Publications by authors named "Ming Tang"

675 Publications

Evaluation of Apigenin Inhibiting Lactate Dehydrogenase Activity Based on CdTe Quantum Dots Fluorescence.

J Biomed Nanotechnol 2021 Sep;17(9):1806-1811

Laboratory of Controllable Preparation and Application of Nanomaterials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.

Lactate dehydrogenase (LDH) is one of key enzymes in glucose metabolism pathway, which plays a critical role in cell metabolism. Inhibition of LDH can inhibit glycolysis process, thereby inhibiting the occurrence and development of tumor cells. Two kinds of LDH inhibitors, apigenin and emodin, were obtained by testing the IC of several natural products in LDH enzyme reaction. The IC of apigenin was about 1/3 of LDH inhibitor sodium oxalate. A new method to evaluate the performance of LDH inhibitors based on CdTe QDs was established at the same time, which provides a new idea for research on LDH enzyme inhibitors.
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http://dx.doi.org/10.1166/jbn.2021.3158DOI Listing
September 2021

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks.

J Vis Exp 2021 09 25(175). Epub 2021 Sep 25.

Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Sciences, Guizhou Normal University;

The root microbiome plays an important role in plant growth and environmental adaptation. Network analysis is an important tool for studying communities, which can effectively explore the interaction relationship or co-occurrence model of different microbial species in different environments. The purpose of this manuscript is to provide details on how to use the weighted correlation network algorithm to analyze different co-occurrence networks that may occur in microbial communities due to different ecological environments. All analysis of the experiment is performed in the WGCNA package. WGCNA is an R package for weighted correlation network analysis. The experimental data used to demonstrate these methods were microbial community data from the NCBI (National Center for Biotechnology Information) database for three niches of the rice (Oryza sativa) root system. We used the weighted correlation network algorithm to construct co-abundance networks of microbial community in each of the three niches. Then, differential co-abundance networks among endosphere, rhizoplane and rhizosphere soil were identified. In addition, the core genera in network were obtained by the "WGCNA" package, which plays an important regulated role in network functions. These methods enable researchers to analyze the response of microbial network to environmental disturbance and verify different microbial ecological response theories. The results of these methods show that the significant differential microbial networks identified in the endosphere, rhizoplane and rhizosphere soil of rice.
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http://dx.doi.org/10.3791/62205DOI Listing
September 2021

Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response.

Nat Genet 2021 Oct 30;53(10):1456-1468. Epub 2021 Sep 30.

The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.

Glioma intratumoral heterogeneity enables adaptation to challenging microenvironments and contributes to therapeutic resistance. We integrated 914 single-cell DNA methylomes, 55,284 single-cell transcriptomes and bulk multi-omic profiles across 11 adult IDH mutant or IDH wild-type gliomas to delineate sources of intratumoral heterogeneity. We showed that local DNA methylation disorder is associated with cell-cell DNA methylation differences, is elevated in more aggressive tumors, links with transcriptional disruption and is altered during the environmental stress response. Glioma cells under in vitro hypoxic and irradiation stress increased local DNA methylation disorder and shifted cell states. We identified a positive association between genetic and epigenetic instability that was supported in bulk longitudinally collected DNA methylation data. Increased DNA methylation disorder associated with accelerated disease progression and recurrently selected DNA methylation changes were enriched for environmental stress response pathways. Our work identified an epigenetically facilitated adaptive stress response process and highlights the importance of epigenetic heterogeneity in shaping therapeutic outcomes.
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http://dx.doi.org/10.1038/s41588-021-00926-8DOI Listing
October 2021

Identification of the Short Neuropeptide F and Short Neuropeptide F Receptor Genes and Their Roles of Food Intake in .

Insects 2021 Sep 19;12(9). Epub 2021 Sep 19.

College of Forestry, Northwest A&F University, Xianyang 712100, China.

The short neuropeptide F (sNPF) is an essential signaling molecule that is evolutionarily conserved and involved in a broad range of physiological functions in the invertebrates, by interacting with sNPF receptors, which belong to G protein-coupled receptors (GPCR). However, the function of sNPF in regulating the food intake of has been unclear. In this study, we cloned and characterized cDNAs encoding sNPF and sNPF receptor in the and made bioinformatics predictions on the deduced amino acid sequences. They had a high degree of similarity to that of Quantitative real-time reverse transcription PCR (qRT-PCR) revealed that the transcript levels of both sNPF and sNPFR varied across developmental stages and body parts. In addition, the sNPF and sNPFR expression levels were upregulated in starved beetles, and the expression levels recovered after re-feeding. Furthermore, RNAi knockdown by the injection of sNPF and sNPFR dsRNA into beetles significantly increased mortality and reduced their food intake and body weight, and also caused decrease of glycogen and free fatty acid and increase of trehalose. These results indicate that sNPF signaling pathway plays an important role in the regulation of food intake and provides a potential molecular target for the eco-friendly control strategies of this pest.
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http://dx.doi.org/10.3390/insects12090844DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8469826PMC
September 2021

Using different machine learning models to classify patients into mild and severe cases of COVID-19 based on multivariate blood testing.

J Med Virol 2021 Sep 20. Epub 2021 Sep 20.

Department of Critical Care Medicine, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China.

COVID-19 is a serious respiratory disease. The ever-increasing number of cases is causing heavier loads on the health service system. Using 38 blood test indicators on the first day of admission for the 422 patients diagnosed with COVID-19 (from January 2020 to June 2021) to construct different machine learning (ML) models to classify patients into either mild or severe cases of COVID-19. All models show good performance in the classification between COVID-19 patients into mild and severe disease. The area under the curve (AUC) of the random forest model is 0.89, the AUC of the naive Bayes model is 0.90, the AUC of the support vector machine model is 0.86, and the AUC of the KNN model is 0.78, the AUC of the Logistic regression model is 0.84, and the AUC of the artificial neural network model is 0.87, among which the naive Bayes model has the best performance. Different ML models can classify patients into mild and severe cases based on 38 blood test indicators taken on the first day of admission for patients diagnosed with COVID-19.
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http://dx.doi.org/10.1002/jmv.27352DOI Listing
September 2021

Managing chronic postsurgical pain after total hip arthroplasty under ten applications of pericapsular nerve group block: A case series.

J Clin Anesth 2021 Sep 13;75:110487. Epub 2021 Sep 13.

Department of Anesthesiology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai, China. Electronic address:

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http://dx.doi.org/10.1016/j.jclinane.2021.110487DOI Listing
September 2021

Impact of salt and exogenous AM inoculation on indigenous microbial community structure in the rhizosphere of dioecious plant, Populus cathayana.

Sci Rep 2021 Sep 15;11(1):18403. Epub 2021 Sep 15.

State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, Guangdong, China.

The sex-specific physical and biochemical responses in dioecious plants to abiotic stresses could result in gender imbalance, and how to ease the current situation by microorganisms is still unclear. Using native soil where poplars were grown, growth parameters, soil physicochemical properties in the rhizosphere soil of different sexes of Populus cathayana exposed to salt stress and exogenous arbuscular mycorrhizal (AM) inoculation were tested. Besides, the sex-specific microbial community structures in the rhizosphere soil of different sexes of Populus cathayana were compared under salt stress. To identify the sex-specific microbial community characteristics related to salinity and AM symbiosis, a combined qPCR and DGGE method was used to monitor microbial community diversity. Seedlings suffered severe pressure by salt stress, reflected in limited growth, biomass, and nutrient element accumulation, especially on females. Exogenous AM inoculation treatment alleviated these negative effects, especially under salt treatment of 75 mM. Compared with salt effect, exogenous AM inoculation treatment showed a greater effect on soil physical-chemical properties of both sexes. Based on DGGE results, salt stress negatively affected fungal richness but positively affected fungal Simpson diversity index, while exogenous AM inoculation treatment showed the opposite effect. Structural equation modeling (SEM) was performed to show the causal relationships between salt and exogenous AM inoculation treatments with biomass accumulation and microbial community: salt and exogenous AM inoculation treatment showed complicated effects on elementary concentrations, soil properties, which resulted in different relationship with biomass accumulation and microbial community. Salt stress had a negative effect on soil properties and microbial community structure in the rhizosphere soil of P. cathayana, whereas exogenous AM inoculation showed positive impacts on most of the soil physical-chemical properties and microbial community status.
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http://dx.doi.org/10.1038/s41598-021-97674-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8443550PMC
September 2021

Cardiac Magnetic Resonance Imaging and Blood Biomarkers for Evaluation of Radiation-Induced Cardiotoxicity in Patients With Breast Cancer: Results of a Phase 2 Clinical Trial.

Int J Radiat Oncol Biol Phys 2021 Sep 9. Epub 2021 Sep 9.

Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan; Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan. Electronic address:

Purpose: Radiation therapy (RT) can increase the risk of cardiac events in patients with breast cancer (BC), but biomarkers predicting risk for developing RT-induced cardiac disease are currently lacking. We report results from a prospective clinical trial evaluating early magnetic resonance imaging (MRI) and serum biomarker changes as predictors of cardiac injury and risk of subsequent cardiac events after RT for left-sided disease.

Methods: Women with node-negative and node-positive (N-/+) left-sided BC were enrolled on 2 institutional review board (IRB)-approved protocols at 2 institutions. MRI was conducted pretreatment (within 1 week of starting radiation), at the end of treatment (last day of treatment ±1 week), and 3 months after the last day of treatment (±2 weeks) to quantify left and right ventricular volumes and function, myocardial fibrosis, and edema. Perfusion changes during regadenoson stress perfusion were also assessed on a subset of patients (n = 28). Serum was collected at the same time points. Whole heart and cardiac substructures were contoured using CT and MRI. Models were constructed using baseline cardiac and clinical risk factors. Associations between MRI-measured changes and dose were evaluated.

Results: Among 51 women enrolled, mean heart dose ranged from 0.80 to 4.7 Gy and mean left ventricular (LV) dose from 1.1 to 8.2 Gy, with mean heart dose 2.0 Gy. T1 time, a marker of fibrosis, and right ventricular (RV) ejection fraction (EF) significantly changed with treatment; these were not dose dependent. T2 (marker of edema) and LV EF did not significantly change. No risk factors were associated with baseline global perfusion. Prior receipt of doxorubicin was marginally associated with decreased myocardial perfusion after RT (P = .059), and mean MHD was not associated with perfusion changes. A significant correlation between baseline IL-6 and mean heart dose (MHD) at the end of RT (ρ 0.44, P = .007) and a strong trend between troponin I and MHD at 3 months post-treatment (ρ 0.33, P = .07) were observed. No other significant correlations were identified.

Conclusions: In this prospective study of women with left-sided breast cancer treated with contemporary treatment planning, cardiac radiation doses were very low relative to historical doses reported by Darby et al. Although we observed significant changes in T1 and RV EF shortly after RT, these changes were not correlated with whole heart or substructure doses. Serum biomarker analysis of cardiac injury demonstrates an interesting trend between markers and MHD that warrants further investigation.
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http://dx.doi.org/10.1016/j.ijrobp.2021.08.039DOI Listing
September 2021

Step-adjusted tree-based reinforcement learning for evaluating nested dynamic treatment regimes using test-and-treat observational data.

Stat Med 2021 Sep 7. Epub 2021 Sep 7.

Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.

Dynamic treatment regimes (DTRs) include a sequence of treatment decision rules, in which treatment is adapted over time in response to the changes in an individual's disease progression and health care history. In medical practice, nested test-and-treat strategies are common to improve cost-effectiveness. For example, for patients at risk of prostate cancer, only patients who have high prostate-specific antigen (PSA) need a biopsy, which is costly and invasive, to confirm the diagnosis and help determine the treatment if needed. A decision about treatment happens after the biopsy, and is thus nested within the decision of whether to do the test. However, current existing statistical methods are not able to accommodate such a naturally embedded property of the treatment decision within the test decision. Therefore, we developed a new statistical learning method, step-adjusted tree-based reinforcement learning, to evaluate DTRs within such a nested multistage dynamic decision framework using observational data. At each step within each stage, we combined the robust semiparametric estimation via augmented inverse probability weighting with a tree-based reinforcement learning method to deal with the counterfactual optimization. The simulation studies demonstrated robust performance of the proposed methods under different scenarios. We further applied our method to evaluate the necessity of prostate biopsy and identify the optimal test-and-treat regimes for prostate cancer patients using data from the Johns Hopkins University prostate cancer active surveillance dataset.
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http://dx.doi.org/10.1002/sim.9177DOI Listing
September 2021

P4HA2-induced prolyl hydroxylation suppresses YAP1-mediated prostate cancer cell migration, invasion, and metastasis.

Oncogene 2021 Oct 1;40(41):6049-6056. Epub 2021 Sep 1.

Department of Genitourinary Medical Oncology and the David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Yes-associated protein 1 (YAP1), a key player in the Hippo pathway, has been shown to play a critical role in tumor progression. However, the role of YAP1 in prostate cancer cell invasion, migration, and metastasis is not well defined. Through functional, transcriptomic, epigenomic, and proteomic analyses, we showed that prolyl hydroxylation of YAP1 plays a critical role in the suppression of cell migration, invasion, and metastasis in prostate cancer. Knockdown (KD) or knockout (KO) of YAP1 led to an increase in cell migration, invasion, and metastasis in prostate cancer cells. Microarray analysis showed that the EMT pathway was activated in Yap1-KD cells. ChIP-seq analysis showed that YAP1 target genes are enriched in pathways regulating cell migration. Mass spectrometry analysis identified P4H prolyl hydroxylase in the YAP1 complex and YAP1 was hydroxylated at multiple proline residues. Proline-to-alanine mutations of YAP1 isoform 3 identified proline 174 as a critical residue, and its hydroxylation suppressed cell migration, invasion, and metastasis. KO of P4ha2 led to an increase in cell migration and invasion, which was reversed upon Yap1 KD. Our study identified a novel regulatory mechanism of YAP1 by which P4HA2-dependent prolyl hydroxylation of YAP1 determines its transcriptional activities and its function in prostate cancer metastasis.
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http://dx.doi.org/10.1038/s41388-021-02000-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8526415PMC
October 2021

Asymmetric dual-SSB modulation for photonic co-frequency mm-wave signals generation and DSP-free receiver.

Opt Lett 2021 Sep;46(17):4366-4369

An asymmetric dual-single-sideband (SSB) modulation scheme for photonic co-frequency millimeter (mm)-wave signals generation and digital signal processing (DSP)-free receiver is experimentally demonstrated for the first time, to the best of our knowledge. To effectively avoid the sideband crosstalk in the traditional symmetric dual-SSB modulation scheme, not only two vector-modulated signals but also two unmodulated sidebands are modulated on the two asymmetric sides of an optical carrier in this scheme. An optical delay line interferometer could easily separate these two asymmetric dual-SSB signals simultaneously in the receiver, and thus the photonic frequency up-conversion is realized. Besides, this scheme is free of dispersion-induced RF power fading thanks to the SSB modulation. By this means, no digital compensation algorithms such as carrier phase recovery, fiber dispersion compensation, and channel equalization are required, contributing to the DSP-free receiver. In our experiment, two 32 GHz 3.2 Gb/s 16-ary quadrature amplitude modulation mm-wave signals are produced using two RF signals with the carrier frequencies of 12 GHz and 20 GHz. The error vector magnitude (EVM) performances of these two mm-wave signals after 25.5 km standard single-mode fiber transmission are better than 3rd Generation Partnership Project requirements without using any digital compensation algorithms.
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http://dx.doi.org/10.1364/OL.437746DOI Listing
September 2021

Genome-Wide Analysis of Nutrient Signaling Pathways Conserved in Arbuscular Mycorrhizal Fungi.

Microorganisms 2021 Jul 22;9(8). Epub 2021 Jul 22.

State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China.

Arbuscular mycorrhizal (AM) fungi form a mutualistic symbiosis with a majority of terrestrial vascular plants. To achieve an efficient nutrient trade with their hosts, AM fungi sense external and internal nutrients, and integrate different hierarchic regulations to optimize nutrient acquisition and homeostasis during mycorrhization. However, the underlying molecular networks in AM fungi orchestrating the nutrient sensing and signaling remain elusive. Based on homology search, we here found that at least 72 gene components involved in four nutrient sensing and signaling pathways, including cAMP-dependent protein kinase A (cAMP-PKA), sucrose non-fermenting 1 (SNF1) protein kinase, target of rapamycin kinase (TOR) and phosphate (PHO) signaling cascades, are well conserved in AM fungi. Based on the knowledge known in model yeast and filamentous fungi, we outlined the possible gene networks functioning in AM fungi. These pathways may regulate the expression of downstream genes involved in nutrient transport, lipid metabolism, trehalase activity, stress resistance and autophagy. The RNA-seq analysis and qRT-PCR results of some core genes further indicate that these pathways may play important roles in spore germination, appressorium formation, arbuscule longevity and sporulation of AM fungi. We hope to inspire further studies on the roles of these candidate genes involved in these nutrient sensing and signaling pathways in AM fungi and AM symbiosis.
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http://dx.doi.org/10.3390/microorganisms9081557DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8401276PMC
July 2021

The Synergy of Arbuscular Mycorrhizal Fungi and Exogenous Abscisic Acid Benefits L. Growth through Altering the Distribution of Zn and Endogenous Abscisic Acid.

J Fungi (Basel) 2021 Aug 19;7(8). Epub 2021 Aug 19.

College of Forestry, Northwest A&F University, Yangling 712100, China.

The simultaneous effects of arbuscular mycorrhizal (AM) fungi and abscisic acid (ABA) on the tolerance of plants to heavy metal (HM) remain unclear. A pot experiment was carried out to clarify the effects of simultaneous applications of AM fungi and ABA on plant growth, Zn accumulation, endogenous ABA contents, proline metabolism, and the oxidative injury of black locust ( L.) exposed to excess Zn stress. The results suggested that exogenously applied ABA positively enhanced AM colonization, and that the growth of plants only with AM fungi was improved by ABA application. Under Zn stress, AM inoculation and ABA application increased the ABA content in the root/leaf (increased by 48-172% and 92%, respectively) and Zn content in the root/shoot (increased by 63-152% and 61%, respectively) in AM plants, but no similar trends were observed in NM plants. Additionally, exogenous ABA addition increased the proline contents of NM roots concomitantly with the activities of the related synthases, whereas it reduced the proline contents and the activity of Δ-pyrroline-5-carboxylate synthetase in AM roots. Under Zn stress, AM inoculation and ABA application decreased HO contents and the production rate of O, to varying degrees. Furthermore, in the roots exposed to Zn stress, AM inoculation augmented the activities of SOD, CAT, POD and APX, and exogenously applied ABA increased the activities of SOD and POD. Overall, AM inoculation combined with ABA application might be beneficial to the survival of black locust under Zn stress by improving AM symbiosis, inhibiting the transport of Zn from the roots to the shoots, increasing the distribution of ABA in roots, and stimulating antioxidant defense systems.
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http://dx.doi.org/10.3390/jof7080671DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8400989PMC
August 2021

neurons in the mouse perifornical area promote infant-directed neglect and aggression.

Elife 2021 08 23;10. Epub 2021 Aug 23.

Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, United States.

While recent studies have uncovered dedicated neural pathways mediating the positive control of parenting, the regulation of infant-directed aggression and how it relates to adult-adult aggression is poorly understood. Here we show that ()-expressing neurons in the hypothalamic perifornical area (PeFA) are activated during infant-directed attacks in males and females, but not other behaviors. Functional manipulations of PeFA neurons demonstrate the role of this population in the negative control of parenting in both sexes. PeFA neurons receive input from areas associated with vomeronasal sensing, stress, and parenting, and send projections to hypothalamic and limbic areas. Optogenetic activation of PeFA axon terminals in these regions triggers various aspects of infant-directed agonistic responses, such as neglect, repulsion, and aggression. Thus, PeFA neurons emerge as a dedicated circuit component controlling infant-directed neglect and aggression, providing a new framework to understand the positive and negative regulation of parenting in health and disease.
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http://dx.doi.org/10.7554/eLife.64680DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8452308PMC
August 2021

Inoculation With Ectomycorrhizal Fungi and Dark Septate Endophytes Contributes to the Resistance of spp. to Pine Wilt Disease.

Front Microbiol 2021 6;12:687304. Epub 2021 Aug 6.

State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China.

Pine wilt disease (PWD) is a deadly disease to pines ( spp.) worldwide. The occurrence of PWD can reduce the relative abundance of root ectomycorrhizal fungi (ECMF) and dark septate endophytes (DSE). However, the effects of exogenous ECMF/DSE inoculation on the rhizosphere microbial community structure of infected by pine wood nematode (PWN) is little known. Here, we tested how ECMF/DSE may improve resistance to PWD by quantifying microbial carbon biomass and soil enzymatic activity among different treatments at 6 and 9 months after PWN infection. Denaturing gradient gel electrophoresis (DGGE) was used to study the microbial community structure at 3, 6, and 9 months after PWN infection in the rhizosphere of seedlings inoculated with ECMF/DSE. The results showed that exogenous ECMF/DSE inoculation reduced the disease severity caused by PWN infection. After PWN infection, the rhizosphere microbial carbon of seedlings inoculated with , , , and was 38.16, 49.67, 42.11, and 96.05% higher than that of the control group, respectively. Inoculation of ECMF/DSE inhibited the decrease of rhizosphere microbial biomass caused by PWN infection. The richness and diversity of rhizosphere fungi at 9 months were reduced by PWN infection but partially recovered by the exogenous fungi (ECMF/DSE) inoculation except for , which indicates a role of ECMF/DSE in maintaining stability of the microbial community. Inoculation with ECMF/DSE increased the beneficial bacterial ( sp., sp., etc.) and fungal groups (, , etc.) of in the rhizosphere. In summary, exogenous ECMF/DSE inoculation could increase resistance to PWD probably by improving the rhizosphere microenvironment.
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http://dx.doi.org/10.3389/fmicb.2021.687304DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8377431PMC
August 2021

USP12 downregulation orchestrates a protumourigenic microenvironment and enhances lung tumour resistance to PD-1 blockade.

Nat Commun 2021 08 11;12(1):4852. Epub 2021 Aug 11.

State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Oncogenic activation of KRAS and its surrogates is essential for tumour cell proliferation and survival, as well as for the development of protumourigenic microenvironments. Here, we show that the deubiquitinase USP12 is commonly downregulated in the Kras-driven mouse lung tumour and human non-small cell lung cancer owing to the activation of AKT-mTOR signalling. Downregulation of USP12 promotes lung tumour growth and fosters an immunosuppressive microenvironment with increased macrophage recruitment, hypervascularization, and reduced T cell activation. Mechanistically, USP12 downregulation creates a tumour-promoting secretome resulting from insufficient PPM1B deubiquitination that causes NF-κB hyperactivation in tumour cells. Furthermore, USP12 inhibition desensitizes mouse lung tumour cells to anti-PD-1 immunotherapy. Thus, our findings propose a critical component downstream of the oncogenic signalling pathways in the modulation of tumour-immune cell interactions and tumour response to immune checkpoint blockade therapy.
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http://dx.doi.org/10.1038/s41467-021-25032-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8357983PMC
August 2021

Enabling long range distributed vibration sensing using multicore fiber interferometers.

Opt Lett 2021 Aug;46(15):3685-3688

We report a novel long range distributed fiber optic vibration sensor using two counter-propagating interferometers, which are space-division multiplexed in different cores of a seven-core fiber. The proposed system requires only one laser source. Thanks to the spatially separated structure of the two interferometers, it no longer suffers from the coherent Rayleigh backscattering noise, and, since forward transmitting CW light instead of weak backscattering light is used, as a result, the sensing range can be significantly extended. On the other hand, because the two interferometers are implemented in one single compact multicore fiber, the output temporal waveforms have good correlation; therefore, the sampled waveforms can be used directly to determine the vibration location through cross correlation, and no additional complicated data processing (e.g., time-frequency analysis methods) is required. For proof of concept, we achieved distributed vibration detection with 38.5 km sensing range, and the root mean square error of positioning is estimated to be about 54.9 m with 120 measurements. The proposed system has the unique advantages of simple setup, high sensitivity, large dynamic range, ultra-long sensing range, etc.
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http://dx.doi.org/10.1364/OL.425843DOI Listing
August 2021

Site selection of straw collection and storage facilities considering carbon emission reduction.

Environ Sci Pollut Res Int 2021 Jul 27. Epub 2021 Jul 27.

School of Transportation, Jilin University, Changchun, 130025, China.

Straw recycling has generated high collection and transportation costs. Scientifically informed collection, storage, and transportation methods can reduce automobile exhaust emissions and high transportation costs. According to the relevant statistics, China's total theoretical straw resources reached 920 million tons in 2020. Due to such regional and seasonal straw surpluses, however, comprehensive utilization technologies need to be improved, and farmers' awareness of environmental protection needs to be strengthened. In some areas, open burning of straw is still practiced, causing environmental pollution and wasting resources. This study used cost and carbon emission metrics in a dual-objective planning model to plan the site selection of straw collection and storage facilities. Compared with the current manual calculation in various links in straw supply logistics, modeling can resolve the contradiction between cost and carbon emission considerations and can help meet the goal of Pareto optimum while ensuring supply, reducing costs for enterprises, and providing decision-making assistance for the government. This paper uses transportation theory and a dual-objective, mixed-integer model to study the field of biomass energy. Through the planning and design of the biomass raw material supply chain, the system efficiency is improved, and the studied company can obtain more profits. This article also explores the role of controlling carbon emissions in the field of biomass energy. It is believed that the government not only needs to guide corporate decision-making by charging carbon taxes but also needs to support enterprises in participating in the field of biomass power generation through active policy guidance.
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http://dx.doi.org/10.1007/s11356-021-15581-zDOI Listing
July 2021

The deubiquitinase USP16 functions as an oncogenic factor in K-RAS-driven lung tumorigenesis.

Oncogene 2021 Sep 22;40(36):5482-5494. Epub 2021 Jul 22.

State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

K-RAS mutation and molecular alterations of its surrogates function essentially in lung tumorigenesis and malignant progression. However, it remains elusive how tumor-promoting and deleterious events downstream of K-RAS signaling are coordinated in lung tumorigenesis. Here, we show that USP16, a deubiquitinase involved in various biological processes, functions as a promoter for the development of K-RAS-driven lung tumor. Usp16 deletion significantly attenuates K-ras-mutation-induced lung tumorigenesis in mice. USP16 upregulation upon RAS activation averts reactive oxygen species (ROS)-induced p38 activation that would otherwise detrimentally influence the survival and proliferation of tumor cells. In addition, USP16 interacts with and deubiquitinates JAK1, and thereby promoting lung tumor growth by augmenting JAK1 signaling. Therefore, our results reveal that USP16 functions critically in the K-RAS-driven lung tumorigenesis through modulating the strength of p38 and JAK1 signaling.
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http://dx.doi.org/10.1038/s41388-021-01964-6DOI Listing
September 2021

Reprogramming of bivalent chromatin states in NRAS mutant melanoma suggests PRC2 inhibition as a therapeutic strategy.

Cell Rep 2021 Jul;36(3):109410

Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA. Electronic address:

The dynamic evolution of chromatin state patterns during metastasis, their relationship with bona fide genetic drivers, and their therapeutic vulnerabilities are not completely understood. Combinatorial chromatin state profiling of 46 melanoma samples reveals an association of NRAS mutants with bivalent histone H3 lysine 27 trimethylation (H3K27me3) and Polycomb repressive complex 2. Reprogramming of bivalent domains during metastasis occurs on master transcription factors of a mesenchymal phenotype, including ZEB1, TWIST1, and CDH1. Resolution of bivalency using pharmacological inhibition of EZH2 decreases invasive capacity of melanoma cells and markedly reduces tumor burden in vivo, specifically in NRAS mutants. Coincident with bivalent reprogramming, the increased expression of pro-metastatic and melanocyte-specific cell-identity genes is associated with exceptionally wide H3K4me3 domains, suggesting a role for this epigenetic element. Overall, we demonstrate that reprogramming of bivalent and broad domains represents key epigenetic alterations in metastatic melanoma and that EZH2 plus MEK inhibition may provide a promising therapeutic strategy for NRAS mutant melanoma patients.
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http://dx.doi.org/10.1016/j.celrep.2021.109410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8369408PMC
July 2021

Effects of Word Semantic Transparency, Context Length, and L1 Background on CSL Learners' Incidental Learning of Word Meanings in Passage-Level Reading.

J Psycholinguist Res 2021 Jul 21. Epub 2021 Jul 21.

Department of Chinese and Bilingual Studies, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, Hong Kong.

This study investigated the effects of semantic transparency of Chinese disyllabic compound words on Chinese as a second language (CSL) learners' incidental learning of word meanings in sentence-level reading and passage-level reading. The accuracy of the learners' lexical inferencing was compared among various types of words (transparent, semi-transparent, and opaque words), different context lengths (sentence and passage contexts), and learners with different L1 backgrounds (with and without a Chinese character background in their L1s). In the study, ninety CSL adult learners were asked to infer the meanings of target words in the sentence context and the passage context. The results indicated that the effects of semantic transparency and context length on inferencing accuracy were significant, while the effect of L1 background was not. It was also found that there were significant interactions between transparency and context length as well as between transparency and L1 background.
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http://dx.doi.org/10.1007/s10936-021-09786-zDOI Listing
July 2021

Enhancer reprogramming in PRC2-deficient malignant peripheral nerve sheath tumors induces a targetable de-differentiated state.

Acta Neuropathol 2021 09 20;142(3):565-590. Epub 2021 Jul 20.

Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Malignant peripheral nerve sheath tumors (MPNSTs) are soft tissue sarcomas that frequently harbor genetic alterations in polycomb repressor complex 2 (PRC2) components-SUZ12 and EED. Here, we show that PRC2 loss confers a dedifferentiated early neural-crest phenotype which is exclusive to PRC2-mutant MPNSTs and not a feature of neurofibromas. Neural crest phenotype in PRC2 mutant MPNSTs was validated via cross-species comparative analysis using spontaneous and transgenic MPNST models. Systematic chromatin state profiling of the MPNST cells showed extensive epigenomic reprogramming or chromatin states associated with PRC2 loss and identified gains of active enhancer states/super-enhancers on early neural crest regulators in PRC2-mutant conditions around genomic loci that harbored repressed/poised states in PRC2-WT MPNST cells. Consistently, inverse correlation between H3K27me3 loss and H3K27Ac gain was noted in MPNSTs. Epigenetic editing experiments established functional roles for enhancer gains on DLX5-a key regulator of neural crest phenotype. Consistently, blockade of enhancer activity by bromodomain inhibitors specifically suppressed this neural crest phenotype and tumor burden in PRC2-mutant PDXs. Together, these findings reveal accumulation of dedifferentiated neural crest like state in PRC2-mutant MPNSTs that can be targeted by enhancer blockade.
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http://dx.doi.org/10.1007/s00401-021-02341-zDOI Listing
September 2021

Lighting quantity indexes for lighting traditional Chinese paintings based on pigments protection and substrates protection in museums.

Opt Express 2021 Jul;29(14):22667-22678

In museum lighting, traditional Chinese paintings are the artworks with the highest light sensitivity. They are vulnerable to the color damage to pigments and the mechanical damage to substrates after the irradiation from light sources. As the basis of effective preventive protection, the research on the two lighting quantity indexes of illuminance and annual exposure (illuminance × time) is currently missing. In this study, the halogen lamp was used as the experimental light source to conduct a 1440 h irradiation experiment on the samples of paper and silk substrates under 4 illuminance levels, respectively, and the test of infrared spectrum was carried out on the samples every 240 h. The oxidation index of paper and crystallinity degree of silk were calculated then. Three-dimensional visual curved surface plots of mechanical damage to samples with the change of illuminance and time were established and then fitted into damage evaluation equations, which revealed and described mathematically the mechanical damage law of samples. Through the equations, the recommended values of illuminance and annual exposure for samples could be calculated. Combining the previous researches on pigments, the lighting quantity indexes of traditional Chinese paintings with different combinations of substrates and pigments were proposed.
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http://dx.doi.org/10.1364/OE.429923DOI Listing
July 2021

Geometric shaping optimization of 64-APSK constellation in discrete nonlinear frequency division multiplexing systems.

Opt Lett 2021 Jul;46(14):3368-3371

We experimentally demonstrated a geometric shaped (GS) 64-ary amplitude phase shift keying (64-APSK) eigenvalue transmission. The signal is modulated on the scatter coefficient of a single eigenvalue and linear minimum mean square error (LMMSE) estimator is used to reduce the noise. The channel response is estimated by transmitting a normally distributed 64-APSK constellation through a communication link. Based on the polar coordinates distribution of the received constellation, the diameter distributions for each circle can be obtained so that circles with larger noise can obtain larger judgment width. After optimization, the experimental results show that the Q-factor gain is 1.13 dB under 22 dB received optical signal to noise ratio (OSNR) configuration and 0.88 dB after 900 km transmission compared with normally distributed APSK configuration.
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http://dx.doi.org/10.1364/OL.430391DOI Listing
July 2021

HieRFIT: A hierarchical cell type classification tool for projections from complex single-cell atlas datasets.

Bioinformatics 2021 Jul 13. Epub 2021 Jul 13.

Informatics Group, Harvard University, Cambridge, MA, USA.

Motivation: The emergence of single-cell RNA sequencing (scRNA-seq) has led to an explosion in novel methods to study biological variation among individual cells, and to classify cells into functional and biologically meaningful categories.

Results: Here, we present a new cell type projection tool, HieRFIT (Hierarchical Random Forest for Information Transfer), based on hierarchical random forests. HieRFIT uses a priori information about cell type relationships to improve classification accuracy, taking as input a hierarchical tree structure representing the class relationships, along with the reference data. We use an ensemble approach combining multiple random forest models, organized in a hierarchical decision tree structure. We show that our hierarchical classification approach improves accuracy and reduces incorrect predictions especially for inter-dataset tasks which reflect real life applications. We use a scoring scheme that adjusts probability distributions for candidate class labels and resolves uncertainties while avoiding the assignment of cells to incorrect types by labeling cells at internal nodes of the hierarchy when necessary.

Availability: HieRFIT is implemented as an R package, and it is available at (https://github.com/yasinkaymaz/HieRFIT/releases/tag/v1.0.0). t.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btab499DOI Listing
July 2021

Cloning and Expression of the Neuropeptide F and Neuropeptide F Receptor Genes and Their Regulation of Food Intake in the Chinese White Pine Beetle .

Front Physiol 2021 18;12:662651. Epub 2021 Jun 18.

College of Forestry, Northwest A&F University, Xianyang, China.

Neuropeptide F (NPF) is an important signaling molecule that acts as a neuromodulator to regulate a diversity of physiological and behavioral processes from vertebrates to invertebrates by interaction with NPF receptors, which are G protein-coupled receptors (GPCR). However, nothing is known about NPF in Chinese white pine beetle, , a destructive pest of natural and coniferous forests in the middle Qinling Mountains of China. We have cloned and characterized cDNAs encoding one NPF precursor and two NPF receptors in and made bioinformatics predictions according to the deduced amino acid sequences. They were highly similar to that of The transcription levels of these genes were different between larvae and adults of sexes, and there were significant differences among the different developmental stages and tissues and between beetles under starvation and following re-feeding states. Additionally, downregulation of NPF and NPFR by injecting dsRNA into beetles reduced their food intake, caused increases of mortality and decreases of body weight, and also resulted in a decrease of glycogen and free fatty acid and an increase of trehalose. These results indicate that the NPF signaling pathway plays a significant positive role in the regulation of food intake and provides a potential target for the sustainable management of this pest.
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http://dx.doi.org/10.3389/fphys.2021.662651DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8249871PMC
June 2021

Arbuscular Mycorrhizal Fungi Increase Pb Uptake of Colonized and Non-Colonized Root and Deliver Extra Pb to Colonized Root Segment.

Microorganisms 2021 Jun 2;9(6). Epub 2021 Jun 2.

College of Forestry, Northwest A&F University, Yangling 712100, China.

Arbuscular mycorrhizal (AM) fungi establish symbiosis and improve the lead (Pb) tolerance of host plants. The AM plants accumulate more Pb in roots than their non-mycorrhizal counterparts. However, the direct and long-term impact of AM fungi on plant Pb uptake has been rarely reported. In this study, AM fungus () colonized and non-colonized roots of were separated by a split-root system, and their differences in responding to Pb application were compared. The shoot biomass accumulation and transpiration were increased after inoculation, whereas the biomass of both colonized and non-colonized roots was decreased. Lead application in the non-colonized root compartment increased the colonization rate and up-regulated the relative expressions of and in the colonized root compartments. inoculation increased Pb uptake in both colonized and non-colonized roots, and transferred Pb to the colonized root segment. The Pb transferred through the colonized root segment had low mobility and might be sequestrated and compartmented in the root by The Pb uptake of roots might follow water flow, which is facilitated by MtPIP2. The quantification of Pb transfer via the mycorrhizal pathway and the involvement of MtPIP2 deserve further study.
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http://dx.doi.org/10.3390/microorganisms9061203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8229133PMC
June 2021

Regulating glucose metabolism using nanomedicines for cancer therapy.

J Mater Chem B 2021 Jul;9(29):5749-5764

Laboratory of Controllable Preparation and Application of Nanomaterials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China. and CAS Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China.

The regulation of glucose metabolism is a research focus in cancer treatment. Glucose metabolism is essential for maintaining the growth and proliferation of tumor cells, thus offering us great opportunities for tumor treatment. Recently, much progress has been made in efficient cancer treatment by regulating the pathway of glucose metabolism with nanomedicines due to the rapid development of nanotechnology and promising drug targets. In this review, we first introduced the pathway of cell energy supply from the perspective of aerobic and anaerobic processes. Then, we discussed the recent research progress in regulating glucose metabolism for various tumor resistance strategies including heat resistance, multiple drug resistance, and hypoxia. Finally, we presented the prospects and challenges of developing multifunctional nanoagents for efficient chemotherapy, hyperthermia, dynamic therapy and so on by regulating glucose metabolism.
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http://dx.doi.org/10.1039/d1tb00218jDOI Listing
July 2021

Thermal state and evolving geodynamic regimes of the Meso- to Neoarchean North China Craton.

Nat Commun 2021 Jun 23;12(1):3888. Epub 2021 Jun 23.

Key Laboratory of Mineral Resources, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China.

Constraining thickness and geothermal gradient of Archean continental crust are crucial to understanding geodynamic regimes of the early Earth. Archean crust-sourced tonalitic-trondhjemitic-granodioritic gneisses are ideal lithologies for reconstructing the thermal state of early continental crust. Integrating experimental results with petrochemical data from the Eastern Block of the North China Craton allows us to establish temporal-spatial variations in thickness, geothermal gradient and basal heat flow across the block, which we relate to cooling mantle potential temperature and resultant changing geodynamic regimes from vertical tectonics in the late Mesoarchean (~2.9 Ga) to plate tectonics with hot subduction in the early to late Neoarchean (~2.7-2.5 Ga). Here, we show the transition to a plate tectonic regime plays an important role in the rapid cooling of the mantle, and thickening and strengthening of the lithosphere, which in turn prompted stabilization of the cratonic lithosphere at the end of the Archean.
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http://dx.doi.org/10.1038/s41467-021-24139-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222299PMC
June 2021

SIRT7: a sentinel of genome stability.

Open Biol 2021 06 16;11(6):210047. Epub 2021 Jun 16.

Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, People's Republic of China.

SIRT7 is a class III histone deacetylase that belongs to the sirtuin family. The past two decades have seen numerous breakthroughs in terms of understanding SIRT7 biological function. We now know that this enzyme is involved in diverse cellular processes, ranging from gene regulation to genome stability, ageing and tumorigenesis. Genomic instability is one hallmark of cancer and ageing; it occurs as a result of excessive DNA damage. To counteract such instability, cells have evolved a sophisticated regulated DNA damage response mechanism that restores normal gene function. SIRT7 seems to have a critical role in this response, and it is recruited to sites of DNA damage where it recruits downstream repair factors and directs chromatin regulation. In this review, we provide an overview of the role of SIRT7 in DNA repair and maintaining genome stability. We pay particular attention to the implications of SIRT7 function in cancer and ageing.
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http://dx.doi.org/10.1098/rsob.210047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8205529PMC
June 2021
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