RDscan: Extracting RNA-disease relationship from the literature based on pre-training model

With the rapid advancements in molecular biology and genomics, a multitude of connections between RNA and diseases has been unveiled, making the efficient and accurate extraction of RNA-disease (RD) relationships from extensive biomedical literature crucial for advancing research in this field. This study introduces RDscan, a novel text mining method developed based on the pre-training and fine-tuning strategy, aimed at automatically extracting RD-related information from a vast corpus of literature using pre-trained biomedical large language models (LLM). Initially, we constructed a dedicated RD corpus by manually curating from literature, comprising 2,082 positive and 2,000 negative sentences, alongside an independent test dataset (comprising 500 positive and 500 negative sentences) for training and evaluating RDscan. Subsequently, by fine-tuning the Bioformer and BioBERT pre-trained models, RDscan demonstrated exceptional performance in text classification and named entity recognition (NER) tasks. In 5-fold cross-validation, RDscan significantly outperformed traditional machine learning methods (Support Vector Machine, Logistic Regression and Random Forest). In addition, we have developed an accessible webserver that assists users in extracting RD relationships from text. In summary, RDscan represents the first text mining tool specifically designed for RD relationship extraction, and is poised to emerge as an invaluable tool for researchers dedicated to exploring the intricate interactions between RNA and diseases. Webserver of RDscan is free available at https://cellknowledge.com.cn/RDscan/.

Light Enables the Cathodic Interface Reaction Reversibility in Solid-State Lithium-Oxygen Batteries

Limited triple-phase boundaries arising from the accumulation of solid discharge product(s) in solid-state cathodes (SSCs) pose a challenge to high-property solid-state lithium-oxygen batteries (SSLOBs). Light-assisted SSLOBs have been gradually explored as an ingenious system; however, the fundamental mechanisms of the SSCs interface behavior remain unclear. Here, we discovered that light assistance can enhance the fast inner-sphere charge transfer in SSCs and regulate the discharge products with spherical particles generated via the surface growth model. Moreover, the high photoelectron excitation and transportation capabilities of SSCs can retard cathodic catalytic decay by avoiding structural degradation of the cathode with a reduced charge voltage. The light-induced SSLOBs exhibited excellent stability (170 cycles) with a low discharge-charge polarization overpotential (0.27 V). Furthermore, transparent SSLOBs with exceptional flexibility, mechanical stability, and multiform shapes were fabricated for theory-to-practical applications in sunlight-induced batteries. Our study opens new opportunities for the introduction of solar energy into energy storage systems.

First Measurement of η Meson Production in Neutrino Interactions on Argon with MicroBooNE

We present a measurement of η production from neutrino interactions on argon with the MicroBooNE detector. The modeling of resonant neutrino interactions on argon is a critical aspect of the neutrino oscillation physics program being carried out by the DUNE and Short Baseline Neutrino programs. η production in neutrino interactions provides a powerful new probe of resonant interactions, complementary to pion channels, and is particularly suited to the study of higher-order resonances beyond the Δ(1232). We measure a flux-integrated cross section for neutrino-induced η production on argon of 3.22±0.84(stat)±0.86(syst) 10^{-41}  cm^{2}/nucleon. By demonstrating the successful reconstruction of the two photons resulting from η production, this analysis enables a novel calibration technique for electromagnetic showers in GeV accelerator neutrino experiments.

Generation and characterization of temperature-sensitive alleles encoding GPI anchored proteins Psu1 and Dfg502 in Schizosaccharomyces pombe

Glycosyl-phosphatidylinositol (GPI) anchored proteins are implicated in remodeling of the yeast cell wall during growth and division. Schizosaccharomyces pombe proteins, Psu1 , Dfg501 , and Dfg502 are predicted GPI anchored proteins with likely cell wall modifying activity. Here, we isolated and characterized null and temperature-sensitive alleles that will allow further analysis of the function of these proteins and S. pombe cell wall formation. Our data confirm that Psu1 is necessary for cell separation, maintaining proper cell shape, and viability. Additionally, we found that Dfg501 and Dfg502 share a redundant and essential function necessary for cell separation and viability.

Applications of single‑cell omics and spatial transcriptomics technologies in gastric cancer (Review)

Gastric cancer (GC) is a prominent contributor to global cancer-related mortalities, and a deeper understanding of its molecular characteristics and tumor heterogeneity is required. Single-cell omics and spatial transcriptomics (ST) technologies have revolutionized cancer research by enabling the exploration of cellular heterogeneity and molecular landscapes at the single-cell level. In the present review, an overview of the advancements in single-cell omics and ST technologies and their applications in GC research is provided. Firstly, multiple single-cell omics and ST methods are discussed, highlighting their ability to offer unique insights into gene expression, genetic alterations, epigenomic modifications, protein expression patterns and cellular location in tissues. Furthermore, a summary is provided of key findings from previous research on single-cell omics and ST methods used in GC, which have provided valuable insights into genetic alterations, tumor diagnosis and prognosis, tumor microenvironment analysis, and treatment response. In summary, the application of single-cell omics and ST technologies has revealed the levels of cellular heterogeneity and the molecular characteristics of GC, and holds promise for improving diagnostics, personalized treatments and patient outcomes in GC.

ncRS: A resource of non-coding RNAs in sepsis

Sepsis, a life-threatening condition triggered by the body's response to infection, presents a significant global healthcare challenge characterized by disarrayed host responses, widespread inflammation, organ impairment, and heightened mortality rates. This study introduces the ncRS database (http://www.ncrdb.cn), a meticulously curated repository housing 1144 experimentally validated non-coding RNAs (ncRNAs) intricately linked with sepsis. ncRS offers comprehensive RNA data, exhaustive experimental insights, and integrated annotations from diverse databases. This resource empowers researchers and clinicians to decipher ncRNAs' roles in sepsis pathogenesis, potentially identifying vital biomarkers for early diagnosis and prognosis, thus facilitating personalized treatments.

Cm-siRPred: Predicting chemically modified siRNA efficiency based on multi-view learning strategy

The rational modification of siRNA molecules is crucial for ensuring their drug-like properties. Machine learning-based prediction of chemically modified siRNA (cm-siRNA) efficiency can significantly optimize the design process of siRNA chemical modifications, saving time and cost in siRNA drug development. However, existing in-silico methods suffer from limitations such as small datasets, inadequate data representation capabilities, and lack of interpretability. Therefore, in this study, we developed the Cm-siRPred algorithm based on a multi-view learning strategy. The algorithm employs a multi-view strategy to represent the double-strand sequences, chemical modifications, and physicochemical properties of cm-siRNA. It incorporates a cross-attention model to globally correlate different representation vectors and a two-layer CNN module to learn local correlation features. The algorithm demonstrates exceptional performance in cross-validation experiments, independent dataset, and case studies on approved siRNA drugs, and showcasing its robustness and generalization ability. In addition, we developed a user-friendly webserver that enables efficient prediction of cm-siRNA efficiency and assists in the design of siRNA drug chemical modifications. In summary, Cm-siRPred is a practical tool that offers valuable technical support for siRNA chemical modification and drug efficiency research, while effectively assisting in the development of novel small nucleic acid drugs. Cm-siRPred is freely available at https://cellknowledge.com.cn/sirnapredictor/.

MCSdb, a database of proteins residing in membrane contact sites

Organelles do not act as autonomous discrete units but rather as interconnected hubs that engage in extensive communication by forming close contacts called "membrane contact sites (MCSs)". And many proteins have been identified as residing in MCS and playing important roles in maintaining and fulfilling specific functions within these microdomains. However, a comprehensive compilation of these MCS proteins is still lacking. Therefore, we developed MCSdb, a manually curated resource of MCS proteins and complexes from publications. MCSdb documents 7010 MCS protein entries and 263 complexes, involving 24 organelles and 44 MCSs across 11 species. Additionally, MCSdb orchestrates all data into different categories with multitudinous information for presenting MCS proteins. In summary, MCSdb provides a valuable resource for accelerating MCS functional interpretation and interorganelle communication deciphering.

Generation and characterization of temperature-sensitive alleles of the glucanosyltransferase Gas1 in Schizosaccharomyces pombe

The Schizosaccharomyces pombe Gas family of β-1,3-glucanosyltransferases modify the cell wall by elongating β-1,3-glucan chains. While gas1Δ cells are inviable under standard laboratory growth conditions, they are viable in the presence of an osmotic stabilizer. Even under these conditions however, gas1Δ cells are slow-growing and display cell separation and morphology defects. Here, we isolated and characterized two gas1 temperature-sensitive alleles. Our data support that Gas1 is the primary S. pombe β-1,3-glucanosyltransferase important for cell separation and cell viability and provide useful tools for further analysis of S. pombe cell wall formation.

Towards the role of apprehension and anxiety as antecedents of EFL students' burnout

How students experience the learning process is of great importance because it affects the enthusiasm they feel during this process. Although many studies have been conducted on apprehension, anxiety, and burnout in both teachers and students, few focus on the relationship between these three variables. To this end, the three variables in this review study are first defined. Then, the relationship between EFL learners' apprehension and their anxiety and burnout is discussed. It seems that the more apprehensive and anxious one feels, the more likely they feel burned out. Finally, the implications of this study and suggestions for further studies are presented.

The Cdc14 phosphatase, Clp1, does not affect genome expression

Schizosaccharomyces pombe Clp1 is a Cdc14-family phosphatase that reverses mitotic Cdk1 phosphorylation. Despite evolutionary conservation, Clp1 's mammalian orthologs do not share this function. Rather, higher eukaryotic Cdc14 enzymes act in DNA repair, ciliogenesis, and gene regulation. To examine if Clp1 regulates gene expression, we compared the transcriptional profiles of cells lacking Clp1 function to that of wildtype. Because clp1∆ cells are sensitive to the actin depolymerizing drug, LatrunculinA, we also investigated whether a transcriptional response was involved. Our results indicate that Clp1 does not detectably affect gene expression and highlight the organism-specific functions of this conserved phosphatase family.

Improving astaxanthin-loaded chitosan/polyvinyl alcohol/graphene oxide nanofiber membranes and their application in periodontitis

Periodontitis is a chronic inflammatory disease primarily driven by host inflammation and plaque-induced immune responses. Controlling the host inflammatory response and improving the periodontal inflammatory microenvironment are crucial to promoting periodontal tissue regeneration. In this study, the blended nanofiber membranes previously prepared by our research group were improved, and we developed multifunctional chitosan/polyvinyl alcohol/graphene oxide/astaxanthin coaxial nanofiber membranes. Scanning electron microscopy showed that the prepared nanofibers had a smooth surface and a uniform diameter distribution. The mechanical property test results showed that the coaxial nanofiber membranes exhibited higher tensile strength compared to the blended nanofiber membranes, which increased from 4.50 ± 0.32 and 3.70 ± 0.45 MPa to 7.12 ± 0.22 and 5.62 ± 0.79 MPa respectively. Drug release studies indicated that the "shell-core" structure of coaxial nanofibers significantly reduced the initial burst release of astaxanthin (ASTA), with only 13.49 % and 10.71 % release in the first 24 h, and drug release lasted for over a week. Animal experiments confirmed that the coaxial nanofiber membranes loaded with ASTA promoted periodontal bone defect repair while inhibiting periodontal inflammation. In conclusion, the prepared coaxial nanofiber membranes are a promising sustained-release drug system for treating periodontitis.

Search for Heavy Neutral Leptons in Electron-Positron and Neutral-Pion Final States with the MicroBooNE Detector

We present the first search for heavy neutral leptons (HNLs) decaying into νe^{+}e^{-} or νπ^{0} final states in a liquid-argon time projection chamber using data collected with the MicroBooNE detector. The data were recorded synchronously with the NuMI neutrino beam from Fermilab's main injector corresponding to a total exposure of 7.01×10^{20} protons on target. We set upper limits at the 90% confidence level on the mixing parameter |U_{μ4}|^{2} in the mass ranges 10≤m_{HNL}≤150  MeV for the νe^{+}e^{-} channel and 150≤m_{HNL}≤245  MeV for the νπ^{0} channel, assuming |U_{e4}|^{2}=|U_{τ4}|^{2}=0. These limits represent the most stringent constraints in the mass range 35 Collapse

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[Reappraisals of biological behaviors of PDGFRA mutant gastrointestinal stromal tumor]

Objective: To investigate the biological behavior spectrum of platelet-derived growth factor alpha receptor (PDGFRA)-mutant gastrointestinal stromal tumor (GIST), and to compare the clinical values of the Zhongshan method of benign and malignant evaluation with the modified National Institutes of Health (NIH) risk stratification. Methods: A total of 119 cases of GIST with PDGFRA mutation who underwent surgical resection at Zhongshan Hospital, Fudan University from 2009 to 2020 were collected. The clinicopathological data, follow-up records, and subsequent treatment were reviewed and analyzed statistically. Results: There were 79 males and 40 females. The patients ranged in age from 25 to 80 years, with a median age of 60 years. Among them, 115 patients were followed up for 1-154 months, and 13 patients progressed to disease. The 5-year disease-free survival (DFS) and overall survival (OS) were 90.1% and 94.1%, respectively. According to the modified NIH risk stratification, 8 cases, 32 cases, 38 cases, and 35 cases were very-low risk, low risk, intermediate risk, and high risk, and 5-year DFS were 100.0%, 95.6%, 94.3%, and 80.5%, respectively. There was no significant difference in prognosis among the non-high risk groups, only the difference between high risk and non-high risk groups was significant (P=0.029). However, the 5-year OS was 100.0%, 100.0%, 95.0% and 89.0%, and there was no difference (P=0.221). According to the benign and malignant evaluation Zhongshan method, 43 cases were non-malignant (37.4%), 56 cases were low-grade malignant (48.7%), 9 cases were moderately malignant (7.8%), and 7 cases were highly malignant (6.1%). The 5-year DFS were 100.0%, 91.7%, 77.8%, 38.1%, and the difference was significant (P<0.001). The 5-year OS were 100.0%, 97.5%, 77.8%, 66.7%, the difference was significant (P<0.001). Conclusions: GIST with PDGFRA gene mutation shows a broad range of biological behavior, ranging from benign to highly malignant. According to the Zhongshan method, non-malignant and low-grade malignant tumors are common, the prognosis after surgery is good, while the fewer medium-high malignant tumors showed poor prognosis after surgical resection. The overall biological behavior of this type of GIST is relatively inert, which is due to the low proportion of medium-high malignant GIST. The modified NIH risk stratification may not be effective in risk stratification for PDGFRA mutant GIST.

Prevotella copri exhausts intrinsic indole-3-pyruvic acid in the host to promote breast cancer progression: inactivation of AMPK via UHRF1-mediated negative regulation

Emerging evidence has revealed the novel role of gut microbiota in the development of cancer. The characteristics of function and composition in the gut microbiota of patients with breast cancer patients has been reported, however the detailed causation between gut microbiota and breast cancer remains uncertain. In the present study, 16S rRNA sequencing revealed that Prevotella, particularly the dominant species Prevotella copri, is significantly enriched and prevalent in gut microbiota of breast cancer patients. Prior-oral administration of P. copri could promote breast cancer growth in specific pathogen-free mice and germ-free mice, accompanied with sharp reduction of indole-3-pyruvic acid (IPyA). Mechanistically, the present of excessive P. copri consumed a large amount of tryptophan (Trp), thus hampering the physiological accumulation of IPyA in the host. Our results revealed that IPyA is an intrinsic anti-cancer reagent in the host at physiological level. Briefly, IPyA directly suppressed the transcription of UHRF1, following by the declined UHRF1 and PP2A C in nucleus, thus inhibiting the phosphorylation of AMPK, which is just opposite to the cancer promoting effect of P. copri. Therefore, the exhaustion of IPyA by excessive P. copri strengthens the UHRF1-mediated negative control to inactivated the energy-controlling AMPK signaling pathway to promote tumor growth, which was indicated by the alternation in pattern of protein expression and DNA methylation. Our findings, for the first time, highlighted P. copri as a risk factor for the progression of breast cancer.

Astragaloside IV enhances the sensitivity of breast cancer stem cells to paclitaxel by inhibiting stemness

Background

Chemotherapy is one of the common treatments for breast cancer. The induction of cancer stem cells (CSCs) is an important reason for chemotherapy failure and breast cancer recurrence. Astragaloside IV (ASIV) is one of the effective components of the traditional Chinese medicine (TCM) Astragalus membranaceus, which can improve the sensitivity of various tumors to chemotherapy drugs. Here, we explored the sensitization effect of ASIV to chemotherapy drug paclitaxel (PTX) in breast cancer from the perspective of CSCs.

Methods

The study included both in vitro and in vivo experiments. CSCs from the breast cancer cell line MCF7 with stem cell characteristics were successfully induced in vitro. Cell viability and proliferation were detected using the Cell Counting Kit-8 (CCK-8) and colony formation assays, and flow cytometry and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) methods were performed to detect cell apoptosis. Stemness-related protein expression was determined by western blotting (WB) and immunohistochemistry (IHC). Body weight, histopathology, and visceral organ damage of mice were used to monitor drug toxicity.

Results

The expression of stemness markers including Sox2, Nanog, and ALDHA1 was stronger in MCF7-CSCs than in MCF7. PTX treatment inhibited the proliferation of tumor cells by promoting cell apoptosis, whereas the stemness of breast cancer stem cells (BCSCs) resisted the effects of PTX. ASIV decreased the stemness of BCSCs, increased the sensitivity of BCSCs to PTX, and synergistically promoted PTX-induced apoptosis of breast cancer cells. Our results showed that the total cell apoptosis rate increased by about 25% after adding ASIV compared with BCSCs treated with PTX alone. The in vivo experiments demonstrated that ASIV enhanced the ability of PTX to inhibit the growth of breast cancer. WB and IHC showed that ASIV reduced the stemness of CSCs.

Conclusions

In this study, the resistance of breast cancer to PTX was attributed to the existence of CSCs; ASIV weakened the resistance of MCF7-CSCs to PTX by significantly attenuating the hallmarks of breast cancer stemness and improved the efficacy of PTX.

Cryptanshinone extract of Salvia miltiorrhiza stimulates pediatric acute myeloid leukemia stem cell apoptosis and the anti-inflammatory mechanism via accelerating microRNA-211-5p to supress Janus kinase 2/signal transducer and activator of transcription 3 signaling pathway activation

This study was designed to explore cryptanshinone (CPT) extract of Salvia miltiorrhiza stimulating pediatric acute myeloid leukemia (AML) stem cell (LSC) apoptosis and anti-inflammatory mechanism via accelerating microRNA (miR)-211-5p to restrain Janus kinase 2 (JAK2)/signal transducer and activator of transcription 3 (STAT3) pathway activation. Obtaining blood samples from pediatric acute myeloid leukemia patients and healthy volunteers and detecting miR-211-5p and JAK2 were performed. Purchase of the human AML cell line KG1a was conducted, and sorting of KG1a cells was to gain LSC. Test of miR-211-5p and JAK2, the phosphorylation of JAK2/STAT3 was implemented. Pretreatment of LSCs was with CPT. Variation of miR-211-5p and JAK2 in LSCs was via plasmid transfection to explore their actions in cell advancement with apoptosis and inflammation. Identification of the targeting of miR-211-5p with JAK2 was implemented. In results: MiR-211-5p was declined in endometrial cancer, while JAK2 was elevated; CPT was available to boost LSC apoptosis and restrain the inflammation; elevated miR-211-5p or repressive JAK2 was available to strengthen the acceleration of CPT on LSCs apoptosis and the repression of inflammation; MiR-211-5p targeted JAK2; augmented JAK2 was available to turn around the action of elevated miR-211-5p. We conclude that CPT extract of Salvia miltiorrhiza stimulated pediatric LSC apoptosis and restrained the inflammation via accelerating microRNA (miR)-211-5p to suppress JAK2/STAT3 pathway activation.

MetaboliteCOVID: A manually curated database of metabolite markers for COVID-19

In the realm of unraveling COVID-19's intricacies, numerous metabolomic investigations have been conducted to discern the unique metabolic traits exhibited within infected patients. These endeavors have yielded a substantial reservoir of potential data pertaining to metabolic biomarkers linked to the virus. Despite these strides, a comprehensive and meticulously structured database housing these crucial biomarkers remains absent. In this study, we developed MetaboliteCOVID, a manually curated database of COVID-19-related metabolite markers. The database currently comprises 665 manually selected entries of significantly altered metabolites associated with early diagnosis, disease severity, prognosis, and drug response in COVID-19, encompassing 337 metabolites. Additionally, the database offers a user-friendly interface, containing abundant information for querying, browsing, and analyzing COVID-19-related abnormal metabolites in different body fluids. In summary, we believe that this database will effectively facilitate research on the functions and mechanisms of COVID-19-related metabolic biomarkers, thereby advancing both basic and clinical research on COVID-19. MetaboliteCOVID is free available at: https://cellknowledge.com.cn/MetaboliteCOVID.

All-in-one self-floating porous foams as robust heat-blocking layers for efficient photothermal conversion and solar desalination

Solar-driven interfacial evaporation is a highly efficient and ecofriendly technology for producing freshwater. Herein, self-floating plasmon Ag/black TiO2/carbon porous layered foams (Ag-BTCFs) were demonstrated as efficient solar-thermal convectors using freeze-drying cast-molding and high-temperature surface hydrogenation strategies. This all-in-one three-dimensional (3D) cross-linked self-floating porous layered foam material with full-spectrum absorption can fully harvest sunlight (∼95.45%) and effectively block heat transfer to its sublayer. The synergy of sufficient utilization of absorbed ultraviolet radiation by black TiO2 (b-TiO2), visible light absorption by Ag nanoparticles (Ag NPs) via localized surface plasmon resonance, and near-infrared absorption by layered-amorphous carbon can achieve full-solar-spectrum absorption to concentrate thermal energy. In addition to their synergistic effect, they are conducive to the relaxation of hot electrons when utilizing photogenerated holes to degrade pollutants in domestic wastewater. The steam generation efficiency of Ag-BTCFs is up to 1.79 kg m-2h-1 due to their solar energy conversion efficiency of 81.74% under 1 sun irradiation, which is five times higher than the evaporation rate of pure water. Notably, the material's efficient ion removal rate of 99.80% for solar desalination indicates its high potential for various applications. This strategy provides new insights for fabricating recyclable heat-blocking layer systems against thermal loss to enhance solar steam generation.

The role of ncRNA regulatory mechanisms in diseases-case on gestational diabetes

Non-coding RNAs (ncRNAs) are a class of RNA molecules that do not have the potential to encode proteins. Meanwhile, they can occupy a significant portion of the human genome and participate in gene expression regulation through various mechanisms. Gestational diabetes mellitus (GDM) is a pathologic condition of carbohydrate intolerance that begins or is first detected during pregnancy, making it one of the most common pregnancy complications. Although the exact pathogenesis of GDM remains unclear, several recent studies have shown that ncRNAs play a crucial regulatory role in GDM. Herein, we present a comprehensive review on the multiple mechanisms of ncRNAs in GDM along with their potential role as biomarkers. In addition, we investigate the contribution of deep learning-based models in discovering disease-specific ncRNA biomarkers and elucidate the underlying mechanisms of ncRNA. This might assist community-wide efforts to obtain insights into the regulatory mechanisms of ncRNAs in disease and guide a novel approach for early diagnosis and treatment of disease.

Characterization of Pik1 function in fission yeast reveals its conserved role in lipid synthesis and not cytokinesis

Phosphatidylinositol (PI)-4-phosphate (PI4P) is a lipid found at the plasma membrane (PM) and Golgi in cells from yeast to humans. PI4P is generated from PI by PI4-kinases and can be converted into PI-4,5-bisphosphate [PI(4,5)P2]. Schizosaccharomyces pombe have two essential PI4-kinases - Stt4 and Pik1. Stt4 localizes to the PM, and its loss from the PM results in a decrease of PM PI4P and PI(4,5)P2. As a result, cells divide non-medially due to disrupted cytokinetic ring-PM anchoring. However, the localization and function of S. pombe Pik1 has not been thoroughly examined. Here, we found that Pik1 localizes exclusively to the trans-Golgi and is required for Golgi PI4P production. We determined that Ncs1 regulates Pik1, but unlike in other organisms, it is not required for Pik1 Golgi localization. When Pik1 function was disrupted, PM PI4P but not PI(4,5)P2 levels were reduced, a major difference compared with Stt4. We conclude that Stt4 is the chief enzyme responsible for producing the PI4P that generates PI(4,5)P2. Also, that cells with disrupted Pik1 do not divide asymmetrically highlights the specific importance of PM PI(4,5)P2 for cytokinetic ring-PM anchoring.

Accurately identifying hemagglutinin using sequence information and machine learning methods

Introduction

Hemagglutinin (HA) is responsible for facilitating viral entry and infection by promoting the fusion between the host membrane and the virus. Given its significance in the process of influenza virus infestation, HA has garnered attention as a target for influenza drug and vaccine development. Thus, accurately identifying HA is crucial for the development of targeted vaccine drugs. However, the identification of HA using in-silico methods is still lacking. This study aims to design a computational model to identify HA.

Methods

In this study, a benchmark dataset comprising 106 HA and 106 non-HA sequences were obtained from UniProt. Various sequence-based features were used to formulate samples. By perform feature optimization and inputting them four kinds of machine learning methods, we constructed an integrated classifier model using the stacking algorithm.

Results and discussion

The model achieved an accuracy of 95.85% and with an area under the receiver operating characteristic (ROC) curve of 0.9863 in the 5-fold cross-validation. In the independent test, the model exhibited an accuracy of 93.18% and with an area under the ROC curve of 0.9793. The code can be found from https://github.com/Zouxidan/HA_predict.git. The proposed model has excellent prediction performance. The model will provide convenience for biochemical scholars for the study of HA.

P450Rdb: a manually curated database of reactions catalyzed by cytochrome P450 enzymes

INTRODUCTION

Cytochrome P450 enzymes (P450s) are recognized as the most versatile catalysts worldwide, playing vital roles in numerous biological metabolism and biosynthesis processes across all kingdoms of life. Despite the vast number of P450 genes available in databases (over 300,000), only a small fraction of them (less than 0.2%) have undergone functional characterization.

OBJECTIVES

To provide a convenient platform with abundant information on P450s and their corresponding reactions, we introduce the P450Rdb database, a manually curated resource compiles literature-supported reactions catalyzed by P450s.

METHODS

All the P450s and Reactions were manually curated from the literature and known databases. Subsequently, the P450 reactions organized and categorized according to their chemical reaction type and site. The website was developed using HTML and PHP languages, with the MySQL server utilized for data storage.

RESULTS

The current version of P450Rdb catalogs over 1,600 reactions, involving more than 590 P450s across a diverse range of over 200 species. Additionally, it offers a user-friendly interface with comprehensive information, enabling easy querying, browsing, and analysis of P450s and their corresponding reactions. P450Rdb is free available at http://www.cellknowledge.com.cn/p450rdb/.

CONCLUSIONS

We believe that this database will significantly promote structural and functional research on P450s, thereby fostering advancements in the fields of natural product synthesis, pharmaceutical engineering, biotechnological applications, agricultural and crop improvement, and the chemical industry.

Automatic Prediction of Metastasis-Free Survival (MFS) Using Prostate-Specific Membrane Antigen (PSMA) PET for Oligometastatic Castration-Sensitive Prostate Cancer (omCSPC)

PURPOSE/OBJECTIVE(S)

Recent data have shown the promise of metastasis-directed therapy (MDT) to improve outcomes in omCSPC patients. Response biomarkers are still needed to identify patients at an early time point who will not respond to the treatment. We have shown that PSMA PET-CT SUVmax changes over time may be a useful response biomarker that correlates with MFS, an important endpoint in these omCSPC patients. This study investigated radiomic imaging biomarkers derived from PSMA-PET acquired pre- and post-MDT for MFS prediction, which may provide better features to discriminate response in the future to improve the outcome of these patients.

MATERIALS/METHODS

We accrued an international multi-institutional cohort of omCSPC patients treated with stereotactic ablative radiation therapy (SABR) MDT. The cohort includes 32 patients from Institution 1 (USA) and 38 patients from Institution 2 (Europe). Both pre- and 6-month post-treatment PSMA-PET/CT were acquired. Combat was used for data harmonization in the image domain to minimize imaging variations across institutions. We defined the GTV volume as zone 1 and a 3-5 mm expansion ring area outside the GTV as zone 2 for radiomics analysis. 874 radiomics features (214 original and 660 wavelet filtered features) were extracted from both zones using open-source software and used together for MFS prediction. Function Chi2 was used to select the most significant five features. Several machine learning models (Random Forest, Logistic regression, Support Vector Machine, Naïve Bayesian) were implemented to predict MFS. The models were tested using both a leave-one-out strategy and cross-validation across the two institutions.

RESULTS

In the leave-one-out biomarker using 70 patients, random forest achieved the best accuracy, with MFS predicted correctly for 56 (80% of 70) patients. The five radiomic features identified based on their ability to predict MFS included Entropy, Skewness, and Compactness from zone 1, Skewness, and Mesh volume from zone 2. In the cross-institution tests, random forest predicted MFS correctly for 24 (75% of 32) patients when being trained using 38 Institution 2 patients and validated against 32 Institution 1 patients. Vice versa, the model predicted MFS correctly for 28 (74% of 38) patients when being trained using Institution 1 patients and validation using Institution 2 patients. The five features identified for prediction included Entropy and Skewness from both zones and Flatness from zone 1.

CONCLUSION

Our study demonstrated the promise of using pre- and post-MDT PSMA-PET-based imaging radiomic biomarkers for MFS prediction for omCSPC patients. Imaging biomarkers predictive of MFS were identified in both GTV and the ring area outside GTV. Over 74% prediction accuracy was achieved in the cross-institution validation test. The model provides a valuable tool for prognosis prediction early following MDT, which opens up a unique opportunity for monitoring or treatment interventions for patients identified with poor prognoses to improve outcomes.

Elevated levels of sphingolipid MIPC in the plasma membrane disrupt the coordination of cell growth with cell wall formation in fission yeast

Coupling cell wall expansion with cell growth is a universal challenge faced by walled organisms. Mutations in Schizosaccharomyces pombe css1, which encodes a PM inositol phosphosphingolipid phospholipase C, prevent cell wall expansion but not synthesis of cell wall material. To probe how Css1 modulates cell wall formation we used classical and chemical genetics coupled with quantitative mass spectrometry. We found that elevated levels of the sphingolipid biosynthetic pathway's final product, mannosylinositol phosphorylceramide (MIPC), specifically correlated with the css1-3 phenotype. We also found that an apparent indicator of sphingolipids and a sterol biosensor accumulated at the cytosolic face of the PM at cell tips and the division site of css1-3 cells and, in accord, the PM in css1-3 was less dynamic than in wildtype cells. Interestingly, disrupting the protein glycosylation machinery recapitulated the css1-3 phenotype and led us to investigate Ghs2, a glycosylated PM protein predicted to modify cell wall material. Disrupting Ghs2 function led to aberrant cell wall material accumulation suggesting Ghs2 is dysfunctional in css1-3. We conclude that preventing an excess of MIPC in the S. pombe PM is critical to the function of key PM-localized proteins necessary for coupling growth with cell wall formation.

Membrane binding of endocytic myosin-1s is inhibited by a class of ankyrin repeat proteins

Myosin-1s are monomeric actin-based motors that function at membranes. Myo1 is the single myosin-1 isoform in Schizosaccharomyces pombe that works redundantly with Wsp1-Vrp1 to activate the Arp2/3 complex for endocytosis. Here, we identified Ank1 as an uncharacterized cytoplasmic Myo1 binding partner. We found that in ank1Δ cells, Myo1 dramatically redistributed from endocytic patches to decorate the entire plasma membrane and endocytosis was defective. Biochemical analysis and structural predictions suggested that the Ank1 ankyrin repeats bind the Myo1 lever arm and the Ank1 acidic tail binds the Myo1 TH1 domain to prevent TH1-dependent Myo1 membrane binding. Indeed, Ank1 overexpression precluded Myo1 membrane localization and recombinant Ank1 reduced purified Myo1 liposome binding in vitro. Based on biochemical and cell biological analyses, we propose budding yeast Ank1 and human OSTF1 are functional Ank1 orthologs and that cytoplasmic sequestration by small ankyrin repeat proteins is a conserved mechanism regulating myosin-1s in endocytosis.

Hybrid-Supervised Deep Learning for Proton-Acoustic Reconstruction for 3D In Vivo Proton Dose Verification

PURPOSE/OBJECTIVE(S)

Proton-acoustic (PA) image has shown great potential to provide real-time 3D dose verification of proton therapy. However, the PA image quality suffers from severe limited view artifacts, which significantly impairs its accuracy for dose verification. In this study, we developed a hybrid-supervised deep learning method for PA reconstruction to address the limited-view issues.

MATERIALS/METHODS

Our method consists of two stages. In the first stage, a transformer-based network was proposed to reconstruct initial pressure maps from protoacoustic signals. The network was first trained using supervision by the iteratively reconstructed pressure map and then fine-tuned using transfer learning and self-supervision based on the data fidelity constraint. In the second stage, the PA image was further enhanced by a 3D U-net. The final PA images were converted to dose maps using conversion coefficients derived from CT images. Data from 126 prostate cancer patients treated by proton therapy were collected under an IRB protocol and were split into 86 and 40 patients for model training and testing, respectively. Data of each patient contains the planning CT scan, the corresponding clinical treatment plan, and the dose map calculated by commercial software. The radiofrequency signals were generated by performing proton acoustic simulation based on CT images and the ground truth pressure map derived from the treatment plan. An ultrasound detector matrix with 64 × 64 size and 500kHz central frequency was simulated under the perineum to acquire the signals in the prostate area. In the testing results, the method's accuracy was evaluated using Root-mean-squared-error (RMSE) and structural-similarity-index-measure (SSIM) between the reconstructed and ground truth pressure map and dose distribution.

RESULTS

Testing results showed that the reconstructed pressure map achieved an average RMSE/SSIM of 0.0292/0.96, demonstrating excellent 3D information with details. Dose maps derived from the pressure map achieved an average RMSE/SSIM of 0.018/0.99 with a gamma index of 94.7% and 95.7% for 1%/3 mm and 1%/5 mm criteria compared to the ground truth dose maps. The reconstruction time was 6s, which can be further reduced using GPU.

CONCLUSION

Our study achieves start-of-the-art performance in the challenging task of direct reconstruction from limited-view radiofrequency signals, demonstrating the great promise of PA imaging as a highly efficient and accurate tool for in-vivo 3D proton dose verification. Such high-precision 3D online dose verification can substantially reduce the range uncertainties of proton therapy to significantly improve its precision and outcomes.

Insight into the enhancement effect of amino functionalized carbon nanotubes on the H2S removal performance of nanofluid system

By constructing nanofluid system, trace functionalized nanoparticles can significantly enhance the absorption performance of basic liquid. In this work, amino functionalized carbon nanotubes (ACNTs) and carbon nanotubes (CNTs) were introduced into alkaline deep eutectic solvents to build nanofluid systems and used for the dynamic absorption of H2S. The experiment results showed that the introduction of nanoparticles can significantly enhance the H2S removal performance of original liquid. When performing H2S removal experiments, the optimal mass concentrations of ACNTs versus CNTs were 0.05 % and 0.01 %, respectively. The characterization showed that the surface morphology and structure of the nanoparticles unchanged significantly during the absorption-regeneration process. A double mixed gradientless gas-liquid reactor was used to explore the gas-liquid absorption kinetics characteristics of the nanofluid system. It was found that the gas-liquid mass transfer rate increased significantly after the addition of nanoparticles. The highest total mass transfer coefficient of the nanofluid system of ACNTs was increased to more than 400 % of the value before the addition of nanoparticles. The analysis showed that the shuttle effect and hydrodynamic effect of nanoparticles play important role in the process of enhancing gas-liquid absorption, and the amino functionalization enhanced the shuttle effect of nanoparticles significantly.

Control of the Bright-Dark Exciton Splitting Using the Lamb Shift in a Two-Dimensional Semiconductor

We investigate the exciton fine structure in atomically thin WSe_{2}-based van der Waals heterostructures where the density of optical modes at the location of the semiconductor monolayer can be tuned. The energy splitting Δ between the bright and dark exciton is measured by photoluminescence spectroscopy. We demonstrate that Δ can be tuned by a few meV as a result of a significant Lamb shift of the optically active exciton that arises from emission and absorption of virtual photons triggered by the vacuum fluctuations of the electromagnetic field. We also measure strong variations of the bright exciton radiative linewidth as a result of the Purcell effect. All these experimental results illustrate the strong sensitivity of the excitons to local vacuum field fluctuations. We find a very good agreement with a model that demonstrates the equivalence, for our system, of a classical electrodynamical transfer matrix formalism and quantum-electrodynamical approach. The bright-dark splitting control we demonstrate here in the weak light-matter coupling regime should apply to any semiconductor structures.

First Double-Differential Measurement of Kinematic Imbalance in Neutrino Interactions with the MicroBooNE Detector

We report the first measurement of flux-integrated double-differential quasielasticlike neutrino-argon cross sections, which have been made using the Booster Neutrino Beam and the MicroBooNE detector at Fermi National Accelerator Laboratory. The data are presented as a function of kinematic imbalance variables which are sensitive to nuclear ground-state distributions and hadronic reinteraction processes. We find that the measured cross sections in different phase-space regions are sensitive to different nuclear effects. Therefore, they enable the impact of specific nuclear effects on the neutrino-nucleus interaction to be isolated more completely than was possible using previous single-differential cross section measurements. Our results provide precision data to help test and improve neutrino-nucleus interaction models. They further support ongoing neutrino-oscillation studies by establishing phase-space regions where precise reaction modeling has already been achieved.

Isolation of mutant alleles of the U6 snRNA m 6 A methyltransferase Mtl16 and characterization of their genetic interactions with splicing mutants in Schizosaccharomyces pombe

Schizosaccharomyces pombe Dim1 is a conserved essential component of the U4/U6.U5 tri-snRNP complex essential for pre-mRNA splicing. In a synthetic lethal screen with the temperature-sensitive dim1-35 mutant, we isolated multiple alleles of non-essential mtl16 that encodes the U6 snRNA m 6 A methyltransferase. Further genetic analysis revealed strong and specific negative genetic interactions between mtl16 and a mutation in the Dim1 binding partner, Prp31, and between dim1-35 and a mutation in the Prp31 binding partner, Prp6. Our work provides additional tools to study pre-mRNA splicing in S. pombe and biological confirmation of the importance of the Prp6-Prp31-Dim1-U6 snRNA interactions for pre-mRNA splicing.

Pyrotinib plus capecitabine for trastuzumab-resistant, HER2-positive advanced breast cancer (PICTURE): a single-arm, multicenter phase 2 trial

BACKGROUND

Patients with human epidermal growth factor receptor 2 (HER2)-positive advanced breast cancer and primary resistance to trastuzumab have a poor clinical outcome and lack good evidence to inform clinical decision. This study investigated the efficacy and safety of pyrotinib plus capecitabine in this population.

METHODS

This phase 2 trial was conducted at 16 sites in China. Patients received oral pyrotinib 400 mg once daily and capecitabine 1000 mg/m2 twice a day on days 1-14 of each 21-day cycle until disease progression or intolerable toxicity. The primary endpoint was investigator-assessed progression-free survival (PFS).

RESULTS

Between June 2019 and September 2021, 100 patients were enrolled with a median age of 51 years (range, 24-69). All patients had been treated with trastuzumab and 21 (21.0%) patients had prior use of pertuzumab. As of August 31, 2022, the median follow-up duration was 20.1 months (range, 1.3-38.2). The median PFS was 11.8 months (95% confidence interval [CI], 8.4-15.1), which crossed the pre-specified efficacy boundary of 8.0 months. The objective response rate was 70.0% (70/100), with a median duration of response of 13.8 months (95% CI, 10.2-19.3). The disease control rate was 87.0% (87/100). The median overall survival was not reached. The most common grade ≥ 3 treatment-emergent adverse event was diarrhea (24 [24.0%]). No treatment-related deaths occurred.

CONCLUSIONS

Pyrotinib plus capecitabine can be considered to be a treatment option in HER2-positive advanced breast cancer patients who have shown primary resistance to trastuzumab. Even in the era of modern anti-HER2 treatments, this clinical setting warrants more investigations to meet unmet needs.

TRIAL REGISTRATION

ClinicalTrials.gov, NCT04001621. Retrospectively registered on June 28, 2019.

[Analysis of respiratory syncytial virus nonstructural protein 1 amino acid variation and clinical characteristics]

Objective: To investigate the relationship between amino acid variations of respiratory syncytial virus (RSV) nonstructural protein (NS) 1 and the clinical characteristics. Method: A retrospective case review was conducted. From December 2018 to January 2020, a total of 81 cases of hospitalized children who were tested only positive for RSV by RT-PCR or PCR at the Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University were included in the study. The NS1 genes of RSV subtype A and subtype B were amplified by PCR and sequenced. The amino acid sequences were analyzed. The Chi-square test and Mann-Whitney rank sum test were used to compare the clinical characteristics and type Ⅰ interferon levels of children with or without NS1 variation in the variation and non-variation groups. Results: Among 81 cases, there were 58 males and 23 females. There were 11 cases in the variation group, the age of onset was 2.0 (1.0, 11.0) months, included 4 cases of subtype A (variant sites were: 2 cases for Lys33Gln, one case for Gly2Asp, Pro67Ser, Leu137Phe, respectively) and 7 cases of subtype B (variant sites were: two cases for Val121Ile, one case for Tyr30Cys, Val65Met, Asn85Ser, Ser118Asn, Asp124Asn, respectively). These variant sites all appeared at a very low frequency 0.08 (0.04, 0.29) % in the NCBI PROTEIN database. There were 70 cases in non-variation group, the onset age was 3.5 (1.0, 7.0) months. The proportion of dyspnea in the variation group was higher than that in the non-variation group (10/11 vs. 47% (33/70), χ²=7.31, P<0.01). Conclusions: There are some variant sites in nonstructural protein NS1 of RSV. Children may be prone to have dyspnea with NS1 variations.

Overexpression of potato ORANGE (StOR) and StOR mutant in Arabidopsis confers increased carotenoid accumulation and tolerance to abiotic stress

ORANGE (OR) plays essential roles in regulating carotenoid homeostasis and enhancing the ability of plants to adapt to environmental stress. However, OR proteins have been functionally characterized in only a few plant species, and little is known about the role of potato OR (StOR). In this study, we characterized the StOR gene in potato (Solanum tuberosum L. cv. Atlantic). StOR is predominantly localized to the chloroplast, and its transcripts are tissue-specifically expressed and significantly induced in response to abiotic stress. Compared with wild type, overexpression of StOR increased β-carotene levels up to 4.8-fold, whereas overexpression of StORHis with a conserved arginine to histidine substitution promoted β-carotene accumulation up to 17.6-fold in Arabidopsis thaliana calli. Neither StOR nor StORHis overexpression dramatically affected the transcript levels of carotenoid biosynthetic genes. Furthermore, overexpression of either StOR or StORHis increased abiotic stress tolerance in Arabidopsis, which was associated with higher photosynthetic capacity and antioxidative activity. Taken together, these results indicate that StOR could be exploited as a potential new genetic tool for the improvement of crop nutritional quality and environmental stress tolerance.

Characterization of Pik1 function in fission yeast reveals its conserved role in lipid synthesis and not cytokinesis

Phosphatidylinositol (PI)-4-phosphate (PI4P) is a lipid found at the plasma membrane (PM) and Golgi in cells from yeast to humans. PI4P is generated from PI by PI4-kinases and can be converted to PI-4,5-bisphosphate [PI(4,5)P 2 ]. Schizosaccharomyces pombe have 2 essential PI4-kinases: Stt4 and Pik1. Stt4 localizes to the PM and its loss from the PM results in a decrease of PM PI4P and PI(4,5)P 2 . As a result, cells divide non-medially due to disrupted cytokinetic ring-PM anchoring. However, the localization and function of S. pombe Pik1 has not been thoroughly examined. Here, we found that Pik1 localizes exclusively to the trans-Golgi and is required for Golgi PI4P production. We determined that Ncs1 regulates Pik1, but unlike in other organisms, it is not required for Pik1 Golgi localization. When Pik1 function was disrupted, PM PI4P but not PI(4,5)P 2 levels were reduced, a major difference with Stt4. We conclude that Stt4 is the chief enzyme responsible for producing the PI4P that generates PI(4,5)P 2 . Also, that cells with disrupted Pik1 do not divide asymmetrically highlights the specific importance of PM PI(4,5)P 2 for cytokinetic ring-PM anchoring.

Summary statement

Fission yeast Pik1 localizes exclusively to the trans-Golgi independently of Ncs1, where it contributes to PI4P but not PI(4,5)P 2 synthesis. Pik1 does not affect cytokinesis.

[Efficacy and safety of endoscopic diaphragm incision in children with congenital duodenal diaphragm]

Objective: To explore the efficacy and safety of endoscopic diaphragm incision in pediatric congenital duodenal diaphragm. Methods: Eight children with duodenal diaphragm treated by endoscopic diaphragm incision in the Department of Gastroenterology of Guangzhou Women and Children's Medical Center from October 2019 to May 2022 were enrolled in this study. Their clinical data including general conditions, clinical manifestations, laboratory and imaging examinations, endoscopic procedures and outcomes were retrospectively analyzed. Results: Among the 8 children, 4 were males and 4 females. The diagnosis was confirmed at the age of 6-20 months; the age of onset was 0-12 months and the course of disease was 6-18 months. The main clinical manifestations were recurrent non-biliary vomiting, abdominal distension and malnutrition. One case complicated with refractory hyponatremia was first diagnosed with atypical congenital adrenal hyperplasia in the endocrinology department. After treatment with hydrocortisone, the blood sodium returned to normal, but vomiting was recurrent. One patient underwent laparoscopic rhomboid duodenal anastomosis in another hospital but had recurred vomiting after the operation, who was diagnosed with double duodenal diaphragm under endoscope. No other malformations were found in all the 8 cases. The duodenal diaphragm was located in the descending part of the duodenum, and the duodenal papilla was located below the diaphragm in all the 8 cases. Three cases had the diaphragm dilated by balloon to explore the diaphragm opening range before diaphragm incision; the other 5 had diaphragm incision performed after probing the diaphragm opening with guide wire. All the 8 cases were successfully treated by endoscopic incision of duodenal diaphragm, with the operation time of 12-30 minutes. There were no complications such as intestinal perforation, active bleeding or duodenal papilla injury. At one month of follow-up, their weight increased by 0.4-1.5 kg, with an increase of 5%-20%. Within the postoperative follow-up period of 2-20 months, all the 8 children had duodenal obstruction relieved, without vomiting or abdominal distension, and all resumed normal feeding. Gastroscopy reviewed at 2-3 months after the operation in 3 cases found no deformation of the duodenal bulbar cavity, and the mucosa of the incision was smooth, with a duodenal diameter of 6-7 mm. Conclusion: Endoscopic diaphragm incision is safe, effective and less invasive in pediatric congenital duodenal diaphragm, with favorable clinical applicability.

First Measurement of Quasielastic Λ Baryon Production in Muon Antineutrino Interactions in the MicroBooNE Detector

We present the first measurement of the cross section of Cabibbo-suppressed Λ baryon production, using data collected with the MicroBooNE detector when exposed to the neutrinos from the main injector beam at the Fermi National Accelerator Laboratory. The data analyzed correspond to 2.2×10^{20} protons on target running in neutrino mode, and 4.9×10^{20} protons on target running in anti-neutrino mode. An automated selection is combined with hand scanning, with the former identifying five candidate Λ production events when the signal was unblinded, consistent with the GENIE prediction of 5.3±1.1 events. Several scanners were employed, selecting between three and five events, compared with a prediction from a blinded Monte Carlo simulation study of 3.7±1.0 events. Restricting the phase space to only include Λ baryons that decay above MicroBooNE's detection thresholds, we obtain a flux averaged cross section of 2.0_{-1.7}^{+2.2}×10^{-40}  cm^{2}/Ar, where statistical and systematic uncertainties are combined.

Fission yeast CK1 promotes DNA double-strand break repair through both homologous recombination and non-homologous end joining

The CK1 family are conserved serine/threonine kinases with numerous substrates and cellular functions. The fission yeast CK1 orthologues Hhp1 and Hhp2 were first characterized as regulators of DNA repair, but the mechanism(s) by which CK1 activity promotes DNA repair had not been investigated. Here, we found that deleting Hhp1 and Hhp2 or inhibiting CK1 catalytic activities in yeast or in human cells activated the DNA damage checkpoint due to persistent double-strand breaks (DSBs). The primary pathways to repair DSBs, homologous recombination and non-homologous end joining, were both less efficient in cells lacking Hhp1 and Hhp2 activity. In order to understand how Hhp1 and Hhp2 promote DSB repair, we identified new substrates using quantitative phosphoproteomics. We confirmed that Arp8, a component of the INO80 chromatin remodeling complex, is a bona fide substrate of Hhp1 and Hhp2 that is important for DSB repair. Our data suggest that Hhp1 and Hhp2 facilitate DSB repair by phosphorylating multiple substrates, including Arp8.

Membrane binding of endocytic myosin-1s is inhibited by a class of ankyrin repeat proteins

Myosin-1s are monomeric actin-based motors that function at membranes. Myo1 is the single myosin-1 isoform in Schizosaccharomyces pombe that works redundantly with Wsp1-Vrp1 to activate the Arp2/3 complex for endocytosis. Here, we identified Ank1 as an uncharacterized cytoplasmic Myo1 binding partner. We found that in ank1Δ cells, Myo1 dramatically redistributed from endocytic patches to decorate the entire plasma membrane and endocytosis was defective. Biochemical analysis and structural predictions suggested that the Ank1 ankyrin repeats bind the Myo1 lever arm and the Ank1 acidic tail binds the Myo1 TH1 domain to prevent TH1-dependent Myo1 membrane binding. Indeed, Ank1 over-expression precluded Myo1 membrane localization and recombinant Ank1 blocked purified Myo1 liposome binding in vitro. Based on biochemical and cell biology analyses, we propose budding yeast Ank1 and human OSTF1 are functional Ank1 orthologs and that cytoplasmic sequestration by small ankyrin repeat proteins is a conserved mechanism regulating myosin-1s in endocytosis.

Summary

Fission yeast long-tailed myosin-1 binds Ank1. Ank1 ankyrin repeats associate with the Myo1 lever arm and Ank1 acidic tail binds the Myo1 TH1 domain to inhibit Myo1 membrane binding. Ank1 orthologs exists in budding yeast (Ank1) and humans (OSTF1).

[Clinicopathological features and prognostic factors of gastric intermediate-risk gastrointestinal stromal tumor after surgical resection: a retrospective study]

Objective: To investigate the clinicopathological features, treatment and prognosis of gastric intermediate-risk gastrointestinal stromal tumor (GIST), so as to provide a reference for clinical management and further research. Methods: A retrospective observational study of patients with gastric intermediate-risk GIST, who underwent surgical resection between January 1996 and December 2019 at Zhongshan Hospital of Fudan University, was carried out. Results: Totally, 360 patients with a median age of 59 years were included. There were 190 males and 170 females with median tumor diameter of 5.9 cm. Routine genetic testing was performed in 247 cases (68.6%, 247/360), and 198 cases (80.2%) showed KIT mutation, 26 cases (10.5%) showed PDGFRA mutation, and 23 cases were wild-type GIST. According to "Zhongshan Method"(including 12 parameters), there were 121 malignant and 239 non-malignant cases. Complete follow-up data were available in 241 patients; 55 patients (22.8%) received imatinib therapy, 10 patients (4.1%) experienced tumor progression, and one patient (PDGFRA mutation, 0.4%) died. Disease-free survival (DFS) and overall survival rate at 5 years was 96.0% and 99.6%, respectively. Among the intermediate-risk GIST, there was no difference in DFS between the overall population, KIT mutation, PDGFRA mutation, wild-type, non-malignant and malignant subgroups (all P>0.05). However, the non-malignancy/malignancy analysis showed that there were significant differences in DFS among the overall population (P<0.01), imatinib treatment group (P=0.044) and no imatinib treatment group (P<0.01). Adjuvant imatinib resulted in potential survival benefit for KIT mutated malignant and intermediate-risk GIST in DFS (P=0.241). Conclusions: Gastric intermediate-risk GIST shows a heterogeneous biologic behavior spectrum from benign to highly malignant. It can be further classified into benign and malignant, mainly nonmalignant and low-grade malignant. The overall disease progression rate after surgical resection is low, and real-world data show that there is no significant benefit from imatinib treatment after surgery. However, adjuvant imatinib potentially improves DFS of intermediate-risk patients with tumors harboring KIT mutation in the malignant group. Therefore, a comprehensive analysis of gene mutations in benign/malignant GIST will facilitate improvements in therapeutic decision-making.

Abstract P4-01-43: PyrotInib in combination with Capecitabine for trasTUzumab-REsistant, HER2-positive advanced breast cancer (PICTURE): a multicenter phase 2 trial

Background: Approximately 10% of patients with HER2-positive breast cancer have primary resistance to trastuzumab, leading to poor prognosis. Although several trials enrolled those hard-to-treat patients, there has been no strong evidence available for the clinical decision making. This multicenter phase 2 trial aimed to investigate the activity and safety of pyrotinib plus capecitabine only in those patients with trastuzumab-resistant, HER2-positive advanced breast cancer. Methods: Patients from 17 sites in China received pyrotinib 400 mg once a day and capecitabine 1000 mg/m2 twice a day on days 1-14 every 21 days until disease progression or intolerable toxicity. Based on the definitions used in prior clinical trials, primary trastuzumab resistance was defined as progression during trastuzumab treatment (Group 1) or within 12 months after completing trastuzumab treatment in the (neo)adjuvant setting (trastzuzumab should have been for ≥9 weeks, Group 2), or progression within 6 months after the initiation of trastuzumab treatment in the advanced setting (treatment should have been for ≥6 weeks, Group 3). The primary endpoint was progression-free survival (PFS). The study is registered with ClinicalTrials.gov, NCT04001621. Results: Between June 2019 and September 2021, a total of 100 patients enrolled; 35 (35.0%) patients had hormone receptor (HR)-positive disease, and 65 (65.0%) had HR-negative disease. Prior use of trastuzumab, pertuzumab and antibody-drug conjugate was reported in 100%, 21.0% and 2.0% of patients, respectively. By the data cutoff on July 10, 2022, the median follow-up duration was 23.4 months (95%CI, 20.5-25.6) with 66 PFS events documented. Median PFS was 11.8 months (95%CI, 8.4-15.1) in the overall population. Patients in Group 2 (n=49) had the longest median PFS of 17.8 months (95%CI, 13.8-not reached), which was significantly different from either 8.2 months (95%CI, 3.0-20.7; p = 0.001) in Group 1 (n=21) or 5.6 months (95%CI, 4.1-6.9; p &lt; 0.001) in Group 3 (n=30). No significant difference in median PFS was observed in subgroup by HR status (HR-positive: 9.7 months [95%CI, 6.4-18.4]; HR-negative: 12.3 months [95%CI, 8.2-17.8]; p = 0.764). Objective response rate was 70.0% (95%CI, 60.0%-78.8%). Overall survival data was immature. The most common grade ≥3 treatment-emergent adverse events included diarrhea (24.0%), palmar-plantar erythrodysaesthesia syndrome (9.0%), neutrophil count decreased (7.0%), hypokalemia (5.0%), and decreased appetite (5.0%). No treatment-related deaths occurred. Conclusions: Pyrotinib plus capecitabine resulted in a promising PFS that crossed the pre-specified efficacy boundary in patients with HER2-positive advanced breast cancer who met the traditional definition of primary trastuzumab resistance. Patients in Group 2 had a significant longer PFS than those in either Group 1 or Group 3, highlighting the need to re-define primary trastuzumab resistance and to clarify efficacy of new anti-HER2 biologicals for each subpopulation.

Citation Format: Xichun Hu, Jun Cao, Yue’e Teng, Hui-Ping Li, Lili Zhang, Quchang Ouyang, Weimin Xie, Yueyin Pan, Zhenchuan Song, Xiaoling Ling, Xiaohong Wu, Jingwei Xu, Li Li, Liping Ren, Hong Wang, Dongxian Zhou, Jing Luo. PyrotInib in combination with Capecitabine for trasTUzumab-REsistant, HER2-positive advanced breast cancer (PICTURE): a multicenter phase 2 trial [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-01-43.

Serial multiple mediation of psychological empowerment and job burnout in the relationship between workplace bullying and turnover intention among Chinese novice nurses

AIM

This study aimed to examine the direct and indirect effects of workplace bullying on turnover intention using the serial multiple mediators of psychological empowerment and job burnout.

DESIGN

A cross-sectional study was conducted.

METHODS

A convenience sample of 506 novice nurses from five Triple A hospitals in China's S province from November 2020 to February 2021 and were evaluated using online questionnaires on workplace bullying, psychological empowerment, job burnout, and turnover intention.

RESULTS

The prevalence of turnover intention was 51.9%. In the serial multiple mediator model, workplace bullying had a direct effect (c = 0.452, p < 0.001) and indirect effect (c' = 0.229, p < 0.001) on turnover intention through the serial multiple mediators of psychological empowerment (B = -0.093, p = 0.020) and job burnout (B = 0.127, p < 0.001); hence, the proposed model explained the total variance of 32.2% in turnover intention.

PATIENT OR PUBLIC CONTRIBUTION

Nursing managers should use effective measures for strengthening the psychological empowerment to minimize novice nurse burnout and turnover intention resulting from workplace bullying.

Genome-wide analysis of WRKY transcription factor genes in Toona sinensis: An insight into evolutionary characteristics and terpene synthesis

WRKY transcription factors (TFs), one of the largest TF families, serve critical roles in the regulation of secondary metabolite production. However, little is known about the expression pattern of WRKY genes during the germination and maturation processes of Toona sinensis buds. In the present study, the new assembly of the T. sinensis genome was used for the identification of 78 TsWRKY genes, including gene structures, phylogenetic features, chromosomal locations, conserved protein domains, cis-regulatory elements, synteny, and expression profiles. Gene duplication analysis revealed that gene tandem and segmental duplication events drove the expansion of the TsWRKYs family, with the latter playing a key role in the creation of new TsWRKY genes. The synteny and evolutionary constraint analyses of the WRKY proteins among T. sinensis and several distinct species provided more detailed evidence of gene evolution for TsWRKYs. Besides, the expression patterns and co-expression network analysis show TsWRKYs may multi-genes co-participate in regulating terpenoid biosynthesis. The findings revealed that TsWRKYs potentially play a regulatory role in secondary metabolite synthesis, forming the basis for further functional characterization of WRKY genes with the intention of improving T. sinensis.

[Clinical significance of pathological diagnosis and genetic abnormalities detection in gastrointestinal stromal tumor using endoscopic biopsy]

Objective: To investigate the clinical significance of pathological diagnosis and genetic abnormalities detection of gastrointestinal stromal tumor (GIST) using endoscopic biopsy. Methods: Patients with GIST diagnosed by endoscopic biopsy (from January 1st, 2016 to August 1st, 2018, at Zhongshan Hospital, Fudan University) were included in this study. This retrospective study evaluated the histopathologic and immunohistochemical (IHC) features, genetic abnormalities of the tumors and the treatment and clinical course of the patients. Results: Totally 4 095 cases of GIST were collected, among which 67 patients (67/4 095, 1.6%) underwent endoscopic biopsy. Forty-eight patients (71.6%) were male and 19 (28.4%) were female, with a mean age of 61 years (range 31-90 years). Fifty-nine lesions were located in stomach and eight in duodenum. Of all the 67 cases, 47 were spindle type, 14 were epithelioid type, and 6 mixed type. IHC staining showed the positive rates were 100.0% (64/64) for DOG1, 98.4% (62/63) for CD117, 87.5% (56/64) for CD34, 3.6% (2/56) for S-100 protein, 12.1% (7/58) for α-SMA, 12.3% (7/57) for desmin and 4.0% (2/50) for CKpan. Morphologically, 34 cases were malignant; three cases (all epithelioid type) were originally misdiagnosed as poorly differentiated carcinoma; missed-diagnosis were found in four cases (spindle type) due to the insufficient diagnostic tumor cells. The genetic abnormality detection rate in the biopsy tissue was 38.8% (26/67),among them two patients were lost to follow up after biopsy, 33 patients received surgical resection, 16 cases underwent operation after neoadjuvant therapy and 16 patients with advanced disease underwent continuous imatinib therapy, with the genetic testing rate of 6.1% (2/33), 10/16 and 14/16, respectively. Conclusions: Endoscopic biopsy is a useful but rare method for the preoperative diagnosis of GIST. For majority of biopsy, accurate pathological diagnosis and auxiliary examination can be completed to guide clinical treatment. A thorough history in combination with endoscopic finding is essential to avoid misdiagnosis (epithelioid type) and missed diagnosis (spindle type) in suspicious cases. Genetic testing should be recommended in patients who will undergo targeted therapy after endoscopic biopsy, and it can provide valuable information and guidance for clinical treatment.

First Constraints on Light Sterile Neutrino Oscillations from Combined Appearance and Disappearance Searches with the MicroBooNE Detector

We present a search for eV-scale sterile neutrino oscillations in the MicroBooNE liquid argon detector, simultaneously considering all possible appearance and disappearance effects within the 3+1 active-to-sterile neutrino oscillation framework. We analyze the neutrino candidate events for the recent measurements of charged-current ν_{e} and ν_{μ} interactions in the MicroBooNE detector, using data corresponding to an exposure of 6.37×10^{20} protons on target from the Fermilab booster neutrino beam. We observe no evidence of light sterile neutrino oscillations and derive exclusion contours at the 95% confidence level in the plane of the mass-squared splitting Δm_{41}^{2} and the sterile neutrino mixing angles θ_{μe} and θ_{ee}, excluding part of the parameter space allowed by experimental anomalies. Cancellation of ν_{e} appearance and ν_{e} disappearance effects due to the full 3+1 treatment of the analysis leads to a degeneracy when determining the oscillation parameters, which is discussed in this Letter and will be addressed by future analyses.

Construction of a combined hypoxia-related genes model for Hepatocellular carcinoma prognosis

BACKGROUND

Hepatocellular carcinoma (HCC) is the most common liver malignancy where tumorigenesis and metastasis are believed to be tied to the hallmarks of hypoxia and tumor microenvironment (TME).

METHODS

In this study, to investigate the relationships among hypoxia, TME, and HCC prognosis, we collected two independent datasets from a public database (TCGA-LIHC for identification, GSE14520 for validation) and identified the hypoxia-related differentially expressed genes (DEGs) from the TCGA data, and the univariable Cox regression and lasso regression analyses were performed to construct the prognosis model. An HCC prognosis model with 4 hypoxia-related DEGs ("NDRG1", "ENO1", "SERPINE1", "ANXA2") was constructed, and high- and low-risk groups of HCC were established by the median of the model risk score.

RESULTS

The survival analysis revealed significant differences between the two groups in both datasets, with the results of the AUC of the ROC curve of 1, 3, and 5 years in two datasets indicating the robustness of the prognosis model. Meanwhile, for the TCGA-LIHC data, the immune characteristics between the two groups revealed that the low-risk group presented higher levels of activated NK cells, monocytes, and M2 macrophages, and 7 immune checkpoint genes were found upregulated in the high-risk group. Additionally, the two groups have no difference in molecular characteristics (tumor mutational burden, TMB). The proportion of recurrence was higher in the high-risk group, and the correlation between the recurrence month and risk score was negative, indicating high-risk correlates with a short recurrence month.

CONCLUSION

In summary, this study shows the association among hypoxic signals, TME, and HCC prognosis and may help reveal potential regulatory mechanisms between hypoxia, tumorigenesis, and metastasis in HCC. The hypoxia-related model demonstrated the potential to be a predictor and drug target of prognosis.