1.Research on The Genealogical Inference Efficiency of High-density SNPs
Jing LI ; Yi-Jie SUN ; Wen-Ting ZHAO ; Zi-Chen TANG ; Jing LIU ; Cai-Xia LI
Progress in Biochemistry and Biophysics 2026;53(3):740-753
ObjectiveThis study aims to explore the potential of different orders of magnitude single-nucleotide polymorphism (SNP) locus combinations for predicting distant kinship relationships. A high-density SNP locus set was constructed, and a comprehensive assessment of its inference capability was conducted. MethodsFirstly, we selected three commercial chip panels, CGA (Chinese genotyping array, Illumina), GSA (Global screening array, Illumina), Affy (23MF_V2 high-density SNP array, Affymetrix) and merged them after quality control, forming a high-density SNP locus panel(1 180 k). Secondly, we selected 161 samples and collected their peripheral blood samples by using whole-genome sequencing technology. Within this sample population, the levels of kinship relationships fully covered the range from level 1 to level 9, and the number of kinship pairs at each level was consistently maintained at over 50 pairs. From 161 samples data of whole-genome sequencing, the 1 180 k locus set was extracted, which is referred to as the high-density SNP locus set in the following text. The kinship inference was conducted using the identity-by-descent (IBD) algorithm with the selected optimal parameters. To comprehensively evaluate the performance of the high-density SNP locus set in kinship inference, we compared it with the three commercial chip panels, the intersection of these three chip loci, and the control sets constructed by randomly reducing the number of the high-density SNP locus set. Based on the changes in the IBD lengths, as well as the dynamic trends in prediction accuracy, we conducted a scientific assessment of the kinship inference capability of the high-density SNP locus set. ResultsAfter screening, a set of 1 184 334 autosomal SNPs was obtained. During the process of screening the optimal IBD length threshold, the result revealed that 0 cM, 1 cM, and 2 cM all demonstrated good applicability. However, to avoid the issue of a large amount of redundant information caused by setting a too low IBD length threshold, this study ultimately selected 2 cM as the optimal threshold. Compared with the average results of three chip panels, the high-density SNP locus set increased the total IBD length and the average IBD length across levels 1-9; the accuracy of the confidence interval for level 8 was 70.97%, which represented a 3.50% improvement; the average confidence interval accuracy for levels 1-8 was 91.39%, representing a 1.00% increase; and the false negative rates at levels 8 and 9 were reduced by 2.42% and 6.76%, respectively. The system efficacy of the high-density SNP locus set for kinship inference of first to eighth degree relationships reached 98.91%. Through random reduction of the high-density SNP locus set results, it is found that increasing the number of SNPs with the panel, the detection efficiency of IBD length showed a significant upward trend. At the same time, the overall trend in the accuracy of kinship relationship prediction as well as the confidence interval accuracy also indicated that both metrics steadily increased with the addition of more loci. ConclusionThe results show that the high-density SNPs panel significantly enhances the efficacy of distant kinship inference, accurately covering kinship degrees, with the average confidence interval accuracy for first to eighth degree relationships stably above 90%. The study finds that increasing the number of SNPs panel can improve the ability to predict distant kinship.
2.Role of extracellular vesicle-mediated intercellular communication in female follicle reproduction,preimplantation embryo development and implantation
Jing LIU ; Xiaoli ZHAO ; Tian XIA
Chinese Journal of Tissue Engineering Research 2026;30(1):218-228
BACKGROUND:Extracellular vesicles mediate intercellular signal transduction through the proteins,nucleic acids,and lipids they carry,thereby influencing the function of target cells.This vesicle-mediated communication mechanism is involved in regulating female reproductive development.OBJECTIVE:To summarize and analyze the regulatory roles of extracellular vesicle-mediated intercellular communication in female reproductive development.METHODS:A search was conducted in the PubMed database using the search terms"extracellular vesicles,exosomes,reproduction,maternal-embryo communication,maternal-fetal crosstalk,embryo implantation,endometrium,oviduct,follicle."The initial screening was carried out by reading the titles and abstracts of the literature,and then the literature with poor relevance to the research purpose,outdated content,and duplication was excluded according to the inclusion and exclusion criteria.Ultimately,69 relevant articles were included for comprehensive analysis.RESULTS AND CONCLUSION:Extracellular vesicles play a crucial role in key processes of female reproductive development,from folliculogenesis to implantation.(1)Extracellular vesicles mediate intercellular communication within the follicle,particularly the interactions between oocytes and follicular cells,which are essential for follicle development and maturation.(2)Extracellular vesicles and their contents facilitate interactions between the embryo and the fallopian tube,influencing the trajectory of embryonic development.(3)Extracellular vesicles and their contents promote implantation by mediating bidirectional communication between the embryo and the endometrium.Uterine-derived extracellular vesicles regulate processes such as embryo adhesion,invasion,and decidualization,while embryo-derived extracellular vesicles modulate endometrial receptivity,convey embryonic signals,and adjust the endometrial microenvironment.Studying the roles of extracellular vesicles in female reproductive development can provide valuable insights into the mechanisms of infertility and support the development of new therapeutic strategies.
3.Role of extracellular vesicle-mediated intercellular communication in female follicle reproduction,preimplantation embryo development and implantation
Jing LIU ; Xiaoli ZHAO ; Tian XIA
Chinese Journal of Tissue Engineering Research 2026;30(1):218-228
BACKGROUND:Extracellular vesicles mediate intercellular signal transduction through the proteins,nucleic acids,and lipids they carry,thereby influencing the function of target cells.This vesicle-mediated communication mechanism is involved in regulating female reproductive development.OBJECTIVE:To summarize and analyze the regulatory roles of extracellular vesicle-mediated intercellular communication in female reproductive development.METHODS:A search was conducted in the PubMed database using the search terms"extracellular vesicles,exosomes,reproduction,maternal-embryo communication,maternal-fetal crosstalk,embryo implantation,endometrium,oviduct,follicle."The initial screening was carried out by reading the titles and abstracts of the literature,and then the literature with poor relevance to the research purpose,outdated content,and duplication was excluded according to the inclusion and exclusion criteria.Ultimately,69 relevant articles were included for comprehensive analysis.RESULTS AND CONCLUSION:Extracellular vesicles play a crucial role in key processes of female reproductive development,from folliculogenesis to implantation.(1)Extracellular vesicles mediate intercellular communication within the follicle,particularly the interactions between oocytes and follicular cells,which are essential for follicle development and maturation.(2)Extracellular vesicles and their contents facilitate interactions between the embryo and the fallopian tube,influencing the trajectory of embryonic development.(3)Extracellular vesicles and their contents promote implantation by mediating bidirectional communication between the embryo and the endometrium.Uterine-derived extracellular vesicles regulate processes such as embryo adhesion,invasion,and decidualization,while embryo-derived extracellular vesicles modulate endometrial receptivity,convey embryonic signals,and adjust the endometrial microenvironment.Studying the roles of extracellular vesicles in female reproductive development can provide valuable insights into the mechanisms of infertility and support the development of new therapeutic strategies.
4.Effect and mechanism of Liujunzi Pills on gut microbiota of rats with spleen Qi deficiency syndrome.
Tao ZHANG ; Nian CHEN ; Qin-Yao JIA ; Xiao-Xia LEI ; Jie WANG ; Jia-Qing ZHAO ; Ying WEI ; Jing WEN
China Journal of Chinese Materia Medica 2025;50(15):4333-4341
This article aims to explore the effect and mechanism of Liujunzi Pills on the intestinal microbiota of rats with spleen Qi deficiency syndrome. The raw Rhei Radix et Rhizoma water extract(1 g·mL~(-1)) was used to prepare spleen Qi deficiency rat models. A total of 44 SD male rats were randomly divided into a control group, a model group, Liujunzi Pills groups at high(3.24 g·kg~(-1)), medium(1.62 g·kg~(-1)), low(0.81 g·kg~(-1)) doses, and Shenling Baizhu San(2.50 g·kg~(-1)) group. The drug effect was evaluated by observing the following aspects: spleen index, fecal water content, body weight, and intestinal propulsion index. Gut microbiota analysis and 16S rRNA gene sequencing were conducted on feces. Enzyme-linked immunosorbent assay(ELISA) and UV spectrophotometry were used to detect interleukin-1β(IL-1β) and adenosine triphosphate(ATP) levels in small intestine tissues. Hematoxylin-eosin staining and transmission electron microscopy were employed to observe changes in intestinal pathology and microstructure. The results show that, compared with the control group, fecal moisture content is significantly increased while spleen index, body weight, and intestinal propulsion index are significantly reduced in rats of the model group, indicating the successful establishment of the model. The above symptoms can be improved by both Shenling Baizhu San and Liujunzi Pills. Compared with the control group, in the model group, the gut microbiota abundance is changed with an unbalanced development: the abundance of beneficial bacteria within the Bacteroidetes phylum is reduced, accompanied by a significantly decreased Shannon index, and reduced signal levels of nicotinamide adenine dinucleotide phosphate(NADPH)-related enzymes relevant to mitochondria. However, Liujunzi Pills and Shenling Baizhu San can significantly improve the Bacteroidetes phylum abundance in gut microbiota, microbial diversity, and NADPH activity in the model group. Additionally, compared with the control group, the ATP level is decreased and the IL-1β level is increased in small intestinal tissues of the model group, with shorter small intestinal epithelial villi and decreased mitochondrial number. The above symptoms can be improved by Liujunzi Pills and Shenling Baizhu San. In conclusion, Liujunzi Pills can treat spleen Qi deficiency syndrome by enhancing mitochondrial function to regulate gut microbiota balance and diversity.
Animals
;
Gastrointestinal Microbiome/drug effects*
;
Drugs, Chinese Herbal/pharmacology*
;
Male
;
Rats, Sprague-Dawley
;
Rats
;
Qi
;
Spleen/metabolism*
;
Splenic Diseases/metabolism*
;
Humans
;
Interleukin-1beta/genetics*
;
Bacteria/drug effects*
;
Feces/microbiology*
;
Adenosine Triphosphate/metabolism*
5.Preliminary efficacy observation of 3D printed functional spinal external fixation brace combined with McKenzie therapy in the treatment of lumbar disc herniation.
Ning-Xia WANG ; Ping CHEN ; Hai-Dong WANG ; Jing JI ; Fang-Hong NIAN ; Xin LIU ; Chong-Fei JIN ; Duo-Ming ZHAO ; Hao-Lin LI ; Wei-Gang CHENG ; Gui-Lin LAI ; Guo-Biao WU
China Journal of Orthopaedics and Traumatology 2025;38(10):1047-1054
OBJECTIVE:
To observe the clinical efficacy of 3D printing spinal external fixator combined with McKenzie therapy for patients with lumbar dics herniation (LDH).
METHODS:
Sixty patients with LDH between January 2022 and January 2023 were enrolled. Among them, 30 patients were given McKinsey training. According to different treatment methods, all patients were divided into McKenzie group and McKenzie + 3D printing group, 30 patients in each group. The McKenzie group provided McKenzie therapy. The McKenzie + 3D printing group were treated with 3D printing spinal external fixation brace on the basis of McKenzie therapy. Patients in both groups were between 25 and 60 years of age and had their first illness. In the McKenzie group, there were 19 males and 11 females, with an average age of (48.57±5.86) years old, and the disease duration was (7.03 ±2.39) months. The McKenzie + 3D printing group, there were 21 males and 9 females, with an average age of (48.80±5.92) years old, and the disease duration was(7.30±2.56) months. Pain was evaluated using the visual analogue scale (VAS), and lumbar spine function was assessed using the Oswestry disability index (ODI) and the Japanese Orthopaedic Association (JOA) score. VAS, ODI and JOA scores were compared between two groups before treatment and at 1, 3, 6, 9 and 12 months after treatment.
RESULTS:
All patients were followed up for 12 months. The VAS for the McKenzie combined with 3D printing group before treatment and at 1, 3, 6, 9, and 12 months post-treatment were(6.533±0.860), (5.133±1.008), (3.933±0.868), (2.900±0.759), (2.067±0.640), (1.433±0.504), respectively. In the McKenzie group, the corresponding scores were (6.467±0.860), (5.067±1.048), (4.600±0.968), (3.533±1.008), (2.567±0.728), (1.967±0.809), respectively. The ODI of the McKenzie group before treatment and at 1, 3, 6, 9, and 12 months post-treatment were (41.033±6.810)%, (37.933±6.209)%, (35.467±6.962)%, (27.567±10.081)%, (20.800±7.531)%, (13.533±5.158)%, respectively. For the McKenzie combined with 3D printing group, the corresponding ODI were(38.033±5.605)%, (33.000±6.192)%, (28.767±7.045)%, (22.200±5.517)%, (17.700±4.836)%, (11.900±2.771)%, respectively. The JOA scores of the McKenzie combined with 3D printing group before treatment and at 1, 3, 6, 9, and 12 months post-treatment were(8.900±2.074), (13.133±2.330), (15.700±3.583), (20.400±3.480), (22.267±3.084), (24.833±2.640), respectively. In the McKenzie group, the corresponding scores were(9.200±2.091), (12.267±2.406), (15.333±3.198), (18.467±2.240), (20.133±2.751), (22.467±2.849), respectively. Before the initiation of treatment, no statistically significant differences were observed in the VAS, ODI, and JOA scores between two groups (P>0.05). At 3, 6, 9, and 12 months post-treatment, the VAS in the McKenzie combined with 3D printing group was significantly lower than that in the McKenzie group, and the difference was statistically significant (P<0.05). The comparison of ODI between two groups at 1, 3, 6, 9, and 12 months post-treatment revealed statistically significant differences (P<0.05). At 6, 9, and 12 months post-treatment, the JOA score in the McKenzie combined with 3D printing group was significantly higher than that in the McKenzie-only group, and the difference was statistically significant (P<0.05).
CONCLUSION
The combination of 3D printed functional spinal external fixation brace with McKenzie therapy can significantly improve and maintain lumbar function in patients with LDH.
Humans
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Male
;
Female
;
Middle Aged
;
Printing, Three-Dimensional
;
Intervertebral Disc Displacement/surgery*
;
External Fixators
;
Lumbar Vertebrae/surgery*
;
Adult
;
Braces
;
Treatment Outcome
6.The application of machine learning in the auxiliary diagnosis of specific learning disorder.
Hao ZHAO ; Shu-Lan MEI ; Jing-Yu WANG ; Xia CHI
Chinese Journal of Contemporary Pediatrics 2025;27(11):1420-1425
Specific learning disorder (SLD) is a common neurodevelopmental disorder in children that significantly affects academic performance and quality of life. At present, diagnosis mainly relies on standardized tests and professional evaluations, a process that is complex and time-consuming. Multiple studies have shown that machine learning can analyze diverse data, including test scores, handwriting samples, eye movement data, neuroimaging data, and genetic data, to automatically learn the relationships between input features and output labels and achieve efficient prediction. It shows great potential for early screening, auxiliary diagnosis, and research on underlying mechanisms in SLD. This article reviews the applications of machine learning in the auxiliary diagnosis of SLD and discusses its performance when handling different data types.
Humans
;
Machine Learning
;
Specific Learning Disorder/diagnosis*
;
Child
7.Clinical analysis of 49 cases of malignant lymphoma of the head and neck in children.
Yanli QU ; Heng ZHAO ; Xuli MA ; Xia LI ; Jing MA
Journal of Clinical Otorhinolaryngology Head and Neck Surgery 2025;39(5):476-481
Objective:To analyze the clinical characteristics of malignant lymphoma of the head and neck in children, and to improve the understanding and diagnosis and treatment of this type of disease by otolaryngologists. Methods:Clinical data of 49 children with malignant lymphoma of the head and neck hospitalized in the Department of Otorhinolaryngology, Head and Neck Surgery of Kunming Children's Hospital from 2013-2021 were retrospectively analyzed and statistically analyzed according to gender, age distribution, duration of the disease, site of onset, type of pathology and survival status. Results:A total of 49 cases of malignant lymphoma of the head and neck in children were collected, of which, 39 were male and 10 female. The minimum age was 3 years, the maximum was 14 years and 4 months, the median age of onset was 7 years, and the largest percentage (51.02%) of children was in the school age(6-12 years). The duration of the disease ranged from 5 days to 2 years, with a median of 1 month, and the site of the lesion was located in the neck in the majority of cases, 41(83.67%). The pathologic types of hodgkin lymphoma(HL) were 25 cases(51.02%) and non-hodgkin lymphoma(NHL) were 24 cases(48.98%), and among hodgkin lymphomas, mixed-cell classical hodgkin lymphoma was the most common, with 9 cases(18.37%); among non-hodgkin lymphomas,originated from B-cells in 16 cases (32.65%) and from T-cells in 7 cases (14.29%), with Burkitt's lymphoma being the most numerous of B-cell origin in 13 cases (26.53%), and T-cell lymphoblastoid lymphoma being the most common of T-cell origin in 4 cases (8.16%). The follow-up period was from 22 days to 6 years and 10 months, with 3 cases losing, 43 cases surviving, 3 cases dying, with a survival rate of 93
Humans
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Male
;
Female
;
Child
;
Head and Neck Neoplasms/therapy*
;
Child, Preschool
;
Retrospective Studies
;
Adolescent
;
Lymphoma/therapy*
;
Survival Rate
;
Hodgkin Disease
;
Prognosis
;
Infant
;
Lymphoma, Non-Hodgkin
8.Facilitation of mucosal healing by estrogen receptor β in ulcerative colitis through suppression of branched-chain amino acid transport and subsequent triggering of autophagy in colonic epithelial cells.
Yilei GUO ; Yanrong ZHU ; Jing ZHANG ; Yue HE ; Mianjiang ZHAO ; Haochang LIN ; Zhifeng WEI ; Yufeng XIA ; Yue DAI
Acta Pharmaceutica Sinica B 2025;15(1):168-187
Colonic mucosal healing is the ultimate goal of ulcerative colitis (UC) treatment, but it remains difficult to realize. Given the higher incidence of UC in males and the beneficial effect of estrogen on UC, we conducted this study to examine the therapeutic potential of estrogen receptor β (ERβ), the primary ER subtype in colon, on mucosal healing in UC. Our study is the first to report that ERβ activation degree was positively correlated with mucosal healing in patients with UC. Furthermore, ERβ activation enhanced mucosal healing in mice with dextran sulfate sodium-induced and biopsy-induced colonic injuries. Mechanistically, ERβ activation promoted autophagy of colonic epithelial cells by inhibiting branched-chain amino acid transport, leading to focal adhesion kinase (FAK) activation. Activated FAK promoted focal adhesion turnover and colonic epithelial cell migration, ultimately facilitating mucosal healing. ERβ -/- colitis mice exhibited impaired mucosal healing compared to wild-type littermates, highlighting the crucial effect of ERβ. Importantly, combination with ERβ-agonist diarylpropionitrile enhanced the amelioration of 5-aminosalicylic acid, a standard UC treatment agent, against mouse colitis. These findings attest to the crucial role of ERβ activation in colonic mucosal healing and may further inform the development of novel strategies for UC treatment.
9.Anterior Cingulate Cortex Contributes to the Hyperlocomotion under Nitrogen Narcosis.
Bin PENG ; Xiao-Bo WU ; Zhi-Jun ZHANG ; De-Li CAO ; Lin-Xia ZHAO ; Hao WU ; Yong-Jing GAO
Neuroscience Bulletin 2025;41(5):775-789
Nitrogen narcosis is a neurological syndrome that manifests when humans or animals encounter hyperbaric nitrogen, resulting in a range of motor, emotional, and cognitive abnormalities. The anterior cingulate cortex (ACC) is known for its significant involvement in regulating motivation, cognition, and action. However, its specific contribution to nitrogen narcosis-induced hyperlocomotion and the underlying mechanisms remain poorly understood. Here we report that exposure to hyperbaric nitrogen notably increased the locomotor activity of mice in a pressure-dependent manner. Concurrently, this exposure induced heightened activation among neurons in both the ACC and dorsal medial striatum (DMS). Notably, chemogenetic inhibition of ACC neurons effectively suppressed hyperlocomotion. Conversely, chemogenetic excitation lowered the hyperbaric pressure threshold required to induce hyperlocomotion. Moreover, both chemogenetic inhibition and genetic ablation of activity-dependent neurons within the ACC reduced the hyperlocomotion. Further investigation revealed that ACC neurons project to the DMS, and chemogenetic inhibition of ACC-DMS projections resulted in a reduction in hyperlocomotion. Finally, nitrogen narcosis led to an increase in local field potentials in the theta frequency band and a decrease in the alpha frequency band in both the ACC and DMS. These results collectively suggest that excitatory neurons within the ACC, along with their projections to the DMS, play a pivotal role in regulating the hyperlocomotion induced by exposure to hyperbaric nitrogen.
Animals
;
Gyrus Cinguli/drug effects*
;
Male
;
Mice, Inbred C57BL
;
Locomotion/drug effects*
;
Neurons/drug effects*
;
Mice
;
Nitrogen/toxicity*
;
Inert Gas Narcosis/physiopathology*
;
Corpus Striatum/physiopathology*
10.Administration of Porphyromonas gingivalis in pregnant mice enhances glycolysis and histone lactylation/ADAM17 leading to cleft palate in offspring.
Xige ZHAO ; Xiaoyu ZHENG ; Yijia WANG ; Jing CHEN ; Xiaotong WANG ; Xia PENG ; Dong YUAN ; Ying LIU ; Zhiwei WANG ; Juan DU
International Journal of Oral Science 2025;17(1):18-18
Periodontal disease is a risk factor for many systemic diseases such as Alzheimer's disease and adverse pregnancy outcomes. Cleft palate (CP), the most common congenital craniofacial defect, has a multifaceted etiology influenced by complex genetic and environmental risk factors such as maternal bacterial or virus infection. A prior case-control study revealed a surprisingly strong association between maternal periodontal disease and CP in offspring. However, the precise relationship remains unclear. In this study, the relationship between maternal oral pathogen and CP in offspring was studied by sonicated P. gingivalis injected intravenously and orally into pregnant mice. We investigated an obvious increasing CP (12.5%) in sonicated P. gingivalis group which had inhibited osteogenesis in mesenchyme and blocked efferocytosis in epithelium. Then glycolysis and H4K12 lactylation (H4K12la) were detected to elevate in both mouse embryonic palatal mesenchyme (MEPM) cells and macrophages under P. gingivalis exposure which further promoted the transcription of metallopeptidase domain17 (ADAM17), subsequently mediated the shedding of transforming growth factor-beta receptor 1 (TGFBR1) in MEPM cells and mer tyrosine kinase (MerTK) in macrophages and resulted in the suppression of efferocytosis and osteogenesis in palate, eventually caused abnormalities in palate fusion and ossification. The abnormal efferocytosis also led to a predominance of M1 macrophages, which indirectly inhibited palatal osteogenesis via extracellular vesicles. Furthermore, pharmacological ADAM17 inhibition could ameliorate the abnormality of P. gingivalis-induced abnormal palate development. Therefore, our study extends the knowledge of how maternal oral pathogen affects fetal palate development and provides a novel perspective to understand the pathogenesis of CP.
Animals
;
Female
;
Porphyromonas gingivalis
;
Pregnancy
;
Mice
;
Cleft Palate/etiology*
;
Glycolysis

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