An essential signaling function of cytoplasmic NELFB is independent of RNA polymerase II pausing.

The four-subunit negative elongation factor (NELF) complex mediates RNA polymerase II (Pol II) pausing at promoter-proximal regions. Ablation of individual NELF subunits destabilizes the NELF complex and causes cell lethality, leading to the prevailing concept that NELF-mediated Pol II pausing is essential for cell proliferation. Using separation-of-function mutations, we show here that NELFB function in cell proliferation can be uncoupled from that in Pol II pausing. NELFB mutants sequestered in the cytoplasm and deprived of NELF nuclear function still support cell proliferation and part of the NELFB-dependent transcriptome. Mechanistically, cytoplasmic NELFB physically and functionally interacts with prosurvival signaling kinases, most notably phosphatidylinositol-3-kinase/AKT. Ectopic expression of membrane-tethered phosphatidylinositol-3-kinase/AKT partially bypasses the role of NELFB in cell proliferation, but not Pol II occupancy. Together, these data expand the current understanding of the physiological impact of Pol II pausing and underscore the multiplicity of the biological functions of individual NELF subunits.

TDG generation in a ski-jump spillway with a fully or partial-flip bucket.

Ski-jump spillways are frequently used as discharge structures for high dams during floods with high energy heads. The selection of bucket types at the end of spillways has a pronounced effect on the hydraulics of jet characteristics, such as trajectories and entrained air features. However, there is no literature reporting how changes in the bucket types influence TDG generation. This study compares the hydraulic characteristics and TDG mass transfer properties of a hydraulic project under construction using both the traditional fully-flip bucket and the partial-flip bucket configurations. The results indicate that, the use of the partial-flip bucket at the end of the spillway significantly disperses the water flow and yields better energy dissipation effects. At low flow rates (lower than 400 m3/s for the dam in this study), there is little difference in the downstream TDG saturation between the traditional fully-flip bucket and the partial-flip bucket, the average difference is 1.6 % in three cases with a low flow rate. However, at high flow rates (higher than 400 m3/s), the partial-flip bucket generates more TDG compared to the traditional fully-flip bucket, reaching up to 6.2 % at the maximum flow rate. This phenomenon stems from significant changes in the hydrodynamics of the stilling basin at high flow rates due to variations in the flip bucket type. When strict control of TDG generation is necessary downstream of dams, the use of the partial-flip bucket should be carefully considered. This is because, at high flow rates, the partial-flip bucket might result in higher TDG saturation than the fully-flip bucket.

CDCA7 promotes TGF-ß-induced epithelial-mesenchymal transition via transcriptionally regulating Smad4/Smad7 in ESCC.

Cell division cycle associated 7 (CDCA7) is a copy number amplification gene that contributes to the metastasis and invasion of tumors, including esophageal squamous cell carcinoma (ESCC). This present study aimed at clarifying whether high expression of CDCA7 promotes the metastasis and invasion of ESCC cell lines and exploring the underlying mechanisms implicated in epithelial-mesenchymal transition (EMT) of ESCC. The role of CDCA7 in the regulation of ESCC metastasis and invasion was evaluated using ESCC cell lines. Expression of EMT-related markers including E-cadherin, N-cadherin, Vimentin, Snail, and Slug, transforming growth factor ß (TGF-ß) signaling pathway including Smad2/3, p-Smad2/3, Smad4, and Smad7 were detected in CDCA7 knockdown and overexpressed cell lines. Dual-luciferase reporter assay and rescue assay were used to explore the underlying mechanisms that CDCA7 contributed to the metastasis and invasion of ESCC. High CDCA7 expression significantly promoted the metastasis and invasion of ESCC cell lines both in vivo and in vitro. Additionally, the expression of CDCA7 positively correlated with the expression of N-cadherin, Vimentin, Snail, Slug, TGF-ß signaling pathway and negatively correlated with the expression of E-cadherin. Furthermore, CDCA7 transcriptionally regulated the expression of Smad4 and Smad7. Knockdown of CDCA7 inhibited the TGF-ß signaling pathway and therefore inhibited EMT. Our data indicated that CDCA7 was heavily involved in EMT by regulating the expression of Smad4 and Smad7 in TGF-ß signaling pathway. CDCA7 might be a new therapeutic target in the suppression of metastasis and invasion of ESCC.

A deep learning-based drug repurposing screening and validation for anti-SARS-CoV-2 compounds by targeting the cell entry mechanism.

The recent outbreak of Corona Virus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a severe threat to the global public health and economy, however, effective drugs to treat COVID-19 are still lacking. Here, we employ a deep learning-based drug repositioning strategy to systematically screen potential anti-SARS-CoV-2 drug candidates that target the cell entry mechanism of SARS-CoV-2 virus from 2635 FDA-approved drugs and 1062 active ingredients from Traditional Chinese Medicine herbs. In silico molecular docking analysis validates the interactions between the top compounds and host receptors or viral spike proteins. Using a SARS-CoV-2 pseudovirus system, we further identify several drug candidates including Fostamatinib, Linagliptin, Lysergol and Sophoridine that can effectively block the cell entry of SARS-CoV-2 variants into human lung cells even at a nanomolar scale. These efforts not only illuminate the feasibility of applying deep learning-based drug repositioning for antiviral agents by targeting a specified mechanism, but also provide a valuable resource of promising drug candidates or lead compounds to treat COVID-19.

Large-range lithography nano-alignment without phase unwrapping by a dual-frequency moiré fringe heterodyne.

Moiré fringe is an effective approach to realize nano-alignment. However, affected by short periodicity and phase unwrapping, moiré fringe technology has small alignment ranges and redundant algorithms, making it difficult to meet practical application requirements. To solve the problem, we propose a large-range lithography nano-alignment method without phase unwrapping by a dual-frequency moiré fringe heterodyne. This method obtains four sets of moiré fringes from the main and differential alignment marks and then calculates the misalignment information using the heterodyne method. In this approach, both large alignment range and high alignment accuracy are achieved while avoiding the phase unwrapping process. The experimental results verified the rationality and feasibility of the proposed method.

LncRNA GABPB1-IT1 inhibits the tumorigenesis of renal cancer via the miR-21/PTEN axis.

Long noncoding RNA (lncRNA) (GABPB1-IT1) has been reported to be downregulated in lung cancer, while its expression and function in other cancers are unknown. In this study, the expression levels of GABPB1-IT1 in tissue samples from 62 ccRCC patients were measured by performing RT-qPCR. Potential base pairing formed between GABPB1-IT1 and miR-21 was explored using the online program IntaRNA 2.0 and further confirmed by Dual-luciferase activity assay and RNA pulldown assay. The role of GABPB1-IT1 and miR-21 in regulating the expression of PTEN was evaluated by RT-qPCR and Western blot. The role of GABPB1-IT1, miR-21, and PTEN in regulating the proliferation of Caki-2 cells was explored by CCK-8 assay. It was observed that GABPB1-IT1 was downregulated in ccRCC and predicted poor survival. GABPB1-IT1 directly interacted with miR-21, while it did not regulate the expression of each other. Moreover, upregulation of PTEN, which is a target of miR-21, was observed in ccRCC cells with overexpression of GABPB1-IT1. Overexpression of GABPB1-IT1 and PTEN decreased the proliferation rates of ccRCC cells. In addition, overexpression of GABPB1-IT1 reduced the enhancing effects of miR-21 on cell proliferation. Therefore, GABPB1-IT1 may upregulate PTEN by sponging miR-21 in ccRCC to inhibit cancer cell proliferation. Our study characterized a novel GABPB1-IT1/miR-21/PTEN axis in ccRCC.

High-order spatial phase shift method realizes modulation analysis through a single-frame image.

For the modulation-based structured illumination microscopy system, how to obtain modulation distribution with an image has been a research hotspot. However, the existing frequency-domain single-frame algorithms (mainly including the Fourier transform method, wavelet method, etc.) suffer from different degrees of analytical error due to the loss of high-frequency information. Recently, a modulation-based spatial area phase-shifting method was proposed; it can obtain higher precision by retaining high-frequency information effectively. But for discontinuous (such as step) topography, it would be somewhat smooth. To solve the problem, we propose a high-order spatial phase shift algorithm that realizes robust modulation analysis of a discontinuous surface with a single-frame image. At the same time, this technique proposes a residual optimization strategy, so that it can be applied to the measurement of complex topography, especially discontinuous topography. Simulation and experimental results demonstrate that the proposed method can provide higher-precision measurement.

Efficient Fourier single-pixel imaging based on weighted sorting.

Fourier single-pixel imaging (FSI) has attracted increased attention in recent years with the advantages of a wide spectrum range and low cost. FSI reconstructs a scene by directly measuring the Fourier coefficients with a single-pixel detector. However, the existing sampling method is difficult to balance the noise suppression and image details within a limited number of measurements. Here we propose a new sampling strategy for FSI to solve this problem. Both the generality of the spectral distribution of natural images in the Fourier domain and the uniqueness of the spectral distribution of the target images in the Fourier domain are considered in the proposed method. These two distributions are summed with certain weights to determine the importance of the Fourier coefficients. Then these coefficients are sampled in order of decreasing importance. Both the simulations and experiments demonstrate that the proposed method can capture more key Fourier coefficients and retain more details with lower noise. The proposed method provides an efficient way for Fourier coefficient acquisition.

CRISP-view: a database of functional genetic screens spanning multiple phenotypes.

High-throughput genetic screening based on CRISPR/Cas9 or RNA-interference (RNAi) enables the exploration of genes associated with the phenotype of interest on a large scale. The rapid accumulation of public available genetic screening data provides a wealth of knowledge about genotype-to-phenotype relationships and a valuable resource for the systematic analysis of gene functions. Here we present CRISP-view, a comprehensive database of CRISPR/Cas9 and RNAi screening datasets that span multiple phenotypes, including in vitro and in vivo cell proliferation and viability, response to cancer immunotherapy, virus response, protein expression, etc. By 22 September 2020, CRISP-view has collected 10 321 human samples and 825 mouse samples from 167 papers. All the datasets have been curated, annotated, and processed by a standard MAGeCK-VISPR analysis pipeline with quality control (QC) metrics. We also developed a user-friendly webserver to visualize, explore, and search these datasets. The webserver is freely available at http://crispview.weililab.org.

Urological Tumor: A Narrative Review of Tertiary Lymphatic Structures.

BACKGROUND: Tertiary lymphoid structures (TLSs), as ectopic lymphoid-like tissues, are highly similar to secondary lymphoid organs and are not only involved in chronic inflammation and autoimmune responses but are also closely associated with tumor immunotherapy and prognosis. The complex composition of the urological tumor microenvironment not only varies greatly in response to immunotherapy, but the prognostic value of TLSs in different urological tumors remains controversial. SUMMARY: We searched PubMed, Web of Science, and other full-text database systems. TLSs, kidney cancer, uroepithelial cancer, bladder cancer, and prostate cancer as keywords, relevant literature was searched from the time the library was built to 2023. Systematically explore the role and mechanism of TLSs in urological tumors. It includes the characteristics of TLSs, the role and mechanism of TLSs in urological tumors, and the clinical significance of TLSs in urological tumors. KEY MESSAGES: The prognostic role of TLSs in different urological tumors was significantly different. It is not only related to its enrichment in the tumor but also highly correlated with the location of the tumor. In addition, autoimmune toxicity may be a potential barrier to its role in the formation of TLSs through induction. Therefore, studying the mechanisms of TLSs in autoimmune diseases may help in the development of antitumor target drugs.

Research on the purification enhancement of ecological ponds: Integrating water cycle optimization and plants layout.

The hydrodynamic conditions of ponds are generally poor, which seriously affects the long-term water quality guarantee. In this research, the numerical simulation method was used to establish an integrated model of hydrodynamics and water quality for the simulation of the plant purification effect in ponds. Based on the flushing time using the tracer method, the purification rate of plants was introduced to consider the purification effect of plants on water quality. In-situ monitoring was carried out at the Luxihe pond in Chengdu, and the model parameters such as the purification rate of typical plants were calibrated. The degradation coefficient of NH3-N in the non-vegetated area was 0.014 d-1 in August and 0.010 d-1 in November. In areas with vegetation, the purification rate of NH3-N was 0.10-0.20 g/(m2·d) in August and 0.06-0.12 g/(m2·d) in November. The comparison of the results in August and November showed that due to the higher temperature in August, the plant growth effect was better, and the degradation rate of pollutants and the purification rate of pollutants by plants were higher. The flushing time distribution of the proposed Baihedao pond under the conditions of terrain reconstruction, water replenishment, and plant layout was simulated, and the frequency distribution curve of flushing time was used to evaluate the results. Terrain reconstruction and water replenishment can significantly improve the water exchange capacity of ponds. The reasonable planting of plants can reduce the variability of the water exchange capacity. Based on this combined with the purification effect of plants on NH3-N, the layout plan of Canna, Cattails, and Thalia in ponds was proposed.

Establishing a quantitative assessment methodology framework of water conservation based on the water balance method under spatiotemporal and different discontinuous ecosystem scales.

Water conservation (WC) is an essential terrestrial ecosystem service that mitigates surface runoff and replenishes groundwater, which has received considerable attention under the dual pressures of climate change and human activity. However, there is insufficient understanding of the trends in WC changes on temporal (annual, monthly, daily), spatial, and ecosystem scales. This study proposed a quantitative assessment methodology framework (QAMF) for analyzing the spatiotemporal variation of WC under different discontinuous ecosystems. The QAMF mainly used models and methods such as the hydrological model (SWAT), calibration and uncertainty program (SWAT-CUP), WC calculation formula (water balance method), and spatial analysis method (empirical orthogonal function and wavelet analysis). It was applied to the source region of the Yellow River (SRYR), where the ecological landscape pattern underwent varying degrees of degradation, and WC capacity decreased. The results show that: Firstly, the constructed SWAT in the SRYR had high accuracy, and the proposed formula for calculating WC was suitable for multi-temporal scale analysis of WC in spatially distributed discontinuous basins. Secondly, the annual and monthly WC were respectively 81.00-184.13 mm and -28.58-107.64 mm, and daily WC was positive during extreme precipitation periods and negative during dry periods. The regulating effect of WC was fully reflected on the daily scale, partially reflected on the monthly scale, and absent on the annual scale. Third, the crucial WC area was mainly distributed in the southeast, and there was a significant primary yearly cycle of WC in the SRYR. Finally, different ecosystems exhibited different WC capabilities, and protecting the diversity of ecosystems played an essential role in maintaining and improving the WC function in the SRYR. This project has great scientific significance and technological support for scientifically evaluating the WC capacity in the SRYR.

An N-glycoproteomic site-mapping analysis reveals glycoprotein alterations in esophageal squamous cell carcinoma.

BACKGROUND: Aberrant glycosylation has been recognized as a hallmark of cancer and N-glycosylation is one of the main types of glycosylation in eukaryotes. Although N-glycoproteomics has made contributions to the discovery of biomarkers in a variety of cancers, less is known about the abnormal glycosylation signatures in esophageal squamous cell carcinoma (ESCC). METHODS: In this study, we reported the proteomics and N-glycoproteomic site-mapping analysis of eight pairs of ESCC tissues and adjacent normal tissues. With zic-HILIC enrichment, TMT-based isobaric labeling, LC-MS/MS analysis, differentially expressed N-glycosylation was quantitatively characterized. Lectin affinity enrichment combined with western blot was used to validate the potential biomarkers in ESCC. RESULTS: A series of differentially expressed glycoproteins (e.g., LAMP2, PLOD2) and enriched signaling pathways (e.g., metabolism-related pathway, ECM-receptor interaction, focal adhesion) were identified. Besides that, seven significantly enriched motifs were found from the identified N-glycosylation sites. Three clusters were identified after conducting the dynamic profiling analysis of glycoprotein change during lymph node metastasis progression. Further validation found that the elevated fucosylation level of ITGB1, CD276 contributed to the occurrence and development of ESCC, which might be the potential biomarkers in ESCC. CONCLUSION: In summary, we characterized the N-glycosylation and N-glycoprotein alterations associated with ESCC. The typical changes in glycoprotein expression and glycosylation occupancy identified in our study will not only be used as ESCC biomarkers but also improve the understanding of ESCC biology.

Single-exposure height-recovery structured illumination microscopy based on deep learning.

Modulation-based structured illumination microscopy (SIM) is performed to reconstruct three-dimensional (3D) surface topography. Generally speaking, modulation decoding algorithms mainly include a phase-shift (PS) method and frequency analysis technique. The PS method requires at least three images with fixed PSs, which leads to low efficiency. Frequency methods could decode modulation from a single image, but the loss of high-frequency information is inevitable. In addition, these methods all need to calculate the mapping relationship between modulation and height to recover the 3D shape. In this paper, we propose a deep learning enabled single-exposure surface measurement method. With only one fringe image, this method can directly restore the height information of the object. Processes such as denoising, modulation calculation, and height mapping are all included in the neural network. Compared with traditional Fourier methods, our method has higher accuracy and efficiency. Experimental results demonstrate that the proposed method can provide accurate and fast surface measurement for different structures.

FAT1 downregulation enhances stemness and cisplatin resistance in esophageal squamous cell carcinoma.

Primary or acquired drug resistance accounts for the failure of chemotherapy and cancer recurrence in esophageal squamous cell carcinoma (ESCC). However, the aberrant mechanisms driving drug resistance are not fully understood in ESCC. In our previous study, FAT Atypical Cadherin 1 (FAT1) was found to inhibit the epithelial-mesenchymal transition (EMT) process in ESCC. EMT plays a critical role in the development of drug resistance in multiple cancer types. Besides, it equips cancer cells with cancer stem cell (CSC)-like characters that also are associated with chemotherapy resistance. Whether FAT1 regulates the stemness or drug resistance of ESCC cells is worth being explored. Here we found that FAT1 was downregulated in ESCC spheres and negatively correlated with stemness-associated markers including ALDH1A1 and KLF4. Knocking down FAT1 enhanced the sphere-forming ability, resistance to cisplatin and drug efflux of ESCC cells. Additionally, FAT1 knockdown upregulated the expression of drug resistance-related gene ABCC3. Furtherly, we found FAT1 knockdown induced the translocation of ß-catenin into nucleus and enhanced its transcriptional activity. The result of ChIP showed that ß-catenin was enriched in ABCC3 promoter. Furthermore, ß-catenin promoted expression of ABCC3. In conclusion, FAT1 knockdown might enhance the stemness and ABCC3-related cisplatin resistance of ESCC cells via Wnt/ß-catenin signaling pathway. FAT1 and its downstream gene ABCC3 might be potential targets for overcoming chemoresistance in ESCC.

S-transform application in phase extraction of spectrally resolved interferometry measuring step height.

Spectrally resolved interferometry is widely used in the measurement of distance, displacement, film thickness, and surface morphology in micro/nano-scale geometric measurement. The core of spectrally resolved white-light interferometry is phase extraction. Temporal phase shifting, Fourier transform, wavelet transform, and other methods are commonly used in phase extraction of spectrally resolved interferometry. The S-transform, providing frequency-dependent resolution and having good time-frequency characteristics, is widely used in power quality disturbance analysis, seismic wave analysis, and phase recovery in profilometry. S-transform is used to extract the phase of the spectrally resolved white-light interferometry signal measuring step height. Compared with Fourier transform and wavelet transform, it is proved that S-transform is a feasible method in phase extraction of spectrally resolved interferometry measuring step height.

Diverse AR-V7 cistromes in castration-resistant prostate cancer are governed by HoxB13.

The constitutively active androgen receptor (AR) splice variant 7 (AR-V7) plays an important role in the progression of castration-resistant prostate cancer (CRPC). Although biomarker studies established the role of AR-V7 in resistance to AR-targeting therapies, how AR-V7 mediates genomic functions in CRPC remains largely unknown. Using a ChIP-exo approach, we show AR-V7 binds to distinct genomic regions and recognizes a full-length androgen-responsive element in CRPC cells and patient tissues. Remarkably, we find dramatic differences in AR-V7 cistromes across diverse CRPC cells and patient tissues, regulating different target gene sets involved in CRPC progression. Surprisingly, we discover that HoxB13 is universally required for and colocalizes with AR-V7 binding to open chromatin across CRPC genomes. HoxB13 pioneers AR-V7 binding through direct physical interaction, and collaborates with AR-V7 to up-regulate target oncogenes. Transcriptional coregulation by HoxB13 and AR-V7 was further supported by their coexpression in tumors and circulating tumor cells from CRPC patients. Importantly, HoxB13 silencing significantly decreases CRPC growth through inhibition of AR-V7 oncogenic function. These results identify HoxB13 as a pivotal upstream regulator of AR-V7-driven transcriptomes that are often cell context-dependent in CRPC, suggesting that HoxB13 may serve as a therapeutic target for AR-V7-driven prostate tumors.

Removal of Cd(II) using dithiocarboxyl cornstalk and the waste filtrate.

A novel adsorbent, called dithiocarboxyl cornstalk (DTCS), was developed, and the effects of various parameters on the adsorption performance for Cd(II) with DTCS were investigated in this work. The results suggested that DTCS presented the efficient removal capacity for Cd(II) when the pH values, adsorption temperature, and oscillation rate were 3.0 to 6.0, 313 K, and 150 rpm, respectively. The adsorption kinetic data were more agreed with pseudo-second-order kinetic model, and the isotherm data could be characterized by Freundlich model. The thermodynamic data indicated the adsorption process was endothermic and spontaneous. The FTIR and SEM confirmed the chemisorption between Cd(II) and DTCS. Furthermore, to eliminate the secondary pollution, the waste filtrate generated in the preparation of DTCS was employed to remove Cd(II) through flocculation experiments. The results showed that the waste filtrate is a potential flocculant for the treatment of wastewater containing Cd(II).

MYH9 promotes cell metastasis via inducing Angiogenesis and Epithelial Mesenchymal Transition in Esophageal Squamous Cell Carcinoma.

Non-muscle myosin heavy chain 9 (MYH9) is one novel low frequency mutated gene identified in esophageal squamous cell carcinoma (ESCC) using next-generation sequencing. However, its clinical relevance, potential function and mechanisms remain elusive. Methods: Genomic sequencing datas from 104 esophageal squamous cell carcinoma (ESCC) cases were screened a series of low frequency mutant genes. MYH9 was selected to further analyze its clinical significance, function and PCR-array was performed to explore its potential mechanism. Results: MHY9 is a low frequency mutant gene with a mutation frequency of 2.88% in ESCC. Immunohistochemical analysis showed that MYH9 expression was significantly higher in ESCC tumor tissues, and the expression levels were associated with lymph node metastasis of ESCC patients. Moreover, we found that MYH9 knock-down led to inhibition of cell migration and invasion. PCR-array showed MYH9 knockdown led to a significant change of genes expression associated with angiogenesis and epithelial-to-mesenchymal transition (EMT). This observation is further confirmed in TCGA database of LUSC (lung squamous cell carcinoma), CESC (cervical squamous cell carcinomas) and HNSC (head and neck squamous cell carcinoma). Conclusions: Collectively, our study identifies a novel role and mechanism of MYH9, highlights a significance of MYH9 as a metastatic biomarker, and offers potential therapeutic targets for ESCC patients harboring MYH9 mutations.

Considering gemcitabine-based combination chemotherapy as a potential treatment for advanced oesophageal cancer: A meta-analysis of randomised trials.

BACKGROUND: Gemcitabine has been proved to be effective in many advanced cancer. However, almost all trials failed to demonstrate the response rate of gemcitabine-based combination schedules on oesophageal cancer (EC). METHODS: A systematic meta-analysis of randomised clinical trials (RCTs) was performed to investigate the efficacy of gemcitabine-based combination chemotherapy in EC treatment. Clinical trials were collected during the period ranging from January 2000 to November 2018 by searching different databases. Odds-ratios (ORs) of response rate (RR), disease control rate (DCR) and grade 3-4 toxicity rates (TRs) were extracted as presented in retrieved studies. RESULTS: Fourteen trials (1024 patients) were selected for the final analysis. The results showed that RR and DCR of gemcitabine-based combination chemotherapy demonstrated a significant advantage for non-gemcitabine therapy (OR for RR: 1.51; 95% CI: 1.16-1.96; P = .002; OR for DCR: 1.66; 95% CI: 1.19-2.32, P = .003). Toxicities of gemcitabine-based combination chemotherapy on gastrointestinal tract (OR, 0.39; 95% CI: 0.24-0.63, P = .0001) were less frequent compared to that of the non-gemcitabine therapy. CONCLUSION: The improvements of gemcitabine-based combination chemotherapy on RR, CDR and reduction of gastrointestinal tract, hepatic and renal for EC patients suggests that the combined chemotherapy based on gemcitabine could be a potential treatment options for advanced EC.