The shear-accelerated II-I phase transition of isotactic poly(1-butene)

The II-I phase transition of isotactic poly(1-butene) (iPBu) leads to improved mechanical performance. However, this will take several weeks and increase storage and processing costs. In this work, shear forces were introduced into the supercooled iPBu melt, and the effects of isothermal crystallization temperature (Tc) and shear temperature (Tshear) on crystallization and phase transition were explored. Shear-induced transcrystalline morphology of Form II with a significantly shortened crystallization induction period can be observed at relatively high Tc (105 °C). Besides, the shear-induced Form II can transit to Form I faster than the unsheared one. In addition, the phase transition rate increases as the Tshear decreases, with the fastest rate occurring at Tshear of 120 °C. The half transition time (t1/2) is measured as 6.3 hours, much shorter than the 20.7 hours required for unsheared samples. The accelerated phase transition of iPBu can be attributed to the stretching of molecular chains resulting from shear treatment. This study provides a quantitative analysis of the influence of the shear treatment and the Tshear on the II-I phase transition rate. And it also presents a cost-effective and straightforward approach for expediting the phase transition process. This article is protected by copyright. All rights reserved.

Fish skin mucosal surface becomes a barrier of antibiotic resistance genes under apramycin exposure

Antibiotic resistance genes (ARGs) are a kind of emerging environmental contamination, and are commonly found in antibiotic application situations, attracting wide attention. Fish skin mucosal surface (SMS), as the contact interface between fish and water, is the first line of defense against external pollutant invasion. Antibiotics are widely used in aquaculture, and SMS may be exposed to antibiotics. However, what happens to SMS when antibiotics are applied, and whether ARGs are enriched in SMS are not clear. In this study, Zebrafish (Danio rerio) were exposed to antibiotic and antibiotic resistant bacteria in the laboratory to simulate the aquaculture situation, and the effects of SMS on the spread of ARGs were explored. The results showed that SMS maintained the stability of the bacterial abundance and diversity under apramycin (APR) and bacterial exposure effectively. Until 11 days after stopping APR exposure, the abundance of ARGs in SMS (mean value was 3.32×10-3 copies/16S rRNA copies) still did not recover to the initial stage before exposure, which means that enriched ARGs in SMS were persistently remained. Moreover, non-specific immunity played an important role in resisting infection of external contamination. Besides, among antioxidant proteins, superoxide dismutase showed the highest activity. Consequently, it showed that SMS became a barrier of antibiotic resistance genes under APR exposure, and ARGs in SMS were difficult to remove once colonized. This study provided a reference for understanding the transmission, enrichment process, and ecological impact of antibiotics and ARGs in aquatic environments.

Protective effect of resveratrol on nickel-refining fumes-induced inflammatory damage

Nickel (Ni), a ductile and hard silver-white transition metal, is commonly found in occupational environments and can harm the human body. Since it is a toxic compound, long-term Ni exposure can cause pneumonia, rhinitis, and other types of respiratory inflammatory diseases. Resveratrol (Res) is a plant antitoxin polyphenol, which also has anti-cancer and anti-inflammatory properties. In this report, the toxicity of Ni-refining fumes on the human lung bronchial epithelial (BEAS-2B) cells, as well as the protective effects of Res were investigated in vitro, and the specific mechanism of its anti-inflammatory effect was explained. The experimental observations of this study revealed that Ni-refining fumes induce BEAS-2B cell damage, increase reactive oxygen species (ROS) content, activate NLRP3 (LRR-, NOD-, and pyrin domain-containing 3) inflammasome, and promote the secretion of the cytokine Interleukin (IL)-1β, leading to cellular inflammation and reducing cell activity. Resveratrol (20 μmol/L) activated sirtuin 1 (SIRT1) in BEAS-2B cells to increase protein and mRNA expression. SIRT1 was observed to inhibit the transcriptional activity of nuclear factor-kappaB (NF-κB), reduced the expression of NLRP3 protein and mRNA, and inhibited NLRP3 inflammation. The level of inflammasome activation and IL-1β overexpression could reduce the inflammatory damage caused by the Ni-refining fume particles on the BEAS-2B cells and exert anti-inflammatory protective effects. In vivo experiments further confirmed that resveratrol could effectively alleviate the acute inflammatory injuries caused due to exposure to the Ni-refining fume particles in the lung tissues of the Wistar rats, and verified that resveratrol could exert its anti-inflammatory impact through the SIRT1-NF-κB-NLRP3 pathway. These results provide an important theoretical basis for developing novel protective drugs and investigating the mechanism of action for inflammatory injury in occupational populations caused by exposure to nickel and other heavy metals.

Morules and β-catenin predict POLE mutation status in endometrial cancer: A pathway to more cost-effective diagnostic procedures

OBJECTIVES

The characterization of DNA polymerase epsilon (POLE) mutations has transformed the classification of endometrial endometrioid carcinomas (EECs), highlighting the need for efficient identification methods. This study aims to examine the relationship between distinct morphologic features-namely, squamous morules and squamous differentiation (SD), as well as β-catenin expression-and the POLE mutation status in endometrial cancer (EC).

METHODS

Our study included 35 POLE-mutated (POLEmut) EC cases and 395 non-POLEmut EEC cases.

RESULTS

Notably, we observed no presence of morules in POLEmut cases, while SD was identified in 20% of instances. Conversely, morules and SD were identified in 12.7% and 26.1% of non-POLEmut EC cases, respectively, with morules consistently linked to a POLE wild-type status. The nuclear β-catenin expression is typically absent in tumors with wild-type POLE (wt-POLE) status.

CONCLUSIONS

Our findings suggest that the presence of either morules or nuclear β-catenin expression in EEC could practically rule out the presence of POLE mutations. These morphologic and immunohistochemical features can be used as preliminary screening tools for POLE mutations, offering significant savings in time and resources and potentially enhancing clinical decision-making and patient management strategies. However, further validation in larger, multi-institutional studies is required to fully understand the implications of these findings on clinical practice.

Correction: Cyanobacterial extracellular antibacterial substances could promote the spread of antibiotic resistance: impacts and reasons

Correction for 'Cyanobacterial extracellular antibacterial substances could promote the spread of antibiotic resistance: impacts and reasons' by Rui Xin et al., Environ. Sci.: Processes Impacts, 2023, 25, 2139-2147, https://doi.org/10.1039/D3EM00306J.

Occurrence characteristics and influencing factors of antibiotic resistance genes in rural groundwater in Henan Province

This study determined the antibiotic-resistant gene (ARG) contents of 34 groundwater samples in Henan Province collected from September to October 2022, then assessed the roles of both water quality parameters and intI1 in ARG propagation in groundwater. The results show that there existed universal ARG pollution in groundwater, and sulfonamides-, β-lactem-, and tetracycline-resistance genes were the most prevalent gene types during the time. Sul1 contributed the majority proportion of the total resistance genes (TARGs). The prevalence of ESBLs gene blaTEM and the occurrence of Carbapenems resistant gene blaOXA-1 suggests the pollution of high-risk ARGs in groundwater demands more attention. IntI1 is prevalent and had a significantly positive correlation with almost 50% ARGs, indicating its contribution to ARG propagation in groundwater. Well types contribute little to ARG propagation in rural groundwater of Henan, which means the protective facilities established by the local government for public wells can effectively prevent contamination from exogenous ARGs. However, the economic level has no impact on the abundance of ARGs in rural groundwater, which suggests the local government should pay greater attention to investment in controlling ARG pollution in Henan rural areas.

Exploring the potential of a new marine bacterium associated with plastisphere to metabolize dibutyl phthalate and bis(2-ethylhexyl) phthalate by enrichment cultures combined with multi-omics analysis

Phthalic acid esters (PAEs) plasticizers are virulent endocrine disruptors that are mixed into plastics while fabricating and can filter out once they release into the surrounding environments. Plastic surfaces serve as new habitats for microorganisms, referred to as 'plastisphere'. Previous metagenomic investigations of the 'plastisphere' indicated that marine plastic surfaces may harbor microbes that degrade PAEs plasticizers. To our knowledge, the potential of microorganisms in the marine 'plastisphere' to metabolize PAEs is poorly understood. In this study, by screening the natural microbial community on plastic debris that had been deployed in situ for up to 20 months, a novel marine bacterium, Microbacterium esteraromaticum DEHP-1, was successfully isolated, which could degrade and mineralize 10-200 mg/L dibutyl phthalate (DBP) and bis(2-ethylhexyl) phthalate (DEHP). According to the results of gas chromatography-mass spectrometry (GC-MS) and whole genome mining of strain DEHP-1, we found that strain DEHP-1 may metabolize DBP by successive removal of the ester side chain by esterase 2518 to produce mono-butyl phthalate (MBP) and phthalic acid (PA), whereas the degradation of DEHP may take place by the direct action of monooxygenase 0132 on the fatty acid side chain of the DEHP molecule to produce di-n-hexyl phthalate (DnHP) and DBP, and then the subsequent hydrolysis of DBP by de-esterification to PA and finally into the tricarboxylic acid (TCA) cycle. Non-targeted metabolomics results showed that intracellular degradation of PAEs did not happen. However, exposure to PAEs was found to significantly affect pathways such as arginine and proline, riboflavin, glutathione and lysine degradation. Therefore, the intracellular metabolic behavior of strain DEHP-1 exposed to PAEs was proposed for the first time. This study sheds light on the metabolic capacity and strategies of bacteria in the marine 'plastisphere' to effectively degrade PAEs and highlights the importance of marine microbes in mitigating plastic poisonousness.

Investigation of the antimicrobial susceptibility patterns of marine cyanobacteria in Bohai Bay: Cyanobacteria may be important hosts of antibiotic resistance genes in marine environment

Marine cyanobacteria, as widely distributed and photosynthetically autotrophic bacteria in the ocean, may contribute to the global dissemination of antibiotic resistance genes (ARGs) and develop a different antimicrobial susceptibility pattern from heterotrophic bacteria and cyanobacteria from freshwater environments. However, studies on antimicrobial susceptibility and the carriage of ARGs in marine cyanobacteria are still very limited. In this study, the antibiotic resistance characteristics of cyanobacteria in nearshore waters were examined through field monitoring and laboratory investigations, which included PCR detection and ARG transformation. The results showed a positive correlation between marine cyanobacteria and some ARGs in the nearshore waters of Bohai Bay. Moreover, most screened cyanobacteria showed high minimum inhibitory concentration (MIC) values for polymyxins, tetracyclines, kanamycin, and sulfonamides, moderate MIC values for streptomycin, chloramphenicol, rifampicin, and norfloxacin, and low MIC values for roxithromycin and cephalosporins. The blaTEM, blaKPC, sul1, sul2, strA, tetA, tetB, tetC, tetM, mdfA, and intI1 genes were detected in the screened marine cyanobacteria. The highest detection rates were observed for blaTEM (93.3 %), sul1 (56.6 %), sul2 (90 %), and strA (73.3 %). The detection rate of tetA (33.3 %) was the highest among the tetracycline resistance genes, and mdfA, a multidrug-resistant pump gene with resistance to tetracycline, also showed a high detection level (23.3 %). Overall, most of the screened marine cyanobacteria were found to tolerate multiple antibiotics in seawater, and the condition of the ARGs carriage was serious. Furthermore, the screened marine Synechocystis sp. C12-2 demonstrated the ability to accept ARGs on the RP4 plasmid through natural transformation and showed reduced sensitivity to ampicillin, suggesting the possibility that some marine cyanobacteria could acquire ARGs from the environment through horizontal gene transfer. Thus, marine cyanobacteria may play an important role in the propagation of marine ARGs.

Epitaxy-Directed Self-Assembly of Copolymers and Polymer Blends

Directed self-assembly of materials into patterned structures is of great importance since the performance of them depends remarkably on their multiscale hierarchical structures. Therefore, purposeful structural regulation at different length scales through crystallization engineering provides an opportunity to modify the properties of polymeric materials. Here, an epitaxy-directed self-assembly strategy for regulating the pattern structures including phase structure as well as crystal modification and orientation of each component for both copolymers and polymer blends is reported. Owing to the specific crystallography registration between the depositing crystalline polymers and the underlying crystalline substrate, not only order phase structure with controlled size at nanometer scale but also the crystal structure and chain orientation of each component within the separated phases for both copolymers and polymer blend systems can be precisely regulated.

Tracking the extracellular and intracellular antibiotic resistance genes across whole year in wastewater of intensive dairy farm

Monitoring the annual variation of antibiotic resistance genes (ARGs) in livestock wastewater is important for determining the high-risk period of transfer and spread of animal-derived antibiotic resistance into the environment. However, the knowledge regarding the variation patterns of ARGs, especially intracellular ARGs (iARGs) and extracellular ARGs (eARGs), over time in livestock wastewater is still unclear. Herein, we conducted a year-round study to trace the profiles of ARGs at a Chinese-intensive dairy farm, focusing on the shifts observed in different months. The results showed significant differences in the composition and variation between iARGs and eARGs. Tetracycline, sulfonamide, and macrolide resistance genes were the major types of iARGs, while cfr was the major type of eARG. The environmental adaptations of the host bacteria determine whether ARGs appear as intracellular or extracellular forms. The total abundance of ARGs was higher from April to September, which can be attributed to the favorable climatic conditions for bacterial colonization and increased antibiotic administration during this period. Integron was found to be highly correlated with most iARGs, potentially playing a role in the presence of these genes within cells and their similar transmission patterns in wastewater. The intracellular and extracellular bacterial communities were significantly different, primarily because of variations in bacterial adaptability to the high salt and anaerobic environment. The intracellular co-occurrence network indicated that some dominant genera in wastewater, such as Turicibacter, Clostridium IV, Cloacibacillus, Subdivision5_genera_incertae_sedis, Saccharibacteria_genera_incertae_sedis and Halomonas, were potential hosts for many ARGs. To the best of our knowledge, this study demonstrates, for the first time, the annual variation of ARGs at critical points in the reuse of dairy farm wastewater. It also offers valuable insights into the prevention and control of ARGs derived from animals.

Cyanobacterial extracellular antibacterial substances could promote the spread of antibiotic resistance: impacts and reasons

Many studies have shown that antibiotic resistance genes (ARGs) can be facilitated by a variety of antibacterial substances. Cyanobacteria are photosynthetic bacteria that are widely distributed in the ocean. Some extracellular substances produced by marine cyanobacteria have been found to possess antibacterial activity. However, the impact of these extracellular substances on ARGs is unclear. Therefore, we established groups of seawater microcosms that contained different concentrations (1000, 100, 10, 1, 0.1, 0.01, and 0 μg mL-1) of cyanobacterial extracellular substances (CES), and tracked the changes of 17 types of ARGs, the integron gene (intI1), as well as the bacterial community at different time points. The results showed that CES could enrich most ARGs (15/17) in the initial stage, particularly at low concentrations (10 and 100 μg mL-1). The correlation analysis showed a positive correlation between several ARGs and intI1. It is suggested that the abundance of intI1 increased with CES may contribute to the changes of these ARGs, and co-resistance of CES may be the underlying reason for the similar variation pattern of some ARGs. Moreover, the results of qPCR and high-throughput sequencing of 16S rRNA showed that CES had an inhibitory impact on the growth of bacterial communities. High concentrations of CES were found to alter the structure of bacterial communities. Co-occurrence networks showed that bacteria elevated in the high concentration group of CES and might serve as the potential hosts for a variety of ARGs. In general, marine cyanobacteria could play an important role in the global dissemination of ARGs and antibiotic-resistant bacteria (ARBs).

Current Progress and Challenges in Large-Scale 3D Mitochondria Instance Segmentation

In this paper, we present the results of the MitoEM challenge on mitochondria 3D instance segmentation from electron microscopy images, organized in conjunction with the IEEE-ISBI 2021 conference. Our benchmark dataset consists of two large-scale 3D volumes, one from human and one from rat cortex tissue, which are 1,986 times larger than previously used datasets. At the time of paper submission, 257 participants had registered for the challenge, 14 teams had submitted their results, and six teams participated in the challenge workshop. Here, we present eight top-performing approaches from the challenge participants, along with our own baseline strategies. Posterior to the challenge, annotation errors in the ground truth were corrected without altering the final ranking. Additionally, we present a retrospective evaluation of the scoring system which revealed that: 1) challenge metric was permissive with the false positive predictions; and 2) size-based grouping of instances did not correctly categorize mitochondria of interest. Thus, we propose a new scoring system that better reflects the correctness of the segmentation results. Although several of the top methods are compared favorably to our own baselines, substantial errors remain unsolved for mitochondria with challenging morphologies. Thus, the challenge remains open for submission and automatic evaluation, with all volumes available for download.

Identification and validation of functional roles for three MYC-associated genes in hepatocellular carcinoma

BACKGROUND

Aberrations in MYC underlie a large proportion of liver hepatocellular carcinoma (LIHC) cases; however, MYC is difficult to target because of its undruggable structure. We aimed to uncover MYC-associated molecular targets to provide new strategies for LIHC treatment.

METHODS

LIHC transcriptome datasets and clinical information were obtained from The Cancer Genome Atlas. A series of bioinformatics analyses were performed for 370 patients who were stratified based on the median MYC expression level (high-MYC group and low-MYC group). Correlation analysis was performed to determine relationships between the expression of key MYC-associated genes and prognosis, DNA promotor methylation, and immune cell infiltration. Gene ontology and Kyoto Encyclopedia of Genes and Genomes Pathway enrichment analyses were performed to elucidate the functions of these genes in LIHC. Their expression and functions in LIHC were further verified using transgenic mice overexpressing c-Myc under control of the hepatocyte-specific promoter (Alb-Cre).

RESULTS

AURKB, CCNB2, and CDKN3 were overexpressed in LIHC patients with high MYC expression and were associated with poor prognosis. Upregulation of these 3 genes was significantly correlated with hypomethylated promoter status, advanced T stage, metastasis, and immune cell infiltration in LIHC patients. Functional enrichment analyses indicated that these genes participate in the "p53 signaling pathway" and "cell cycle". Furthermore, RT-PCR and IHC analysis revealed that their mRNA and protein expression levels were upregulated in an Alb-Cre;cMYClsl/- mouse model. Drugs that target these 3 MYC-related genes were identified.

CONCLUSION

Taken together, our results identify biomarkers of potential utility for managing liver cancer therapy owing to their significance in tumorigenesis, proliferation, and tumor immunity.

Co(II)-Based Metal-Organic Framework Derived CA-CoNiMn-CLDHs with Peroxidase-like Activity for Colorimetric Detection of Phenol

Given the serious harm of toxic phenol to human health and the ecological environment, it is urgent to develop an efficient, low-cost and sensitive nanoenzyme-based method to monitor phenol. MOF-derived nanozyme has attracted wide interest due to its hollow polyhedra structure and porous micro-nano frameworks. However, it is still a great challenge to synthesize MOF-derived multimetal synergistic catalytic nanoenzymes in large quantities with low cost. Herein, we reported the synthetic strategy of porous hollow CA-CoNiMn-CLDHs with ZIF-67 as templates through a facile solvothermal reaction. The prepared trimetallic catalyst exhibits excellent peroxidase-like activity to trigger the oxidative coupling reaction of 4-AAP and phenol in the presence of H2O2. The visual detection platform for phenol based on CA-CoNiMn-CLDHs is constructed, and satisfactory results are obtained. The Km value for CA-CoNiMn-CLDHs (0.21 mM) is lower than that of HRP (0.43 mM) with TMB as the chromogenic substrate. Because of the synergistic effect of peroxidase-like activity and citric acid functionalization, the built colorimetric sensor displayed a good linear response to phenol from 1 to 100 μM with a detection limit of 0.163 μM (3σ/slope). Additionally, the CA-CoNiMn-CLDHs-based visual detection platform possesses high-chemical stability and excellent reusability, which can greatly improve economic benefits in practical applications.

Optimal Sparse Regression Trees

Regression trees are one of the oldest forms of AI models, and their predictions can be made without a calculator, which makes them broadly useful, particularly for high-stakes applications. Within the large literature on regression trees, there has been little effort towards full provable optimization, mainly due to the computational hardness of the problem. This work proposes a dynamic-programming-with-bounds approach to the construction of provably-optimal sparse regression trees. We leverage a novel lower bound based on an optimal solution to the k-Means clustering algorithm on one dimensional data. We are often able to find optimal sparse trees in seconds, even for challenging datasets that involve large numbers of samples and highly-correlated features.

Strain-induced 3D-oriented crystallites in natural rubber/chitin nanofiber composites

Natural rubber (NR) composites containing bio-based chitin nanofibers (ChNFs) exhibit a wide range of mechanical properties - from rubber to plastic behavior - with increasing chitin contents. A constrained 3-dimensional network can be formed by mixing natural rubber latex and a modified zwitterionic rigid chitin counterpart. By inclusion of highly anisotropic chitin nanofibers (30 wt%), strain-induced NR crystallization occurs at a much lower strain of 50%. More intriguingly, 2D-WAXD results reveal that the strain-induced crystallization of NR/ChNFs composites show 3-dimensionally oriented crystallite formation behaving similar to "3D-single crystals orientation" when the content of ChNFs is over 5 wt%. It is suggested that not only c-axis (NR chains) orients along the stretching direction, but also the a- and b-axes deliberately arrange along the normal direction and transverse direction, respectively. Structure and morphology in 3-dimensional spaces after strain-induced crystallization of the NR/ChNFs30 composite are investigated in detail. Therefore, this study might pave a new way to enhance mechanical properties by incorporation of ChNFs, obtaining 3-dimensionally oriented crystallites of novel multifunctional NR/ChNFs composite with shape memory ability.

Sm-Doped PIN-PMN-PT Transparent Ceramics with High Curie Temperature, Good Piezoelectricity, and Excellent Electro-Optical Properties

Transparent piezoelectric materials are capable of coupling several physical effects such as optics, acoustics, electricity, and mechanical deformation together, which expands applications for mechanical-electro-optical multifunctional devices. However, piezoelectricity, transparency, and Curie temperature restrict each other, so it is difficult to achieve high piezoelectricity with both good transparency and a high Curie point. In this paper, Sm-doped 24Pb(In_1/2Nb_1/2)O₃-42Pb(Mg_1/3Nb_2/3)O₃-34PbTiO₃ (PIN-PMN-PT) transparent ceramic with a high piezoelectric coefficient of 905 pC/N, excellent electro-optical coefficient of 814 pm/V, and high Curie-point of 179 °C is fabricated. Sm doping effect on the phase structures, piezoelectricity, ferroelectricity, optical transparency, electro-optical properties, and thermal stability is systematically investigated. Compared with PMN-PT transparent ceramics, PIN-PMN-PT transparent ceramics exhibit better temperature stability. Electro-optical modulation and energy conversion are achieved using PIN-PMN-PT transparent piezoelectric ceramic, which indicates that it has great potential to develop mechanical-electrical-optical multifunctional coupling devices for optical communication, energy harvesting, photoacoustic imaging, and so on.

Oncogenic lncRNA MALAT-1 recruits E2F1 to upregulate RAD51 expression and thus promotes cell autophagy and tumor growth in non-small cell lung cancer

INTRODUCTION

LncRNA MALAT-1 expression is involved in regulating activities of non-small-cell lung cancer (NSCLC) cells. This study aimed to investigate the effects of lncRNA MALAT-1 on chemosensitivity of NSCLC cells by regulating autophagy.

METHODS

We first validated the expression of lncRNA MALAT-1 in NSCLC cell lines. NSCLC cell lines with high lncRNA MALAT-1 expression were exposed to doxorubicin (DOX) to assess chemosensitivity. Further LncMAP database retrieval and ChIP, RIP and luciferase activity assays were conducted to explore interplay between lncRNA MALAT-1, RAD51, and E2F1. Immunofluorescence staining was performed to evaluate formation of autophagosomes in NSCLC cells. Ectopic expression and knockdown methods were used for in vitro mechanism experiments and in vivo substantiation.

RESULTS

LncRNA MALAT-1 was overexpressed in NSCLC cells, and could promote NSCLC cell autophagy and inhibit its chemosensitivity. In vitro cell mechanism verification experiments showed that lncRNA MALAT-1 could recruit transcription factor E2F1 to bind to the promoter of RAD51, so as to promote the transcriptional expression of RAD51. In addition, cell function experiments in vitro showed that ectopically expressed lncRNA MALAT-1 promoted NSCLC cell autophagy and inhibited its chemosensitivity, while RAD51 knockdown negated its effect. Finally, in vivo animal experiments confirmed that lncRNA MALAT-1 silencing could impede the tumor growth.

CONCLUSIONS

Taken together, this study revealed that silencing lncRNA MALAT-1 enhanced chemosensitivity of NSCLC cells by promoting autophagy, highlighting a feasible approach to prevent chemoresistance in NSCLC treatment.

Nomogram prediction model of postoperative pneumonia in patients with lung cancer: A retrospective cohort study

Background

The prediction model of postoperative pneumonia (POP) after lung cancer surgery is still scarce.

Methods

Retrospective analysis of patients with lung cancer who underwent surgery at The Fourth Hospital of Hebei Medical University from September 2019 to March 2020 was performed. All patients were randomly divided into two groups, training cohort and validation cohort at the ratio of 7:3. The nomogram was formulated based on the results of multivariable logistic regression analysis and clinically important factors associated with POP. Concordance index (C-index), receiver operating characteristic (ROC) curve, calibration curve, Hosmer-Lemeshow goodness-of-fit test and decision curve analysis (DCA) were used to evaluate the predictive performance of the nomogram.

Results

A total of 1252 patients with lung cancer was enrolled, including 877 cases in the training cohort and 375 cases in the validation cohort. POP was found in 201 of 877 patients (22.9%) and 89 of 375 patients (23.7%) in the training and validation cohorts, respectively. The model consisted of six variables, including smoking, diabetes mellitus, history of preoperative chemotherapy, thoracotomy, ASA grade and surgery time. The C-index from AUC was 0.717 (95%CI:0.677-0.758) in the training cohort and 0.726 (95%CI:0.661-0.790) in the validation cohort. The calibration curves showed the model had good agreement. The result of DCA showed that the model had good clinical benefits.

Conclusion

This proposed nomogram could predict the risk of POP in patients with lung cancer surgery in advance, which can help clinician make reasonable preventive and treatment measures.

Research Progress in Elucidating the Mechanisms Underlying Resveratrol Action on Lung Cancer

Resveratrol has several functions, including protection of the heart and nervous system and exerts antidiabetic, anti-inflammatory, anti-aging, and antitumor effects. It is reported to impede the occurrence and development of tumors in cancer cell lines, animal models, and clinical studies. In vitro and in vivo experiments show that it exerts preventive or adjuvant therapeutic effects in pancreatic, colorectal, prostate, liver, and lung cancers. Mechanistic research reports show that resveratrol can induce tumor cell apoptosis and autophagy, inhibit cell cycle and angiogenesis, regulate nuclear factors and cyclooxygenase signal transduction pathways, and inhibit carcinogens' metabolic activation and alter tumor-related expression patterns; anti-oxidation affects tumor cell proliferation, metastasis, and apoptosis. However, the exact mechanism underlying its action remains unclear. This review highlights multiple aspects of the biological impacts and mechanisms underlying resveratrol action on the occurrence and development of lung cancer.

MATERIAL TRANSFORMERS: DEEP LEARNING LANGUAGE MODELS FOR GENERATIVE MATERIALS DESIGN

Pre-trained transformer language models on large unlabeled corpus have produced state-of-the-art results in natural language processing, organic molecule design, and protein sequence generation. However, no such models have been applied to learn the composition patterns for generative design of material compositions. Here we train a series of seven modern transformer models (GPT, GPT-2, GPT-Neo, GPT-J, BLMM, BART, and RoBERTa) for materials design using the expanded formulas of the ICSD, OQMD, and Materials Projects databases. Six different datasets with/out non-charge-neutral or balanced electronegativity samples are used to benchmark the generative design performances and uncover the biases of modern transformer models for the generative design of materials compositions. Our experiments show that the materials transformers based on causal language models can generate chemically valid materials compositions with as high as 97.54\% to be charge neutral and 91.40\% to be electronegativity balanced, which has more than six times higher enrichment compared to the baseline pseudo-random sampling algorithm. Our language models also demonstrate high generation novelty and their potential in new materials discovery is proved by their capability to recover the leave-out materials. We also find that the properties of the generated compositions can be tailored by training the models with selected training sets such as high-bandgap samples. Our experiments also show that different models each have their own preference in terms of the properties of the generated samples and their running time complexity varies a lot. We have applied our materials transformers to discover a set of new materials as validated using DFT calculations. All our trained materials transformer models and code can be accessed freely at \url{http://www.github.com/usccolumbia/MTransformer}.

Comprehensive analysis to identify a novel PTEN-associated ceRNA regulatory network as a prognostic biomarker for lung adenocarcinoma

Lung adenocarcinoma (LUAD) is one of the most prevalent forms of lung cancer. Competitive endogenous RNA (ceRNA) plays an important role in the pathogenesis of lung cancer. Phosphatase and tensin homolog (PTEN) is one of the most frequently deleted tumour suppressor genes in LUAD. The present study aimed to identify a novel PTEN-associated-ceRNA regulatory network and identify potential prognostic markers associated with LUAD. Transcriptome sequencing profiles of 533 patients with LUAD were obtained from TCGA database, and differentially expressed genes (DEGs) were screened in LUAD samples with PTEN high- (PTENhigh) and low- (PTENlow) expression. Eventually, an important PTEN-related marker was identified, namely, the LINC00460/miR-150-3p axis. Furthermore, the predicted target genes (EME1/HNRNPAB/PLAUR/SEMA3A) were closely related to overall survival and prognosis. The LINC00460/miR-150-3p axis was identified as a clinical prognostic factor through Cox regression analysis. Methylation analyses suggested that abnormal regulation of the predicted target genes might be caused by hypomethylation. Furthermore, immune infiltration analysis showed that the LINC00460/miR-150-3p axis could alter the levels of immune infiltration in the tumour immune microenvironment, and promote the clinical progression of LUAD. To specifically induce PTEN deletion in the lungs, we constructed an STP mouse model (SFTPC-rtTA/tetO-cre/Ptenflox/+). Quantitative PCR (qPCR) and immunohistochemical (IHC) analysis were used to detect predicted target genes. Therefore, we revealed that the PTEN-related LINC00460/miR-150-3p axis based on ceRNA mechanism plays an important role in the development of LUAD and provides a new direction and theoretical basis for its targeted therapy.

Impact of the COVID-19 pandemic on urban human mobility - A multiscale geospatial network analysis using New York bike-sharing data

The COVID-19 pandemic breaking out at the end of 2019 has seriously impacted urban human mobility and poses great challenges for traffic management and urban planning. An understanding of this influence from multiple perspectives is urgently needed. In this study, we propose a multiscale geospatial network framework for the analysis of bike-sharing data, aiming to provide a new perspective for the exploration of the pandemic impact on urban human mobility. More specifically, we organize the bike-sharing data into a network representation, and divide the network into a three-scale structure, ranging from the whole bike system at the macroscale, to the network community at the mesoscale and then to the bicycle station at the microscale. The spatiotemporal analysis of bike-sharing data at each scale is combined with visualization methods for an intuitive understanding of the patterns. We select New York City, one of the most seriously influenced city by the pandemic, as the study area, and used Citi Bike bike-sharing data from January to April in 2019 and 2020 in this area for the investigation. The analysis results show that with the development of the pandemic, the riding flow and its spatiotemporal distribution pattern changed significantly, which had a series of effects on the use and management of bikes in the city. These findings may provide useful references during the pandemic for various stakeholders, e.g., citizens for their travel planning, bike-sharing companies for bicycle dispatching and bicycle disinfection management, and governments for traffic management.

Stimulating the expression of sphingosine kinase 1 (SphK1) is beneficial to reduce acrylamide-induced nerve cell damage

Sphingosine kinase 1 (SphK1) is an important signaling molecule for cell proliferation and survival. However, the role of SphK1 in acrylamide (ACR)-induced nerve injury remains unclear. The purpose of this study was to investigate the role and potential mechanism of SphK1 in ACR-induced nerve injury. Liquid chromatography triple quadrupole tandem mass spectrometry (LC-MS/MS) and reverse transcription-quantitative PCR (RT-qPCR) were used to detect sphingosine 1-phosphate (S1P) content in serum and SphK1 content in whole blood from an occupational work group exposed to ACR compared to a non-exposed group. For in vitro experiments, SphK1 in human SH-SY5Y neuroblastoma cells was activated using SphK1-specific activator phorbol 12-myristate 13-acetate (PMA). Our research also utilized cell viability assays, flow cytometry, western blots, RT-qPCR and related protein detection to assess activity of the mitogen activated protein kinase (MAPK) signaling pathway. The results of the population study showed that the contents of SphK1 and S1P in the ACR-exposed occupational contact group were lower than in the non-exposed group. The results of in vitro experiments showed that expression of SphK1 decreased with the increase in ACR concentration. Activating SphK1 improved the survival rate of SH-SY5Y cells and decreased the apoptosis rate. Activating SphK1 in SH-SY5Y cells also regulated MAPK signaling, including enhancing the phosphorylation of extracellular signal-regulated protein kinases (ERK) and inhibiting the phosphorylation of c-Jun N-terminal kinase (JNK) and p38. These results suggest that activating SphK1 can protect against nerve cell damage caused by ACR.

Antibiotic resistomes in water supply reservoirs sediments of central China: main biotic drivers and distribution pattern

Water supply reservoirs form one of the critical drinking water resources. Their water quality directly affects human health. However, reservoir sediments have not received adequate attention in antibiotic resistance genes (ARGs) dissemination, though they reflect long-term ARGs contamination of water supply reservoirs. Moreover, the physicochemical parameters in water supply reservoir sediments are generally better than those in the other media. Thus, the main ARGs biotic drivers of the media would demonstrate their unique characteristics. In this study, sediment samples were collected from 10 water supply reservoirs in central China, and the antibiotic resistomes were determined with the metagenomic method. As revealed from the results, 174 ARGs (18 ARG types) were detected in the reservoir sediment. Besides, multidrug-, sulfonamide-, and vancomycin-ARGs were the dominant ARGs in the sediment samples. The macrolide-resistant Microcystis was prevalent (100% detection frequency with 0.35% average percentage) in reservoir sediments and posed potential risks to human health. Furthermore, the results of the Mantel test and VPA demonstrated that mobile genetic elements (MGEs) were the more essential biotic drivers in ARG contents of reservoir sediments rather than the bacteria community.

TCSP: a Template-Based Crystal Structure Prediction Algorithm for Materials Discovery

Fast and accurate crystal structure prediction (CSP) algorithms and web servers are highly desirable for the exploration and discovery of new materials out of the infinite chemical design space. However, currently, the computationally expensive first-principles calculation-based CSP algorithms are applicable to relatively small systems and are out of reach of most materials researchers. Several teams have used an element substitution approach for generating or predicting new structures, but usually in an ad hoc way. Here we develop a template-based crystal structure prediction (TCSP) algorithm and its companion web server, which makes this tool accessible to all materials researchers. Our algorithm uses elemental/chemical similarity and oxidation states to guide the selection of template structures and then rank them based on the substitution compatibility and can return multiple predictions with ranking scores in a few minutes. A benchmark study on the 98290 formulas of the Materials Project database using leave-one-out evaluation shows that our algorithm can achieve high accuracy (for 13145 target structures, TCSP predicted their structures with root-mean-square deviation < 0.1) for a large portion of the formulas. We have also used TCSP to discover new materials of the Ga-B-N system, showing its potential for high-throughput materials discovery. Our user-friendly web app TCSP can be accessed freely at www.materialsatlas.org/crystalstructure on our MaterialsAtlas.org web app platform.

Exploring the Whole Rashomon Set of Sparse Decision Trees

In any given machine learning problem, there might be many models that explain the data almost equally well. However, most learning algorithms return only one of these models, leaving practitioners with no practical way to explore alternative models that might have desirable properties beyond what could be expressed by a loss function. The Rashomon set is the set of these all almost-optimal models. Rashomon sets can be large in size and complicated in structure, particularly for highly nonlinear function classes that allow complex interaction terms, such as decision trees. We provide the first technique for completely enumerating the Rashomon set for sparse decision trees; in fact, our work provides the first complete enumeration of any Rashomon set for a non-trivial problem with a highly nonlinear discrete function class. This allows the user an unprecedented level of control over model choice among all models that are approximately equally good. We represent the Rashomon set in a specialized data structure that supports efficient querying and sampling. We show three applications of the Rashomon set: 1) it can be used to study variable importance for the set of almost-optimal trees (as opposed to a single tree), 2) the Rashomon set for accuracy enables enumeration of the Rashomon sets for balanced accuracy and F1-score, and 3) the Rashomon set for a full dataset can be used to produce Rashomon sets constructed with only subsets of the data set. Thus, we are able to examine Rashomon sets across problems with a new lens, enabling users to choose models rather than be at the mercy of an algorithm that produces only a single model.

[Seasonal Variation and Influencing Factor Analysis of Antibiotic Resistance Genes in Water Supply Reservoirs of Central China]

This study quantified an integron gene intI1 and 19 antibiotic resistance genes(ARGs) to identify the ARGs pollution characteristics in 11 drinking water reservoirs of central China. The results indicated that the ARGs abundance did not change significantly over time in the studied reservoir waterbodies. Tetracycline, sulfonamide, and β-lactam ARGs were dominant. The high abundance and detection rate of two sulfonamide ARGs(sul1 and sul2) suggested that they were the predominant ARGs. No polymyxin resistance genes(mcr-1) were detected, which indicated that the antibiotic restriction policy of China has achieved positive outcomes. Compared with that in other environmental media, the ARGs abundance in the reservoir environment was low. The correlation analysis showed relevance between the water quality indicators and the ARGs, which suggested that the water quality indexes can be used as ARGs pollution indicators in the reservoir environment. The abundance and detection rate of carbapenem ARGs were low owing to their dosage restriction and high degradability. Tetracycline ARGs were closely related to the other resistance gene types, which might have been due to horizontal gene transfer. Although the overall correlation between intI1 and ARGs was modest, it might be the main reason for the spread of several individual ARGs in the reservoir environment.

Downregulation of miR-23b by transcription factor c-Myc alleviates ischemic brain injury by upregulating Nrf2

Ischemic brain injury (IBI) is a common acute cerebral vessel disease that occurs secondary to blockage in arteries, mainly characterized by insufficient blood supply to the brain. The transcription factor c-Myc in IBI continues to be implicated in numerous studies. This study was conducted with emphasis placed on the underlying mechanism of c-Myc in IBI. Clinical samples were collected from IBI patients. Middle cerebral artery occlusion (MCAO) was induced in mice by inserting a suture from the external carotid artery to the anterior cerebral artery through the internal carotid artery to mechanically block the blood supply at the origin of the middle cerebral artery, and cortical neurons from mice were exposed to oxygen glucose deprivation (OGD) conditions for IBI model in vitro construction. RT-qPCR was performed to determine microRNA-23b (miR-23b) expression. TUNEL staining and Western blot analysis was conducted to detect apoptosis. The regulatory relationship was analyzed by dual-luciferase reporter gene assay. After loss- and gain-of-function assays, triphenyltetrazolium chloride staining was carried out to detect the area of cerebral infarction, after which the spatial memory in mice was evaluated with Morris water maze test. As per our findings, miR-23b was upregulated in the serum of IBI patients and OGD-treated murine primary neurons. Silencing of miR-23b resulted in reduced OGD-induced neuronal apoptosis. miR-23b inversely targeted nuclear factor erythroid 2-related factor 2 (Nrf2) and c-Myc negatively regulated miR-23b expression. Overexpression of c-Myc and inhibition of miR-23b led to reduced neurological scores of infarction area, neuronal apoptosis, shortened platform arrival time and significantly increased the time spent on the platform quadrant and the times of crossing the platform in vivo. Collectively, downregulated miR-23b by c-Myc might alleviate IBI by upregulating Nrf2.

The power and the promise of circRNAs for cancer precision medicine with functional diagnostics and prognostic prediction

Circular RNA (circRNA) is a large class of covalently closed circular RNA. As a member of competitive endogenous RNA (ceRNA), it participates in the regulation of circRNA-miRNA-mRNA network and plays an important role in the regulation of physiology and pathology. CircRNA is produced by the reverse splicing of exon, intron or both, forming exon or intron circRNA. Studies have shown that circRNA is a ubiquitous molecule, which exceeds the linear mRNA distributed in human cells. Because of its covalent closed-loop structure, circRNA is resistant to RNase R, which is more stable than linear mRNA; circRNA is highly conserved in different species. It was found that circRNA competitively adsorbs miRNA, as a miRNA sponge, to involve in the expression regulation of a variety of genes and plays an important role in tumor development, invasion, metastasis and other processes. These molecules offer new potential opportunities for therapeutic intervention and serve as biomarkers for diagnosis. In this paper, the origin, characteristics and functions of circRNA and its role in tumor development, invasion and metastasis, diagnosis and prognosis are reviewed.

Protein disulfide isomerase inhibits endoplasmic reticulum stress response and apoptosis via its oxidoreductase activity in colorectal cancer

Protein disulfide isomerase (PDI), a principal endoplasmic reticulum resident oxidoreductase chaperone, is known to play a role in malignancies. This study aims to explore the molecular mechanism by which PDI regulates endoplasmic reticulum stress and the apoptosis signaling pathway in colorectal cancer (CRC). We determined the expression of PDI in CRC tissues and adjacent normal tissues. Gain- and loss- of function assays were conducted to evaluate the effects of PDI on oxidative stress, endoplasmic reticulum stress, and apoptosis in CRC cells, as reflected by hydrogen peroxide (H₂O₂) level and the expression of related proteins. PDI protein expression was upregulated in CRC tissues. Small molecule inhibitor of PDI or PDI knockdown reduced CRC cell viability and induced apoptosis. Overexpression of wild-type PDI augmented the viability of CRC cells and inhibited endoplasmic reticulum stress response and apoptosis. Small molecule inhibitor of PDI or PDI knockdown increased intracellular H₂O₂ level and activated apoptosis signaling pathway, which could be reversed by wild-type PDI restoration. Moreover, the catalytic active site of C-terminal of PDI was found to be indispensable for the regulatory effects of PDI on H₂O₂ levels, apoptosis and cell viability in CRC cells. Collectively, PDI inhibits endoplasmic reticulum stress and apoptosis of CRC cells through its oxidoreductase activity, thereby promoting the malignancy of CRC.

A miR-212-3p/SLC6A1 Regulatory Sub-Network for the Prognosis of Hepatocellular Carcinoma

Introduction

Hepatocellular carcinoma (HCC) is a liver cancer with a poor prognosis. Owing to the complexity and limited pathogenic mechanism research on HCC, the molecular targeted therapy has been hindered.

Methods

In this study, we categorized transcriptome data into low-Myc and high-Myc expression groups in 365 HCC samples, screened the differentially expressed RNAs, including 441 DE-lncRNAs, 99 DE-miRNAs and 612 DE-mRNAs, constructed a lncRNA-miRNA-mRNA regulatory network, and selected a hub triple regulatory network through cytoHubba analysis. Through Gene ontology and KEGG pathway, a hub regulatory network was particularly enriched in the “Wnt signaling pathway” and “Cytochrome P450-arranged by substrate type” by Metascape. The prognostic genes in the hub regulatory network were evaluated by the RNA expression analysis, Kaplan–Meier (KM) survival analysis, and correlation analysis.

Results

The results showed that miR-212-3p/SLC6A1 axis was a potential prognostic model for HCC. Furthermore, IHC analysis showed down-regulated expression of SLC6A1 in HCC tissues and Alb-Cre;Myc mouse liver cancer tissues. The genetics and epigenetic analysis indicated that SLC6A1 expression was negatively correlated with DNA methylation. Immune infiltration analysis showed a negative relation between SLC6A1 and T cell exhaustion/monocyte in liver cancer tissues.

Conclusion

In summary, the study revealed that miR-212-3p/SLC6A1 axis could serve as a crucial therapeutic target for HCC.

Basic approaches, challenges and opportunities for the discovery of small molecule anti-tumor drugs

Chemotherapy is one of the main treatments for cancer, especially for advanced cancer patients. In the past decade, significant progress has been made with the research into the molecular mechanisms of cancer cells and the precision medicine. The treatment on cancer patients has gradually changed from cytotoxic chemotherapy to precise treatment strategy. Research into anticancer drugs has also changed from killing effects on all cells to targeting drugs for target genes. Besides, researchers have developed the understanding of the abnormal physiological function, related genomics, epigenetics, and proteomics of cancer cells with cancer genome sequencing, epigenetic research, and proteomic research. These technologies and related research have accelerated the development of related cancer drugs. In this review, we summarize the research progress of anticancer drugs, the current challenges, and future opportunities.

The power and the promise of organoid models for cancer precision medicine with next-generation functional diagnostics and pharmaceutical exploitation

As organ-specific three-dimensional cell clusters derived from cancer tissue or cancer-specific stem cells, cancer-derived organoids are organized in the same manner of the cell sorting and spatial lineage restriction in vivo, making them ideal for simulating the characteristics of cancer and the heterogeneity of cancer cells in vivo. Besides the applications as a new in vitro model to study the physiological characteristics of normal tissues and organs, organoids are also used for in vivo cancer cell characterization, anti-cancer drug screening, and precision medicine. However, organoid cultures are not without limitations, i.e., the lack of nerves, blood vessels, and immune cells. As a result, organoids could not fully replicate the characteristics of organs but partially simulate the disease process. This review attempts to provide insights into the organoid models for cancer precision medicine.

Construction of a Myc-associated ceRNA network reveals a prognostic signature in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) remains an extremely lethal disease worldwide. High-throughput methods have revealed global transcriptome dysregulation; however, a comprehensive investigation of the complexity and behavioral characteristics of the competing endogenous RNA (ceRNA) network in HCC is lacking. In this study, we extracted the transcriptome (RNA) sequencing data of 371 HCC patients from The Cancer Genome Atlas platform. With the comparison of the high Myc expression (Myc^high) tumor and low Myc expression (Myc^low) tumor groups in HCC, we identified 1,125 differentially expressed (DE) mRNAs, 589 long non-coding RNAs (lncRNAs), and 93 microRNAs (miRNAs). DE RNAs predicted the interactions necessary to construct an associated Myc ceRNA network, including 19 DE lncRNAs, 5 miRNAs, and 72 mRNAs. We identified a significant signature (long intergenic non-protein-coding [LINC] RNA 2691 [LINC02691] and LINC02499) that effectively predicted overall survival and had protective effects. The target genes of microRNA (miR)-212-3p predicted to intersect with DE mRNAs included SEC14-like protein 2 (SEC14L2) and solute carrier family 6 member 1 (SLC6A1), which were strongly correlated with survival and prognosis. With the use of the lncRNA-miRNA-mRNA axis, we constructed a ceRNA network containing four lncRNAs (LINC02691, LINC02499, LINC01354, and NAV2 antisense RNA 4), one miRNA (miR-212-3p), and two mRNAs (SEC14L2 and SLC6A1). Overall, we successfully constructed a mutually regulated ceRNA network and identified potential precision-targeted therapies and prognostic biomarkers.

microRNA-320b suppresses HNF4G and IGF2BP2 expression to inhibit angiogenesis and tumor growth of lung cancer

We examined the effect of microRNA-320b (miR-320b) on tumor growth and angiogenesis in lung cancer and also determined its downstream molecular mechanisms. Lung cancer tissues and adjacent non-cancerous tissues were collected from 66 patients with lung cancer. miR-320b expression was experimentally determined to be expressed at low level in cancer tissues. The results of gain-of-function experiments suggested that miR-320b overexpression suppressed cancer cell invasion, tube formation, tumor volume and angiogenesis in xenografted nude mice. Hepatocyte nuclear factor 4 gamma (HNF4G) was identified as a target of miR-320b based on in silico analysis. Dual-luciferase reporter gene assays further identified the binding relationship between HNF4G and miR-320b. Lung cancer tissues exhibited increased expression of HNF4G and insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2). Meanwhile, HNF4G knockdown suppressed IGF2BP2 expression, thereby repressing cancer cell invasion and tube formation. Furthermore, IGF2BP2 modified m6A to increase the expression of thymidine kinase 1 (TK1), thus promoting angiogenesis. In nude mice, restoration of TK1 reversed the suppressive effect of miR-320b overexpression on tumor growth rate and CD31 expression. In conclusion, miR-320b suppresses lung cancer growth and angiogenesis by inhibiting HNF4G, IGF2BP2 and TK1.

MicroRNA-499 serves as a sensitizer for lung cancer cells to radiotherapy by inhibition of CK2α-mediated phosphorylation of p65

The present study aimed to define the tumor-suppressive role of microRNA-499 (miR-499) in lung cancer cells and its underlying mechanism. First, qRT-PCR analysis revealed poor expression of miR-499 in clinical samples and cell lines of lung cancer. Next, we performed loss- and gain-of-function experiments for the expression of miR-499 in lung cancer cells exposed to irradiation (IR) to determine the effect of miR-499 expression on cell viability and apoptosis as well as tumor growth. Results showed that overexpression of miR-499 inhibited cell viability, enhanced the radiosensitivity of lung cancer cells, and promoted cell apoptosis under IR. Furthermore, CK2α was verified to be a target of miR-499, and miR-499 was identified to repress p65 phosphorylation by downregulating CK2α expression, which ultimately diminished the survival rate of lung cancer cells under IR. Collectively, the key findings of the study illustrate the tumor-inhibiting function of miR-499 and confirmed that miR-499-mediated CK2α inhibition and altered p65 phosphorylation enhances the sensitivity of lung cancer cells to IR.

Aberrantly DNA Methylated-Differentially Expressed Genes in Pancreatic Cancer Through an Integrated Bioinformatics Approach

Pancreatic cancer remains one of the chief contributors to cancer related deaths on a global scale, with its diagnosis often associated with poor prognosis and high mortality. Accumulating literature continues to highlight the role of aberrant DNA methylation in relation to pancreatic cancer progression. Integrated bioinformatics approaches in the characterization of methylated-differentially expressed genes (MeDEGs) in pancreatic cancer were employed to enhance our understanding of the potential underlying molecular mechanisms of this cancer. We initially identified differentially expressed genes (DEGs) between 178 pancreatic cancer samples and 4 normal samples and differentially methylated genes (DMGs) based on 185 pancreatic cancer samples as well as 10 normal samples by analyzing RNA sequencing data in the TCGA database. Eventually, 31 MeDEGs including 5 hypomethylated/upregulated genes and 26 hypermethylated/downregulated genes were identified. Univariate Cox model and Kaplan–Meier method revealed that, among 31 MeDEGs, 5 hypermethylated/downregulated genes (ZNF804A, ZFP82, TRIM58, SOX17, and C12orf42) were correlated with poor survival of patients with pancreatic cancer. KEGG pathway enrichment analysis by GSEA 3.0 and the protein–protein interaction (PPI) network revealed that these 5 MeDEGs were enriched in numerous cancer-related pathways in addition to interacting with each other, highlighting a significant role in the development of pancreatic cancer. Taken together, the key findings of the current study demonstrate that ZNF804A, ZFP82, TRIM58, SOX17, and C12orf42 are hypermethylated/downregulated genes in pancreatic cancer and may be associated, through their modulation of specific pathways, with unfavorable pancreatic cancer prognosis.

Paving the way for small-molecule drug discovery

Small-molecule drugs are organic compounds affecting molecular pathways by targeting important proteins, which have a low molecular weight, making them penetrate cells easily. Small-molecule drugs can be developed from leads derived from rational drug design or isolated from natural resources. As commonly used medications, small-molecule drugs can be taken orally, which enter cells to act on intracellular targets. These characteristics make small-molecule drugs promising candidates for drug development, and they are increasingly favored in the pharmaceutical market. Despite the advancements in molecular genetics and effective new processes in drug development, the drugs currently used in clinical practice are inadequate due to their poor efficacy or severe side effects. Therefore, developing new safe and efficient drugs is a top priority for disease control and curing.

[The study of the protection function of the sphingosine kinase 1 in the nerve cell damage caused by acrylamide]

Objective: To study the protective effect and effect of SphK1 overexpression on the injury of nerve cells induced by acrylamide. Methods: ACR with 99% purity was prepared into 1.25 mmol/L and 2.5 mmol/L solutions. SH-SY5Y cells were divided into control group (NC group) , experimental group and SphK1 activator group. The experimental group was given ACR solution with final concentration of 1.25 mmol/L and 2.5 mmol/L respectively for 24 h. In the SphK1 activator group, on the basis of the exposure concentration of the experimental group, the SphK1 specific activator (12-) phorbol tetradecanoate (-13-) acetate (PMA) solution[prepared by dimethyl sulfoxide (DMSO) , the final concentration was 100 nmol/l], and other treatments were the same as the experimental group. Control group (NC group) added PMA solution into normal cells. Western blot was used to detect the expression of SphK1 protein; CCK-8 was used to detect the proliferation of SH-SY5Y cells; hoechst33342 method was used to observe the morphological changes of nerve cells; flow cytometry was used to analyze the apoptosis of cells. Results: Compared with NC group, the expression of SphK1 protein in the experimental group and the SphK1 activator group was significantly lower (P<0.05) . Compared with the experimental group, the expression of SphK1 protein in each concentration of SphK1 activator group was increased, and the difference was statistically significant (P<0.05) . In addition to 1.25 mmol/L SphK1 activator group, compared with NC group, the relative growth survival rate of experimental group and 2.5 mmol/L SphK1 activator group were lower, the difference was statistically significant (P<0.05) . Compared with the experimental group, the relative survival rate of cells in the SphK1 activator group was higher, and the difference was statistically significant (P<0.05) . With the increase of exposure concentration, the cells in the experimental group showed the morphological characteristics of early apoptosis at ACR 1.25 mmol/L and late apoptosis at ACR 2.5 mmol/L. Compared with NC group, the apoptosis rate of experimental group and SphK1 activator group at ACR 2.5 mmol/L was significantly different (P<0.05) ; compared with experimental group, the apoptosis rate of SphK1 activator group at ACR 2.5 mmol/L was lower, the difference was statistically significant (P<0.05) . Conclusion: The SphK1 excessive expression plays the protective function to the nerve cell damage caused by acrylamide.

Mobile genetic elements are the Major driver of High antibiotic resistance genes abundance in the Upper reaches of huaihe River Basin

Rivers are considered a vital reservoir of antibiotic resistance genes (ARGs) and are critical to disseminate ARGs. The present study delved into the ARGs pollution of the sediments in the upper reaches of Huaihe river, one of the seven longest rivers in China, by high-throughput quantitative PCR. Subsequently, the relationship between ARGs and the bacterial community/mobile genetic elements (MGEs) was determined. As revealed from the results, the overall ARGs ranged from 2.65×10^-3 to 6.14×10^-2/16S copies, and the abundance of ARGs in the tributaries was significantly higher than that in the mainstreams (p<0.05). Moreover, the ARGs introduced by tributaries were capable of affecting the whole mainstream of Huaihe river. As suggested from the results of co-occurrence analysis and pRDA analysis, MGEs were reported as the major driver to disseminate ARGs in the upper reaches of Huaihe river basin. The larger the MGEs proportion, the higher the likelihood of ARGs transferring from antibiotic resistance bacteria to human pathogens in Huaihe river.