Biosynthesis and Assembly Logic of Fungal Hybrid Terpenoid Natural Products.

In recent decades, fungi have emerged as significant sources of diverse hybrid terpenoid natural products, and their biosynthetic pathways are increasingly unveiled. This review mainly focuses on elucidating the various strategies underlying the biosynthesis and assembly logic of these compounds. These pathways combine terpenoid moieties with diverse building blocks including polyketides, nonribosomal peptides, amino acids, p-hydroxybenzoic acid, saccharides, and adenine, resulting in the formation of plenty of hybrid terpenoid natural products via C-O, C-C, or C-N bond linkages. Subsequent tailoring steps, such as oxidation, cyclization, and rearrangement, further enhance the biological diversity and structural complexity of these hybrid terpenoid natural products. Understanding these biosynthetic mechanisms holds promise for the discovery of novel hybrid terpenoid natural products from fungi, which will promote the development of potential drug candidates in the future.

Application, knowledge and training needs regarding comprehensive geriatric assessment among geriatric practitioners in healthcare institutions: a cross-sectional study.

BACKGROUND: This study aimed to investigate the actual application, knowledge, and training needs of comprehensive geriatric assessment (CGA) among geriatric practitioners in China. METHODS: A total of 225 geriatric practitioners attending the geriatric medicine or geriatric nursing training were recruited for this cross-sectional study. The questionnaire included demographics, healthcare institution characteristics, the actual application, knowledge, training needs, and barriers to CGA and geriatric syndromes (GS). RESULTS: Physicians and nurses were 57.3% and 42.7%, respectively. 71.1% were female, with a median age was 35 years. Almost two-thirds (140/225) of geriatric practitioners reported exposure to CGA in their clinical practice. The top five CGA evaluation items currently used were malnutrition risk (49.8%), fall risk (49.8%), activity of daily living (48.0%), pain (44.4%), and cognitive function (42.7%). Median knowledge scores for the management procedures of GS ranged from 2 to 6. Physicians identified medical insurance payment issues (29.5%) and a lack of systematic specialist knowledge and technology (21.7%) as the two biggest barriers to practicing geriatrics. Nurses cited a lack of systematic specialist knowledge and technology (52.1%) as the primary barrier. In addition, physicians and nurses exhibited significant differences in their knowledge of CGA-specific evaluation items and management procedures for GS (all P < 0.05). However, there were no significant differences in their training needs, except for polypharmacy. CONCLUSIONS: The rate of CGA application at the individual level, as well as the overall knowledge among geriatric practitioners, was not adequate. Geriatric education and continuous training should be tailored to address the specific roles of physicians and nurses, as well as the practical knowledge reserves, barriers, and training needs they face.

Alterations of nasal microbiome in eosinophilic chronic rhinosinusitis.

BACKGROUND: Exposure to microbes may be important in the development of chronic rhinosinusitis (CRS). Dysbiosis of the nasal microbiome is considered to be related to CRS with nasal polyps (CRSwNP). The link between the nasal microbiota and eosinophilic CRSwNP (eCRSwNP) has rarely been studied. OBJECTIVE: The aim of this study was to rigorously characterize nasal dysbiosis in a cohort of patients with eCRSwNP and compare the nasal microbiomes of these patients with those of healthy controls (HCs). METHODS: We performed a cross-sectional study of 34 patients with eCRSwNP, 10 patients without CRSwNP, and 44 HCs by using 16S rRNA gene sequencing. An independent cohort of 14 patients with eCRSwNP, 9 patients without CRSwNP, and 11 HCs was used to validate the results. RESULTS: Compared with the nasal microbiome of healthy controls, the nasal microbiome of patients with eCRSwNP was characterized by higher α-diversity (Shannon and Chao1 index) and a distinct composition of microbes. Notably, the distinct differences in microbial composition between patients with eCRSwNP and HCs were significantly correlated with eCRSwNP disease status. Furthermore, in a diagnostic model generated by using these differences, a combination of 15 genera could be used to distinguish patients with eCRSwNP from HCs, with an area under the curve of approximately 0.8 in both the exploration and validation cohorts. CONCLUSION: Our study establishes the compositional alterations in the nasal microbiome in eCRSwNP and suggests the potential for using the nasal microbiota as a noninvasive predictive classifier for the diagnosis of eCRSwNP.

Biosynthesis of Cosmosporasides Reveals the Assembly Line for Fungal Hybrid Terpenoid Saccharides.

Fungal hybrid terpenoid saccharides constitute a new and growing family of natural products with significant biomedical and agricultural activities. One representative family is the cosmosporasides, which feature oxidized terpenoid units and saccharide moieties; however, the assembly line of these building blocks has been elusive. Herein, a cos cluster from Fusarium orthoceras was discovered for the synthesis of cosmosporaside C (1) by genome mining. A UbiA family intramembrane prenyltransferase (UbiA-type PT), a multifunctional cytochrome P450, an α,ß-hydrolase, an acetyltransferase, a dimethylallyl transferase (DMAT-type PT) and a glycosyltransferase function cooperatively in the assembly of the scaffold of 1 using primary central metabolites. The absolute configuration at C4, C6 and C7 of 1 was also established. Our work clarifies the unexpected functions of UbiA-type and DMAT-type PTs and provides an example for understanding the synthetic logic of hybrid terpenoid saccharides in fungi.

IL-10 Dampens an IL-17-Mediated Periodontitis-Associated Inflammatory Network.

Emerging evidence suggests comprehensive immune profiling represents a highly promising, yet insufficiently tapped approach to identify potentially prognostic signatures for periodontitis. In this report, we agnostically identified a periodontitis-associated inflammatory expression network with multiple biomarkers identified within gingival crevicular fluid samples from study participants by applying principal component analysis. We identified an IL-17-dominated trait that is associated with periodontal disease and is inversely modified by the level of IL-10. IL-10 mitigated chemokine CXCL5 and CXCL1 expressions in IL-17-stimulated peripheral blood monocytic cells and peripheral blood monocytic cell-derived macrophages. Il10-deficient mice presented more bone loss, which was associated with more Il17 and IL-17-mediated chemokine and cytokine expression at the transcriptional levels in comparison with control wild-type mice in both the Porphyromonas gingivalis-induced experimental murine periodontitis and ligature-induced alveolar bone-loss models. The dampening effect of IL-10 on the excessive signaling of IL-17 appeared to be mediated by innate immune cells populations rather than by gingival epithelial cells, which are the major cell target for IL-17 signaling. Additionally, elevated IL-17 response in Il10-deficient mice specifically elicited an M1-skewing macrophage phenotype in the gingiva that was associated with the advanced bone loss in the ligature model. In summary, IL-17 dominated an inflammatory network characteristic of periodontitis, and IL-10 dampens this excessive IL-17-mediated periodontitis trait.

Clinical efficacy of photodynamic therapy on halitosis: a systematic review and meta-analysis.

Halitosis is a widespread health problem with complex factors, and therapeutic effects sometimes are unsatisfactory. Plenty of clinical trials have tried to prove the effectiveness of photodynamic therapy (PDT), but the results are indeterminate. This study aimed to evaluate the clinical efficacy of PDT on halitosis. We searched PubMed, Cochrane Library, Embase, Web of Science, and Scopus from inception to August 10, 2022, and only studies about the PDT on halitosis were included. The criteria for meta-analysis comprised randomized controlled trials (RCTs) comparing the treatment of PDT with tongue scraper (TS) immediately after the halitosis therapy and during a 7-, 14-, 30-, and 90-day follow-up. Eight eligible studies involving 345 patients were included in this study. It was shown that PDT (MD = - 34.49, 95% CI [- 66.34, - 2.64], P = 0.03) or PDT + TS (MD = - 67.72, 95% CI [- 101.17, - 34.28], P < 0.001) had better efficacy than TS on the H2S concentration reduction immediately after the halitosis therapy. No significant differences were observed in reducing the H2S among TS, PDT alone, and PDT + TS at the follow-up. Besides, no difference between PDT and TS was found in the reduction of CH3SCH3 and CH3SH. Based on the current evidence, PDT and PDT + TS demonstrate efficacy in the treatment of halitosis in the short term, and PDT was shown to be a beneficial and promising therapeutic method.

The value of CT radiomics features to predict visceral pleural invasion in ≤3 cm peripheral type early non-small cell lung cancer.

OBJECTIVE: To investigate predictive value of CT-based radiomics features on visceral pleural invasion (VPI) in ≤3.0 cm peripheral type early non-small cell lung cancer (NSCLC). METHODS: A total of 221 NSCLC cases were collected. Among them, 115 are VPI-positive and 106 are VPI-negative. Using a stratified random sampling method, 70% cases were assigned to training dataset (n = 155) and 30% cases (n = 66) were assigned to validation dataset. First, CT findings, imaging features, clinical data and pathological findings were retrospectively analyzed, the size, location and density characteristics of nodules and lymph node status, the relationship between lesions and pleura (RAP) were assessed, and their mean CT value and the shortest distance between lesions and pleura (DLP) were measured. Next, the minimum redundancy-maximum relevance (mRMR) and least absolute shrinkage and selection operator (LASSO) features were extracted from the imaging features. Then, CT imaging prediction model, texture feature prediction model and joint prediction model were built using multifactorial logistic regression analysis method, and the area under the ROC curve (AUC) was applied to evaluate model performance in predicting VPI. RESULTS: Mean diameter, density, fractal relationship with pleura, and presence of lymph node metastasis were all independent predictors of VPI. When applying to the validation dataset, the CT imaging model, texture feature model, and joint prediction model yielded AUC = 0.882, 0.824 and 0.894, respectively, indicating that AUC of the joint prediction model was the highest (p < 0.05). CONCLUSION: The study demonstrates that the joint prediction model containing CT morphological features and texture features enables to predict the presence of VPI in early NSCLC preoperatively at the highest level.

Clonality, virulence genes, and antibiotic resistance of Staphylococcus aureus isolated from blood in Shandong, China.

BACKGROUND: Bloodstream infection (BSI) caused by Staphylococcus aureus (S. aureus) can be life-threatening and pose a great challenge to infection control and clinical treatment. However, little information exists regarding the characterization of S. aureus in BSI patients in Shandong, China. To identify the clonality, virulence genes, and antibiotic resistance of S. aureus in blood, a total of 101 nonrepetitive blood isolates were collected. The antibiotic resistance phenotypes were determined, and virulence genes were analyzed with polymerase chain reaction (PCR). Finally, the genetic relatedness was investigated with Staphylococcus chromosomal cassette mec (SCCmec) typing for methicillin-resistant S. aureus (MRSA) isolates, Staphylococcal protein A (spa), and multilocus sequence typing (MLST) for all of 101 isolates. RESULTS: Of the 101 S. aureus isolates, 24 MRSA isolates and 77 methicillin-susceptible S. aureus (MSSA) isolates were identified. Overall, MRSA isolates had higher resistance rates than MSSA isolates when exposed to any of the 15 antibiotics tested in this study except for trimethoprim/sulfamethoxazole. Among the 17 virulence genes tested in this study, hla, hld, and hlg could be detected in all isolates. MRSA isolates were more likely to carry seb and hlb genes, while MSSA isolates were more likely to carry seg and sei genes. Thirty-five sequence types (STs) and 49 spa types were identified, of which ST59-t437 and ST398-t571 were the most abundant. These two genotypes were also the most abundant ST-spa types in MRSA and MSSA isolates, but their abundances shifted over time, with ST398-t571 being the predominant genotype from 2016 to 2017, and ST59-t437 from 2018 to 2020. Besides, all the ST59-t437 isolates harbored hlgb gene, whereas most (88.9%) ST398-t571 did not. In addition, twenty-four MRSA isolates were subject to SCCmec typing. SCCmec IVa was the most prevalent SCCmec type, and all the ST59-t437 MRSA isolates were SCCmec IVa. We also observed 15 new STs, and some of them were MRSA. CONCLUSION: These findings provide additional observations and epidemiological data for blood S. aureus isolates, which can improve future infection-control measures and aid in potential clinical treatments in hospitals and other clinical settings.

Impaired function of epithelial plakophilin-2 is associated with periodontal disease.

BACKGROUND AND OBJECTIVES: Plakophilin-2 (PKP2) is an intracellular desmosomal anchoring protein that has been implicated in a genome-wide association study, in which genetic variants of PKP2 are associated with Porphyromonas gingivalis (P.gingivalis) -dominant periodontal dysbiosis. In this study, we compared the ex vivo PKP2 expression in periodontitis gingival biopsies to periodontitis-free subjects and assessed the in vitro role of PKP2 in gingival epithelial barrier function and the mechanism by which P.gingivalis modulates PKP2 expression. MATERIAL AND METHODS: Using reverse transcription quantitative real-time PCR (RT-qPCR), we determined PKP2 mRNA expression levels in gingival biopsies collected from 11 periodontally healthy, 10 experimental gingivitis, and 10 chronic periodontitis subjects. PKP2 protein expression in gingival biopsies was detected by immunohistochemistry. We then challenged primary gingival epithelial cells with bacteria including P.gingivalis, Campylobacter rectus, and various Toll-like receptor agonists. Western blot and immunofluorescence staining were used to detect protein expression. Inhibitors blocking proteases pathways were tested for P.gingivalis-mediated PKP2 protein degradations. We also knocked down endogenous epithelial PKP2 using lentiviral short-hairpin RNA (shRNA) and evaluated cell proliferation, spreading, and barrier function. RESULTS: Periodontitis gingival biopsies had approximately twofold less PKP2 mRNA than did healthy controls (p < .05). PKP2 protein was predominantly expressed in gingival epithelium. In primary gingival epithelial cells, P.gingivalis challenge increased PKP2 mRNA levels, while protein expression decreased, which suggests that P.gingivalis has a protein degradation mechanism. Cysteine proteases inhibitors greatly attenuated P.gingivalis-mediated PKP2 protein degradation. Epithelial cells with deficient PKP2 exhibited inhibited cell proliferation and spreading and failed to form monolayers. Finally, P.gingivalis impaired gingival epithelial barrier function. CONCLUSIONS: PKP2 appears to be critical in maintaining gingival epithelial barrier function and is susceptible to degradation by cysteine proteases produced by P.gingivalis. Our findings have identified a mechanism by which P.gingivalis impairs epithelial barrier function by promoting PKP2 degradation.

Immunoglobulin G4-related periodontitis: case report and review of the literature.

BACKGROUND: Immunoglobulin G4-related disease (IgG4-RD) is a chronic inflammatory systemic disease of unknown etiology that can affect one or multiple organs. The disease can mimic many infectious and inflammatory diseases, mainly causing organ enlargement or hyperplasia. Its diagnosis primarily relies on clinical, serologic, and histological features (lymphoplasmacytic infiltrates, storiform fibrosis, and obliterative phlebitis of IgG4 + plasma cells). Here, we report a rare case of IgG4-related periodontitis, and review the relevant literatures. CASE PRESENTATION: A 38-year-old Chinese man visited the Department of Periodontics with gingival enlargement, loose teeth, and tooth loss. The patient had very poor oral hygiene and a large amount of calculus. Gingivae were edematous with deep periodontal pockets and attachment loss. Panoramic radiography showed alveolar bone loss. Serologic examination showed that IgG was 23.70 g/L and IgG4 concentration was 2.800 g/L. There was significant lymphoplasmacytic infiltration, a storiform pattern of fibrosis, and mitotic figures with hematoxylin and eosin staining; immunohistochemical staining showed 10 scattered IgG4-positive plasma cells in a high-power field. The patient was diagnosed as IgG4-related periodontitis. He received a course of corticosteroids with periodontal therapy, and the enlargement was significantly improved without recurrence. CONCLUSION: IgG4-RD in the oral and maxillofacial region mainly involves salivary glands, but this rare case was characterized by enlarged gingivae. The differential diagnosis of IgG4-RD should be based on the clinical features and serologic (IgG4) and histopathological examinations. Corticosteroid therapy is effective for most IgG4-RD patients. Taken together, we hope this case report and the literature review can help dentists to improve their understanding of the IgG4-RD.

LncRNA TP73-AS1 is a novel regulator in cervical cancer via miR-329-3p/ARF1 axis.

Cervical cancer holds one of the highest morbidity and mortality in various types of cancers. It even leads to the most number of cancer-related deaths of women. A lot of research has indicated that the anomalous expression of long noncoding RNAs (lncRNAs) would induce carcinogenesis and is associated with poor prognosis of patients with cancer. However, the function and mechanism of many lncRNAs still call for further research. Tumor Protein P73 Antisense RNA 1 (TP73-AS1) is no exception. LncRNA TP73-AS1 has been found to promote cancer progressions in various cancers. It is upregulated in cervical cancer cells. The proliferation and migration ability of cervical cancer cells can also be boosted by TP73-AS1 in return. Meanwhile, miRNA-329-3p is downregulated in cervical cancer cells and could bind with both TP73-AS1 and ADP Ribosylation Factor 1 (ARF1). TP73-AS1 inhibited miR-329-3p expression while miR-329-3p inhibited ARF1 expression. More importantly, TP73-AS1 can positively regulate ARF1 expression. Based on all these experiments, TP73-AS1 regulates ARF1 expression by competitively binding with miR-329-3p, thus regulating cervical cancer progression. Further rescue assays confirmed TP73-AS1 regulates cervical cell proliferation and migration via miR-329-3p/ARF1. TP73-AS1 might serve as a novel regulator in cervical cancer.

Heterologous and Engineered Biosynthesis of Nematocidal Polyketide-Nonribosomal Peptide Hybrid Macrolactone from Extreme Thermophilic Fungi.

Fungal polyketide-nonribosomal peptide (PK-NRP) hybrid macrolactones are a growing family of natural products with biomedical and agricultural activities. One of the most important families is the thermolides, which are produced by extreme thermophilic fungi and exhibit strong nematocidal activity. We show here that the genes ThmABCE from Talaromyces thermophilus NRRL 2155 are critical for thermolide synthesis. Two separate single-module hrPKS (ThmA) and NRPS (ThmB) enzymes collaborate to synthesize the core macrolactone backbone (6 or 7), and the NRPS ThmB-CT domain catalyzes the key macrocyclization step in PK-NRP intermediate release via ester bond formation, representing a novel function of fungal NRPS C domains. We also show that heterologous and engineered expression of the Thm genes in the type strains of Aspergillus nidulans and Escherichia coli not only dramatically enhances the yields of thermolides but also affords different esterified analogues, such as butyryl- (thermolides J and K, 15 and 16), hexanoyl-, and octanyl- derivatives or mixed thermolides. Thermolides L and M (18 and 19), discovered via genome mining-based combinatorial biosynthesis, represent the first l-phenylalanine-based thermolides. Our work shows a unique biosynthetic mechanism of PK-NRP hybrid macrolactones from extremophiles, which led to the discovery of novel compounds and furthers our biosynthetic knowledge.

Surgical retrieval of PICC-related right atrial thrombus in a child with acute lymphoblastic leukemia: a case report.

BACKGROUND: Peripherally inserted central catheters (PICCs) are widely used in cancer patients for administering chemotherapy drugs, antibiotics, and nutrients. PICC-related thrombi are not uncommon and may result in pulmonary embolism and the formation of thrombi in the right atrium. The latter are associated with an increased risk of subsequent morbidity or mortality because of their potential for embolization in the pulmonary vasculature. CASE PRESENTATION: A 16-year-old male with acute lymphoblastic leukemia (ALL) was admitted to our hospital after an echocardiographic examination revealed a ring-like structure in the right atrium that was still present after 6 months' anticoagulation treatment with aspirin. The boy had had a PICC inserted 2 years previously for chemotherapy; the PICC was intact and successfully removed 18 months after insertion when chemotherapy is finished. Subsequent computer tomography and radiography differentiated right atrial ring-shaped mass with a diameter of approximately 15 mm. Cardiac surgery was performed to remove the mass which was found to be a calcified thrombus. CONCLUSION: Although this is a rare occurrence, recognition of the possibility of a calcified thrombus may minimize the misdiagnosis of PICC-related thrombus and allow surgical retrieval if the thrombus is sufficiently large.

Massively Parallel Quantum Chemistry: A high-performance research platform for electronic structure.

The Massively Parallel Quantum Chemistry (MPQC) program is a 30-year-old project that enables facile development of electronic structure methods for molecules for efficient deployment to massively parallel computing architectures. Here, we describe the historical evolution of MPQC's design into its latest (fourth) version, the capabilities and modular architecture of today's MPQC, and how MPQC facilitates rapid composition of new methods as well as its state-of-the-art performance on a variety of commodity and high-end distributed-memory computer platforms.

Population genetic dynamics of Himalayan-Hengduan tree peonies, Paeonia subsect. Delavayanae.

According to the present taxonomical treatment, Paeonia subsect. Delavayanae consists of only two species (P. delavayi and P. ludlowii) endemic to the Himalayan-Hengduan Mountains. Although P. ludlowii can be distinguished from P. delavayi on the basis of a series of morphological characters, the species delimitation remains controversial because the more widespread one, P. delavayi, exhibits considerable morphological diversity. Both chloroplast DNA markers and nuclear microsatellites or simple sequence repeats (nSSR) are used herein to reveal genetic diversity and relationships of the two taxa included in this subsection, and ecological niche modeling (ENM) is employed to get insights into their paleodistribution. Our results show that genetic boundaries between the two currently recognized species are unclear, probably due to recent divergence. Paeonia ludlowii is budding from P. delavayi, probably by genetic isolation but also by shifting its niche to the harsher upland Tibetan conditions. Paeonia delavayi itself would be, however, under active speciation, showing significant genetic differentiation and morphological diversity. Whereas P. ludlowii would have endured the Pleistocene glacial periods by in situ persistence in local, small refugia, a 'dual' model seems to apply for P. delavayi (in situ persistence and retreat to refugia). The rarity of P. ludlowii and high evolutionary potential of P. delavayi imply high priority for in situ conservation of both taxa. The Himalayan-Hengduan Mountains are an ideal arena for differentiation within subsect. Delavayanae of Paeonia, by means of expansions/contractions/displacements, vertical migrations, and local survival/extinctions in response to the Neogene climate fluctuations and geological changes.

The role of TNF alpha polymorphism and expression in susceptibility to nasal polyposis.

OBJECTIVE: In this study, we first performed a meta-analysis to assess the role of single-nucleotide polymorphism (SNP) within tumor necrosis factor alpha (TNF alpha) gene and TNF alpha expression in the risk of nasal polyposis. METHODS: STATA 12.0 software was utilized to conduct the Mantel-Haenszel statistics, Cohen statistics, Begg's test, Egger's tests and sensitivity analysis. RESULTS: We systemically carried out the database retrieval and initially identified 486 articles. After screening, 15 articles were included in our meta-analysis. For TNF alpha rs1800629 G/A SNP, compared with control group, an increased risk of nasal polyposis of case group was observed in the models of A vs. G [p (P value of association) = 0.009, OR (odds ratio) = 1.35], GA vs. GG (p = 0.001, OR = 1.69), GA+AA vs. GG (p = 0.010, OR = 1.47). The similar results were observed in Caucasian subgroup (p < 0.05, OR > 1). For TNF alpha rs361525 G/A SNP, no significant difference between control and case group was detected (all p > 0.05). In addition, a significant difference exists between case and control groups in the meta-analyses of TNF alpha expression in nasal mucosal cells, secreted TNF alpha (p < 0.05, OR > 1), but not serum TNF alpha (p = 0.090). CONCLUSION: The present meta-analysis revealed that TNF alpha rs1800629, increased TNF alpha expression and secretion of nasal mucosal cells were associated with an increased risk of nasal polyposis.

Oxidative damage and antioxidative indicators in 48 h germinated rice embryos during the vitrification-cryopreservation procedure.

KEY MESSAGES: Cu/Zn SOD and other genes may be critical indicators of a stress response to reactive oxygen species (ROS) accumulation in 48 h germinated rice embryos subjected to vitrification cryopreservation. In the current study, reactive oxygen species (ROS) accumulation was investigated in 48 h germinated rice embryos during the vitrification-cryopreservation process. We found that vitrification-cryopreservation significantly affected ROS levels, especially superoxide anion levels, in 48 h germinated rice embryos. Malonaldehyde content in the apical meristems of germinated embryos was significantly positively correlated with the rate of superoxide anion generation and the highest levels of malonaldehyde content were reached after vitrification treatment. Cell viability in 48 h germinated embryos was significantly negatively correlated with the rate of superoxide anion generation, malonaldehyde content, and electrolyte leakage. Spatial and temporal patterns in ROS accumulation in these embryos existed during the vitrification procedure. Among the vitrification-cryopreservation treatments we assessed, the preculture treatment was found to stimulate superoxide anion generation and to activate the response system in the apical meristems of germinated embryos. Loading treatments motivated the catalase and ascorbate peroxidase activities. During the vitrification-dehydration treatment, oxidative stress reached the highest levels causing an antioxidative response. This response involved antioxidant enzymes promoting detoxification of ROS. Based on a comprehensive correlation analysis involving ROS accumulation, cell viability, the activities of antioxidant enzymes, and gene expression profiles, Cu/Zn SOD, CAT1, APX7, GR2, GR3, MDHAR1, and DHAR1 may be critical indicators of oxidative stress affected by the vitrification-cryopreservation treatments. The investigation of these antioxidative responses in 48 h germinated rice embryos may, therefore, provide useful information with respect to plant vitrification-cryopreservation.

Massively Parallel Implementation of Explicitly Correlated Coupled-Cluster Singles and Doubles Using TiledArray Framework.

A new distributed-memory massively parallel implementation of standard and explicitly correlated (F12) coupled-cluster singles and doubles (CCSD) with canonical O(N6) computational complexity is described. The implementation is based on the TiledArray tensor framework. Novel features of the implementation include (a) all data greater than O(N) is distributed in memory and (b) the mixed use of density fitting and integral-driven formulations that optionally allows to avoid storage of tensors with three and four unoccupied indices. Excellent strong scaling is demonstrated on a multicore shared-memory computer, a commodity distributed-memory computer, and a national-scale supercomputer. The performance on a shared-memory computer is competitive with the popular CCSD implementations in ORCA and Psi4. Moreover, the CCSD performance on a commodity-size cluster significantly improves on the state-of-the-art package NWChem. The large-scale parallel explicitly correlated coupled-cluster implementation makes routine accurate estimation of the coupled-cluster basis set limit for molecules with 20 or more atoms. Thus, it can provide valuable benchmarks for the merging reduced-scaling coupled-cluster approaches. The new implementation allowed us to revisit the basis set limit for the CCSD contribution to the binding energy of π-stacked uracil dimer, a challenging paradigm of π-stacking interactions from the S66 benchmark database. The revised value for the CCSD correlation binding energy obtained with the help of quadruple-ζ CCSD computations, -8.30 ± 0.02 kcal/mol, is significantly different from the S66 reference value, -8.50 kcal/mol, as well as other CBS limit estimates in the recent literature.

Monte Carlo explicitly correlated second-order many-body perturbation theory.

A stochastic algorithm is proposed and implemented that computes a basis-set-incompleteness (F12) correction to an ab initio second-order many-body perturbation energy as a short sum of 6- to 15-dimensional integrals of Gaussian-type orbitals, an explicit function of the electron-electron distance (geminal), and its associated excitation amplitudes held fixed at the values suggested by Ten-no. The integrals are directly evaluated (without a resolution-of-the-identity approximation or an auxiliary basis set) by the Metropolis Monte Carlo method. Applications of this method to 17 molecular correlation energies and 12 gas-phase reaction energies reveal that both the nonvariational and variational formulas for the correction give reliable correlation energies (98% or higher) and reaction energies (within 2 kJ mol-1 with a smaller statistical uncertainty) near the complete-basis-set limits by using just the aug-cc-pVDZ basis set. The nonvariational formula is found to be 2-10 times less expensive to evaluate than the variational one, though the latter yields energies that are bounded from below and is, therefore, slightly but systematically more accurate for energy differences. Being capable of using virtually any geminal form, the method confirms the best overall performance of the Slater-type geminal among 6 forms satisfying the same cusp conditions. Not having to precompute lower-dimensional integrals analytically, to store them on disk, or to transform them in a nonscalable dense-matrix-multiplication algorithm, the method scales favorably with both system size and computer size; the cost increases only as O(n4) with the number of orbitals (n), and its parallel efficiency reaches 99.9% of the ideal case on going from 16 to 4096 computer processors.

Effect of Mir-122 on Human Cholangiocarcinoma Proliferation, Invasion, and Apoptosis Through P53 Expression.

BACKGROUND Bile duct carcinoma is a common digestive tract tumor with high morbidity and mortality. As a kind of important non-coding RNA, microRNA (miR) plays an important role in post-transcriptional regulation. MiR-122 is the most abundant miR in the liver. Multiple studies have shown that miR-122 level is reduced in a variety of liver tumors and can be used as a specific marker for liver injury. P53 is a classic tumor suppressor gene that can induce tumor cell apoptosis through various pathways. Whether miR-122 affects p53 in bile duct carcinoma still needs investigation. MATERIAL AND METHODS miR inhibitor or mimics was transfected to bile duct carcinoma cells to evaluate its function on proliferation, invasion, apoptosis, and p53 expression. RESULTS MiR-122 overexpression reduced cell invasion and migration ability, and inhibited cell apoptosis and p53 expression. Inhibiting miR-122 caused the opposite results. CONCLUSIONS Upregulating miR-122 can suppress bile duct carcinoma cell proliferation and induce apoptosis. MiR-122 could be used as a target for bile duct carcinoma treatment, which provides a new strategy for cholangiocarcinoma patients.