Identification and validation of a DNA methylation-driven gene-based prognostic model for clear cell renal cell carcinoma.

BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is a malignant tumor with heterogeneous morphology and poor prognosis. This study aimed to establish a DNA methylation (DNAm)-driven gene-based prognostic model for ccRCC. METHODS: Reduced representation bisulfite sequencing (RRBS) was performed on the DNA extracts from ccRCC patients. We analyzed the RRBS data from 10 pairs of patient samples to screen the candidate CpG sites, then trained and validated an 18-CpG site model, and integrated the clinical characters to establish a Nomogram model for the prognosis or risk evaluation of ccRCC. RESULTS: We identified 2261 DMRs in the promoter region. After DMR selection, 578 candidates were screened, and was correspondence with 408 CpG dinucleotides in the 450 K array. We collected the DNAm profiles of 478 ccRCC samples from TCGA dataset. Using the training set with 319 samples, a prognostic panel of 18 CpGs was determined by univariate Cox regression, LASSO regression, and multivariate Cox proportional hazards regression analyses. We constructed a prognostic model by combining the clinical signatures. In the test set (159 samples) and whole set (478 samples), the Kaplan-Meier plot showed significant differences; and the ROC curve and survival analyses showed AUC greater than 0.7. The Nomogram integrated with clinicopathological characters and methylation risk score had better performance, and the decision curve analyses also showed a beneficial effect. CONCLUSIONS: This work provides insight into the role of hypermethylation in ccRCC. The targets identified might serve as biomarkers for early ccRCC diagnosis and prognosis biomarkers for ccRCC. We believe our findings have implications for better risk stratification and personalized management of this disease.

White matter BOLD signals at 7 Tesla reveal visual field maps in optic radiation and vertical occipital fasciculus.

There is growing evidence that blood-oxygen-level-dependent (BOLD) activity in the white matter (WM) can be detected by functional magnetic resonance imaging (fMRI). However, the functional relevance and significance of WM BOLD signals remain controversial. Here we investigated whether 7T BOLD fMRI can reveal fine-scale functional organizations of a WM bundle. Population receptive field (pRF) analyses of the 7T retinotopy dataset from the Human Connectome Project revealed clear contralateral retinotopic organizations of two visual WM bundles: the optic radiation (OR) and the vertical occipital fasciculus (VOF). The retinotopic maps of OR are highly consistent with post-mortem dissections and diffusion tractographies, while the VOF maps are compatible with the dorsal and ventral visual areas connected by the WM. Similar to the grey matter (GM) visual areas, both WM bundles show over-representations of the central visual field and increasing pRF size with eccentricity. Hemodynamic response functions of visual WM were slower and wider compared with those of GM areas. These findings clearly demonstrate that WM BOLD at 7 Tesla is closely coupled with neural activity related to axons, encoding highly specific information that can be used to characterize fine-scale functional organizations of a WM bundle.

Longitudinal resting-state functional connectivity and regional brain atrophy-based biomarkers of preclinical cognitive impairment in healthy old adults.

BACKGROUND: Intervention against age-related neurodegenerative diseases may be difficult once extensive structural and functional deteriorations have already occurred in the brain. AIM: Investigating 6-year longitudinal changes and implications of regional brain atrophy and functional connectivity in the triple-network model as biomarkers of preclinical cognitive impairment in healthy aging. METHODS: We acquired longitudinal cognitive scores and magnetic resonance imaging (MRI) data from 74 healthy old adults. Resting-state functional MRI (rs-fMRI) analysis was conducted using FSL6.0.1 to examine functional connectivity changes and regional brain morphometries were quantified using FreeSurfer5.3. Finally, we cross-validated and compared two support vector machine (SVM) regression models to predict future 6-year cognition score from the baseline regional brain atrophy and resting-state functional connectivity (rs-FC) measures. RESULTS: After a 6-year follow-up, our results (P < 0.05-corrected) indicated significant connectivity reduction within all the three brain networks, significant differences in regional brain volumes and cortical thickness. We also observed significant improvement in episodic memory and significant decline in executive functions. Finally, comparing the two models, we observed that regional brain atrophy predictors were more efficient in approximating future 6-year cognitive scores (R = 0.756, P < 0.0001) than rs-FC predictors (R = 0.6, P < 0.0001). CONCLUSION: This study used longitudinal data to keep subject variability low and to increase the validity of the results. We demonstrated significant changes in structural and functional MRI over 6 years. Our findings present a potential neuroimaging-based biomarker to detect cognitive impairment and prevent risks of neurodegenerative diseases in healthy old adults.

White matter hyperintensities induce distal deficits in the connected fibers.

White matter hyperintensities (WMH) are common in elderly individuals and cause brain network deficits. However, it is still unclear how the global brain network is affected by the focal WMH. We aimed to investigate the diffusion of WMH-related deficits along the connecting white matters (WM). Brain magnetic resonance imaging data and neuropsychological evaluations of 174 participants (aged 74 ± 5 years) were collected and analyzed. For each participant, WMH lesions were segmented using a deep learning method, and 18 major WM tracts were reconstructed using automated quantitative tractography. The diffusion characteristics of distal WM tracts (with the WMH penumbra excluded) were calculated. Multivariable linear regression analysis was performed. We found that a high burden of tract-specific WMH was related to worse diffusion characteristics of distal WM tracts in a wide range of WM tracts, including the forceps major (FMA), forceps minor (FMI), anterior thalamic radiation (ATR), cingulum cingulate gyrus (CCG), corticospinal tract (CST), inferior longitudinal fasciculus (ILF), superior longitudinal fasciculus-parietal (SLFP), superior longitudinal fasciculus-temporal (SLFT), and uncinate fasciculus (UNC). Furthermore, a higher mean diffusivity (MD) of distal tracts was linked to worse attention and executive function in the FMI, right CCG, left ILF, SLFP, SLFT, and UNC. The effect of WMH on the microstructural integrity of WM tracts may propagate along tracts to distal regions beyond the penumbra and might eventually affect attention and executive function.

Surface modification and effects on tribology by laser texturing in Al2O3.

We investigate the surface modification by laser texturing and effects thereof on the tribological performance in Al2O3. By detailed observation for microstructure evolution, it has been shown that there were three distinct modification morphologies by laser treatment: dense surface microfeatures, "coral" dendritic structures, and coarse grains. X-ray diffraction (XRD) results indicated that there was no formation of metastable phases due to low supercooling in solidification in the nanosecond laser regime. The formation of AlN compounds in the laser-treated region was examined by using x-ray photoelectron spectroscopy (XPS), which led to dense surface microfeatures and randomly distributed pores formation in the laser treated region. The formation of "coral" dendritic structures on the edge of groove and coarse grains in the vicinity of the laser surface was attributed to the fast-cooling rates. Wear tests were carried out to analyze the effect of laser texturing on tribological performance. The results of coefficients of friction (COF) illustrated that laser texturing can significantly improve COFs for dry friction; however, it decreases the COFs for wet friction. The mechanism of wear was explained based on a SEM measurement for worn surfaces; the formation of surface texture can store abrasive particles and debris lead to hydrodynamic lubricant film formation and the COFs significantly reducing for wet friction.

AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species.

BACKGROUND: Function genomic studies will generally result in lists of genes that may provide clues for exploring biological questions and discovering unanticipated functions, based on differential gene expression analysis, differential epigenomic analysis or co-expression network analysis. While tools have been developed to identify biological functions that are enriched in the genes sets, there remains a need for comprehensive tools that identify functional enrichment of genes for both model and non-model species from a different function classification perspective. RESULTS: We developed AllEnricher, a tool that calculates gene set function enrichment, with user-defined updatable libraries backing up for both model and non-model species as well as providing comprehensive functional interpretation from multiple dimensions, including GO, KEGG, Reactome, DO and DisGeNET. CONCLUSIONS: AllEnricher incorporates up to date information from different public resources and provides a comprehensive resolution for biologists to make sense out of specific gene sets, making it an advanced open-source tool for gene set function analysis.

Mechanism of Rate Acceleration of Radical C-C Bond Formation Reaction by a Radical SAM GTP 3',8-Cyclase.

While the number of characterized radical S-adenosyl-l-methionine (SAM) enzymes is increasing, the roles of these enzymes in radical catalysis remain largely ambiguous. In radical SAM enzymes, the slow radical initiation step kinetically masks the subsequent steps, making it impossible to study the kinetics of radical chemistry. Due to this kinetic masking, it is unknown whether the subsequent radical reactions require rate acceleration by the enzyme active site. Here, we report the first evidence that a radical SAM enzyme MoaA accelerates the radical-mediated C-C bond formation. MoaA catalyzes an unprecedented 3',8-cyclization of GTP into 3',8-cyclo-7,8-dihydro-GTP (3',8-cH2GTP) during the molybdenum cofactor (Moco) biosynthesis. Through a series of EPR and biochemical characterizations, we found that MoaA catalyzes a shunt pathway in which an on-pathway intermediate, GTP C-3' radical, abstracts H-4' atom from (4'R)-5'-deoxyadenosine (5'-dA) to transiently generate 5'-deoxyadenos-4'-yl radical (5'-dA-C4'•) that is subsequently reduced stereospecifically to yield (4'S)-5'-dA. Detailed kinetic characterization of the shunt and the main pathways provided the comprehensive view of MoaA kinetics and determined the rate of the on-pathway 3',8-cyclization step as 2.7 ± 0.7 s-1. Together with DFT calculations, this observation suggested that the 3',8-cyclization by MoaA is accelerated by 6-9 orders of magnitude. Further experimental and theoretical characterizations suggested that the rate acceleration is achieved mainly by constraining the triphosphate and guanine base positions while leaving the ribose flexible, and a transition state stabilization through H-bond and electrostatic interactions with the positively charged R17 residue. This is the first evidence for rate acceleration of radical reactions by a radical SAM enzyme and provides insights into the mechanism by which radical SAM enzymes accelerate radical chemistry.

Cytochrome P450 family member CYP96B5 hydroxylates alkanes to primary alcohols and is involved in rice leaf cuticular wax synthesis.

Odd-numbered primary alcohols are components of plant cuticular wax, but their biosynthesis remains unknown. We isolated a rice wax crystal-sparse leaf 5 (WSL5) gene using a map-based cloning strategy. The function of WSL5 was illustrated by overexpression and knockout in rice, heterologous expression in Arabidopsis and transient expression in tobacco leaves. WSL5 is predicted to encode a cytochrome P450 family member CYP96B5. The wsl5 mutant lacked crystalloid platelets on the surface of cuticle membrane, and its cuticle membrane was thicker than that of the wild-type. The wsl5 mutant is more tolerant to drought stress. The load of C23 -C33 alkanes increased, whereas the C29 primary alcohol reduced significantly in wsl5 mutant and WSL5 knockout transgenic plants. Overexpression of WSL5 increased the C29 primary alcohol and decreased alkanes in rice leaves. Heterologous expression of WSL5 increased the C29 primary alcohol and decreased alkanes, secondary alcohol, and ketone in Arabidopsis stem wax. Transient expression of WSL5 in tobacco leaves also increased the production C29 primary alcohol. WSL5 catalyzes the terminal hydroxylation of alkanes, yielding odd-numbered primary alcohols, and is involved in the formation of epidermal wax crystals on rice leaf, affecting drought sensitivity.

Multi-omics profiling highlights lipid metabolism alterations in pigs fed low-dose antibiotics.

BACKGROUND: In order to study the relations of hepatocellular functions, weight gain and metabolic imbalance caused by low-dose antibiotics (LDA) via epigenetic regulation of gene transcription, 32 weaned piglets were employed as animal models and randomly allocated into two groups with diets supplemented with 0 or LDA (chlorotetracycline and virginiamycin). RESULTS: During the 4 weeks of the experiment, LDA showed a clear growth-promoting effect, which was exemplified by the significantly elevated body weight and average daily gain. Promoter methylome profiling using liquid hybridization capture-based bisulfite sequencing (LHC-BS) indicated that most of the 745 differential methylation regions (DMRs) were hypermethylated in the LDA group. Several DMRs were significantly enriched in genes related with fatty acids metabolic pathways, such as FABP1 and PCK1. In addition, 71 differentially expressed genes (DEGs) were obtained by strand-specific transcriptome analysis of liver tissues, including ALOX15, CXCL10 and NNMT, which are three key DEGs that function in lipid metabolism and immunity and which had highly elevated expression in the LDA group. In accordance with these molecular changes, the lipidome analyses of serum by LC-MS identified 38 significantly differential lipids, most of which were downregulated in the LDA group. CONCLUSIONS: Our results indicate that LDA could induce epigenetic and transcriptional changes of key genes and lead to enhanced efficiency of lipid metabolism in the liver.

A longitudinal study reveals the alterations of the Microtus fortis colonic microbiota during the natural resistance to Schistosoma japonicum infection.

The gut microbiota has been demonstrated to associate with protection against helminth infection and mediate via microbial effects on the host humoral immunity. As a non-permissive host of Schistosoma japonicum, the Microtus fortis provides an ideal animal model to be investigated, because of its natural self-healing capability. Although researches on the systemic immunological responses have revealed that the host immune system contributes a lot to the resistance, the role of gut microbiome remains unclear. In this study, we exposed the M. fortis to the S.japonicum infection, carried out a longitudinal research (uninfected control, infected for 7 days, 14 days, 21 days, and 31 days) on their colonic microbiota based on the 16S rRNA gene amplicon sequencing. The bacterial composition disclosed a disturbance-recovery alteration followed by the resistance to S. japonicum. The alpha diversity of colon microbiota was reduced after the infection, but it gradually recovered along with self-healing process. Further LEfSe analysis revealed that phyla shifted from Firmicutes to Bacteroidetes, which were mainly driven by an increase of Ruminococcaceae and a depletion of Muribaculaceae in the family level along the Control-Infection-Recovery (CIR) process. We identified a temporary blooming of Lactobacillaceae and Lactobacillus in the mid infection stage (D14). As a recognized probiotics repository, we speculate the increased abundance of Lactobacillaceae in M. fortis colonic microbiota might relate to the natural resistance to the schistosome. Besides, potential microbial functions were also significantly changed in the resistance process. These results demonstrate the remarkable alterations of reed vole colonic microbiota in both community structure and potential functions along with the resistance to S. japonicum infection. The identified microbial biomarkers might offer new ways for drug development to conquer human schistosomiasis.

Plasmon-Enhanced Catalysis: Distinguishing Thermal and Nonthermal Effects.

In plasmon-enhanced heterogeneous catalysis, illumination accelerates reaction rates by generating hot carriers and hot surfaces in the constituent nanostructured metals. In order to understand how photogenerated carriers enhance the nonthermal reaction rate, the effects of photothermal heating and thermal gradients in the catalyst bed must be confidently and quantitatively characterized. This is a challenging task considering the conflating effects of light absorption, heat transport, and reaction energetics. Here, we introduce a methodology to distinguish the thermal and nonthermal contributions from plasmon-enhanced catalysts, demonstrated by illuminated rhodium nanoparticles on oxide supports to catalyze the CO2 methanation reaction. By simultaneously measuring the total reaction rate and the temperature gradient of the catalyst bed, the effective thermal reaction rate may be extracted. The residual nonthermal rate of the plasmon-enhanced reaction is found to grow with a superlinear dependence on illumination intensity, and its apparent quantum efficiency reaches ∼46% on a Rh/TiO2 catalyst at a surface temperature of 350 °C. Heat and light are shown to work synergistically in these reactions: the higher the temperature, the higher the overall nonthermal efficiency in plasmon-enhanced catalysis.

A ß-Ketoacyl-CoA Synthase Is Involved in Rice Leaf Cuticular Wax Synthesis and Requires a CER2-LIKE Protein as a Cofactor.

Cuticular waxes are complex mixtures of very-long-chain fatty acids (VLCFAs) and their derivatives, forming a natural barrier on aerial surfaces of terrestrial plants against biotic and abiotic stresses. In VLCFA biosynthesis, ß-ketoacyl-CoA synthase (KCS) is the key enzyme, catalyzing the first reaction in fatty acid elongation and determining substrate specificity. We isolated a rice (Oryza sativa) wax crystal-sparse leaf 4 (WSL4) gene using a map-based cloning strategy. WSL4 is predicted to encode a KCS, a homolog of Arabidopsis (Arabidopsis thaliana) CER6. Complementation of the mutant wsl4-1 with WSL4 genomic DNA rescued the cuticular wax-deficient phenotype, confirming the function of WSL4 The load of wax components longer than 30 carbons (C30) and C28 were reduced markedly in wsl4-1 and wsl4-2 mutants, respectively. Overexpression of WSL4 increased the cuticular wax load in rice leaves. We further isolated a cofactor of WSL4, OsCER2, a homolog of Arabidopsis CER2, by coimmunoprecipitation and confirmed their physical interaction by split-ubiquitin yeast two-hybrid experiments. Expression of WSL4 alone in elo3 yeast cells resulted in increased C24 but did not produce VLCFAs of greater length, whereas expressing OsCER2 alone showed no effect. Coexpression of WSL4 and OsCER2 in elo3 yeast cells yielded fatty acids up to C30. OsCER2 with a mutated HxxxD motif (H172E, D176A, and D176H) interrupted its interaction with WSL4 and failed to elongate VLCFAs past C24 when expressed with WSL4 in elo3 yeast cells. These results demonstrated that WSL4 was involved in VLCFA elongation beyond C22 and that elongation beyond C24 required the participation of OsCER2.

Activating MoS2 for pH-Universal Hydrogen Evolution Catalysis.

MoS2 presents a promising catalyst for the hydrogen evolution reaction (HER) in water splitting, but its worse catalytic performance in neutral and alkaline media than in acidic environment may be problematic for practical application. This is because the other half reaction of water splitting, i.e., oxygen evolution reaction, often needs to be implemented in alkaline environment. Here we demonstrate a universal strategy that may be used to significantly improve the HER catalysis of MoS2 in all kinds of environments from acidic to alkaline, proton intercalation. Protons may be enabled to intercalate between monolayer MoS2 and underlying substrates or in the interlayer space of thicker MoS2 by two processes: electrochemically polarizing MoS2 at negative potentials (vs RHE) in acidic media or immersing MoS2 into certain acid solutions like TFSI. The improvement in catalytic performance is due to the activity enhancement of the active sites in MoS2 by the intercalated protons, which might be related with the effect of the intercalated protons on electrical conductance and the adsorption energy of hydrogen atoms. The enhancement in catalytic activity by the intercalated proton is very stable even in neutral and alkaline electrolytes.

Excitation energies from particle-particle random phase approximation with accurate optimized effective potentials.

The optimized effective potential (OEP) that gives accurate Kohn-Sham (KS) orbitals and orbital energies can be obtained from a given reference electron density. These OEP-KS orbitals and orbital energies are used here for calculating electronic excited states with the particle-particle random phase approximation (pp-RPA). Our calculations allow the examination of pp-RPA excitation energies with the exact KS density functional theory (DFT). Various input densities are investigated. Specifically, the excitation energies using the OEP with the electron densities from the coupled-cluster singles and doubles method display the lowest mean absolute error from the reference data for the low-lying excited states. This study probes into the theoretical limit of the pp-RPA excitation energies with the exact KS-DFT orbitals and orbital energies. We believe that higher-order correlation contributions beyond the pp-RPA bare Coulomb kernel are needed in order to achieve even higher accuracy in excitation energy calculations.

Charge transfer excitations from particle-particle random phase approximation-Opportunities and challenges arising from two-electron deficient systems.

The particle-particle random phase approximation (pp-RPA) is a promising method for studying charge transfer(CT) excitations. Through a detailed analysis on two-electron deficient systems, we show that the pp-RPA is always able to recover the long-distance asymptotic -1/R trend for CT excitations as a result of the concerted effect between orbital energies and the pp-RPA kernel. We also provide quantitative results for systems with relatively short donor-acceptor distances. With conventional hybrid or range-separated functionals, the pp-RPA performs much better than time-dependent density functional theory (TDDFT), although it still gives underestimated results which are not as good as TDDFT with system-dependent tuned functionals. For pp-RPA, there remain three great challenges in dealing with CT excitations. First, the delocalized frontier orbitals in strongly correlated systems often lead to difficulty with self-consistent field convergence as well as an incorrect picture with about half an electron transferred. Second, the commonly used density functionals often underestimate the energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital (LUMO) for the two-electron deficient species, resulting in systems with delocalized orbitals. Third, the performance of pp-RPA greatly depends on the energy difference between the LUMO and a higher virtual orbital. However, the meaning of the orbital energies for higher virtual orbitals is still not clear. We also discuss the performance of an approximate pp-RPA scheme that uses density functional tight binding (pp-DFTB) as reference and demonstrate that the aforementioned challenges can be overcome by adopting suitable range-separated hybrid functionals. The pp-RPA and pp-DFTB are thus promising general approaches for describing charge transfer excitations.

All The Catalytic Active Sites of MoS2 for Hydrogen Evolution.

MoS2 presents a promising low-cost catalyst for the hydrogen evolution reaction (HER), but the understanding about its active sites has remained limited. Here we present an unambiguous study of the catalytic activities of all possible reaction sites of MoS2, including edge sites, sulfur vacancies, and grain boundaries. We demonstrate that, in addition to the well-known catalytically active edge sites, sulfur vacancies provide another major active site for the HER, while the catalytic activity of grain boundaries is much weaker. The intrinsic turnover frequencies (Tafel slopes) of the edge sites, sulfur vacancies, and grain boundaries are estimated to be 7.5 s-1 (65-75 mV/dec), 3.2 s-1 (65-85 mV/dec), and 0.1 s-1 (120-160 mV/dec), respectively. We also demonstrate that the catalytic activity of sulfur vacancies strongly depends on the density of the vacancies and the local crystalline structure in proximity to the vacancies. Unlike edge sites, whose catalytic activity linearly depends on the length, sulfur vacancies show optimal catalytic activities when the vacancy density is in the range of 7-10%, and the number of sulfur vacancies in high crystalline quality MoS2 is higher than that in low crystalline quality MoS2, which may be related with the proximity of different local crystalline structures to the vacancies.

Plastidial Disproportionating Enzyme Participates in Starch Synthesis in Rice Endosperm by Transferring Maltooligosyl Groups from Amylose and Amylopectin to Amylopectin.

Plastidial disproportionating enzyme1 (DPE1), an α-1,4-d-glucanotransferase, has been thought to be involved in storage starch synthesis in cereal crops. However, the precise function of DPE1 remains to be established. We present here the functional identification of DPE1 in storage starch synthesis in rice (Oryza sativa) by endosperm-specific gene overexpression and suppression. DPE1 overexpression decreased amylose content and resulted in small and tightly packed starch granules, whereas DPE1 suppression increased amylose content and formed heterogeneous-sized, spherical, and loosely packed starch granules. Chains with degree of polymerization (DP) of 6 to 10 and 23 to 38 were increased, while chains with DP of 11 to 22 were decreased in amylopectin from DPE1-overexpressing seeds. By contrast, chains with DP of 6 to 8 and 16 to 36 were decreased, while chains with DP of 9 to 15 were increased in amylopectin from DPE1-suppressed seeds. Changes in DPE1 gene expression also resulted in modifications in the thermal and pasting features of endosperm starch granules. In vitro analyses revealed that recombinant DPE1 can break down amylose into maltooligosaccharides in the presence of Glc, while it can transfer maltooligosyl groups from maltooligosaccharide to amylopectin or transfer maltooligosyl groups within and among amylopectin molecules in the absence of Glc. Moreover, a metabolic flow of maltooligosyl groups from amylose to amylopectin was clearly identifiable when comparing DPE1-overexpressing lines with DPE1-suppressed lines. These findings demonstrate that DPE1 participates substantially in starch synthesis in rice endosperm by transferring maltooligosyl groups from amylose and amylopectin to amylopectin.

Accurate and efficient calculation of excitation energies with the active-space particle-particle random phase approximation.

An efficient method for calculating excitation energies based on the particle-particle random phase approximation (ppRPA) is presented. Neglecting the contributions from the high-lying virtual states and the low-lying core states leads to the significantly smaller active-space ppRPA matrix while keeping the error to within 0.05 eV from the corresponding full ppRPA excitation energies. The resulting computational cost is significantly reduced and becomes less than the construction of the non-local Fock exchange potential matrix in the self-consistent-field (SCF) procedure. With only a modest number of active orbitals, the original ppRPA singlet-triplet (ST) gaps as well as the low-lying single and double excitation energies can be accurately reproduced at much reduced computational costs, up to 100 times faster than the iterative Davidson diagonalization of the original full ppRPA matrix. For high-lying Rydberg excitations where the Davidson algorithm fails, the computational savings of active-space ppRPA with respect to the direct diagonalization is even more dramatic. The virtues of the underlying full ppRPA combined with the significantly lower computational cost of the active-space approach will significantly expand the applicability of the ppRPA method to calculate excitation energies at a cost of O(K4), with a prefactor much smaller than a single SCF Hartree-Fock (HF)/hybrid functional calculation, thus opening up new possibilities for the quantum mechanical study of excited state electronic structure of large systems.

Analytic gradients, geometry optimization and excited state potential energy surfaces from the particle-particle random phase approximation.

The energy gradient for electronic excited states is of immense interest not only for spectroscopy but also for the theoretical study of photochemical reactions. We present the analytic excited state energy gradient of the particle-particle random phase approximation (pp-RPA). The analytic gradient formula is developed from an approach similar to that of time-dependent density-functional theory (TDDFT). The formula is verified for both the Hartree-Fock and (Generalized) Kohn-Sham reference states via comparison with finite difference results. The excited state potential energy surfaces and optimized geometries of some small molecules are investigated, yielding results of similar or better quality compared to adiabatic TDDFT. The singlet-to-triplet instability in TDDFT resulting in underestimated energies of the lowest triplet states is eliminated by pp-RPA. Charge transfer excitations and double excitations, which are challenging for most adiabatic TDDFT methods, can be reasonably well captured by pp-RPA. Within this framework, ground state potential energy surfaces of stretched single bonds can also be described well.

Immunogenic cell death inducers for cancer therapy: An emerging focus on natural products.

BACKGROUND: Immunogenic cell death (ICD) is a specific form of regulated cell death induced by a variety of stressors. During ICD, the dying cancer cells release damage-associated molecular patterns (DAMPs), which promote dendritic cell maturation and tumor antigen presentation, subsequently triggering a T-cell-mediated anti-tumor immune response. In recent years, a growing number of studies have demonstrated the potential of natural products to induce ICD and enhance tumor cell immunogenicity. Moreover, there is an increasing interest in identifying new ICD inducers from natural products. PURPOSE: This study aimed to emphasize the potential of natural products and their derivatives as ICD inducers to promote research on using natural products in cancer therapy and provide ideas for future novel immunotherapies based on ICD induction. METHOD: This review included a thorough search of the PubMed, Web of Science, Scopus, and Google Scholar databases to identify natural products with ICD-inducing capabilities. A comprehensive search for clinical trials on natural ICD inducers was also conducted using ClinicalTrials.gov, as well as the approved patents using the Espacenet and CNKI Patent Database. RESULTS: Natural compounds that induce ICD can be categorized into several groups, such as polyphenols, flavonoids, terpenoids, and alkaloids. Natural products can induce the release of DAMPs by triggering endoplasmic reticulum stress, activation of autophagy-related pathways, and reactive oxygen species generation, etc. Ultimately, they activate anti-tumor immune response and improve the efficacy of cancer treatments. CONCLUSION: A growing number of ICD inducers from natural products with promising anti-cancer potential have been identified. The detailed information presented in this review will contribute to the further development of natural ICD inducers and cancer treatment strategies based on ICD-induced responses.