Training machine learning potentials for reactive systems: A Colab tutorial on basic models

In the last several years, there has been a surge in the development of machine learning potential (MLP) models for describing molecular systems. We are interested in a particular area of this field - the training of system-specific MLPs for reactive systems - with the goal of using these MLPs to accelerate free energy simulations of chemical and enzyme reactions. To help new members in our labs become familiar with the basic techniques, we have put together a self-guided Colab tutorial (https://cc-ats.github.io/mlp_tutorial/), which we expect to be also useful to other young researchers in the community. Our tutorial begins with the introduction of simple feedforward neural network (FNN) and kernel-based (using Gaussian process regression, GPR) models by fitting the two-dimensional Müller-Brown potential. Subsequently, two simple descriptors are presented for extracting features of molecular systems: symmetry functions (including the ANI variant) and embedding neural networks (such as DeepPot-SE). Lastly, these features will be fed into FNN and GPR models to reproduce the energies and forces for the molecular configurations in a Claisen rearrangement reaction.

Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions

In enzyme mechanistic studies and mutant design, it is highly desirable to know the individual residue contributions to the reaction free energy and barrier. In this work, we show that such free energy contributions from each residue can be readily obtained by postprocessing ab initio quantum mechanical molecular mechanical (ai-QM/MM) free energy simulation trajectories. Specifically, through a mean force integration along the minimum free energy pathway, one can obtain the electrostatic, polarization, and van der Waals contributions from each residue to the free energy barrier. Separately, a similar analysis procedure allows us to assess the contribution from different collective variables along the reaction coordinate. The chorismate mutase reaction is used to demonstrate the utilization of these two trajectory analysis tools.

[Opportunities and challenges in an emerging interdisciplinary research field-cardio-oncology]

The field of oncology has made remarkable progress over the past two decades. With the aging of the population, the number of cancer survivors is increasing. At the same time, cancer therapy-related cardiovascular toxicity (CTR-CVT) has become an important cause that seriously affects the quality of life and survival of cancer patients. In this context, cardio-oncology, an emerging interdisciplinary field, emerged. The types and treatment strategies of oncological diseases are heterogeneous, and the management of cancer patients also requires the participation of multiple disciplines. Currently, there are still insufficient clinical research and evidence-based practice in the field of cardio-oncology, resulting in a lack of standardization in its diagnosis and treatment. Additionally, the training model of physicians in cardio-oncology is still being explored. This article provides a comprehensive exploration of the opportunities and challenges faced by physicians and researchers in the field of cardio-oncology. It also delves into the prevailing landscape of clinical research in China and outlines the future training model for physicians in cardio-oncology.

Hybrid Metal-Ligand Interfacial Dipole Engineering of Functional Plasmonic Nanostructures for Extraordinary Responses of Optoelectronic Properties

Programmable manipulation of inorganic-organic interfacial electronic properties of ligand-functionalized plasmonic nanoparticles (NPs) is the key parameter dictating their applications such as catalysis, photovoltaics, and biosensing. Here we report the localized surface plasmon resonance (LSPR) properties of gold triangular nanoprisms (Au TNPs) in solid state that are functionalized with dipolar, conjugated ligands. A library of thiocinnamate ligands with varying surface dipole moments were used to functionalize TNPs, which results in ∼150 nm reversible tunability of LSPR peak wavelength with significant peak broadening (∼230 meV). The highly adjustable chemical system of thiocinnamate ligands is capable of shifting the Au work function down to 2.4 eV versus vacuum, i.e., ∼2.9 eV lower than a clean Au (111) surface, and this work function can be modulated up to 3.3 eV, the largest value reported to date through the formation of organothiolate SAMs on Au. Interestingly, the magnitude of plasmonic responses and work function modulation is NP shape dependent. By combining first-principles calculations and experiments, we have established the mechanism of direct wave function delocalization of electrons residing near the Fermi level into hybrid electronic states that are mostly dictated by the inorganic-organic interfacial dipole moments. We determine that both interfacial dipole and hybrid electronic states, and vinyl conjugation together are the key to achieving such extraordinary changes in the optoelectronic properties of ligand-functionalized, plasmonic NPs. The present study provides a quantitative relationship describing how specifically constructed organic ligands can be used to control the interfacial properties of NPs and thus the plasmonic and electronic responses of these functional plasmonics for a wide range of plasmon-driven applications.

Bridging semiempirical and ab initio QM/MM potentials by Gaussian process regression and its sparse variants for free energy simulation

Free energy simulations that employ combined quantum mechanical and molecular mechanical (QM/MM) potentials at ab initio QM (AI) levels are computationally highly demanding. Here, we present a machine-learning-facilitated approach for obtaining AI/MM-quality free energy profiles at the cost of efficient semiempirical QM/MM (SE/MM) methods. Specifically, we use Gaussian process regression (GPR) to learn the potential energy corrections needed for an SE/MM level to match an AI/MM target along the minimum free energy path (MFEP). Force modification using gradients of the GPR potential allows us to improve configurational sampling and update the MFEP. To adaptively train our model, we further employ the sparse variational GP (SVGP) and streaming sparse GPR (SSGPR) methods, which efficiently incorporate previous sample information without significantly increasing the training data size. We applied the QM-(SS)GPR/MM method to the solution-phase SN2 Menshutkin reaction, NH3+CH3Cl→CH3NH3++Cl-, using AM1/MM and B3LYP/6-31+G(d,p)/MM as the base and target levels, respectively. For 4000 configurations sampled along the MFEP, the iteratively optimized AM1-SSGPR-4/MM model reduces the energy error in AM1/MM from 18.2 to 4.4 kcal/mol. Although not explicitly fitting forces, our method also reduces the key internal force errors from 25.5 to 11.1 kcal/mol/Å and from 30.2 to 10.3 kcal/mol/Å for the N-C and C-Cl bonds, respectively. Compared to the uncorrected simulations, the AM1-SSGPR-4/MM method lowers the predicted free energy barrier from 28.7 to 11.7 kcal/mol and decreases the reaction free energy from -12.4 to -41.9 kcal/mol, bringing these results into closer agreement with their AI/MM and experimental benchmarks.

Machine learning based implicit solvent model for aqueous-solution alanine dipeptide molecular dynamics simulations

Inspired by the recent work from Noé and coworkers on the development of machine learning based implicit solvent model for the simulation of solvated peptides [Chen et al., J. Chem. Phys., 2021, 155, 084101], here we report another investigation of the possibility of using machine learning (ML) techniques to "derive" an implicit solvent model directly from explicit solvent molecular dynamics (MD) simulations. For alanine dipeptide, a machine learning potential (MLP) based on the DeepPot-SE representation of the molecule was trained to capture its interactions with its average solvent environment configuration (ASEC). The predicted forces on the solute deviated only by an RMSD of 0.4 kcal mol-1 Å-1 from the reference values, and the MLP-based free energy surface differed from that obtained from explicit solvent MD simulations by an RMSD of less than 0.9 kcal mol-1. Our MLP training protocol could also accurately reproduce combined quantum mechanical molecular mechanical (QM/MM) forces on the quantum mechanical (QM) solute in ASEC environment, thus enabling the development of accurate ML-based implicit solvent models for ab initio-QM MD simulations. Such ML-based implicit solvent models for QM calculations are cost-effective in both the training stage, where the use of ASEC reduces the number of data points to be labelled, and the inference stage, where the MLP can be evaluated at a relatively small additional cost on top of the QM calculation of the solute.

Facilitating ab initio QM/MM free energy simulations by Gaussian process regression with derivative observations

In combined quantum mechanical and molecular mechanical (QM/MM) free energy simulations, how to synthesize the accuracy of ab initio (AI) methods with the speed of semiempirical (SE) methods for a cost-effective QM treatment remains a long-standing challenge. In this work, we present a machine-learning-facilitated method for obtaining AI/MM-quality free energy profiles through efficient SE/MM simulations. In particular, we use Gaussian process regression (GPR) to learn the energy and force corrections needed for SE/MM to match with AI/MM results during molecular dynamics simulations. Force matching is enabled in our model by including energy derivatives into the observational targets through the extended-kernel formalism. We demonstrate the effectiveness of this method on the solution-phase S_N2 Menshutkin reaction using AM1/MM and B3LYP/6-31+G(d,p)/MM as the base and target levels, respectively. Trained on only 80 configurations sampled along the minimum free energy path (MFEP), the resulting GPR model reduces the average energy error in AM1/MM from 18.2 to 5.8 kcal mol^-1 for the 4000-sample testing set with the average force error on the QM atoms decreased from 14.6 to 3.7 kcal mol^-1 Å^-1. Free energy sampling with the GPR corrections applied (AM1-GPR/MM) produces a free energy barrier of 14.4 kcal mol^-1 and a reaction free energy of -34.1 kcal mol^-1, in closer agreement with the AI/MM benchmarks and experimental results.

Circadian nuclear receptor Rev-erbalpha is expressed by platelets and potentiates platelet activation and thrombus formation

Background

Adverse cardiovascular events have day/night patterns with peaks in the morning, potentially related to endogenous circadian clock control of platelet activation. Circadian nuclear receptor Rev-erbα is an essential and negative component of the circadian clock.

Purpose

We aim to investigate the expression profile and biological function of Rev-erbα in platelets.

Methods and results

Here we report the presence and functions of circadian nuclear receptor Rev-erbα in human and mouse platelets. Both human and mouse platelet Rev-erbα showed a circadian rhythm that positively correlated with platelet aggregation. Global Rev-erbα knockout and platelet-specific Rev-erbα knockout mice exhibited defective in hemostasis as assessed by prolonged tail-bleeding times. Rev-erbα deletion also reduced ferric chloride-induced carotid arterial occlusive thrombosis, prevented collagen/epinephrine-induced pulmonary thromboembolism, and protected against microvascular microthrombi obstruction and infarct expansion in an acute myocardial infarction model. In vitro thrombus formation assessed by CD41-labeled platelet fluorescence intensity was significantly reduced in Rev-erbα knockout mouse blood. Platelets from Rev-erbα knockout mice exhibited impaired agonist-induced aggregation responses, integrin αIIbβ3 activation and α-granule release. Consistently, pharmacological inhibition of Rev-erbα by specific antagonists decreased platelet activation markers in both mouse and human platelets. Mechanistically, mass spectrometry and co-immunoprecipitation analyses revealed that Rev-erbα potentiated platelet activation via oligophrenin-1-mediated RhoA/ERM (ezrin/radixin/moesin) pathway.

Conclusion

We provide the first evidence that circadian protein Rev-erbα is functionally expressed in platelets and potentiates platelet activation and thrombus formation. Rev-erbα may serve as a novel therapeutic target for managing thrombosis-based cardiovascular disease.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): This work was supported by grants from the National Science Fund for Distinguished Young Scholars (81625002), the National Natural Science Foundation of China (81930007).

Accelerating Ab Initio Quantum Mechanical and Molecular Mechanical (QM/MM) Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semiempirical QM/MM Hamiltonian

Molecular dynamics (MD) simulations employing ab initio quantum mechanical and molecular mechanical (ai-QM/MM) potentials are considered to be the state of the art, but the high computational cost associated with the ai-QM calculations remains a theoretical challenge for their routine application. Here, we present a modified protocol of the multiple time step (MTS) method for accelerating ai-QM/MM MD simulations of condensed-phase reactions. Within a previous MTS protocol [Nam J. Chem. Theory Comput. 2014, 10, 4175], reference forces are evaluated using a low-level (semiempirical QM/MM) Hamiltonian and employed at inner time steps to propagate the nuclear motions. Correction forces, which arise from the force differences between high-level (ai-QM/MM) and low-level Hamiltonians, are applied at outer time steps, where the MTS algorithm allows the time-reversible integration of the correction forces. To increase the outer step size, which is bound by the highest-frequency component in the correction forces, the semiempirical QM Hamiltonian is recalibrated in this work to minimize the magnitude of the correction forces. The remaining high-frequency modes, which are mainly bond stretches involving hydrogen atoms, are then removed from the correction forces. When combined with a Langevin or SIN(R) thermostat, the modified MTS-QM/MM scheme remains robust with an up to 8 (with Langevin) or 10 fs (with SIN(R)) outer time step (with 1 fs inner time steps) for the chorismate mutase system. This leads to an over 5-fold speedup over standard ai-QM/MM simulations, without sacrificing the accuracy in the predicted free energy profile of the reaction.

Doubly Polarized QM/MM with Machine Learning Chaperone Polarizability

A major shortcoming of semiempirical (SE) molecular orbital methods is their severe underestimation of molecular polarizability compared with experimental and ab initio (AI) benchmark data. In a combined quantum mechanical and molecular mechanical (QM/MM) treatment of solution-phase reactions, solute described by SE methods therefore tends to generate inadequate electronic polarization response to solvent electric fields, which often leads to large errors in free energy profiles. To address this problem, here we present a hybrid framework that improves the response property of SE/MM methods through high-level molecular-polarizability fitting. Specifically, we place on QM atoms a set of corrective polarizabilities (referred to as chaperone polarizabilities), whose magnitudes are determined from machine learning (ML) to reproduce the condensed-phase AI molecular polarizability along the minimum free energy path. These chaperone polarizabilities are then used in a machinery similar to a polarizable force field calculation to compensate for the missing polarization energy in the conventional SE/MM simulations. Because QM atoms in this treatment host SE wave functions as well as classical polarizabilities, both polarized by MM electric fields, we name this method doubly polarized QM/MM (dp-QM/MM). We demonstrate the new method on the free energy simulations of the Menshutkin reaction in water. Using AM1/MM as a base method, we show that ML chaperones greatly reduce the error in the solute molecular polarizability from 6.78 to 0.03 ų with respect to the density functional theory benchmark. The chaperone correction leads to ∼10 kcal/mol of additional polarization energy in the product region, bringing the simulated free energy profiles to closer agreement with the experimental results. Furthermore, the solute-solvent radial distribution functions show that the chaperone polarizabilities modify the free energy profiles through enhanced solvation corrections when the system evolves from the charge-neutral reactant state to the charge-separated transition and product states. These results suggest that the dp-QM/MM method, enabled by ML chaperone polarizabilities, provides a very physical remedy for the underpolarization problem in SE/MM-based free energy simulations.

Circadian disruption on the susceptibility to sepsis-induced cardiac dysfunction: a prospective multi-modal imaging study

Background

Sepsis is a significant cause of mortality, and cardiac dysfunction is one of the vital predictors for mortality of sepsis. However, the factors associated with the susceptibility to sepsis-induced cardiac dysfunction remain unclear. Disruption of circadian rhythms can profoundly influence cardiac health; however, to the knowledge of the authors, the relationship of circadian disruption to cardiac involvement in patients with sepsis is unknown.

Purpose

We aim to investigate the impact of circadian disruption on the susceptibility to sepsis-induced cardiac dysfunction.

Methods

Study patient data were obtained from the image database of EARLY-MYO-SEPSIS (EARLY assessment of MYOcardial tissue characteristics by multi-modal imaging in SEPSIS) registry, which was a prospective, multi-center registry of sepsis patients who have undergone cardiac magnetic resonance imaging (MRI) and echocardiography from 8 sites (clinical trial number NCT04513795). Cardiac involvement was evaluated using a comprehensive assessment comprising of echocardiography (with global longitudinal strain calculation), cardiac MRI and cardiac biomarker evaluation. Logistic regression was performed to identify independent predictors of left ventricular systolic dysfunction in sepsis.

Results

A total of 216 intensive care unit patients with sepsis was enrolled in the present analysis. Septic patients with a history of circadian disruption (i.e., sleep insufficiency <6 hours) presented more cardiac involvements (as indicated by edema on the cardiac MRI along with cardiac deformation and increased cardiac biomarkers) compared with those without circadian disruption history. Moreover, septic patients with a history of circadian disruption had increased mortality and incidence of heart failure. A history of circadian disruption was identified as an independent predictor of left ventricular systolic dysfunction in sepsis.

Conclusions

Our data from EARLY-MYO-SEPSIS registry demonstrated a previously unappreciated circadian sensitivity to sepsis-induced cardiac dysfunction.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): This work was supported by grants from the National Science Fund for Distinguished Young Scholars (81625002) and National Natural Science Foundation of China (81930007)

Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions

Despite recent advances in the development of machine learning potentials (MLPs) for biomolecular simulations, there has been limited effort on developing stable and accurate MLPs for enzymatic reactions. Here we report a protocol for performing machine-learning-assisted free energy simulation of solution-phase and enzyme reactions at the ab initio quantum-mechanical/molecular-mechanical (ai-QM/MM) level of accuracy. Within our protocol, the MLP is built to reproduce the ai-QM/MM energy and forces on both QM (reactive) and MM (solvent/enzyme) atoms. As an alternative strategy, a delta machine learning potential (ΔMLP) is trained to reproduce the differences between the ai-QM/MM and semiempirical (se) QM/MM energies and forces. To account for the effect of the condensed-phase environment in both MLP and ΔMLP, the DeePMD representation of a molecular system is extended to incorporate the external electrostatic potential and field on each QM atom. Using the Menshutkin and chorismate mutase reactions as examples, we show that the developed MLP and ΔMLP reproduce the ai-QM/MM energy and forces with errors that on average are less than 1.0 kcal/mol and 1.0 kcal mol^-1 Å^-1, respectively, for representative configurations along the reaction pathway. For both reactions, MLP/ΔMLP-based simulations yielded free energy profiles that differed by less than 1.0 kcal/mol from the reference ai-QM/MM results at only a fraction of the computational cost.

Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force

First-principles determination of free energy profiles for condensed-phase chemical reactions is hampered by the daunting costs associated with configurational sampling on ab initio quantum mechanical/molecular mechanical (AI/MM) potential energy surfaces. Here, we report a new method that enables efficient AI/MM free energy simulations through mean force fitting. In this method, a free energy path in collective variables (CVs) is first determined on an efficient reactive aiding potential. Based on the configurations sampled along the free energy path, correcting forces to reproduce the AI/MM forces on the CVs are determined through force matching. The AI/MM free energy profile is then predicted from simulations on the aiding potential in conjunction with the correcting forces. Such cycles of correction-prediction are repeated until convergence is established. As the instantaneous forces on the CVs sampled in equilibrium ensembles along the free energy path are fitted, this procedure faithfully restores the target free energy profile by reproducing the free energy mean forces. Due to its close connection with the reaction path-force matching (RP-FM) framework recently introduced by us, we designate the new method as RP-FM in collective variables (RP-FM-CV). We demonstrate the effectiveness of this method on a type-II solution-phase SN2 reaction, NH3 + CH3Cl (the Menshutkin reaction), simulated with an explicit water solvent. To obtain the AI/MM free energy profiles, we employed the semiempirical AM1/MM Hamiltonian as the base level for determining the string minimum free energy pathway, along which the free energy mean forces are fitted to various target AI/MM levels using the Hartree-Fock (HF) theory, density functional theory (DFT), and the second-order Møller-Plesset perturbation (MP2) theory as the AI method. The forces on the bond-breaking and bond-forming CVs at both the base and target levels are obtained by force transformation from Cartesian to redundant internal coordinates under the Wilson B-matrix formalism, where the linearized FM is facilitated by the use of spline functions. For the Menshutkin reaction tested, our FM treatment greatly reduces the deviations on the CV forces, originally in the range of 12-33 to ∼2 kcal/mol/Å. Comparisons with the experimental and benchmark AI/MM results, tests of the new method under a variety of simulation protocols, and analyses of the solute-solvent radial distribution functions suggest that RP-FM-CV can be used as an efficient, accurate, and robust method for simulating solution-phase chemical reactions.

Interligand communication in a metal mediated LL'CT system - a case study

A series of oxo-Mo(iv) complexes, [MoO(Dt²⁻)(Dt⁰)] (where Dt²⁻ = benzene-1,2-dithiol (bdt), toluene-3,4-dithiol (tdt), quinoxaline-2,3-dithiol (qdt), or 3,6-dichloro-benzene-1,2-dithiol (bdtCl₂); Dt⁰ = N,N′-dimethylpiperazine-2,3-dithione (Me₂Dt⁰) or N,N′-diisopropylpiperazine-2,3-dithione (ⁱPr₂Dt⁰)), possessing a fully oxidized and a fully reduced dithiolene ligand have been synthesized and characterized. The assigned oxidation states of coordinated dithiolene ligands are supported with spectral and crystallographic data. The molecular structure of [MoO(tdt)(ⁱPr₂Dt⁰)] (6) demonstrates a large ligand fold angle of 62.6° along the S⋯S vector of the Dt⁰ ligand. The electronic structure of this system is probed by density functional theory (DFT) calculations. The HOMO is largely localized on the Dt²⁻ ligand while virtual orbitals are mostly Mo and Dt⁰ in character. Modeling the electronic spectrum of 6 with time dependent (TD) DFT calculations attributes the intense low energy transition at ∼18 000 cm⁻¹ to a ligand-to-ligand charge transfer (LL′CT). The electron density difference map (EDDM) for the low energy transition depicts the electron rich Dt²⁻ ligand donating charge density to the redox-active orbitals of the electron deficient Dt⁰ ligand. Electronic communication between dithiolene ligands is facilitated by a Mo-monooxo center and distortion about its primary coordination sphere.

The interligand communication between non-innocent dithiolene ligands of different oxidation states has been described in a Mo system. The fully reduced ene-dithiolate (Dt²⁻) acts as a donor moiety to the oxidized dithione (Dt⁰) in an LL′CT process.

[Perinatal outcomes on mortality and influencing factors among HIV-infected mothers in Sichuan province]

Objective: To explore the influencing factors on perinatal mortality of pregnant women with HIV infection to reduce the mother-to-child transmission in Sichuan province. Methods: In this study, 4 786 perinatal infants of the HIV-infected pregnant women were included. Related data on perinatal epidemiology was reported by all the 183 medical and health care institutions where the HIV prevention of mother-to-child transmission program was initiated in 2005-2016. Univariate χ(2) test and multivariate logistic regression methods were used to analyze the perinatal mortality outcomes and influencing factors. Results: The overall perinatal mortality rate was 25.7‰ (123/4 786) among HIV-infected pregnant women, with annual downwarding trend (trend χ(2)=32.220, P=0.000). Perinatal mortality rate appeared the highest (χ(2)=4.130, P=0.042), with more fetal deaths and stillbirths and less early neonatal death within 7 days in Liangshan county (χ(2)=29.626, P=0.000). Results from the multivariate logistic regression analysis showed that fewer pregnant numbers would contribute to the, lower perinatal mortality rate (1-2 pregnancies OR=0.417, 95%CI: 0.184-0.943; 3-4 pregnancies OR=0.447, 95%CI: 0.223-0.895). Perinatal deaths were more likely to be prevented if LPV/r protease inhibitor-based triple antiviral therapy was provided (OR=0.530, 95%CI: 0.285- 0.986) or delivery was taken place in the hospital (hospital of municipal-level and above OR=0.222, 95%CI:0.098-0.499; county-level hospital OR=0.282, 95%CI: 0.166-0.480; township-level hospital OR=0.134, 95%CI: 0.031-0.586) among HIV-infected pregnant women. However, premature delivery or neonatal asphyxia would increase the risk of perinatal mortality (premature delivery OR=8.285, 95%CI: 5.073-13.533; neonatal asphyxia OR=9.624, 95%CI: 4.625-20.028). Conclusions: The perinatal mortality rate of HIV-infected pregnant women appeared significantly higher than that in the province or the whole country. Strategies involving LPV/r-based triple antiviral therapy, promotion of hospital delivery, reducing the incidence rates of premature deliveries and neonatal asphyxia, should be strengthened.

Identifying Thermal Decomposition Products of Nitrate Ester Explosives Using Gas Chromatography-Vacuum Ultraviolet Spectroscopy: An Experimental and Computational Study

Analysis of nitrate ester explosives (e.g., nitroglycerine) using gas chromatography-vacuum ultraviolet spectroscopy (GC-VUV) results in their thermal decomposition into nitric oxide, water, carbon monoxide, oxygen, and formaldehyde. These decomposition products exhibit highly structured spectra in the VUV that is not seen in larger molecules. Computational analysis using time-dependent density functional theory (TDDFT) was utilized to investigate the excited states and vibronic transitions of these decomposition products. The experimental and computational results are compared with those in previous literature using synchrotron spectroscopy, electron energy loss spectroscopy (EELS), photoabsorption spectroscopy, and other computational excited state methods. It was determined that a benchtop GC-VUV detector gives comparable results to those previously reported, and TDDFT could predict vibronic spacing and model molecular orbital diagrams.

[HIV positive rate from different detection methods in medical institutions in China: a Meta analysis]

Objective: To analyze the HIV positive detection rate from different detection channels in Chinese medical institutions. Methods: A Meta-analysis was conducted. First of all, the literature on HIV testing of medical institutions in China was systematically searched on China National Knowledge Infrastructure, Wanfang Data Knowledge Service Platform, VIP Information Chinese journal Service platform and PubMed. Secondly, a self-made information table was used to collect the basic information, HIV positive number and test number of the literature. Finally, R 4.0.2 software was used to calculate the pooled HIV detection rate and 95%CI of the whole population, detection approaches subgroups and regions subgroups, and then the forest map was drawn. Funnel plot was used to analyze publication bias. Results: A total of 45 studies which covered 22 provinces. Meta analysis showed that the pooled HIV positive rate was 0.82‰ (95%CI: 0.62‰-1.04‰). Subgroup analysis showed that the HIV positive rate of STD outpatient was the highest (3.01‰ (95%CI: 1.76‰-4.58‰), followed by other patients (1.43‰ (95%CI: 1.00‰-1.93‰)). The HIV positive rate of western China was the highest (1.14‰ (95%CI: 0.72‰-1.63‰)). The HIV positive rate in 2008-2017 was higher than in 2000-2007. The Egger test indicated no publication bias (t=-0.737, P=0.465). Conclusion: The HIV positive detection rate of patients in medical institutions in China was at a low level, but the positive rate of patients in STD clinics was relatively high. Therefore, the HIV testing should be further expanded in this population. Secondly, HIV screening should be strengthened for other patients.

Comparison of trans-catheter closure of paravalvular leak versus surgical approach-outcomes and cost analysis

Background

The outcomes and costs of trans-catheter closure (TC) of paravalvular leak (PVL) compared with surgical closure (SC) are rarely described.

Purpose

The aim of the study was to assess the outcomes and hospital costs of patients who underwent TC or SC of PVL in our center.

Methods

Patients who underwent TC and SC of PVL between Jan. 2016 and Dec. 2019 were enrolled. Baseline characteristics, procedural, in-hospital and mid-term outcomes and hospital costs were compared.

Results

A total of 141 patients were studied (TC, n=65 and SC, n=76). The patients were elder in TC group (56.8±12.8 years vs. 50.1±12.8 years, p=0.002). Technical success was higher in SC group (83.1% vs. 98.7%, p<0.001). Procedure room time (93±38 min vs. 395±132 min, p<0.001), intensive care unit time (0 h vs. 25 h, p<0.001), length of stay from hospitalization to discharge (7 days vs. 21 days, p<0.001) and costs (¥45090±19343 vs. ¥164165±94300, p<0.001) were significantly less in TC group. After risk adjustment, there was no significant differences between in 30 days survival between TC group and SC group. However, the residual PVLs were less in SC group (43.1% vs. 12.0%, p=0.012). At a median follow-up of 21 months, there was a trend towards reduce all-cause death following TC versus SC (OR=0.054, 95% CI: 0.070 to 0.445, p=0.007).

Conclusions

SC for PVL is associated with higher technical rates and less residual shunt. But, the shorter length of stay and lower resources use with TC group significantly reduce hospital costs. In addition, TC achieve a better mid-term results in survival.

Funding Acknowledgement

Type of funding source: None

Global longitudinal diastolic strain rate as a novel marker for predicting adverse outcomes in hypertrophic cardiomyopathy by cardiac magnetic resonance tissue tracking

AIM

To examine the prognostic value of global peak diastolic strain rate (PDSR) derived from cardiac magnetic resonance (CMR) tissue tracking (CMR-TT) in predicting adverse outcomes in hypertrophic cardiomyopathy (HCM) patients.

MATERIALS AND METHODS

A total of 98 patients diagnosed with HCM (44 patients had left ventricle [LV] outflow tract obstruction [LVOTO] and 54 patients did not) were enrolled and followed for the specified endpoint. LV global myocardial mechanics was assessed in all participants using CMR-TT at study entry.

RESULTS

Compared with the non-obstructive subgroup, the obstructive subgroup demonstrated deteriorated magnitude of LV global radial, circumferential, and longitudinal PDSR (all p<0.05). After a mean follow-up period of 4.5 years, 24 patients reached an endpoint before the end of the study. Furthermore, when using the specified cut-off value (0.33 1/s) of longitudinal PDSR, the Kaplan-Meier curve demonstrated that patients with lower longitudinal PDSR had a significantly lower freedom from major adverse cardiovascular events (MACE) compared with their counterparts in the non-obstructive, obstructive, and overall cohorts (all log-rank p<0.05). Multivariable analysis showed that longitudinal PDSR remained the strongest predictor of outcome after adjusting for baseline and CMR variables (hazard ratio, 2.65; 95% confidence interval, 2.21-11.44; p<0.05).

CONCLUSION

CMR-TT-derived longitudinal PDSR is probably considered a novel and easy-to-perform marker for predicting adverse outcomes in HCM patients, which is beneficial to risk stratification. Further confirmatory studies are needed.

[A multicenter randomized prospective study of concurrent chemoradiation with 60 Gy versus 50 Gy for inoperable esophageal squamous cell carcinoma]

Objective: To determine whether 60 Gy is superior to standard 50 Gy for definitive concurrent chemoradiation(CCRT) in esophageal squamous cell carcinoma (ESCC) using modern radiation technology in a phase Ⅲ prospective randomized trial. Methods: From April 2013 to May 2017, 331 patients from 22 hospitals who were pathologically confirmed with stage ⅢA-ⅣA ESCC were randomized to 60 Gy or 50 Gy with random number table. Total of 305 patients were analyzed, including 152 in 60 Gy group and 153 in 50 Gy group. The median age was 63 years, 242(79.3%) males and 63(20.7%) females. The median length of primary tumor was 5.6 cm. The clinical characteristics between two groups were comparable. All patients were delivered 2 Gy per fraction, 5 fractions per week. Concurrent weekly chemotherapy with docetaxel (25 mg/m(2)) and cisplatin (25 mg/m(2)) and 2 cycles consolidation chemotherapy with docetaxel (70 mg/m(2)) and cisplatin (25 mg/m(2), d1-3) were administrated. The primary endpoint was local/regional progression-free survival (LRPFS). The data were compared with Pearson chi-square test or Fisher's exact test. Results: At a median follow-up of 27.3 months, the disease progression rate was 37.5% (57/152), 43.8% (67/153) in the high and standard-dose group, respectively (χ(2)=1.251, P=0.263). The 1, 2, 3-year LRPFS rate was 75.4%, 56.8%, 52.1% and 74.2%, 58.4%, 50.1%, respectively (HR: 0.95, 95%CI: 0.69-1.31, P=0.761). The 1, 2, 3-year overall survival rate was 84.1%, 64.8%, 54.1% and 85.4%, 62.9%, 54.0%, respectively (HR: 0.98, 95%CI: 0.71-1.38, P=0.927). The 1, 2, 3-year progression-free survival rate was 70.8%, 54.2%, 48.5% and 65.5%, 51.9%, 45.1%, respectively (HR: 0.93, 95%CI: 0.68-1.26, P=0.621). The incidence rates in toxicities between the two groups were similar except for higher rate of severe pneumonitis in high dose group (χ(2)=11.596, P=0.021). Conclusions: The efficacy in disease control is similar between 60 Gy and 50 Gy using modern radiation technology concurrent with chemotherapy for ESCC. The 50 Gy should be recommended as the regular radiation dose with CCRT for ESCC.

The relationship between regulatory T cells and radiation therapy

Radiation therapy (RT) is an effective treatment for cancer. Approximately, 70% of cancer patients receive RT in China. The immune-modulating effect of radiation therapy have gained considerable interest in recent years and there have been multiple reports of synergy between radiation and immunotherapy. Regulatory T cells (Tregs) are a group of T cell subsets with immunosuppressive function, which is correlated with cancer. Tregs are involved in the pathogenesis, development, treatment and prognosis of tumors by cell-cell contact, cytokines, and cell metabolism. Based on the immunological characteristics of Tregs, this article reviews the interaction between RT and immune molecules, aiming to provide new ideas for RT combined with immunotherapy.

Correlation between gene polymorphism and opioid efficacy in patients with gastric or intestinal cancer

OBJECTIVE

To explore the correlation between gene polymorphism and opioid efficacy in patients with gastric or intestinal cancer.

PATIENTS AND METHODS

Fifty-nine patients who underwent laparoscopic surgery for gastric or intestinal cancer under general anesthesia were included and randomly divided into oxycodone (n=30) and sufentanil groups (n=29) by reproducible random number generation method. Single nucleotide polymorphisms (SNPs) of four alleles: μ-opioid receptor gene OPRM1 A118G, cytochrome P450 (CPY450) enzyme system: CPY3A4*1G, CYP3A5*3, and CYP2D6*10 were detected by PCR-pyrosequencing. Patients in sufentanil group received intravenous sufentanil injection during anesthesia induction, intraoperative maintenance, and postoperative analgesia, while those in oxycodone group received oxycodone. Patients' postoperative VAS score, opioid use, and prevalence of adverse reactions were recorded.

RESULTS

The genotype distribution of OPRM1 A118G, CYP3A4*1G, CYP3A5*3, and CYP2D6*10 in Chinese gastric cancer/intestinal cancer patients accorded with the Hardy-Weinberg law (p>0.05). OPRM1 A118G polymorphism correlated with postoperative VAS score and medication dosage, in oxycodone group (p<0.05), while it didn't with those of sufentanil group. The VAS scores in GG group were higher than that in AA group and AG group at T6-T9, (p<0.05); the postoperative pain remedies times in GG group were more than that in the AA and AG groups (p=0.002). CYP3A4*1G polymorphism related to postoperative VAS score, medication dosage and prevalence of adverse reactions in sufentanil group (p<0.05), while it didn't with those of oxycodone group (p>0.05). The total intraoperative medication in AA group was less than that in GG and GA groups (p<0.01), with a higher prevalence of respiratory depression (p=0.01). Nor was there any correlation of CYP3A5*3 and CYP2D6*10 polymorphisms with the efficacy, postoperative VAS score, pain remedies times, postoperative 24 h medication dosage, or prevalence of adverse reactions in oxycodone and sufentanil groups.

CONCLUSIONS

Gene polymorphism affects the efficacy and adverse reactions of opioids in patients undergoing laparoscopic gastric or intestinal cancer surgery.

Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching

An efficient and accurate reference potential simulation protocol is proposed for producing ab initio quantum mechanical/molecular mechanical (AI-QM/MM) quality free energy profiles for chemical reactions in a solvent or macromolecular environment. This protocol involves three stages: (a) using force matching to recalibrate a semi-empirical quantum mechanical (SE-QM) Hamiltonian for the specific reaction under study; (b) employing the recalibrated SE-QM Hamiltonian (in combination with molecular mechanical force fields) as the reference potential to drive umbrella samplings along the reaction pathway; and (c) computing AI-QM/MM energy values for collected configurations from the sampling and performing weighted thermodynamic perturbation to acquire an AI-QM/MM corrected reaction free energy profile. For three model reactions (identity SN2 reaction, Menshutkin reaction, and glycine proton transfer reaction) in aqueous solution and one enzyme reaction (Claisen arrangement in chorismate mutase), our simulations using recalibrated PM3 SE-QM Hamiltonians well reproduced QM/MM free energy profiles at the B3LYP/6-31G* level of theory all within 1 kcal mol-1 with a 20 to 45 fold reduction in the computer time.

Exploring Cycloreversion Reaction of Cyclobutane Pyrimidine Dimers Quantum Mechanically

The cyclobutane pyrimidine dimer (CPD) is a major photoproduct of deoxyribonucleic acid (DNA) that is damaged by ultraviolet light. This DNA lesion can be repaired by DNA photolyase with the aid of UV light and two cofactors. To understand the repair mechanism of CPD and whether protonation of CPD participates in the DNA repair process, the cycloreversion reactions of four CPD models and proton transfers between the adjacent residue Glu283 and CPD models were explored through the quantum mechanical method. Two-dimensional maps of potential energy surface in a vacuum and in implicit water solution were calculated at the ωB97XD/6-311++G(2df,2pd) level. One-dimensional potential energy profiles were computed for proton transfer reactions. Among the models that have been considered, both in a vacuum and in water solution, the results indicate that the most likely repair mechanism involves CPD^•2- radical anion splitting in a stepwise manner. C5-C5' splits first, and C6-C6' splits later. The computed free energies of activation of the two splitting steps are 0.9 and 3.1 kcal/mol, respectively. The adjacent Glu283 may stabilize the CPD^•2- radical anion through hydrogen bond and increase the quantum yield; however, protonating the CPD radical anion by Glu283 cannot accelerate the rate of ring opening.

Mapping Free Energy Pathways for ATP Hydrolysis in the E. coli ABC Transporter HlyB by the String Method

HlyB functions as an adenosine triphosphate (ATP)-binding cassette (ABC) transporter that enables bacteria to secrete toxins at the expense of ATP hydrolysis. Our previous work, based on potential energy profiles from combined quantum mechanical and molecular mechanical (QM/MM) calculations, has suggested that the highly conserved H-loop His residue H662 in the nucleotide binding domain (NBD) of E. coli HlyB may catalyze the hydrolysis of ATP through proton relay. To further test this hypothesis when entropic contributions are taken into account, we obtained QM/MM minimum free energy paths (MFEPs) for the HlyB reaction, making use of the string method in collective variables. The free energy profiles along the MFEPs confirm the direct participation of H662 in catalysis. The MFEP simulations of HlyB also reveal an intimate coupling between the chemical steps and a local protein conformational change involving the signature-loop residue S607, which may serve a catalytic role similar to an Arg-finger motif in many ATPases and GTPases in stabilizing the phosphoryl-transfer transition state.

Effects of dietary energy and lipase levels on nutrient digestibility, digestive physiology and noxious gas emission in weaning pigs

Objective

This study was conducted to evaluate the effect of dietary energy and lipase supplementation on growth performance, nutrient digestibility, serum profiles, intestinal morphology, small intestinal digestive enzyme activities, biochemical index of intestinal development and noxious gas emission in weaning pigs.

Methods

A total of 240 weaning pigs ([Yorkshire×Landrace]×Duroc) with an average body weight (BW) of 7.3±0.12 kg were used in this 28-d experiment. Weaning pigs were randomly allocated to 4 dietary treatments in a 2×2 factorial arrangement with 2 levels of energy (net energy = 2,470 kcal/kg for low energy diet and 2,545 kcal/kg for basal diet) and 2 levels of lipase (0 and 1.5 U/g of lipase) according to BW and sex. There were 6 replications (pens) per treatment and 10 pigs per pen (5 barrows and 5 gilts).

Results

Weaning pigs fed the low energy diet had lower (p<0.05) gain-to-feed ratio (G:F) throughout the experiment, apparent digestibility of dry matter, nitrogen, ether extract, and gross energy during d 0 to 14, average daily gain during d 15 to 28, lipase activity in duodenum and ileum and protein/DNA in jejunum (p<0.05), respectively. Lipase supplementation had no effect on growth performance but affected apparent nutrient digestibility (p<0.05) on d 14 and enhanced lipase activity in the duodenum and ileum and protease activity in duodenum and jejunum of pigs (p<0.05) fed the low energy diet. Lipase reduced serum low-density lipoprotein cholesterol (LDL-C) and triglyceride (TG), NH₃ production (p<0.05) from the feces.

Conclusion

The low energy diet decreased G:F throughout the experiment and nutrient digestibility during d 0 to 14 as well as lipase activity in duodenum and ileum. Lipase supplementation increased nutrient digestibility during d 0 to 14 and exerted beneficial effects on lipase activity in duodenum and ileum as well as protease activity in duodenum and jejunum, while reduced serum LDL-C, TG and fecal NH₃.

Elucidating the role of surface passivating ligand structural parameters in hole wave function delocalization in semiconductor cluster molecules

This article describes the mechanisms underlying electronic interactions between surface passivating ligands and (CdSe)₃₄ semiconductor cluster molecules (SCMs) that facilitate band-gap engineering through the delocalization of hole wave functions without altering their inorganic core. We show here both experimentally and through density functional theory calculations that the expansion of the hole wave function beyond the SCM boundary into the ligand monolayer depends not only on the pre-binding energetic alignment of interfacial orbitals between the SCM and surface passivating ligands but is also strongly influenced by definable ligand structural parameters such as the extent of their π-conjugation [π-delocalization energy; pyrene (Py), anthracene (Anth), naphthalene (Naph), and phenyl (Ph)], binding mode [dithiocarbamate (DTC, -NH-CS₂^-), carboxylate (-COO^-), and amine (-NH₂)], and binding head group [-SH, -SeH, and -TeH]. We observe an unprecedentedly large ∼650 meV red-shift in the lowest energy optical absorption band of (CdSe)₃₄ SCMs upon passivating their surface with Py-DTC ligands and the trend is found to be Ph- < Naph- < Anth- < Py-DTC. This shift is reversible upon removal of Py-DTC by triethylphosphine gold(i) chloride treatment at room temperature. Furthermore, we performed temperature-dependent (80-300 K) photoluminescence lifetime measurements, which show longer lifetime at lower temperature, suggesting a strong influence of hole wave function delocalization rather than carrier trapping and/or phonon-mediated relaxation. Taken together, knowledge of how ligands electronically interact with the SCM surface is crucial to semiconductor nanomaterial research in general because it allows the tuning of electronic properties of nanomaterials for better charge separation and enhanced charge transfer, which in turn will increase optoelectronic device and photocatalytic efficiencies.

Multiple ATP-binding cassette transporters are involved in insecticide resistance in the small brown planthopper, Laodelphax striatellus

ATP-binding cassette (ABC) transporters are membrane-bound proteins involved in the movement of various substrates, including drugs and insecticides, across the lipid membrane. Demonstration of the role of human ABC transporters in multidrug resistance has led to speculation that they might be an important mechanism controlling the fate of insecticides in insects. However, the role of ABC transporters in insects remains largely unknown. The small brown planthopper, Laodelphax striatellus Fallén, has developed resistance to most of the insecticides used for its control. Our goals were to identify the ABC transporters in La. striatellus and to examine their involvement in resistance mechanisms, using related strains resistant to chlorpyrifos, deltamethrin and imidacloprid, compared with the susceptible strain. Based on the transcriptome of La. striatellus, 40 full-length ABC transporters belonging to the ABCA-ABCH subfamilies were identified. Quantitative PCR revealed that over 20% of genes were significantly up-regulated in different resistant strains, and eight genes from the ABCB/C/D/G subfamilies were up-regulated in all three resistant strains, compared with the susceptible strain. Furthermore, synergism studies showed verapamil significantly enhanced insecticide toxicity in various resistant strains but not in the susceptible strain. These results suggest that ABC transporters might be involved in resistance to multiple insecticides in La. striatellus.

Toward Determining ATPase Mechanism in ABC Transporters: Development of the Reaction Path-Force Matching QM/MM Method

Adenosine triphosphate (ATP)-binding cassette (ABC) transporters are ubiquitous ATP-dependent membrane proteins involved in translocations of a wide variety of substrates across cellular membranes. To understand the chemomechanical coupling mechanism as well as functional asymmetry in these systems, a quantitative description of how ABC transporters hydrolyze ATP is needed. Complementary to experimental approaches, computer simulations based on combined quantum mechanical and molecular mechanical (QM/MM) potentials have provided new insights into the catalytic mechanism in ABC transporters. Quantitatively reliable determination of the free energy requirement for enzymatic ATP hydrolysis, however, requires substantial statistical sampling on QM/MM potential. A case study shows that brute force sampling of ab initio QM/MM (AI/MM) potential energy surfaces is computationally impractical for enzyme simulations of ABC transporters. On the other hand, existing semiempirical QM/MM (SE/MM) methods, although affordable for free energy sampling, are unreliable for studying ATP hydrolysis. To close this gap, a multiscale QM/MM approach named reaction path-force matching (RP-FM) has been developed. In RP-FM, specific reaction parameters for a selected SE method are optimized against AI reference data along reaction paths by employing the force matching technique. The feasibility of the method is demonstrated for a proton transfer reaction in the gas phase and in solution. The RP-FM method may offer a general tool for simulating complex enzyme systems such as ABC transporters.