Biomedical big data, characterized by its massive scale, multi-dimensionality, and heterogeneity, offers novel perspectives for disease research, elucidates biological principles, and simultaneously prompts changes in related research methodologies. Biomedical ontology, as a shared formal conceptual system, not only offers standardized terms for multi-source biomedical data but also provides a solid data foundation and framework for biomedical research. In this review, we summarize enrichment analysis and deep learning for biomedical ontology based on its structure and semantic annotation properties, highlighting how technological advancements are enabling the more comprehensive use of ontology information. Enrichment analysis represents an important application of ontology to elucidate the potential biological significance for a particular molecular list. Deep learning, on the other hand, represents an increasingly powerful analytical tool that can be more widely combined with ontology for analysis and prediction. With the continuous evolution of big data technologies, the integration of these technologies with biomedical ontologies is opening up exciting new possibilities for advancing biomedical research.
Deep Learning ; Biological Ontologies ; Humans ; Big Data ; Biomedical Research

Cardiovascular disease (CVD), chronic kidney disease (CKD), and metabolic disorders are the 3 major chronic diseases threatening human health, which are closely related and often coexist, significantly increasing the difficulty of disease management. In response, the American Heart Association (AHA) proposed a novel disease concept of “cardiovascular-kidney-metabolic (CKM) syndrome” in October 2023, which has triggered widespread concern about the co-treatment of heart and kidney diseases and the prevention and treatment of metabolic disorders around the world. This review posits that effectively managing CKM syndrome requires a new and multidimensional paradigm for diagnosis and risk prediction that integrates biological insights, advanced technology and social determinants of health (SDoH). We argue that the core pathological driver is a “metabolic toxic environment”, fueled by adipose tissue dysfunction and characterized by a vicious cycle of systemic inflammation and oxidative stress, which forms a common pathway to multi-organ injury. The at-risk population is defined not only by biological characteristics but also significantly impacted by adverse SDoH, which can elevate the risk of advanced CKM by a factor of 1.18 to 3.50, underscoring the critical need for equity in screening and care strategies. This review systematically charts the progression of diagnostic technologies. In diagnostics, we highlight a crucial shift from single-marker assessments to comprehensive multi-marker panels. The synergistic application of traditional biomarkers like NT-proBNP (reflecting cardiac stress) and UACR (indicating kidney damage) with emerging indicators such as systemic immune-inflammation index (SII) and Klotho protein facilitates a holistic evaluation of multi-organ health. Furthermore, this paper explores the pivotal role of non-invasive monitoring technologies in detecting subclinical disease. Techniques like multi-wavelength photoplethysmography (PPG) and impedance cardiography (ICG) provide a real-time window into microcirculatory and hemodynamic status, enabling the identification of early, often asymptomatic, functional abnormalities that precede overt organ failure. In imaging, progress is marked by a move towards precise, quantitative evaluation, exemplified by artificial intelligence-powered quantitative computed tomography (AI-QCT). By integrating AI-QCT with clinical risk factors, the predictive accuracy for cardiovascular events within 6 months significantly improves, with the area under the curve (AUC) increasing from 0.637 to 0.688, demonstrating its potential for reclassifying risk in CKM stage 3. In the domain of risk prediction, we trace the evolution from traditional statistical tools to next-generation models. The new PREVENT equation represents a major advancement by incorporating key kidney function markers (eGFR, UACR), which can enhance the detection rate of CKD in primary care by 20%-30%. However, we contend that the future lies in dynamic, machine learning-based models. Algorithms such as XGBoost have achieved an AUC of 0.82 for predicting 365-day cardiovascular events, while deep learning models like KFDeep have demonstrated exceptional performance in predicting kidney failure risk with an AUC of 0.946. Unlike static calculators, these AI-driven tools can process complex, multimodal data and continuously update risk profiles, paving the way for truly personalized and proactive medicine. In conclusion, this review advocates for a paradigm shift toward a holistic and technologically advanced framework for CKM management. Future efforts must focus on the deep integration of multimodal data, the development of novel AI-driven biomarkers, the implementation of refined SDoH-informed interventions, and the promotion of interdisciplinary collaboration to construct an efficient, equitable, and effective system for CKM screening and intervention.

This study aims to investigate the effects of renin inhibitor aliskiren on kidney injury in human angiotensinogen-renin (AGT-REN) double transgenic hypertensive (dTH) mice and explore its possible mechanism. The dTH mice were divided into hypertension group (HT group) and aliskiren intervention group (HT+Aliskiren group), while wild-type C57BL/6 mice were served as the control group (WT group). Blood pressure data of mice in HT+Aliskiren group were collected after 28 d of subcutaneous penetration of aliskiren (20 mg/kg), and the damage of renal tissue structure and collagen deposition were observed by HE, Masson and PAS staining. The ultrastructure of kidney was observed by transmission electron microscope. Coomassie bright blue staining and biochemical analyzer were used to detect renal function injury. The expression of renin-angiotensin system (RAS) was determined by ELISA and immunohistochemistry. The contents of superoxide dismutase (SOD) and malondialdehyde (MDA) in kidney were determined by chemiluminescence method. The content of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase subunit p47^phox, inducible nitric oxide synthase (iNOS), 3-nitrotyrosine (3-NT), NADPH oxidase 2 (NOX2) and NADPH oxidase 4 (NOX4) were detected by Western blot analysis. The results showed that compared with WT group, the blood pressure of mice in HT group was significantly increased. The renal tissue structure in HT group showed glomerular sclerosis, severe interstitial tubular injury, and increased collagen deposition. In addition, 24 h urinary protein, serum creatinine and urea levels increased. Serum and renal tissue levels of angiotensin II (Ang II) were increased, serum angiotensin-(1-7) [Ang-(1-7)] expression was decreased, and renal Ang-(1-7) expression was elevated. The expressions of ACE, Ang II type 1 receptor (AT₁R) and MasR in renal tissue were increased, while the expression of ACE2 was decreased. MDA content increased, SOD content decreased, and the expressions of p47^phox, iNOS, 3-NT, NOX2 and NOX4 were increased. However, aliskiren reduced blood pressure in dTH mice, improved renal structure and renal function, reduced Ang II and Ang-(1-7) levels in serum and renal tissue, reduced the expression of ACE and AT₁R in renal tissue, increased the expression of ACE2 and MasR in renal tissue, and decreased the above levels of oxidative stress indexes in dTH mice. These results suggest that aliskiren may play a protective role in hypertensive renal injury by regulating the balance between ACE-Ang II-AT₁R and ACE2-Ang-(1-7)-MasR axes and inhibiting oxidative stress.
Animals ; Fumarates/therapeutic use* ; Mice ; Renin/antagonists & inhibitors* ; Amides/therapeutic use* ; Mice, Inbred C57BL ; Hypertension/physiopathology* ; Mice, Transgenic ; Kidney/pathology* ; Angiotensinogen/genetics* ; Renin-Angiotensin System/drug effects* ; NADPH Oxidases/metabolism* ; Male ; Antihypertensive Agents/pharmacology* ; Humans ; Superoxide Dismutase/metabolism* ; NADPH Oxidase 4

The study was aimed at identifying the diversity of tick species in selected areas of Qinghai,to analyze the genetic differentiation characteristics of tick-borne spotted fever group rickettsiae(SFGR),and to provide the theoretical basis for SFGR prevention and control in the region.The 16S rRNA gene was used for molecular biological identification of 446 collected tick samples,and the infection characteristics of SFGR in tick samples were determined according to the SFGR outer membrane protein A(ompA)gene.Haplotype analysis,phylogenetic tree construction,and estimation of differentiation times for SFGR were conducted in DNASP v6,IQ-tree v2.2.0,and BEAST v2.7.4 software.The obtained 446 tick samples belonged to three categories:(1)Haemaphy-salis spp.,including Haemaphysalis qinghaiensis(n=192)and H.danieli(n=37);(2)Dermacentor spp.,including Dermacentor ever-estianus(n=121),D.nuttalli(n=55),and D.silvarum(n=36);and(3)Hyalomma marginatum(n=5).Rickettsia raoultii was de-tected in D.everestianus,D.silvarum,D.nuttalli,H.qinghaiensis,and H.danieli,with infection rates of 95.9%,80.6%,69.1%,4.1%,and 2.7%,respectively.R.sibirica subsp.sibirica BJ-90 was found only in D.silvarum and D.nuttalli,with infection rates of 5.6%and 1.8%,respectively.The Candidatus R.gannanii F107 was found in H.danieli and H.qinghaiensis,with infection rates of 16.2%and 7.8%,respectively.Ca.R.hongyuanensis was detected only in H.qinghaiensis,with a prevalence of 16.3%.The prevalence of R.aeschlimannii was 20%and 2.7%in Hy.marginatum and H.danieli,respectively.Haplotype and nucleotide polymorphism analy-ses revealed 13 haplotypes in R.raoultii,with haplotype H13 as the dominant haplotype(42/192);seven haplotypes in Ca.R.ganna-nii F107,with haplotype H4 as the dominant haplotype(4/18);and three haplotypes in Ca.R.hongyuanensis,with haplotype H1 as the dominant haplotype(11/13).The phylogenetic tree indicated that the sequences of R.raoultii in selected areas of Qinghai and R.rhipicephali clustered into one branch;Ca.R.hongyuanensis and Ca.R.gannanii F107 clustered into one branch;and R.sibirica subsp.sibirica BJ-90 clustered into one branch with R.sibirica.Estimates of differentiation time revealed that the mean differentiation time for the six Rickettsia was approximately 2 000 Mya(95%CI:1 999.08-2 001.02 Mya).The tick species distributed in selected ar-eas of Qinghai are diverse,and this study provides the first report of Hy.marginatum in Qinghai Province.SFGR significantly varied in prevalence among tick species and showed high genetic diversity.

Objective To analyze the research status and hotspots in the field of astragalus polysaccharides;To provide references for further research.Methods Research literature about astragalus polysaccharides was retrieved from CNKI,Wanfang Data,VIP,PubMed,and Web of Science databases from 1st,Jan.2013 to 1st,July 2023.NoteExpress 3.7 software was used to manage the literature and ultimately establish a database.Excel 2019,CiteSpace 6.2.2R and VOSviewer 1.6.18 were used to visually analyze the publication volume,authors,institutions,and keywords of the included literature.Results A total of 2 462 articles were included,with 1 284 Chinese articles and 1 178 English articles.The main research institutions were Gansu University of Chinese Medicine,Shandong University of Traditional Chinese Medicine,and Beijing University of Chinese Medicine.The core authors of Chinese literature were Liu Yongqi,Wang Hongxin,Lu Meili,etc.The core authors of English literature included Zhang Wei,Li Ke,Yang Xiaojun,etc.High-frequency keywords of Chinese literature included Astragali Radix,rats,polysaccharides,cell apoptosis,and oxidative stress,etc.High frequency keywords in English literature included expression,in vitro,oxidative stress,apoptosis,etc.Conclusion The research on astragalus polysaccharides focuses on their pharmacological effects and mechanisms.Intestinal flora,immune regulation,autophagy and apoptosis are the hot action mechanisms in this field.The focus of disease research involves tumor and diabetes,and antiviral,anti infection and other pharmacological effects are the research trend.

The study was aimed at identifying the diversity of tick species in selected areas of Qinghai,to analyze the genetic differentiation characteristics of tick-borne spotted fever group rickettsiae(SFGR),and to provide the theoretical basis for SFGR prevention and control in the region.The 16S rRNA gene was used for molecular biological identification of 446 collected tick samples,and the infection characteristics of SFGR in tick samples were determined according to the SFGR outer membrane protein A(ompA)gene.Haplotype analysis,phylogenetic tree construction,and estimation of differentiation times for SFGR were conducted in DNASP v6,IQ-tree v2.2.0,and BEAST v2.7.4 software.The obtained 446 tick samples belonged to three categories:(1)Haemaphy-salis spp.,including Haemaphysalis qinghaiensis(n=192)and H.danieli(n=37);(2)Dermacentor spp.,including Dermacentor ever-estianus(n=121),D.nuttalli(n=55),and D.silvarum(n=36);and(3)Hyalomma marginatum(n=5).Rickettsia raoultii was de-tected in D.everestianus,D.silvarum,D.nuttalli,H.qinghaiensis,and H.danieli,with infection rates of 95.9%,80.6%,69.1%,4.1%,and 2.7%,respectively.R.sibirica subsp.sibirica BJ-90 was found only in D.silvarum and D.nuttalli,with infection rates of 5.6%and 1.8%,respectively.The Candidatus R.gannanii F107 was found in H.danieli and H.qinghaiensis,with infection rates of 16.2%and 7.8%,respectively.Ca.R.hongyuanensis was detected only in H.qinghaiensis,with a prevalence of 16.3%.The prevalence of R.aeschlimannii was 20%and 2.7%in Hy.marginatum and H.danieli,respectively.Haplotype and nucleotide polymorphism analy-ses revealed 13 haplotypes in R.raoultii,with haplotype H13 as the dominant haplotype(42/192);seven haplotypes in Ca.R.ganna-nii F107,with haplotype H4 as the dominant haplotype(4/18);and three haplotypes in Ca.R.hongyuanensis,with haplotype H1 as the dominant haplotype(11/13).The phylogenetic tree indicated that the sequences of R.raoultii in selected areas of Qinghai and R.rhipicephali clustered into one branch;Ca.R.hongyuanensis and Ca.R.gannanii F107 clustered into one branch;and R.sibirica subsp.sibirica BJ-90 clustered into one branch with R.sibirica.Estimates of differentiation time revealed that the mean differentiation time for the six Rickettsia was approximately 2 000 Mya(95%CI:1 999.08-2 001.02 Mya).The tick species distributed in selected ar-eas of Qinghai are diverse,and this study provides the first report of Hy.marginatum in Qinghai Province.SFGR significantly varied in prevalence among tick species and showed high genetic diversity.

Objective To analyze the research status and hotspots in the field of astragalus polysaccharides;To provide references for further research.Methods Research literature about astragalus polysaccharides was retrieved from CNKI,Wanfang Data,VIP,PubMed,and Web of Science databases from 1st,Jan.2013 to 1st,July 2023.NoteExpress 3.7 software was used to manage the literature and ultimately establish a database.Excel 2019,CiteSpace 6.2.2R and VOSviewer 1.6.18 were used to visually analyze the publication volume,authors,institutions,and keywords of the included literature.Results A total of 2 462 articles were included,with 1 284 Chinese articles and 1 178 English articles.The main research institutions were Gansu University of Chinese Medicine,Shandong University of Traditional Chinese Medicine,and Beijing University of Chinese Medicine.The core authors of Chinese literature were Liu Yongqi,Wang Hongxin,Lu Meili,etc.The core authors of English literature included Zhang Wei,Li Ke,Yang Xiaojun,etc.High-frequency keywords of Chinese literature included Astragali Radix,rats,polysaccharides,cell apoptosis,and oxidative stress,etc.High frequency keywords in English literature included expression,in vitro,oxidative stress,apoptosis,etc.Conclusion The research on astragalus polysaccharides focuses on their pharmacological effects and mechanisms.Intestinal flora,immune regulation,autophagy and apoptosis are the hot action mechanisms in this field.The focus of disease research involves tumor and diabetes,and antiviral,anti infection and other pharmacological effects are the research trend.

Objective To observe the efficacy and safety of Morinda officinalis oligosaccharides in the continuation treatment of mild and moderate depression.Methods An open,single-arm,multi-center design was adopted in our study.Adult patients with mild and moderate depression who had received acute treatment of Morinda officinalis oligosaccharides were enrolled and continue to receive Morinda officinalis oligosaccharides capsules for 24 weeks,the dose remained unchanged during continuation treatment.The remission rate,recurrence rate,recurrence time,and the change from baseline to endpoint of Hamilton Depression Scale(HAMD),Hamilton Anxiety Scale(HAMA),Clinical Global Impression-Severity(CGI-S)and Arizona Sexual Experience Scale(ASEX)were evaluated.The incidence of treatment-related adverse events was reported.Results The scores of HAMD-17 at baseline and after treatment were 6.60±1.87 and 5.85±4.18,scores of HAMA were 6.36±3.02 and 4.93±3.09,scores of CGI-S were 1.49±0.56 and 1.29±0.81,scores of ASEX were 15.92±4.72 and 15.57±5.26,with significant difference(P＜0.05).After continuation treatment,the remission rate was 54.59％(202 cases/370 cases),and the recurrence rate was 6.49％(24 cases/370 cases),the recurrence time was(64.67±42.47)days.The incidence of treatment-related adverse events was 15.35％(64 cases/417 cases).Conclusion Morinda officinalis oligosaccharides capsules can be effectively used for the continuation treatment of mild and moderate depression,and are well tolerated and safe.

Objective To investigate the efficacy of Bushen Tiaojing Decoction,a prescription derived from Daying Decoction which recorded in Jing Yue Quan Shu(The Complete Works of ZHANG Jing-Yue)and with herbs added,combined with human recombinant interferon-α-2b for the treatment of endometriosis(EMs)and to observe its effects on humoral immunity,serum carbohydrate antigen 125(CA125)and anti-endometrial antibody(EMAb)levels of EMs patients.Methods A total of 86 cases of EMs patients with kidney deficiency and blood stasis syndrome were randomly divided into observation group and control group,with 43 cases in each group.The control group was treated with human recombinant interferon-α-2b alone,and the observation group was treated with Bushen Tiaojing Decoction combined with human recombinant interferon-α-2b.The course of treatment covered one month.The changes of humoral immune factors of immunoglobulin A(IgA),complement 3(C3)and complement 4(C4),endometrial ectopic mass diameter,and the levels of pathology-relevant factors of CA1 25 and EMAb in the two groups before and after treatment were observed.Moreover,the clinical efficacy and safety of the two groups were evaluated.Results(1)After one month of treatment,the total effective rate of the observation group was 97.67％(42/43),and that of the control group was 81.40％(35/43).The intergroup comparison(tested by chi-square test)showed that the efficacy of the observation group was significantly superior to that of the control group(P＜0.05).(2)After treatment,the serum IgA level of the two groups was significantly higher than that before treatment(P＜0.05),and the serum C3 and C4 levels were significantly lower than those before treatment(P＜0.05).The increase of serum IgA level and the decrease of serum C3 and C4 levels in the observation group were significantly superior to those in the control group(P＜0.01).(3)After treatment,the serum CA125 and EMAb levels and the diameter of endometrial ectopic mass in the two groups were significantly lower than those before treatment(P＜0.05),and the decrease of serum CA125 and EMAb levels and the diameter of endometriosis mass in the observation group was significantly superior to that in the control group(P＜0.01).(4)The total incidence of adverse reactions in the observation group was 6.98％(3/43)and that in the control group was 11.63％(5/43),and the difference between the two groups was not significant(P＞0.05).Conclusion Bushen Tiaojing Decoction combined with human recombinant interferon-α-2b has a significant clinical effect for the treatment of EMs patients with kidney deficiency and blood stasis syndrome.The combined therapy is effective on improving the levels of humoral immune factors,serum CA125 and EMAb,and reducing endometrial ectopic mass,with high safety.

Objective To analyze the characteristics of healthcare-associated infection(HAI)in patients in liver transplantation intensive care unit(ICU),and provide basis for the effective prevention and control of liver post-transplantation infection.Methods Targeted surveillance data of HAI in liver transplantation ICU from 2018 to 2022 were analyzed retrospectively.Incidence,incidence trend,infection site,pathogens and drug resistance were analyzed.Results A total of 3 762 liver transplantation patients were surveilled,106 patients developed 133 cases of HAI,with an incidence of 2.82％and a case incidence of 3.54％.There was no significant difference among the years(P=0.473).Infection mainly occurred within 2 weeks after admission to ICU,accounting for 85.85％.The main infection sites included blood system(26.32％),respiratory system(22.56％),and surgical site(19.55％).The average utilization rates of central veinous catheterization,urethral catheterization,and ventilator were 85.77％,70.58％,and 40.83％,respectively.The incidences of central line-associated bloodstream infection(CLABSI),catheter-associated urinary tract infection(CAUTI),and ventilator-associated pneumonia(VAP)were 0.54‰,0.33‰,and 1.84‰,respectively.A total of 131 strains of pathogens were detected,of which Gram-negative bac-teria accounted for 38.17％and Gram-positive bacteria accounted for 29.77％.The top three pathogens were Kleb-siella pneumoniae(15.27％),Enterococcus faecium(11.45％),and Acinetobacter baumannii(9.16％).Conclusion Effective prevention and control measures should be taken based on the characteristics of HAI in the liver transplan-tation ICU,so as to curb bacterial resistance and reduce liver post-transplantation HAI.