Development and validation of nomograms to predict survival of primary cervical lymphoma: A surveillance, epidemiology, and end results (SEER) database analysis.

Due to the rarity of primary cervical lymphoma (PCL), the long-term survival of patients with cervical lymphoma and factors influencing survival are unknown. This study aimed to compare the survivals of patients with PCL and those with other cervical tumors and construct a clinical prediction model to assess the prognosis of patients with PCL. Patients with PCL from the Surveillance, Epidemiology, and End Results database were allocated randomly in a 7:3 ratio to the training and validation sets. Cox proportional hazard and Fine-Gray models were used to verify independent factors influencing overall survival (OS) and disease-specific survival (DSS), and nomograms were constructed. Receiver operating characteristic curve analysis and decision curve analysis (DCA) were used to test the performance and clinical utility of the models, respectively. We included 206 patients with PCL. The areas under the curves (AUCs) and DCA showed that all models had clinical benefits; The models constructed in this study had a predictive performance for patients with PCL. It can guide clinicians to rationalize the treatment plan for patients.

Development and validation of nomograms to predict survival of neuroendocrine carcinoma in genitourinary system: A population-based retrospective study.

Neuroendocrine carcinoma (NEC) is a rare yet potentially perilous neoplasm. The objective of this study was to develop prognostic models for the survival of NEC patients in the genitourinary system and subsequently validate these models. A total of 7125 neuroendocrine neoplasm (NEN) patients were extracted. Comparison of survival in patients with different types of NEN before and after propensity score-matching (PSM). A total of 3057 patients with NEC, whose information was complete, were extracted. The NEC influencing factors were chosen through the utilization of the least absolute shrinkage and selection operator regression model (LASSO) and the Fine & Gary model (FGM). Furthermore, nomograms were built. To validate the accuracy of the prediction, the efficiency was verified using bootstrap self-sampling techniques and receiver operating characteristic curves. LASSO and FGM were utilized to construct three models. Confirmation of validation was achieved by conducting analyses of the area under the curve and decision curve. Moreover, the FGS (DSS analysis using FGM) model produced higher net benefits. To maximize the advantages for patients, the FGS model disregarded the influence of additional occurrences. Patients are expected to experience advantages in terms of treatment options and survival assessment through the utilization of these models.

Westerlies-driven transboundary transport of atmospheric mercury to the north-central Tibetan Plateau.

The transboundary mercury (Hg) pollution has caused adverse effects on fragile ecosystems of the Tibetan Plateau (TP). Yet, knowledge of transport paths and source regions of atmospheric Hg on the inland TP remains poor. Continuous measurements of atmospheric total gaseous mercury (TGM) were conducted in the central TP (Tanggula station, 5100 m a.s.l., June-October). Atmospheric TGM level at Tanggula station (1.90 ± 0.30 ng m-3) was higher than the background level in the Northern Hemisphere. The identified high-potential source regions of atmospheric TGM were primarily located in the northern South Asia region. TGM concentrations were lower during the Indian summer monsoon (ISM)-dominant period (1.81 ± 0.25 ng m-3) than those of the westerly-receding period (2.18 ± 0.40 ng m-3) and westerly-intensifying period (1.91 ± 0.26 ng m-3), contrary to the seasonal pattern in southern TP. The distinct TGM minima during the ISM-dominant period indicated lesser importance of ISM-transported Hg to Tanggula station located in the northern boundary of ISM intrusion, compared to stations in proximity to South and Southeast Asia source regions. Instead, from the ISM-dominant period to the westerly-intensifying period, TGM concentrations showed an increasing trend as westerlies intensified, indicating the key role of westerlies in transboundary transport of atmospheric Hg to the inland TP.

The association between three prevalent autoimmune disorders and the likelihood of developing prostate cancer: a Mendelian randomization study.

Numerous studies establish a significant correlation between autoimmune disorders (AIDs) and prostate cancer (PCa). Our Mendelian randomization (MR) analysis investigates the potential connection between rheumatoid arthritis (RA) and PCa, aiming to confirm causal links between systemic lupus erythematosus (SLE), hyperthyroidism, and PCa. Summary statistics from genome-wide association studies provided data on PCa and three AIDs. MR analysis, using IVW as the main approach, assessed causal relationships, validated by sensitivity analysis. IVW revealed a correlation between genetically anticipated RA and PCa, notably in Europeans (OR = 1.03; 95% CI 1.01-1.04, p = 2*10-5). Evidence supported a lower PCa risk in individuals with SLE (OR = 0.94; 95% CI 0.91-0.97, p = 2*10-4) and hyperthyroidism (OR = 0.02; 95% CI 0.001-0.2, p = 2*10-3). Weighted mode and median confirmed these findings. No pleiotropic effects were observed, and MR heterogeneity tests indicated dataset homogeneity. Our study establishes a causal link between RA, SLE, hyperthyroidism, and PCa.

A novel polycyclic quinazoline and three quinolines alkaloids from marine-derived fungus trichoderma longibrachiatum QD01 with anti-bacterial and anti-quorum sensing activities.

A novel polycyclic quinazoline alkaloid (1) along with one new natural quinoline alkaloid (2) and two known quinoline alkaloids (3,4) were isolated from the marine-derived fungus Trichoderma longibrachiatum QD01. Structural determinations of those isolates were established by comprehensive spectroscopic analyses and literature comparison. Single-crystal X-ray diffraction analysis of novel compound verified its structure and stereochemistry, representing the first characterised crystal structure of a trimeric-type of tetrahydroquinazoline. Compound 4 exhibited potential antibacterial and anti-quorum sensing activity against C. violaceum and C. violaceum CV026. The sub-MIC of 4 observably decreased the violacein production in C. violaceum CV026 by 55% on 15 µg/mL. Furthermore, molecular docking results revealed that 4 has stronger binding interactions with CviR receptor than ligand C6-HSL with lower binding energy of -8.68 kcal/mol. Hydrogen bond and π-π interactions formed by Trp84, Tyr88, Trp111, and Phe126 were predicted to play an important role in the inhibition against C. violaceum CV026.

Protocol for automated N-glycan sequencing using mass spectrometry and computer-assisted intelligent fragmentation.

Biological functions of glycans are intimately linked to fine details in branches and linkages, which make structural identification extremely challenging. Here, we present a protocol for automated N-glycan sequencing using multi-stage mass spectrometry (MSn). We describe steps for release/purification and derivation of glycans and procedures for MSn scanning. We then detail "glycan intelligent precursor selection" to computationally guide MSn experiments. The protocol can be used for both discrete individual glycans and isomeric glycan mixtures. For complete details on the use and execution of this protocol, please refer to Sun et al.,1 Huang et al.,2 and Huang et al.3.

Renal pelvis metastasis following surgery for breast angiosarcoma: a case report and literature review.

Renal metastasis of breast angiosarcoma is rare. This article reports the medical records of a patient diagnosed with breast angiosarcoma who underwent radical mastectomy and was found to have multiple lung metastases 3 years after surgery and renal pelvic metastasis 4 years after surgery. The patient underwent robot-assisted laparoscopic radical nephroureterectomy and sleeve resection of the intramural segment of the ureter, and postoperative pathology and immunohistochemical staining confirmed the diagnosis of renal pelvic metastasis of breast angiosarcoma. The patient received anlotinib for lung metastases following surgery and was followed up for 4 months after surgery. Currently, the patient has symptoms of coughing and hemoptysis but no other discomfort. The diagnosis and treatment of this rare malignant tumor remain challenging.

Synthesizing Pd-based high entropy alloy nanoclusters for enhanced oxygen reduction.

We report the synthesis of uniform Pd-based high-entropy alloy clusters via rapid Joule heating. The quinary PdMnFeCuNi clusters exhibit 4.95 times higher mass activity than the Commercial Pt/C for the oxygen reduction reaction, and outstanding stability with only 2 mV decay in the half-wave potential after 20 000 cycles of testing.

Protein-centric omics analysis reveals circulating complements linked to non-viral liver diseases as potential therapeutic targets.

BACKGROUND/AIMS: To evaluate the causal correlation between complement components and non-viral liver diseases and their potential use as druggable targets. METHODS: We conducted Mendelian randomization (MR) to assess the causal role of circulating complements in the risk of non-viral liver diseases. A complement-centric protein interaction network was constructed to explore biological functions and identify potential therapeutic options. RESULTS: In the MR analysis, genetically predicted levels of complement C1q C chain (C1QC) were positively associated with the risk of autoimmune hepatitis (odds ratio 1.125, 95% confidence interval 1.018-1.244), while complement factor H-related protein 5 (CFHR5) was positively associated with the risk of primary sclerosing cholangitis (PSC;1.193, 1.048- 1.357). On the other hand, CFHR1 (0.621, 0.497-0.776) and CFHR2 (0.824, 0.703-0.965) were inversely associated with the risk of alcohol-related cirrhosis. There were also significant inverse associations between C8 gamma chain (C8G) and PSC (0.832, 0.707-0.979), as well as the risk of metabolic dysfunction-associated steatotic liver disease (1.167, 1.036-1.314). Additionally, C1S (0.111, 0.018-0.672), C7 (1.631, 1.190-2.236), and CFHR2 (1.279, 1.059-1.546) were significantly associated with the risk of hepatocellular carcinoma. Proteins from the complement regulatory networks and various liver diseaserelated proteins share common biological processes. Furthermore, potential therapeutic drugs for various liver diseases were identified through drug repurposing based on the complement regulatory network. CONCLUSION: Our study suggests that certain complement components, including C1S, C1QC, CFHR1, CFHR2, CFHR5, C7, and C8G, might play a role in non-viral liver diseases and could be potential targets for drug development.

Molecular characteristics and pathogenicity of a novel chicken astrovirus variant.

It is well-established that the genetic diversity, regional prevalence, and broad host range of astroviruses significantly impact the poultry industry. In July 2022, a small-scale commercial broiler farm in China reported cases of growth retardation and a 3% mortality rate. From chickens displaying proventriculitis and pancreatitis, three chicken astroviruses (CAstV) isolates were obtained and named SDAU2022-1-3. Complete genomic sequencing and analysis revealed the unique characteristics of these isolates from known CAstV strains in ORF1a, ORF1b, and ORF2 genes, characterized by an unusually high variability. Analysis of amino acid mutations in ORF1a, ORF1b, and ORF2 indicated that the accumulation of these mutations played a pivotal role in the emergence of the variant strain. Inoculation experiments demonstrated that affected chickens exhibited liver and kidney enlargement, localized proventricular hemorrhage, and a dark reddish-brown appearance in about two-thirds of the pancreas. Histopathological examination unveiled hepatic lymphocytic infiltration, renal tubular epithelial cell swelling, along with lymphocytic proventriculitis and pancreatitis. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis indicated viremia and viral shedding at 3 days post-infection (dpi). The proventriculus displayed the highest viral loads, followed by the liver, kidney, duodenum, and pancreas. Liver parameters (AST and ALT) and kidney parameters (UA and UN) demonstrated mild damage consistent with earlier findings. While the possibility of new mutations in the ORF2 gene of CAstV causing proventriculitis and pancreatitis warrants further investigation, these findings deepen our comprehension of CAstV's pathogenicity in chickens. Additionally, they serve as valuable references for subsequent research endeavors.

EMNGly: predicting N-linked glycosylation sites using the language models for feature extraction.

MOTIVATION: N-linked glycosylation is a frequently occurring post-translational protein modification that serves critical functions in protein folding, stability, trafficking, and recognition. Its involvement spans across multiple biological processes and alterations to this process can result in various diseases. Therefore, identifying N-linked glycosylation sites is imperative for comprehending the mechanisms and systems underlying glycosylation. Due to the inherent experimental complexities, machine learning and deep learning have become indispensable tools for predicting these sites. RESULTS: In this context, a new approach called EMNGly has been proposed. The EMNGly approach utilizes pretrained protein language model (Evolutionary Scale Modeling) and pretrained protein structure model (Inverse Folding Model) for features extraction and support vector machine for classification. Ten-fold cross-validation and independent tests show that this approach has outperformed existing techniques. And it achieves Matthews Correlation Coefficient, sensitivity, specificity, and accuracy of 0.8282, 0.9343, 0.8934, and 0.9143, respectively on a benchmark independent test set.

Development and validation of machine-learning models for the difficulty of retroperitoneal laparoscopic adrenalectomy based on radiomics.

Objective: The aim is to construct machine learning (ML) prediction models for the difficulty of retroperitoneal laparoscopic adrenalectomy (RPLA) based on clinical and radiomic characteristics and to validate the models. Methods: Patients who had undergone RPLA at Shanxi Bethune Hospital between August 2014 and December 2020 were retrospectively gathered. They were then randomly split into a training set and a validation set, maintaining a ratio of 7:3. The model was constructed using the training set and validated using the validation set. Furthermore, a total of 117 patients were gathered between January and December 2021 to form a prospective set for validation. Radiomic features were extracted by drawing the region of interest using the 3D slicer image computing platform and Python. Key features were selected through LASSO, and the radiomics score (Rad-score) was calculated. Various ML models were constructed by combining Rad-score with clinical characteristics. The optimal models were selected based on precision, recall, the area under the curve, F1 score, calibration curve, receiver operating characteristic curve, and decision curve analysis in the training, validation, and prospective sets. Shapley Additive exPlanations (SHAP) was used to demonstrate the impact of each variable in the respective models. Results: After comparing the performance of 7 ML models in the training, validation, and prospective sets, it was found that the RF model had a more stable predictive performance, while xGBoost can significantly benefit patients. According to SHAP, the variable importance of the two models is similar, and both can reflect that the Rad-score has the most significant impact. At the same time, clinical characteristics such as hemoglobin, age, body mass index, gender, and diabetes mellitus also influenced the difficulty. Conclusion: This study constructed ML models for predicting the difficulty of RPLA by combining clinical and radiomic characteristics. The models can help surgeons evaluate surgical difficulty, reduce risks, and improve patient benefits.

Development and validation of nomograms to predict survival of primary adrenal lymphoma: a population-based retrospective study.

While it is known that accurate evaluation of overall survival (OS) and disease-specific survival (DSS) for patients with primary adrenal lymphoma (PAL) can affect their prognosis, no stable and effective prediction model exists. This study aimed to develop prediction models to evaluate survival. This study enrolled 5448 patients with adrenal masses from the SEER Program. The influencing factors were selected using the least absolute shrinkage and selection operator regression model (LASSO) and Fine and Gray model (FGM). In addition, nomograms were constructed. Receiver operating characteristic curves and bootstrap self-sampling methods were used to verify the discrimination and consistency of the nomograms. The independent influencing factors for PAL survival were selected by LASSO and FGM, and three models were built: the OS, DSS, and FGS (DSS analysis by FGM) model. The areas under the curve and decision curve analyses indicated that the models were valid. This study developed survival prediction models to predict OS and DSS of patients with PAL. The FGS model was more accurate than the DSS model in the short term. Above all, these models should offer benefits to patients with PAL in terms of the treatment modality choice and survival evaluation.

Tensile-Strained Holey Pd Metallene toward Efficient and Stable Electrocatalysis.

Noble metal-based metallenes are attracting intensive attention in energy catalysis, but it is still very challenging to precisely control the surface structures of metallenes for higher catalytic properties on account of their intrinsic thermodynamic instability. Herein, the synthesis of tensile-strained holey Pd metallene by oxidative etching is reported using hydrogen peroxide, which exhibits highly enhanced catalytic activity and stability in comparison with normal Pd metallene toward both oxygen reduction reaction and formic acid oxidation. The pre-prepared Pd metallene functions as a catalyst to decompose hydrogen peroxide, and the Pd atoms in amorphous regions of Pd metallene are preferentially removed by the introduced hydrogen peroxide during the etching process. The greatly enhanced ORR activity is mainly determined by the strong electrostatic repulsion between intermediate O* and the dopant O, which balances the adsorption strength of O* on Pd sites, ultimately endowing a weakened adsorption energy of O* on TH-Pd metallene. This work creates a facile and economical strategy to precisely shape metallene-based nanoarchitectures with broad applications for energy systems and sensing devices.

Establishment and validation of clinical prediction model for hemorrhoid recurrence after procedure for prolapse and hemorrhoids.

This study aimed to establish a clinical model to predict the risk of hemorrhoid recurrence after procedure for prolapse and hemorrhoids. The clinical data of patients who underwent stapler hemorrhoidal mucosal circumcision in Shanxi Bethune Hospital from April 2014 to June 2017 were collected retrospectively and followed up regularly after the operation. Finally, 415 patients were included, which were divided into training group (n = 290) and verification group (n = 125). Logistic regression method was used to select meaningful predictors. The prediction model was constructed with nomographs, and the model was evaluated with correction curve, receiver operating characteristic curve and C index. The decision analysis curve was used to determine the clinical utility of the nomogram. Birth history, muscle attachment, postoperative anal urgency, anal resting pressure, postoperative nutritional index, body mass index, Wexner score, and hemorrhoid grading were included in the nomogram. The area under the curve of the prediction model was 0.813 and 0.679, respectively, in the training and verification groups, and 0.839 and 0.746, respectively, for the 5-year recurrence rate. The C index (0.737) and clinical decision curve showed that the model had high clinical practical value. The prediction model of hemorrhoid recurrence risk after hemorrhoidectomy based on multiple clinical indicators can be used for individualized prediction of hemorrhoid recurrence in patients after hemorrhoidectomy, and early intervention measures can be given to individuals with a high recurrence risk to reduce the risk of recurrence.

Identification and screening of fungicides against Piper nigrum basal Fusarium wilt disease in Hainan, China.

Fusarium wilt has occurred in the main Piper nigrum cultivation regions, which seriously affects the yield and quality of P. nigrum. To identify the pathogen of this disease, the diseased roots were collected from a demonstration base in Hainan Province. The pathogen was obtained by tissue isolation method and confirmed by pathogenicity test. Based on the morphological observation, sequence analyses of TEF1-α nuclear gene, Fusarium solani was identified as the pathogen causing P. nigrum Fusarium wilt and induced symptoms on inoculated plants, including chlorosis, necrotic spots, wilt, drying, and root rot. The experiments for the antifungal activity showed that all the 11 fungicides selected in this study showed certain inhibitory effects on the colony growth of F. solani, where 2% kasugamycin AS, 45% prochloraz EW, 25 g·L-1 fludioxonil SC and 430 g·L-1 tebuconazole SC exhibited relative higher inhibitory effects with EC50 as 0.065, 0.205, 0.395, and 0.483 mg·L-1 , respectively, and were selected to perform SEM analysis and test in seeds in vitro. The SEM analysis showed that kasugamycin, prochloraz, fludioxonil, and tebuconazole might have exerted their antifungal effect by damaging F. solani mycelia or microconidia. These preparations were applied as a seed coating of P. nigrum Reyin-1. The kasugamycin treatment was most effective in reducing the harmful impact of F. solani on the seed germination. These results presented herein provide useful guidance for the effective control of P. nigrum Fusarium wilt.

Predicting the antigenic evolution of SARS-COV-2 with deep learning.

The relentless evolution of SARS-CoV-2 poses a significant threat to public health, as it adapts to immune pressure from vaccines and natural infections. Gaining insights into potential antigenic changes is critical but challenging due to the vast sequence space. Here, we introduce the Machine Learning-guided Antigenic Evolution Prediction (MLAEP), which combines structure modeling, multi-task learning, and genetic algorithms to predict the viral fitness landscape and explore antigenic evolution via in silico directed evolution. By analyzing existing SARS-CoV-2 variants, MLAEP accurately infers variant order along antigenic evolutionary trajectories, correlating with corresponding sampling time. Our approach identified novel mutations in immunocompromised COVID-19 patients and emerging variants like XBB1.5. Additionally, MLAEP predictions were validated through in vitro neutralizing antibody binding assays, demonstrating that the predicted variants exhibited enhanced immune evasion. By profiling existing variants and predicting potential antigenic changes, MLAEP aids in vaccine development and enhances preparedness against future SARS-CoV-2 variants.

Brushite-coated Mg-Nd-Zn-Zr alloy promotes the osteogenesis of vertebral laminae through IGF2/PI3K/AKT signaling pathway.

Biodegradable magnesium (Mg) alloys have been extensively investigated in orthopedic implants due to their suitable mechanical strength and high biocompatibility. However, no studies have reported whether Mg alloys can be used to repair lamina defects, and the biological mechanisms regulating osteogenesis are not fully understood. The present study developed a lamina reconstruction device using our patented biodegradable Mg-Nd-Zn-Zr alloy (JDBM), and brushite (CaHPO4·2H2O, Dicalcium phosphate dihydrate, DCPD) coating was developed on the implant. Through in vitro and in vivo experiments, we evaluated the degradation behavior and biocompatibility of DCPD-JDBM. In addition, we explored the potential molecular mechanisms by which it regulates osteogenesis. In vitro, ion release and cytotoxicity tests revealed that DCPD-JDBM had better corrosion resistance and biocompatibility. We found that DCPD-JDBM extracts could promote MC3T3-E1 osteogenic differentiation via the IGF2/PI3K/AKT pathway. The lamina reconstruction device was implanted on a rat lumbar lamina defect model. Radiographic and histological analysis showed that DCPD-JDBM accelerated the repair of rat lamina defects and exhibited lower degradation rate compared to uncoated JDBM. Immunohistochemical and qRT-PCR results showed that DCPD-JDBM promoted osteogenesis in rat laminae via IGF2/PI3K/AKT pathway. This study shows that DCPD-JDBM is a promising biodegradable Mg-based material with great potential for clinical applications.

An accurate, efficient, and economical identification technology for black twig borer based on species-specific cytochrome C oxidase subunit I PCR assay.

Xylosandrus compactus (Eichhoff) (Coleoptera: Curculionidae, Scolytinae) is a worldwide invasive species that causes huge economic loss and environmental damage in many countries. Traditional morphological characteristics make it hard to identify scolytines due to their tiny size. Besides, the intercepted insect samples are incomplete, and the limitation of insect (larvae and pupae) morphology makes morphological identification more difficult. The majority of the damage is caused by adults and fungi that serve as nutrition for their larvae. They destroy plant trunks, branches, and twigs, affecting plant transport tissues in both weak and healthy plants. An accurate, efficient, and economical molecular identification technique for X. compactus not restricted by professional taxonomic knowledge is necessary. In the present study, a molecular identification tool based on the mitochondrial DNA gene, cytochrome C oxidase subunit I (COI) was developed. A species-specific COI (SS-COI) PCR assay was designed to identify X. compactus regardless of the developmental stage. Twelve scolytines commonly found in eastern China, namely Xylosandrus compactus, X. crassiusculus, X. discolor, X. germanus, X. borealis, X. amputates, X. eupatorii, X. mancus, Xyleborinus saxesenii, Euwallacea interjectus, E. fornicatus, and Acanthotomicus suncei, were included in the study. Additionally, specimens of X. compactus from 17 different areas in China, as well as a specimen collected from the United Stated, were also analyzed. Results demonstrated the accuracy and high efficiency of the assay, regardless of the developmental stage or the type of specimen. These features provide a good application prospect for fundamental departments and can be used to prevent the harmful consequences of the spread of X. compactus.