Understanding decision curve analysis in clinical prediction model research.

BACKGROUND: Many medical graduate students lack a thorough understanding of decision curve analysis (DCA), a valuable tool in clinical research for evaluating diagnostic models. METHODS: This article elucidates the concept and process of DCA through the lens of clinical research practices, exemplified by its application in diagnosing liver cancer using serum alpha-fetoprotein levels and radiomics indices. It covers the calculation of probability thresholds, computation of net benefits for each threshold, construction of decision curves, and comparison of decision curves from different models to identify the one offering the highest net benefit. RESULTS: The paper provides a detailed explanation of DCA, including the creation and comparison of decision curves, and discusses the relationship and differences between decision curves and receiver operating characteristic curves. It highlights the superiority of decision curves in supporting clinical decision-making processes. CONCLUSION: By clarifying the concept of DCA and highlighting its benefits in clinical decisionmaking, this article has improved researchers' comprehension of how DCA is applied and interpreted, thereby enhancing the quality of research in the medical field.

The Structural Characteristics and Bioactivity Stability of Cucumaria frondosa Intestines and Ovum Hydrolysates Obtained by Different Proteases.

The study aimed to investigate the effects of alcalase, papain, flavourzyme, and neutrase on the structural characteristics and bioactivity stability of Cucumaria frondosa intestines and ovum hydrolysates (CFHs). The findings revealed that flavourzyme exhibited the highest hydrolysis rate (51.88% ± 1.87%). At pH 2.0, the solubility of hydrolysate was the lowest across all treatments, while the solubility at other pH levels was over 60%. The primary structures of hydrolysates of different proteases were similar, whereas the surface hydrophobicity of hydrolysates was influenced by the types of proteases used. The hydrolysates produced by different proteases were also analyzed for their absorption peaks and antioxidant activity. The hydrolysates of flavourzyme had ß-fold absorption peaks (1637 cm-1), while the neutrase and papain hydrolysates had N-H bending vibrations. The tertiary structure of CFHs was unfolded by different proteases, exposing the aromatic amino acids and red-shifting of the λ-peak of the hydrolysate. The alcalase hydrolysates showed better antioxidant activity in vitro and better surface hydrophobicity than the other hydrolysates. The flavourzyme hydrolysates displayed excellent antioxidant stability and pancreatic lipase inhibitory activity during gastrointestinal digestion, indicating their potential use as antioxidants in the food and pharmaceutical industries.

Loading of Amino Acids onto RNA in a Putative RNA-Peptide World.

RNA is a molecule that can both store genetic information and perform catalytic reactions. This observed dualism places RNA into the limelight of concepts about the origin of life. The RNA world concept argues that life started from self-replicating RNA molecules, which evolved toward increasingly complex structures. Recently, we demonstrated that RNA, with the help of conserved non-canonical nucleosides, which are also putative relics of an early RNA world, had the ability to grow peptides covalently connected to RNA nucleobases, creating RNA-peptide chimeras. It is conceivable that such molecules, which combined the information-coding properties of RNA with the catalytic potential of amino acid side chains, were once the structures from which life emerged. Herein, we report prebiotic chemistry that enabled the loading of both nucleosides and RNAs with amino acids as the first step toward RNA-based peptide synthesis in a putative RNA-peptide world.

Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry.

We present DeepNovo-DIA, a de novo peptide-sequencing method for data-independent acquisition (DIA) mass spectrometry data. We use neural networks to capture precursor and fragment ions across m/z, retention-time, and intensity dimensions. They are then further integrated with peptide sequence patterns to address the problem of highly multiplexed spectra. DIA coupled with de novo sequencing allowed us to identify novel peptides in human antibodies and antigens.

Retrospective reversal of extinction of conditioned fear by instruction.

In the present study, we examined the impact of verbal instruction during extinction of human fear-conditioning. We extended the study of Raes, De Houwer, Verschuere, and De Raedt (2011) by controlling for context conditioning and recording unconditioned stimulus expectancy online in a within-subject design. We informed participants of an alternative reason for the absence of the aversive unconditioned stimulus after extinction had been carried out, to see if such instruction could induce retrospective protection from extinction. The results demonstrated that both the expectancy of an aversive outcome and conditioned skin conductance were significantly increased for the conditioned stimulus targeted by the instruction. Thus extinction was reversed by the concurrent presence of an alternative cause for the absence of the unconditioned stimulus.

Comprehensive analysis of IGF2BP3 with expression features, prognosis, immune modulation and stemness in hepatocellular carcinoma and pan-cancer.

Insulin like growth factor 2 mRNA binding protein 3 (IGF2BP3) is a critical m6A reader. It encodes proteins that contain several KH domains, which are important in RNA binding, RNA synthesis and metabolism. Lots of researches have studied the malignant potential of m6A readers in tumors. However, the biological functional analysis of IGF2BP3 in hepatocellular carcinoma (HCC) and pan-cancer is not comprehensive. In this study, we used a bioinformatics approach to comprehensively analyze the significance of IGF2BP3 in HCC through analyzing its expression, mutation, prognosis, protein-protein interaction (PPI) network, functional enrichment, and the correlation with ferroptosis, stemness as well as immune modulation in HCC. IGF2BP3 presented a negative correlation with the ferroptosis molecule NFE2L2, and a positive correlation with the ferroptosis molecule SLC1A5 as well as the immune checkpoint HAVCR2. In addition, we also analyzed IGF2BP3 expression, prognosis and immune modulation in pan-cancer, revealing the prognostic value of IGF2BP3 in a variety of tumors. Finally, we verified the biological functions of IGF2BP3 in HCC through various experiments. The data showed that IGF2BP3 may enhance the proliferation, colony formation and invasion capacities of HCC cells, and IGF2BP3 is mainly positively correlated with the expression level of stemness marker SOX2. In conclusion, IGF2BP3 had a potential to be a new perspective biomarker in forecasting the immune response, ferroptosis, stemness and prognosis of HCC or even pan-cancer.

Recent Advances in Nanozyme-Based Materials for Inflammatory Bowel Disease.

Inflammatory bowel disease (IBD) is a type of chronic inflammatory disorder that interferes with the patient's lifestyle and, in extreme situations, can be deadly. Fortunately, with the ever-deepening understanding of the pathological cause of IBD, recent studies using nanozyme-based materials have indicated the potential toward effective IBD treatment. In this review, the recent advancement of nanozymes for the treatment of enteritis is summarized from the perspectives of the structural design of nanozyme-based materials and therapeutic strategies, intending to serve as a reference to produce effective nanozymes for moderating inflammation in the future. Last but not least, the potential and current restrictions for using nanozymes in IBD will also be discussed. In short, this review may provide a guidance for the development of innovative enzyme-mimetic nanomaterials that offer a novel and efficient approach toward the effective treatment of IBD.

Multi-functional nanogel with cascade catalytic performance for treatment of diabetic oral mucosa ulcer.

Introduction: Diabetic oral mucosa ulcers face challenges of hypoxia, hyperglycemia and high oxidative stress, which result in delayed healing process. Oxygen is regarded as an important substance in cell proliferation, differentiation and migration, which is beneficial to ulcer recovery. Methods: This study developed a multi-functional GOx-CAT nanogel (GCN) system for the treatment of diabetic oral mucosa ulcers. The catalytic activity, ROS scavenge and oxygen supply ability of GCN was validated. The therapeutic effect of GCN was verified in the diabetic gingival ulcer model. Results: The results showed that the nanoscale GCN was capable of significantly eliminating intracellular ROS, increasing intracellular oxygen concentration and accelerating cell migration of human gingival fibroblasts, which could promote diabetic oral gingival ulcer healing in vivo by alleviating inflammation and promoting angiogenesis. Discussion: This multifunctional GCN with ROS depletion, continuous oxygen supply and good biocompatibility, which might provide a novel therapeutic strategy for effective treatment of diabetic oral mucosa ulcers.

Tilapia (Oreochromis mossambicus) allergens characterized by ELISA, SDS-PAGE, 2D gels, Western blotting and MALDI-TOF mass spectrometry.

Parvalbumins have long been identified as major allergens in fish, but our research has found that parvalbumins are not the main cause of allergic reactions to tilapia. After homogenization, proteins were extracted from freshwater tilapia to react with a pooled sera sample taken from patients (n = 20) tested to be allergic to tilapia. Enzyme-linked immunosorbent assay revealed immunoglobulin E antibody activity, followed by sodium dodecyl sulphate polyacrylamide gel electrophoresis, Western blot, 2D electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to carry out protein separation and analysis. Protein identification against different databases yielded three known high molecular weight proteins as tilapia allergens: chromosome undetermined SCAF7145, fructose-bisphosphate aldolase A and enolase 3 (beta muscle). A fourth, new, unidentified protein with two T-cell receptors was discovered.

Evaluating the efficacy of a ferrous-ion-chelating peptide from Alaska pollock frame for the improvement of iron nutritional status in rats.

This study aimed to investigate the effects of ferrous-ion-chelating peptides from Alaska pollock frames (APFP-Fe) on iron deficiency in anaemic rats. We hydrolysed the Alaska pollock frames to obtain a peptide with an average molecular weight of 822 Da. The bioavailability of APFP-Fe was tested using animal experiments. Wistar rats were randomly divided into six groups: an iron deficiency control group, a normal control group, and iron deficiency groups treated with ferrous sulfate (FeSO4) or low-, medium-, or high-dose APFP-Fe. Rats in the iron deficiency groups were fed an iron-deficient diet to establish the iron deficiency anaemia (IDA) model. After the model was established, different iron supplements were given to rats once per day via intragastric administration for 21 days. The results showed that APFP-Fe had restorative effects, returning the body weight, weight gain, height, and haematological parameters in IDA rats to normal levels. In addition, compared with FeSO4, APFP-Fe promoted significant weight gain and effectively improved haemoglobin, serum iron and transferrin levels, and recovery of the capacity of iron binding with transferrin, especially at the medium and high doses. These findings suggest that APFP-Fe is an effective source of iron for improving the iron nutritional status in IDA rats and shows promise as a new source of iron supplementation.

Effects of three products from Antarctic krill on the nitrogen balance, growth, and antioxidation status of rats.

A few studies conducted over the past few decades have demonstrated the health benefits of a diet rich in marine products, but limited studies have investigated the effects of different krill products on the nitrogen balance and their potential health benefits. In our study, after a 14-day acclimation period, 50 female Sprague-Dawley rats were randomly assigned to five groups, each of which was fed a different diet, for 28 days. We then evaluated the effect of krill protein complex (KPC), krill powder, and defatted krill powder on the nitrogen balance, growth, and antioxidant activity through analyses of MDA, CAT, GSH-Px, and T-SOD. An in vivo analysis suggested that the nitrogen retention rate, protein digestibility, and bioutilization of krill products were equal to those of casein. Moreover, the KPC diet resulted in the highest nitrogen intake and retention among the groups, and the biological value and net protein utilization obtained with KPC were higher than those obtained with defatted krill powder, which was consistent with the weight gains observed for these two groups. The hematological test also showed that KPC contributed to the production of functional proteins in the body. The antioxidant activity analysis indicated that higher GSH-Px and T-SOD activities were obtained with krill products and KPC, respectively, compared with casein. The results from this study suggested that krill proteins could promote growth and improve the antioxidant status of an organism. Although further studies on the safety of krill products for human consumption are needed, this work provides insights into the use of krill proteins as a potential substitute for other proteins and restructured foods.

[Screening of the Stable Expressing HPV18 E5 Protein Cell Line and its Influence on Cell Proliferation and the Cell Cycle].

We wished to screen the cell line that stably expresses the HPV18E5 protein, and to ascertain the influence of HPV18E5 protein on cell proliferation and the cell cycle. The HPV18E5 gene was amplified by the polymerase chain reaction. Then, the His-tag pSecTag-HPV18E5 eukaryotic expression vector was constructed by digestion ligation and connection. The recombinant plasmid was transfected into Balb/c3T3 cells with lipofectamine, and positive cell lines were screened by a culture medium containing bleomycin. HPV18E5 expression in cells was confirmed by western blotting and immuno-enzymatic methods. The influence of HPV18E5 on cell proliferation and the cell cycle were detected by Cell Counting Kit-8 and flow cytometry, respectively. The pSecTag-HPV18E5 eukaryotic expression vector was constructed. After 21-day selection in a culture medium containing 400 µg/mL bleomycin, stably expressing HPV18E5 protein cells were harvested. Compared with control groups, cell proliferation in HPV18E5 stably expressed cells was obviously increased, as was the S phase in the cell cycle. Our results suggested that HPV18E5 influences cell proliferation and the cell cycle. Our study has laid the foundation of the biologic properties of HPV18E5 protein, which will aid further studies on the mechanism of action of carcinogenesis.

Infection and integration of high-risk human papillomavirus in HPV-associated cancer cells.

High-risk human papillomaviruses (HPV) have been associated with many human cancers in clinical studies. Integration of HPV into the human genome is a suspected etiological factor in the induction of some HPV-associated cancers. The characteristics of HPV integration in certain HPV-integrated cancer cells remain unclear. In this study, ten HPV-associated carcinoma cell lines were evaluated for the presence, genotype, and integration status of HPV by nested polymerase chain reaction. The HPV genome did not insert in the genome of a mammary cancer cell line (MCF7), adrenal neuroblastoma cell line (NH-6), or three esophageal carcinoma cell lines (KYSE150, KYSE450 and KYSE140). HPV type 18 DNA did infect cell lines of tongue cancer (Tca83), hepatocellular carcinoma (Hep G2), and lung carcinoma (A549), but the HPV type 18 genes were not transcribed into mRNA. However, HPV type 18 integrated into the genomes of the esophageal carcinoma cell lines EC9706 and EC109, and the integration sites for both cell lines were in loci 8q24, which is a gene desert area adjacent to fragile sites. We speculate that HPV transcripts are more likely to integrate near highly susceptible fragile sites. This study suggests that HPV integration is still a significant issue that needs to be fully examined and can possibly be used as individualized biomarkers for the early diagnosis of HPV-related cancers.

Integrated HPV genomes tend to integrate in gene desert areas in the CaSki, HeLa, and SiHa cervical cancer cell lines.

AIMS: The integration preferences of human papillomavirus (HPV) have been intensively studied and contested over recent years. To disclose the integration preferences of high-risk HPV in cervical cancer, HPV transcriptional sites and features in different cervical cancer cell lines were identified. MAIN METHODS: In this study, three cervical cancer cell lines (CaSki, HeLa, and SiHa) were subjected for HPV genome status determination by amplification of papillomavirus oncogene transcripts (APOT) assay. The numbers of viral copies in human genomes and numbers of viral-human fusion mRNAs in three HPV-integrated cervical cancer cell lines were measured and analysed. KEY FINDINGS: The results revealed that the gene desert region 8q24 of the HPV type 18 integrated HeLa cell line and the 13q21-22 region of the HPV type 16 integrated CaSki and SiHa cell lines were hotspots for HPV integration, and the numbers of viral copies in the human genomes of the three cell lines that we detected were not in accordance with those reported in previous studies. SIGNIFICANCE: Integration of the HPV genome into the host cell chromosome suggests that persistent HPV infection is vital for malignant cell transformation and carcinogenesis. This study provides information to benefit health care professionals seeking more comprehensive and accurate diagnostics for HPV-related disease"? Please check, and amend as necessary.

Characterization of allergens isolated from the freshwater fish blunt snout bream (Megalobrama amblycephala).

Fish are an important source of dietary protein for humans throughout the world. However, they are recognized as one of the most common food allergens and pose a serious health problem in countries where fish consumption is high. Many marine fish allergens have been extensively studied, but relatively little is known about freshwater fish allergens. This study identified two main allergens from blunt snout bream (Megalobrama amblycephala), a freshwater fish widely consumed in China. Sera from 11 patients with convincing clinical history of blunt snout bream allergy were utilized in IgE immunoblot analysis to identify prominent allergens. Several blunt snout bream proteins revealed specific binding to serum IgE, with the 47 and 41 kDa proteins being the most immunodominant among them. Two-dimensional gel electrophoresis (2D SDS-PAGE) enabled resolution of the 47 and 41 kDa proteins into several protein spots with distinct isoelectric points. 2D SDS-PAGE along with IgE immunoblot analysis further confirmed the strong reactivity of these protein spots with the pooled sera from blunt snout bream-sensitive patients. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis of the peptides generated by trypsin digestion of the different spots corresponding to the 47 and 41 kDa proteins indicated that these spots were isoforms of enolase and muscle creatine kinase, respectively. The potential allergenicity of these proteins was further verified by an bioinformatics approach using the full-length and 80 amino acid sliding window FASTA searches, which revealed a significant amino acid sequence homology between blunt snout bream allergens and several known inhaled and crustacean allergens.