessels were similar between the two groups (both P>0.05). Moreover, there were no significant differences in major perioperative complications (i.e., repeat thoracotomy, incision infection, stroke) and mortality between the two groups (all P>0.05). Conclusion: MICS is an alternative treatment for patients with multi-vessel CAD with better perioperative outcomes compared with conventional CABG.

Tissue-specific features of the T cell repertoire after allogeneic hematopoietic cell transplantation in human and mouse.

T cells are the central drivers of many inflammatory diseases, but the repertoire of tissue-resident T cells at sites of pathology in human organs remains poorly understood. We examined the site-specificity of T cell receptor (TCR) repertoires across tissues (5 to 18 tissues per patient) in prospectively collected autopsies of patients with and without graft-versus-host disease (GVHD), a potentially lethal tissue-targeting complication of allogeneic hematopoietic cell transplantation, and in mouse models of GVHD. Anatomic similarity between tissues was a key determinant of TCR repertoire composition within patients, independent of disease or transplant status. The T cells recovered from peripheral blood and spleens in patients and mice captured a limited portion of the TCR repertoire detected in tissues. Whereas few T cell clones were shared across patients, motif-based clustering revealed shared repertoire signatures across patients in a tissue-specific fashion. T cells at disease sites had a tissue-resident phenotype and were of donor origin based on single-cell chimerism analysis. These data demonstrate the complex composition of T cell populations that persist in human tissues at the end stage of an inflammatory disorder after lymphocyte-directed therapy. These findings also underscore the importance of studying T cell in tissues rather than blood for tissue-based pathologies and suggest the tissue-specific nature of both the endogenous and posttransplant T cell landscape.

Folic Acid Supplementation Promotes Hypomethylation in Both the Inflamed Colonic Mucosa and Colitis-Associated Dysplasia.

PURPOSE: The purpose of this study was to assess the effect of folic acid (FA) supplementation on colitis-associated colorectal cancer (CRC) using the azoxymethane/dextran sulfate sodium (AOM/DSS) model. METHODS: Mice were fed a chow containing 2 mg/kg FA at baseline and randomized after the first DSS treatment to receive 0, 2, or 8 mg/kg FA chow for 16 weeks. Colon tissue was collected for histopathological evaluation, genome-wide methylation analyses (Digital Restriction Enzyme Assay of Methylation), and gene expression profiling (RNA-Seq). RESULTS: A dose-dependent increase in the multiplicity of colonic dysplasias was observed, with the multiplicity of total and polypoid dysplasias higher (64% and 225%, respectively) in the 8 mg FA vs. the 0 mg FA group (p < 0.001). Polypoid dysplasias were hypomethylated, as compared to the non-neoplastic colonic mucosa (p < 0.05), irrespective of FA treatment. The colonic mucosa of the 8 mg FA group was markedly hypomethylated as compared to the 0 mg FA group. Differential methylation of genes involved in Wnt/ß-catenin and MAPK signaling resulted in corresponding alterations in gene expression within the colonic mucosa. CONCLUSIONS: High-dose FA created an altered epigenetic field effect within the non-neoplastic colonic mucosa. The observed decrease in site-specific DNA methylation altered oncogenic pathways and promoted colitis-associated CRC.

High-resolution analyses of associations between medications, microbiome, and mortality in cancer patients.

Discerning the effect of pharmacological exposures on intestinal bacterial communities in cancer patients is challenging. Here, we deconvoluted the relationship between drug exposures and changes in microbial composition by developing and applying a new computational method, PARADIGM (parameters associated with dynamics of gut microbiota), to a large set of longitudinal fecal microbiome profiles with detailed medication-administration records from patients undergoing allogeneic hematopoietic cell transplantation. We observed that several non-antibiotic drugs, including laxatives, antiemetics, and opioids, are associated with increased Enterococcus relative abundance and decreased alpha diversity. Shotgun metagenomic sequencing further demonstrated subspecies competition, leading to increased dominant-strain genetic convergence during allo-HCT that is significantly associated with antibiotic exposures. We integrated drug-microbiome associations to predict clinical outcomes in two validation cohorts on the basis of drug exposures alone, suggesting that this approach can generate biologically and clinically relevant insights into how pharmacological exposures can perturb or preserve microbiota composition. The application of a computational method called PARADIGM to a large dataset of cancer patients' longitudinal fecal specimens and detailed daily medication records reveals associations between drug exposures and the intestinal microbiota that recapitulate in vitro findings and are also predictive of clinical outcomes.