A time-resolved multi-omics atlas of transcriptional regulation in response to high-altitude hypoxia across whole-body tissues.

High-altitude hypoxia acclimatization requires whole-body physiological regulation in highland immigrants, but the underlying genetic mechanism has not been clarified. Here we use sheep as an animal model for low-to-high altitude translocation. We generate multi-omics data including whole-genome sequences, time-resolved bulk RNA-Seq, ATAC-Seq and single-cell RNA-Seq from multiple tissues as well as phenotypic data from 20 bio-indicators. We characterize transcriptional changes of all genes in each tissue, and examine multi-tissue temporal dynamics and transcriptional interactions among genes. Particularly, we identify critical functional genes regulating the short response to hypoxia in each tissue (e.g., PARG in the cerebellum and HMOX1 in the colon). We further identify TAD-constrained cis-regulatory elements, which suppress the transcriptional activity of most genes under hypoxia. Phenotypic and transcriptional evidence indicate that antenatal hypoxia could improve hypoxia tolerance in offspring. Furthermore, we provide time-series expression data of candidate genes associated with human mountain sickness (e.g., BMPR2) and high-altitude adaptation (e.g., HIF1A). Our study provides valuable resources and insights for future hypoxia-related studies in mammals.

Molecular Insights into the Effects of F16L and F19L Substitutions on the Conformation and Aggregation Dynamics of Human Calcitonin.

Human calcitonin (hCT) regulates calcium-phosphorus metabolism, but its amyloid aggregation disrupts physiological activity, increases thyroid carcinoma risk, and hampers its clinical use for bone-related diseases like osteoporosis and Paget's disease. Improving hCT with targeted modifications to mitigate amyloid formation while maintaining its function holds promise as a strategy. Understanding how each residue in hCT's amyloidogenic core affects its structure and aggregation dynamics is crucial for designing effective analogues. Mutants F16L-hCT and F19L-hCT, where Phe residues in the core are replaced with Leu as in nonamyloidogenic salmon calcitonin, showed different aggregation kinetics. However, the molecular effects of these substitutions in hCT are still unclear. Here, we systematically investigated the folding and self-assembly conformational dynamics of hCT, F16L-hCT, and F19L-hCT through multiple long-time scale independent atomistic discrete molecular dynamics (DMD) simulations. Our results indicated that the hCT monomer primarily assumed unstructured conformations with dynamic helices around residues 4-12 and 14-21. During self-assembly, the amyloidogenic core of hCT14-21 converted from dynamic helices to ß-sheets. However, substituting F16L did not induce significant conformational changes, as F16L-hCT exhibited characteristics similar to those of wild-type hCT in both monomeric and oligomeric states. In contrast, F19L-hCT exhibited substantially more helices and fewer ß-sheets than did hCT, irrespective of their monomers or oligomers. The substitution of F19L significantly enhanced the stability of the helical conformation for hCT14-21, thereby suppressing the helix-to-ß-sheet conformational conversion. Overall, our findings elucidate the molecular mechanisms underlying hCT aggregation and the effects of F16L and F19L substitutions on the conformational dynamics of hCT, highlighting the critical role of F19 as an important target in the design of amyloid-resistant hCT analogs for future clinical applications.

Simultaneous detection of dental caries and fissure sealant in intraoral photos by deep learning: a pilot study.

BACKGROUND: Deep learning, as an artificial intelligence method has been proved to be powerful in analyzing images. The purpose of this study is to construct a deep learning-based model (ToothNet) for the simultaneous detection of dental caries and fissure sealants in intraoral photos. METHODS: A total of 1020 intraoral photos were collected from 762 volunteers. Teeth, caries and sealants were annotated by two endodontists using the LabelMe tool. ToothNet was developed by modifying the YOLOX framework for simultaneous detection of caries and fissure sealants. The area under curve (AUC) in the receiver operating characteristic curve (ROC) and free-response ROC (FROC) curves were used to evaluate model performance in the following aspects: (i) classification accuracy of detecting dental caries and fissure sealants from a photograph (image-level); and (ii) localization accuracy of the locations of predicted dental caries and fissure sealants (tooth-level). The performance of ToothNet and dentist with 1year of experience (1-year dentist) were compared at tooth-level and image-level using Wilcoxon test and DeLong test. RESULTS: At the image level, ToothNet achieved an AUC of 0.925 (95% CI, 0.880-0.958) for caries detection and 0.902 (95% CI, 0.853-0.940) for sealant detection. At the tooth level, with a confidence threshold of 0.5, the sensitivity, precision, and F1-score for caries detection were 0.807, 0.814, and 0.810, respectively. For fissure sealant detection, the values were 0.714, 0.750, and 0.731. Compared with ToothNet, the 1-year dentist had a lower F1 value (0.599, p < 0.0001) and AUC (0.749, p < 0.0001) in caries detection, and a lower F1 value (0.727, p = 0.023) and similar AUC (0.829, p = 0.154) in sealant detection. CONCLUSIONS: The proposed deep learning model achieved multi-task simultaneous detection in intraoral photos and showed good performance in the detection of dental caries and fissure sealants. Compared with 1-year dentist, the model has advantages in caries detection and is equivalent in fissure sealants detection.

Clinical influencing factors of vital pulp therapy on pulpitis permanent teeth with 2 calcium silicate-based materials: A randomized clinical trial.

BACKGROUND: Compared with traditional root canal therapy (RCT), vital pulp therapy (VPT) is a personalized and minimally invasive method for the treatment of pulpitis caused by dental caries. However, there are still no clear guidelines for VPT because high-quality randomized clinical trials are scarce. This prospective cohort study evaluated the clinical efficacy of VPT with the light-curable calcium silicate-based material TheraCal LC (TH) and bioceramic material iRoot BP Plus (BP) in reversible and irreversible pulpitis permanent teeth with carious exposures. METHODS: 115 teeth with reversible or irreversible pulpitis caused by deep care were randomly divided into 2 groups. TheraCal LC and iRoot BP Plus were used for the pulp capping. Direct pulp capping (DPC), partial pulpotomy (PP) and full pulpotomy (FP) were performed based on observation of the exposed pulp. Postoperative discomforts were enquired and recorded via follow-up phone calls. Clinical and radiographic evaluations were performed 3, 6, and 12 months postoperatively. RESULTS: The overall clinical success rate in the first year was 90.4% (47/52) in both groups. The TH group required less operating time, showed lower levels of pain, and had shorter pain duration post-operative (P < .001). According to the binary logistic regression model, preoperative pain duration was significantly correlated with the prognosis of VPT (P = .011). CONCLUSION: VPT with TheraCal LC and iRoot BP Plus in pulpitis permanent carious teeth both achieved good clinical outcomes, and TheraCal LC can be easily operated for clinical use. Preoperative pain duration of the affected tooth might have a significant correlation with the prognosis of VPT.

Association between gut microbiota and central retinal artery occlusion: A two-sample Mendelian randomization study.

PURPOSE: The gut microbiota might be closely related to central retinal artery occlusion (CRAO), but the causality has not been well defined. Two-sample Mendelian randomization (MR) study was used to reveal the potential causal effect between the gut microbiota and CRAO. METHODS: Data for gut microbiota were obtained from the genome-wide association studies of the Dutch Microbiome Project (DMP) (n = 7738) and the MiBioGen consortium (n = 18,340), and data on CRAO were obtained from samples of FinnGen project (546 cases and 344,569 controls). Causalities of exposures and outcomes were explored mainly using the inverse variance weighted method. In addition, multiple sensitivity analyses including MR-Egger, weighted median (WM), simple mode, weighted mode, and MR Pleiotropy RESidual Sum and Outlier were simultaneously applied to validate the final results. RESULTS: We identified three microbial pathways (two risk factors/one protective factor) and seven microbial taxa (two risk factors/five protective factors) associated with CRAO in the DMP study. Based on the data from the MiBioGen consortium, we identified seven microbial taxa (two risk factors/five protective factors) associated with CRAO, including the Eubacterium genus, which was consistently identified as a risk factor in both the DMP and the MiBioGen consortium MR analyses. CONCLUSION: Our study implicates the potential causal effects of specific microbial taxa and pathways on CRAO, potentially providing new insights into the prevention and treatment of CRAO through specific gut microbial taxa and pathway. Since our conclusion is a hypothesis derived from secondary genome-wide association studies (GWAS) data analysis, further research is needed for confirmation.

Advancing Alzheimer's research: Radiomics visualization of the default mode network in cerebral perfusion imaging.

OBJECTIVE: Alzheimer's disease, an irreversible neurological condition, demands timely diagnosis for effective clinical intervention. This study employs radiomics analysis to assess image features in default mode network cerebral perfusion imaging among individuals with cognitive impairment. METHODS: A radiomics analysis of cerebral perfusion imaging was conducted on 117 patients with cognitive impairment. They were divided into training and validation sets in a 7:3 ratio. Least Absolute Shrinkage and Selection Operator (LASSO) and Random Forest were employed to select and model image features, followed by logistic regression analysis of LASSO and Random Forest results. Diagnostic performance was assessed by calculating the area under the curve (AUC). RESULTS: In the training set, LASSO achieved AUC of 0.978, Random Forest had an AUC of 0.933. In the validation set, LASSO had AUC of 0.859, Random Forest had AUC of 0.986. By conducting Logistic Regression analysis in combination with LASSO and Random Forest, we identified a total of five radiomics features, with four related to morphology and one to textural features, originating from the medial prefrontal cortex and middle temporal gyrus. In the training set, Logistic Regression achieved AUC of 0.911, while in the validation set, it attained AUC of 0.925. CONCLUSION: The medial prefrontal cortex and middle temporal gyrus are the two brain regions within the default mode network that hold the highest significance for Alzheimer's disease diagnosis. Radiomics analysis contributes to the clinical assessment of Alzheimer's disease by delving into image data to extract deeper layers of information.

Distribution and Risk Assessment of Organophosphate Esters in Agricultural Soils and Plants in the Coastal Areas of South China.

Organophosphate esters (OPEs) are frequently used as flame retardants and plasticizers in various commercial products. While initially considered as substitutes for brominated flame retardants, they have faced restrictions in some countries due to their toxic effects on organisms. We collected 37 soil and crop samples in 20 cities along the coast of South China, and OPEs were detected in all of them. Meanwhile, we studied the contamination and potential human health risks of OPEs. In soil samples, the combined concentrations of eight OPEs varied between 74.7 and 410 ng/g, averaging at 255 ng/g. Meanwhile, in plant samples, the collective concentrations of eight OPEs ranged from 202 to 751 ng/g, with an average concentration of 381 ng/g. TDCIPP, TCPP, TCEP, and ToCP were the main OPE compounds in both plant and soil samples. Within the study area, the contaminants showed different spatial distributions. Notably, higher OPEs were found in coastal agricultural soils in Guangdong Province and crops in the Guangxi Zhuang Autonomous Region. The results of an ecological risk assessment show that the farmland soil along the southern coast of China is at high or medium ecological risk. The average non-carcinogenic risk and the carcinogenic risk of OPEs in soil through ingestion and dermal exposure routes are within acceptable levels. Meanwhile, this study found that the dietary intake of OPEs through food is relatively low, but twice as high as other studies, requiring serious attention. The research findings suggest that the human risk assessment indicates potential adverse effects on human health due to OPEs in the soil-plant system along the coast of South China. This study provides a crucial foundation for managing safety risks in agricultural operations involving OPEs.

Associations between regular physical exercise and physical, emotional, and cognitive health of older adults in China: an 8-year longitudinal study with propensity score matching.

Background: The importance of healthy aging is growing in China as it has the largest number of older adults in the world and is one of the fastest-aging countries. This study aimed to examine the predictive value of regular physical exercise in relation to the physical, emotional, and cognitive health among samples of adults aged ≥60 years in China during an 8-year period. Methods: A total of 10,691 older adults were extracted from two waves of national data from the China Family Panel Studies in 2010 and 2018. To minimize the impact of selection bias on the findings, a longitudinal propensity score matching (LPSM) method was used to examine the relationships between regular physical exercise and emotional health (depression), between regular physical exercise and physical health (instrumental activities of daily living), and between regular physical exercise and cognitive health (cognitive ability) of older adults. After LPSM, 856 older adults were included in the study. In the regular physical exercise group, the average age of participants at baseline year was 65.67 years, with an average age of 65.90 years for 238 men and 65.45 years for 190 women, and in the non-physical exercise group, their average age at baseline year was 65.70 years, with an average age of 65.45 years for 253 men and 65.98 years for 175 women. Results: LPSM indicated that regular physical exercise has been found to be effective in improving physical function and reducing depressive symptoms in old adults, even after controlling for background differences. However, the sensitivity analysis suggests that the positive association between regular physical exercise and cognitive function may not be sufficiently valid. Conclusion: The findings of this study indicate that engaging in long-term structured and repetitive physical exercise can have a significant positive effect on reducing depressive symptoms and improving the physical function of older adults. As a result, incorporating regular physical exercise into the lifestyle of older adults is recognized as an effective strategy for promoting healthy aging and reducing the strain on public health resources.

ProteoMutaMetrics: machine learning approaches for solute carrier family 6 mutation pathogenicity prediction.

The solute carrier transporter family 6 (SLC6) is of key interest for their critical role in the transport of small amino acids or amino acid-like molecules. Their dysfunction is strongly associated with human diseases such as including schizophrenia, depression, and Parkinson's disease. Linking single point mutations to disease may support insights into the structure-function relationship of these transporters. This work aimed to develop a computational model for predicting the potential pathogenic effect of single point mutations in the SLC6 family. Missense mutation data was retrieved from UniProt, LitVar, and ClinVar, covering multiple protein-coding transcripts. As encoding approach, amino acid descriptors were used to calculate the average sequence properties for both original and mutated sequences. In addition to the full-sequence calculation, the sequences were cut into twelve domains. The domains are defined according to the transmembrane domains of the SLC6 transporters to analyse the regions' contributions to the pathogenicity prediction. Subsequently, several classification models, namely Support Vector Machine (SVM), Logistic Regression (LR), Random Forest (RF), and Extreme Gradient Boosting (XGBoost) with the hyperparameters optimized through grid search were built. For estimation of model performance, repeated stratified k-fold cross-validation was used. The accuracy values of the generated models are in the range of 0.72 to 0.80. Analysis of feature importance indicates that mutations in distinct regions of SLC6 transporters are associated with an increased risk for pathogenicity. When applying the model on an independent validation set, the performance in accuracy dropped to averagely 0.6 with high precision but low sensitivity scores.

Suppression of Pseudomonas aeruginosa type III secretion system by a novel calcium-responsive signaling pathway.

Expression of the type III secretion system (T3SS) in Pseudomonas aeruginosa is exquisitely controlled by diverse environmental or host-related signals such as calcium (Ca2+), however, the signal transduction pathways remain largely elusive. In this study, we reported that FleR, the response regulator of the two-component system FleS/FleR, inhibits T3SS gene expression and virulence of P. aeruginosa uncoupled from its cognate histidine kinase FleS. Interestingly, FleR was found to repress T3SS gene expression under Ca2+-rich conditions independently of its DNA-binding domain. FleR activates the elevation of intracellular c-di-GMP contents and FleQ serves as the c-di-GMP effector to repress T3SS gene expression through the Gac/Rsm pathway. Remarkably, we found that AmrZ, a member of the FleR regulon, inhibits T3SS gene expression by directly targeting the promoter of exsCEBA in an expression level-dependent manner. This study revealed an intricate regulatory network that connects P. aeruginosa T3SS gene expression to the Ca2+ signal.

[Genetic dissection of rice resistance to bacterial blight].

Bacterial blight, a major disease in rice, poses a serious impact on rice production. In this study, a doubled haploid (DH) population derived from a cross between the introduced japonica cultivar 'Maybelle' and the indica landrace 'Baiyeqiu' was used to investigate the pathogenicity of four pathogen races causing bacterial blight. The results showed that the pathogenicity of all the pathogen races exhibited continuous, transgressive distribution in the DH population. Moreover, strong correlations existed between every two pathogen races, with the correlation coefficients ranging from 0.3 to 0.6. A total of 12 quantitative trait loci (QTLs) distributed on chromosomes 1, 2, 3, 5, 6, 7, 9, and 12 were detected for rice bacterial blight, explaining 4.95% to 16.05% of the phenotype. Among these QTLs, a major QTL located in the interval RM6024-RM163 on chromosome 5 was detected in three pathogen races. In addition, the pyramiding of the positive alleles can apparently improve the rice resistance to bacterial blight. This study is of great significance for broadening the genetic resources with resistance to bacterial blight in China.

Nomogram Based on US and Clinicopathologic Characteristics: Axillary Nodal Evaluation Following Neoadjuvant Chemotherapy in Patients With Node-Positive Breast Cancer.

BACKGROUND: To develop a convenient modality to predict axillary response to neoadjuvant chemotherapy (NAC) in breast cancer patients. MATERIALS AND METHODS: In this multi-center study, a total of 1019 breast cancer patients with biopsy-proven positive lymph node (LN) receiving NAC were randomly assigned to the training and validation groups at a ratio of 7:3. Clinicopathologic and ultrasound (US) characteristics of both primary tumors and LNs were used to develop corresponding prediction models, and a nomogram integrating clinicopathologic and US predictors was generated to predict the axillary response to NAC. RESULTS: Axillary pathological complete response (pCR) was achieved in 47.79% of the patients. The expression of estrogen receptor, human epidermal growth factor receptor -2, Ki-67 score, and clinical nodal stage were independent predictors for nodal response to NAC. Location and radiological response of primary tumors, cortical thickness and shape of LNs on US were also significantly associated with nodal pCR. In the validation cohort, the discrimination of US model (area under the curve [AUC], 0.76) was superior to clinicopathologic model (AUC, 0.68); the combined model (AUC, 0.85) demonstrates strong discriminatory power in predicting nodal pCR. Calibration curves of the nomogram based on the combined model demonstrated that substantial agreement can be observed between the predictions and observations. This nomogram showed a false-negative rates of 16.67% in all patients and 10.53% in patients with triple negative breast cancer. CONCLUSION: Nomogram incorporating routine clinicopathologic and US characteristics can predict nodal pCR and represents a tool to aid in treatment decisions for the axilla after NAC in breast cancer patients.

Global responses to tris(1-chloro-2-propyl) phosphate and tris(2-butoxyethyl) phosphate in Escherichia coli: Evidences from biomarkers, and metabolic disturbance using GC-MS and LC-MS metabolomics analyses.

Tris(1-chloro-2-propyl) phosphate (TCPP) and tris(2-butoxyethyl) phosphate (TBEP) as pollutants of emerging concern have aroused the rising attention due to their potential risks on aquatic ecosystem and public health. Nevertheless, there is a lack of toxicological mechanisms exploration of TCPP and TBEP at molecular levels. Herein, the toxicity effects and molecular mechanism of them were fully researched and summarized on Escherichia coli (E.coli). Acute exposure to them significantly activated antioxidant defense system and caused lipid peroxidation, as proved by the changes of antioxidant enzymes and MDA. The ROS overload resulted in the drop of membrane potential as well as the downregulated synthesis of ATPase, endorsing that E. coli cytotoxicity was ascribed to oxidative stress damage induced by TCPP and TBEP. The combination of GC-MS and LC-MS based metabolomics validated that TCPP and TBEP induced metabolic reprogramming in E.coli. More specifically, the responsive metabolites in carbohydrate metabolism, lipids metabolism, nucleotide metabolism, amino acid metabolism, and organic acids metabolism were significantly disturbed by TCPP and TBEP, confirming the negative effects on metabolic functions and key bioprocesses. Additionally, several biomarkers including PE(16:1(5Z)/15:0), PA(17:1(9Z)/18:2(9Z,12Z)), PE(19:1(9Z)/0:0), and LysoPE(0:0/18:1(11Z)) were remarkably upregulated, verifying that the protection of cellular membrane was conducted by regulating the expression of lipids-associated metabolites. Collectively, this work sheds new light on the potential molecular toxicity mechanism of TCPP and TBEP on aquatic organisms, and these findings using GC-MS and LC-MS metabolomics generate a fresh insight into assessing the effects of OPFRs on target and non-target aquatic organisms.

One-step hydrothermal growth of porous nickel manganese layered double hydroxide nanosheet film towards efficient visible-light modulation.

Electrochromic smart windows have attracted great attention due to their dynamic regulation of the solar spectrum. NiO and MnO2 are typical anodic coloration materials and widely investigated as complementary electrodes with WO3. However, NiO and MnO2 films often cannot be bleached to complete transparency, resulting in low transmittances and low optical modulations in the short-wavelength visible region. Herein, we report a porous nickel manganese layered double hydroxide (NiMn-LDH) nanosheet film directly grown on fluorine-doped tin oxide (FTO) glass using a one-step hydrothermal method, which demonstrates a high transmittance of 80.1% at 550 nm (without deduction of FTO glass). Induced by the double-redox couples of Ni2+/Ni3+ and Mn3+/Mn4+ associated synergistic electrochromic effect, the as-grown NiMn-LDH film electrode exhibits a large optical modulation of 68.5% at 550 nm, and a large solar irradiation modulation of 59.0% in the visible region of 400-800 nm. After annealing at 450 °C for 2 h, the NiMn-LDH film can be transformed into Ni6MnO8 film with a reduced optical modulation of 30.0% at 550 nm. Furthermore, the NiMn-LDH film electrode delivers an areal capacitance of 30.8 mF cm-2 at a current density of 0.1 mA cm-2. These results suggest that the as-prepared NiMn-LDH film electrode is a promising candidate for both electrochromic and energy storage applications.

Protocol for generating mouse morula-like cells resembling 8- to 16-cell stage embryo cells.

Generating cell types with properties of embryo cells with full developmental potential is of great biological importance. Here, we present a protocol for generating mouse morula-like cells (MLCs) resembling 8- to 16-cell stage embryo cells. We describe steps for induction, via increasing Stat3 activation, and the isolation of MLCs. We then detail procedures for segregating MLCs into blastocyst cell fates and how to create embryo-like structures from them. This system provides a stem-cell-based embryo model to study early embryo development. For complete details on the use and execution of this protocol, please refer to Li et al.1.

Quadruple Control Electrochromic Devices Utilizing Ce4W9O33 Electrodes for Visible and Near-Infrared Transmission Intelligent Modulation.

Electrochromic smart windows are promising for building energy savings due to their dynamic regulation of the solar spectrum. Restricted by materials or traditional complementary device configuration, precisely and independently controlling of visible (VIS) and near-infrared (NIR) light is still on the drawing board. Herein, a novel Zn2+ electrochemically active Ce4W9O33 electrode is reported, which demonstrates three distinct states, including VIS and NIR transparent "bright and warm" state, VIS and NIR opaque "dark and cool" state, VIS transparent and NIR opaque "bright and cool" state. A dual-operation mode electrochromic platform is also presented by integrating Ce4W9O33/NiO complementary device and Zn anode-based electrochromic device (Ce4W9O33/Zn/NiO device). Such a platform enables an added VIS opaque and NIR transparent "dark and warm" state, thus realizing four color states through individually controlling Ce4W9O33 and NiO electrodes, respectively. These results present an effective approach for facilitating electrochromic windows more intelligent to weather/season conditions and personal preferences.

Selenium nanoparticles/carboxymethyl chitosan/alginate antioxidant hydrogel for treating steroid-induced osteonecrosis of the femoral head.

Oxidative stress plays a crucial role in steroid-induced osteonecrosis of the femoral head (SONFH). Although several antioxidant strategies have been investigated for treating SONFH, their antioxidant efficiencies and therapeutic effects remain unsatisfactory. Here, we developed a selenium nanoparticles/carboxymethyl chitosan/alginate (SeNPs/CMC/Alg) antioxidant hydrogel and evaluated its ability to treat SONFH. In vitro assays indicated that the SeNPs/CMC/Alg hydrogel exhibited excellent properties, such as low cytotoxicity, sustained SeNPs release, and favorable antioxidant activity. Under oxidative stress, the SeNPs/CMC/Alg hydrogel promoted reactive oxygen species (ROS) elimination and enhanced the osteogenic and proangiogenic abilities of bone marrow mesenchymal stem cells (BMSCs). After establishing a rabbit model of SONFH, the SeNPs/CMC/Alg hydrogel was transplanted into the femoral head after core decompression (CD) surgery. Radiographic and histological analyses revealed that the hydrogel treatment alleviated SONFH by eliminating ROS and promoting osteogenesis and angiogenesis compared to those in the CD and CMC/Alg groups. In vitro and in vivo studies indicated that the Wnt/ß-catenin signaling pathway was activated by the SeNPs/CMC/Alg hydrogel in both hydrogen peroxide-conditioned BMSCs and necrotic femoral heads. These findings indicate that local transplantation of the SeNPs/CMC/Alg hydrogel is beneficial for treating SONFH, as it promotes ROS elimination and activation of the Wnt/ß-catenin signaling pathway.

Identification of lethal species in amanita section Phalloideae based on nucleotide signature and specific TaqMan-MGB probe and primer.

Amanita section Phalloideae consists of lethal toxic mushroom species, causing many fatal poisoning incidents worldwide. Molecular techniques of nucleotide signatures and single nucleotide polymorphism (SNP) detection could be used to develop a specific method for identifying lethal section (sect.) Phalloideae species. A comparison of 38 sequenced and 228 validated sequences from sect. Phalloideae species showed a 17-base pair nucleotide signature and an SNP site between the lethal and non-lethal species. A specific minor groove binder probe was designed based on them. The results indicated that this method exhibited excellent specificity for the lethal subgroup, good detection in samples subjected to simulated gastric digestion (60 min boiling and 120 min digestion), and a 10 pg./µL detection limit. This method enables accurate detection of target species in samples under complex conditions and can provide evidence for poisoning incidents caused by lethal sect. Phalloideae species to assist in targeted treatment strategies.

Anti-HER2 therapy response assessment for guiding treatment (de-)escalation in early HER2-positive breast cancer using a novel deep learning radiomics model.

OBJECTIVES: Anti-HER2 targeted therapy significantly reduces risk of relapse in HER2 + breast cancer. New measures are needed for a precise risk stratification to guide (de-)escalation of anti-HER2 strategy. METHODS: A total of 726 HER2 + cases who received no/single/dual anti-HER2 targeted therapies were split into three respective cohorts. A deep learning model (DeepTEPP) based on preoperative breast magnetic resonance (MR) was developed. Patients were scored and categorized into low-, moderate-, and high-risk groups. Recurrence-free survival (RFS) was compared in patients with different risk groups according to the anti-HER2 treatment they received, to validate the value of DeepTEPP in predicting treatment efficacy and guiding anti-HER2 strategy. RESULTS: DeepTEPP was capable of risk stratification and guiding anti-HER2 treatment strategy: DeepTEPP-Low patients (60.5%) did not derive significant RFS benefit from trastuzumab (p = 0.144), proposing an anti-HER2 de-escalation. DeepTEPP-Moderate patients (19.8%) significantly benefited from trastuzumab (p = 0.048), but did not obtain additional improvements from pertuzumab (p = 0.125). DeepTEPP-High patients (19.7%) significantly benefited from dual HER2 blockade (p = 0.045), suggesting an anti-HER2 escalation. CONCLUSIONS: DeepTEPP represents a pioneering MR-based deep learning model that enables the non-invasive prediction of adjuvant anti-HER2 effectiveness, thereby providing valuable guidance for anti-HER2 (de-)escalation strategies. DeepTEPP provides an important reference for choosing the appropriate individualized treatment in HER2 + breast cancer patients, warranting prospective validation. CLINICAL RELEVANCE STATEMENT: We built an MR-based deep learning model DeepTEPP, which enables the non-invasive prediction of adjuvant anti-HER2 effectiveness, thus guiding anti-HER2 (de-)escalation strategies in early HER2-positive breast cancer patients. KEY POINTS: • DeepTEPP is able to predict anti-HER2 effectiveness and to guide treatment (de-)escalation. • DeepTEPP demonstrated an impressive prognostic efficacy for recurrence-free survival and overall survival. • To our knowledge, this is one of the very few, also the largest study to test the efficacy of a deep learning model extracted from breast MR images on HER2-positive breast cancer survival and anti-HER2 therapy effectiveness prediction.

Transformation process and phytotoxicity of sulfamethoxazole and N4-acetyl-sulfamethoxazole in rice.

Sulfonamide antibiotics, extensively used in human and veterinary therapy, accumulate in agroecosystem soils through livestock manure and sewage irrigation. However, the interaction between sulfonamides and rice plants remains unclear. This study investigated the transformation behavior and toxicity of sulfamethoxazole (SMX) and its main metabolite, N4-acetyl-sulfamethoxazole (NASMX) in rice. SMX and NASMX were rapidly taken up by roots and translocated acropetally. NASMX showed higher accumulating capacity, with NASMX concentrations up to 20.36 ± 1.98 µg/g (roots) and 5.62 ± 1.17 µg/g (shoots), and with SMX concentrations up to 15.97 ± 2.53 µg/g (roots) and 3.22 ± 0.789 µg/g (shoots). A total of 18 intermediate transformation products of SMX were identified by nontarget screening using Orbitrap-HRMS, revealing pathways such as deamination, hydroxylation, acetylation, formylation, and glycosylation. Notably, NASMX transformed back into SMX in rice, a novel finding. Transcriptomic analysis highlights the involvements of cytochrome P450 (CYP450), acetyltransferase (ACEs) and glycosyltransferases (GTs) in these biotransformation pathways. Moreover, exposure to SMX and NASMX disrupts TCA cycle, amino acid, linoleic acid, nucleotide metabolism, and phenylpropanoid biosynthesis pathways of rice, with NASMX exerting a stronger impact on metabolic networks. These findings elucidate the sulfonamides' metabolism, phytotoxicity mechanisms, and contribute to assessing food safety and human exposure risk amid antibiotic pollution.