Influence of environmental filtering and spatial processes on macroinvertebrate community in urban lakes in the Taihu Lake Basin, China.

Studies identifying the relative importance of multiple ecological processes in macroinvertebrate communities in urban lakes at a basin scale are rare. In this study, 14 urban lakes in the Taihu Lake Basin were selected to explore the relative importance of environmental filtering and spatial processes in the assembly of macroinvertebrate communities. Our findings revealed significant spatiotemporal variations in macroinvertebrate communities, both between lakes and across seasons. We found that environmental filtering exerted a greater influence on taxonomic total beta diversity and its individual components (species turnover and nestedness) compared to spatial processes. Key environmental variables such as water depth, water temperature, total dissolved solids, chlorophyll a, and lake surface area were found to be crucial in shaping macroinvertebrate communities within these urban lakes. The observed high spatial heterogeneity in environmental conditions, along with intermediate basin areas, good connectivity and short distances between lakes, and the high dispersal ability of dominant taxa, likely contributed to the dominance of environmental filtering in macroinvertebrate community assembly. Our study contributes to a better understanding of the underlying mechanisms governing macroinvertebrate community assembly in urban lakes, thereby providing valuable insights for studies on community ecology and water environmental protection in urban lakes.

The virtual staining method by quantitative phase imaging for label free lymphocytes based on self-supervised iteration cycle-consistent adversarial networks.

Quantitative phase imaging (QPI) provides 3D structural and morphological information for label free living cells. Unfortunately, this quantitative phase information cannot meet doctors' diagnostic requirements of the clinical "gold standard," which displays stained cells' pathological states based on 2D color features. To make QPI results satisfy the clinical "gold standard," the virtual staining method by QPI for label free lymphocytes based on self-supervised iteration Cycle-Consistent Adversarial Networks (CycleGANs) is proposed herein. The 3D phase information of QPI is, therefore, trained and transferred to a kind of 2D "virtual staining" image that is well in agreement with "gold standard" results. To solve the problem that unstained QPI and stained "gold standard" results cannot be obtained for the same label free living cell, the self-supervised iteration for the CycleGAN deep learning algorithm is designed to obtain a trained stained result as the ground truth for error evaluation. The structural similarity index of our virtual staining experimental results for 8756 lymphocytes is 0.86. Lymphocytes' area errors after converting to 2D virtual stained results from 3D phase information are less than 3.59%. The mean error of the nuclear to cytoplasmic ratio is 2.69%, and the color deviation from the "gold standard" is less than 6.67%.

Dynamic three-dimensional deformation measurement by polarization-multiplexing of full complex amplitude.

This paper provides an extensive discussion of a complex amplitude-based dynamic three-dimensional deformation measurement method, in which the phase and amplitude of the speckle field are used for out-of-plane and in-plane deformation calculation respectively. By determining the optimal polarization states of the speckle field and reference field from the comprehensive analysis of measurement mathematical model in the principle of polarization multiplexing, the 3-step phase-shifting interferograms and one speckle gram can be directly recorded by a polarization camera in a single shot. The out-of-plane deformation would be recovered from the subtraction of speckle phases that are demodulated by a special least square algorithm; speckle gram with improved quality is offered for correlation computation to obtain in-plane deformation. The advancement and significance of the optimized strategy are intuitively demonstrated by comparing the measurement accuracy under different combinations of polarization states. Finally, the dynamic thermal deformation experiment reveals the potential in practical real-time applications.

Importance of DNA nanotechnology for DNA methyltransferases in biosensing assays.

DNA methylation is the process by which specific bases on a DNA sequence acquire methyl groups under the catalytic action of DNA methyltransferases (DNMT). Abnormal changes in the function of DNMT are important markers for cancers and other diseases; therefore, the detection of DNMT and the selection of its inhibitors are critical to biomedical research and clinical practice. DNA molecules can undergo intermolecular assembly to produce functional aggregates because of their inherently stable physical and chemical properties and unique structures. Conventional DNMT detection methods are cumbersome and complicated processes; therefore, it is necessary to develop biosensing technology based on the assembly of DNA nanostructures to achieve rapid analysis, simple operation, and high sensitivity. The design of the relevant program has been employed in life science, anticancer drug screening, and clinical diagnostics. In this review, we explore how DNA assembly, including 2D techniques like hybridization chain reaction (HCR), rolling circle amplification (RCA), catalytic hairpin assembly (CHA), and exponential isothermal amplified strand displacement reaction (EXPAR), as well as 3D structures such as DNA tetrahedra, G-quadruplexes, DNA hydrogels, and DNA origami, enhances DNMT detection. We highlight the benefits of these DNA nanostructure-based biosensing technologies for clinical use and critically examine the challenges of standardizing these methods. We aim to provide reference values for the application of these techniques in DNMT analysis and early cancer diagnosis and treatment, and to alert researchers to challenges in clinical application.

Sedation versus general anesthesia on all-cause mortality in patients undergoing percutaneous procedures: a systematic review and meta-analysis.

BACKGROUND: The comparison between sedation and general anesthesia (GA) in terms of all-cause mortality remains a subject of ongoing debate. The primary objective of our study was to investigate the impact of GA and sedation on all-cause mortality in order to provide clarity on this controversial topic. METHODS: A systematic review and meta-analysis were conducted, incorporating cohort studies and RCTs about postoperative all-cause mortality. Comprehensive searches were performed in the PubMed, EMBASE, and Cochrane Library databases, with the search period extending until February 28, 2023. Two independent reviewers extracted the relevant information, including the number of deaths, survivals, and risk effect values at various time points following surgery, and these data were subsequently pooled and analyzed using a random effects model. RESULTS: A total of 58 studies were included in the analysis, with a majority focusing on endovascular surgery. The findings of our analysis indicated that, overall, and in most subgroup analyses, sedation exhibited superiority over GA in terms of in-hospital and 30-day mortality. However, no significant difference was observed in subgroup analyses specific to cerebrovascular surgery. About 90-day mortality, the majority of studies centered around cerebrovascular surgery. Although the overall pooled results showed a difference between sedation and GA, no distinction was observed between the pooled ORs and the subgroup analyses based on RCTs and matched cohort studies. For one-year all-cause mortality, all included studies focused on cardiac and macrovascular surgery. No difference was found between the HRs and the results derived from RCTs and matched cohort studies. CONCLUSIONS: The results suggested a potential superiority of sedation over GA, particularly in the context of cardiac and macrovascular surgery, mitigating the risk of in-hospital and 30-day death. However, for the longer postoperative periods, this difference remains uncertain. TRIAL REGISTRATION: PROSPERO CRD42023399151; registered 24 February 2023.

RhMED15a-like, a subunit of the Mediator complex, is involved in the drought stress response in Rosa hybrida.

BACKGROUND: Rose (Rosa hybrida) is a globally recognized ornamental plant whose growth and distribution are strongly limited by drought stress. The role of Mediator, a multiprotein complex crucial for RNA polymerase II-driven transcription, has been elucidated in drought stress responses in plants. However, its physiological function and regulatory mechanism in horticultural crop species remain elusive. RESULTS: In this study, we identified a Tail module subunit of Mediator, RhMED15a-like, in rose. Drought stress, as well as treatment with methyl jasmonate (MeJA) and abscisic acid (ABA), significantly suppressed the transcript level of RhMED15a-like. Overexpressing RhMED15a-like markedly bolstered the osmotic stress tolerance of Arabidopsis, as evidenced by increased germination rate, root length, and fresh weight. In contrast, the silencing of RhMED15a-like through virus induced gene silencing in rose resulted in elevated malondialdehyde accumulation, exacerbated leaf wilting, reduced survival rate, and downregulated expression of drought-responsive genes during drought stress. Additionally, using RNA-seq, we identified 972 differentially expressed genes (DEGs) between tobacco rattle virus (TRV)-RhMED15a-like plants and TRV controls. Gene Ontology (GO) analysis revealed that some DEGs were predominantly associated with terms related to the oxidative stress response, such as 'response to reactive oxygen species' and 'peroxisome'. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment highlighted pathways related to 'plant hormone signal transduction', in which the majority of DEGs in the jasmonate (JA) and ABA signalling pathways were induced in TRV-RhMED15a-like plants. CONCLUSION: Our findings underscore the pivotal role of the Mediator subunit RhMED15a-like in the ability of rose to withstand drought stress, probably by controlling the transcript levels of drought-responsive genes and signalling pathway elements of stress-related hormones, providing a solid foundation for future research into the molecular mechanisms underlying drought tolerance in rose.

A Foggy Weather Simulation Algorithm for Traffic Image Synthesis Based on Monocular Depth Estimation.

This study addresses the ongoing challenge for learning-based methods to achieve accurate object detection in foggy conditions. In response to the scarcity of foggy traffic image datasets, we propose a foggy weather simulation algorithm based on monocular depth estimation. The algorithm involves a multi-step process: a self-supervised monocular depth estimation network generates a relative depth map and then applies dense geometric constraints for scale recovery to derive an absolute depth map. Subsequently, the visibility of the simulated image is defined to generate a transmittance map. The dark channel map is then used to distinguish sky regions and estimate atmospheric light values. Finally, the atmospheric scattering model is used to generate fog simulation images under specified visibility conditions. Experimental results show that more than 90% of fog images have AuthESI values of less than 2, which indicates that their non-structural similarity (NSS) characteristics are very close to those of natural fog. The proposed fog simulation method is able to convert clear images in natural environments, providing a solution to the problem of lack of foggy image datasets and incomplete visibility data.

Genome-Wide Extrachromosomal Circular DNA Profiling of Paired Hepatocellular Carcinoma and Adjacent Liver Tissues.

Hepatocellular carcinoma (HCC) develops through multiple mechanisms. While recent studies have shown the presence of extrachromosomal circular DNA (eccDNA) in most cancer types, the eccDNA expression pattern and its association with HCC remain obscure. We aimed to investigate this problem. The genome-wide eccDNA profiles of eight paired HCC and adjacent non-tumor tissue samples were comprehensively elucidated based on Circle-seq, and they were further cross-analyzed with the RNA sequencing data to determine the association between eccDNA expression and transcriptome dysregulation. A total of 60,423 unique eccDNA types were identified. Most of the detected eccDNAs were smaller than 1 kb, with a length up to 182,363 bp and a mean sizes of 674 bp (non-tumor) and 813 bp (tumor), showing a greater association with gene-rich rather than with gene-poor regions. Although there was no statistical difference in length and chromosome distribution, the eccDNA patterns between HCC and adjacent non-tumor tissues showed significant differences at both the chromosomal and single gene levels. Five of the eight HCC tissues showed significantly higher amounts of chromosome 22-derived eccDNA expression compared to the non-tumor tissue. Furthermore, two genes, SLC16A3 and BAIAP2L2, with a higher transcription level in tumor tissues, were related to eccDNAs exclusively detected in three HCC samples and were negatively associated with survival rates in HCC cohorts from public databases. These results indicate the existence and massive heterogeneity of eccDNAs in HCC and adjacent liver tissues, and suggest their potential association with dysregulated gene expression.

Novel Oxidation Oligomer of Chlorogenic Acid and (-)-Epigallocatechin and Its Quantitative Analysis during the Processing of Keemun Black Tea.

Not only do flavan-3-ols participate in the formation of chromogenic oxidation products such as theaflavins, but chlorogenic acid (3-caffeoylquinic acid, CQA) is also involved in the enzymatic oxidation during black tea processing. The critical oxidation product of CQA and (-)-epigallocatechin (EGC) were identified as an adduct containing benzobicyclo[3.2.2]nonenone structure, which was named as the dichlorogeniccatechin (DCGC) oligomer. It was composed of two molecules of CQA and one molecule of EGC. The effects of the initial reactant ratio and reaction time on the generation of DCGC were also analyzed. A high proportion of CQA promoted the production of DCGC, but a high proportion of EGC inhibited the DCGC formation. In addition, the content of DCGC in Keemun black tea during processing was determined. The content of DCGC highly increased after withering but decreased after drying. This study provides a new perspective for the investigation of other oxidation oligomers in black tea.

Flexible dynamic quantitative phase imaging based on division of focal plane polarization imaging technique.

This paper proposes a flexible and accurate dynamic quantitative phase imaging (QPI) method using single-shot transport of intensity equation (TIE) phase retrieval achieved by division of focal plane (DoFP) polarization imaging technique. By exploiting the polarization property of the liquid crystal spatial light modulator (LC-SLM), two intensity images of different defocus distances contained in orthogonal polarization directions can be generated simultaneously. Then, with the help of the DoFP polarization imaging, these images can be captured with single exposure, enabling accurate dynamic QPI by solving the TIE. In addition, our approach gains great flexibility in defocus distance adjustment by adjusting the pattern loaded on the LC-SLM. Experiments on microlens array, phase plate, and living human gastric cancer cells demonstrate the accuracy, flexibility, and dynamic measurement performance for various objects. The proposed method provides a simple, flexible, and accurate approach for real-time QPI without sacrificing the field of view.

Fast and robust calibration method of liquid-crystal spatial light modulator based on polarization multiplexing.

We propose a fast and robust method for calibrating Spatial Light Modulators (SLMs) based on polarization phase-shifting interferometry. Our method effectively calibrates the SLM by addressing both the static aberration and nonlinear phase response, utilizing specially designed gray images loaded sequentially onto the SLM. Notably, we introduce a novel kinoform that effectively eliminates the influence of tilt phase shift between two shots of the polarization camera. This results in a highly accurate phase aberration map and phase modulation curve with exceptional stability, making it an ideal method to calibrate the SLM with exceptional efficiency and precision in real applications.

A novel biosensor based on tetrahedral DNA nanostructure and terminal deoxynucleotidyl transferase-assisted amplification strategy for fluorescence analysis of uracil-DNA glycosylase activity.

Tetrahedral DNA nanostructure (TDN), as a classical bionanomaterial, which not only has excellent structural stability and rigidity, but also possesses high programmability due to strict base-pairs complementation, is widely used in various biosensing and bioanalysis fields. In this study, we first constructed a novel biosensor based on Uracil DNA glycosylase (UDG) -triggered collapse of TDN and terminal deoxynucleotidyl transferase (TDT)-induced insertion of copper nanoparticles (CuNPs) for fluorescence and visual analysis of UDG activity. In the presence of the target enzyme UDG, the uracil base modified on the TDN were specifically identified and removed to produce an abasic site (AP site). Endonuclease IV (Endo.IV) could cleave the AP site, making the TDN collapse and generating 3'-hydroxy (3'-OH), which were then elongated under the assistance of TDT to produce poly (T) sequences. Finally, Copper (II) sulfate (Cu2+) and l-Ascorbic acid (AA) were added to form CuNPs using poly (T) sequences as templates (T-CuNPs), resulting in a strong fluorescence signal. This method exhibited good selectivity and high sensitivity with a detection limit of 8.6 × 10-5 U/mL. Moreover, the strategy has been successfully applied to the screening of UDG inhibitors and the detection of UDG activity in complex cell lysates, which means that it has promising applications in clinical diagnosis and biomedical research.

Foliar spraying with a mixture of transpiration inhibitor-rhamnolipid reduces the Cd content in rice grains.

A field experiment was conducted to investigate the effectiveness and mechanisms of foliar spraying of transpiration inhibitor (TI) and different amounts of rhamnolipid (Rh) on the Cd content in rice grain. The contact angle of TI on the rice leaves was significantly reduced when it was combined with one critical micelle concentration of Rh. The Cd concentration in the rice grain in the presence of TI, TI + 0.5Rh, TI + 1Rh, and TI + 2Rh significantly decreased by 30.8 %, 41.7 %, 49.4 %, and 37.7 % respectively, compared with the control treatment. Specifically, the Cd content with TI + 1Rh was as low as 0.182 ± 0.009 mg/kg, which meets the national food safety requirements (< 0.2 mg/kg). The rice yield and plant biomass of TI + 1Rh were highest compared to the other treatments, possibly because of the alleviation of oxidative stress due to Cd. The hydroxyl and carboxyl concentrations in the soluble components in the leaf cells for the TI + 1Rh treatment were the highest compared to the other treatments. Our results demonstrated that the foliar spraying of TI + 1Rh is an efficient method to reduce Cd accumulation in rice grain. It holds potential for the future development of safe food production in soils polluted with Cd.

Accurate dynamic 3D deformation measurement based on the synchronous multiplexing of polarization and speckle metrology.

An accurate dynamic 3D deformation measurement method realized by the combination of phase-shifting speckle interferometry and speckle correlation is proposed. By converting the speckle field and the reference field into a circular polarized and linear polarized state, the three-step phase-shifting speckle interferograms and one specklegram were recorded directly and simultaneously within a single image by using a polarization camera. Then, the out-of-plane deformation was demodulated from the synchronous phase-shifting fringe patterns, and the in-plane deformation was measured by performing correlation calculations by using specklegrams with the effect of the reference field ignored. Thus, the full-field 3D deformation was obtained precisely. Experimental results demonstrated the accuracy and dynamic measurement ability of the proposed method, which is compact and feasible for actual dynamic scenes.

Double-wing switch nanodevice-mediated primer exchange reaction for the activity analysis of cancer biomarker FEN1.

DNA damage repair is one of the foremost factors leading to changes in tumor drug resistance. The analysis of Flap endonuclease 1 (FEN1), a kind of pivotal enzyme in various DNA metabolic pathways, has been of great support to tumor research and the development of chemotherapeutics. Nevertheless, few analytical techniques can achieve quantitative and simplified FEN1 measurement. Here, we constructed a double-wing switch nanodevice (DWSN)-mediated primer exchange technique for rapid and label-free quantification of FEN1 activity. Target FEN1 triggered the generation of numerous telomeric repeat fragments in different lengths through recognizing the three-base mismatched sites on the DWSN to release the 5'-Flaps. Further binding to the fluorescent dye ThT resulted in significantly enhanced fluorescence. This study broke the limitation of traditional single-site identification and demonstrated good sensitivity and specificity with detection limits up to 0.55 mU. Besides, the extraordinary analytical performance allowed the method to be utilized to monitor FEN1 extracted from cells and clinical serum samples and to compare the effect of targeted FEN1 inhibitors.

Single-shot quantitative phase imaging with phase modulation of a liquid crystal spatial light modulator (LC-SLM) under white light illumination.

We propose a novel, to the best of our knowledge, single-shot quantitative phase imaging (QPI) technique with the phase modulation of a liquid crystal spatial light modulator (LC-SLM) under white light illumination. By studying the phase modulation characteristics of an LC-SLM under white light illumination, images captured at different wavelengths are equivalent to those captured at different defocus distances when loading a Fresnel lens pattern on the LC-SLM. Consequently, a color camera is able to simultaneously acquire multi-intensity images at different defocus distances. Finally, the phase is retrieved from a single-shot color image using the transport of intensity equation. To demonstrate the flexibility and accuracy of our method, a photoetched phase object and human red blood cells are quantitatively measured. An investigation of living yeast cells is conducted to verify the dynamic measurement capability. The proposed method provides a simple, efficient, and flexible means to accomplish real-time high-resolution quantitative phase imaging without sacrificing the field of view (FOV), which can be further integrated into a conventional microscope to achieve real-time microscopic QPI.

Gene-microRNA Network Analysis Identified Seven Hub Genes in Association with Progression and Prognosis in Non-Small Cell Lung Cancer.

INTRODUCTION: Lung cancer is the leading cause of cancer deaths in the world and is usually divided into non-small cell lung cancer (NSCLC) and small cell lung cancer. NSCLC is dominant and accounts for 85% of the total cases. Currently, the therapeutic method of NSCLC is not so satisfactory, and thus identification of new biomarkers is critical for new clinical therapy for this disease. METHODS: Datasets of miRNA and gene expression were obtained from the NCBI database. The differentially expressed genes (DEGs) and miRNAs (DEMs) were analyzed by GEO2R tools. The DEG-DEM interaction was built via miRNA-targeted genes by miRWalk. Several hub genes were selected via network topological analysis in Cytoscape. RESULTS: A set of 276 genes were found to be significantly differentially expressed in the three datasets. Functional enrichment by the DAVID tool showed that these 276 DEGs were significantly enriched in the term "cancer", with a statistic p-value of 1.9 × 10-5. The subdivision analysis of the specific cancer types indicated that "lung cancer" occupies the largest category with a p-value of 2 × 10-3. Furthermore, 75 miRNAs were shown to be differentially expressed in three representative datasets. A group of 13 DEGs was selected by analysis of the miRNA-gene interaction of these DEGs and DEMs. The investigation of these 13 genes by GEPIA tools showed that eight of them had consistent results with NSCLC samples in the TCGA database. In addition, we applied the KMplot to conduct the survival analysis of these eight genes and found that seven of them have a significant effect on the prognosis survival of patients. We believe that this study could provide effective research clues for the prevention and treatment of non-small cell lung cancer.

Characterization of the complete chloroplast genome of orchid family species Paphiopedilum bellatulum.

The genus Paphiopedilum is well known as the lady's slipper orchid in Orchidaceae family. Paphiopedilum bellatulum (Rchb.f.) Stein 1892, has important medicinal and ornamental value, which occurs in the tropical Asia. However, in recent decades, it was threatened with extinction by significantly reduced small population size. In this study, we sequenced and characterized the complete chloroplast genome of P. bellatulum based on the Illumina Hiseq platform. The size of P. bellatulum chloroplast genome was 156,567 bp, including a large single-copy (LSC) region of 88,243 bp, a small single-copy (SSC) region of 3652 bp, and two inverted repeat regions (IRs) of 32,336 bp. The overall GC contents of the chloroplast genome were 35.71%. A total of 122 genes were annotated, including 76 protein-coding genes, 38 transfer RNAs (tRNAs), and eight ribosomal RNAs (rRNAs). The phylogenetic analysis indicated that P. bellatulum formed a close relationship with another Paphiopedilum species P. wenshanense. The results will provide helpful genetic resource for further phylogenetic studies of the genus Paphiopedilum.

Sign-singularity solution in single-frame speckle interferometry with vortex-phase modulation.

We propose a sign-singularity solution in single-shot digital speckle interferometry based on vortex-phase modulation. The vortex phase is introduced through the reference beam as variation information by a reflective liquid crystal spatial light modulator. The sign singularity is eliminated with the help of a single spiral speckle fringe pattern. To effectively obtain the deformation phase, the measurement process is specially designed on the consideration of the modulation principle of the vortex phase, which is discussed in terms of theoretical analysis and simulation results. Experiments on out-of-plane deformation measurement reveal the feasibility of the proposed method and suggest the potential in actual dynamic measurement applications.

The fluorescence amplification strategy based on 3D DNA walker and CRISPR/Cas12a for the rapid detection of BRAF V600E.

Circulating tumor DNA (ctDNA) is a fragment of single- or double-stranded DNA originating from tumor or circulating tumor cells and provides accurate information regarding the molecular characteristics of tumors. Therefore, sensitive detection of ctDNA is of great significance to mutation analysis and clinical diagnosis. Among various ctDNAs, the BRAF V600E is related to aggressive behavior, disease recurrence, and disease-specific mortality in papillary thyroid carcinoma. Herein, we selected the BRAF V600E gene sequence as an in vitro biomarker, and established a fluorescence detection strategy combined 3D DNA walker with CRISPR/Cas12a. In the presence of the target ctDNA, 3D DNA walker could identify and bind it, and thus released a large amount of output DNAs through cyclic cleavage with the assistance of specific endonuclease (Nb.BbvCI). The output DNAs were specifically bound to crRNA and activated the non-specific trans-cleavage activity of Cas12a. Finally, the fluorescence signal was significantly enhanced. Notably, this method can detect the BRAF V600E in a range of 1 fM ~ 20 nM with a detection limit of 0.37 fM without DNA polymerase. Due to the powerful amplification capability of 3D DNA walker and high specificity and programmability of CRISPR/Cas12a, the entire process took only a maximum of 70 min. Furthermore, it can be potentially used for the detection of ctDNA in human serum. In summary, this method not only provides a platform for the rapid detection of ctDNA, but also shows good potential for early clinical diagnosis and biomedical research.