Consistent Construction of the Density Matrix from Surface Hopping Trajectories.

Proper construction of the density matrix based on surface hopping trajectories remains a difficult problem. Due to the well-known overcoherence in traditional surface hopping simulations, the electronic wave function cannot be used directly. In this work, we propose a consistent density matrix construction method, which takes the advantage of occupation of active states to rescale the coherence calculated by wave functions and ensures the intrinsic consistency of the density matrix. This new trajectory analysis method can be used for both Tully's fewest switches surface hopping (FSSH) and our recently proposed branching corrected surface hopping (BCSH). As benchmarked in both one- and two-dimensional standard scattering models, the new approach combined with BCSH trajectories achieves highly accurate time-dependent spatial distributions of adiabatic populations and coherence compared to exact quantum results.

Learning Decoherence Time Formulas for Surface Hopping from Quantum Dynamics.

Surface hopping simulations have achieved great success in many different fields, but their reliability has long been limited by the overcoherence problem. We here present a general machine learning assisted approach to identify optimal decoherence time formulas for surface hopping using exact quantum dynamics as references. In order to avoid computationally expensive force calculations, we use the nuclear kinetic energy and the adiabatic energy difference to iteratively generate the descriptor space. Through multilayer screening of the candidate descriptors and discrete optimization of the relevant parameters, we obtain new energy-based decoherence time formulas. As benchmarked in thousands of diverse multilevel systems and six standard scattering models, surface hopping with our new decoherence time formulas nearly reproduces the exact quantum dynamics while maintaining high efficiency. Thereby, our approach provides a promising avenue for systematically improving the accuracy of surface hopping simulations in complex systems from quantum dynamics data.

Prominin-1 promotes restitution of the murine extrahepatic biliary luminal epithelium following cholestatic liver injury.

BACKGROUND AND AIMS: Restitution of the extrahepatic biliary luminal epithelium in cholangiopathies is poorly understood. Prominin-1 (Prom1) is a key component of epithelial ciliary body of stem/progenitor cells. Given that intrahepatic Prom1-expressing progenitor cells undergo cholangiocyte differentiation, we hypothesized that Prom1 may promote restitution of the extrahepatic bile duct (EHBD) epithelium following injury. APPROACH AND RESULTS: Utilizing various murine biliary injury models, we identified Prom1-expressing cells in the peribiliary glands of the EHBD. These Prom1-expressing cells are progenitor cells which give rise to cholangiocytes as part of the normal maintenance of the EHBD epithelium. Following injury, these cells proliferate significantly more rapidly to re-populate the biliary luminal epithelium. Null mutation of Prom1 leads to significantly >10-fold dilated peribiliary glands following rhesus rotavirus-mediated biliary injury. Cultured organoids derived from Prom1 knockout mice are comprised of biliary progenitor cells with altered apical-basal cellular polarity, significantly fewer and shorter cilia, and decreased organoid proliferation dynamics consistent with impaired cell motility. CONCLUSIONS: We, therefore, conclude that Prom1 is involved in biliary epithelial restitution following biliary injury in part through its role in supporting cell polarity.

TWEAK/FN14 promotes profibrogenic pathway activation in Prominin-1-expressing hepatic progenitor cells in biliary atresia.

BACKGROUND AND AIMS: Biliary atresia (BA), a congenital cholestatic liver disease, commonly culminates in end-stage liver disease. We previously demonstrated in BA that Prominin-1 ( Prom1 )-expressing hepatic progenitor cells (HPCs) expand within regions of developing fibrosis, giving rise to cholangiocytes within biliary ductular reactions. Null mutation of Prom1 or ablation of cells expressing Prom1 significantly diminishes fibrogenesis. FN14, the receptor for TNF-like weak inducer of apoptosis (TWEAK), is expressed by HPCs. TWEAK/FN14 signaling promotes fibrosis in multiple organ systems. Therefore, we hypothesized that TWEAK/FN14 signaling mediates Prom1 -expressing HPC proliferation leading to profibrogenic ductular reactions in BA. APPROACH AND RESULTS: The experimental mouse model of BA mediated by perinatal rhesus rotavirus (RRV) infection resulted in increased co-expression of Fn14 in Prom1 -expressing HPCs within regions of ductular reactions. FN14 antagonist L524-0366 decreased ductular reactions, biliary fibrosis and periportal fibroblast activation in RRV injury. L524-0366 inhibition also demonstrated loss of downstream noncanonical NF-kB signaling expression in RRV injury. Murine HPC organoids demonstrated accelerated organoid growth and proliferation when treated with recombinant TWEAK. Increased organoid proliferation with recombinant TWEAK was lost when also treated with L524-0366. Analysis of a large publicly available RNA sequencing database of BA and normal control patients revealed significant increases in expression of PROM1 , FN14 , and genes downstream of TNF signaling and noncanonical NF-κB signaling pathways in BA infants. Infants who failed to achieve bile drainage after hepatoportoenterostomy had higher relative levels of FN14 expression. CONCLUSION: TWEAK/FN14 signaling activation in Prom1 -expressing HPCs contributes to proliferation of profibrogenic ductular reactions in BA.

A unified framework of mixed quantum-classical dynamics with trajectory branching.

As popular mixed quantum-classical dynamics methods, trajectory surface hopping and Ehrenfest mean field have been widely utilized to simulate nonadiabatic dynamics. Recently, we have proposed the branching-corrected surface hopping and the branching-corrected mean field methods, both of which closely reproduce the exact quantum dynamics in a series of standard scattering models. Here, the mixed surface hopping and mean field with branching correction (BCSHMF) is presented as a unified framework of mixed quantum-classical dynamics. As benchmarked in thousands of diverse three-level and four-level scattering models, BCSHMF achieves high reliability and flexibility, implying that surface hopping and mean field are compatible with each other in nature, and trajectory branching is essential for the mixed quantum-classical description of nonadiabatic dynamics.

Consensus-Related Performance of Triplex MASs Based on Partial Complete Graph Structure.

This article mainly studies first-order coherence related to the robustness of the triplex MASs consensus models with partial complete graph structures; the performance index is studied through algebraic graph theory. The topologies of the novel triplex networks are generated by graph operations and the approach of graph spectra is applied to calculate the first-order network coherence. The coherence asymptotic behaviours of the three cases of the partial complete structures are analysed and compared. We find that under the condition that the number of nodes in partial complete substructures n tends to infinity, the coherence asymptotic behaviour of the two sorts of non-isomorphic three-layered networks will be increased by r-12(r+1), which is irrelevant to the peripheral vertices number p; when p tends to infinity, adding star copies to the original triplex topologies will reverse the original size relationship of the coherence under consideration of the triplex networks. Finally, the coherence of the three-layered networks with the same sorts of parameters, but non-isomorphic graphs, are simulated to verify the results.

A mixed deterministic-stochastic algorithm of the branching corrected mean field method for nonadiabatic dynamics.

We present a new algorithm of the branching corrected mean field (BCMF) method for nonadiabatic dynamics [J. Xu and L. Wang, J. Phys. Chem. Lett. 11, 8283 (2020)], which combines the key advantages of the two existed algorithms, i.e., the deterministic BCMF algorithm based on weights of trajectory branches (BCMF-w) and the stochastic BCMF algorithm with random collapse of the electronic wavefunction (BCMF-s). The resulting mixed deterministic-stochastic BCMF algorithm (BCMF-ws) is benchmarked in a series of standard scattering problems with potential wells on the excited-state surfaces, which are common in realistic systems. In all investigated cases, BCMF-ws holds the same high accuracy while the computational time is reduced about two orders of magnitude compared to the original BCMF-w and BCMF-s algorithms, thus promising for nonadiabatic dynamics simulations of general systems.

Clinical characteristics and related risk factors of disease severity in 101 COVID-19 patients hospitalized in Wuhan, China.

Coronavirus disease 2019 (COVID-19) broke out in December 2019. Due its high morbility and mortality, it is necessary to summarize the clinical characteristics of COVID-19 patients to provide more theoretical basis for future treatment. In the current study, we conducted a retrospective analysis of the clinical characteristics of COVID-19 patients and explored the risk factors for the severity of illness. A total of 101 COVID-19 patients hospitalized in Leishenshan Hospital (Wuhan, China) was classified into three sub-types: moderate (n = 47), severe (n = 36), and critical (n = 18); their clinical data were collected from the Electronic Medical Record. We showed that among the 101 COVID-19 patients, the median age was 62 years (IQR 51-74); 50 (49.5%) patients were accompanied by hypertension, while 25 (24.8%) and 22 (21.8%) patients suffered from diabetes and heart diseases, respectively, with complications. All patients were from Wuhan who had a definite history of exposure to the epidemic area. Multivariate logistic regression analysis revealed that older age, diabetes, chronic liver disease, percentage of neutrophils (N%) > 75%, CRP > 4 mg/L, D-dimer > 0.55 mg/L, IL-2R > 710 U/mL, IL-8 > 62 pg/mL, and IL-10 > 9.1 pg/mL were independent variables associated with severe COVID-19. In conclusion, we have identified the independent risk factors for the severity of COVID-19 pneumonia, including older age, diabetes, chronic liver disease, higher levels of N%, CRP, D-dimer, IL-2R, IL-8, and IL-10, providing evidence for more accurate risk prediction.

Branching and phase corrected surface hopping: A benchmark of nonadiabatic dynamics in multilevel systems.

Since the seminal work of Tully [J. Chem. Phys. 93, 1061 (1990)], two-level scattering models have been extensively adopted as the standard benchmark systems to assess the performance of different trajectory surface hopping methods for nonadiabatic dynamics simulations. Here, we extend the branching and phase corrections to multilevel systems and combine them with both the traditional fewest switches surface hopping (FSSH) and its variant global flux surface hopping (GFSH) algorithms. To get a comprehensive evaluation of the proposed methods, we construct a series of more challenging and diverse three-level and four-level scattering models and use exact quantum solutions as references. Encouragingly, both FSSH and GFSH with the branching and phase corrections produce excellent and nearly identical results in all investigated systems, indicating that the new surface hopping methods are robust to describe multilevel problems and the reliability is insensitive to the definition of self-consistent hopping probabilities in the adiabatic representation. Furthermore, the branching correction is found to be especially important when dealing with strongly repulsive potential energy surfaces, which are common in realistic systems, thus promising for general applications.

Urea-based amino sugar agent clears murine liver and preserves protein fluorescence and lipophilic dyes.

Five established clearing protocols were compared with a modified and simplified method to determine an optimal clearing reagent for three-dimensionally visualizing fluorophores in the murine liver, a challenging organ to clear. We report successful clearing of whole liver lobes by modification of an established protocol (UbasM) using only Ub-1, a urea-based amino sugar reagent, in a simpler protocol that requires only a 24-h processing time. With Ub-1 alone, we observed sufficiently preserved liver tissue structure in three dimensions along with excellent preservation of fluorophore emissions from endogenous protein reporters and lipophilic tracer dyes. This streamlined technique can be used for 3D cell lineage tracing and fluoroprobe-based reporter gene expression to compare various experimental conditions.

In vivo therapeutic success of MicroRNA-155 antagomir in a mouse model of pulmonary fibrosis induced by bleomycin.

BACKGROUND/AIMS: MicroRNAs (miRNAs) play critical regulatory roles in the pathogenesis of pulmonary fibrosis. The aim of this study was to explore whether miRNA antagomirs could serve as potential therapeutic agents in interstitial lung diseases. METHODS: A mouse model of pulmonary fibrosis was established by intratracheal injection of bleomycin (BLM). Using microarray analysis, up-regulated miRNAs were identified during the development of pulmonary fibrosis. miR-155 was chosen as the candidate miRNA. Fifteen mice were then randomized into the following three groups: BLM + antagomiR-155 group, treated with BLM plus intravenously injected with antagomiR-155; BLM group, treated with intratracheal BLM plus phosphate-buffered saline (PBS); and a control group, treated with PBS only. Lung tissues were collected for histopathological analysis, hydroxyproline measurement, and Western blotting. Enzyme-linked immunosorbent assays were used for the measurement of cytokines associated with pulmonary fibrosis. RESULTS: Histological changes and hydroxyproline levels induced by BLM were significantly inhibited by antagomiR-155. The levels of interleukin 4 (IL-4) and transforming growth factor-ß (TGF-ß) expression were increased after BLM treatment. However, miR-155 silencing decreased the expression of IL-4, TGF-ß, and interferon-γ. TGF-ß-activated kinase 1/mitogen-activated protein kinase kinase kinase 7 (MAP3K7)-binding protein 2 (TAB2) of the mitogen-activated protein kinase (MAPK) signaling pathway, was activated by BLM and inhibited by in vivo silencing of miR-155 via antagomiR-155. CONCLUSION: In vivo treatment with antagomiR-155 alleviated the pathological changes induced by BLM and may be a promising therapeutic strategy for pulmonary fibrosis.

Branching Corrected Mean Field Method for Nonadiabatic Dynamics.

When nonadiabatic dynamics are described on the basis of trajectories, severe trajectory branching occurs when the nuclear wave packets on some potential energy surfaces are reflected while those on the remaining surfaces are not. As a result, the traditional Ehrenfest mean field (EMF) approximation breaks down. In this study, two versions of the branching corrected mean field (BCMF) method are proposed. Namely, when trajectory branching is identified, BCMF stochastically selects either the reflected or the nonreflected group to build the new mean field trajectory or splits the mean field trajectory into two new trajectories with the corresponding weights. As benchmarked in six standard model systems and an extensive model base with two hundred diverse scattering models, BCMF significantly improves the accuracy while retaining the high efficiency of the traditional EMF. In fact, BCMF closely reproduces the exact quantum dynamics in all investigated systems, thus highlighting the essential role of branching correction in nonadiabatic dynamics simulations of general systems.

Prominin-1-expressing hepatic progenitor cells induce fibrogenesis in murine cholestatic liver injury.

Cholestatic liver injury is associated with intrahepatic biliary fibrosis, which can progress to cirrhosis. Resident hepatic progenitor cells (HPCs) expressing Prominin-1 (Prom1 or CD133) become activated and participate in the expansion of cholangiocytes known as the ductular reaction. Previously, we demonstrated that in biliary atresia, Prom1(+) HPCs are present within developing fibrosis and that null mutation of Prom1 significantly abrogates fibrogenesis. Here, we hypothesized that these activated Prom1-expressing HPCs promote fibrogenesis in cholestatic liver injury. Using Prom1CreERT2-nLacZ/+ ;Rosa26Lsl-GFP/+ mice, we traced the fate of Prom1-expressing HPCs in the growth of the neonatal and adult livers and in biliary fibrosis induced by bile duct ligation (BDL). Prom1-expressing cell lineage labeling with Green Fluorescent Protein (GFP) on postnatal day 1 exhibited an expanded population as well as bipotent differentiation potential toward both hepatocytes and cholangiocytes at postnatal day 35. However, in the adult liver, they lost hepatocyte differentiation potential. Upon cholestatic liver injury, adult Prom1-expressing HPCs gave rise to both PROM1(+) and PROM1(-) cholangiocytes contributing to ductular reaction without hepatocyte or myofibroblast differentiation. RNA-sequencing analysis of GFP(+) Prom1-expressing HPC lineage revealed a persistent cholangiocyte phenotype and evidence of Transforming Growth Factor-ß pathway activation. When Prom1-expressing cells were ablated with induced Diphtheria toxin in Prom1CreERT-nLacZ/+ ;Rosa26DTA/+ mice, we observed a decrease in ductular reactions and biliary fibrosis typically present in BDL as well as decreased expression of numerous fibrogenic gene markers. Our data indicate that Prom1-expressing HPCs promote biliary fibrosis associated with activation of myofibroblasts in cholestatic liver injury.

Branching corrected surface hopping: Resetting wavefunction coefficients based on judgement of wave packet reflection.

We present a new interpretation of the decoherence correction in surface hopping by examining the inconsistency of the traditional time-dependent Schrödinger equation and propose an elegant decoherence correction algorithm to deal with wave packet branching. In contrast to the widely used approaches based on decoherence rates, our branching corrected surface hopping (BCSH) resets the wavefunction directly after wave packet branching is identified through prediction of trajectory reflection. The appealing simplicity and reliability of BCSH are demonstrated in a series of widely studied one-dimensional and two-dimensional scattering models using exact quantum solutions and existing surface hopping approaches as references. The BCSH approach exhibits a high performance in all investigated systems, showing good potential for applications in general nonadiabatic dynamics simulations.

Prominin-1 Promotes Biliary Fibrosis Associated With Biliary Atresia.

In patients with biliary atresia (BA), the extent of intrahepatic biliary fibrosis negatively correlates with successful surgical bypass of the congenital cholangiopathy as well as subsequent transplant-free survival. We recently linked the expansion of a population of prominin-1 (Prom1)-expressing hepatic progenitor cells to biliary fibrogenesis. Herein, we hypothesized that Prom1-expressing progenitor cells play a role in BA-associated fibrosis. Rhesus rotavirus (RRV)-mediated experimental BA was induced in newborn mice homozygous for the transgene Prom1cre-ert2-nlacz , which was knocked in to the Prom1 gene locus, thus creating functional Prom1 knockout (KO) mice, and their wildtype (WT) littermates. Clinical data and tissue samples from BA infants from the Childhood Liver Disease Research Consortium were analyzed. Extrahepatic biliary obliteration was present in both WT and KO mice; there was no difference in serum total bilirubin (TBili) levels. The intrahepatic periportal expansion of the PROM1pos cell population, typically observed in RRV-induced BA, was absent in KO mice. RRV-treated KO mice demonstrated significantly fewer cytokeratin-19 (CK19)-positive ductular reactions (P = 0.0004) and significantly less periportal collagen deposition (P = 0.0001) compared with WT. RRV-treated KO mice expressed significantly less integrin-ß6, which encodes a key biliary-specific subunit of a transforming growth factor (TGF) ß activator (P = 0.0004). Infants with successful biliary drainage (Tbili ≤1.5 mg/dL within 3 months postoperatively), which is highly predictive of increased transplant-free survival, expressed significantly less hepatic PROM1, CK19, and COLLAGEN-1α compared with those with TBili >1.5 (P < 0.05). Conclusion: Prom1 plays an important role in biliary fibrogenesis, in part through integrin-mediated TGF pathway activation.

Rivaroxaban treatment for cancer-associated venous thromboembolism in a patient with heparin-induced thrombocytopenia: a case report.

Low molecular weight heparin (LMWH) is the first-line therapy in acute cancer-associated venous thromboembolism (CAT). However, heparin-induced thrombocytopenia (HIT) is a life-threatening adverse drug reaction that occurs in anticoagulation therapy with LMWH. This article reports the case of a 66-year-old Chinese male who received nadroparin 4100IU twice daily for treating CAT. Unfortunately, the epistaxis persisted and the blood count examination revealed serious thrombocytopenia on postoperative day 5. The patient was diagnosed with HIT and thereafter LMWH therapy was replaced with rivaroxaban. During three months follow-up, the patient had a good recovery without recurrent CAT or bleeding.

Leukotriene B4 receptor 2 regulates the proliferation, migration, and barrier integrity of bronchial epithelial cells.

The airway epithelium plays a crucial role in the pathogenesis of asthma. The functions of leukotriene B4 receptor 2 (BLT2) on the airway epithelial cells remains unknown. In our study, BLT2 expression in 16HBE bronchial epithelial cells were manipulated by transfection with BLT2 overexpression plasmid or BLT2 small interference RNA. 16HBE cells were then exposed to BLT2 antagonist (LY255283) or BLT2 agonist (12(S)-hydroxyheptadeca-5Z,8E,10E-trienoic acid [12-HHT] or CAY10583). The results showed that BLT2 overexpression, 12-HHT stimulation, or CAY10583 treatment resulted in the enhanced proliferation and migration of 16HBE cells. In addition, BLT2 showed an inhibitory effect on epithelial permeability as illustrated by the measurement of transepithelial electrical resistance (TER) and epithelial permeability, and a promoting effect on the levels of tight junction proteins (occludin and claudin-4) and phosphorylated p38 as demonstrated by real-time PCR and Western blotting analyses. These results suggest BLT2 as a key determinant of airway epithelial barrier integrity. On the contrary, RNAi-mediated knockdown or LY255283 treatment had reversed effects on the proliferation, migration, and epithelial barrier integrity. Together, our findings suggest the critical roles of BLT2 on the functions of bronchial epithelial cells and that BLT2 agonists are potential therapeutic agents for asthma treatment.

Notch signaling promotes ductular reactions in biliary atresia.

BACKGROUND: Biliary atresia (BA) is a congenital, progressive, fibro-obliterative disease of the extrahepatic biliary tree and the most common cause of end-stage liver disease in children. BA is characterized by extensive intrahepatic proliferating ductular reactions that may contribute to biliary fibrosis. Lineage tracing during experimental cholestasis indicates that cells within ductular reactions derive from PROM1-expressing hepatic progenitor cells. Given the role of Notch signaling in normal biliary development, we hypothesize that activated Notch signaling promotes the formation of ductular reactions in BA. METHODS: Liver samples collected from BA infants at Kasai portoenterostomy and age-matched controls, as well as from wild-type and Prom1 knockout mice with 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC)-induced experimental cholestasis were analyzed histologically using immunofluorescence and by quantitative polymerase chain reaction. RESULTS: Increased expression of genes encoding Notch ligand JAG1 and its receptor NOTCH2 was observed in BA livers compared with control by quantitative polymerase chain reaction analyses. Livers of DDC-treated mice, which exhibit cytokeratin-19-positive ductular reactions typical of BA livers, demonstrated significant increases in the expression level of the gene encoding Notch2, as well as downstream Notch target gene Hes1 compared with control. Prom1 knockout mice exhibit diminished ductular reactions and decreased levels of Jag1 and Hes1 compared with littermate controls. CONCLUSIONS: Human BA and cholestasis induced by DDC are associated with Notch signaling activation. Null mutation of Prom1 is associated with decreased ductular reactions and decreased Notch signaling activation during DDC treatment. These data are consistent with Notch signaling promoting ductular reactions of Prom1 expressing progenitor cells in BA.

Hepatic Prominin-1 expression is associated with biliary fibrosis.

BACKGROUND: Intrahepatic biliary fibrosis, as seen with cholestatic liver injuries such as biliary atresia, is mechanistically distinct from fibrosis caused by hepatocyte toxicity. We previously demonstrated the expansion of cells expressing the stem/progenitor cell marker Prominin-1, within regions of developing fibrosis in biliary atresia. Thus, we hypothesized that Prominin-1 expression is biliary fibrosis-specific. METHODS: Gene expression of Prominin-1 was analyzed in adult mice undergoing either cholestatic bile duct ligation or hepatotoxic carbon tetrachloride administration by quantitative polymerase chair reaction. Lineage tracing of Prominin-1-expressing cells and Collagen-1α-expressing cells was performed after bile duct ligation in Prominin-1cre-ert2-lacz;Gfplsl and Collagen-1αGfp transgenic mice, respectively. RESULTS: Prominin-1 expression increased significantly after bile duct ligation compared with sham (6.6 ± 0.9-fold change at 2 weeks, P < .05) but not with carbon tetrachloride (-0.7 ± 0.5-fold change, not significant). Upregulation of Prominin-1 was observed histologically throughout the liver as early as 5 days after bile duct ligation in Prominin-1cre-ert2-lacz mice by LacZ staining in nonhepatocyte cells. Lineage tracing of Prominin-1-expressing cells labeled prior to bile duct ligation in Prominin-1cre-ert2-lacz;Gfplsl mice, demonstrated increasing colocalization of GREEN FLUORESCENT PROTEIN with biliary marker CYTOKERATIN-19 within ductular reactions up to 5 weeks after bile duct ligation consistent with biliary transdifferentiation. In contrast, rare colocalization of GREEN FLUORESCENT PROTEIN with mesenchymal marker α-SMOOTH MUSCLE ACTIN in Prominin-1cre-ert2-lacz;Gfplsl mice and some colocalization of GREEN FLUORESCENT PROTEIN with PROMININ-1 in Collagen-1αGfp mice, indicate minimal contribution of Prominin-1 progenitor cells to the pool of collagen-producing myofibroblasts. CONCLUSION: During biliary fibrosis Prominin-1-expressing progenitor cells transdifferentiate into cells within ductular reactions. This transdifferentiation may promote fibrosis.