1.Development of an Analytical Software for Forensic Proteomic SAP Typing
Feng HU ; Meng-Jiao WANG ; Jia-Lei WU ; Dong-Sheng DING ; Zhi-Yuan YANG ; An-Quan JI ; Lei FENG ; Jian YE
Progress in Biochemistry and Biophysics 2025;52(9):2406-2416
ObjectiveThe proteome of biological evidence contains rich genetic information, namely single amino acid polymorphisms (SAPs) in protein sequences. However, due to the lack of efficient and convenient analysis tools, the application of SAP in public security still faces many challenges. This paper aims to meet the application requirements of SAP analysis for forensic biological evidence’s proteome data. MethodsThe software is divided into three modules. First, based on a built-in database of common non-synonymous single nucleotide polymorphisms (nsSNPs) and SAPs in East Asian populations, the software integrates and annotates newly identified exonic nsSNPs as SAPs, thereby constructing a customized SAP protein sequence database. It then utilizes a pre-installed search engine—either pFind or MaxQuant—to perform analysis and output SAP typing results, identifying both reference and variant types, along with their corresponding imputed nsSNPs. Finally, SAPTyper compares the proteome-based typing results with the individual’s exome-derived nsSNP profile and outputs the comparison report. ResultsSAPTyper accepts proteomic DDA mass spectrometry raw data (DDA acquisition mode) and exome sequencing results of nsSNPs as input and outputs the report of SAPs result. The pFind and Maxquant search engines were used to test the proteome data of 2 hair shafts of2 individuals, and both obtained SAP results. It was found that the results of the Maxquant search engine were slightly less than those of pFind. This result shows that SAPTyper can achieve SAP fingding function. Moreover, the pFind search engine was used to test the proteome data of 3 hair shafts from 1 European person and 1 African person in the literature. Among the sites fully matched by the literature method, sites detected by SAPTyper are also included; for semi-matching sites, that is, nsSNPs are heterozygous, both literature method and SAPTyper method had the risk of missing detection for one type of the allele. Comparing the analysis results of SAPTyper with the SAP test results reported in the literature, it was found that some imputed nsSNP sites identified by the literature method but not detected by SAPTyper had a MAF of less than 0.1% in East Asian populations, and therefore they were not included in the common nsSNP database of East Asian populations constructed by this software. Since the database construction of this software is based on the genetic variation information of East Asian populations, it is currently unable to effectively identify representative unique common variation sites in European or African populations, but it can still identify SAP sites shared by these populations and East Asian populations. ConclusionAn automated SAP analysis algorithm was developed for East Asian populations, and the software named SAPTyper was developed. This software provides a convenient and efficient analysis tool for the research and application of forensic proteomic SAP and has important application prospects in individual identification and phenotypic inference based on SAP.
2.Establishment of UPLC-DAD fingerprint of raw and vinegar Bupleurum bupleurum and study on spectral effect relationship of anti-hepatic fibrosis
Ni-Ping CHEN ; Yan WANG ; Yan DONG ; Yang-Xin XIAO ; Ji-Yuan TU ; Yan-Ju LIU ; Zhong-Shi ZHOU
Chinese Pharmacological Bulletin 2024;40(6):1145-1152
Aim To establish the fingerprint of raw bupleurum and vinegar bupleurum,investigate the difference in their anti-liver fibrosis effects,and ex-plore the relationship between the chemical composition of raw bupleurum and vinegar bupleurum and their an-ti-liver fibrosis efficacy.Methods The fingerprints of 10 batches of raw bupleuri and 10 batches of bupleuri were established by UPLC method.The liver fibrosis cell model in vitro was established by TGF-β induced LX-2 hepatic stellate cells.The liver fibrosis cell mod-el was analyzed with collagen type Ⅰ(col1a1)and α-smoothmuscleactin.The expression of α-SMA protein was used as the pharmacodynamic index.MetaboAna-lyst5.0 was used to screen the difference markers af-fecting the quality of raw bupledges and vinegar bu-pledges with VIP value>1 as the criterion.Orthogo-nal partial least squares discriminant analysis(OPLS-DA)was used to screen the main components of raw bupleurum and vinegar bupleurum against liver fibro-sis.Results There were 18 peaks in the UPLC fin-gerprints of raw bupleurum and vinegar bupleurum,and the analysis results showed that there were nine main differences between raw bupleurum and vinegar bupleurum,among which peaks 9,7 and 6 could be considered as bupleurin d,bupleurin a and bupleurin f.The results of spectral effect relationship showed that the main components of bupleurum anti-liver fibrosis were peaks 11,12,14,15 and 18.Conclusions The established fingerprint method of raw bupleurum and vinegar bupleurum is simple and feasible,and the important components of anti-liver fibrosis activity are screened through the spectrum effect relationship,which provides a basis for clarifying the material basis of anti-liver fibrosis effect of raw bupleurum and vine-gar bupleurum.
3.Exploring the effects of sirolimus on the growth and development of zebrafish embryo models
Zi-Xin ZHANG ; Tong QIU ; Jiang-Yuan ZHOU ; Xue-Peng ZHANG ; Xue GONG ; Kai-Ying YANG ; Yu-Ru LAN ; Si-Yuan CHEN ; Yi JI
Chinese Pharmacological Bulletin 2024;40(12):2368-2374
Aim To explore the effects of sirolimus on the growth and development of motor,vascular,nerv-ous,and immune systems through zebrafish models.Methods After 3 hours of fertilization of zebrafish embryos,different concentrations of sirolimus were add-ed to the growth environment,and the growth and de-velopment of the embryos was recorded.Transgenic ze-brafish models labeled with blood vessels,nerves or im-mune cells were used to compare the drug effects on the growth and development of those systems.Results At the concentration of 0.5 μmol·L-1,the hatching rate and the body length(P<0.01)were significantly smaller than those of the control group,and movement was also significantly slowed down.Meanwhile,the length of axons of the nervous system,the development of intersegmental vessels,and the growth of immune cells were significantly delayed by drug treatment.But when the concentration was below 0.1 μmol·L-1,there was no statistically difference between the control group and the sirolimus group.Conclusions When the concentration of sirolimus exceeds a certain level,it can significantly slow down the growth and development of movement,blood vessels,nervous system and im-mune system of zebrafish.Therefore,in clinical prac-tice,it is important to monitor the blood concentration of sirolimus in children on time.
4.Comparison of open reduction hollow nail anchoring system with loop plate fixation under arthroscopy for the treat-ment of posterior cruciate ligament avulsion fractures
Rong WU ; Zhan-Feng ZHANG ; Wei WENG ; Hong-Hang YANG ; Ji-Kang MIN ; Jian-Wei SUN ; Zhe-Yuan SHEN
China Journal of Orthopaedics and Traumatology 2024;37(6):583-590
Objective To compare clinical effect between open reduction and fixation with cannulated screw and threaded rivet via posteromedial approach versus arthroscopic Endobutton plate fixation in treating posterior cruciate ligament avulsion fractures.Methods Clinical data of 38 patients with posterior cruciate ligament avulsion fractures from July 2020 to December 2021 were analyzed retrospectively,and divided into open reduction and internal fixation group(posterior medial approach hollow anchor system fixation)and arthroscopic fixation group(Endobutton with loop plate fixation under arthroscopy).There were 20 patients in open reduction and internal fixation group,including 16 males and 4 females,aged from 26 to 74 years old with an average of(42.9±18.8)years old;13 patients on the left side and 7 patients on the right side;12 patients were classi-fied to type Ⅱ and 8 patiens with type Ⅲ according to Meyers-McKeever fractures classification;14 patients were grade Ⅱ and 6 patients were grade Ⅲ in back drawer test.There were 18 patients in arthroscopic fixation group,including 11 males and 7 fe-males;aged from 24 to 70 years old with an average of(53.5±13.4)years old;11 patients on the left side and 7 patients on the right side;10 patients were classified to type Ⅱ and 8 patiens with type Ⅲ according to Meyers-McKeever fractures classifica-tion;11 patients were grade Ⅱ and 7 patients were grade Ⅲ in back drawer test.Operation time,blood loss,and quality of im-mediate reduction were compared between two groups.Knee range of motion,knee back drawer test,and International Knee Documentation Committee(IKDC)grading,KT2000 stability evaluation and Lysholm function score of knee joint were com-pared at 6 months after operation.Results All patients were followed up for 8 to 16 months with an average of(12.3±1.9)months.There were no complications such as incision infection,fracture malunion or non-union,and internal fixation loosening occurred.The avulsion fractures of knee joint were reached to imaging healing standard at 6 months after operation.Operation time and blood loss in open reduction and internal fixation group were(56.4±7.1)min and(63.2±10.2)ml,while(89.9±7.4)min and(27.7±8.7)ml in arthroscopic fixation group,respectively,and had significant difference between two groups(P<0.05).There were no differences in immediate reduction quality(x2=0.257,P=0.612),knee joint range of motion at 6 months after opertaion(t=0.492,P=0.626),knee joint rear drawer test(x2=0.320,P=0.572),IKDC classification of knee joint(x2=0.127,P=0.938),KT2000stability evaluation(x2=0.070,P=0.791),and knee Lysholmfunction score(t=0.092,P=0.282)between two groups.Conclusion Posterior medial approach with hollow anchoring system fixation and arthroscopic Endobutton with loop plate fixa-tion for the treatment of posterior cruciate ligament tibial occlusion avulsion fracture could achieve satisfactory clinical results,and arthroscopic surgery has less bleeding,but also has a longer learning curve and longer operation time than traditional inci-sion surgery.The surgeon needs to make a choice according to clinical situation of patient and their own surgical inclination.
5.Three-dimensional finite element analysis of lumbar disc herniation under different body positions
Ben-Jing YIN ; Yu LU ; Fu-Tao JI ; Rong-Neng QIU ; Yuan-Yang XIE ; Ge CHEN ; Tian-Li XU ; Chao-Yu BAO ; Ju-Bao LI
China Journal of Orthopaedics and Traumatology 2024;37(6):599-604
Objective To campare biomechanical effects of different postural compression techniques on three-dimensional model of lumbar disc herniation(LDH)by finite element analysis.Methods Lumbar CT image of a 48-year-old female patient with LDH(heighted 163 cm,weighted 53 kg)was collected.Mimics 20.0,Geomagic Studio,Solidwords and other software were used to establish three-dimensional finite element model of LDH on L4,5 segments.Compression techniques under horizon-tal position,30° forward bending and 10° backward extension were simulated respectively.After applying the pressure,the ef-fects of compression techniques under different positions on stress,strain and displacement of various tissues of intervertebral disc and nerve root were observed.Results L4,5 segment finite element model was successfully established,and the model was validated.When compression manipulation was performed on the horizontal position,30° flexion and 10° extension,the annular stress were 0.732,5.929,1.286 MPa,the nucleus pulposus stress were 0.190,1.527,0.295 MPa,and the annular strain were 0.097,0.922 and 0.424,the strain sizes of nucleus pulposus were 0.153,1.222 and 0.282,respectively.The overall displace-ment distance of intervertebral disc on Y direction were-3.707,-18.990,-4.171 mm,and displacement distance of nerve root on Y direction were+7.836,+5.341,+3.859 mm,respectively.The relative displacement distances of nerve root and interverte-bral disc on Y direction were 11.543,24.331 and 8.030 mm,respectively.Conclusion Compression manipulation could make herniated intervertebral disc produce contraction and retraction trend,by increasing the distance between herniated interverte-bral disc and nerve root,to reduce symptoms of nerve compression,to achieve purpose of treatment for patients with LDH,in which the compression manipulation is more effective when the forward flexion is 30°.
6.Effect of ureteral wall thickness at the site of ureteral stones on the clinical efficacy of ureteroscopic lithotripsy
Wei PU ; Jian JI ; Zhi-Da WU ; Ya-Fei WANG ; Tian-Can YANG ; Lyu-Yang CHEN ; Qing-Peng CUI ; Xu XU ; Xiao-Lei SUN ; Yuan-Quan ZHU ; Shi-Cheng FAN
Journal of Regional Anatomy and Operative Surgery 2024;33(12):1077-1081
Objective To investigate the effect of varying ureteral wall thickness(UWT)at the site of ureteral stones on the clinical efficacy of ureteroscopic lithotripsy(URL).Methods The clinical data of 164 patients with ureteral stones in our hospital were retrospectively analyzed.According to different UWT,the patients were divided into the mild thickening group(84 cases,UWT<3.16 mm),the moderate thickening group(31 cases,UWT 3.16 to 3.49 mm),and the severe thickening group(49 cases,UWT>3.49 mm),and the differences of clinical related indicators among the three groups were compared.Results The incidence of postoperative renal colic and leukocyte disorder in the mild thickening group and the moderate thickening group were lower than those in the severe thickening group,and the differences were statistically significant(P<0.05).The postoperative catheterization time in the mild thickening group and the moderate thickening group were shorter than that in the severe thickening group,and the incidences of secondary lithotripsy,residual stones and stone return to kidney in the mild thickening group and the moderate thickening group were lower than those in the severe thickening group,with statistically significant differences(P<0.05).The length of hospital stay and hospitalization cost in the mild thickening group and the moderate thickening group were shorter/less than those in the severe thickening group,with statistically significant differences(P<0.05).Conclusion With the increase of UWT(especially when UWT>3.49 mm),the incidence of postoperative complications and hospitalization cost of URL increase to varying degrees,and the surgical efficacy decreases.In clinical work,UWT measurement holds potential value in predicting the surgical efficacy and complications of URL.
7.Construction of an evaluation index system for clinical practice bases of nursing graduate students majoring in midwifery from a practical perspective
Xuqian SHEN ; Yufang GAO ; Lei SONG ; Meiling YUAN ; Rui YANG ; Zitong JI ; Longlong WANG
Chinese Journal of Modern Nursing 2024;30(1):55-62
Objective:To establish a comprehensive and detailed evaluation index system for clinical practice bases of nursing graduate students majoring in midwifery, providing reference for promoting the construction of clinical practice bases for nursing graduate students majoring in midwifery in China.Methods:Based on the theoretical framework of international midwifery practice basic skills, an evaluation index system for clinical practice bases of nursing graduate students majoring in midwifery was established through literature analysis and Delphi method. Analytic hierarchy process was used to calculate the weights of indicators at all levels.Results:This study conducted two rounds of consultation with 20 experts. In the two rounds of consultation, the positivity coefficients of experts were 84.38% and 74.07%, and the authority coefficients of the expert groups were 0.91 and 0.94, respectively. The total Cronbach's α coefficients of the index system were 0.930 and 0.965, respectively, and the Kendall harmony coefficients of the overall indicators were 0.230 and 0.297 ( P<0.01). The final evaluation index system for clinical practice bases of nursing graduate students majoring in midwifery included five primary indicators, 14 secondary indicators, and 76 connotation indicators. Conclusions:Based on the service purpose of maternal and child health and the functional positioning of the base, this study constructs a scientific and reliable evaluation index system for clinical practice bases of nursing graduate students majoring in midwifery.
8.Clinical Characteristics of CD4-CD56+Blastic Plasmacytoid Dendritic Cell Neoplasm
He-Sheng HE ; Yuan-Feng WEI ; Xin-Yue JI ; You-Hai XU ; Yu-Qiong YANG ; Xiao-Ke JIN
Journal of Experimental Hematology 2024;32(2):588-594
Objective:To explore the clinical manifestations,pathological features,immunophenotype,as well as diagnosis,treatment and prognosis of patients with CD4-CD56+blastic plasmacytoid dendritic cell neoplasm(BPDCN),in order to further understand the rare disease.Methods:The clinical data,laboratory examinations and treatment regimens of two patients with CD4-CD56+BPDCN in the First Affiliated Hospital of Wannan Medical College were retrospectively analyzed.Results:The two patients were both elderly males with tumor involved in skin,bone marrow,lymph nodes,etc.Immunohistochemical results of skin lesions showed that both CD56 and CD123 were positive,while CD4,CD34,TdT,CD3,CD20,MPO and EBER were negative.Flow cytometry of bone marrow demonstrated that CD56,CD123,and CD304 were all positive,while specific immune markers of myeloid and lymphoid were negative.Two patients were initially very sensitive to acute lymphoblastic leukemia or lymphomatoid chemotherapy regimens,but prone to rapid relapse.The overall survival of both patients was 36 months and 4 months,respectively.Conclusion:CD4-CD56+BPDCN is very rare and easily misdiagnosed as other hematological tumors with poor prognosis.Acute lymphoblastic leukemia or lymphomatoid therapy should be used first to improve the poor prognosis.
9.Effect of CD8+CD28-T Cells on Acute Graft-Versus-Host Disease after Haploidentical Hematopoietic Stem Cell Transplantation
An-Di ZHANG ; Xiao-Xuan WEI ; Jia-Yuan GUO ; Xiang-Shu JIN ; Lin-Lin ZHANG ; Fei LI ; ZHEN-Yang GU ; Jian BO ; Li-Ping DOU ; Dai-Hong LIU ; Meng LI ; Chun-Ji GAO
Journal of Experimental Hematology 2024;32(3):896-905
Objective:To investigate the effect of CD8+CD28-T cells on acute graft-versus-host disease(aGVHD)after haploidentical hematopoietic stem cell transplantation(haplo-HSCT).Methods:The relationship between absolute count of CD8+CD28-T cells and aGVHD in 60 patients with malignant hematological diseases was retrospectively analyzed after haplo-HSCT,and the differences in the incidence rate of chronic graft-versus host disease(cGVHD),infection and prognosis between different CD8+CD28-T absolute cells count groups were compared.Results:aGVHD occurred in 40 of 60 patients after haplo-HSCT,with an incidence rate of 66.67%.The median occurrence time of aGVHD was 32.5(20-100)days.At 30 days after the transplantation,the absolute count of CD8+CD28-T cells of aGVHD group was significantly lower than that of non-aGVHD group(P=0.03).Thus the absolute count of CD8+CD28-T cells at 30 days after transplantation can be used to predict the occurrence of aGVHD to some extent.At 30 days after transplantation,the incidence rate of aGVHD in the low cell count group(CD8+CD28-T cells absolute count<0.06/μl)was significantly higher than that in the high cell count group(CD8+CD28-T cells absolute count ≥0.06/μl,P=0.011).Multivariate Cox regression analysis further confirmed that the absolute count of CD8+CD28-T cells at 30 days after transplantation was an independent risk factor for aGVHD,and the risk of aGVHD in the low cell count group was 2.222 times higher than that in the high cell count group(P=0.015).The incidence of cGVHD,fungal infection,EBV infection and CMV infection were not significantly different between the two groups with different CD8+CD28-T cells absolute count.The overall survival,non-recurrent mortality and relapse rates were not significantly different between different CD8+CD28-T cells absolute count groups.Conclusion:Patients with delayed CD8+CD28-T cells reconstitution after haplo-HSCT are more likely to develop aGVHD,and the absolute count of CD8+CD28-T cells can be used to predict the incidence of aGVHD to some extent.The absolute count of CD8+CD28-T cells after haplo-HSCT was not associated with cGVHD,fungal infection,EBV infection,and CMV infection,and was also not significantly associated with the prognosis after transplantation.
10.Sperm ultrastructure in patients with partial globozoospermia
Hao-Ran LIU ; Liu YANG ; Hui TIAN ; Yuan-Yuan JI ; Xiao-Fang HAN ; Xiang HUANG
National Journal of Andrology 2024;30(10):867-871
Objective:To investigate the morphological and ultrastructural differences between normal and round-headed sperm and the outcomes of assisted reproduction in patients with partial globozoospermia.Methods:We collected clinical information and semen samples from 6 cases of partial globozoospermia confirmed in our hosptials from March 2023 to March 2024,performed Diff-Quik staining of the samples,observed the sperm morphology under the light microscope and transmission electron microscope,compared the ultrastructures between round-headed and normal spermatozoa,and analyzed the clinical outcomes of assisted reproduction in the pa-tients.Results:Under the light microscope,the the round-headed sperm had no acrosomal structure,some with tail abnormalities;while under the transmission electron microscope,they exhibited dissolved plasma membrane,acrosomal absence,small acrosomes,nucleoplasmic granulation,huge central vacuoles,swelling,absence or irregular arrangement of mitochondria in the neck,and disor-ganized or missed 9+2 microtubules in the tail.All the 6 patients underwent intracytoplasmic sperm injection(ICSI),and 1 of them achieved pregnancy.Conclusion:The sperm organelle is morphologically damaged and ultrastructurally abnormal in some patients with partial globozoospermia,which may be a key factor for their infertility,and ICSI can help some of them to achieve fertility.

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