CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data.

CellMarker 2.0 (http://bio-bigdata.hrbmu.edu.cn/CellMarker or http://117.50.127.228/CellMarker/) is an updated database that provides a manually curated collection of experimentally supported markers of various cell types in different tissues of human and mouse. In addition, web tools for analyzing single cell sequencing data are described. We have updated CellMarker 2.0 with more data and several new features, including (i) Appending 36 300 tissue-cell type-maker entries, 474 tissues, 1901 cell types and 4566 markers over the previous version. The current release recruits 26 915 cell markers, 2578 cell types and 656 tissues, resulting in a total of 83 361 tissue-cell type-maker entries. (ii) There is new marker information from 48 sequencing technology sources, including 10X Chromium, Smart-Seq2 and Drop-seq, etc. (iii) Adding 29 types of cell markers, including protein-coding gene lncRNA and processed pseudogene, etc. Additionally, six flexible web tools, including cell annotation, cell clustering, cell malignancy, cell differentiation, cell feature and cell communication, were developed to analysis and visualization of single cell sequencing data. CellMarker 2.0 is a valuable resource for exploring markers of various cell types in different tissues of human and mouse.

Varied immune responses of HBV-specific B cells in patients undergoing pegylated interferon-alpha treatment for chronic hepatitis B.

BACKGROUND & AIMS: The changes of HBV-specific B-cells in chronic hepatitis B (CHB) patients underwent pegylated interferon-alfa (PEG-IFNα) treatment and achieved functional cure remain unclear. We aimed to evaluate the alterations in HBV-specific B-cells during treatment and therefore explored the mechanism of functional recovery of HBsAg-specific B-cells. METHODS: We included 39 nucleos(t)ide analogues-treated CHB patients who received sequential combination therapy with PEG-IFNα and 8 treatment-naive CHB patients. HBV-specific B-cells were characterized ex vivo using fluorescent labeled HBsAg and HBcAg. The frequency, phenotype, and subsets of HBV-specific B-cells and follicular helper T cells (Tfh-cells) were detected using flow cytometry. The functionality of HBV-specific B-cells was quantified through ELISpot assays. RESULTS: During treatment, the fraction of activated memory B-cells (MBCs) among HBsAg-specific B-cells and the expression of IgG, CXCR3, and CD38 increased. Antibody-secretion capacity of HBsAg-specific B-cell was restored after treatment only in patients with a functional cure and it showed a positive correlation with serum hepatitis B surface antibody levels. The phenotype and function of HBsAg-specific B-cells differed between patients with and without functional cure. Patients with functional cure exhibited IgG+ classical MBCs and plasmablasts in HBsAg-specific B-cells. HBcAg-specific B-cells displayed both attenuated antibody secretion with reduced IgG expression and an IgM+ atypical type of MBCs after treatment, irrespective of with and without functional cure. The number of CD40L+ Tfh-cells increased after PEG-IFNα treatment and positively correlated with HBsAg-specific B-cell activation. CONCLUSIONS: After PEG-IFNα treatment, HBsAg- and HBcAg-specific B-cells exhibit various changes in antibody secretion. Their functional differences are reflected in the alterations in phenotypes and subtypes. The presence of CD40L+ Tfh-cells is associated with the active recovery of HBsAg-specific B-cells. IMPACT AND IMPLICATIONS: HBV-related complications and hepatocellular carcinoma remain the leading causes of mortality from chronic liver disease worldwide, and a cure is rarely achieved with antiviral therapies. Elucidating the immunological mechanisms underlying the functional cure of CHB patients offers a promising therapeutic strategy for viral clearance, such as therapeutic vaccine. We analyzed the alterations in HBV-specific B-cells in patients treated with PEG-IFNα and identified novel pathways for immunotherapeutic boosting of B cell immunity.

Theoretical Study of the Photocyclization Reaction-Induced Dual Aggregation-Induced Emission Phenomenon.

Photochromic molecules with aggregation-induced emission (AIE) effects are of great value and prospective in various practical applications. To explore its inherent mechanism, the open isomer ap-BBTE and the closed isomer c-BBTE were chosen to perform the theoretical calculation using the quantum mechanics/molecular mechanics model combined with thermal vibration correlation function formalism. The calculations show that the photocyclization (PC) reaction from ap-BBTE to c-BBTE facilitates an improvement in the AIE effect. It is found that the fluorescence quantum yield (ΦF) enhancement of ap-BBTE is attributed to the restriction of the low-frequency rotational motion of the benzothiophene moiety and the high-frequency stretching vibrations of the C-C bond between the benzothiophene and benzylbis(thiadiazole) vinyl groups after aggregation. For c-BBTE, the increase in ΦF upon aggregation is mainly due to the suppression of the high-frequency stretching vibration of the C-C bond between the benzothiophene and the benzobis(thiadiazole) vinyl groups. In addition, the AIE effect was also enhanced from ap-BBTE to c-BBTE, which is consistent with the experimental phenomenon. The corresponding emission spectrum red-shifted from ap-BBTE to c-BBTE in both dilute solution and the crystalline state due to the improved intramolecular conjugation of c-BBTE. Moreover, the PC reaction from ap-BBTE to c-BBTE easily occurs in an excited state with a low energy barrier transition state by forming a C-C bond between benzothiophene groups effectively in dilute solution. Our calculations provide theoretical guidance for the further rational design of efficient AIE luminogens.

Uric acid metabolism promotes apoptosis against Bombyx mori nucleopolyhedrovirus in silkworm, Bombyx mori.

The white epidermis of silkworms is due to the accumulation of uric acid crystals. Abnormal silkworm uric acid metabolism decreases uric acid production, leading to a transparent or translucent phenotype. The oily silkworm op50 is a mutant strain with a highly transparent epidermis derived from the p50 strain. It shows more susceptibility to Bombyx mori nucleopolyhedrovirus (BmNPV) infection than the wild type; however, the underlying mechanism is unknown. This study analysed the changes in 34 metabolites in p50 and op50 at different times following BmNPV infection based on comparative metabolomics. The differential metabolites were mainly clustered in six metabolic pathways. Of these, the uric acid pathway was identified as critical for resistance in silkworms, as feeding with inosine significantly enhanced larval resistance compared to other metabolites and modulated other metabolic pathways. Additionally, the increased level of resistance to BmNPV in inosine-fed silkworms was associated with the regulation of apoptosis, which is mediated by the reactive oxygen species produced during uric acid synthesis. Furthermore, feeding the industrial strain Jingsong (JS) with inosine significantly increased the level of larval resistance to BmNPV, indicating its potential application in controlling the virus in sericulture. These results lay the foundation for clarifying the resistance mechanism of silkworms to BmNPV and provide new strategies and methods for the biological control of pests.

Nature of Hops, Coordinates, and Detailed Balance for Nonadiabatic Simulations in the Condensed Phase.

Photoinduced processes play a crucial role in a multitude of important molecular phenomena. Accurately modeling these processes in an environment other than a vacuum requires a detailed description of the electronic states involved as well as how energy flows are coupled to the surroundings. Nonadiabatic effects must also be included in order to describe the exchange of energy between electronic and nuclear degrees of freedom correctly. In this work, we revisit the ring-opening reaction 1,3-cylohexadiene (CHD) in a solvent environment. Using our newly developed Interface for Non-Adiabatic Quantum mechanics/molecular mechanics in Solvent (INAQS) we trace the evolution of the reaction via hybrid quantum mechanics/molecular mechanics (QM/MM) surface hopping with a focus on the solvent's participation in the nonadiabatic relaxation process and the long-time approach to equilibrium. We explicitly include the MM solvent contribution to the nonadiabatic coupling vector─enabling an accurate approach to equilibrium at long times─and find that in highly multidimensional systems gradients can have little or nothing to do with the nonadiabatic couplings.

DeePKS + ABACUS as a Bridge between Expensive Quantum Mechanical Models and Machine Learning Potentials.

Recently, the development of machine learning (ML) potentials has made it possible to perform large-scale and long-time molecular simulations with the accuracy of quantum mechanical (QM) models. However, for different levels of QM methods, such as density functional theory (DFT) at the meta-GGA level and/or with exact exchange, quantum Monte Carlo, etc., generating a sufficient amount of data for training an ML potential has remained computationally challenging due to their high cost. In this work, we demonstrate that this issue can be largely alleviated with Deep Kohn-Sham (DeePKS), an ML-based DFT model. DeePKS employs a computationally efficient neural network-based functional model to construct a correction term added upon a cheap DFT model. Upon training, DeePKS offers closely matched energies and forces compared with high-level QM method, but the number of training data required is orders of magnitude less than that required for training a reliable ML potential. As such, DeePKS can serve as a bridge between expensive QM models and ML potentials: one can generate a decent amount of high-accuracy QM data to train a DeePKS model and then use the DeePKS model to label a much larger amount of configurations to train an ML potential. This scheme for periodic systems is implemented in a DFT package ABACUS, which is open source and ready for use in various applications.

Identification of optimal reference genes in Bombyx mori (Lepidoptera) for normalization of stress-responsive genes after challenge with pesticides.

Pesticides are frequently used to control pests in agriculture due to their ease of use and effectiveness, but their use causes serious economic losses to sericulture when their production overlaps with agriculture. However, no suitable internal reference genes (RGs) have been reported in the study of silkworms in response to pesticides. In this study, a standard curve was established to detect the expression levels of seven RGs in different tissues of different silkworm strains after feeding with pesticides using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR), including BmGAPDH, BmActin3, BmTBP, BmRPL3, Bm28sRNA, Bmα-tubulin, and BmUBC, and the stability of them was evaluated by using NormFinder, geNorm, Delta CT, BestKeeper, and RefFinder. The results showed that BmGAPDH and Bmα-tubulin were relatively stable in the midgut after feeding with fenvalerate, BmGAPDH and Bmactin3 were relatively stable in the fat body, and Bmα-tubulin and Bmactin3 were relatively stable in the hemolymph, indicating that Bmactin3 was the most suitable RG when evaluating fenvalerate, followed by BmGAPDH and Bmα-tubulin. Besides, BmGAPDH and Bmactin3 were relatively stable in the midgut after treatment with DDVP, BmGAPDH and Bmα-tubulin were relatively stable in the fat body, and BmGAPDH and Bmα-tubulin were relatively stable in the hemolymph, indicating that Bmα-tubulin was the most stable RG when evaluating DDVP, followed by BmGAPDH and Bmactin3. Of note, BmGAPDH was shared by the two pesticides. The results will be valuable for RG selection in studying the pesticide response mechanism of silkworms and other lepidopteran insects.

Cavity quantum-electrodynamical time-dependent density functional theory within Gaussian atomic basis. II. Analytic energy gradient.

Following the formulation of cavity quantum-electrodynamical time-dependent density functional theory (cQED-TDDFT) models [Flick et al., ACS Photonics 6, 2757-2778 (2019) and Yang et al., J. Chem. Phys. 155, 064107 (2021)], here, we report the derivation and implementation of the analytic energy gradient for polaritonic states of a single photochrome within the cQED-TDDFT models. Such gradient evaluation is also applicable to a complex of explicitly specified photochromes or, with proper scaling, a set of parallel-oriented, identical-geometry, and non-interacting molecules in the microcavity.

Intermolecular Charge-Transfer-Induced Strong Optical Emission from Herringbone H-Aggregates.

Luminescence in molecular aggregates can be quenched either by intermolecular charge transfer or by forming a dipole-forbidden lower Frenkel exciton in H-aggregate. Taking intermolecular charge transfer and excitonic coupling into a three-state model through localized diabatization, we demonstrate that the low-lying intermolecular charge-transfer state could couple with the upper bright Frenkel exciton to form dipole-allowed S1 that lies below the dark state, which accounts for the recent experimentally discovered strong luminescence in organic light-emitting transistors (OLETs) system with DPA and dNaAnt herringbone aggregates. The condition of forming such bright state is that the electron and hole transfer integrals, te and th, are of the same sign, and should be notably larger than the excitonic coupling (J), that is , te × th > 2J2. This theoretical finding not only rationalizes recent experiments but unravels an exciting scenario where strong luminescence and high charge mobilities become compatible, which is a preferable condition for both OLETs and electrically pumped lasing.

Enhanced Reverse Intersystem Crossing Promoted by Triplet Exciton-Photon Coupling.

Polaritons are hybrid light-matter states formed via strong coupling between excitons and photons inside a microcavity, leading to upper and lower polariton (LP) bands splitting from the exciton. The LP has been applied to reduce the energy barrier of the reverse intersystem crossing (rISC) process from T1, harvesting triplet energy for fluorescence through thermally activated delayed fluorescence. The spin-orbit coupling between T1 and the excitonic part of the LP was considered as the origin for such an rISC transition. Here we propose a mechanism, namely, rISC promoted by the light-matter coupling (LMC) between T1 and the photonic part of LP, which is originated from the ISC-induced transition dipole moment of T1. This mechanism was excluded in previous studies. Our calculations demonstrate that the experimentally observed enhancement to the rISC process of the erythrosine B molecule can be effectively promoted by the LMC between T1 and a photon. The proposed mechanism would substantially broaden the scope of the molecular design toward highly efficient cavity-promoted light-emitting materials and immediately benefit the illumination of related experimental phenomena.

Theoretical Characterizations of TADF Materials: Roles of ΔG and the Singlet-Triplet Excited States Interconversion.

The thermally activated delayed fluorescence (TADF) phenomenon has attracted increasing attention because it can harvest 100% of the electro-pumped carriers to form singlet bound excited state for fluorescence. It is generally believed that the small energy gap between S1 and T1 (ΔEST) is essential for TADF to facilitate the reverse intersystem crossing (rISC). However, for a few donor-acceptor (D-A) organic compounds with small ΔEST, the TADF phenomenon is absent, indicating that ΔEST might not be a good molecular descriptor. Here, using our self-developed thermal vibration correlation function (TVCF) formalism in combination with quantum chemistry calculations, we revisit the key factors that dominate the TADF property for 11 D-A systems with small ΔEST. Based on our theoretical results in comparison to experiments, we conclude that the activation energy ΔG is a good molecular descriptor to characterize the TADF performance because a significantly better linear relationship is observed between ΔG and the rISC rate constant (krISC) compared to that between ΔEST and krISC. These findings provide deeper understanding of the TADF mechanism, shedding light on the molecular design of high-performance TADF materials.

Quantum-electrodynamical time-dependent density functional theory within Gaussian atomic basis.

Inspired by the formulation of quantum-electrodynamical time-dependent density functional theory (QED-TDDFT) by Rubio and co-workers [Flick et al., ACS Photonics 6, 2757-2778 (2019)], we propose an implementation that uses dimensionless amplitudes for describing the photonic contributions to QED-TDDFT electron-photon eigenstates. This leads to a Hermitian QED-TDDFT coupling matrix that is expected to facilitate the future development of analytic derivatives. Through a Gaussian atomic basis implementation of the QED-TDDFT method, we examined the effect of dipole self-energy, rotating-wave approximation, and the Tamm-Dancoff approximation on the QED-TDDFT eigenstates of model compounds (ethene, formaldehyde, and benzaldehyde) in an optical cavity. We highlight, in the strong coupling regime, the role of higher-energy and off-resonance excited states with large transition dipole moments in the direction of the photonic field, which are automatically accounted for in our QED-TDDFT calculations and might substantially affect the energies and compositions of polaritons associated with lower-energy electronic states.

Organic Laser Molecule with High Mobility, High Photoluminescence Quantum Yield, and Deep-Blue Lasing Characteristics.

Here, we design and synthesize an organic laser molecule, 2,7-diphenyl-9H-fluorene (LD-1), which has state-of-the-art integrated optoelectronic properties with a high mobility of 0.25 cm2 V-1 s-1, a high photoluminescence quantum yield of 60.3%, and superior deep-blue laser characteristics (low threshold of Pth = 71 µJ cm-2 and Pth = 53 µJ cm-2 and high quality factor (Q) of ∼3100 and ∼2700 at emission peaks of 390 and 410 nm, respectively). Organic light-emitting transistors based on LD-1 are for the first time demonstrated with obvious electroluminescent emission and gate tunable features. This work opens the door for a new class of organic semiconductor laser molecules and is critical for deep-blue optical and laser applications.

Novel "turn on-off" paper sensor based on nonionic conjugated polythiophene-coated CdTe QDs for efficient visual detection of cholinesterase activity.

An increasing number of patients are living with Alzheimer's disease (AD); thus, the need for a method to detect AD early and sensitively has become urgent, and the demand for an intelligent analytical platform is growing year by year. Abnormal levels of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) are known to be indicative of AD. In this work, a novel conjugated polythiophene (CP) compound was successfully combined with CdTe quantum dots (QDs) to improve their selectivity and sensitivity. The QDs successfully enabled the detection of low concentrations of AChE by turning on the fluorescence of the CdTe/CP via the interaction between CP and thiocholine produced by ATCh hydrolysis and aggregation induced emission enhancement (AIEE). Under optimal conditions, we reached a low detection limit of 0.14 U L-1, which is 7.9 times lower than that of pristine QDs. More importantly, an efficient, inexpensive, and disposable paper-based platform, which allows the efficient visual detection of AChE activity via the color variation of CdTe/CP, was designed. Moreover, the accuracy of the method was demonstrated by conducting a recovery test in human serum, in which the recoveries reached 107% and 110%, proving that CdTe/CP has considerable potential to be used for analyzing real biological samples. The advantages of this method are its simplicity, fast detection capability, affordability, and the fact that it can be used for on-site detection of AChE activity. Furthermore, it has certain guiding significance for detecting AD.

Strong Solid-State Fluorescence Induced by Restriction of the Coordinate Bond Bending in Two-Coordinate Copper(I)-Carbene Complexes.

The photophysical properties of two-coordinate copper(I) complexes have become a new research hotspot due to their nearly perfect luminescent properties and low price and promising applications in organic light-emitting diodes (OLEDs). In this work, we employ the hybrid quantum mechanics and molecular mechanics (QM/MM) approach, coupled with our early developed thermal vibration correlation function (TVCF) rate formalism, to study the aggregation effect on the luminescent properties of the cyclic (alkyl)(amino)carbene-copper(I)-Cl complex. Our calculations reveal that the transition properties changes from metal-ligand-charge-transfer (MLCT) in solution to hybrid halogen ligand charge-transfer (XLCT) and MLCT in solid state, which induces the blue-shifted emission spectra from solution to solid phase. Upon aggregation, the restriction of the bending vibrations of the C-Cu-Cl and Cu-C-N bonds largely slow down the nonradiative decay, which induces strong fluorescence. This study provides a clear rationalization for the highly efficient fluorescence character of two-coordinate Cu(I) complexes.

The long non-coding RNA PTTG3P promotes cell growth and metastasis via up-regulating PTTG1 and activating PI3K/AKT signaling in hepatocellular carcinoma.

BACKGROUND: Dysfunctions of long non-coding RNA (lncRNAs) have been associated with the initiation and progression of hepatocellular carcinoma (HCC), but the clinicopathologic significance and potential role of lncRNA PTTG3P (pituitary tumor-transforming 3, pseudogene) in HCC remains largely unknown. METHODS: We compared the expression profiles of lncRNAs in 3 HCC tumor tissues and adjacent non-tumor tissues by microarrays. In situ hybridization (ISH) and quantitative real-time polymerase chain reaction (qRT-PCR) were applied to assess the level of PTTG3P and prognostic values of PTTG3P were assayed in two HCC cohorts (n = 46 and 90). Artificial modulation of PTTG3P (down- and over-expression) was performed to explore the role of PTTG3P in tumor growth and metastasis in vitro and in vivo. Involvement of PTTG1 (pituitary tumor-transforming 1), PI3K/AKT signaling and its downstream signals were validated by qRT-PCR and western blot. RESULTS: We found that PTTG3P was frequently up-regulated in HCC and its level was positively correlated to tumor size, TNM stage and poor survival of patients with HCC. Enforced expression of PTTG3P significantly promoted cell proliferation, migration, and invasion in vitro, as well as tumorigenesis and metastasis in vivo. Conversely, PTTG3P knockdown had opposite effects. Mechanistically, over-expression of PTTG3P up-regulated PTTG1, activated PI3K/AKT signaling and its downstream signals including cell cycle progression, cell apoptosis and epithelial-mesenchymal transition (EMT)-associated genes. CONCLUSIONS: Our findings suggest that PTTG3P, a valuable marker of HCC prognosis, promotes tumor growth and metastasis via up-regulating PTTG1 and activating PI3K/AKT signaling in HCC and might represent a potential target for gene-based therapy.

The requisite electronic structure theory to describe photoexcited nonadiabatic dynamics: nonadiabatic derivative couplings and diabatic electronic couplings.

Electronically photoexcited dynamics are complicated because there are so many different relaxation pathways: fluorescence, phosphorescence, radiationless decay, electon transfer, etc. In practice, to model photoexcited systems is a very difficult enterprise, requiring accurate and very efficient tools in both electronic structure theory and nonadiabatic chemical dynamics. Moreover, these theoretical tools are not traditional tools. On the one hand, the electronic structure tools involve couplings between electonic states (rather than typical single state energies and gradients). On the other hand, the dynamics tools involve propagating nuclei on multiple potential energy surfaces (rather than the usual ground state dynamics). In this Account, we review recent developments in electronic structure theory as directly applicable for modeling photoexcited systems. In particular, we focus on how one may evaluate the couplings between two different electronic states. These couplings come in two flavors. If we order states energetically, the resulting adiabatic states are coupled via derivative couplings. Derivative couplings capture how electronic wave functions change as a function of nuclear geometry and can usually be calculated with straightforward tools from analytic gradient theory. One nuance arises, however, in the context of time-dependent density functional theory (TD-DFT): how do we evaluate derivative couplings between TD-DFT excited states (which are tricky, because no wave function is available)? This conundrum was recently solved, and we review the solution below. We also discuss the solution to a second, pesky problem of origin dependence, whereby the derivative couplings do not (strictly) satisfy translation variance, which can lead to a lack of momentum conservation. Apart from adiabatic states, if we order states according to their electronic character, the resulting diabatic states are coupled via electronic or diabatic couplings. The couplings between diabatic states |ΞA⟩ and |ΞB⟩ are just the simple matrix elements, ⟨ΞA|H|ΞB⟩. A difficulty arises, however, because constructing exactly diabatic states is formally impossible and constructing quasi-diabatic states is not unique. To that end, we review recent advances in localized diabatization, which is one approach for generating adiabatic-to-diabatic (ATD) transformations. We also highlight outstanding questions in the arena of diabatization, especially how to generate multiple globally stable diabatic surfaces.

Comparison between GW and Wave-Function-Based Approaches: Calculating the Ionization Potential and Electron Affinity for 1D Hubbard Chains.

We calculate the ionization potential and electron affinity of 1D Hubbard chains with a variety of different site energies from two perspectives: (i) the physics-based GW approximation and (ii) the chemistry-based configuration interaction (CI) approach. Results obtained from all methods are compared against the exact values for three classes of systems: metallic, impurity doped, and molecular (semiconducting/insulating) systems. Although all methods are reasonably accurate for weakly correlated systems, the GW method is significantly more reliable for strongly correlated systems with little disorder unless explicit double excitations are included in the CI. In principle, our results should offer some intuition about the choice of methodologies as well as state references for different classes of physical systems.

First-order derivative couplings between excited states from adiabatic TDDFT response theory.

We present a complete derivation of derivative couplings between excited states in the framework of adiabatic time-dependent density functional response theory. Explicit working equations are given and the resulting derivative couplings are compared with derivative couplings from a pseudo-wavefunction ansatz. For degenerate excited states, i.e., close to a conical intersection (CI), the two approaches are identical apart from an antisymmetric overlap term. However, if the difference between two excitation energies equals another excitation energy, the couplings from response theory exhibit an unphysical divergence. This spurious behavior is a result of the adiabatic or static kernel approximation of time-dependent density functional theory leading to an incorrect analytical structure of the quadratic response function. Numerical examples for couplings close to a CI and for well-separated electronic states are given.

Derivative couplings between TDDFT excited states obtained by direct differentiation in the Tamm-Dancoff approximation.

Working within the Tamm-Dancoff approximation, we calculate the derivative couplings between time-dependent density-functional theory excited states by assuming that the Kohn-Sham superposition of singly excited determinants represents a true electronic wavefunction. All Pulay terms are included in our derivative coupling expression. The reasonability of our approach can be established by noting that, for closely separated electronic states in the infinite basis limit, our final expression agrees exactly with the Chernyak-Mukamel expression (with transition densities from response theory). Finally, we also validate our approach empirically by analyzing the behavior of the derivative couplings around the T1/T2 conical intersection of benzaldehyde.