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Due to the exponential growth of clinical data and its inherent privacy sensitivity, ensuring robust privacy and security in medical database systems remains a critical challenge. This article reviews recent advances in Access Control, Data Encryption, and Blockchain technologies. Access control covers the framework design based on multi-institution attribute encryption, Elliptic Curve Cryptography (ECC) and Selective Ring Access Control (SRAC) mechanism. Data encryption discusses the encryption schemes of Fully Homomorphic Encryption (FHE), SFO-optimized Multi-Key Homomorphic Encryption (MHE-SFO) and Parallel AES (P-AES) combined with RSA. In blockchain applications, it introduces the permissioned public chain architecture based on fog computing and the management methodology of introducing sufficiency scoring (sfmd). Regarding these technologies, the article also points out the limitations of deep learning models, data encryption performance and searchability, and blockchain, suggesting future research to enhance data and search efficiency, privacy protection, trustworthy Artificial Intelligence (AI) and blockchain efficiency through techniques like semi-supervised learning, explainable AI, lightweight encryption and decentralized software. This article provides a comprehensive and in-depth review that can help readers in this field better understand the current and future directions.

Blockchain technology is increasingly being used in personal data protection. Inspired by the importance of data security, this paper proposes a personal data protection mechanism based on blockchain, combined with distributed hash tables and cryptography, to enhance users' control over the data generated using web applications. This paper designs this mechanism's system model and describes the three aspects in detail: data storage mechanism, data encryption mechanism, and data trading mechanism. Among them, the data storage mechanism restricts user data to be stored only in the local storage space of the user terminal, the decentralized blockchain network, and the distributed hash table network to ensure that enterprises providing network applications cannot privately store user interaction data, the encryption mechanism is responsible for encrypting all user data recorded in the network and allows users to control the key of the data to ensure the security of the user data in the blockchain and distributed hash tables, the data transaction mechanism allows users to trade their data, and to incentivize enterprises to assist users in collecting personal data, data transaction contracts are built into the data transaction mechanism, allowing enterprises to receive a share of the revenue from user data transactions. Then, for data transactions, use the Stackelberg game to simulate the revenue sharing between users and service providers in data trading to incentivize enterprises providing web services to assist users in collecting their data. The simulation results show that when the number of users is 1000, the revenues of this scheme for service providers are 31%, 561%, and 19% higher than the existing scheme. Finally, the personal data protection platform is implemented by code to verify the feasibility of the theory proposed in this paper in personal data protection.

Background Helicobacter pylori ( H. pylori ) is a global infectious carcinogen. We aimed to evaluate the prevalence of H. pylori infection in the healthcare-utilizing population undergoing physical examinations at a tertiary hospital in Guangxi, China. Furthermore, gastroscopies were performed on selected participants to scrutinize the endoscopic features of H. pylori infection among asymptomatic individuals. Subjects and methods This study involved 22,769 participants who underwent H. pylori antibody serology screenings at the hospital between 2020 and 2023. The 14C-urea breath test was employed to determine the current H. pylori infection status of 19,307 individuals. Concurrently, 293 participants underwent gastroscopy to evaluate their endoscopic mucosal abnormalities. The risk correlation and predictive value of endoscopic mucosal traits, Hp infection status, and 14C-urea breath test(14C-UBT) outcomes were investigated in subsequent analyses. Results Serum Ure, CagA, and VacA antibodies were detected in 43.3%, 27.4%, and 23.6% of the 22,769 subjects that were screened, respectively. The population exhibited 27.5% and 17.2% positive rates for immune type I and II, respectively. Male participants exhibited lower positive rates of serum antibodies than females. The positive rates and predictive risks of the antibodies increased with age, and the highest positive rates were observed in the 50–60 age subgroup. Based on the outcomes of serological diagnostic techniques, it was observed that the positive rate was significantly higher compared to that of non-serological diagnostic methods, specifically the 14C-UBT results (43.3% versus 14.97%). Among the other cohort ( n  = 19,307), the 14C-UBT revealed a 14.97% positivity rate correlated with age. The 293 individuals who underwent gastroscopy from 14C-UBT Cohort were found to be at an increased risk of a positive breath test if they exhibited duodenal bulb inflammation, diffuse redness, or mucosal edema during the gastroscopy visit. Conclusion The prevalence of Helicobacter pylori infection is high among the population of Wuzhou, Guangxi, China. Type I H. pylori strains, distinguished by their enhanced virulence, are predominant in this region. In the framework of this population-based study, age has been identified as an independent risk factor for H. pylori infection. Additionally, distinct mucosal manifestations observed during gastroscopy can facilitate the identification of healthcare-utilizing individuals with active H. pylori infections.

Purpose: Paired Box 5 (PAX5) is a transcription factor that is widely associated with carcinogenesis. PAX5 can maintain Epstein-Barr virus (EBV) latency in B cells, while a close association exists between EBV infection and nasopharyngeal carcinoma (NPC). However, there are very few reports on the correlation between PAX5 and NPC development. The aim of this study was to investigate the role of PAX5 in NPC. Patients and Methods: The clinical value and prognostic significance of PAX5 in NPC and the association with PAX5 expression and immune cell infiltration were analyzed by multiple GEO datasets. In vivo and in vitro experiments including real-time PCR, Western blot, CCK-8 assay, and methylation sequencing were used to validate the results of bioinformatics analysis. Results: The expression of PAX5 was significantly reduced in NPC tissues, with the low expression being correlated with advanced clinical stage, low tumor mutation burden and immune activation, high relative expression of EBV, poor survival for NPC patients. PAX5 exhibited excellent diagnostic performance and had potential as a predictive factor for response to the immune checkpoint inhibitors therapy. Enrichment analysis suggested that the low expression of PAX5 was associated with the dysregulation of Hippo and Wnt signaling pathways. The promoter of PAX5 gene was hypermethylated in NPC tissues. Furthermore, the in vitro and in vivo experiments revealed that NPC tissue and cell lines had low mRNA expression levels of PAX5, the PAX5 promoter was hypermethy-lated in NPC cell lines, and PAX5 overexpression inhibited NPC cell proliferation and tumor growth in nude mice. Conclusion: PAX5 may be a tumor suppressor and serve as a novel potential diagnostic and prognostic marker for NPC. Keywords: nasopharyngeal carcinoma, transcription factor, PAX5, prognosis, immunity, Epstein-Barr virus

Paired Box 5 (PAX5) is a transcription factor that is widely associated with carcinogenesis. PAX5 can maintain Epstein-Barr virus (EBV) latency in B cells, while a close association exists between EBV infection and nasopharyngeal carcinoma (NPC). However, there are very few reports on the correlation between PAX5 and NPC development. The aim of this study was to investigate the role of PAX5 in NPC. The clinical value and prognostic significance of PAX5 in NPC and the association with PAX5 expression and immune cell infiltration were analyzed by multiple GEO datasets. In vivo and in vitro experiments including real-time PCR, Western blot, CCK-8 assay, and methylation sequencing were used to validate the results of bioinformatics analysis. The expression of PAX5 was significantly reduced in NPC tissues, with the low expression being correlated with advanced clinical stage, low tumor mutation burden and immune activation, high relative expression of EBV, poor survival for NPC patients. PAX5 exhibited excellent diagnostic performance and had potential as a predictive factor for response to the immune checkpoint inhibitors therapy. Enrichment analysis suggested that the low expression of PAX5 was associated with the dysregulation of Hippo and Wnt signaling pathways. The promoter of PAX5 gene was hypermethylated in NPC tissues. Furthermore, the in vitro and in vivo experiments revealed that NPC tissue and cell lines had low mRNA expression levels of PAX5, the PAX5 promoter was hypermethylated in NPC cell lines, and PAX5 overexpression inhibited NPC cell proliferation and tumor growth in nude mice. PAX5 may be a tumor suppressor and serve as a novel potential diagnostic and prognostic marker for NPC.

The procedures of ultrasonic extraction and clean-up were optimized for the determination of polycyclic aromatic hydrocarbons （PAHs） in marine sediments. Samples were ultrasonically extracted, and the extracts were purified with a miniaturized silica gel chromatographic column and analyzed with high performance liquid chromatography （HPLC） with a fluorescence detector. Ultrasonication with methanol-dichloromethane （2：1, v/v） mixture gave higher extraction efficiency than that with dichloromethane. Among the three elution solvents used in clean-up step, dichloromethane-hexane （2：3, v/v） mixture was the most satisfactory. Under the optimized conditions, the recoveries in the range of 54.82% to 94.70% with RSDs of 3.02% to 23.22% for a spiked blank, and in the range of 61.20% to 127.08% with RSDs of 7.61% to 26.93% for a spiked matrix, were obtained for the 15 PAHs studied, while the recoveries for a NIST standard reference SRM 1941b were in the range of 50.79% to 83.78% with RSDs of 5.24% to 21.38%. The detection limits were between 0.75 ng L-1 and 10.99 ng L-1for different PAHs. A sample from the Jiaozhou Bay area was examined to test the established methods.

Background In the pig production industry, artificial insemination (AI) plays an important role in enlarging the beneficial impact of elite boars. Understanding the genetic architecture and detecting genetic markers associated with semen traits can help in improving genetic selection for such traits and accelerate genetic progress. In this study, we utilized a weighted single-step genome-wide association study (wssGWAS) procedure to detect genetic regions and further candidate genes associated with semen traits in a Duroc boar population. Overall, the full pedigree consists of 5284 pigs (12 generations), of which 2693 boars have semen data (143,113 ejaculations) and 1733 pigs were genotyped with 50 K single nucleotide polymorphism (SNP) array. Results Results show that the most significant genetic regions (0.4 Mb windows) explained approximately 2%~ 6% of the total genetic variances for the studied traits. Totally, the identified significant windows (windows explaining more than 1% of total genetic variances) explained 28.29, 35.31, 41.98, and 20.60% of genetic variances (not phenotypic variance) for number of sperm cells, sperm motility, sperm progressive motility, and total morphological abnormalities, respectively. Several genes that have been previously reported to be associated with mammal spermiogenesis, testes functioning, and male fertility were detected and treated as candidate genes for the traits of interest: Number of sperm cells, TDRD5 , QSOX1 , BLK , TIMP3 , THRA , CSF3 , and ZPBP1 ; Sperm motility, PPP2R2B , NEK2 , NDRG , ADAM7 , SKP2 , and RNASET2 ; Sperm progressive motility, SH2B1 , BLK , LAMB1 , VPS4A , SPAG9 , LCN2, and DNM1 ; Total morphological abnormalities, GHR , SELENOP , SLC16A5 , SLC9A3R1 , and DNAI2 . Conclusions In conclusion, candidate genes associated with Duroc boars’ semen traits, including the number of sperm cells, sperm motility, sperm progressive motility, and total morphological abnormalities, were identified using wssGWAS. KEGG and GO enrichment analysis indicate that the identified candidate genes were enriched in biological processes and functional terms may be involved into spermiogenesis, testes functioning, and male fertility.

Background Gene expression programs are intimately linked to the interplay of active cis regulatory elements mediated by chromatin contacts and associated RNAs. Genome-wide association studies (GWAS) have identified many variants in these regulatory elements that can contribute to phenotypic diversity. However, the functional interpretation of these variants remains nontrivial due to the lack of chromatin contact information or limited contact resolution. Furthermore, the distribution and role of chromatin-associated RNAs in gene expression and chromatin conformation remain poorly understood. To address this, we first present a comprehensive interaction map of nuclear dynamics of 3D chromatin-chromatin interactions (H3K27ac BL-HiChIP) and RNA-chromatin interactions (GRID-seq) to reveal genomic variants that contribute to complex skeletal muscle traits. Results In a genome-wide scan, we provide systematic fine mapping and gene prioritization from GWAS leading signals that underlie phenotypic variability of growth rate, meat quality, and carcass performance. A set of candidate functional variants and 54 target genes previously not detected were identified, with 71% of these candidate functional variants choosing to skip over their nearest gene to regulate the target gene in a long-range manner. The effects of three functional variants regulating KLF6 (related to days to 100 kg), MXRA8 (related to lean meat percentage), and TAF11 (related to loin muscle depth) were observed in two pig populations. Moreover, we find that this multi-omics interaction map consists of functional communities that are enriched in specific biological functions, and GWAS target genes can serve as core genes for exploring peripheral trait-relevant genes. Conclusions Our results provide a valuable resource of candidate functional variants for complex skeletal muscle-related traits and establish an integrated approach to complement existing 3D genomics by exploiting RNA-chromatin and chromatin-chromatin interactions for future association studies.

Background This study aimed to investigate the relationship between total serum testosterone level (TT) and metabolic syndrome (MetS) among adult female population. Subgroup analysis further stratified the population by menopausal status to address the potential hormonal difference in postmenopausal women. Methods A total of 1966 participants from the National Health and Nutrition Examination Survey (NHANES) 2011–2012 cycle was included for analysis in this study. MetS was defined based on the National Cholesterol Education Program Adult Treatment Panel III guidelines. Serum TT was collected during the physical examination of the NHANES program and divided into quartiles (Q) in this analysis. Menopausal status was determined based on NHANES Reproductive Health Questionnaire. Logistic regression models were applied for analysis. Results The odds of MetS in Q2: 12.99–19.38 ng/mL (OR = 0.641, 95%CI 0.493–0.835, P < 0.01), Q3: 19.39–28.38 ng/mL (OR = 0.476, 95%CI 0.362–0.626, P < 0.001), and Q4: ≥28.40 ng/mL (OR = 0.390, 95%CI 0.294–0.517, P < 0.001) were statistically lower compared to the reference Q1: <12.99 ng/mL. For the postmenopausal group, a significantly lower odds of MetS was observed in the Q2 (OR = 0.689, 95%CI 0.486–0.977, P < 0.05) and Q4 (OR = 0.606, 95%CI 0.399–0.922, P < 0.05), while the odds of Q3 (OR = 0.439, 95%CI 0.248–0.779, P < 0.01) and Q4 (OR = 0.464, 95%CI 0.261–0.825, P < 0.01) were significantly lower than the reference Q1 in the premenopausal group. Conclusions Elevated TT levels are associated with incremental reductions in the odds of metabolic syndrome among adult females. Although, serum testosterone level is associated with the occurrence of metabolic syndrome in both the postmenopausal and the premenopausal group, the patterns of the relationship are different.

Background Lateral Organ Boundaries Domain ( LBD ) genes arise from charophyte algae and evolve essential functions in land plants in regulating organ development and secondary metabolism. Although diverse plant species have been investigated to construct the phylogeny of LBD gene family, a detailed and reliable ancestry that characterizes their evolutionary patterns has not been revealed. Results We develop an improved bioinformatic method that allows robust detection of 431 LBD genes in 11 high-quality land plant genomes. Phylogenetic analysis classifies the LBD genes into six subfamilies which support the existence of 7 ancient gene lineages. Phylogenetic relationship and gene collinearity are combined to retrace 11 ancestor genes for seed plants and 18 ancestor genes for angiosperms, which improves the resolution of LBD gene ancestry. The ancient gene lineages are strictly preserved in current plant genomes, including the previously controversial class IB gene in Selaginella moellendorphii , suggesting extreme reluctance of LBD genes to be lost during evolution. Meanwhile, whole-genome and dispersed gene duplications substantially expand LBD gene family in angiosperms, and elaborate functions of LBD genes through frequent expression pattern change and protein sequence variation. Conclusions Through phylogenetic and gene collinearity analyses, we retrace the landscape of LBD gene ancestry which lays foundation for elucidating evolutionary diversification of LBD genes in land plants.