Search

Supplementary text S1. Supplementary Figure 1: Chromatin Profiles of Primary GC. Supplementary Figure 2: Epithelial features of GC promoters. Supplementary Figure 3: GC Somatic Promoter Features. Supplementary Figure 4: Association of Somatic Promoters with Gene Expression in GC and Other Tumor Types. Supplementary Figure 5: Changes in DNA methylation at CpG island containing promoters. Supplementary Figure 6: Expression distribution of alternative and canonical isoforms. Supplementary Figure 7: Characterization of RASA3 Isoform. Supplementary Figure 8: Characterization of MET Isoforms. Supplementary Figure 9: Immunogenicity of N-terminal peptides. Supplementary Figure 10: Immunogenicity Assay and Nanostring Profiling. Supplementary Figure 11: Functional Assessment of Peptide Immunogenicity. Supplementary Figure 12: EZH2 Inhibition. Supplementary Figure 13: Unannotated somatic promoters.

Association between genotype and toxicity Grade 3 or greater

Purpose: Germline polymorphisms may affect chemotherapy efficacy and toxicity. We examined the effect of polymorphisms in drug metabolism and DNA repair genes on pathologic response rates, survival, and toxicity for patients randomized to surgery alone or perioperative ECF chemotherapy in the MRC MAGIC trial.Experimental Design: DNA was extracted from nontumor resection formalin-fixed paraffin-embedded (FFPE) blocks. ERCC1, ERCC2, XRCC1, DYPD, and OPRT SNPs were evaluated using Sequenom, GSTP1, GSTT1 deletion, and TYMS (TS) 5′ 2R/3R using multiplex PCR. Post PCR amplification, TS 2R/3R and GSTT1 samples underwent gel electrophoresis.Results: Polymorphism data were available for 289 of 456 (63.4%) operated patients. No polymorphism was statistically significantly associated with pathologic response to chemotherapy. Median overall survival (OS) for patients treated with surgery alone with any TS genotype was not different (1.76 years 2R/2R, 1.68 years 2R/3R, 2.09 years 3R/3R). Median OS for patients with a TS 2R/2R genotype treated with chemotherapy was not reached, whereas median OS for 2R/3R and 3R/3R patients were 1.44 and 1.60 years, respectively (log rank P value = 0.0053). The P value for the interaction between treatment arm and genotype (3R/3R and 3R/2R vs. 2R/2R) was 0.029. No polymorphism was statistically significantly associated with chemotherapy toxicity.Conclusions: In MAGIC, patients with a TS 2R/2R genotype appeared to derive a larger benefit from perioperative ECF chemotherapy than patients with 3R containing genotypes. Further exploration of this potential predictive biomarker in this patient population is warranted. Clin Cancer Res; 23(24); 7543–9. ©2017 AACR.

Percentage of somatic variants based on 6 mutation types in Asian lung cancers.

Supplementary Tables 1-4 from Prediction of Clinical Outcome in Multiple Lung Cancer Cohorts by Integrative Genomics: Implications for Chemotherapy Selection

Clinical and tissue information on 30 lung cancer patients (S1); Recurrent somatic variants based on presence of the same variant in the COSMIC database or presence of the same variant within the dataset (S2); Variants of the category 'three or more different variants with predicted functional impact within a gene' (S3); Somatic structural variations (S4); Summary of the sequencing statistics by Complete Genomics for 30 tumor/normal paired samples (S5); Validation of somatic variants by Ion Torrent or Sanger sequencing (S6); Validation of EGFR mutations by Sanger sequencing (S7).

Asian nonsmoking populations have a higher incidence of lung cancer compared with their European counterparts. There is a long-standing hypothesis that the increase of lung cancer in Asian never-smokers is due to environmental factors such as second-hand smoke. We analyzed whole-genome sequencing of 30 Asian lung cancers. Unsupervised clustering of mutational signatures separated the patients into two categories of either all the never-smokers or all the smokers or ex-smokers. In addition, nearly one third of the ex-smokers and smokers classified with the never-smoker–like cluster. The somatic variant profiles of Asian lung cancers were similar to that of European origin with G.C>T.A being predominant in smokers. We found EGFR and TP53 to be the most frequently mutated genes with mutations in 50% and 27% of individuals, respectively. Among the 16 never-smokers, 69% had an EGFR mutation compared with 29% of 14 smokers/ex-smokers. Asian never-smokers had lung cancer signatures distinct from the smoker signature and their mutation profiles were similar to European never-smokers. The profiles of Asian and European smokers are also similar. Taken together, these results suggested that the same mutational mechanisms underlie the etiology for both ethnic groups. Thus, the high incidence of lung cancer in Asian never-smokers seems unlikely to be due to second-hand smoke or other carcinogens that cause oxidative DNA damage, implying that routine EGFR testing is warranted in the Asian population regardless of smoking status. Cancer Res; 74(21); 6071–81. ©2014 AACR.

Supplementary Methods from Prediction of Clinical Outcome in Multiple Lung Cancer Cohorts by Integrative Genomics: Implications for Chemotherapy Selection

Supplementary Figures 1-6 from Prediction of Clinical Outcome in Multiple Lung Cancer Cohorts by Integrative Genomics: Implications for Chemotherapy Selection

Supplementary Figure Legends 1-6 from Prediction of Clinical Outcome in Multiple Lung Cancer Cohorts by Integrative Genomics: Implications for Chemotherapy Selection

Legend for Supplementary Figures S1-S2.

Classical swine fever virus (CSFV) is a member of the genus Pestivirus, which causes serious economic losses. The re-emergence of the disease in Japan in 2018 has increased awareness of CSFV. In this study, Balb/c mice were immunized with plant-derived E2 protein, and four monoclonal antibodies (mAbs) 4B11, 7B3, 11A5 and 6F3 were generated. Two of these mAbs, 4B11 and 7B3, effectively blocked CSFV infection of PK-15 cells. Both mAbs recognized a novel linear epitope, 256CLIGNTTVKVHASDER271. The neutralizing ability of anti-CSFV serum decreased 63%, when pre-incubated with the linear peptide at 200 μg/mL. Structural analysis showed that this linear epitope is present at the border of Domain C and Domain D on the surface of the E2 protein. Alignment of amino acid sequences showed that the epitope was conserved in different subgroups of CSFV but not in other members of the Pestivirus genus. Consistently with the analysis above, this epitope distinguished antibodies against CSFV from those against bovine viral diarrhea virus (BVDV). Our study provides an ideal candidate peptide for new vaccine design and differential diagnosis of CSFV. These findings will contribute to the control and eradication of classical swine fever.

To explore the relationship between the dry matter contents of potato tubers and metabolic enzymes, an experiment was designed. Ten individual indicators, including metabolic enzymes, could be reduced to 4 comprehensive indicators by using a principal component analysis. Using these 4 components as independent variables (X) and the dry matter content as the dependent variable (Y), the following linear regression equation was obtained: Y = ‒51.802 ‒ 1.022X5 ‒ 0.034X6 + 0.872X9 + 0.286X10 (R2 = 0.889, P = 0.012). In a comparison between the dry matter contents (22.74, 16.58 and 20.72%) calculated according to the equation and the measured value (22.96, 17.09 and 19.75%), the absolute error was < 1% and the estimation accuracy was > 95%. These results indicated that the linear regression equation can be used to predict accurately and quickly the dry matter contents during the tuber enlargement stage. Bangladesh J. Bot. 50(2): 253-259, 2021 (June)

Vaccination is an effective method to control the spread of classical swine fever virus (CSFV), which is a major cause of economic losses to the swine industry. Although serological detection assays are commonly used to assess immune status, current methods for monitoring of antibodies (Abs) are time-consuming, expensive, and require cell culture and virus manipulation. To address these problems, the E2 protein of CSFV was expressed in transgenic rice seeds as a labeled antigen for the development of an immunochromatographic test strip (ICTS) for rapid, precise, and cost-effective detection of Abs. The ICTS has a reasonable sensitivity of 1:128,000 for detection of serum Abs against CSFV and no cross-reactivity with Abs of other porcine viruses. The similarity of the results between the proposed ICTS and a commercial enzyme-linked immunosorbent assay was 94.1% (128/136) for detection of serum Abs from immunized animals and 92.3% (72/78) for detection of maternally derived Abs. The proposed assay was successfully used to monitor Abs against E2 of both pigs and rabbits immunized with a live attenuated vaccine or an E2 subunit vaccine. The results confirmed that the ICTS can be applied to detect Ab levels in animals with different immunological backgrounds. The ICTS based on plant-derived E2 is a relatively inexpensive, rapid, and accurate assay for detection of Abs against CSFV and avoids the risk of contamination by animal products.

Several transition metal oxides, including La1–xSrxCoO3, are promising materials to realize resistive switching devices for neuromorphic applications, as they can undergo a metal-to-insulator trans...

Although epigallocatechin-3-gallate (EGCG), the major polyphenol in green tea, has been shown to have many benefits, the effect of EGCG exposure in utero on adult uterine development is unclear. In this study, pregnant C57BL/6 mice were exposed to 1 mg/kg body weight (bw) EGCG dissolved in drinking water from gestational days 0.5-16.5. A significant decrease in uterine weight was observed in the adult female mice, accompanied by uterine atrophy, inflammation, and fibrosis in the endometrium. Uterine atrophy was attributed to the thinning of the endometrial stromal layer and a significant reduction in endometrial cell proliferation. The expression levels of related proteins in the NF-κB and RAF/MEK/ERK signaling pathways were significantly increased, which might be responsible for the occurrence of inflammation. Activation of the transforming growth factor beta (TGF-β1)/Smad signaling pathway might be involved in the development of endometrial fibrosis. The changes in the expression of estrogen receptor α, β (ERα, ERβ), progesterone receptor (PGR), and androgen receptor (AR) might lead to changes in the aforementioned signaling pathways. The promoter region methylation level of Esr2 was increased, and the expression of DNMT3A was evaluated. Our study indicates a risk of EGCG intake during pregnancy affecting uterine development in offspring.

The aim of this study was to develop a semi-quantitative immunochromatographic method for rapid detection of Newcastle disease virus (NDV) antibodies by expressing HN protein in rice endosperm bioreactor. The recombinant plasmid pUC57-HN was digested by

Oxide-based photoelectrodes recently have been at the forefront of research for photoelectrochemical water splitting. While most oxide-based photoanodes suffer from severe electron–hole recombinati...

In this paper, the phase transformation mechanism of various carbon sources in the synthesis of diamond by direct detonation method was studied. Through designing comparison experiment and the X-ra...

Epigallocatechin gallate (EGCG) has a wide consumption for its health advantages. The current study investigates the effects of prenatal EGCG administration on glucose metabolism and obesity in adulthood. Pregnant C57BL/6J mice were supplemented with EGCG in drinking water (3 µg/mL) for 16 d. Abdominal obesity was observed in both male and female adult mice, which was associated with the upregulation of adipose-specific genes, including C/ebpα and Srebf1 (Srebf1 only in males), and the downregulation of genes related to lipolysis, such as Acox1, Atgl and Pdk4 (only in males) in visceral adipose tissue. Elevated fasting glucose levels and hyperinsulinemia were observed in adult males, while females exhibit lower glucose level in glucose tolerance test, which might be due to reduced glucagon levels. Though hepatic expression of the insulin receptor signaling pathway was upregulated in males and was not altered in females, prenatal treatment with EGCG downregulated the expression of this signaling pathway in the skeletal muscle of adult mice, which was further demonstrated in primary human skeletal muscle cells treated with EGCG. The methylation levels in promotor of genes related to the insulin receptor signaling were matched with their transcription in mice, while the expression of acetylated histones was downregulated in human skeletal muscle cells. These results suggest that EGCG consumption during pregnancy should be a risk factor for the disruption of glucose homeostasis in adulthood.

Background: DNA methylation signatures describing distinct histological subtypes of oesophageal cancer have been reported. We studied DNA methylation in samples from the MRC OE02 phase III trial, which randomised patients with resectable oesophageal cancer to surgery alone (S) or neoadjuvant chemotherapy followed by surgery (CS).Aim: The aim of the study was to identify epigenetic signatures predictive of chemotherapy benefit in patients with oesophageal adenocarcinoma (OAC) from the OE02 trial and validate the findings in an independent cohort.Methods: DNA methylation was analysed using the Illumina GoldenGate platform on surgically resected OAC specimens from patients in the OE02 trial. Cox proportional hazard analysis was performed to select probes predictive of survival in the CS arm. Non-negative matrix factorisation was used to perform clustering and delineate DNA methylation signatures. The findings were validated in an independent cohort of patients with gastroesophageal adenocarcinoma treated with neoadjuvant chemotherapy.Results: A total of 229 patients with OAC were analysed from the OE02 trial (118 in the CS arm and 111 in the S arm). There was no difference in DNA methylation status between the CS and S arms. A metagene signature was created by dichotomising samples into two clusters. In cluster 1, patients in the CS arm had significant overall survival (OS) benefit (median OS CS: 931 days vs. S: 536 days [HR: 1.54, P = 0.031]). In cluster 2, patients in the CS arm had similar (or worse) OS compared with patients in the S arm (CS: 348 days vs. S: 472 days [HR: 0.70, P = 0.1], and test of interaction was significant (p = 0.005). In the validation cohort (n = 13), there was no difference in DNA methylation status in paired pre- and post-treatment samples. When the epigenetic signature was applied, cluster 1 samples had better OS (median OS, cluster 1: 1174 days vs. cluster 2: 392 days, HR: 3.47, p = 0.059)Conclusions: This is the first and largest study of DNA methylation in patients with OAC uniformly treated in a randomised phase III trial. We identified an epigenetic signature that may serve as a predictive biomarker for chemotherapy benefit in OAC. (C) 2019 Elsevier Ltd. All rights reserved.

Phenanthrene (Phe) is a polycyclic aromatic hydrocarbon widely present in foods and drinking water. To explore the detrimental effects of Phe on body metabolism, female Kunming mice were treated with Phe in drinking water at concentrations of 0.05, 0.5 and 5 ng/mL. After exposure for 270 d, the animals exhibited dose-dependent reduced body weight and increased water consumption. The dose-dependent accumulation of Phe in the brain decreased hypothalamic neuron numbers, upregulated hypothalamic expression of anaplastic lymphoma kinase, elevated norepinephrine levels in white adipose tissue (WAT) and further activated lipolysis in WAT, leading to a reduction in fat mass. Brown adipose tissue formation was reduced, accompanied by the inhibition of the bone morphogenetic protein signaling pathway. A simultaneous reduced serum levels of antidiuretic hormone (arginine vasopressin) might be one of the reasons for increased water consumption. The present results indicate an environmental etiology and prevention way for the development of emaciation-thirst disease.

Background: Cytokine storms are a common complication in severely ill patients with COVID-19, for which corticosteroid therapy (CsT) is used as adjuvant treatment. Therefore, we evaluated the efficacy and safety of CsT in patients with COVID-19.Methods: A single-center, retrospective cohort study was conducted in 1,392 severely ill patients with COVID-19 from Wuhan Huoshenshan Hospital. Patients received at least one dose (1–2 mg·kg-1·day-1 for 3–5 days) of methylprednisolone were divided into CsT group, whereas the rest were assigned into the non-CsT group. Results: Of 1,392 patients, 116 were assigned to the CsT group and 1,226 to the non-CsT group. Patients in the CsT group showed comparable mortality rate (1.8% vs. 1.2%, P > 0.99) and viral clearance time (44.5 days vs. 46.0 days, P = 0.48), but longer hospitalization time (21 days vs. 12 days, P < 0.001) than those in non-CsT group. During CsT, the proportion of lymphocytes was lower (14.7 % vs. 18.5 %, P = 0.01), while neutrophils was higher (77.1 % vs. 69.8 %, P < 0.001), than before treatment. The C-reactive protein (CRP) level was significantly lower after CsT (3.1 mg/L vs. 9.5 mg/L, P < 0.001). Furthermore, indicators of liver function (gamma-glutamyl transferase [GGT], alanine aminotransferase [ALT], and aspartate aminotransferase [AST]) and cardiac function (brain natriuretic peptide [BNP], α-hydroxybutyrate dehydrogenase [α-HBDH], and lactate dehydrogenase [LDH]) increased significantly during CsT but returned to normal after CsT. Patients who developed liver damage showed higher GGT, ALT, AST, LDH, Cre, and CRP; patients who developed heart injury had higher AST, LPH, CRP, lymphocyte (LYM), glucose, BNP, and α-HBDH; and patients who developed kidney failure had higher α-HBDH, LDH, CRP, and LYM values than before CsT. Additionally, patients who received CsT with cardiovascular disease showed a continuous elevation in D-dimer levels.Conclusions: CsT effectively attenuates the inflammatory response in severely ill patients with COVID-19 at a relatively low dose in a short duration; however, CsT increases the risk of hepatic and cardiac abnormalities.

Polycyclic aromatic hydrocarbons (PAHs) are a risk factor for the occurrence of cardiac diseases. The present study was conducted to investigate the influence of prenatal exposure to a mixed PAHs on heart and the underlying mechanism. Pregnant mice were orally administered with a mixture of 8 kinds of PAHs (0, 5, 50, 500 μg/kg body weight) once every 2 days for a total of 8 dosages. The mixed PAHs contained naphthalene, acenaphthylene, phenanthrene, fluoranthene, pyrene, benzo[a]pyrene, dibenzo[a,h]anthracene and benzo[g,h,i]perylene at a weight ratio of 10: 10: 10: 10: 10: 1: 1: 1. The adult males, not females, showed significantly decreased heart/body weight ratio, which was attributed to the loss of cardiac fiber and the increase of cell apoptosis. The protein expression of transforming growth factor β1 and its downstream transcription factors, Smad3 and Smad4, was significantly downregulated, which caused the loss of cardiac fiber. The downregulated phosphatidylinositol 3-kinase and AKT led to increased expression of caspase3, caspase9, BAX and reduced expression of Bcl-2, which was responsible for the increased cell apoptosis. Different levels of aromatic hydrocarbon receptor and sex hormone receptors between males and females were associated with the distinct effect on heart.

Author(s): Chiu, IT; Lee, MH; Cheng, S; Zhang, S; Heki, L; Zhang, Z; Mohtashami, Y; Lapa, PN; Feng, M; Shafer, P; N'Diaye, AT; Mehta, A; Schuller, JA; Galli, G; Ramanathan, S; Zhu, Y; Schuller, IK; Takamura, Y | Abstract: Topotactic transformations involve structural changes between related crystal structures due to a loss or gain of material while retaining a crystallographic relationship. The perovskite oxide La0.7Sr0.3CoO3 (LSCO) is an ideal system for investigating phase transformations due to its high oxygen vacancy conductivity, relatively low oxygen vacancy formation energy, and strong coupling of the magnetic and electronic properties to the oxygen stoichiometry. While the transition between cobaltite perovskite and brownmillerite (BM) phases has been widely reported, further reduction beyond the BM phase lacks systematic studies. In this paper, we study the evolution of the physical properties of LSCO thin films upon exposure to highly reducing environments. We observe the rarely reported crystalline Ruddlesden-Popper phase, which involves the loss of both oxygen anions and cobalt cations upon annealing where the cobalt is found as isolated Co ions or Co nanoparticles. First-principles calculations confirm that the concurrent loss of oxygen and cobalt ions is thermodynamically possible through an intermediary BM phase. The strong correlation of the magnetic and electronic properties to the crystal structure highlights the potential of utilizing ion migration as a basis for emerging applications such as neuromorphic computing.

ObjectiveGenomic structural variations (SVs) causing rewiring of cis-regulatory elements remain largely unexplored in gastric cancer (GC). To identify SVs affecting enhancer elements in GC (enhancer-based SVs), we integrated epigenomic enhancer profiles revealed by paired-end H3K27ac ChIP-sequencing from primary GCs with tumour whole-genome sequencing (WGS) data (PeNChIP-seq/WGS).DesignWe applied PeNChIP-seq to 11 primary GCs and matched normal tissues combined with WGS profiles of >200 GCs. Epigenome profiles were analysed alongside matched RNA-seq data to identify tumour-associated enhancer-based SVs with altered cancer transcription. Functional validation of candidate enhancer-based SVs was performed using CRISPR/Cas9 genome editing, chromosome conformation capture assays (4C-seq, Capture-C) and Hi-C analysis of primary GCs.ResultsPeNChIP-seq/WGS revealed ~150 enhancer-based SVs in GC. The majority (63%) of SVs linked to target gene deregulation were associated with increased tumour expression. Enhancer-based SVs targeting CCNE1, a key driver of therapy resistance, occurred in 8% of patients frequently juxtaposing diverse distal enhancers to CCNE1 proximal regions. CCNE1-rearranged GCs were associated with high CCNE1 expression, disrupted CCNE1 topologically associating domain (TAD) boundaries, and novel TAD interactions in CCNE1-rearranged primary tumours. We also observed IGF2 enhancer-based SVs, previously noted in colorectal cancer, highlighting a common non-coding genetic driver alteration in gastric and colorectal malignancies.ConclusionIntegrated paired-end NanoChIP-seq and WGS of gastric tumours reveals tumour-associated regulatory SV in regions associated with both simple and complex genomic rearrangements. Genomic rearrangements may thus exploit enhancer-hijacking as a common mechanism to drive oncogene expression in GC.

The use of coordination complexes as building units within covalent organic frameworks (COFs) has significant potential to diversify the structures and properties of this class of materials. Here, we present a synergistic coordination and reticular chemistry approach to the design of a series of crystalline scandium–covalent organic frameworks (Sc–COFs), featuring tunable levels of metal incorporation. Removal of scandium from the material with the highest metal content results in a metal-imprinted COF (MICOF) that exhibits high affinity and capacity for Sc3+ ions in acidic environments and in the presence of competing metal ions. In particular, the selectivity of this MICOF for Sc3+ over common impurity ions such as La3+ and Fe3+ surpasses that of all reported scandium adsorbents. Importantly, analogous materials can be prepared starting from earth-abundant transition metals, highlighting the versatility of this approach for the development of tailor-made metal–COFs and MICOFs for applications involving selective metal ion capture.

Immune checkpoint inhibitors (ICIs) have emerged as one of the most promising therapeutic options for patients with advanced cancer. The aim of the present study was to investigate the prognostic value of somatic mutations in mismatch repair (MMR) genes in metastatic cancers after ICI treatment, as well as their association with tumor mutational burden (TMB). Information regarding gene mutations in mismatch repair and the survival time of patients with advanced cancer following ICI treatment was collected from the cBioPortal database. The prognostic value of somatic mutations in MMR genes and the association between the mutation status and TMB score were analyzed among multiple types of cancer. Somatic mutation frequency in the MMR genes was identified to be 7% among all patients, which varied across different types of cancer. Somatic mutations in the MMR genes were associated with improved overall survival time in all tested patients (P=0.004). Following stratification by type of ICI treatment, a significant association was observed between somatic mutations in the MMR genes and overall survival time in patients treated with cytotoxic T-lymphocyte-associated protein 4 inhibitors (P=0.01). In addition, marked but non-significant association between somatic mutations in the MMR genes and overall survival time was revealed in patients administered with programmed death-1/programmed death-ligand-1 inhibitors (P=0.09). Multivariate Cox proportional hazards regression analysis demonstrated that somatic mutations in MMR genes were significantly associated with overall survival time (hazard ratio, 0.683; 95% confidence interval, 0.497-0.938; P=0.01). Patients with somatic mutations in the MMR genes demonstrated higher TMB compared with those not harboring mutations (P

Epidemiological studies have indicated that polycyclic aromatic hydrocarbons were related to diabetes and insulin resistance. However, studies in mammals on the development of diabetes caused by polycyclic aromatic hydrocarbons are lacking. Pregnant mice were orally exposed to phenanthrene (0, 60 and 600 μg kg−1 body weight) once every 3 days during gestation. In adult mouse offspring, in-utero phenanthrene exposure caused glucose intolerance and decreased insulin levels in females, while caused elevated fasting blood glucose and insulin levels in males. Serum resistin and interleukin-6 levels were elevated in offspring of both sexes. Serum adiponectin levels were decreased in females but increased in males. The insulin receptor signals were upregulated in the liver and downregulated in the skeletal muscle of F1 females, while they were inhibited in both tissues of F1 males. The visceral fat weight and body weight of the treated mice were not increased, suggesting that phenanthrene is not an obesogen, which is supported by the nonsignificant alteration in pparγ transcription in visceral adipose tissue. The transcription of retn in visceral adipose tissue was upregulated in both sexes, and that of adipoq was downregulated in females but upregulated in males, which were matched with the promoter methylation levels of these genes. The results indicated that phenanthrene exposure during gestation could disturb adipocytokine levels via epigenetic modification in adult offspring, and further influence glucose metabolism. These results might be helpful for understanding nonobesogenic pollutant-induced insulin resistance and preventing against diabetes without obesity.

Environmental pollutants are thought to be a risk factor for the prevalence of hepatic steatosis. Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous, and human exposure is inevitable. In the present study, phenanthrene (Phe) was used as a representative PAH to investigate the effects of in utero exposure to PAH on hepatic lipid metabolism and the toxicological mechanism involved. Pregnant mice (C57BL/6J) were orally administered Phe (0, 60, 600 and 6000 μg kg−1 body weight) once every 3 days with 6 doses in total. F1 female mice aged 125 days showed significantly elevated hepatic lipid levels in the liver. The protein expression of hepatic peroxisome proliferator-activated receptors (PPARβ and PPARγ) and retinoid X receptors (RXRs) was upregulated; the transcription of genes related to lipogenesis, such as srebp1 (encoding sterol regulatory element binding proteins), acca (acetyl-CoA carboxylase), fasn (fatty acid synthase) and pcsk9 (proprotein convertase subtilisin/kexin type 9), showed an upregulation, while the mRNA levels of the lipolysis gene lcat (encoding lecithin cholesterol acyl transferase) were downregulated. These results could be responsible for lipid accumulation. The promoter methylation levels of pparγ were reduced and were the lowest in the 600 μg kg−1 group, and the promoter methylation levels of lcat were significantly increased in all the Phe treatments. These changes were matched with the alterations in their mRNA levels, suggesting that prenatal Phe exposure could induce abnormal lipid metabolism in later life via epigenetic modification.

Improving the mechanical performance of nanocrystalline functional oxides can have major implications for stability and resilience of battery cathodes, development of reliable nuclear oxide fuels, strong and durable catalytic supports. By combining Monte Carlo simulations, experimental thermodynamics, and in-situ transmission electron microscopy, we demonstrate a novel toughening mechanism based on interplay between the thermo-chemistry of the grain boundaries and crack propagation. By using zirconia as a model material, lanthanum segregation to the grain boundaries was used to increase the toughness of individual boundaries and simultaneously promote a smoother energy landscape in which cracks experience multiple deflections through the grain boundary network, ultimately improving fracture toughness.

The asymmetric hydrogenation of biomass-derived molecules for the preparation of single enantiomer compounds is an effective method to reduce the rapid consumption of fossil resources. Porous organic frameworks (POFs) with pure organic surfaces may provide unusual confinement effects for organic substrates in chiral catalysis. Here, a series of POF catalysts are designed with chiral active centers decorated into sharply defined one-dimensional channels with diameters in the range of 1.2-2.9 nm. Due to the synergistic effect originating from the conjugated inner wall, the POF material (aperture size 2.4 nm) concentrates over 90% of aromatic species into the porous architecture, and its affinity is one or two orders of magnitude higher than those of classical porous solids. As determined by PBE+D3 calculation, the phenyl fragment reveals strong π-π interaction for steric hindrance around the metal active site to achieve stronger asymmetric induction. Therefore, this POF catalyst achieves high conversion (>99% yield) and enantioselectivity (>99% ee) for various substrates. The advantages of using the POF platform as a chiral catalyst can provide new perspectives on POF-based solid-state host-guest chemistry and asymmetric heterogeneous catalysis.

Carbon nanotubes (CNTs) are one of the strongest known materials. When assembled into fibres, however, their strength becomes impaired by defects, impurities, random orientations and discontinuous lengths. Fabricating CNT fibres with strength reaching that of a single CNT has been an enduring challenge. Here, we demonstrate the fabrication of CNT bundles (CNTBs) that are centimetres long with tensile strength over 80 GPa using ultralong defect-free CNTs. The tensile strength of CNTBs is controlled by the Daniels effect owing to the non-uniformity of the initial strains in the components. We propose a synchronous tightening and relaxing strategy to release these non-uniform initial strains. The fabricated CNTBs, consisting of a large number of components with parallel alignment, defect-free structures, continuous lengths and uniform initial strains, exhibit a tensile strength of 80 GPa (corresponding to an engineering tensile strength of 43 GPa), which is far higher than that of any other strong fibre.

© 2018 the Owner Societies. The effect of La3+doping on the structure and ionic conductivity change in nanocrystalline yttria-stabilized zirconia (YSZ) was studied using a combination of Monte Carlo and molecular dynamics simulations. The simulation revealed the segregation of La3+at eight tilt grain boundary (GB) structures and predicted an average grain boundary (GB) energy decrease of 0.25 J m-2, which is close to the experimental values reported in the literature. Cation stabilization was found to be the main reason for the GB energy decrease, and energy fluctuations near the grain boundary are smoothed out with La3+segregation. Both dynamic and energetic analysis on the Σ13(510)/[001] GB structure revealed La3+doping hinders O2-diffusion in the GB region, where the diffusion coefficient monotonically decreases with increasing La3+doping concentration. The effect was attributed to the increase in the site-dependent migration barriers for O2-hopping caused by segregated La3+, which also leads to anisotropic diffusion at the GB.

Epigallocatechin-3-gallate (EGCG), which is a major polyphenol in tea, has an unclear effect on cardiac development. In the present study, mice (C57BL/6) were exposed in utero to EGCG dissolved in drinking water (3 μg/ml) for 16 days. A significant decrease in the heart/body weight ratio was observed in adult males but not in adult females. The protein expression levels of TGF-β1 and its downstream transcription factors SMAD3 and SMAD4 were significantly decreased in male hearts. The PI3K/AKT signaling pathway was inhibited, the expression of proapoptotic proteins, such as BAX, Cleaved Caspase3 and Cleaved Caspase9, was elevated, and the level of antiapoptotic proteins, such as BCL-2, was decreased. A reduced heart/body weight ratio may be associated with the loss of cardiac fibers and an increase in myocardial apoptosis. The cardiac levels of aromatic hydrocarbon receptor and androgen receptor were elevated only in males, which may explain the sexual dimorphism in the effects. The promoter methylation levels of pik3r1, tgf-β, smad4 were elevated, and those of ahr were reduced, explaining the mechanism underlying the cardiac histological alteration caused by prenatal exposure to EGCG. The results suggest that ingestion of EGCG during pregnancy may be a risk factor for cardiac development in offspring.

Phenanthrene (Phe) is a tricyclic polycyclic aromatic hydrocarbon with high bioavailability under natural exposure. However, there are few studies on the reproductive toxicity of Phe in mammals. In this study, male Kunming mice were gavaged once every two days with Phe (5, 50, and 500 ng/kg) for 28 weeks. The accumulation levels of Phe in the testis were dose-dependently increased. Histopathological staining showed that Phe exposure reduced the number of spermatogonia, sperm and Sertoli cells. The percentage of testicular apoptotic cells was significantly increased, which was further verified by the upregulated BAX protein. The expression of the GDNF/PI3K/AKT signaling pathway was downregulated, which might suppress the self-renewal and differentiation of spermatogonial stem cells. Meanwhile, Phe exposure inhibited the expression of Sertoli cell markers (Fshr, WT1, Sox9) and the Leydig cell marker Cyp11a1, indicating damage to the function of Sertoli cells and Leydig cells. Serum estrogen and testicular estrogen receptor alpha were significantly upregulated, while androgen receptor expression was downregulated. These alterations might be responsible for impaired spermatogenesis. This study provides new insights for evaluating the reproductive toxicity and potential mechanisms of Phe in mammals.

Core/shell structured composites of hollow spherical CoFe2O4 and CNTs were in situ synthesized using a CVD method with ethanol as a carbon source. CoFe2O4 hollow spheres were used as cores, catalysts and magnetic ingredients simultaneously. It was found that the shell of CNTs uniformly grew on the surface of CoFe2O4 hollow sphere cores. The reflection loss reached −32.8 dB at 11.7 GHz for the core/shell composites with a thickness of 2 mm.

Purpose: A comprehensive molecular analysis was conducted to identify prognostic and predictive markers for adjuvant S-1 chemotherapy in stage II/III Japanese gastric cancer (GC) patients and to evaluate their potential suitability for alternative cytotoxic or targeted drugs. Experimental Design: We investigated genetic polymorphisms of enzymes potentially involved in 5-fluoruracil (5-FU) metabolism as well as platinum resistance, previously identified genomic subtypes potentially predicting 5-FU benefit, and mRNA expression levels of receptor tyrosine kinases and KRAS as potential treatment targets in a single institution cohort of 252 stage II/III GC patients treated with or without S-1 after D2 gastrectomy. Results: 88% and 62% GC had a potentially 5-FU sensitive phenotype by SNP analyses of TS 3'UTR, and TS 5'UTR, respectively. 24%, 46%, 40%, 5%, and 44% GC had a potentially platinum sensitive phenotype by SNP analyses of GSTP1, ERCC1 rs11615, ERCC1 rs3212986, ERCC2, and XRCC1, respectively. High HER2, EGFR, FGFR2, or MET mRNA expression was observed in 49%, 66%, 72%, and 54% GC, respectively. High HER2 expression was the only significant prognosticator (HR=3.912, 95%CI: 1.706-8.973, p=0.0005). High HER2 (p=0.031), low EGFR (p=0.124), high MET (p=0.165) RNA expression, and TS 5'UTR subtype 2R/2R, 2R/3C, or 3C (p=0.058) were significant independent predictors for S-1 resistance. Conclusions: The present study suggests that platinum-based or RTK targeted agents could be alternative treatment options for a substantial subgroup of Japanese GC patients currently treated with S-1. HER2, EGFR, MET, and TS 5'UTR SNP appear to be promising predictive markers for S-1 resistance warranting validation in an independent GC series.

The atomic layer etching of chlorinated germanium surfaces under argon bombardment was simulated using molecular dynamics with a newly fitted Tersoff potential. The chlorination energy determines the threshold energy for etching and the number of etched atoms in the bombardment phase. Etch rate is determined by bombardment energy.

Purpose: A comprehensive molecular analysis was conducted to identify prognostic and predictive markers for adjuvant S-1 chemotherapy in stage II/III Japanese gastric cancer (GC) patients and to evaluate their potential suitability for alternative cytotoxic or targeted drugs.Experimental Design: We investigated genetic polymorphisms of enzymes potentially involved in 5-fluoruracil (5-FU) metabolism as well as platinum resistance, previously identified genomic subtypes potentially predicting 5-FU benefit, and mRNA expression levels of receptor tyrosine kinases and KRAS as potential treatment targets in a single institution cohort of 252 stage II/III GC patients treated with or without S-1 after D2 gastrectomy.Results: 88% and 62% GC had a potentially 5-FU sensitive phenotype by SNP analyses of TS 3'UTR, and TS 5'UTR, respectively. 24%, 46%, 40%, 5%, and 44% GC had a potentially platinum sensitive phenotype by SNP analyses of GSTP1, ERCC1 rs11615, ERCC1 rs3212986, ERCC2, and XRCC1, respectively. High HER2, EGFR, FGFR2, or MET mRNA expression was observed in 49%, 66%, 72%, and 54% GC, respectively. High HER2 expression was the only significant prognosticator (HR=3.912, 95%CI: 1.706-8.973, p=0.0005). High HER2 (p=0.031), low EGFR (p=0.124), high MET (p=0.165) RNA expression, and TS 5'UTR subtype 2R/2R, 2R/3C, or 3C (p=0.058) were significant independent predictors for S-1 resistance.Conclusions: The present study suggests that platinum-based or RTK targeted agents could be alternative treatment options for a substantial subgroup of Japanese GC patients currently treated with S-1. HER2, EGFR, MET, and TS 5'UTR SNP appear to be promising predictive markers for S-1 resistance warranting validation in an independent GC series.

Transcriptional reactivation of telomerase catalytic subunit (TERT) is a frequent hallmark of cancer, occurring in 90% of human malignancies. However, specific mechanisms driving TERT reactivation remain obscure for many tumor types and in particular gastric cancer (GC), a leading cause of global cancer mortality. Here, through comprehensive genomic and epigenomic analysis of primary GCs and GC cell lines, we identified the transcription factor early B cell factor 1 (EBF1) as a TERT transcriptional repressor and inactivation of EBF1 function as a major cause of TERT upregulation. Abolishment of EBF1 function occurs through 3 distinct (epi)genomic mechanisms. First, EBF1 is epigenetically silenced via DNA methyltransferase, polycomb-repressive complex 2 (PRC2), and histone deacetylase activity in GCs. Second, recurrent, somatic, and heterozygous EBF1 DNA-binding domain mutations result in the production of dominant-negative EBF1 isoforms. Third, more rarely, genomic deletions and rearrangements proximal to the TERT promoter remobilize or abolish EBF1-binding sites, derepressing TERT and leading to high TERT expression. EBF1 is also functionally required for various malignant phenotypes in vitro and in vivo, highlighting its importance for GC development. These results indicate that multimodal genomic and epigenomic alterations underpin TERT reactivation in GC, converging on transcriptional repressors such as EBF1.