The genomes of Dahlia pinnata, Cosmos bipinnatus, and Bidens alba in tribe Coreopsideae provide insights into polyploid evolution and inulin biosynthesis.

BACKGROUND: The Coreopsideae tribe, a subset of the Asteraceae family, encompasses economically vital genera like Dahlia, Cosmos, and Bidens, which are widely employed in medicine, horticulture, ecology, and food applications. Nevertheless, the lack of reference genomes hinders evolutionary and biological investigations in this tribe. RESULTS: Here, we present 3 haplotype-resolved chromosome-level reference genomes of the tribe Coreopsideae, including 2 popular flowering plants (Dahlia pinnata and Cosmos bipinnatus) and 1 invasive weed plant (Bidens alba), with assembled genome sizes 3.93 G, 1.02 G, and 1.87 G, respectively. We found that Gypsy transposable elements contribute mostly to the larger genome size of D. pinnata, and multiple chromosome rearrangements have occurred in tribe Coreopsideae. Besides the shared whole-genome duplication (WGD-2) in the Heliantheae alliance, our analyses showed that D. pinnata and B. alba each underwent an independent recent WGD-3 event: in D. pinnata, it is more likely to be a self-WGD, while in B. alba, it is from the hybridization of 2 ancestor species. Further, we identified key genes in the inulin metabolic pathway and found that the pseudogenization of 1-FEH1 and 1-FEH2 genes in D. pinnata and the deletion of 3 key residues of 1-FFT proteins in C. bipinnatus and B. alba may probably explain why D. pinnata produces much more inulin than the other 2 plants. CONCLUSIONS: Collectively, the genomic resources for the Coreopsideae tribe will promote phylogenomics in Asteraceae plants, facilitate ornamental molecular breeding improvements and inulin production, and help prevent invasive weeds.

Shared and task-specific brain functional differences across multiple tasks in children with developmental dyslexia.

Different tasks have been used in examining the neural functional differences associated with developmental dyslexia (DD), and consequently, different findings have been reported. However, very few studies have systematically compared multiple tasks in understanding what specific task differences each brain region is associated with. In this study, we employed an auditory rhyming task, a visual rhyming task, and a visual spelling task, in order to investigate shared and task-specific neural differences in Chinese children with DD. First, we found that children with DD had reduced activation in the opercular part of the left inferior frontal gyrus (IFG) only in the two rhyming tasks, suggesting impaired phonological analysis. Children with DD showed functional differences in the right lingual gyrus/inferior occipital gyrus only in the two visual tasks, suggesting deficiency in their visuo-orthographic processing. Moreover, children with DD showed reduced activation in the left dorsal inferior frontal gyrus and increased activation in the right precentral gyrus across all of the three tasks, suggesting neural signatures of DD in Chinese. In summary, our study successfully separated brain regions associated with differences in orthographic processing, phonological processing, and general lexical processing in DD. It advances our understanding about the neural mechanisms of DD.

Sagittal en bloc resection of thoracolumbar tumours: a report of thirty one cases.

PURPOSE: To develop a novel classification of sagittal en bloc resection (SEBR) based on anatomical locations for thoracolumbar spine tumors and assess the clinical outcomes of this surgical procedure. METHODS: 31 patients with thoracolumbar tumours treated with SEBR were enrolled in this study. The individualized surgical strategy was adopted based on our surgical classification. Demographics, perioperative outcomes, complications and postoperative outcomes were assessed. RESULTS: Based on our surgical classifications, patients were divided into four types. All bony resection margins were negative, wide resection was achieved in 25 patients, marginal resection in four, and intralesional resection in two. 18 patients underwent anterior reconstruction. Complications were encountered in five patients, and instrumentation failure occurred in one patient. The median follow-up was 24 (range, 6-72) months and recurrence was found in only one patient. CONCLUSION: SEBR is a safe and effective surgical procedure for patients with thoracolumbar spinal tumours in specific anatomical locations. The proposed surgical classification covers all SEBR types and is easy to apply, it may assist surgical decision-making in patients with spinal tumours.

Physiological occlusal force attenuates replacement root resorption of replanted teeth: an experimental animal study.

BACKGROUND: Tooth avulsion represents the most severe form of dental trauma, necessitating tooth replantation as the primary treatment. However, the risk of replacement root resorption (RRR) poses a significant threat to tooth retention following replantation. This study preliminarily aimed to investigate the effect of physiological occlusal force on RRR after the replantation of avulsed teeth and to explore the potential underlying mechanisms. METHODS: Thirty-six 4-week-old male Sprague-Dawley rats underwent extraction and immediate replantation of their left maxillary molars. The rats were randomly divided into two major groups: the occluded (n = 18) group, where the opposite mandibular teeth were preserved; non-occluded (n = 18) group, where the opposite mandibular teeth were extracted. Within each major group, there were three subgroups corresponding to 7 days, 14 days, and 2 months, resulting in a total of six subgroups, (n = 6 per subgroup). The right maxillary first molars served as the normal control. Various periodontal characteristics were assessed using haematoxylin-eosin (H&E), tartrate-resistant acid phosphatase (TRAP) staining, and micro-computed tomography (micro-CT). RESULTS: Histological staining revealed that under occlusal force, the early stage (day 7) after tooth replantation mainly manifested as root surface resorption, especially in the non-occluded group, which gradually diminished over time. Cementum and periodontal ligament (PDL) repair was observed on day 14. Micro-CT analysis indicated a significant decrease in PDL width in the non-occluded group two months after replantation, consistent with the histological findings, signifying severe RRR in the non-occluded group. CONCLUSIONS: This study provides preliminary evidence that physiological occlusal force may attenuate osteoclastogenesis during the early stage of tooth replantation, thereby reducing the occurrence of RRR and promoting periodontal healing.

Impaired neurogenesis induced by fluoride via the Notch1 signaling and effects of carvacrol intervention.

The negative regulation on neurogenesis has been implicated in fluoride neurotoxicity, while the evidence is limited. To explore whether fluoride interferes with neurogenesis via the Notch1 signaling and the potential alleviation effects of carvacrol (CAR), we conducted in vivo and in vitro experiments, as well as epidemiological analyses in this study. The results showed that urinary fluoride levels and circulating Notch1 levels were associated with IQ levels in boys. NaF-treated rats had fewer neurons, lower densities of dendritic spines, depressed neurogenesis, and impaired learning and memory abilities. In vitro experiments using undifferentiated PC12 cells mimicking neurogenesis revealed that NaF suppressed differentiation and neurite outgrowth. Besides, Notch1 signaling activation was detected in vivo and in vitro. The latter was confirmed using an in vitro model supplemented with DAPT, a potent Notch1 inhibitor. Furthermore, CAR supplementation negatively regulated NICD1 and Hes1 expressions and promoted hippocampal neurogenesis, thereby improving neurological functions in NaF-treated rats. These findings indicated that the inhibition of neurogenesis in hippocampi induced by fluoride via Notch1 signaling activation may be one of the underlying mechanisms of its neurotoxicity, and that CAR significantly alleviated the neurotoxicity of NaF via the Notch1 signaling.

PD-L1 expression in ovarian clear cell carcinoma using the 22C3 pharmDx assay.

BACKGROUND: Ovarian clear cell carcinoma (OCCC), well known for its chemoresistance to platinum-based chemotherapy, exhibited a good response in clinical trials of anti-PD-1/PD-L1 inhibitors. By assessing PD-L1 expression, we sought to determine the potential therapeutic benefit of PD-1/PD-L1 inhibitors in OCCC. METHODS AND RESULTS: The retrospective study included 152 individuals with OCCC between 2019 and 2022 at Peking Union Medical College Hospital. Paired tumors of primary versus recurrent lesions (17 pairs from 15 patients) or primary versus metastatic lesions (11 pairs from 9 patients) were also included. The 22C3 pharmDx assay and whole sections were used for PD-L1 immunohistochemical staining. Pathologists with experience in premarket clinical trials evaluated PD-L1 expression based on various diagnostic criteria (TPS 1%, CPS 1, or CPS 10). The number and percentage of positive PD-L1 cases were 34 (22.4%, TPS ≥ 1%) and 59 (38.8%, CPS ≥ 1), respectively. Thirty-three (21.7%) of the cases had high PD-L1 expression (CPS ≥ 10). Half of the platinum-resistant patients (11/22) were PD-L1 positive (CPS ≥ 1). In addition, positive PD-L1 expression (CPS ≥ 1) was related to clinicopathological characteristics that represented a worse prognosis, such as advanced stages, lymph node metastasis, and distant metastasis (p = 0.032, p < 0.001 and p = 0.003, separately). PD-L1 was expressed equally or more in the recurrent lesion compared with its matched primary lesion. CONCLUSIONS: In conclusion, anti-PD-1/PD-L1 inhibitors are a promising therapeutic choice for OCCC. For evaluation of PD-L1 expression, CPS is more recommended than TPS. Evaluation of recurrent lesion was still suitable and predictive when the primary tumor tissue was not available. Distant metastatic lesions can serve as alternative samples for PD-L1 evaluation, while usage of lymphatic metastatic lesions is not recommended.

Hemodynamic Impairment of Blood Pressure and Stroke Mechanisms in Symptomatic Intracranial Atherosclerotic Stenosis.

BACKGROUND: Hemodynamic impairment of blood pressure may play a crucial role in determining the mechanisms of stroke in symptomatic intracranial atherosclerotic stenosis). We aimed to elucidate this issue and assess the impacts of modifications to blood pressure on hemodynamic impairment. METHODS: From the Third China National Stroke Registry III, computed fluid dynamics modeling was performed using the Newton-Krylov-Schwarz method in 339 patients with symptomatic intracranial atherosclerotic stenosis during 2015 to 2018. The major exposures were translesional systolic blood pressure (SBP) drop and poststenotic mean arterial pressure (MAP), and the major study outcomes were cortex-involved infarcts and borderzone-involved infarcts, respectively. Multivariate logistic regression models and the bootstrap resampling method were utilized, adjusting for demographics and medical histories. RESULTS: In all, 184 (54.3%) cortex-involved infarcts and 70 (20.6%) borderzone-involved infarcts were identified. In multivariate logistic model, the upper quartile of SBP drop correlated with increased cortex-involved infarcts (odds ratio, 1.92 [95% CI, 1.03-3.57]; bootstrap analysis odds ratio, 2.07 [95% CI, 1.09-3.93]), and the lower quartile of poststenotic MAP may correlate with increased borderzone-involved infarcts (odds ratio, 2.07 [95% CI, 0.95-4.51]; bootstrap analysis odds ratio, 2.38 [95% CI, 1.04-5.45]). Restricted cubic spline analysis revealed a consistent upward trajectory of the relationship between translesional SBP drop and cortex-involved infarcts, while a downward trajectory between poststenotic MAP and borderzone-involved infarcts. SBP drop correlated with poststenotic MAP negatively (rs=-0.765; P<0.001). In generating hemodynamic impairment, simulating blood pressure modifications suggested that ensuring adequate blood pressure to maintain sufficient poststenotic MAP appears preferable to the reverse approach, due to the prolonged plateau period in the association between the translesional SBP drop and cortex-involved infarcts and the relatively short plateau period characterizing the correlation between poststenotic MAP and borderzone-involved infarcts. CONCLUSIONS: This research elucidates the role of hemodynamic impairment of blood pressure in symptomatic intracranial atherosclerotic stenosis-related stroke mechanisms, underscoring the necessity to conduct hemodynamic assessments when managing blood pressure in symptomatic intracranial atherosclerotic stenosis.

Integrating single-cell and spatial analysis reveals MUC1-mediated cellular crosstalk in mucinous colorectal adenocarcinoma.

BACKGROUND: Mucinous colorectal adenocarcinoma (MCA) is a distinct subtype of colorectal cancer (CRC) with the most aggressive pattern, but effective treatment of MCA remains a challenge due to its vague pathological characteristics. An in-depth understanding of transcriptional dynamics at the cellular level is critical for developing specialised MCA treatment strategies. METHODS: We integrated single-cell RNA sequencing and spatial transcriptomics data to systematically profile the MCA tumor microenvironment (TME), particularly the interactome of stromal and immune cells. In addition, a three-dimensional bioprinting technique, canonical ex vivo co-culture system, and immunofluorescence staining were further applied to validate the cellular communication networks within the TME. RESULTS: This study identified the crucial intercellular interactions that engaged in MCA pathogenesis. We found the increased infiltration of FGF7+/THBS1+ myofibroblasts in MCA tissues with decreased expression of genes associated with leukocyte-mediated immunity and T cell activation, suggesting a crucial role of these cells in regulating the immunosuppressive TME. In addition, MS4A4A+ macrophages that exhibit M2-phenotype were enriched in the tumoral niche and high expression of MS4A4A+ was associated with poor prognosis in the cohort data. The ligand-receptor-based intercellular communication analysis revealed the tight interaction of MUC1+ malignant cells and ZEB1+ endothelial cells, providing mechanistic information for MCA angiogenesis and molecular targets for subsequent translational applications. CONCLUSIONS: Our study provides novel insights into communications among tumour cells with stromal and immune cells that are significantly enriched in the TME during MCA progression, presenting potential prognostic biomarkers and therapeutic strategies for MCA. KEY POINTS: Tumour microenvironment profiling of MCA is developed. MUC1+ tumour cells interplay with FGF7+/THBS1+ myofibroblasts to promote MCA development. MS4A4A+ macrophages exhibit M2 phenotype in MCA. ZEB1+ endotheliocytes engage in EndMT process in MCA.

Exclusion-zone water inside and outside of plant xylem vessels.

The fourth phase of water has garnered increased attention within the scientific community due to its distinct properties that differentiate it from regular water. This unique state seems to arise potentially from a liquid crystalline structure, which has been observed near various hydrophilic surfaces to possess the capability of excluding microspheres. Consequently, it has been labeled as exclusion zone (EZ) water. When in contact with hydrophilic surfaces, water could exhibit the ability to form organized layers of EZ water. In this study, we investigated the quick buildup of EZ water exposed to xylem vessels of four vegetable plants: cabbage, celery, asparagus, and pumpkin. Among them, pumpkin vessels showed larger EZs, up to 240 ± 56 µm in width. The width of EZ water found near the xylem vessels of the other plants ranged from 133 ± 22 to 142 ± 20 µm. EZ water generally excludes a wide range of particles, including polystyrene microspheres with various surface modifications, as well as silica microspheres. This implies that the formation of EZ water is not an artificial result of using specific microsphere types but rather demonstrates EZ's ability to exclude particles regardless of their composition. Inside single xylem vessels of the pumpkin, we could observe the dynamics of EZ buildup, growing from the inside edge of the vessel toward the center. The relationship between vessel diameter, vessel length, and salt concentration on EZ generation inside the xylem vessel was also explored. The results showed that EZ water can build up both inside and outside the xylem vessels. Our findings suggest that EZ generation inside xylem vessels is associated with water flow, likely driven by a proton gradient. Further research is warranted to elucidate the role of EZ water in the physiology of living plants, particularly considering the limitations of the current experiments conducted on cut-out xylem vessel samples.

Effect of Overheating on the Tensile Properties of Nickel-Based Superalloy GH4720Li.

Aero-engines can be exposed to One Engine Inoperative (OEI) conditions during service, and the resulting overheating effect may significantly impact their structural integrity and flight safety. This paper focuses on the influence of overheating on the microstructural evolution and tensile properties of the GH4720Li alloy, a nickel-based polycrystalline superalloy commonly used in turbine disks. Based on the typical OEI operating conditions of a real aero-engine, a series of non-isothermal high-temperature tensile tests involving an OEI stage of 800 °C were conducted. The effects of OEI-induced overheating on the microstructure and tensile properties of the GH4720Li alloy were investigated. The results showed that, after OEI treatment, the primary γ' phase in this alloy was partially dissolved. The GH4720Li superalloy also exhibited numerous microcracks at the grain boundaries, resulting in complex effects on its tensile properties. The alloy's yield strength and ultimate tensile strength were slightly decreased, whereas its ductility decreased considerably. The OEI-induced embrittlement phenomenon was mainly caused by the non-uniform distribution of the tertiary γ' phase within grains. The formation of microcracks nucleated at the interfaces between the primary γ' precipitates and γ matrix phase was another key factor.

Study on the Performance of a High-Speed Motor, Considering the Effect of Temperature on the Properties of High-Strength Non-Oriented Silicon Steel.

Considering the high-speed and high power density technical specifications of new energy vehicle motors, there is a growing demand for rotor strength as motor peak speeds reach 20,000 r/min and beyond. The utilization of non-oriented silicon steel with a high yield strength in rotors has emerged as a promising approach to increase motor speed. However, the magnetic and mechanical properties of high-strength silicon steel under variable temperature conditions have not been fully explored, particularly in regards to their impact on motor torque, efficiency, and speed. This manuscript investigates the behavior of high-strength silicon steel before and after annealing and at different temperatures, analyzing its influence on high-speed motor performance. The validity and feasibility of this study are confirmed through prototype testing, providing a comprehensive reference for engineering design.

Quinomycins with an unusual N-methyl-3-methylsulfinyl-alanine residue from a Streptomyces sp.

Four new echinomycin congeners, quinomycins M-P (1-4) were isolated from the cultures of the soil-derived Streptomyces sp. CPCC205575. The planar structures were determined by comprehensive analyses of NMR and HRESIMS/MS data. The absolute configurations were elucidated by the advanced Marfey's method combined with biosynthetic gene analysis. Compounds 1-4 represent the first examples of quinomycin-type natural products with the sulfur atom at the N,S-dimethylcysteine residue oxidized as a sulfoxide group forming the unusual N-methyl-3-methylsulfinyl-alanine residue. Bioassay results revealed that the oxidation of the sulfur atom at the Cys or Cys' residues led to dramatic decrease of cytotoxicity and antimicrobial activity.

Cardiovascular Disease Burden Attributable to High Sodium Intake in China: A Longitudinal Study from 1990 to 2019.

BACKGROUND: Overconsumption of sodium has been identified as a key driving factor for diet-related cardiovascular diseases (CVDs). China, being a country bearing a hefty burden of CVD, has a large population with diverse cultural traditions and ethnic beliefs, which complicates the patterns of dietary sodium intake, necessitating a systematic investigation into the profile of the high sodium intake (HSI)-related burden of CVD within its subregions. This study aims to estimate the evolving patterns of HSI-induced CVD burden across China from 1990 to 2019. METHODS: The methodology used in the Global Burden of Disease Study was followed to assess deaths and disability-adjusted life years (DALYs) by age, sex, region, and socio-demographic index (SDI). The estimated annual percentage change (EAPC) was calculated to quantify the secular changes in the age-standardized mortality rate (ASMR) and age-standardized DALY rate (ASDR). RESULTS: In 2019, 0.79 million deaths and 1.93 million DALYs of CVD were attributed to HSI, an increase of 53.91% and 39.39% since 1990, respectively. Nevertheless, a downward trend in ASMR (EAPC: -1.45, 95% CI: -1.55, -1.35) and ASDR (EAPC: -1.61, 95% CI: -1.68, -1.53) was detected over time. ASMR and ASDR were higher for males, individuals aged ≥60 years, and regions with low-middle SDI. A markedly negative association between the EAPC in both ASMR and ASDR and the SDI was found in 2019 (ρ = -0.659, p < 0.001 and ρ = -0.558, p < 0.001, respectively). CONCLUSIONS: The HSI-induced CVD burden is gender-, age-, and socioeconomic-dependent. Integrated and targeted strategies for CVD prevention are anticipated in the future throughout China.

Biological response to Przewalski's horse reintroduction in native desert grasslands: a case study on the spatial analysis of ticks.

BACKGROUND: Reintroduction represents an effective strategy for the conservation of endangered wildlife, yet it might inadvertently impact the native ecosystems. This investigation assesses the impact of reintroducing endangered Przewalski's horses into the desert grassland ecosystem of the Kalamaili Nature Reserve (KNR), particularly its effect on the spatial distribution of ticks. In a 25 km2 core area of Przewalski's horse distribution, we set up 441 tick sampling sites across diverse habitats, including water sources, donkey trails, and grasslands, recording horse feces and characteristics to analyze the occurrence rate of ticks. Additionally, we gathered the data of 669 fresh feces of horses. To evaluate the spatial dynamics between these feces and ticks, we used methods such as Fixed Kernel Estimation (FKE), Moran's I spatial autocorrelation index, and Generalized Linear Models (GLM). RESULTS: The dominant species of ticks collected in the core area were adult Hyalomma asiaticum (91.36%). Their occurrence rate was higher near donkey trails (65.99%) and water sources (55.81%), particularly in areas with the fresh feces of Przewalski's horses. The ticks' three risk areas, as defined by FKE, showed significant overlap and positive correlation with the distribution of Przewalski's horses, with respective overlap rates being 90.25% in high risk, 33.79% in medium risk, and 23.09% in low risk areas. Moran's I analysis revealed a clustering trend of the fresh feces of Przewalski's horses in these areas. The GLM confirmed a positive correlation between the distribution of H. asiaticum and the presence of horse fresh feces, alongside a negative correlation with the proximity to water sources and donkey trails. CONCLUSIONS: This study reveals the strong spatial correlation between Przewalski's horses and H. asiaticum in desert grasslands, underlining the need to consider interspecific interactions in wildlife reintroductions. The findings are crucial for shaping effective strategies of wildlife conservation and maintaining ecological balance.

The genomes of seven economic Caesalpinioideae trees provide insights into polyploidization history and secondary metabolite biosynthesis.

The Caesalpinioideae subfamily contains many well-known trees that are important for the sustainability of the economy and human health, but the lack of genomic resources hindered the breeding and utilization of these plants. Here, we present chromosome-level reference genomes for two food and industrial trees Gleditsia sinensis (921 Mb) and Biancaea sappan (872 Mb), three shade and ornamental trees Albizia julibrissin (705 Mb), Delonix regia (580 Mb) and Acacia confusa (566 Mb), as well as two pioneer and hedgerow trees Leucaena leucocephala (1,338 Mb) and Mimosa bimucronata (641 Mb). Phylogeny inference showed that the mimosoid clade has a much higher evolution rate than the other clades of Caesalpinioideae. Macrosynteny comparison showed that the fusion and broken of an unstable chromosome was responsible for the difference in the basic chromosome number 13 and 14 for Caesalpinioideae. After the ancient whole genome duplication shared by all Caesalpinioideae species (CWGD, ∼72.0 MYA), we found two recent successive WGD events LWGD-1 (16.2-19.5 MYA) and LWGD-2 (7.1-9.5 MYA) in L. leucocephala. Then, ∼40% gene loss and genome size contraction occurred during the diploidization process in L. leucocephala. For the secondary metabolites, we identified all the gene copies involved in mimosine metabolism for these species and revealed that the abundance of mimosine biosynthesis genes in L. leucocephala largely explains its high mimosine production. Moreover, we identified all the potential genes involved in triterpenoid saponin biosynthesis in G. sinensis, which is more complete than the previous transcriptome-derived unigenes. Our analyzing results and the genomic resources will facilitate the biological studies of Caesalpinioideae and promote the utilization of valuable secondary metabolites.

Ice sheet and precession controlled subarctic Pacific productivity and upwelling over the last 550,000 years.

The polar oceans play a vital role in regulating atmospheric CO2 concentrations (pCO2) during the Pleistocene glacial cycles. However, despite being the largest modern reservoir of respired carbon, the impact of the subarctic Pacific remains poorly understood due to limited records. Here, we present high-resolution, 230Th-normalized export productivity records from the subarctic northwestern Pacific covering the last five glacial cycles. Our records display pronounced, glacial-interglacial cyclicity superimposed with precessional-driven variability, with warm interglacial climate and high boreal summer insolation providing favorable conditions to sustain upwelling of nutrient-rich subsurface waters and hence increased export productivity. Our transient model simulations consistently show that ice sheets and to a lesser degree, precession are the main drivers that control the strength and latitudinal position of the westerlies. Enhanced upwelling of nutrient/carbon-rich water caused by the intensification and poleward migration of the northern westerlies during warmer climate intervals would have led to the release of previously sequestered CO2 from the subarctic Pacific to the atmosphere. Our results also highlight the significant role of the subarctic Pacific in modulating pCO2 changes during the Pleistocene climate cycles, especially on precession timescale ( ~ 20 kyr).

TROP2 is highly expressed in triple-negative breast cancer CTCs and is a potential marker for epithelial mesenchymal CTCs.

Circulating tumor cells (CTCs) are the seeds of distant metastases of malignant tumors and are associated with malignancy and risk of metastasis. However, tumor cells undergo epithelial-mesenchymal transition (EMT) during metastasis, leading to the emergence of different types of CTCs. Real-time dynamic molecular and functional typing of CTCs is necessary to precisely guide personalized treatment. Most CTC detection systems are based on epithelial markers that may fail to detect EMT CTCs. Therefore, it is clinically important to identify new markers of different CTC types. In this study, bioinformatics analysis and experimental assays showed that trophoblast cell surface antigen 2 (TROP2), a target molecule for advanced palliative treatment of triple-negative breast cancer (TNBC), was highly expressed in TNBC tissues and tumor cells. Furthermore, TROP2 can promote the migration and invasion of TNBC cells by upregulating EMT markers. The specificity and potential of TROP2 as an EMT-associated marker of TNBC CTCs were evaluated by flow cytometry, immunofluorescence, spiking experiments, and a well-established CTC assay. The results indicated that TROP2 is a potential novel CTC marker associated with EMT, providing a basis for more efficacious markers that encompass CTC heterogeneity in patients with TNBC.

Hierarchical joint analysis of marginal summary statistics-Part I: Multipopulation fine mapping and credible set construction.

Recent advancement in genome-wide association studies (GWAS) comes from not only increasingly larger sample sizes but also the shift in focus towards underrepresented populations. Multipopulation GWAS increase power to detect novel risk variants and improve fine-mapping resolution by leveraging evidence and differences in linkage disequilibrium (LD) from diverse populations. Here, we expand upon our previous approach for single-population fine-mapping through Joint Analysis of Marginal SNP Effects (JAM) to a multipopulation analysis (mJAM). Under the assumption that true causal variants are common across studies, we implement a hierarchical model framework that conditions on multiple SNPs while explicitly incorporating the different LD structures across populations. The mJAM framework can be used to first select index variants using the mJAM likelihood with different feature selection approaches. In addition, we present a novel approach leveraging the ideas of mediation to construct credible sets for these index variants. Construction of such credible sets can be performed given any existing index variants. We illustrate the implementation of the mJAM likelihood through two implementations: mJAM-SuSiE (a Bayesian approach) and mJAM-Forward selection. Through simulation studies based on realistic effect sizes and levels of LD, we demonstrated that mJAM performs well for constructing concise credible sets that include the underlying causal variants. In real data examples taken from the most recent multipopulation prostate cancer GWAS, we showed several practical advantages of mJAM over other existing multipopulation methods.

A novel framework for high resolution air quality index prediction with interpretable artificial intelligence and uncertainties estimation.

Accurate air quality index (AQI) prediction is essential in environmental monitoring and management. Given that previous studies neglect the importance of uncertainty estimation and the necessity of constraining the output during prediction, we proposed a new hybrid model, namely TMSSICX, to forecast the AQI of multiple cities. Firstly, time-varying filtered based empirical mode decomposition (TVFEMD) was adopted to decompose the AQI sequence into multiple internal mode functions (IMF) components. Secondly, multi-scale fuzzy entropy (MFE) was applied to evaluate the complexity of each IMF component and clustered them into high and low-frequency portions. In addition, the high-frequency portion was secondarily decomposed by successive variational mode decomposition (SVMD) to reduce volatility. Then, six air pollutant concentrations, namely CO, SO2, PM2.5, PM10, O3, and NO2, were used as inputs. The secondary decomposition and preliminary portion were employed as the outputs for the bidirectional long short-term memory network optimized by the snake optimization algorithm (SOABiLSTM) and improved Catboost (ICatboost), respectively. Furthermore, extreme gradient boosting (XGBoost) was applied to ensemble each predicted sub-model to acquire the consequence. Ultimately, we introduced adaptive kernel density estimation (AKDE) for interval estimation. The empirical outcome indicated the TMSSICX model achieved the best performance among the other 23 models across all datasets. Moreover, implementing the XGBoost to ensemble each predicted sub-model led to an 8.73%, 8.94%, and 0.19% reduction in RMSE, compared to SVM. Additionally, by utilizing SHapley Additive exPlanations (SHAP) to assess the impact of the six pollutant concentrations on AQI, the results reveal that PM2.5 and PM10 had the most notable positive effects on the long-term trend of AQI. We hope this model can provide guidance for air quality management.