SnapHiC-G: identifying long-range enhancer-promoter interactions from single-cell Hi-C data via a global background model.

Harnessing the power of single-cell genomics technologies, single-cell Hi-C (scHi-C) and its derived technologies provide powerful tools to measure spatial proximity between regulatory elements and their target genes in individual cells. Using a global background model, we propose SnapHiC-G, a computational method, to identify long-range enhancer-promoter interactions from scHi-C data. We applied SnapHiC-G to scHi-C datasets generated from mouse embryonic stem cells and human brain cortical cells. SnapHiC-G achieved high sensitivity in identifying long-range enhancer-promoter interactions. Moreover, SnapHiC-G can identify putative target genes for noncoding genome-wide association study (GWAS) variants, and the genetic heritability of neuropsychiatric diseases is enriched for single-nucleotide polymorphisms (SNPs) within SnapHiC-G-identified interactions in a cell-type-specific manner. In sum, SnapHiC-G is a powerful tool for characterizing cell-type-specific enhancer-promoter interactions from complex tissues and can facilitate the discovery of chromatin interactions important for gene regulation in biologically relevant cell types.

Development and validation of a preoperative CT­based radiomics nomogram to differentiate tuberculosis granulomas from lung adenocarcinomas: an external validation study.

BACKGROUND: An accurate and non-invasive approach is urgently needed to distinguish tuberculosis granulomas from lung adenocarcinomas. This study aimed to develop and validate a nomogram based on contrast enhanced-compute tomography (CE-CT) to preoperatively differentiate tuberculosis granuloma from lung adenocarcinoma appearing as solitary pulmonary solid nodules (SPSN). METHODS: This retrospective study analyzed 143 patients with lung adenocarcinoma (mean age: 62.4 ± 6.5 years; 54.5% female) and 137 patients with tuberculosis granulomas (mean age: 54.7 ± 8.2 years; 29.2% female) from two centers between March 2015 and June 2020. The training and internal validation cohorts included 161 and 69 patients (7:3 ratio) from center No.1, respectively. The external testing cohort included 50 patients from center No.2. Clinical factors and conventional radiological characteristics were analyzed to build independent predictors. Radiomics features were extracted from each CT-volume of interest (VOI). Feature selection was performed using univariate and multivariate logistic regression analysis, as well as the least absolute shrinkage and selection operator (LASSO) method. A clinical model was constructed with clinical factors and radiological findings. Individualized radiomics nomograms incorporating clinical data and radiomics signature were established to validate the clinical usefulness. The diagnostic performance was assessed using the receiver operating characteristic (ROC) curve analysis with the area under the receiver operating characteristic curve (AUC). RESULTS: One clinical factor (CA125), one radiological characteristic (enhanced-CT value) and nine radiomics features were found to be independent predictors, which were used to establish the radiomics nomogram. The nomogram demonstrated better diagnostic efficacy than any single model, with respective AUC, accuracy, sensitivity, and specificity of 0.903, 0.857, 0.901, and 0.807 in the training cohort; 0.933, 0.884, 0.893, and 0.892 in the internal validation cohort; 0.914, 0.800, 0.937, and 0.735 in the external test cohort. The calibration curve showed a good agreement between prediction probability and actual clinical findings. CONCLUSION: The nomogram incorporating clinical factors, radiological characteristics and radiomics signature provides additional value in distinguishing tuberculosis granuloma from lung adenocarcinoma in patients with a SPSN, potentially serving as a robust diagnostic strategy in clinical practice.

Development and validation of a [18F]FDG PET/CT-based radiomics nomogram to predict the prognostic risk of pretreatment diffuse large B cell lymphoma patients.

OBJECTIVE: In this study, based on PET/CT radiomics features, we developed and validated a nomogram to predict progression-free survival (PFS) for cases with diffuse large B cell lymphoma (DLBCL) treated with immunochemotherapy. METHODS: This study retrospectively recruited 129 cases with DLBCL. Among them, PET/CT scans were conducted and baseline images were collected for radiomics features along with their clinicopathological features. Radiomics features related to recurrence were screened for survival analysis using univariate Cox regression analysis with p < 0.05. Next, a weighted Radiomics-score (Rad-score) was generated and independent risk factors were obtained from univariate and multivariate Cox regressions to build the nomogram. Furthermore, the nomogram was tested for their ability to predict PFS using time-dependent receiver operating characteristic (ROC) curves, calibration curves, and decision curve analysis (DCA). RESULTS: Blood platelet, Rad-score, and gender were included in the nomogram as independent DLBCL risk factors for PFS. We found that the training cohort areas under the curve (AUCs) were 0.79, 0.84, and 0.88, and validation cohort AUCs were 0.67, 0.83, and 0.72, respectively. Further, the DCA and calibration curves confirmed the predictive nomogram's clinical relevance. CONCLUSION: Using Rad-score, blood platelet, and gender of the DLBCL patients, a PET/CT radiomics-based nomogram was developed to guide cases' recurrence risk assessment prior to treatment. The developed nomogram can help provide more appropriate treatment plans to the cases. KEY POINTS: • DLBCL cases can be classified into low- and high-risk groups using PET/CT radiomics based Rad-score. • When combined with other clinical characteristics (gender and blood platelet count), Rad-score can be used to predict the outcome of the pretreatment of DLBCL cases with a certain degree of accuracy. • A prognostic nomogram was established in this study in order to aid in assessing prognostic risk and providing more accurate treatment plans for DLBCL cases.

GuidePro: a multi-source ensemble predictor for prioritizing sgRNAs in CRISPR/Cas9 protein knockouts.

MOTIVATION: The efficiency of CRISPR/Cas9-mediated protein knockout is determined by three factors: sequence-specific sgRNA activity, frameshift probability and the characteristics of targeted amino acids. A number of computational methods have been developed for predicting sgRNA efficiency from different perspectives. However, an integrative method that combines all three factors for rational sgRNA selection is still lacking. RESULTS: We developed GuidePro, a two-layer ensemble predictor that enables the integration of multiple factors for the prioritization of sgRNAs in protein knockouts. Tested on independent datasets, GuidePro outperforms existing methods and demonstrates consistent superior performance in predicting phenotypes caused by protein loss-of-function, suggesting its robustness for prioritizing sgRNAs in various applications of CRISPR/Cas9 knockouts. AVAILABILITY AND IMPLEMENTATION: GuidePro is available at https://github.com/MDhewei/GuidePro. A web application for prioritizing sgRNAs that target protein-coding genes in human, monkey and mouse genomes is available at https://bioinformatics.mdanderson.org/apps/GuidePro. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Light grazing facilitates carbon accumulation in subsoil in Chinese grasslands: A meta-analysis.

Grazing by livestock greatly affects the soil carbon (C) cycle in grassland ecosystems. However, the effects of grazing at different intensities and durations on the dynamics of soil C in its subsoil layers are not clearly understood. Here, we compiled data from 78 sites (in total 122 published studies) to examine the effects of varying grazing intensities and durations on soil C content at different depths for grasslands in China. Our meta-analysis revealed that grazing led to an overall decrease in soil C content and productivity of above-ground vegetation (e.g., above-ground biomass and litter) but an increase in below-ground biomass. Specifically, the effects of grazing on soil C content became less negative or even positive with increasing soil depths. An increase of soil C content was consequently found under light grazing (LG), although soil C content still decreased under moderate and heavy grazing. The increase in soil C content under LG could be largely attributed to the increase of soil C content in subsoil layers (>20 cm), despite that soil C content in surface soil layer (0-20 cm) decreased. Moreover, the magnitude of increase in soil C content under LG in subsoil layers increased with grazing duration. A possible reason of the increase in soil C content in the subsoil layers was due to the increases in below-ground biomass. Our study highlights that LG may modify the allocation of C input and promote its accumulation in subsoil layers, thus offsetting the negative impact of grazing on surface soil C content, a finding that has significant implications for C sequestration in grasslands.

Revealing the spatio-temporal variability of evapotranspiration and its components based on an improved Shuttleworth-Wallace model in the Yellow River Basin.

Identifying the spatio-temporal variations of evapotranspiration (ET) from its components (soil evaporation and plant transpiration) can greatly improve our understanding of water-cycle and biogeochemical processes. However, partitioning evapotranspiration into evaporation (E) and transpiration (T) at regional scale with high accuracy still remains a challenge. This study has aimed to reveal the spatio-temporal variations of evapotranspiration and its components by using an improved Shuttleworth-Wallace (SWH) model to partition ET in the Yellow River Basin during 1981-2010. The environmental factors affecting the spatial and temporal variations of evapotranspiration and its components were also assessed. Results showed that the mean annual ET, T and E in the Yellow River Basin were 372.18 mm, 179.64 mm, and 192.54 mm, respectively, over the last 30 years. The spatial pattern of mean annual ET and T displayed a decreasing trend from southeast to northwest in the Yellow River Basin, and the temporal variation showed a significant increasing trend with rates of 1.72 mm yr-1 and 1.54 mm yr-1, respectively. It meant that T accounted for the variations of ET, while E showed no significant changes in recent decades. Moreover, the normalized differential vegetation index (NDVI) and temperature were identified as the main factors controlling the variations of ET and T in the Yellow River Basin. Among them, the area with NDVI as the dominant factor for ET and T could reach 63.82% and 78.47% of the whole basin respectively. However, the variations of E were affected by complex factors, and evaporation in the western alpine region was mainly controlled by temperature. Our findings are expected to not only have implications for developing sustainable policies of water management and ecological restoration in this region, but also provide valuable insight in methodology of ET partitioning in regional or global scale.

Combination of Circulating miRNA-320a/b and D-Dimer Improves Diagnostic Accuracy in Deep Vein Thrombosis Patients.

BACKGROUND D-dimer tests have been widely used to rule-out deep venous thrombosis (DVT), but with low specificity. Circulating microRNAs (miRNAs) are novel promising biomarkers in diverse diseases. The purpose of our study was to identify the diagnostic abilities of circulating miRNA-320a/b and to assess their correlation with plasma D-dimer in DVT and post-thrombotic syndrome (PTS) patients. MATERIAL AND METHODS Plasma samples were taken from 30 DVT patients, 30 PTS patients, and 30 age- and sex-matched healthy volunteers. Quantitative real-time PCR (qPCR) assay and turbidimetric immunoassay were conducted to assess the concentrations of miRNA-320a/b and D-dimer in plasma. RESULTS Circulating miRNA-320a and miRNA-320b were significantly upregulated in DVT patients with fold changes of 1.58 and 1.79, respectively. The receiver operating characteristic (ROC) curve analysis showed area under the curve (AUC) values of 0.70 (95% CI: 0.56-0.83) for miRNA-320a and 0.79 (95% CI: 0.67-0.90) for miRNA-320b. Moreover, plasma levels of miRNA-320b were associated with D-dimer values (r=0.52, 95% CI: 0.19-0.74) in DVT. However, no significant changes in plasma miRNA-320a/b and D-dimer were detected in PTS patients. CONCLUSIONS Compared with controls, circulating miRNA-320a/b was differentially expressed in DVT. Simultaneous detection of miRNA-320a/b with D-dimer may improve diagnostic accuracy of DVT.

Platelet-to-lymphocyte ratio, neutrophil-to-lymphocyte ratio, and platelet indices in patients with acute deep vein thrombosis.

BACKGROUND: Inflammation is associated with an increased risk of thrombotic events and complete blood count (CBC) is an easily measured test. The purpose of this study was to evaluate the value of CBC relative parameters including mean platelet volume (MPV), platelet-to-lymphocyte ratio (PLR), mean platelet volume-to-lymphocyte ratio (MPVLR), and neutrophil-to-lymphocyte ratio (NLR) for patients with acute deep vein thrombosis (DVT). PATIENTS AND METHODS: A total of 115 patients with unprovoked DVT of the lower extremities and 105 controls were recruited in this study. Blood samples were drawn from all participants to obtain the concentrations of CBCs and D-dimers. RESULTS: MPVs (P = 0.044), PLRs (P = 0.005), MPVLRs (P = 0.001), and NLRs (P < 0.0001) were significantly higher in acute DVT patients compared to controls. The MPV was inversely correlated with platelet count (P < 0.0001) and the NLR was positively associated with D-dimers (P = 0.002) and the PLR (P < 0.0001). Notably, on multivariate logistic regression analysis, NLRs and D-dimers were independent risk factors of acute DVT (OR: 1.889, P = 0.024; OR: 1.009, P < 0.0001, respectively). CONCLUSIONS: MPV, PLR, MPVLR, and NLR have potential diagnostic values for patients with unprovoked DVT. NLR is an independent risk factor related to DVT.

Integrative analysis of Anoikis-related genes reveals that FASN is a novel prognostic biomarker and promotes the malignancy of bladder cancer via Wnt/ß-catenin pathway.

Bladder cancer (BC) exhibits diversity in clinical outcomes and is characterized by heterogeneity. Anoikis, a form of programmed cell death, plays a crucial role in facilitating tumor invasion and metastasis. This study comprehensively investigated the genetic landscape of BC progression, identifying 300 differentially expressed Anoikis-related genes (DE-ARGs) through in-depth analysis of the GSE13507 datasets. Functional enrichment analysis revealed associations with diverse diseases and biological processes. Employing machine learning algorithms, a logistic regression model based on nine marker genes demonstrated superior accuracy in distinguishing BC from normal samples. Validation in TCGA datasets highlighted the prognostic significance of LRP1, FASN, and SIRT6, suggesting their potential as cancer biomarkers. Particularly, FASN emerged as an independent prognostic indicator, regulating BC cell proliferation and metastasis through the Wnt/ß-catenin pathway. The study provides crucial insights into altered genetic landscapes and potential therapeutic strategies for BC, emphasizing the significance of FASN in BC prognosis and progression.

Quorum sensing regulation in Microcystis aeruginosa: Insights into AHL-mediated physiological processes and MC-LR production.

Quorum sensing (QS) is a widespread regulatory mechanism in Gram-negative bacteria, primarily involving the secretion of N-acyl homoserine lactone (AHL) to facilitate population density sensing. However, the existence of QS in blue-green algae, a subset of photoautotrophic Gram-negative bacteria forming high-density communities in water blooms, remains elusive. This study delves into the unexplored realm of QS in Microcystis aeruginosa (M. aeruginosa) by investigating AHL-related regulatory mechanisms and their impact on various physiological processes. Utilizing high-performance liquid chromatography coupled with mass spectrometry (HPLC-MS) and biosensors, a hitherto unknown long-chain AHL exhibiting a mass-to-charge ratio of 318 was identified in sterile M. aeruginosa cultures. Our investigation focused on discerning correlations between AHL activity fluctuations and key parameters such as microcystin (MC-LR) production, algal density, photosynthesis, buoyancy, and aggregation. Furthermore, the AHL extract was introduced during the logarithmic stage of M. aeruginosa cultures to observe the response in physiological processes. The results revealed that AHL, functioning as an autoinducer (AI), positively influenced algal growth and photosynthesis, as evidenced by the upregulated photosynthetic conversion efficiency of PSI and chlorophyll synthesis gene (psbA). AI also played a crucial role in altering surface characteristics through the synthesis of polysaccharides and proteins in EPS, subsequently promoting cell aggregation. Concomitantly, AI upregulated mcyD, enhancing the synthesis of MC-LR. Notably, our investigation pinpointed the initiation of QS in Microcystis at a density of approximately 1.22 × 10^7 cells/mL. This groundbreaking evidence underscores the regulatory role of AI in governing the physiological processes of growth, aggregation, buoyancy, and MC-LR production by activating pertinent gene expressions. This study significantly expands the understanding of QS in AHL, providing crucial insights into the regulatory networks operating in blue-green algae.

Integrating land-sea coordination into construction of an ecological security pattern for urban agglomeration: a case study in the Guangdong-Hong Kong-Macao Greater Bay Area.

The construction of ecological security pattern (ESP) is of great scientific significance for solving the problem of habitat fragmentation in urban environment. However, previous studies mainly focused on the ESP in land area, leaving the sea area to be ignored. This study took the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) and its offshore area as an example and integrated the land-sea coordination into the construction of ESP based on the minimum resistance model, gravity model, and graph theory centrality. The results showed that there are 171 and 56 ecological sources for land area and offshore area, accounting for 31.46% and 21.51% of total area, respectively. Twenty-four important ecological corridors with a total length of 2738.05 km were identified in GBA, and the width is proposed to be less than 100 m. Moreover, the α, ß, and γ index of the ecological network in the study area is 0.19, 1.33, and 0.5, respectively, indicating that the ecological network structure is complex and the connectivity between ecological nodes is good. The ecological restoration area includes 286.6 km2 of ecological pinch points and 140.44 km2 of ecological barrier. The overall ESP of the study area is "one ring, two belts, and four zones." The main body of the area with a superior ecological environment is distributed in a ring-like pattern near the outer edge of the study area, and two belts (important ecological corridor and ecological corridor) are distributed in a network. According to the ecological characteristics, the study area was divided into four zones: ecological preservation areas, ecological restoration areas, limited construction areas, and optimized construction areas. The ESP established herein institute provides a reference for the revision of ecological space control and optimization measures in the GBA. It also provides effective and systematic means to solve ecological problems in the current territorial spatial planning and territorial ecological restoration of coastal urban agglomeration.

Prediction of preoperative lymph-vascular space invasion and survival outcomes of cervical squamous cell carcinoma by utilizing 18F-FDG PET/CT imaging at early stage.

OBJECTIVE: To establish nomograms for predicting preoperative lymph-vascular space invasion (LVSI) and survival outcomes of cervical squamous cell carcinoma (CSCC) based on PET/CT radiomics. METHODS: One hundred and twenty-three patients with CSCC and LVSI status were enrolled retrospectively. Independent predictors of LVSI were identified through clinicopathological factors and PET/CT metabolic parameters. We extracted 1316 features from PET and CT volume of interest, respectively. Additionally, four models (PET-RS: radiomic signature of PET only; CT-RS: radiomic signature of CT only; PET/CT-RS + clinical data; PET/CT-RS: radiomic signature of PET and CT) were established to predict LVSI status. Calculation of radiomics scores of PET/CT was executed for assessment of the survival outcomes, followed by development of nomograms with radiomics (NR) or without radiomics (NWR). RESULTS: One hundred and twenty-three patients with pathologically confirmed CSCC had been categorized into two sets (training and testing sets). It was found that only maximum standardized uptake value (SUVmax) and squamous cell carcinoma antigen were independent predictors of LVSI. Meanwhile, the PET/CT-RS + clinical data outperformed the other three models in the training set [area under the curve (AUC): 0.91 vs. 0.861 vs. 0.81 vs. 0.814] and the testing set (AUC: 0.885 vs. 0.857 vs. 0.783 vs. 0.798). Additionally, SUVmax and LVSI had been demonstrated to be independent prognostic indicators for progression-free survival and overall survival. Decision curve analysis and calibration curve indicated that NRs were superior to NWRs. The survival outcomes were assessed. CONCLUSION: PET/CT-based radiomic signature nomogram enables a new method for preoperative prediction of LVSI and survival prognosis for patients with CSCC.

Draw on advantages and avoid disadvantages: CT-derived individualized radiomic signature for predicting chemo-radiotherapy sensitivity in unresectable advanced non-small cell lung cancer.

BACKGROUND: Presently, the options of concurrent chemo-radiotherapy (CCR) in patients with locally advanced non-small cell lung cancer (LA-NSCLC) are controversial and there is no reliable prediction tool to stratify poor- and good-responders. Although radiomic analysis has provided new opportunities for personalized medicine in oncological practice, the repeatability and reproducibility of radiomic features are critical challenges that hinder their widespread clinical adoption. This study aimed to develop a qualitative radiomic signature based on the within-sample rank of radiomics features, and to use this novel method to predict CCR sensitivity in LA-NSCLC, avoiding the variability of quantitative signatures to multicenter effect. METHODS: We retrospectively analyzed 125 patients with stage III NSCLC who received treatment from our hospital. Radiomic features were extracted from pretreatment plain CT scans and constructed as feature pairs based on their within-sample rank. Fisher and univariate Cox analyses were performed to select feature pairs significantly associated with patients' overall survival (OS). NSCLC-Radiomic (R422) cohort including 104 NSCLC patients was used as an independent testing cohort. NSCLC-Radiogenomic (RG211) cohort with matched RNA sequencing profiles, was used for functional enrichment analysis to reveal the underlying biological mechanism reflected by the signature. RESULTS: A qualitative signature, consisting of 15 radiomic feature pairs (termed as 15-RiFPS), was developed based on the Genetic Algorithm, which could optimally distinguish responder from non-responder with significantly improved OS if they received CCR treatment (log-rank P = 0.0009, HR = 13.79, 95% CIs 1.83-104.1). The performance of 15-RiFPS was validated in an independent public cohort (log-rank P = 0.0037, HR = 2.40, 95% CIs 1.30-4.40). Furthermore, the transcriptomic analyses provided biological pathways ('glutathione metabolic process', 'cellular oxidant detoxification') underlying the signature. CONCLUSIONS: We developed a CT-derived 15-RiFPS, which could potentially help predict individualized therapeutic benefit of CCR in patients with LA-NSCLC. Additionally, we investigated the underlying intra-tumoral biological characteristics behind 15-RiFPS which would accelerate its clinical application. This approach could be applied to a wider range of treatments and cancer types.

The interaction mechanisms of algal organic matter (AOM) and various types and aging degrees of microplastics.

Algal blooms can produce substantial amounts of algal organic matter (AOM). Microplastics (MPs) in aquatic environments inevitably interact with AOM. Meanwhile, the aging and type of MPs may increase the uncertainty surrounding interaction. This study focused on polyethylene (PE) and polylactic acid (PLA) to investigate their interaction with AOM before and after aging. The results shw that PLA has a stronger adsorption capacity for AOM than PE. Meanwhile, aging enhanced and weakened the adsorption of PE and PLA for AOM. Compared to unaged PE (UPE) and aged PLA (APLA), aged PE (APE) and unaged PLA (UPLA) more significantly promote the humification of AOM and alter its functional groups. 2D-IR-COS analysis reveals that the sequence of functional group changes in AOM interacting with MPs is influenced by the type and aging of MPs. After interacting with AOM, surface roughness increased for all MPs. FTIR and XPS analyses show that the addition of AOM accelerated the oxidation of MPs surfaces, especially for UPE and APLA, with oxygen content increasing by 9.32 % and 1 %. Aging enhances the interaction between PE and AOM, while weakening the interaction between PLA and AOM. These findings provide new insights into understanding the interplay between AOM and MPs.

Identifying Migration Routes of Wild Asian Elephants in China Based on Ecological Networks Constructed by Circuit Theory Model.

Humans overlap with Asian elephants, resulting in frequent costly human-elephant conflicts, which disturb and even threaten local residents. In this study, we treat provincial and national nature reserves where Asian elephants still exist and other alternative habitats suitable for Asian elephants in southern Yunnan, China, as ecological patches. By using this approach, we can treat the terrain and surface state factors that hinder the migration of Asian elephants as a form of ecological resistance surface. We can then use a circuit theory model and remote sensing data to construct an ecological network, which allows us to identify ecological corridors and ecological pinch points. Herein, the possible migration routes of wild Asian elephants were identified. The main results are as follows: (1) In the study area, dense forests with steep slopes and high altitudes, cultivated land, and building land have greater migration resistance, while the gently undulating shrubs, bamboo forests, and grasslands far away from the city have less migration resistance. (2) There are three ecological corridor groups in the study area, mainly composed of shrub and grassland. The ecological corridors identified in this paper are the most likely migration routes of wild Asian elephants in China, and areas with higher simulated current densities reflect a higher probability of Asian elephants passing through. (3) According to the analysis, the ecological pinch points in the study area are 602 km2 in total, and woodland and grassland account for 89.2% of the total ecological pinch area. The areas where the pinch points are located have a high probability of Asian elephants passing through and a narrow space. Our findings can provide suggestions and solutions for the current conservation of wild Asian elephant species, alleviate human-elephant conflicts, promote the harmonious coexistence between humans and nature, and provide reference for biological protection and biological reserve planning.

Superiority of FAPI-PET/CT for examining multiple malignant tumors: a retrospective study.

To compare the diagnostic value of [18F]-AlF-NOTA-FAPI-04 PET/CT and [18F]-FDG PET/CT for primary and metastatic lesions in different types of tumors. A retrospective analysis was conducted on 51 patients with 11 different types of tumors. Among them, 20 patients underwent PET/CT, and 31 patients underwent restaging. The patients were diagnosed using [18F]-AlF-NOTA-FAPI-04 PET/CT and [18F]-FDG PET/CT scan techniques, and adverse reactions were recorded. Thickness of primary lesions, metastasis, and lymph node involvement were analyzed and confirmed by histological analysis. The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of [18F]-AlF-NOTA-FAPI-04 PET/CT and [18F]-FDG PET/CT were calculated. Neither [18F]-AlF-NOTA-FAPI-04 PET/CT nor [18F]-FDG PET/CT scan techniques caused adverse reactions in the patients. [18F]-AlF-NOTA-FAPI-04 PET/CT performed well in detecting recurrence, with a positive rate of 100%, higher than 71.0% of [18F]-FDG PET/CT. Compared with [18F]-FDG PET/CT, [18F]-AlF-NOTA-FAPI-04 PET/CT identified 6 types of malignant tumors more clearly, and could improve the detection rate of primary and metastatic tumors (97.0% vs. 84.8%, P<0.001). [18F]-AlF-NOTA-FAPI-04 PET/CT exhibited a higher sensitivity for detecting lymph node (81.8% vs. 50.0%, P<0.05) than [18F]-FDG PET/CT. Additionally, [18F]-AlF-NOTA-FAPI-04 PET/CT demonstrated higher diagnostic sensitivity (67.39% vs. 58.7%, P=0.387) and accuracy (82.14% vs. 60.71%, P=0.377) for detecting metastatic lesions compared to [18F]-FDG PET/CT. [18F]-AlF-NOTA-FAPI-04 PET/CT outperforms [18F]-FDG PET/CT in diagnosing primary and metastatic lesions across various types of tumors, especially in identifying lymph node, visceral, and peritoneal metastases. It can improve diagnostic efficiency and accuracy, thereby positively influencing clinical decision-making for optimal patient management.

Differentiating thymic epithelial tumors from mediastinal lymphomas: preoperative nomograms based on PET/CT radiomic features to minimize unnecessary anterior mediastinal surgery.

PURPOSE: Clinical feasibility nomograms were developed to facilitate the differentiation between thymic epithelial tumors (TETs) and mediastinal lymphomas (MLs), aiming to minimize the occurrence of non-therapeutic thymectomy. METHODS: A total of 255 patients diagnosed with TETs or MLs underwent pre-treatment 18F-FDG PET/CT. Comprehensive clinical and imaging data were collected, including age, gender, lactate dehydrogenase (LDH) level, pathological results, presence of myasthenia gravis symptoms, B symptoms, mass size, location, morphology, margins, density, and metabolic parameters derived from PET/CT. Radiomic features were extracted from the region of interest (ROI) of the primary lesion. Feature selection techniques were employed to identify the most discriminative subset of features. Machine learning methods were utilized to build candidate models, which were subsequently evaluated based on their area under the curve (AUC). Finally, nomograms were constructed using the optimal model to provide a clinical tool for improved diagnostic accuracy. The performance of the radiomic models was evaluated by their calibration, discrimination, and clinical utility. RESULTS: Several independent risk factors were identified for distinguishing TETs from MLs, including average standardized uptake value (SUVavg), LDH, age, mass size, and radiomic score (rad-score). Significance was observed in differentiating the two types of tumors based on these factors. The best clinical efficacy was demonstrated by the combined model, with an impressive AUC of 0.954. Decision curve analysis and calibration curves indicated that the combined model was clinically advantageous for discriminating TETs from MLs. Besides, the results of external validation showed a sensitivity of 0.8 and a specificity of 0.78. CONCLUSION: Preoperatively, the differentiation of TETs from MLs can be facilitated by the utilization of the combined clinical information and radiomics model. This approach holds promise in minimizing the occurrence of unnecessary anterior mediastinal surgeries.

Development and validation of 18F-FDG PET/CT radiomics-based nomogram to predict visceral pleural invasion in solid lung adenocarcinoma.

OBJECTIVES: This study aimed to establish a radiomics model based on 18F-FDG PET/CT images to predict visceral pleural invasion (VPI) of solid lung adenocarcinoma preoperatively. METHODS: We retrospectively enrolled 165 solid lung adenocarcinoma patients confirmed by histopathology with 18F-FDG PET/CT images. Patients were divided into training and validation at a ratio of 0.7. To find significant VPI predictors, we collected clinicopathological information and metabolic parameters measured from PET/CT images. Three-dimensional (3D) radiomics features were extracted from each PET and CT volume of interest (VOI). Receiver operating characteristic (ROC) curve was performed to determine the performance of the model. Accuracy, sensitivity, specificity and area under curve (AUC) were calculated. Finally, their performance was evaluated by concordance index (C-index) and decision curve analysis (DCA) in training and validation cohorts. RESULTS: 165 patients were divided into training cohort (n = 116) and validation cohort (n = 49). Multivariate analysis showed that histology grade, maximum standardized uptake value (SUVmax), distance from the lesion to the pleura (DLP) and the radiomics features had statistically significant differences between patients with and without VPI (P < 0.05). A nomogram was developed based on the logistic regression method. The accuracy of ROC curve analysis of this model was 75.86% in the training cohort (AUC: 0.867; C-index: 0.867; sensitivity: 0.694; specificity: 0.889) and the accuracy rate in validation cohort was 71.55% (AUC: 0.889; C-index: 0.819; sensitivity: 0.654; specificity: 0.739). CONCLUSIONS: A PET/CT-based radiomics model was developed with SUVmax, histology grade, DLP, and radiomics features. It can be easily used for individualized VPI prediction.

An innovative strategy to control Microcystis growth using tea polyphenols sustained-release particles: preparation, characterization, and inhibition mechanism.

Allelochemicals have been shown to inhibit cyanobacterial blooms for several years. In view of the disadvantages of "direct-added" mode, natural and pollution-free tea polyphenolic allelochemicals with good inhibitory effect on cyanobacteria were selected to prepare sustained-release particles by microcapsule technology. Results showed that the encapsulation efficiency of tea polyphenols sustained-release particles (TPSPs) was 50.6% and the particle size ranged from 700 to 970 nm, which reached the nanoscale under optimum preparation condition. Physical and chemical properties of TPSPs were characterized to prove that tea polyphenols were well encapsulated and the particles had good thermal stability. The optimal dosage of TPSPs was determined to be 0.3 g/L, at which the inhibition rate on Microcystis aeruginosa in logarithmic growth period could be maintained above 95%. Simultaneous decrease in algal density and chlorophyll-a content indicated that the photosynthesis of algal cells was affected leading to cell death. Significant changes of antioxidant enzyme activities suggested that Microcystis aeruginosa's antioxidant systems had been disrupted. Furthermore, TPSPs increased the concentration of O2- which led to lipid peroxidation of cell membrane and a subsequent increase in malondialdehyde (MDA) content. Meanwhile, the protein content, nucleic acid content, and electrical conductivity in culture medium rose significantly indicating the cell membrane was irreversibly damaged. This work can provide a basis for the utilization of environmentally friendly algal suppressants.

Integrated transcriptomic and metabolomic analysis of Microcystis aeruginosa exposed to artemisinin sustained-release microspheres.

Artemisinin sustained-release microspheres (ASMs) have been shown to inhibit Microcystis aeruginosa (M. aeruginosa) blooms. Previous studies have focused on inhibitory mechanism of ASMs on the physiological level of M. aeruginosa, but the algal inhibitory mechanism of ASMs has not been comprehensively and profoundly revealed. The study proposed to reveal the toxicity mechanism of ASMs on M. aeruginosa based on transcriptomics and metabolomics. After exposure to 0.2 g·L-1 ASMs for 7 days, M. aeruginosa biomass was significantly inhibited, with an inhibition rate (IR) of 47 % on day 7. Transcriptomic and metabolomic results showed that: (1) 478 differentially expressed genes (DEGs) and 251 differential metabolites (DMs) were obtained; (2) ASMs inhibited photosynthesis by blocking photosynthetic pigment synthesis, destroying photoreaction centers and photosynthetic carbon reactions; (3) ASMs reduced L-glutamic acid content and blocked glutathione (GSH) synthesis, leading to an imbalance in the antioxidant system; (4) ASM disrupted nitrogen metabolism and the hindered synthesis of various amino acids; (5) ASMs inhibited glyoxylate cycle and TCA cycle. This study provides an important prerequisite for the practical application of ASMs and a new perspective for the management of harmful algal blooms (HABs).