Gold nanoclusters-based fluorescence sensor array for herbicides qualitative and quantitative analysis.

Herbicides have been extensively used around the world, which poses a potential hazard to humans and wildlife. Accurate detection of herbicides is crucial for the environment and human health. Herein, a simple and sensitive fluorescence sensor array was constructed for discrimination and identification of herbicides. Fluorescent gold nanoclusters modified with 11-mercaptoundecanoic acid or reduced glutathione were prepared, respectively. Metal ions quenched the fluorescence of nanoclusters through coordination and leading to the aggregation of gold nanoclusters. The addition of auxin herbicides (2,4-dichlorophenoxyacetic acid, 2-methyl-4-chlorophenoxyacetic acid, decamba, picloram, quinclorac) restored the fluorescence of nanoclusters with different degrees. The mechanism study showed auxin herbicides can bind with metal ions and re-disperse the gold nanoclusters from the aggregation state. The "on-off-on" fluorescent sensor array was constructed basic on above detection mechanism. Combined with principal component analysis (PCA) and hierarchical cluster analysis (HCA) methods, auxin herbicides are well separated on 2D/3D PCA score plots and HCA dendrogram in the range of 40-500 µm. In addition, the fluorescence sensor array performed successful in detecting real samples and blind samples. The developed sensor system shows a promising in practical detection of herbicides.

Outcomes in patients treated with frontline immune checkpoint inhibition (ICI) for advanced NSCLC with KRAS mutations and STK11/KEAP1 comutations across PD-L1 levels.

INTRODUCTION: In patients with advanced NSCLC (aNSCLC), the impact of KRAS mutations (m) and comutations with STK11 and KEAP1 on outcomes across different PD-L1 levels remains incompletely understood. We aimed to investigate the frequency of KRAS mutations and comutations across PD-L1 levels, and the association between these mutations and survival, stratified by PD-L1 expression. METHODS: We conducted a nationwide cohort study of patients diagnosed with aNSCLC between 2016 and 2021 treated with frontline (chemo)immunotherapy, who underwent molecular genotyping including KRAS, STK11, and KEAP1. Real-world overall survival (OS) and progression-free survival (rwPFS) were estimated using Kaplan-Meier methodology. Cox multivariable regressions were used to evaluate the association between KRASm and survival across different PD-L1 strata, and to assess whether the association between KRASm and survival differed by PD-L1 level. Finally, within subgroups defined by PD-L1 expression, we used interaction terms to assess whether co-mutations with STK11 and KEAP1 moderated the association between KRAS mutation and survival. RESULTS: Of our 2593-patient cohort, 982 (37.9 %) were KRASm and 1611 (62.1 %) KRASwt. KRASm were enriched in the PD-L1 ≥50 % cohort (334/743, 45 %), but within patients with KRASm, co-mutations with STK11 and KEAP1 were enriched in the PD-L1 0 % cohort. KRASm was associated with significantly worse OS in the PD-L1 0 % cohort compared to the PD-L1 ≥50 % cohort (P for interaction = 0.008). On adjusted analyses stratified by PD-L1, KRASm was associated with worse survival only in the PD-L1 0 % group (OS HR 1.46, p = 0.001). KEAP1 and STK11 comutations were most strongly associated with worse OS in the PD-L1 0 % subgroup; patients with triple KRASm/KEAPm/STK11m PD-L1 0 % NSCLC experienced the worst outcomes. CONCLUSIONS: KRASm are associated with worse overall survival in PD-L1 negative NSCLC; however, this association is largely driven by comutations with STK11 and KEAP1, which are enriched in PD-L1 negative tumors.

Enhancing phenotype recognition in clinical notes using large language models: PhenoBCBERT and PhenoGPT.

To enhance phenotype recognition in clinical notes of genetic diseases, we developed two models-PhenoBCBERT and PhenoGPT-for expanding the vocabularies of Human Phenotype Ontology (HPO) terms. While HPO offers a standardized vocabulary for phenotypes, existing tools often fail to capture the full scope of phenotypes due to limitations from traditional heuristic or rule-based approaches. Our models leverage large language models to automate the detection of phenotype terms, including those not in the current HPO. We compare these models with PhenoTagger, another HPO recognition tool, and found that our models identify a wider range of phenotype concepts, including previously uncharacterized ones. Our models also show strong performance in case studies on biomedical literature. We evaluate the strengths and weaknesses of BERT- and GPT-based models in aspects such as architecture and accuracy. Overall, our models enhance automated phenotype detection from clinical texts, improving downstream analyses on human diseases.

A High-Efficiency Bioorthogonal Tumor-Membrane Reactor for In Situ Selective and Sustained Prodrug Activation.

The site-specific activation of bioorthogonal prodrugs has provided great opportunities for reducing the severe side effects of chemotherapy. However, the precise control of activation location, sustained drug production at the target site, and high bioorthogonal reaction efficiency in vivo remain great challenges. Here, we propose the construction of tumor cell membrane reactors in vivo to solve the above problems. Specifically, tumor-targeted liposomes with efficient membrane fusion capabilities are generated to install the bioorthogonal trigger, the amphiphilic tetrazine derivative, on the surface of tumor cells. These predecorated tumor cells act as many living reactors, transforming the tumor into a "drug factory" that in situ activates an externally delivered bioorthogonal prodrug, for example intratumorally injected transcyclooctene-caged doxorubicin. In contrast to the rapid elimination of cargo that is encapsulated and delivered by liposomes, these reactors permit stable retention of bioorthogonal triggers in tumor for 96 h after a single dose of liposomes via intravenous injection, allowing sustained generation of doxorubicin. Interestingly, an additional supplement of liposomes will compensate for the trigger consumed by the reaction and significantly improve the efficiency of the local reaction. This strategy provides a solution to the efficacy versus safety dilemma of tumor chemotherapy.

CaSnRK2.4-mediated phosphorylation of CaNAC035 regulates abscisic acid synthesis in pepper (Capsicum annuum L.) responding to cold stress.

Plant NAC transcription factors play a crucial role in enhancing cold stress tolerance, yet the precise molecular mechanisms underlying cold stress remain elusive. In this study, we identified and characterized CaNAC035, an NAC transcription factor isolated from pepper (Capsicum annuum) leaves. We observed that the expression of the CaNAC035 gene is induced by both cold and abscisic acid (ABA) treatments, and we elucidated its positive regulatory role in cold stress tolerance. Overexpression of CaNAC035 resulted in enhanced cold stress tolerance, while knockdown of CaNAC035 significantly reduced resistance to cold stress. Additionally, we discovered that CaSnRK2.4, a SnRK2 protein, plays an essential role in cold tolerance. In this study, we demonstrated that CaSnRK2.4 physically interacts with and phosphorylates CaNAC035 both in vitro and in vivo. Moreover, the expression of two ABA biosynthesis-related genes, CaAAO3 and CaNCED3, was significantly upregulated in the CaNAC035-overexpressing transgenic pepper lines. Yeast one-hybrid, Dual Luciferase, and electrophoretic mobility shift assays provided evidence that CaNAC035 binds to the promoter regions of both CaAAO3 and CaNCED3 in vivo and in vitro. Notably, treatment of transgenic pepper with 50 µm Fluridone (Flu) enhanced cold tolerance, while the exogenous application of ABA at a concentration of 10 µm noticeably reduced cold tolerance in the virus-induced gene silencing line. Overall, our findings highlight the involvement of CaNAC035 in the cold response of pepper and provide valuable insights into the molecular mechanisms underlying cold tolerance. These results offer promising prospects for molecular breeding strategies aimed at improving cold tolerance in pepper and other crops.

Enhancing Phenotype Recognition in Clinical Notes Using Large Language Models: PhenoBCBERT and PhenoGPT.

To enhance phenotype recognition in clinical notes of genetic diseases, we developed two models - PhenoBCBERT and PhenoGPT - for expanding the vocabularies of Human Phenotype Ontology (HPO) terms. While HPO offers a standardized vocabulary for phenotypes, existing tools often fail to capture the full scope of phenotypes, due to limitations from traditional heuristic or rule-based approaches. Our models leverage large language models (LLMs) to automate the detection of phenotype terms, including those not in the current HPO. We compared these models to PhenoTagger, another HPO recognition tool, and found that our models identify a wider range of phenotype concepts, including previously uncharacterized ones. Our models also showed strong performance in case studies on biomedical literature. We evaluated the strengths and weaknesses of BERT-based and GPT-based models in aspects such as architecture and accuracy. Overall, our models enhance automated phenotype detection from clinical texts, improving downstream analyses on human diseases.

Continuous Cropping Inhibits Photosynthesis of Polygonatum odoratum.

Polygonatum odoratum (Mill.) Druce possesses widespread medicinal properties; however, the continuous cropping (CC) often leads to a severe consecutive monoculture problem (CMP), ultimately causing a decline in yield and quality. Photosynthesis is the fundamental process for plant growth development. Improving photosynthesis is one of the most promising approaches to increase plant yields. To better understand how P. odoratum leaves undergo photosynthesis in response to CC, this study analyzed the physiochemical indexes and RNA-seq. The physiochemical indexes, such as the content of chlorophyll (chlorophyll a, b, and total chlorophyll), light response curves (LRCs), and photosynthetic parameters (Fv/Fm, Fv/F0, Fm/F0, Piabs, ABS/RC, TRo/RC, ETo/RC, and DIo/RC) were all changed in P. odoratum under the CC system. Furthermore, 13,798 genes that exhibited differential expression genes (DEGs) were identified in the P. odoratum leaves of CC and first cropping (FC) plants. Among them, 7932 unigenes were upregulated, while 5860 unigenes were downregulated. Here, the DEGs encoding proteins associated with photosynthesis and carbon assimilation showed a significant decrease in expression under the CC system, such as the PSII protein complex, PSI protein complex, Cytochorome b6/f complex, the photosynthetic electron transport chain, light-harvesting chlorophyll protein complex, and Calvin cycle, etc., -related gene. This study demonstrates that CC can suppress photosynthesis and carbon mechanism in P. odoratum, pinpointing potential ways to enhance photosynthetic efficiency in the CC of plants.

Trogocytosis of cancer-associated fibroblasts promotes pancreatic cancer growth and immune suppression via phospholipid scramblase anoctamin 6 (ANO6).

In pancreatic ductal adenocarcinoma (PDAC), the fibroblastic stroma constitutes most of the tumor mass and is remarkably devoid of functional blood vessels. This raises an unresolved question of how PDAC cells obtain essential metabolites and water-insoluble lipids. We have found a critical role for cancer-associated fibroblasts (CAFs) in obtaining and transferring lipids from blood-borne particles to PDAC cells via trogocytosis of CAF plasma membranes. We have also determined that CAF-expressed phospholipid scramblase anoctamin 6 (ANO6) is an essential CAF trogocytosis regulator required to promote PDAC cell survival. During trogocytosis, cancer cells and CAFs form synapse-like plasma membranes contacts that induce cytosolic calcium influx in CAFs via Orai channels. This influx activates ANO6 and results in phosphatidylserine exposure on CAF plasma membrane initiating trogocytosis and transfer of membrane lipids, including cholesterol, to PDAC cells. Importantly, ANO6-dependent trogocytosis also supports the immunosuppressive function of pancreatic CAFs towards cytotoxic T cells by promoting transfer of excessive amounts of cholesterol. Further, blockade of ANO6 antagonizes tumor growth via disruption of delivery of exogenous cholesterol to cancer cells and reverses immune suppression suggesting a potential new strategy for PDAC therapy.

Endogenous listeria monocytogenes endophthalmitis in a cirrhotic patient.

Endogenous endophthalmitis caused by listeria monocytogenes is rare and serious, which is easily misdiagnosed initially. We present one case of endogenous endophthalmitis due to listeria monocytogenes in a cirrhotic patient, whose diagnosis was delayed 17 days after admission.

Integrated Analysis of microRNA and RNA-Seq Reveals Phenolic Acid Secretion Metabolism in Continuous Cropping of Polygonatum odoratum.

Polygonatum odoratum (Mill.) Druce is an essential Chinese herb, but continuous cropping (CC) often results in a serious root rot disease, reducing the yield and quality. Phenolic acids, released through plant root exudation, are typical autotoxic substances that easily cause root rot in CC. To better understand the phenolic acid biosynthesis of P. odoratum roots in response to CC, this study performed a combined microRNA (miRNA)-seq and RNA-seq analysis. The phenolic acid contents of the first cropping (FC) soil and CC soil were determined by HPLC analysis. The results showed that CC soils contained significantly higher levels of p-coumaric acid, phenylacetate, and caffeic acid than FC soil, except for cinnamic acid and sinapic acid. Transcriptome identification and miRNA sequencing revealed 15,788 differentially expressed genes (DEGs) and 142 differentially expressed miRNAs (DEMs) in roots from FC and CC plants. Among them, 28 DEGs and eight DEMs were involved in phenolic acid biosynthesis. Meanwhile, comparative transcriptome and microRNA-seq analysis demonstrated that eight miRNAs corresponding to five target DEGs related to phenolic acid synthesis were screened. Among them, ath-miR172a, ath-miR172c, novel_130, sbi-miR172f, and tcc-miR172d contributed to phenylalanine synthesis. Osa-miR528-5p and mtr-miR2673a were key miRNAs that regulate syringyl lignin biosynthesis. Nta-miR156f was closely related to the shikimate pathway. These results indicated that the key DEGs and DEMs involved in phenolic acid anabolism might play vital roles in phenolic acid secretion from roots of P. odoratum under the CC system. As a result of the study, we may have a better understanding of phenolic acid biosynthesis during CC of roots of P. odoratum.

Model performance and interpretability of semi-supervised generative adversarial networks to predict oncogenic variants with unlabeled data.

BACKGROUND: It remains an important challenge to predict the functional consequences or clinical impacts of genetic variants in human diseases, such as cancer. An increasing number of genetic variants in cancer have been discovered and documented in public databases such as COSMIC, but the vast majority of them have no functional or clinical annotations. Some databases, such as CiVIC are available with manual annotation of functional mutations, but the size of the database is small due to the use of human annotation. Since the unlabeled data (millions of variants) typically outnumber labeled data (thousands of variants), computational tools that take advantage of unlabeled data may improve prediction accuracy. RESULT: To leverage unlabeled data to predict functional importance of genetic variants, we introduced a method using semi-supervised generative adversarial networks (SGAN), incorporating features from both labeled and unlabeled data. Our SGAN model incorporated features from clinical guidelines and predictive scores from other computational tools. We also performed comparative analysis to study factors that influence prediction accuracy, such as using different algorithms, types of features, and training sample size, to provide more insights into variant prioritization. We found that SGAN can achieve competitive performances with small labeled training samples by incorporating unlabeled samples, which is a unique advantage compared to traditional machine learning methods. We also found that manually curated samples can achieve a more stable predictive performance than publicly available datasets. CONCLUSIONS: By incorporating much larger samples of unlabeled data, the SGAN method can improve the ability to detect novel oncogenic variants, compared to other machine-learning algorithms that use only labeled datasets. SGAN can be potentially used to predict the pathogenicity of more complex variants such as structural variants or non-coding variants, with the availability of more training samples and informative features.

Silica Cross-Linked Micelle-Based Theranostic System for the Imaging and Treatment of Acute and Chronic Kidney Injury.

Acute kidney injury (AKI) is a common and serious disease with high mortality and morbidity, and the persistent inflammatory environment brought about by AKI promotes its deterioration into chronic kidney disease (CKD). An efficient and timely targeted drug delivery to the renal tubules is crucial for AKI treatment. Here, we prepared silica cross-linked micelles (SCLMs) with different sizes and studied their targeting ability to the injured kidney. It is found that the SCLMs with a size of 13 nm could rapidly accumulate and remain in the damaged kidney. Immunofluorescence results confirmed that SCLMs are selectively located in the damaged tubular cells but cannot be found in healthy renal tissue. Therefore, fluorescent dye-labeled SCLMs were used for the imaging of the injured kidney, which could reflect the status of the kidney injury. Furthermore, atorvastatin, an antioxidative and anti-inflammatory drug, was loaded in SCLMs as the therapeutic agents for the treatment of ischemia/reperfusion-induced AKI and CKD. Renal function indexes, such as tubular necrosis, collagen deposition, and inflammation, were effectively improved after the treatment.

Targeting Warburg effect to rescue the suffocated photodynamic therapy: A cancer-specific solution.

The cancer photodynamic therapy (PDT) is limited by a congenital defect, namely the tumor hypoxia. Cancer cells are characterized by the vigorous oxygen-consuming glycolysis, which is well-known as the "Warburg effect" and one of the primary causes for the hypoxia. Herein, we employed the glucose metabolism as the cancer-specific target to enhance the performance of PDT. The Salvianolic acid B as the inhibitor of glucose uptake and aerobic glycolysis was concomitantly delivered with the photosensitizer chlorin e6 by a redox-responsive organosilica cross-linked micelle. The results demonstrated that the Salvianolic acid B suppressed the glucose metabolism, retarded the oxygen consumption to retain adequate oxygen as the ammo for PDT, which remarkably improve the efficacy of PDT both in vitro and in vivo. Our study not only provides an alternative strategy to address the hypoxia problem for PDT, but also enhances the selectivity of the treatment by targeting the cancer-specific Warburg effect.

Assessments of Somatic Variant Classification Using the Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists Guidelines: A Report from the Association for Molecular Pathology.

To assess the clinical implementation of the 2017 Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists, identify content that may result in classification inconsistencies, and evaluate implementation barriers, an Association for Molecular Pathology Working Group conducted variant interpretation challenges and a guideline implementation survey. A total of 134 participants participated in the variant interpretation challenges, consisting of 11 variants in four cancer cases. Results demonstrate 86% (range, 54% to 94%) of the respondents correctly classified clinically significant variants, variants of uncertain significance, and benign/likely benign variants; however, only 59% (range, 39% to 84%) of responses agreed with the working group's consensus intended responses regarding both tiers and categories of clinical significance. In the implementation survey, 71% (157/220) of respondents have implemented the 2017 guidelines for variant classification and reporting either with or without modifications. Collectively, this study demonstrates that, although they may not yet be optimized, the 2017 guideline recommendations are being adopted for standardized somatic variant classification. The working group identified significant areas for future guideline improvement, including the need for a more granular and comprehensive classification system and education resources to meet the growing needs of both laboratory professionals and medical oncologists.

Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer.

Somatic mutations are a major source of cancer development, and many driver mutations have been identified in protein coding regions. However, the function of mutations located in miRNA and their target binding sites throughout the human genome remains largely unknown. Here, we built detailed cancer-specific miRNA regulatory networks across 30 cancer types to systematically analyze the effect of mutations in miRNAs and their target sites in 3' untranslated region (3' UTR), coding sequence (CDS), and 5' UTR regions. A total of 3,518,261 mutations from 9,819 samples were mapped to miRNA-gene interactions (mGI). Mutations in miRNAs showed a mutually exclusive pattern with mutations in their target genes in almost all cancer types. A linear regression method identified 148 candidate driver mutations that can significantly perturb miRNA regulatory networks. Driver mutations in 3'UTRs played their roles by altering RNA binding energy and the expression of target genes. Finally, mutated driver gene targets in 3' UTRs were significantly downregulated in cancer and functioned as tumor suppressors during cancer progression, suggesting potential miRNA candidates with significant clinical implications. A user-friendly, open-access web portal (mGI-map) was developed to facilitate further use of this data resource. Together, these results will facilitate novel noncoding biomarker identification and therapeutic drug design targeting the miRNA regulatory networks. SIGNIFICANCE: A detailed miRNA-gene interaction map reveals extensive miRNA-mediated gene regulatory networks with mutation-induced perturbations across multiple cancers, serving as a resource for noncoding biomarker discovery and drug development.

Real-Time Visualization of the Antioxidative Potency of Drugs for the Prevention of Myocardium Ischemia-Reperfusion Injury by a NIR Fluorescent Nanoprobe.

The burst of the reactive oxygen species (ROS) is the culprit of myocardial ischemia-reperfusion injury. As direct ROS scavengers, antioxidants are clinically documented drugs for the prevention of reperfusion injury. However, some drugs give disappointing therapeutic performance despite their good in vitro effects. Therefore, in vivo assessments are necessary to screen the antioxidants before clinical trials. However, traditional methods such as histological study require invasive and complicated preprocessing of the biological samples, which may fail to reflect the actual level of the unstable ROS with a very short lifetime. Peroxynitrite (ONOO-) is a characteristic endogenous ROS produced during reperfusion. Here, we modified the ONOO--responsive near-infrared fluorescent probe on a myocardium-targeting silica cross-linked micelle to prepare a nanoprobe for the real-time monitoring of ONOO- during coronary reperfusion. A ROS-stable cyanine dye was co-labeled as an internal reference to achieve ratiometric sensing. The nanoprobe can passively target the infarcted myocardium and monitor the generation of ONOO- during reperfusion in real-time. The antioxidants, carvedilol, atorvastatin, and resveratrol, were used as model drugs to demonstrate the capability of the nanoprobe to evaluate the antioxidative potency in situ. The drugs were either loaded and delivered by the nanoprobe to compare their in vivo efficacy under similar concentrations or administered intraperitoneally as a free drug to take their pharmacokinetics into account. The imaging results revealed that pharmacokinetics might be the determinant factor that influences the efficacy of the antioxidants.

Pepper bHLH transcription factor CabHLH035 contributes to salt tolerance by modulating ion homeostasis and proline biosynthesis.

Members of the bHLH family of transcription factors play important roles in multiple aspects of plant biological processes, for instance, abiotic stress responses. Previously, we characterized CaNAC035, a gene that positively regulates stress tolerance and identified CabHLH035, a CaNAC035-interacting protein in pepper (Capsicum annuum L.). In this study, we describe the role of CabHLH035 in the response to salt stress. Our results show that the expression of CabHLH035 increased following salt treatment. Transient expression of CabHLH035 (CabHLH035-To) in pepper enhanced salt tolerance, ectopic expression of CabHLH035 in Arabidopsis increased the salt stress tolerance, whereas knocking down the expression of CabHLH035 in pepper plants resulted in decreased salt tolerance. Homologs of the Salt Overly Sensitive 1 (SOS1) and pyrroline-5-carboxylate acid synthetase (P5CS) genes showed drastically increased expression in transgenic Arabidopsis plants expressing CabHLH035 and CabHLH035-To plants, but expression decreased in CabHLH035-silenced plants. Our results also showed that CabHLH035 can directly bind to the CaSOS1 and CaP5CS gene promoters and positively activate their expression. We found that transgenic Arabidopsis plants, ectopic expression of CabHLH035 and pepper plants transiently overexpressing CabHLH035 (CabHLH035-To) showed lower Na+ and higher proline contents in response to NaCl treatment, while CabHLH035-silenced plants had higher Na+ and lower proline concentrations. Overall, CabHLH035 plays important roles in salt tolerance through its effects on the intracellular Na+ : K+ ratio and proline biosynthesis.

The complete chloroplast genome of Digitaria sanguinalis (Graminales: Gramineae).

Digitaria sanguinalis (Linnaeus) Scopoli 1722 is an annual herbal plant that has important medicinal and ecological value. The chloroplast genome was 138,079 bp in length. In total, 129 genes were predicted, including 82 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. The overall AT content of the genome was 61.39%. The phylogenetic analysis showed that D. sanguinalis and D. glauca formed a base clade in Panicoideae close to Thyridolepis xerophila. This study will help to understand the genetic diversity of the Digitaria plants.